title: Retinoic acid induces Snai1 in stem cells of the preimplantation blastocyst to initiate differentiation

status: Public on Jan 12 2015

city: Torino

first: Francesco

last: Neri

state: Italy

address: Via Nizza 52

institute: University of Torino

summary: Although much is known about the pluripotency self-renewal circuitry, the molecular events that lead embryonic stem cells (ESCs) exit from pluripotency and begin differentiation are largely unknown. We found that the zinc finger transcription factor Snai1, involved in gastrulation and epithelial- mesenchymal transition (EMT) is already expressed in the inner cell mass of the preimplantation blastocysts. In ESCs Snai1 does not respond to TGFα or BMP4 signalling but it is induced by retinoic acid (RA) treatment, which induces the binding, on the Snai1 promoter, of the retinoid receptors RARγ and RXRα the dissociation of the Polycomb repressor compex 2 (PRC2) which results in the decrease of H3K27me3 and the increase of histone H3K4me3. Snai1 mediates the repression of pluripotency genes by binding directly to the promoters of Nanog, Nr5a2, Tcl1, c-Kit, and Tcfcp2l1. The transient activation of Snai1 in embryoid bodies induces the expression of the markers of all three germ layers. These results suggest that Snai1 is a key factor that triggers ESCs exit from the pluripotency state and initiate their differentiation processes.

overall_design: microarray analysis of embryonic stem cells (ESC) expressing Snail-ER at various time points of induction with 4-OHT

first: Salvatore

last: Oliviero

first: Federico

last: Galvagni


title: siRNAs in C2C12

status: Public on Jan 14 2015

city: La Jolla

first: Roy

middle: M

last: Williams

state: CA

address: 3030 Science Park Road

department: Regenerative Medicine

country: USA

institute: The Scripps Research Institute

summary: The two catalytic subunits of the SWI/SNF chromatin remodeling complex - Brg1 and Brm - have been often implicated as essential components of common biological processes, suggesting a functional redundancy between these two proteins. For instance, earlier works indicated that both proteins are required for the activation of the myogenic program. However, their mutually exclusive pattern of incorporation in SWI/SNF complexes with variable composition and functional heterogeneity predicts that Brg1- and Brm-based SWI/SNF complexes execute specific functions to coordinate gene expression in multistep programs, such as skeletal myogenesis. We detected a distinct expression profile of Brg1 and Brm during the myogenic program, with Brm being upregulated in differentiating myocytes. Genetic knockdown of either Brg1 or Brm in skeletal myoblasts, followed by gene expression analysis, revealed discrete functions during myogenic differentiation. While Brm is required for the exit from the cell cycle at the early stages of differentiation, by repressing CyclinD1 transcription, Brg1 is required for the activation of muscle gene transcription. Interestingly, at later stages of differentiation Brg1 and Brm cooperate to the activation of a cluster of common target genes. Thus, Brg1 and Brm appear to coordinate activation and repression of distinct subsets of genes during initial phase myogenesis, and converge to cooperatively activate the expression of muscle genes at later stages.

overall_design: C2C12 myoblasts treated with siBRM or siBRG1 or siSCR in growth medium (GM) and differentiated by medium replacemnte (DM ). Celles were collected at 18h and 48h from the onset of DM for RNA extraction and microarray analysis. Arrays were used to generate 6 data sets in duplicate.To address the question of which genes were regulated by BRM and/or BRG1 the fold changes in gene expression were calculated between  Scrambled siRNA and the BRM or BRG1 siRNA.  The experiments were repeated at 2 different time points (18 hours and 48 hours) .

first: Sonia

last: Albini

first: Paula

last: Coutinho


title: A MEIG1/PACRG complex in the manchette is essential for building the sperm flagella

status: Public on Jan 23 2015

city: Columbus

first: Kellie

middle: J.

last: Archer

state: OH

address: 1841 Neil Ave

department: Division of Biostatistics

institute: Ohio State University

summary: Meig1-deficient mice show male germ cell development defect after they are 28 days old. To understand if the phenotype was caused by altered gene expression due to MEIG1 deficiency, total testicular RNA was isolated from 22 day old and  28 day old wild type and Meig1-deficient mice, microarray was conducted and gene expression was compared between wld-type and Meig1-deficient mice at the two time points.

overall_design: Total testicular RNA was extracted from 22 day or 28 day old wild-type and Meig1-deficient mice, and gene expression was compared between wild-type and Meig1-deficient mice at the two time points.

first: Wei

last: Li

first: Waixin

last: Tang

first: Maria

middle: E

last: Teves

first: Zhengang

last: Zhang

first: Ling

first: Hongfei

middle: J

first: Darrell

last: Peterson

first: David

middle: C

first: Jerome

middle: F

last: Strauss

first: Zhibing


title: Gene expression profiles reveal the effect of a high-fat diet in brown fat development

status: Public on Jan 08 2015

city: Daegu

first: Sanggyu

last: Lee

address: 1370 Sankyuk-dong, Bukgu

country: South Korea

institute: Kyungpook National University

summary: Genome-scale analysis of the genetic factors that govern the development of white and brown adipose tissue is still far from complete. In order to identify the key genes that regulate the development of white and brown adipose tissue in mice, the transcriptome analysis was performed on adipose tissues

overall_design: Total RNA obtained from interscapular brown adipose tissue of C57BL/6J mice fed normal diet or high fat diet for 2, 4, 8, 20 and 24 weeks

first: Hyeng

middle: S

last: Kim

first: Zae

middle: Y

last: Ryoo


title: Gene Expression Test for Operational Renal Allograft Tolerance

city: San Francisco

first: Matthew

middle: James

last: Vitalone

address: 475 Brannan st

department: BIOMARC

institute: CPMCRI

summary: Genomic Analysis of more than 400 patients from multi-center transplant programs and clinical trials provides a non-invasive QPCR based gene expression test for operational renal allograft tolerance

overall_design: 3 group comparison of blood from TOL, CAN and Non-transplant healthy controls (HD) allografts. Biological replicates: 16 TOL, 10 CAN and 5 HC

first: Silke

last: Roedder

first: Minh-thien

last: Vu

first: Li

first: Michael

last: Alonso

first: Szu-chuan

last: Hsieh

first: Hong

last: Dai

first: Tara

last: Sigdel

first: Adriana

last: Zeevi

first: Oscar

last: Salvatierra

first: Sam

last: Strober

first: Ed

last: Engelman

first: Josefina

last: Alberu

first: Minnie

last: Sarwal


title: Enhancer Sequence Variants and Transcription Factor Deregulation Synergize to Construct Pathogenic Regulatory Circuits in B Cell Lymphoma (array)

status: Public on Jan 15 2015

city: St. Louis

first: Jacqueline

last: Payton

state: MO

address: 660 S. Euclid Ave

department: Pathology and Immunology

institute: Washington University School of Medicine

summary: Most B cell lymphomas arise in the germinal center (GC), where humoral immune responses evolve from potentially oncogenic cycles of mutation, proliferation, and clonal selection. Although lymphoma gene expression diverges significantly from GC-B cells, underlying mechanisms that alter the activities of corresponding regulatory elements (REs) remain elusive. Here we define the complete pathogenic circuitry of human follicular lymphoma (FL), which activates or decommissions transcriptional circuits from normal GC-B cells and commandeers enhancers from other lineages. Moreover, independent sets of transcription factors, whose expression is deregulated in FL, target commandeered versus decommissioned REs. Our approach reveals two distinct subtypes of low-grade FL, whose pathogenic circuitries resemble GC-B or activated B cells. Remarkably, FL-altered enhancers also are enriched for sequence variants, including somatic mutations, which disrupt transcription factor binding and expression of circuit-linked genes. Thus, the pathogenic regulatory circuitry of FL reveals distinct genetic and epigenetic etiologies for GC-B transformation.

overall_design: Gene expression analysis was performed for follicular lymphoma, pheriphal blood and germinal center B cells using Affymetrix Human Gene 1.0 ST and 2.0 ST arrays

first: Eugene

last: Oltz

first: Olivia

middle: I

last: Koues


title: Microarray analysis of chimeric CD4+CD28null and CD4+CD28+ T-cells in humanized mice.

status: Public on Jan 05 2015

city: New Haven

first: JOSE

middle: DAVID

last: HERAZO MAYA

state: CT

address: 300 Cedar Street

department: Medicine

institute: Yale University

summary: The major goal of this experiment was to identify the overall changes in gene expression of human CD4+CD28 null T-cells that develop after repetitive [xeno] antigen stimulation, in comparison to normal CD4+CD28+ T-cells.  These cells were derived by adoptive transfer of human CD4 T-cells from a normal donor (all CD28+) into immunodeficient mice.

overall_design: Chimeric human CD4+CD28+ were isolated from 4 mice, and chimeric human CD4+CD28 null cells from two of these animals after expansion and T-cell differentiation in vivo.  Animals were euthanized, and single cell suspensions of splenocytes derived.  CD4 T-cell subpopulations were isolated by fluoresence activated cell sorting, RNA was extrated, labeled and hybridized to whole human gene expression arrays. Overall changes in the gene expression were identified using GEDI (gene expression dynamic inspector). 603 genes were found to be statistically significant (P<0.05) between the CD4+CD28+ and CD4+CD28null cells. Candidate genes were validated using qRT-PCR

first: Jose

last: Herazo-Maya

first: Steve

last: Duncan

first: Jianmin

last: Xue


title: ADRM1 amplified metastasis gene in gastric cancer

status: Public on Jan 01 2015

city: Santa Monica

first: HSIAOWANG

last: CHEN

address: 2825 Santa Monica Blvd

institute: UCLA

summary: Selected genes within the 1 Mb minimal amplified region on 20q13.3 driven by ADRM1 in gastric cancer cell line AGS were analyzed by Gene expression Microarray.

overall_design: Gene Expression of ADRM1, HRH3, MTG2, LAMA5 and OSBPL2 were then compared in 16 Gastric cancer cell lines to a reference composed of mixed gastric cancer cell lines.

first: Marlena

last: Fejzo

first: Hsiao-Wang

last: Chen

first: Judy

last: Dering

first: Dennis

last: Slamon


title: The N-glycosylated isoform of β-integrin as a potential biomarker and target in HER-2+ BC refractory to HER-2 targeted therapies.

city: Edmonton

first: Kathryn

last: Graham

state: Alberta

address: 11560 University Ave

department: Oncology

country: Canada

institute: University of Alberta

type: Expression profiling by genome tiling array

summary: Acquired resistance to trastuzumab, a rationally designed HER-2 targeting antibody, remains a major hurdle in management of HER-2 positive breast cancer (HER-2+ BC) patients.  Potential resistance mechanisms are numerous, derived primarily from studies where HER-2 positive cell lines are chronically exposed to trastuzumab.  Recent evidence suggests a role for epithelial-mesenchymal transition (EMT) in trastuzumab resistance, but a definitive link between the two has been difficult to establish because relevant model systems are lacking.  When sub-populations of trastuzumab sensitive SKBR-3 cells were isolated using cloning rings, an (EMT) occurred spontaneously in several (3/8) clones.  SKBR-3 EMT-clones featured increased spindle morphology, expressed N-glycosylated β1-integrin, and decreased HER-2, all characteristics shared by JIMT-1, a cell lines with intrinsic resistance to trastuzumab. SKBR-3 EMT-clones were characterized by gene expression profiling and mammosphere formation.  The N-glycosylated isoform of β-itnegrin was targeted with β-integrin inhibiting antibody, AIIB2. Transcriptional profiling revealed that SKBR-3 EMT-clones underwent a shift from a luminal molecular subtype to a more aggressive mesenchymal/ basal phenotype. Isolating clones from SKBR-3 cells with enforced expression of a β-integrin isoform lacking extensive N-glycosylation failed to increase the likelihood for spontaneous EMT in SKBR-3.  However, specific inhibition of the heavily N-glycosylated variant of β1-integrin expressed by SKBR-3 EMT-clones restored epithelial morphology and impaired mammosphere formation.  Furthermore, when SKBR-3 EMT-clones were treated with relevant doses of trastuzumab and lapatinib, they showed “spontaneous” resistance.   In this study we describe a model of spontaneous EMT following clonal selection in HER-2+ cell line, SKBR-3.  Using this model we establish the first direct link between EMT and resistance to HER-2 targeted therapies. We also identify the N-glycosylated isoform of β-integrin as a potential biomarker and target in HER-2+ BC refractory to HER-2 targeted therapies.

