title: A systematic evaluation of miRNA:mRNA interactions involved in the migration and invasion of breast cancer cells [HG-U133_Plus_2]

city: Augusta

first: Huidong

last: Shi

department: Georgia Cancer Center

institute: Augusta University

summary: In this study we performed a systematic evaluation of functional miRNA-mRNA interactions associated with the aggressiveness of breast cancer cells using a combination of integrated miRNA and mRNA expression profiling, bioinformatics prediction, and functional assays. Analysis of the miRNA expression identified 11 miRNAs that were differentially expressed, including 7 down-regulated (miR-200c, miR-205, miR-203, miR-141, miR-34a, miR-183, and miR-375) and 4 up-regulated miRNAs (miR-146a, miR-138, miR-125b1 and miR-100), in aggressive cell lines when compared to normal and less aggressive cell lines. Transient overexpression of miR-200c, miR-205, and miR-375 in MDA-MB-231 cells led to the inhibition of cell migration and invasion. The integrated analysis of miRNA and mRNA expression identified 35 known and novel target genes of miR-200c, miR-205, and mir-375, including CFL2, LAMC1, TIMP2, ZEB1, CDH11, PRKCA, PTPRJ, PTPRM, LDHB, and SEC23A. Surprisingly, the majority of these genes (27 genes) were target genes of miR-200c, suggesting that it plays a more important role in regulating the aggressiveness of breast cancer cells. We characterized one of the target genes of miR-200c, CFL2, and demonstrated that CFL2 is overexpressed in aggressive breast cancer cell lines and can be significantly down-regulated by exogenous miR-200c. Tissue microarray analysis further revealed that CFL2 expression in primary breast cancer tissue correlated with tumor grade. To our knowledge, this study is the first systematic screening of functional miRNA target genes in aggressive breast cancer cells. The results obtained from this study may improve our understanding of the role of these candidate miRNAs and their target genes in relation to breast cancer aggressiveness and ultimately lead to the identification of novel biomarkers associated with prognosis.

overall_design: Affymetrix U133 plus arrays were performed according to the manufacturer's directions on RNA extracted from 12 breast cancer cell lines including 4 aggressive cell lines, 6 less aggressive cell lines and 2 imortalized breast epithelium cell lines

first: Daya

last: Luo

first: Nikki

last: Harvel


title: Expression data from human cumulus cells isolated from oocytes at MI and MII stages in polycystic ovary syndrome (PCOS) patients

status: Public on Jun 05 2013

city: Yan tai

first: Xin

last: Huang

state: Shan dong

address: Yuhuangding east street 20

department: Reproduction Medical Centre

country: China

institute: Yuhuangding hospital of Yantai

summary:
Polycystic ovary syndrome (PCOS) is a common endocrine and metabolic disorder that is characterized by increased circulating androgen levels, anovulatory infertility, and frequently, insulin resistance and hyperinsulinemia.The abnormity of oocyte nuclear maturity is the main reason for anovulatory infertility and pregnancy loss in PCOS patients.The bidirectional exchanges between oocyte and contiguous CCs are important for oocyte competence acquisition, early embryonic development and CC expansion.Gene expression profiles of CCs has been suggested to predict embryo development and pregnancy outcome.
We used microarrays to detail the global programme of gene expression of CCs isolated from oocytes at metaphase I (CCMI) and metaphase II (CCMII) stage under controlled ovarian stimulation (COS) cycle in PCOS patients.

overall_design: Cumulus cells were isolated from oocyte at stage metaphase 1(MI)and stage metaphase II (MII) of PCOS patients for RNA extraction and hybridization on Affymetrix microarrays. For microarray analysis, we used three chips for each CC category. That is, CCMI1,CCMI2,CCMI3,CCMII1,CCMII2 and CCMII3.

first: Cuifang

last: Hao


title: Dual targeting of MYC and CYCLON by BET bromodomain inhibition optimizes Rituximab response in lymphoma.

status: Public on Jun 01 2013

city: Grenoble

first: Anouk

last: Emadali

country: France

institute: Institut Albert Bonniot

summary:
Immuno-chemotherapy regimens elicit high response rates in B-cell non-Hodgkin lymphoma but heterogeneity in response duration is observed, with some patients achieving cure and others showing refractory disease or relapse. Using a transcriptome-powered targeted proteomics screen, we discovered a gene regulatory circuit involving the nuclear factor CYCLON which characterizes aggressive disease and resistance to the anti-CD20 monoclonal antibody, Rituximab, in high-risk B-cell lymphoma. CYCLON knockdown was found to inhibit the aggressivity of MYC-overexpressing tumors in mice and to modulate gene expression programs of biological relevance to lymphoma. Furthermore, CYCLON knockdown increased the sensitivity of human lymphoma B cells to Rituximab in vitro and in vivo. Strikingly, this effect could be mimicked by in vitro treatment of lymphoma B cells with a small molecule inhibitor for BET bromodomain proteins (JQ1). In summary, this work has identified CYCLON as a new MYC cooperating factor that drives aggressive tumor growth and Rituximab resistance in lymphoma. This resistance mechanism is amenable to next-generation epigenetic therapy by BET bromodomain inhibition, thereby providing a new combination therapy rationale for high-risk lymphoma.
We have identified CYCLON has a nuclear factor involved in tumor progression and treatment resistance in aggressive lymphoma. In order to get further insights into the molecular mechanisms related to the expression of this factor, we used Raji cells to compared  gene expression profiles of control and CYCLON knock-down cell lines.

overall_design: Stable cell lines have been established using lentiviral transduction of Raji Burkitt lymphoma B cells with either a control (non-targeting) shRNA sequence or CYCLON shRNA constructs under puromycin selection. Non-transduced cells were also analyzed as a control. 4 replicates were analyzed for each conditions.

first: Sophie

last: Rousseaux

first: Saadi

last: Khochbin

first: Mary

last: Callanan


title: MicroRNA-27a regulates lipid metabolism and inhibits hepatitis C virus replication in human hepatoma cells

city: Kanazawa

first: Masao

last: Honda

address: Takara-Machi 13-1

department: Gastroenterology

country: Japan

institute: Kanazawa University

summary:
Gene expression profiling was carried out in Huh-7.5 cells in which miR-27a was over- or under-expressed. Transfection of cells with pre-miR-27a and pre-miR-control, or anti-miR-27a and anti-miR-control enabled down- and up-regulated genes to be determined, respectively.
Replication and infectivity of the lipotrophic hepatitis C virus (HCV) is regulated by cellular lipid status. Among differentially expressed micro (mi)RNAs, we found that miR-27a was preferentially expressed in HCV-infected compared with hepatitis B virus (HBV)-infected liver. Gene expression profiling of Huh-7.5 cells showed that miR-27a regulates lipid metabolism by targeting the lipid synthetic transcriptional factor, RXRα, and the lipid transporter, ABCA1

overall_design:
Carrying out a Target Scan (Release 5.2) of miR-27a predicted 921 candidate target genes, and functional gene ontology enrichment analysis of these genes by MetaCore (Thomson Reuters, NY) showed that miR-27a could target the signaling pathways of cytoskeleton remodeling and lipid metabolism .   To examine whether these signaling pathways were regulated by miR-27a, gene expression profiling was carried out in Huh-7.5 cells in which miR-27a was over- or under-expressed. Transfection of cells with pre-miR-27a and pre-miR-control, or anti-miR-27a and anti-miR-control enabled down- and up-regulated genes to be determined, respectively.
Huh-7.5 cells with miR-27a over- or under-expressed

first: Takayoshi

last: Shirasaki

first: Tetsuro

last: Shimakam

first: Rika

last: Horii

first: Taro

last: Yamashita

first: Yoshio

last: Sakai

first: Akito

first: Hikari

last: Okada

first: Risa

last: Watanabe

first: Seishi

last: Murakami

first: MinKyung

last: Yi

first: Stanley

middle: M

last: Lemon

first: Shuichi

last: Kaneko


title: Integration of high-resolution methylome and transcriptome analyses to dissect epigenomic changes in childhood acute lymphoblastic leukemia

status: Public on Jun 04 2013

city: Montreal

first: Stephan

last: Busche

state: Quebec

address: 740 Dr. Penfield Avenue

department: Human Genetics

country: Canada

institute: McGill University

type: Methylation profiling by genome tiling array

summary: B-cell precursor acute lymphoblastic leukemia (pre-B ALL) is the most common pediatric cancer. Although the genetic origin of the disease remains unclear, epigenetic modifications including DNA methylation are suggested to contribute significantly to leukemogenesis. We assessed the DNA methylation status of 402,842 CpG-sites across the genome (Illumina 450k array) in tumor and remission samples of 46 pre-B ALL patients, thus generating the most comprehensive single CpG-site resolution pre-B ALL methylomes so far. Unsupervised hierarchical clustering of CpG-site neighborhood, protein-coding gene, or miRNA gene associated methylation levels separated the tumor cohort according to major pre-B ALL subtypes, and methylation in CpG islands, shores, and in regions around the transcription start site of protein-coding genes strongly correlated with transcript expression. Focusing on samples carrying the t(12;21)(p13;q22) translocation (ETV6-RUNX1 fusion gene) we identified subtype-specific methylation of 430 CpG-sites. Pathway analyses implied the associated genes in hematopoiesis and cancer. Further intersection with transcriptome data identified methylation to impact expression of 18 genes. In summary, our data illustrate the power of methylation profiling to classify leukemic subtypes and to identify subtype-specific methylation markers. Further, we demonstrate that integration of methylome and transcriptome alterations allows the study of downstream effects of individual genomic rearrangements in cancer.

overall_design: Bisulfite converted DNA of tumor (isolated on day of diagnosis) and remission (isolated after disease remission) samples derived from 46 patients of French-Canadian origin diagnosed with pre-B ALL were analyzed on the Illumina Infinium HumanMethylation 450k BeadChips.

first: Bing

last: Ge

first: Ramon

last: Vidal

first: Jean-François

last: Spinella

first: Virginie

last: Saillour

first: Chantal

last: Richer

first: Jasmine

last: Healy

first: Shu-Huang

last: Chen

first: Arnaud

last: Droit

first: Daniel

last: Sinnett

first: Tomi

last: Pastinen


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

status: Public on Jun 03 2013

city: Los Angeles

first: Markus

last: Müschen

state: CA

address: 4650 Sunset Blvd

department: Childrens Hospital Los Angeles

country: USA

institute: University of Southern California

summary: In order to investigate the function of Bcor in ALL, we isolated bone marrow cells from Bcor fl/Y mice and transformed them with BCR-ABL1. In a second transduction the BCR-ABL1 driven pre-B cells were transformed either with CRE-ERT2 or ERT2 (PMIP) and after 2 days of treatment with 4OH-Tamoxifen (0.5 micromolar) subjected to gene expression analysis.

overall_design: Two days after treatment with 4OH-Tamoxifen (0.5 micromolar) total RNA of Puromycin resistant cells was extracted and subjected to gene expression analysis.

first: seyedmehdi

last: shojaee


title: A systematic evaluation of miRNA: mRNA interactions involved in the migration and invasion of breast cancer cells

first: Huidong

last: Shi

state: GA

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

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

platform_organism:
Homo sapiens
synthetic construct

overall_design: Refer to individual Series

first: Daya

last: Luo

first: Nikki

last: Harvel


title: Gene expression data of BCR-ABL1 transformed B cell precursors from ETV5 wild-type and ETV5 knockout mice

summary: To elucidate the mechanism of ETV5-mediated pre-B cell survival signaling, we investigated the gene expression pattern in BCR-ABL1-transformed ETV5+/+ and ETV5-/- B cell precursors.

