title: The miR-200 family and targets, ZEB1 and ZEB2, modulate uterine quiescence and contractility during pregnancy and labor

status: Public on Oct 30 2010

city: Dallas

first: Carole

middle: R

last: Mendelson

address: 5323 Harry Hines Blvs

department: Biochemistry

institute: University of Texas Southwestern Medical Center

summary: Throughout most of pregnancy, uterine quiescence is maintained by increased progesterone receptor (PR) transcriptional activity, while spontaneous labor is initiated/facilitated by a concerted series of biochemical events that activate inflammatory pathways and negatively impact PR function. In this study, we uncovered a new regulatory pathway whereby miRNAs serve as hormonally-modulated and conserved mediators of contraction-associated genes in the pregnant uterus from mouse to human. Using miRNA and gene expression microarray analyses of uterine tissues, we identified a conserved family of miRNAs, the miR-200 family, that is highly induced at term in both mice and humans, as well as two coordinately downregulated targets, zinc finger E-box binding homeobox proteins, ZEB1 and ZEB2, which act as transcriptional repressors. We also observed upregulation of the miR-200 family and downregulation of ZEB1 and ZEB2 in two different mouse models of preterm labor. We further demonstrated that ZEB1 is directly upregulated by the action of P4/PR at the ZEB1 promoter. Excitingly, we observed that ZEB1 and ZEB2 inhibit expression of the contraction- associated genes, oxytocin receptor and connexin-43 and block oxytocin-induced contractility in human myometrial cells. Together, these findings implicate the miR-200 family and their targets ZEB1 and ZEB2 as novel progesterone/PR- mediated regulators of uterine quiescence and contractility during pregnancy and labor, and shed new light on the molecular mechanisms involved in preterm birth.

overall_design: RNA was purified from mouse myometrium (miRNeasy kit, Qiagen). miRNA microarray was performed (LC Sciences) on 18 biological replicates of murine myometrium at 15.5 dpc and an equal number of replicates at 18.5 dpc. Gene expression microarray assays were performed (UT Southwestern Medical Center) on the same 36 samples as detailed further in SI Materials and Methods.

first: Nora

last: Renthal

first: C

last: Chen

last: Williams

first: R

middle: D

last: Gerard

first: J

last: Prange-Kiel


title: Genomic profiling combined with gene expression profiling in primary central nervous system lymphoma

status: Public on Nov 13 2010

city: Seoul

first: Chang Ohk

last: Sung

address: Song-Pa gu,Pung-nap dong

department: Pathology

country: South Korea

institute: Asan Medical Center

type: Genome variation profiling by genome tiling array

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

overall_design: Refer to individual Series

first: Young-Hyeh

last: Ko

first: Chang-Ohk

first: Sang-Cheol

last: Kim

first: Sivasundaram

last: Karnan

first: Kennosuke

last: Karube

first: Hyung-Jin

last: Shin

first: Do-Hyun

last: Nam

first: Yeon-Lim

last: Suh

first: Seok-Hyung

first: Ji-Yeon

first: Soek-Jin

first: Won-Seog

first: Masao

last: Seto


title: Transcriptional changes in Sohlh1 knockout and Sohlh2 knockout mouse newborn ovaries

status: Public on Oct 22 2010

city: Pittsburgh

first: Aleksandar

last: Rajkovic

state: PA

address: 204 Craft Ave. Suite A230

department: Dept. of Obstetrics, Gynecology & Reproductive Sciences

country: USA

institute: Magee-Womens Research Institute

summary: Sohlh1 and Sohlh2 are germ cell-specific basic helix-loop-helix transcription factors critical in early folliculogenesis. We discovered that Sohlh1 and Sohlh2 knockout females lose oocytes after birth and few remains by postnatal day 14. Here, we show that many genes preferentially expressed in the oocytes are misregulated by Sohlh1 and/or Sohlh2 deficiency.

overall_design: Total RNA samples isolated from wildtype, Sohlh1 KO and Sohlh2 KO mouse newborn ovaries were arrayed on the Illumina BeadChip MouseWG-6 2.0 arrays. We have 4 replicates for wildtype and Sohlh1 KO and 3 replicates for Sohlh2 KO.

first: Hyo

middle: W

last: Ahn


title: Transcriptional changes in Sohlh1/Sohlh2 double knockout newborn mouse ovaries

summary: Sohlh1 and Sohlh2 are germ cell-specific basic helix-loop-helix transcription factors critical in early folliculogenesis. Differential genes expression by both Sohlh1 and Sohlh2 deficiency in mouse newborn ovaries was accessed using microarray. RNA samples from Sohlh1/ Sohlh2 double knockout and wild-type newborn ovaries were arrayed on the Illumina beadchip mouse WG-6 2.0.

overall_design: Total RNA isolated from wildtype and Sohlh1/Sohlh2 double KO mouse newborn ovary were used to run Illumina BeadChip MouseWG-6 2.0 arrays.


title: Gene expression profiling of retinoblastoma Y79 cell line grown with scaffold compared to cells without scaffold

status: Public on Oct 01 2010

city: Bangalore

first: Genotypic

last: technology

state: Karnataka

address: 259, Apoorva 4th cross,80 feet Road,RMV 2ND STAGE

country: India

institute: Genotypic Technology

summary: Retinoblastoma Y79 cell line was grown on 3D scaffolds and compared its gene expression profile with Y79 cells grown without scaffold.

overall_design: Agilent one-color experiment, Organism: Human, Agilent-014850 Whole Human Genome Microarray 4x44K G4112F, Labeling kit: Agilent Quick-Amp labeling Kit (p/n5190-0442)

first: Moutushy

last: Mitra

first: Chandana

last: Mohanty

first: Anju

last: harilal

first: Sanjeeb

middle: K

last: Sahoo

first: Subramanian

last: Krishnakumar


title: Gene expression profiles in gastric mucosa from a transgenic mice infected with H. pylori and immunized with BabA

status: Public on Jan 04 2011

city: Stockholm

first: Qiang

last: Pan-Hammarström

address: F79, Huddinge Hospital

department: Laboratory Medicine

country: Sweden

institute: Karolinska Institute

summary:
Many vaccination studies have revealed various degrees of protection in mouse models. However, the mechanism of protection is not fully understood. The aim of this study was to identify genes specifically expressed in H. pylori infection and prophylactic immunized mice. A prophylactic immunization with purified protein of H. pylori BabA combining with the mucosal CTA1-DD adjuvant was performed in a-1,3/4-fucosyltransferase transgenic FVB/N mice. Gene expression profile was analysed from the gastric mucosa among untreated, the infected and immunized mice. There were a set of genes were upregulated or downregulated respectively, in infected mice as compared with untreated mice. These include the adipokines released form adipose tissue, adhesion molecules and actin cytoskeletal rearragemet associated genes. In immunized mice, however, the host response was not as strong as in infected mice and significantly changed genes were completely overlapped with those in infected mice. The expression data from genechip was confirmed by quantitative real-time PCR assay. The microarray analysis suggests that genes such as actin cytoskeletal molecules and adipokines may be as potential targets of H. pylori infection. Prophylactic immunization with purified protein of H. pylori BabA combining with the mucosal CTA1-DD adjuvant could reduce bacteria colonization without induced a severe degree of inflammation.
Keywords: response to treatment

overall_design: The gastric antrum form three groups of mice were prepared for Affymetrix gene chip analysis, using samples from the infected group, untreated control group (not immunized and not challenged) and the immunized group (challenged J99 four weeks after immunization). Four mice in each group were analysis by microarray.

first: Sicheng

last: Wen


title: Regulation of early folliculogenesis by Sohlh1 and Sohlh2 in mouse ovary


title: Orientsia tsutsugamushi stimulates an original gene expression program in human monocytes: relationship with gene expression in patients with scrub typhus

status: Public on Sep 21 2010

city: marseille

first: adil

last: ef

address: 27 bd jean Moulin

country: France

institute: URMITE

summary: Orientia tsutsugamushi, an obligate intracellular bacterium, is the causative agent of scrub typhus. As O. tsutsugamushi is detected in circulating monocytes during acute phase of scrub typhus, we wondered if this organism was able to infect monocytes. We showed here that O. tsutsugamushi replicated in monocytes from healthy donors. Using human whole genome microarrays, we found that O. tsutsugamushi the expression of genes in which up-regulated and down-modulated genes were equally distributed. , the expression of type I interferon, interferon-stimulated genes and M1-associated genes was significantly up-regulated. Second, O. tsutsugamushi the expression of apoptosis-related genes and induced cell death in monocytes. Live organisms were indispensable to type I interferon response and apoptosis and enhanced the expression of M1 cytokines. These findings were related to the transcriptional changes found in mononuclear cells from patients with scrub typhus. Hence, a microarray study revealed the up-regulation of 613 genes and the down-modulation of 517 genes. Importantly, IFN-related genes were specifically enriched and some features of M1 polarization were observed in patients, as found in O. tsutsugamushi-stimulated cells. Our results provide a comprehensive understanding of scrub typhus pathogenesis in which IFN-mediated activation of monocytes appears as critical.

overall_design:
Monocytes (1.5 x 105 per assay) were incubated with or without 3 x 105 O. tsutsugamushi organisms in RPMI 1640 containing 10% FBS, 20 mM HEPES and 2 mM L-glutamine (Invitrogen) for 2 hours.
The raw data, from the Agilent feature extraction software, were preprocessed with background subtraction and quantile normalization. This pretreatment was performed by using a bioconductor limma package, called Agi4x44PreProcess (http://www.bioconductor.org/packages/2.3/bioc/html/ Agi4x44PreProcess.html)

first: Wiwit

last: Tantibhedhyangkul

first: Thanavadee

last: Prachason

first: Duangdao

last: Waywa

first: Adil

last: El Filali

first: Eric

last: Ghigo

first: Wanna

last: Thongnoppakhun

first: Didier

last: Raoult

first: Yupin

last: Suputtamongkol

first: Christian

last: Capo

first: Chanin

last: Limwongse

first: Jean-Louis

last: Mege


title: Comparison of gene expression in CD13 wild type versus Knock out Macrophages

status: Public on Sep 30 2010

city: Farmington

first: Anupinder

last: Kaur

state: CT

address: 400 Farmington Avenue

department: Genetics and Developmental Biology

institute: UCHC

summary: The robust and consistent expression of the CD13 cell surface marker on very early as well as differentiated myeloid hematopoietic cells has prompted numerous investigations seeking to define roles for CD13 in myeloid cells.  To directly address the function of myeloid CD13 we created a CD13 null mouse and assessed the responses of purified primary macrophages or dendritic cells from wild type and CD13 null animals in cell assays and inflammatory disease models where CD13 has been previously implicated.  We find that mice lacking CD13 develop normally with normal hematopoietic profiles.  Moreover, in in vitro assays, CD13 appears to be largely dispensable for the aspects of phagocytosis, proliferation and antigen presentation that we tested, but may contribute to adhesion to endothelial cells.  In vivo assessment of four inflammatory disease models showed that lack of CD13 has little effect on disease onset or progression.  Nominal alterations in gene expression levels between CD13 wild type and null macrophages argue against compensatory mechanisms.   Analysis of the dataset with Ingenuity Pathway Analysis software did not suggest that loss of CD13 resulted in a purturbation of any specific biological pathways, processes or networks.  Therefore, while CD13 is highly expressed on myeloid cells and is a reliable marker of the myeloid lineage of both normal and leukemic cells, it is not a critical regulator of hematopoietic development, hemostasis or myeloid cell function.

overall_design:
Method:

	RNA was isolated from resting peritoneal or bone marrow derived macrophages from wild type or CD13 null mice using Trizol according to the manufacturer’s protocol.  For quality control, RNA purity and integrity was evaluated by denaturing gel electrophoresis, OD 260/280 ratio and analysis on an Agilent 2100 Bioanalyzer (Agilent Technologies, Palo Alto, CA).  Total RNA was amplified and purified using the Ambion Ilumina RNA amplification kit (Ambion, www.ambion.com).  Briefly, 300 ng of total RNA was reverse transcribed to cDNA using a T7 oligo(dT) primer. Second-strand cDNA was synthesized, in vitro transcribed and labeled with biotin-16-UTP. The labeled cRNA was analyzed on the Agilent 2100 Bioanalyzer and quantitated by Nanodrop analysis (www.nanodrop.com). The labeled cRNAs were hybridized to the Mouse WholeGenome- 6 BeadChip (Illumina Inc.,) for 16 hours at 58°C, as per manufacturer's instructions. The BeadChips were washed, stained with streptavidin-Cy3 and scanned on the Illumina BeadArray Reader.

