title: Cooperation of IRF-4 and IRF-8 deficiencies in the development of hematological malignancies

status: Public on Aug 22 2010

city: Waltham

first: Ruibao

last: Ren

address: 415 South St.

institute: Brandeis University

summary:
We found that mice deficient in both IRF-4 and IRF-8 develop from a very early age a more aggressive CML-like disease than mice deficient in IRF-8 alone. IRF-4 deficiency dramatically enhanced the effect of IRF-8 deficiency on expansion of granulocyte-monocyte progenitors (GMPs). All mice deficient in both IRF-4 and IRF-8 eventually develop and succumb to a B-lymphoblastic leukemia/lymphoma at approximately 25 weeks of age. The results demonstrate that IRF-4 and IRF-8 deficiencies can cooperate in the development of both myeloid and lymphoid tumors.
To gain insights into how loss of IRF-4 affects the transcriptional program underlying leukemogenesis, we analyzed the genome-wide transcription profiles of GMPs from WT, IRF-8 KO and IRF-4/8 DKO mice. Microarray analysis revealed genes differentially expressed in IRF-4/8 DKO and IRF-8 KO GMPs, including genes that are involved in cell growth regulation and/or tumorigenesis.

overall_design: Total RNA was extracted from GMPs (Lin-/IL-7R-/Sca1-/Kit+/CD34+/FcRII/IIIhi) of wild type, IRF8 KO and IRF4/8 DKO mice (two samples each group) using the Qiagen RNAeasy Micro kit. Affymetrix Mouse Genome 430 2.0 microarray with 45,000 probe sets was used at the BIDMC Genomics Center. Hybridization data were normalized and expression values were determined using the PM/MM difference model by dChip 1.3 (DNA-Chip analyzer).

first: Seung-Hee

last: Jo


title: Effects of ACE2 on BMPR2 mutation-mediated defects in gene expression

status: Public on Aug 25 2010

city: Nashville

first: James

last: West

state: TN

address: 4200 E 9TH Ave, Box B133

department: Medicine

country: USA

institute: Vanderbilt University

summary: BMPR2 mutation causes pulmonary arterial hypertension (PAH); ACE2 treatment can resolve established BMPR2-mediated PAH. The purpose of this study was to uncover the molecular mechanism behind this.

overall_design: Four groups: +/- ACE2 and +/- BMPR2 transgene, two arrays each, each array a pool of three animals.

first: Jennifer

last: Johnson


title: UGE and UGM Reveal Novel Signaling Pathways and Ligand-Receptor Interactions in the Primitive Prostate Stem Cell Niche

status: Public on Aug 29 2010

city: New York

first: Roy

last: Blum

state: NY

address: 552 First Ave

department: Cancer Institute

institute: New York University

summary:
We isolated fetal murine urogenital sinus epithelium and urogenital sinus mesenchyme and determined their global gene expression profiles to define their differentially expressed regulators. To distinguish gene expression patterns that are shared by other developing epithelial/mesenchymal compartments in the embryo from those that pertain to the prostate stem cell niche, we also determine the global gene expression of epidermis and dermis of the same embryos. We identified a distinctive core of transcripts that were differentially regulated in the prostate stem cell niche. Our analysis indicates that several of the key transcriptional components that are likely to be active in the embryonic prostate stem cell niche regulate processes such as self-renewal (e.g., E2f and Ap2), lipid metabolism (e.g., Serbp1) and cell migration (e.g., Areb6 and Rreb1). Several of the promoter binding motifs that are enriched in the profiles are shared between the prostate epithelial/mesenchymal compartments and their epidermis/dermis counterparts, indicating their likely relevance in epithelial/mesenchymal signaling in primitive cellular compartments. We also focused on defining ligand-receptor interactions that may be relevant in controlling signals in the stem cell niche and identified the Wnt/beta-catenin, ephrin, Notch, sonic hedgehog, FGF, TGF-beta and bone morphogenic signaling pathways as being of likely relevance in the prostate stem cell niches. Members of the integrins family including those that bind extracellular matrix proteins such as laminin and activate latent TGF-beta are also expressed in the prostate niche.development.

Keywords: Differential gene expression

overall_design: Six biological replicate experiments were performed for UGE. Five biological replicate experiments were performed for UGM. Four biological replicate experiments were performed for Epidermis. Four biological replicate experiments were performed for Dermis.

first: Rashmi

last: Gupta

first: Patricia

middle: E

last: Burger

first: Christopher

middle: S

last: Ontiveros

first: Sarah

middle: N

last: Salm

first: Xiaozhong

last: Xiong

first: Jiri

last: Zavadil

first: Alexander

last: Kamb

first: Holger

last: Wesche

first: Lisa

last: Marshall

first: Gene

last: Cutler

first: Sean

last: Wang

first: David

last: Moscatelli

first: E

middle: L

last: Wilson


title: Expression data from DC-induced Hopx-deficient and sufficient regulatory T cells after immunization

city: New Haven

first: Daniel

last: Hawiger

state: CT

address: 300 Cedar St. TAC-S570

institute: Yale University

summary: We found that Hopx is required for the function of DC-induced regulatory T cells in vivo. We used microarrays to identify relevant Hopx-targets in such cells after antigenic re-challenge in vivo.

overall_design: CD25/Foxp3 double positive DC-induced Hopx-deficient and sufficient regulatory T cells were FACS sorted to high purity

first: Richard

last: Flavell


title: Expression data from mouse neonatal ovarian xenobiotic culture experiments

status: Public on Aug 21 2010

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 three ovotoxic agents, 4-Vinylcyclohexene Diepoxide (VCD), Methoxychlor (MXC), and Menadione (MEN), all of which target immature follicles. Neonatal mouse ovaries (PND3-4) were cultured in the presence of 4-Vinylcyclohexene Diepoxide (50uM), Methoxychlor (50uM), and Menadione (5uM) 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 xenobiotic containing media for 96 hours. The ovaries were then collected for RNA extraction and hybridization on Affymetrix microarrays (Mouse 430 version 2.0 GeneChip).

first: Victoria

middle: J

last: Pye

middle: P

first: Eileen

middle: A

last: McLaughlin


title: Global analysis of gene expression by SV40 T antigen in mouse embryo fibroblasts

status: Public on Aug 31 2010

city: Pittsburgh

first: Ulka

last: Sachdev-Ost

address: 300 Halket Street Suite 5414

institute: University of Pittsburgh School of Medicine

summary: SV40 large T antigen (TAg) contributes to cell transformation, in part, by targeting two well characterized tumor suppressors, pRb and p53. TAg expression affects the transcriptional circuits controlled by Rb and by p53. We have performed a microarray analysis to examine the global change in gene expression induced by wild-type TAg and TAg-mutants, in an effort to link changes in gene expression to specific transforming functions. For this analysis we have used MEFs expressing TAg or infected by SV40. Our analysis indicates that TAg can induce interferon-stimulated genes in MEFs and that this induction depends upon the LXCXE motif and p53 binding.

overall_design: Two independent wild-type MEFs and three independent MEF cell lines expressing TAg and the mutants were used. Additionally, three independent mock and SV40 infections were conduted in MEFs. Total RNA was isolated from with the RNeasy kit. Total RNA was processed by the Genomics and Proteomics Core Laboratories at the University of Pittsburgh and hybridized to the Affymetrix GeneChip Mouse Genome 430 2.0 array. MAS 5.0 was used to obtain the present/absent calls and CEL files were normalized by RMA to obtain log2 expression values.

first: Abhilasha

middle: V

last: Rathi

first: Paul

middle: G

last: Cantalupo

first: Saumendra

last: Sarkar

first: James

middle: M

last: Pipas


title: Expression data of LPS-stimulated bone marrow macrophages induced by M-CSF from wild-type and Jmjd3-/- mice.

city: Kyoto

first: Osamu

last: Takeuchi

state: Kyoto

address: Yoshida-konoe-cho, Sakyo-ku,

department: Grad School of Medicine

country: Japan

institute: Kyoto University

summary:
Jmjd3 is critical for proper M2 macropahge inducution in response to M-CSF and showed defects in response to LPS.
We used microarrays to examine gene expression profiles in wild-type and Jmjd3-/- M-CSF-derived macrophages.

overall_design: Bone marrow macrophages induced by M-CSF from wild-type and Jmjd3-/- mice were stimulated with LPS for 4 hours, followed by RNA extraction. Then hybridization on affymetrix microarrays was performed.

first: Takashi

last: Satoh


title: The gene encoding the hematopoietic stem cell regulator CCN3 (NOV) is under direct cytokine control through the transcription factors STAT5a/b.

city: Bethesda

first: WeiPing

last: Chen

state: MD

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

department: GCL

institute: NIDDK/NIH

summary: Cytokines control the biology of hematopoietic stem and progenitor cells in part through the transcription factors STAT5a/b.  CCN3/NOV has been reported as a positive regulator of hematopoietic stem and progenitor cells.  We report microarray analyses of Lineage- Sca-1+ c-Kit+ (KSL) cells in the presence and absence of STAT5a/b.  Expression of the ccn3 gene was induced over 100-fold in control, but not STAT5a/b-null cells, upon stimulation with a cocktail containing IL-3, IL-6, SCF, TPO and Flt3 ligand.  Among the cytokines, IL-3 elevated ccn3 mRNA level in Lineage- c-Kit+ (KL) cells and 32D cells.  ChIP assays using 32D cells revealed IL-3-induced binding of STAT5a/b to a GAS site in the ccn3 gene promoter.  This is the first report to link two molecules with importance in the regulation of HSCs, CCN3 and STAT5a/b.  We report that the regulation and expression of the ccn3 gene is directly controlled by IL-3 through the transcription factors STAT5a/b.

overall_design: Six Control and Six Stat5a/b-null KSL cells, including three biological replications, were unstimulated or stimulated with a cocktail containing IL-3, IL-6, SCF, TPO and FL.

first: Akiko

last: Kimura

first: Cyril

last: Martin

first: Gertraud

middle: W

last: Robinson

last: Simone

first: Weiping

first: Mark

middle: C

last: Wickre

first: John

last: O'Shea

first: Lothar

last: Hennighausen


title: mRNA expression profile in mouse lung development

status: Public on Aug 17 2010

city: Rochester

first: Jie

last: Dong

state: MN

address: 200 1st SW

department: Thoracic Surgery

institute: Mayo Clinic

summary: We performed miRNA and mRNA profiling over a 7-point time course, encompassing all recognized stages of lung development and explore dynamically regulated miRNAs and potential miRNA-mRNA interaction networks specific to mouse lung development

overall_design: replicated time course of mouse lung development in 7 time points

first: Dennis

last: Wigle


title: Expression data of wild type and miR-155 knockout bone marrow derived dendritic cells treated with lipopolysaccharide (LPS)

status: Public on Aug 16 2010

city: Pasadena

first: Aadel

last: Chaudhuri

state: CA

address: 1200 E California Blvd

institute: Caltech

summary: We used microarrays to look at overall gene expression differences between miR-155-/- and WT dendritic cells under inflammatory conditions.

overall_design: Bone marrow from either wild type or miR-155-/- C57Bl/6 mice was differentiated into dendritic cells by incubating with GM-CSF.  These cells were then stimulated with LPS, and gene expression was performed.

first: Ryan

last: O'Connell


title: Mouse Embryonic Stem Cell E14Tg2A.4 BMP2 Responses

status: Public on Aug 15 2010

first: Qiaoran

last: Xi

address: 1275, York ave.

department: Cancer biology and genetics

institute: MSKCC

summary: Study was carried out to investigates the acute responses of mouse ES cells to BMP-2.

overall_design: E14 cells were treated with BMP-2 at 25ng/ml for 1hour or untreated for the same time. The RNA were extracted and labeled to applied for microaaray.