overall_design: BCR-ABL1 transformed B cell precursors of ETV5wild-type and ETV5 knockout mice were subjected to RNA isolation


title: Role and function of SPRY1/2 in BCR-ABL1 driven pre-B cells

summary: In order to investigate the function of SPRY1 and SPRY2  in ALL, we isolated bone marrow cells from Spry1 and 2 fl/fl mice and transformed them with BCR-ABL1. In a second transduction the BCR-ABL1 driven pre-B cells were transformed either with CRE-ERT2 or ERT2 (PMIP) and after 2 days of treatment with 4OH-Tamoxifen (0.5 micromolar) subjected to gene expression analysis.


title: COHCAP HCT116 Mutant Comparison [methylation]

status: Public on Jun 08 2013

city: Duarte

first: Charles

middle: David

last: Warden

address: 1500 East Duarte Rd

department: Department of Molecular and Cellular Biology

institute: City of Hope

summary: Genome-wide expression and methylation differences are compared for a normal HCT116 cell line and a derived mutant with altered DNA methylation patterns.

overall_design:
The data compares the effect of a gene mutation on genome-wide expression (and methylation).  This data is being published as a technical test of utility for a novel integrative genomic algorithm (COHCAP)
Keywords: parental, mutant

first: Hua

last: Yu

first: Heehyoung

last: Lee

first: Richard

last: Jove


title: Expression data for resting and activated B and T cells

city: Utrecht

first: sjoerd

last: holwerda

address: Uppsalalaan 8

country: Netherlands

institute: Hubrecht Institute

summary:
The IgH locus encodes for part of the antibody exposed by B cells and is important for the immune system. In B cells, one allele produces protein, the other must remain silenced. It was proposed that both alleles reside in different nuclear compartments and that this is important to maintain mono-allelic productivity. Here we challenge this concept. We provide detailed genome-wide contact maps, which show that IgH adopts different nuclear locations in immune versus other cells but also demonstrate that in B cells both alleles reside in the same environment. Nuclear positioning is therefore not important to maintain allelic exclusion.
We did a gene expression analysis on resting (Day 0) and in vitro activated (Day 4) B and T cells in triplicate

overall_design: Splenic B cells and T cells were separately isolated from spleen, using magnetic activated cell sorting, and activated in vitro for 4 days

first: Sjoerd

middle: B

last: Holwerda

first: Harmen

middle: G

last: van de Werken

first: Claudia

middle: R

last: de Almeida

first: Ingrid

last: Bergen

first: Marjolein

middle: W

last: de Bruijn

first: Marjon

middle: J

last: Verstegen

first: Marieke

last: Simonis

first: Erik

last: Splinter

first: Patrick

last: Wijchers

first: Rudi

last: Hendriks

first: Wouter

last: de Laat


title: Identification of the chemokine CCL28 as a growth and survival factor for human hematopoietic stem- and progenitor cells

city: Lund

first: Shamit

last: Soneji

address: Sölvegatan 19

department: Biomedicinskt Centrum

country: Sweden

institute: Lund University

summary:
To discover novel growth factors for hematopoietic stem- and progenitor cells (HSPCs), we have assessed cytokine responses of cord blood (CB)-derived CD34+ cells in a high-content growth factor screen. We identify the immunoregulatory chemokine (C-C motif) ligand 28 (CCL28) as a novel growth factor that directly stimulates proliferation of primitive hematopoietic cells from different ontogenetic origins.
Microarrays are used to compare the expression profiles of HSPCs expanded in SCF, TPO and CCL28 respectively.

overall_design: HSPCs were cultured in Serum-Free Expansion Medium with SCF, SCF + TPO, and SCF + CCL28 respectively, and hybridised microarrays in triplicate.

first: C

last: Karlsson

first: S

first: L

last: Larsson


title: Microarray analysis of C. rodentium infected colons

city: Saint Louis

first: Ansuman

last: Satpathy

state: MO

address: 660 S. Euclid Ave.

department: Pathology and Immunology

institute: Washington University in St. Louis

summary: Defense against attaching and effacing (A/E) bacteria requires the sequential generation of IL-23 and IL-22 to induce protective mucosal responses. While the critical source of IL-22 has been identified as CD4+ and Nkp46+ innate lymphoid cells (ILCs), the precise source of IL-23 is unclear. Here, we use genetic techniques to deplete specific classical dendritic cell (cDC) subsets and analyze immunity to the A/E pathogen Citrobacter rodentium. We find that Zbtb46+ cDCs, and specifically Notch2-dependent intestinal CD11b+ cDCs, but not Batf3-dependent CD103+ cDCs, are required for IL-23 production and immunity against C. rodentium. Notch2 controls cDC differentiation at a terminal step mediated by lymphotoxin signaling. Importantly, these results provide the first demonstration of a non-redundant function of CD11b+ cDCs in vivo.

overall_design:
Analysis of genes differentially expressed between WT, Batf3 KO and Notch2 KO colons following C. rodentium infection.
Mice were infected with 2 x 10^9 C. rodentium and colons harvested at either Day 4 or Day 9.

first: Kenneth

last: Murphy


title: Microarray analysis of WT and Notch2-deficient classical DC subsets

overall_design:
Analysis of Notch2-dependent genes in CD11b+ and DEC205+ splenic classical DC subsets.
Splenocytes were harvested from littermate WT Notch2 f/f C57Bl/6 or Notch2 CD11c-cre C57Bl/6 mice and DC subsets sorted to >95% purity on the FACSAriaII.


title: Microarray analysis of WT ESAM+ and ESAM- cDC subsets

overall_design:
Analysis of differentially expressed genes in ESAM+ and ESAM- CD11b+ and DEC205+ splenic classical DC subsets.
Splenocytes were harvested from WT C57Bl/6 or WT Cx3cr1-gfp mice and cDC subsets sorted to >95% purity on the FACSAriaII.


title: Expression data from human antigen presenting cells expressing HIV-1 Tat alleles and mutants

city: BOSTON

first: NAYOUNG

last: KIM

state: MA

address: 61 BINNEY

department: MEDICINE

institute: BOSTON CHILDREN'S HOSPITAL

summary:
HIV-1 Tat induces the expression of interferon (IFN)-inducible genes in immature dendritic cells (iDC) in the absence of IFN production. We evaluated how three alleles of Tat and some Tat mutants differ in cellular gene modulation and whether a similar gene induction pattern could be detected by treating cells with IFN’s.  The three alleles and mutants, with the exception of mutants TatSF21-47 and TatSF2G48-R57A that do not localize in the nucleous, modulated to different degrees IFN-inducible genes without concomitant induction of IFN’s. The first exon TatSF21-72 and the minimal transactivator TatSF21-58, all induced genes to a significantly greater extent than full-length Tat. The 2nd exon appears to diminish the gene modulation that can be observed when the first exon alone is expressed.
To investigate what domain of Tat are critical to the host-pathogen interactions that are Tat-dependent during HIV infection, we evaluated a variety of Tat-mutants and found that in antigen presenting cells, blood-derived myeloid iDC and macrophages, the second exon of Tat reduces innate immunological responses which are maximal when a Single exon Tat is expressed.

overall_design: 1X10e6 macrophages were infected with  HIVBal (20 ng of p24/ 106 cells) for 10 days and with adenoviruses expressing TatHXB2 or LacZ control (5 pfu per cell). Cells infected with Ad-Tat or Ad-LacZ were collected at 24 hours and cells infected with HIV or treated  with medium were harvested at 7d and 10d post-infection. THP-Mac were infected with Ad-Tat or Ad-tTA control  for 24 hours. RNA was isolated and mRNA expression levels were analyzed by microarrays. adenovirus expressing HIV Tat  for 30 hours.  and  then RNA was isolated, labeled, and prepared for hybridization on Affymetrix microarrays.

first: Nayoung

last: Kim

first: Sami

last: Kukkonen


title: Notch2-dependent classical dendritic cells orchestrate intestinal immunity against attaching and effacing bacterial pathogens


title: HIV-1 Tat Second Exon limits the Extent of Tat-mediated Modulation of Interferon-Stimulated Genes in Antigen Presenting cells


title: LEF1 in Burkitt lymphoma

city: Regensburg

first: Katharina

last: Meyer

address: Josef Engert Street 9

department: Statistical Bioinformatics

country: Germany

institute: Institute for Functional Genomics

summary: Recently global gene expression profiling of patients samples lead to a molecular definition of Burkitt Lymphoma (BL) with lymphocyte enhancer-binding factor 1 (LEF1) as a signature gene. Here we report the discovery of nucleic LEF1 in a very high proportion of BL cases (15/18) and LEF1 target genes. Germinal center B cells were devoid of detectable nuclear LEF1 expression as mantle cell lymphoma (0/5), marginal zone lymphoma (0/6), follicular lymphoma (0/12) or diffuse large B cell lymphoma (DLBCL) (1/31). Using whole genome gene expression profiling after transient knockdown of LEF1 in BL cell lines, new LEF1 target genes were identified. The joint expression of these genes in primary BL samples shows that LEF1 is not only expressed aberrantly in BL but also transcriptionally active. Our study identified aberrantly expressed LEF1 and its target genes suggesting an important functional role in BLs.

overall_design: 3 biological replicates scrb siRNA vs LEF1 si RNA , 4 siRNA are pooled

first: N

last: Walther

first: A

last: Ulrich

first: M

last: Vockerodt

first: F

last: von Bonin

first: W

last: Klapper

first: K

last: Eberth

first: T

last: Pukrop

first: R

last: Spang

last: Trümper

first: D

last: Kube


title: A genome-wide comparative study of DNA methylation in great apes

city: Barcelona

first: Irene

last: Hernando

address: Dr Aiguader 88

country: Spain

institute: UPF/CSIC

summary: DNA methylation is an epigenetic modification involved in regulatory processes such as cell differentiation during development, X-chromosome inactivation, genomic imprinting and susceptibility to complex diseases. These changes can be inherited through generations and likely have played an important role during human evolution. We performed a comparative analysis of CpG methylation patterns between humans and all great apes (chimpanzee, bonobo, gorilla and orangutan) on a total of 32 individuals.Our analysis identified ~1,000 genes with significantly altered methylation patterns among the great apes, including ~200 with a methylation pattern unique to humans. Analysis of genes with human-specific epigenetic patterns identified enrichments for several functional categories that are key for human-specific traits, such as advanced facial expressions or equilibrium related to bipedalism. We also found a highly significant positive correlation between the genomic distance genome-wide and the methylation levels. In a pairwise comparison, we observed that ~9% (~30,000) of CpGs assayed show significant methylation differences between human and chimpanzee, including promoter regions of 879 genes (11.9% of those tested), suggesting that epigenetic changes have occurred at high frequency during recent primate evolution and represent an important substrate for adaptive modification of genome function. Epigenetic changes among primates are highly enriched for sites showing intermediate DNA methylation levels might be related to regulatory elements, and we observed a significant relationship between changes in DNA methylation and gene expression across multiple different tissues. We also identified a significant positive relationship between the rate of coding variation within genes and alterations of promoter methylation, suggesting concerted evolution between protein sequence and gene regulation. Contrastingly, our analysis also identified scores of genes that are perfectly conserved at the amino acid level between human and chimp, yet which show significant epigenetic difference between these two species. We conclude that epigenetic alterations represent an important force during primate evolution and has been systematically under explored in evolutionary comparative genomics.

