title: Pemetrexed alters inflammatory profile in EA.hy 926 cells grown under low-folate conditions.

status: Public on Oct 03 2012

address: 421 Curie Blvd

summary: Pemetrexed is an antifolate drug used in the treatment of lung cancer. EA.hy 926 cells grown under low (Lo) and normal (Hi) folate conditions were treated with PMX. Microarray analysis was used to examine changes in gene expression due to PMX treatment.

overall_design: Hi and Lo cells were grown to confluence and maintained in fresh medium for 24 hours prior to treatment with 0.5uM PMX for 48 hours.

first: Alexander


title: Epigenetic polymorphism and the stochastic formation of differentially methylated regions in normal and cancerous tissues (Gene Expression data)

status: Public on Sep 24 2012

city: Rehovot

first: Gilad

last: Landan

address: 234 Herzl Street

country: Israel

institute: Weizmann Institute of Science

summary: DNA methylation has been comprehensively profiled in normal and cancer cells, but the dynamics that form, maintain and reprogram differentially methylated regions remain enigmatic. We show that methylation patterns within populations of cells from individual somatic tissues are heterogeneous and polymorphic. Using in vitro evolution of immortalized fibroblasts for over 300 generations, we track the dynamics of polymorphic methylation at regions developing significant differential methylation on average. The data indicate that changes in population-averaged methylation occur through a stochastic process that generates a stream of local and uncorrelated methylation aberrations. Despite the stochastic nature of the process, nearly deterministic epigenetic remodeling emerges on average at loci that lose or gain resistance to methylation accumulation. Changes in the susceptibility to methylation accumulation are correlated with changes in histone modifications and CTCF occupancy.  Characterizing epigenomic polymorphism within cell populations is therefore critical for understanding methylation dynamics in normal and cancer cells.

overall_design: Gene expression profiled in duplicate throughout the microevolutionary timecourse using Affymetrix Gene 1.0 ST arrays.


title: Transcriptional profiling in facioscapulohumeral muscular dystrophy to identify candidate biomarkers

status: Public on Sep 19 2012

city: Boston

first: Fedik

last: Rahimov

state: MA

address: 3 Blackfan Circle, CLS 15030.4

department: Genetics

country: USA

institute: Boston Children's Hospital

summary: Facioscapulohumeral muscular dystrophy (FSHD) is a progressive neuromuscular disorder caused by contractions of repetitive elements within the macrosatellite D4Z4 on chromosome 4q35. In order to develop mRNA-based biomarkers of affected muscles, we used GeneChip Gene 1.0 ST arrays for global analysis of gene expression in muscle biopsy specimens obtained from FSHD subjects and their unaffected first degree relatives.

overall_design: FSHD typically affects biceps muscles more severely than deltoid muscles. To examine muscle-specific expression changes associated with FSHD while controlling for background genetic variation, we analyzed RNA extracted from both biceps and deltoids of FSHD subjects and unaffected first-degree relatives.


title: Expression data from trisomy 21 and euploid induced pluripotent stem cell hematopoietic progenitors

city: University Park

first: Ross

last: Hardison

state: PA

address: 303 Wartik Lab

institute: Pennsylvania State University

summary: We modeled human Trisomy 21 primitive hematopoiesis using induced pluripotent stem cells (iPSCs).  Primitive multipotent progenitor populations generated from Trisomy 21 iPSCs showed normal proliferative capacity and megakaryocyte production, enhanced erythropoiesis and reduced myeloid development compared to euploid iPSCs.

overall_design: CD41+/235+ iPSC-derived progenitor cells were flow cytometrically sorted for RNA extraction and hybridization onto Affymetrix microarrays.

first: Stella

middle: T

last: Chou

first: Mitchell

middle: J

last: Weiss


title: ZNF750 in late keratinocyte differentiation

city: Beer Sheva

first: Idan

last: Cohen

address: Ben-Gurion Boulevard

department: Dept. of Molecular Genetics and Virology

institute: Ben Gurion University

summary: Disrupted skin barrier due to altered keratinocyte differentiation is common in pathologic conditions such as atopic dermatitis, ichthyosis and psoriasis. However, the molecular cascades governing keratinocyte terminal differentiation are still poorly understood. We have previously demonstrated that a dominant mutation in ZNF750 leads to a clinical phenotype that reminiscent of psoriasis and seborrheic dermatitis. We defined ZNF750 as a nuclear effector that is strongly activated in and essential for keratinocyte terminal differentiation. ZNF750 knockdown in HaCaT keratinocytes markedly reduced the expression of  epidermal late differentiation markers, including gene subsets of epidermal differentiation complex and skin barrier formation such as FLG, LOR, SPINK5, ALOX12B and DSG1, known to be mutated in various human skin diseases. Furthermore, ZNF750 over-expression in undifferentiated cells induced terminal differentiation genes. Thus, ZNF750 is a regulator of keratinocyte terminal differentiation, and with its downstream targets can serve in future elucidation of therapeutics for common disease of skin barrier

overall_design: Gene expression analysis: To determine the differentaition signature for HaCaT keratinocytes, with ZNF750 gene silencing, total RNA was isolated in biologic triplicates from cells induced to differentiate for twelve days and hybridized to Affymerix Human Gene 1.0 ST arrays.

first: I

first: R

middle: Y

last: Birnbaum

first: O

middle: S

last: Birk


status: Public on Sep 14 2012

city: La Jolla

first: David

last: Gorkin

state: California

address: 9500 Gilman Dr. CMM-East 2071

institute: Ludwig Institute for Cancer Research

type: Genome binding/occupancy profiling by high throughput sequencing

summary: Using ChIP-seq for p300 and H3K4me1, we identified 2,489 putative melanocyte enhancer loci in the mouse genome. We demonstrated that these putative enhancers are evolutionarily constrained, enriched for sequence motifs predicted to bind key melanocyte transcription factors, located near genes relevant to melanocyte biology, and capable of driving reporter gene expression with high frequency in cultured melanocytes and in melanocytes of transgenic zebrafish.

overall_design: ChIP-seq for EP300 and H3K4me1 in the mouse melanocyte cell line melan-a.

middle: U

first: Dongwon

last: Lee

first: Xylena

last: Reed

first: Christopher

last: Fletez-Brant

first: Seneca

middle: L

last: Bessling

first: Stacie

middle: K

last: Loftus

first: Michael

middle: A

last: Beer

first: William

last: Pavan

first: Andrew

last: McCallion


title: EZH2 promotes a bi-lineage identity in basal-like breast cancer cells

status: Public on Sep 21 2012

city: Jerusalem

first: Ittai

last: Ben-Porath

address: Faculty of Medicine, Ein kerem

department: Developmental Biology and Cancer Research

institute: Hebrew University of Jerusalem

summary: The mechanisms regulating breast cancer differentiation state are poorly understood. Of particular interest are molecular regulators controlling the highly aggressive and poorly differentiated traits of basal-like breast carcinomas. Here we show that the Polycomb factor EZH2 maintains the differentiation state of basal-like breast cancer cells, and promotes the expression of progenitor-associated and basal-lineage genes. Specifically, EZH2 regulates the composition of basal-like breast cancer cell populations by promoting a “bi-lineage” differentiation state, in which cells co-express basal- and luminal-lineage markers. We show that human basal-like breast cancers contain a subpopulation of bi-lineage cells, and that EZH2-deficient cells give rise to tumors with a decreased proportion of such cells. Bi-lineage cells express genes that are active in normal luminal progenitors, and possess increased colony formation capacity, consistent with a primitive differentiation state. We found that GATA3, a driver of luminal differentiation, performs a function opposite to EZH2, acting to suppress bi-lineage identity and luminal progenitor gene expression. GATA3 levels increase upon EZH2 silencing, leading to the observed decrease in bi-lineage cell numbers. Our findings reveal a novel role for EZH2 in controlling basal-like breast cancer differentiation state and intra-tumoral cell composition.

overall_design: Total of four treatments (HCC70 cells stably expressing shEZH2, shEED, or EZH2 cDNA, and MDA-MB-468 cells stably expressing shEZH2) were done in duplicates, each with its own control.

first: Roy

middle: Z

last: Granit

first: Yael

last: Gabai

first: Tal

last: Hadar

last: Karamansha

first: Leah

last: Liberman

first: Ithai

last: Waldhorn

first: Irit

last: Gat-Viks

first: Aviv

last: Regev

first: Bella

last: Maly

first: Tamar

last: Peretz


title: LXR activation induces insulin resistance in primary human adipocytes

status: Public on Sep 29 2012

city: Stockholm

first: Annie

last: Pettersson

address: Hälsovägen 7

department: Dept. of medicine, Huddinge

country: Sweden

institute: Karolinska Institutet

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

summary: The effects of LXR stimulation by GW3965 treatment on global mRNA and miRNA expression in primary human in vitro differentiated adipocytes was investigated using microarray profiling.

platform_organism:
Homo sapiens
synthetic construct

overall_design:
Preadipocytes were isolated from human adipose tissue obtained from healthy subjects and differentiated in vitro. Around day 11 of differentiation cells were treated with the Liver X Receptor agonist GW3865 for 24 h and lysed. Total RNA as prepared and hybridised biotinylated complementary RNA to Gene 1.0 ST Arrays using standardized protocols (Affymetrix Inc., Santa Clara, CA). The GeneChip Operating Software Version 1.4 was used for analysis. Arrays were normalized using PLIER and all samples were subjected to an all-probeset scaling-to-target signal of 100.

Preadipocytes were isolated from human adipose tissue obtained from healthy subjects and differentiated in vitro. Around day 11 of differentiation cells were treated with the Liver X Receptor agonist GW3865 for 12 h and lysed. Total RNA was prepared and and labelled using the FlashTag biotin HSR labeling kit (Genisphere Inc., Hatfield, PA) according to the supplier's protocol. The labelled samples were placed in a hybridization cocktail mix containing 4% formamide and hybridised overnight to Affymetrix miRNA Arrays (Affymetrix Inc.) following the indicated Genisphere protocol. The arrays were washed, stained and scanned in an Affymetrix GCS 3000 scanner. Signal intensities and present calls were generated by using the microRNA QC tool by Affymetrix using default settings i.e. Background Adjustment: BC-CG adjust, Normalization: Quantile: Summarization: Median Polish.

first: A

middle: M

first: B

last: Stenson

first: I

last: Dahlman

first: J

last: Laurencikiene


title: Gene expression before or 3 hours after t-RA treatment in HeLa cells expressing an shRNA control or shRNA against PARG

status: Public on Sep 15 2012

city: Illkirch

first: Frédéric

last: Coin

address: 1, rue laurent fries

department: Functional Genomics and Cancer

country: France

institute: IGBMC

summary: The goal of this experiment was to compare gene expression after t-RA treatment in cells with or without the presence of the PolyADP ribose Glycohydrolase protein (PARG)

overall_design: Microarray analysis of gene expression before or 3 hours after t-RA treatment in Hela cells expressing an shRNA control or shRNA against PARG

first: Izarn

last: Iltis

first: Frederic


title: Analysis of Nkx2-1-regulated gene expression in A549 lung carcinoma cells

status: Public on Sep 05 2012

city: Cincinnati

first: Yutaka

last: Maeda

state: OH

address: 3333 Burnet Avenue

department: Pulmonary Biology

institute: Cincinnati Children's Hospital

summary: A transcription factor Nkx2-1 (also known as TTF-1) regulates the expression of different sets of genes.  Gene expression analysis was performed using mRNAs from Nkx2-1-induced A549 cells compared to that from the control A549 cells. We used microarrays to detail the global program of gene expression controlled by Nkx2-1 and identified distinct classes of up-regulated and down-regulated genes.

overall_design: mRNAs were isolated from control and Nkx2-1-induced A549 cells and hybridized on Affymetrix microarrays.  We sought to identify genes influenced by Nkx2-1.

