title: A novel metabolic monitoring system identified nutrition-mediated microbial interactions

city: Tsuruoka

first: Shinji

last: Fukuda

state: Yamagata

address: 246-2 Mizukami, Kakuganji

department: Institute for Advanced Biosciences

institute: Keio University

summary: "Omics" technologies have been developed to understand the whole complex microbial systems; however, most omics studies reported so far were utilized to analyze the living matters of “single-species”. To understand the cell-cell interaction in the gut microbial complex, we selected to examine the interaction of Escherichia coli O157:H7 (O157) and Bifidobacterium longum (BL), known as a pathogenic and a commensal bacteria, as a first step for understanding the whole gut microbial complex. We have developed a novel time-lapse 2D-NMR metabolic profiling system in order to measure the extracellular metabolites, which are considered a key factor to understand the bacterial crosstalk. Furthermore, in combination with transcriptome and proteome analysis, we found that the relationship between BL and O157 could be partially regarded as the producer and the consumer of nutrients, especially in the case of serine and aspartate metabolism. These findings suggest that our novel profiling systems could be a powerful tool toward understanding crosstalk of the whole microbial complex such as the gut, industrial bioreactors or environmental microbial communities.

sample_organism:
Escherichia coli
Bifidobacterium longum

platform_organism:
Escherichia coli
Bifidobacterium longum

overall_design: In vitro mono and coculture were performed. All experiments were performed in duplicate.

first: Yumiko

last: Nakanishi

first: Hiroshi

last: Ohno

first: Jun

last: Kikuchi


title: Genomic profiles of mouse liver tissue harboring deletion of RB and/or p53, untreated or post-hepatocarcinogen treatment [expression data]

status: Public on Sep 20 2011

city: PHILADELPHIA

first: Adam

last: Ertel

state: PA

address: 233 S 10TH ST

department: Cancer Biology

country: USA

institute: Thomas Jefferson University

summary: The retinoblastoma (RB) and p53 tumor suppressors are critical regulators of the cell cycle with profound impact on both normal cell biology and disease etiology. In the context of human cancers, compound inactivation of RB and p53 is a frequent occurrence; however, the cooperation of these tumor suppressors in driving tumorigenesis has proven to be intricate and dependent on both the tissue and type of cancer. Hepatocellular carcinoma (HCC) is a highly complex disease characterized by numerous molecular abnormalities (e.g. p53, RB, TGFβ) and chromosomal aberrations associated with environmental factors (e.g. Hepatitis B/C Virus, Aflatoxin B1). Despite extensive research, how each of these facets of disease development cooperates in promoting tumorigenesis is ultimately unknown.  In the current study, we present a mouse model of liver tumorigenesis, in which the impact of RB and p53 loss is modified by the tissue environment. While loss of RB and p53 promotes deregulation of transcriptional programs associated with advanced disease, these changes are not sufficient to drive spontaneous tumorigenesis in the liver. However, in response to carcinogen-induced damage, distinct and cooperative roles of RB and p53 are revealed, which critically impact cell cycle control, checkpoint response, genome stability, and ultimately tumor development.

overall_design: Mice that are transgenic for Cre recombinase under the albumin promoter and harboring loxP sites within the Rb and/or p53 genes. For gene expression microarray analysis, mice were aged to 14 days, and treated for 24 hours with diethylnitrosamine (DEN) or saline as a control. For CGH analysis, mice were aged to 6 months post-DEN treatment. Liver tissue was obtained from dissected tumors and compared to normal liver tissue of 6-month old, saline-treated littermates. CGH analysis includes 5 individual tumor samples and 2 control samples (each consisting of a pool of 3 normal mouse liver DNA).

first: A

middle: K

last: McClendon

first: Erik

middle: S

last: Knudsen

first: Sankar

last: Addya


title: Gene expression profiles of mouse liver tissue harboring deletion of RB and/or p53, untreated or post-hepatocarcinogen treatment

type: Genome variation profiling by genome tiling array

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

overall_design: Refer to individual Series


title: BT474 and BT474-J4 microarray data

city: Collegeville

first: Yuan

last: Liu

address: 1250 South Collegeville Rd

department: Biomarker

institute: GlaxoSmithKline

summary: These data provide scientific information to understand the mechanism of action of lapatinib resistance in HER2-positive patients and to test the combination of HER2-targeted agents and GSK1363089 (foretinib) in the clinic by using an acquired lapatinib-resistant cell line.

overall_design: Cell lines (BT474, an HER2-positive and lapatinib-sensitive cell line; BT474-J4, an acquired lapatinib-resistant cell line) were treated with lapatinib alone (1uM), foretinib (GSK1363089) alone (0.1 uM), a combination of lapatinib (1 uM) and foretinib (0.1 uM), or DMSO control for 24 hours. Triplicates were performed.

first: Li

first: Tona

last: Gilmer

first: Anne-Marie

last: Martin


title: Identification of a Myometrial Molecular Profile for Dystocic Labor

status: Public on Sep 17 2011

city: Dublin

first: Donal

last: Brennan

address: Holles Street

department: UCD School of Medicine, National Maternity Hospital

country: Ireland

institute: University College Dublin

summary:
This study identifies a transciptomic myometrial profile associated with dystocia in spontanous nulliparous term labour
We used microarrays to compare myometrial biopsies obtained at cesarean section from women in spontaneous term labour

overall_design: Women in spontaneous labour undergoing cesarean section for dystocia (slow progressing labour) compared to women who had progressed in the second stage


title: Gene expression profiles of E14 ESCs treated with low levels of the HDAC inhibitor VPA for 4 hrs

city: Jerusalem

first: Eran

last: Meshorer

address: Edmond J. Safra campus

department: Genetics

country: Israel

institute: The Hebrew University of Jerusalem

summary: Gene expression profiles of E14 embryonic stem cells (ESCs) before and after treatment with low levels of the histone deacetylase (HDAC) inhibitor valproic acid (VPA).

overall_design: E14 cells were treated with valproic acid for 4 hrs in duplicates. Cells were harvested along with untreated control E14 cells. RNA was isolated from the cells and hybridized on Affymetrix chips.

first: Hadas

last: Hezroni


title: Transcriptome analysis of mouse cerebral cortical neural progenitor cells

city: Duarte

first: Xiwei

last: Wu

state: CA

address: 1500 E. Duarte Rd.

department: Computational and Quantitative Medicine

institute: City of Hope National Medical Center

summary: Transcriptome analysis of neural progenitor/stem cells is limited by the lack of a reliable method for cell isolation. We have designed a genetic dual reporter strategy that can allow prospective isolation of cortical neural progenitor cells and their neuronal progeny form the same animals. These cells should be a good cell source for comparative global analysis.

overall_design: Cortical neural progenitor cells and their neuronal progeny were purified using a dual reporter strategy. The purified cells were used for comparative expression profiling.

first: Qiang

last: Lu

last: Wang


title: Gene expression profiles of E14 ESCs treated with low levels of HDAC inhibitors for 16 hrs

summary: Gene expression profiles of E14 embryonic stem cells (ESCs) before and after treatment with low levels of the histone deacetylase (HDAC) inhibitors valproic acid (VPA) and sodium butyrate (NaBu).

overall_design: E14 cells were treated with VPA or NaBu for 16 hrs in duplicates. Cells were harvested along with untreated control E14 cells. RNA was isolated from the cells and hybridized on Affymetrix chips.


title: Microarray analysis of genes associated with cell surface NIS protein levels in breast cancer

status: Public on Sep 16 2011

city: Columbus

first: Sissy

last: Jhiang

state: OH

address: 1645 Neil Ave

department: Physiology and Cell Biology

institute: The Ohio State University

summary: Na+/I- symporter (NIS)-mediated iodide uptake allows radioiodine therapy for thyroid cancer.  NIS is also expressed in breast tumors, raising potential for radionuclide therapy of breast cancer.  However, NIS expression in most breast cancers is low and may not be sufficient for radionuclide therapy.  A better understanding of the mechanisms of NIS regulation in breast cancer may lead to strategies for increasing cell surface NIS and radioactive iodide uptake (RAIU) in breast cancer.  The MCF-7 cell line is the only human breast cancer cell line with inducible endogenous NIS expression. Kogai et al. [2000] first reported that trans-retinoic acid (tRA) induces NIS mRNA expression in MCF-7 cells and it was later reported that a combination treatment of tRA and hydrocortisone (tRA/H) further increases tRA-induced NIS expression/function in MCF-7 cells (Kogai et al., 2005; Dohan et al., 2006).  In this study, we used gene expression profiling to identify genes that correlate with NIS expression in MCF-7 cells such that mechanisms underlying NIS modulation may be elucidated.

overall_design: MCF-7 cells were treated with DMSO vehicle, tRA (1µM), or tRA(1µM)/H(1µM) for 12 hours and total RNA was extracted.  There are two replicates for each treatment group.

middle: M


title: Human Mesenchymal Stem Cells in Cardiomyocyte Co-Culture

city: Greenville

first: Barbara

last: Muller-Borer

state: NC

address: 115 Heart Drive, East Carolina Heart Institute, Room 2247

department: Cardiovascular Sciences

institute: East Carolina University

summary: Evaluate the change in transcription factors that have a role in human mesenchymal stem cell (hMSC)  commitment to a cardiomyocyte lineage when co-cultured for 4 days with rat neonatal cardiomyocytes and before acquiring a recognizable cardiac phenotype.

overall_design: A myocardial microenvironment was generated by dissociating neonatal rat hearts and establishing cardiomyocyte primary cultures. HumanMSCs constitutively labeled with dsRed localized to the cell's mitochondria were either grown separately (control) or added to the cardiomyocyte primary cultures and grown for 4 days. dsRed fluorescent hMSCs were harvested from co-cultures at 4 days using a FACscan flow cytometer. The RNA for the microarray analysis was prepared from three biologically separate samples of hMSCs co-cultured for 4 days and from hMSCs grown separately for 4 days (control).

first: Nadia

middle: N

last: Malouf

first: Gwyn

last: Esch


title: Expression data from Parkinson's iPSCs with four copies of SNCA, and equivalent cell lines from an unaffected first degree relative

status: Public on Sep 15 2011

city: Edinburgh

first: Tilo

last: Kunath

address: 5 LIttle France Drive

department: Centre for Regenerative Medicine

country: United Kingdom

institute: University of Edinburgh

summary:
A major barrier to research on Parkinson’s disease (PD) is inaccessibility of diseased tissue for study. One solution is to derive induced pluripotent stem cells (iPSCs) from patients with PD and differentiate them into neurons affected by disease. We created an iPSC model of PD caused by triplication of SNCA encoding α-synuclein. α-Synuclein dysfunction is common to all forms of PD, and SNCA triplication leads to fully penetrant familial PD with accelerated pathogenesis. After differentiation of iPSCs into neurons enriched for midbrain dopaminergic subtypes, those from the patient contain double α-synuclein protein compared to those from an unaffected relative, precisely recapitulating the cause of PD in these individuals. A measurable biomarker makes this model ideal for drug screening for compounds that reduce levels of α-synuclein, and for mechanistic experiments to study PD pathogenesis.
This gene expression microarray study was carried out as part of the validation process for demonstrating that the generated iPSC lines are pluripotent.