Analysis:

Microarray data was extracted, normalized and analyzed using Illumina GenomeStudio software. Illumina MouseWG-6 v 2.0 Expression BeadChip (Illumina, San Diego, CA) contains 50-mer gene specific oligonucleotide probes corresponding to 45,281 mouse transcript variants.  There is on average a 30-fold redundancy for each transcript per array. Intensity data were normalized using the Quantile algorithm in GenomeStudio. Differential expression of each gene, relative to the respective control was evaluated using the Illumina custom error model that calculates a p value as a function of intensity, differential and biological, technical and nonspecific variation.  Those samples with p values less than 0.05 were deleted, the relative expression of CD13 null vs. wild type calculated and expressed as fold wild type, and the data ranked from low to high expression relative to wild type values.  The dataset was further analyzed using the Ingenuity Pathway Analysis software (Ingenuity Systems, http://www.ingenuity.com).

first: Linda

middle: H

last: Shapiro


title: Postnatal Growth Restriction and Gene Expression Changes in a Mouse Model of Fetal Alcohol Syndrome (Liver)

city: Herston

first: Suyinn

last: Chong

state: Queensland

address: 300 Herston Rd

department: Division of Genetics and Population Health

country: Australia

institute: Queensland Institute of Medical Research

summary: Growth restriction, craniofacial dysmorphology and central nervous system defects are the main diagnostic features of fetal alcohol syndrome. Studies in humans and mice have reported that the growth restriction can be prenatal and/or postnatal, but the underlying mechanisms remain unknown.  We recently described a mouse model of moderate gestational ethanol exposure that produces measurable phenotypes in line with fetal alcohol syndrome, e.g. craniofacial changes and growth restriction in adolescent mice. Here we further characterize the growth restriction phenotype by measuring body weight at gestational day 16.5, cross-fostering from birth to weaning, and extending our observations into adulthood. Furthermore, in an attempt to unravel the molecular events contributing to the growth phenotype, we have compared gene expression patterns in the liver and kidney of non-fostered ethanol-exposed and control mice at postnatal day 28.  We find that the ethanol-induced growth phenotype is not detectable prior to birth, but is present at weaning, even in mice that have been cross-fostered to unexposed dams. This suggests a postnatal growth restriction phenotype that is not due to deficient postpartum care by dams that drank ethanol, but rather a physiological result of ethanol exposure in utero. We also find that, despite some catch-up growth after five weeks of age, the effect extends into adulthood, consistent with longitudinal studies in humans.  Genome-wide gene expression analysis revealed interesting ethanol-induced changes in the liver, including genes involved in the metabolism of exogenous and endogenous compounds, iron homeostasis and lipid metabolism.

overall_design: Gene expression changes in the livers of offspring exposed to alcohol in utero compared to controls.


title: Bone marrow-derived myofibroblasts contribute to the mesenchymal stem cell niche and promote tumor growth

city: New York

first: Michael

last: Quante

state: NY

address: 1130 St. Nicholas Av

department: Digestive and Liver Disease

institute: Columbia University Medical Center

summary:
Carcinoma-associated fibroblasts (CAFs) that express α-smooth-muscle-actin (αSMA+) contribute to cancer progression, but their precise origin and role in tumorigenesis is not established. Using mouse models of inflammation-induced gastric cancer, we show that at least 20% of CAFs originate from bone marrow and derive from mesenchymal stem cells (MSCs). Surprisingly, we find that αSMA+ myofibroblasts (MF) are niche cells normally present in bone marrow and increase markedly in the bone marrow and blood during progression to dysplasia. MSC-derived CAFs that are recruited to the dysplastic stomach express IL-6, Wnt5α and BMP4 and show DNA hypomethylation. Bone marrow (BM)-derived CAFs strongly promote tumor growth in organotypic and xenograft models. In addition, CAFs are generated from MSCs and are recruited to distant tumor sites in a TGF-β- and SDF-1α-dependent manner. Carcinogenesis therefore involves the expansion and relocation of normal bone marrow niche cells to the tumor site where they create a new niche to sustain cancer progression.
Since resident (non-BM-derived) CAFs could not be cultured and directly compared to BM-derived CAFs, we additionally isolated total RFP(+) gastric CAFs from aSMA-RFP mice with Helicobacter felis-induced dysplasia, and compared them to GFP(+) BM-derived gastric CAFs from mice with H. felis-induced dysplasia mice that had been transplanted with UBC-EGFP bone marrow. The RFP+ CAFs (HF CAF) represent total CAFs (of which only 20% were BM-derived), while the latter represented only BM-derived CAFs (BM CAF). We compared their gene expression using the Illumina array (MouseWG-6v2) directly after FACS sorting. Interestingly, the GFP+ BM-derived CAFs expressed higher levels of inflammatory genes (IL-6, IL-1β, IL-33) and a number of tumor and stem cell associated factors (CCL5, SPP1, Notch3, MMP9, CD47, CXCR4, PARP10,) compared to the total (RFP+) population of gastric CAFs.

overall_design: Comparison of bone marrow-derived GFP-labeled gastric CAFs versus all gastric CAFs.

first: Shui

middle: P

last: Tu

first: Hiroyuki

last: Tomita

first: Tamas

last: Gonda

first: Sophie

middle: S

last: Wang

first: Shigeo

last: Takashi

first: Gwang

last: Baik

first: Wataru

last: Shibata

first: Bethany

last: DiPrete

first: Kelly

last: Betz

first: Richard

last: Friedman

first: Andrea

last: Varro

first: Benjamin

last: Tycko

first: Timothy

middle: C


title: Peroxisomes are signaling patforms for antiviral innate immunity

status: Public on Nov 04 2010

city: Boston

first: Jonathan

last: Kagan

state: MA

address: 300 Longwood Ave, Enders 649

institute: Children's Hospital Boston

summary: Analysis of the transcriptional response of mouse embryonic fibroblasts to reovirus infection.  The hypothesis tested was that both peroxisomal and mitochondrial MAVS is capable of inducing the expression of antiviral genes.

overall_design: mRNA isolated from MAVS-expressing cells after infection for various times with reovirus

first: Evelyn

last: Dixit


title: Postnatal Growth Restriction and Gene Expression Changes in a Mouse Model of Fetal Alcohol Syndrome

first: Suyinn


title: Gene expression analysis of CBFbeta knockdown PPC1 cells

status: Public on Sep 01 2010

city: Shreveport

first: Shari

last: Meyers

state: LA

address: 1501 Kings Highway

department: Biochemistry and Molecular Biology

institute: LSU Health Sciences Center-Shreveport

summary: Whole genome array expression analysis was performed to identify changes in gene expression associated with the downregulation of the Core Binding Factor subunit CBFbeta.

overall_design: PPC1 cells were infected with lentivirus containing either a control non-target shRNA or a shRNA specific for human CBFbeta. The cells were collected and lysed in Tri-reagent. Biological triplicates were analyzed for both control and knockdown cells.

first: Nathan

last: Davis


title: Postnatal Growth Restriction and Gene Expression Changes in a Mouse Model of Fetal Alcohol Syndrome (Kidney)

last: Chong

overall_design: Gene expression changes in the kidneys of offspring exposed to alcohol in utero compared to controls.


title: Gene expression profile of human melanocytes derived from iPS cells

status: Public on Aug 26 2010

city: Tokyo

first: Shigeki

middle: Ohta

last: Ohta

state: Tokyo

address: 35 Shinanomachi shinjyuku-ku

department: Institute for Advanced Medical Research

country: Japan

institute: Keio University

summary: This experiment was designed to show the similarity among normal human epidermal melanocytes, melanocytes derived from human 3F-induced pluripotent stem (iPS) cells, and human 3F-iPS cells.

overall_design: Human 3F-iPS cells without c-myc were established and then differentiated into melanocytes. The differentiated cells were collected and the gene expression profile was compared to normal human epidermal melanocytes (NHEMs) and orginal 3F-iPS cells.

first: S


title: Therapy with bone marrow cells recovers gene expression alterations in hearts of mice with chronic chagasic cardiomyopathy

status: Public on Sep 17 2010

city: Prairie View

first: Dumitru

middle: Andrei

last: Iacobas

state: TX

address: Ann Preston St

department: Undergraduate Medical Academy

institute: Prairie View A&M University

summary: Chronic chagasic cardiomyopathy is one of the leading causes of heart failure in Latin American countries, being associated with intense inflammatory response and fibrosis. We have previously shown that bone marrow mononuclear cell (BMC) transplantation improves inflammation, fibrosis and ventricular diameter in hearts of mice with chronic Chagas’ disease. Here we investigated alterations of gene expression in the hearts of chronic chagasic mice submitted or not to BMC therapy. C57Bl/6 mice chronically infected with T. cruzi (6 months) were transplanted with BMC or saline i.v. and sacrificed 2 months later. RNA was extracted from the hearts of normal controls, chagasic and BMC transplanted mice and microarray analysis was performed using MO30k oligonucleotide arrays.  Out of the 9390 unigenes quantified in all samples, 1702 had their expression altered in chronic chagasic hearts compared to those of normal mice. Major categories of significantly upregulated genes were related to inflammation, fibrosis and immune responses, while genes involved in mitochondrion function were downregulated. When BMC-treated chagasic hearts were compared to infected mice, 1631 (96%) of the alterations detected in infected hearts were not found, although an additional 109 genes were altered by treatment, indicating a remarkable 84% transcriptomic recovery. Immunofluorescence and morphometric analyses confirmed the effects of BMC therapy in the pattern of inflammatory-immune response and expression of adhesion molecules. Our results demonstrate important immunomodulatory effects of BMC therapy in chagasic cardiomyopathy and indicate potentially relevant factors involved in the pathogenesis of the disease that may provide new therapeutic targets.