overall_design: RNA was isolated from 10 breast cancer cell lines in triplicate. Pairwise gene expression differences were compared between each of the SKBR-3 cell lines (SKBR-3/ b1, SK-EV-C4, and SK-B1-C1). Features selected had at least a 2X difference in at least one comparison, with a one-way ANOVA corrected p-value of >0.05. In addition, expression profiles from SKBR-3/ EV and SK-B1-C1 cell were compared and a differential gene list was generated to include genes that differed by at least 1.5X, with a t-test p-value of >0.02 (unpaired, Bonferroni corrected).  A total of 1940 entities met these criteria and the expression of these genes was investigated in all breast cancer cell lines.

first: David

last: Lesnaik


title: Quantitative proteomics cell bilayer (qPCB) method for studying cell-cell communication

city: Berlin

first: Christopher

last: Weidner

address: Ihnestraße 63

department: Otto Warburg Laboratory

country: Germany

institute: Max Planck-Institute for Molecular Genetics

summary: Cellular communication is a fundamental process in biology. We developed an in vitro procedure for quantitatively analyzing proteome-wide changes triggered by interaction of different cell types. Using an adipocyte-macrophage bilayer co-culture model we detected thousands of proteins and deciphered regulatory pathways involved in low-grade inflammation leading to insulin resistance. The method can be applied for multiple cell-cell combinations to gain understanding in cellular interaction.

overall_design: 2 cell lines (3T3-L1 adipocytes [A] and RAW 264.7 macrophages [R]), cultivated both as monolayer (condition 1 [O]) and together in a bilayer experiment (condition 2 [B]); 2-3 biological replicates per treatment (10 samples in total)

first: Weidner

last: Christopher

first: Freiwald

last: Anja

first: Sauer

last: Sascha


title: Gene expression profiling of interferon-alpha-treated HTLV-1-infected CD4+ T cell lines

city: Leuven

first: Rekin's

last: Janky

address: Herestraat 49 Box 816

department: Nucleomics Core

country: Belgium

institute: VIB

summary:
Background: Interferon-alpha (IFN-a) contributes extensively to the host immune response upon viral infection through antiviral, pro-apoptotic, antiproliferative and immunomodulatory activities. Although extensively documented in various types of human cancers and viral infections, controversy exists in the exact mechanism of action of IFN-a in human immunodeficiency virus type 1 (HIV-1) and human T lymphotropic virus type 1 (HTLV-1) retroviral infections.

Principal Findings: IFN-a displayed robust anti-HIV-1 effects in HTLV-1/HIV-1 co-infected MT-4 cells in vitro, demonstrated by the dose-dependent inhibition of the HIV-1-induced cytopathic effect (IC50 = 83.5IU/ml, p < 0.0001) and p24 secretion (IC50 = 1.2 IU/ml, p < 0.0001). In contrast, IFN-a treatment did not affect cell viability nor HTLV-1 viral RNA levels in HTLV-1 mono-infected cell lines, based on flow cytometry and nCounter analysis. However, we were able to confirm the previously described posttranscriptional inhibition of HTLV-1 p19 secretion by IFN-a, both in cell lines (p = 0.0045) as well as in adult T cell leukemia patient samples (p = 0.031). In addition, through microarray and nCounter analysis, we demonstrated significant transcriptional activation of interferon-stimulated genes and intact IFN-a signaling in HTLV-1-infected cell lines.

Conclusions: Taken together, our results indicate that both the absence of in vitro antiproliferative and pro-apoptotic activity, as well as the modest posttranscriptional antiviral activity of IFN-a against HTLV-1, was not due to a cell intrinsic defect in IFN-a signalisation, but rather represents a retrovirus-specific phenomenon, considering the robust HIV-1 inhibition in co-infected cells.

overall_design: The microarray experiment consists of 46 hybridizations in total. For MT-2 cells, triplicate samples (from three independent RNA experiments) were used for untreated (C), IFN-a-, A-, and A+IFN-a-treated cells, duplicate samples for Q2- and Q3-treated cells (from two independent RNA experiments), and one sample for IFN-b-treated cells. For MT-4 cells, quadruplicate samples (from four independent RNA experiments) were used for untreated (C), IFN-a-, A-, and A+IFN-a-treated cells, and duplicate samples for Q2-, Q3-, and IFN-b-treated cells (from two independent RNA experiments). A (AZT) , Q2, and Q3 are drug candidates.

first: Britta

last: Moens

first: Kimberly

last: Dée

first: Anne-Mieke

last: Vandamme

first: Johan

last: Van Weyenbergh


title: Gene Expression Profiling of Human High-Grade Serous Ovarian Tumor Samples

status: Public on Jan 07 2015

address: 2825 Santa Monica Blvd. Suite 200

institute: UCLA School of Medicine

summary: The goal of the study was to further delineate the molecular signatures associated with high-grade serous ovarian cancer in order to develop validated clinically useful prognostic signatures with the potential to guide therapy decisions.   Fresh frozen samples were prospectively collected from a series of 174 consecutive women with high-grade serous ovarian, primary peritonial, or fallopian tube cancer who underwent surgery by a gynecologic oncologist at Mayo Clinic betweern 1994 and 2005.  All patients received postoperative chemotherapy with a platinum agent, and 75% received a taxane.  All patients signed an Institutional Review Board approved consent for bio-banking, clinical data extraction and molecular analysis. Median follow-up time was 35 months (range, 1-202 months).  Fourteen patients (8%) were included in the TCGA study.

overall_design: High grade serous ovarian tumors (n=174) were compared to a reference pool of 106 ovarian samples. Mixed reference includes normal, benign, borderline, and malignant sample of various histolgies.

first: Gottfried

last: Konecny

first: Chen

last: Wang

first: Ellen

last: Goode

first: Lynn

last: Hartmann

first: Charles

last: Ginther

first: Hsiao-wang


title: Global analysis of TGF-beta-regulated gene expression in MCF10Ca1h (M3) breast tumor xenografts

city: Bethesda

first: Howard

last: Yang

state: MD

address: 37 CONVENT DR, Room 5120

department: CCR

institute: NCI

summary:
TGF-betas have complex roles in tumorigenesis,  with context-dependent effects that can either suppress or promote tumor progression. We have previously shown that TGF-beta has tumor suppressor activity in the MCF10Ca1h (M3) human breast cancer xenograft model.  To identify potential molecular players in the tumor suppressor responses,  we performed global gene expression analyses.
To determine which genes were regulated by TGF-beta in this tumor model in vivo,  we performed gene expression arrays on tumors derived from xenografts of M3 cells with and without expression of a dominant negative TGF-beta receptor to block activity of endogenous TGF-beta.

overall_design: Tumor xenografts of MCF10Ca1h (M3) cells that had been transduced ex vivo with pLPCX retrovirus with no insert (CON),  or pLPCX expressing dominant negative type II TGF-beta receptor (dnTbRII) were harvested for gene expression analysis. Six biological replicates of each tumor type were used for a total of 12 samples

first: Misako

last: Sato

first: Mitsutaka

last: Kadota

first: Binwu

last: Tang

middle: H

first: Robert

last: Clifford

first: Aleksandra

last: Michalowski

first: Maxwell

middle: P

last: Lee

first: Lalage

last: Wakefield


title: Triiodothytonine (T3) response is changed after KLF9 knockdown in HepG2-TRbeta overexpressing cells.

status: Public on Dec 31 2014

city: Houston

first: Paul

last: Webb

address: 6670 Bertner Ave

department: Genomic Medicine

institute: Houston Methodist Research Institute

summary: Analysis of T3 response in HepG2-TRbeta cells transfected with siRNA (siCtrl or siKLF9) at gene expression level.The hypothesis tested in the present study was that TR/KLF9 axis is responsible for many of T3 downstream efects. Results provide information of the changr in T3 response after KLF9 knockdown.response

overall_design: Total RNA was obtained from HepG2-TR beta cells transfected with siCtrl or siKLF9 and treated with T3 for 0, 8 or 24 hours. T3 response in siKLF9 samples was compared to response in siCtrl samples.

first: Webb

last: Paul

first: Cvoro

last: Aleksandra


title: Activation of beta-catenin in hepatocellular carcinoma (mouse Ctnnb1 knockout)

first: Sangbae

last: Kim

state: TX

address: 1 Baylor plaza

department: HGSC

institute: Baylor Colleage of Medicine

summary: CTNNB1 is the most frequently mutated gene in hepatocellular carcinoma (HCC). However, its clinical relevance remains controversial. We determined an evolutionarily conserved β-catenin signature by comparative analysis of gene expression data from human HCC (GSE43619) and a mouse model.

overall_design: We generated gene expression data from 4 tumor tissues from a mouse Ctnnb1 knockout model (Ctnnb1 flox(ex3)/+) and 4 normal liver tissues from control wild-type mice.

first: David

middle: D

last: Moore

first: Bingning

last: Dong

first: Ju

first: Yun

last: Park


title: Effect of long-term vitamin D supplementation on colonic gene expression in IL-10 Knockout mice at young adulthood

status: Public on Jan 02 2015

city: Toronto

first: Elena

last: Comelli

state: ON

address: 150 College Street

department: Nutritional Sciences

institute: University of Toronto

summary: Low vitamin D status has been implicated in the progression of inflammatory bowel disease (IBD). This study used interleukin (IL)-10 knockout (KO) mice, that develop an intestinal inflammation when housed in a non-sterile environment, to determine if supplementation with vitamin D throughout life impacts colonic gene expression. Results provide important information on the intestinal response to vitamin D in inflamed mice.

overall_design: Female IL-10 knock out mice were randomized to 25 (Low, L) or 5000 (High, H) IU vitamin D/kg of diet throughout pregnancy and lactation. At weaning, offspring received the same or opposite diet as their mother until age 3 months. This resulted in four vitamin D interventions: HH, HL, LH, or LL where the first letter represents the diet consumed by dams during pregnancy and lactation and the second letter represents the diet consumed by offspring from weaning through to 3 months of age. Global gene expression was analyzed in the proximal colon of 3 months old mice (n=6 per group, for a total of 24 samples; samples came from different litters and moms IDs are given in the samples table below). Samples were stored at -80C.

first: Andrea

last: Glenn

first: Kristina

middle: A

last: Fielding

first: Jianmin

last: Chen

first: Wendy

last: Ward


title: Hypoxia-induced stem-like cancer cells resistance to VEGFR inhibition

city: Paris

first: Anne

last: Janin

address: 1 Av C Vellefaux

country: France

institute: University Paris 7, INSERM, APHP

type: Genome variation profiling by genome tiling array

summary: Developing strategies to overcome the frequent resistance to VEGF/VEGFR inhibitors in patients is a major challenge in antiangiogenic therapy for cancer. Targeting the VEGF pathway in vivo induces hypoxia and therefore enables to study drug-induced hypoxia in tumors. Hypoxia also occurs in the spontaneous evolution of cancers, particularly around areas of necrosis.  Using cell markers such as CD133, CXCR4, or ALDH1, we identified stem-like cells in peri-necrotic areas in human biopsies and xenografts models of renal cancers. These stem-like cells were able in vitro to self-renew, form carcinoma spheres and had a tumorigenic potency, thus showing characteristics of stem-like cancer cells. In xenografted human renal cell carcinoma, we further demonstrated a strong link between necrosis, either spontaneous or treatment-induced, and the presence of CD133/CXCR4 double positive stem-like cells. Hypoxia increased their tumorigenic potency, induced overexpression of metallothionein2A, which we here identified as critical regulator of resistance to VEGFR-inhibition.

