title: Identification of a CD271-associated signaling network in human malignant melanoma cells

city: Berlin

first: Christian

last: Regenbrecht

address: Chariteplatz 1

department: Tumor stem cells

institute: Charité University Medicine Berlin, Germany

summary:
Background: Large-scale genomic analyses of patient cohorts have revealed extensive heterogeneity between individual tumors, contributing to treatment failure and drug resistance. In malignant melanoma, heterogeneity is thought to arise as a consequence of the differentiation of melanoma-initiating cells that are defined by cell-surface markers like CD271 or CD133.
Results: Here we identified the nerve growth factor receptor (CD271) as a crucial determinant of melanoma cell tumorigenicity, stem-like properties, heterogeneity and plasticity. Stable shRNA mediated knock-down of CD271 in patient-derived melanoma cells abrogated their tumor-initiating and colony-forming capacity. A genome-wide expression profiling and gene-set enrichment analysis revealed novel connections of CD271 with melanoma-associated genes like CD133 and points to a neural crest stem cell (NCSC) signature lost upon CD271 knock-down. In a meta-analysis, we found CD271 linked to the neural crest specifier SOX10 and observed a shared set of 271 differentially regulated genes. To dissect the connection of CD271 and CD133 we analyzed 10 patient-derived melanoma-cell lines for cell-surface expression of both markers compared to established cell lines MeWo and A375. We found CD271+ cells in the majority of cell lines analyzed as well as in a set of 16 different patient-derived melanoma metastases. Strikingly, only 2/12 cell lines harbored a CD133+ sub-set that in addition comprised a fraction of cells of a CD271+/CD133+ phenotype. Those cells were found in the label-retaining fraction and in vitro deduced from CD271+ but not CD271 knock-down  cells.
Conclusions: Our present study provides a deeper insight into the regulation of melanoma cell properties and points CD271 out as a regulator of several melanoma-associated genes. Further, our data strongly suggest CD271 is a crucial determinant of stem-like properties of melanoma cells like colony-formation and tumorigenicity.

overall_design:
For knock-down of CD271 (NGFR), melanoma cells were transfected with 2 µg of each shRNA plasmid;
#2: 5’-ACAACCTCATCCCTGTCTATT-3’; #3: 5’-CCCGAGCACATAGA CTCCTTT-3’ and #4: 5’-CCGAGCACATAGACTCCTTTA-3’ or
control shRNA (shCtl 5’-GGAATCTCATTCGATGCATAC-3’; all from Quiagen) using Lipofectamine2000 (Invitrogen). Cells were selected with puromycin (10µg/ ml) over a period of two weeks.
Whole genome expression profiling of CD271k.d. cells (shRNA#4) and shCtl. cells was performed with three biological replicates. Illumina raw data of BeadChip HumanHT-12V4 platform were summarized via the BeadStudio without normalization and background correction. Follow-up processing was done via the R/Bioconductor environment employing packages lumi, limma and q-value. Data were normalized with quantile normalization. Genes were termed significantly differentially expressed when the average detection p-value of at least one case was < 0.05  the ratio was outside the interval [0.75,1.33], one of the p-values from limma test, Student's t-test, Welch test and Wilcoxon test was < 0.05. At least one of the q-values corresponding to one of these tests < 0.05.

first: Torben

last: Redmer


title: Transcriptome-based network analysis reveals a spectrum model of human macrophage activation [Expression]

status: Public on Feb 13 2014

city: Bonn

first: Joachim

last: Schultze

state: NRW

address: Carl-Troll-Strasse 31

department: Genomics and Immunoregulation

country: Germany

institute: LIMES (Life and Medical Sciences Center Genomics and Immunoregulation)

type:
Expression profiling by array
Third-party reanalysis

summary: Macrophage activation is associated with profound transcriptional reprogramming. Although much progress has been made in the understanding of macrophage activation, polarization and function, the transcriptional programs regulating these processes remain poorly characterized. We stimulated human macrophages with diverse activation signals, acquiring a dataset of 299 macrophage transcriptomes. Analysis of this dataset revealed a spectrum of macrophage activation states extending the current M1 versus M2-polarization model. Network analyses identified central transcriptional regulators associated with all macrophage activation complemented by regulators related to stimulus-specific programs. Applying these transcriptional programs to human alveolar macrophages from smokers and patients with chronic obstructive pulmonary disease (COPD) revealed an unexpected loss of inflammatory signatures in COPD patients. Finally, by integrating murine data from the ImmGen project we propose a refined, activation-independent core signature for human and murine macrophages. This resource serves as a framework for future research into regulation of macrophage activation in health and disease.

overall_design:
Illumina: To better understand the transcriptional program of human macrophages a set of different stimuli were used to activate and differentiate human macrophages in vitro. These macrophages were then assessed by transcriptomics and analyzed by different approaches using gene co-regulation analysis, SOM-clustering, hierarchical clustering, reverse network engineering and statistical models such as ANOVA.

Affymetrix: To understand the relationship of in vivo macrophages with in vitro stimulations, two alveaolar macrophage datasets GSE13896 (COPD patients, smokers and non-smokers) and GSE2125 (asthmatic patients, smokers and non-smokers)  were downloaded and processed together. In total, the combined dataset consists of 12 COPD samples, 15 asthmatic, 49 smoker samples and 39 non-smokers as control. Clustering of the samples (such as correlation network, principal component analysis and hierarchical clustering) and Gene Set Enrichment Analysis was performed on differentially expressed genes from 28 in vitro conditions.

first: J

last: Xue

first: S

middle: V

last: Schmidt

last: Sander

first: A

last: Draffehn

first: W

last: Krebs

first: I

last: Quester

first: D

last: De Nardo

first: T

middle: D

last: Gohel

first: M

last: Emde

first: L

last: Schmidleithner

first: H

last: Ganesan

last: Nino-Castro

middle: R

last: Mallmann

last: Labzin

last: Theis

last: Kraut

last: Beyer

first: E

last: Latz

middle: C

last: Freeman

last: Ulas

middle: L


title: Transcriptional analysis of human tonsil Tfh cells

status: Public on Nov 12 2013

city: Cleveland

first: Peter

middle: A

last: Wilkinson

state: Ohio

address: 2103 Cornell Road

department: Pathology / Systems Biology & Bioinformatics

country: USA

institute: Case Western Reserve University

summary: Follicular helper CD4 T (Tfh) cells provide B cells with signals that are important for the generation of high-affinity Abs and immunological memory and, therefore, are critical for the protective immunity elicited by most human vaccines. In this study we sought to define the  gene expression signature of bona fide GC Tfh and Tfh cells.

overall_design: The CD4+ T cell subsets CD45RO+CXCR5-, CD45RO+CXCR5int (Tfh cells), and CD45RO+CXCR5hi (GC Tfh cells) were isolated from 6 tonsil samples for gene expression analysis.

last: Kroenke

middle: K

last: Haddad

last: Crotty

first: K

last: Ghneim

middle: J

last: Cameron

first: P


title: Gene expression profiling of oral and genital lichen planus epithelium and normal oral and genital epithelium

status: Public on Nov 08 2013

city: Umeå

first: Karin

last: Danielsson

address: Byggnad 6M

department: Medicalbiosciences

country: Sweden

institute: Umeå University

summary: Comparing gene expression in Oral and genital lichen planus with normal oral and genital epithelium trying to idenitfy differently expressed genes in lichen planus compared to normal epithelium

overall_design: Total RNA obtained from oral and genital lichen planus epithelium compared with normal oral and genital epithelium

first: Philp

last: Coates

first: Majid

last: Ebrahimi

first: Elisabet

last: Nylander

first: Ylva-Britt

last: Wahlin


title: KD of Fibroblast specific TF

city: Yokohama

first: Yasuhiro

last: Tomaru

state: Kanagawa

address: 1-7-22 Suehicho

department: Omics Science Center

country: Japan

institute: RIKEN

summary: Combinatorial knock down of LHX9, OSR1, PRRX1, TWIST2, fibroblast specific transcription factors and adipogenic induction by medium change induce transdifferentiation from fibroblast to adipocyte. Adipogenesis from meshencymal stem cell (MSC) and human preadipocyte (PreADP) were used for general reference of adipogenesis.

overall_design: 54 Samples total with 3 replicates each of sample and treatment types.

first: Y

middle: T

last: Hasegawa


title: Transcriptional analysis of human blood CXCR5+ CD4 T cell populations

summary: The vast majority of currently licensed human vaccines work on the basis of long-term protective antibody responses. Generation of long term humoral immunity is a complex process predominantly dependent on germinal centers and CD4 T cell help to B cells. Follicular helper T cells (Tfh) are the specialized CD4 T cells for B cell help. However, whether such cells develop memory in humans and can be tracked in human blood has been enigmatic. We identified a subpopulation of blood CXCR5+ PD-1+CXCR3- resting CD4 T cells that are most related to Tfh cells of lymphoid tissue by gene expression profile and phenotype. Functional analysis showed that these memory Tfh cells were specialized for helping B cells. Moreover, these cells correlate with a clinically important outcome: development of potent neutralizing antibodies against HIV in HIV+ individuals.

overall_design: CD4 T cells were enriched from fresh blood of 5 normal donors by magnetic beads negative selection. Following enrichment, CD14-CD16-CD19-CD8-CD4+CD45RA- cells from each donor were FACS sorted into the following 5 populations: CXCR5-, CXCR5+PD1+CXCR3-, CXCR5+PD1+CXCR3+, CXCR5+PD1-CXCR3-, and CXCR5+PD1-CXCR3+. The gene expression profile of each cell population was determined.

last: Locci

first: S


title: Statin induced changes in gene expression in EBV-transformed and native B-cells

city: Riverside

first: Eugene

last: Bolotin

state: CA

address: 900 university ave

department: Cell Biology and Neuroscience

institute: UC Riverside

summary: Statin-induced gene expression differences observed in LCLs may be influenced by their transformation, and thus differ from those observed in native B-cells.  To assess this possibility, we prepared LCLs and purified B-cells from the same donors, and compared mRNA profiles after 24hr incubation with simvastatin (2µM) or sham buffer.

overall_design: We prepared LCLs and purified B-cells from the same donors, and compared mRNA profiles after 24hr incubation with simvastatin (2µM) or sham buffer. Genes involved in cholesterol metabolism were similarly regulated between the two cell types under both the statin and sham treated conditions, and the statin-induced changes were significantly correlated.

first: Marisa

middle: W

last: Medina

first: Ronald

middle: M

last: Krauss


title: Expression data from gastroesphageal cancers and adjascent normal tissue

status: Public on Nov 07 2013

city: Bronx

first: Juan

last: Lin

state: NY

address: 1300 Morris Park Ave.

institute: Albert Einstein College of Medicine

summary: The primary objective of this study was to determine the effectiveness of bortezomib alone or in combination with irinotecan in patients with advanced gastric and gastroesphageal cancer.  A secondary objecitve was to determine whether treatment was associated with changes in gene expression in the tumor and normal adjascent tissue.

overall_design: Tumor biopsies and biopsies of normal adjascent tissue were obtained before therapy and 24 hours after therapy. Differences in gene expression were evaluated between tumor and normal tissue (N=8 patients), and between post-treatment and pretreatment specimens for bortezomib alone (N=2 patients) and bortezomib plus irinotecan (N=10 patients).


title: Genome-wide expression analysis of VprBP knockdown in DU145 cells

city: Los Angeles

first: Kyunghwan

last: Kim

state: California

address: 1450 Biggy Street NRT6517

department: Biochemistry and Molecular Biology

institute: University of Southern California

summary: VprBP has been implicated in transcriptionally silent chromatin formation and cell cycle regulation, but the molecular basis underlying such effects remains unclear. To investigate the role of VprBP on gene regulation, genme-wide gene expression analysis is carried out in DU145 cells expressing either control shRNA or VprBP shRNA.