first: Jeffrey

last: Whitsett


title: Peripheral blood RNA gene expression profiling in patients with bacterial meningitis

city: Perth

first: Sulev

last: Koks

state: Western Australia

address: 90 South Street

department: Centre for Molecular Medicine and Innovative Therapeutics

country: Australia

institute: Murdoch University

summary: The aim of present study was to describe the genetic pathways activated during the community acquired bacterial meningitis (BM) by using genome-wide RNA expression profiling combined with functional annotation of transcriptional changes. We included 21 patients with BM hospitalized in 2008. The control group consisted of 18 healthy subjects. The RNA was extracted from whole blood, globin mRNA was depleted and gene expression profiling was performed with GeneChip Human Gene 1.0 ST Arrays enabling the analysis of 28,869 genes. Gene expression profile data were analyzed using Bioconductor packages and Bayesian modeling. Functional annotation of the enriched gene sets was used to define changed genetic networks. We also analyzed if the gene expression profile depends on the clinical course and outcome. In order to verify the genechip results, we chose ten functionally relevant genes with high statistical significance (CD177, IL1R2, IL18R1, IL18RAP, OLFM4, TLR5, CPA3, FCER1A, IL5RA, IL7R) and performed quantitative real-time (qRT) PCR.We identified the significant differences at p values of <0.05 in 8569 genes and after False Discovery Rate (FDR) correction, total of 5500 genes remained significant at p value of <0.01. Quantitative RT-PCR confirmed differential expression for selected genes. Functional annotation and network analysis indicated that most of the genes were related to activation of humoral and cellular immune responses (enrichment score 43). Those changes were found in adults and in children with BM compared to the healthy controls. Gene expression profile didn’t depend on the clinical outcome, but there was very strong influence by the type of the pathogen. This study demonstrates a strong functional genomic evidence of the over-active immune response during bacterial meningitis. This hyperactive response possibly explains the complicated clinical course of this disease.

overall_design: 22 bacterial meningitis patients and 18 healthy controls

first: Margit

last: Lill

last: Kõks

first: Ursel

last: Soomets

first: Leonard

middle: C

last: Schalkwyk

first: Cathy

last: Fernandes

first: Irja

last: Lutsar

first: Pille

last: Taba


title: Human Pluripotent Cell Derived Endothelial Cell Characterization

status: Public on Sep 01 2012

city: San Francisco

first: Deepak

last: Srivastava

state: CA

address: 1650 Owens St

department: GICD

institute: J. David Gladstone Institute

summary:
Human ES or iPS Cells were differentiated into endothelial cells (ECs) defined by expression of CD31 (PECAM1) and CD144 (VE-Cadherin) on the cell surface. All ES or iPS derived ECs were greater than 90% double positive for these two markers.
These in vitro derived ECs were compared to each other and to ECs from primary cell sources; arterial (aortic Ecs), venous (saphenous vein) and lymphatic.

overall_design: ES and iPS cells were differentiated into Ecs using a directed differentiation protocol using sequential addition of growth factors to recapitulate endogenous differentiation (FGF, BMP4, Activin, VEGF). These ECs were grown until 21 days after the start of differentiation. Primary cells were obtained from a commercial vendor and grown to passage 3 to minimize cellular senescence and in vitro artifacts. The RNA was cleaned and DNAse digested on RNeasy columns (Qiagen, Valencia, CA). RNA was amplified, fragmented and labeled using NuGEN Technologies Applause Plus kits and the manufacturer's instructions. Labeled samples were then hybridized to Affymetrix Human Gene 1.0 ST GeneChips. The GeneChips were then washed and stained on Affymetrix 450 Fluidics Stations and scanned on an Affymetrix 3000 Scanner according to standard protocols.

first: Mark

last: White


title: Expression data from human hematopoietic stem and progenitor compartments from patients with acute myeloid leukemia with normal karyotype and healthy controls

city: Bronx

first: Boris

last: Bartholdy

state: NY

address: 1300 Morris Park Ave

department: Cell Biology

institute: Albert Einstein College of Medicine

summary: We applied a novel approach of parallel transcriptional analysis of multiple, highly fractionated stem and progenitor populations from patients with acute myeloid leukemia (AML) and a normal karyotype. We isolated phenotypic long-term HSC (LT-HSC), short-term HSC (ST-HSC), and committed granulocyte-monocyte progenitors (GMP) from individual patients, and measured gene expression profiles of each population, and in comparison to their phenotypic counterparts from age-matched healthy controls.

overall_design: Bone marrow samples from AML patients with normal karyotype and age-matched healthy controls were used in this study. Hematopoietic stem and progenitor compartments were purified by multiparameter-high speed fluorescence-activated cell sorting (FACS) from CD34+ enriched bone marrow to isolate LT-HSC (Lin-/CD34+/CD38-/CD90+), ST-HSC (Lin-/CD34+/CD38-/CD90-), and GMP (Lin-/CD34+/CD38+/CD123+/CD45R+).

first: Britta

last: Will

first: Laura

last: Barreyro

first: Ulrich

last: Steidl


title: Silencing of the WFS1 gene in HEK cells induces pathways related to neurodegeneration and mitochondrial damage.

summary: The gene WFS1 encodes a protein with unknown function although its functional deficiency causes different neuropsychiatric and neuroendocrine syndromes. In the present study, we aimed to find the functional networks influenced by the time-dependent silencing of WFS1 in HEK cells. We performed whole genome gene expression profiling (Human Gene 1.0 ST Arrays) in HEK cells 24, 48, 72 and 96 hours after transfection with three different WFS1 siRNAs. In order to verify silencing we performed quantitative RT-PCR and western blot analysis. Analysis was conducted in two ways. First we analyzed the overall effect of the siRNA treatment on the gene expression profile. As a next step we performed time-course analysis separately for different siRNAs and combined for all siRNAs.  Quantitative RT-PCR and western blot confirmed clear silencing of WFS1 gene expression after 48 hours. Eleven genes had an FDR value less than 10% and most of them were genes related to the mitochondrial dysfunction and apoptosis. Time-course analysis confirmed significant correlation between WFS1 silencing and changes in the expression profiles of several genes. The pathways that were influenced significantly by WFS1 silencing were related to mitochondrial damage and neurodegenerative diseases. Our findings suggest the role of WSF1 gene in cell survival and its involvement in the degenerative diseases.

overall_design: 54 samples; whole genome gene expression profiling (Human Gene 1.0 ST Arrays) in HEK cells 24, 48, 72 and 96 hours after transfection with three different WFS1 siRNAs.

first: Rupert

middle: W

last: Overall

first: Mithu

last: Guha

first: Eero

last: Vasar


title: Identification of novel genes associated with human glioblastoma (GBM) tumor-initiating cells (TICs)

status: Public on Sep 11 2012

city: Genova (GE)

first: Massimiliano

last: Monticone

address: Largo R. Benzi, 10

country: Italy

institute: IRCCS AOU San Martino – IST, Genova

summary:
Most patients affected by Glioblastoma multiforme (GBM) experience a recurrence of the disease because of the spreading of tumor-initiating cells (TICs) beyond surgical boundary. Unveiling and targeting molecular mechanisms causing this process is a logic goal to impair GBM killing ability.
In an orthotopic xenograph model, we have noticed that GBM TICs isolated from several patients may fall into two classes of invasive behavior: nodular or diffuse. In order to identify genes responsible for the diffusive type of invasion, we have compared by genome expression analysis, cultured GBM TICs belonging to the two classes. This analysis allowed us to identify a small group of regulated genes in the diffusive type of GBM TICs. The gene ontology process of cell adhesion and the localization of the gene product functions to the plasmamembrane resulted significantly associated to this gene set. Real time RT-PCR and immunofluorescence analyses performed for a selected subgroup of regulated genes/gene products confirmed the results obtained by the expression analysis. Some of the genes that we found upregulated in our screening were already proven to be involved in Glioma cell invasion supporting our study. However, we have also identified genes that were not previously implicated in this process. To assess whether these are required to sustain TICs GBM invasion, we silenced a subset of them and evaluated in Boyden chamber the invasive ability of the cells.
Our study provides novel target genes to be evaluated for the inhibition of GBM diffusion within the SNC.

overall_design: As we observed that GBM TICs may fall into two classes of “in vivo” invasive behavior in mouse orthotopic transplantation: expansive or highly diffusive, resulting in the host’s white and gray matters substitution, we decided to identify genes associated with the latter phenotype by microarray analysis. Three replicates of each class were analyzed.

first: Antonio

last: Daga

first: Simona

last: Candiani

first: Emanuela

last: Biollo

first: Andrea

last: Fabiano

first: Francesco

last: Romeo

first: Alice

last: Melotti

first: Giorgio

last: Corte

first: Patrizio

last: Castagnola


title: MCF10A cells expressing HER2 and HER3 and grown in three-dimensional cultures

city: Basel

first: Tim

last: Roloff

address: Maulbeerstrasse 66

department: Functional Genomics

country: Switzerland

institute: FMI

summary: The tyrosine kinase receptors HER2 and HER3 play an important role in breast cancer. The HER2/HER3 heterodimer is a critical oncogenic unit associated with reduced relapse-free and decreased overall survival. We provide gene expression profile of the mammary epithelial cells MCF10A expressing HER2, HER3 or HER2/HER3 and grown in three-dimensional cultures for 15 days in the presence of heregulin, a known HER3-ligand that stabilizes and activates the HER2/HER3 heterodimer.

overall_design: The mammary epithelial cells MCF10A were transduced with retroviral vectors expressing HER2, HER3 or both. Cells from each group were grown for 15 days in three-dimensional cultures. At the end of the experiment, RNA was extracted for gene expression analysis.

first: Nicola

last: Aceto

first: Stephane

last: Thiry

first: Tim-C

first: Mohamed

last: Bentires-Alj


title: Expression data from human hematopoietic stem and progenitor compartments from patients with acute myeloid leukemia with monosomy 7 and healthy controls

first: Boris

last: Bartholdy

summary: We applied a novel approach of parallel transcriptional analysis of multiple, highly fractionated stem and progenitor populations in a genetically defined subset of AML (AML with monosomy 7). We isolated phenotypic long-term HSC (LT-HSC), short-term HSC (ST-HSC), and committed granulocyte-monocyte progenitors (GMP) from individual patients with AML, and measured gene expression profiles of each population, and in comparison to their phenotypic counterparts from age-matched healthy controls.

overall_design: Bone marrow samples from AML patients bearing monosomy 7 and age-matched healthy controls were used in this study. Hematopoietic stem and progenitor compartments were purified by multiparameter-high speed fluorescence-activated cell sorting (FACS) from CD34+ enriched bone marrow to isolate LT-HSC (Lin-/CD34+/CD38-/CD90+), ST-HSC (Lin-/CD34+/CD38-/CD90-), and GMP (Lin-/CD34+/CD38+/CD123+/CD45R+).

first: Laura

last: Barreyro

first: Ulrich

last: Steidl


title: Gene expression profiling of MCF-7 cells treated with 6-shogaol

city: Bukit Jalil

first: Chee-Onn

last: Leong

country: Malaysia

institute: International Medical University

summary: A total of 18 genes were up-regulated and 11 genes were down-regulated > 2-fold following 6-shogaol treatment

overall_design: Microarray experiments were performed in duplicate as follows: MCF-7 cells were treated with 10 uM of 6-shogaol or control vehicle (0.1% DMSO) for 48 h. Total RNA from cells was extracted using Qiagen RNA isolation kit (Qiagen, Valencia, CA, USA) according to the manufacturers’ protocol. RNA purity was examined by spectrophotometric determination at 260/280 nm. The microarray hybridizations were carried out using the Affymetrix Human Gene 1.0 ST arrays.