overall_design:
6 sample were collected and analysed for gene expression: 2 samples are human tumors xenografted into nude mice, 2 samples are human tumor renal kidney spheres cultured under hypoxic conditions and 2 other samples are human tumor renal kidney spheres cultured under normoxic conditions
Two DNA samples were analysed with CGH array : 1 tumor stem cell cultured in normoxic condition and one human renal carcinoma xenografted into nude mice.

first: Mariana

last: Varna

first: Guilhem

last: Bousquet

first: Jean-Paul

last: Feugeas

first: Guillaume

last: Gapihan

first: Irmine

last: Ferreira

first: Christophe

last: Leboeuf

first: Niclas

last: Setterblad

first: Arnaud

last: Duval

first: Pierre

last: Mongiat-Artus

first: Philippe

last: Bertheau

first: Stéphane

last: Germain


title: Human dental pulp cells cultured in FBS vs. chemically defined conditions

status: Public on Dec 25 2014

city: Gifu City

first: Ken-ichi

last: Tezuka

state: Gifu

address: 1-1 Yanagido

department: Gifu University Graduate School of Medicine

country: Japan

summary: Human dental pulp cells (hDPCs) are one of the promising resources for regenerative medicine and tissue engineering, including derivation of induced pluripotent stem cells (iPSCs). However, our current protocol uses reagents of animal origin, mainly fetal bovine serum (FBS) with potential risk of infectious diseases and unwanted immunogenicity. This time, we designed a chemically defined protocol to isolate and maintain the growth and differentiation potentials of hDPCs.

overall_design: To investigate the effect of chemically defined condition on global gene expression in DPCs, we cultured them in FBS and chemically defined conditions.

first: Tomoko

last: Kawaguchi


title: Human Dental Pulp Cells Mature vs. Immature stages

institute: Gifu University Graduate School of Medicine

summary: We report screening of genes differentially expressed in cells isolated from immature and mature third molar teeth. Among them, a homeobox transcription factor, distal-less homeobox 4 (DLX4) was highly expressed in immature human dental pulp cells, and significantly enhanced iPSC colony formation in combination with OCT3/4, SOX2, and KLF4 to the level comparable with that using classical combination of Yamanaka's factors, OCT3/4, SOX2, KLF4, and c-MYC.

overall_design: To investigate the effect of developmental stage of teeth on global gene expression, we compared DPCs isolated from immature (14-16yr) and mature (23-60yr) teeth.

first: Naritaka

last: Tamaoki


title: HOX genes: potential candidates furthering the development of larynx squamous cell carcinoma.

city: Ribeirao Preto

first: Wilson

middle: Araújo

last: Silva Jr

state: Sao Paulo

address: Rua Catao Roxo, 2501

department: Genetics

country: Brazil

institute: University of Sao Paulo

summary: Larynx squamous cell carcinoma (LSCC) is the second most aggressive cancer from head and neck (HSCC). Survival of LSCC patients has been found worsening, albeit significant advances in technology and therapeutics were made. We sought to clarify new genetic targets driven the development of LSCC. Analyzing tumors revealed that eight members of the homeobox gene family (HOX) were expressed 200 times more in LSCC samples than in normal larynx tissue. qPCR analysis validated all transcriptomic findings for the HOX gene family. Receiver Operating Characteristic statistical method (ROC curve) predicted that 8 members of the HOX gene family differentiate tumors from their normal surrounding tissue. Enabling the comparison of patient clinics with gene expression data, ROC curve analysis yet revealed that HOXC8 and HOXD11 genes are related to the tumor differentiation degree and regional lymph node metastasis, respectively. From siRNA assay, we found that HOXC8 and HOXD11 genes are essential for the expansion of FADU cell colonies. Our findings strongly suggest that members of the HOX family might be associated with the development of LSCC.

overall_design: Twenty nine cancer samples and thirteen margin samples were collected from patients undergoing surgical ablation of LSCC according to Ethic Committee guideline and patient pre-informed signed consents. Whole human genome microarray analysis was applied to investigate new genetic targets in LSCC.

first: Rafaela

middle: B

last: Bueno

first: Vinicius

last: Kannen

first: Achim

last: Jungbluth

first: Daniel

middle: G

last: Pinheiro

first: Luiza

last: Araújo

first: Bruna

middle: R

last: Muys

first: Aline

last: Fonseca

first: Jessica

last: Plaça

first: Rodrigo

last: Panepucci

first: Luciano

last: Neder

first: Fabiano

last: Saggioro

first: Rui

last: Mamede

first: David

middle: L

last: Figueiredo


title: MITF drives endolysosomal biogenesis and potentiates Wnt signaling in melanoma cells

status: Public on Dec 24 2014

first: HSIAOWANG

last: CHEN

summary: Canonical Wnt signaling plays an important role in development and disease, regulating transcription of target genes and stabilizing many proteins phosphorylated by Glycogen Synthase Kinase 3 (GSK3). We observed that the MiT family of transcription factors, which includes the melanoma oncogene MITF and the lysosomal master regulator TFEB, had the highest phylogenetic conservation of three consecutive putative GSK3 phosphorylation sites in animal proteomes. This prompted us to examine the relationship between MITF, endolysosomal biogenesis and Wnt signaling. Here we report that MITF expression levels correlated with the expression of a large subset of lysosomal genes in melanoma cell lines. MITF expression in the Tetracycline-inducible C32 melanoma model caused a marked increase in vesicular structures, and increased expression of late endosomal proteins such as Rab7, LAMP1, and CD63. These late endosomes were not functional lysosomes as they were less active in proteolysis, yet were able to concentrate Axin1, phospho-LRP6, phospho-β-Catenin, and GSK3 in the presence of Wnt ligands. This relocalization significantly enhanced Wnt signaling by increasing the number of multivesicular bodies (MVBs) into which the Wnt signalosome/destruction complex becomes localized upon Wnt signaling. We also show that the MITF protein was stabilized by Wnt signaling, through the novel C-terminal GSK3 phosphorylations identified here. MITF stabilization caused an increase in MVB biosynthesis, which in turn increased Wnt signaling, generating a positive feed-back loop that may function during the proliferative stages of melanoma. The results underscore the importance of misregulated endolysosomal biogenesis in Wnt signaling and cancer.

overall_design: Expression of selected Lysosomal genes and CLEAR element plus MITF were compared in 51 melanoma cell lines to a mixed reference pool containing equal amounts of 47 melanoma cell lines.

first: Hsiao-Wang

last: Chen

first: Judy

last: Dering

first: Diego

last: Ploper


title: Triiodothyronine (T3) response in liver of FGF21 knockout mice

first: Paul

last: Webb

summary: Thyroid hormone (TH) influences metabolic pathways by binding to specific receptors (TRs), which are conditional transcription factors. T3 works through TRs to induce fibroblast growth factor (FGF) 21, a peptide hormone that is usually induced in fasting and influences lipid and carbohydrate metabolism via local hepatic and systemic endocrine effects. While administered TH and FGF21 display overlapping actions, including reductions in serum lipids, current models suggest that these hormones act independently in vivo. Here, we examined mechanisms of TH regulation of FGF21 expression and tested the possibility that FGF21 is required for induction of hepatic TH-responsive genes. We confirm that active TH (T3) and the TRβ selective thyromimetic GC-1 increase FGF21 transcript and peptide levels in mouse liver and that this effect requires TRβ. T3 also induces FGF21 in cultured hepatocytes and this effect involves direct actions of TRβ1, which binds a TRE within intron 2 of FGF21. Gene expression profiles in wild type and FGF21 knockout mice are highly similar indicating that FGF21 is dispensable for the majority of hepatic T3 gene responses. A small subset of genes displays diminished T3 response in the absence of FGF21. However, most of these are not obviously involved in T3-dependent hepatic lipid and carbohydrate metabolic processes. Accordingly, T3-dependent effects upon serum lipids are maintained in the FGF21-/- background. Our findings suggest that T3 regulates genes involved in classical hepatic metabolic responses independently of FGF21.

overall_design: Total RNA was obtained from mouse liver of WT and FGF21-/- treated with DMSO or T3

first: Aijun

last: Zhang

first: Douglass

last: Sieglaff

first: Xuefeng

last: Xia


title: Genome-wide expression analysis of the effects of a parasitic nematode's secreted exosomes on mammalian cells.

city: Irapuato

first: Cei

last: Abreu-Goodger

state: Guanajuato

address: Km. 9.6 Libramiento Nte Carr Leon-Irapuato

country: Mexico

institute: Langebio - Cinvestav

summary: We show that a gastrointestinal nematode that infects mice, Heligmosomoides polygyrus, secretes vesicles packaged with specific microRNAs (miRNAs) and Y RNAs as well as a nematode-specific Argonaute protein. The vesicles are of intestinal origin and are enriched for homologs of mammalian proteins found in exosomes, including heat shock proteins, tetraspanins and an ESCORT protein. The nematode-derived vesicles are internalized by mouse intestinal epithelial cells and mediate changes in expression of host genes involved in inflammation and immunity, including the receptor for the alarmin IL33 as well as a key regulator of MAPK signaling, DUSP1.

overall_design: A total of 12 samples were analyzed, from 4 different conditions: medium, exosome-treated, LPS and LPS+exosomes, each with 3 biological replicates. One of the 'medium' replicates was discarded due to outlier behaviour.

first: Amy

last: Buck

first: Gillian

last: Coakley

first: Fabio

last: Simbari

first: Sujai

last: Kumar

first: Thierry

last: Le Bihan

first: Marissa

last: Lear

first: Yvonne

last: Harcus

first: Mark

last: Blaxter

first: Alasdair

last: Ivens

first: Rick

middle: M

last: Maizels


title: Gene expression of HCT116 cells after stimulation with oncostatin M (OSM)

status: Public on Dec 13 2014

city: München

first: Florian

last: Beigel

address: Marchioninistr. 15

department: Medizinische Klinik und Poliklinik II

institute: Klinikum Grosshadern

summary: To evaluate gene expression profiles in intestinal epithelial cells (IEC) after OSM stimulation, we have employed whole genome microarray expression profiling as a discovery platform to identify relevant genes which are potentially of interest to reveal the role of OSM in intestinal inflammation.  The most strongly up-regulated genes were SERPINS, which belong to the family of serin peptidase inhibitors with antiprotease activities, most of them serine and cysteine proteases. SERPINB4, SERPINB3 and SERPINA3 were the genes with the strongest up-regulation, also verified in qPCR. OSM-induced SERPIN up-regulation may contribute to anti-apoptotic and proliferative effects of OSM in IEC.

overall_design: HCT116 cells were starved overnight with medium containing 1% FCS after reaching 70% confluency. On the next day, cells were stimulated in quadruplicates with 100 ng/mL OSM or left unstimulated. RNA was isolated 6 hours after stimulation and RNA concentration and purity was measured.

first: Matthias

last: Friedrich

first: Corina

last: Probst

first: Karl

last: Sotlar

first: Burkhard

last: Göke

first: Julia

last: Diegelmann

first: Stephan

last: Brand


title: UV Photoprotection and Long-lasting Pigmentation from UVA and/or UVB

status: Public on Dec 12 2014

city: BETHESDA

first: Vincent

middle: J.

last: Hearing

address: BG 37 RM 2132B 37 CONVENT DR

institute: National Cancer Institute

summary: To test whether there is a photoprotective benefit after different types of suberythemal repetitive UV, a 1.5 MED challenge dose was applied 1 week after the initial 2 weeks of repetitive irradiation.  To determine what different mechanisms and/or factors might be involved in physiological pigmentary responses of the skin to different types of UV, we used whole human genome microarrays and immunohistochemical analyses to characterize human skin in situ to examine how melanocyte-specific proteins and paracrine melanogenic factors are regulated by repetitive exposure to suberythemal doses of different types of UV (UVA and/or UVB).