sample_organism:
Gorilla gorilla gorilla
Pan paniscus
Pongo pygmaeus
Pongo abelii
Homo sapiens
Pan troglodytes schweinfurthii
Pan troglodytes troglodytes
Pan troglodytes verus
Gorilla beringei graueri

overall_design: 32 samples analyzed in total: 9 humans, 5 chimpanzees, 6 bonobos, 6 gorillas and 6 orangutans. Blood-derived DNA methylation levels were assessed using Illumina Infinium HumanMethylation450 BeadChip.  We performed a strict filtering step to remove divergent probes based on the number and location of mismatches with their target site in each species genome assembly tested, this resulted in the retention of 133,908 shared across all the species.

last: Hernando-Herraez

first: Tomas

last: Marques-Bonet

first: Andrew

last: Sharp

first: Paras

last: Garg

first: Javier

last: Prado-Martinez

first: Marcos

last: Fernandez-Callejo

first: Holger

last: Heyn

first: Christina

last: Hvilsom

first: Manel

last: Esteller


title: Expression data from long-term Ebf1-deficient, CD19+, Bcl2tg cells

city: Freiburg

first: Senthilkumar

last: Ramamoorthy

address: Stübeweg 51

department: Cellular & Molecular Immunology

institute: Max Planck Institute of Immunobiology and Epigenetics

type:
Expression profiling by array
Third-party reanalysis

summary:
An assessment of a role of Ebf1 in committed B lineage cells.
In this study, we adopted the strategy of deleting Ebf1 after reconstitution of Rag2-/-Il2rg-/- mice and found that committed pre-B cells could be converted into T cells and ILCs upon deletion of Ebf1.

overall_design:
We used µ-arrays to gain insight into changes in gene expression of CD19+ Ebf1-deficient cells.
The dataset was compared with microarray data available for different hematopoietic developmental stages (GSE15907).
The complete dataset is linked below as a supplementary file.

first: Robert

last: Nechanitzky

first: Duygu

last: Akbas

first: Stefanie

last: Scherer

first: Fabio

last: Savarese

first: Rudolf

last: Grosschedl


title: Temporal induction of immunoregulatory processes coincides with age-dependent resistance to viral-induced type 1 diabetes

city: Milwaukee

first: Martin

last: Hessner

state: WI

address: 8701 Watertown Plank Road

department: Pediatrics

institute: Medical College of Wisconsin

sample_organism:
Homo sapiens
Rattus norvegicus

platform_organism:
Homo sapiens
Rattus norvegicus

first: Yi-Guang

last: Chen

first: John

last: Mordes

first: Elizabeth

last: Blankenhorn

first: Himala

last: Kashmiri

first: Mary

last: Kaldunski

first: Shuang

last: Jia

first: Rhonda

last: Geoffrey


title: Temporal induction of immunoregulatory processes coincides with age-dependent resistance to viral-induced type 1 diabetes [human]

summary: A need exists for biomarkers in T1D that can 1) sensitively and specifically detect disease-related immune activity prior to, and independent of, measurement of auto-antibodies towards islet cell antigens; 2) define immunopathological mechanisms; and 3) monitor changes in the inflammatory state associated with disease progression or response to therapeutic intervention.  In an effort to fill this gap, we have applied a novel bioassay to both human and BB rat T1D whereby the complex milieu of inflammatory mediators present in plasma can be indirectly detected through their ability to drive transcription in peripheral blood mononuclear cells drawn from healthy, unrelated donors.  The resultant gene expressions are comprehensively measured with a microarray.  In our human studies, we find that plasma of recent-onset T1D patients induces expression of a pro-inflammatory signature consisting in part of many interleukin-1 (IL-1) regulated genes related to immunological activation and immunocyte chemotaxis compared to unrelated healthy controls.  This signature has been found to resolve in long-standing T1D subjects (>10 years post-onset), thus associating it with active autoimmunity.  Importantly, this signature has been detected in pre-onset samples of progressors to T1D years prior to onset and prior to development of auto-antibodies directed towards islet antigens.

overall_design: Fresh PBMCs of a healthy control donor were isolated by density gradient centrifugation. These cells were then stimulated with 20% plasma from a longitudinally monitored sibling of a T1D patient that progressed to T1D (n= 6 timepoints) at 37C in 5% CO2.  Gene expression analysis was perfromed in order to evaluate the transcriptional signature associated with T1D pathogenesis.

first: Xujing

last: Wang


title: Signaling pathways of HPAIV

status: Public on May 31 2013

city: Hannover

first: Dorothee

last: Viemann

state: Deutschland

address: Carl-Neuberg-Straße 1

department: Department of Pediatric Pulmonology, Allergy and Neonatology

institute: Hannover Medical School

summary:
Highly pathogenic avian influenza viruses (HPAIV) induce severe inflammation in poultry and men. There is still an ongoing threat that these viruses may acquire the capability to freely spread as novel pandemic virus strains that may cause major morbidity and mortality. One characteristic of HPAIV infections is the induction of a cytokine burst that strongly contributes to viral pathogenicity. It has been suggested, that this cytokine overexpression is an intrinsic feature of infected cells and involves hyperinduction of p38 mitogen activated protein kinase (MAPK). Here we investigate the role of MAPK p38 signaling in the antiviral response against HPAIV in mice as well as in endothelial cells, the latter a primary source for cytokines during systemic infections.
Global gene expression profiling of HPAIV infected endothelial cells in the presence of the MAP kinase p38-specific inhibitor SB202190 revealed, that inhibition of MAPK p38 leads to reduced expression of interferon (IFN) and other cytokines after A/Thailand/1(KAN-1)/2004 (H5N1) and A/FPV/Bratislava/79 (H7N7) infection. Furthermore, the expression of interferon stimulated genes (ISGs) after treatment with IFN or conditioned media from HPAIV infected cells was decreased when the target cells were preincubated with SB202190. Finally, promoter analysis confirmed a direct impact of p38 MAPK on the IFN-enhanceosome and ISG-promoter activity. In vivo inhibition of MAP kinase p38 greatly diminishes virus induced cytokine expression concomitant with reduced viral titers, thereby protecting mice from lethal infection.
These observations show, that MAPK p38 acts on two levels of the antiviral IFN response: Initially the kinase regulates IFN induction and at a later stage MAPK p38 controls IFN signaling and thereby expression of IFN-stimulated genes. Thus, inhibition of MAP kinase p38 may be an antiviral strategy that significantly protects mice from lethal influenza via suppression of overshooting cytokine expression.

overall_design: HUVEC were infected with FPV in the presence or absence of a p38 MAP kinase inhibitor

first: Yvonne

last: Börgeling


title: Effect of Tgfbr2 disruption on gene expression in the aorta of Fbn1 wild-type and Fbn1C1039G mice

city: new haven

first: qingle

last: li

state: ct

address: 10 Amistad st

institute: yale universtiy

summary: We used microarrays to characterize the global changes in gene expression within the ascending aorta of mice due to conditional disruption of TGF-β signaling in smooth muscle and/or due to heterozygous fibrillin-1 mutation.

overall_design: Myh11-CreERT2.Tgfbr2f/f (abbreviated as Cre.Tgfbr2) mice were cross-bred to Fbn1C1039G/+ (abbreviated as Fbn1C/+) mice and treated with vehicle or tamoxifen for 5 d starting at 4 wk of age to generate 4 groups of animals: 1) Cre.Tgfbr2-Veh: controls with intact TGF-β signaling and wild-type fibrillin-1 expression; 2) Cre.Tgfbr2-Tmx: conditional disruption of Tgfbr2 in smooth muscle with wild-type fibrillin-1 expression; 3) Fbn1C1039G.Cre.Tgfbr2-Veh: heterozygous expression of mutant fibrillin-1 with intact TGF-β signaling; and 4) Fbn1C1039G.Cre.Tgfbr2-Tmx: conditional disruption of Tgfbr2 in smooth muscle with heterozygous expression of mutant fibrillin-1. The animals were euthanized at 6 weeks of age and their ascending aortas (from above the coronary arteries to the first arch branch) were collected and total RNA was extracted.

first: Wei

last: Li

first: Rahmat

last: Ali

first: George

last: Tellides


title: Expression data from CD138+ cells obtained from MM patients at diagnosis

city: Bologna

first: Carolina

last: Terragna

address: Via Massarenti, 9

department: Department of Experimental, Diagnostic and Specialty Medicine - DIMES

country: Italy

institute: Institute of Hematology "L.A.Seràgnoli"

summary: Thalidomide-dexamethasone (TD) combination is an effective induction therapy for newly diagnosed multiple myeloma patients, candidates for subsequent autologous stem cell transplantation (ASCT). Since maximization of tumor response before ASCT may favorably affect the clinical outcomes, we designed a study to identify a gene expression profile (GEP) signature predictive of attainment of complete response to TD induction therapy. CD138+ bone marrow samples obtained at diagnosis from 112/311 patients were analyzed. Two subsequent time phases were planned. Firstly, a GEP supervised analysis, performed on a training set of 32 patients, allowed to identify 157 probe sets differentially expressed in complete responder + near complete responder (CR+nCR) versus ≤partial responder patients. Than, we generated an 8-gene GEP signature predicting at diagnosis the probability to achieve CR+nCR to TD induction therapy. The performance of this assay was subsequently validated in an 80 patients training set. The 8-gene signature provide a negative predictive value of 93% and a positive predictive value of 44%. The 8 genes were down-regulated in patients who achieved at least a nCR. These results could be an important first step to adopting a diagnostic assay, used to determine, at diagnosis, patients who will respond more favourably to a particular treatment strategy.

overall_design: This series of microarray experiments contains the gene expression profiles of purified plasma cells (PCs) obtained from 32 newly diagnosed multiple myeloma (MM). PCs were purified from bone marrow specimens, using CD138 immunomagnetic microbeads. The purity of the positively selected PCs was assessed by flow cytometry and was > 90% in all cases. 5 micrograms of total RNA was processed and hybridized to the Affymetrix HG U133 Plus 2.0 GeneChip following the manufacturer's instructions.

first: C

first: M

last: Renzulli

first: D

last: Remondini

first: E

last: Tagliafico

first: F

last: Di Raimondo

last: Patriarca

first: G

last: Martinelli

last: Roncaglia

first: L

last: Masini

first: P

last: Tosi

last: Zamagni

last: Tacchetti

first: A

last: Ledda

last: Brioli

last: Angelucci

first: N

last: Testoni

last: Marzocchi

last: Galieni

last: Gozzetti

last: Martello

last: Dico

last: Cavo


title: Patient-derived Human Breast Cancer Xenografts

status: Public on May 30 2013

city: Houston

first: Chad

middle: A.

last: Shaw

state: TX

address: 1 Baylor Plaza

department: Molecular and Human Genetics

institute: BCM

summary: Breast cancer research is hampered by difficulties in obtaining and studying primary human breast tissue, and by the lack of in vivo preclinical models that reflect patient tumor biology accurately. To overcome these limitations, we propagated a cohort of human breast tumors grown in the epithelium-free mammary fat pad of SCID/Beige and NOD/SCID/IL2γ-receptor null (NSG) mice, under a series of transplant conditions.  Both models yielded stably transplantable xenografts at comparably high rates (~23% and ~19%, respectively). Of the conditions tested, xenograft take rate was highest in the presence of a low-dose estradiol pellet. Overall, 32 stably transplantable xenograft lines were established, representing unique 25 patients. Most tumors yielding xenografts were “triple-negative” (ER-PR-HER2+) (n=19). However, we established lines from three ER-PR-HER2+ tumors, one ER+PR-HER2-, one ER+PR+HER2- and one “triple-positive” (ER+PR+HER2+) tumor. Serially passaged xenografts show biological consistency with the tumor of origin, are phenotypic stability across multiple transplant generations at the histological, transcriptomic, proteomic, and genomic levels, and show comparable treatment responses. Xenografts representing 12 patients, including two ER+ lines, showed metastasis to the mouse lung. These models thus serve as a renewable, quality-controlled tissue resource for preclinical studies investigating treatment response and metastasis.

overall_design: The study was designed to determine how stable patient-derived xenografts are across multiple transplant generations in mice, and to determine how closely xenografts established with pre-treatment samples cluster with xenografts established with post-treatment samples. Overall, pre-treatment and post-treatment samples derived from the same patient cluster together, and multiple transplant generations of xenografts derived from an individual patient cluster together.

first: Michael

middle: T

last: Lewis

middle: A


title: Expression data from 45 Month Slovak Children with high POPs exposure

city: Washington DC

first: Sisir

middle: K.

last: Dutta

state: DC

address: 415 College Street, NW

department: Biology

institute: Howard University

summary:
Exposure to Persistant Organic Pollutants (POPs) is known to cause serious health effects in human but the gene expression profiles leading to development of differnet diseases and disorders are not fully understood. The knowledge of global gene expression will help us to devlop early disease or disorder biomarkers for POP induced health effects.
We used microarrays to detail the global gene expression profile underlying the effects of high POP exposure to Slovak 45 month children leading to identification of distinct classes of up-regulated and down-regulated genes and cellular processes.