overall_design: We compared RNA samples extracted from whole hearts of 4 control, 4 chagasic and 4 BMC-treated chagasic mice by analyzing hybridization to microarrays printed by Duke University (http://www.ncbi.nlm.nih.gove/geo/query/acc.cgi?acc=GPL8938) spotted with MO30k mouse Operon version 3.0 70-mer oligonucleotides. The hybridization protocol (see Soares et al, 2010), the slide type and the scanner settings were uniform throughout the entire experiment to minimize the technical noise. Briefly, 20 ug total RNA extracted in Trizol from each of the twelve samples (individual hearts) was reverse transcribed in the presence of fluorescent Alexa Fluor® 555- and Alexa Fluor®647-aha-dUTPs (Invitrogen, Carlsbad, CA) to obtain labeled cDNA. Red and green labeled samples of biological replicas were then co-hybridized (“multiple yellow” strategy, 22) overnight at 50° C. After washing (0.1% SDS and 1% SSC) to remove the non-hybridized cDNA, each array was scanned at 630V (635 nm) and 580V (532 nm) with GenePix 4100B scanner (Axon Instruments, Union City, CA) and images were primarily analyzed with GenePixPro 6.0 (Molecular Devices, Sunnyvale, CA). Microarray data were processed as described previously (Soares et al, 2010).  A gene was considered as significantly up- or down-regulated when comparing four hearts from one condition to those from another if the absolute fold change was >1.5x and the p-vlaue of the Sutdent”s heteroscedastic t-test of equality of the means of the distributions with a Bonferroni-type adjustment for each redundancy group (set of spots probing the same gene) was <0.05.

first: Milena

middle: B

last: Soares

first: Ricardo

last: Lima

first: Leonardo

middle: L

last: Rocha

first: Bruno

last: Souza

first: Juliana

middle: F

last: Vasconcelos

last: dos Santos

first: Sanda

first: Regina

last: Goldenberg

middle: A

first: Herbert

last: Tanowitz

first: David

last: Spray

first: Antonio

last: de carvalho


title: Insulin resistance induced by physical inactivity is associated with multiple transcriptional changes in skeletal muscle in young men

city: Sharnbrook

first: Natalie

last: Hiscock

address: Colworth House

country: United Kingdom

institute: Unilever R&D

summary: Rationale: Physical inactivity is a risk factor for insulin resistance. We examined the effect of nine days of bed rest on basal and insulin stimulated expression of genes potentially involved in insulin action by applying hypothesis-generating microarray in parallel with candidate gene real-time PCR approaches in 20 healthy, young men. Furthermore, we investigated whether bed rest affected DNA methylation in the promoter region of the peroxisome proliferator-activated receptor gamma coactivator 1 alpha (PPARGC1A) gene. Subjects were re-examined after four weeks of retraining. Findings: Bed rest induced insulin resistance and altered the expression of more than 4,500 genes. These changes were only partly normalized after four weeks of retraining. Pathway analyses revealed significant down-regulation of 34 pathways, predominantly those of genes associated with mitochondrial function including PPARGC1A. Despite induction of insulin resistance, bed rest resulted in a paradoxically increased response to acute insulin in the general expression of genes, particularly those involved in inflammation and endoplasmatic reticulum (ER) stress. Furthermore, bed rest changed gene expressions of several insulin resistance and diabetes candidate genes. We also observed a trend toward increased PPARGC1A DNA methylation after bed rest. Conclusions: Impaired expression of PPARGC1A and other genes involved in mitochondrial function as well as a paradoxically increased response to insulin of genes involved in inflammation and ER stress may contribute to the development of insulin resistance induced by bed rest. Lack of complete normalization of changes after four weeks of exercise retraining underscores the importance of maintaining a minimum of daily physical activity.

overall_design: 50 samples were collected (5 samples from 10 subjects) and included in this study. Ten technical repeats were also performed in this analysis

first: A

last: Alibegovic

first: M

last: Sonne

first: L

last: Højbjerre

first: J

last: Bork-Jensen

last: Jacobsen

first: E

last: Nilsson

first: K

last: Færch

first: N

first: B

last: Mortensen

last: Friedrichsen

last: Stallknecht

first: F

last: Dela

last: Vaag


title: Molecular and functional characterization of alloantigen-specific anergic T-cell suitable for cell therapy

status: Public on Aug 17 2010

city: Bergisch-Gladbach

first: Stefan

last: Tomiuk

address: Friedrich-Ebert-Str. 68

department: Bioinformatics

country: Germany

institute: Miltenyi Biotec GmbH

summary: IL-10 is an immunomodulant cytokine that plays a central role in controlling inflammation, down-regulating immune responses, and inducing immunological tolerance. IL-10 inhibits the expression of costimulatory molecules and the secretion of inflammatory cytokines by antigen-presenting cells (APC), directly suppresses T-cell proliferation, and promotes T-cell anergy. In this study we demonstrate that IL-10 inhibits primary allogeneic proliferation in total PBMC and induces antigen(Ag)-specific T-cell hyporesponsiveness. IL-10-induced anergy is TGF-beta independent, is associated with a decrease of Ag-specific CTLp frequency, and can be obtained among cells with different degree of HLA disparity. The use of tolerogenic dendritic cells (DC) differentiated in the presence of IL-10 (DC-10) allows a more consistent anergy induction, even in the context of HLA matched donors. Importantly, alloAg-IL-10/DC-10-anergized T cells preserve their ability to respond to nominal and third party Ags. Microarray experiments were conducted on different mixed lymphocyte cultures aiming at the identification of gene expression profiles characteristic for the various T cell populations. Independently from the APC used to anergized T cells, the resulting T cell populations exhibit a specific gene signature. Based on the results of this study, we developed a method suitable for GMP scale up and for the generation of a population of anergic Ag-specific T cells for cellular therapy.

overall_design: The dataset comprises 12 samples divided into four sample groups each representing a certain kind of allogeneic mixed lymphocyte culture, i.e. peripheral blood mononuclear cells (PBMC) mixed with CD3-depleted cells (MEC, monocyte-enriched cells) with or without IL-10 treatment, and PBMC mixed with mature or IL-10 treated dendritic cells (DCs). Each group includes three biological replicates with cells collected from different donors.

first: Rosa

last: Bacchetta

first: Silvia

last: Gregori

first: Giorgia

last: Serafini

first: Claudia

last: Sartirana

first: Ute

last: Schulz

first: Elisabetta

last: Zino

first: Katharina

last: Fleischhauer

first: Uwe

last: Janßen

first: Maria

middle: G

last: Roncarolo


title: Differential Effects of TiO2 Nanotubes on Vascular Cells

status: Public on Aug 14 2010

city: San Francisco

first: Andrea

middle: J

last: Barczak

state: CA

address: 1550 4th St Rock Hall 545

institute: UCSF Sandler Center Functional Genomics Core Facility

summary: The response of primary human endothelial (ECs) and vascular smooth muscle cells (VSMCs) to TiO2 nanotube arrays is studied through gene expression analysis.  Microarrays revealed that nanotubes enhanced EC proliferation and motility, decreased VSMC proliferation, and decreased expression of molecules involved in inflammation and coagulation in both cell types.  Network generated from significantly affected genes suggests that cells may be sensing nanotopographical cues via pathways previously implicated in sensing shear stress.

overall_design: DNA microarrays were used to analyze the response of primary human endothelial (ECs) and vascular smooth muscle cells (VSMCs) to nanotopographical TiO2 surfaces. The experiment incorporated a 1 color design and used Agilent arrays that contained roughly 44,00 60mer probes that provide complete coverage of the human genome. 19 arrays were hybridized and represent 4 biological replicates for each group ( with the exception of group VSMC-NT30, which has 3 biological replicates). Data was analyzed separately for each cell type ( EC or VSMC). Gene expression comparisons were made between control cells grown on flat titanium (Ti) and cells grown on either 30nm nanotubes (NT30) or 100nm nantubes ( NT-100).


title: Myc-regulated gene expression in human fibroblasts

status: Public on Jul 26 2010

city: Kyoto

first: Shinya

last: Yamanaka

address: 53 Kawahara-machi, Shogoin, Sakyo-ku

institute: Center for iPS Cell Research and Applicaton (CiRA), Kyoto University

summary: Myc regulates many gene expression during cell growth, development, or other many cellular events. C-Myc is a well known molecule which expression increase in many cancers. Overexpression of c-Myc causes cell transformation, apoptosis, etc. There are several Myc family genes in human, mouse, or other species. The function of N-Myc was well characterized and was similar to that of c-Myc. However, the function of L-Myc is not clearly examined. To examine the function of L-Myc, we perfomed microarray analyses using L-Myc overexpressed human fibroblasts.

overall_design: Adult human fibroblasts were transduced with Myc and their mutants and were used for microarray analyses.

first: Masato

last: Nakagawa

first: Nanako

last: Takizawa

first: Megumi

last: Kumazaki


title: In vivo gene expression changes in human blood cells in response to radiation therapy.

status: Public on Aug 05 2010

first: Thomas

last: Templin

address: 630 West 168th Street

summary: Our in vivo study measures miRNA and gene expression changes in human blood cells in response to ionizing radiation in order to develop miRNA signatures that can be used as biomarkers for radiation exposure. Blood was collected from 8 radiotherapy patients immediately prior to and at 4 h after total body irradiation with 1.25 Gy X-rays. Both miRNA and gene expression changes were measured by means of quantitative PCR and microarray hybridization, respectively. Patients were in complete remission at the time of blood collection. Out of 223 differentially expressed genes, 37 were both downregulated and predicted targets of the upregulated miRNAs. Both miRNA and gene control of biological processes such as hemopoiesis and the immune response is increased after irradiation, whereas metabolic processes are underrepresented among all differentially expressed genes and the genes controlled by miRNAs.

overall_design: Sixteen human whole-blood samples were included in this study. Eight samples were collected shortly before total body irradiation. The other 8 samples were collected at 4 h after total body irradiation with 1.25 Gy X-rays.

first: Sunirmal

last: Paul

first: Sally

last: Amundson

first: Lubomir

last: Smilenov


title: DLK1 Is a Novel Regulator of Bone Mass That Mediates Estrogen-Deficiency Induced Bone Loss in Mice

status: Public on Oct 15 2010

city: Odense C

first: Basem

last: Abdallah

address: J.B. Winslows Vej 25

department: Dept. of Endocrinology

country: Denmark

institute: Odense University Hospital

summary: DLK1/FA-1 (delta-like 1/fetal antigen-1) is a transmembrane protein belonging to Notch/Delta family that acts as a membrane-associated or a soluble protein to regulate regeneration of a number of adult tissues. Here, we examined the role of DLK1/FA-1 in bone biology using osteoblast-specific-Dlk1 over-expressing mice (Col1-Dlk1). Col1-Dlk1 mice displayed growth retardation and significantly reduced total body weight and bone mineral density (BMD). μCT-scanning revealed a reduced trabecular and cortical bone volume fraction. Tissue-level histomorphometric analysis demonstrated decreased bone formation rate and enhanced bone resorption in Col1-Dlk1 as compared to WT. At a cellular level, DLK1 markedly reduced the total number of bone marrow (BM)-derived CFU-F, as well as their osteogenic capacity. In a number of in vitro culture systems, DLK1 stimulated osteoclastogenesis indirectly through osteoblast-dependent increased production of pro-inflammatory bone resorbing cytokines (e.g, Il7, Tnfa and Ccl3). We found that ovariectomy (ovx)-induced bone loss was associated with increased production of DLK1 in bone marrow by activated T-cells. However, Dlk1-/- mice were protected from ovx-induced bone loss. Thus, we identified DLK1 as a novel regulator of bone mass that function to inhibit bone formation and to stimulate bone resorption. Increasing DLK1 production by T-cells under estrogen deficiency suggests its possible use as a therapeutic target for preventing postmenopausal bone loss.

overall_design: Calvarial osteoblasts were grown from neonatal mice overexpressing Dlk1 and their non-transgenic littermate controls. Three separate cultures from each of the two genotypes were combined and analysed by Affymetrix microarray MOE430 2.0.