overall_design: Total RNA was isolated from mock- or VprBP-depleted DU145 cells

first: Jin-Man

first: Joong-Sun

first: Jongkyu

last: Choi

first: Yong

middle: S

last: Lee

first: Nouri

last: Neamati

first: Jin

last: Song

first: Kyu

last: Heo

first: Woojin

last: An


title: Novel Oncogenic PDGFRA Mutations in Pediatric High-Grade Gliomas

status: Public on Nov 06 2013

city: Memphis

first: Chunxu

last: Qu

state: TN

address: 262 Danny Thomas Pl

department: Pathology

institute: St Jude Children's Research Institute

summary: The outcome for children with high-grade gliomas (HGG) remains dismal, with a two-year survival rate of only 10-30%.  Approximately half of pediatric HGGs are diffuse intrinsic pontine glioma (DIPG), a brainstem tumor that arises almost exclusively in children.  Genome-wide analyses of copy number imbalances previously showed that platelet derived growth factor receptor alpha (PDGFRA) is the most frequent target of focal amplification in pediatric HGGs.  To determine whether the PDGFRA is also targeted by more subtle mutations not detected by copy number analysis, we sequenced all PDGFRA coding exons from a cohort of pediatric HGGs.  Somatic activating mutations were identified in 14.4% (13/90) of non-brainstem pediatric HGGs and 4.7% (2/43) of DIPGs, including missense mutations and in-frame deletions and insertions not previously described. 40% of tumors with mutation showed concurrent amplification, while 60% carried heterozygous mutations. Six different mutations impacting different domains all resulted in ligand-independent receptor activation that was blocked by small molecule inhibitors of PDGFR.  Expression of mutants in p53-null primary mouse astrocytes conferred a proliferative advantage in vitro, and generated HGGs in vivo with complete penetrance when implanted into brain. The gene expression signatures reflected the spectrum of human diffuse HGGs. PDGFRA intragenic deletion of exons 8 and 9 were previously shown in adult HGG, but were not detected in 83 non-brainstem pediatric HGG and 57 DIPGs. Thus, a distinct spectrum of mutations confers constitutive receptor activation and oncogenic activity to PDGFR in childhood HGG.

overall_design: To better understand the consequence of PDGFRα mutation in pediatric gliomagenesis, retroviral constructs expressing wild-type PDGFRα or six selected PDGFRα mutants that affect different regions of the receptor were generated for functional studies. p53-null primary mouse astrocyte (PMA) cultures were chosen as a relevant cellular background to assess PDGFRα function.

first: Barbara

last: Paugh

first: Xiaoyan

last: Zhu

first: Suzanne

last: Baker


title: Disulphide bond inhibitors in 2 cancer cell lines

city: Toronto

first: Nicholas

last: Harding

state: ON

address: 101 College St

department: Informatics and Biocomputing Platform

country: Canada

institute: OICR

summary: To elucidate which ER cargo maturation processes may be oxygen dependent, we first reasoned that the transcriptional response may be tailored specifically to counteract the mechanism of the imposed stress.  Therefore, we compared the transcriptional regulation of the ERome during anoxic conditions to ER stress caused by lack of glycosylation (tunicamycin) or chaperone inactivation by calcium depletion (thapsigargin)

overall_design: In two cancer cell lines (colon carcinoma HCT116, and hepatocellular carcinoma Hep G2) cells were given one of 4 treatments. 24 hours of 0.0% O2 (Anoxia), 1.5 µg/ml tunicamycin or 0.3 µM thapsigargin with a control 21% O2 (Normoxia).  Cells were exposed to hypoxia and anoxia in H35 and H85 HypOxystations (Don Whitley Scientific). 3 biological replicates of each experiment were carried out. Total of 24 samples.

first: M

last: Koritzinsky

first: T

last: van den Beucken

first: N

first: K

last: Chu

first: P

last: Boutros

first: I

last: Braakman

first: B

middle: G

last: Wouters


title: Expression data from Arabidopsis flowers under drought stress

city: University Park

first: Zhao

last: SU

state: PA

address: 354 N. Frear

department: Biology

institute: The Penn State University

summary: We also used microarray analysis to examine transcriptomic changes under drought, identifying thousands of genes that potentially mediate drought responses in the flower, including genes encoding transcription factors that likely play crucial regulatory roles.

overall_design: Arabidopsis were well-watered until after just bolting (after 24 days growth with the main stem about 1 cm high) when drought treatment was started by withholding water (defined as day 0 for drought treatment). The relative soil moisture content decreased sharply and, after about 80 hours (defined as day 3 for drought treatment), the relative soil moisture content was near 35% of the soil water-holding capacity. The soil water condition was maintained by daily watering until almost all the fruits were mature and ready to harvest (about 50 days). For well-watered (control) plants, 90% of the soil water-holding capacity was maintained until tissue harvest or after seed maturation (pots were weighed and watered twice per day). Unopened flower samples were collected, from both treated and control plants, at day 0, 3, 4, 5, 10.

last: Su

first: Hong

last: Ma


title: regulatory T cells in human pregnancy

status: Public on Nov 04 2013

city: Kingswood

first: Grant

last: Parnell

state: NSW

address: Nepean Hospital

department: Nepean Clinical School

country: Australia

institute: University of Sydney

summary: Transplacental immune programming refers to the concept that during  pregnancy, significant crosstalk occurs between the maternal and fetal immune  system, with consequent long‐term effects especially for the offspring. In this  study, we searched for evidence of transplacental programming in cellular  immunity. We made the surprising observation that there is a stringent and  specific correlation of regulatory T cells (Treg) between the mother and the  fetus. Gene microarray analysis indicates that interleukin 10 (IL‐10) might be  involved in transplacental Treg alignment. This is further supported by the direct  correlation of IL‐10 at a protein level between maternal fetal dyads. In vitro data  provide evidence that IL‐10 may regulate the homeostatic balance between  Tregs and non‐Tregs through selective upregulation of the anti‐apoptotic  molecule Bcl‐2 in Tregs. Induction of IL‐10 might be triggered by fetus‐derived  estriol (E3), which readily crosses the placenta and correlates with maternal IL‐  10 levels. Our study represents the first example of transplacental regulation of  cellular immunity between the mother and the fetus. These novel findings might  have major implications for pregnancy related‐changes in the maternal and fetal  immune system, and provide possible mechanistic insights into how prenatal  influences can lead to subsequent immunopathologies, such as allergy and  autoimmunity.

overall_design: T-reg and non-Treg samples of non pregnant women, and matched cord blood and maternal blood T-regs and non-T-regs

first: Brigitte

last: Santner‐Nanan

first: Peter

last: Hsu

first: Bei

last: Xu

first: Angela

last: Makris

first: Benjamin

last: Tang

first: Annemarie

last: Hennessy

first: Michael

last: Peek

first: Ralph

last: Nanan


title: CD44 is a negative cell surface marker for pluripotent stem cell identification during human fibroblast reprogramming

status: Public on Nov 05 2013

city: Singapore

first: Vivek

last: Tanavde

state: Singapore

address: 30 Biopolis Street, #07-01, Matrix

department: Genome and Gene Expression Data Analysis Division

country: Singapore

institute: Bioinformatics Institute, A*STAR, Singapore

summary: Analysis of different iPSC clones in comparison to parental fibroblasts and Pluripotent ESC and iPSC lines

overall_design: Total RNA obtained from iPSC clones generated with CytoTune reprogramming of BJ Fbiroblasts and compared to parent BJ fibroblasts and known pluripotent H9 ESC and Gibco Episomal iPSC lines.

first: Uma

last: Lakshmipathy


title: Analysis for expression of genes in human leukemic cell line Jurkat treated with Me6TREN or Phosphate Buffered Saline (PBS) control

status: Public on Nov 01 2013

city: Beijing

first: Jing

last: Zhang

address: 27 Taiping Road

country: China

institute: Beijing Institute of Transfusion Medicine

summary: mRNA from cells treated with or without small molecule Me6TREN for 24 hour was analyzed for differential gene expression. The hypothesis tested in the present study was that specific genes were up- or down-regulated via certain signaling pathways. Results provide important information to study the response of cellular functions triggered by Me6TREN.

overall_design: Total RNA obtained from human Jurkat cells subjected to 24 hours in vitro Me6TREN and PBS-treated control cells was amplified and hybridized to Illumina HT12 human whole-genome arrays.

first: Yanhua

last: Li

first: Xuetao

last: Pei


title: Sex chromosome parent-of-origin effects on gene expression in Drosophila melanogaster

city: Bloomington

first: Colin

last: Meiklejohn

state: IN

address: Jordan Hall, 1001 E. 3rd St.

department: Biology Department

institute: Indiana University

summary: RNA was extracted from adult male and adult female Drosophila melanogaster with reversed sex-chromosome parent-of-origin (e.g. maternal-X/paternal-Y vs. paternal-X/maternal-Y)

overall_design: Parent-of-origin effects were assayed in X/Y males, XY/Y males, and XY/X females.  Direct comparisons were made between individuals with the same karyotype (e.g. X/Y males or XY/Y males) incorporating dye-swaps.

first: Bernardo

last: Lemos

first: Alan

last: Branco

first: Pan-Pan

last: Jiang

first: Daniel

last: Hartl


title: Human Bone Marrow Stromal Cells cultured on 3D nanofiber scaffolds or 2D films

city: Gaithersburg

first: Carl

last: Simon

state: MD

address: 100 Bureau Drive

department: Biomaterials Group

institute: NIST

summary:
Microarray analysis was used to evaluate expression differences from a single donor human bone marrow stromal cells (hBMSCs) as a function of varied polymer-based tissue engineering scaffolds.  These scaffolds include polycaprolactone (PCL) nanofibers (PCL_NF), films (PCL_SC), poly D,L-lactic acid (PDLLA) nanofibers (PDLLA_NF), films (PDLLA_SC), tissue culture polystyrene (TCPS) and TCPS with osteogenic supplements (TCPS_OS).
The results revealed that scaffold structure was able to significantly affect gene expression, with nanofiber scaffolds inducing similar gene expression patterns to hBMCSs cultured with osteogenic media.

overall_design:
A library of scaffolds prepared from polycaprolactone or poly D,L-lactic acid was sythesized and cultured with hBMSCs for 14 days with RNA extracted from cells on Day 1 and Day 14.  Gene expression analysis was performed using BRB ArrayTools. SC = spun coat, BNF = big nanofiber, TCPS = tissue culture polystyrene, TCPS+OS = tissue culture polystyrene with osteogenic supplements.
This data forms is part of a pending publication:  Baker et al. Ontology Analysis of Global Gene Expression Differences of Human Bone Marrow Stromal Cells Cultured on 3D Scaffolds or 2D Films and is a subset of the 72 array data referenced in ( Kumar et al. The determination of stem cell fate by 3D scaffold structures through the control of cell shape, Biomaterials (2011) 32, 9188-9196.)  The 72 array data set is submitted separately to GEO as GSE50743.


title: Human Bone Marrow Stromal Cells cultured on polymer scaffolds with varied properties

summary:
Microarray analysis was used to evaluate expression differences from a single donor human bone marrow stromal cells (hBMSCs) as a function of varied polymer-based tissue engineering scaffolds.
The results revealed that gene expression patterns of hBMSCs grouped according to scaffold.