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

first: Somiranjan

last: Ghosh

first: Partha

last: S. Mitra

middle: K

first: Tomas

last: Trnovec

first: Lubica

last: Pulkovicova

first: Eric

middle: P

last: Hoffman

first: Irva

last: Hertz-Picciotto

first: Dean

last: Sonneborn

first: Svetlana

last: Ghimbovschi


title: Expression data from immortalized human lung small airway epithelial cells

status: Public on May 29 2013

city: Tokyo

first: Masato

last: Enari

address: 5-1-1 Tsukiji

institute: National Cancer Center

summary:
In lung cancer progression, p53 mutations are more often observed in invasive tumors than in non-invasive tumors, suggesting that p53 is involved in tumor invasion and metastasis. To understand the nature of p53 function as a tumor suppressor, it is crucial to elucidate the detailed mechanism of the alteration in epithelial cells, the main origin of solid tumors, following p53 inactivation.
To elucidate the mechanism by which p53 loss enhances invasive and motile activities in human lung small airway epithelial cells (SAECs), we performed comprehensive expression profiling analyses between p53 knockdown and control cells using GeneChip Human Genome U133 plus 2.0 arrays.

overall_design: SAECs were infected with lentiviruses for the expressions of CDK4 devoid of binding ability to p16INK4A, Cyclin D1 and TERT to generate immotalized SAECs. At 18 population doublings, immortalized SAECs were transfected with the siRNAs (si-control, si-p53-#1 or si-p53-#2) and used for RNA extraction and hybridization on Affymetrix microarrays.

first: Hitoshi

last: Ichikawa


title: Expression data of Enterohemorrhagic E. coli O157:H7 (EHEC) strain 86-24 when cultured with Bacteroides thetaiotaomicron VPI-5482

city: Dallas

first: Meredith

middle: Mathis

last: Curtis

address: 6000 Harry Hines Blvd

department: Microbiology

institute: University of Texas Southwestern Medical Center

summary:
Regulation of EHEC gene expression by the gut commensal bacterium B. thetaiotaomicron. EHEC is a human pathogen that colonizes in the colon where B. thetaiotaomicron is a predominant commensal.
We used microarrays to evaluate global regulation of EHEC when cultured with B. thetaiotaomicron.

overall_design: EHEC and B. thetaiotaomicron were co-cultured in vitro under strict anaerobic conditions in low-glucose Dulbecco's modified Eagle's medium (DMEM). Total RNA from bacteria grown to mid-logarithmic phase was extracted and hybridized to an Affymetrix E. coli 2.0 gene chip according to manufacturer's specifications: http//www.affymetrix.com/support/technical/manual/expression_manual.affx

first: Vanessa

last: Sperandio


title: Expression data by telomere elongation

city: Koto-ku

first: kyotaro

last: HIRASHIMA

state: Tokyo

address: 3-8-31 Ariake

department: Cancer Chemotherapy Center

institute: The JFCR-Cancer Inst.

summary: Limitless reproductive potential is one of the hallmarks of cancer cells1. This ability is accomplished by maintaining telomeres, which erosion otherwise causes cellular senescence or death. Human cancer cells often maintain shorter telomeres than do cells in surrounding normal tissues2-5. While most cancer cells activate telomerase, which can elongate telomeres6, it remains elusive why cancer cells keep telomeres short. Here we show that forced elongation of telomeres in cancer cells promotes their differentiation in a tumor microenvironment in vivo. We elongated telomeres of human prostate cancer PC-3 cells, which possess short telomeres7, by enhancing their telomerase activity. The resulting cells with long telomeres retain an ability to form tumors in a mouse xenograft model. Strikingly, these tumors exhibit many duct-like structures and reduced N-cadherin expression, reminiscent of well-differentiated adenocarcinoma. These phenotypic changes are caused by telomere elongation per se but not enhanced telomerase activity. Gene expression profiling revealed that telomere elongation correlates with inhibition of cell-cycle processes. Together, our results suggest a functional contribution of short telomeres to tumor malignancy by regulating cancer cell differentiation.

overall_design: Two samples are telomere-elongated cells, both in the presence and absence of the exogenous hTERT. The other two samples are control cell lines.

first: Kyotaro

last: Hirashima

first: Hiroyuki

last: Seimiya


title: Expression data from immature dendritic cells (iDC) expressing HIV-1 Tat alleles and mutants

first: NAYOUNG

last: KIM

summary:
HIV-1 Tat induces the expression of interferon (IFN)-inducible genes in immature dendritic cells (iDC) in the absence of IFN production. We evaluated how three alleles of Tat and some Tat mutants differ in cellular gene modulation and whether a similar gene induction pattern could be detected by treating cells with IFN’s.  The three alleles and mutants, with the exception of mutants TatSF21-47 and TatSF2G48-R57A that do not localize in the nucleous, modulated to different degrees IFN-inducible genes without concomitant induction of IFN’s. The first exon TatSF21-72 and the minimal transactivator TatSF21-58, all induced genes to a significantly greater extent than full-length Tat. The 2nd exon appears to diminish the gene modulation that can be observed when the first exon alone is expressed.
We investigated the effect of various Tat alleles and mutants on host cell gene expression in immature dendritic cells (iDC). The cells were infected with adenoviruses expressing the Tat constructs.

overall_design: The Tat alleles and mutants are under a tetracycline inducible promoter and are expressed only in cells co-infected with Ad-tTA, which expresses the tetracycline responsive transactivator. 10e6 iDC were infected with 5 plague forming units per cell of the adenoviruses and cells were collected  10 and 20 hours post-infection. RNA was isolated and mRNA expression levels were analyzed by microarrays. As controls we used cells that were left uninfected and cells that were infected with Ad-LacZ, which expresses beta-galactosidase.

first: Nayoung

last: Kim

first: Sami

last: Kukkonen

first: Anna

last: Aldovini


title: Identification of a predictive gene signature to recMAGE A3 antigen-specific cancer immunotherapy in metastatic melanoma and non-small-cell lung cancer

city: Rixensart

first: Fernando

last: Ulloa Montoya

address: rue de l'Institut, 89

country: Belgium

institute: GlaxoSmithKline Biologicals

summary:
Purpose:  To evaluate the presence of a gene expression signature present before treatment as predictive of response to treatment with MAGE‑A3
immunotherapeutic in metastatic melanoma patients and to validate its predictivity in adjuvant therapy of early-stage lung cancer.

overall_design:
Patients were participants in two Phase II studies of the recombinant MAGE‑A3 antigen combined with immunological adjuvants.  mRNA from tumor samples (biopsies) collected before MAGE-A3 immunotherapy was analyzed by microarray hybridization and by quantitative polymerase chain reaction (qRT-PCR).  The melanoma microarray dataset was used to discover and crossvalidate a gene expression signature and classifier discriminative of Responders (R) versus Non-Responders (NR) patients; the gene signature and classifier were then applied to an adjuvant lung cancer study. Patients that were not included for analysis are denoted as NE (Non-evaluable).
GSK Biologicals

first: Benjamin

last: Dizier

last: Ulloa-Montoya

first: Frédéric

middle: F

last: Lehmann

first: Jamila

last: Louahed

first: Olivier

last: Gruselle

first: Vincent

last: Brichard


title: Reversal of glucocorticoid resistance by AKT inhibition in T-ALL

city: Utrecht

first: Jules

last: Meijerink

address: Uppsalalaan 8

institute: Princess Máxima Center for Pediatric Oncology

summary: Glucocorticoid resistance is a major driver of therapeutic failure in T-cell acute lymphoblastic leukemia  (T-ALL). Here we used a systems biology approach, based on the reverse engineering of signaling regulatory  networks, which identified the AKT1 kinase as a signaling factor driving glucocorticoid resistance in T-ALL.  Indeed, activation of AKT1 in T-ALL lymphoblasts impairs glucocorticoid-induced apoptosis. Mechanistically,  AKT1 directly phosphorylates the glucocorticoid receptor NR3C1 protein at position S134 and blocks  glucocorticoid-induced NR3C1 translocation to the nucleus. Consistently, inhibition of AKT1 with MK-2206  increases the response of T-ALL cells to glucocorticoid therapy both in T-ALL cell lines and in primary patient  samples thus effectively reversing glucocorticoid resistance in vitro and in vivo. These results warrant the  clinical testing of ATK1 inhibitors and glucocorticoids, in combination, for the treatment of T-ALL.

overall_design: This study includes 228 T-ALL samples of which 117 samples are re-analysis of GSE26713.

first: Rob

last: Pieters


title: Expression data by telomere elongation in vivo (xenograft)

overall_design: Two cell lines are telomere-elongated cells, both in the presence and absence of the exogenous hTERT. The other two lines are control PC-3 cell lines. We extracted RNA from four independent xenograft tumors per original cell line.


title: Identification of Sp1 targets involved in proliferation and cancer

first: Carlos

last: Ciudad

state: Barcelona

address: Av. Juan XXIII-27

department: Biochemistry and Molecular Biology

institute: University of Barcelona

summary: Sp1 is a transcription factor able to regulate many genes through its DNA binding domain, containing three zinc fingers. We were interested in identifying target genes regulated by Sp1, with a special emphasis to those involved in proliferation and cancer. Our approach was to treat HeLa cells with a siRNA directed against Sp1 mRNA (siSp1) to decrease the expression of Sp1 and, in turn, the genes activated by this transcription factor. Sp1 siRNA treatment led to a great number of differentially expressed genes as determined by whole genome cDNA microarray analysis.  Underexpressed genes were selected since they represent putative genes activated by Sp1. These underexpressed genes were classified in six Gene Onthology categories, namely proliferation and cancer, mRNA processing, lipidic metabolism, glucidic metabolism, transcription and translation. Putative Sp1 binding sites were found in the promoters of the selected genes using the MatchTM software. After literature mining, 11 genes were selected for further validation of their expression levels using RT-real time PCR. Underexpression was confirmed for the 11 genes plus Sp1 in HeLa cells after siSp1 treatment. Additionally, EMSA and chromatin immunoprecipitation assays were performed to test for binding between Sp1 and the promoters of these genes. We observed binding of Sp1 to the promoters of RAB20, FGF21, IHPK2, ARHGAP18, NPM3, SRSF7, CALM3, PGD and Sp1 itself. Finally, the mRNA levels of RAB20, FGF21 and IHPK2, three genes related with proliferation and cancer, were determined after overexpression of Sp1 in HeLa cells, to confirm their relationship with Sp1.