title: Mx-Cre mediated deletion of SRF in murine hematopoietic LSK (Lin-Sca1+c-Kit+) cells

status: Public on Aug 12 2010

city: Villejuif

first: Virginie

last: PENARD

address: 39 rue Camille Desmoulins

department: Institut Gustave Roussy

country: France

institute: INSERM U985

summary: Analysis of hematopoietic LSK(Lin-Sca1+c-Kit+) cells lacking the Serum response factor (SRF) gene. Results provide insight into the role of SRF in regulating genetic programs important for hematopoietic stem cell development

overall_design: Comparison of the gene expression profile between murine Lin-Sca1+c-Kit+ cells from Mx-Cre C57BL/6 Srf WT (3) and C57BL/6 Srf KO (3). Cells were sorted by flow cytometry and RNA was harvested and hybridized to Affymetrix MOE430A.

last: Penard-Lacronique


title: Genes differentially regulated by the glucocorticoid receptor in developing skin of the GR knock out and wt embryos.

city: Valencia

first: Paloma

last: Perez

address: Jaime Roig 11

country: Spain

institute: Instituto Biomedicina Valencia, Consejo Superior Investigaciones Científicas

summary: To understand the transcriptional program by which GR regulates skin development, we performed a microarray analysis using the skin of E18.5 GR-/- and GR+/+ mouse embryos.

overall_design: RNA from four dorsal skin samples from GR-/- and GR+/+ E18.5 mouse embryos was collected and analyzed using Affymetrix Mouse Genome 430 2.0 GeneChips.

first: Lisa

last: Sevilla

first: Pilar

last: Bayo

first: Victor

last: Latorre

first: Ana

last: Sanchis

last: Pérez


title: Expression data from sorted Treg cells from WT or motheaten mice

status: Public on Aug 13 2010

city: Charlottesville

first: David

last: Mullins

state: VA

address: 345 Crispell Dr. Rm G525

department: Microbiology

institute: University of Virginia

summary:
The importance of regulatory T cells (Treg) for immune tolerance is well recognized, yet the signaling molecules influencing their suppressive activity are relatively poorly understood. We identified the cytoplasmic tyrosine phosphatase SHP-1 as a novel ‘endogenous brake’ and modifier of the suppressive ability of Treg cells; consistent with this notion, loss of SHP-1 expression strongly augments the ability of Treg cells to suppress inflammation in a mouse model. Specific harmacological inhibition of SHP-1 enzymatic activity via the cancer drug sodium stibogluconate (SSG) potently augmented Treg cell suppressor activity both in vivo and ex vivo.
We evaluated the gene expression profiles of sorted T reg cells (CD4+CD25+) from wild type (wt) mice and mice that were heterozygous (he) or homozygous (me) for SHP-1 knockout (motheaten phenotype).

overall_design: T reg (CD4+CD25+) cells were isolated form wild type (WT) mice and that were heterozygous (he) or homozygous (me) for SHP-1 knockout (motheaten phenotype); totalRNA was isolated using Arcturus reagents; aRNA was generated and amplified using Arcturus reagents; and labeled product was hybridized to Affymetrix chips to asses gene expression patterns.

first: Ulrike

last: Lorenz


title: HOP homeobox (Hopx) and Histone deacetylase-2 (Hdac2) deficiency effect on the embryonic heart

status: Public on Aug 19 2010

city: Philadelphia

first: Jonathan

last: Epstein

state: PA

address: 421, Curie Blvd

department: Cell and Developmental Biology

institute: University of Pennsylvania, School of Medicine

summary:
Analysis of heart ventricles from Hopx, Hdac2, and both Hopx-Hdac2 deficient embryos at embryonic day E16.5. Results provide insight into the role of Hopx and Hdac2 in cardiac development.
We used microarrays to detail the global programme of gene expression underlying cardiogenesis by Hopx and Hdac2 and identified distinct classes of up-regulated and down-regulated genes during this process.

overall_design: Mouse embryonic ventricles were selected at E16.5 for RNA extraction and hybridization on Affymetrix microarrays. We obtained three independent embryonic ventricles for WT, Hopx-null, Hdac2-null, and Hopx-Hdac2 double null genotypes.

first: Chinmay

last: Trivedi

first: Qiaohong

last: Wang


title: Gene expression profile of murine bone marrow endosteal populations

status: Public on Aug 10 2010

city: Tokyo

first: Fumio

last: Arai

address: 35 Shinano-machi, Shinjuku-ku

institute: School of Medicine, Keio University

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

overall_design: Refer to individual Series


city: Lincoln

first: Jean-Jack

middle: M.

last: Riethoven

state: NE

address: 1901 Vine Street

department: Beadle Center for Biotechnology

institute: University of Nebraska-Lincoln

summary:
Activated AMPK and prostaglandins are involved in the response to conjugated linoleic acid and are sufficient to cause lipid reductions in adipocytes.
Trans-10, cis-12 conjugated linoleic acid (t10c12 CLA) reduces triglyceride levels in adipocytes. AMP-activated protein kinase (AMPK) was recently demonstrated to be involved in the emerging pathways regulating this response. This study investigated the role of AMPK and inflammation in lowering triglyceride levels by testing the following hypotheses: 1) A moderate activator of AMPK, such as metformin, and an inflammatory response are sufficient to reduce triglycerides, and 2) Strong activation of AMPK is also sufficient. These experiments were performed by adding compounds that affect these pathways and measuring their effects in 3T3-L1 adipocytes. Tumor necrosis factor α (TNF-α), an inflammatory cytokine, increased the ability of metformin to reduce triglycerides, but TNF-α was observed to activate AMPK. A comparison of metformin, phenformin, TNF-α, and t10c12 CLA found a correlation between AMPK activity level and triglyceride reduction. Inhibitors of the prostaglandin (PG) biosynthetic pathway interfered with t10c12 CLA's ability to reduce triglycerides. Inhibitors of MAPK/ERK kinase or Jun N-terminal kinase interfered with the phosphorylation of phospholipase A2 and triglyceride reductions.

Keywords: control/treatment

overall_design:
Mouse 3T3-L1 RNA was isolated from control (LA) and treatment (CLA, phenformin) samples for analysis on microarrays with three biological replicates per sample.

Limma data are available in the Supplementary files 'GSE17404_limma_CLAvsLA.txt', 'GSE17404_limma_PFMvsLA.txt', and 'GSE17404_limma_PFMvsCLA.txt'.

first: Shan

last: Jiang

first: Han

last: Chen

first: Zhigang

first: Yuannan

last: Xia

first: Jess

last: Miner

first: Michael

last: Fromm


title: Exon Array Analysis of Asthmatic Chronic Rhinosinusitis with Nasal Polyps

first: Douglas

last: Plager

address: 200 First Street SW

department: Dermatology

institute: Mayo Clinic Rochester

summary: Asthmatic chronic rhinosinusitis with nasal polyps (aCRSwNP) is a common disruptive eosinophilic disease.  Therefore, we sought to identify gene expression changes in nasosinus inflamed mucosa and adjacent polyp tissue from subjects with aCRSwNP.

overall_design: Twelve asthmatic chronic rhinosinusitis (aCRS) subjects (11 with nasal polyps; aCRSwNP) provided inflamed nasosinus mucosa (11 samples) and adjacent polyp (10 samples) or a small mixed mucosa and polyp specimen (1 sample) (thus, 22 samples overall).  Inflamed mucosa or polyp was from the middle meatus or anterior ethmoid cavity.  As control samples, nasosinus tissue was collected from the inferior turbinate or uncinate process from normal or rhinitis subjects without nasal polyps (n=17); 4 had physician-diagnosed allergic rhinitis (AR), 2 had suspected AR, 1 had suspected vasomotor rhinitis, and 10 had no signs of nasosinus disease, allergy, or atopy.  All 4 AR subjects chose to donate tissue outside of their known allergy season(s).

first: Hirohito

last: Kita


title: Global changes of expression patterns of vaccinia virus infected lungs of C57BL/6 mice.

city: Gainesville

first: Amanda

middle: Dawn

last: Rice

email: amandad.rice@gmail.com, amandar@ufl.edu

state: FL

address: 1600 SW Archer Rd

institute: University of Florida

summary:
Vaccinia virus infection of mouse lungs produces a focal infection within the lung remaining at the large bronchi throughout the course of infection. Animals die of respiratory failure with little edema and few infiltrating immune cells. It is well established that poxviruses control the host immune system by encoding multiple host defense pathway antagonists.
The goal of this study was to examine the local response to infection within the lung given that the virus controls the host immune response.

overall_design: The global changes exhibited over the course of a lung infection with vaccinia virus were analyzed by arrays of lungs harvested from 1 to 5 day post infection using Affymetrix Mouse 430A 2.0 arrays.

first: Richard

last: Moyer

middle: D


title: Expression data from mouse aorta during and following transient hyperglycaemia

status: Public on Aug 09 2010

city: Coventry

first: Yi-Fang

address: Gibbet Hill Road

department: Biological Sciences

country: United Kingdom

institute: Warwick University

summary: Immediate and early effects of transient hyperglycaemia were examined using fully- reversible transgenic diabetic mice. Transient hyperglycaemia altered expression of 769 arterial genes, of which 200 did not reverse following  recovery from hyperglycaemia. Many such genes are known to promote atherogenesis, including several implicated in arterial calcification and inflammation. This supports the view that hyperglycaemia causes not only very early deleterious changes in arterial gene expression but that to a large extent these persist for some time after restoration of normal blood glucose levels in vivo. Together, results support the contention that avoiding excess CVD risk in diabetes requires very early correction of hyperglycaemia.

overall_design: As shown previously (Pelengaris et al., 2002 Cell), c-MycERTAM protein is activated in pancreatic beta cells of adult transgenic mice, by daily intraperitoneal (IP) administration of tamoxifen (TAM; Sigma-Aldrich, Dorset, UK) (1 mg/0.2 ml in peanut oil). Inactivation of c-MycERTAM protein was achieved through withdrawal of TAM. Adult female mice, 3-6 months of age, inbred into CBA-C57Bl/6 background and maintained under barrier conditions, were treated with TAM for up to 7 days (Myc ‘ON’) and then monitored during recovery for more than 4 months (140 days) (Myc ‘OFF’). Experimental timepoints were: Days 2, 4 and 7: c-Myc ‘ON’; days 0, 11, 26: c-Myc ‘OFF’. Biological replicates: each timepoint included 3 biological replicates (n=3 mice).

first: S

last: Zervou

first: Y

middle: F

last: Abouna

first: D

last: Pelengaris

first: M

last: Khan


title: A large intergenic non-coding RNA induced by p53 mediates global gene repression in the p53 transcriptional response

city: Cambridge

first: Mitchell

last: Guttman

state: MA

address: 7 Cambridge Center

institute: Broad Institute

summary: Recently, more than a thousand large intergenic non-coding RNAs (lincRNAs) have been reported.  These RNAs are evolutionarily conserved in mammalian genomes and thus presumably function in diverse biological processes. Here, we report the identification of lincRNAs that are regulated by p53. One of these lincRNAs (lincRNA-p21) serves as a repressor in p53-dependent transcriptional responses.  Inhibition of lincRNA-p21 affects the expression of hundreds of gene targets enriched for genes normally repressed by p53. The observed transcriptional repression by lincRNA-p21 is mediated through the physical association with hnRNP-K. This interaction is required for proper genomic localization of hnRNP-K at repressed genes and regulation of p53 mediated apoptosis. We propose a model whereby transcription factors activate lincRNAs that serve as key repressors by physically associating with repressive complexes and modulating their localization to sets of previously active genes.

overall_design:
Gene expression profiles of different p53 inducible mouse embryonic fibroblasts (p53LSL/LSL MEFs) across different time points after DNA damage.
A large intergenic noncoding RNA induced by p53 mediates global gene repression in the p53 transcriptional response.

