title: miRNA analysis is useful to diagnosis of liver disease, and evaluation of the grade of liver disease.

status: Public on Nov 05 2012

city: Tokushima city

first: toshihito

last: tanahashi

address: Kuramoto-cho 3-18-15

country: Japan

institute: Tokushima University

summary: miRNAs have been found to circulate in the blood in a cell-free form; their potential as readily accessible disease markers is currently evaluated. Here, we investigated if miRNA expression profile in peripheral blood can be useful as disease parameter in patients with chronic hepatitis C (CHC), chronic hepatitis B (CHB), non-alcoholic steatohepatitis (NASH), and normal liver (NL). RNA from exosome rich fraction was extracted from serum of patients with 64 CHC, 4 CHB, 7 NASH, and 12 healthy volunteers. miRNA expression profile was analyzed by microarray. Histological evaluation for the degree of inflammation and fibrosis in liver disease patients was also performed. miRNA expression profile according to the degree of liver fibrosis and inflammation was established. Diagnosis of fibrosis, inflammation by using miRNA expression pattern was shown with accuracy 67.2~89.1%, 67.2~76.5%, respectively. Moreover, miRNA expression profile in several liver diseases was also established. Classification among CHC, CHB, NASH, and NL was well tolerated and reproducible. The expression pattern of miRNA in peripheral blood showed not only the useful parameter of the grade and stage of liver disease, but also diagnostic tool for liver disease.

overall_design:
chronic hepatitis HCV; 64 samples
chronic hepatitis HBV; 4 samples
non-alcoholic steatohepatitis; 7 samples
healthy volunteers; 12 samples


title: A modified lung allograft renal capsule model to investigate the differentiation of lung epithelial cells from murine embryonic stem cells

status: Public on Aug 29 2012

city: Farmington

first: Todd

middle: James

last: Jensen

state: CT

address: 263 Farmington Avenue   MC3501

department: Center for Vascular Biology

country: USA

institute: University of Connecticut Health Center

summary: Analysis of epithelial type cell formation with mouse embyronic stem cells following 11 days of differentiation using the small molcule IDE2 as well as FGF2 and FGF10 growth factors. Up-regulation of selected lung epithelial genes will provide evidence as to whether these IDE2-based differentiation protocols result in a higher yield of alveolar-epithelial type cells.

overall_design: Total RNA was isolated following 11 days of differentiation in culture using IDE2 with or without FGF2 or FGF 10. Undifferentiated embryonic stem cells were taken as a control

first: Blair

last: Roszell

first: Ariel

last: Seaton

first: Fan

last: Zhang

first: Anupinder

last: Kaur

first: Eric

middle: D

last: Girard

first: Christine

last: Finck


title: cDNA microarray analysis of mouse embryonic stem cells-derived hematopoietic progenitors compared to native hematopoietic stem cells

status: Public on Nov 15 2012

city: Austin

first: Irina

last: Fernandez

state: TX

address: 107 West Dean Keeton st

department: Biomedical Engineering

institute: University of Texas at Austin

summary: In this study, we compared gene expression profiles of c-kit+Sca-1+ cells generated in vitro from mouse ESCs using static and bioreactor-based cultures with native HSCs isolated from mouse fetal liver (FL) or bone marrow (BM).

overall_design: total RNA obtained from ckit+Sca-1+ cells isolated  from mouse embryonic stem cells (ES) differentiated for 7 days in Static, Spinner flask and Synthecon compared to RNA isolated from ckit+Sca-1+ cells from mouse bone marrow, mouse fetal liver and mouse ES cells undifferentiated.

first: Krista

last: Fridley

first: Krishnendu

last: Roy


title: Gene expression profile changes in brains of VSV-infected wild-type and Ifit2 knockout mice at 6 days after infection

status: Public on Nov 14 2012

city: Cleveland

first: Ganes

middle: C.

last: Sen

address: 9500 Euclid Avenue NE-20

institute: Cleveland Clinic

summary: Vesicular stomatitis virus replicates with marked effciency in Ifit2 knockout mouse brains late after infection (6 days after intranasal inoculation), compared to wt brains. Changes in gene expression, especially of interferon-stimulated genes, between late in infection (at 6 d p.i.) compared to early during infection (2 d p.i.) were examined in comparison to wild-type.

overall_design: Total RNA extracted from mouse brains of wt or Ifit2 knockout mice at 6 days after infection, compared to RNA from 2 days after infection.

middle: C


title: Effect of small molecules on activated astrocytes and microglia cells

status: Public on Nov 03 2012

city: Münster

first: Susanne

last: Höing

address: Röntgenstraße 20

department: Cell and Developmental Biology

country: Germany

institute: Max Planck Institute for Molecular Biomedicine

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

overall_design: Refer to individual Series


title: Proteogenomics of synaptosomal mitochondrial oxidative stress

status: Public on Jul 17 2012

city: Novato

first: Simon

last: Melov

state: CA

address: 8001 Redwood Blvd

institute: Buck Institute for Research on Aging

summary: There has been increasing interest in the quantification and characterization of messages and proteins at the synapse, due to its importance in neurodegenerative disease, most notably Alzheimer’s disease. Here, we report the transcriptomic and proteomic changes that occur in synaptosomes from frontal cortices of Sod2 null mice. Constitutively null Sod2 mice were differentially dosed with the synthetic catalytic antioxidant EUK-189, which can extend the lifespan of these mice, as well as uncover or prevent neurodegeneration due to endogenous oxidative stress. This approach facilitated insight into quantification of trafficked messages and proteins to the synaptosome. We used two complementary methods to investigate the nature of the synaptosome under oxidative stress; either whole genome gene expression microarrays or mass spectrometry-based proteomics using isobaric tagging for relative and absolute quantitation (iTRAQ) of proteins. We have characterized the relative enrichments of gene ontologies at both gene and protein expression that occur due to mitochondrial oxidative stress in the synaptosome, which may lead to new avenues of investigation in understanding the regulation of the synaptic function in normal and diseased states. As a result of using these approaches, we report for the first time an activation of the mTOR pathway in synaptosomes isolated from Sod2 null mice, confirmed by an upregulation of the phosphorylation of 4E-BP1.

overall_design: mRNA was extracted from synaptosome samples of individual mice from each genotype/treatment group (N=9-11 per group/treatment). 200ng of the purified total RNA was then amplified one round using Ambion’s Illumina RNA Amplification Kit, to prepare cRNA for labeling and hybridization to Illumina’s MouseRef-8 v2.0 expression bead chips as per the manufacturers instructions (Illumina, San Diego, CA, USA).

first: James

middle: M

last: Flynn

first: Gregg

middle: A

last: Czerwieniec

first: Sung

middle: W

last: Choi

first: Nicholas

middle: U

last: Day

first: Bradford

last: Gibson

first: Alan

last: Hubbard


title: Genome-Wide Study Based On Abasic Site Revealed Selective RNA Oxidation In Neuro 2a Cells

status: Public on Oct 01 2012

city: Hershey

first: Penn State

last: COM

state: PA

address: 500 University Drive

department: Genome Sciences Facility

institute: Penn State College of Medicine

summary: To investigate selectivity of mRNA oxidation, total RNA and oxidized RNA isolated from Neuro 2a cells before and after H2O2 treatment were employed for microarray analysis. It was found that selective oxidation of mRNA already occurs under normal culture conditions but was increased by H2O2, especially in a subset of mRNAs related to certain functions. Moreover, mRNA oxidation level is also related to its abundance or stability (half-life time). This shows for the first time that mRNA oxidation is associated with RNA homeostasis including function, stability and abundance depending on cellular redox status in a genome-wide scale.

overall_design:
Neuro 2a cells received hydrogen peroxide treatment or no treatment as a control. Samples were applied for RNA extraction and ARP labeling, which could bind with apurinic/apyrimidinic sites, and then a pull-down process to isolate oxidized RNA. Total RNA and oxidized RNA were used for subsequent transcriptomic profiling.

4 types of samples were analyzed:
Basal-total: untreated N2a cells labeled with ARP, but not processed for the pull-down assay.
Ox-total: hydrogen peroxide-treated N2a cells labeled with ARP, but not processed for the pull-down assay.
Basal-ARP: untreated N2a cells labeled with ARP, and processed for the pull-down assay. ARP-derivatized RNA, which is also oxidized RNA, was concentrated and used for the microarray analysis.
Ox-ARP: hydrogen peroxide-treated N2a cells labeled with ARP, and processed for the pull-down assay. ARP-derivatized RNA, which is also oxidized RNA, was concentrated and used for the microarray analysis.

first: Song

last: Han

first: Mikiei

last: Tanaka

first: Robert

last: Brucklacher

first: Han

last: Yan

first: Matthew

last: Mitschelen

first: Julie

last: Farley

first: Willard

last: Freeman

first: William

middle: E

last: Sonntag


title: Control of RelB during dendritic cell activation integrates canonical and non-canonical NFkB pathways

city: La Jolla

first: Vincent

middle: Feng-Sheng

last: Shih

address: UCSD m/c 0375, NSB 3318 9500, Gilman Dr.

department: Chemistry and Biochemistry

institute: UCSD

summary: Dendritic cells (DC) play central roles in coordinating appropriate immune responses to pathogens.  In the present study, the genes regulated by NFkB activators, RelB and cRel, in PAMP-induced bone marrow dendritic cells (BMDCs) activation was examined.

overall_design: Total RNA extracted from WT, relb-/-, crel-/-relb-/- bone marrow derived dendritic cells (BMDCs) were subjected to stimulation with CpG or Pam3CSK4.

middle: F

first: Alexander

last: Hoffmann


title: Sca-1 is an early-response target of histone deacetylase inhibitors and marks hematopoietic cells with enhanced function

status: Public on Sep 25 2012

city: Groningen

first: Leonid

last: Bystrykh

state: Groningen

address: A. Deusinglaan 1

department: European Research Institute for the Biology of Ageing - ERIBA

country: Netherlands

institute: University Medical Center Groningen

summary:
Expression profiles of LSK cells stimulated for 24h in the presence or in the absence of of valproic acid (VPA)
The molecular process that underlies the biological effects of valproic acid (VPA), a widely used histone deacetylase inhibitor, on HSPCs was investigated by studying the early-response genes of VPA. Genome-wide gene expression studies revealed overrepresentation of genes involved in glutathione metabolism, receptor and signal transducer activity and changes in the HSPCs surface profile following short, 24h VPA treatment. Sca-1, a well-known and widely used stem cell surface marker, was identified as a prominent VPA target.VPA strongly preserved Sca-1 expression on LSK cells, but also re-activated Sca-1 on committed progenitor cells that were Sca-1 negative, thereby reverting them to the LSK phenotype. We demonstrated that re-acquired Sca-1 expression coincided with induced self-renewal capacity as measured by in vitro re-plating assays, while Sca-1 itself was not required for the biological effects of VPA as demonstrated using Sca-1 deficient progenitor cells. We show that VPA can induce several genes involved in signal transduction of which Sca-1 was shown to mark cells with increased self-renewal capacity.

overall_design: These data consist of total mRNA obtained from hematopoietic cells cultured for 24h in the presence or absence of valproic acid. All samples were analyzed in independent biological triplicates.