title: Gene expression of PBMC of chinese nickel refinery workers when compared to the gene expression profile of PBMCs from referent subjects

status: Public on Aug 28 2012

city: Tuxedo

first: Adriana

last: Arita

address: 57 Old Forge Road

institute: New York University

summary:
Up to date the studies examining the gene expression profiles in response to exposure to nickel compounds have only been conducted using in vitro tissue culture systems.
Here, we have compared the gene expression profiles in peripheral blood mononuclear cells (PMCs) of eight nickel refinery workers in Jinchang, China to the expression profiles of referent subjects with only environmental exposure.

overall_design: PBMC RNA was collected from eight nickel refinery workers in China and ten reference subjects with only environmental exposure to nickel. PBMC RNA was labeled and hybridized to Affymetrix Genechip arrays 2.0. Gene expression profiles between nickel refinery workers and referent subjects was compared.

first: Max

last: Costa


title: Prolactin-inducible Stat5a-mediated and Stat5b-mediated gene profiles

status: Public on Aug 29 2012

city: PHILADELPHIA

first: Adam

last: Ertel

address: 233 S 10TH ST

department: Cancer Biology

institute: Thomas Jefferson University

summary: Stat5a and Stat5b proteins are highly homologous with greater than 90% amino acid identity and share binding to the palindromic Stat5 consensus sequence, TTCNNNGAA, but individual roles of each transcription factor in breast cancer have not been thoroughly evaluated.  To determine the degree of similarity between transcripts modulated by Stat5a and Stat5b proteins in human breast cancer, we utilized genome-wide transcript profiling to identify genes regulated specifically by Stat5a or Stat5b in response to prolactin.

overall_design: Stat5a or Stat5b was transiently overexpressed using adenoviral gene delivery in MCF7 breast cancer cells followed 16 hr serum starvation and a brief 4 hr exposure to 10nM human prolactin to identify immediate-early transcripts modulated by each transcription factor.  Basal activation of Stat5a or Stat5b was not present in cells not stimulated with prolactin.  mRNA from each condition was harvested and validated using the Agilent bioanalyzer.  cDNA was generated and genome-wide transcript profiling was performed in triplicate using the Affymetrix HuGene 1.0 ST array.

first: Amy

middle: R

last: Peck

first: Hallgeir

last: Rui


title: Expression data from human memory CD4 T-cells stimulated with autologous monocytes pulsed with HCMV

status: Public on Aug 15 2012

city: Frederiksberg C

first: Helle

last: Jensen

address: Stigbojlen 7

department: Section of Biomedicine

country: Denmark

institute: LIFE, University of Copenhagen

summary: The present study reports an unbiased analysis of the genetic profile and regulation of NKG2D expressing CD4 T-cells.An Affymetrix microarray analysis was used to explore the genetic profile of NKG2D+ versus NKG2D- CD4 T-cells. The genetic profile was studied by single gene analysis and gene set enrichment analysis. I found that several immune regulatory receptors was regulated differently in NKG2D+ versus NKG2D- CD4 T-cells. Futhermore, I found that NKG2D+ CD4 T-cells display a genetic profile of cytotoxic T-cells. The gene set enrichment analysis revealed a change in 19 processes, including ARF GTPase activator activity; RNA splicing; Signal transduction; Interspecies interaction between organisms; Regulation of ARF GTPase activity; Cell motility; Mitosis; Cell cycle; Anaphase-promoting complex-dependent proteasomal ubiquitin-dependent protein catabolic process; Induction of apoptosis by extracellular signals; Negative regulation of apoptosis; mRNA export from nucleus; Positive regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle; Cell division; Protein polymerization; Spliceosome assembly; Microtubule-based movement; Immune response; mRNA processing.

overall_design: Human CD4 T-cells were isolated from buffy coat by anti-CD4 conjugated magnetic beads. Memory CD4 T-cells were sorted, labeled with CFSE and stimulated with autologous monocytes pulsed with HCMV. HCMV stimulated CD4 T-cells were sorted as CFSE-NKG2D+ or CFSE-NKG2D- and processed for microarray analysis.


title: Novel antioxidative peptides with potential to reduce psoriatic changes in PBMCs

status: Public on Aug 22 2012

first: Sulev

last: Koks

summary:
Oxidative damage contributes significantly to the pathogenesis of psoriasis. We recently developed antioxidative peptides (UPF peptides) activating the endogenous glutathione system (GSH). In the present study, we analyzed gene expression profiles in the samples of psoriasis patients to find if these peptides could reduce oxidative damage during psoriasis.
Peripheral blood mononuclear cells (PBMCs) from patients with psoriasis and from healthy controls were collected and cultivated. Cultured PBMCs were incubated with two different UPF peptides for 12 hours. Gene expression analysis was performed with Affymetrix Human Gene 1.0 ST arrays and with quantitative real-time PCR. Gene expression profile in the PBMCs of patients with psoriasis indicated significant up-regulation of the immune response pathway. Treatment with UPF peptides normalized the gene expression pattern in psoriasis samples. Therefore, treatment with antioxidative drugs have potential anti-psoriatic activity.

overall_design: 5 healthy controls (C1-5), 5 psoriasis patients (P1-5), 2 different drugs (upf17 peptide, upf1 peptide) and a control drug. Overall, 30 samples and six groups: PSOR, PSORUPF1, PSORUPF17, CON, CONUPF1, CONUPF17.

first: Ursel

last: Soomets

first: Külli

last: Kingo

first: Leonard

last: Schalkwyk

first: Cathy

last: Fernandes

first: Michael

last: Parsons

first: Riina

last: Mahlapuu

last: Kõks


title: Expression data of inducible stable cell lines overexpressing Ero1alpha WT and  Ero1alpha C104A/C131A

status: Public on Sep 07 2012

city: Copenhagen N

first: Henning Gram

last: Hansen

address: Ole Maaløesvej 5

department: Department of Biology

institute: University of Copenhagen

summary:
The overall cellular response to oxidative stress generated by Ero1α in the lumen of the mammalian endoplasmic reticulum (ER) is poorly characterized. Here, we investigate the effects of overexpressing a hyperactive mutant (C104A/C131A) of Ero1α.
Using microarray analysis, we demonstrate that the cell reacts to the oxidative challenge caused by Ero1α hyperactivity by turning on the unfolded protein response. Our findings suggest that the hyperoxidation generated by Ero1α-C104A/C131A is addressed in the ER lumen and is unlikely to exert oxidative injury throughout the cell.

overall_design: Human embryonic kidney 293 Flp-In T-REx cells (Invitrogen) overexpressing Ero1α-WT and Ero1α-C104A/C131A were grown in triplicates and expression was either not induced or induced doxycycline (dox) for 24 h. Extracted RNA was hybridized on Affymetrix microarrays and genes with significantly different expression levels between the four categories were identified by a two-way analysis of variance (ANOVA), where the cell line (Ero1α-WT or Ero1α-C104A/C131A) and induction status (-dox/+dox) were used as the two factors for the p-value calculation.

first: Henning

middle: G

first: Jonas

middle: D

last: Schmidt

first: Cecilie

last: Soltoft

first: Henrik

last: Geertz-Hansen

first: Agnieszka

last: Juncker

first: Christian

last: Appenzeller-Herzog

first: Lars

last: Ellgaard


title: Suppression of IFN-induced transcription underlies IFN defects generated by activated Ras/MEK in human cancer cells

status: Public on Aug 02 2012

city: St. John's

first: Sherri

last: Christian

state: Newfoundland

address: 232 Elizabeth Ave

department: Biochemistry

country: Canada

institute: Memorial University of Newfoundland

summary: Certain oncolytic viruses exploit activated Ras signalling in order to replicate in cancer cells. Constitutive activation of the Ras/MEK pathway is known to suppress the effectiveness of the interferon (IFN) antiviral response, which may contribute to Ras-dependent viral oncolysis. Here, we identified 10 human cancer cell lines (out of 16) with increased sensitivity to the anti-viral effects of IFN-α after treatment with the MEK inhibitor U0126, suggesting that the Ras/MEK pathway underlies their reduced sensitivity to IFN. To determine how Ras/MEK suppresses the IFN response in these cells, we used DNA microarrays to compare IFN-induced transcription in IFN-sensitive SKOV3 cells, moderately resistant HT1080 cells, and HT1080 cells treated with U0126. We found that 267 genes were induced by IFN in SKOV3 cells, while only 98 genes were induced in HT1080 cells at the same time point. Furthermore, the expression of a distinct subset of IFN inducible genes, that included RIGI, GBP2, IFIT2, BTN3A3, MAP2, MMP7 and STAT2, was restored or increased in HT1080 cells when the cells were co-treated with U0126 and IFN. Bioinformatic analysis of the biological processes represented by these genes revealed increased representation of genes involved in the anti-viral response, regulation of apoptosis, cell differentiation and metabolism. Furthermore, introduction of constitutively active Ras into IFN sensitive SKOV3 cells reduced their IFN sensitivity and ability to activate IFN-induced transcription. This work demonstrates for the first time that activated Ras/MEK in human cancer cells induces downregulation of a specific subset of IFN-inducible genes.

overall_design: HT1080 cancer cells treated for 6 hours or 12 hours with interferon-alpha (500U/ml), the MEK inhibitor U0126 (20uM) or both, triplicate biological samples (18 samples). SKOV3 cells treated with interferon-alpha (500U/ml) for 6h, triplicate biological samples (6 samples).

first: Dong

last: Zu

first: Maria

last: Licursi

first: Yumiko

last: Komatsu

first: Theerawat

last: Pongnopparat

first: Dianne

last: Codner

first: Kensuke

last: Hirasawa


title: A microRNA network regulates expression and biosynthesis of CFTR and CFTR-ΔF508.

status: Public on Sep 04 2012

city: Iowa City

first: Shyam

last: Ramachandran

address: 240G EMRB

department: Pediatrics

institute: Univ of Iowa

summary: Production of functional proteins requires multiple steps including gene transcription and post-translational processing.  MicroRNAs (miRNA) can regulate individual stages of these processes.  Despite the importance of the cystic fibrosis transmembrane conductance regulator (CFTR) channel for epithelial anion transport, how its expression is regulated remains uncertain.  We discovered that microRNA-138 regulates CFTR expression through its interactions with the transcriptional regulatory protein SIN3A.  Treating airway epithelia with a miR-138 mimic increased CFTR mRNA and also enhanced CFTR abundance and transepithelial Cl- permeability independently of elevated mRNA levels.  A miR-138 anti-miR had the opposite effects.  Importantly, miR-138 altered the expression of many genes encoding proteins that associate with CFTR and may influence its biosynthesis.  The most common CFTR mutation, ΔF508, causes protein misfolding, degradation, and cystic fibrosis. Remarkably, manipulating the miR-138 regulatory network also improved biosynthesis of CFTR-ΔF508 and restored Cl- transport to cystic fibrosis airway epithelia.  This novel miRNA-regulated network directs gene expression from the chromosome to the cell membrane, indicating that an individual miRNA can control a cellular process broader than previously recognized.  This discovery also provides new therapeutic avenues for restoring CFTR function to cells affected by the most common cystic fibrosis mutation.

overall_design: 12 samples of Calu-3 cells representing different interventions.


title: Context-specific microRNA analysis: identification of functional microRNAs and their mRNA targets

city: Rehovot

first: Noa

last: Bossel Ben-Moshe

address: Hertzl Street

institute: Weizmann

summary: MicroRNAs (miRs) function primarily as post-transcriptional negative regulators of gene expression through binding to their mRNA targets. Reliable prediction of a miR’s targets is a considerable bioinformatic challenge of great importance for inferring the miR’s function. Sequence-based prediction algorithms have high false-positive rates, are not in agreement, and are not biological context specific. Here we introduce CoSMic (Context-Specific MicroRNA analysis), an algorithm that combines sequence-based prediction with miR and mRNA expression data. CoSMic differs from existing methods—it identifies miRs that play active roles in the specific biological system of interest and predicts with less false positives their functional targets. We applied CoSMic to search for miRs that regulate the migratory response of human mammary cells to epidermal growth factor (EGF) stimulation. Several such miRs, whose putative targets were significantly enriched by migration processes were identified. We tested three of these miRs experimentally, and showed that they indeed affected the migratory phenotype; we also tested three negative controls. In comparison to other algorithms CoSMic indeed filters out false positives and allows improved identification of context-specific targets. CoSMic can greatly facilitate miR research in general and, in particular, advance our understanding of individual miRs’ function in a specific context.