[1] MEF profiling: p53 LSL/LSL MEFs were treated with adenoCRE for p53 restoration or adenoGFP as control for 24h and treated with 500nM doxorubicin for the indicated times.
[2] hnRNPKKD profiling: p53 LSL/LSL MEFs were treated with adenoCRE for p53 restoration for 24h, transfected with siRNA oligos targeting different transcripts for 24h and then treated with 100nM doxorubicin for 13h.
[3] lincP21KD profiling: p53 LSL/LSL MEFs were treated with adenoCRE for p53 restoration for 24h, transfected with siRNA oligos targeting different transcripts for 24h and then treated with 100nM doxorubicin for 13h.
[4] RAS profiling: For p53 restoration, cultured tumor cell lines were incubated with 500nM 4-hydroxytamoxifen for the indicated times.

first: Maite

last: Huarte

first: John

last: Rinn


title: Gene regulation in the hyperoxia mouse retina

status: Public on Aug 06 2010

city: Acton

first: Riccardo

last: Natoli

state: ACT

address: Sullivans Creek Road

department: CMBE

institute: ANU

summary: PURPOSE: Hyperoxia is toxic to photoreceptors, and this toxicity may be important in the progress of retinal dystrophies. This microarray study examines gene expression induced in the C57BL/6J mouse retina by hyperoxia over the 14-day period during which photoreceptors first resist, then succumb to, hyperoxia.   METHODS: Young adult C57BL/6J mice were exposed to hyperoxia (75% oxygen) for up to 14 days. On day 0 (control), day 3, day 7, and day 14, retinal RNA was extracted and processed on Affymetrix GeneChip Mouse Genome 430 2.0 arrays. Microarray data were analyzed using GCOS Version 1.4 and GeneSpring Version 7.3.1.   RESULTS: The overall numbers of hyperoxia-regulated genes increased monotonically with exposure. Within that increase, however, a distinctive temporal pattern was apparent. At 3 days exposure, there was prominent upregulation of genes associated with neuroprotection. By day 14, these early-responsive genes were downregulated, and genes related to cell death were strongly expressed. At day 7, the regulation of these genes was mixed, indicating a possible transition period from stability at day 3 to degeneration at day 14.   CONCLUSIONS: Microarray analysis of the response of the retina to prolonged hyperoxia demonstrated a temporal pattern involving early neuroprotection and later cell death, and provided insight into the mechanisms involved in the two phases of response. As hyperoxia is a consistent feature of the late stages of photoreceptor degenerations, understanding the mechanisms of oxygen toxicity may be important therapeutically.

overall_design: 4 timepoints in total, 0d (control), 3d, 7d and 14d and a replicate per timepoint. Total of 8 chips.

first: Provis

last: Jan

first: Krisztina

last: Valter

first: Jonathan

last: Stone


title: Murine M7 leukemia derived from retroviral insertional mutagenesis of Gata1s fetal progenitors depends on IGF signaling

status: Public on Aug 01 2010

city: Boston

first: Zhe

last: Li

department: Division of Hematology/Oncology

institute: Children's Hospital Boston

summary:
The goal of this study is to derive a mouse model of human Down Syndrome (DS) megakaryocytic leukemia involving mutations in the hematopoietic transcription factor, GATA1 (called GATA1s mutation). We achieved this through transduction of Gata1s mutant fetal progenitors by MSCV-based retrovirus expressing a GFP marker, followed by in vitro selection (for immortalized cell lines), and then in vivo selection (for transformed cell lines) through transplantation.
Here we report one such cell line [T6(6)] that gives rise to megakaryocytic leukemia (M7 leukemia) upon transplantation. We show knockdown of IGF1R in these cells leads to their reduced proliferation.

overall_design: IGF1R was knocked down in these cells using a tet-regulatable shRNA-based lentiviral system. Cells infected with the empty vector or those infected with shRNA construct against IGF1R but in the absence of Doxycycline were used as controls. The latter cells in the presence of Doxycycline exhibited reduced IGF1R at the RNA level.

first: Stuart

last: Orkin


title: RNA expression data from glomeruli lacking von Hippel-Lindau protein in podocytes

status: Public on Aug 03 2010

city: Kansas City

first: Brooke

last: Steenhard

state: KS

address: 3901 Rainbow Blvd

department: Anatomy and Cell Biology

institute: Univ of KS Medical Center

summary:
We and others have previously shown that glomerular endothelial cells and podocytes express hypoxia-inducible transcription factors (HIFs).  HIFs bind to hypoxia response elements in target genes, such as vascular endothelial growth factor, which is continually produced by podocytes throughout life.  To further assess function of HIFs in podocyte biology, podocin-Cre mice were mated with floxed von Hippel-Lindau (VHL) mice to selectively delete VHL, a component of an E3 ligase complex responsible for degradation of HIFs in normoxia.
We reasoned that cells lacking VHL would overexpress stable HIFs and upregulate hypoxia-responsive genes.  Progeny from these crosses displayed two phenotypes, non-proteinuric with glomerular basement membrane (GBM) defects and proteinuric with GBM defects and end-stage renal failure at ~6 months of age.  Gene changes associated with the mild, non-proteinuric phenotype were studied using isolated glomeruli from wildtype and Pod-Cre fVHL mice.

overall_design: At 4 weeks of age, urine was collected and urinary albumin was quantified by Albuwell elisa from Pod-Cre fVHL litters. At 6 weeks of age, glomeruli from 3 wildtype littermate controls and 3 non-proteinuric Pod-Cre fVHL mice were collected using the magnetic bead method.  RNA was extracted and hybridized to Affymetrix microarrays.

first: Dale

middle: R

last: Abrahamson


title: Rescue of murine Gata1s mutant M7 leukemic cells by full-length Gata1

summary:
In this project, we studied a mouse model of human Down Syndrome (DS) megakaryocytic leukemia involving mutations in the GATA1 transcription factor (called GATA1s mutation). The model was generated through retroviral insertional mutagenesis in Gata1s mutant fetal liver progenitors. In this study, we analyzed the dependency of these leukemic cells on the Gata1s mutant protein.
Here we report Gata1s mutant leukemic cells were dependent on this mutant protein. Introduction of the full-length Gata1 protein to these cells led to their reduced proliferation and increased differentiation along the megakaryocytic lineage.

overall_design: We transduced leukemic cells with Gata1/estrogen receptor fusion cDNA (Gata1-ER) and generated stable cell lines. Addition of beta-estradiol to culture medium led to activation of the full-length Gata1 protein in synchronized leukemic cells. Gene expression profiles were collected at multiple time points.


title: Analysis of mir-223 knockout cultured neutrophils versus wild-type cultured neutrophils, by microarray profiling

city: Singapore

first: Huili

last: Guo

address: 28 Medical Drive

country: Singapore

institute: National University of Singapore

summary: MicroRNAs (miRNAs) are endogenous ~22-nucleotide RNAs that mediate important gene-regulatory events by pairing to the mRNAs of protein-coding genes to direct their repression. Repression of these regulatory targets leads to decreased translational efficiency and/or decreased mRNA levels, but the relative contributions of these two outcomes have been largely unknown, particularly for endogenous targets expressed at low-to-moderate levels. Here, we use ribosome profiling to measure the overall effects on protein production and compare these to simultaneously measured effects on mRNA levels. For both ectopic and endogenous miRNA regulatory interactions, lowered mRNA levels account for most (≥84%) of the decreased protein production. These results show that changes in mRNA levels closely reflect the impact of miRNAs on gene expression and indicate that destabilization of target mRNAs is the predominant reason for reduced protein output.

overall_design: Examine mRNA expression levels in mir-223 knockout cultured neutrophils, versus wild-type cultured neutrophils.

first: H

first: N

middle: T

last: Ingolia

first: J

middle: S

last: Weissman

last: Bartel


title: Murine M7 leukemia derived from retroviral insertional mutagenesis of Gata1s fetal progenitors

summary:
The goal of this study is to derive a mouse model of human Down Syndrome (DS) megakaryocytic leukemia involving mutations in the hematopoietic transcription factor, GATA1 (called GATA1s mutation). We achieved this through transduction of Gata1s mutant fetal progenitors by MSCV-based retrovirus expressing a GFP marker, followed by in vitro selection (for immortalized cell lines), and then in vivo selection (for transformed cell lines) through transplantation.
Here we report one such cell line [T6(6)] that gives rise to megakaryocytic leukemia (M7 leukemia) upon transplantation.

overall_design: Since the leukemic cells were retrovirally tagged with a GFP reporter, we sorted GFP+ leukemic blasts and generated their expression profiles by microarray.


title: A comprehensive methylome map of lineage commitment from hematopoietic progenitors

city: Stanford

first: Jun

last: Seita

address: Lokey Stem Cell Building #G3101, 265 Campus Drive

department: Institute for Stem Cell Biology and Regenerative Medicine

institute: Stanford University

summary: Epigenetic modifications must underlie lineage-specific differentiation since terminally differentiated cells express tissue-specific genes, but their DNA sequence is unchanged. Hematopoiesis provides a well-defined model of progressive differentiation in which to study the role of epigenetic modifications in cell fate decisions. Multi-potent progenitors (MPPs) can differentiate into all blood cell lineages, while downstream progenitors commit to either myeloerythroid or lymphoid lineages. While DNA methylation is critical for myeloid versus lymphoid differentiation, as demonstrated by the myeloerythroid bias in Dnmt1 hypomorphs {Broske, 2009 #6}, a comprehensive DNA methylation map of hematopoietic progenitors, or of any cell lineage, does not exist. Here we have generated a mouse DNA methylation map, examining 4.6 million CpG sites throughout the genome including all CpG islands and shores, examining MPPs, all lymphoid progenitors (ALPs), common myeloid progenitors (CMPs), granulocyte/macrophage progenitors (GMPs), and thymocyte progenitors (DN1, DN2, DN3). Interestingly, differentiation towards the myeloid lineage corresponds with a net decrease in DNA methylation, while lymphoid commitment involves a net increase in DNA methylation, but both show substantial dynamic changes consistent with epigenetic plasticity during development. By comparing lineage-specific DNA methylation to gene expression array data, we find many examples of genes and pathways not previously known to be involved in lymphoid/myeloid differentiation, such as Gcnt2, Arl4c, Gadd45α, and Jdp2. Several transcription factors, including Meis1 and Prdm16 were methylated and silenced during differentiation, suggesting a role in maintaining an undifferentiated state. Additionally, epigenetic modification of modifiers of the epigenome appears to be important in hematopoietic differentiation. Our results directly demonstrate that modulation of DNA methylation occurs during lineage-specific differentiation, often correlating with gene expression changes, and define a comprehensive map of the methylation and transcriptional changes that accompany myeloid versus lymphoid fate decisions.