overall_design: 5 samples were analysed:  two clonal iPSC lines from each of two genotypes (four in total; AST denoting alpha-synuclein triplication and NAS denoting normal alpha-synuclein), a human embryonic stem cell line (SHEF4). All cultured in self-renewal conditions, mTeSR1

first: Michael

middle: J

last: Devine

first: Mina

last: Ryten

first: Petr

last: Vodicka

first: Alison

last: Thomson

first: Henry

last: Houlden

first: Tom

last: Burdon

first: Fatima

last: Cavaleri

first: Nicola

last: Drummond

first: Masumi

last: Nagano

first: Jan-Willem

last: Taanman

first: Anthony

middle: H

last: Schapira

first: Katrina

last: Gwinn

first: John

last: Hardy

first: Patrick

middle: A

last: Lewis


title: Bisphenol A Regulates the Expression of DNA Repair Genes in Human Breast Epithelial Cells (expression data)

city: Charlottesville

first: Yong

last: Huang

state: VA

address: 1340 Jefferson Park Ave

department: Medicine

institute: University of Viginia

summary: Xenoestrogens are part of a group of agents termed endocrine disruptors because of their capacity to perturb normal hormonal actions. It has been suggested that xenoestrogens may contribute to the development of hormone-dependent cancers, such as breast and endometrial cancers. Bisphenol A (BPA) is polymerized to manufacture polycarbonate plastic and epoxy resins. Human exposure occurs when BPA leaches from plastic-lined food and beverage cans. In the present work we are aiming to determine if BPA has carcinogenic properties by using an in vitro system. For this purpose the human breast epithelial cells MCF-10F were treated with 10-3M to 10-9M BPA continuously for two weeks. The MCF-10F cells treated with 10-3M and 10-4M BPA died, indicating that these concentrations were toxic for the human breast epithelial cells. The cells treated with 10-5M to 10-9M BPA were evaluated for formation of solid masses in collagen and invasion capacity, both phenotypes that are indicators of cell transformation. MCF-10F treated with 10-5M, 10-6M, 10-7M, 10-8M and 10-9M BPA formed a high percentage of solid masses (34.6%, 20%, 42.4%, 31.8% and 32.2%, respectively). Ten passages after BPA treatments, the invasive capacities of the cells were evaluated using Boyden chambers. The invasion capacity was lower in the cells treated at high concentrations of BPA (10-5M and 10-6M), and there was an increased invasion for the cells treated at low BPA concentration (10-9M) although, in all the cases the differences were not significant to the controls. Expression and DNA methylation analyses were performed with the cells treated with 10-5M and 10-6M BPA. We found that these cells showed an increased expression of BRCA1, BARD1, CtIP, RAD51 and BRCC3, all genes involved in DNA repair, and downregulation of PDCD5 and BCL2L11 (also known as BIM), both involved in apoptosis. The upregulation of CtIP was related to hypomethylation of the promoter/exon1 of this gene. Furthermore, BPA induced silencing of BCL2L11 by hypermethylation. This is the first demonstration that BPA induces neoplastic transformation of breast epithelial cells and that aberrant DNA methylation of genes involved in DNA repair and apoptosis could be involved in the initiation of the neoplastic process.

overall_design: MCF-10F, a normal-like human breast epithelial cell (HBEC) line that is ERalpha-negative PR-negative, was maintained in high-calcium medium at 37°C and 5% CO2 until confluent. These cells were treated with different concentrations of BPA continuously for two weeks, adding fresh media every day. As controls, MCF-10F cells were not treated and maintained in the regular media or treated with 0.284% DMSO (vehicle). The cells treated with 10-5M or 10-6M BPA after the invasion assay were collected and expanded during 6 passages. RNA was isolated from the cells  using an RNA extraction kit (Qiagen).

first: Sandra

middle: V

last: Fernandez


title: Bisphenol A Regulates the Expression of DNA Repair Genes in Human Breast Epithelial Cells

type: Methylation profiling by genome tiling array


title: Knockdown effect of CDK8 or CDK19 in HeLa S3 cell

city: Toyama

first: Taiki

last: Tsutsui

country: Japan

institute: Univ. Toyama

summary: Mediator complex has been known as pivotal regulator of RNA polymerase II. Mediator complex has two CDK subunits in vertebrates, named CDK8 and CDK19.  To elucidate functional difference between CDK8 and CDK19 in human cell, we employ siRNA mediate knockdown assay using HeLa S3 cell line. According to this assay these CDKs possess highly redundancy in HeLa S3 cell transcription regulation mechanism but in several genes, each CDK shows gene specific regulatory function.

overall_design: HeLa S3 cells were seeded on 6-well plate at 4 x 104 cells per well in 2ml antibiotic free DMEM medium before 24hr transfection. We transfect siRNA using Lipofectamine 2000 (invitrogen) according to its manual and siRNA final concentration in the medium was 20nM. After culturing for 48hr, transfection medium was changed to fresh antibiotic containing medium. Then the cells were incubated for additional 12hr and then RNA was prepared using RNeazy column (QIAGEN). Five μg of prepared RNA was subjected to the gene expression analysis using Human Genome U133 Plus 2.0 (Affymetrix) followed by characterizations with GeneSpring software (Agilent) and Pathway Analysis software (Ingenuity). In this analysis we employ two individual siRNA against each CDK and three replicates in each condition.

first: Yosiaki

last: Ohkuma


title: Lung adenocarcinoma invasion and progression

city: New York

first: Charles

last: Powell

state: NY

address: One Gustave Levy Place, Box 1232

department: MEDICINE/PULMONARY

institute: Mount Sinai School of Medicine

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus


title: Gene expression analysis of lung cancer using long time stored formalin-fixed and paraffin embedded (FFPE) tissue

city: Stockholm

first: Therese

last: Hogfeldt

address: Cancer Centre Karolinska, R:8

country: Sweden

institute: Karolinska Institutet

summary: This study was performed to evaluated RNA extraction and gene expression analysis of FFPE specimen stored for more than 20 years. Using long time stored FFPE material; large retrospective studies correlating molecular features with therapeutic response and clinical outcome, can be performed. Quantitative PCR (qPCR) was used to evaluate RNA extraction methods and to compare gene expression profiles of FFPE and fresh frozen (FF) tissue. Extracted RNA was subsequently subjected to microarray analysis and compared to qPCR data. The Ambion RecoverAll kit appears to be particularly suited for RNA extraction of long time stored FFPE tissues. Gene expression analysis using Affymetrix platform displayed a high degree of correlation for endogenous control genes comparing FF and FFPE tissues. We conclude that high quality gene expression signatures can be recognized using Affymetrix gene expression platform on FFPE tissue stored for more than 20 years. However, a general interpretation must be done with caution as different FFPE procedures have varying effects on RNA quality.

overall_design: Three RNA extraction methods from Roche (Basel, Switzerland), Ambion (Austin, TX, USA) and Qiagen (Hilden, Germany), designed for FFPE material was used. The methods were compared using qPCR. For the qPCR analysis, two different concentrations of input cDNA were used (20ng and 100ng) and 32 human endogenous control genes were examined. RNA from the Ambion FFPE kit was further analyzed by using microarray. Amplification of RNA prior to microarray analysis was performed using Nugen technologies (San Carlos, CA, USA). Nugen has developed amplification kits both for FFPE and FF materials: WT- ovation FFPE RNA amplification System V2 (Nugen FFPE), Ovation FF RNA Amplification System V2 (Nugen V2 FF) and Ovation FF Pico RNA Amplification System (Nugen PICO FF). The Nugen FFPE kit, designed for FFPE material was only used for FFPE tissue. The Nugen Pico FF kit, designed to target small amounts of FF RNA (>500 pg) and the Nugen V2 FF kit designed to target total FF RNA, were only used for FF tissue. Affymetrix standard amplification protocol (Affy FF) designed for FF RNA was also included as the standard method for amplification.

last: Jacobson

first: Joachim

last: Lundahl

first: Håkan

last: Mellstedt

first: Ali

last: Moshfegh


status: Public on Sep 12 2011

first: Yael

last: Strulovici-Barel

address: 1300 York Avenue

department: Department of Genetic Medicine

institute: Weill Cornell Medical College

summary:
Disparate Oxidant-related Gene Expression of Human Small Airway Epithelium Compared to Autologous Alveolar Macrophages in Response to the In Vivo Oxidant Stress of Cigarette Smoking
The oxidant burden of cigarette smoking induces lung cell dysfunction, and play a significant role in the pathogenesis of lung disease. Two cell populations directly exposed to the oxidants in cigarette smoke are the small airway epithelium and alveolar macrophages. Of these, the epithelium appears to be more vulnerable to smoking, becoming disordered in differentiation, repair and function, while alveolar macrophages become activated, without becoming diseased. In this context, we asked: for the same individuals, what is the baseline trancriptome of oxidant-related genes in small airway epithelium compared to alveolar macrophages and do the responses of the transcriptome of these 2 cell populations differ substantially to inhaled cigarette smoke? To address these questions we used microarray gene expression and TaqMan analysis to assess the gene expression profile of known oxidant-related genes in paired samples recovered by bronchoscopy from small airway epithelium and alveolar macrophages from the same healthy nonsmokers and normal smokers. Of the 155 oxidant-related genes surveyed, 122 (77%) were expressed in both cell populations in nonsmokers. However, of the genes expressed by both cell populations, oxidant related gene expression levels were higher in alveolar macrophages (67 genes, 43%) than small airway epithelium (37 genes, 24%). There were more oxidant-related genes uniquely expressed in the small airway epithelium (17%), than in alveolar macrophages (5%). In healthy smokers, the majority of oxidant-related genes were expressed in both cell populations, but there were marked differences in the numbers of oxidant-related genes that smoking up- or down-regulated. While smoking up-regulated 15 genes (10%) and down-regulated 7 genes (5%) in the small airway epithelium, smoking had far less effect on alveolar macrophages [only 4 (3%) genes up-regulated, and only 1 (0.6%) down-regulated]. Only a small number of smoking responsive oxidant-related genes overlapped between the two cell types (2 up-regulated, and no down-regulated genes). Consistent with this observation, pathway analysis of smoking-responsive genes in the small airway epithelium showed oxidant-related pathways dominated, but in alveolar macrophages immune-response pathways dominated. Thus, the responses of the oxidant-related transcriptome of cells with an identical genome and exposed to the same oxidant stress of cigarette smoking are very different, with responses of oxidant-related genes of alveolar macrophages far more subdued than that of small airway epithelium, consistent with the clinical observation that, while the small airway epithelium is vulnerable, alveolar macrophages are not "diseased" in response to the oxidant stress of cigarette smoking.

overall_design: Gene expression profiles of known oxidant-related genes in paired samples recovered by bronchoscopy from small airway epithelium and alveolar macrophages from the same healthy nonsmokers and normal smokers.

first: Brendan

last: Carolan

first: Ben-Gary

last: Harvey

first: Neil

middle: R

last: Hackett

first: Timothy

middle: P

last: O'Connor

first: Patricia

last: Cassano

first: Ronald

middle: G

last: Crystal


title: Blood vessels restrain pancreas branching, differentiation and growth

status: Public on Sep 14 2011

city: jerusalem

first: Yuval

last: Dor

address: ein-karem

institute: Hadassah medical school

summary: How organ size and form are controlled during development is a major question of biology. Blood vessels have been shown to be essential for early development of the liver and pancreas, and are fundamental to normal and pathological tissue growth. Here we report that non-nutritional signals from blood vessels surprisingly act to restrain pancreas growth. Elimination of endothelial cells increases the size of embryonic pancreatic buds. Conversely, VEGF-induced hypervascularization decreases pancreas size. The growth phenotype results from vascular restriction of pancreatic tip cell formation, lateral branching and differentiation of the pancreatic epithelium into endocrine and acinar cells. The effects are seen both in vivo and ex vivo, indicating a perfusion-independent mechanism. Thus the vasculature controls pancreas morphogenesis and growth by reducing branching and differentiation of primitive epithelial cells.