overall_design:
A library of scaffolds prepared from polycaprolactone (PCL) or poly D,L-lactic acid (PDLLA) was sythesized and cultured with hBMSCs for 14 days with RNA extracted from cells on Day 1 and Day 14. Gene expression analysis was performed using BRB ArrayTools. GF = gas foam, SC = spun coat, BNF = big nanofiber, SNF = small nanofiber, FFF = free-form fabricated, TCPS = tissue culture polystyrene, TCPS+OS = tissue culture polystyrene with osteogenic supplements.
The 72 arrays data was used previously in the publication: Kumar et al. The determination of stem cell fate by 3D scaffold structures through the control of cell shape, Biomaterials (2011) 32, 9188-9196. A companion data set of 24 arrays was submitted separately to GEO as GSE50744 and will be referenced to Baker et al. Ontology Analysis of Global Gene Expression Differences of Human Bone Marrow Stromal Cells Cultured on 3D Scaffolds or 2D Films


title: Massive Transcriptional Perturbation in Subgroups of Diffuse Large B-cell Lymphomas

city: Leipzig

first: Maciej

last: Rosolowski

address: Härtelstr. 16-18

institute: Institute for Medical Informatics, Statistics and Epidemiology (IMISE)

summary: Based on the assumption that molecular mechanisms involved in cancerogenesis are characterized by groups of coordinately expressed genes, we developed and validated a novel method for analyzing transcriptional data called Correlated Gene Set Analysis (CGSA). Using 50 extracted gene sets we identified three different profiles of tumors in a cohort of 364 Diffuse large B-cell (DLBCL) and related mature aggressive B-cell lymphomas other than Burkitt lymphoma. The first profile had high level of expression of genes related to proliferation whereas the second profile exhibited a stromal and immune response phenotype. These two profiles were characterized by a large scale gene activation affecting genes which were recently shown to be epigenetically regulated, and which were enriched in oxidative phosphorylation, energy metabolism and nucleoside biosynthesis. The third and novel profile showed only low global gene activation similar to that found in normal B cells but not cell lines. Our study indicates novel levels of complexity of DLBCL with low or high large scale gene activation related to metabolism and biosynthesis and, within the group of highly activated DLBCLs, differential behavior leading to either a proliferative or a stromal and immune response phenotype.

overall_design: 72 samples from normal cells and lymphoma cell lines including: 8 samples of naïve B cells, 13 samples of germinal center (GC) B cells, 9 samples of postGC B cells, 10 tissue samples of tonsils and 32 samples of 28 different lymphoma cell lines were hybridized to HGU133A Affymetrix GeneChips.

first: Jürgen

last: Läuter

first: Dmitriy

last: Abramov

first: Hans

last: Drexler

last: Hummel

first: Wolfram

last: Klapper

first: Roderick

last: MacLeod

first: Shoji

last: Pellissery

first: Friedemann

last: Horn

first: Reiner

last: Siebert

first: Markus

last: Loeffler


title: BMP4-directed trophoblast differentiation of human embryonic stem cells is mediated through a ΔNp63+ cytotrophoblast stem cell state

city: La Jolla

first: Mana

last: Parast

address: 9500 Gilman drive #0695

institute: University of California San Diego

summary: We show that FCM-BMP4-treated hESC differentiate into bona fide CTB by direct comparison to primary human placental tissues and isolated CTB through gene expresson profiling.

overall_design: We have compared gene expression profiling of FCM-BMP4-treated hESC to a panel of fetal tissues and first trimester tissues. Moreover, we have analysed the expression profiles of cells after shRNA knock-down of p63 compared to Scramble upon BMP4 treatment. Difference in expression between CTB trimester 1 / trimester 3 and PSC were compared the difference between FCM-BMP4-treated hESC and PSC at each time point collected.

first: Yingchun

last: Li

first: Matteo

last: Moretto-Zita

first: Francesca

last: Soncin

first: Anna

last: Wakeland

first: Lynlee

last: Wolfe

first: Sandra

last: Leon-Garcia

first: Raj

last: Pandian

first: Donald

last: Pizzo

first: Li

last: Cui

first: Kristopher

last: Nazor

first: Jeanne

middle: F

last: Loring

first: Christopher

middle: P

last: Crum

first: Louise

last: Laurent


title: Mitocans target tryptophan metabolism to remove the mimicry of tumour-initiating cells

city: Gold Coast

first: Michael

middle: Peter

last: Stapelberg

state: Queensland

address: Parklands Drive

institute: Griffith University

summary: Following therapy, tumour-initiating cells (TICs) survive and give rise to second-line tumours. Gene set enrichment analysis of microarray data and microRNA analysis confirmed the validity of spheroid cultures as models of TICs for breast and prostate cancer and mesothelioma cell lines. Pathway analysis revealed increased Trp metabolism in all types of TICs with indoleamine 2,3-dioxygenase (IDO) as the rate-limiting enzyme. TICs also expressed higher levels of the Trp uptake system consisting of CD98 and LAT1 with functional consequences. Mitocans, represented by vitamin E (VE) analogues, suppressed IDO1 in TICs with functional mitochondrial complex II, a target for the agents. IDO1 expression was regulated via a mechanism involving both transcriptional and post-transcriptional mechanisms. IDO1 increase and its suppression by VE analogues were replicated in TICs from primary human glioblastomas. Our work points to Trp metabolism as a novel mechanism of TICs to bypass the immune surveillance and to VE analogues as agents that remove this ‘mimicry’.

overall_design: Total RNA obtained from from breast cancer (MCF7), mesothelioma (IstMes2) and prostate cancer (LNCaP) adherent cell lines was compared to their corresponding sphere cultures

first: Jiri

last: Neuzil


title: Epigenetic silencing of noncoding RNA nc886 provokes oncogenes during esophageal tumorigenesis

status: Public on Oct 31 2013

city: Houston

first: Sangbae

last: Kim

state: TX

address: 1 Baylor plaza

department: HGSC

institute: Baylor Colleage of Medicine

summary: nc886 is a 101 nucleotides long non-coding RNA that is also known as a precursor microRNA or a vault RNA. nc886 has been suggested to be a tumor suppressor, mainly inferred by its expression pattern as well as its genomic location at human chromosome 5q31, a locus for a tumor suppressor gene(s).

overall_design:
Pre-clinical study
In order to understand potential roles of nc886 in esophageal squamous cell carcinoma (ESCC), we performed the knockdown of nc886 in nonmalignant HET-1A cells and ESCC cell lines (TE-1 and TE-8) and identified and analyzed genes whose expression is activated by nc886 knockdown in ESCC.

first: Hyun-Sung

last: Lee

first: Yong-Sun

first: Ju-Seog


title: Human whole blood microarray study to compare patients with tuberculosis, sarcoidosis, pneumonia, and lung cancer (sarcoidosis)

city: London

first: Chloe

last: Bloom

address: The Ridgeway

country: United Kingdom

institute: MRC National Institute for Medical Research

summary: This study used whole blood transcriptional signatures from patients with sarcoidosis before and during immunosuppressive treatment

overall_design: There were 7 pneumonia patients, the same patients were sampled before and after their treatment

middle: I

first: Christine

last: Graham

first: Matthew

last: Berry

first: Fotini

last: Rozakeas

first: Paul

last: Redford

first: Yuanyuan

last: Wang

first: Zhaohui

last: Xu

first: Katalin

last: Wilkinson

first: Robert

first: Yvonne

last: West

first: Makoto

last: Miyara

first: Diane

last: Bouvry

first: Valeyre

last: Dominique

first: Guy

last: Gorochov

first: Derek

last: Blankenship

first: Mitra

last: Saadatian

first: Phillip

last: Vanhems

first: Huw

last: Beynon

first: Rama

last: Vancheeswaran

first: Mel

last: Wickremasinghe

first: Damien

last: Chaussabel

first: Jacques

last: Banchereau

first: Virginia

last: Pascual

first: Ling-pei

last: Ho

first: Marc

last: Lipman

first: Anne

last: O’Garra


title: Human whole blood microarray study to compare patients with tuberculosis, sarcoidosis, pneumonia, and lung cancer (training)

first: Chloe

last: Bloom

summary: This study used whole blood transcriptional signatures from patients with tuberculosis compared to those with similar pulmonary diseases, sarcoidosis, pneumonia and primary lung cancer. TB and sarcoidosis had similar signatures that were distinct from pneumonia and lung cancer.

overall_design: There were 16 TB, 25 sarcoidosis, 8 pneumonia, 8 lung cancer and 38 healthy controls

first: Christine

last: Graham

first: Matthew

last: Berry

first: Fotini

last: Rozakeas

first: Paul

last: Redford

first: Yuanyuan

last: Wang

first: Zhaohui

last: Xu

first: Katalin

last: Wilkinson

first: Robert

first: Yvonne

last: West


title: Human whole blood microarray study to compare patients with tuberculosis, sarcoidosis, pneumonia, and lung cancer (validation)

summary: This study used whole blood transcriptional signatures from patients with tuberculosis, sarcoidosis and healthy controls.

overall_design: There were 8 TB, 11 sarcoidosis and 23 healthy controls

first: Makoto

last: Miyara

first: Diane

last: Bouvry

first: Valeyre

last: Dominique

first: Guy

last: Gorochov

first: Derek

last: Blankenship

first: Mitra

last: Saadatian

first: Phillip

last: Vanhems

first: Huw

last: Beynon

first: Rama

last: Vancheeswaran

first: Mel


title: Gene expression profile of MRKHS patients

status: Public on Nov 22 2013

city: Naples

first: mariateresa

last: giuliano

address: Via L. De Crecchio 7

department: Experimental Medicine

country: Italy

institute: Second University of Naples

summary: The gene expression profile of vaginal cells isolated from MRKHS patients, compared with those without MRKHS, presented alterations of developmental genes such as HOXB family, the Notch ligands JAG1 and DLL1 and MUC1, which can represent key elements in the pathogenesis of MRKHS, thus suggesting a potential alteration of networks involved in the formation of the female reproductive tract.

overall_design: This study included sixteen MRKHS patients, diagnosed by clinical examination, trans abdominal and pelvic ultrasonography, nuclear magnetic resonance (NMR) and/or vaginoscopy, that underwent reconstruction of neovagina in the Department of Gynecologic-Obstetrical and Urologic Sciences of Sapienza University of Rome between 2007 and 2011, and five control subjects with no known reproductive tract defects or developmental malformations. 8 patients and 5 controls were analyzed using Illumina beadarray.

first: C

last: Nodale

first: S

last: Ceccarelli

first: M

last: Giuliano

last: Cammarota

last: D'Amici

first: E

last: Vescarelli

first: D

last: Maffucci

first: F

last: Bellati

first: P

middle: B

last: Panici

last: Romano

first: A

last: Angeloni

last: Marchese


title: Gene expression analysis of MCF7 breast cancer cells cultured as xenografts, in two dimensional cultures, in polyHEMA anchorage independent three dimansional cell culture models and in Matrigel three dimensional cultures.

status: Public on Oct 30 2013

city: Turku

first: Vesa

last: Hongisto

address: Itainen Pitkakatu 4c

department: Medical Biotechnology

country: Finland

institute: VTT Technical Research Centre of Finland

summary: The traditional method for studying cancer in vitro is to grow immortalized cancer cells in two-dimensional (2D) monolayers on plastic. However, many cellular features are impaired in these unnatural conditions and big alterations in gene expression in comparison to tumors have been reported. Three-dimensional (3D) cell culture models have become increasingly popular and are suggested to be better models than 2D monolayers due to improved cell-to-cell contacts and structures that resemble in vivo architecture.  The aim of this study was to compare gene expression patterns of MCF7 breast cancer cells when grown as xenografts, in 2D, in polyHEMA coated anchorage independent 3D models and in Matrigel on-top 3D cell culture models. Surprisingly small variations in gene expression patterns were observed between the models indicating that 3D and xenograft are not always that different from 2D cell cultures.