middle: M

first: Nicholas

last: Ditzel

first: Amer

last: Mahmood

first: Adiba

last: Isa

first: Gunnhildur

last: Traustadottir

first: Arndt

last: Schilling

first: María-José

last: Ruiz-Hidalgo

first: Jorge

last: Laborda

first: Michael

last: Amling

first: Moustapha

last: Kassem


title: Gene expression profiling of 3T3 fibroblast cells cultured with degradable metallic materials

status: Public on Jul 24 2010

city: Quebec

first: Jacques

last: Couet

address: 2725 chemin Sainte-Foy

country: Canada

institute: Centre de Recherche de l'Hopital Laval

summary: Metals have been used for coronary artery stent materials in order to prevent stenosis caused by atherosclerosis. Degradable metallic materials (DMMs) are considered to be useful to avoid in-stent restenosis and late thrombosis.  A new DMM, Fe-35Mn alloy, was fabricated through powder metallurgy in order to satisfy the ideal criteria of cardiovascular stent made of DMM. Since in-stent restenosis is mediated by the extracellular matrix production, which is mostly regulated by fibroblasts, the gene expression profile of 3T3 fibroblasts in the presence of Fe-35Mn alloy was then investigated. The mechanism of cellular responses in the presence of DMM is then expected to be clearly described through the gene profiling experiment.

overall_design: 3T3 fibroblast cells derived from mouse (Mus musculus) embryo (BALB/3T3 clone A31, ATTC) were put in the culture and treated with iron, manganese, and Fe-35Mn alloy for 24 hour in parallel and followed by the RNA extraction. Six technical replicates were included for treated cells as well as control cells.

first: J

first: A

last: Purnama

first: H

last: Hermawan

first: D

last: Mantovani


title: Different propensity in hematopoietic differentiation potential among distinct human pluripotent stem cell lines

city: MAdrid

first: Gustavo

last: Melen

state: Madrid

address: Avda. Menendez Pelayo 65

country: Spain

institute: FIB Hospital NIño Jesus

summary: Lineage-specific differentiation potential varies among different human pluripotent stem cell (hPSC) lines. A stem cell bank may advice researchers on which hPSCs exhibit the highest differentiation potential for a certain lineage. In this study, we aimed at characterizing the hematopoietic differentiation potential from 14 hESC/iPSC lines through the embryoid body (hEB) differentiation system.

overall_design: We carried out gene expression profiling on six different hESC lines grouped according to their ability to differentiate towards hematopoietic lineage: SHEF1, AND1 and H1 were considered as good (high CD45 expression and high CFU potential), whereas H9, HS181 and VAL3 were selected as poor-blood differentiating lines (low CD45 expression and low CFU potential). Human ESC samples were collected during the exponential cell growth phase and stabilized in RNA later. 500 ng of each total RNA sample was labelled with Cy3 using the Quick-Amp Labelling kit and hybridized with the Gene Expression Hybridization kit to a Whole Human Genome Oligo Microarray (Agilent Technologies) following the Manufacturer’s instructions. Each cell line was analyzed as independent duplicates. H9 hESC line was used as the baseline.

first: Verónica

last: Ramos-Mejía

first: Laura

last: Sánchez

first: Iván

last: Gutiérrez-Aranda

first: Gertrudis

last: Ligero

first: Jose

last: Cortés

first: Pedro

last: Real

first: Clara

last: Bueno

first: Pablo

last: Menéndez


title: Gene expression patterns of EBV negative BJAB B-lymphoma lines stably and conditionally expressing EBNA-1

status: Public on Jul 17 2010

city: Iowa City

first: Ramakrishna

last: Sompallae

state: IA

address: 285 Newton Road, 5292 CBRB

department: Iowa Institute of Human Genetics

institute: University of Iowa

summary:
EBNA-1 is expressed in all EBV-associated malignancies and may play a role in transcription regulation through its DNA binding ability. This is our attempt to examine the effect of EBNA-1 on the expression of cellular genes. We have compared the transcription profiles of conditional and stable EBNA-1 transfected sublines of the EBV negative B-cell lymphoma BJAB where EBNA-1 was expressed for few days, few months or years.
The non-specific effects were accounted by comparing the gene expression profiles of untransfected cells or cells transfected with the empty vector or cultured in the presence or absence of doxycycline.

overall_design: Stable and inducible EBNA-1 expressing cells compared with EBNA-1 lacking cells.  Biological replicates: 3 transfected replicates for each condition

first: Simone

last: Callegari

first: Siamak

last: Kamranvar

first: Maria

last: Masucci


title: Chronic Hypoxia predicts Poor Prognosis in Hepatocellular Carcinoma

status: Public on Jul 20 2010

city: Leuven

first: Rekin's

last: Janky

address: Herestraat 49 Box 816

department: Nucleomics Core

country: Belgium

institute: VIB

summary:
Background - Hepatocellular carcinomas (HCCs) are heterogeneous tumors with respect to etiology, cell of origin and biology. The course of the disease is unpredictable and is in part dependent on the tumor microenvironment. One of the microenvironmental factors is hypoxia, which is known to promote aggressiveness in other malignant tumors. We hypothesized that certain regions in HCC exist with chronic hypoxia and a characteristic gene expression pattern. Moreover, during the development of HCC there is an important contribution of this chronic hypoxia on prognosis via this gene expression. Until now, most research has been performed in acute hypoxic models (< 24 hours).
Methods – Human hepatoblastoma cells HepG2 were cultured in either normoxic (20% O2) or hypoxic (2% O2) conditions for 72 hrs, the time it takes to adapt to chronic hypoxia. After 3 days the cells were harvested and analyzed by microarray technology. The highly significant differentially expressed genes were selected and used to assess the clinical value of our in vitro chronic hypoxia gene signature in four published patient studies. Three of these independent microarray studies on HCC patients were used as training sets to determine a minimal prognostic gene set and one study was used for validation. Gene expression analysis and correlation with clinical outcome was assessed with the bioinfomatic method of Goeman et al ().
Results – In the HepG2 cells, 3592 genes were differentially expressed in cells cultured at 2% oxygen for 72 hrs. Out of these, 265 showed a high significant change (2-fold change and p=0.0001). The level of gene expression after 72 hrs was different from the acute hypoxic response (during the first 24 hours) and represented chronicity. Using computational methods we identified 7 out of the 265 highly significant genes that showed correlation with prognosis in all three different training sets and this was independently validated in a 4th dataset. With our approach we could include the largest number of HCC patients in one single study.
Conclusion – We identified a 7-gene signature, which is associated with chronic hypoxia and predicts prognosis in patients with HCC. In the future this signature could be used as a diagnostic tool. In addition, chronic hypoxia gene expression information can be used in the search for new therapeutic targets.

overall_design: Two conditions were compared and each sample has a biological replicate. Samples are hybridized in dye-swap, resulting in 4 hybridizations.

first: Hannah

last: van Malenstein

first: Olivier

last: Gevaert

first: Louis

last: Libbrecht

first: Anneleen

last: Daemen

first: Joke

last: Allemeersch

first: Frederik

last: Nevens

first: Paul

last: Van Hummelen

first: David

last: Cassiman

first: Bart

last: De Moor

first: Chris

last: Verslype

first: Jos

last: van Pelt


title: IMR90 bystander experiment 0.5 Gy alpha particle

status: Public on Jul 21 2010

first: Shanaz

middle: Adi

last: Ghandhi

address: 630, W 168th street

department: Center for Radiological Research

summary: The existence of a radiation bystander effect, in which non-irradiated cells respond to signals from irradiated cells, is well established. It raises concerns for the interpretation of risks from exposure to low doses of ionizing radiation. Sparse data exists about the bystander signaling mechanisms and the ability to transmit damaging effects both spatially and temporally. To understand early signaling and cellular changes in bystanders, we have measured global gene expression 30 minutes after direct and bystander exposure to alpha particle in primary human lung fibroblasts. Gene ontology and pathway analyses suggested that the earliest measured changes at 30 minutes after treatment are in cell structure, motility and adhesion categories and a significant number of genes belong to the category of inflammation and cell-to-cell communication. We investigated time course gene expression profiles of matrix metalloproteinases 1 and 3 (MMP1 and MMP3), chemokine ligands 2, 3 and 5 (CXCL2, CXCL3 and CXCL5), interleukins 1a, 1b, 6 and 33 (IL1A, IL1B, IL6 and IL33) growth differentiation factor 15 (GDF15) and superoxide dismutase2 (SOD2) by real time quantitative PCR. These encode proteins involved in cellular signaling via the NFkappaB pathway and time course of mRNA levels revealed an increased response at 30 minutes after irradiation followed by another wave at 4 to 6 hours. We also investigated protein modifications in the AKT-GSK-3 signaling pathway and found that in irradiated cells AKT and GSK3beta are hyper-phosphorylated at 30 minutes and this effect is maintained until 4 hours after exposure. In bystanders there is a similar response with a delay of 30 minutes. In irradiated cells, inactivated GSK3beta led to decreased phosphorylation of beta-catenin. Our results are the first to show that the radiation induced bystander signal can induce a widespread gene expression response as early as 30 minutes after exposure and that these changes are accompanied by protein modification of signaling modules such as AKT and GSK3beta.

overall_design: There are 12 total samples, 4 corresponding biological replicates of IMR90 cells that were not irradiated (control=C), irradiated (alpha=A) and bystander (B), cells were harvested 0.5 hr after treatment

first: Sally

last: Amundson


title: To compare the expression profile of CD8 T cells from mice vaccinated with Ad85A via the intranasal (IN) or intradermal (ID) routes isolated from lungs or spleen.

status: Public on Aug 24 2010

city: Oxford

first: Lian

middle: Ni

last: Lee

address: Peter Medawar Building, South Parks Road

department: Nuffield Dept of Medicine

institute: University of Oxford

summary: In Balb/c mice, the presence of effector CD8 T cells in lungs after intra-nasal (IN) immunization with replication deficient recombinant Adenovirus expressing the 85A antigen from Mycobacterium tuberculosis (MTb) (Ad85A) correlates with protection against aerosol MTb infection. In order to identify differentially expressed transcripts which contribute to protection by IN immunized lung CD8 T cells, total RNA from CD8 T cells isolated from target tissue (lungs) and lymphoid organ (spleen ) after a protective (IN) and non-protective (intradermal, ID) immunization regime will be analyzed in a whole-genome microarray study.

overall_design: Total RNA from CD8 T cells isolated from lungs or spleens of Balb/c mice 3 weeks post-immunization with Ad85A through the IN (protective) or ID (non-protective) route will be compared.

middle: N

first: Dilair

last: Baban

first: Elma

middle: Z

last: Tchilian

first: Peter

last: Beverley


title: An Association Between Gene Expression and Better Survival in Female Mice Following Myocardial Infarction

status: Public on Aug 31 2010

city: La Jolla

first: Roy

last: Williams

address: 3030 Science Park Road

department: Regenerative Medicine

institute: The Scripps Research Institute

summary: Following myocardial infarction, the prognosis for females is better than males. Estrogen is thought to be protective, but clinical trials with hormone replacement failed to show protection. Here, we sought to identify novel mechanisms that might explain this sex-based difference. By diverging from the traditional focus on sex hormones, we employed a conceptually novel approach to this question by using a non-biased approach to measure global changes in gene expression following infarction.

overall_design: Three days after coronary artery ligation surgery, RNA was extracted from left ventricular samples (infarct excluded) using the QIAGEN RNeasy Fibrous Tissue Mini Kit. Four groups were compared with a 2x2 design: male and female, sham and coronary artery ligation, with five mice per group.