overall_design: mRNA expression of 8 hematopoietic progenitor populations [MPPFL-(5), MPPFL+(3), CMP(3), GMP(3), CLP(3), DN1(3), DN2(3), DN3(3)] were compared

first: Hong

last: Ji

first: Lauren

last: Ehrlich

first: Peter

last: Murakami

first: Akiko

last: Doi

first: Paul

last: Lindau

first: Hwajin

last: Lee

first: Martin

last: Aryee

first: Rafael

last: Irizarry

first: Kitai

last: Kim

first: Derrick

last: Rossi

first: Matthew

last: Inlay

first: Thomas

last: Serwold

first: Holger

last: Karsunky

first: Lena

last: Ho

first: George

middle: Q

last: Daley

first: Irving

middle: L

first: Andrew

last: Feinberg


title: Genome-wide analysis of adipose tissue gene expression in twin-pairs discordant for physical activity for over 30 years

status: Public on Jul 31 2010

city: Jyväskylä

first: Heikki

last: Kainulainen

address: Seminaarinmäki

department: Department of Biology of Physical Activity

country: Finland

institute: University of Jyväskylä

summary: The high physical activity/high aerobic fitness phenotype predicts low morbidity and mortality more strongly than any other known biological risk factor. Inherited and/or acquired properties of skeletal muscle seem to be linked with aerobic fitness and other cardio-metabolic risk factors. However, physical activity-induced changes in muscle and fat tissue-related complex molecular networks and their links with cardio-metabolic disease risk are not comprehensively understood. In the present study, we show that among the physically active members of twin pairs, as compared to their inactive co-twins, gene expression in musculus vastus lateralis tissue samples is chronically up-regulated for the central pathways or genes related to energy metabolism, including oxidative phosphorylation, lipid metabolism and supportive metabolic pathways. In addition to aerobic fitness, upregulation of these pathways is associated in particular with high HDL cholesterol levels. In fat tissue we found physical activity-induced increases in the expression of polyunsaturated fatty acid metabolism and in branched chain amino acid degradation genes, increases which were associated with decreased ‘high-risk’ ectopic body fat and low glucose levels. Consistent with other findings, plasma lipidomics analyses showed up-regulation of the triacylglycerols containing the polyunsaturated fatty acids. The findings indicate the main pathways in skeletal muscle and fat tissue that mediate the chronic effects of physical activity on reduced cardio-metabolic disease risk, including the increase in aerobic fitness. Up-regulation of oxidative energy metabolism seems to be a common underlying mechanism.

overall_design:
Total RNA obtained from the biopsy samples of adipose tissue from two mono- and four dizygotic twin pairs that had been followed for their discordance for physical activity for 32 years.

The supplementary file 'GSE20536_non-normalized.txt' contains non-normalized data for Samples GSM516113-GSM516124.

first: Urho

last: Kujala

first: Tuija

last: Leskinen


title: Effect of Mineralocorticoid Receptor deletion on glucocorticoid signalling in the macropahge

status: Public on Jul 30 2010

city: ann arbor

first: mort

last: lab

state: MI

address: 1150 W Med Ctr Dr

department: Physiology

institute: University of Michigan

summary:
Inappropriate excess of the steroid hormone aldosterone, which is a mineralocorticoid receptor (MR) agonist, is associated with increased inflammation and risk of cardiovascular disease. MR antagonists are cardioprotective and antiinflammatory in vivo, and evidence suggests that they mediate these effects in part by aldosterone- independent mechanisms.
We used affymetrix to characterize the effect of Mineralocorticoid Receptor deletion on macrophage transcriptional profile, and identify its requirement in normal glucocorticoid signalling.

overall_design: We isolated mouse peritoneal macrophages from Myeloid MRKO mice and Floxed Controls, cultured in the presence or absence of corticosterone. RNA was extracted for Affymetrix cDNA hybridization. Each sample was pooled from experiments performed in triplicate.

first: Michael

last: Usher

first: Sheng

middle: Z

last: Duan

first: Christine

last: Ivaschenko

first: Ryan

last: Frieler

first: Stefan

last: Berger

first: Gunther

last: Schutz

first: Carey

last: Lumeng

first: Richard

last: Mortensen


title: Array profiling of dystrophin-deficient mice with a secondary glycosylation defect

city: Columbus

first: Paul

last: Martin

state: OH

address: 700 Children's Drive

institute: Columbus Children's Research Institute

summary: A deletion in the CMAH gene in humans occurred approximately 3.5 million years ago. This resulted in the inactivation of the CMP-Neu5Ac hydroxylase enzyme, and hence, in the specific deficiency in N-glycolylneuraminic acid (Neu5Gc), a form of sialic acid, in all modern humans. Although there is evidence that this molecular milestone in the origin of humans may have led to the evolution of human-specific pathogens, how deficiency in Neu5Gc might alter progression of non-infectious human diseases remains unanswered.  Here, we have investigated cardiac and skeletal muscle gene expression changes in mdx mice, a model of Duchenne muscular dystrophy (DMD), that do or do not carry the human-like inactivating mutation in the mouse Cmah gene.  We have evidence that Neu5Gc-deficiency in humans might explain some of the discrepancies in the disease phenotype between mdx mice and DMD patients.

overall_design: The study had four groups of mice: 1) Wild type, 2) Cmah KO (mice carrying a human-like mutation in the Cmah gene and hence have human-like deficiency in Neu5Gc sialic acid), 3) mdx (mouse model for Duchenne Muscular Dystrophy), and 4) mdx mice deficient in Cmah. Gene expression was studied in heart and gastrocnemius muscle samples. Three replicates per group/tissue.

first: K

last: Chandrasekharan

first: P


title: Gene expression profiling of mouse splenic Dendritic cells subsets

status: Public on Jul 28 2010

city: REHOVOT

first: Steffen

last: Jung

address: Herzl

department: Immunology and Regenerative Biology

country: Israel

institute: The Weizmann Institute of Science

summary: We describe a novel subset of CD8+ DCs in lymphoid organs of naïve mice characterized by expression of the CX3CR1 chemokine receptor. CX3CR1+CD8+ DCs lack hallmarks of classical CD8+ DCs, including IL12 secretion, the capacity to cross-present antigen and their developmental independence of the transcriptional factor BatF3. Gene expression profiling showed that CX3CR1+CD8+ DCs resemble CD8- cDCs. The microarray analysis further revealed a unique plasmacytoid DC (PDC) gene signature of CX3CR1+ CD8+ DCs. A PDC relationship of the cells is further supported by the fact that they harbor characteristic D-J immunoglobulin gene rearrangements and that development of CX3CR1+CD8+ DCs requires E2-2, the critical transcriptional regulator of PDCs. Thus, CX3CR1+ CD8+ DCs represent a unique DC subset, related to but distinct from PDCs.

overall_design: After collagenase D digestion, spleens from Cx3cr1gfp/+ C57BL/6 mice were enriched for CD11c+ cells by magnetic separation according to the manufacturer’s protocol (MiltenyiBiotec GmbH). Splenic CD11chi cells were isolated using the FACS ARIA high-speed sorter (Becton-Dickinson). Total RNA was extracted and subjected to gene expression profiling using the Mouse Genome 430.2 Affymetrix GeneChip

first: Liat

last: Bar-On

first: Tal

last: Birnberg

first: Kanako

last: Lewis

first: Dunja

last: Bruder

first: Jan

last: Buer

first: Kenneth

last: Murphy

first: Boris

last: Reizis


title: Expression data analysis in lungs from mice induced for pulmonary arterial hypertension (PAH) by inhalation of Stachybotrys chartarum spores

status: Public on Jul 29 2010

first: kayoko

last: shimodaira

address: 6-11-1 Omorinishi, Ota-ku

institute: Toho University School of Medicine

summary:
It has been reported that repeated intra-tracheal instillation of S. chartarum spores induced significant pulmonary arterial remodeling in mice, which resulted in pathological changes like human pulmonary arterial hypertension (PAH) and elevation right ventricle systolic pressure.
Then, we used microarrays to know the complex molecular mechanisms that underlie pathogenesis of PAH.

overall_design: Isolates of Stachybotrys chartarum were used. Ddy mice were anesthetized and the spore suspension was intratracheally injected 12 times, i.e. 1×104 spores into each mouse at 4-5 day intervals for 8 weeks. Mice were sacrificed one week after the final injection and then examined. Lung tissue specimens from mice model of PAH (n=3) and normal controls (n=3) were obtained. RNA targets preparation were performed according to the manufacturer's protocol using GeneChip(R) 3' IVT Express Kit (Affymetrix). One hundred nanograms of total RNA was converted into double-stranded cDNA template for transcription. In vitro transcription synthesized amplified RNA (aRNA) and incorporated a biotin-conjugated nucleotide. After purification and fragmentation of aRNA, 12.5 ug of them was hybridized to GeneChip(R) Mouse Genome 430 2.0 Array (Affymetrix).The Probe Array was scanned using a GeneChip(R) Scanner 3000 7G.

first: Kayoko

last: Shimodaira

first: Yoichiro

last: Okubo

first: Minoru

last: Shinozaki

first: Eri

last: Ochiai

first: Katuhiko

last: Kamei

first: Kazutoshi

last: Shibuya


title: Gene expression profile of murine bone marrow endosteal populations (2)

first: Fumio

last: Arai

summary: A subset of osteoblasts functions as a key component of the hematopoietic stem cell niche. But it is still unclear that the precise cellular and molecular contribution of endosteal cell populations on the HSC supportive microenvironment. We purified the endosteal cells and subdivided them into mesenchymal progenitor cells (MPCs: PDGF-Ra(+)Sca-1(+)) and two osteoblast populations (PDGF-Ra(-)Sca-1(-) and PDGF-Ra(+)Sca-1(-)). In this study, to clarify the characteristics of these fractionated cells in detail, gene expression analysis were performed using the GeneChip Mouse Genome Array 430 2.0 (Affymetrix).

overall_design: The bone fragments of femur and tibiae were treated with collagenase and endosteal cells were obtained. For enrichment of non-hematopoietic and non-endothelial population, CD45(-)CD31(-)Ter119(-) population was isolated and then the expressions of Sca-1 and PDGF-Ra was analyzed by FACS. FACS analysis showed that CD45(-)CD31(-)Ter119(-) cells were subdivided into PDGF-Ra(+)Sca-1(+), PDGF-Ra(-)Sca-1(-) and PDGF-Ra(+)Sca-1(-). These three populations were sorted and RNA samples were used for amplification, labeling, and hybridization to independent arrays.

first: Yuka

last: Nakamura

first: Isao

last: Kobayashi

first: Toshio

last: Suda


title: Gene expression profile of murine bone marrow endosteal populations (1)

summary: A subset of osteoblasts functions as a key component of the hematopoietic stem cell niche. But it is still unclear that the precise cellular and molecular contribution of endosteal cell populations on the HSC supportive microenvironment. We purified the endosteal cells and subdivided them into mesenchymal progenitor cells (MPCs: ALCAM(-)Sca-1(+)) and two osteoblast populations (ALCAM(-)Sca-1(-) and ALCAM(+)Sca-1(-)). In this study, to clarify the characteristics of these fractionated cells in detail, gene expression analysis were performed using the GeneChip Mouse Genome Array 430 2.0 (Affymetrix).

overall_design: The bone fragments of femur and tibiae were treated with collagenase and endosteal cells were obtained. For enrichment of non-hematopoietic and non-endothelial population, CD45(-)CD31(-)Ter119(-) population was isolated and then the expressions of Sca-1 and activated leukocyte cell adhesion molecule (ALCAM) was analyzed by FACS. FACS analysis showed that CD45(-)CD31(-)Ter119(-) cells were subdivided into ALCAM(-)Sca-1(+), ALCAM(-)Sca-1(-) and ALCAM(+)Sca-1(-). These three populations were sorted and RNA samples were used for amplification, labeling, and hybridization to independent arrays.


title: Lmnadelta9 mouse gene expression study

city: Bethesda

first: Lidia

last: Hernandez

address: 10 Center Drive

department: CCR/MOB

institute: National Cancer Institute

summary:
Lmnadelta9 mice derived in the C57bl6X129S3/J background have been identified as exhibiting a progeric phenotype. Using this mouse model we show that a truncated variant of Lamin A (Lmna∆9) causes the proliferative arrest of post-natal  fibroblasts. Arrest is due to the cells inability to produce a functional extracellular matrix (ECM).
We used microarrays to compare gene expression of adult primary fibroblasts from wildtype and Lmnadelta9 mice in order to understand whether the Lmnadelta9 adult MEF defective proliferation is due to alterations of specific signaling associated with ECM functions.

