title: Mitochondrial DNA mutations induce supression of nuclear encoded mitochondrial Genes in skeletal muscle

status: Public on May 01 2010

city: Tokyo

first: Takuya

last: Miyakawa

address: 1-1-1 Yayoi, Bunkyo-ku

institute: The University of Tokyo

summary: To identify and analyze mtDNA mutation-responsive genes, a comparison of gastrocnemius muscle tissues from WT (control) and D257A mice was conducted. We examined changes in gene expression in the muscle associated with mtDNA mutations.

overall_design:
1) Types of experiments:
a) Effect of mitochondrial DNA (mtDNA) mutations
b) Effect of aging
c) WT (13 month-old Polg+/+ mice) vs. D257A (13 month-old PolgD257A/D257A) mice

2) Experimental factors:
a) Type of gene: PolgD257A/D257A
b) Time (age)

3) Number of hybridizations in the study: ~10

4) A common reference RNA was not used.

5) Quality control measures were not used. No replicates were done. Dye swap was not used.

first: Chie

last: Nakayama

first: Shinichi

last: Someya

first: Tomas

last: Prolla

first: Masaru

last: Tanokura


title: Chromatin Analysis of Wilms Tumor Highlights Stem Cell Properties and a Renal Developmental Network

status: Public on May 05 2010

city: Cambridge

first: Noam

last: Shoresh

state: MA

address: 7 Cambridge Center

department: Epigenomics

country: USA

institute: Broad Institute

type: Genome binding/occupancy profiling by high throughput sequencing

summary: Wilms tumors are pediatric cancers thought to arise from kidney-specific stem cells. In order to identify transcriptional and epigenetic mechanisms that drive these malignant cells, we compared genomewide chromatin profiles of Wilms tumors to embryonic stem (ES) cells and normal kidney.

overall_design: Data represent examination of genome-wide chromatin modifications in primary Wilms tumors, fetal and mature kidney.

first: Aviva

middle: P

last: Aiden

first: Miguel

middle: N

last: Rivera


title: mRNA profiling of iPSCs and derivative NT-ESCs

status: Public on Apr 28 2010

city: Boston

first: Matthias

last: Stadtfeld

address: 185 Cambridge Street

institute: MGH

summary: Pluripotent cells can be derived from somatic cells by either overexpression of defined transcription factors (resulting in induced pluripotent stem cells (iPSCs)) or by nuclear transfer or cloning (resulting in NT-ESCs). To determine whether cloning further reprograms iPSCs, we used iPSCs as donor cells in nuclear transfer experiments.

overall_design: An iPSC clone derived from tail-tip fibroblasts using adenoviral vectors was used as donor cell in nuclear transfer experiments. RNA was isolated from both parental iPSC clone and derivative NT-ESCs lines and analyzed.

first: Konrad

last: Hochedlinger


title: Expression data from testis of day-7 Sohlh1 knock-out mice

status: Public on Apr 27 2010

city: Pittsburgh

first: Aleksandar

last: Rajkovic

state: PA

address: 204 Craft Ave. Suite A230

department: Dept. of Obstetrics, Gynecology & Reproductive Sciences

institute: Magee-Womens Research Institute

summary: Sohlh1 and Sohlh2 encode a germ cell-specific basic helix-loop-helix transcriptional regulator critical in spermatogonial differentiation. Seven-day-old Sohlh1 or Sohlh2 knockout and wild-type testes were arrayed on the Affy 430 2.0 platform.

overall_design: The following mice were analyzed at postnatal day 7: wild-type, Sohlh1-/-, and Sphlh2-/-. 4 samples/group.