first: Marta

last: Walasek

middle: V

first: Sandra

last: Olthof

first: Gerald

last: de Haan

first: Ronald

last: van Os


title: Gene expression analysis of pluripotent and differentiated genes during EB formation treated with streptozotocin, o-glacnacylation inhibitor

status: Public on Jul 06 2012

city: Youngun dong, jongro gu,Seoul

first: Taewan

last: Kim

address: biomedical science building 202ho

department: biomedical science

country: South Korea

institute: Seoul National University of medicine

summary: O-linked-N-acetylglucosamine (O-GlcNAc) has emerged as a critical regulator of diverse cellular processes, but its role in embryonic stem cells (ESCs) and pluripotency has not been investigated. Here we show that O-GlcNAcylation directly regulates core components of the pluripotency network. Blocking O-GlcNAcylation disrupts ESC self-renewal and reprogramming of somatic cells to induced pluripotent stem cells. The core reprogramming factors Oct4 and Sox2 are O-GlcNAcylated in ESCs, but the O-GlcNAc modification is rapidly removed upon differentiation. O-GlcNAc modification of Threonine 228 in Oct4 regulates Oct4 transcriptional activity and is important for inducing many pluripotency related genes, including Klf2, Klf5, Nr5a2, Tbx3 and Tcl1. A T228A point mutation that eliminates this O-GlcNAc modification reduces the capacity of Oct4 to maintain ESC self-renewal and reprogram somatic cells. Overall, our study makes a direct connection between O-GlcNAcylation of key regulatory transcription factors and the activity of the pluripotency network.

overall_design: 2 of E14 stem cell, 2 of  embryonic body at day 2, 2 of  embryonic body at day 2 treated with streptozotocin, 1 of ZHBTc4 stem cell treated with doxicyclin, and 1 of ZHBTc4 stem cell treated with doxicyclin and streptozotocin were analysed

first: Hong-Duk

last: Youn

first: Hyonchol

last: Jang

first: Tae


title: Transcriptional profiling analysis of pre-selected DP thymocytes in response to positive and negative selection signals

status: Public on Jul 01 2012

city: Saint Louis

first: Wan-Lin

last: Lo

address: 425 S Euclid Ave, campus box 8118

institute: Washington University in St Louis

summary: Sustained Ca2+ entry into CD4+CD8+ double-positive thymocytes is required for positive selection. We identified a voltage-gated Na+ channel (VGSC), essential for positive selection of CD4+ T cells. Pharmacological inhibition of VGSC activity inhibited sustained Ca2+ influx induced by positive-selecting ligands and in vitro positive selection of CD4+ but not CD8+ T cells. In vivo shRNA knockdown of Scn5a specifically inhibited positive selection of CD4+ T cells. Ectopic expression of VGSC in peripheral AND CD4+ T cells bestowed the ability to respond to a positively selecting ligand, directly demonstrating VGSC expression was responsible for increased sensitivity. Thus active VGSCs in thymocytes provides a mechanism by which a weak positive selecting signal can induce sustained Ca2+ signals required for CD4+ T cell development.

overall_design:
Pre-selected AND DP thymocytes were stimulated with plate bound peptide-loaded I-Ek Ig dimers. Genes were differentially regulated by positive and negative selection signals.
The goal of this study is to identify ion-channel related genes critical for thymic positive selection, given the sustained Ca2+ entry into double positive thymocytes is required for positive selection. Total RNA of pre-selected AND thymocytes stimulated with I-Ek Ig dimers loaded with the positively-selecting peptide gp250, the negatively-selecting agonist peptide MCC, or the non-selecting control peptide Hb were used for the transcriptional profiling analysis. We found 28 genes were differentially down-regulated by MCC stimulation but upregulated by gp250 stimulation. One of them, scn4b, was ion-channel related.

first: Paul

last: Allen


title: Site-specific cytosine-5 methylation by the mouse RNA methyltransferases Dnmt2 and NSun2 promotes tRNA stability and protein synthesis

status: Public on Jul 04 2012

city: Heidelberg

first: Francesca

last: Tuorto

address: Im Neuenheimer Feld 580

department: Epigenetics

institute: German Cancer Research Center

summary: Mouse embryonic fibroblast (MEFs) cell lines and liver samples from Dnmt2 and Nsun2 single mutant, double mutant and wildtype mice were used to identify potential mRNA substrates of both proteins.

overall_design: MEFs were derived from day 13.5 embryos and immortalized by transfection with a plasmid expressing the SV40 large-T antigen. Total RNA of MEFs cell line at passage 9 and total RNA extracted from 2 months old mouse liver tissues of Dnmt2, Nsun2 single mutant, double mutant and wildtype mice were arrayed on Illumina MouseRef8 v2 chips.

first: Reinhard

last: Liebers

first: Tanja

last: Musch

first: Matthias

last: Schaefer

first: Sarah

last: Hofmann

first: Stefanie

last: Kellner

first: Michaela

last: Frye

first: Mark

last: Helm

first: Georg

last: Stöcklin

first: Frank

last: Lyko


title: Transcriptome analysis of garlic induced hepatoprotection against alcoholic fatty liver

city: TAIPEI

first: Lee-Yan

last: Sheen

address: No. 1, Sec 4, Roosevelt Road,

department: Institute of Food Science and Technology

country: Taiwan

institute: National Taiwan University

summary: Alcohol induced fatty liver cause a dangerous health problem and is the major cause of morbidity and mortality worldwide. Garlic (Allium sativum) is documented to possess anti-fatty liver properties. However the exact molecular mechanisms are unknown. The main aim of this experiment is to elucidate the underlying pathways through which garlic ameliorates alcohol induced fatty liver. Dially disulfide and garlic oil were the garlic compounds used in this study. Leiber DeCarli ethanol liquid diet was to induce fatty liver in C57BL/6 mice model. Also the expression impaired by alcohol induced fatty liver is another aim of this study.

overall_design: Leiber-Decarli ethanol diet was used to induce fatty liver in male C57BL/6 mice (n=12).  For control, Lieber-DeCarli liquid control diet was fed to mice (n=4). The control mice were pair-fed to the ethanol mice. After adaptation, the ethanol fed mice were divided into three groups viz. alcohol (n=4), dially disulfide [DADS] (n=4) and garlic oil [GO] (n=4). The study started with the administration of DADS (15 mg/kg bw) or GO (50 mg/kg bw) mixed in 0.1 ml olive oil through gavage. For the control and alcohol groups, same amount of olive oil (0.1 ml) was gavaged. The mice were gavaged daily for 4 weeks. The mice were euthanized by CO2 and blood was collected by cardiac puncture. Liver, kidney, spleen, lungs and hearts were collected and their weights recorded. A portion of liver was snap frozen in liquid nitrogen (200 mg) for RNA extraction.

first: Raghu

last: Rajasekaran

first: Shin-Kuang

last: Chen

first: Hen-Hao

last: Hsiao

first: Chun-Ting

last: Liu

first: Mong-Hsun

last: Tsai

first: Xiaojia

last: Tang

first: Krishna

middle: R

last: Kalari

first: Subbaya

last: Subramanian


title: Comparison of mouse epithelial tumor initiating cells to mesenchymal tumor initiating cells generated by EMT

status: Public on Sep 01 2012

first: Roy

last: Williams

address: 3030 Science Park Road

department: Regenerative Medicine

institute: The Scripps Research Institute

summary: The differentiation of stem-like cells of tumors may contribute to the cellular heterogeneity of breast cancers. We report the propagation of highly enriched mouse mammary cancer stem cells  that retain the potential to differentiate both in vivo and in culture and their use to identify chemical compounds that influence both self-renewal and differentiation. We identify epithelial tumor initiating cells (ETIC) that expresses lineage markers of both basal and luminal mammary cell lineages and retains the potential to generate heterogeneous tumors similar to the tumor of origin from even single cells. ETIC can progress through a Rho associated coil-coil protein kinase 1 (ROCK1) dependent, epithelial to mesenchymal transition to generate a second cell  type capable of  initiating tumors of limited heterogeneity. The propagation of ETIC will increase the opportunities for identifying new therapeutic compounds that may inhibit or prevent progression of some types of breast cancer. These data compare the gene expression pattern of ETIC and MTIC.

overall_design: Total RNA obtained from ETIC and MTIC cells, allowing the comparison of gene expression patterns and the selection of potential targets.

first: David

last: Castro

first: Jochen

last: Maurer

first: Robert

last: Oshima


title: Molecular profiling of activated neurons by phosphorylated ribosome capture [Illumina BeadArray]

status: Public on Sep 20 2012

city: New York

first: Zachary

last: Knight

state: NY

address: 1230 York Ave

institute: Rockefeller University

summary: We report that phosphorylated ribosomes can be immunoprecipitated from mouse brain homogenates, enriching for mRNAs that were selectively expressed  in activated neurons

overall_design: Mice were given an injection of concentrated salt solution (2M NaCl, 325 uL) or PBS, and then sacrificed 2h later and hypothalami dissected.  Tissue homogenates were prepared from hypothalamus and phosphorylated ribosomes immunoprecipitated using pS6 244/247 antibodies.  The immunoprecipitated RNA and total RNA from both control and salt treated animals were then purified and analyzed by Illumina Microarray.

first: Jeffrey

last: Friedman


title: Differences in hepatic gene expression between lactating and non-lactating sows as assessed by genome-wide transcript profiling

status: Public on May 31 2012

city: Gießen

last: Ringseis

address: Heinrich-Buff-Ring 26-32

department: Institute of Animal Nutrition and Nutrition Physiology

institute: JLU Gießen

summary:
Background: While the mechanisms underlying the lactation-induced adaptations of intermediary metabolism and immune response have been extensively studied in rodents and dairy cows, little is known in this regard in sows. Therefore, the present study aimed to explore the lactation-induced changes in hepatic gene expression in sows during lactation.
Results: Using a porcine whole-genome microarray a total of 632 differentially expressed genes in the liver of lactating compared to non-lactating sows (each n = 10) could be identified. Enrichment analysis revealed that the differentially expressed genes were mainly involved in fatty acid metabolism, pyruvate metabolism, glutathione metabolism, glycine, serine and threonine metabolism, citrate cycle, glycerophospholipid metabolism, PPAR signaling, nitrogen metabolism, and focal adhesion. The most striking observation with respect to intermediary metabolism was that genes involved in fatty acid catabolism, the catabolism of gluconeogenic amino acids, the citrate cycle and the respiratory chain were up-regulated in the liver of sows during lactation. With respect to immune response, it could be demonstrated that genes encoding acute phase proteins and genes involved in tissue repair were up-regulated and genes encoding focal adhesion molecules were down-regulated in the liver of sows during lactation.
Conclusion: The results from this study indicate that energy-generating pathways and pathways involved in the delivery of gluconeogenic substrates are induced in the liver of sows during lactation. The alterations of expression of genes encoding proteins involved in immune response suggest that lactation in sows may cause an adaptive immune response which possibly counteracts hepatic inflammation.

overall_design: For microarray analyses, four RNA pools each, for the non-lactating group (n = 4) and the lactating group (n = 4), were prepared from eight individual sows per group. To each RNA pool, RNA from two different sows per group contributed identical amounts of RNA.

first: Susann

last: Rosenbaum

first: Klaus

last: Eder


title: mTOR inhibitors synergistically induce regression, reversal of gene expression and autophagy in hepatocellular carcinoma

status: Public on Jul 12 2012

city: Cambridge

first: Manway

state: MA

address: 250 Massachusetts Avenue

institute: Novartis Institutes for Biomedical Research

summary: The mTOR-allosteric inhibitor, RAD001, in combination with a PI3K/mTOR ATP-site competitive inhibitor, BEZ235, causes gene reprogramming, autophagy and tumor regression, in a mouse model approximating human HCC with poor prognosis, leading to an investigator Phase 1B-2 clinical trial.

overall_design: Comparative study of total RNA obtained from normal and tumor liver tissue under RAD001, BEZ235, or RAD001 + BEZ235.