first: Quanhai

last: Chen

first: Timothy

middle: D

last: O’Connell


title: Gene expression data from P. gingivalis infected Mouse

status: Public on Jul 15 2010

city: Gainesville

first: Kesavalu

middle: Naidu

last: Lakshmyya

state: FL

address: 1600 SW Archer road, D11-24

department: Periodontology

institute: University of Florida, College of Dentistry

summary:
The objectives of this investigation were to examine changes in the host transcriptional profiles during a Porphyromonas gingivalis infection using a murine calvarial model of inflammation and bone resorption.  P. gingivalis strain 381 was injected into the subcutaneous soft tissue over the calvaria of BALB/c mice for 3 days, after which the soft tissues and calvarial bones were excised.  RNA was isolated from infected soft tissues and calvarial bones and analyzed for transcript profiles using Murine GeneChip® MG-MOE430A Affymetrix arrays to provide a molecular profile of the events that occur following infection of these tissues.
We used mouse microarrays to detail the molecular profile of the events that occur following infection of calvarial and bone tissues and identified distinct classes of up- and down-regulated genes during this process.

overall_design: P. gingivalis was injected at 1.5 x 10E9 (N = 10) into the soft tissues overlying the calvaria of the mice for 3 days. A control group (N = 9) was injected with vehicle once daily for 3 days. Mice were euthanized 8 h after the last injection.  The calvarial bones and overlying soft tissues from 5 mice in each group were excised, snap frozen in liquid nitrogen, and stored at –80°C until RNA isolation. Total RNA was isolated from the frozen calvarial tissue and calvarial bone from each mouse (P. gingivalis infected and control animals) with Trizol reagent (Invitrogen, CA).  Equal amounts of RNA from samples were labeled and hybridized on a mouse GeneChip following the protocol described in the GeneChip Expression Analysis Technical manual (Affymetrix, Santa Clara, CA). After hybridization, the GeneChip arrays were stained and scanned in an Affymetrix GCS 3000 7G Scanner.

first: Lakshmyya

last: Kesavalu

first: Archana

last: Meka

first: Vasudevan

last: Bakthavatchalu

first: Sabapathi

last: Sathishkumar

first: Cecilia

last: Lopez

first: Raj

middle: K

last: Verma

first: Shannon

last: Wallet

first: Indraneel

last: Bhattacharyya

first: Brendan

last: Boyce

first: Martin

last: Handfield

first: Richard

last: Lamont

first: Henry

middle: V

last: Baker

first: Jeffrey

last: Ebersole


title: cryopreserved CD34 positive human umbilical cord blood cells

first: Jun

last: Yasuda

address: 3-8-31, Ariake, Koto-ku

department: Cell Biology

institute: The JFCR-Cancer Institute

summary: Human umbilical cord blood cells (UCB) is an important alternative resource for the hematopoietic stem cells in treatment of leukemia and other non-malignant diseases. The failure of hematopoiesis reconstruction by the UCB is known to be associated with several clinicopathological features of host patients. There are very few reports available, however, seeking for the association with the quality of umbilical cord blood cells (UCB) themselves. Here we try to address the quality of UCBs by transfusion to the lethally irradiated immunocompromized mice. The cryopreserved CD34+ UCBs cells from twelve different single human donors were transplanted to the irradiated NOD/shi-scid Jic mice. In parallel, total RNAs of the UCBs were subjected to the gene expression profiling with oligonucleotide microarrays. The UCBs from three donors failed to establish the engraftment in the host mice whereas other 9 UCBs succeeded to various extents. Oligonucleotide microarray analysis indicated that 71 genes, including HOXB4 and ETS2, were specifically overexpressed and 23 genes were suppressed more than 2 fold in the successful UCBs comparing with the failed ones (p<0.005, Student’s t-test). Functional annotation analyses revealed that the genes mediated cell growth and cell cycle regulations were enriched in successful UCBs comparing with the failed ones. Our results suggest that the hematopoiesis reconstitution ability may vary among the cryopreserved UCBs and the quality can be distinguished with certain sets of gene expression.

overall_design: The gene expression in human umbilical cord blood cells (UCBs) was measured before transplantation to the lethally irradiated immunocompromized mice. UCBs from 12 individuals were examined.

first: Kazuhiro

last: Sudo

first: Yukio

last: Nakamura


title: Genome wide transcriptional profiling of c-Cbl deficient hematopoietic stem and progenitor cells

status: Public on Aug 12 2010

city: New Haven

first: Chozha Vendan

last: Rathinam

address: 300 Cedar St

department: Immunobiology

institute: Yale School Of Medicine

summary: Expression of genes that are differentially expressed between c-Cbl control and c-Cbl mutant hematopoietic stem and progenitor cells were identified through this approach. Interestingly, several leukemia associated genes, particularly transcription factors, were differentially expressed between c-Cbl WT and c-Cbl mutant hematopoietic stem and progenitor cells.

overall_design: Hematopoietic stem and progenitor cells of c-Cbl control  and c-Cbl mutant mice were sorted based on their defined immunophenotype. Gene expression studies were performed using Illumina microarray chips.

first: Chozhavendan

last: Flavell


title: Effects of Continuous Infusion of 20-Hydroxyecdysone in C57BL/6 Mice

city: Urbana

first: Diana

last: Cheng

state: IL

address: 1115 Plant Sciences Laboratory, 1201 South Dorner Drive

department: Natural Resources and Environmental Sciences

institute: University of Illinois Urbana Champaign

summary: 20-Hydroxyecdysone (20E) is the most abundant phytoecdysteroid produced by several plant families and has been attributed with numerous pharmacological properties in animals including anabolic and immune modulating effects.  However, the in vivo bioactivity of phytoecdysteroids in mammals remains ambiguous, and moreover, the mechanism of action in mammals has yet to be determined.  In this study, the physiological and gene expression effects of 20E were analyzed in C57BL/6 mice given a continuous infusion of saline or 20E (5 mg/kg/day) for five or fifteen days using subcutaneously implanted Alzet® osmotic pumps.  The weights of the total body, muscle groups and organs were recorded and carcass composition was determined to evaluate changes in nutrient partitioning.  There was a significant increase (p = 0.01) in the weight of triceps brachii in mice treated with 20E for five days (115 +/- 8 mg) compared to mice treated with saline for five days (88 +/- 3 mg), however, there were no differences in the other measured parameters.  To determine potential mechanisms of action of 20E in skeletal muscle, Illumina’s Mouse Whole Genome-6 v2.0 Expression BeadChips were used to evaluate changes in gene expression after 20E infusion.  False Discovery Rate correction of microarray data did not reveal any beadtypes that were differentially expressed.  Therefore, Ingenuity Pathways Analysis (IPA) was used to identify genes with the most evidence for differential expression in the context of biological functions and pathways.  IPA provided evidence for 20E involvement in processes including cellular growth and proliferation and cell-to-cell signaling and interaction.  Overall, the data suggests that 20E does not have potent anabolic properties.  IPA identified potential lead biological processes and pathways of 20E.

overall_design: Total RNA was extracted from the triceps brachii of C57BL/6 mice given a continuous infusion of saline or 20E (5 mg/kg/day) for 5 or 15 days using subcutaneously implanted Alzet® osmotic pumps to evaluate gene expression effects of 20E on mouse muscle.

first: Louis

middle: W

last: Kutzler

first: Jenny

last: Drnevich

first: John

last: Killefer

first: Mary

last: Lila


title: mRNA expression data from differentiation of human ESCs into definitive endoderm, Cyt49 on matrigel

status: Public on Jul 30 2010

city: San Diego

first: Andrew

last: Hinton

address: 3525 John Hopkins Ct.

department: Pediatrics

institute: UC, San Diego

summary:
hESCs can differentiate into the three primary embryonic lineages (endoderm, mesoderm, ectoderm) as well as extraembryonic tissues. Definitive endoderm (DE) is the first step into the pathway to endoderm derived tissues: pancreas, liver, gut, lung.
We used microarrays to detail the changes in mRNA expression during the transition from pluripotent hESCs into definitive endoderm.

overall_design: hESCs (Cyt49) were differentiated in the presence of Activin A and Wnt3A under low serum conditions to induce DE formation. Samples were collected at day 0, day 2 and day 4.


title: Siah2-dependent concerted activity of HIF and FoxA2 regulates formation of neuroendocrine prostate tumors

status: Public on Jul 13 2010

first: Roy

last: Williams

summary: Neuroendocrine (NE) carcinoma and NE differentiation (NED) of human prostate tumor are hallmarks of aggressive human prostate cancer. Here we reveal that HIF-1a cooperation with FoxA2, a transcription factor expressed in NE tissue, is required for determining NE phenotype. Reduced HIF-1a expression, as seen in the E3 ubiquitin ligase Siah2 mutant mice, converted NE tumors to atypical hyperplasia when crossed with the TRAMPTg mice. Significantly, HIF-1a cooperation with FoxA2 enables the trans-activation of select HRE-regulated genes such as Hes6, Plod2 and Jmjd1a, whose expression is notably higher in metastatic prostate adenocarcinomas. Our findings disclose the requirement for spatial and timely regulation of FoxA2 and HIF-1a for NE/NED in prostate tumors.

overall_design: 12 prostate tumor samples were analyzed during normoxia and hypoxia, with different FOX/HIF genotypes. The pivotal samples are represented as duplicates.

first: Ze'ev

last: Ronai

first: Jianfei

last: Qi


title: A distinct microRNA signature for definitive endoderm derived from human embryonic stem cells

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

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

overall_design: Refer to individual Series


title: Gene expression profie of OSMF (Oral Submucous Fibrosis) tissues compared with the expression in normal oral tissues

status: Public on Jun 30 2010

city: Bangalore

first: Paturu

last: Kondaiah

address: CV Raman Avenue

department: MRDG

institute: IISc

summary:
ABSTRACT:

Background: Oral Submucous Fibrosis (OSF) is a chronic inflammatory disease   resulting in progressive fibrosis of the oral soft tissues.  Habit of   chewing betel quid has been proposed as an important etiological factor in   the development of this disease. But the exact mechanism of pathogenesis is   still not clear.

Methods: We took microarray approach to identify differentially regulated   genes in 10 OSF tissues against 8 pooled normal tissues using   oligonucleotide arrays.  Microarray results have been confirmed by qRT-PCR.   Regulation of genes in epithelial and fibroblast cells was studied after   treatment with arecoline, TGF-b and LAP followed by qRT-PCR.

Results: Total number of genes found to be commonly regulated in OSF   (p<=0.05 and Fold change>=1.5) tissues are 5288 and among them 2884 are   up-regulated and 2404 are down-regulated. Extra cellular matrix genes that   have been reported in OSF such as collagens, fibronectin and cytokines ET1,   CTGF and TGF-b1 are among the up regulated genes.  The list of up and down   regulated genes also includes RARRES1, TGM2, THBS1, CHGB, MMP3, SPP1 and   ALOX12, C4orf7 respectively.  Analysis of microarray data revealed TGF-?   pathway as a principal gene network involved in the development of OSF.   Intriguingly, there was no regulation of CTGF and THBS1 in fibroblasts by   arecoline.  However, TGF-b1 treatment regulated all these genes in both   epithelial and fibroblast cells.