overall_design: The aim of our study was to evaluate, by using whole genome microarrays, the effects of a siRNA against the transcription factor of Sp1 in HeLa cells. Using this methodology genes activated by Sp1 could be downregulated. The obtective was to determine new genes regulated at the cellular level. Triplicate samples were hybridized for each experimental condition (6 samples in total). The samples provided were analyzed using the specific software GeneSpring GX.

first: Sabine

last: Welten

first: Audrey

last: Belloc

first: Carlota

last: Oleaga

last: Sole

first: Nuria

last: Mencia

first: Elisabet

last: Selga

first: Alicia

last: Tapias

first: Veronique

last: Noe


title: Comparison of gene expression profiles of HT29 cells treated with Instant Caffeinated Coffee or Caffeic Acid versus control.

summary:
A summary of the work associated to these microarrays is the following:

Background: Phenolic compounds present in coffee are antioxidants in vitro that might protect against cardiovascular disease and certain types of cancer in humans.
Objective: Our aim was to identify differentially expressed genes upon incubation of HT-29 human colon cancer cells with instant caffeinated coffee (ICC) or caffeic acid (CA) using microarrays.
Results: In HT-29 cells incubated with ICC, 77 genes were overexpressed whereas 162 were underexpressed. Upon incubation with CA, 12 genes were overexpressed whereas 33 were underexpressed. A list of five overexpressed genes and eleven underexpressed genes were found in common between the two conditions and was use to construct a biological association network. In the generated network, STAT5B and ATF-2 appeared as highly interconnected nodes. STAT5B overexpression was confirmed at the mRNA and protein levels. For ATF-2, the changes in mRNA levels were confirmed for both ICC and CA, whereas the decrease in protein levels was only observed in CA-treated cells. The levels of cyclin D1, a target gene for both STAT5B and ATF-2 transcription factors, decreased dramatically in breast cancer cells treated with CA or ICC.
Conclusions: Coffee polyphenols are able to affect gene expression in cancer cells through the modulation of STA5B and ATF-2 transcription factors.

overall_design: The aim of our study was to evaluate, by using whole genome microarrays, the effects of one cup of coffee, either regular caffeinated coffee or a coffee polyphenol, such as caffeic acid, on HT-29 gene expression, Three experimental approaches were conducted to assess the effects of coffee on HT29 cells. I) Incubation with non cytotoxic concentrations of ICC (7 µg/mL) for 24h. (Group ICC); II) Incubation with non cytotoxic concentrations of CA (1.68 µg/mL) for 24h. (Group CA); III) non treatment of HT-29 to refered as a control (Group CNT). Triplicate samples were hybridized for each experimental condition (9 samples in total). The samples provided were analyzed using the specific software GeneSpring GX.

first: Maria

last: Izquierdo-Pulido


title: Global gene expression analysis of amniotic fluid cell-free RNA from recipient twins with twin-twin transfusion syndrome [Set 1]

status: Public on May 28 2013

city: Medford

first: Heather

middle: C

last: Wick

address: 161 College Ave

department: Department of Computer Science

institute: Tufts University

summary:
To understand the biological pathways involved in twin-twin transfusion syndrome (TTTS) by performing global gene expression analysis of amniotic fluid (AF) cell-free RNA
Analysis of paired data from TTTS cases and controls revealed differential expression of 801 genes, which were significantly enriched for neurological disease and cardiovascular system pathways. We also identified cardiovascular genes and pathways associated with the presence of critically abnormal Doppler measurements in Stage III TTTS recipients.

overall_design: Prospective whole transcriptome microarray study analyzing cell-free RNA in AF from TTTS recipient twins and singleton controls. Significantly differentially-regulated genes in TTTS cases (N= 8) vs. matched controls (N = 8) were identified and pathways analyses performed. Significant gene expression differences between Stage II TTTS recipients (N = 5) and Stage III TTTS recipients with abnormal Doppler measurements (N = 5) were also analysed.

first: Lisa

last: Hui

first: Kenneth

last: Moise Jr

first: Anthony

last: Johnson

first: Francois

last: Luks

first: Sina

last: Haeri

first: Kirby

middle: L

first: Diana

last: Bianchi


title: Expression profiling of glioblastoma cancer stem cells

city: Cambridge

first: Esther

last: Rheinbay

address: 7 Cambridge Center

institute: Broad Institute

summary: Glioblastoma (GBM) is thought to be driven by a sub-population of cancer stem cells (CSCs) that self-renew and recapitulate tumor heterogeneity, yet remain poorly understood. Here we present a comparative epigenomic analysis of GBM CSCs that reveals widespread activation of genes normally held in check by Polycomb repressors. These activated targets include a large set of developmental transcription factors (TFs) whose coordinated activation is unique to the CSCs. We demonstrate that a critical factor in the set, ASCL1, activates Wnt signaling by repressing the negative regulator DKK1. We show that ASCL1 is essential for maintenance and in vivo tumorigenicity of GBM CSCs. Genomewide binding profiles for ASCL1 and the Wnt effector LEF1 provide mechanistic insight and suggest widespread interactions between the TF module and the signaling pathway. Our findings demonstrate regulatory connections between ASCL1, Wnt signaling and collaborating TFs that are essential for the maintenance and tumorigenicity of GBM CSCs.

overall_design: Two replicates for MGG4, MGG6, MGG23 and NS; four replicates for MGG8

first: E

first: A

middle: S

last: Chi

first: C

last: Epstein

first: B

middle: E

last: Bernstein


title: Histone modification and TF ChIP-Seq for glioblastoma cell lines and neural stem cells

type: Genome binding/occupancy profiling by high throughput sequencing

overall_design: Histone modification profiling for multiple marks by ChIP-Seq in untreated glioblastoma cancer stem cells, glioblastoma non-stem cells and neural stem cells

first: M

last: Suvà

first: S

middle: M

last: Gillespie


title: Global gene expression analysis of amniotic fluid cell-free RNA from recipient twins with twin-twin transfusion syndrome [Set 2]


title: The Y chromosome as a regulatory element shaping immune cell transcriptomes and susceptibility to autoimmune disease

city: Burlington

first: Laure

last: Case

address: 89 Beaumont Ave

institute: University of Vermont

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

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

platform_organism:
Mus musculus
synthetic construct

overall_design: Refer to individual Series


title: Effects of Thyroxine Exposure on Osteogenesis in Mouse Calvarial Pre-Osteoblasts

city: Augusta

first: James

last: Cray Jr.

institute: Georgia Regents University

summary: Thyroid hormone has a positive effect on endochondral bone growth. Few studies have looked at the interaction between thyroid hormone exposures and intramembranous bone derived cells. We used microarray as one tool to determine the gene expression profile of intramembranous (calvarial) derived murine pre-osteoblsts after thyroxine exposure.

overall_design: We isolated whole RNA from MC3T3-E1 cells treated with proliferation media or proliferation media with thyroxine at a dose of 10^-6 mol./liter for 3 or 7 days in culture. We then used an Affymetrix array and compared expression profiles between control and experimental treatments.


title: Gene expression data from T-cell progenitors developing in response to DLL4 stimulation in the plastic thymus

city: Basel

first: Nadine

last: Gehre

department: Biomedicine

country: Switzerland

institute: University Basel

summary:
Since the first description of the involvement of Notch signaling in homeostasis especially of T cells, there is great effort in research to find new target genes of Notch that are involved in T cell development in the thymus. We developed a stroma cell free system that is able to induce T cell development in vitro called the plastic thymus. Having this new tool we decided to use the gene expression technique to get an expanded and more global picture of the changes in gene expression in T cell progenitor induced by Notch signaling via DLL4-Fc.
We used microarrays to detail the global programme of gene expression in developing T-cell progenitors induced by Notch signaling.

overall_design: T cell progenitors generated in the plastic thymus, defined as CD93 lo, c-Kit+ cells were sorted on day 5, RNA was isolated and gene expression was analyzed using Affymetrix GeneChip Mouse Gene 1.0 ST Array. PC5B7 cultured with IL7 and SCF were stimulated with 2 μg/ml plate bound DLL4-Fc and compared to cells cultured without the Notch ligand.

first: Antonius

last: Rolink

first: Corinne

last: Engdahl


title: Identification of metastasis associated genes in clear cell renal cell carcinoma

status: Public on May 25 2013

city: Beijing

first: xu

last: zhang

address: Fuxing road

institute: PLA general hospital

summary:
This study investigates the genes that promote clear cell renal cell carcimoma (ccRCC) metastasis using 4 primary metastatic and 5 non-metastatic tumor samples.
U133 plus 2.0 array was used to identify the diffrently expressed genes between the primary metastatic and non metastatic ccRCC samples

overall_design: To identify differences in gene expression assoctiated with ccRCC metastasis, 4 primary metastatic and 5 non-metastatic ccRCC samples were used to perform expression profiling.

first: Xu

last: Zhang

first: Xin

last: Ma

first: Dong

last: Ni

first: Hong-zhao

last: Li

first: Yu

last: Gao


title: Breast Cancer Gene Expression Analysis

status: Public on May 26 2013

city: Dublin

first: Colin

last: Clarke

address: Collin's Av.

department: NICB

country: Ireland

institute: Dublin City University

summary:
Analysis of 104 breast cancer biopsies (removed prior to any treatment with tamoxifen or chemotherapeutic agents) from patients aged between 31 years and 89 years at the time of diagnosis (mean age = 58 years). Twenty were less than 50 years and seventy-seven women were 50 years, or older, at diagnosis. The size of the tumours ranged between 0.6 cm and 8.0 cm (mean = 2.79 cm). Eighteen tumours were T1 (<2 cm) in maximal dimension; 83 were T2 (2–5 cm) and 3 tumours were T3 (>5 cm). Eighty-two were invasive ductal carcinoma, 17 were invasive lobular and five were tumours of special type (two tubular and three mucinous). Eleven tumours were grade 1; 40 were grade 2; and 53 were grade 3. Sixty-seven tumours were oestrogen receptor (ER) positive and 34 were ER negative (ER status was determined by Enzyme Immuno-Assay (EIA); a positive result was defined as more than 200 fmol/g protein). ER status was not available for 3 patients. Forty-five tumours had no axillary metastases and 59 tumours had metastasised to axillary lymph nodes. Sixty-nine women were treated with post-operative tamoxifen; 26 did not receive tamoxifen. Fifty patients were treated with adjuvant systemic chemotherapy (CMF +/− adriamycin); 45 patients did not receive chemotherapy. Details regarding tamoxifen and systemic chemotherapy were not available for 9 patients. Maximal follow-up was 3,026 days with a mean follow-up of 1,887 days.
17 normal breast tissues were also assayed.

overall_design: Gene expression profiling of 104 breast cancer and 17 normal breast biopsies.

first: Stephen

last: Madden

first: Padraig

last: Doolan

first: Helena

last: Joyce

first: Sinead

last: Aherne

first: Lorraine

last: O' Driscoll

first: William

last: Gallagher

first: Bryan

last: Hennesy

first: Michael

last: Moriarty

first: John

last: Crown

first: Susan

last: Kennedy

first: Martin

last: Clynes


title: Epigenomic profiling of glioblastoma stem cells

first: Esther

last: Rheinbay


title: "Off-context" gene expression in lung cancer identifies a group of metastatic-prone tumors

status: Public on May 24 2013

city: La Tronche

first: Sophie

last: Rousseaux

address: Bd de la Chantourne

department: IAB

institute: INSERM-UGA

summary: An unexplored consequence of epigenetic alterations associated with cancer is the ectopic expression of tissue-restricted genes. Here, a new strategy was developed to decipher genome-wide expression data in search for these “off-context” gene activations, which consisted first, in identifying a large number of tissue-specific genes normally epigenetically silenced in most somatic cells and second, in using them as cancer biomarkers on an “on/off” basis. Applying this concept to analyze whole-genome transcriptome data in lung cancer, we discovered a specific group of 26 genes whose expression was a strong and independent predictor of poor prognosis in our cohort of 293 lung tumours, as well as in two independent external populations. In addition, these 26 classifying genes enabled us to isolate a homogenous group of metastatic-prone highly aggressive tumours, whose characteristic gene expression profile revealed a high proliferative potential combined to a significant decrease in immune and signaling functions. This work illustrates a new approach for a personalized management of cancer, with applications to any cancer type.

overall_design:
This study is part of the Cartes d'Identite des Tumeurs (CIT) program from the french Ligue Nationale Contre le Cancer (http://cit.ligue-cancer.net).