overall_design: Gene expression analysis of MCF7 breast cancer cells cultured as xenografts for 43 days, in two dimensional cultures for seven days (2D7d), in polyHEMA three dimensional cell culture models for four and seven days (PH7d and PH7d), and in Matrigel three dimensional cultures for four and seven days (MG4d and MG7d). Two biological replicates was included for each sample.

first: Sandra

last: Nyberg

first: Vidal

last: Fey

first: John-Patric

last: Mpindi

first: Olli

last: Kallioniemi

first: Merja

last: Perälä


title: Expression of ZAP70 in CLL activates NF-κB signalling

status: Public on Oct 22 2013

city: Gent

first: Valerie

last: Pede

address: De Pintelaan 185

country: Belgium

institute: Ghent University

summary: Chronic lymphocytic leukemia (CLL) is a disease with a highly variable prognosis. The clinical course can however be predicted thanks to prognostic markers. Poor prognosis is associated with expression of a B cell receptor (BCR) from unmutated immunoglobulin variable heavy-chain genes (IgVH) and expression of zeta associated protein of 70 kDa (ZAP-70). The reason why ZAP-70 expression is associated with poor prognosis and whether the protein has a direct pathogenic function is at present unknown. By transfer of ZAP-70 to CLL cells, we show here that expression of ZAP-70 in CLL cells leads to increased expression of the NF-κB target genes interleukin-1β (IL-1β), IL-6 and IL-8 upon BCR triggering. This could be blocked by inhibition of NF-κB signaling through inhibition of IκB kinases (IKK). Transcriptome analysis identified a NF-κB RelA signature imposed by ZAP-70 expression in BCR stimulated CLL cells. We conclude that ZAP-70 acts directly as an amplifier of NF-κB signaling in CLL cells which could be an underlying mechanism for its association with poor prognosis and which may represent a therapeutic target.

overall_design: 22 patient samples, Stimulated for 3h or 24h, Electroporated with capped ZAP-70 mRNA or uncapped ZAP-70 mRNA (negative control)

first: Ans

last: Rombout

first: Jolien

last: Vermeire

first: Evelien

last: Naessens

first: Hanne

last: Vanderstraeten

first: Jan

last: Philippé

first: Bruno

last: Verhasselt


title: Gene expression analysis of estrogen receptor mutants, S463P, Y537S and D538G in MCF7 cells

status: Public on Oct 25 2013

city: New York

first: Sarat

last: Chandarlapaty

address: 1275 York Ave

department: HOPP

institute: MSKCC

summary:
Analysis of MCF7 cells transfected with ER mutants (S463P, Y537S and D538G) in phenol-red free, charcoal stripped FBS media and regular DMEM/F12 media. Results provide insight on the gene expression profiles induced by the various ER mutants.
Total RNA extracted from transfected cells 48 hours after transfection

overall_design: 36 samples were analyzed, triplicates for each constructs (GFP vector control, WT, S463P, Y537S, D538G and S463P/D538G) for each type of media

first: Weiyi

last: Toy


title: Human whole blood microarray study to compare patients with tuberculosis, sarcoidosis, pneumonia, and lung cancer (test)

first: Chloe

last: Bloom

overall_design: There were 11 TB, 25 sarcoidosis, 6 pneumonia, 8 lung cancer and 52 healthy controls

first: Christine

last: Graham

first: Matthew

last: Berry

first: Fotini

last: Rozakeas

first: Paul

last: Redford

first: Yuanyuan

last: Wang

first: Zhaohui

last: Xu

first: Katalin

last: Wilkinson

first: Robert

first: Yvonne

last: West

first: Makoto

last: Miyara

first: Diane

last: Bouvry

first: Valeyre

last: Dominique

first: Guy

last: Gorochov

first: Derek

last: Blankenship

first: Mitra

last: Saadatian

first: Phillip

last: Vanhems

first: Huw

last: Beynon

first: Rama

last: Vancheeswaran

first: Mel

last: Wickremasinghe

first: Damien

last: Chaussabel

first: Jacques

last: Banchereau

first: Virginia

last: Pascual

first: Ling-pei

last: Ho

first: Marc

last: Lipman

first: Anne

last: O’Garra


title: TMEM88 knockdown during human embryonic stem cell cardiac differentiation

status: Public on Oct 21 2013

city: Seattle

first: Nathan

last: Palpant

state: WA

address: 850 Republican St

institute: University of Washington

summary: TMEM88 is indispensable for heart development and acts in the pre-cardiac mesoderm to specify lineage commitment of the cardiovascular progenitor cell through inhibition of Wnt signaling.

overall_design: 2 different lentiviruses expression shRNA targeting different domains of the TMEM88 locus were transduced into undifferentiated hES cells. Cells were puromycin selected then differentiated along the cardiac lineage. Total RNA was taken at day 5 of differentiation when the cardiovascular progenitor cell arises. 1 sample for each shRNA and 2 samples for control shRNA were analyzed by array

first: Charles

middle: E

last: Murry


title: Identification of miRNA targets in breast cancer cells (Ago2-IP)

city: Memphis

first: Meiyun

last: Fan

address: 19 S. Manassas Street

institute: University of Tennessee

summary: miRNAs regulate mRNA stability and translation through the action of the RNAi-induced silencing complex. In this study, we systematically identified endogenous miRNA target genes by using AGO2 immunoprecipitation (AGO2-IP) and microarray analyses in two breast cancer cell lines, MCF7 and MDA-MB-231, representing luminal and basal-like breast cancer, respectively. The expression levels of ~70% of the AGO2-IP mRNAs were increased by DROSHA or DICER1 knockdown. In addition, integrated analysis of miRNA expression profiles, mRNA-AGO2 interaction, and the 3'-UTR of mRNAs revealed that >60% of the AGO2-IP mRNAs were putative targets of the fifty most abundantly expressed miRNAs.

overall_design: To identify mRNAs associated with AGO2, cell lysate was precleaned with control IgG and immunoprecipitated with anti-human Ago2 (Clone 2E12-1C9, Abnova). Total RNA from cell lysate or coimmunoprecipitated with AGO2 was extracted with Trizol and subjected to microarray analysis, with three biological repeats for each experimental condition.

first: Raisa

last: Krutilina

first: Jing

last: Sun

first: Aarti

last: Sethuraman

first: Chuan

middle: H

last: Yang

first: Zhaohui

last: Wu

first: Junming

last: Yue

first: Lawrence

last: Pfeffer


title: Identification of miRNA targets in breast cancer cells (DICER1 and DROSHA knockdown)

overall_design: To identify mRNAs responsive to miRNA synthesis inhibition, total RNA was prepared from control cells and cells that stably express small hairpin RNA against DICER1 or DROSHA. Expression array analysis was performed with duplicates for each cell type.


title: Transcriptional reprogramming and stimulation of leaf respiration by elevated CO2 concentration is diminished, but not eliminated, under limiting nitrogen supply.

status: Public on Oct 15 2013

city: Urbana

first: Robert

middle: John Cody

last: Markelz

state: IL

address: 1206 W Gregory Dr

department: Plant Biology

institute: University of Illinois

overall_design: Arabidopsis plants were grown in either ambient (370 ppm) or elevated (750 ppm) CO2 with either ample N supply or limiting N supply. Leaf tissue was harvested from youngest most fully expanded leaves 35 days after plant germination at either midday or midnight.

first: R

first: Andrew

middle: D

last: Leakey


title: Identification of miRNA targets in breast cancer cells

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

overall_design: Refer to individual Series


title: Microarray study using whole blood and purified leucocyte populations from healthy controls and patients with tuberculosis or sarcoidosis with tuberculosis and sarcoidosis

first: Chloe

last: Bloom

summary: Whole blood and purified leucocyte populations were compared to determine which cell types the whole blood interferon-inducible signature, found in both tuberculosis and sarcoidosis, was present in. This study agreed with previous publication that the neutrophil was the dominant cell in tuberculosis and also showed it was the dominant cell type in sarcoidosis.

overall_design: There were 5 patients in each group of healthy controls, tuberculosis and sarcoidosis. The cell types were whole blood, PBMCs, monocytes (CD14), T cells (CD8 and CD4) and neutrophils (CD15).

first: Christine

last: Graham

first: Fotini

last: Rozakeas

first: Yuanyuan

last: Wang

first: Paul

last: Redford

last: O'Garra


title: Genome-wide expression profiling of HepG2 liver cells after berberine chloride treatment

status: Public on Oct 17 2013

city: Taipei

first: Ting-fang

last: Lo

address: 128 Academia Road, Section 2, Nankang, Taipei 115, Taiwan

department: Institute of Biological Chemistry

country: Taiwan

institute: Academia Sinica

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


title: SMAD4 regulated through HDAC4 is associated with chemoresistance in MCF-7 cells

city: Daejeon

first: Seong-Lan

last: Yu

address: Gasuwon-dong

department: Myunggok Medical Research Institute

country: South Korea

institute: Konyang university

summary: HDACs play crucial role in epigenetic modulation through deacetylation of histone and non-histone substrates in critical process of normal development and cancer. Moreover, HDAC inhibitors have been considered as new agent by effects such as cell cycle arrest, apoptosis, anti-angiogenic effects and autophagy and utilized in clinical applications for chemotherapy. we previously reported that HDAC 1, 4, 6 and 8 were higly expressed in MDA-MB-231 than MCF-7 cells and HDAC1, 6 and 8 excepting HDAC4 were associated with invasion that is very important factor in cancer progression. However, HDAC4 did not affect in invasion. To investigate interaction between chemoresistance and HDAC4 expression, we establish stable cells overexpressing HDAC4 in MCF-7 cells. Cells overexpressed HDAC4 were increased cytotoxicity about 5-FU and identified 356 differentially expressed genes using Ilumina array. Based on array result, we selected SMAD4 as a candidate gene related with chemoresistance because SMAD4 was previously reported evaluation of chemoresistance to 5-FU. We purpose that HDAC4 regulated with SMAD4 expression through acetylation in SMAD4 promoter region.  HDAC4 directly bound a part of SMAD4 promoter.

overall_design: Total RNA obtained from cells overexpressed HDAC4 cDNA in MCF-7 compared to control cells.

first: S

middle: L

first: J

last: Kang


title: Human whole blood microarray study to compare patients with tuberculosis, sarcoidosis, pneumonia, and lung cancer (pneumonia treated)

summary: This study used whole blood transcriptional signatures from patients with pneumonia before and after succesful antibiotic treatment

overall_design: There were 5 pneumonia patients, the same patients were sampled before and after their treatment

first: Matthew

middle: R

last: Berry

last: Xu

first: Katalin

middle: A

last: Wilkinson

first: Yvonne

last: West

first: Makoto

last: Miyara

first: Diane

last: Bouvry

first: Valeyre

last: Dominique

first: Guy

last: Gorochov

first: Derek

last: Blankenship

first: Mitra

last: Saadatian

first: Phillip

last: Vanhems

first: Huw

last: Beynon

first: Rama

last: Vancheeswaran

first: Mel

last: Wickremasinghe

first: Damien

last: Chaussabel

first: Jacques

last: Banchereau

first: Virginia

last: Pascual

first: Ling-pei

last: Ho

first: Marc

last: Lipman

first: Anne

last: O’Garra


title: Global analysis of off-target genes by GAPDH siRNA

status: Public on Oct 03 2013

city: Chicago

first: Xiaowei

last: Wang

address: 909 S Wolcott Ave, Rm 5137

institute: University of Illinois at Chicago

summary: A GAPDH siRNA was overexpressed in HeLa cells and microarray expression profiling was performed to experimentally identify the off-targets of this siRNA at the transcriptome level. Among all predicted siRNA off-targets by MirTarget2, the majority were downregulated by at least 10% (i.e. less than 90% remaining gene expression). Moreover, more than one fifth were downregulated by at least 30%. The gene knockdown data is consistent with previous observations that siRNA off-targets are generally silenced at a more moderate level as compared to silencing of the single intended target

overall_design: GAPDH siRNA was transfected into HeLa cells, and the unintended off-targets was identified by microarrays 24 hours post transfection.