first: Hala

last: Thomas

first: Carol

last: Mercer

first: Larissa

middle: S

last: Carnevalli

first: Jongsun

last: Park

first: Jesper

middle: B

last: Andersen

first: Elizabeth

last: Conner

first: Kazuhiro

last: Tanaka

first: Tomoo

last: Matsutani

first: Akio

last: Iwanami

first: Bruce

middle: J

last: Aronow

first: Liu

last: Manway

first: Michel

last: Maira

first: Snorri

last: Thorgeirsson

first: Paul

last: Mischel

first: George

first: Sara

last: Kozma


title: Regulation of Embryonic and Induced Pluripotency by Aurora Kinase-p53 Signaling

status: Public on May 30 2012

city: san francisco

first: Yen-Sin

last: Ang

state: CALIFORNIA

address: 1650 Owens Street

institute: Gladstone Institute, UCSF

summary: Illumina Beadchip array analyses of mouse embryonic stem cell gene expression profiles in the presence of or upon knockdown of Aurka. An ES complementation 'rescue' system was employed to measure the effects of knockdown (minus Dox). Aurka was rescued to wildtype levels in the presence of Dox (plus Dox). A control rescue ES cell line, with a Luciferase-targeting shRNA, was also assessed.

overall_design: Total of 12 samples; Aurka_R (+/-Dox) and Control_R (+/-Dox); all performed in triplicates

first: Dung-Fang

last: Lee

first: Jie

last: Su

first: Xonia

last: Carvajal-Vergara

first: Betty

last: Chang

first: Ana

last: Sevilla

first: Ruiying

last: Zhao

first: Christoph

last: Schaniel

first: Sonia

last: Mulero-Navarro

first: Carlos

last: Pereira

first: Julian

last: Gingold

first: Hung-Liang

last: Wang

first: Henia

last: Darr

first: Andrew

last: Williamson

first: Xiaohong

last: Niu

first: Francesca

last: Aguilo

first: Elsa

last: Flores

first: Yuh-Pyng

last: Sher

first: Mien-Chie

last: Hung

first: Anthony

last: Whetton

last: Gelb

first: Kateri

last: Moore

first: Hans-Willem

last: Snoeck

first: Avi

last: Ma'ayan

first: Ihor

last: Lemischka


title: Genome-wide analysis of macrophage gene expression upon Bcl3 knockdown

status: Public on Aug 07 2012

first: Vivien

middle: Ya-Fan

address: 9500 Gilman Drive, NSB, 3325A

summary: By binding to specific DNA elements, known collectively as “κB sites”, contained within the promoters/enhancers of target genes, NF-κB regulates gene expression. We found that the identity of the central base pair (bp) of κB sites profoundly impacts the transcriptional activity of NF-κB dimers.  RelA dimers prefer an A/T bp at this position for optimum transcriptional activation (A/T-centric) and discriminate against G/C-centric κB sites.  The p52 homodimer, in contrast, activates transcription from G/C-centric κB sites in complex with Bcl3 but represses transcription from the A/T-centric sites.  The p52:Bcl3 complex binds to these two classes of κB sites in distinct modes permitting recruitment of coactivator, corepressor, or both coactivator and corepressor complexes in promoters containing G/C, A/T or both G/C and A/T-centric sites.  Therefore, through sensing of bp differences within κB sites, NF-κB dimers modulate biological programs by activating, repressing and altering expression of effector genes.

overall_design: Total RNA extracted from bone marrow derived macrophages (BMDMs) with Bcl3 siRNA knockdown or mouse scramble siRNA knockdown were subjected to LPS stimulation.

middle: Y

first: Gourisankar

last: Ghosh

first: Alexander

last: Hoffmann


title: Murine forestomach epithelial sheets: Controls vs. Sox2 overexpression mutants

status: Public on May 09 2012

city: Camden

first: Xiaoxin

middle: Luke

last: Chen

state: NJ

address: 403 Haddon Avenue

institute: Coriell Institute for Medical Research

summary: Transcriptional profiling of adult forestomach epithelium comparing K5-CreER controsl with K5-CreER;Rosa26Sox2/Sox2 mutants. Two doses of tamoxifen were given and four weeks later the epithelal sheets were harvested for RNA extraction. Goal was to determine the effects of Sox2 overexpression on epithelial phenotypic changes.

overall_design: Two-condition experiment, wildtype Vs Sox2 overexpression mutant. Biological replicates: 3 control replicates, 3 mutant replicates.

first: Hao

first: Jianwen

last: Que


title: Antisense oligonucleotides targeting nuclear RNA for in vivo correction of myotonic dystrophy

status: Public on Jun 28 2012

city: Rochester

first: Stephen

last: Welle

address: 601 Elmwood Avenue

institute: University of Rochester

summary: This study examined the effects of antisense oligonucleotides (ASOs) on the muscle transcriptome in a transgenic mouse model of myotonic dystrophy.  Two ASOs were tested in HSALR transgenic mice.  Both of the ASOs targeted mRNA from a human skeletal actin (hACTA1) transgene.  This transgene contains an expanded CTG repeat in the 3’ untranslated region (UTR) (Mankodi et al “Myotonic dystrophy in transgenic mice expressing an expanded CUG repeat” Science 2000; 289:1769-72).  ASO 445235 targeted the hACTA1 transcript in the 3’ UTR, downstream from the expanded repeat.  ASO 190401 targeted the hACTA1 transcript in the coding region.  The HSALR mice received 4 weeks of biweekly subcutaneous injections of vehicle (saline), ASO 190401, or ASO 445236 (n = 4 per group), at a dose of 25 mg/kg per injection.  Wild-type mice of the same strain background received saline injections (n = 4).  One week after the final injection, quadriceps muscle was harvested for RNA analysis.

overall_design: Four conditions, four arrays per condition, to compare WT and HSALR trangenic mice without treatment (saline) and to examine the effect of two oligos (vs. saline) in the HSALR transgenic mice.

first: Charles

last: Thornton


title: LIX11 vs H37Rv under Log vs stationary phase growth

status: Public on Jun 02 2012

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: Transcription analysis of ΔpknK mutant (LIX11) versus wild type H37Rv during logarithmic and stationary phase growth. This will elucidate the genes regulated by PknK during transition from logarithmic growth to stationary phase growth.

overall_design: Two color Experiment,Organism: Mycobacterium tuberculosis, Genotypic Technology designed Custom Mycobacterium tuberculosis H37Rv Whole Genome 8x15k GE Microarray (AMADID-26323 and AMADID-23057

first: Vandana

last: Malhotra

first: Blessing

middle: P

last: Okon

first: Josephine

last: Clark-Curtiss


title: Hepatic gene expression in wild type and SHPKO mice fed chow or western diet

status: Public on May 17 2012

city: Rootstown

first: Yoonkwang

last: Lee

address: 4209 State Route 44

department: Integrative Medical Sciences

institute: Northeast Ohio Medical University

summary: SHP (small heterodimer partner; NR0B2) belongs to the nuclear hormone receptor superfamily, which regulates numerous developmental and metabolic cellular functions. To study physiological function of SHP, we generated congenic SHP-/- mice on C57Bl/6 background. When the congenic SHP-/- mice were challenged with a western diet (harlan, TD.88137) for 22 weeks, they were resistant to diet induced obesity and hepatic steatosis compared to WT controls. However, their hepatic insulin sensitivity was compromised when assessed with phospho-Akt levels after insulin injection. Therefore, we investigated hepatic gene expression using illumina beadchip array to explore mechanisms underneath the unique liver physiology in SHP-/- mice.

overall_design: Livers were collected from C57Bl/6 wild type and C57Bl/6 SHP-/- mice fed chow or western diet. The 1 microgram of total RNA obtained from individual mouse (n=4 per group) and subjected to illumina beadchip gene expression profiling.


title: A PPARγ-FGF1 axis is required for adaptive adipose remodeling

status: Public on Apr 23 2012

first: Ruth

middle: T

last: Yu

address: 10010 N Torrey Pines Rd

department: Gene Expression Lab

institute: Salk Institute

summary: We identify fibroblast growth factor 1 (FGF1) as a critical transducer in adipose tissue remodeling and link its regulation to peroxisome proliferator activated-receptor γ (PPARγ), the adipocyte master regulator and target of the thiazolidinedione (TZD) class of insulin sensitizing drugs. We show that FGF1 is highly induced in adipose tissue in response to high-fat diet (HFD) and that mice lacking FGF1 develop an aggressive diabetic phenotype coupled to aberrant adipose expansion when challenged with HFD. Mechanistically, we show that transcription of FGF1 is directly regulated by an adipocyte-selective proximal PPAR response element, and that this PPARγ-FGF1 axis is evolutionarily conserved in mammals. This work describes the first phenotype of the FGF1 knockout mouse and establishes FGF1 as a new member of the NR-FGF axis critical for maintaining metabolic homeostasis and insulin sensitization.

overall_design: Total RNA was obtained from epidydimal white adipose tissue (eWAT) and livers from 6 month old wild-type and FGF1-/- mice after 16 weeks on normal chow or high-fat diets.

first: Johan

last: Jonker

first: Ronald

last: Evans


title: A specific Peroxisome Proliferator-Activated Receptor (PPAR)-delta agonist is hepatoprotective and attenuates liver fibrogenesis

status: Public on Apr 19 2012

summary: PPARδ is emerging as a key metabolic regulator with pleiotropic actions on various tissues including fat, skeletal muscle and liver. The aim of our study was to assess the effect of either the well-validated PPARδ agonist GW501516, or a novel PPARδ agonist KD3010 in mouse models of liver fibrosis. KD3010, but not GW501516, treated mice had markedly less liver injury induced by carbon tetrachloride (CCl4) injections. Deposition of extracellular matrix proteins was lower in the KD3010 group as compared to the vehicle or GW501516 treated group. Interestingly, profibrogenic CTGF was significantly induced by GW501516, but not KD3010, following CCl4 treatment. The hepatoprotective and antifibrotic effect of KD3010 was confirmed in a model of cholestasis-induced liver injury and fibrosis using bile duct ligation for three weeks. Hepatocytes were identified as targets for PPARδ agonist, and primary hepatocytes treated with KD3010 showed decreased serum starvation or CCl4-induced cell death, while GW501516 treated hepatocytes were not protected.  KD3010 treatment of hepatocytes decreased reactive oxygen species (ROS) production after CCl4 exposure. In conclusion, our data demonstrate that a novel PPARδ agonist has hepatoprotective and antifibrotic effects in animal models of liver fibrosis. Given the oral availability and the favorable pharmacologic profile of KD3010, ligand activation of PPARδ represents an attractive and promising target for patients with chronic liver diseases.

overall_design: Total RNA was extracted from primary mouse hepatocytes treated with DMSO or PPARd agonists (KD3010, GW1516)

first: Keiko

last: Iwaisako

first: Bernd

last: Schnabl

first: Elizabeth

middle: M


title: Promoter DNA methylation couples genome-defense mechanisms to epigenetic reprogramming in the mouse germline (part 2)

status: Public on Aug 01 2012

first: Jamie

last: Hackett

address: Tennis Court Road

country: United Kingdom

institute: Gurdon Institue

summary: Mouse primordial germ cells (PGCs) erase global DNA methylation (5mC) as part of the comprehensive epigenetic reprogramming that occurs during PGC development. 5mC plays an important role in maintaining stable gene silencing and repression of transposable elements (TE) but it is not clear how the extensive loss of DNA methylation impacts on gene expression and TE repression in developing PGCs. Using a novel epigenetic disruption and recovery screen and genetic analyses, we identified a core set of germline-specific genes that are dependent exclusively on promoter DNA methylation for initiation and maintenance of developmental silencing. These gene promoters appear to possess a specialised chromatin environment that does not acquire any of the repressive H3K27me3, H3K9me2, H3K9me3 or H4K20me3 histone modifications when silenced by DNA methylation. Intriguingly, this methylation-dependent subset is highly enriched in genes with roles in suppressing TE activity in germ cells. We show that the mechanism for developmental regulation of the germline genome-defence genes involves DNMT3B-dependent de novo DNA methylation. These genes are then activated by lineage-specific promoter demethylation during distinct global epigenetic reprogramming events in migratory (~E8.5) and post-migratory (E10.5-E11.5) PGCs. We propose that genes involved in genome defence are developmentally regulated exclusively by promoter DNA methylation as a sensory mechanism that is coupled to the potential for TE activation during global 5mC erasure, thereby acting as a failsafe to ensure TE suppression and maintain genomic integrity in the germline.