overall_design: MCF10A cells were transfected using Oligofectamine transfection reagent (Invitrogen), with siRNA oligonucleotides directed at hsa-miR-20a, hsa-miR-671-5p and a non-targeting control (purchased from Dharmacon). Total RNA was extracted from biological duplicates at four time-points following EGF stimulation (t=0,30,60,120 min.). RNA was isolated and was hybridized to Affymetrix GeneChip Human Gene 1.0 ST arrays.

first: Roi

last: Avraham

first: Merav

last: Kedmi

first: Amit

last: Zeisel

first: Assif

last: Yitzhaky

first: Yosef

last: Yarden

first: Eytan

last: Domany


title: Expression profiling of purified hematopoietic stem cells from patients with MDS and healthy controls

status: Public on Aug 01 2012

first: Britta

last: Will

address: 1300 Morris Park Avenue

summary: Gene expression analysis on purified human long-term hematopoietic stem cells (LT-HSC; CD34+CD38-CD90+) and short-term HSC (ST-HSC; CD34+CD38-CD90-) derived from healthy control patients and patients with myelodysplastic syndrome (MDS)

overall_design: Analysis of gene experssion of ST-HSCs and LT-HSCs derived from two patients with MDS and three healthy controls

last: Verma

first: Ulrich

last: Steidl


title: Analysis of gene expression during Calcium induced differentiation of human primary keratinocytes (NHEK)

status: Public on Jul 19 2012

city: Irvine

first: Amelia

middle: Soto

last: Hopkin

address: 250 Sprague Hall

department: Biological Chemistry & Medicine

institute: University of California Irvine

summary: Human primary keratinocytes were collected at 0, 1, 3, 6, 12, 24 and 48 hours after addition of 1.8mM Calcium and RNA was extracted.

overall_design: Primary normal human keratinocytes (NHEK) were collected and RNA was extracted 0, 1, 3, 6, 12, 24, and 48 after addition of 1.8mM Calcium.

first: Bogi

last: Andersen


title: Gene expression profiling and pathway analysis of human bronchial epithelial cells exposed to airborne particulate matter collected from Saudi Arabia

city: New York

first: Hong

last: Sun

address: 341 East 25 Street

department: Medicine

institute: NYU School of Medicine

summary:
Whole transcript expression was profiled using the Affymetrix 1.0 array in human bronchial epithelial cells exposed to PM collected from Saudi Arabia for 1 or 4 days. The differentially expressed genes were identified and analyzed for enriched networks and pathways using Ingenuity Pathway Analysis (IPA).
We have identified 140 and 230 genes that significantly changed more than 1.5 fold after PM exposure for 1 or 4 days, respectively. IPA analysis revealed that different exposure durations triggered distinct pathways. Genes involved in NRF2-mediated response to oxidative stress were up-regulated after 1 day exposure. In contrast, cells exposed for 4 days exhibited significantly changes in genes related to cholesterol and lipid synthesis pathways.

overall_design: We analyzed gene expression profiles from 12 samples collected at two different time points, including 2 untreated controls, 2 normal PM treated samples and 2 storm PM treated samples for each time point.

first: Magdy

last: Shamy

first: Thomas

last: Kluz

first: Mianhua

last: Zhong

first: Freda

last: Laulicht

first: Mansour

last: Alghamdi

first: Mamdouh

middle: I

last: Khoder

first: Lung-Chi

last: Chen

first: Max

last: Costa


title: Analysis of gene expression in differentiated human primary keratinocytes depleted for Grainyhead like 3 (GRHL3)

summary: Human primary keratinocytes were depleted of GRHL3 by siRNA and induced to differentiated for 2 days by addition of Calcium

overall_design: Primary normal human keratinocytes were transfected with GRHL3 or scrambled control siRNA using RNAi max (Life Technologies). 24 hours post transfection medium was raised to 1.8mM to induce differentiation.  Cells were collected 48 hours later.


title: Expression & polysome association in pluripotent human embryonic stem cells

first: Natali

last: Molotski

address: Rehovot

department: Biological Chemistry

institute: Weizmann Institute of Science

summary: The goal was to measure the expression and polysome association of genes with polysomes in human embryonic stem cells

overall_design: H9 human embryonic stem cells were kept in pluripotent conditions. Total RNA and polysome extracts were isolated.

first: Yoav

last: Soen


title: HCMV infection of human neural precursor cells: Human neural precursor cell expression

status: Public on Jul 22 2012

city: Newark

first: Saleena

last: Ghanny

address: 185 South Orange Ave

institute: Rutgers University

summary:
HCMV -treated and control human adult neural precurso cells (NPC) were used to extract RNA for profiling on DNA arrays
Primary adult hippocampus-derived neural precursor cells were used at passage # 2-4 for HCMV infection, followed by RNA extraction at indicated times

overall_design: Primary adult neural precursor cells were infected with HCMV strains Towne and TR (O.1MOI) and RNA was extracted at 72 hrs postinfection for expression profiling on both HCMV and Affymetrix DNA arrays

first: Liliana

last: Soroceanu


title: Elevating Sox2 levels deleteriously affects the growth of glioblastoma and medulloblastoma cells.

status: Public on Aug 25 2012

city: Omaha

first: Angie

last: Rizzinio

state: NE

address: 986805 Nebraska Medical Center

department: Eppley Institute for Research in Cancer and Allied Diseases

institute: University of Nebraska Medical Center

summary:
Induction of the transcription factor Sox2 from a doxycycline-inducible promoter in iSox2-DAOY medulloblastoma cells.
Affymetrix microarrays were used to characterize the gene expression profile of iSox2-DAOY cells in the absence and presence of doxycycline.

overall_design: Human DAOY medulloblastoma cells were engineered to express epitope tagged Sox2 under the control of a doxycycline inducible promoter, to produce iSox2-DAOY cells. iSox2-DAOY cells were FACS sorted into CD133 low and high populations. The CD133 low population was cultured in the absence and presence of 0.5 µg/mL doxycycline for 24 hours. RNA was extracted from cells cultured without and with doxycycline, and was used for microarray analysis.

first: Jesse

last: Cox

first: Phillip

last: Wilder

last: Rizzino


title: Expression data in induced pluripotent stem cells (iPSCs) derived from a DNA repair deficient fibroblast

status: Public on Jul 13 2012

city: La Jolla

first: Jason

last: Nathanson

address: 2880 Torrey Pines Rd, Rm 3807

department: Cellular and Molecular Medicine

institute: University of Californa San Diego

summary:
Cockayne syndrome (CS) is an autossomal human disorder characterized by premature aging along with other symptoms. At the molecular level, CS is characterized by a deficiency in the Transcription-couple DNA repair pathway caused by a mutation mainly in ERCC6 gene and the absence of its functional protein. It has been shown that the presence of DNA damage and the lack of some functional proteins related to DNA repair constitute a barrier for somatic cell reprogramming.  Recently, it was demonstrated that one protein involved in Genome Global Repair controls the expression of an important pluripotent gene, highligting its importance for cellular reprogramming.
We used microarray to confirm cellular reprogramming of CS fibroblasts at the molecular level and detail the expression of some genes invoved in cell death and aging control that might explain the unique characteristics of these iPSCs.

overall_design: Normal (wild type) and fibroblasts from a CS patient were reprogrammed and independent clones were isolated. After sucessive passages in culture, total RNA from donor fibroblasts, iPSCs clones and human embryonic stem cell line (HUES6) were isolated and transcriptional analysis using human genome Affimetrix Gene Chip arrays were performed. HUES6 was used to demonstrate that CS and normal iPSCS  show a global gene expression similar to an embryonic stem cell, confirming that both fibroblasts were successfully reprogrammed. We also used  fibroblasts from CS to point out the diiferences in global gene expression after reprogramming. We sought to use normal (control) iPSCs to compare the levels of some genes involved in cell death and aging in iPSCs from CS fibroblasts.

first: A

last: Muotri

first: G

last: Yeo


title: Human cartilage zone arrays

first: Shawn

middle: Patrick

last: Grogan

address: 10550 N. Torrey Pines Road, MEM161

department: MEM

institute: TSRI

summary:
Objective. Identify novel genes and pathways specific to superficial (SZ), middle (MZ) and deep zones (DZ) of normal articular cartilage.
Methods.  Articular cartilage was obtained from knees of 4 normal human donors. The cartilage zones were dissected on a microtome. RNA was analyzed on human genome arrays. Data obtained with human tissue were compared to bovine cartilage zone specific DNA arrays. Genes differentially expressed between zones were evaluated using direct annotation for structural or functional features, and by enrichment analysis for integrated pathways or functions.
Results. The greatest differences were observed between SZ and DZ in both human and bovine cartilage. The MZ was transitional between the SZ and DZ and thereby shared some of the same pathways as well as structural/functional features of the adjacent zones. Cellular functions and biological processes enriched in the SZ relative to the DZ, include most prominently ECM receptor interactions, cell adhesion molecules, regulation of actin cytoskeleton, ribosome-related functions and signaling aspects such as Interferon gamma, IL4, CDC42Rac and Jak-Stat. Two pathways were enriched in the DZ relative to the SZ, including PPARG and EGFR_SMRTE.
Conclusion. These differences in cartilage zonal gene expression identify new markers and pathways that govern the unique differentiation status of chondrocyte subpopulations.

overall_design: 12 samples, 4 donors, 3 conditions each donor (SZ, MZ and DZ), 0 donor replicates, comparisons made between SZ, MZ and DZ to identify differentially expressed genes.

middle: P

first: Stuart

middle: F

last: Duffy

first: Chantal

last: Pauli

first: James

last: Koziol

first: Andrew

last: Su

first: Darryl

last: D'Lima

first: Martin

last: Lotz


title: Expression data from Hodgkin lymphoma cell lines L-428 and L-1236: L-428 and L-1236 cells were transduced with tGFP-EBF1 or as control tGFP-only.

status: Public on Nov 01 2012

city: Frankfurt

first: Claudia

last: Döring

address: Theodor Stern Kai 7

department: Medical School, Institite of Pathology

country: Germany

institute: Johann Wolfgang-Goethe University Frankfurt a.M.

summary:
The transcription factor network in Hodgkin lymphoma (HL) represents a unique composition of proteins found in no other hematopoietic cell. An aberrant downregulation of the B cell transcription factor EBF1 is observed in the B cell-derived Hodgkin and Reed/Sternberg (HRS) tumor cells. Herein, we elucidated the consequences of the down regulation of this factor in HL.
To obtain a more comprehensive overview of EBF1 regulated genes in cHL cell lines, we performed a gene chip analysis comparing gene expression in tGFP-EBF1-transduced L-1236 and L-428 cells compared to samples transduced with vectors encoding only tGFP.

overall_design: 12 total samples were analyzed. Three independent samples were analyzed per condition and cell line.We generated the following pairwise comparisons using Bioconductor: tGFP-EBF1 L-428 < tGFP L-428;  tGFP-EBF1 L-1236 < tGFP L-1236. Genes with an FDR≤ 5 % and a fold-change ≥ 2.0 and ≤ -2.0 were selected.