title: Integrative DNA methylation and gene expression analysis in high-grade soft tissue sarcomas [gene expression]

status: Public on Nov 16 2013

city: Heidelberg

first: Marcus

last: Renner

address: Im Neuenheimer Feld 224

department: General Pathology

institute: Institute of Pathology

summary: We used the Infinium HumanHT-12 platform to profile gene expression in 79 primary, untreated high-grade soft tissue sarcomas, representing eight relevant subtypes, two non-neoplastic fat samples and 13 representative sarcoma cell lines.

overall_design: Marcus, Renner

first: Thomas

last: Wolf

first: Gunhild

last: Mechtersheimer


title: Gene expression profile upon IL-22 stimulation, forced expression of Hes1, or IL-22 stimulation under forced expression of Hes1, in human colon carcinoma-derived LS174T cells

status: Public on Oct 01 2013

city: Tokyo

first: Ryuichi

last: Okamoto

state: Please Select

address: Tokyo Medical and Dental University

institute: Tokyo Medical and Dental University

summary:
A human colon carcinoma-derived cell line LS174T was modified to overexpress Hes1, a bHLH-type transcription factor, upon doxycycline addition (designated as LS174T-tetON-Hes1 cells), using the T-rex system (Invitrogen). We have previously shown that these cells can overexpress Hes1 under the control of CMV promoter (Zheng et al, Inflamm Bowel Dis, 17;2251-2260, 2011), and the amont of the overexpressed Hes1 protein reaches to the maximal level in early as 3 hours from doxycycline addition (100ng/ml), which persists for up to 24 hours. In the present experiment,  LS174T-tetON-Hes1 cells were treated with recombinant human IL-22 (20ng/ml) alone, doxycycline alone (100ng/ml), co-treated by both IL-22 and doxycycline, or left untreated (Control) for 24 hours, and subjected for analysis.
Experiment was done using a modified sub-line of LS174T cell (LS174T-tetON-Hes1 cells), in which overexpression of Hes1 can be induced by a Doxycycline dependent manner.

overall_design: Four-condition experiment, Control vs. IL-22 stimulation, Control vs Doxycycline addition (Hes1 overexpression) and Control vs IL22 stimulation+Doxycycline addition  (Hes1 overexpression). Biological replicates: One for each condition, independently grown and harvested. One replicate per array.

first: Tatsuro

last: Murano


title: High-throughput 3D screening reveals differences in drug sensitivities between culture models of JIMT1 breast cancer cells.

first: Vesa

last: Hongisto

summary:
The traditional method for studying cancer in vitro is to grow immortalized cancer cells in two-dimensional (2D) monolayers on plastic. However, many cellular features are impaired in these unnatural conditions and big alterations in gene expression in comparison to tumors have been reported. Three-dimensional (3D) cell culture models have become increasingly popular and are suggested to be better models than 2D monolayers due to improved cell-to-cell contacts and structures that resemble in vivo architecture.
The aim of this study was to develop a simple high-throughput 3D drug screening method and to compare drug responses in JIMT1 breast cancer cells when grown in 2D, in polyHEMA coated anchorage independent 3D models and in Matrigel on-top 3D cell culture models. We screened 102 compounds with multiple concentrations and biological replicates for their effects on cell proliferation. The cells were either treated immediately upon plating or they were allowed to grow in 3D for four days prior to the drug treatment. Big variations in drug responses were observed between the models indicating that comparisons of culture model influenced drug sensitivities cannot be made based on effects of a single drug. However, we show with the 63 most prominent drugs that, in general, JIMT1 cells grown on Matrigel were significantly more sensitive to drugs than cells grown in 2D cultures, while responses of cells grown in polyHEMA resembled those of 2D. Furthermore, comparison of gene expression profiles of the cell culture models to xenograft tumors indicated that cells cultured in Matrigel and as xenografts most closely resembled each other. In this study we also suggest that 3D cultures can provide a platform for systematic experimentation of larger compound collections in a high-throughput mode and be used as alternatives for traditional 2D screens towards better comparability to in vivo state.

overall_design: Gene expression analysis of JIMT1 breast cancer cells cultured as xenografts for 43 days, in two dimensional cultures for seven days (2D7d), in polyHEMA three dimensional cell culture models for four and seven days (PH7d and PH7d),  and in Matrigel three dimensional cultures for four and seven days (MG4d and MG7d). Two biological replicates was included for each sample.

first: Sandra

last: Nyberg

first: Vidal

last: Fey

first: John-Patric

last: Mpindi

first: Olli

last: Kallioniemi

first: Merja

last: Perälä


title: Regulation of gene expression by YAP1

first: Sangbae

last: Kim

summary: In order to define YAP1-specific gene expression patterns in gastric cancer, the constitutively active mutant YAP1 (YAP1-S127A) was over-expressed in MKN45 gastric cancer cells. Defined gene expression signature was later used to stratify gastric cancer patients according to the presence of the YAP1-activated signature.

overall_design: Three groups of samples are included: 1. Mock control; 2. Vector control; 3. YAP-S127A expression. Gene expression profiles of YAP-S127A mutant-expressing cells were compared to that of mock and vector control. Experiments were done in MKN45 gastric cancer cells.

first: Sung

last: Lee

first: Woojin

last: Jeong

first: Ju


title: Gene expression changes associated with progression of Irf8–/– CML-like disease into blast crisis after β-catenin activation

status: Public on Sep 26 2013

city: Berlin

first: Marina

last: Scheller

address: Robert-Rössle-Str. 10

institute: MDC Berlin

summary:
Progression and disease relapse of chronic myeloid leukemia (CML) depends on leukemia-initiating cells (LIC) that resist treatment. Using mouse genetics, we observed that compound constitutive activation of β-catenin and deletion of Irf8 results in progression of CML-like disease into fatal blast crisis, elevated leukemic potential of BCR-ABL-induced LICs, and accumulation of Imatinib-resistant LICs in GMP-like populations. We found that progression of the disease is tightly connected to the magnitude of gene expression and that activated β-catenin enhances a pre-existing Irf8-deficient gene signature that was defined as a “progression specific signature” (PSS). We identified β-catenin as an amplifier of disease progression and as a critical step in the shift of CML to blast crisis. Collectively, our data uncover Irf8 as a roadblock for β-catenin-driven leukemia and imply both factors as targets in combinatorial therapy.
We used microarrays to identify the gene expression signature in GMPs underlying CML-like disease progression and identified distinct classes of up- and down-regulated genes during this process defined as a “progression specific signature (PSS)”.

overall_design: GMP populations were sorted from three to four independent pools of control MxCre–Ctnnb1(Ex3)fl/+, Ctnnb1(Ex3)∆/+, Irf8–/–Ctnnb1(Ex3)fl/+ and Irf8–/–Ctnnb1(Ex3)∆/+ mice for RNA extraction and hybridization on Affymetrix Mouse 430_2 chip arrays (MG-430 PM peg arrays; Affymetrix GeneChip). Cells were sorted using FACSAria (BD Biosciences Immunocytometry Systems, San Jose, CA) flow cytometers and GMPs defined as lineage depleted Lin– Sca-1–c-Kit+CD34+FcR II/IIIhi population. All mice were treated with 400µg polyinosinic-polycytidylic acid (poly(I:C)) (Amersham) on day 0, 3 and 5 to induce β-catenin activation (MxCre-dependent excision of Exon3 in the β-catenin gene). Harvesting of bone marrow cells were performed 10-14 days after the last poly(I:C) injection. We used heterozygous inducible MxCre+Ctnnb1(Ex3)fl/+ mice because of the dominant effect from a single activated Ctnnb1 allele. To validate excision efficiency, genomic DNA from harvested cells was subjected to PCR, as previously described (Huelsken et al., 2001; Scheller et al., 2006).

first: Jörg

last: Schönheit

first: Karin

last: Zimmermann

first: Ulf

last: Leser

first: Frank

last: Rosenbauer

first: Achim

last: Leutz


title: Transcriptome analysis in flavonoid overaccumulating and lacking Arabidopsis.

status: Public on Sep 27 2013

city: Yokohama

first: Ryo

last: Nakabayashi

address: 1-7-22 Suehiro-cho, Tsurumi-ku

institute: RIKEN CSRS

summary: TranscriptoTranscriptome profiling using DNA microarrays of the aerial parts of the wild-type and other plants was conducted to examine if either MYB overexpression or flavonoid overaccumulation is responsible for the expression of stress-related genes involved in both the biotic and abiotic stress response.

overall_design: Comparative transcriptome analysis using DNA microarray in flavonoid overaccumulating and lacking Arabidopsis.

first: Keiko

last: Yonekura-Sakakibara

first: Kaoru

last: Urano

first: Makoto

last: Suzuki

first: Yutaka

last: Yamada

first: Tomoko

last: Nishizawa

first: Fumio

last: Matsuda

first: Mikiko

last: Kojima

first: Hitoshi

last: Sakakibara

first: Kazuo

last: Shinozaki

first: Anthony

middle: J

last: Michael

first: Takayuki

last: Tohge

first: Mami

last: Yamazaki

first: Kazuki

last: Saito


title: Expression analysis of YAP and Angiomotin target genes

city: Philadelphia

first: Louise

middle: C

last: Showe

address: 3601 Spruce St

institute: The Wistar Institute

summary: To assess  changes in gene expression regulated by Yap1 or Angiomotin,  either Yap1 or Angiomotin were knocked down in HEK293 cells  using shRNA and expression was assessed by microarray analysis and compared to expression patterns of wildtype cells.

overall_design: Microarray analysis was performed to compare gene expression in Amot-KD, Yap-KD, and control HEK293 cells. Samples from three individual experiments for each of the three groups were analyzed.

first: Chunling

last: Yi

first: Zhewei

last: Shen

first: Anat

last: Stemmer-Rachamimov

first: Noor

last: Dawany

first: Scott

last: Troutman

first: Qin

last: Liu

first: Marco

last: Giovannini

first: Akihiko

last: Shimono

first: Marius

last: Sudol

first: Lars

last: Holmgren

first: Ben

middle: Z

last: Stanger

first: Joseph

last: Kissil


title: Genome-wide analysis of BRCA1 and PALB2 [TNF-alpha stimulation]

status: Public on Sep 30 2013

city: Miami

first: Alessandro

last: Gardini

state: FL

address: 1501 NW 10 Avenue

department: Sylvester Comprehensive Cancer Center

institute: University of Miami

summary: Breast and ovarian cancer susceptibility genes, BRCA1 and PALB2 have enigmatic roles in cellular growth and mammalian development.  While these genes are essential for growth during early developmental programs, inactivation later in adulthood leads to increased growth and formation of tumors, leading to their designation as tumor suppressors.  We performed genome-wide analysis assessing their chromatin residence and gene expression responsiveness using high throughput sequencing in breast epithelial cells.  These experiments revealed a critical role for BRCA1 and PALB2 in transcriptional responsiveness to NF-kB, a crucial mediator of growth and inflammatory response during development and cancer.  Importantly, we also uncovered a vital role for these proteins in response to retinoic acid (RA), a growth inhibitory signal in breast cancer cells, which may constitute the basis for their tumor suppressor activity.