title: A53T-α-synuclein overexpression mouse model   signaling and striatal synaptic plasticity

city: Tuebingen

first: Michael

last: Bonin

state: BW

address: CAlwerstr. 7

department: Medical Genetics

country: Germany

institute: University Tuebingen

summary: Parkinson’s disease (PD), the second most frequent neurodegenerative disorder at old age, can be caused by elevated expression, or the A53T mutation, of the presynaptic protein alpha-synuclein (SNCA). PD is characterized pathologically by the preferential vulnerability of the dopaminergic nigrostriatal projection neurons. Here, we used two mouse lines overexpressing human A53T-SNCA around ages 6 and 18 months and studied striatal dysfunction in the absence of neurodegeneration to understand early disease mechanisms.  High pressure liquid chromatography analysis of striatal neurotransmitter content demonstrated that dopamine (DA) levels correlated directly with the level of expression of SNCA, an observation also observed in SNCA deficient mice. In the striatum of aged A53TSNCA overexpressing mice, where DA levels were elevated, a paradoxical upregulation of dopamine receptors DRD1A and DRD2 was detected by immunoblots and autoradiography, findings compatible with the notion of abnormal vesicle release. Extensive transcriptome studies via microarrays and quantitative real-time RT-PCR validation of altered Homer1, Cb1, Atf2 and Pde7b transcript levels indicated a progressive reduction in the postsynaptic DA response. As functional consequences, long term depression was absent in corticostriatal slices from aged transgenic mice and an insidious decrease of spontaneous locomotor activity of these animals was found in open field tests. Taken together, the dysfunctional neurotransmission and decreased synaptic plasticity seen in the A53T-SNCA overexpressing mice reflects early functional changes within the basal ganglia resulting from synucleinopathy prior to frank neurodegeneration. Thus, preclinical stages of PD may be modeled in this mouse.  Parkinson’s disease (PD), the second most frequent neurodegenerative disorder at old age, can be caused by elevated expression, or the A53T mutation, of the presynaptic protein alpha-synuclein (SNCA). PD is characterized pathologically by the preferential vulnerability of the dopaminergic nigrostriatal projection neurons. Here, we used two mouse lines overexpressing human A53T-SNCA around ages 6 and 18 months and studied striatal dysfunction in the absence of neurodegeneration to understand early disease mechanisms.  High pressure liquid chromatography analysis of striatal neurotransmitter content demonstrated that dopamine (DA) levels correlated directly with the level of expression of SNCA, an observation also observed in SNCA deficient mice. In the striatum of aged A53TSNCA overexpressing mice, where DA levels were elevated, a paradoxical upregulation of dopamine receptors DRD1A and DRD2 was detected by immunoblots and autoradiography, findings compatible with the notion of abnormal vesicle release. Extensive transcriptome studies via microarrays and quantitative real-time RT-PCR validation of altered Homer1, Cb1, Atf2 and Pde7b transcript levels indicated a progressive reduction in the postsynaptic DA response. As functional consequences, long term depression was absent in corticostriatal slices from aged transgenic mice and an insidious decrease of spontaneous locomotor activity of these animals was found in open field tests. Taken together, the dysfunctional neurotransmission and decreased synaptic plasticity seen in the A53T-SNCA overexpressing mice reflects early functional changes within the basal ganglia resulting from synucleinopathy prior to frank neurodegeneration. Thus, preclinical stages of PD may be modeled in this mouse.

overall_design: Tissue was dissected from the brain of 6 months old (2 WT / 2 TgA / 2 TgB striata, 2 WT / 2 TgA / 2 TgB brainstems/midbrains, 2 WT / 2 TgA / 2 TgB cerebella) and of 18+ months old mice (4 WT / 2 TgA / 2 TgB striata, 6 WT / 4 TgA / 3 TgB brainstems/midbrains, 6 WT / 5 TgA / 4 TgB cerebella). Tissues from individual, particularly old mice up to 28 months age were included here to strengthen the definition of progression markers reflecting old age.