overall_design: For transcriptome analysis, RNA was isolated using QIAGEN RNeasy micro Kit from pancreatic buds of Pdx1-tTA (n=3) and littermate Pdx1-tTA; TET-VEGF (n=3) e12.5 embryos, or from e12.5 wild type pancreatic buds explanted and treated  with VEGFR2i (n=5) or vehicle (n=5) for 2 days. Pooled samples were hybridized to Affymetrix mouse gene 1.0 st arrays. The arrays were RMA normalized using Partek Genomic Suite 6.5. Differentially regulated genes were selected based on p-values and ratios using t-test.

first: Judith

last: Magenheim

first: Ohad

last: Ilovich

first: Alon

last: Lazarus

first: Agnes

last: Klochendler

first: Oren

last: Ziv

first: Roni

last: Werman

first: Ayat

last: Hija

first: Ondine

last: Cleaver

first: Eyal

last: Mishani

first: Eli

last: Keshet


title: Expression data from Columbia Lung Adenocarcinoma Human Tumor Cells

first: Charles

last: Powell

summary:
The World Health Organization has subclassified adenocarcinoma based upon predominant cell morphology and growth pattern such as bronchioloalveolar carcinoma (BAC), adenocarcinoma with mixed subtypes (AC-mixed), and homogenously invasive tumors with a variety of histological patterns
Pure invasive adenocarcinomas are often devoid of bronchioloalveolar morphology. The clinical importance of lung adenocarcinoma invasion is supported by several recent studies  indicating that the risk of death in non-mucinous BAC  is significantly lower than that of pure invasive tumors and in tumors with greater than 0.6 cm of fibrosis or linear invasion (J Thorac Oncol 6:244-285)
To identify human tumor cell signatures associated with lung adenocarcinoma subtype and invasion, we performed microarray gene expression profiling of microdissected tumor cells noninvasive AC  and AC-Mixed invasive tumors.

overall_design: 17 cases of noninvasive AC tumors and 23 cases of AC-mixed subtype invasive lung adenocarcinomas resected from 2002 to 2006 were examined (Columbia Lung Adenocarcinoma dataset)

first: Alain

middle: C

last: Borczuk


title: Genome-wide Analyses of Diffuse Intrinsic Pontine Gliomas

status: Public on Sep 21 2011

city: Memphis

first: Chunxu

last: Qu

state: TN

address: 262 Danny Thomas Pl

department: Pathology

institute: St Jude Children's Research Institute

type:
Expression profiling by array
Genome variation profiling by SNP array

summary:
Purpose: More than 90% of children with diffuse intrinsic pontine glioma (DIPG) die within 2 years of diagnosis. There is a dire need to identify therapeutic targets, however lack of patient material for research has limited progress. We evaluated a large cohort of diffuse intrinsic pontine gliomas (DIPGs) to identify recurrent genomic abnormalities and gene expression signatures underlying DIPG.
Patients and Methods:  We used single nucleotide polymorphism arrays to evaluate genomic copy number imbalances in 43 DIPGs from 40 patients and in 8 low-grade exophytic brainstem gliomas. Gene expression arrays were used to evaluate expression signatures from 27 DIPGs, 6 low-grade exophytic brainstem gliomas and 66 low-grade gliomas arising outside the brainstem.
Results: Frequencies of specific large-scale and focal imbalances varied significantly between DIPGs and pediatric glioblastomas outside the brainstem.  Focal amplifications of genes within the receptor tyrosine kinase-Ras-PI3-kinase signaling pathway were found in 47% of DIPG, with PDGFRA and MET showing the highest frequency. 30% of DIPG contained focal amplifications of cell-cycle regulatory genes controlling RB phosphorylation, and 21% had concurrent amplification of genes from both pathways.  Some tumors showed heterogeneity in amplification patterns. DIPGs showed distinct gene expression signatures relating to developmental processes compared to pediatric glioblastomas arising outside the brainstem, while expression signatures of low-grade exophytic brainstem gliomas were similar to low-grade gliomas outside the brainstem.

overall_design:
Copy number analaysis: 43 DIPG samples, 8 Low Grade Gliomas using SNP6.0.  Available matched normals are also profiled with SNP6.0.
Expression analysis: 29 DIPG samples, 6 Low grade samples

Please contact Suzanne Baker at Suzanne.Baker@stjude.org for CEL files and genotype calls.

first: Barbara

last: Paugh

first: Alberto

last: Broniscer

first: Claudia

last: Miller

first: Junyuan

last: Zhang

first: James

last: Olson

first: Russell

last: Geyer

first: Susan

last: Chi

first: Nasjla

last: da Silva

first: Arzu

last: Onar-Thomas

first: Justin

last: Baker

first: Amar

last: Gajjar

first: David

middle: W

last: Ellison

first: Suzanne


title: Expression data of genes that regulate reactive oxygen species in bone marrow mononuclear cells from patients with Shwachman-Diamond syndrome

city: Toronto

first: Saswati

last: Sen

state: ON

address: 555 university avenue

country: Canada

institute: Hospital for Sick Children

summary:
Although anemia is common in Shwachman-Diamond syndrome (SDS), the underlying mechanism remains unclear. We asked whether SBDS, which is mutated in most SDS patients, is critical for erythroid development. We found that SBDS expression is high early during erythroid differentiation. Inhibition of SBDS in CD34+ hematopoietic stem cells and early progenitors (HSC/Ps) and K562 cells led to slow cell expansion during erythroid differentiation. Induction of erythroid differentiation resulted in markedly accelerated apoptosis in the knockdown cells; however, proliferation was only mildly reduced. The percentage of cells entering differentiation was not reduced.
Differentiation also increased the oxidative stress in SBDS-knockdown K562 cells, and antioxidants enhanced the expansion capability of differentiating SBDS-knockdown K562 cells and colony production of SDS patient HSC/Ps. Erythroid differentiation also resulted in reduction of all ribosomal subunits and global translation. Furthermore, stimulation of global translation with leucine improved the erythroid cell expansion of SBDS-knockdown cells and colony production of SDS patient HSC/Ps. Leucine did not reduce the oxidative stress in SBDS-deficient K562 cells. These results demonstrate that SBDS is critical for normal erythropoiesis. Erythropoietic failure caused by SBDS-deficiency is at least in part related to elevated ROS levels and translation insufficiency since antioxidants and leucine improved cell expansion.

overall_design: Bone marrow mononuclear cells from nine SDS patients and nine control patients were selected for RNA extraction and hybridization on Affymetrix microarrays.

first: Yigal

last: Dror

first: Piya

last: Rujkijyanont

first: Joseph

last: Beyene

first: Fahad

last: Khan

first: Peter

last: Jaqsa


title: Genome wide gene expression profiles of distal colon from 5% DSS-treated mice after administration of various siRNA against TNFa.

status: Public on Sep 10 2011

city: Barcelona

first: Evarist

middle: Planet

last: Letschert

state: Spain

address: C/ Baldiri Reixac 10

department: Biostatistics

country: Spain

institute: IRB Barcelona

summary:
Differential gene expression assessed in siTNF-OMe-P treated animals showed significant correlation between improved colon integrity and clinical parameters of colitis with reduced TLR activation, tissue regeneration and reduced pro-inflammatory cytokines, as compared to all treatment groups.
This data shows the changes in gene expression profile associated with effective silencing of TNFa by a chemically-modified siRNA in the colon of colitic mice.

overall_design: We performed genome-wide gene expression profiling of 5% DSS-treated mice after intrarectal administration of a)siRNA against TNFa (siTNF), b)siRNA against TNFa modified with O-Methyl nucleotides (siTNF-OMe), c)siRNA against TNFa modified with O-Methyl-propanediol nucleotides (siTNF-OMe-P) and d) siControl (scrambled siRNA).

first: Jose

last: Perales

first: Ramon

last: Eritja

first: Sandra

last: Ocampo


title: Transcriptional pathway signatures for the Aurora inhibitor Danusertib

city: Nerviano

first: Roberta

last: Bosotti

state: MI

address: viale Pasteur,10

department: Biotechnology

country: Italy

institute: Nerviano Medical Sciences srl

summary: Treatment with Aurora inhibitors has been shown to induce diverse biological responses in different tumor cell lines, in part depending on their p53 status. To characterize at the transcriptional level the effects of Danusertib we analyzed by microarray different tumor cell lines, with WT or mutant p53 status, that showed differential cell cycle response upon drug treatment.

overall_design: We analyzed the effects of Danusertib treatment in different tumor cell lines derived from ovary (A2780, p53WT), breast (MCF-7, p53WT and MDA-MB-468, p53 mut) and colon carcinoma (HCT116, p53 WT and Colo205, p53 mut). Cell line were treated (TRT) or left unreated (CTRL) for 24 hrs with 1 uM Danusertib.

last: Healy

first: Antonella

last: Isacchi


title: Expression analysis of mutant U2AF35 transduced cells

city: Tokyo

first: Aiko

last: Sato-Otsubo

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

institute: University of Tokyo

summary: In this study, to obtain the biological impact of the mutated U2AF35, HeLa and TF-1 cells were retrovirally transduced with either mock, wild-type or S34F mutant of U2AF35, and Expression array was performed.

overall_design: Expression analysis was performed for mock, wild-type U2AF35 or S34F mutant transduced HeLa and MDS-derived TF-1 cell line in triplicate.

first: Kenichi

last: Yoshida

first: Masashi

last: Sanada

first: Yuichi

last: Shiraishi

first: Yasunobu

last: Nagata

first: Yusuke

last: Sato

first: Ayana

last: Kon

last: Shiosaka

first: Ryoichiro

last: Kawahata

first: Seishi

last: Ogawa


title: Gene expression profiles of familial Alzheimer's disease with presenilin 2 mutation patient-specific induced pluripotent stem cells

first: Takuya

last: Yagi

address: 35-Shinanomachi Shinjuku-ku

institute: Keio University

summary: We established two clones of induced pluripotent stem cells (iPSC) with the presenilin 2 mutation, N141 (PS2-1 iPSC and PS2-2 iPSC) by retroviral transduction of primary human fibroblasts. To show the similarity among  201B7 iPSC, PD01-25 iPSC(Sporadic Parkinson's disease patient derived iPSC), PS2-1 iPSC, PS2-2 iPSC, this experiment was designed.

overall_design: Undifferentiated  201B7 iPSC, PD01-25 iPSC, PS2-1 iPSC and PS2-2 iPSC were collected. Then, they were applied in this experiment.

first: Daisuke

last: Ito


title: PCPTC screening

status: Public on Sep 09 2011

city: Uppsala

first: Mårten

last: Fryknäs

address: Akademiska sjh ingång 61

department: Medical sciencies

institute: Uppsala university

summary: Primary cultures of patient tumor cells (PCPTC) were used in a cell-based cytotoxicity screen. Microarray-based mRNA profiling was used to identify the mechanism-of-action for the small molecule VLX 50.

overall_design: MCF7 cells were treated with the PCPTC screening hit VLX 50 or DMSO control for 6h prior to RNA isolation. One sample per treatment. Data were analyzed using both MAS5.0 and RMA.

first: Marten

last: Fryknas


title: Expression data from human primary fibroblasts treated with Trypanosoma cruzi-conditioned medium

city: Quito

first: Jaime

middle: Alfredo

last: Costales

address: 12 de Octubre y Patria

department: Biological Sciences

country: Ecuador

institute: Pontificia Universidad Catolica del Ecuador

summary:
The intracellular pathogen Trypanosoma cruzi secretes an activity that blocks TGF-β-dependent induction of connective tissue growth factor (CTGF/CCN2).  Here, we address the mechanistic basis for T. cruzi-mediated interference of
CTGF/CCN2 expression by examining host cell signaling pathways and the global inhibitory effect on TGF-β-dependent gene expression. We show that the expression of a discrete subset of TGF-β-inducible genes involved in cell proliferation, wound repair, and immune regulation are blocked by the soluble T. cruzi activity, demonstrating that this parasite-derived activity has broad, but specific effects on fibroblast gene regulation.