overall_design: Total RNA isolated from control p53-/- or sample Dnmt1-/- (p53-/-) mouse embryonic fibroblasts

middle: A


title: Exacerbated T cell lymphoma in NOD.Stat5bTg mice is caused by selective activation of Stat5b in CD8+ thymocytes and can be prevented by inhibition of the Stat5b signaling pathway with chemoprevention agents

status: Public on Apr 10 2012

city: Augusta

first: Jin-Xiong

last: She

state: GA

department: Center for Biotechnology and Genomic Medicine

institute: Medical College of Georgia

summary: This study demonstrated that genetic background is critical to the STAT5B-mediated lymphomagenesis probably through regulation of STAT5B activation, which results in the alteration of many tumorigenic genes.  Chemopreventive compounds that can reduce STAT5B phosphorylation and/or the STAT5B signaling pathway can efficiently block lymphomagenesis, demonstrating that the NOD.Stat5bTg mouse is an excellent model for testing novel chemopreventive strategies.

overall_design: To elucidate the molecular mechanism underlying the activation of Stat5b upon lymphoma onset, we profiled gene expression in thymocytes of NOD.Stat5b mice, Gene expression was analyzed with the Illumina's MouseRef-8 v2.0 Expression beadchips

first: Bo

first: Bing

last: Yi

first: Rui

last: Mao

first: Haitao

last: Liu

first: Jinhua

last: Wang

last: Guo

last: Peiper

first: Warren

last: Leonard

first: Jin-xiong


title: Conditional elimination of c-Met signaling in the liver aggravates oxidative stress and cholestasis, and deregulates lipid metabolism, under a high cholesterol diet

status: Public on Jul 11 2012

city: Bethesda

first: Daekwan

last: Seo

state: MD

address: 37 Convent Dr. Rm 4140

department: NCI

institute: NIH

summary:
Background: Genetic elimination of c-Met signaling in the liver has been shown to impact many cellular pathways involved in repair, regeneration, lipid homeostasis and redox balance. In this study, we analyzed a nutritional model of hepatic steatosis in Met fl/fl ; Alb-Cre +/- (MetKO) mice in a 129SV/C57BL/6 background fed a high cholesterol diet for 30 days.

Methods: Liver injury was determined by histopathology and plasma enzymes, transcriptomic changes were examined using gene expression microarrays, and evaluation of key molecules involved in liver damage and lipid homestasis were evaluated by Western blot analysis.

Results: We observed that in comparison with wild type mice subjected to the same diet, MetKO mice developed a strong liver lipid deposition, inflammatory infiltration and increment in total bile acids synthesis and liver damage markers. Global transcriptomic changes analysis confirmed the steatosis and cholestasis induced by the high cholesterol diet. In addition, we found affected pathways related to amino acids, glutathione and lipid metabolism, oxidative stress and mitochondria dysfunction. Oxidative stress exacerbation was corroborated by lipid and protein oxidation in liver tissue. To address further, Western blot studies revealed downregulation on Erk, NF-kB and Nrf2 survival pathways and target genes (cyclin D1, SOD1, gamma-GCS), an increment in proapoptotic proteins (p53, caspase 3) and changes in nuclear receptors such as RAR and RXR, which were increased, and CAR, FXR and PPAR alfa, which were decreased, in the MetKO diet. These results are in agreement with the steatosis and cholestasis phenotype.

Conclusion: Our data provide evidence of c-Met signaling involvement in lipid metabolism, and bile acids synthesis and excretion. Disruption of these pathways leads to liver dysfunction, improper metabolism and hepatocellular damage.

overall_design: Global transcriptome changes between WT mice vs. c-Met KO mice fed a 2% cholesterol and 0.5% sodium cholate diet (high cholesterol) or a Chow regular diet (Chow) as control. Mice were fed a high cholesterol or chow regular diet for 30 days. Liver tissue was obtained, and RNA was extracted and subjected to Illumina microarray analysis.

first: Luis

last: Gomez-Quiroz

first: Deakwan

first: Matthew

last: Gillen

first: Snorri

last: Thorgeirsson


title: MIR-204 target genes

status: Public on Mar 31 2012

city: San Antonio

first: Yidong

last: Chen

state: Texas

address: 8403 Floyd Curl Drive, MSC 7784

department: Population Health Sciences

institute: UT Health Science Center at San Antonio

summary: The aim of this study is to discover genes regulated by miR-204. Differential gene expression in HEK-293 cells transfected with miR-204-mimic compared to HEK-293 cells transfected with control oligo (HEK-293 control) was analyzed using the Agilent Human Whole Genome 4x44K gene expression array (Agilent Technologies, Santa Clara, CA).

overall_design: HEK-293 cells were transfected with either miR-204 or a control, and gene expression was analyzed using the Agilent Human Whole Genome 4x44K array. A dye-swap was performed.

first: Rao

last: Manjeet

first: J

last: Imam

first: Jennifer

last: Rebeles

first: Hung-I

middle: H


title: Expression analysis of genes regulated by RBPJ (Notch) and Axin2 (Wnt) mediated signaling in mouse cardiogenesis at E9.25

status: Public on Jun 21 2012

city: Berlin

first: Alexandra

last: Klaus

state: Berlin

department: Signal Transduction, Invasion and Metastasis of Epithelial Cells

institute: MDC (Max Delbrück Center)

summary: Progenitor cells of the first and second heart fields (FHF and SHF) depend on cardiac-specific transcription factors for their differentiation. In mouse mutant embryos, we define the hierarchy of signaling events that controls the expression of cardiac-specific transcription factors during commitment of SHF progenitors at E9.25. Wnt and Bmp act downstream of Notch/RBPJ at this developmental stage. Mutation of Axin2, the negative regulator of canonical Wnt signaling, enhances Wnt and Bmp signals and suffices to rescue the cardiac differentiation arrest caused by loss of RBPJ. By analysis of isolated cardiac progenitors, embryo cultures in the presence of pharmacological inhibitors, and Bmp triple mutants, we could classify the expression of heart-specific transcription factors of SHF progenitors according to their dependence on either Wnt or Bmp signals, Nkx2-5, Isl1, Baf60c  and Gata4, SRF,  Mef2c, respectively.

overall_design: Total RNA from whole embryonic hearts of control mice was compared to MesP1-cre:RBPJlox/lox (KO), MesP1-cre:RBPJlox/lox//Axin2-/- (DKO), MesP1-cre:RBPJlox/+//Axin2-/- (hetDKO) and MesP1-cre:RBPJlox/lox//Axin2+/- (DKOhet) mutant mouse embryos.

first: Walter

last: Birchmeier


title: Genome-wide analysis of gene expression in WT and Erk2 deficient CD4 T cells

status: Public on Jul 01 2012

city: La Jolla

first: Chiungfang

last: Chang

address: 9500 Gilman Drive

department: Biological Science

institute: University of California, San Diego

summary: Effective immune responses depend upon appropriate T cell differentiation in accord with the nature of an infectious agent, and the contingency of differentiation depends minimally on T cell antigen receptor, co-receptor, and cytokine signals. In this reverse genetic study we show that the Map Kinase, Erk2, is nonessential for T cell proliferation in the presence of optimum co-stimulation. Instead, it has opposite polar effects on T-bet and Gata3 expression and hence on Th1 and Th2 differentiation. Alternatively, in the presence of TGFbeta, the Erk pathway suppresses a large program of gene expression effectively limiting the differentiation of Foxp3+ T reg cells. In the latter case, the mechanisms involved include suppression of Gata3 and Foxp3, induction of Tbx21, phosphorylation of Smad2,3, and possibly suppression of Socs2, a positive inducer of Stat5 signaling. Consequently, loss of Erk2 severely impeded Th1 differentiation while enhancing the development of Foxp3+ induced T regulatory cells. Selected profiles of gene expression under multiple conditions of T cell activation illustrate the opposing consequences of Erk pathway signaling.

overall_design:
Analysis of the Th1 and iTreg differentiation regulated by Erk2.
Total RNA obtained from WT or Erk2 deficient CD4 T cells in different conditions.

first: S

last: Hedrick

first: C


title: Effects of internal low dose irradiation from 131I on gene expression in normal mouse tissue

status: Public on May 18 2012

city: Göteborg

first: Emil

last: Schüler

address: Gula stråket 2B

country: Sweden

institute: University of Gothenburg

summary: Transcriptomic profiling of normal mouse tissue following 131I irradiation.

overall_design: Total RNA was isolated from fresh-frozen tissue samples.

first: Toshima

middle: Z

last: Parris

first: Nils

last: Rudqvist

first: Khalil

last: Helou

first: Eva

last: Forssell-Aronsson


title: Altered de novo lipogenesis contributes to low adipose stores in cystic fibrosis mice.

status: Public on Jun 18 2012

city: Cleveland

first: Aura

last: Perez

state: OH

address: 10900 Euclid Avenue

department: Pediatrics

institute: CWRU

summary: Cystic fibrosis (CF) mouse models exhibit exocrine pancreatic function yet do not develop adipose stores to the levels of non-CF mice. CF mice homozygous for the Cftr mutation (F508del) at 3 weeks (post-weaning) and 6 weeks (young adult) of age had markedly less adipose tissue than non-CF mice. Both 3- and 6-week old mice had dietary lipid absorption and fecal lipid excretion comparable to non-CF controls. Fractional hepatic de novo synthesis of palmitate and stearate (de novo lipogenesis, DNL) as determined by deuterium incorporation was reduced in CF mice. At 3 weeks of age, F508del mice had significantly decreased DNL of palmitate and stearate, by 83% and 80%, respectively. By 6 weeks of age, DNL rates in non-CF mice remained unchanged as compared to 3-week old mice, while DNL rates of F508del mice were still reduced, by 33% and 40%, respectively. Adipose tissue fatty acid profiles were comparable in CF and non-CF mice, indicating that adipose differences are quantitative, not qualitative. A correspondingly lower content of deuterium-labeled fatty acids was found in CF adipose tissue, consistent with reduced deposition of newly made hepatic triglycerides and/or decreased adipose tissue lipogenesis. Hepatic transcriptome analysis revealed lower mRNA expression from several genes involved in fatty acid biosynthesis, suggesting down-regulation of several enzymes in fatty acids synthesis as a mechanism for the reduced lipogenesis. These novel data provide a model for altered fat and fatty acid metabolism in CF, independent of malabsorption, and may partly explain the inability of pancreatic enzyme replacement therapy to completely restore normal body mass to CF patients

overall_design: ∆F508 CF mice and its WT littermates (3-weeks old females, C57BL/6J) were examined. RNA extracted from snapped-frozen livers, 4 replicates per genotype.

first: A

first: Mitchell

middle: L

last: Drumm


title: Ctnnb1-targeted genes in mouse post-meiotic germ cells

status: Public on Mar 20 2012

first: Yidong

summary: To determine differential gene expression in Ctnnb1 CKO mice testis compared to CTRL mice testis.