293 lung tumor samples and 14 non-tumoral lung samples were analyzed.

first: Alexandra

last: Debernardi

first: Baptiste

last: Jacquiau

first: Anne-Laure

last: Vitte

first: Aurore

last: LeBescont

first: Aurelien

last: Vesin

first: Hélène

last: Nagy-Mignotte

first: Denis

last: Moro-Sibilot

first: Pierre-Yves

last: Brichon

first: Sylvie

last: Lantuejoul

first: Mary

last: Callanan

first: David

middle: G

last: Beer

first: Jean-François

last: Timsit

first: Christian

last: Brambilla

first: Elisabeth

first: Saadi

last: Khochbin

last: De Reynies


title: Vector-transduced neurons transcriptome profiles

status: Public on May 22 2013

city: Rome

first: Valerio

last: Licursi

address: via degli Apuli, 4

department: c/o Dept. Biology and Biotechnologies "C. Darwin", Sapienza University of Rome

institute: Institute of Molecular Biology and Pathology (IBPM), National Research Council (CNR)

summary:
With the goal of specifically dissecting the toxicogenomic signatures of the helper-dependent (HD) human (HAd5) and canine (CAV-2) adenovirus, the VSV-G-pseudotyped SIN HIV-1 (LV) and the Adenoviral-associated vector 2/9 for human neurons (AAV2/9), we transduced a bona fide human neuronal system with HD-HAd5, HD-CAV-2, LV and AAV2/9, we analysed the transcriptional response of more than 47,000 transcripts using gene chips.
Chip data showed that HD-CAV-2 and LV vectors both activated the innate arm of the immune response, including Toll-like receptors and hyaluronan circuits. LV vector induced as well an IFN response. Moreover, HD-CAV-2 and LV vectors affected DNA damage pathways - at 5 days in opposite directions - suggesting a differential response of the p53 and ATM pathways to the vector genomes. As a general response to the vectors, human neurons activated pro-survival genes and neuron morphogenesis.

overall_design: Total RNAs extracted from transduced hmNPCs cells at 2 h and 5 days post-infection with HD-HAd, HD-CAV-2, LV and AAV2/9 vectors were hybridizated on Affymetrix microarrays and paired pair wise comparisons were performed between the mock and vector transduced hmNPCs cells. Each condition was tested in three replicates.

first: Stefania

last: Piersanti

first: Letizia

last: Astrologo

first: Rossella

last: Costa

first: Enrica

last: Roncaglia

first: Aurelie

last: Gennetier

first: Sandy

last: Ibanes

first: Miguel

last: Chillon

first: Rodolfo

last: Negri

first: Enrico

last: Tagliafico

first: Eric

last: Kremer

first: Isabella

last: Saggio


title: Human gastric cancer cells MKN28 gene expression results: MKN28 cells vs. MKN28 cells with transcription factor Sox2 overexpression

city: Xi'an

first: Wang

last: Simeng

address: Changle Road

department: Xijing Hospital of Digestive Diseases

institute: Fourth Military Medical University

summary: Gene expression profiling of gastric cancer cells MKN28 infected with Sox2 lentivirus comparing with MKN28 infected with control lentivirus

overall_design: Transfected cell lines, MKN28-Sox2 vs. MKN28-NC

first: Simeng

last: Wang

first: Jun

last: Tie


title: Global gene expression analysis of amniotic fluid cell-free RNA from recipient twins with twin-twin transfusion syndrome

first: Heather

last: Wick

first: Lisa

last: Hui

first: Kenneth

last: Moise Jr

first: Anthony

last: Johnson

first: Francois

last: Luks

first: Sina

last: Haeri

first: Kirby

first: Diana

last: Bianchi


title: Lymph node CD4+ T cell expression data from naïve C57BL/6J and C57BL/6J-ChrY^SJL

status: Public on May 17 2013

first: Laure

last: Case

summary: Understanding the DNA elements that constitute and control the regulatory genome is critical for the appropriate therapeutic management of complex diseases. Here, using chromosome Y (ChrY) consomic mouse strains on the C57BL/6J background, we show that susceptibility to two diverse animal models of autoimmune disease, including experimental allergic encephalomyelitis (EAE) and experimental myocarditis, correlates with the natural variation in copy number of Sly and Rbmy multicopy ChrY genes. In the B6 background, ChrY possesses gene regulatory properties that impact both genome-wide gene expression and the presence of alternative splice variants in pathogenic CD4+ T cells compared to CD4+ T cells. An inverse correlation exists between the number of Sly and Rbmy ChrY gene copies and the number of significantly upregulated genes in immune cells, thereby supporting a link between copy number variation of Sly and Rbmy and the ChrY genetic element exerting regulatory properties. Thus, these data establish ChrY as a member of the regulatory genome in mammals due to its ability to regulate gene expression and alternative splicing in immune cells linked to disease.

overall_design: Three biological replicates for each strain were pooled from the axillary, brachial, and inguinal lymph nodes from 5 mice for each replicate. RNA was isolated from CD4+TCRB+ FAC sorted cells.

first: Emma

middle: H

last: Wall

first: Julie

last: Dragon

first: Naresha

last: Saligrama

first: Dimitry

middle: N

last: Krementsov

first: Mohamad

last: Moussawi

first: James

last: Zachary

first: Sally

last: Huber

first: Elizabeth

last: Blankenhorn

first: Cory

last: Teuscher


title: Expression data from immortal and senescence-programmed Huh7 clones

status: Public on May 23 2013

city: Ankara

first: Mehmet

last: Ozturk

address: Faculty of Science Building

department: BilGen Genetics and Biotechnology Research Center

country: Turkey

institute: Bilkent University

summary:
Cellular senescence is a tumor suppressor mechanism, and immortalization facilitates neoplastic transformation. Both mechanisms may be highly relevant to hepatocellular carcinoma (HCC) development and its molecular heterogeneity. Cellular senescence appears to play a major role in liver diseases. Chronic liver diseases are associated with progressive telomere shortening leading senescence that is observed highly in cirrhosis, but also in some HCC. We previously described the generation of immortal and senescence-programmed clones from HCC-derived Huh7 cell line.
We used microarrays to detail the global programme of gene expression profiles of immortal and senescent-programmed clones.

overall_design: Immortal C11I and G11I clones were tested after PD 150. Senescence-programmed clones were tested at proliferating presenescent (C3P, G12P) and senescent (C3S, G12S) stages. Proliferating presenescent cells were tested at PD 20-30 with >85% BRDU positivity, and senescent cells were <5% BRDU positive and >50% SABG positive. The clones were plated in triplicate and subjected to RNA extraction.

first: M


title: Oncogenic SDH mutation underlies global epigenomic instability in gastrointestinal stromal tumor

city: Bethesda

first: Yuelin

middle: Jack

last: Zhu

state: MD

address: 9000 Rockville Pike

department: Genetics Branch, Center for Cancer Research

institute: NCI

summary: We have discovered a striking connection between mitochondrial dysfunction and epigenomic instability, manifested by global biallelic DNA cytosine 5-methylation and loss of 5-hydroxymethycytosine within succinate dehydrogenase (SDH)-null gastrointestinal stromal tumors (GIST) relative to those bearing KIT or PDGFRA tyrosine kinase driver mutations. The duality of Krebs versus kinase molecular and epigenomic profiles in GIST provides compelling evidence linking mitochondrial process to nuclear structure and function and underscores an essential role for succinate metabolism in the maintenance of epigenomic programming and tumor suppression.

overall_design:
Illumina GoldenGate Methylation Cancer Panel I:  Bisulfite-converted DNA from 144 samples were analyzed with the Illumina GoldenGate Methylation Cancer Panel I array.
Illumina HumanMethylation450 BeadChip: Bisulfite-converted gDNAs from 76 samples were analyzed with the Illumina 450K Infinium Methylation assay.

first: J

last: Killian

first: Su

middle: Y

last: Kim

first: Markku

last: Miettinen

first: Carly

last: Smith

first: Maria

last: Tsokos

first: Martha

last: Quezado

first: William

middle: I

first: Mona

last: Jahromi

first: Robert

last: Walker

first: Jerzy

last: Lasota

first: Zengfeng

last: Wang

first: Laura

last: Jones

first: Joshua

middle: J

last: Waterfall

middle: D

last: Schiffman

first: Maureen

last: O’Sullivan

first: Constantine

last: Stratakis

first: Lee

last: Helman

first: Paul

last: Meltzer


title: Epigenetic determinants of muscle stem cell quiescence and chronological aging

city: Palo Alto

first: Ling

last: Liu

address: 300 Pasteur Drive

institute: Stanford University

summary: Skeletal muscle is a post-mitotic tissue that exhibits an extremely low turnover in the absence of disease or injury. At the same time, muscle possesses remarkable regenerative capacity mediated by satellite cells (SCs) that reside in close association with individual myofibers, underneath the fiber’s basal lamina. Consistent with the low turnover of the muscle, SCs in adult animals are mitotically quiescent and therefore provide an excellent model to study stem cell quiescence. As an organism grows older, the resident stem cells are exposed to a deteriorating environment and experience chronological aging. In stem cells with high turnover, the effects of chronological aging are superimposed upon the effects of the replicative aging that results from DNA replication and cell division. On the contrary, SCs experience minimal replicative aging due to their low turnover. They are thus a good model to study the consequence of chronological aging of quiescent stem cells. We performed microarray analysis of quiescent and activated SCs from both young and aged mice to understand the global gene expression profile underlying stem cell properties such as quiecence and self-renewal, and to understand how the transcriptome of a quiescent stem cell pouplation changes with age.