overall_design: Seven volunteers with skin type II-III were irradiated with UVA, UVB or UVA+UVB radiation for 2 weeks (5 times per week, 10 times total) after preliminary determination of their MEDs. A UVA+UVB challenge dose of 1.5X the MED was applied 1 week later.  Biopsies were taken before the challenge dose, immediately after the challenge dose, 4 days after the challenge, and 15 weeks after the challenge.

first: Sergio

last: Coelho

first: Lanlan

last: Yin

first: Julio

middle: C

last: Valencia

first: Dominik

last: Ebsen

first: Christoph

last: Smuda

first: Andre

last: Mahns

first: Ludger

last: Kolbe

middle: J


title: A natural plant derived compound, Withaferin A exploits the stress pathway to induce antitumor immunity

city: Miami

first: Annalise

last: Smith

state: FL

address: 1580 NW 10th Avenue

department: Microbiology and Immunology

institute: University of Miami

summary: Analysis of the global effect of plant derived compound Withaferin A on gene expression in rat her-2/neu expressing murine cancer cells at an early time point of 6hrs post treatment. Pathway analyses were performed to determine which metabolic pathways were significantly affected by the Withaferin A.

overall_design: Total RNA was isolated from rat her-2/neu cells treated with Withaferin A for 6hrs or untreated cells.

first: Samita

last: Andreansky


title: Genome-wide analysis of gene expression in brown adipose tissue (BAT) of mice lacking CD36.

status: Public on Dec 11 2014

city: Berkeley

first: Andreas

last: Stahl

address: 119 Morgan Hall, #3104

department: Nutritional Sciences and Toxicology

institute: University of California Berkeley

summary: Analysis of gene expression in BAT lacking CD36. The hypothesis tested in the present study was that genes involved in lipid metabolism and mitochondrial function would be misregulated. Results provide important information about the role of CD36 in BAT.

overall_design: Total RNA was obtained from the BAT of control and Cd36-/- mice subjected to an overnight fast.

first: Melissa

last: Kazantzis

first: Candice

last: Herber

first: Courtney

last: Anderson


title: Role of Bank1 in the Secretion of IL6 and Expression of Type I Interferon Inducible Genes Through the Control of p38 Signaling and the eIF4E Translation Initiation Complex

city: Richmond

first: Mikhail

last: Dozmorov

state: VA

address: 830 E Main St

department: Biostatistics

institute: Virginia Commonwealth University

summary: Bank1 is an adaptor protein primarily expressed in B-cells with a little understood role in B-cell signaling. Studies involving human systemic lupus erythematosus showed that genetic variants in the human BANK1 gene were associated with SLE. Our studies have suggested that BANK1 could have an endosomal intracellular localization suggesting that it could play a role in endosomal-dependent signaling induced by nucleic acids such as the Tlr9 agonist CpG. To investigate this we used a Bank1 deficient mouse.   Deficiency of Bank1 led to an important reduction in p38 phosphorylation, without affecting Erk or Jnk after CpG stimulation, and a reduction in IL-6 production. In addition, our data demonstrates the reduced transcription and phosphorylation of eIF4E and reduced phosphorylation of the MAP kinase signal-integrating kinases Mnk1/2, confirming the effect on molecules that are direct targets of p38 that are also involved in protein translation initiation. Furthermore, Bank1 deficient B-cells show stronger up- and down-regulation of type-1 interferon response genes and genes repressed during such responsesupregulation of interferon response genes. Our data clearly shows that Bank1 has previously unrecognized and specific roles in the CpG-induced production of IL-6 by splenic B lymphocytes via p38 signaling and suggests a unique role that involves the regulation of the translation initiation complex and type 1 interferon responses of major impact in viral infections and autoimmunity.

overall_design: Bank1-/- vs. WT B-cell stimulated with CpG timecourse

first: Ying-Yu

last: Wu

first: Ramesh

last: Kumar

first: Mohammed

middle: S

last: Haque

first: Marta

last: Alarcón-Riquelme


title: Genome-wide analysis of atypical NK cell subset in mouse model of Systemic Lupus Erythematosus (SLE)

status: Public on Dec 04 2014

city: Rockville

first: Silvia

last: Bolland

address: 12441 Parklawn Drive

department: AFGS

institute: NIAID

summary: Exploratory study to identify genome-wide changes in expression between conventional NK cells isolated from B6 WT and NK1.1+ cells from TLR7tg mice

overall_design: Isolated splenic NK1.1+ cells are compared between B6 WT and TLR7tg mice

first: Elisaveta

last: Voynova

first: Jeff

last: Skinner

first: Timothy

last: Myers


title: Global gene transcriptional profiles in RAW 264.7 cells following mica fine particle stimulation

city: Seoul

first: Myunghwan

last: Jung

address: 1 Gwanak-ro

department: Veterinary Medicine

institute: Seoul National University

summary: We focused on how mica fine particle influences macrophage activities.

overall_design: We analyzed altered transcription in RAW 264.7 cells at 0, 12, and 48 h following the stimulation with 100 µg/mL of mica fine particles.

first: Han

last: Yoo


title: MCF10A-based xenograft model of breast cancer

first: Howard

last: Yang

type: Genome binding/occupancy profiling by genome tiling array

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

overall_design: Refer to individual Series


title: Epigenetic regulations in the IFNγ signalling pathway: IFNγ-mediated MHC class I upregulation on tumour cells is associated with DNA demethylation of antigen-presenting machinery genes [RVPC3_DAC]

status: Public on Dec 08 2014

city: Prague

first: Milan

last: Reinis

address: Videnska 1083

country: Czech Republic

institute: Institute of Molecular Genetics of the ASCR, v. v. i.

summary: Reversible MHC class I deficiency on tumour cells is commonly caused by coordinated silencing of antigen-presenting machinery genes and restorable by IFNγ. Here we describe association of  DNA demethylation of selected antigen-presenting machinery gene regulatory regions located in the MHC genomic locus (TAP-1, TAP-2, LMP-2, LMP-7) upon IFNγ treatment with MHC class I upregulation on tumour cells. Our novel findings demonstrate that IFNγ acts as an epigenetic modifier upregulating the expression of antigen-presenting machinery genes through DNA demethylation.  Our data also cast more light on the role of DNA methylation in tumour cell escape from specific immunity.

overall_design: RVP3 cultured cells treated with DAC/TSA or nothing. 3 biological replicates per condition.

first: Veronika

last: Vlková

first: Ivan

last: Štěpánek

last: Hrušková

first: Filip

last: Šenigl

last: Mayerová

first: Jana

last: Šímová

last: Bieblová

first: Marie

last: Indrová

first: Tomas

last: Hejhal

first: Nicolas

last: Dérian

first: David

last: Klatzmann

first: Adrien

last: Six

last: Reiniš


title: Epigenetic regulations in the IFNγ signalling pathway: IFNγ-mediated MHC class I upregulation on tumour cells is associated with DNA demethylation of antigen-presenting machinery genes [TC1A9_DAC]

overall_design: TC-1/A9 cultured cells treated with DAC/TSA or nothing. 3 biological replicates per condition.


title: Effect of ARF on the transcription of p53 target genes in homologous recombination deficient cells

city: Oxford

first: Ana

middle: Rita

last: Carlos

address: Old Road Campus Research Building

department: The CR-UK/MRC Gray Institute for Radiation Oncology and Biology

country: United Kingdom

institute: University of Oxford

summary: ARF is a tumour suppressor activated by oncogenic stress, which stabilizes p53. Although p53 is a key component of the response to DNA damage, a similar function for ARF has not been ascribed. In this work we show that homologous recombination (HR) -deficient primary mouse and human cells accumulate DNA damage, which triggers checkpoint signalling and ARF activation. We also show that in the absence of ARF p53 is induce in response to DNA damage, but surprisingly fails to trigger senescence. The hypothesis tested in this study was that ARF deficiency alters the spectrum of genes activated by p53 in response to HR deficiency. Using mRNA microarray analysis and expression profiling, we identified genes upregulated in wild type primary MEFs treated with RAD51 shRNA, whose expression was not induced in similarly treated Arf -/- primary MEFs. Clustering analysis of p53 transcriptional targets with increased expression in RAD51-depleted cells revealed three groups: genes requiring functional ARF for their expression, genes transcribed in an ARF-independent manner and genes that are upregulated in both ARF-proficient and ARF-deficient cells. Among the genes in the last group we found Cdkn1a(p21), encoding the p21 inhibitor of cyclindependent kinases and well-characterized effector of the p53 role in promoting senescence. The subset of p53 targets requiring ARF for their transcription was specifically upregulated in response to RAD51 inhibition in wild type, but not Arf -/- MEFs. Among these genes, two encoded the dual specificity phosphatase (DUSP) family members DUSP4 and DUSP7, which act as ERK phosphatases and negative regulators of the MAPK kinase pathway in mammalian cells.

overall_design: Four samples were analysed (WT or ARF negative cells transfected with GFP or RAD51 shRNAs) in duplicate. Samples treated with GFP shRNA are the reference samples and the ones treated with RAD51 shRNA are the experimental ones (RAD51 depletion leads to HR deficiency). The WT cell line is our control cell line to study the effect of HR deficiency on the transcription of p53 target genes

first: Jose

last: Escandell

first: Panagiotis

last: Kotsantis

first: Natsuko

last: Suwaki

first: Peter

last: Bouwman

first: Sophie

last: Badie

first: Cecilia

last: Folio

first: Javier

last: Benitez

first: Gonzalo

last: Gomez-Lopez

last: Pisano

first: Jos

last: Jonkers

first: Madalena

last: Tarsounas


title: Epigenetic regulations in the IFNγ signalling pathway: IFNγ-mediated MHC class I upregulation on tumour cells is associated with DNA demethylation of antigen-presenting machinery genes

first: Milan

last: Reinis

first: Veronika

last: Vlková

first: Ivan

last: Štěpánek

last: Hrušková

first: Filip

last: Šenigl

last: Mayerová

first: Jana

last: Šímová

last: Bieblová

last: Indrová

last: Hejhal


title: Microarray analyses of the effects of prenatal metformin exposure on the gene expression profile of liver, brain and subcutaneous adipose tissue of neonatal mice

city: Kuopio

first: Merja

last: Heinäniemi

address: Yliopistonranta 1

country: Finland

institute: university of eastern finland

summary: The aim of the study was to characterise the effects of prenatal metformin exposure on a tissue gene expression level in mice. The data consists of two models, regular diet (study I) and  high fat diet (study II) model. In  both models, metformin (300 mg/kg) or control agent (water) was administered to pregnant female mice from the embryonic day E0.5 untill E17.5.  In the high fat diet model, the dams had been on a high fat diet (60% of fat) for one month prior to and during the gestation. The diet was changed to regular diet from E18.5. The pups were sacrificed by decapitation at postnatal day 4 and brain (study I),  liver (studies I and II) and subcutaneous adipose tissue (study II) were taken for further microarray analyses.

overall_design: In study I,there are 3 replicates in each group of interest: brain_male_ctrl; brain_male_met; liver_male_ctrl; liver_male_met; liver_female_ctrl; liver_female_met. In study II, there are 6 replicates in each group of interest: liver_male_ctrl; liver_male_met; wat_male_ctrl; wat_male_met.

first: Henriikka

last: Salomäki

first: Markku

last: Koulu


title: Whole genome transcription profile of activated pre-B cells

city: Umeå

first: Thomas

last: Grundström

address: Analysvägen 1

department: Department of Molecular Biology

country: Sweden

institute: Umeå University

summary: To search for rapid changes in gene expression following pre-BCR activation, we performed DNA microarray analysis of activated pre-B cells with and without anti-m heavy chain  treatment for 3 hour.The expression of only small subset of genes differed significantly.