overall_design: The Agilent Mouse Whole Genome 4x44K array (Samples are from pooled total testes RNA from 4 CTRL and 4 Ctnnb1 CKO mice; dye-swap was performed.)

first: Yao-Fu

first: Manjeet

last: Rao


title: Integral roles for Rev-erb alpha and Rev-erb beta in the circadian clock function [Expression array]

status: Public on Mar 29 2012

first: Ruth

last: Yu

summary: The circadian clock acts at the genomic level to coordinate internal behavioral and physiologic rhythms via the CLOCK-BMAL transcriptional heterodimer.  Although the nuclear receptors REV-ERBα and β have been proposed to contribute to clock function, their precise roles and importance remain unresolved.  To establish their regulatory potential we generated comparative cistromes of both Rev-erb isoforms, which revealed shared recognition at over ~50% of their total sites and extensive overlap with the master clock regulator Bmal.  While Rev-erbα has been shown to directly regulate Bmal expression, the cistromic analysis reveals a more profound connection between Bmal and Rev-erbα and β regulatory circuits than previously suspected. Genes within the intersection of the Bmal and Rev-erb cistromes are highly enriched for both clock and metabolic functions. As predicted by the cistromic analysis, dual depletion of Rev-erbα/β function by creating double-knockout mice (DKOs) profoundly disrupted circadian expression of core clock and lipid homeostatic genes. As a result, DKOs show strikingly altered circadian wheel-running behavior and deregulated lipid metabolism.  These data reveal an integral role of Rev-erbα/β in clock function as well as provide a cistromic basis for the integration of circadian rhythm and metabolism.

overall_design: Total RNA was obtained from livers of wild-type and Liver-specific Reverb alpha/beta double knockout mice at ZT 0, 4, 8, 12, 16, and 20.

first: Han

last: Cho

first: Ronald

last: Evans


title: Copy number alteration in Wilms' tumor with custom-designed miRNA probes

last: Chen

type: Genome variation profiling by genome tiling array

summary: The aim of this study is to discover loss of specific miRNA loci in Wilms' tumors using array CGH. Custom arrays were designed based on the Agilent 2x105K Human Whole Genome Genomic microarray with Agilent’s eArray program (https://earray.chem.agilent.com/earray/), with additional probes that cover all miRNA regions (200 bps before, within and after each miRNA from miRBase v13, with  each probe in triplicates to enhance the reliability). All custom-designed probes were designed in UCSC hg18. Probes from Agilent’s database were lifted-over from hg19 to hg18 (LiftOver tool: http://genome.ucsc.edu).

overall_design: The Agilent 2x105K custom-design whole genome microarray was used to analyze genomic alterations in Wilms' tumor samples compared to normal human genomic DNA (Promega p/n G1523).

first: Rao

last: Manjeet

first: J

last: Imam

first: Jennifer

first: Kihoon

last: Yoon

first: Hung-I


title: Analysis of differential genetic expression by dietary intervention using moderate-carbohydrate restriction diet supplemented with calorie restriction mimetic multiple phytochemicals extracts(MCDmp) in B16F10 xenografted mouse model.

status: Public on Mar 21 2012

city: Seoul

first: Jong-Doo

last: Lee

address: 250 seonsan-ro seodaemum-gu

institute: Yonsei University

type: Genome binding/occupancy profiling by genome tiling array

summary: We performed survival analysis of control and MCDmp groups, and explored underlying tumor suppression mechanisms after dietary intervention, focused on alterations in the energy-dependent signaling pathways, and global gene expression differences on cDNA microarray study, or histone modification on ChIP-on-chip analysis.

overall_design: Illumina arrays: Five- week- old male C57BL6 mice were randomly divided into two groups and fed control diet (control group, LabDiet, Brentwood, MO, USA) or MCDmp formula (Treat group) in a specific pathogen free zone. All procedures were approved by the institutional animal use and care committee. Following a preliminary feeding of each diet formula for one week, 1 × 106 B16F10 cells (suspended with 100 μl of PBS) were subcutaneously injected into the back of the mice. After 24 days of diet supplementation, all mice were sacrificed. Tumor tissue was excised for cDNA microarray.

first: Jong

middle: D

first: Min-Ah

last: Choi


title: miRNA and Wilms' tumor

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

overall_design: Refer to individual Series


title: Effect of dietary methyl donor depletion on gene expression in normal colons of ApcMin mice

status: Public on May 01 2012

city: West Haven

first: Petr

last: Protiva

address: 950 Campbell Avenue

institute: Yale University and VA CT Healthcare System

overall_design: Expression profiles of normal colons in ApcMin mice that were fed methyl deficient diet for 11 weeks vs controls fed methyl donor sufficient diets


title: Histone H3 lysine 9 di-methylation as an epigenetic signature of the interferon response (WT and G9a deficient MEFs)

status: Public on Mar 02 2012

city: New York

first: Terry

last: Fang

address: 1230 York Ave

institute: Rockefeller University

summary: Effective anti-viral immunity depends on the ability of infected cells or cells triggered with virus-derived nucleic acids to produce type I interferon (IFN), which activates transcription of numerous antiviral genes. However, disproportionately strong or chronic IFN expression is a common cause of inflammatory and autoimmune diseases. Here we describe an epigenetic mechanism that determines cell-type specific differences in IFN and IFN-stimulated gene expression in response to exogenous signals. We identify di-methylation of histone H3 at lysine 9 (H3K9me2) as a suppressor of IFN and IFN-inducible antiviral gene expression. We show that levels of H3K9me2 at IFN and IFN stimulated genes (ISG) correlate inversely with the scope and amplitude of IFN and ISG expression in fibroblasts and dendritic cells. Accordingly, genetic ablation or pharmacological inactivation of lysine methyltransferase G9a, which is essential for the generation of H3K9me2, resulted in phenotypic conversion of fibroblasts into highly potent IFN-producing cells and rendered these cells resistant to pathogenic RNA viruses. In summary, our studies implicate H3K9me2 and enzymes controlling its abundance as key regulators of innate antiviral immunity.

overall_design: Examination of gene expression in response to PolyI:C in WT and G9a deficient MEFs

middle: C

first: Alexander

last: Tarakhovsky


title: Analysis of differential gene expression during functional beta-cell maturation in the mouse

status: Public on Feb 18 2012

first: Doug

last: Melton

address: 7 Divinity Ave

department: Stem Cell and regenerative Biology

institute: Harvard University

summary: Global gene expression is tested in FACS-sorted beta-cells from PDX1-GFP transgenic mice at different ages (E18.5, P1, P10 and adult)

overall_design: Total RNA obtained from FACS-sorted beta-cells from PDX1-GFP transgenic mice at different ages (E18.5, P1, P10 and adult)

first: Douglas

first: Barak

last: Blum


title: Expression data from mouse neonatal ovarian 3MC culture experiments

status: Public on Feb 16 2012

city: Newcastle

middle: Peter

last: Sobinoff

state: NSW

address: University Drive

department: Science and IT

country: Australia

institute: University of Newcastle Australia

summary: Mammalian females are born with a finite number of non-renewing primordial follicles, the majority of which remain in a quiescent state for many years. Due to their non-renewing nature, these resting oocytes are particularly vulnerable to xenobiotic insult, resulting in premature ovarian senescence and the formation of dysfunctional oocytes.  In this study we characterised the mechanisms of ovotoxicity for the ovotoxic agent 3-methylcholanthrene (3MC), which targets immature follicles. Neonatal mouse ovaries (PND3-4) were cultured in the presence of 3MC (5 µM) for 96 hours to observe their effects on the ovarian transcriptome. This was done in the hopes of gaining a better understanding of the mechanisms underpinning xenobiotic induced pre-antral ovotoxicity.

overall_design: Ovaries from day 3-4 Swiss neonatal mice were cultured in 3MC containing media for 96 hours. The ovaries were then collected for RNA extraction and hybridization on an Illumina Sentrix Mouse ref-8 v2 Beadchip

first: Eileen

last: McLaughlin


title: Histone H3 lysine 9 di-methylation as an epigenetic signature of the interferon response (WT and G9a deficient DCs)

overall_design: Examination of gene expression in response to PolyI:C in WT and G9a deficient DCs


title: eQTL study of bone marrow derived macrophages and endothelial cells from DBA2xAKR F2 mice

status: Public on Mar 14 2012

first: Jeff

last: Hsu

address: 9500 Euclid Ave

department: Cellular and Molecular Medicine

institute: Cleveland Clinic Lerner Research Institute

summary: An eQTL analysis between DBA/2J and AKR/J mice strains on the ApoE null background was done in bone marrow derived macrophages and endothelial cells to identify modifier genes that affect atherosclerosis susceptibility.

overall_design: DBA/2J mice were crossed with AKR/J mice and their offspring crossed with each other to yield an F2 generation.  Bone marrow derived macrophages were cultured and gene expression quantified using Illumina's MouseRef-8 v2 arrays in 170 F2 mice for an eQTL study.  In addition primary endothelial cells derived from the aorta of 48 male F2 mice were also assayed using arrays for eQTL mapping.  Lesion area in the aortic root was also quantified in these samples.

first: Jeffrey

first: Johnathan

last: Smith


title: Sex-Dependent Programming of Glucose and Fatty Acid Metabolism in Mouse Offspring by Maternal Protein Restriction

status: Public on Feb 08 2012

city: Groningen

first: vincent

last: bloks

institute: UMCG

summary:
Analysis of glucose and Lipid metabolism in male and female offspring after protein restriction of the mother

Male offspring showed features of metabolic syndrome after receiving a high fat diet, regardless of the diet of the dam. Glucose and lipid metabolism in male offspring was unaltered. Insulin sensitivity and hepatic fatty acid storage in female offspring of low-protein-fed dams changed in such a way that it resembled the male pattern of insulin sensitivity and hepatic fatty acid storage. Microarray analysis on hepatic gene expression patterns confirmed these findings. We therefore conclude that in mice, maternal protein restriction does not change the response of glucose and fatty acid metabolism to a high fat diet in male offspring, but does program metabolism in female offspring in such a way that it resembles male metabolism. Our findings might have implications for potential future gender-specific treatment of the features of metabolic diseases.

overall_design: Total RNA obtained from liver (16 samples per gender) were compared in the different groups. In total, 4 groups per gender, each group consisting of 4 biological replicates.

first: E

last: van Straten

first: V

middle: W

last: Bloks

first: T

last: Plosch

last: van Dijk

first: J

middle: F

last: Baller

first: N

last: Huijkman

first: I

last: Kuipers

first: HJ

last: Verkade


title: Genome-wide analysis of gene expression in Eµ-Myc and Eµ-Myc Wrn Δhel/Δhel murine lymphomas

status: Public on Feb 25 2012

city: Seattle

first: Russell

last: Moser

state: WA

address: 1100 Fairview Avenue N.

department: Human Biology

institute: Fred Hutchinson Cancer Research Center

summary: Transcriptional profiling Myc-driven lymphomas to determine pathways by which Wrn deficiency impairs tumor development

overall_design: Total RNA isolated from Eµ-Myc and Eµ-Myc Wrn Δhel/Δhel murine B-cell lymphomas (n=4)

first: R

last: Davison

first: C

last: Grandori


title: Innate response activator B cells are sentinels that guard against polymicrobial sepsis

status: Public on Feb 07 2012

city: Cambridge

first: Martin

last: Etzrodt

address: 185 Cambridge St

department: Center for Systems Biology

institute: Massachusetts General Hospital

summary:
Innate immunity is fundamental to recognition and clearance of bacterial infection. The relevant cells and molecules that orchestrate an effective response, however, remain incompletely understood. Here we describe a previously unknown population of B cells, which we have named innate response activator (IRA) B cells that recognize bacteria directly through TLR-4-MyD88 and protect against polymicrobial sepsis.
IRA-B cells have a unique IgM high CD23 low CD43 + CD93+ GM-CSF+ signature, develop and diverge from B1a B cells, require BAFFR, and adhere to tissue via VLA-4 and LFA-1.