Conclusion: We demonstrate over expression of novel genes in OSF and suggest   that OSF development involves TGF-b pathway in an epithelial-stromal   cooperation.  Targeting TGF-b signaling could be an alternate strategy to   treat OSF.

overall_design: Two-condition experiment: 10 OSF tissues against 8 pooled normal tissues

first: Imran

last: Khan

first: Prasoon

last: Agarwal


title: Gene expression profiling of gastric cancer

status: Public on Jul 08 2010

first: Akhilesh

last: Pandey

email: pandey@jhmi.edu, arivusudar@ibioinformatics.org, sameerkumar.iob@gmail.com, microarray@ibioinformatics.org

address: UnitI, Discoverer building, ITPL

institute: Institute of Bioinformatics

summary: Surgically resected gastric adenocarcinoma samples and their paired disease-free (R0) marginal nonmalignant tissue were obtained from 14 patients with gastric adenocarcinoma. RNA was isolated using the RNAeasy Kit (Qiagen Valencia, CA) from 15 mg of tissue.  The quality of total RNA and its integrity was assessed using the Bioanalyzer 2100 (Agilent, Palo Alto, CA) and RIN value (RNA Integrity Number) was recorded for all the samples for intact 18S and 28S rRNA. Total RNA (800 ng) from each sample was reverse transcribed and linear amplified using the low RNA input linear amplification kit (Agilent Technologies). After synthesis of the first and second strand of cDNA, the product was used in an in vitro transcription reaction to generate cRNAs in the presence of cyanine 3-labeled UTP (Cy3) for normal and cyanine 5-labeled UTP (Cy5) for tumor. Fragmented Cy3-labeled cRNA of the control sample were mixed with equal amounts of Cy5-labeled cRNA from the gastric tumor sample, and the mixtures were hybridized onto 44K whole human genome DNA microarrays (Agilent Technologies) for 17 hrs at 65°C with constant rotation (10 rpm). Subsequently, the arrays were washed according to manufacturer’s instructions. The slides were scanned using an Agilent microarray scanner (G2565AA), and the images were processed using the Agilent feature extraction software AFE 9.5. GeneSpring GX v10.1 (Agilent Technologies) was used to analyze the expression profiles obtained after microarray hybridization. The feature extraction files from all the samples were uploaded to GeneSpring. Following intensity-dependent normalization (Lowess), the data was subjected to statistical analysis. A two tailed student’s t-test was used to determine significance of the differences observed between the normal and tumor samples. Benjamini Hochberg algorithm was used to compute false discovery rates. Genes were filtered based on P value threshold of 0.001 and false discovery rate of less than 1%.

overall_design: Transcriptional profiling of normal vs. tumor tissues from 14 patients with gastric cancer. Two-color experiment.


title: Genome-wide analysis of effects of obovatol on lipopolysaccharide (LPS)-induced gene expression in microglia

status: Public on Jul 05 2010

city: Daegu

first: Kyoungho

last: Suk

address: 101 Dong-In, Joong-gu

department: Department of Pharmacology

institute: Kyungpook National University School of Medicine

summary: Transcriptional profiling of BV-2 microglial cells comparing control untreated BV-2 cells with LPS-treated BV-2 cells or obovatol/LPS-treated BV-2 cells. Objective was to determine the effect of obovatol on LPS-induced gene expression in microglia.

overall_design: Total RNA obtained from BV-2 microglial cells, which were treated with lipopolysaccharide (LPS) or LPS/obovatol compared to untreated BV-2 cells. Biological replicates: 1 control replicates, 1 LPS-treated replicates, 1 obovatol+LPS-treated replicates.

first: Jiyeon

last: Ock


title: Genes regulated by PCK Inhibitors, enzastaurin and Go, in CAL-27 cells, a SCCHN cell line

status: Public on Jul 12 2010

city: Chicago

first: Wen

last: Kuo

department: Medicine/Hema/Onc

institute: University of Chicago

summary:
Efficacy of the Multi-Kinase Inhibitor Enzastaurin is Dependent on Cellular Signaling Context
Testing a panel of SCCHN cell lines revealed variable sensitivity to enzastaurin which correlated significantly with baseline cyclin D1 protein expression. Moreover, sensitivity and resistance could be reversed, respectively, by expression or depletion of cyclin D1. Furthermore, analysis of sensitive and resistant cell lines revealed distinct differences in cyclin D1 regulation. Enzastaurin modulated cyclin D1 synthesis via an AKT regulated pathway in the former while high level CCND1 gene amplification was present in the latter. These results underscore the critical relevance of cellular signaling context in developing cancer therapies, in general, and suggest that enzastaurin, in particular, would be most effective in tumors where baseline cyclin D1 expression is low to moderate and physiologically regulated.

overall_design: CAL-27 cells were treated with the inhibitors for 24 hours and the gene expression from each group were analyzed

first: Marsha

last: Rosner

first: Ezra

last: Cohen


title: Signaling from the secretory granule to the nucleus: Uhmk1 and PAM

status: Public on Jun 23 2010

city: Farmington

first: Richard

middle: E

last: Mains

address: 263 Farmington Ave

department: Neuroscience

institute: University of Connecticut Health Center

summary: Neurons and endocrine cells package peptides in secretory granules (large dense core vesicles; LDCVs) for storage and stimulated release.  Studies of PAM, an essential secretory granule membrane enzyme, revealed a pathway that can relay information from secretory granules to the nucleus, resulting in alterations in gene expression.  The cytosolic domain of PAM, a type 1 membrane enzyme essential for the production of amidated peptides, is basally phosphorylated by Uhmk1 and other Ser/Thr kinases.  Proopiomelanocortin processing in AtT-20 corticotrope tumor cells was increased when Uhmk1 expression was reduced.  Uhmk1 was concentrated in the nucleus, but cycled rapidly between nucleus and cytosol.  Endoproteolytic cleavage of PAM releases a soluble cytosolic domain (CD) fragment that localizes to the nucleus.  Localization of PAM-CD to the nucleus was decreased when PAM-CD with phosphomimetic mutations was examined and when active Uhmk1 was simultaneously over-expressed.  Membrane-tethering Uhmk1 did not eliminate its ability to exclude PAM-CD from the nucleus, suggesting that cytosolic Uhmk1 could cause this response.  Microarray analysis demonstrated the ability of PAM to increase expression of a small subset of genes, including aquaporin 1 (Aqp1) in AtT-20 cells.  Aqp1 mRNA levels were higher in wildtype mice than in mice heterozygous for PAM, indicating that a similar relationship occurs in vivo.  Expression of PAM-CD also increased Aqp1 levels while expression of Uhmk1 diminished Aqp1 expression. The outlines of a pathway that ties secretory granule metabolism to the transcriptome are thus apparent.

overall_design: Three separate clones of AtT-20 mouse corticotrope tumor cells stably transfected with doxycycline-inducible rat PAM-1 (clones 14, 6_1, 6_2) were treated with cotrol or doxycycline medium for 48 hours.  Total mRNA was isolated and hybridized to an Illumina MouseWG-6 v 2.0 whole genome BeadChip.

first: Victor

middle: P

last: Francone

first: Chitra

last: Rajagopal

first: Betty

last: Eipper


title: Gene expression in mouse embryonic heart

city: Charleston

first: Jeremy

last: Barth

state: SC

address: 173 Ashley Ave, BSB 627

institute: MUSC

summary: This study was conducted to examine normal gene expression in the heart during mouse embryonic development.

overall_design: Wild type embryo hearts (n=5) were collected at stage E12.5 and total RNA was isolated for analysis by Affymetrix mouse genome 430A GeneChip.

first: W

middle: S

last: Argraves

last: Fresco

first: Marion

last: Cooley

middle: L


title: Control of mammary stem cell function by steroid hormone signalling.

status: Public on Jun 18 2010

city: Parkville

first: Gordon

last: Smyth

state: Vic

address: 1G Royal Pde

institute: Walter and Eliza Hall Institute of Medical Research


title: Effects of Ionizing Radiation on Self Renewal and Pluripotency of Human Embryonic Stem Cells

status: Public on Jun 16 2010

city: Stanford

first: Kitchener

middle: D.

last: Wilson

address: S140 Grant Bldg

institute: Stanford University

summary: Human embryonic stem cells (hESCs) present a novel platform for in vitro investigation of the early embryonic cellular response to ionizing radiation. Thus far, no study has analyzed the genome-wide transcriptional response to ionizing radiation in hESCs. In this study, we use Agilent microarrays to analyze the global gene expression changes in H9 hESCs after low (0.4 Gy), medium (2 Gy), and high (4 Gy) dose irradiation.

overall_design: Undifferentiated H9 hESCs were cultured on Matrigel in feeder-free conditions, and exposed to ionizing radiation at the indicated dosage (or control) from a Cesium-137 irradiator. Total RNA was isolated 24 hours after irradiation in the same feeder-free culture conditions. Experiment was repeated three times for each group, yielding a total of 12 distinct samples.

first: Mei

last: Huang


title: Comparison of CD44+/CD24- sorted fraction with 'rest' fraction of NBLE cells and primary breast cancer-derived cells

status: Public on Jun 09 2010

first: Anurag

last: Paranjape

address: CVRaman road

institute: Indian Institute of Science

summary:
TSV40ER and hTERT immortalized mammospheres undergo transformation in culture to generate breast cancer stem cells

The stem cell hypothesis of cancer predicts that cancers arise from the transformation of normal stem/progenitor cells present within adult tissues. However, the molecular mechanisms that lead to the transformation of these cells remain largely unknown, mainly owing to the lack of suitable model systems. In this study, we have generated an immortalized breast epithelial cell line, NBLE, by over-expressing the SV40 Early Region and the catalytic domain of human telomerase into mammosphere-derived cells that are enriched in breast stem/progenitor cells. While primary mammospheres fail to grow beyond four passages in suspension culture, NBLE cells propagated continuously generating spheres at a high frequency of 35%. These cells also expressed stemness-related genes, and differentiated into both luminal and myoepithelial lineages. Interestingly, after around 135 population doublings in culture, the late passage cells exhibited a mesenchymal morphology and contained >90% of CD44+/CD24Low/- cells resembling breast cancer stem cells. When injected subcutaneously into nude mice, the late passage NBLEs formed invasive tumors closely resembling breast adenocarcinomas, the most common type of breast cancer. The transformed NBLE cells showed hyperactivation of Wnt, Hh and TGFbeta pathways, suggesting that the deregulation of these self-renewal pathways may have in part contributed to tumorigenesis. Gene expression analysis further revealed a high degree of similarity with breast cancer stem cells. Thus, our study provides a unique model system to study signaling pathways involved in self-renewal, differentiation, and transformation of breast stem/progenitor cells. Additionally, the NBLE cells can be utilized for screening drugs specifically targeting breast cancer stem cells.

NBLE cells were generated by over-expressing SV40ER and hTERT into mammosphere-derived cells. These cells harnored CD44+/CD24- fraction that resembled breast cancer stem cells. To understand the unique gene expression of this fraction we performed microarray on CD44+/CD24- versus rest fractions from NBLE cells (Rep 1 and Rep 2). To see if this gene profile has any similarity with breast cancer stem cells, we performed CD44+/CD24- versus rest microarray on two primary breast tumors (CB272 and CB258-Rep1 andRep2).

overall_design:
Whole genome gene expression profiling microarray based comparison of immortalized and transformed mammospheres derived cells.