overall_design: The mouse bone marrow derived pre-B cells were grown with IL-7 on limiting amounts of S17 stromal cells and activated by incubation with goat F(ab’)2 anti-mouse μ heavy chain (Southern Biotechnologies) at 5 μg/ml for 3 hour.

first: Verma-Gaur

last: Jiyoti

first: Grundström

last: Thomas


title: Gene expression data from mouse hormone receptor positive mammary epithelial cells during early pregnancy

status: Public on Dec 02 2014

city: Singapore

first: Alexandra

last: Pietersen

address: 11 Hospital Drive

country: Singapore

institute: National Cancer Centre Singapore

summary:
The aim of this study was to identify transcriptional changes in hormone receptor positive (HR+) cells during the dynamic morphogenesis in mammary epithelium during early pregnancy. HR+ cells translate the systemic hormonal signals that indicate pregnancy into local instructions for the generation of alveoli (milk-producing units). We previously found that IGF-2 is produced by HR+ cells, but this is only detectable in early pregnancy and not in virgin animals. This data set was generated to charachterize what other genes become expressed in HR+ cells specifically during a time of active proliferation and cellular communication.
The gene expression profile at 3 days of pregnancy shows a marked upregulation of genes involved in cell division. By the 7th day of pregnancy the HR+ cells induce expression of several secreted molecules. Taken together with EdU incorporation analysis, we find that HR+ cells first undergo an expansion phase and subsequently express paracrine stimulators of alveolar and basal mammary epithelial cells during early pregnancy.

overall_design:
HR+ mammary epithelial cells were sorted by FACS directly into lysis buffer. We used CD49b and Sca1 to identify the HR+ cells. The RNA from the lysed cells was amplified and labeled with biotin. We harvested samples from virgin, 3-day and 7-day pregnant FVB mice and used 3 individual animals per time point.
1.5 μg of biotinylated a/cRNA from each sample was hybridized at 58°C for 16 hours using the Illumina Whole-Genome Gene Expression Direct Hybridization Assay system with the Illumina Mouse WG-6 v2.0 (six-sample BeadChip) platform. The signal was developed using streptavidin-Cy3 and the BeadChips were scanned with an Illumina BeadArray Reader. Raw signals were logarithmically transformed (to base 2) and quantile normalized with Partek Genomics Suite, version 6.6. The background noise from the array was determined at 100.


title: Genome-wide analysis of gene expression in lung cells from metformin treated Mycobacterium tuberculosis infected mice

first: jinmiao

last: chen

address: 8A Biomedical Grove, #04-06 Immunos

institute: Singapore Immunology Network

summary: Analysis of Metfromin induced changes in the lung cells of Mycobacterium tuberculosis infected mouse at gene expression level. The hypothesis tested in the present study was whether metformin has any effect on the host immune response in Mycobacterium tuberculosis infected mice? Results provide important information on the effect of metformin on the inflammatory response and immune activation associated with mycobacterial infection. In conclusion, Metfromin normalizes the chronic inflammation associated with Mycobacterium tuberculosis infection.

overall_design: Total RNA obtained from lung cells of untreated and metformin (500 mg/Kg) treated Mycobacterium tuberculosis infected mouse. The treatment was started day 7 post-infection and was given for 30 days post-initiation.

first: Amit

last: Singhal

first: Francesca

last: Zolezzi

first: Jinmiao

last: Chen

first: Michael

last: Poidinger

first: Gennaro

last: De Libero


title: Distinct luminal type mammary carcinomas arise from orthotopic Trp53 null mammary transplantation of juvenile versus adult mice

status: Public on Dec 01 2014

first: David

last: Nguyen

address: 1 Cyclotron Road, MS-977

department: Cell & Molecular Biology

institute: Lawrence Berkeley National Laboratory

summary: Age and physiological status like menopause are key factors in mammary development and are associated with breast cancer risk. Less clear is what factors influence breast cancer intrinsic subtypes that are associated with prognosis.    Here, we investigated the age of the host in a mammary chimera model.  The mammary glands of wildtype BALB/c mice were cleared of endogenous epithelium at 3 weeks of age and subsequently transplanted during puberty (5 weeks) or upon maturation (10 weeks) with syngeneic Trp53null mammary fragments.  The Trp53null mammary epithelium undergoes a high rate of neoplastic transformation, such that carcinomas arise over the course of a year.   Tumors arose more rapidly (p=0.003, log-rank test) when transplanted to adult hosts (AH, n=89) compared to tumors arising following transplantation into juvenile hosts (JH, n=55).  However, JH tumors grew several times faster than AH tumors, were more perfused as indicated by 2-fold larger blood vessels (p=0.015), and exhibited a 2-fold higher mitotic index (p=0.009). Transplantation into juvenile hosts (JH) gave rise to 80% ER positive tumors compared to 60% in adult hosts.  However, tumor cells were significantly more ER immunoreactive (p=0.0001) in JH tumors compared to those in AH tumors and were more highly positive for insulin like growth factor receptor  phosphorylation (p=0.026).   Expression profiles of JH (n=15) and AH (n=12) tumors identified 243 differentially expressed genes.  The main biological processes enriched in JH tumors were organ morphology, proliferation, and lipid metabolism.  An expression profile of juvenile versus adult (JVA) tumors revealed a luminal transcriptional program, characterized by expression of Foxa1, Igf2, Ccnd1 and Fgfr2.  The human homologs of JVA genes (JVAh) were used to create two centroids (AHh or JHh) to classify human breast cancers from archival microarray datasets in two-dimensional space.  Luminal human breast cancers were more like JH tumors compared to basal-like cancers, whereas luminal A tumors were more like JH tumors than luminal B tumors.  Consistent with this, JVAh genes segregated human luminal A from luminal B breast cancers via hierarchical clustering.  The distinct biology of tumors arising from tissue undergoing morphogenesis in the context of puberty suggests that young age at neoplastic transformation promotes a luminal tumor phenotype and supports the contention that the tumor intrinsic subtype is influenced by physiological status at the time of putative initiation.

overall_design: Trp53null mammary fragments were transplanted in the inguinal mammary glands of syngeneic BALB/c mice. The endogenous mammary ducts of the inguinal glands of the recipient mouse were surgically removed when the recipients were 3-weeks old. Recipient mice were transplanted at either 5 weeks of age (pubertal/juvenile) or 10 weeks of age (adult hosts). Chimeric mice were palpated 2-3 times per week for 13 months, starting six months after transplantation.

first: Lynn

last: Hlatky

first: Jian-Hua

last: Mao

first: Mary

last: Barcellos-Hoff


title: Transcriptional profiling reveals functional links between RasGrf1 and Pttg1 in pancreatic beta cells

city: Salamanca

first: Alberto

last: Fernández-Medarde

state: Salamanca

address: Campus Miguel de Unamuno

country: Spain

institute: Instituto de Biología Molecular y Celular del Cáncer-IBMCC

summary: We used microarrays to investigate gene expression changes in the pancreas of RasGrf1 KO mice. These animals have a reduction in the number and size of the pancreatic islets which lead to lower levels of insulin and glucagon in their blood.

overall_design: Manually selected pancreatic islets from collagenase-P digests of WT and RasGrf1 KO mice pancreases were used for RNA extraction using the TRIZOL protocol. RNA was further purified using Qiagen Rneasy mini kit. RNA from three different animals was pooled to obtain enough RNA for each microarray hybridization

first: L

last: Manyes

first: M

last: Arribas

first: C

last: Gomez

first: N

last: Calzada

first: A

last: Fernandez-Medarde

first: E

last: Santos


title: Gene expression profiles of nurse-like cells (NLCs) generated in vitro from chronic lymphocytic leukemia in presence of lenalidomide

status: Public on Nov 24 2014

city: Modena

first: Rossana

last: Maffei

state: Modena

address: Via del Pozzo 71

department: Dept of Hematology and Oncology

country: Italy

institute: University of Modena and Reggio Emilia

summary: NLCs were generated in vitro by culturing PBMCs from CLL patients for 10 days with/without the addition of 0.5 µM lenalidomide. Then, nonadherent cells were removed by vigorous pipetting and the remaining adherent cells were harvested for analyses. We inspected the whole-genome gene expression profiles of NLCs (control sample vs. lenalidomide-treated sample) derived from 4 CLL patients by microarray. Supervised analysis identified 584 genes differentially expressed upon lenalidomide treatment, 352 up-regulated and 232 down-regulated (p<0.05).

overall_design: RNA was extracted with the RNeasy Plus Mini kit (Qiagen, Valencia, CA, USA). Large-scale gene expression profiling (GEP) was performed by hybridizing RNA from NLCs treated or not with lenalidomide 0.5 µM for 10 days (n=4) on 4X44K Whole Human Genome Microarray (Agilent Technologies, Palo alto, CA). Genes were defined as differentially expressed between groups (NLCs CTRL vs. NLCs LENALIDOMIDE) at p<0.05 (paired t-test) and fold change ± 1.5 by using Gene Spring GX v12.6 (Agilent) software.

first: Stefania

last: Fiorcari


title: Genome-wide analysis of gene expression in wild-type and Sp4 hypomorphic mouse cerebellum

status: Public on Nov 27 2014

city: Boston

first: Grace

last: Gill

state: MA

address: 136 Harrison Ave

department: Genetics Program

institute: Tufts University

summary: Transcription factor Sp4 controls dendritic patterning during development of cerebellar granule neurons in culture by limiting branch formation and promoting activity-dependent pruning (Ramos et al., 2007). Sp4 is associated with neuropsychiatric disorders such as major depressive disorder, schizophrenia and bipolar disorder.  In order to identify target genes of Sp4, we compared global gene expression in the cerebella of wild type and Sp4 hypomorph mice (Sp4neo-/-; Zhou et al, 2005).  The results identify candidate Sp4 target genes that may contribute to neuronal development and neuropsychiatric disorders.

overall_design: Total RNA from postnatal Day 21 cerebella of 3 pairs of WT and Sp4 hypomorphic littermate mice were compared.

first: Xinxin

last: Sun


title: Identification of novel metastases-suppressor genes involved in lung cancer brain metastases formation.

status: Public on Nov 18 2014

city: Ibbenbüren

first: Dirk

last: Kemming

address: Roggenkampstr.

institute: ELA

summary: Initial screening for potential metastases suppressors down regulated by methylation was performed using lung cancer cell line models specific for site-specific metastasation. Gene expression profiling and qRT-PCR validations were conducted on tumor tissues from primary lung cancer (LC) and brain metastasis. HERC5 was further characterized for the methylation pattern.

overall_design: Three human lung cancer cell lines H1993, H1395 and were compared to the (SV40)-transformed human bronchial epithelial cell line BEAS-2B  in order to find genes, which might be specifically involved in brain metastasis formation. The cell lines were treated with 5-Aza-2'-deoxycytidine in order to find genes potentially down regulated by methylation. The non-tumorigenic cell line BEAS-2B was used to control for stress response after the treatment with 5-Aza-2'-deoxycytidine.