overall_design: VCAM+/CD31-/CD45-/Sca1- quiescent satellite cells (QSCs) were isolated by FACS from hindlimb muscle of uninjured 2-3- or 22-24-month old mice. Activated satellite cells (ASCs) were isolated from hindlimb muscles of BaCl2-injured mice of the same age 36, 60 and 84 hours after injury using the same cell surface marker combination. YFP-expressing cells were isolated from 2-3-month old Pax7CreER/+; ROSA26eYFP/+ mice in which satellite cells are labeled geneticall by YFP expression. Total RNA was extracted from cells with the Trizol reagent according to manufacturer's instructions. RNA was then processed and assayed with Affymetrix Mouse Gene 1.0 ST arrays.

first: Tom

last: Cheung

first: Thomas

last: Rando


title: Expression data from cirrhosis and HCC tissue samples

first: Mehmet

last: Ozturk

summary:
Hepatocellular carcinoma (HCC) is the fifth most-common cancer worldwide causing nearly 600,000 deaths esch year. Approximately 80% of HCC develops on the background of cirrhosis.It is necessary to identify novel genes involved in HCC to implement new diagnostic and treatment options. However, the molecular pathogenesis of HCC largely remains unsolved. Only a few genetic alterations, namely those affecting p53, β-catenin and p16INK4a have been implicated at moderate frequencies of these cancers. Early detection of HCC with appropriate treatment can decrease tumor-related deaths
We used microarrays to detail the global programme of gene expression profiles of cirrhosis and tumor liver samples.

overall_design: 15 cirrhosis and 15 HCC samples were collected with informed constent of each patient. Surgically resected tissues were snap frozen in liquid nitrogen and stored at -80C, and subjected to RNA extraction. Histology slides were prepared for all samples and scored by an experienced scientist. For the tumor samples, tissues were resected from inside the tumor, while tissues were resected from adjacent tissue sorrounding the tumor for non-tumor samples.

first: M


title: Expression data from 5-week-old mouse prostate

status: Public on May 15 2013

city: Athens

first: Xuanyang

last: Li

address: 315 Riverbend Rd

department: Biochemistry&Molecular Biology

institute: University of Georgia

summary:
Heparan sulfate (HS) is a linear, sulfated polysaccharide, and expresses abundantly in prostate and PCa tissues. Intriguingly, the HS content and sulfation modifications appear to increase when the prostate becomes malignance, suggesting that HS may critically modulate PCa pathogenesis.
We specifically ablated Ext1, the enzyme that initiates HS biosynthesis, in mouse prostate at late development stage. And used microarray to detail the gene expressions affected by Ext1 ablation and identified distinct classes of up-regulated genes during this process.

overall_design: Prostate tissues were removed from euthanized mice at 5 weeks old for RNA extraction and hybridization on Affymetrix microarrays. We sought to compare gene expression during tumorigenesis among the wildtype, prostate specific knockout of Pten and double knockout of Pten and Ext1 in prostate.

first: Lianchun


title: HGAL Enhances BCR-mediated Syk Activation, Leading to Lymphoid Hyperplasia and Amyloidosis

city: Houston

first: Michael

middle: R

last: Green

address: 1515 Holcombe Blvd, Unit 903

department: Lymphoma/Myeloma

institute: MD Anderson Cancer Center

summary: Gene expression data from CD22+B220+ FACS-purified splenocytes of adult Sca1-HGAL knock-in CBAxC57BL/6J mice or wild-type littermates.

overall_design: Transgenic mice expressing HGAL (GCET2) under control of the Sca1 (Ly-6E.1) promoter were generated. CD22 and B220 dual-positive B-cells were FACS purified from spleens of adult transgenic mice and wildtype littermates, total-RNA was isolated, and transcriptional profiling performed using GeneChip® Mouse Gene 1.0 ST Arrays.

first: Izidore

last: Lossos

first: Isidro

last: Sánchez-García

first: Ash

middle: A

last: Alizadeh


title: Gene methylation profiles in offspring born before vs. after maternal bariatric surgery

status: Public on May 16 2013

city: Quebec

first: Frederic

last: Guenard

address: 2440, Hochelage blvd

institute: Laval University

summary: Evaluate differences in gene methylation levels between offspring born after maternal bariatric surgery and their siblings born before surgery

overall_design: Offspring born after maternal bariatric surgery (AMS, N=25) vs. offspring born before maternal surgery (BMS, N=25)

first: Frédéric

last: Guénard

first: Yves

last: Deshaies

first: Katherine

last: Cianflone

first: John

last: Kral

first: Picard

last: Marceau

first: Marie-Claude

last: Vohl


title: Expression profiling by array in ATLL

city: Osaka-Sayama

first: Tomonori

last: Higuchi

state: Osaka

address: 377-2 Ohno-Higashi

department: Department of Microbiology

institute: Kinki University Faculty of Medicine

summary:
Previously, we have shown that an AP-1 family member Fra-2, which is hardly expressed in normal mature T cells, is consistently over-expressed in adult T-cell leukemia/lymphoma (ATLL), and together with JunD, upregulates CCR4 and many other genes including proto-oncogenes c-Myb, MDM2, Bcl-6, and SOX4. SOX4 is frequently overexpressed in many solid tumors and considered to be a potential oncogene.
To identify downstream target genes of SOX4 and analyze SOX4 oncogenic pathway in ATLL , we compared gene expression profiles of ST1 cells transfected with SOX4 siRNA or control siRNA using the Affymetrix high density oligonucleotide microarray.

overall_design: The ATL-derived cell line ST1 was transfected with control siRNA or SOX4 siRNA using Nucleofector® (Lonza, Basel, Switzerland). To determine the high-viability of the cells transfected with siRNAs, the cells were counted after 6 h on FACSCalibur (Becton Dickinson, Mountain View, CA) by gating out cells stained with propidium iodide. The transfection efficiency of RNAs was close to 95%, as determined by using fluorescent siRNA (Qiagen). After 48 h, total RNA samples were prepared and confirmed to be of good quality with the Agilent 2100 Bioanalyzer (Agilent Technologies, Waldbronn, Germany). In addition,  quantitative PCR confirmed that SOX4 siRNA effectively reduced SOX4 mRNA in ST1 cells.

first: Takashi

last: Nakayama

first: Kazuto

last: Nishio

first: Tokuzo

last: Arao

first: Osamu

last: Yoshie


title: Estrogen inhibits lipid content in liver exclusively from membrane receptor signaling

status: Public on May 14 2013

city: Dublin 2

first: Harry

middle: Myles

last: Harvey

address: York Street

institute: Royal COllege of Surgeons in Ireland

summary:
Membrane estrogen receptor (ER) alpha stimulates AMP kinase to suppress SREBP1 processing and lipids in liver
Here we present evidence that signaling from membrane-localized ERalpha similarly suppresses a subset of mRNAs in the livers of female WT and membrane only estrogen receptor (MOER) transgenic mice but not in estrogen receptor knock out (ERKO) mice

overall_design: Three month old wild type, MOER and ERKO mice were ovariectomized and utilized per IRB-approved. Following ovariectomy and recovery the animals were injected intraperitoneally with PPT (100 μg) or oil placebo (0.1 mL) daily for 3 days. Whole livers were removed upon euthanasia.

first: Ellis

last: Levin

first: Brian

first: Ali

last: Pedram

first: Mahnaz

last: Razandi

first: Fiona

last: O'Mahony


title: Usp22 depletion in E14 mouse ESCs

city: Philadelphia

first: Steven

middle: B

last: McMahon

state: PA

department: Cancer Biology

institute: Thomas Jefferson University

summary:
Mouse ESCs depleted of the epigenetic modifying enzyme Usp22 fail to differentiate properly.  Ectopic expresison of Usp22 results in spontaneous differnetiation.
In order to understand the transcriptional program underlying this biological defect, whole genome expression analysis was performed.

overall_design: E14 mESCs were infected with lentivirus containing shRNA targeting Usp22 or control (Luc).  RNA was extracted from both samples and subjected to expression analysis by affymetrix array.

first: Robyn

middle: T

last: Sussman


title: Prdm5 suppresses ApcMin-driven intestinal adenomas and regulates monoacylglycerol lipase expression

status: Public on May 11 2013

city: Torino

first: Raffaele

last: Calogero

state: To

address: Via Nizza 52

department: Molecular Biotechnology Center

institute: University of Torino

summary: PRDM proteins are tissue specific transcription factors often deregulated in diseases, particularly in cancer where different members have been found to act as oncogenes or tumor suppressors. PRDM5 is a poorly characterized member of the PRDM family for which several studies have reported a high frequency of promoter hypermethylation in cancers of gastrointestinal origin.  We report here the characterization of Prdm5 knockout mice in the context of intestinal carcinogenesis. We demonstrate that loss of Prdm5 increases the number of adenomas throughout the murine small intestine on an ApcMin background. By genome-wide ChIP-seq and transcriptome analyses we identify loci encoding proteins involved in metabolic processes as prominent PRDM5 targets and characterize monoacylglycerol lipase (Mgll) as a direct PRDM5 target in human colon cancer cells and in Prdm5 mutant mouse intestines. Moreover, we report the downregulation of PRDM5 protein expression in human colon neoplastic lesions. In summary, our data provide the first causal link between Prdm5 loss and intestinal carcinogenesis and uncover an extensive and novel PRDM5 target repertoire likely facilitating the tumor suppressive functions of PRDM5.

overall_design:
Two experimental conditions: wt and ko mice for PRDM5. Each experimental condition was replicated three times.

This submission represents transcriptome component of study.

first: Giorgio

last: Galli

first: Hinke

last: Multhaupt

first: Matteo

last: Carrara

first: Kristian

last: Honnens de Lichtenberg

first: Ib

last: Christensen

first: Dorte

last: Linnemann

first: Eric

last: Santoni-Rugiu

first: Anders

last: Lund


title: Co-culture of human hematopoietic stem cells with osteoblasts affects mono/macrophage versus erythroid lineage choice.

status: Public on May 10 2013

city: Modena

first: Rossella

last: Manfredini

address: Via Gottardi 100

department: Life Sciences

institute: Centre for Regenerative Medicine

summary:
Hematopoietic stem cells (HSCs) are located in the bone marrow in a specific microenvironment referred as the hematopoietic stem cell niche, where HSCs interact with a variety of stromal cells. Though several components of the stem cell niche have been identified, the regulatory mechanisms through which such components regulate the stem cell fate are still unknown. In order to address this issue, we investigated how osteoblasts (OBs) can affect the molecular and functional phenotype of HSCs and vice versa.   Our data showed that CD34+ cells cultured with OBs give rise to higher total cell numbers, produce more CFU and maintain a higher percentage of CD34+CD38- cells compared to control culture. Moreover, clonogenic assay and long-term culture results showed that OBs enhance HSC differentiation towards the mono/macrophage lineage at the expense of the granulocytic and erythroid ones. Finally, GEP analysis allowed us to identify several cytokine-receptor networks, such as WNT pathway, and transcription factors, as TWIST1 and FOXC1, that could be activated by co-culture with OBs and could be responsible for the biological effects reported above.
Altogether our results indicate that OBs are able to affect both HPC maintenance and differentiation capacity by modulating mono/macrophage and erythroid commitment.

overall_design: We set up a co-culture system composed of human CD34+ cells in culture with human OBs. After coculture, CD34+ cells and the hematopoietic cell fraction were separated from OBs and analyzed by gene expression profiling (GEP), clonogenic assay and long-term culture.