overall_design: MCF-7 cells were infected with PALB2, BRCA1, p65/RelA and non targeting (SCR) shRNAs. After puromycin selection, cells were stimulated with 10ng/ml TNF-alpha 1 hour

first: Matteo

last: Cesaroni

first: Ramin

last: Shiekhattar


city: Lyon

first: stéphane

last: ansieau

address: 28 rue Laennec

department: Centre Léon Bérard

country: France

institute: Inserm U590

summary: The SNAI1 and SNAI2 embryonic genes are reactivated in numerous cancer types, including carcinomas. They promote cancer cell dissemination by inducing an epithelial-to-mesenchymal transition (EMT) and by protecting cells from anoikis. We now have demonstrated that the sequentially related SNAI3 gene is aberrantly reactivated in human breast carcinomas. To compare the functional properties of the three SNAIL family members, the transcription factors were ectopically expressed in immortalized mammary epithelial cells.

overall_design: Immortalized human mammary epithelial cells (HMEC-hTERT cells) or MCF10A cells were infected with SNAIL retroviral expression constructs. The gene expression profiles of the resulting cell lines, cultured in standard conditions or after plating them 24h in low-adherent (LA) conditions, were performed.

first: Fabienne

last: Barbet

first: Marjorie

last: Carrere

first: Baptiste

last: Gras

first: Anne

last: Wierinckx

first: Alain

last: Puisieux

first: Stéphane

last: Ansieau


title: Expression of DND41 cell lines treated with 1µM Dexamethasone for 24h after shPTEN infection

first: Alberto

last: Ambesi-Impiombato

address: 1130 St. Nicholas Avenue

department: ICG

institute: Columbia University

summary: Glucocorticoid resistance is a major driver of therapeutic failure in T-cell acute lymphoblastic leukemia (T-ALL). Here we identify the AKT1 kinase as a signaling factor driving glucocorticoid resistance in T-ALL. Mechanistically, AKT1 directly phosphorylates the glucocorticoid receptor NR3C1 protein and blocks glucocorticoid-induced NR3C1 transcription by inhibiting glucocorticoid-induced NT3C1 translocation to the nucleus. Consistently, pharmacologic inhibition of AKT1 increases the response of T-ALL cells to glucocorticoid therapy and effectively reverses glucocorticoid resistance in vitro and in vivo. These results warrant the clinical testing of AKT1 inhibitors and glucocorticoids in combination for the treatment of T-ALL.

overall_design: Gene Expression Analysis of DND41 cell lines infected with shPTEN or shLUC and treated with 1µM Dexamethasone vs DMSO for 24h, in triplicate.

first: Adolfo

last: Ferrando


title: Genome-wide analysis of BRCA1 and PALB2 [RA stimulation]

overall_design: MCF-7 cells were infected with PALB2, BRCA1 and  non targeting (SCR) shRNAs. After puromycin selection, cells were stimulated with 10microM Retinoic Acid (RA) for 24 hours


title: The influence of folate supplementation on global gene expression in normal colonic mucosa of subjects with colorectal adenoma

city: London

first: Matthew

last: Arno

state: LONDON

address: 150 Stamford Street

department: Genomics Centre

institute: King's College London

summary: Background: We tested the hypothesis that short-term supplementation with a physiological dose of folate can alter global gene expression in the colon of subjects with colorectal adenoma using a randomised double blind placebo controlled trial design.  Materials and Methods: Fourteen subjects with histologically confirmed colorectal adenoma, randomised to receive folic acid (400µg/d, n=6) or placebo (n=8) for 10 weeks, had blood samples and colonic tissue biopsies collected before and after the intervention. Blood samples were used to determine serum and red cell folate, plasma homocysteine, and genetic polymorphisms in methylenetetrahydrofolate reductase (MTHFR C677T) and methionine synthase (MS A2756G). RNA extracted from normal-appearing colonic tissue samples was used to determine global gene expression in the colon using Affymetrix Microarray GeneChips. Microarray results were confirmed by quantitative real time RT-PCR.  Two methods were used to analyse the microarray data: (1) differences between pre- and post-intervention gene expression values in the folic acid and placebo groups separately using paired-sample t tests; (2) differences between the folic acid and placebo groups in the ratio of post-intervention to pre-intervention gene expression values using independent sample t-tests.    Results: (1) Following intervention, sixty seven genes were up-regulated and 13 genes were down-regulated in the folic acid group, while 21 genes were up-regulated and none were down-regulated in the placebo group (P<0.05, adjusted for multiple testing).  (2) Thirty six genes were up-regulated and 18 genes were down-regulated in the folic acid group when compared with placebo, but none of these were statistically significant after adjustment for multiple testing.  These genes are involved in multiple pathways, including cell cycle, signal transduction, cell differentiation, transport, cell division, cell motility, protein transport and immune response.  There were no genes involved in 1-carbon metabolism that were altered in expression, although several genes involved in neoplasia were up-regulated.  Conclusions:  These results indicate that while folic acid can modify gene expression, it is difficult to separate its effects from the natural variability in gene expression in the colon.

overall_design: Fourteen patients with colorectal adenoma were treated with either folate supplementation (6 subjects) or a placebo (8 subjects) for 10 weeks in a randomised double-blind trial. Colonic biopsies of normal tissue were taken before and after the intervention, and analysed for gene expression.

first: Maria

last: Pufulete


title: Drug Synergy Screen and Network Modeling in Dedifferentiated Liposarcoma (DDLS) part 1

status: Public on Sep 24 2013

city: Cambridge

first: Martin

last: Miller

address: Robinson Way

department: Cancer research UK, Cambridge Institute

institute: University of Cambridge

summary:
Analysis of gene expression levels in two DDLS tumor-derived cell lines DDLS8817 and LPS141 growing in culture in basal conditions
The goal of this gene transcript study was to determine the expression level of genes used in signaling network modeling in DDLS

overall_design: RNA was isolated from asynchronously growing DDLS8817 and LPS141 cultures growing in basal conditions using the Qiagen RNEasy kit. Three replicates of each cell line

first: Evan

last: Molinelli

first: Jayasree

middle: S

last: Nair

first: Tahir

last: Sheikh

first: Rita

last: Samy

first: Xiaohong

last: Jing

first: Qin

last: He

first: Anil

last: Korkut

first: Aimee

middle: M

last: Crago

first: Samuel

last: Singer

first: Gary

middle: K

last: Schwartz

first: Chris

last: Sander


title: Drug Synergy Screen and Network Modeling in Dedifferentiated Liposarcoma (DDLS)

type: Genome variation profiling by genome tiling array

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

overall_design: Refer to individual Series


title: Hypoxia-independent downregulation of hypoxia inducible factor 1 targets by androgen deprivation therapy in prostate cancer.

status: Public on Oct 02 2013

city: Oslo

first: Heidi

last: Lyng

address: Montebello

department: Department of Radiation Biology

country: Norway

institute: Oslo University Hospital

summary: Hypoxia inducible factor 1 (HIF1) has been shown to cooperate with the androgen receptor (AR) in activation of oncogenic pathways in prostate cancer (PCa). Here we hypothesized that HIF1 also plays a role in PCa response to androgen deprivation therapy (ADT). Comparison of gene expression profiles of androgen exposed (AE) and androgen deprived (AD) CWR22 PCa xenografts identified 596 upregulated and 748 downregulated genes after ADT. Gene ontology (GO) analysis of the differentially expressed genes showed significant enrichment of the biological processes cell proliferation, cell cycle and metabolism and suggested suppression of these processes after ADT. A set of 80 hypoxia-inducible genes were identified in 22Rv1 and LNCaP cell lines treated with hypoxia and showed considerable overlap (53%) with the downregulated genes. Immunostaining of the hypoxia marker pimonidazole showed no difference between AE- and AD-tumors. Comparison of the differentially expressed genes with lists of 1115 direct AR- and 276 direct HIF1-target genes identified 138 AR- and 40 HIF1-targets that were regulated after ADT, including six shared AR- and HIF1-targets for which downregulation was confirmed with RT-PCR. Most HIF1-targets were downregulated and included in the significant biological processes and the set of hypoxia-inducible genes. The downregulation of HIF1-targets was consistent with decreased HIF1A immunostaining in AD- compared to AE-tumors (p=0.002). A decrease in HIF1A immunostaining after ADT was also demonstrated in a cohort of 35 PCa patients (p<0.001). These data suggest suppressed HIF1-signaling after ADT and a shared role of HIF1 and AR in the regressive phase of PCa after ADT.

overall_design: Prostate cancer xenografts were subjected to adrogen deprivation therapy and analysed with regard to changes in gene expressions. Cell culture experiments were performed to generate prostate cancer specific gene lists associated with hypoxia.

first: Harald

last: Ragnum

first: Kathrine

last: Røe

first: Ruth

last: Holm

first: Ljiljana

last: Vlatkovic

first: Jahn

last: Nesland

first: Eva-Katrine

last: Aarnes

first: Anne

last: Ree

first: Kjersti

last: Flatmark

first: Therese

last: Seierstad

first: Wolfgang

last: Lilleby


title: Expression data from volatile treated and insect damaged Arabidopsis thaliana

city: Beijing

first: Sufang

last: Zhang

address: No.2 Dong Xiao Fu, Wan Shou Shan, Haidian District

institute: Research Institute of Forest Ecology, Environment and Protection, Chinese Academy of Forestry

summary:
Plant volatiles can mediate plant-plant communication in the sense that plants attacked by herbivores can signal their unattacked neighbors of danger by emitting HIPVs. We call this the priming effect. Since the plant defense response is a systematic process involving numerous pathways and genes,to characterize the priming process, a time course study using a genome-wide microarray may provide more accurate information about the priming process. Furthermore, to what extent do the priming process and direct defense share similar gene expression profiles or pathways are also not clear.
We used microarray to detect the priming effect of plant volatiles to healthy Arabidopsis thaliana, and the effect of direct leafminer feeding to Arabidopsis thalianas.

overall_design: A system using Lima bean plants, from which HIPVs can be effectively induced by leafminer feeding, as emitters and Arabidopsis thaliana as receivers is used to track the priming process between neighbor plants. The Arabisopsis thaliana seedlings were treated by volatiles from leafminer fed lima bean for 24h or 48h for RNA extraction and hybridization on Affymetrix microarrays. The Arabisopsis thaliana seedlings fed by leafminer directly were also collected The for RNA extraction and hybridization on Affymetrix micorarrays. We want to explore the response of Arabidopsis thaliana to priming volatiles during a 24h-48h time course. We also want to compare the effect of priming and direct leafminer feeding.

first: Le

last: Kang

first: Jianing

last: We


title: Gene expression profiles of 2D- and 3D-cultured fallopian tube secretory epithelial cells

city: Los Angeles

first: Kate

last: Lawrenson

state: CA

address: 1450 Biggy Street

department: Preventive Medicine

institute: University of Southern California

summary:
Background: Fallopian tube secretory epithelial cells (FTSECs) have been implicated as a cell-of-origin for high-grade serous epithelial ovarian cancer. However, there are relatively few in vitro models of this tissue type available for use in studies of FTSEC biology and malignant transformation. In vitro three-dimensional (3D) cell culture models aim to recreate the architecture and geometry of tissues in vivo and restore the complex network of cell-cell/cell-matrix interactions that occur throughout the surface of the cell membrane.

Results: We have established and characterized 3D spheroid culture models of primary FTSECs. FTSEC spheroids contain central cores of hyaline matrix surrounded by mono- or multi-layer epithelial sheets. We found that 3D culturing alters the molecular characteristics of FTSECs compared to 2D cultures of the same cells. Gene expression profiling identified more than a thousand differentially expressed genes between 3D and 2D cultures of the same FTSEC lines. Pathways significantly under-represented in 3D FTSEC cultures were associated with cell cycle progression and DNA replication. This was also reflected in the reduced proliferative indices observed in 3D spheroids stained for the proliferation marker MIB1. Comparisons with gene expression profiles of fresh fallopian tube tissues revealed that 2D FTSEC cultures clustered with follicular phase tubal epithelium, whereas 3D FTSEC cultures clustered with luteal phase samples.