first: Harriet

last: Wikman


title: Wide methylation analysis in vestibular schwannoma [Affymetrix exon level analysis]

status: Public on Nov 30 2014

city: Badalona

first: Miguel

last: Torres-Martin

state: Barcelona

address: Carretera de Canyet, s/n

department: Clinical Genomics Unit

institute: Hospital Universitari Germans Trias i Pujol

summary: Vestibular schwannomas are intracranial tumors that affects unilateral and sporadically or bilateral when is associated to Neurofibromatosis type 2 syndrome. The hallmark of the disease is the biallelic inactivation by NF2 gene mutation or LOH of chromosome 22q, where this gene harbors. In this work, we used  Infinium HumanMethylation 450K BeadChip  microarrays in a series of 36 vestibular schwannomas, 4 non-vestibular schwannomas and 5 healthy nerves. Our results shows a trend to hypomethylation in schwannomas. Furthermore, HOX genes, located at 4 clusters in the genome, displayed hypomethylation in numerous CpG sites in vestibular but not in non-vestibular schwannomas. Additionally, several microRNA and protein-coding genes were found hypomethylated at promoter regions and confirmed by expression analysis; including miRNA-199a1, miRNA-21, MET and PMEPA1. We also detected methylation patterns that might be involved in alternative transcripts of several genes such as NRXN1 or MBP; that would increase the complexity of methylation-expression. Overall, our results shows specific epigenetic signatures in several coding genes and microRNA that could be used in the finding of potential therapeutic targets.

overall_design: Microarrays of vestibular and 4 non-vestibular schwannomas were used in Affymetrix Human Gene 1.0 ST, at exon level. Batch correction was performed between tumors and controls to avoid batch effect.

first: Luis

last: Lassaletta

first: Barbara

last: Melendez

first: Juan

last: Rey


title: Genome-wide analysis of gene expression of Flk1Cre;ETV2 CKO mouse yolk sacs.

status: Public on Nov 17 2014

city: Des Moines

first: Chunfa

last: Jie

state: IA

address: 3200 Grand Ave

institute: Des Moines University

summary: To identify genes critical for vascular development, we generated mice where ETV2 is inactivated in FLK1+ cells by a loxP-Cre recombination approach.  Results provide a detailed insight into the function of ETV2 in emrbyonic vasculare formation.

overall_design: Total RNA obtained from E9.5 yolk sacs from Flk1Cre;ETV2 CKO and control mice.

first: Changwon

last: Park


title: Gene expression changes induced by the pan-PIM inhibitor ETP-39010 in 4 peripheral T cell lymphoma cell lines

status: Public on Nov 14 2014

city: Madrid

first: Esperanza

last: Martín-Sánchez

address: Melchor Fernandez Almagro 3

institute: Spanish National Cancer Research Centre (CNIO)

summary: Peripheral T cell lymphoma (PTCL) is a very aggressive disease which currently lacks efficient targeted therapy. New therapeutic strategies are needed to improve the very poor outcome of these patients. In these study we hypothesized that PIM kinases could be of therapeutic value in PTCL because we found an overexpression of PIM1 and PIM2, but not PIM3, in PTCL cases, cell lines and primary tumoral T cells from Sezary Syndrome patients, compared with reactive lymph nodes and normal T cells from healthy donors, respectively. In order to understand the mechanism of action of this pan-PIM inhibitor in PTCL, 4 cell lines (DERL7, HuT78, SR786 and MyLa) were treated with 10 μM of ETP-39010 for 0, 2, 4, 6, 10 and 24 h, and gene expression profiling was performed.

overall_design: 4 PTCL cell lines (DERL7, HuT78, SR786 and MyLa) were treated with DMSO and 10 μM of the pan-PIM inhibitor ETP-39010, and hybridized using the Universal Human Reference RNA (Stratagene, La Jolla, CA) as the reference sample.

first: Socorro

last: Rodríguez-Pinilla

last: Piris


title: Gene expression signatures for Nanog-positive and Nanog-negative hepatocellular carcinoma cells

status: Public on Nov 13 2014

city: Chong qing

first: junjie

last: shen

address: Gaotanyan 30, Shapingba District

country: China

institute: Institute of Pathology and Southwest Cancer Center

summary: Whole genome microarray expression profiling of  HCC cell line (Huh7) and patients derive primary HCC cells (T1115 and T1224) expressing Nanog or not. Results provide insight into the role of Nanog in transcriptional regulation.

overall_design: Using Nanog promoter as a reporter system, we sorted the Nanog-positive and Nanog-negative cells from Huh7, T1115 and T1224 by FACS, respectively. Each group is composed of a Nanog negative control and two independent Nanog positive samples.

first: Juanjuan

last: Shan

first: Junjie

last: Shen

first: Limei

last: Liu

first: Feng

last: Xia

first: Chuan

last: Xu

first: Guangjie

last: Duan

first: Yanmin

first: Qinghua

last: Ma

first: Zhi

last: Yang

first: Qianzhen

last: Zhang

first: Leina

first: Jia

first: Senlin

first: Xiaochu

last: Yan

first: Ping

last: Bie

first: Youhong

last: Cui

first: Xiu-wu

last: Bian

first: Cheng

last: Qian


title: Hepatic Farnesoid X-Receptor Isoforms α2 and α4 Differentially Modulate Bile Salt and Lipoprotein Metabolism in Mice

status: Public on Nov 11 2014

city: Groningen

first: vincent

last: bloks

department: Pediatrics

country: Netherlands

institute: UMCG

summary: The nuclear receptor FXR acts as an intracellular bile salt sensor that regulates synthesis and transport of bile salts within their enterohepatic circulation. In addition, FXR is involved in control of a variety of crucial metabolic pathways. Four FXR splice variants are known, i.e. FXRα1-4. Although these isoforms show differences in spatial and temporal expression patterns as well as in transcriptional activity, the physiological relevance hereof has remained elusive. We have evaluated specific roles of hepatic FXRα2 and FXRα4 by stably expressing these isoforms using liver-specific self-complementary adeno-associated viral vectors in total body FXR knock-out mice. The hepatic gene expression profile of the FXR knock-out mice was largely normalized by both isoforms. Yet, differential effects were also apparent; FXRα2 was more effective in reducing elevated HDL levels and transrepressed hepatic expression of Cyp8B1, the regulator of cholate synthesis. The latter coincided with a switch in hydrophobicity of the bile salt pool. Furthermore, FXRα2-transduction caused an increased neutral sterol excretion compared to FXRα4 without affecting intestinal cholesterol absorption. Our data show, for the first time, that hepatic FXRα2 and FXRα4 differentially modulate bile salt and lipoprotein metabolism in mice.

overall_design: Total RNA obtained from liver were compared in the 2 different groups, 6 isoform fxr2 transduced frx-/- mice were compared with 6 isoform fxr4 transduced frx-/- mice. All animals received chow diet supplemeted with 0.5% cholate (CA).

first: M

last: Boesjes

first: V

middle: W

last: Bloks

first: J

last: Hageman

first: T

last: Bos

last: van Dijk

first: H

last: Wolters

last: Havinga

last: Jonker

first: F

last: Kuipers

first: A

middle: K

last: Groen


title: Genome-wide analysis of telomerase-regulated genes in MLL-AF9 acute myeloid leukemia stem cells (LSCs)

city: Herston

first: Steven

last: Lane

address: 300 Herston Road

country: Australia

institute: QIMR Berghofer Medical Research Institute

summary:
Genome-wide transcriptional profiling of purified telomerase deficient (Terc-/-) and WT LSCs was performed in order to gain insights into the mechanisms underlying the susceptibilities of Terc-/- LSCs in vivo.
Results provide important information on the response of LSCs to telomerase deficiency, such as telomerase-dependent genes, and dysregulated cellular functions including cell cycle, DNA replication, recombination and repair, altered cellular morphology, cellular function and maintenance, and activated programmed cell death.

overall_design: Total RNA obtained from G3 Terc-/- LSCs compared to WT LSCs (MLLAF9gfp+, lin-, kit+, Fcgr+) purified from primary recipients at individual disease onset.

first: Claudia

last: Bruedigam

first: Frederik

middle: O

last: Bagger


title: Telomerase Inhibition Effectively Targets Mouse and Human AML Stem Cells and Delays Relapse Following Chemotherapy

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

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus

overall_design: Refer to individual Series


title: Enhanced skeletal muscle regeneration upon Bmi1 gain of function is driven by Mt1-mediated protection from oxidative stress.

city: Trieste

first: Danilo

last: Licastro

department: Genomica Funzionale

institute: CBM

summary: Three independently prepared satellite cell cultures isolated from STOPFloxBmi1 mice, treated with Adeno-Cre (A-Cre) infection and induced to differentiate for 2 days were analysed by whole-genome Illumina platform mouse v2 as compared to the same cells treated with Adeno-GFP (A-GFP).

overall_design: 6 samples,2 condition with 3 biological replicates per condition

first: Xinyu

middle: X

last: Zhang

first: Silvia

last: Marino


title: Genome-wide analysis of gene expression in DJ-1 deficient muscle cells

status: Public on Nov 07 2014

city: Toronto

first: Minna

last: Woo

state: Ontario

address: Room 10-601D, 101 College Street

country: Canada

institute: University of Toronto

summary: Excessive reactive oxygen species (ROS) underlie the pathogenesis of multiple disorders. Nevertheless, physiological levels of ROS are required for intracellular signalling and maintenance of metabolic homeostasis. DJ-1, a Parkinson’s disease-associated protein, is involved in the regulation of oxidative stress. Our aim in this study was to determine the effect of DJ-1 disruption on gene expression in muscle cells. To this end, we transfected a murine myoblast cell line, C2C12 cells with siRNA targeting DJ-1.

overall_design: C2C12 myoblasts purchased from ATCC were transfected with scramble or DJ-1 siRNA, and 48 hours later, cells were induced to differentiate into myotubes. 4 days later, myotubes were harvested and processed for RNA extraction and hybridization.


title: Genome-wide measurement of gene expression changes with Bptf knockout in mouse embryonic fibroblasts

status: Public on Nov 06 2014

city: Richmond

first: Joseph

middle: William

last: Landry

state: Virginia

address: 401 College Street

department: Human and Molecular Genetics

country: USA

institute: Virginia Commonwealth University

summary: Gene expression frequently requires the action of chromatin remodeling complexes and it is assumed that these complexes have common gene targets across cell-types. Contrary to this belief, we show that Bptf, an essential and unique subunit of the Nucleosome Remodeling Factor (NURF), largely regulates cell-type-restricted gene expression across diverse cell-types. Unexpectedly, cell-type-restricted gene expression is accomplished through both physical and functional interactions between NURF and the ubiquitous multivalent factor Ctcf. We go on to show in these cell types, that Bptf influences the regulatory activity of Ctcf binding sites in a cell type-restricted manner. Detailed studies of Ctcf binding sites in embryonic stem cells (ESC) show that Bptf prevents Klf4 binding upstream of H2-K1, and facilitates RNA polymerase elongation through Ccnd1, to regulate genes important for embryonic development. In total, these studies provide mechanisms by which prominent chromatin remodeling complexes can maintain cell-type-restricted gene expression through ubiquitous factors like Ctcf.

overall_design:
Analysis of gene expression changes in mouse embryonic cells with Bptf knockout using TetO-Cre expression system.
Three independent cell lines with knockout or control genotypes were depleted of Bptf prior to extracting total RNA for microarray analysis.

first: Zhijun

last: Qiu


title: Allele specific gene expression in tissue

city: Montreal

first: Tomi

middle: Markku

last: Pastinen

state: Quebec

address: 740, Dr. Penfield Avenue

institute: McGill University and Génome Québec Innovation Centre

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

summary: This set of data was used to identify cis-regulatory SNPs by measuring allelic gene expression. From analyzing cis-regulatory SNPs from different tissues,  cis-regulatory SNPs common across tissues or the cell-type specific  were cataloged.

overall_design:
International Hapmap Project - Yoruba samples, genotypes and allele ratios were obtained using Illumina HumanOmni 1M Beadchips.
CEU Samples, genotypes and allele ratios were obtained using Illumina Human1M-Duov3 DNA Analysis BeadChip (Human1M-Duov3_B)

first: Bing

last: Ge


title: Gene expression analysis of mtDNA-depleted (Rho) mouse embryonic fibroblasts

status: Public on Nov 03 2014

city: Parkville

first: Matthew

last: Ritchie

state: Victoria

address: 1G Royal Parade

department: Epigenetics and Development Division

institute: The Walter and Eliza Hall Institute of Medical Research

summary: Genome-wide transcriptional profiles of parental and mtDNA-depleted mouse embryonic fibroblasts. Analysis revealed a downregulation of ChrM genes.