Two-color experiment, NBLE-CD44+/CD24- labelled with Cy5 and NBLE-Rest labelled with Cy3

first: Tamoghna

last: Mandal

first: Geetashree

last: Mukherjee

first: Annapoorni

last: Rangarajan


title: Expression analysis of dendritic cells, macrophages and monocytes

status: Public on Jun 07 2010

city: Regensburg

first: Maja

last: Klug

address: Franz-Josef-Strauss-Allee 11

department: Hematology

institute: University Hospital Regensburg

summary: Expression profiles at different time points during dendritic cell differentiation (induced by specific culture conditions) including monocytes as well as expression profiles between monocytes and completely differentiated cells (macrophages at day7 and dendritic cells at day7, respectively) were compared.  Monocyte-derived dendritic cells (DC) were obtained by culturing elutriated monocytes with 20U/ml IL-4, 280U/ml GM-CSF and 10% FCS; monocyte-derived macrophages (MAC) were obtained by culturing elutriated monocytes with 2% AB serum.

overall_design: Three to seven biological replicates that are derived from independent healthy donors were included. One-color based gene expression. 2 datasets: dendritic cell kinetic study and comparison of monocyte, macrophage, and dendritic cells

first: Lucia

last: Schwarzfischer

first: Claudia

last: Gebhard

first: Michael

last: Rehli


title: Effects of a high-fat maternal diet and embryonic Cited2 genotype on gene expression and development in mouse

status: Public on Jun 24 2010

first: Shoumo

last: Bhattacharya

address: Roosevelt Drive

department: RDM Cardiovascular Medicine

institute: Wellcome Centre For Human Genetics, University of Oxford

summary:
Deficiency of the transcription factor Cited2 in mice results in cardiac malformation, adrenal agenesis, neural tube, placental defects, and partially penetrant left-right patterning defects resulting from an abnormal Nodal->Pitx2c pathway. Here we show that a maternal high-fat diet more than doubles the penetrance of laterality defects and, surprisingly, induces palatal clefting in Cited2 deficient embryos. Both maternal diet and Cited2 deletion reduce embryo weight and kidney and thymus volume.
Expression profiling identified 40 embryonic transcripts including Pitx2 that were significantly affected by embryonic genotype-maternal diet interaction.  We show that a high-fat diet reduces Pitx2c levels >2 fold in Cited2 deficient embryos and that Pitx2c deficiency results in cleft palate. Taken together, these results define a novel interaction between maternal high-fat diet and embryonic Cited2 deficiency that affects Pitx2c expression and results in abnormal laterality and cleft palate.

overall_design: Two-factor design: diet (high fat or control) and genotype (Cited2 knockout or wildtype) with n=3 for each of the 4 factor combinations

first: Jamie

last: Bentham

first: Anna

last: Michell

first: Helen

last: Lockstone

first: Jennifer

last: Taylor

first: Daniel

last: Andrew

first: Jurgen

last: Schneider

first: Nigel

middle: A

last: Brown


title: Analysis of gene expression in the mouse embryo pharyngeal arch

first: Jeremy

last: Barth

summary: This study was conducted to examine normal gene expression in the pharyngeal arch during mouse embryonic development

overall_design: Wild type embryonic tissue containing the pharyngeal arches was collected from five independent samples (n=5) at stage E10.5 by dissection. Total RNA was isolated for analysis by Affymetrix mouse genome 430A GeneChip.

first: W

last: Argraves

first: Victor

last: Fresco

first: Marion

last: Cooley


title: Gene expression profiles of TiPS, HDF-iPS, ES and T cells

status: Public on Jun 03 2010

city: Tokyo

first: Shinsuke

last: Yuasa

address: 35-Shinanomachi Shinjuku-ku

institute: Keio University

summary: To show the similarity among TiPSCs, HDF-iPSCs and ESCs and the differences between TiPSCs and T cells, this experiment was designed.

overall_design: Undifferentiated TiPSCs, HDF-iPSCs and ESCs were collected. And stimulated peripheral circulating terminally differentiated T cells were collected. Then, they were applied in this experiment.


title: Hypoxia response by human breast cancer cell MDA-MB-231 sublines

city: Princeton

first: Yibin

last: Kang

state: NJ

address: LTL 254, Washington Road

department: Molecular Biology

institute: Princeton University

summary: Two MDA-MB-231 sublines, SCP2 and LM2 (4175), were applied to low oxygen (1%) for 0, 6 and 24 hours, then profiled for RNA expression.

overall_design: Two sublines, each sublines has three conditions: 0h, 6h and 24h for hypoxia treatment. Each condition has two repeats. Total 12 samples

first: Xin

last: Lu


title: Molecular Characterization of Treponema denticola infection-induced bone and soft tissue transcriptional profiles

status: Public on Nov 16 2010

first: Kesavalu

last: Lakshmyya

address: 1600 SW Archer road, D11-24

institute: University of Florida, College of Dentistry

summary:
The objectives of this investigation were to examine changes in the host transcriptional profiles during a Treponema denticola infection using a murine calvarial model of inflammation and bone resorption.  T. denticola ATCC 35404 was injected into the subcutaneous soft tissue over the calvaria of BALB/c mice for 3 days, after which the soft tissues and calvarial bones were excised.  RNA was isolated from infected soft tissues and calvarial bones and analyzed for transcript profiles using Murine GeneChip® MG-MOE430A Affymetrix arrays to provide a molecular profile of the events that occur following infection of these tissues.
We used mouse microarrays to detail the molecular profile of the events that occur following infection of calvarial and bone tissues and identified distinct classes of up- and down-regulated genes during this process.

overall_design: T. denticola was injected at 1.5 x 109 (N = 10) into the soft tissues overlying the calvaria of the mice for 3 days. A control group (N = 9) was injected with vehicle once daily for 3 days. Mice were euthanized 8 h after the last injection.  The calvarial bones and overlying soft tissues from 5 mice in each group were excised, snap frozen in liquid nitrogen, and stored at –80°C until RNA isolation. Total RNA was isolated from the frozen calvarial tissue and calvarial bone from each mouse (T. denticola infected and control animals) with Trizol reagent (Invitrogen, CA).  Equal amounts of RNA from samples were labeled and hybridized on a mouse GeneChip following the protocol described in the GeneChip Expression Analysis Technical manual (Affymetrix, Santa Clara, CA). After hybridization, the GeneChip arrays were stained and scanned in an Affymetrix GCS 3000 7G Scanner.

first: Lakshmyya

last: Kesavalu

first: Archana

last: Meka

first: Vasudevan

last: Bakthavatchalu

first: Sabapathi

last: Sathishkumar

first: Cecilia

last: Lopez

first: Raj

last: Verma

first: Shannon

last: Wallet

first: Indraneel

last: Bhattacharyya

first: Brendan

middle: F

last: Boyce

first: Jeffrey

last: Mans

first: Richard

middle: J

last: Lamont

first: Henry

last: Baker

last: Ebersole


title: Regulation of gene expression program by Fsp27 in white and brown adipose tissue

status: Public on Jul 07 2010

city: Beijing

first: Yinxin

last: Zhang

address: Room C131, School of Medicine, Tsinghua University

department: School of Life Sciences

country: China

institute: Tsinghua University

summary:
Background: Brown and white adipose tissues (BAT and WAT) play critical roles in controlling energy homeostasis and in the development of obesity and diabetes. Fsp27 is expressed in both BAT and WAT and promotes lipid storage and the development of obesity and diabetes. In addition, Fsp27-deficient white adipocytes acquired certain BAT-like properties including reduced lipid droplet size and increased mitochondrial activity. Using microarray and semi-quantitative real-time PCR analyses, we systematically analyzed the gene expression profile in Fsp27-deficient WAT and BAT.
Results: We observed that BAT-selective genes were significantly up-regulated, whereas WAT-selective genes were down-regulated in the WAT of Fsp27-/- mice. Expression levels of BAT-selective genes were also dramatically up-regulated in the WAT of leptin and Fsp27 double deficient mice. Furthermore, we observed that expression levels of genes in multiple metabolic pathways including oxidative phosphorylation, the TCA cycle and fatty acid synthesis and oxidation were increased in the Fsp27-/- WAT. In contrast, expression levels for extracellular matrix remodeling, the classic complement pathway and TGF-β signaling"were down-regulated in the WAT of Fsp27-/- mice. Most importantly, regulatory factors that determine BAT identity such as CEBPα/β, PRDM16 and major components in the cAMP pathway were markedly up-regulated in the WAT of Fsp27-/- mice. Interestingly, we observed distinct gene expression profiles in the BAT of Fsp27-/- mice.
Conclusion: Our data suggest that Fsp27 acts at upstream to control gene expression of diverse pathways, in particular the expression of regulatory factors that determine the identity of BAT and WAT. Therefore, Fsp27 is an important molecular determinant for the identity of WAT, and loss of Fsp27 leads to the conversion of WAT to a BAT-like tissue.

overall_design: Total RNAs were extracted from individual gonadal WAT of five pairs of 3-month-old wild-type and Fsp27-null male mice. Equal amounts of RNA from five pairs of mice with each genotype were pooled to form RNA pools (total 45 μg). Duplicate experiments were carried out.

first: De

last: Li

first: Yue

last: Wang

first: Bofu

last: Xue

first: Linkang

last: Zhou

first: Li

last: Xu

first: Zilong

last: Wen

first: Peng

first: Jianli

last: Sang


title: Gene Expression in Mutant P0 Cre Dicer Mouse Sciatic Nerves

status: Public on Jun 04 2010

first: Beth

last: Yun

address: 303 E.  Superior St.

department: Neurology and The Center for Genetic Medicine

institute: Northwestern University

summary: The hypothesis is that genes involved in the immature schwann cell and promyelinating state will be upregulated and genes that are involved in the myelnating state will be down regulated.

overall_design: Bioconductor limma package [1,2,3,4] was used to preprocess 6 samples from mouse tissue-cultured cells, which are hybridized to Mouse WG-6 version 2 Illumina Array. To remove batch effects, the complete dataset were normalized by RMA. Before doing statistical analysis, we filter the probe-sets by present/absent calls using the Wilcoxon signed rank-based algorithm. 18,420 genes out of 45,281 genes were kept and the remaining ones were removed as “Absent” to reduce false positive rate. We identified differentially expressed gene list by fitting linear models to the normalized expression values. The empirical Bayes shrinkage was applied to t-statistics using the limma package in Bioconductor. In general, selected genes have greater than 2.0 fold-change and less than 0.05 fdr adjusted p-value.

first: Rajeshwar

last: Awatramani

first: Gang

last: Feng

first: Simon

last: Lin

first: Pan

last: Du


title: Genome-wide analysis of adult Pitx2c heterozygous mice

city: Münster

first: Peter

middle: Christian

last: Kahr

address: Grevener Straße 1

institute: University Hospital Münster

summary: Analysis of the expression profile of adult mice heterozygous for Pitx2 isoform C.

overall_design: Total RNA obtained from isolated left and right atria from 5 Pitx2c heterozygous mice and 5 wild-type littermates.

first: Nigel

last: Brown

middle: C


title: Hepatocytes obtained from mouse GPSCs are functional and show similar expression profiles to fetal primary hepatocytes

status: Public on Jun 01 2010

city: Candiolo

first: Enzo

last: Medico

state: TO

address: Strada Prov. 142, km 3,95

department: Oncology

country: Italy

institute: Candiolo Cancer Institute, University of Torino

summary:
Germline cell-derived pluripotent stem cells (GPSCs) are similar to embryonic stem (ES) cells in that they can proliferate intensively and differentiate into a variety of cell types, including cardiomyocytes and neurons. In this report, mouse GPSCs were induced to differentiate into hepatocytes with very high efficiency, and demonstrated, for the first time, to be functional.  These hepatocytes were characterised at cellular and molecular levels. The GPSC-derived hepatocytes not only expressed hepatic markers, but were also metabolically active as shown by albumin and haptoglobin secretion, urea synthesis, glycogen storage and indocyanine green uptake.
Previous studies have revealed some inherent differences in gene expression between undifferentiated mouse ES cells and GPSCs.  We wanted to investigate whether this difference may impact on the hepatocyte differentiation capacity of the GPSCs. Large-scale gene expression profiling revealed a strong similarity between GPSC and ES cells at different stages of induced hepatic differentiation. Moreover, Pearson correlation analysis of the microarray datasets revealed that, at late hepatic differentiation stages, the in vitro-derived cells were closer to fetal mouse primary hepatocytes. Thus, adult GPSCs offer great potential for cell ment therapy for a wide variety of liver diseases.

overall_design:
Mouse ES cells and GPSCs at various times of hepatocyte differentiation, compared to embryonal (E16) and postnatal (PN1) mouse primary hepatocytes.