overall_design: B cell subsets are sorted from the spleen and peritoneum of C57BL/6 mice that were given intraperitoneal injections of LPS once daily for four days.

first: Philipp

last: Rauch

first: Aleksey

last: Chudnovskiy

first: Clinton

middle: S

last: Robbins

first: Georg

last: Weber

first: Ingo

last: Hilgendorf

first: Jose-Luiz

last: Figueiredo

first: Yoshiko

last: Iwamoto

first: Rostic

last: Gorbatov

first: Majd

last: Mouded

first: Mikael

last: Pittet

first: Matthias

last: Nahrendorf

first: Ralph

last: Weissleder

first: Filip

middle: K

last: Swirski


status: Public on Feb 04 2012

city: Amsterdam

first: Derk

last: Amsen

address: Meibergdreef 9

institute: AMC

summary: Generation of effective immune responses requires expansion of rare antigen-specific CD4+ T cells. The magnitude of the response is ultimately determined by proliferation and survival. Both processes are tightly controlled to limit responses to innocuous antigens. Sustained expansion occurs only when innate immune sensors are activated by microbial stimuli or by adjuvants, which has important implications for vaccination. The molecular identity of the signals controlling sustained T cell responses is not fully clear. Here we describe a prominent role for the Notch pathway in this process. Co-activation of Notch allows accumulation of far greater numbers of activated CD4+ T cells than stimulation via T cell receptor and classical co-stimulation alone. Notch does not overtly affect cell cycle entry or progression of CD4+ T cells. Instead, Notch protects activated CD4+ T cells against apoptosis after an initial phase of clonal expansion. Notch induces a broad anti-apoptotic gene expression program, which protects against intrinsic as well as extrinsic apoptosis pathways. Both Notch1 and Notch2 receptors and the canonical effector RBPJ are involved in this process. Correspondingly, CD4+ T cell responses to immunization with protein antigen are strongly reduced in mice lacking these components of the Notch pathway. Our findings therefore show that Notch controls the magnitude of CD4+ T cell responses by promoting cellular longevity.

overall_design: Naïve CD4+ T cells were activated for 1 day (1 control sample and 1 experimental sample) or 3 days (3 control samples and 3 experimental samples) with antibodies to CD3 soluble and CD28 in the presence of recombinant Delta4-Ig (experimental samples) or control Ig (control samples).

first: Christina

last: Helbig

first: Perry

last: Moerland


title: Transcriptional response to soybean aphid infestation in susceptible and resistant soybean plants

status: Public on Jan 31 2012

city: Ames

first: Matthew

last: Studham

state: IA

address: 2214 Molecular Biology Bldg.

institute: Iowa State University

summary:
Soybean aphids are phloem-feeding pests that can cause significant yield losses in soybean plants. Soybean aphids thrive on susceptible soybean lines but not on resistant lines.
We used microarrays to characterize the soybean plant's transcriptional defense against aphids in two related cultivars, a susceptible line and a resistant line with the Rag1 aphid-resistance gene. We measured trancript levels in leaves after one and seven days of aphid infestation.

overall_design: This was a full-factorial experiment with three factors: soybean variety (susceptible SD01-76R,resistant LD05-16060), aphid treatment (control, aphids), and infestation duration (1 day, 7 days). There were three replicates per treatment, for a total of 24 samples. The experiment was carried out in a growth chamber. At the V3 growth stage, thirty aphids were added to the third trifoliate leaves of the aphid-treated plants. Each plant had a net to prevent aphid movement among different plants. The aphids were removed prior to sampling.

middle: E

first: Gustavo

last: MacIntosh


title: Matrix metalloproteinase-9 and TIMP-1 in peripheral nerve: Implications for myelin formation

status: Public on Feb 28 2012

first: Andrei

last: Chernov

address: 9500 Gilman Dr

department: Anesthesiology

institute: University of California San Diego

summary: Remyelination is a key step in functional nerve regeneration performed by Schwann cells (SC). We have demonstrated that matrix metalloproteinase (MMP)-9 is a major regulator of signal transduction and phenotypic switching in SCs. Herein, genome-wide transcriptional profiling, followed by Ingenuity Pathway Analysis revealed the MMP-9 signaling network and its endogenous inhibitor, TIMP-1, among the top induced genes of the injured sciatic nerve, that co-distributed with MMP-9 in myelinating SCs and the paranodal/nodal areas of myelinated fibers. Homo- and heterodimers of the active and proMMP-9 were purified from injured nerves using gelatin-sepharose. MMP-9 gene deletion increased the number of immature, GFAP+ mSC and post-mitotic cell counts that correlate with shorter myelin internodes in remyelinated fibers lacking MMP-9. MMP-9 is essential to nodal clustering of voltage-gated Na+ (Nav) channels. MMP inhibitor therapy diminished the expression of Nav 1.7 and 1.8. These data established the essential role of MMP-9 in guiding SC differentiation toward myelin production and in molecular assembly of the myelin domains. Modification of Nav channels in myelinated fibers may thus provide an important therapeutic approach for a number of facilitates regeneration and attenuated neuropathic pain.

overall_design: Gene expression profiling of total RNAs extracted from murine sciatic nerves, dorsal root ganglion and spinal cords at day 1 and day 5 post injury.

middle: V

first: Veronica

last: Shubayev

first: Alex

middle: Y

last: Strongin


title: Expression profiles of 7-day cultured HSPCs in the presence or absence of valproic acid and/or lithium

status: Public on Jan 24 2012

first: Leonid

last: Bystrykh

address: A. Deusinglaan 1

department: European Research Institute for the Biology of Ageing - ERIBA

institute: University Medical Center Groningen

summary: Two small molecules, valproic acid (VPA) and lithium (Li), were tested to inhibit differentiation of hematopoietic stem/progenitor (HSPC) cells in culture. HSPCs exposed to VPA and Li during differentiation-inducing culture preserved an immature cell phenotype, provided radioprotection to lethally irradiated recipients and enhanced in vivo repopulating potential. Furthermore, VPA and Li synergistically preserved expression of stem cell-related genes and repressed genes involved in differentiation. Target genes were collectively co-regulated during normal hematopoietic differentiation. Additionally, transcription factor networks were identified as possible primary regulators. Our results demonstrate that the combination of VPA and Li potently prevents differentiation at the biological and the molecular level, and provide evidence to suggest that combinatorial screening of chemical compounds may uncover possible additive/synergistic effects to modulate stem cell fate decisions.

overall_design: These data consist of total mRNA obtained from hematopoietic cells cultured for 7 days in the presence or absence of valproic acid and/or lithium. All samples were analyzed in independent biological triplicates.

first: Marta

last: Walasek

first: Vinvent

last: van den Boom

first: Sandra

last: Olthof

first: Albertina

last: Ausema

first: Martha

last: Ritsema

first: Gerwin

last: Huls

first: Gerald

last: de Haan

first: Ronald

last: van Os


title: Genome-wide analysis of atrial left-right differences in two different mouse strains

status: Public on Dec 31 2011

city: Münster

first: Peter

middle: Christian

last: Kahr

address: Grevener Straße 1

institute: University Hospital Münster

summary: Two wild-type mouse strains (Swiss Agouti and MF1) were investigated regarding the mRNA expression patterns of their left and right atria at 12 months of age.

overall_design: Eight samples of each strain, four with left atrium and four with right atrium examined.

first: P

first: I

last: Piccini


title: Spatial segregation of BMP/Smad signaling affects osteoblast differentiation in C2C12 cells

first: Raghu

last: Bhushan

address: Thielallee 63

department: Institut für Chemie und Biochemie

institute: Freie Universität

summary:
Analysis of BMP-2 induced gene expression of C2C12 cells treated with the endocytosis inhibitor dynasore to identify gene expression profiles which are sensitive to endocytosis inhibition.
Our data highlight the importance of endocytosis for transmission of an extracellular BMP-2 signal into the nucleus to activate a transcriptional gene network

overall_design: Total RNA obtained from C2C12 cells stimulated with BMP-2 together with the endocytosis inhibitor dynasore or DMSO as control compared to unstimulated cells treated with dynasore or DMSO alone.

first: Eva

last: Heining

first: Petra

last: Knaus


title: Expression analysis of stepwise induction of iPS cells

status: Public on Dec 29 2011

city: Saint Louis

first: Jianxin

last: Bao

institute: Washington University

summary:
We were able to achieve an initial stable intermediate phase by the transduction of Oct4, Klf4, and c-Myc. Furthermore, over-expression of Sox2 in these intermediate stage cells leads to final iPS cell phase.
After examining the gene expression profiles from the initial to final iPS cell phases, we have identified Sox2 downstream genes important for iPS cell induction.

overall_design: 4 groups of cells are analyzed. Each group contains cells from 4 indepent dishes. The four groups are: ES cells, iPS cells, intermediate stage cells (OKM cells) and MEFs

first: Bao

last: Jianxin

first: Lin

last: Zhaoyu


title: Genome-wide analysis of gene expression perturbed by RORa in MEFs subjected to control and 12 hour DNA damaged condition.

status: Public on Dec 30 2011

city: Pohang

first: Bhin

last: Jin-hyuk

address: Ji-gok research center, hyoja-dong, Nam-gu

department: Department of Chemical engineering

institute: POSTECH

summary: In order to investigate the role of RORa on the expression of damage responsive genes across the whole genome, we performed a microarray analysis from RNAs isolated from wild type MEFs or staggerer MEFs in control and damaged conditions.

overall_design: Wild type MEFs and staggerer MEFs were treated doxorubicin for 12 hours. Cells were then lysed and RNA isolated.

first: Sung

last: Baek

first: Daehee

last: Hwang

first: Hyunkyung

last: Kim

first: Jinhyuk

last: Bhin


title: Defective Drosha Processing Contributes to Downregulation of MiR-15/-16 in Chronic Lymphocytic Leukemia.

city: ULM

first: Danilo

last: Allegra

address: Albert-Einstein-Allee 23

institute: University Hospital of Ulm

summary: MIR15A and MIR16-1, located in chromosomal band 13q14, are tumor suppressor miRNAs often deleted and downregulated in chronic lymphocytic leukemia (CLL). This downregulation is not only due to loss of 13q, as it occurs also in 13q+/+ CLL patients. We found that a subgroup of CLL patients has a dysregulation of miR-15 /-16 processing intermediates due to defective processing by Drosha. These patients have reduced levels of miR-15a, miR-16 and miR-15b (another member of the miR-15 family), but not of most other miRNAs. Thus, we show that modulation of miRNA maturation leads to specific downregulation of a family of tumor suppressor miRNAs in leukemic cells.

overall_design: 11 normal processing CLL sample; 12 processing defective CLL patients

first: Angela

last: Philippen

first: Hartmut

last: Döhner

first: Stefan

last: Stilgenbauer

first: Daniel

last: Mertens


title: Expression profile of Gli1-expressing keratinocytes from mouse skin

status: Public on Dec 01 2011

first: Jeffrey

last: Zhao

address: 1275 York Avenue

department: Genomics Core

institute: Memorial Sloan Kettering Cancer Center

summary: To assess if Hedgehog (Hh) responding cells in the skin have a unique expression profile, isolated keratinocytes that express the Hh response gene Gli1 were collected by FACS and their gene expression was compared to sorted CD34-expressing cells from the middle bulge region of the hair follicle and to cells from the interfollicular epidermis (IFE) by hybridization of isolated RNA to gene expression microarrays.