overall_design: Mcl1 knockout mouse embryonic fibroblasts (transformed with SV40 large T antigen) were cultured for 7 days with Ethidium Bromide (100 ng/mL) in DMEM supplemented with Glucose (4.5 g/L), Uridine (50 ug/mL) and Sodium Pyruvate (100 ug/mL). Depletion of mtDNA was assessed by quantitative real-time PCR. Total RNA was isolated and up to 250 ng of total RNA per sample was labelled and hybridized to Illumina Mouse WG6V2 expression BeadChip platform. Three replicate samples were available for each population.

middle: E


title: C/EBPα and PPARγ-specific transcriptional programs in mature adipocytes in vivo

status: Public on Nov 04 2014

city: Dallas

first: Qiong

middle: A.

last: Wang

address: 5323 Harry Hines Blvd.

department: Internal Medicine

institute: UT Southwestern Medical Center

summary: We took a systematic approach to determine the transcriptional programs that are specifically regulated by C/EBPα in mature white adipocytes of mice on chow diet or high fat diet. The hypothesis tested in the present study was that C/EBPα, as a lipogenic transcription factor, has unique direct targets compared to PPARγ. Our inducible adipocyte specific knockout system allows us to test the direct targets of C/EBPα and PPARγ in adipocytes by short-term C/EBPα or PPARγ elimination in mature adipocytes in vivo. Results indicate that although it has been shown that C/EBPα and PPARγ cross-regulate each other, they have distinct direct responsive targets. Moreover, there are very few C/EBPα specific targets in mice on a chow diet, most of the C/EBPα targets in mature adipocytes are genes modulated by HFD feeding.

overall_design: Total RNA obtained from subcutaneous adipose tissue of Adn-C/EBPα-/- mice on doxycycline chow diet for 3 days,  doxycycline high fat diet for 3 days or 1 month and  Adn-PPARγ-/- mice on doxycycline chow diet for 3 days, compared to control littermates.

middle: A

first: Philipp

last: Scherer


title: Genome-wide analysis of mouse 4T1 tumor cells derived clone (4T1ch9) gene expression subjected to transduction with STC1-specific or non-targeting shRNA  lentiviral particles

status: Public on Nov 01 2014

city: Westmead

first: Andy

middle: C-M

last: Chang

state: New South Wales

address: 214 Hawkesbury Rd

department: Cancer Unit

institute: Children's Medical Research Institute

summary: Analysis of genes regulated by STC1 down-regulation in mouse 4T1 derived clone, 4T1ch9.  STC1 expression is associated with tumor growth and metastasis.  This study looks at genes affected when STC1 expression is down-regulated by STC1 shRNA.

overall_design: Total RNA isolated from shRNA transduced cells subjected to puromycin selection for  5-6 days.


title: Purification and ex vivo expansion of fully functional salivary gland stem cells

first: lalitha

middle: sy

last: nanduri

state: Groningen

address: Antonius deusinglaan 1

department: cell biology

institute: university medical center groningen

summary: Analysis of genes that are enriched in long-term self-renewing salivary gland stem cells. And analysis of genes that are enriched in the organoids containing differentiated salivary gland cells.

overall_design: Total RNA extracted from long-term self-renewing CD24hi/CD29hi passage-10 cells and compared to that of non-selfrenewing CD24hi/CD29hi passage-0 cells. Total RNA extracted from differentiated organoids compared with that of undifferentiated primary sphere cells.

first: Lalitha

last: Nanduri

first: Rob

middle: P

last: Coppes


title: EWS/WT1 co-operates with the loss of p53 to exert its oncogenic effects and up-regulates canonical Wnt pathway signaling.

first: Paul

last: Ekert

state: Vic

department: Cell Signalling and Cell Death

institute: Walter and Eliza Hall Institute of Medical Research

summary: The t(11;22)(p13;q12) translocation is pathognomonic for the highly aggressive desmoplastic small round cell tumour (DSRCT). The translocation fuses exon 7 of the EWS gene to exon 8 of the WT1 gene (EWS/WT1). Two splice variants of EWS/WT1 exist, arising from the presence (+KTS) or absence (-KTS) of three amino acids: lysine, threonine and serine between zinc fingers 3 and 4. To investigate the oncogenic properties of both isoforms of EWS/WT1, we over-expressed EWS/WT1 in untransformed murine embryonic fibroblasts (MEFs).  We demonstrate that neither isoform of EWS/WT1 is sufficient to transform wild type MEFs, however the oncogenic potential of both isoforms is unmasked by the loss of p53.  Expression of EWS/WT1 in MEFs lacking at least one allele of p53 resulted in enhanced cell proliferation, clonogenic survival and anchorage-independent growth.  In addition EWS/WT1 expression in wild type MEFs attenuated several p53-dependent responses, including cell cycle arrest after irradiation and daunorubicin induced apoptosis.  We show that DSRCT commonly have copy number amplification of MDM2 and MDMX, suggesting loss of p53 function in the tumours.  Expression of either isoform of EWS/WT1 in MEFs induced characteristic mRNA expression profiles, including up-regulation of canonical Wnt pathway signaling.  This was validated in cell lines and in a series of DSCRT, which confirmed canonical Wnt pathway activation in the tumours.  We show for the first time that both isoforms of EWS/WT1 have oncogenic potential and that in addition to co-operating with loss of p53 function can also further attenuate p53-mediated responses.  In addition we provide the first link between EWS/WT1 and Wnt pathway signaling.  These data provide novel insights into the function of the EWS/WT1 fusion protein which characterizes DSCRT.

overall_design: Four independently generated pools of wild type MEFs were infected with tetracycline repressible EWS/WT1+KTS, EWS/WT1-KTS or GFP, selected with hygromycin and protein expression confirmed.  Four GFP, four KTS+ and four KTS- samples were hybridized to the Ilumina BeadChip.

first: Pratiti

last: Bandopadhayay

first: Anissa

middle: M

last: Jabbour

first: Christoperh

last: Riffkin

first: Marika

last: Salmanidis

first: Lavinia

last: Gordon

first: Dean

last: Popovski

first: David

last: Ashley

first: Neil

last: Watkins

last: Thomas

first: Elizabeth

last: Algar

middle: G


title: Identification of cytokine signals regulated by Caspase-9

first: Matthew

last: Ritchie

summary: Genome-wide transcriptional profiles of the hematopoietic stem and progenitor cell (HSPCs)-enriched population derived from bone marrow chimeras reconstituted with Caspase-9 or Bak and Bax deficient fetal liver cells. Gene ontology analysis revealed changes in the expression of genes associated with interferon responses.

overall_design: HSPCs (Lineage-Kit+CD45.2+) were flow sorted from the femur and tibia of bone marrow chimeras 12-16 weeks post transplant of 2 million embryonic day (E) 13.5 fetal liver cells. Total RNA was isolated and up to 250 ng of total RNA per sample was labelled and hybridized to Illumina Mouse WG6V2 expression BeadChip platform. Three independent samples were used for each population.


title: Identifying genes regulated by miR-490-3p

status: Public on Oct 18 2014

city: Hong Kong

first: Jing

last: Shen

address: Lo Kwee-Seong Integrated Biomedical Sciences Building, cuhk, Shatin NT

department: sbs

country: Hong Kong

institute: The Chinese University of Hong Kong

summary: To identify the direct target of miR-490-3p, we used whole genome microarray expression profiling to screen for genes potentially regulated by the microRNA.

overall_design: AGS cells were transfected with control mimics or miR-490-3p mimics and gene expression was determined 72 hours after transfection.

first: William

last: Wu


title: Tumor suppression by miR-26 overrides potential oncogenic activity in intestinal tumorigenesis

status: Public on Oct 30 2014

first: Joshua

last: Mendell

state: Texas

address: 6000 Harry Hines Blvd NA 6.200

department: Molecular Biology

summary:
Through a series of mouse genetic studies, we concluded that miR-26 overexpression in intestinal epithelial cells inhibits tumor formation in Apcmin/+ mice.
We isolated intestinal epithelial cells from M2rtTA and M2rtTA; eGFP.miR-26a to assess gene expression changes after the induction of miR-26a expression.

overall_design: Intestinal epithelial cells were isolated from three M2rtTA and three M2rtTA; eGFP.miR-26a mice after treatment with doxycycline for 10 days.  Gene expression was profiled using Illumina microarrays.

first: Lauren

middle: R

last: Zeitels

middle: T


title: Deletion of DUSP5 affects the expression of a subset of TPA-inducible genes

status: Public on Oct 17 2014

city: London

first: Philip

last: East

state: London

address: 1 Midland Road, London

department: Bioinformatics

institute: The Francis Crick Institute

summary: This experiment was designed to determine if deletion of the dual-specificity MAP kinase phosphatase encoded by DUSP5 had any effect on the pattern of gene expression in cells treated with the phorbol ester tumour promoter TPA. Sex matched primary WT and DUSP5 knockout MEFs were isolated from littermate embryos and cultured. Cells were then exposed to TPA for 0, 1 and 3h before isolation of RNA prior to microarray hybrdisation and data analysis. Our results show that the transcript levels of a subset of TPA-inducible genes are altered in cells that lack DUSP5.

overall_design: Primary sex-matched wild type (WT) and DUSP5 knockout (KO) mouse embryonic fibroblasts (MEFs) were derived from littermate day 13.5 embryos. Cells were treated for 0, 1 and 3 hours with TPA, and the experiment was done in triplicate (18 samples in total).

first: Linda

last: Rushworth

first: Stephen

last: Keyse


title: Gene expression in HNSCC cell lines after knockdown of CTTN

city: Heidelberg

first: Madeleine

last: Gross

address: Im Neuenheimer Feld 280

country: Germany

institute: German Cancer Research Center

summary: The gene expression level of CTTN was decreased in HPV-negative HNSCC cell line with an amplification and overexpression of CTTN by performing knockdown experiments using RNA interference. Gene expression profiling and consecutive pathway analyses showed a number of deregulated genes known to be involved in metastatic processes such as migration and invasion. Furthermore, three potential downstream targets of CTTN (MAF, MAFB and PLAC2) were identified.

overall_design: cells with knockdown of CTTN vs. Control,  4 biological replicates

first: Elena

last: Orlova

first: Aristotelis

last: Kittas

first: Niels

last: Grabe

first: Kolja

last: Freier

first: Peter

last: Lichter


title: A dysregulated Acetyl/SUMO switch of FXR promotes hepatic inflammation in obesity

city: Urbana

first: Jongsook

middle: Kim

last: Kemper

state: Illinois

address: 524 Burrill Hall

department: Department of Molecular & Integrative

institute: University of Illinois at Urbana-Champaign

summary: Acetylation of transcriptional regulators is normally dynamically regulated by nutrient status but is often persistently elevated in nutrient-excessive obesity conditions. We investigated the functional consequences of such aberrantly elevated acetylation of the nuclear receptor FXR as a model. Proteomic studies identified K217 as the FXR acetylation site in diet-induced obese mice. In vivo studies utilizing acetylation-mimic and -defective K217 mutants and gene expression profiling revealed that FXR acetylation increased proinflammatory gene expression, macrophage infiltration, and liver cytokine and triglyceride levels, impaired insulin signaling, and increased glucose intolerance. Mechanistically, acetylation of FXR blocked its interaction with the SUMO ligase PIASy and inhibited SUMO2 modification at K277, resulting in activation of inflammatory genes. SUMOylation of agonist-activated FXR increased its interaction with NF-κB but blocked that with RXRα, so that SUMO2-modified FXR was selectively recruited to and trans-repressed inflammatory genes without affecting FXR/RXRα target genes. A dysregulated Acetyl/SUMO switch of FXR in obesity may serve as a general mechanism for diminished anti-inflammatory response of other transcriptional regulators and provide potential therapeutic and diagnostic targets for obesity-related metabolic disorders.