overall_design: Three independent replicate samples of sibling-derived wild-type and Lmna∆9 post-natal fibroblast lines at passage 3 were serum-starved for 72 hours and used as the source of mRNA for microarray analysis. RNA was extracted with Trizol, and hybridized to Affymetrix microarrays.

first: Colin

last: Stewart


title: Plag1 overexpression cooperates with Evi1 overexpression and Gata1s mutation in leading to M7 leukemia

first: Zhe

last: Li

summary:
The goal of this study is to develop a Plag1 signature and determine how its overexpression contributes to  leukemogenesis.
To study this, we transduced an immortalized (but not transformed) cell line (derived from Gata1s mutant fetal liver progenitor through insertional mutagenesis) by Plag1-expressing retrovirus. This turned a non-transformed cell line to a leukemogenic cell line. To study whether Plag1 overexpression led to deregulation of signaling pathways that may contribute to leukemic transformation, we generated microarray gene expression profiles of this cell line transduced with either Plag1 or the empty vector.

overall_design: We generated gene expression profiles by microarray from stable cell lines transduced with either the empty vector or the Plag1-expressing vector.

first: Stuart

last: Orkin


title: Gene expression profiling of neural stem cells derived from iPS cells (iPSc) of Sanfilippo syndrome type B (MPSIIIB)  patient versus control

status: Public on Jul 24 2010

city: Paris

first: Pierre

last: de la Grange

address: 29, rue du Faubourg Saint-Jacques

department: Paris Biotech Santé

institute: GenoSplice technology

summary:
We generated iPSc from skin fibroblasts of two MPSIIIB patients (P1 and P2). MPSIIIB-associated cell defects were prominent in undifferentiated iPSc, in neural stem cells and in their neuronal progeny.
We explored alterations of metabolic pathways in MPSIIIB neural cells by performing gene expression profiling of patient versus control neural stem cells. Exon array transcriptome analysis showed 295 transcripts with increased expression level and 1275 transcripts with decreased expression level in patient versus control neural precursors.

overall_design: Total RNA was extracted from proliferating neurosphere cultures derived from two control (C1 and C3) and three patient (P1.1, P1.3, and P2.3) iPSc clones. We considered a minimal fold change of 1.5 fold and a corrected P value lower than 0.05.

first: D

last: Bohl

first: T

last: Lemonnier

first: S

last: Blanchard

first: J

last: Heard


title: Effect of vitamin A deficiency (VAD) on mouse spermatogonial transcriptome profiles

first: TIN-LAP

last: LEE

address: 2C08 Building 49

department: NICHD

institute: National Institutes of Health

summary:
The objective of this study was to understand the genetic mechanisms of Vitamin-A-Deficiency (VAD)-induced arrest of spermatogonial stem-cell differentiation. Vitamin A and its derivatives (the retinoids) participate in many physiological processes including vision, cellular differentiation and reproduction. VAD affects spermatogenesis, the subject of our present study. Spermatogenesis is a highly regulated process of differentiation and complex morphologic alterations that, in the postnatal testis, leads to the formation of sperm in the seminiferous epithelium. VAD causes early cessation of spermatogenesis, characterized by degeneration of meiotic germ cells, leading to seminiferous tubules containing mostly type A spermatogonia and Sertoli cells. In this study, we investigated the molecular basis of VAD on spermatogenesis in mice. We used adult Balb/C mice fed with a Control or VAD diet for an extended period of time (8-28 weeks) and selected two time points (18 and 25 weeks) for microarray analysis.

To understand the effect of VAD on the spermatogonial stem cell transcriptome, we studied isolated pure populations of spermatogonia from control and vitamin-A-deficient mice from two representative time points (18 and 25 weeks) using Affymetrix GeneChip microarrays. We identified target genes involved in the arrest of spermatogonial differentiation and spermatogenesis. Our results establish a better understanding of the chronology and magnitude of the consequences of VAD on mouse testes and add to the current knowledge of the molecular regulatory mechanisms of germ cell development.

overall_design: Spermatogonia were isolated by the STATPUT procedure with minor modifications. VAD mice were sacrificed at 18 and 25 weeks of VAD treatment for spermatogonia isolation. Decapsulated testes from 2 mice were suspended in RPMI medium containing collagenase (0.6 mg/ml), Hyaluronidase (0.12 mg/ml) and DNAse I (1.25 mg/ml) and incubated at 37ºC for 30 minutes in a shaking water bath. The tissues were then allowed to come down the tube and the supernatant (containing interstitial cells) was removed. The pellet was incubated with 3 ml of 0.25% Trypsin /EDTA (GIBCO, Invitrogen, USA), in the presence of DNAse I (0.2 mg/ml) at 37ºC for 15 minutes in a shaking water bath. The dispersed cells were washed twice with RPMI medium containing 10% heat inactivated FBS to neutralize the protease activity, and filtered through a sterile 0.22 nylon to remove any undigested fragments. Cells of the dissociated seminiferous epithelium were then plated overnight in a 34ºC 3% CO2 incubator. The following day, germ cells, in suspension, were separated by sedimentation with use of a 2-4% BSA gradient. The cells were allowed to sediment for a standard period of 2.5 h, and fractions of 2-ml volume were collected. The cells of each fraction were examined under a phase contrast microscope, and fractions containing cells of similar size and morphology were pooled and spun down by low-speed centrifugation. Purity of spermatogonia was estimated and was routinely higher than 90%. Total RNA was extracted from the isolated germ cells using TRIzol ® Reagent, and cleaned with RNeasy minicolumns. RNA content was determined by measurement of optical density at 260 nm. Only the RNA samples showing an OD 260/280 ratio higher than 1.8 were used for microarray hybridization. Raw expression values in Affymetrix CEL file format were generated by GeneChip Operating Software.

first: Tin-Lap

last: Lee


title: Cell cyclin kinase inhibitor Cdkn2c regulates B cell homeostasis and function in the NZM2410-derived murine lupus susceptibility locus Sle2c1

city: Oklahoma City

first: Igor

last: Dozmorov

state: OK

address: 825 NE 13th Street

department: Arthritis & Immunology

institute: OMRF

summary: Sle2c1 is an NZM2410-derived lupus susceptibility locus that induces an expansion of the B1a cell compartment. B1a cells have a repertoire enriched for autoreactivity, and an expansion of this B cell subset occurs in several mouse models of lupus. Here we showed that expression of Sle2c1 enhances NZB cellular phenotypes that have been associated with autoimmune pathogenesis. A combination of genetic mapping and candidate gene analysis presents Cdkn2c, a gene encoding for cyclin kinase inhibitor p18INK4c (p18), as the top candidate gene for inducing the Slec2c1 associated expansion of B1a cells.  A novel SNP in the Cdkn2c promoter is associated with a significantly reduced Cdkn2c expression in the splenic B cells and B1a cells from Sle2c1-carrying mice, which leads to defective G1 cell cycle arrest in splenic B cells and increased proliferation of Pc B1a cells.  As cell cycle is differentially regulated in B1a and B2 cells, these results suggest that Cdkn2c play a critical role in B1a cell self renewal, and that its impaired expression leads to an accumulation of these cells with high autoreactive potential.

overall_design: Total RNA from peritoneal cavity B cells (B1a) and splenic B cells (Bs) was isolated, with 4 biological replicates each. Gene expression data from C57BL/6 mice were compared with data from B6.Sle2c1 mice.

first: Zhiwei

last: Xu

first: Hari-Hara

last: Potula

first: Anusha

last: Vallurupalli

first: Daniel

last: Perry

first: Henry

last: Baker

first: Laurence

last: Morel


title: Rapamycin effect on Wild Type and TSC deficient Mouse Embryonic Fibroblasts : Time Course

first: Pichai

last: Raman

address: 220 Massachusetts Avenue

institute: Novartis Institutes for BioMedical Research, Inc.

summary:
Aberrant activation of the mammalian target of rapamycin (mTOR) complex 1 (mTORC1) is a common molecular event in a large variety of pathological settings, including genetic tumor syndromes, cancer, and obesity.  However, the cell intrinsic consequences of mTORC1 activation remain poorly defined. Here, we identify global trancriptional changes in TSC1 and TSC2 null MEFs, which exhibit constitutive activation of mTORC1, compared to wild-type littermate control lines.  A rapamycin time course is included to determine those changes that are dependent on mTORC1 signaling, revealing mTORC1 induced and repressed transcripts.
In order to identify mTORC1-dependent transcriptional changes, we compared wild-type MEFs to both Tsc1-/- and Tsc2-/- MEFs following serum starvation, where mTORC1 signaling is off in wild-type cells and fully active in TSC-deficient cells.  All cell lines were serum-starved for 24 h, and the Tsc1-/- and Tsc2-/- cells were treated with a time course of rapamycin prior to the isolation of mRNA for microarray analysis.

overall_design: Immortalized wild-type (Tsc2+/+ p53-/-), Tsc1-/- (p53+/+, 3T3-immortalized), and Tsc2-/- (p53-/-, derived from a littermate of the wild-type cell line) MEFs are the three cell lines used in this study and were derived in the laboratory of David J. Kwiatkowski (Brigham and Women's Hospital, Harvard Medical School, Boston, MA).  Wild-type and null MEFs were grown to 70% confluence in 10 cm plates and were serum starved for 24 h in the presence of vehicle (DMSO) for 24 h or rapamycin (20 nM) for 2, 6, 12, or 24 h.  All vehicle-treated samples (0 h time points) were plated in triplicate and all rapamycin time course samples were plated in duplicate.  For each replicate, expression analysis was performed by hybridization to an Affymetrix Mouse 430_2 oligonucleotide microarray chip.

first: Raman

last: Pichai

first: Murphy

last: Leon

first: Cleaver

last: Stephen

first: Manning

last: Brendan


title: The Effects of Globin on Microarray-based Gene Expression Analysis of Mouse Blood

status: Public on Jul 22 2010

city: Grand Rapids

first: Mary

middle: E

last: Winn

address: 333 Bostwick Ave NE

institute: Van Andel Research Institute

summary: Peripheral whole blood-based gene expression profiling has become one of the most common strategies exploited in the development of clinically relevant biomarkers.  However, the ability to identify biologically meaningful conclusions from gene expression patterns in whole blood is highly problematic. First, it is difficult to know whether or not expression patterns in whole blood capture those in primary tissues.  Second, if explicit steps are not taken to accommodate the extremely elevated expression levels of globin in blood then large-scale multi-probe microarray-based studies can be severely compromised.  Many studies consider the use of mouse blood as a model for human blood in addition to considering blood gene expression levels as a general surrogate for gene expression levels in other tissues.  We explored the effects of globin reduction on peripheral mouse blood in the detection of genes known to be expressed in human tissues.   Globin reduction resulted in 1.) a significant increase in the number of probes detected (5840 ± 944 vs 12411 ± 1904); 2.) increased expression for 4128 probe sets compared to non-globin reduced blood (p < .001, ≥ two-fold); 3.) improved detection of genes associated with many biological pathways and diseases; and 4.) an increased ability to detect genes expressed in 27 human tissues (p < 10-4).  This study suggests that although microarray-based mouse blood gene expression studies that do not consider the effects of globin are severely compromised, globin-reduced mouse whole blood gene expression studies can be used to capture the expression profiles of genes known to contribute to various human diseases.

overall_design: Whole and GLOBINclear-treated paired blood samples from 18 mice representing 3 mice from 6 different isogenic mice strains.