first: Verena

last: Bohle


title: Contact versus contactless signatures in leukemia

status: Public on Jul 10 2012

city: Be'er Yacob

first: Yossi

last: Cohen

address: Zeriffin

department: Hematology

institute: Asaf Harofeh University Hospital

summary: Gene expression profile (GEP) was analyzed in bone marrow (BM) samples from patients with leukemia or leukemic phase of lymphoma at different time points following aspiration. Among numerous changes in GEP evolved over time a discrete subset of > 60 genes exhibited prompt and sustained switch in expression consistently. Similar results were discovered recently in BM samples from patients with multiple myeloma (GSE36036). GEP was also examined in peripheral blood as well as in BM samples depleted of red blood cells (=WBC) and in cultured cells from some of the patients.

overall_design: Comparative gene expression profiling of whole bone marrow samples from patients with leukemia fixed either immediately following aspiration or after delayed RNA fixation. Comparison was also made between cultured bone marrow cells fixed immediately following spread from the bottom well versus after maintenance in suspension (for 120 minutes).

first: Osnat

last: Garach-Jehoshua

first: Adina

last: Bar-Chaim

first: Abraham

last: Kornberg


title: MondoA is highly expressed in acute lymphoblastic leukemia and modulates metabolism, differentiation and survival

city: München

first: Olivia

last: Prazeres da Costa

state: Bavaria

address: Trogerstr. 30

department: Medical Microbiology, Immunology and Hygiene

institute: Technische Universität München

summary: Acute lymphoblastic leukemia (ALL) is the most common childhood cancer. To identify novel candidates for targeted treatment of childhood ALL, we performed a comprehensive transcriptome analysis yielding a set of genes specifically overexpressed in ALL. Among them we identified MondoA - a transcription factor regulating glycolysis in response to glucose availability.   Here, we confirm that MondoA is highly overexpressed ALL, whereas the MondoA paralog, MondoB, is not expressed. Expression studies revealed that MondoA is not regulated by glucose availability in leukemia cells, but by the presence of lactate. An in silico MondoA promoter analysis identified two methylation-prone CpG-islands and four conserved binding sites for runt-related transcription factor 1 (RUNX1). In fact, MondoA and RUNX1 are significantly coexpressed in leukemia and experimental blockage of DNA methylation leads to a further induction of MondoA. In addition, using microarray profiling, gene-set enrichment analysis and RNA interference we provide for the first time evidence that MondoA expression not only increases glucose catabolism, but also maintains a more immature ALL phenotype, which is associated with enhanced survival and clonogenicity of leukemia cells. These data hint to an important contribution of MondoA to leukemia aggressiveness validating MondoA as an attractive candidate for targeted treatment of ALL.

overall_design: Two nonsense shRNA expressing control Nalm6 clones and three MondoA shRNA expressing Nalm6 clones were subjected to microarray analysis.

first: Caroline

last: Wernicke

first: Thomas

last: Grunewald

first: Günther

middle: H

last: Richter

first: Stefan

last: Burdach


title: Expression profiling of mice exposed to multiwalled carbon nanotubes

status: Public on Jun 26 2012

city: Huntington

last: Denvir

state: WV

address: One John Marshall Drive

department: Biochemistry and Microbiology

institute: Marshall University School of Medicine

summary: Mice were aspirated with multiwalled carbon nanotubes in four doses ranging from 10 µg to 80 µg, plus control, and sacrificed after 1, 7, 28, and 56 days. RNA was extracted from the lungs and expression profilling by microarray was performed.

overall_design: This is a reference design two-color experiment. Each array was hybridized with RNA extracted from mouse lung labeled with Cy3, and universal reference RNA labeled with Cy5. Five different doses (0, 10ug, 20ug, 40ug, and 80ug) of multiwalled carbon nanotube aspiration were used and mice were sacrificed after 1, 7, 28, and 56 days. Eight replicates were used at each time/dose condition for a total of 160 arrays.

first: Nancy

last: Guo

first: Dale

last: Porter

first: Maricica

last: Pacurari

first: Mike

last: Wolfarth

first: Vincent

last: Castranova

first: Yong

last: Qian

first: Goran

last: Boskovic


title: Analysis of gene expression in differentiated human primary keratinocytes depleted for MLL2

first: Amelia

last: Hopkin

summary: Human primary keratinocytes were depleted of MLL2 by siRNA and induced to differentiated for 2 days by addition of Calcium

overall_design: Primary normal human keratinocytes were transfected with MLL2 or scrambled control siRNA using RNAi max (Life Technologies). 24 hours post transfection medium was raised to 1.8mM calcium to induce differentiation.  Cells were collected 48 hours later.

middle: S

first: Bogi

last: Andersen


title: HCMV infection of human neural precursor cells

first: Saleena

last: Ghanny

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

sample_organism:
Homo sapiens
Human betaherpesvirus 5
unidentified

platform_organism:
Homo sapiens
Human betaherpesvirus 5

overall_design: Refer to individual Series


title: Expression data from siRNAs against SLC45A3-ELK4 in LNCaP cells.

status: Public on Jul 24 2012

city: Charlottesville

first: Hui

last: Li

address: 345 Crispell Dr.

institute: University of Virginia

summary: SLC45A3-ELK4 is found in LNCaP and other prostate cancer samples. We used microarrays to detail the global changes of gene expression when LNCaP cells were treated with siRNAs against SLC45A3-ELK4.

overall_design: We transfected LNCaP cells with siRNAs against SLC45A3-ELK4 and siGl2 control. 72hrs later, RNAs were harvested.

first: Yanmei

last: Zhang


title: Expression data from SKOV/ip-Fumock- or SKOV/ip-FuEP2/Ex2-derived tumor

status: Public on Jun 22 2012

city: Tokushima

first: Tetsuyuki

last: Takahashi

state: Tokushima

country: Japan

institute: Tokushima University

summary:
We intraperitoneally injected SKOV3 (derived from human ovarian adenocarcinoma) expressing soluble fragment of human EP2 receptor or hIgG Fc (SKOV/ip-FuEP2/Ex2 and (SKOV/ip-Fumock). After 4 week, resulted tumors were lysed and total RNAs were isolated.
By using microarray, We analyzed gene expression and identified distinct classes of up-regulated genes in SKOV/ip-FuEP2/Ex2-derived tumor.

overall_design: Tumor tissues from SKOV/ip-Fumock or SKOV/ip-FuEP2/Ex2 were lysed and total RNAs were extracted. And then we analyzed expression status by Affymetrix microarrays.


title: Gene expression profiling of the cell death induced by heat stress in DNA-PK-knockdown human cervical carcinoma HeLa cells

city: Toyama

first: Yoshiaki

last: Tabuchi

state: Toyama

address: 2630 Sugitani

department: Life Science Research Center

institute: University of Toyama

summary: The objective of the present study is to investigate the role of DNA-PK inhibition in cell death induced by heat stress (44°C, 60 min). Comparative gene expression analysis was performed with mock cells, negative control siRNA-treated cells and DNA-PK siRNA-treated cells. The expression of DNA-PK was confirmed by Western blotting. Gene expression was analyzed using GeneChip oligonucleotide microarrays and computational gene expression analysis tools.

overall_design: DNA-PK-knockdown human cervical carcinoma HeLa cells were treated with heat (44°C, 60 min) and then were cultured at 37°C for 6 h. Total RNA samples were prepared from the cells. Gene expression was analyzed by an Affymetrix GeneChip® system with GeneChip Human Gene 1.0 ST arrays. Sample preparation for array hybridization was carried out as described in the manufacturer's instructions.

first: Seisuke

last: Okazawa

first: Yukihiro

last: Furusawa

first: Ayako

last: Kariya

first: Takashi

last: Kondo

first: Kazuyuki

last: Tobe


title: Expression data from primary ovarian samples and matched abdominal deposits

status: Public on Jun 15 2012

city: Melbourne

first: Prof David

last: Bowtell PhD.

state: VIC

address: Locked Bag 1 A' Beckett St

department: Research Division

institute: PeterMacCallum Cancer Centre

summary: We used unsupervised hierarchical clustering to analyse expression in primary ovarian tumors and associated abdominal deposits. GeneGo pathway analysis of differentially expressed genes between primary tumors and deposits revealed 4 of the top 10 pathways related to cytoskeleton remodeling and cell adhesion.

overall_design: Primary ovarian tumours and matched abdominal deposits were selected for RNA extraction and hybridization on Affymetrix microarrays.

first: Prue

last: Cowin

first: Joshy

last: George

first: David

last: Bowtell


title: Expression of MALT1 oncogene in mouse hematopoietic stem/progenitor cells recapitulates the pathogenesis of human MALT lymphoma

city: Pamplona

first: Victor

last: Segura

state: Navarra

address: Avda. Pío XII, 55

department: Unit of Proteomics, Genomics and Bioinformatics

country: Spain

institute: FIMA

summary:
Comparison of gene expression profiling analysis of bone marrow isolated CD34+ cells from patients with MALT lymphoma vs. healthy individuals revealed a large number of differentially expressed genes that included NF-kB target genes, genes involved in inflamatory signalling and immunoglobulin genes, suggesting an early lymphoid B-cell priming.
Chromosomal translocations involving MALT1 gene are hallmarks of mucosa-associated lymphoid tissue (MALT) lymphoma. However, targeting these translocations to mouse B-cells has failed to reproduce human disease. Here, we induced MALT1 expression in mouse Sca1+Lin- hematopoietic stem/progenitor cells (HS/PCs), leading to the development of tumors recapitulating the clinical, histopathological and molecular features of human MALT lymphomas. Ablation of the p53 gene induced transformation of MALT lymphoma to diffuse large-cell lymphoma of activated B-cell type (ABC-DLBCL). Human CD34+ cells isolated from MALT lymphoma patients displayed an abnormal transcriptional program that was shared by MALT lymphoma cells, transgenic mouse Sca1+Lin- cells and Sca1-MALT1-induced lymphomas. Our study shows that MALT lymphoma can be modeled in mice by targeting MALT1 oncogene to HS/PCs.

overall_design: 10 samples were analyzed of which 5 are CD34+ cells sorted from the bone marrow of MALT patients and are compared to the other 5 CD34+ cells sorted from the bone marrow of healthy donors.

first: Jose

last: Martinez-Climent

first: Lorena

last: Fontan

first: Isidro

last: Sanchez-Garcia

first: Carolina

last: Vicente-Dueñas

first: Cesar

last: Cobaleda


title: Effect of NPAP1/C15orf2 overexpression on transcriptome of HEK293 cells

status: Public on Jun 18 2012

city: Essen

first: Ludger

last: Klein-Hitpass

address: Virchowstr. 173

department: Universitaetsklinikum

institute: Institut fuer Zellbiologie

summary: To gain insight into the function of Nuclear pore associated protein 1 (NPAP1, formerly C15orf2), we overexpressed NPAP1 in HEK293 cells. We detected no significant difference between NPAP1-expression of induced and uninduced cells in three technical replicates, exept for an approximately 10-fold increase in the NPAP1 transcript itself. This indicates that overexpression of NPAP1 does not change mRNA expression profiles of HEK293 cells. We used microarrays to investigate global gene expression changes depending on the level of NPAP1/C15orf2

overall_design: We compared NPAP1 overexpressing cells to untreated cells, which do not express detectable amounts of NPAP1 protein, to determine global gene expression changes.