overall_design: FXR-WT or the FXR-K217Q mutant was expressed in lean mice and FXR-WT or the FXR-K217R mutant was expressed in obese mice by adenoviral infection. One week after infection, mice were treated with GW4064 (30 mg/kg in corn oil) overnight before sacrifice and hepatic expression was analyzed by Illumina microarray.

first: Dong-Hyun

last: Kim

first: Zhen

last: Xiao

first: Sanghoon

last: Kwon

first: Xiaoxiao

last: Sun

first: Daniel

last: Ryerson

first: David

last: Tkac

first: Ping

last: Ma

first: Shwu-Yuan

first: Cheng-Ming

last: Chiang

first: Edward

last: Zhou

first: H

last: Xu

first: Jorma

middle: J

last: Palvimo

first: Lin-Feng

last: Chen

first: Byron


title: Long noncoding RNA as putative biomarkers for protstate cancer detection [Set 2]

city: Durham

first: Jian-Liang

last: Li

state: NC

address: 111 TW Alexander Dr

institute: NIEHS

summary: To identify which lncRNAs are differentially expressed in prostate cancer, the total RNA from prostate cancer cell lines (PC3, LNCaP), normal epithelial prostatic cells and the pool of 10 prostate tumor tissues and 10 adjacent normal prostate tissues were screened using SurePrint G3 human lncRNA microarrays (Agilent). The SurePrint G3 Human Gene array contains 16,472 lincRNAs and 34,127 mRNA genes.

overall_design: Gene expression in prostate cell lines and pooled tissue samples was measured. Three independent experiments (biological replicates) for cell lines (epithelial cells, PC3 and LNCap) and two independent experiments (technical replicates) for pooled prostate tissues (tumor and adjacent normal) samples were performed.

first: Bongyong

last: Lee

first: Joseph

last: Mazar

first: Jian

middle: L

first: Subramaniam

last: Govindarajan

first: Ranjan

last: Perera


title: Analysis of cardiac gene expression in juvenile versus mature mice with repressed CELF activity (MHC-CELFdelta)

status: Public on Oct 16 2014

city: Cleveland

first: John

last: Barnard

state: Ohio

address: 9500 Euclid Ave.

department: Quantitative Health Sciences

institute: Cleveland Clinic Foundation

summary: CUG-BP, Elav-like family (CELF) proteins regulate alternative splicing.  In MHC-CELFdelta transgenic mice, CELF-mediated alternative splicing is disrupted in heart muscle via expression of a nuclear dominant negative CELF protein under an alpha-myosin heavy chain promoter.  MHC-CELFdelta mice develop dilated cardiomyopathy and contractile dysfunction by 3 weeks of age, shortly after the transgene is activated and splicing defects appear.  Cardiac function and heart size spontaneously recover with age in a low-expressing (mild) line of MHC-CELFdelta mice despite persistence of dominant negative protein expression and splicing defects, whereas there is no recovery in a higher-expressing (severe) line that also experiences early muscle death and fibrosis.  In this study, we explored the basis for this functional recovery by comparing the gene expression profiles in the hearts of low- and high-expressing lines of MHC-CELFdelta mice to those of wild type littermates at 3 weeks (when cardiac dysfunction is maximal) and 24 weeks (when the low-expressing line has recovered) using microarrays.  We found that differences in gene expression are greatly reduced in older animals from the low-expressing line, but were exacerbated in the high-expressing line.  We did not find evidence of a new compensatory pathway being activated in the low-expressing line with age, and propose that recovery may occur due to developmental stage-specific compatibility of CELF-dependent splice variants with the changing cellular environment of cardiomyocytes.

overall_design: Microarray analysis was performed on total RNA extracted from whole hearts of female mice: three MHC-CELFdelta-10 (high-expressing line) and three MHC-CELFdelta-574 (low-expressing line) were collected at 3 weeks, and five MHC-CELFdelta-10 and five MHC-CELFdelta-574 were collected at 24 weeks.  Two wild type mice from each line were collected at each time point (n = 4 total wild type at 3 weeks, and n = 4 total wild type at 24 weeks).

first: Twishasri

last: Dasgupta

first: Samantha

last: Stillwagon

first: Andrea

middle: N

last: Ladd


title: Differential gene expression analysis of fetal liver cells of R26-LSL-KITD816V:Vav-iCre mice related to controls

city: Bonn

first: Natalie

last: Haas

address: Sigmund-Freud-Str. 25

department: Department of Developmental Pathology

institute: University of Bonn Medical School/ Institute of Pathology

summary: Analysis of differential gene expression. The influence of a constitutively activated mutant Kit receptor on gene expression in fetal hematopoietic cells was analyzed. Results provide information of genes and cellular processes that are influenced by Kit signaling.

overall_design: Total RNA obtained from embryonic day E13.5 fetal liver of double transgenic R26-LSL-KITD816V:Vav-iCre mice compared to single transgenic controls. R26-LSL-KITD816V mice have been registered with the mouse genome database (MGI:5516508, allele named Gt(ROSA)26sorTM1(GFP-cKIT*)Hsc). Vav-iCre mice have been described by De Boer et al. in 2003.

first: Hubert

last: Schorle

first: Holger

last: Fröhlich

first: Deena

last: Gergis


title: MeWo/IMP-3 v.s. MeWo/vec

status: Public on Oct 23 2014

city: Taipei

first: Yi-Shuan

last: Sheen

address: 7 Chun-Shan South Road

department: Dermatology

country: Taiwan

institute: Natioanl Taiwan University Hospital

summary: IMP-3 Promotes Migration and Invasion of Melanoma Cells by Modulating the Expression of HMGA2 and Predicts Poor Prognosis in Melanoma

overall_design: Two-condition experiment,MeWo/IMP-3 v.s. MeWo/vec. Biological replicates: 2 control replicates, 2 transfected replicates.


title: 40 IPF patients and 8 healthy controls

status: Public on Oct 14 2014

city: South San Francisco

first: Alex

last: Abbas

state: CA

address: 1 DNA Way

institute: Genentech, Inc.

summary:
There is microscopic spatial and temporal heterogeneity of pathologic changes in idiopathic pulmonary fibrosis (IPF) lung tissue, which may relate to heterogeneity in pathophysiological mediators of disease and clinical progression.
We measured gene expression in samples from lung biopsies or explants in order to assess relationships with pathological features and systemic biomarkers.

overall_design: RNA was extracted directly from lung tissue samples from 40 IPF patients or 8 healthy controls.

first: Alexander

first: Daryle

last: DePianto

first: Sanjay

last: Chandriani

first: Guiquan

last: Jia

first: Elsa

last: N'Diaye

first: Steven

last: Kauder

first: Sabyasachi

last: Biswas

first: Connie

last: Ha

first: Zora

last: Modrusan

first: Harold

last: Collard

first: Jackson

last: Egen

first: Paul

last: Wolters

last: Arron


city: Bethesda

first: WeiPing

last: Chen

state: MD

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

department: GCL

institute: NIDDK/NIH

summary:
Indoxyl sulfate (IS) is a uremic toxin and ligand of the aryl-hydrocarbon receptor (Ahr), a transcriptional regulator. Elevated serum IS may contribute to the progression of kidney disease. Therefore, we assessed mouse podocyte damage mediated by IS. Ahr was predominantly localized to the podocyte nucleus in vivo and in vitro. In isolated glomeruli, IS-exposure for 2 – 24 h induced Cyp1a1 expression, the most sensitive biomarker of Ahr activation. Mice exposed to IS for 4–8 weeks exhibited microalbuminuria, and mild glomerular injury characterized by ischemic changes, partial podocyte foot process effacement, as well as vascular and tubulointerstitial damage. Chronically IS-exposed kidneys exhibited decreased mRNA, decreased protein levels, and altered staining patterns for podocin, synaptopodin, and non-muscle myosin IIA (Myh9). Immortalized podocytes, upon differentiation, exhibited Ahr nuclear translocation beginning 30 min after 1 mM IS-exposure. At 2 h, there was a dose-dependent decrease in podocyte mRNA expression of WT1, Podxl, Snypo, Myh9, Actn4, and Cd2ap. After 24 h of exposure to IS, podocytes were smaller, had fewer actin/Myh9 fibers, and decreased viability. Ahr-RNAi decreased mRNA expression of podocyte-specific proteins and inhibited Cyp1a1 induction by IS-exposure. Combinations of Ahr-RNAi and IS-exposure further decreased Myh9 expression. In immortalized human podocytes, IS treatment caused cell injury, decreased mRNA expression of podocyte-specific proteins, integrins, collagens, cytoskeletal proteins, and bone morphogenetic proteins, and increased cytokine and chemokine expression. Thus, chronic IS-exposure causes glomerular damage by activating Ahr, altering podocyte function, differentiation, and morphology, and inducing a pro-inflammatory phenotype.
Podocyte cells treated with Indoxyl sulfate, a uremic toxin and aryl-hydrocarbon receptor ligand, mediates progressive glomerular disease by damaging podocytes

overall_design: Human podocyte cell line treated with or without 3-Indoxyl sulfate (1mM/0.1%DMSO) in three replications

first: Osamu

last: Ichii

first: Saori

last: Ostuka

first: Teppei

last: Nakamura

first: Yasuhiro

last: Kon

first: Weiping

first: Avi

middle: Z

last: Rosenberg

first: Jeffrey

middle: B

last: Kopp

first: Moin

last: Saleem


title: Expression data from TAp73+/+ and TAp73-/- MEFs

status: Public on Oct 11 2014

city: Singapore

first: Kanaga

last: Sabapathy

state: Singapore

address: 11 Hospital Drive

institute: National Cancer Centre Singapore

summary: The aim of the experiment was to analyse the gene expression differences between MEFs containing TAp73 or without TAp73, at basal levels in normal culture conditions, and upon treatment with hypoxia (by incubation in 1% oxygen) for 4 or 8 hrs. The analysis indicate that absence of TAp73 leads to changes in multiple cellular and biological processes.

overall_design: TAp73-/- and Tap73+/+ MEFs that were untreated, or treated with hypoxia (in 1% oxygen)  for 4 and 8 hours were used for gene expression analysis

first: Iqbal

last: Dulloo


title: Gene expression profiling of tumor-adjacent histologically normal lung tissues from lung SCC patients

status: Public on Oct 06 2014

city: Beijing

first: Bangrong

last: Cao

address: NO.17 Panjiayuannanli, Chaoyang District, Beijing, P.R.China

institute: Cancer Institute & Hospital, Chinese Academy of Medical Sciences

summary: Tumor-adjacent noncancerous tissues often exhibited abnormalities on molecular levels, which is described as field effect of cancerization. Accumulated evidence demonstrated that filed effect may also play important role in cancer progression. In the present study, we found that the gene expression profile in noncancerous lung tissues adjacent to lung squamous cell carcinoma (SCC) was significantly associated with regional lymph node status of patients. Significance Analysis of Microarrays (SAM) showed that 121 genes were significantly associated with lymph node metastasis (delta=0.75, FDR=0.069). Interestingly, all of the significant genes were up-regulated in the lymph node positive samples. For these genes, the most significant biological GO terms were extracellular structure organization, cell adhesion, regulation of cell motion/migration, and vessel development, etc, which were also involved in EMT process supported by another experiment in vitro.

overall_design: Tumor-adjacent histologically normal lung tissues were collected from 60 primary lung SCC patients, of whom 34 (56.7%) suffered regional lymph node metastasis. Gene expression profiling analysis of these samples was performed using Agilent 4x44K human whole genome gene expression microarray (G4112F).

first: Lin

last: Feng

first: Yan

last: Liu

first: Yu

first: Shujun

last: Cheng

first: Yanning

last: Gao

first: Kaitai

last: Zhang