Conclusions: This 3D model of fallopian tube secretory epithelial cells will advance our ability to study the underlying biology and etiology of fallopian tube tissues and the pathogenesis of high-grade serous epithelial ovarian cancer.

overall_design: 3 primary FTSEC lines were plated in 2D, or in 3D on polyHEMA coated plates

first: Simon

last: Gayther


title: Therapeutic potential of induced neural stem cells for spinal cord injury

first: Kyungtae

last: Lim

address: Tennis Court Road

department: The Wellcome Trust/Cancer Research UK Gurdon Institute

summary:
The spinal cord does not spontaneously regenerate after injury and a treatment that ensures functional recovery after spinal cord injury (SCI) is still not available. Recently, fibroblasts have been directly converted into induced neural stem cells (iNSCs) following the forced expression of different combinations of transcription factors. Although directly converted iNSCs have been considered as a potentialcell source for clinical applications, their therapeutic potential has not been investigated yet. Here we show that iNSCs directly converted from mouse fibroblasts enhance the functional recovery after SCI in rats.
Mouse embryonic fibroblasts (MEFs) were directly converted into iNSCs using four transcription factors (Brn4, Sox2, Klf4 and c-Myc). iNSCs showed gene expression profiles similar to cNSCs as determined by microarray analysis.

overall_design: MEFs were derived from C3H mouse strain embryos at embryonic day (E)13.5 after removing the head and all internal organs including the gonads and the spinal cord. 5x10^4 fibroblasts were transduced with replication-defective retroviral particles coding for Sox2, Klf4, c-Myc, and Brn4. After 48 h, the transduced fibroblasts were cultured in standard NSC medium. iNSC clusters were observed 4-5 weeks after transduction and expanded. Both MEFs and cNSCs were used as negative and positive control, respectively.

first: Jung

last: Hyun

first: Dong

middle: W

last: Han


title: Comparative intraindividual transcriptome analysis of B-precursor ALL of childhood

status: Public on Sep 17 2013

city: Hamburg

first: Thomas

last: Streichert

address: Martinistr. 52, Campus Forschung N27, 2. OG

department: Institute For Clinical Chemistry / Central Laboratories

institute: University Medical Center Hamburg-Eppendorf

summary: The objective of this study was the assessment of transcriptional dysregulation in particular with regard to B-cell differentiation factors. Most studies focus on cross-section analyses of various leukemia subtypes to identify differentially regulated genes lacking suitable reference models. Here we applied comparative intraindividual transcriptome analysis of B-precursor ALL of childhood, which introduces a side-by-side analysis of leukemic cells and matched normal lymphoblasts from the same individual in complete continuous remission after the end of re-induction therapy. This approach reduces noise by eliminating interindividual variability.

overall_design: Comparative matched pair analysis of (single sorted) initial leukemia and single sorted lymphoblasts isolated from the same individual, n=4 pairs, reference samples are the single sorted normal lymphoblasts. Please note that there are sorted samples form only three of the patients. Due to experimental circumstances, a "sorted" sample from the last patient was not included.

first: Martin

last: Horstmann

first: Benjamin

last: Otto


title: Cavin-3 Dictates the Balance Between ERK and Akt Signaling

city: Dallas

first: Peter

last: Michaely

address: 5323 Harry Hines Blvd.

department: Cell Biology

institute: UT Southwestern Medical Center

summary: Cavin-3 is a tumor suppressor protein of unknown function. Using a combination of in vivo knockout and in vitro gain/loss of function approaches, we show that cavin-3 dictates the balance between ERK and Akt signaling. Loss of cavin-3 increases Akt signaling at the expense of ERK, while gain of cavin-3 increases ERK signaling at the expense Akt. Cavin-3 facilitates signal transduction to ERK by anchoring caveolae, a lipid-raft specialization that contains an ERK activation module, to the membrane skeleton of the plasma membrane. Loss of cavin-3 reduces the number of caveolae, thereby separating this ERK activation module from signaling receptors. Loss of cavin-3 promotes Akt signaling through suppression of EGR1 and PTEN. The in vitro consequences of the loss of cavin-3 include induction of Warburg metabolism (aerobic glycolysis), accelerated cell proliferation and resistance to apoptosis. The in vivo consequences of cavin-3 loss are increased lactate production and cachexia.

overall_design: 9 total samples, consisting of 3 cavin-3 siRNA groups (0 days, 3 days and 8 days) one set was untreated, one set was serum starved, one set was serum starved and then treated with EGF for 1 hr.


title: Genome-wide analysis of berberine chloride-responsive gene expression in HepG2 liver cell line

city: Taipei

first: Ting-fang

last: Lo

address: 128 Academia Road, Section 2, Nankang, Taipei 115, Taiwan

institute: Academia Sinica

summary: Berberine, an isoquinoline alkaloid isolated from many medicinal herbs such as Coptis chinensis, has a wide range of pharmacological effects.  Here, we used gene expression microarray to analyze gene expression profiles of HepG2 human hepatoma cell line after berberine chloride treatment or 0.08% DMSO as control.

overall_design: Comparing gene expression profiles of 40 µM berberine-treated HepG2 human hepatoma cell line to those of control cells sampled after 4 hours treatment. A 50 mM stock solution of Berberine chloride was prepared in DMSO. Cells were treated with 40 µM berberine chloride or 0.08% DMSO as control.

first: Ting-Fang

first: Shui-Tein

last: Chen


title: Anaplastic thyroid carcinoma cell lines (HTH83 and TL3) infected with LAMC2 shRNA

status: Public on Oct 10 2013

city: Singapore

first: Lizhen

last: Liu

address: 14 Medical Drive

institute: Cancer Science Institute

summary:
Laminin-5 gamma-2 (LAMC2) is highly expressed in anaplastic thyroid carcinoma and associated with tumor progression, migration and invasion by modulating signaling of EGFR LAMC2 was highly expressed in ATC samples and cell lines compared to normal thyroid tissues. Silencing LAMC2 by shRNA in ATC cells moderately inhibited cell growth in liquid culture and dramatically decreased growth in soft agar and in xenografts growing in immunodeficient mice. Silencing LAMC2 caused cell cycle arrest and significantly suppressed migration, invasion and wound healing of ATC cells. Rescue experiments by overexpressing LAMC2 in LAMC2 knockdown cells, reversed the inhibitory effects as shown by increased cell proliferation and colony formation. Microarray data demonstrated that LAMC2 shRNA significantly altered expression of genes associated with migration, invasion, proliferation and survival. Immunoprecipitation studies showed that LAMC2 was bound to EGFR in ATC cells. Silencing of LAMC2 partially blocked EGF-mediated activation of EGFR and its downstream pathway.
Anaplastic thyroid carcinoma (ATC) is an aggressive malignancy having no effective treatment. Laminin subunit gamma-2 (LAMC2) is an epithelial basement membrane protein involved in cell migration and tumour invasion and might represent an ideal target for the development of novel therapeutic approaches for ATC. LAMC2 was highly expressed in ATC samples and cell lines compared to normal thyroid tissues. Silencing LAMC2 by shRNA in ATC cells moderately inhibited cell growth in liquid culture and dramatically decreased growth in soft agar and in xenografts growing in immunodeficient mice. Silencing LAMC2 caused cell cycle arrest and significantly suppressed migration, invasion and wound healing of ATC cells. Rescue experiments by overexpressing LAMC2 in LAMC2 knockdown cells, reversed the inhibitory effects as shown by increased cell proliferation and colony formation. Microarray data demonstrated that LAMC2 shRNA significantly altered expression of genes associated with migration, invasion, proliferation and survival. Immunoprecipitation studies showed that LAMC2 was bound to EGFR in ATC cells. Silencing of LAMC2 partially blocked EGF-mediated activation of EGFR and its downstream pathway. LAMC2 was highly expressed in ATC samples and cell lines compared to normal thyroid tissues. Silencing LAMC2 by shRNA in ATC cells moderately inhibited cell growth in liquid culture and dramatically decreased growth in soft agar and in xenografts growing in immunodeficient mice. Silencing LAMC2 caused cell cycle arrest and significantly suppressed migration, invasion and wound healing of ATC cells. Rescue experiments by overexpressing LAMC2 in LAMC2 knockdown cells, reversed the inhibitory effects as shown by increased cell proliferation and colony formation. Microarray data demonstrated that LAMC2 shRNA significantly altered expression of genes associated with migration, invasion, proliferation and survival. Immunoprecipitation studies showed that LAMC2 was bound to EGFR in ATC cells. Silencing of LAMC2 partially blocked EGF-mediated activation of EGFR and its downstream pathway.

overall_design: Anaplastic thyroid carcinoma cell lines (HTH83 and TL3) were infected with scrambled shRNA and LAMC2 shRNA and stable clones from each cell line were generated and used for RNA extraction and hybridization on Illumina Microarray. We compared scrambled shRNA stable cells with LAMC2 shRNA stable cells.

first: Manoj

last: Garg

first: Deepika

last: Kanojia

first: Ryoko

last: Okamoto

first: Saket

last: Jain

first: Vikas

last: Madan

first: Wenwen

last: Chien

first: Abhishek

last: Sampath

first: Ling-Wen

last: Ding

first: Meng

last: Xuan

first: Jonathan

last: Said

first: Ngan

last: Doan

first: Li-Zhen

first: Henry

last: Yang

first: Sigal

last: Gery

first: Glenn

last: Braunstein

first: H

middle: P

last: Koeffler


title: Gene expression changes due to influenza virus induced miRNAs

status: Public on Sep 15 2013

city: Evanston

first: William

last: Buggele

address: 2200 Campus Dr.

institute: Northwestern University

summary: The goal of this experiment was to determine gene expression changes during influenza A virus infection as the result of expression influenza virus inducible miRNAs in A549 cells.

overall_design: The gene expression profiling experiment was performed with 4 groups (mock infected, influenza A virus infected, influenza A virus infected in the presence of exogenous miR-141, miR-374b, miR-449b, miR-518b, and miR-1263, and influenza A virus infected in the presence of exogenous miR-147b, miR-190b, miR-199a, miR-512-5p, and miR-874 with 3 biological replicates for each group. Total RNA was purified from A549 cells that were mock infected or infected with influenza A virus (A/WSN/33, 5pfu/cell) alone or in the presence of miRNA mimics 10 hours after treatment.


title: Global gene expression changes in patient-derived CML cell line K562 after short- and long-term BCR-ABL kinase inhibition.

city: San Francisco

first: Neil

last: Shah

address: 513 Parnassus

institute: UCSF

summary: K562 cells were treated with the BCR-ABL kinase inhibitor dasatinib over an extended period of time to determine how BCR-ABL inhibition affects BCR-ABL-dependent negative feedback and erythropoietin receptor (EPO-R) signaling.  Specifically, what types of changes (upregulation versus downregulation) occur in both the negative and positive regulators of growth-factor receptor signaling.

overall_design: Total RNA was extracted from K562 cells treated with 0.2% DMSO for 24hrs or 100nM dasatinib for 4hrs, 8hrs, and 24hrs.

first: Jennifer

last: Asmussen

first: Elisabeth

last: Lasater

first: Cheryl

last: Tajon

first: Juan

last: Oses-Prieto

first: Young-wook

last: Jun

first: Barry

last: Taylor

first: Alma

last: Burlingame

first: Charles

last: Craik


title: Gene expression analysis in wild-type and OsGRX8 overexpression line in response to various treatments

status: Public on Sep 23 2013

city: New Delhi

first: Mukesh

last: Jain

state: New Delhi

address: New Mehrauli Road

country: India

institute: Jawaharlal Nehru University

summary:
Glutaredoxins (GRXs) are the ubiquitous oxidoreductase enzymes, which play important role in defense against various stresses. To analyze the function of a CC-type rice GRX gene, OsGRX8, we overexpressed it into Arabidopsis constitutively. The physiological analyses revealed that overexpression of GRX gene enhanced abiotic stress tolerance in transgenic plants as compared to wild-type.
We used microarrays to study the global effect of overexpression of OsGRX8 in Arabidopsis under control and various treatments.