first: Lisa

last: Neumann


title: Gene Expression of ESC and iPSC lines after specific differentiation

first: Sergio

last: Ruiz

address: 10010 North Torrey Pine Rd

department: Gene Expression Laboratory

institute: Salk Institute for Biological Studies

summary: We cultured hESC and hiPSC lines and compared the transcriptome of untreated cells with cells treated with Activin or BMP4 during 5 days

overall_design: Pluripotent cell lines cultured in feeder-free conditions were treated with 100 ng/ml of activin or 50 ng/ml BMP4 daily during 5 days and collected for analysis

first: Sachin

last: Kumar

first: Juan

last: Izpisua Belmonte


title: Cancer stem cell subpopulations within the CD44high human breast cancer stem cell compartment

status: Public on Jun 12 2012

city: Odense

first: Rikke

last: Leth-Larsen

address: JB Winsloewsvej 25

department: Institute of Molecular Medicine

institute: University of Southern Denmark

summary:
The CD44hi compartment in human breast cancer is enriched in tumor-initiating cells, however the functional heterogeneity within this subpopulation remains poorly defined. From a human breast cancer cell line with a known bi-lineage phenotype we have isolated and cloned two CD44hi populations that exhibited mesenchymal/Basal B and luminal/Basal A features, respectively. Rather than CD44+/CD24-,Basal B (G4) cells, only CD44hi/CD24lo, epithelioid Basal A (A4) cells retained a tumor-initiating capacity in NOG mice, form mammospheres and exhibit resistance to standard chemotherapy.
Microarray data obtained from Affymetrix Human Gene 1.0 ST Array

overall_design: Five replicates of A4 and 5 replicates of G4

first: Henrik

middle: J

last: Ditzel


title: Claudin 1 mediates TNFα-induced gene expression and cell migration in human lung carcinoma cells

status: Public on Jun 13 2012

city: Toronto

first: Mingyao

last: Liu

state: Ontario

address: 101 College Street

department: Surgery

institute: University of Toronto

summary: Epithelial-mesenchymal transition (EMT) is an important mechanism in carcinogenesis. To determine the mechanisms that are involved in the regulation of EMT is crucial to develop new biomarkers and therapeutic targets towards cancers. In this study, when TGFß1 and TNFa were used to induce EMT in human lung carcinoma A549 cells, we were surprised to find an increase in an epithelial cell tight junction marker, Claudin 1. We further identified that it was the TNFa and not the TGFß1 that induced the fibroblast-like morphology changes. TNFa also caused the increase in Claudin-1 gene expression and protein levels in Triton X-100 soluble cytoplasm fraction. Down-regulation of Claudin-1, using small interfering RNA (siRNA), inhibited 75% of TNFa-induced gene expression changes. Claudin-1 siRNA effectively blocked TNFa-induced molecular functional networks related to inflammation and cell movement. Wound-healing assay showed that Claudin-1 siRNA was able to significantly reduce TNF-enhanced cell migration. Furthermore, over expression of Claudin 1 with a Claudin 1-pcDNA3.1/V5-His vector enhanced cell migration. In conclusion, these observations indicate that Claudin 1 acts as a critical signal mediator in TNFa-induced gene expression and cell migration in human lung cancer cells. Further analyses of these cellular processes may be helpful in developing novel therapeutic strategies.

overall_design: 4 groups (with or without TNFα, control or Claudin 1 siRNA) of human lung adenocarcinoma A549 cells with 3 replicates per group.

first: Atsushi

last: Shiozaki

first: Xiao-hui

last: Bai

first: Shan-Yu

last: Fung

first: Shaf

last: Keshavjee


title: The HDAC inhibitor Givinostat modulates key hematopoietic genes in JAK2V617F cells, affecting proliferation, differentiation and apoptosis

status: Public on Jul 17 2012

city: MILAN

first: Luca

last: Agnelli

address: Venezian 1

department: Department of Advanced Diagnostics

institute: IRCCS Istituto Nazionale dei Tumori

summary: We investigated the mechanism of action of the HDAC inhibitor Givinostat in JAK2V617F cells. We confirm that the drug inhibits colony formation and proliferation and induces apoptosis at doses 2-3 fold lower in JAK2V617F (HEL, UKE1 and SET2) compared to JAK2 wild type cell lines (K562, KU812, THP1 and KG1). By global gene expression analysis, we observed  293 common genes in HEL and UKE1 modulated at 6 hour by Givinostat (179 up and 114 down), of which 8/8 were validated by RTQ-PCR. 25, 28 and 33 modulated genes are implicated in the regulation of proliferation, apoptosis and hematopoiesis, respectively. Interestingly, 9 genes, known to be deregulated in MPN (myeloproliferative neoplasms) patients cells, were normalized by Givinostat. The hematopoietic transcription factors NFE2 and C-MYB were downmodulated by the drug specifically in JAK2V617F cells, and ETS1 was upregulated in all cell lines, at both the RNA and protein levels. Modulation of NFE2 and C-MYB was JAK2 dependent, as shown by use of the JAK2 inhibitor AG490. Finally, we suggest that the inhibition of NFE2 and induction of ETS1, also observed in freshly isolated CD34+ cells from MPN patients, may be at least in part responsible for the observed inhibition of erythroid differentiation by the drug.

overall_design:
Gene expression profiling, JAK2V617F cell lines, ITF2357.

This series of microarray experiments contains the gene expression profiles of independent triplicates of HEL and UKE1 erythroleukemia cell lines bearing the JAK2V617F mutation, before and after ITF2357 treatment. 100 nanograms of total RNA were processed, and fragmented biotin-labelled single-stranded DNA target was hybridized to the GeneChip® Gene 1.0 ST array following the Affymetrix  manufacturer's instructions.

first: Ariel

last: Amaru

first: Katia

last: Todoerti

last: Donadoni

first: Anna

last: Pellicioli

first: Giacomo

last: Tuana

first: Antonino

last: Neri

first: Guido

last: Finazzi

first: Alessandro

last: Rambaldi

first: Martino

last: Introna

first: Luigia

last: Lombardi

first: Josée

last: Golay


title: Genome-wide mRNA expression profiles induced by infection with the pandemic and seasonal influenza A viruses in macrophages

status: Public on Jun 10 2012

city: Mexico

first: Sandra

middle: Lorena

last: Romero-Cordoba

state: Mexico

address: Periférico Sur No. 4809, Col. Arenal Tepepan, Delegación Tlalpan. México, D.F.

department: Cancer Genomics

country: Mexico

institute: National Instute of Genomic Medicine

summary: Infection with pandemic A/H1N1 influenza virus induces high levels of circulating and lung pro-inflammatory cytokines and chemokines in experimental models and humans. These inflammatory mediators contribute to poor clinical outcomes of this infection. To compare the regulation of inflammatory responses in seasonal versus pandemic influenza A virus infections, we analyzed the expression of mRNA by the human gene st 1.0 array (affymetrix). We identifed a number of differentially expressed genes by infection of the A/H1N1 compared to the seasonal virus. Gene ontology analysis of these genes found that most of them are involved in several aspects of immunity. These studies suggest that factors inherent in the pandemic A/H1N1 viral strain may augment the production of inflammatory mediators by inhibiting SOCS- 1 expression and that infection with this viral strain also modifies the expression of several immunity related genes and pathways .

overall_design: The experimental design consist in 1 pool and its replicate containing 5 independent experiments from treated macrophages with Influenza A/H1N1 virus, and 1 more pool and its replicate containing 5 independent experiments from treated macrophages with seasonal influenza A virus. By this way, the total number of the samples analyzed was 10 in 4 microarrays.

first: Gustavo

last: Ramírez

first: Alfredo

last: Cruz-Lagunas

first: Luis

last: Jiménez-Alvarez

first: Enrique

last: Espinosa

first: Blanca

last: Ortiz-Quintero

first: Teresa

last: Santos-Mendoza

first: Martha

last: Torres

last: Herrera

first: Elsy

last: Canché-Pool

first: Carlos

last: Cabello

first: Lorena

last: Orozco

first: Irma

last: Aguilar

last: Hidalgo-Miranda

first: Andrew

last: Tager

first: Benjamin

middle: T

last: Suratt

first: Annie

last: Pardo

first: Moisés

last: Selman

first: Joaquin

last: Zuñiga


title: Microarray gene-expression profiles of 45 matching pairs of pancreatic tumor and adjacent non-tumor tissues from 45 patients with pancreatic ductal adenocarcinoma

status: Public on Jul 09 2012

city: Bethesda

first: Perwez

last: Hussain

address: 37 Convent Drive

institute: NCI/NIH

summary:
In order to identify biologically relevant tumor markers with prognostic significance, we set out to analyze gene expression profiling of tumor and adjacent non-tumor tissues from PDAC cases.
We compared the microarray gene-expression profiles of 45 matching pairs of pancreatic tumor and adjacent non-tumor tissues. This data set were used to obtained genes that were differentially expressed and associated with survival. 51 genes were selected for further validation.

overall_design: 90 total samples were analyzed. We compared gene expression profile of 45 pairs of pancreatic tumor and adjacent non-tumor tissues using Affymetrix GeneChip Human Gene 1.0 ST arrays.  Tumor gene expression profiles were distinctly different from non-tumor profiles. Using ANOVA in Partek®, 7352 independent genes were found to be differentially expressed in tumors (P<0.01). We next performed Cox-regression analysis and identified 928 of the differentially expressed genes that were associated with survival (P<0.1). The list of genes was then subjected to pathway and biomarker analyses using Ingenuity Pathways Analysis (IPA). Based on literatures supporting their roles in cancer, 51 genes were selected for further analyses

first: S


title: Exon Level Expression Profiling in D54 with or without TIP-1 expression

status: Public on Jun 06 2012

city: nashville

first: Miaojun

last: Han

state: TN

address: 1161 21st Ave S

institute: Vanderbilt University

summary: D54 stable cell lines that transfected with control shRNA and TIP-1 shRNA were cultured overnight. Isolated the total RNA of these cell lines to do microarray. Try to get more information about the difference in the mRNA level in these cell lines.

overall_design: We analyzed gene expression from 5 subjects: 2 control D54 (two independent clones) and  3 shRNA TIP-1  D54 cells (3 differenct shRNA to scilence TIP-1 expression) using the Affymetrix Human Exon 1.0 ST platform. Array data was processed by Affymetrix Exon Array Computational Tool. No techinical replicates were performed.

first: Maiojun

first: Hailun

last: Wang

first: Zhaozhong


title: Gene expression microarray data by Moutan Cortex Radicis (MCR) in the LPS-stimulated human gingival fibroblast

status: Public on Jun 28 2012

city: Seoul

first: Sabina

last: Lim

address: #1 Hoegi-dong Dongdaemoon-gu

country: South Korea

institute: East-West Medical Research Institute, Kyung Hee University

summary:
The Moutan Cortex Radicis (MCR) has been used as an analgesic, sedative and anti-inflammatory agent.
This study investigated the changes in gene expression by MCR treatment when stimulated with lipopolysaccharide (LPS) in cultured human gingival fibroblasts (HGFs) and the gene expression changes by the MCR when challenged with LPS using a microarray chip.

overall_design: Human gingival fibroblast were divided into three experimental groups; 1, C: Control, 2, LPS: LPS-treatment only, 3, MCR40: LPS- and MCR40-treatments. Total RNA was isolated from each experimental fibroblast (3 experimental group × 1 sample of each experimental group = total 3 samples).

first: Yeong-Gon

last: Choi


title: Gene expression from induced CB-derived neurons at different time of differentiation

status: Public on Jun 05 2012

city: barcelona

first: Alessandra

last: Giorgetti

address: doctor aiguader 88

institute: CMRB

summary:
Gene expression from cord blood stem cells and respective derived neuronal cells at different times point of differentiation:CD133+ cells;

Keywords: Expression Profiling by array

overall_design: We analyzed 3 arrays from each condition and 2 arrays for the positive controls:CB CD133+ untreated,CB-iNCs after SOX2 and cMYC overexpression, CB-neurons after differentiation (6 weeks), HUES6-NPCs control, HUES6-neurons control

first: Juan

last: Izpisua Belmonte


title: Gene expression profiling of primary human hepatocytes treated with IFN-alpha or IFN-gamma

status: Public on Jun 09 2012

city: Basel

first: Zuzanna

last: Makowska

address: Hebelstrasse 20

department: Biomedicine

institute: University of Basel

summary:
Approximately 50% of patients with chronic hepatitis C (CHC) have a sustained virologic response (SVR) to treatment with pegylated interferon (pegINF)-α and ribavirin. Non-response to treatment is associated with constitutively increased expression of IFN-stimulated genes (ISGs) in the liver. Treatment of patients with acute hepatitis C (AHC) is more effective, with SVR rates >90%. We investigated mechanisms of the different responses of patients with CHC and AHC to pegIFN-α therapy. We analyzed IFN signaling and ISG expression in liver samples from patients with acute hepatitis C (AHC), patients with chronic hepatitis (CHC), and individuals without hepatitis C (controls) using microarray, immunohistochemical, and protein analyses. Findings were compared with those from primary human hepatocytes stimulated with IFN-α or IFN-γ, as reference sets. Expression levels of 100s of genes, primarily those regulated by IFN-γ, were altered in liver samples from patients with AHC compared with controls. Expression of IFN-γ–stimulated genes was induced in liver samples from patients with AHC, whereas expression of IFN-α–stimulated genes was induced in samples from patients with CHC. In an expression analysis of negative regulators of IFN-α signaling, we did not observe differences in expression of SOCS1 or SOCS3 between liver samples from patients with AHC and those with CHC. However, USP18 (another negative regulator of IFN-α signaling), was upregulated in liver samples of patients with CHC that did not respond to therapy, but not in AHC. In conclusion, differences in expression of ISGs might account for the greater response of patients with AHC, compared to those with CHC, to treatment with pegINF-α and ribavirin. Specifically, USP18 is upregulated in liver samples of patients with CHC that do not respond to therapy, but not in patients with AHC.