first: Matthew

last: Zapala

first: Iiris

last: Hovatta

first: Elizabeth

last: Lillie

first: Nicholas

middle: J

last: Schork


title: The effects of subchronic arsenate exposure on gene expression in the mouse lung

city: Research Triangle Park

first: Russell

middle: Scott

last: Thomas

state: NC

address: 6 Davis Drive

institute: The Hamner Institutes for Health Sciences

summary: Eight week old female C57BL/6 mice were exposed to arsenate in drinking water (50 ppm) for a period of twelve weeks (n = 5).  Control animals received distilled deionized water (n = 5).  Lung tissue was dissected and used for RNA isolation and gene expression microarray analysis.

first: Frank

last: Boellmann


title: Skeletal muscle gene expression in twin-pairs discordant for their physical activity for over 30 years

first: Heikki

last: Kainulainen

summary: The high physical activity/high aerobic fitness phenotype predicts low morbidity and mortality more strongly than any other known biological risk factor. Inherited and/or acquired properties of skeletal muscle seem to be linked with aerobic fitness and other cardio-metabolic risk factors3. However, physical activity-induced changes in muscle and fat tissue-related complex molecular networks and their links with cardio-metabolic disease risk are not comprehensively understood. Here we show that among the physically active members of twin pairs, as compared to their inactive co-twins, gene expression in musculus vastus lateralis tissue samples is chronically up-regulated for the central pathways or genes related to energy metabolism, including oxidative phosphorylation, lipid metabolism and supportive metabolic pathways. In addition to aerobic fitness, upregulation of these pathways is associated in particular with high HDL cholesterol levels. In fat tissue we found physical activity-induced increases in polyunsaturated fatty acid metabolism and in branched chain amino acid degradation, which increases were associated with decreased ‘high-risk’ ectopic body fat and low glucose levels. Consistent with other findings plasma lipidomics analyses showed up-regulation of the triacylglycerols containing the polyunsaturated fatty acids. The findings indicate the main pathways in skeletal muscle and fat tissue that mediate the chronic effects of physical activity on reduced cardio-metabolic disease risk, including the increase in aerobic fitness. Up-regulation of oxidative energy metabolism seems to be a common underlying mechanism.

overall_design: Total RNA obtained from the biopsy samples of m. vastus lateralis from three mono- and seven dizygotic twin pairs that had been  followed for their discordance for physical avtivity for 32 years.

first: Urho

last: Kujala

first: Tuija

last: Leskinen


title: Transcriptional and Phenotypic Reprogramming of Tumors by Host Stroma Deficient in TNFα Signaling

status: Public on Jul 20 2010

city: Chicago

first: Sean

middle: Pravin

last: Pitroda

state: IL

address: 5841 South Maryland Avenue, MC 1105

department: Radiation and Cellular Oncology

institute: The University of Chicago

summary:
Background: We previously demonstrated that B16F1 melanoma tumors growing in syngeneic germline-deleted TNFR1,2 -/- mice were more sensitive to ionizing radiation (IR) compared to tumors growing in C57BL/6 wild-type mice; however, the mechanisms linked to this difference in radiosensitivity are not fully understood.
Methodology/ Principal Findings: We used DNA microarrays to identify alterations in the expression of functional gene clusters associated with the radiosensitization of B16F1 tumors growing in TNFR1,2 -/- mice. At the basal level, disruption of host stromal TNFα signaling resulted in the over-expression of tumor genes involved in extracellular matrix remodeling and angiogenesis. Phenotypically, these tumors exhibited a reduced vascular density, which induced the expression of oxidative stress signaling pathways and increased levels of tissue hypoxia and necrosis. These alterations were paralleled by the suppression of genes involved in chromosomal stability and key effectors of the ATM-dependent/ non-homologous end-joining pathways including phosphorylated-ATM, BRCA1, and RAD51, which resulted in greater DNA double-strand breaks and caspase 3 activation following IR treatment.
Conclusions/ Significance: Taken together, these results demonstrate that disruption of TNFα signaling in the host stroma mediates transcriptional and phenotypic changes in tumors which may alter tumor radiosensitivity. These results suggest a critical role for TNFα in the maintenance of tumor-associated vasculature and radioresistance. They also indicate that TNFα signaling blockade in stromal cells may represent a strategy for tumor radiosensitization.

overall_design: To investigate the genes associated with the radiosensitization of B16F1 melanoma tumors in the context of disrupted stromal TNFα signaling, we performed expression profiling of B16F1 tumors grown in syngeneic TNFR 1, 2 -/- and wild-type C57BL/6 mice. Tumors were lysed to collect total RNA, pooled by treatment group according to total RNA level, and analyzed in duplicates with Affymetrix GeneChip® Mouse Genome 430 2.0 Arrays.

middle: P

first: Nikolai

middle: N

last: Khodarev

first: Hua

last: Liang

first: Helena

last: Mauceri

last: Filippo

first: Dhara

last: MacDermed

first: Michael

middle: A

last: Beckett

first: Harold

middle: G

last: Sutton

first: Ralph

last: Weichselbaum


title: Comprehensive profiling of the early lung immune responses in the mouse model of tuberculosis

status: Public on Jul 21 2010

city: PITTSBURGH

first: Dongwan

middle: Don

last: Kang

address: 130 DeSoto Street

institute: University of Pittsburgh

summary: The lung host immune responses following M.tuberculosis infection in the mouse model of tuberculosis were assayed by studying the gene expression profiles at day 0, day 12, 15 and 21 post infection

overall_design: Mice were infected with M.tuberculosis via the aerosol route and the host gene induction during early immune response studied

first: Yinyao

last: Lin

first: Javier-Rangel

last: Moreno

first: Troy

last: Randall

first: Shabaana

last: Khader


title: Systemic inflammation modulates Fc receptor expression on microglia in chronic neurodegeneration

city: London

first: Katie

middle: Sarah

last: Lunnon

address: De crespigny Park

department: Old Age Psychiatry

institute: Institute of Psychiatry

summary:
To investigate the inflammatory response in neurodegenerative disease during an episode of systemic inflammation using the ME7 prion model.
Comparison of ME7-infected mice with mice innoculated with Normal brain homogenate (NBH). 18 weeks post-innoculation mice were administered 500ug/kg LPS or an equivalent volume of saline as a control.

overall_design: Total RNA was extracted from the hippocampus, amplified and reverse transcribed to cDNA using WT ovation kit and hybridised to mouse 430_2.0 Affymetrix Arrays. There were three biological replicates (individual  mice) per group.

first: Jessica

last: Teeling

first: Richard

last: Reynolds

first: Martin

last: Glennie

first: Suzanne

last: Szak

first: V

middle: H

last: Perry


title: Gene expression profiling of mouse p53-deficient epidermal carcinoma defines molecular determinants of human cancer malignancy (testing dataset)

city: Madrid

first: Ramon

last: Garcia-Escudero

state: Madrid

address: Avda Complutense 40, Ed 70A

department: Biomedical Innovation

institute: CIEMAT

summary: The epidermal specific ablation of Trp53 gene leads to the spontaneous development of aggressive tumors in mice through a process that is accelerated by the simultaneous ablation of Rb gene. Since alterations of p53-dependent pathway are common hallmarks of aggressive, poor prognostic human cancers, these mouse models can recapitulate the molecular features of some of these human malignancies. To evaluate this possibility, gene expression microarray analysis was performed in mouse samples. The mouse tumors display increased expression of cell cycle and chromosomal instability associated genes. Remarkably, they are also enriched in human embryonic stem cell gene signatures, a characteristic feature of human aggressive tumors. Using cross-species comparison and meta-analytical approaches, we also observed that spontaneous mouse tumors display robust similarities with gene expression profiles of human tumors bearing mutated TP53, or displaying poor prognostic outcome, from multiple body tissues. We have obtained a 20-gene signature whose genes are overexpressed in mouse tumors and can identify human tumors with poor outcome from breast cancer, astrocytoma and multiple myeloma. This signature was consistently overexpressed in additional mouse tumors using microarray analysis. Two of the genes of this signature, AURKA and UBE2C, were validated in human breast and cervical cancer as potential biomarkers of malignancy. Our analyses demonstrate that these mouse models are promising preclinical tools aimed to search for malignancy biomarkers and to test targeted therapies of prospective use in human aggressive tumors and/or with p53 mutation or inactivation.

overall_design: Control skin was compared with skin tumors arising in k14Cre;p53loxP/loxP and k14Cre;p53loxP/loxP;pRbloxP/loxP animals, giving a mouse p53-tumor signature

first: Ramón

last: García-Escudero

first: Ana

middle: B

last: Martínez-Cruz

first: Mirentxu

last: Santos

first: Carmen

last: Segrelles

first: Marta

last: Dueñas

first: Corina

last: Lorz

first: Cristina

last: Saiz

first: Agueda

last: Buitrago-Pérez

first: Clotilde

last: Costa

first: Guillermo

last: Garaulet

first: Jesus

middle: M

last: Paramio


title: Gene expression profiling of mouse p53-deficient epidermal carcinoma defines molecular determinants of human cancer malignancy (training dataset)


title: Expression data from Ts1Cje and disomic C57BL/6 adult neurospheres

status: Public on Jul 16 2010

city: East Melbourne

first: Chelsee

last: Hewitt

state: VIC

address: St Andrews Place

department: Pathology

institute: The Peter MacCallum Cancer Centre

summary: Down syndrome is the most common form of genetic mental retardation. How Trisomy 21 causes mental retardation remains unclear and its effects on adult neurogenesis have not been addressed. To gain insight into the mechanisms causing mental retardation we used microarrays to investigate gene expression differences between Ts1Cje (a mouse model of Down syndrome) and C57BL/6 littermate control neurospheres. The neurospheres were generated from neural stem cells and progenitors isolated from the lateral walls of the lateral ventricles from adult mice.

overall_design: RNA was extracted for hybridization to arrays from 3 pairs of Ts1Cje and disomic C57BL/6 littermate control 7-day old adult neurosphere cultures.

first: King-Hwa

last: Ling

first: Tobias

middle: D

last: Merson

first: Ken

last: Simpson

first: Matthew

last: Ritchie

first: Sarah

last: King

first: Melanie

last: Pritchard

first: Gordon

middle: K

last: Smyth

first: Tim

last: Thomas

first: Hamish

middle: S

last: Scott

first: Anne

last: Voss


title: Arginine utilization following mycobacteria infection in macrophages is dependent on autocrine-paracrine signaling

status: Public on Jul 14 2010

city: Memphis

first: Geoffrey

last: Neale

state: TN

address: 262 Danny Thomas Place

department: Hartwell Center

institute: St Jude Childrens Research Hospital

summary: Nitric oxide (NO) produced by macrophages (MØs) is toxic to both host tissues and invading pathogens and its regulation is therefore essential to suppress host cytotoxicity. MØ arginase 1 (Arg1) inhibits NO production by competing with NO synthases for arginine, the common substrate of NO synthases and arginases. Two signal transduction pathways control Arg1 expression in MØs. First, a MyD88-dependent pathway induces Arg1 in intracellular infections, while a second Stat6-dependent pathway is required for Arg1 expression in alternativelyactivated MØs. We found that mycobacteria-infected MØs produce soluble factors that induce Arg1 in an autocrine-paracrine manner via Stat3. We identify these factors as IL-6, IL-10 and GCSF. We further establish that Arg1 expression is controlled by the MyD88-dependent production of IL-6, IL-10 and G-CSF rather than cell intrinsic MyD88 signaling to Arg1. Our data reveal the MyD88-dependent pathway of Arg1induction following BCG infection requires Stat3 activation and may result in the development of an immunosuppressive niche in granulomas due to the induced Arg1 production in surrounding uninfected MØs

overall_design: We used microarrays to perform genome wide expression analysis in mycobacteria-infected macrophages from C57Bl/6 WT and MyD88-knockout mice.