overall_design: Dissociated keratinocytes isolated form back skin of Gli1-eGFP/+ mice (2 mice pooled for each replicate) in adult telogen were sorted based on GFP expression and immunostaining for CD34. Only viable, single cells with immunostaining for α6 Integrin (to mark basal keratinocytes) were collected. GFP(+) cells were collected as the Gli1 cohort. GFP(-) CD34(+) cells were collected as the CD34 cohort, and GFP(-) CD34(-) cells were collected as interfollicular epidermis (IFE) cohort. Total RNA was extracted from each cell population and labeled for hybridization to gene expression microarrays. The experiment was preformed in triplicate, however RNA from the Gli1(+) cells in one replicate was of insufficient quality to analyze. For staining of isolated keratinocytes, cells were incubated on ice for 1 hour in SMEM containing 1%BSA and 15μL of anti-CD49f-PE antibody (BDBioscience) plus 5μL anti-CD34-APC antibody (eBioscience) for each 100μL total volume for each 2 million cells. Immediately prior to sorting, DAPI (Invitrogen) was added to the washed cells at 1μg/mL final concentration.

first: Isaac

last: Brownell

first: Elizabeth

last: Guevara

first: C

middle: B

last: Bai

first: Cynthia

last: Loomis

first: Alexandra

last: Joyner


title: REST Couples Loss of Pluripotency with Neural Induction and Neural Differentiation

status: Public on Dec 08 2011

city: London

first: Caroline

middle: Emma

last: Johnston

address: 125 Coldharbour Lane

institute: Kings College London

summary: Neural differentiation of embryonic stem cells (ESCs) requires coordinated repression of the pluripotency regulatory programme and reciprocal activation of the neurogenic regulatory programme. Upon neural induction, ESCs rapidly repress expression of pluripotency genes followed by staged activation of neural progenitor and differentiated neuronal and glial genes. The transcriptional factors that underlie pluripotency are partially characterized, whereas those underlying neural induction are much less explored, and the factors that coordinate these two developmental programs are completely unknown. One transcription factor, REST (RE1 silencing transcription factor), has been linked with terminal differentiation of neural progenitors, and more recently and controversially, with control of pluripotency. Here, we show that in the absence of REST, coordination of pluripotency and neural induction is lost and there is a resultant delay in repression of pluripotency genes and a precocious activation of both neural progenitor and differentiated neuronal and glial genes. Further, we show that REST is not required for production of radial glia-like progenitors but is required for their subsequent maintenance and differentiation into neurons, oligodendrocytes and astrocytes. We propose that REST acts as a regulatory hub that coordinates timely repression of pluripotency with neural induction and neural differentiation.

overall_design: We have investigated the role of REST in the coupling of pluripotency and neural induction and neurogenesis using Rest-null mouse ESCs (mESCs) in conjunction with a novel mESC neural differentiation protocol. Differential expression between Rest-null ESCs and controls was tested using Illumina Mouse Ref-8 v2 BeadArray technology. Three replicates were used for Rest-null and three for control. Data analysis was performed using Bioconductor libraries beadarray and limma.

last: Soldati

first: A

last: Bithell

first: K

last: Wong

first: S

last: Teng

first: V

last: Beglopoulos

first: L

last: Stanton

first: N

middle: J

last: Buckley


title: NSD2 links dimethylation of histone H3 at lysine 36 to oncogenic programming [Transduction]

status: Public on Nov 29 2011

city: Houston

first: kaifu

last: chen

address: 1 Baylor plaza, suite 450A

institute: Baylor College of Medicine

summary: NSD2 (also named MMSET and WHSC1) is a histone lysine methyltransferase that is implicated in diverse diseases and commonly overexpressed in multiple myeloma due to a recurrent t(4;14) chromosomal translocation.  However, the precise catalytic activity of NSD2 is obscure, preventing progress in understanding how this enzyme influences chromatin biology and myeloma pathogenesis.  Here we show that dimethylation of histone H3 at lysine 36 (H3K36me2) is the principal chromatin-regulatory activity of NSD2.  Catalysis of H3K36me2 by NSD2 is sufficient for gene activation.  In t(4;14)-positive myeloma cells, the normal genome-wide and gene-specific distribution of H3K36me2 is obliterated, creating a chromatin landscape that selects for a transcription profile favorable for myelomagenesis.  Catalytically active NSD2 confers xenograft tumor formation and invasion capacity upon t(4;14)-negative cells and NSD2 promotes oncogenic transformation of primary cells in an H3K36me2-dependent manner.  Together our findings establish H3K36me2 as the primary product generated by NSD2, and demonstrate that genomic disorganization of this canonical chromatin mark initiates oncogenic programming.

overall_design: Genome-wide expression profiling of p19ARF-/- mouse embryonic fibroblasts stably transduced with control vector or wild-type NSD2. Each cell line is tested in triplicate.

first: Alex

last: Kuo

first: Peggie

last: Cheung

first: Kaifu

last: Chen

first: Barry

middle: M

last: Zee

first: Josh

last: Lauring

first: Yuanxin

last: Xi

first: Ben

middle: H

last: Park

first: Xiaobing

last: Shi

first: Mitomu

last: Kioi

first: Benjamin

middle: A

last: Garcia

first: Wei

last: Li

first: Or

last: Gozani


title: Type 1 interferon and pattern recognition receptor signaling following particulate matter inhalation

status: Public on Dec 18 2011

city: Morgantown

first: Patti

middle: Christine

last: Zeidler-Erdely

state: WV

address: 1095 Willowdale Road

department: HELD

institute: CDC/NIOSH

summary: This study utilized microarray technology as an exploratory search for mechanisms of systemic effects after welding fume inhalation.  In addition, the applicability of this methodological approach for determining specific exposure-induced responses was examined.

overall_design: C57Bl/6J mice were exposed to gas metal arc-stainless steel (GMA-SS) welding fume by inhalation for 10 days (3 hours/day) at 40 mg/m3. Microarray analysis was done on lung, blood and aorta from n=4 mice exposed to welding fume or air (control).

first: Aaron

last: Erdely


title: Cryptochromes mediate rhythmic repression of the glucocorticoid receptor

status: Public on Dec 22 2011

city: La Jolla

first: Ruth

middle: T

last: Yu

state: CA

address: 10010 N Torrey Pines Rd

department: Gene Expression Lab

institute: Salk Institute

summary: The circadian transcriptional repressors cryptochromes 1 (Cry1) and 2 (Cry2) interact with the C-terminus of the glucocorticoid receptor (GR) and are required for transrepression in response to the synthetic GR ligand dexamethasone (Dex) in mouse embryonic fibroblasts.  Dex induction of many genes was increased in Cry-deficient fibroblasts suggesting that cryptochromes oppose transactivation in addition to contributing to transrepression.  In mice, genetic loss of Cry1 and/or Cry2 resulted in glucose intolerance and constitutively high levels of circulating corticosterone, suggesting reduced glucocorticoid suppression of the hypothalamic-pituitary-adrenal axis coupled with increased sensitivity to the hyperglycemic effects of glucocorticoid-mediated transactivation in the liver. Cry1 and Cry2 association with a GRE in the Pck1 promoter was stimulated by Dex, and Dex-induced transcription of pck1 was strikingly increased in Cry-deficient livers.  Finally, cry1-/-;cry2-/- mice subjected to 8 weeks of chronic Dex treatment exhibited incomplete suppression of circulating corticosterone and greater glucose intolerance compared with wildtype littermates subjected to the same chronic treatment, consistent with enhanced transcriptional response to the synthetic glucocorticoid ligand.

overall_design: Total RNA was obtained from WT and Cry1/2 KO MEFs treated with Dexamethasone (1uM) or control EtOH for 16 hours.

first: Katja

last: Lamia

first: Ronald

last: Evans


title: Gene expression profile of developing adipose tissue in vivo

city: new york

first: kivanc

last: birsoy

address: 1230 Rockefeller University

institute: Rockefeller University

summary: Obesity is characterized by an increase in the size and the number of adipocytes. However, the mechanisms responsible for the formation of adipocytes during development and the molecular mechanisms regulating their increase and maintenance in adulthood are poorly understood.  Here, we report the use of leptin-luciferase BAC transgenic mice to track white adipose tissue (WAT) development and guide the isolation and molecular characterization of adipocytes during development using DNA microarrays. These data reveal distinct transcriptional programs that are regulated during murine WAT development in vivo.

overall_design: Developing mouse adipose tissue from at least 3 embryos were pooled for embryonic and postnatal time points.

first: Kivanc

last: Birsoy

first: Matthew

last: Rodeheffer

first: Jeffrey

last: Friedman


title: Gene expression profile of murine tolerant, self-antigen specific CD8 T cells

status: Public on Feb 16 2012

first: Andrea

last: Schietinger

address: 1959 NE Pacific Street

department: Immunology

institute: University of Washington

summary:
Genomewide microarray analysis of murine tolerant, self-antigen specific CD8 T cells to identify genes and pathways underlying peripheral T cell tolerance
Gene signature of tolerant CD8 T cells was compared to the signatures of naïve T cells, memory T cells, rescued T cells (=tolerant T cells undergoing homeostatic proliferation in lymphopenic, tolerogenic Alb:GAG mice), and re-tolerized T cells (=previously rescued T cells post homeostatic proliferation isolated from lymphoreplete wild-type B6 mice).

overall_design: Total RNA obtained from various sort-purified transgenic CD8 T cell subsets (naïve, memory, tolerant, rescued, and re-tolerized) isolated from spleens of different host mice

first: Philip

middle: D

last: Greenberg

first: Ryan

last: Basom

last: Delrow


title: Unraveling the role of ZBED6 in transcriptional regulation by whole transcriptome analysis after RNAi in mouse myoblasts

status: Public on Nov 04 2011

city: Uppsala

first: Carl-Johan

last: Rubin

address: Husargatan 3

department: Dedp. Med. Biochem. & Microbiol.

institute: Uppsala University

summary: ZBED6 is a novel transcription factor unique to placental mammals and has evolved from a domesticated DNA transposon. Here we further characterize the functional significance of ZBED6 based on transcriptome analysis of mouse myoblasts after Zbed6 silencing. ZBED6 appears as an important transcriptional regulator since differential expression of more than 1,000 transcripts was consistently observed after Zbed6 silencing and these changes correlated with increased myotube formation. Up-regulated genes were associated with muscle contractile fibers and muscle organ development, while down-regulated genes were associated with ribosome function. Thirty-four small nucleolar RNAs showed differential expression and all increased in expression after Zbed6 silencing. This is particularly interesting since ZBED6 shows a strong enrichment in the nucleolus. There was an overrepresentation of genes with ZBED6 binding sites among the up-regulated genes after silencing, suggesting that ZBED6 acts as a repressor at many loci. Many genes showed significant down-regulation after Zbed6 silencing, which begs the question of whether ZBED6 acts as an activator at some of these loci or if they all represent secondary effects. The colocalization of histone marks and ZBED6 binding sites defined by a previous ChIP-seq analysis was evaluated. There was a strong association between ZBED6 binding sites and the H3K4me3, H3K4me2 and H3K27ac modifications, which are usually found at active promoters, but no association with the repressive marks H3K27me3 and H3K36me3. We propose that ZBED6 preferentially binds to active promoters and modulates transcriptional activity by a novel mechanism rather than by recruiting repressive histone modifications.

overall_design: C2C12 cells were either exposed to siRNA targeting ZBED6 or negative control siRNAs. Cells in each treatment group were cultured for 48 and 96 hours before RNA was collected. Each treatment and time point was represented by three biological replicates.