(Interferon-γ Stimulated Genes, but not USP18, are Expressed in Livers of Patients with Acute Hepatitis C; Dill MT, Makowska Z et al, Gastroenterology 2012 (in press))

overall_design: Primary human hepatocytes from 2 donors were analyzed. From each donor there are 5 samples: untreated cells, cells treated with interferon alpha (1000 IU/ml) for 6 and 24 hours and cells treated with interferon gamma (1000 IU/ml) for 6 and 24 hours.

first: Michael

last: Dill

first: Francois

last: Duong

first: Franzisca

last: Merkofer

first: Magdalena

last: Filipowicz

first: Thomas

last: Baumert

first: Luigi

last: Tornillo

last: Terraciano

first: Markus

last: Heim


title: Characterization of Anaplastic Large Cell Lymphoma Stem Cells

status: Public on Jun 25 2012

city: Cambridge

first: Naushad

last: Moti

state: Cambridgeshire

address: Hills Road

department: Department of Pathology

country: United Kingdom

institute: University of Cambridge

summary: Anaplastic Large Cell Lymphoma (ALCL) is propagated by cancer stem cells which are identified by their ability to efflux dye and hence reside in the side population (SP) on FACS analysis. In order to understand the origins of these ALCL SP cells we purified SP and main population (MP; SP-depleted) cell from the ALCL cell lines. On comparison of the gene expression signatures derived from these 2 cellular populations distinct branches dividing the SP and MP populations present indicating that they are distinct subsets within the bulk tumour.

overall_design: SP and MP cells from human Anaplastic Large Cell Lymphoma (ALCL) cell lines was selected RNA extraction and hybridization on Affymetrix microarrays. We sought to obtain pure populations of SP and MP cells. Cells were stained with Hoechst 33342 dye and were analysed on FACS. The cells were then sorted in triplicates and subjected to RNA extraction.

first: Rifat

last: Hamoudi

first: Suzanne

last: Turner


title: Adaptation During Ovarian Cancer Metastasis Reveals a Predictive Gene Signature

status: Public on Jun 01 2012

city: PROVIDENCE

first: Alexander

last: Brodsky

state: RI

address: 593 Eddy St.

department: MCB

institute: Rhode Island Hospital/Brown University

summary:
We characterized the genetic copy number and expression differences between matched ovarian primary tumors and omental metastases.
Differentially expressed genes revealed that metastases proliferate more and are less apoptotic.
Differentially expressed genes revealed a predictive expression signature when applied to other gene expression datasets.

overall_design: 18 samples from 9 matched pairs of primary ovarian tumors and metastases from the omentum were collected.


title: Expression data from melanoma subpopulations

city: Vienna

first: Mario

last: Mikula

address: Waehringergürtel 18-20

department: General Dermatology

country: Austria

institute: Medical University Vienna

summary: We aimed at identifying lymphangiogenic subpopulations by comparative analysis of single cell clones derived from a melanoma of a single patient. Selected clones were grafted into SCID mice, where they induced lymphangiogenesis and metastasized into sentinel nodes, whereas non-lymphangiogenic clones from the same patient did not metastasize. RNA isolated from primary SCID mouse tumors were used for transcriptome analysis.

overall_design: A total of 16 Samples were analysed, 4 per group. Parental pool MCM1(C), nonlymphangiogenic MCM1G(G), lymphangiogenic MCM1D(D1), lymphangiogenic and very metastatic MCM1DLN(D2).

first: Peter

last: Petzelbauer


title: Expression data of cHL cell lines after FOXO1 activation

city: Ulm

first: Alexey

last: Ushmorov

address: Albert-Einstein-Allee 11

department: Institute of Physiological Chemistry

institute: Ulm University

summary: FOXO1 is highly expressed in normal B cells and in most types of non-Hodgkinl lymphoma. In Hodgkin and Reed-Sternberg cells of classical Hodgkin lymphoma(cHL) expression of FOXO1 is low or absent. We overexpressed constitutively active mutant of FOXO1 fused in frame with estrogen receptor ligand-binding domain (FOXO1(3A)ER), which can be activated by 4-Hydroxytamoxifen (4-OHT), in cHL cell lines KM-H2 and L428. Activation of the FOXO1 with 4-OHT resulted in inhibition of proliferation and apoptosis. Using gene-expression array we found that FOXO1 activates transcription of known and potential tumor suppressor genes: CDKN1B, PMAIP1, BCL2L11, TNFSF10, FBXO32, CBLB). Of note, FOXO1 repressed transcription of several cytokines and cytokine receptors, which are known tobe involved in pathogenesis of cHL (e.g. CCL5, CXCR5, TNFRSF8). Taken togather our data indicate important role of FOXO1 repression in pathogenesis of cHL.

overall_design: KM-H2, L428, L1236, UH0-1, and SUP-HD1 cells expressing constitutively active mutant of human FOXO1 fused in frame with estrogen receptor ligand-binding domain were incubated with 200 µcle (ethanol).  After 24 h, total RNA was isolated with RNeasy mini kit (QIAGEN). Microarray analyses were performed using 200 ng of total RNA as starting material and 5.5 ug ssDNA per hybridization (GeneChip Fluidics Station 450; Affymetrix, Santa Clara, CA). The total RNAs were amplified and labeled following the Whole Transcript (WT) Sense Target Labeling Assay (http://www.affymetrix.com). Labeled ssDNA was hybridized to Human Gene 1.0 ST Affymetrix GeneChip arrays (Affymetrix, Santa Clara, CA). The chips were scanned with a Affymetrix GeneChip Scanner 3000 and subsequent images analyzed using Affymetrix Expression Console Software (Affymetrix). Probe level data were obtained using the robust multichip average (RMA) normalization algorithm.

first: Linka

last: Xie

first: Hanfeng

last: Guan

last: Wirth


title: Gene expression and genotype in normal heart

status: Public on Jul 04 2012

city: Christchurch

first: Anna

last: Pilbrow

address: 2 Riccarton Avenue

department: Medicine

country: New Zealand

institute: University of Otago Christchurch

summary: Genome-wide association studies have identified a small region at chromosome 9p21.3 strongly associated with coronary heart disease risk. The region contains no protein-coding genes and the mechanism underlying its association with heart disease is unknown. We investigated associations between rs1333049, a single nucleotide polymorphism representing the 9p21.3 locus, and levels of cardiac gene expression in myocardial tissue from donors with no documented history of heart disease.

overall_design: Individual myocardial gene expression profiles were generated with Affymetrix Human Gene 1.0 ST arrays (n=108). DNA genotyping was performed with Taqman assays. Associations between genotype and gene expression were analyzed assuming a recessive effect.

first: Lasse

last: Folkersen

first: John

last: Pearson

first: Chris

last: Brown

first: Les

last: McNoe

first: Nancy

last: Wang

first: Wendy

middle: E

last: Sweet

first: W

last: Tang

middle: A

last: Black

first: Richard

last: Troughton

first: A

last: Richards

first: Anders

last: Franco-Cereceda

last: Gabrielsen

first: Per

last: Eriksson

first: Christine

last: Moravec

first: Vicky

last: Cameron


title: Profiles of Epigenetic Histone Post-translational Modifications at Type 1 Diabetes Susceptible Genes

city: Duarte

last: Chen

address: 1500 Duarte Road

department: Diabetes

country: USA

institute: City of Hope

type: Genome binding/occupancy profiling by genome tiling array

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

overall_design: Refer to individual Series


title: Cytotoxic effects of Bortezomib in Myelodysplastic syndrome/Acute Myeloid Leukemia depend on autophagy-mediated lysosomal degradation of TRAF6 and repression of PSMA1

city: Columbia

first: Jing

last: Fang

state: SC

address: 715 Sumter Street

department: Drug Discovery and Biomedical Sciences

institute: University of South Carolina

summary: Bortezomib (Velcade©) is widely used for the treatment of various human cancers, however, its mechanisms of action are not fully understood, particularly in myeloid malignancies. Bortezomib is a selective and reversible inhibitor of the proteasome. Paradoxically, we find that Bortezomib induces proteasome-independent degradation of TRAF6 protein, but not mRNA, in Myelodysplastic syndrome (MDS) and Acute Myeloid Leukemia (AML) cell lines and primary cells. The reduction in TRAF6 protein coincides with Bortezomib-induced autophagy, and subsequently with apoptosis in MDS/AML cells. RNAi-mediated knockdown of TRAF6 sensitized Bortezomib-sensitive and -resistant cell lines, underscoring the importance of TRAF6 in Bortezomib-induced cytotoxicity. Bortezomib-resistant cells expressing an shRNA targeting TRAF6 were resensitized to the cytotoxic effects of Bortezomib due to down-regulation of the proteasomal subunit alpha-1 (PSMA1). To uncover the molecular consequences following loss of TRAF6 in MDS/AML cells, we applied gene expression profiling and identified an apoptosis gene signature. Knockdown of TRAF6 in MDS/AML cell lines or patient samples resulted in rapid apoptosis and impaired malignant hematopoietic stem/progenitor function. In summary, we describe novel mechanisms by which TRAF6 is regulated through Bortezomib/autophagy-mediated degradation and by which it alters MDS/AML sensitivity to Bortezomib by controlling PSMA1 expression.

overall_design: TF-1 cells were transduced with lentivirus encoding shRNA targeting human TRAF6 and a negative control (pLKO) for 2.5 days. GFP positive cells were sorted for RNA exctration, labeling, and hybridization. A total of four samples were included, and two groups are assigned. Two replicates are for each group. Comparison comprises mRNA expression profile of TRAF6 knockdown (shT6) v.s. control vector (pLKO).