overall_design: Primary human fibroblasts were treated with TGF-β, T. cruzi conditioned medium (PCM) and  TGF-β/ PCM simultaneously. Untreated cells were also included as controls.  Total RNA was extracted and gene expression levels analyzed with Affymetrix microarrays. Three independent biological replicates were included for each type of treatment.

first: Glenn

last: Mott

first: Barbara

last: Burleigh


title: Genome-wide activity-dependent MeCP2 phosphorylation regulates nervous system development and function [visual cortex]

status: Public on Sep 08 2011

city: Brookline

first: Harrison

middle: Wren

last: Gabel

state: MA

address: 7 Linden St Apt 3

department: Neurobiology

institute: Harvard Medical School

summary:
Autism spectrum disorders such as Rett syndrome (RTT) have been hypothesized to arise from defects in experience-dependent synapse maturation. RTT is caused by mutations in MECP2, a nuclear protein that becomes phosphorylated at S421 in response to neuronal activation. We show here that disruption of MeCP2 S421 phosphorylation in vivo results in defects in synapse development and behavior, implicating activity-dependent regulation of MeCP2 in brain development and RTT. We investigated the mechanism by which S421 phosphorylation regulates MeCP2 function and show by chromatin immunoprecipitation-sequencing that this modification occurs on MeCP2 bound across the genome. The phosphorylation of MeCP2 S421 appears not to regulate the expression of specific genes; rather, MeCP2 functions as a histone-like factor whose phosphorylation may facilitate a genome-wide response of chromatin to neuronal activity during nervous system development. We propose that RTT results in part from a loss of this experience-dependent chromatin remodeling.
Gene expression analysis of RNA isolated from P17 mouse visual cortex was performed comparing global gene expression between Wild-Type and MeCP2 S421A knock-in mice.

overall_design: We isolated RNA from the visual cortex of 4 wild-type and 4 MeCP2 S421A littermate P17 Mice, and analyzed mRNA expression using the Affymetrix Mouse Gene 1.0 ST microarray platform.

first: Sonia

last: Cohen

first: Martin

last: Hemberg

first: Ashley

last: Hutchinson

first: L

last: Sadacca

first: Daniel

last: Ebert

first: David

last: Harmin

first: Rachel

last: Greenberg

first: Zhaolan

last: Zhou

first: William

last: Wetsel

first: Anne

middle: E

last: West

first: Michael


title: Primary Lung Cancer Specimens

status: Public on Sep 06 2011

city: Dallas

first: Luc

last: Girard

state: TX

address: 5323 Harry Hines Blvd

department: Hamon Center for Therapeutic Oncology Research

institute: UT Southwestern Medical Center

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

overall_design: Refer to individual Series


title: UMCCC Primary Lung Cancer Specimens

summary: Develop an EGFR mutation gene expression signature to aid in predicting response and clinical outcome and to identify genes associated with the EGFR-dependent phenotype

overall_design: 17 primary lung adenocarcinomas were analyzed with Affymetrix U133-plus2

first: John

middle: D

last: Minna

last: Beer

first: Pierre

last: Saintigny

first: Li

last: Zhang


title: Very small embryonic-like stem cells purified from umbilical cord blood lack stem cell characteristics

status: Public on Sep 03 2011

city: Leipzig

first: Andreas

last: Heider

state: Bayern

address: Semmelweisstr. 14

department: Biologie

country: Germany

institute: Universität Leipzig

summary: Very small embryonic-like (VSEL) cells have been described as putatively pluripotent stem cells present in murine bone marrow and human umbilical cord blood (hUCB) and as such are of high potential interest for regenerative medicine. However, there remain some questions concerning the precise identity and properties of VSEL cells, particularly those derived from hUCB. For this reason, we have carried out an extensive characterisation of purified populations of VSEL cells from a large number of UCB samples. Consistent with a previous report, we find that VSEL cells are CXCR4+, have a high density, are indeed significantly smaller than HSC and have an extremely high nuclear/cytoplasmic ratio. Their nucleoplasm is unstructured and stains strongly with Hoechst 33342. A comprehensive FACS screen for surface markers characteristic of embryonic, mesenchymal, neuronal or hematopoietic stem cells revealed negligible expression on VSEL cells. These cells failed to expand in vitro under a wide range of culture conditions known to support embryonic or adult stem cell types and a microarray analysis revealed the transcriptional profile of VSELs to be clearly distinct both from well-defined populations of pluripotent and adult stem cells and from the mature hematopoietic lineages. Finally, we detected an aneuploid karyotype in the majority of purified VSEL cells by fluorescence in situ hybridisation. These data support neither an embryonic nor an adult stem cell like phenotype, suggesting rather that hUCB VSEL are an aberrant and inactive population that is not comparable to murine VSEL.

overall_design: VSEL cells (Lin-CD45-CXCR4+CD34-)  and CD34+ VSEL cells (Lin-CD45-CXCR4+CD34+) from three individual fresh cord blood units were double sorted to highest purity and subjected to array analysis.

first: Ralitza

last: Danova-Alt

first: Dietmar

last: Egger

last: Cross

first: Rüdiger

last: Alt


title: Comparison of mRNA expression in circulating T-cells from patients with severe asthma

status: Public on Sep 01 2011

city: Sandwich

first: Ketan

middle: Anilkumar

last: Patel

address: Ramsgate Road

department: WWRD

institute: Pfizer

summary: Comparison of mRNA expression showed widespread changes in the circulating CD8+ but not CD4+ T-cells from patients with severe asthma. No changes were observed in the CD4+ and CD8+ T-cells in non-severe asthmatics versus healthy controls. Bioinformatics analysis showed that the changes in CD8+ T-cell mRNA expression were associated with multiple pathways involved in T-cell activation. As with mRNAs, we also observed widespread changes in expression of non-coding RNA species including natural antisense, pseudogenes, intronic long ncRNAs and long intergenic long ncRNAs in CD8+ T-cells from severe asthmatics. Measurement of the miRNA expression profile showed selective down-regulation of miR-28-5p in CD8+ T-cells and reduction of miR-146a and miR-146b in both CD4+ and CD8+ T-cells.

overall_design: mRNA samples were collected from circulating CD4+ and CD8+ T-cells from healthy donors as well as donors with severe and non-severe asthma.

first: Eleni

last: Tsitsiou

first: Andrew

last: Williams

first: Sterghios

last: Moschos

first: Christos

last: Rossios

first: Xiaoying

last: Jiang

first: Oona

last: Adams

first: Patricia

last: Macedo

first: Richard

last: Booton

last: Gibeon

first: Kian

middle: F

last: Chung

first: Mark

last: Lindsay


title: Atorvastatin, rosuvastatin and rifampicin effect on human primary hepatocyte transcriptome

status: Public on Sep 05 2011

city: Ljubljana

first: Peter

last: Juvan

address: Zaloska 4

department: Institute of Biochemistry

country: Slovenia

institute: Faculty of Medicine, University of Ljubljana


title: Expression data from oral squamous cell carcinoma (OSCC)-derived cell lines and normal oral keratinocytes

status: Public on Sep 02 2011

city: Durham

first: Wenbin

last: Wei

address: Stockton Road

department: Biosciences

institute: Durham University

summary: Oral squamous cell carcinoma (OSCC) is a lethal disease and early death usually occurs as a result of local invasion and regional lymph node metastases. We used microarrays to identify down or upregulated genes in OSCCs compared with non-malignant controls.

overall_design:
To identify genes whose transcription is deregulated in
OSCC, the gene expression profiles of eight OSCC cell lines (H-series and M9) and three primary cultures of normal oral keratinocytes (NKs) were examined using Affymetrix HG-U133A and HG-U133 Plus 2.0 arrays.

first: LeeFah

last: Yap

first: Max

last: Robinson

first: Victor

last: Lopes

first: Ian

last: Paterson


title: Expression data from Thymocytes of WT, TCF-1-deficient and β-catenin transgenic mice

city: duarte

first: ruiqing

last: wang

state: ca

address: 1500 duarte rd

institute: city of hope

summary:
Both TCF-1 and its coactivator β-catenin are known to be required for supporting normal double positive (DP) thymocyte survival through upregulating Bcl-xL. However, the downstream factors mediating this effect remained unknown.
We used microarray to compare the global expression difference among WT, TCF-1-deficient, and β-catenin transgenic thymocytes to search for the genes that are down-regulated and up-regulated in TCF-1-deficient and β-catenin transgenic thymocytes, respectively.

overall_design: We focus on the genes that are significantly down-regulated and up-regulated in TCF-1-deficient and β-catenin transgenic thymocytes, respectively, to select for those genes that are potential target genes of β-catenin/TCF-1 pathway. And then those genes are subject to IPA pathway analysis searching for genes that are involved in thymocyte development and cell death.

first: Ruiqing

last: Wang


title: Expression data from human endometrium

first: Glyn

last: Bradley

state: Kent

institute: Pfizer Ltd

summary: The purpose of this study was to compare and contrast the expression of mRNA sequences in samples of endometrial glandular epithelium taken at discrete points in the menstrual cycle of healthy female subjects.  This study was approved by the Erasme Hospital Ethics Committee and was conducted at the Pfizer Clinical Research Unit at the Erasme hospital, Brussels.  The study was conducted in accordance with the Declaration of Helsinki on Ethical Principals for Medical Research Involving Human Subjects, adopted by the General Assembly of the World Medical Association (1996).  In addition, the study was conducted in accordance with the protocol, the principles of the International Conference on Harmonization guideline on Good Clinical Practice and applicable local regulatory requirements and laws.  Written informed consent was obtained from all participants in this study prior to screen. Female healthy subjects were between 20 and 39 years of age and had a regular menstrual cycle.  A total of 23 endometrial biopsies were taken from women at different stages of their menstrual cycle (mid & late follicular; early & mid luteal phases) by pipelle catheter.  Glandular epithelium was laser capture microdissected and total RNA was purified, labelled and hybridized to Affymetrix HG-U133 Plus 2 chips using standard protocols. The resulting data were subjected to a principal component analysis and assessment by a proprietary methodology, the causal reasoning engine.  Using this analysis we describe new progesterone marker genes and a robust methodology which may be useful for identifying endometrial pharmacological response genes or diagnostic disease markers.

overall_design: A single sample was taken from each of 20 human subjects at time points across the menstrual cycle.

first: Paul

last: O'Regan

first: Nick

last: Pullen


title: Inferring drug-induced gene regulatory relationships in primary human hepatocytes

city: Tuebingen

first: Michael

last: Bonin

state: BW

address: CAlwerstr. 7

department: Medical Genetics

institute: University Tuebingen

summary: Statins are widely used cholesterol-lowering drugs that inhibit HMG-CoA reductase, a key enzyme in cholesterol synthesis. In some cases, however, these drugs may cause a number of toxic side effects in hepatocytes and skeletal muscle tissue. Currently, the specific molecular mechanisms that cause these adverse effects are not sufficiently understood. In this work, genome-wide RNA expression changes in primary human hepatocytes of six individuals were measured at five time points upon atorvastatin treatment. A novel systems-level analysis workflow was applied to reconstruct regulatory mechanisms based on these drug-response data and available knowledge about transcription factor binding specificities, protein-protein interactions and protein-drug interactions. Several previously unknown transcription factors, regulatory cofactors and signaling molecules were found to be involved in atorvastatin-responsive gene expression. Some novel relationships, e.g., the regulatory influence of nuclear receptor NR2C2 on CYP3A4, were successfully validated in wet-lab experiments.