first: Suzana

last: Gispert

first: Georg

last: Auburger


title: Tob1 is a Constitutively Expressed Repressor of Liver Regeneration

status: Public on May 15 2010

first: Hasan

middle: Huseyin

last: Otu

address: 4 Blackfan Circle Rm. 238

department: Medicine

institute: Harvard Medical School

summary: How proliferative and inhibitory cell signals integrate to control liver regeneration remains poorly understood.  A screen for antiproliferative factors repressed after liver injury identified Tob1, a member of the PC3/BTG1 family of mitoinhibitory molecules as a target for further evaluation.  Tob1 protein decreases after 2/3 hepatectomy in mice secondary to post-transcriptional mechanisms.  Deletion of Tob1 increases hepatocyte proliferation and accelerates restoration of liver mass after hepatectomy.  Down-regulation of Tob1 is required for normal liver regeneration and Tob1 controls hepatocyte proliferation in a dose-dependent fashion.  Tob1 associates directly with both Caf1 and the Cyclin/cdk complex to modulate kinase activity.  In addition, Tob1 has significant effects on the transcription of critical cell cycle components, including E2F targets and genes involved in p53 signaling.  These studies provide direct evidence that levels of an inhibitory factor control the rate of liver regeneration.  Our data identify Tob1 as a crucial check-point molecule that acts by by modulating levels and activity of cell cycle proteins.

overall_design: Samples from wild type and Tob1 null mice as normal adults and 24 hours after 2/3 hepatectomy are used.  Each experimental point used data from two chips, each having a different set of three pooled animals. In summary we had 8 chips: 2 for WT time 0, 2 for WT time 24, 2 for KO time 0, 2 for KO time 24.

middle: H


title: Aberrant silencing of imprinted genes on chromosome 12qF1 in mouse induced pluripotent stem cells

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

overall_design: Refer to individual Series


title: Comparison of gene expression in whole blood of mice subjected to hypobaric hypoxia at Mt. Everest in vivo.

status: Public on Apr 25 2010

city: Tübingen

first: Gabriel

last: Willmann

address: Schleichstrasse 12-16

institute: University Eye Hospital and Centre for Ophthalmology Tübingen

summary: To determine hypoxia mediated changes in whole blood, normal swiss webster mice were gradually exposed to a chronic hypobaric hypoxic environment up to 8500m, for 2 weeks in vivo. Control, age-matched mice were maintained under normoxic conditions in Kathmandu (c. 1300 mts above sea level).

overall_design:
Purpose: To examine and characterize the expression profile of genes expressed at hypobaric hypoxia on Mt. Everest of whole blood in comparison to the control.
Methods: At the beginning of the experiment mice were divided into two groups, control (room condition, Kathmandu, Nepal) and hypoxic (hypoxic condition). For conditioning, the hypoxic group was exposed to lower levels of hypobaric hypoxia during our mountaineering expedition to Mt Everest. The oxygen level was decreased according to our climbing protocol from 21% to about 7% over a period of 15 days. Food and water were changed daily during the course of the experiment. After 15 days animals were euthanized after whole blood extraction from V. Cava for further analysis. RNA from whole blood was isolated, processed and used for microarray-based expression profiling. Profiles were generated for genes differentially expressed at control versus hypobaric hypoxia in whole blood using a false discovery rate (FDR) of 0%.We validated the profiles by real-time quantitative reverse transcription-polymerase chain reaction (qPCR).
Results: The regional transcriptomes associated with hypobaric hypoxia on Mt. Everest in whole blood were identified. We found 947 genes that were differentially expressed in normobaric hypoxic whole blood compared to control with a 0% FDR and a 2 fold cutoff.
Conclusion: Transcriptome level differences exist between control and hypobaric hypoxia in whole blood. Our definition of the synaptic transcriptome provides insight into the functioning of the unique response to hypoxia in whole blood.

first: Rohit

last: Pokharel

first: Matias

last: Mosqueira

first: Sukhamay

last: Lahiri

first: Tejvir

middle: S

last: Khurana


title: Comparison of gene expression in whole blood of mice subjected to chemical hypoxia in vivo.

summary: To understand hypoxia mediated changes in whole blood, normal C57Bl/10 mice were gradually exposed to a chronic chemical hypoxic environment, for 2 weeks. Control, age-machted mice were maintained under normoxic conditions.