first: Joseph

last: Qualls

first: Peter

last: Murray


title: Pbx1-d Induces T cell Activation and a Decreased Apoptosis in Response to Retinoic Acids (RA)

status: Public on Jul 07 2010

first: Igor

last: Dozmorov

summary:
The hypothesis was tested that the Pbx1-d isoform was responsible for the Sle1a.1 phenotypes in CD4+ T cells.
Jurkat T cells were transfected with a lentiviral  construct expressing Pbx1-d-GFP or control RFP. Pbx1-d over-expression reduced the percentage of late apoptotic cells in response to anti-CD3 and anti-CD28 stimulation as compared with control-Lin28-transfected cells. Overall, these data demonstrate that over-expression of Pbx1-d results in an activated/inflammatory phenotype and in a defective response to RA in Jurkat T cells, strongly suggesting that the increased expression of Pbx1-d is responsible for the Sle1a.1 phenotypes.

overall_design: Jurkat T cells (5 x 105 cells/ml) were transfected with an lentiviral (LV) vector expressing either control (RFP or Lin28) or Pbx1-d-GFP.  Total RNA was extracted from GFP+ or RFP+ FACS-sorted Jurkat T cells transfected LV-GFP-Pbx1-d or LV-RFP, as well as non-transfected cells in 4 independent transfections per group.

first: Carla

last: Cuda

first: Shiwu

last: Li

first: Hari

last: Potula

first: Zhiwei

last: Xu

first: Ed

last: Butfiloski

first: Lung-Ji

last: Chang

first: Eric

last: Sobel

first: Laurence

last: Morel


title: Cell-context dependent Notch target genes

status: Public on Jul 13 2010

city: Kiel

first: Ralf

last: Schwanbeck

address: Otto-Hahn-Platz 9

department: Biochemistry

country: Germany

institute: University of Kiel

summary:
Notch signaling regulates a variety of developmental cell fates decisions in a cell-context dependent manner. Although Notch signaling directly regulates transcription via the RBP-J/CSL DNA binding protein, little is known about the genes in the respective tissues that are directly activated by Notch.
To analyze how Notch signaling mediates its context dependent functions, we utilized a Tamoxifen(OHT)-inducible system (NERT) to activate Notch1 in embryonic stem cells (ESC) at different stages of mesodermal differentiation combined with global transcriptional analyses.

overall_design: Notch1 signaling pathway was analysed in mouse embryonic stem cells (mESCs) that were kept under self-renewal conditions enabling  ectodermal, or mesodermal gene expression (ESCe or ESCm respectively), or were differentiated into mesodermal progenitors. NotchIC were induced or not induced by hydroxytamoxifen (OHT) and addititionally in some experiments the cells were treated with protein synthesis inhibitor cycloheximide (CHX)  for 4 h.

first: Ursula

last: Just


title: GeneChip expression profiling of Glud1 (glutamate dehydrogenase 1) transgenic mice

status: Public on Jul 12 2010

city: Lawrence

first: Xinkun

last: Wang

address: 2099 Constant Ave

department: Genomics Facility

institute: The University of Kansas

summary:
Glud1 (glutamate dehydrogenase 1) transgenic mice release more excitatory neurotransmitter glutamate to synaptic cleft throughout lifespan and show signs of accelerated aging.
Here we compared transcriptomic profiles of these animals to their wild-type counterparts. The hippocampus was used for the analysis.
Keywords: transgenic analysis

overall_design: Three Glud1 transgenic mice vs. three age-matched wide-type mice. Age: 9-month-old. Tissue: hippocampus.

first: Elias

last: Michaelis


title: Microarray data of prepubertal, peripubertal, and adult oocytes, and from GV and MII oocytes matured in vivo or in vitro

city: Urbana

first: Rebecca

last: Krisher

address: 1207 West Gregory Drive

institute: University of Illinois

summary:
Expression data from prepubertal, peripubertal, and adult derived mouse oocytes, and from germinal vesicle (GV), in vivo matured, and in vitro matured mouse oocytes.

Oocytes derived from prepubertal females, or oocytes matured in vitro, are less developmentally competent compared to adult derived, or in vivo matured, oocytes, indicated by decreased embryonic development.  One potential mechanism for decreased developmental potetential in prepubertal or in vitro matured oocytes is inadequate or inappropriate RNA degradation during oocyte maturation (progression from GV to MII).

To investigate mechanisms involved in establishing oocyte cytoplasmic maturation and developmental competence, Affymetrix GeneChip microarrays were used.

Keywords: Oocyte developmental competence

overall_design: The study encompassed three experimental designs using female B6D2F1 mice: 1) In vitro matured oocytes were obtained from d20 (prepubertal), d26 (peripubertal), and 7-8 wk old (adult) mice; 2) in vivo and in vitro matured oocytes were obtained from  d26 mice; and 3) GV, in vivo matured, and in vitro matured oocytes were obtained from 7-8 wk old mice.  RNA was extracted from pools of 150 oocytes and hybridized onto the Affymetrix microarrays.

first: Melissa

last: Paczkowski

first: Chris

last: Bidwell


title: Murine Bone Marrow Stromal Cell Response to Granulocyte Colony-Stimulating Factor

city: Seattle

first: Adam

last: Greenbaum

state: WA

address: 1100 Fairview Ave N D4-100

department: Oncology

institute: Fred Hutchinson Cancer Research Center

summary:
Neutrophil homeostasis is maintained, in part, by the regulated release of neutrophils from the bone marrow.  Constitutive expression of the chemokine CXCL12 by bone marrow stromal cells provides a key retention signal for neutrophils in the bone marrow through activation of its receptor CXCR4.  Herein, we show that the ELR chemokines CXCL1 and CXCL2 are constitutively expressed by bone marrow endothelial cells and osteoblasts, and CXCL2 expression is induced in endothelial cells during granulocyte colony-stimulating factor (G-CSF)-induced neutrophil mobilization. Neutrophils lacking CXCR2, the receptor for CXCL1 and CXCL2, are preferentially retained in the bone marrow, reproducing a myelokathexis phenotype.  Transient disruption of CXCR4 failed to mobilize CXCR2 neutrophils.  However, doubly deficient neutrophils (CXCR2-/- CXCR4-/-) displayed constitutive mobilization, showing that CXCR4 plays a dominant role. Collectively, these data suggest that CXCR2 signaling is a second chemokine axis that interacts antagonistically with CXCR4 to regulate neutrophil release from the bone marrow.
We used gene expression microarrays to determine the changes in osteoblasts and bone marrow endothelial cells after G-CSF treatment.

overall_design: 3 untreated and G-CSF-treated osteoblast samples and 4 untreated and G-CSF-treated endothelial samples.

first: Kyle

last: Eash

first: Priya

last: Gopalan

first: Daniel

middle: C

last: Link


title: In vitro differentiation of P19CL6 cardiogenic embryonic carcinoma cells

status: Public on Jul 08 2010

city: Charleston

first: Jeremy

last: Barth

state: SC

address: 173 Ashley Ave, BSB 627

institute: MUSC

summary: Pluripotent P19CL6 embryonic carcinoma cells can be differentiated to a cardiac lineage by culture in the presence of DMSO. The goal of this study was to characterize temporal gene expression patterns associated with cardiogenic differentiation. Gene expression analysis was conducted on differentiating P19CL6 cells at several time points following induction with 1% DMSO. Samples were processed for analysis by Affymetrix GeneChip.

overall_design: Analysis was done on P19CL6 cells growing in the absence of DMSO or in the presence of DMSO for 4, 6, 8, 10 or 12 days. Three independent samples (n=3) were used for all conditions except for 6-day and 12-day DMSO cultures (n=2).

first: Kyu-Ho

last: Lee

first: William

middle: T

last: Pu

middle: L


title: Type I IFN-signaling following Pneumocystis (PC)-infection and clearance in CD4 T cell-competent mice

city: Bozeman

first: Kate

last: McInnerney

state: MT

address: 109 Lewis Hall

department: Microbiology

institute: Montana State University

summary:
Type I IFN-signaling suppresses an excessive IFN-{gamma} response and prevents lung damage and chronic inflammation following Pneumocystis (PC)-infection and clearance in CD4 T cell-competent mice.
Type I IFN -signaling in pulmonary CD11c+ DCs and alveolar macrophages may prevent chronic inflammation following PC lung infection and clearance by suppressing an excessive IFN-g-response via the induction of SOCS1.

overall_design:
IFNAR-/- and wildtype mice were both Pneumocystis infected via itratracheal instillation. Pulmonary CD11c+ cells were isolated from collagen digested lungs at day 7 and day 14 post infection from both wildtype and IFNAR-/- mice using a magnetic cell sorting technique from Miltenyi with CD11c microbeads. Cells from three individual animals per group were isolated and assessed.
Comparison of 2 treatment types at 2 timepoints to determine whether type I IFN signaling is initiated in resident and early recruited pulmonary CD11c+ cells following Pneumocystis lung infection and whether this is relevant to the outcome of the inflammatory response during the initiation of clearance.

first: Nicole

last: Meissner

first: Soo

last: Han

first: Allen

last: Harmsen


title: Expression data from murine follicular dendritic cells

status: Public on Jul 05 2010

city: Yokohama

first: Keiichiro

last: Suzuki

state: Kanagawa

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

department: Research Center for Allergy and Immunology

institute: RIKEN

summary:
Germinal centers (GCs) are clusters of activated B cells built on stromal cells known as follicular dendritic cells (FDCs). In the Peyer’s patches (PPs), GCs are chronically induced by bacteria and are the major sites for generation of gut IgA immune responses. Whether FDCs directly contribute to the IgA production in PP GCs is unknown.
To investigate the role FDCs in gut immune system, we examined comprehensive gene profiles of FDCs purified from PPs or perypheral lymph nodes (pLNs) with or without immunization. We also tried to reconstitute the PP FDC signature in vitro by pulsed or continuous stimulation of pLN FDCs through TLRs, RARs or simultaneously through TLRs and RARs.

overall_design:
The number of samples is as follows; ex vivo naïve pLN FDC=3, ex vivo immunized pLN FDC=2, ex vivo PP FDCs=3, in vitro without stimulation=2, in vitro with LPS stimulation for 5 hours=1, in vitro with LPS stimulation for 72h=1, in vitro with Pam2CSK4 (Pam) stimulation for 96h=2, in vitro with retinoic acid(RA) stimulation for 96h=2,in vitro with RA+Pam stimulation for 96h=2.