overall_design: Whole-genome Affymetrix U133 Plus 2.0 (Affymetrix, Santa Clara, CA) microarray measurements were conducted using samples of primary human hepatocytes cultured from six individuals (i.e., hh62, hh65, hh67, hh79, hh80 and hh81). Each sample was treated with atorvastatin and dimethylsulfoxide (DMSO), which was used as a control substance. Microarray measurements were performed at five time points (6 h, 12 h, 24 h, 48 h and 72 h) after the drug stimulus.

first: Uli

last: Zanger

first: Matthias

last: Reuss

first: Adrian

last: Schroeder


title: Gene expression changes induced by dimerization of intracellular c-Mpl in cord blood CD34+ progenitors

city: Los Angeles

first: chintan

last: parekh

address: 610 Charles Young Drive

institute: UCLA

summary:
Homodimerization of Mpl can also be accomplished in the absence of Tpo, by binding of a synthetic ligand (Chemical inducer of dimerization, CID) to a constitutively expressed fusion protein F36VMpl consisting of a ligand binding domain (F36V) and the intracellular signaling domain of Mpl. In contrast to Tpo stimulation, F36VMpl dimerization in human CD34+ progenitor cells generates robust erythropoiesis.
Microarray gene expression profiling of progenitors demonstrated that F36VMpl dimerization, but not Tpo, results in upregulation of critical erythroid genes.

overall_design: CD34+ cord blood cells were transduced with F36VMpl-GFP (GFP reporter gene) and cultured on MS-5 stroma for 7 days in the presence of CID, Tpo, Epo or no factors (no CID, negative control). CD34+GFP+ cells were sorted on day 7 and subjected to microarray (n=3 independent experiments).

first: Chintan

last: Parekh


title: A five-gene signature is associated with tumor progression and poor prognosis in colorectal cancer

city: Guangzhou

first: Jianming

last: Li

address: Guangzhou North Road

country: China

institute: Southern Medical University

summary: We developed an experimentally derived molecular signature from mouse tumor models that is closely associated with survival of colorectal cancer (CRC) patients.

overall_design: We isolated single cell-derived progenies (SCPs) from the SW480 CRC cell line and compared their metastatic potential in an orthotopic implantation model of murine CRC. We compared the differences in the gene expression profiles of a high metastatic variant SCP51, a low metastatic variant SCP58 and their parent SW480/EGFP.

first: Jummei

last: Hao

first: Yanqing

last: Ding


title: GATA3 Reprograms Basal Breast Cancer Cells towards a Luminal Subtype and Inhibits Metastases through Suppression of Lysyl Oxidase

city: Bethesda

first: Jeffrey

last: Green

state: MD

address: Rm 4054, 37 Convent Drive

institute: NCI

summary: The transcription factor GATA3 is essential for luminal cell differentiation during mammary gland development and critical for formation of the luminal subtypes of breast cancer. Ectopic expression of GATA3 promoted global alterations of the transcriptome of basal triple-negative breast cancer cells resulting in molecular and cellular changes associated with a more differentiated, luminal tumor subtype and a concomitant reduction in primary tumor growth, lung metastasis, and macrophage recruitment at the metastatic site.  Importantly, we demonstrate that the inhibition of metastases by GATA3 results from the suppression of lysyl oxidase (LOX) expression, a metastasis promoting matrix protein that affects cell proliferation, cross-linking of extracellular collagen types, and establishment of the metastatic niche.

overall_design: There are 2 samples sent in triplicates.

first: Isabel

middle: M

last: Chu


title: Establishment and Comparative Characterization of Novel Non-Small Cell Lung Cancer Cell Lines and Their Corresponding Tumor Tissue

status: Public on Aug 31 2011

city: Heidelberg

first: Ruprecht

last: Kuner

address: Im Neuenheimer Feld 460

department: Molecular Genetics

institute: German Cancer Research Center and National Center of Tumor Diseases

summary: Cell lines play an important role for studying tumor biology and novel therapeutic agents. We demonstrated that cell lines represent a useful and reliable in vitro system for studying basic mechanisms in lung cancer. Moreover, we presented 3 novel, comprehensively characterized SCC cell lines.

overall_design: Establishment and Comparative Characterization of Three Non-Small Cell Lung Cancer Cell Lines and Their Corresponding Tumor Tissue

first: Holger

last: Sueltmann

first: Christian

last: Bender

last: Meister

first: Sandra

last: Gottschling


title: Expression data from 45-month-old Slovak children with high PCBs exposure

city: Washington DC

first: Sisir

middle: K.

last: Dutta

state: DC

address: 415 College Street, NW

department: Biology

institute: Howard University

summary:
Exposure to polychlorobiphenyls (PCBs) is known to cause serious health effects in human but the gene expression profiles leading to development of different diseases and disorders are not fully understood. The knowledge of global gene expression will help us to develop early disease or disorder biomarkers for PCB-induced health effects.

We used microarrays to detail the global gene expression profile underlying the effects of high PCB exposure to Slovak 45-month-old children leading to identification of distinct classes of up-regulated and down-regulated genes and cellular processes.

overall_design: Extraction of total RNA was performed by using Qiagen PAXgene Blood RNA Kit IVD according to the manufacturer's instructions. Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 6 microgram of total RNA (Expression Analysis Technical Manual, 2001, Affymetrix). Following fragmentation, 10 microgram of cRNA were hybridized for 16 hr at 45C on GeneChip Human Genome Arrays (HGU133 plus 2.0). GeneChips were washed and stained in the Affymetrix Fluidics Station 450 and scanned using the Affymetrix GeneArray Scanner 3000. The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings and global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 150.

first: Somiranjan

last: Ghosh

first: Partha

middle: S

last: Mitra

middle: K

first: Tomas

last: Trnovec

first: Lubica

last: Pulkovicova

first: Eric

last: Hoffman

first: Irva

last: Hertz-Picciotto

first: Dean

last: Sonneborn

first: Svetlana

last: Ghimbovschi


title: The Effect of Repeated Whole Cigarette Smoke Challenge on Human Air-Liquid Interface Lung Epithelial Cultures

city: Loughborough

first: Iain

last: Dougall

address: Bakewell Road

institute: AstraZeneca R&D Charnwood

summary:
Airway epithelial cells are the first cells of the lungs to be exposed to the toxic agents contained within cigarette smoke. Accordingly, the response of these cells to this challenge is of considerable interest in the context of diseases in which cigarette smoke is a major aetiological factor.
We used Affymetrix microarrays to study the effects of repeated cigarette smoke challenge on three-dimensional human lung airway epithelial cultures.

overall_design: We have used cultures from four individual donors, and compared the effects of repeated cigarette smoke challenge (30mins exposure on four separate days), with no challenge.

first: Sally

last: Stinson

first: Wendy

last: Merrison

first: Matthew

last: Blades

first: Edward

last: Ainscow

first: Nicholas

last: Cox

first: Rebecca

last: Walls

first: Stuart

last: Ball

first: Martyn

last: Foster


title: Identification of Med26 target genes in Human HEK 293T cells

city: Kansas City

first: Chris

last: Seidel

state: MO

department: Genomics

institute: Stowers Institute

summary: Med26 is a subunit of the Human Mediator complex. The Mediator complex is an evolutionarily conserved coregulatory complex that interacts with RNA polymerase II to regulate gene expression. In metazoa, Mediator is composed of some 30 distinct subunits. Mediator exists in multiple, functionally distinct forms that share a common core of subunits and can be distinguished by the presence or absence of a kinase module composed of Med12, Med13, Cdk8, and Cyclin C. In higher eukaryotes, a subset of Mediator complexes is associated with an additional subunit, Med26. This Med26-containing Mediator copurifies from cells with little or no kinase module, but near-stoichiometric Pol II. Evidence suggests that Med26-containing Mediator plays a key role in transcriptional activation however, the mechanism(s) by which Med26 contributes to this process are not known. To identify Med26 target genes, we used Affymetrix U133A plus 2.0 expression arrays to analyze mRNA expression in 293T cells from which Med26 had been depleted by transient transfection by each of three different siRNAs.

overall_design: Three different independent Med26 siRNA knockdowns were compared to a non-targeting control in triplicate, for a total of 12 samples.

first: Hidehisa

last: Takahashi

first: Joan

last: Conaway

first: Ronald


title: Gene expression data from WT and Klf3 KO mouse CD19+ splenic B cells

status: Public on Aug 26 2011

city: Sydney

first: Richard

middle: Carden

last: Pearson

state: NSW

address: Gate 11 Botany Street

department: School of Biotechnology and Biomolecular Sciences

country: Australia

institute: University of New South Wales

summary:
To investigate the roles of Klf3 in B lymphopoiesis, CD19+ B cells were sorted from the spleens of WT and Klf3 KO mice (Molecular and Cellular Biology (2008); 28:3967–3978).
Following RNA extraction, gene expression was compared in WT and Klf3 KO CD19+splenic B cells using Affymetrix microarrays.

overall_design: 4 wildtype and 4 Klf3 KO mice were analysed, aged between 10 and 12 weeks

first: Merlin

last: Crossley


title: Integrative genomic, transcriptomic and RNAi analysis indicates a potential oncogenic role for FAM110B in castration-resistant prostate cancer.

status: Public on Aug 29 2011

city: Helsinki

first: Maija

last: Wolf

address: Biomedicum Helsinki 2U, Tukholmankatu 8,

country: Finland

institute: Institute for Molecular Medicine Finland (FIMM)

summary:
Background: Castration-resistant prostate cancer (CRPC) represents a therapeutic challenge for current medications.
Methods: In order to explore the molecular mechanisms involved in CRPC progression and to identify new therapeutic targets, we analyzed a unique sample set of 11 castration-resistant prostate cancers and 7 advanced tumors by array-CGH and gene expression microarrays. The genome-wide DNA and RNA data were integrated to identify genes whose overexpression was driven by their amplification. To assess the functional role of these genes, their expression was analyzed in a transcriptional dataset of 329 clinical prostate cancers and the corresponding gene products were silenced using RNA interference in prostate cancer cells.
Results: Six recurrent genetic targets were identified in the CRPCs; ATP1B1, AR, FAM110B, LAS1L, MYC and YIPF6. In addition to AR and MYC, FAM110B emerged as a potential key gene involved in CRPC progression in a subset of the tumors. FAM110B was able to regulate AR signaling in prostate cancer cells and FAM110B itself was regulated by androgens. FAM110B siRNA inhibited the growth of prostate cancer cells in vitro, and this effect was substantially enhanced in androgen deficient conditions. Ectopic FAM110B expression in non-cancerous epithelial prostate cells induced aneuploidy and impaired antigen presentation.
Conclusions: The DNA / RNA gene outlier detection combined with siRNA cell proliferation assay identified FAM110B as a potential growth promoting key gene for CRPC. FAM110B appears to have a key role in the androgen signaling and progression of CRPC impacting multiple cancer hallmarks and therefore highlighting a potential therapeutic target.

overall_design:
[1] Gene expression levels from 13 samples were measured using Affymetrix GeneChip Human Genome U133 plus 2.0 arrays. Sample processing and labeling were done according to the protocol provided by Affymetrix. Three micrograms of total RNA from each sample was used for the initial one-cycle cDNA synthesis. Arrays were scanned immediately after staining using a GeneChip scanner (Affymetrix).