overall_design: Wild-type and transgenic Arabidopsis seedlings were grown on MS medium for 14-days in a culture room with a daily photoperiodic cycle of 16h light and 8h dark. Seedlings were incubated in water (control) or 100 µM solution of indole-3-acetic acid (auxin, IAA), 200 mM sodium chloride (salt, NaCl) and 25 µM solution of methyl viologen (MV)for 3h. The 500 ng of total RNA sample isolated from each tissue sample was processed for microarray analysis according to Affymetrix protocol. Two biological replicates for each sample (control, IAA, NaCl and MV) of wild-type and GRX overexpression line were used for microarray analysis.

first: Sharma

last: Raghvendra

first: Priya

last: Pushp

first: Jain

last: Mukesh


title: Molecular classification of mature aggressive B cell lymphoma using digital multiplexed gene expression on formalin-fixed paraffin-embedded biopsy specimens

status: Public on Sep 25 2013

city: Regensburg

first: Christian

last: Kohler

state: Bavaria

address: Am BioPark 9

department: Institute of Functional Genomics

country: Germany

institute: University of Regensburg

first: Neus

last: Masque-Soler

first: Monika

last: Szczepanowski

first: Rainer

last: Spang

first: Wolfram

last: Klapper


title: Identification and validation of a multigene predictor of recurrence in primary laryngeal cancer.

status: Public on Oct 30 2013

city: Thessaloniki

first: elena

last: fountzilas

address: School of Medicine, Pathology Department

department: Medical Oncology

country: Greece

institute: Aristotle University of Thessaloniki, Greece

summary: Background: Local recurrence is the major manifestation of treatment failure in patients with operable laryngeal carcinoma. Established clinicopathological factors cannot sufficiently predict patients that are likely to recur after treatment. Additional tools are therefore required to accurately identify patients at high risk for recurrence.  Methods: Using Affymetrix U133A Genechips, we profiled fresh-frozen tumor tissues from 59 patients with operable laryngeal cancer. All patients were treated locally with surgery, with or without radiation therapy. We performed Cox regression proportional hazards modeling to identify multigene predictors of recurrence. The end-point of our analysis was disease-free survival (DFS). Gene models were directly validated in a separate, similarly treated cohort of 50 patients using Affymetrix chips. In an attempt to further validate our results, we profiled 12 selected genes of our model in formalin-fixed tumor tissues from an independent cohort of 75 patients, using quantitative real time-polymerase chain reaction (qRT-PCR).   Results: We focused on genes univariately associated with DFS (p<0.05) in the training set. Among several gene models comprising different numbers of genes, a 30-gene model demonstrated optimal performance (log-rank, p<0.001). We directly applied these gene models to the validation set, after adjusting for non-biological experimental variability, and observed similar results. Specifically, median DFS, as predicted by the 30-gene model, was 34 and 80 months for high- and low-risk patients, respectively (p=0.01). Hazard Ratio (HR) for recurrence for the high-risk group was 3.87 (95% CI 1.28-11.73, p=0.017). Furthermore, unsupervised hierarchical clustering of the 75 patients, based on the qRT-PCR 12-gene profile, yielded two groups, which differed significantly in DFS (log-rank, p=0.027). HR= for recurrence was 2.26, (95% CI 1.08-4.76, p=0.031).  Conclusion: We have established and validated gene models that can successfully stratify patients with laryngeal cancer, based on their risk for recurrence. Thus, patients with unfavorable prognosis, when accurately identified, could be ideal candidates for the application of more aggressive treatment modalities.

overall_design: Training set comprises 59 samples and validation set 50 samples

first: Elena

last: Fountzilas


title: ER71/ETV2-mediated direct reprogramming of human dermal fibroblasts (HDFs) into endothelial-like cells

status: Public on Sep 12 2013

city: Atlanta

first: Young-sup

last: Yoon

state: Georgia

address: 101 Woodruff Cir

department: Medicine

country: USA

institute: Emory University

summary:
Samples 1-6: HDFs transduced with ER71/ETV2 were sorted on KDR expression at day 7. The isolated KDR+ cells together with human umbilical venous endothelial cells (HUVECs) and untransduced HDFs were subjected to genomic gene expression profiling. A significant number of genes related with vessel development and angiogenesis was significantly upregulated in KDR+ cells, compared to control HDFs. These findings strongly argue that ER71/ETV2 directly reprograms human fibroblasts to functional endothelial-like cells, which could be useful for disease investigation as well as autologous cell therapy.
Samples 7-12: HDFs transduced with ER71/ETV2 were sorted on KDR expression at day 7. The isolated KDR+ cells were further cultured up to day 93. The further cultured cells together with human umbilical venous endothelial cells (HUVECs) and untransduced HDFs were subjected to genomic gene expression profiling. A significant number of genes related with vessel development and angiogenesis was significantly upregulated in the further cultured cells, compared to control HDFs. These findings strongly argue that ER71/ETV2 directly reprograms human fibroblasts to functional endothelial-like cells, which could be useful for disease investigation as well as autologous cell therapy.

overall_design:
Samples 1-6: HDFs transduced with ER71/ETV2 were sorted on KDR expression at day 7. The isolated KDR+ cells together with human umbilical venous endothelial cells (HUVECs) and untransduced HDFs were subjected to genomic gene expression profiling.
Samples 7-12: HDFs transduced with ER71/ETV2 were sorted on KDR expression at day 7. The isolated KDR+ cells were further cultured up to day 93. The further cultured cells together with human umbilical venous endothelial cells (HUVECs) and untransduced HDFs were subjected to genomic gene expression profiling.

first: Changwon

last: Park

first: Sangho

last: Lee

first: Ji

last: Han

first: Ju

middle: Y

last: Kim

first: Kyuwon

last: Cho

first: Eun

first: Sangsung

first: Hyo

last: An

first: Min

last: Sin

first: Shraya

last: Sharma


title: Cyclophilin B supports the survuval of glioblastoma multiforme cells

city: ROCHESTER

first: Richard

last: Bram

state: MN

address: 200 First Street SW

department: Pediatric and Adolescent Medicine

institute: Mayo Clinic

summary: We have found that cyclophilin B (CypB) expression is important for malignant glioblastoma multiforme (GBM) cell proliferation. To identify molecular mechanisms that could explain CypB-dependent survival in human GBM cells, a microarray analysis was performed using RNA prepared from U251MG GBM cells transduced with lentiviral CypB shRNA. These data revealed that about 130 genes were more than 2-fold affected by CypB depletion. Significant alterations in the expression of genes related to cell death, cell proliferation and cell migration were found in the shCypB cells.

overall_design: U251 glioblastoma cells transduced with lentivirus expressing non-target control shRNA (shCON) were compared to cells transduced with lentivirus expressing shRNA sequence against cyclophilin B (shCypB). Cells transduced with the lentiviral shRNA (shCON VS shCypB) for 5 days before total RNA extraction. Three biological replicates of cells treated with each shRNA (shCON or shCypB) were profiled.

first: Jae

last: Choi


title: Differential requirement for Nfil3 during NK cell development

status: Public on Oct 08 2013

city: Barcelona

first: Victoria

last: Core

address: Baldiri Reixac, 10

department: Functional Genomics Core

country: Spain

institute: Institute for Research in Biomedicine

summary:
Nfil3 has multiple functions during conventional NK cell and thymic NK cell development. Nfil3 controls NK cell development from the earliest committed NK cell progenitor stage. Nfil3-/- prepro NK cells retained T-cell potential due to the failure to repress T cell specific genes. At later stages of NK cell development, Nfil3 regulates the formation of mature NK cells by promoting directly or indirectly the expression of transcription factor Eomes. We also demonstrate that Nfil3 is important for thymic NK cell development whereas Trail+ immature NK cells generated in the bone marrow of neonates and in the adult liver develop independent of Nfil3 function.
We used microarrays to analyse the changes in gene expression due to the presence or absence of Nfil3, both in prepro NK cells and ALP cells (all lymphoid progenitors)

overall_design: Samples were obtained on two experimentation dates. Replicate 1 was processed in April 2012, replicate 2 was processed in May 2012.

first: Cyril

last: Seillet

first: Sebastian

last: Carotta


title: Antiviral signaling mediates inhibition of RNAi in mammalian cells

city: Austin

first: Chris

last: Sullivan

address: 2506 Speedway

institute: University of Texas-Austin

summary: Analysis of the interferon response (specifically interferon stimulated genes-ISGs) in human DLD-1 cells that have decreased microRNA expression due to a exon mutation in Dicer. The hypothesis tested in the present study is that ISGs are particularly suspectible to microRNA regulation.

overall_design: Total RNA obtained from both WT and microRNA hypmorphic DLD-1 cells after 3, 8, and 24 hours post interferon treatment

first: Gil

last: Seo


title: Molecular classification of mature aggressive B cell lymphoma using digital multiplexed gene expression on formalin-fixed paraffin-embedded biopsy specimens [Affymetrix]

first: Christian

last: Kohler

summary:
The most frequent mature aggressive B-cell lymphomas are diffuse large B-cell lymphoma (DLBCL) and Burkitt lymphoma (BL). Patients suffering from molecularly defined BL (mBL) but treated with a regimen developed for DLBCL show an unfavorable outcome compared to mBL treated with chemotherapy regimens for BL. Distinguishing BL from DLBCL by conventional histopathology is challenging in lymphomas that have features common to both diseases (aggressive B-cell lymphoma unclassifiable with features of DLBCL and BL [intermediates]). Moreover, DLBCL are a heterogeneous group of lymphomas comprising distinct molecular subtypes: the activated B-cell (ABC)-like, the germinal center B-cell-like (GCB) and the unclassifyable subtype as defined by gene expression profiling (GEP). Attempts to replace GEP with techniques applicable to formalin-fixed paraffin-embedded (FFPE) tissue led to algorithms for immunohistochemical stainings (IHS). Disappointingly, the algorithms yielded conflicting results with respect to their prognostic potential, raising concerns about their validity.  Furthermore, IHS algorithms did not provide a fully resolved classification:  They did not identify mBL; nor did they separate ABC from unclassified DLBCL.

We used digital multiplexed gene expression (DMGE) with FFPE derived RNA to classify agressive B-cell lymphomas. Our assay comprised only 30 genes (10 for the detection of mBL and 20 for the detection of ABC and GCB). We chose these genes by reanalysis of the microarray data reported in a previous study. 39 samples from mature aggressive B-cell lymphomas were analyzed using DMGE (nCounter, NanoString Technologies Inc., Seattle, WA, USA) of FFPE- and fresh-frozen derived RNA. All cases were previously characterized by the Molecular Mechanisms of Malignant Lymphoma (MMML) consortium using the Affymetrix GeneChip technology (gold standard of classification).

overall_design:
29 diffuse large B-Cell lymphoma samples were hybridized to HGU133A Affymetrix GeneChips. In addition, this study contains 22 already published samples whereas 11 of them contribute to GSE22470, 6 contribute to GSE10172,  3 to GSE44164 and 2 to GSE4475. No re-normalisation of published samples was performed.

The dataset representing: (1) 11 samples from GSE22470, (2) 6 samples from GSE10172,  (3) 3 samples from GSE44164 and (4) 2 samples from GSE4475 is linked below as a supplementary file.

first: Neus

last: Masque-Soler

first: Monika

last: Szczepanowski

first: Rainer

last: Spang

first: Wolfram

last: Klapper