In addition, ex vivo FDCs with or without immunizations were compared (3 samples), or in vitro cultured FDCs with or without various stimulations were compared (6 samples)

first: Mikako

last: Maruya

first: Shimpei

last: Kawamoto

first: Katarzyna

last: Sitnik

first: Hiroshi

last: Kitamura

middle: W

last: Agace

first: Sidonia

last: Fagarasan


title: Deficiency in the 15 kDa Selenoprotein Inhibits Tumorigenicity and Metastasis of Colon Cancer Cells

city: Towson

first: Petra

last: Tsuji

state: MD

address: 8000 York Rd

department: Biological Sciences

institute: Towson University

summary: Selenium has cancer preventive activity that is mediated, in part, through selenoproteins. The role of the 15 kDa selenoprotein (Sep15) in colon cancer was assessed by preparing and using mouse colon CT26 cells stably transfected with shRNA constructs targeting Sep15. Metabolic 75Se-labeling and Northern and Western blot analyses revealed that more than 90% of Sep15 was knocked down. Growth of the resulting Sep15-deficient CT26 cells was reduced (p<0.01) and cells formed significantly (p<0.001) fewer colonies in soft agar compared to control CT26 cells. Whereas most (14/15) BALB/c mice injected with control cells developed tumors, few (3/30) mice injected with Sep15 knockdown cells developed tumors (p<0.0001). The ability to form pulmonary metastases had similar results. Mice injected with the plasmid-transfected control cells had >250 lung metastases/mouse; however, mice injected with the Sep15 knockdown cells only had 7.8 +/- 5.4 metastases. To investigate molecular targets affected by Sep15 status, gene expression patterns between control and knockdown CT26 cells were compared. Ingenuity Pathways Analysis was used to analyze the 1045 genes that were significantly (p<0.001) affected by Sep15 deficiency. The highest scored biological functions were cancer and cellular growth and proliferation. Consistent with these observations, subsequent analyses revealed a G2/M cell cycle arrest in Sep15 CT26 knockdown cells. In contrast, to CT26 cells Sep15 knockdown in Lewis Lung Carcinoma (LLC1) cells did not affect anchorage-dependent or –independent cell growth. These data suggest tissue specificity in the cancer protective effects of Sep15 knockdown, which are mediated, at least in part, by influencing the cell cycle.

overall_design: mRNA was isolated from plasmid-transfected control and shSep15 knockdown CT26 cells (three replicates of each). Microarray analysis was performed on Affymetrix Mouse 430_2 gene chips. Three arrays were analyzed from different mRNA samples for each construct.


title: Expression profiling of murine neonatal lung tissue from Carm1 knockouts and wild type controls

city: Boston

first: Manoj

last: Bhasin

address: 330 Brookline Avenue  RN 380E

institute: Beth Israel Deaconess Medical Center

summary: Coactivator associated arginine methyltransferase I (CARM1, also known as Protein aRginine MethylTransferase 4, or PRMT4) regulates gene expression by multiple mechanisms including methylation of histones and coactivation of steroid receptor transcription. Mice lacking CARM1 are smaller than their littermates, fail to breath, and die shortly after birth, demonstrating the critical role of CARM1 in development.We performed gene expression analysis to identify genes that are responsible for hyperproliferaion in CARM1 knockout lung.

overall_design: RNA extracted from murine lung at E18.5 with carm1 knockouts and wild type controls was hybridised to Affymetrix mouse430.2 GeneChips to identify differentially expressed genes in the disease state.

first: Karen

last: O'Brien

first: Meritxell

last: Alberich-Jordà

first: Neelu

last: Yadav

first: Olivier

last: Kocher

first: Annalisa

last: DiRuscio

first: Alexander

last: Ebralidze

first: Elena

last: Levantini

first: Natasha

middle: J

last: Sng

first: Tyler

last: Caron

first: Daehoon

last: Kim

first: Ulrich

last: Steidl

first: Gang

last: Huang

first: Balázs

last: Halmos

first: Scott

last: Rodig

first: Mark

last: Bedford

last: Tenen

first: Susumu

last: Kobayashi


title: Genome-wide analysis of gene expression in EMT cells induced by overexpression of PDGF-D compared with PC3 control cells

city: Detroit

first: Fazlul

middle: H.

last: Sarkar

address: 4100 John R

institute: Wayne State University School of Medicine

summary: Analysis of EMTrelated gene expression levels. The hypothesis tested in the present study was that expression of mesenchymal markers was increased and expression of epithelial markers was downregulated concomitant with increased expression of stem -like cell markers in EMT cells compared with control cells. Results demostrated that overexpression of PDGF-D induced genome-wide gene expression changes which were consistent with EMT phenotype and stem cell signatures.

overall_design: Total RNA isolated from stable PC3 Neo and PC3 PDGF-D cells.


title: Expression file from FGF-10 experiment

status: Public on Jul 01 2010

city: Tainan

first: Vivienne

middle: HJ

last: Lee

address: No.100, Daxue Rd., East Dist., Tainan City 701, Taiwan (R.O.C.)

department: Institute of Clinical Investigation

country: Taiwan

institute: National Cheng Kung University

summary:
Differentiating embryonic stem cells into cardiomyocytes is inefficient, and we discover that FGF-10 can induce embryonic stem cells differentiation into cardiomyocytes.
We use microarray to gain insight into the global gene expression and elucidate the machenism that FGF-10 induces embryonic stem cells differentiation into cardiomyocytes.

overall_design: Two-day embryoid bodies were treated with or without 100 ng/ml FGF10 and RNA was obtained 24 hours later and hybridized by Affymetrix microarray

first: Desy


title: Expression profiling after ICAP1 or constitutive active NOTCH1 over expression in human umbilical vein endothelial cells

status: Public on Jul 02 2010

city: Mannheim

first: Andreas

last: Fischer

address: Ludolf-Krehl-Str. 13-17

department: Joint Research Division Vascular Biology

institute: German Cancer Research Center and Medical Faculty Mannheim, Heidelberg University

summary: ICAP1 (also known as ITG1BP1) is a protein interaction partner of beta1-integrins and the cerebral cavernous malformation protein 1 (CCM1, also known as KRIT1). In mice Icap1 plays an important role for bone development. The function of ICAP1 in endothelial cells is poorly understood. However, the interactions with beta1-integrins and CCM1 suggest that ICAP1 should play an important role also in endothelial cells. We obtained data that ICAP1 might activate the Delta-Notch signaling cascade, a critical regulator of endothelial proliferation, migration and sprouting angiogenesis. This genome-wide expression analysis is aimed to unravelling novel mechanisms or signaling pathways how ICAP1 functions in endothelial cells. Secondly, this study aimed at defining novel target genes of Notch signaling and finally to compare the gene expression patterns of ICAP1 and NOTCH1. We used human umbilical vein endothelial cells (HUVEC) as a model system to study ICAP1 and NOTCH1 functions after adenoviral over expression in comparison to GFP over expression as control. The results of this experiment suggest that ICAP1 and NOTCH1 control a series of genes involved in cell proliferation, migration and angiogenesis. A high proportion of ICAP1-regulated genes is also regulated by NOTCH1 in a very similar manner.

overall_design:
Human umbilical vein endothelial cells were transduced with adenovirus expressing ICAP1, NOTCH1 (only the constitutive active intracellular domain) or GFP as control. 36 hours after transduction total RNA was isolated from duplicates for genome-wide expression analysis
biological replicate: GFP_1, GFP_2
biological replicate: NOTCH1_1, NOTCH1_2
biological replicate: ICAP1_1, ICAP1_2

first: Sven

last: Liebler

first: Joycelyn

last: Wuestehube

first: Arne

last: Bartol


title: Gene expression analysis of leukemic samples in C57BL6 mice

city: Frankfurt/Main

first: Rolf

last: Marschalek

address: Max-von-Laue-Str. 9

department: Inst Pharm Biology

institute: Goethe University

summary:
[original title] Gene expression analysis of leukemic samples derived from AF4-MLL- or AF4-MLL/MLL-AF4-transduced and transplanted hematopoietic stem/precursor cells in C57BL6 mice.

We used microarrays to analyze the global gene expression in leukemic cells with three distinct immunophenotypes.

overall_design: We compared leukemic cells isolated from the bone marrow of diseased mice and compared these profiles with normal bone marrow.

first: L

last: Klein-Hitpass


title: The orphan nuclear hormone receptor ERRβ controls rod photoreceptor survival.

city: Baltimore

first: Seth

last: Blackshaw

address: 733 N. Broadway, Suite 351

department: Neuroscience

institute: The Johns Hopkins University

summary: Mutation of rod photoreceptor-enriched transcription factors is a major cause of inherited blindness. We identified the orphan nuclear hormone receptor ERRβ as selectively expressed in rod photoreceptors.  Overexpression of ERRβ induces expression of rod-specific genes in retinas of both wildtype and in Nrl-/- mice, which lack rod photoreceptors. Mutation of ERRβ results in dysfunction and degeneration of rods, while inverse agonists of ERRβ trigger rapid rod degeneration, which is rescued by constitutively active mutants of ERRβ. ERRβ coordinates expression of multiple genes that are rate-limiting regulators of ATP generation and consumption in photoreceptors.  Furthermore, enhancing ERRβ activity rescues photoreceptor defects that result from loss of the photoreceptor-specific transcription factor Crx. Our findings demonstrate that ERRβ is a critical regulator of rod photoreceptor function and survival, and suggest that ERRβ agonists may be useful in the treatment of certain retinal dystrophies.

overall_design: Affymetrix MOE430 microarrays were used to analyze the expression patterns of P21 mouse retinal tissues. The results were compared across the variable of Genotype, specifically ERRβ knockout versus wildtype.

first: Akishi

last: Onishi

first: Guang-Hua

last: Peng

first: Erin

last: Poth

first: Daniel

first: Jichao

last: Chen

first: Uel

last: Alexis

first: Jimmy

last: de Melo

first: Shiming


title: Expression data from primary MEF lacking either HDAC1, HDAC2 or both

city: Basel

first: Patrick

last: Matthias

address: Maulbeerstrasse 66

country: Switzerland

institute: Friedrich Miescher Institute for Biomed. Research

summary: Previously published data suggested some redundant functions between HDAC1 and HDAC2 in mouse. To test this hypothesis, we used microarrays to have a genome wide analysis at the transcription level of primary MEFs lacking HDAC1, HDAC2.

overall_design: MEF HDAC1 F/F were were transduced with two different retroviruses: one virus expresses the Tamoxifen-inducible cre recombinase Cre-ERT2 and the second virus expresses either a small hairpin micro-RNA against HDAC2 or a scrambled version. HDAC1F/F MEFs expressing either a scrambled micro-RNA or a micro-RNA against HDAC2 can be induced by addition of Tamoxifen to delete HDAC1, thereby generating four different genotypes: WT, HDAC1 KO, HDAC2 knockdown (Kd) and HDAC1/2 KO/Kd.

first: Fabien

last: Cubizolles


title: Bone marrow transcriptomal differences between wild type, Fancc-deficient, Fancg-deficient, and doubly deficient (Fancc/Fancg) mice.

city: Portland

first: Grover

last: Bagby

state: OR

address: 3181 SW Sam Jackson Park Rd.

department: Dept. of Medicine

institute: Oregon Health & Science University

summary: Seeking to challenge the current dogma that the nuclear core-complex proteins function in an entirely epistatic manner, Dr. Clapp's group developed a new double-knockout mouse nullizygous for Fancc and Fancg.   Because the hematopoietic phenotype was more severe than single knockout mice, we reasoned that transcriptomal differences would exist and lead to  the identification of molecular defects unique to each FA gene.

overall_design: RNA was purified from unfractionated and uncultured bone marrow cells from three types of Fanconi anemia gene knockout mice: nullizygous for Fancc, Fancg, or both Fancc and Fancg..   Three wild type C57Bl/6 mice served as controls.  Each of three marrow samples provided one RNA sample (the RNA samples were not pooled).

first: D

last: Clapp


title: Expression data from CC10-rtta/teton-IL-13 tg mice fed with or without doxycycline

city: Cincinnati

first: Li

last: Zuo

address: 3333 Burnet Ave

department: Allergy and Immunology

institute: Cincinanti Children's Hospital

summary:
Morphogenesis of epithelial tissues relies on the precise developmental control of cell polarity and architecture. In the early Drosophila embryo, the primary epithelium forms during cellularisation, following a tightly controlled genetic programme where specific sets of genes are up-regulated. Some of them, for instance, control membrane invagination between the nuclei anchored at the apical surface of the syncytium.
We used microarrays to detail the global programme of gene expression underlying cellularisation and identified distinct classes of regulated genes during EE.

overall_design: CC10-rtta/teton-IL-13 mice were fed either with doxycycline or regular diet (Dox vs. NODOX). Esophaguses were collected and submitted to RNA extraction and hybridization on Affymetrix microarrays.

first: Patricia

last: Fulkerson

first: Carine

last: Blanchard

first: Marc

middle: E

last: Rothenberg