[2] aCGH was performed from 18 prostate cancer samples using 44K arrays by Agilent Technologies. Male genomic DNA (catalog number G1471, Promega, Madison, WI) was used as reference in all hybridizations.

[3] Gene expression changes following FAM110B silencing in LNCaP prostate cancer cells (48 h: pooled FAM110B siRNA vs. Scrambled siRNA; 72 h: FAM110B siRNAs 1 - 4 and pooled siRNA vs. Scrambled siRNA) and ectopic FAM110B over-expression in both RWPE-1 and LNCaP cells (FAM110B-pEGFP vs. pEGFP, 48 h) were analyzed. The raw data for these Samples are available in the 'GSE28403_LNCaP_RWPE-1_Raw_Data.txt' file, which is linked to this record as a supplementary file.

first: Paula

last: Vainio

first: Henrik

last: Edgren

first: Tao

last: He

first: Pekka

last: Kohonen

first: John-Patrick

last: Mpindi

first: Frank

last: Smit

first: Gerald

last: Verhaegh

first: Jack

last: Schalken

first: Merja

last: Perälä

first: Kristiina

last: Iljin

first: Olli

last: Kallioniemi


title: Akt1 is critical in Maintaining the Blood-Testis Barrier Following Exposure to the Neonatal Goitrogen, 6-N-Propylthiouracil (PTU)

status: Public on Sep 04 2011

city: Providence

first: Mary

last: Hixon

state: RI

address: 70 Ship St

institute: Brown University

summary: Akt1 plays a protective role in the postnatal C57BL6 mouse testis following lactational exposure to the neonatal goitrogen, propylthiouracil (PTU). To elucidate the transcriptional profile mediating this phenotypic effect, we monitored changes in testicular gene expression at postnatal days (PNDs) 15 and 25 in Akt1+/+, Akt1+/-, and Akt1-/- testes following exposure to 0.01% PTU allowing us to determine changes in gene expression due to 1.) genotype effects; 2.) exposure effects; and 3.) genotype-by-exposure interactions. Early PTU-dependent gene changes included genes involved in lipid metabolism, spermatid differentiation, meiosis and adhesion. Early Akt1-dependent effects were associated with germ cell development, spermatid development and differentiation, and sperm motility. By PND25, the Akt1 gene-environment interaction had pronounced effects on genes associated with Sertoli cell (SC) differentiation and claudin-associated junctional formation suggesting delayed formation of the blood-testis barrier (BTB). To confirm these observations, biotin tracer experiments demonstrated a permeable blood-testis barrier in PTU-exposed PKBalpha/Akt1-/- tubules as late as PND25 compared to PTU-exposed Akt1+/+ seminiferous tubules. Transmission electron microscopy demonstrated altered SC morphology, aberrant SC localization, and disorganized actin bundle formation. Taken together, loss of Akt1 coupled with postnatal exposure to the neonatal goitrogen, PTU, in the testis contributes to a transcriptional profile associated with impaired integrity of the blood-testis barrier. In summary, the Akt1-/- mouse represents a potentially important model to study BTB formation and reassembly in response to male reproductive toxicants and the various signaling networks which mediate these responses.

overall_design: The microarray analysis employed a balanced factorial design, with one chip created for each of three mice under each experimental condition:  mouse genotype (Akt1+/+, Akt1+/-, and Akt1-/-), exposure (PTU and Control), and age (sacrificed at PND15 and 25), with a total of 36 mice and 36 chips. MoGene 1.0 st v1 arrays were used for the samples from PND 15 and Mouse Genome 430 2.0 arrays were used for the samples from PND 25. One chip, PTU-exposed, Akt1-/-, PND25, was determined to not be of high quality and was not included in the analysis or provided here.

first: Jeena

last: Santos-Ahmed

first: Allison

last: DeLong

first: Luch

last: Boekelheide

first: Caitlin

last: Brown

first: Zhijin

last: Wu


title: Effect of anti-miR-33 treatment on gene expression in non-human primate liver

status: Public on Aug 27 2011

city: San Diego

first: Christine

last: Esau

state: CA

address: 3545 John Hopkins Court

institute: Regulus Therapeutics

summary: In this study the effect of anti-miR-33 treatment on plasma and liver lipid profiles was examined in non-human primates.  A significant increase in plasma HDL-C, and a significant decrease in plasma triglyceride levels were observed.

overall_design: African green monkeys on a Normal chow diet were treated with anti-miR-33 or control anti-miR for 4 weeks and were then switched to a High Carb/Med. Cholesterol diet and treated with anti-miR-33 or control anti-miR for 8 more weeks (n=6/group).  Gene expression profiling was performed on liver biopsies obtained at -5 weeks (baseline),  4 weeks and 12 weeks.

first: Vivek

last: Kaimal


title: Identify the downstream targets of CHIR99021 and XAV939 in EpiSC using microarray analysis

status: Public on Aug 25 2011

city: los angeles

first: Qilong

last: Ying

address: 1425 san pablo st BCC509b

institute: USC

summary:
The requirements for self-renewal differ between EpiSCs and ES cells and the underlying mechanism is largely unknown. Here we show that mouse EpiSCs can be efficiently derived and robustly propagated even from single cells, using two small-molecule inhibitors: CHIR99021 and XAV939.
To better define how CHIR and XAV act together to maintain EpiSC self-renewal, we performed microarray analyses to identify their downstream targets. The data show the genes regulated by addition of CHIR, XAV or both.

overall_design: EpiSCs starved in serum free growth medium (shown in growth protocol) for 12hrs were treated with CHIR (2hrs), XAV(4hrs), or both, after which total RNA was extracted for analysis.

first: Hoon

last: Kim

first: Chih-I

last: Tai


title: Atorvastatin, rosuvastatin and rifampicin effect on human primary hepatocyte transcriptome [Affymetrix platform]

first: Peter

last: Juvan

institute: Faculty of Medicine, University of Ljubljana

summary:
With particular emphasis on interactions between cholesterol homeostasis and drug metabolism we investigate the transcriptome of human primary hepatocytes treated by two commonly prescribed cholesterol lowering drugs atorvastatin and rosuvastatin and by rifampicin that serves as an outgroup as well as a model substance for induction of nuclear receptor PXR.
Expression profiling with Affymetrix whole genome arrays shows that statins induce extensive transcriptome changes.

overall_design: 7 condition experiment: 3 treatments (atorvastatin, rifampicin, rosuvastatin), each measured at 2 time points (24 and 48 hours), and untreated cells. 4-6 biological replicates for each condition.

first: Mateja

last: Hafner

first: Tadeja

last: Režen

first: Damjana

last: Rozman


title: Impact of Gene Expression Profiling Based Risk Stratification in Patients with Myeloma Receiving Initial Therapy with Lenalidomide and Dexamethasone

city: Rochester

first: Shaji

last: Kumar

state: MN

address: 200 First Street SW

department: Hematology

institute: Mayo Clinic

summary:
Detection of specific chromosomal abnormalities by FISH and metaphase cytogenetics allows risk stratification in multiple myeloma (MM); however, gene expression profiling (GEP) based signatures may enable more specific risk categorization.
We examined the utility of two GEP-based risk stratification systems among patients undergoing initial therapy with lenalidomide in the context of a phase 3 trial.

overall_design: The E4A03 clinical trial randomized patients with previously untreated MM to lenalidomide and either standard-dose dexamethasone. Baseline bone marrow samples were obtained from consenting patients. The marrow aspirates were subjected to a fully automated ROBOSEP cell separation system that utilizes immunomagnetic technology to positively select for CD 138+ cells. The purity of the sorting was confirmed by 3-color immunofluorescent slide based assessment on the sorted cells. The plasma cell gene expression proﬁles were analyzed using U133 Plus 2.0 array. All samples were run individually with no pooling. The GEP-70 signature was determined as previously described, using log2 transformed raw MAS 5.0 signals. The GEP15 classification was performed as previously described, with the patients in highest quartile for the risk score being considered as high risk.

first: Hajime

last: Uno


title: Effect of endoplasmic reticulum stress on gene expression in lymphoblastoid cell lines.

status: Public on Aug 23 2011

city: Pittsburgh

first: Adam

last: Rosendorff

state: PA

address: 530 45th Street, 3rd Fl, Bay 9

department: Pathology

institute: University of Pittsburgh

summary: The ER stress inducing agent Thapsigargin (TG) and/or the cytoprotective agent Salubrinal were applied to lymphoblastoid cell lines. TG induced lytic replication as well as a distinct pattern of gene expression changes. This study was designed to identify host genes mediating lytic replication secondary to ER stress.

overall_design: DMSO or TG applied for 6 hrs then washed out, immediately followed by either (i) DMSO, or  (ii) SAL resulting in 4 conditions (DMSO, TG, SAL, or TG+SAL). Total RNA harvested at 3, 24 or 72hrs for Affymetrix analysis.


title: Human embryonic stem cells as a tool to study hepatocyte differentiation

status: Public on Aug 22 2011

city: Charleston

first: Stephen

middle: A

last: Duncan

state: SC

address: 173 Ashley Avenue, BSB 6th Floor, Room 657A

department: Regenerative Medicine and Cell Biology

institute: Medical University South Carolina

summary: The availability of pluripotent stem cells offers the possibility of using such cells to model hepatic disease and development. With this in mind, we previously established a protocol that facilitates the differentiation of both human embryonic stem cells and induced pluritpotent cells into cells with hepatocyte characteristics. The use of highly defined culture conditions and the avoidance of feeder cells or embryoid bodies allowed synchronous and reproducible differentiation to occur. The differentiation toward a hepatocyte–like fate appeared to recapitulate many of the stages normally associated with the formation of hepatocytes in vivo. In the current study we addressed the feasibility of using human pluripotent stem cells to probe the molecular mechanisms underlying human hepatocyte differentiation. We demonstrate i) that human ES cells express a number of mRNAs that characterize each stage in the differentiation process, ii) that gene expression can be efficiently depleted throughout the differentiation time course using shRNAs expressed from lentiviruses, and iii) that the nuclear hormone receptor HNF4a is essential for specification of human hepatic progenitor cells by establishing expression of the network of transcription factors that control hepatocyte cell fate.

overall_design: RNA was collected at each stage of the hepatocyte differentiation protocol and used to probe Affymetrix U133 plus 2.0 arrays during three independent differentiations.


title: Gene expression signature and the prediction of liver metastasis in colorectal cancer by DNA microarray

city: Bunkyo-ku

first: Toshiaki

last: Watanabe

state: Tokyo

department: Department of Surgical Oncology

institute: University of Tokyo

summary:
Samples were taken from colorectal cancers in surgically resected specimens in 189 colorectal cancer patients. The expression profiles were determined using Affymetrix Human Genome U133 Plus 2.0 arrays. Comparison between the sample groups allow to identify a set of discriminating genes that can be used for molecular markers for predicting liver metastasis.