middle: L


title: Genome-wide analysis of gene transcription in myocardium of the doxycycline inducible Tafazzin shRNA knockdown mouse model of Barth syndrome

status: Public on Nov 05 2011

first: Michael

middle: Andrew

last: Kiebish

state: MO

address: 660 South Euclid Avenue, Campus Box 8020

department: Internal Medicine

institute: Washington University School of Medicine

summary: Analysis of the transcriptome of cardiac tissue from mice trangenically engineered with a doxycycline inducible Tafazzin shRNA knockdown to mimic the loss of function of Tafazzin in Barth syndrome.  ShRNA induced knockdown mice were compared to wildtype littermates also fed the doxycyline diet.  The hypothesis was to investigate adaptive metabolic and compensatory gene transcriptional changes in myocardium of the mouse model of Barth syndrome

overall_design: Total RNA obtained from 2 month old cardiac tissue from the doxycycline inducible shRNA Tafazzin knockdown mouse model of Barth syndrome compared to wildtype littermates also fed 625 mg/Kg doxycycline diet

first: Richard

middle: W

last: Gross

first: Xianlin

last: Han


title: Genome-wide analysis of gene transcription in myocardium of mice transgenically expressing human cardiolipin synthase 1 (hCLS1) in cardiac tissue

summary: Analysis of the transcriptome of cardiac tissue from mice transgenically expressing human cardiolipin synthesis.  The hypothesis tested was that cardiac specific transgenic expression of cardiolipin synthase alters myocardial lipidomic flux resulting in compensatory metabolic gene transcriptional changes that will attenuate pathological environmental and dietary insults on bioenergetics.

overall_design: Total RNA obtained from cardiac tissue from transgenic cardiac specific expressing human cardiolipin synthase 1 (hCLS1) mouse model at 4 months of age  compared to wildtype littermates


title: Loss of c-Met Accelerates Development of Liver Fibrosis in Response to CCl4 Exposure through Deregulation of Multiple Molecular Pathways

status: Public on Nov 09 2011

city: Bethesda

first: Daekwan

last: Seo

address: 37 Convent Dr. Rm 4140

department: NCI

institute: NIH

summary:
Background:
HGF/c-Met signaling plays a pivotal role in hepatocyte survival and tissue remodeling during liver regeneration. Treatment with HGF has been shown to accelerate resolution of fibrotic liver lesions in experimental animal models. To formally address the importance of c-Met signaling in hepatocytes in the context of chronic liver injury, we have used hepatocyte-specific Metfl/fl;Alb-Cre+/- conditional knockout mice (KO) and  a model of liver fibrosis.

Methods:
CCl4 was administrated biweekly over a period of 4 weeks (injury phase), and the animals were followed over the next 4 weeks (healing phase). Macroscopic and microscopic changes during the injury and healing phases were monitored by IHC. Deposition of ECM was assessed by Sirius red staining and hydroxiproline content.  Activation of hepatic stellate cells (HSC) was estimated by a-SMA using WB and IHC. Expression levels of the selected key fibrotic molecules were evaluated by RT-qPCR and WB. Time-dependent global transcriptomic changes from whole livers and isolated hepatocytes were examined using gene expression microarrays.

Results:
Loss of HGF/c-Met signaling in hepatocytes altered the hepatic microenvironment and dramatically aggravated hepatic fibrogenesis. Increased liver damage was associated with decreased hepatocyte proliferation, progressive accumulation of HSCs, and delayed fibrinolysis causing increased collagen deposit. Dystrophic calcification of necrotic areas impaired phagocytosis, resulting in sustained inflammatory and fibrogenic signaling further augmenting severity of fibrogenesis. Global gene-expression analysis demonstrated upregulation of key fibrogenic molecules, such as Tgf-Ã¢ and Pdgf-Ã¢, paralleled by a decreased expression of genes important for cell cycle, stress response and regeneration, which could be attributed to the c-Met deficiency in hepatocytes.  Additionally, key chemotactic and inflammatory cytokines, including Ccl2, SDF1/Cxcr4 and Spp1, were upregulated in Metfl/fl;Alb-Cre+/- hepatocytes. However, the major pro-fibrotic signaling originated from the non-parenchymal cell compartments, as revealed by cell type-specific gene expression signatures.

Conclusion:
These results indicate that lack of c-Met signaling in hepatocytes disrupts the balance between extracellular matrix production and degradation and establish a protective role for c-Met against adverse microenvironment leading to the development of fibrotic liver disease.

overall_design: In the present study, we reported a detailed and comprehensive dynamic characterization of the cellular and molecular alterations involved in fibrosis in the liver of c-Met transgenic mice. Liver samples from female animals were collected at various time-points after fibrosis induction using CCL4 ranging from 0 weeks to 3 weeks.  Tissue samples were divided into two parts; one was fixed in 10% formalin for histological evaluation and the other was used for RNA analysis.

first: Jens

middle: U

last: Marquardt

first: Deakwan

first: Snorri

middle: S

last: Thorgeirsson


title: Gene expression profiles of the mouse oviduct during the estrous cycle

status: Public on Jan 01 2012

city: Taipei

first: Chung-Hao

last: Lu

state: Taipei

address: 92, Sec. 2, Zhongshan N. Rd

department: Department of Medical Research

institute: Mackay Memorial Hospital

summary: This study attempted to reveal the profile of the oviductal gene expression at each stage of estrous cycle by microarray analyses

overall_design: The oviductal tissue was separately collected at four stages of the estrous cycle, i.e., proestrus, estrus, metestrus, and diestrus.

first: Robert

middle: K

last: Lee

first: Mong-Hsun

last: Tsai

first: Ling-Yu

last: Yeh

first: Shau-Ping

last: Lin

first: Sheng-Hsiang

last: Li


title: Pitx1 Haploinsufficiency Causes Clubfoot in Humans and Mice

status: Public on Nov 21 2011

first: David

middle: Michael

last: Alvarado

address: 660 South Euclid

department: Orthopaedic Surgery

institute: Washington University in St. Louis

summary: To identify genes regulated by Pitx1 during early hindlimb development, we compared gene expression differences between hindlimb buds from E12.5 Pitx1+/+ and Pitx1-/- mice on the Illumina MouseRef-8 expression Bead Chip.  Genes involved in muscle development GeneGO processes were highly enriched in our dataset, specifically in down-regulated genes. This data is consistent with the reduced muscle volumes that were observed in the clubfoot limbs of our adult mice.

overall_design: Hindlimb buds were collected from Pitx1+/- mated mice at embryonic day E12.5 and genotypes were determined by PCR of DNA isolated from tails.

first: Kevin

last: McCall

first: Hyuliya

last: Aferol

first: Matthew

last: Silva

first: Joel

last: Garbow

first: Marilyn

last: Siegel

last: Dobbs

first: Christina

last: Gurnett


title: Forkhead box protein p1 is a transcriptional repressor of immune signaling in the CNS

status: Public on Nov 01 2011

first: Elizabeth

middle: A.

last: Thomas

address: 10550 N. Torrey Pines Rd

department: Molecular Biology

institute: The Scripps Research Institute

summary: Forkhead box protein P1 (Foxp1), a transcription factor showing highly enriched expression in the striatum, has been implicated in CNS development, but its role in the mature brain is unknown.   In order to ascertain functional roles for Foxp1 in the CNS, we have identified gene targets for Foxp1 in vitro using gene expression microarrays and chromatin immunoprecipitation followed by high-throughput sequencing (ChIP-seq) assays.  Transcriptome-wide analysis of Foxp1-transfected striatal cells revealed widespread expression changes of genes related to immune signaling, cancer, transcriptional regulation, and a curated Huntington’s disease (HD) signaling pathway.   Integrating the microarray expression dataset with Foxp1 binding sequences determined from ChIP-seq analysis resulted in 75 direct targets of Foxp1, which included Foxp1 itself, which were also related to immune processes and the category “genetic disorder”.   These findings demonstrate that Foxp1 is a primary transcriptional repressor of immunological-related gene expression in striatal cells.

overall_design: n=3 wt STHdh striatal cells  and n=3 Foxp1-transfected STHdh striatal cells

first: Bin

last: Tang

first: Lana

last: Schaffer

first: Steven

middle: R

last: Head


title: Identification of cardiomyocyte-derived microvesicles content.

city: Umea

first: Urban

last: Hellman

address: Nus 6M

department: Public health and clinical medicine

institute: Umea University

summary:
Investigation of content of microvesicles exocytosed by cardiomyocytes. The aims of the study were to identify DNA and RNA content in microvesicles from cardiomyocytes.
DNA and RNA were purified from microveicles from cultured cardiomyocytes. Illumina microarrays were used to detect DNA and mRNA molecules and identify them.

overall_design:
Gene expression microarray were used to detect 50 nucleotide long illumina probe sequences in the sequences of the extracted microvesicular DNA.
Terminal deoxynucleotidyl transferase were used to add a poly_T tail to DNA from microvesicles to construct cDNA, possible to label as cRNA and use on the chip to identify part of the sequence of the original DNA.
The microvesicular mRNA content was compared to cardiomyocyte mRNA content (the source of the microvesicles and therefore also the source of microvesicle mRNA).
Two replicates of mRNA from cardiomyocytes and two replicates of mRNA from microvesicles and one sample of DNA from microvesicles were analyzed.

first: Anders

last: Waldenström

first: Gunnar

last: Ronquist


title: Cultured fibroblasts treated with microvesicles from cardiomyocytes

summary:
Investigation of microvesicles exocytosed by cardiomyocytes. The aims of the study were to determine if microvesicles from cardiomyocytes are capable of affecting fibroblasts and causes changes in gene expression.
The study showed that cardiomyocytes microvesicles are capable to cause change in gene expression in fibroblasts.

overall_design:
Microvesicles were purified from media from cultured cardiomyocytes and transfered to cultured fibroblasts. Gene expression in fibroblasts were analyzed with Illumina Beadstation.
Two replicates fibroblasts controls and two replicates of fibroblasts transfected with microvesicle from cultured cardiomyocytes were compared.


title: Cultured cardiomyocytes treated with hyaluronan

summary:
Investigation of the role of hyaluronan in cardiomyocytes . The aims of the study were to determine if cardiomyocytes are capable of detecting hyaluronan and if then intrecellular signaling causes changes in gene expression.
The study showed that cardiomyocytes can bind hyaluronan with following change in gene expression.

overall_design: Cultured cardiomyocytes were treated with hyaluronan in differrent length. Gene expression in cells were analyzed with Illumina Beadstation.

first: Linus

last: Malm

first: Li-Ping

last: Ma

first: Stellan

last: Mörner

first: Michael

last: Fu

first: Anna

middle: E

last: Laurent


title: Cultured fibroblasts treated with media from cardiomyocytes.

summary:
Investigation of the role of hyaluronan in cardiomyocytes. The aims of the study were to determine if cardiomyocytes are capable of signal to fibroblasts to affect their hyaluronan synthesis and if intracellular signaling causes changes in gene expression.
The study showed that cardiomyocytes send a signal to fibroblasts, to causing them to increase hyaluronan synthesis, with following change in gene expression.

overall_design: Media from cultured cardiomyocytes were transfered to cultured fibroblasts. Gene expression in fibroblasts were analyzed with Illumina Beadstation.


title: Gene Array Analysis of Methylthioadenosine Supplementation in Dextran Sulfate Sodium Induced Colitis

status: Public on Dec 20 2011

first: Nancy

last: Benight

address: 1100 Bates Street

summary: Study hypothesized that oral supplementation of methylthioadenosine (MTA) would reduce the inflammatory response in mice exposed to an agent that induces colitis (DSS) and that this reduction in inflammatory response would lead to reduced clinical disease burden.

overall_design: Total RNA was collected from isolated colons of mice in the following treatment groups: untreated controls, DSS only, DSS+MTA