The supplementary file 'GSE19044_non-normalized.txt' contains non-normalized data for Samples GSM471318-GSM471359.

first: Sharmila

last: Fagoonee

first: Fiorella

last: Altruda


title: Gene profiling and prediction of response to anastrozole neoadjuvant treatment in breast cancer

status: Public on May 17 2010

city: Biella

first: vijay

middle: kumar

last: singh

state: Biella

address: via Malta 3

institute: Fondazione "Edo ed Elvo Tempia Valenta"

summary: Transcriptome of 17 tru-cut biopsies and 13 matched surgical samples from ER+ breast tumor patients, treated for 3 months with Anastrozole were anayzed to identify a robust expression signature predictive of response to Anastrozole neoadjuvant treatment in ER+ breast cancer patients and, at the same time, to delineate treatment effects.

overall_design: Each specimen had been hybridized against a Human universal reference used as baseline in each array. Two replicates with dye-swap had been performed for each sample, both before (tru-cut biopsy sample) and after treatment (surgical sample).

first: Vijay

last: Singh

first: Maurizia

middle: M

last: Grand

first: Chiara

last: Ghimenti

first: Maria

last: Scatolini

first: Lea

last: Regolo

first: Enrico

last: Grosso

first: Alberto

last: Zambelli

first: Gian

last: Da Prada

first: Laura

last: Villani

first: Paola

last: Baiardi

first: Silvia

last: Marsoni

last: Costa

first: Giovanna

last: Chiorino


title: Global gene expression responses to low doses of protons in a human 3-dimensional skin model

city: New York

first: Alexandre

last: Mezentsev

address: 630 west 168th Street, VC 15-204

department: Dermatology

institute: Columbia University

summary: Accumulating data suggest that the biological responses to high and low doses of radiation are qualitatively different, necessitating the direct study of low dose responses. Most such studies have utilized 2-dimensional culture systems, which may not fully represent responses in 3-dimensional tissues.  To gain insight into low dose responses in tissue, we have profiled global gene expression in EPI-200, a 3-dimensional tissue model that imitates the structure and function of human epidermis, at 4, 16 and 24 hours after exposure to high (2.5 Gy) and low (0.1 Gy) doses of low LET protons. The most significant gene ontology groups among genes altered in expression were consistent with effects observed at the tissue level, where the low dose was associated with gradual recovery and tissue remodeling, while the high dose resulted in loss of structural integrity and terminal differentiation.  Network analysis of the significantly responding genes suggested that TP53 dominated the response to 2.5 Gy, while HNF4A, a novel transcription factor not previously associated with radiation response, was most prominent in the low dose response.  Thus, these studies address the molecular basis of response to low versus high dose low LET radiation exposure.

overall_design: Radiation induced gene expression in 3-dimensional tissue model, Epi-200, was measured at 4, 16 and 24 hours after exposure to doses of 0, 0.1 and 2.5 Gy of protons. Three independent experiments were performed in the each time (4, 16 and 24 hours) using one tissue sample per a data point.

first: Sally

last: Amundson


title: DNA methylation in progenitor cells

status: Public on May 12 2010

city: Oslo

first: Philippe

last: Collas

address: PO Box 1112 Blindern

department: Institute of Basic Medical Sciences

country: Norway

institute: University of Oslo

type: Methylation profiling by genome tiling array

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

overall_design: Refer to individual Series


title: Transcriptional analysis of an E2F gene signature as a biomarker of activity of the cyclin-dependent kinase inhibitor PHA-793887 in tumor and skin biopsies from a phase I clinical study

status: Public on May 14 2010

city: Nerviano

first: Roberta

last: Bosotti

state: MI

address: viale Pasteur,10

department: Biotechnology

institute: Nerviano Medical Sciences srl

summary: Microarray analysis of transcriptional changes in biopsies of solid tumors from patients treated in a Phase I study with the Cdk inhibitor PHA-793887.

overall_design: 7 patient biopsies pre- and post-treatment in dye swap. Tumors are of different origins, and are described in the accompanying manuscript.

first: G

last: Locatelli

first: R

first: M

last: Ciomei

middle: G

last: Brasca

last: Calogero

first: C

last: Mercurio

first: F

last: Fiorentini

last: Bertolotti

first: E

last: Scacheri

first: A

last: Scaburri

last: Galvani

last: Pesenti

first: T

last: De Baere

first: JC

last: Soria

first: V

last: Lazar

last: Isacchi


title: Opposing roles of polycomb repressive complexes in hematopoietic stem and progenitor cells

status: Public on May 20 2010

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: Polycomb group (PcG) proteins are transcriptional repressors with a central role in the establishment and maintenance of gene expression patterns during development. We have investigated the role of Polycomb Repressive Complexes (PRCs) in hematopoietic stem cells (HSCs) and progenitor populations. We show that mice with loss of function mutations in PRC2 components display enhanced HSC/progenitor population activity, whereas mutations that disrupt PRC1 or PhoRC are associated with HSC/progenitor cell defects. Since the hierarchical model of PRC action would predict synergistic effects of PRC1 and PRC2 mutation, these opposing effects suggest this model does not hold true in HSC/progenitor cells. To investigate the molecular targets of each complex in HSC/progenitor cells, we measured genome-wide expression changes associated with PRC-deficiency, and identified transcriptional networks that are differentially regulated by PRC1 and PRC2. These studies provide new insights into the mechanistic interplay between distinct PRCs and have important implications for approaching PcG proteins as therapeutic targets.

overall_design: Total RNA obtained from foetal liver LSK cells from mouse embryos with genes from different polycomb repressive complexes mutated or knocked-out was compared with wild-type samples.

first: Marnie

last: Blewitt


title: Epigenetic environment of histone H3.3 on promoters revealed by integration of imaging, ChIP-chip, and MeDIP-chip data

last: Collas

type: Genome binding/occupancy profiling by genome tiling array

summary:
Epigenetic environment of histone H3.3 on promoters revealed by integration of imaging and genome-scale chromatin and methyl-DNA immunoprecipitation information.
Chromatin regions with different transcriptional outputs are distinguished by the deposition of histone variants. Histone H3.3 is incorporated into chromatin in a replication-independent manner; yet the relationship between H3.3 deposition, chromatin environment is incompletely understood. We have integrated imaging and genome-scale chromatin and methyl-DNA immunoprecipitation approaches to investigate the genomic distribution of epitope-tagged H3.3 in relation to histone modifications, DNA methylation and transcription.
Results: Imaging shows that H3.3, in contrast to replicative H3.1 or H2B, is enriched in chromatin marked by histone modifications of active genes. A genome-wide survey identifies 1,649 H3.3-enriched promoters, only a subset of which is co-enriched in H3K4me3, H3K9me3 and/or H3K27me3, with a preference for H3K4me3, corroborating imaging data. H3.3-enriched promoters are depleted of H3.3 at the TSS in a transcription-independent manner. H3.3 is found predominantly on CpG-rich unmethylated promoters, creating a condition favourable for transcription. In undifferentiated mesenchymal stem cells, H3.3 target genes are linked to signaling and mesodermal differentiation, suggesting that H3.3 may be a mark of lineage priming.
Conclusions: A minor fraction of H3.3 is targeted to promoters, which are predominantly CpG-rich, DNA unmethylated and devoid of detectable trimethylated H3K4, K9 and K27. Among H3.3 target promoters co-marked by methylated H3, H4K4me3 is preferred, with or without H3K27me3, arguing that in mesenchymal stem cells H3.3 marks transcriptionally active or potentially active promoters.
Key words: Imaging, ChIP-chip, MeDIP-chip, histone H3.3, mesenchymal stem cells

overall_design:
ChIP-chip and MeDIP-chip experiments: Performed with two independent biological replicates.
Gene expression profiling experiments: Total RNA obtained from H3.3-EGFP transfected or empty-EGFP transfected mesenchymal stem cells compared to untransfected mesenchymal stem cells.  Raw expression data linked below as supplementary file (GSE17053_Illumina_non-normalized_data.txt).

first: Andrew

middle: H

last: Reiner

first: Bente

last: Jacobsen


title: Differential gene expression profiles of long bones of telomerase deficient mice (G3-mTERC-/-)

status: Public on May 10 2010

city: odense

first: Hamid

last: Saeed

state: Fyn

address: Winslows parken 1st floor

department: Endocrinology

institute: Odense University Hospital/ University of Southern Denmark

summary: Telomere shortening due to telomerase deficiency leads to accelerated senescence of human skeletal (mesenchymal) stem cells (MSC) in vitro. In order to study the role of telomere shortening in vivo, we studied the phenotype of telomerase deficient mice caused by absence of telomerase RNA component (TERC-/-).  TERC-/- exhibited accelerated age-related bone loss starting at 3 months of age and during 12 months follow up. Bone histomorphometry revealed decreased mineralized surface and bone formation rate as well as increased osteoclast number and size in TERC-/-. Also, serum total deoxy-pyridinoline (tDPD) was increased in TERC-/-. MSC isolated from TERC-/-  exhibited intrinsic defects with reduced total number, lower proliferation rate, decreased expression of osteoblastic (OB) differentiation markers and  formed less in vivo ectopic bone compared to WT cells. The TERC-/--MSC cultures accumulated a larger proportion of senescent ß-galactosidase+ cells and cells exhibiting DNA damage positive for γ-H2AX. Micro-array analysis of bones of TERC-/- and WT revealed significant over-expression of a large number of pro-inflammatory genes and signaling pathways in TERC-/- known to control osteoclast (OC) differentiation. In accordance with that, serum from TERC-/- enhanced OC formation in control bone marrow cultures. Our data demonstrate two mechanisms for age-related bone loss caused by telomerase deficiency: intrinsic osteoblastic defects and creation of pro-inflammatory osteoclast-activating microenvironment. Approaches for re-telomerization of MSC may provide a novel approach for abolishing age-related bone loss.

overall_design: control (WT) and the test (G3 - mTERC-/-) samples

first: Basem

last: Abdallah

first: Moustapha

last: Kassem


title: DNA methylation in progenitor cells: expression study

first: Philippe

summary: We surveyed DNA methylation profiles of all human RefSeq promoters in relation to gene expression and differentiation in adipose tissue, bone marrow and muscle mesenchymal progenitors, as well as in bone marrow-derived hematopoietic progenitors. We unravel strongly overlapping DNA methylation profiles between adipose stem cells (ASCs), bone marrow mesenchymal stem cells (BMMSCs) and muscle progenitor cells (MPCs), while hematopoietic progenitor cells (HPCs) are more epigenetically distant from MSCs seen as a whole. Differentiation resolves a fraction of methylation patterns common to MSCs, generating epigenetic divergence.

overall_design:
RNA was isolated from MSCs isolated from various tissues and from differentiated cells, and hybridized onto Illumina expression arrays. 2-3 replicates per cell type.

The supplementary file 'GSE19773_non-normalized.txt' contains the non-normalized data for Samples GSM493884-GSM493894.