Keywords: repeat

overall_design: One hundred and eighty nine patients who underwent surgical resection of colorectal cancer were included in this study. Patients were evaluated at 3-month intervals for the first postoperative year and at 6-month intervals thereafter. Liver metastases were identified by clinical and laboratory examination, completed by liver ultrasound or CT scan. Patients were divided randomly into a training and a validation set. A training set consisted of 160 patients, while a test set 29 patients.

first: Takashi

last: Kobunai

first: Etsuko

last: Sakamoto

first: Eriko

last: Hashimoto


title: DNA microarrays (time course) of MEFs transduced with SKO plus HDAC7 or MEF2C

status: Public on Aug 18 2011

first: Duanqing

last: Pei

state: Guangdong

address: Room 301, International Business Incubator, Guangzhou science park

department: Center for Molecular Medicine

institute: Guangzhou Institute of Biomedicine and Health, Chinese Academy of Sciences(GIBH.CAS)

summary:
Overexpression HDAC7 can enhance iPS efficiency in SKO by supressing MEF2 factors
We used microarrays to identify changes induced by overexpression of HDAC7 or MEF2C.

overall_design: MEFs were transduced with SKO plus HDAC7 or MEF2C compared to SKO plus empty vector(Flag), GFP as controls. TRIZOL cell lysates were prepared from D6 and D10.

first: Qiang

last: Zhuang

first: Wenzhi

last: He


title: Expression profile of miR-101 transfection in MCF-7 cells compared with scramble control

status: Public on Aug 20 2011

city: Copenhagen

first: Jiayu

last: Wen

address: Ole Maaloes Vej 5

country: Denmark

institute: University of Copenhagen

summary: Autophagy is an evolutionarily conserved mechanism of cellular self-digestion in which proteins and organelles are degraded through delivery to lysosomes. Defects in this process are implicated in numerous human diseases including cancer. To further elucidate regulatory mechanisms of autophagy, we performed a functional screen in search of microRNAs (miRNAs), which regulate the autophagic flux in breast cancer cells. In this study we identified the tumor suppressive miRNA, miR-101, as a potent inhibitor of basal, etoposide- and rapamycin-induced autophagy. Through transcriptome profiling, we identified three novel miR-101 targets, STMN1, RAB5A and ATG4D. siRNA-mediated depletion of these genes phenocopied the effect of miR-101 overexpression, demonstrating their importance in autophagy regulation. Importantly, overexpression of STMN1 could partially rescue cells from miR-101-mediated inhibition of autophagy, indicating a functional importance for this target. Finally, we show that miR-101-mediated inhibition of autophagy can sensitize breast cancer cells to 4-hydroxytamoxifen (4-OHT) mediated cell death. Collectively, these data establish a novel link between two highly important and rapidly growing research fields and present a new role for miR-101 as a key regulator of autophagy.

overall_design: MCF-7 cells were seeded in 6-cm plates and independent triplicate transfections were performed the following day with 50 nM miR-101 or scramble control using Lipofectamine 2000. Total RNA was harvested 24 h after transfection using Trizol reagent. There are a total of six arrays included in this experiment, including three biological replicates of mRNA expression after miR-101 over-expression and three scramble controls in MCF-7 cells.

first: Lisa

middle: B

last: Frankel

first: Michael

last: Lees

first: Maria

last: Høyer-Hansen

first: Thomas

last: Farkas

first: Anders

last: Krogh

first: Marja

last: Jäättelä

middle: H

last: Lund


title: Comparison of C57Bl/KalwRij mouse bone marrow to C57BL6 mouse bone marrow

status: Public on Aug 19 2011

city: Los Angeles

first: Jessica

middle: Aaron

last: Fowler

address: 675 Charles E. Young Drive south

institute: University of California, Los Angeles

summary: Multiple myeloma is a fatal hematological malignancy. In order to develop effective therapeutic approaches, it is critical to understand the pathogenesis of myeloma. The Radl 5T model of multiple myeloma is a clinically relevant murine model where myeloma spontaneously occurs in aged, in-bred C57BlKalwRij mice and can be propagated by intravenous inoculation of 5T myeloma cells into mice of the same strain. Importantly inoculation of 5T myeloma cells into C57Bl6 mice does not result in myeloma, demonstrating that the bone marrow (BM) microenvironment of the C57BlKalwRij strain provides a unique and permissive milieu for myeloma development. We hypothesized that cells of the BM microenvironment may provide essential stimuli for the development of multiple myeloma in vivo. We aim to determine the differences in expression within the bone marrow of C57Bl/KalwRij mice.


title: Robust Gene Expression Signature from Formalin-Fixed Paraffin-Embedded Samples Predicts Prognosis of Non-Small-Cell Lung Cancer Patients

city: Dallas

first: Xilong

last: Li

address: 5323 Harry Hines Blvd

department: Clinical Science

institute: UT Southwestern Medical  Center

summary:
The requirement of frozen tissues for microarray experiments limits the clinical usage of genome-wide expression profiling using microarray technology.
Keywords:  Lung Cancer Prognosis, Gene Expression Signature, Formalin Fixed Paraffin Embedded Samples
The goal of this study is to test the feasibility of developing lung cancer prognosis gene signatures using genome-wide expression profiling of formalin-fixed paraffin-embedded (FFPE) samples, which are widely available and provide a valuable rich source for studying the association of molecular changes in cancer and associated clinical outcomes. FFPE tumor specimens were collected, and total RNA was processed for analysis on the Affymetrix U133 plus 2.0 arrays according to Affymetrix protocols.  The quality control procedure for microarray data analysis was based on the percentage of present calls calculated by the MAS5 package. We selected 55 arrays with at least 15% of probe sets present, and we selected 1400 probe sets that present on all 55 arrays for data analysis. After microarray analysis QC, we used the RMA background correction algorithm to remove non-specific background  noise. A robust regression model was fitted to the probe level data, and the fitted expression values for the probes at the 3' end were used to summarize the probe set expression values.  Quantile-quantile normalization was used to normalize all the arrays. The 55 samples and the derived gene expression values for 1400 genes based on the robust regression model were used to develop gene signatures and were uploaded as supplementary data (GSE29013_fitted_1400_probes.txt).

overall_design: We micro dissected tumor area from FFPE specimen, and used Affymetrix U133 plus 2.0 arrays to obtain gene expression data.

first: Yang

last: Xie

first: Guanghua

last: Xiao

first: Kevin

middle: R

last: Coombes

first: Carmen

last: Behrens

first: Luisa

last: Solis

first: Gabriela

last: Raso

first: Lue

last: Girard

first: Heidi

last: Erickson

first: Jack

last: Roth

first: John

last: Heymach

first: Cesar

last: Moran

first: Kathy

last: Danenberg

last: Minna

first: Ignacio

middle: I

last: Wistuba


title: Sarcoidosis-specific markers from whole blood gene expression

status: Public on Aug 11 2011

city: San Francisco

first: Prescott

middle: Gurney

last: Woodruff

address: 505 Parnassus Ave

department: Medicine

institute: UCSF

summary: We hypothesized that microarray analyses of whole blood gene expression would identify patterns of gene expression useful in the diagnosis for sacroidosis and identify inflammatory mediators relevant to the underlying pathophysiology.

overall_design: We analyzed whole blood RNA from 37 patients with sarcoidosis, 20 healthy controls and 6 patients with hypersensitivity pneumonitis using genome-wide expression microarrays. We developed a classification algorithm using a derivation and validation subset approach, analyzed the most discriminative gene expression changes, and confirmed selected expression changes using flow-cytometry.

middle: G

first: Laura

middle: L

last: Koth


title: Expression data of ribosomal proteins from sorted hematopoietic stems cells from patients with low risk MDS.

status: Public on Aug 14 2011

city: New York

first: Christopher

last: Park

state: NY

address: 1275 York Avenue

institute: MSKCC

summary:
A role for reduced ribosomal protein gene dosage in both DBA and 5q- MDS suggests that other forms of MDS might also involve altered expression of ribosomal protein genes.
We used microarrays to interrogate the expression of ribosomal proteins from purified hematopoietic stems cells from patients with low risk myelodysplastic syndrome and age-matched healthy controls.

overall_design: Hematopoietic stem cells were sorted from 8 patients with low risk myelodysplastic syndrome and 11 age-matched healthy controls, and total RNA was  hybridized to Affymetrix microarrays.

first: Kelly

last: McGowan

middle: Y

first: Gregory


title: The nucleic-acid recognizing Toll-like receptors -3, -7 and -9 cooperatively protect against murine T cell lymphoma caused by endogenous retrovirus

status: Public on Aug 15 2011

city: München

first: Olivia

last: Prazeres da Costa

state: Bavaria

address: Trogerstr. 30

department: Medical Microbiology, Immunology and Hygiene

institute: Technische Universität München

summary: The genome of vertebrates contains endogenous retroviruses (ERVs) that have resulted from ancestral infections by exogenous retroviruses. ERVs are germline encoded, transmitted in a Mendelian fashion and account for about 8% of the human and 9.9% of the murine genome, respectively1, 2. By spontaneous activation and reintegration ERVs may cause insertional mutagenesis and thus participate in the process of malignant transformation or progression of tumor growth3, 4. However, if the innate immune system is able to recognize and control ERVs has not yet been elucidated. Here we report that, in vitro, nucleic-acid sensing TLRs on dendritic cells are activated by retroviral RNA and DNA from infected cells in vitro. Infection of TLR competent wild type mice with murine leukemia virus (MuLV)-like ERV isolates results in non-canonical gene upregulation, independent of type I IFN. In vivo, TLR3, -7 and -9 triple deficient mice (TLR379-/-) and mice with non functional TLR3, 7 and 9 signaling due to a mutation in UNC93B develop spontaneous ERV-induced viremia. More importantly, in TLR379-/- mice ERV-induced viremia correlates with acute T cell lymphoblastic leukemia (T-ALL). Multiple independent TLR379-/- T cell leukemia lines produce infectious MuLV of endogenous origin. These cell lines display de novo retroviral integration into the Nup214 or Notch1 gene locus leading to gene dysregulation that is reminiscent of aberrant Nup214 and Notch1 expression in human T-ALLs5. Overall, our results demonstrate that in addition to their role in innate immune defense against exogenous pathogens, TLR3,-7, and -9 may be essential for the control of endogenous retroviral mediated T-cell lymphomagenesis.

overall_design: The data covers two data sets. The data set covers two comparisons of the expression profile from old and young TLR379-/- knockout. Spleen was taken from and old wild type (C57BL/6 background) to compare it against an old TLR379-/- knockout and also from an young wild type (C57BL/6 background) to compare it against a young TLR379-/- knockout.   The second experiment includes three replicates of the wild type, the Baki-1MuLV infected C57BL/6, and the Sendai infected C57BL/6.


title: Gene expression from head and neck squamous cell carcinoma (SCCHN) cancer cells before and after figitumumab

status: Public on Aug 10 2011

city: Brussels

first: Sandra

last: Schmitz

address: avenue Hippocrate 54

department: Medical Oncology

country: Belgium

institute: UCL

summary:
Patients with palliative SCCHN were treated with figitumumab, an IGF-1R inhibitor. This receptor plays an important role in cell growth, proliferation and differentiation and is often overexpressed in SCCHN. No significant clinical activity was observed in our study
We used microarray to establish hypothesis for treatment resistance

overall_design: Tissue biopsies before and after figitumumab were stored in RNA later, total RNA was extracted and hybridized on Affymetrix microarrays

first: Laurent

last: Knoops


title: Role and function of STAT5 in BCR-ABL1 driven pre-B cells

status: Public on Aug 24 2011

first: Markus

last: Müschen

address: 4650 Sunset Blvd

department: Childrens Hospital Los Angeles

country: USA

institute: University of Southern California

summary: In order to investigate the function of STAT5 in ALL, we isolated bone marrow cells from STAT5 fl/fl mice and transformed them with BCR-ABL1. In a second transduction the BCR-ABL1 driven pre-B cells were transformed either with CRE-GFP or empty vector control (GFP) and subjected to gene expression analysis.

overall_design: Three days post transduction, total RNA of GFP positive sorted cells was extracted and subjected to gene expression analysis.