first: Garrett

last: Rhyasen

first: Lyndsey

last: Bolanos

first: Christopher

last: Rasch

first: Melinda

last: Varney

first: Mark

last: Wunderlich

first: Susumu

last: Goyama

first: Gerrit

last: Jansen

first: Jacqueline

last: Cloos

first: Carmela

last: Rigolino

first: Agostino

last: Cortelezzi

first: James

middle: C

last: Mulloy

first: Esther

middle: N

last: Oliva

first: Maria

last: Cuzzola

first: Daniel

last: Starczynowski


title: Genomic signatures of a global fitness index in a multi-ethnic cohort of women

city: Miami

first: Evadnie

last: Rampersaud

state: FL

address: 1501 NW 10th Ave. BRB

department: John P. Hussman Institute for Human Genomics

institute: University of Miami, Miller School of Medicine

summary: The rates of obesity and sedentary lifestyle are on a dramatic incline, with associated detrimental health effects among women in particular. Although exercise prescriptions are useful for overcoming these problems, success can be hampered by differential responsiveness among individuals in cardiovascular fitness indices (i.e., improvements in strength, lipids, VO2max). Genetic factors appear to play an important role in determining this inter-individual variation in responsiveness.  We performed microarray analyses on mRNA in whole blood from 60 sedentary women from a multi-ethnic cohort who underwent 12 weeks of exercise, to identify gene subsets that were differentially expressed between individuals who experienced the greatest and least improvements in fitness based upon a composite fitness score index. We identified 43 transcripts in 39 unique genes (FDR<10%; FC>1.5) whose expression increased the most in “high” versus “low” premenopausal female responders. Several (TIGD7, UQCRH, PSMA6, WDR12, TFB2M, USP15) have reported associations with fitness-related phenotypes. Bioinformatic analysis of the 39 genes identified 4 miRNAs whose expression has been linked to cardiovascular diseases (ANKRD22: miR-637, LRRFIP1: miR-132, PRKAR2B: miR-92a, RSAD2:miR-192). These 39 genes were enriched in 6 biological pathways, including the oxidative phosphorylation pathway (p=8.08 x 10-3). Two genes, LRRFIP1 and SNORD30, were also identified with lower expression in high responding postmenopausal women.  In summary, we identified gene signatures based on mRNA analysis that define responsiveness to exercise in a largely minority-based female cohort. Importantly, this study validates several genes/pathways previously associated with exercise responsiveness and extends these findings with additional novel genes.

first: Lubov

last: Nathanson

first: Jeffrey

last: Farmer

first: Karyn

last: Meshbane

first: Richard

middle: L

last: Belton

first: Amy

last: Dressen

first: Michael

last: Cuccaro

first: Anthony

last: Musto

first: Sylvia

last: Daunert

first: Sapna

last: Deo

first: Natasha

last: Hudson

first: Jeffery

middle: M

last: Vance

first: David

last: Seo

first: Armando

last: Mendez

first: Derek

last: Dykxhoorn

first: Margaret

last: Pericak-Vance

first: Pascal

last: Goldschmidt-Clermont


title: Expression data from U373 cells expressing EGFP, MAML1-dn and DTX1-myc

first: Roland

middle: Martin

last: Huber

state: BS

summary: Glioblastoma multiforme (GBM) is the most malignant and most common tumor of the central nervous system characterized by rapid growth and extensive tissue infiltration. GBM results in more years of life lost than any other cancer type. Notch signaling has been implicated in GBM pathogenesis through several modes of action. Inhibition of Notch leads to a reduction of cancer-initiating cells in gliomas and reduces proliferation and migration. Deltex1 (DTX1) is part of an alternative Notch signaling pathway distinct from the canonical MAML1/RBPJκ-mediated cascade. In this study, we show that DTX1 activates both the RTK/PI3K/PKB as well as the MAPK/ERK pathway. Moreover, we found the anti-apoptotic factor Mcl-1 to be induced by DTX1. In accordance with this, the clonogenic potential and proliferation rates of glioma cell lines correlated with DTX1 levels. DTX1 knock down mitigated the tumorigenic potential in vivo, and overexpression of DTX1 increased cell migration and invasion of tumor cells accompanied by an elevation of the pro-migratory factors PKBβ and Snail1. Microarray gene expression analysis identified a DTX1-specific transcriptional program - including microRNA-21 - which is distinct from the canonical Notch signaling. We propose the alternative Notch pathway via DTX1 as oncogenic factor in malignant glioma and found low DTX1 expression levels to correlate with prolonged survival of GBM and early breast cancer patients in open source databases.

overall_design: We generated human glioma U373 cell lines stably expressing Enhanced Green Fluorescent Protein (EGFP), human Deltex1-Myc Tag (DTX1-myc), or Master Mind Like 1 - dominant negative (MAML1-dn) to compare differences in overall gene expression. We included 3x EGFP control samples, 3x DTX1-myc, and 3 MAML1-dn samples.

first: Adrian

last: Merlo


title: Functional expression of membrane alanyl-aminopeptidase (CD13/APN) promotes tumor cell proliferation and neoangiogenesis in malignant gliomas.

status: Public on May 28 2012

city: Greifswald

first: Joerg

last: Mostertz

address: F.-L.-Jahnstr 15

department: Competence Center Functional Genomics

institute: Greifswald University

summary: Malignant gliomas are characterized by marked neovascularization and increased tumor cell proliferation. Recently, membrane alanyl-aminopeptidase (CD13/APN) has been identified to play a crucial role in neoangiogenesis. In this study, we show that among various central nervous system tumors, malignant astrocytomas are unique in their high expression levels of functionally active CD13/APN. CD13/APN was found in both tumor cells and tumor vessels of malignant astrocytomas, while in low-grade astrocytomas only endothelial cells of tumor vessels expressed CD13/APN. Inhibitors of the enzymatic activity of CD13/APN significantly reduced the proliferation of U87MG and U138MG malignant glioma cells. Inhibition of CD13/APN mRNA expression by siRNA in glioma cells co-cultured with human umbilical vein endothelial cells (HUVEC) effectively decreased blood vessel formation. Pro-angiogenic factors like bFGF and VEGF induced CD13/APN expression in glioma cells. Treatment of U87MG and U138MG cells with CD13/APN inhibitors resulted in an increased mRNA expression of VEGF and VEGF receptor 2 (VEGF-R2) in these cells. Taken together, these findings provide evidence that CD13/APN promotes tumor cell proliferation and blood vessel formation in malignant astrocytomas. Remarkably, inhibition of CD13/APN induces an angiogenic expression profile via an autocrine feed-back mechanism involving the VEGF/VEGF-R2 system in malignant gliomas.

overall_design: Experimental design includes altogether four samples with two replicate controls (U87_APN_wt_EGFP) and two replicate samples (U87_APN_L243P_EGFP). Replicates are from two independent experiments.

first: Uwe

last: Lendeckel

first: Christian

last: Mawrin


title: Expression data from HCT116 cells

status: Public on May 22 2012

first: Alexandra

last: Graf

address: Spitalgasse 23

institute: Medical University of Vienna

summary:
Advanced colon cancer is characterized by drug resistance and a poor prognosis. In these patients tumor-propagating cells appear to be largely resistant against various targeted drugs including ErbB-inhibitors. The cell surface antigen prominin-1 (CD133) has recently been identified as a potential marker of colon cancer stem cells.
The purpose of this study was to define mRNA expression patterns in CD133+ and CD133- HCT116 cells.

overall_design: To define mRNA expression patterns in CD133+ and CD133- HCT116 cells, gene array analysis were performed using genome-wide human U133 2.0 plus GeneChips (Affymetrix, Santa Clara, CA, USA). 3 repetitions of CD133+ HCT116 cells and 3 repetitions of CD133- HCT116 cells were performed. Robust Multichip Average (RMA) signal extraction and normalization were performed.

first: Peter

last: Valent

last: Laffer


title: The clinical and molecular significance of different types of C4d staining in renal allografts

status: Public on May 29 2012

city: New York

first: Bin

last: Ye

state: NY

address: 1301 Morris Park Ave

department: Genetics

institute: Albert Einstein College of Medicine

summary: We investigated the clinical and molecular significance of minimal peritubular capillary (PTC) and isolated glomerular C4d+ staining using microarrays. Immunohistochemistry for C4d was performed on paraffin-embedded sections. Of the 255 biopsies analyzed, 51% were C4d negative, 4% were minimal, 15% focal or diffuse PTC C4d+, and 31% isolated glomerular C4d+. Minimal and focal/ diffuse PTC C4d+ staining were associated with a higher frequency of donor-specific anti-HLA antibodies (DSA) (67% vs. 82% vs. 25%), antibody mediated rejection (AMR) (66% vs. 89% vs. 19%) and mean glomerulitis (0.88 vs. 0.65 vs. 0.25, p=0.003), interstitial inflammation (1.25 vs. 1.41 vs. 0.79; p=0.003) and peritubular capillaritis scores (1.5 vs. 1.5 vs. 0.34; p < 0.001), compared to the C4d negative group, respectively. There were no differences in the DSA frequency, AMR rate, and Banff scores between isolated glomerular C4d+ and negative patients. While both minimal and focal/diffuse C4d+ biopsies showed increased expression of genes related to the immune response, and interferon-gamma and rejection induced, cytotoxic T cell and constitutive macrophage-associated pathogenesis based transcripts, there was no activation of immune-response related genes in isolated glomerular C4d+ biopsies. In summary, minimal PTC C4d+ staining but not isolated glomerular C4d+ staining is associated with AMR.

overall_design: Total of 92 arrays included in this study. G1. Native pre-implantation biopsies (N= 10); G2. Focal or diffuse PTC C4d+ (N= 13); G3. Minimal PTC C4d+ (N=4); G4. Isolated glomerular C4d+ with glomerular disease (N= 13); G5. Isolated glomerular C4d+ staining without glomerular disease  (N= 15); G6. C4d negative with glomerular disease (N= 12); G7. C4d negative biopsies without evidence of glomerular disease (N=25)

first: Enver

last: Akalin

first: Nicole

last: Hayde

first: Yi

last: Bao

first: James

last: Pullman

first: Brent

last: Calder

first: Monica

last: Chung

first: Daniel

last: Schwartz

first: Ahmed

last: Alansari

last: Glicklich

first: Graciela

last: de Boccardo

first: Min

last: Ling


title: Expression data for effector T cells

status: Public on May 13 2012

city: New Haven

first: Wei

last: Zhang

state: Connecticut

institute: Yale School of Medicine

summary:
In this study, we examined differential gene expression in naïve human CD4+ T cells, as well as in effector Th1, Th17-negative and Th17-enriched CD4- T cell subsets. We observed a marked enrichment for increased gene expression in effector CD4+ T cells compared to naive CD4+ among immune-mediated disease oci genes. Within effector T cells, expression of disease-associated genes was increased in Th17-enriched compared to Th17-negative cells.
We used microarray to examine the gene expresssion profile and level of human naïve, Th1 and effector T cell subsets.

overall_design: Human PBMCs were isolated and sorted to naïve, CD161-CCR6- and CD161+CCR6+ memory T cells. Naïve T cells were differentiatied to Th1 cells, and CD161-CCR6- and CD161+CCR6+ memory T cells were in vitro expanded for Th17-negative and Th17-enriched effector T cells. The gene profile was compared among naive, Th1, Th17-negative, and Th17-enriched cell subsets.

first: John

last: Ferguson

first: Judy

last: Cho


title: Synthetic circuits for tracking human cell fate

status: Public on May 24 2012

city: Boston

first: Mara

middle: Christine

last: Inniss

address: 200 Longwood Ave.

department: Systems Biology

institute: Harvard Medical School

summary:
Cells respond heterogeneously to DNA damage. We engineered genetic circuits to detect differential responses in a population that persist for many days post-stimulus.
We used microarrays to compare memory and non-memory subpopulations 3 days after DNA damage or doxycycline exposure.

overall_design: MD12/p53R2-RE and MD10/TetOx2 cells were either exposed to UV (10uJ/m^2) or doxycycline (1 ug/mL, 24 hours) and allowed to recover 3 days before sortng of memory and non-memory cells and RNA extraction. Two replicates were submitted for each condition (UV memory, UV non-memory, dox memory, dox non-memory)

first: Devin

middle: R

last: Burrill

first: Patrick

last: Boyle

first: Pamela

last: Silver