first: Simona

last: Salati

first: Gina

last: Lisignoli

first: Cristina

last: Manferdini

first: Valentina

last: Pennucci

first: Roberta

last: Zini

first: Elisa

last: Bianchi

first: Ruggiero

last: Norfo

first: Andrea

last: Facchini

first: Sergio

last: Ferrari


title: Inhibitors of Differentiation-1 Promotes Transformation of Human Papillomavirus Type 16-immortalized Cervical Epithelial Cells

city: Chengdu, Sichuan

first: Lingxia

last: Xie

address: South Renmin Road Section 3 NO.20

department: OB & GY

institute: Sichuan University

summary: Our previous study implied a correlation of inhibitors of differentiation-1 (Id-1) to cervical cancer development. However, how Id-1 contributes to cervical carcinogenesis is unknown. In the present study, we investigated the role of Id-1 in transforming cervical cells with an in vitro transformation model. The human papillomavirus (HPV) immortalized cervical epithelial cells (H8) were successfully transformed by exposure to the carcinogen N-nitrosopyrrolidine (NPYR). The results showed that both Id-1 RNA and protein expression were significantly increased in transformed H8 cells, suggesting a possible role of Id-1 in cervical cell transformation. Ectopic expression of Id-1 in H8 cells potentiated NPYR-induced cell transformation. In contrast, silencing of Id-1 suppressed NPYR-induced H8 cell transformation. A cDNA microarray assay was performed, which identified suggested potential cell signaling pathways for NPYR-induced H8 cell transformation. The results suggest that Id-1 plays an oncogenic role in the cervix, which sheds light on cervical cancer development and implies potential target for cervical cancer prevention and therapy.

overall_design: Id-1-shRNA H8 and the control pGIPZ-H8 cells, with or without NPYR treatment, were used for cDNA microarray assay. Total RNA was extracted by using TRIZOL Reagent (Life Technologies, Carlsbad, CA, US) following the manufacturer's instructions. Total RNA was further purified by RNeasy micro kit (QIAGEN, GmBH, Germany) and RNase-free DNase Set (QIAGEN, GmBH, Germany). The RNAs were amplified, labeled and purified by using GeneChip 3' IVT Express Kit (Affymetrix, Santa Clara, CA, US) following the manufacturer's instructions. Array hybridization and wash were performed using GeneChip® Hybridization, Wash and Stain Kit (Affymetrix, Santa Clara, CA, US) in a Hybridization Oven 645 (Affymetrix) and Fluidics Station 450 (Affymetrix) following the manufacturer's instructions. The slides were scanned with GeneChip® Scanner 3000 (Affymetrix) using the Command Console Software 3.1 (Affymetrix) with default settings. Raw data were normalized by using the MAS 5.0 algorithm of GeneSpring Software 11.0 (Agilent Technologies, Santa Clara, CA, US).

first: Jinke

last: Li


title: Hepatitis C Virus Infection Activates a Novel Innate Pathway Involving IKKα in Lipogenesis and Viral Assembly

status: Public on May 08 2013

first: WeiPing

last: Chen

address: Bldg 8, Room 1A11, NIDDK/NIH

department: GCL

institute: NIDDK/NIH

summary: Hepatitis C virus interacts extensively with host factors not only to establish productive infection but also to trigger unique pathological processes. Our recent genome-wide siRNA screen demonstrated that IKKα is a critical host factor for HCV. Here we describe a novel NF-κB-independent and kinase-mediated nuclear function of IKKα in HCV assembly. HCV infection, through its 3’-untranslated region, interacts with DDX3X to activate IKKα, which translocates to the nucleus and induces a CBP/p300-mediated transcriptional program involving SREBPs. This novel innate pathway induces lipogenic genes and enhances core-associated lipid droplet formation to facilitate viral assembly. Chemical inhibitors of IKKα suppress HCV infection and IKKα-induced lipogenesis, offering a proof-of-concept approach for novel HCV therapeutic development. Our results show that HCV commands a novel mechanism to its advantage by exploiting intrinsic innate response and hijacking lipid metabolism, which likely contributes to a high chronicity rate and the pathological hallmark of steatosis in HCV infection.

overall_design: Cells were treated with either non-targeting control siRNA or siRNA against IKKalpha. After 72 h, cells were either mock infected or infected with HCV JFH-1 strain with the M.O.I. of 0.5.

first: Qisheng

first: Helen

last: Cha

first: Véronique

last: Pène

first: T

last: Liang

first: Siddharth

last: Krishnamurthy


title: Gene expression data from primary human bronchial epithelial cells expressing EGFP or DN-GRHL2 for 48h

city: Durham

first: Xia

last: Gao

state: NC

address: 353 Nanaline Duke Bldg. Research Dr.

institute: Duke University

summary:
The airways of the human lung are lined by an epithelium made up of ciliated and secretory luminal cells and undifferentiated p63+ Krt5+ basal cells. The integrity of this epithelium and its ability to act as a selective barrier are critical for normal lung function. In other epithelia there is evidence that transcription factors of the evolutionarily conserved grainyheadlike (GRHL) family play key roles in co-ordinating the expression of numerous proteins required for epithelial morphogenesis, differentiation, remodeling and repair. However, little is known about their function in the adult lung.
We use Affymetrix microarray analysis to compare transcripts in lentivirus transfected primary human bronchial epithelial (HBE) cells expressing either EGFP or DN-GRHL2 for 48h when the transepithelial electrical resistance (TER) reached a threshold level. The goal is to identify direct target genes of GRHL2 and early events in the uncoupling of junctional interactions, including those regulating transepithelial resistance.

overall_design: Primary HBE cells from three donors were infected with EGFP or DN-GRHL2 expression lentivirus. Dox was added for 48h to induce the expression of either EGFP or DN-GRHL2 when TER reached a threshold level in ALI culture.

first: Brigid

last: Hogan


title: Expression data from visceral mesothelium (omentum) and parietal meosthelium

city: Nashville

first: David

last: Bader

address: Pierce

institute: Vanderbilt

summary:
Mesothelia, which cover all coelomic organs and body cavities in vertebrates, perform diverse functions in embryonic and adult life.  Yet, mesothelia are traditionally viewed as simple, uniform epithelia.
We used microarrays to demonstrate distinct differences between visceral and parietal mesothelia, the most basic subdivision of this tissue type, in terms of gene expression.

overall_design: Visceral mesothelium was isolated from the omentum of adult Wt1-cre;Rosa26ReYFP mice. In parallel, parietal mesothelium was isolated by teasing the mesothelium from the underlying skeletal muscle of the body wall of these animals. RNA was then extracted from these native mesothelia samples and used for hybridization in a microarray experiment.

first: Cristi

middle: L

last: Galindo


title: Gene expression data from primary human bronchial epithelial cells expressing EGFP or DN-GRHL2

summary:
The airways of the human lung are lined by an epithelium made up of ciliated and secretory luminal cells and undifferentiated p63+ Krt5+ progenitors. The integrity of this epithelium and its ability to act as a selective barrier are critical for normal lung function. In other epithelia there is evidence that transcription factors of the evolutionarily conserved grainyheadlike (GRHL) family play key roles in co-ordinating the expression of numerous proteins required for epithelial morphogenesis, differentiation, remodeling and repair. However, little is known about their function in the adult lung.
We used Affymetrix microarray analysis to compare transcripts in lentivirus transfected primary human bronchial epithelial (HBE) cells expressing either EGFP or DN-GRHL2 to help identify GRHL2 target genes and their functions in HBE cells.

overall_design: Primary HBE cells from three donors were infected with modified TripZ lentivirus designed to express EGFP or DN-GRHL2 in response to Dox. Dox was added to cells cultured at the air-liquid interface from day 7 to 14.


title: Primary human bronchial epithelial cells expressing EGFP or DN-GRHL2

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

overall_design: Refer to individual Series


title: Characterization of Formaldehyde's Genotoxic Mode of Action by Gene Expression Analysis in TK6 Cells

status: Public on May 13 2013

city: Ulm

first: Karlheinz

last: Holzmann

address: Helmholtzstreet 8/1

department: Medical Faculty

institute: Ulm University

summary: Gene expression analysis has been established as a tool for the characterization of genotoxic mechanisms of chemical mutagens. This approach has been shown to differentiate between DNA reactive genotoxins and non-DNA reactive or indirectly-acting genotoxins. In this context, it has been suggested that expression analysis is capable of distinguishing compounds that cause DNA damage from those that interfere with mitotic spindle function. Formaldehyde (FA) is known to be a DNA-reactive substance which mainly induces chromosomal damage in cultured mammalian cells. However, there has been concern that FA might also act as an aneugen (i.e., induce aneuploidy) but recent cytogenetic studies did not support this assumption. To further characterize FA's genotoxic mode of action, we now used gene expression profiling as a molecular tool to differentiate between clastogenic and aneugenic activity. TK6 cells were exposed to FA for 4 and 24 h and changes in gene expression were analyzed using a whole-genome human microarray. Results were compared to the expression profiles of two DNA-damaging clastogens (methyl methanesulfonate [MMS] and ethyl methanesulfonate [EMS]) and two aneugens (colcemid [COL] and vincristine [VCR]). The gene expression profiles indicated that clastogens and aneugens induce discriminable gene expression patterns. The expression profile of FA showed more similarities to clastogens than to aneugens. Hierarchical clustering analysis as well as several class prediction algorithms revealed a much closer relationship of FA with clastogens than with aneugens. A pathway analysis of differentially regulated genes also demonstrated an overall better agreement of FA with clastogens than with aneugens. Altogether, the results of this study revealed great similarities in gene expression in response to FA and clastogens but did not support an aneugenic activity of FA.

overall_design: Gene expression analysis of untreated TK6 cells or TK6 cells treated with formaldehyde, the DNA-damaging clastogens methyl methanesulfonate or ethyl methanesulfonate, or the aneugens colcemid or vincristine.

first: Stefanie

last: Kuehner

first: Günter

last: Speit


title: Genome-wide gene expression analysis in Thoc5- and CFIm68-depleted HeLa cells

status: Public on May 21 2013

city: Suita

first: Daisuke

last: Okuzaki

address: Yamadaoka 3-1

department: Immunology Frontier Research Center

institute: Osaka univ.

summary: We found that CFIm68, a mRNA cleavage and polyadenylation factor implicated for alternative polyadenylation site choice, was co-purified with Thoc5, a component of human THO/TREX. Microarray analysis using human HeLa cells reveals knockdown of Thoc5 affects the expression of a subset of non-heat shock genes. Notably, depletion of Thoc5 attenuated the expression of the mRNAs polyadenylated at distal, but not proximal, polyadenylation sites, which phenocopied the depletion of CFIm68.

overall_design: Two independent experiments using different siRNAs against Thoc5 (siThoc5-1and siThoc5-2) and CFIm68 (siCFIm68-1and siCFIm68-2) were performed. In both experiments, siDsRed was used as negative control.

first: Jun

last: Katahira


title: Expression data from cultured human ovarian carcinoma cell lines

city: Singapore

first: Tuan Zea

last: Tan

address: 14 Medical Drive, #11-01, Singapore

department: Cancer Science Institute Singapore

country: Singapore

institute: National University of Singapore

summary: The hallmark of human cancer is heterogeneity, mirroring the complexity of genetic and epigenetic alterations acquired during oncogenesis.  We extracted RNA of 34 cultured human ovarian carcinoma cell lines and performed expression microarrays so that cultured cell lines can represent in vivo human tumors.

overall_design: 34 ovarian carcinoma cell lines expression data.

first: Tuan

first: Ruby

last: Huang

first: Noriomi

last: Matsumura

first: Jean-Paul

last: Thiery

first: Seiichi

last: Mori