first: Parham

last: Ramezani-Rad


title: Gene expression analysis of human pediatric mesenchymal stem cells (hpMSCs) upon expression of EWS-FLI-1

status: Public on Aug 05 2011

city: Torino

first: Paolo

last: Provero

address: Via Nizza 52

department: Molecular Biotechnology and Health Sciences

institute: University of Turin

summary: Cancer stem cells (CSCs) display plasticity and self-renewal properties reminiscent of normal tissue stem cells, but the events responsible for their emergence remain obscure. We recently identified CSCs in Ewing sarcoma family tumors (ESFTs) and showed that they retain mesenchymal stem cell (MSC) plasticity. In the present study, we addressed the mechanisms that underlie ESFT CSC development. We show that the EWS-FLI-1 fusion gene, associated with 85%-90% of ESFTs and believed to initiate their pathogenesis, induces expression of the embryonic stem cell (ESC) genes OCT4, SOX2, and NANOG in human pediatric MSCs (hpMSCs) but not in their adult counterparts. Moreover, under appropriate culture conditions, hpMSCs expressing EWS-FLI-1 generate a cell subpopulation displaying ESFT CSC features in vitro. We further demonstrate that induction of the ESFT CSC phenotype is the result of the combined effect of EWS-FLI-1 on its target gene expression and repression of microRNA-145 (miRNA145) promoter activity. Finally, we provide evidence that EWS-FLI-1 and miRNA-145 function in a mutually repressive feedback loop and identify their common target gene, SOX2, in addition to miRNA145 itself, as key players in ESFT cell differentiation and tumorigenicity. Our observations provide insight for the first time into the mechanisms whereby a single oncogene can reprogram primary cells to display a CSC phenotype.

overall_design: 4 samples of hpMSCs expressing EWS-FLI-1 vs. 4 matched samples of empty-vector-infected cells.

first: Nicoló

last: Riggi

first: Mario-Luca

last: Suvá

first: Claudio

last: De Vito

first: Jean-Christophe

last: Stehle

first: Karine

last: Baumer

first: Luisa

last: Cironi

first: Michalina

last: Janiszewska

first: Tanja

last: Petricevic

first: Domizio

first: Stéphane

last: Tercier

first: Jean-Marc

last: Joseph

first: Louis

last: Guillou

first: Ivan

last: Stamenkovic


title: Microarray analysis of gene expression profile in HCT116 colon cancer cells expressed the isoform A or isoform B of the Tazarotene-induced gene 1.

city: Sindian City

first: Shun-Yuan

last: Jiang

state: Taipei county

address: 289 Jianguo Rd

department: Department of Research

country: Taiwan

institute: Buddhist Tzu Chi General Hospital, Taipei Branch

summary: Tazarotene-induced gene 1 (TIG1), also named as retinoic acid receptor responder 1 (RARRES1), is a retinoid inducible type II tumor suppressor gene; the TIG1B isoform inhibits growth and invasion of cancer cells. Expression of TIG1B is frequently downregulated in various cancer tissues; however, the expression and activities of the TIG1A isoform has yet to be analyzed. This study investigated the effects of TIG1A and TIG1B isoforms on gene expression profiles of colon cancer cells. TIG1A, TIG1B and control stable clones derived from HCT116 colon cells were established using the GeneSwitch system. TIG1 isoform expression was induced upon 5 micro Molar of mifepristone (MFP) treatment for 24 hr. Biological triplicate samples were prepared and gene expression profiles were determined by microarray using human genome HGU133 plus 2 array (Affymatrix). Upon induction of TIG1A and TIG1B expression for 24 hr, a total of 129 and 55 genes were significantly altered, respectively. Of the genes analyzed, 23 and 6 genes were up- and downregulated, respectively in both TIG1A and TIG1B expressing cells.

overall_design: TIG1A, TIG1B and control stable clones derived from HCT116 colon cells were established using the GeneSwitch system. Inducible stable clones were plated in 15-cm dishes overnight in maintaining medium free of hygromycin and zeocin. Cells were refreshed with medium containing 5 micro molar of mifepristone and then incubated overnight. Cells were washed with ice-cold PBS and then harvested. Total RNA was prepared. Biological triplicate samples were prepared for control, TIGA and TIG1B stable cells. Samples of cRNA were prepared, labeled with biotin, and then hybridized to Human Genome U133 Plus 2.0 Array.


title: Gene expression data following Cyclin T2 and Cyclin T1 depletion by shRNA in HeLa cells

status: Public on Aug 03 2011

city: Houston

first: Andrew

middle: P

last: Rice

state: TX

address: MS BCM385,One Baylor Plaza

department: Molecular Virology & Microbiology

institute: Baylor College of Medicine

summary: We have characterized gene expression changes in HeLa cells following long term depletion of Cyclin T2 or Cyclin T1 using shRNA

overall_design: HeLa cells were transduced with VSV-G pseudotyped lentiviral vectors expressing shRNA against either Cyclin T2 or Cyclin T1.  As a control, cells were transduced with shRNA vector with four nucleotides mismatch in the Cyclin T1 mRNA that has been previously shown to have minimal effects on mRNA expression levels. The vectors have a GFP reporter that can be used to estimate transduction efficiency.  Five days post-transduction, cells were harvested and total RNA extracted.  Transcriptional profiling was carried out on these RNA samples.  Two independent biological replicate experiments were carried out in this analysis and the xpression values normalized by GC-RMA and averaged.  The following comparisons were made: MM to Cyclin T2 and MM to Cyclin T1.

first: Rajesh

last: Ramakrishnan


title: Expression data of cancer cell lines

city: La Jolla

first: Daniel

last: Nomura

address: 10550 North Torrey Pines Rd. SR107

institute: the Scripps Research Institute

overall_design: Expression profiles of aggressive versus non-aggressive ovarian, breast, melanoma, and prostate cancer cell lines was determined. 231MFP, C8161, SKOV3, DU145, and PC3 are aggressive and MCF7, MUM2C, OVCAR3, and LNCaP are non-aggressive cancer cells. We are not comparing across all of the cell lines--just between C8161 and MUM2C, SKOV3 and OVCAR3, 231MFP and MCF7, and LNCaP/DU145/PC3. Therefore the normalization strategies used are different. We have not used the same normalization strategy

first: Sherry

last: Niessen

first: Benjamin

middle: F

last: Cravatt


title: E.coli response to Antimicrobial Arylamides

city: Philadelphia

first: Bruk

last: Mensa

address: 1010 Stellar Chance Building, 422 Curie Blvd.

department: Biochemistry and Biophysics

institute: University of Pennsylvania, School of Medicine

summary:
We treated logarithmically growing cultures of E.coli with a sub-lethal dose of an antimicrobial arylamide compound (PMX 10070) and Polymyxin B sulfate to measure transcriptional responses in an effort to understand mechanism of action
Treated samples were assayed at time = 20min and time = 60min after arylamide and polymyxin B exposure

overall_design: E.coli were isolated and RNA extracted at different time points after exposure to arylamide, polymyxin B or control

first: William

last: DeGrado


title: RNAi screen identifies Brd4 as a therapeutic target in acute myeloid leukemia

status: Public on Aug 04 2011

city: Cold Spring Harbor

first: Junwei

last: Shi

address: 1 Bungtown Rd

institute: cold spring harbor lab

summary: Epigenetic pathways regulate gene expression by controlling and interpreting chromatin modifications. Cancer cells are characterized by altered epigenetic landscapes and commonly exploit the chromatin regulatory machinery to enforce oncogenic gene expression programs. While chromatin alterations are, in principle, reversible and often amendable to drug intervention, the promise of targeting such pathways therapeutically has been hampered by our limited understanding of cancer-specific epigenetic dependencies. Here we describe a non-biased approach to probe epigenetic vulnerabilities in acute myeloid leukemia (AML) – an aggressive hematopoietic malignancy often associated with aberrant chromatin states. By screening a custom shRNA library targeting known chromatin regulators in a genetically defined AML mouse model, we identify the bromodomain-containing protein Brd4 as a critical requirement for disease maintenance. Suppression of Brd4 using shRNAs or the small-molecule inhibitor JQ1 led to robust anti-leukemic effects in vitro and in vivo, accompanied by terminal myeloid differentiation. Extensive evaluation of JQ1-sensitivity in primary human leukemia samples and in established cell lines revealed a broad activity of this compound against diverse AML subtypes. These effects are, at least in part, due to a requirement for Brd4 in maintaining Myc expression and promoting aberrant self-renewal. Together, our results indicate that Brd4 is a promising therapeutic target in AML and identify a small molecule that efficiently targets Myc. These findings also highlight the utility of RNAi screening as a discovery platform for revealing epigenetic vulnerabilities for direct pharmacologic intervention in cancer.

overall_design: In order to understand downstream targets of Brd4, we performed array in murine or human MLL-AF9/NrasG12D cell line under the condition that Brd4 was suppressed by using shRNAs or the small molecule inhibitor JQ1. To test the hypothesis that Myc might be an important target of Brd4, we performed arrary on murine ectopic Myc overexpression MLL-AF9/NrasG12D cell under JQ1 treatment.

first: Johannes

last: Zuber

first: Eric

last: Wang

first: Amy

last: Rappaport

first: Jun

last: Qi

first: Meredith

middle: J

last: Taylor

first: Christopher

last: Johns

first: James

middle: E

last: Bradner

first: Scott

middle: W

last: Lowe

last: Vakoc


title: Expression of Splicing Factor Genes is Reduced in Human Obesity and Contributes to Enhanced Lipogenesis

city: Boston

first: Mary Elizabeth

last: Patti

state: MA

address: 1 Joslin Place

department: Research Division

institute: Joslin Diabetes Center

summary: Alternative mRNA splicing provides transcript diversity and has been proposed to contribute to several human diseases. Here, we demonstrate that expression of genes regulating RNA processing is decreased in both liver and skeletal muscle of obese humans. To determine the metabolic impact of reduced splicing factor expression, we further evaluated the splicing factor, SFRS10, identified as down-regulated in obese human liver and skeletal muscle and in high fat fed rodents. siRNA-mediated reductions in SFRS10 expression induced lipogenesis and lipid accumulation in cultured hepatocytes. Moreover, SFRS10 heterozygous mice have both increased hepatic lipogenic gene expression and hypertriglyceridemia. We also demonstrate that LPIN1, a key regulator of lipid metabolism, is a splicing target of SFRS10, with reduced SFRS10 levels favoring the lipogenic β isoform of LPIN1. Importantly, LPIN1β-specific siRNA abolished the lipogenic effects of decreased SFRS10 expression. Together, our results indicate reduced expression of SFRS10 alters LPIN1 splicing and induces lipogenesis, demonstrating that reduced splicing factor expression observed in human tissues may contribute to metabolic phenotypes associated with human obesity.

overall_design: Skeletal muscle samples were obtained from 10 lean control subjects and 7 obese subjects with either IGT or DM2 undergoing elective cholecystectomy.  Data for liver samples presented in the same manuscript are available at GEO GSE15653.  In this analysis RNA was isolated for cRNA preparation and hybridized to Affymetrix Human Genome U133 Plus 2.0 microarrays.

first: Jussi

last: Pihlajamäki

first: Carles

last: Lerin

first: Paula

last: Itkonen

first: Tanner

last: Boes

first: Thomas

last: Floss

first: Farrell

last: Dearie

first: Sarah

last: Crunkhorn

first: Furkan

last: Burak

first: Josep

middle: C

last: Jimenez-Chillaron

first: Tiina

last: Kuulasmaa

first: Pekka

last: Miettinen

first: Peter

last: Park

first: Imad

last: Nasser

first: Zhenwen

last: Zhao

first: Zhaiyi

last: Zhang

first: Yan

last: Xu

first: Wolfgang

last: Wurst

first: Stefan

last: Stamm

first: Allison

last: Goldfine

first: Markku

last: Laakso

first: Mary