overall_design:
Purpose: To examine and characterize the expression profile of genes expressed at chemical hypoxia of whole blood in comparison to the control.
Methods: At the beginning of the experiment mice were divided into two groups, control (room condition) and chemical hypoxic (room condition). For conditioning, the chemical hypoxic group was supplemented with 200ng of CoCl2 per 100ml/day. Animal’s weight and food intake were monitored daily. Food and water were changed daily during the course of the experiment. Before and after the experiments the hematocrit was monitored by taking blood from the tail vein of control and hypoxic animals. After 15 days animals were euthanized using CO2 after whole blood extraction from V. Cava for further analysis. RNA from whole blood was isolated, processed and used for microarray-based expression profiling. Profiles were generated for genes differentially expressed at control versus chemical hypoxia in whole blood using a false discovery rate (FDR) of 0%.We validated the profiles by real-time quantitative reverse transcription-polymerase chain reaction (qPCR).
Results: The regional transcriptomes associated with chemical hypoxia in whole blood were identified. We found 3094 genes that were differentially expressed in chemical hypoxic whole blood compared to control with a 0% FDR and a 2 fold cutoff.
Conclusion: Transcriptome level differences exist between control and chemical hypoxia in whole blood. Our definition of the synaptic transcriptome provides insight into the functioning of the unique response to hypoxia in whole blood.


title: Comparison of gene expression in whole blood of mice subjected to normobaric hypoxia in vivo.

summary: To determine hypoxia mediated changes in whole blood, normal C57Bl/10 mice were gradually exposed to a chronic hypoxic environment, equivalent to an altitude of 6500m, for 2 weeks in vivo. Control, age-matched mice were maintained under normoxic, normobaric conditions by exposing them to ambient air in Philadelphia (c. 50 mts above sea level).

overall_design:
Purpose: To determine the expression profile of genes differentially expressed in mouse whole blood upon exposure to normobaric hypoxia in vivo.

Methods: The hypoxic group consisting of 6 C57/BL10 mice was exposed to normobaric hypoxia, in a specially designed and hermetically closed hypoxic chamber, using a gas mixing system Pegas 4000 MF (Columbus Instruments, Ohio, USA). The oxygen level was decreased from 21% to 8% over a period of 14 days. 6 control mice were kept at normal oxygen and pressure levels  by exposing them to ambient air in Philadelphia (c. 50 mts  above sea level).  RNA from whole blood was isolated, processed and used for microarray-based expression profiling. Profiles were generated for genes differentially expressed at control versus normobaric hypoxia in whole blood using a false discovery rate (FDR) of 0%. The Profile was validated by real-time quantitative reverse transcription-polymerase chain reaction (qPCR) on 2 biologically independent samples, not used for generating the profile.

Results: The transcriptomes associated with normobaric hypoxia in whole blood were identified. We found 4723 genes that were differentially expressed in normobaric hypoxic whole blood compared to control with a 0% FDR and a 2 fold cutoff.

Conclusion: Transcriptome level differences exist in the whole blood of animals subjected to normobaric hypoxia. Our definition of the normobaric hypoxia blood transcriptome provides insight into the functioning and response to hypoxia in whole blood.


title: Downstream Targets of HOXB4 in the primitive hematopoietic progenitor EML Cell line

status: Public on Apr 20 2010

city: New Haven

first: Vince

last: Schulz

state: CT

address: 333 Cedar St. LMP 4085

department: Department of Pediatrics

institute: Yale University

type: Genome binding/occupancy profiling by genome tiling array

summary: Enforced expression of the homeobox transcription factor HOXB4 has been shown to enhance hematopoietic stem cell (HSC) self-renewal and expansion ex vivo and in vivo.  In order to investigate the largely unknown downstream targets of HOXB4 in hematopoietic progenitor cells, HOXB4 was constitutively overexpressed in the primitive hematopoietic progenitor cell line, EML.  Gene expression differences were compared between KLS (c-Kit+, Lin-, Sca-1+)-EML cells that overexpressed HOXB4 (KLS-EML-HOXB4) to control KLS-EML cells that were transduced with vector alone.  ChIP-chip was used to identify promoter regions bound by HOXB4.

overall_design: We overexpressed HOXB4 in EML cells.  We isolated 3 separate single cell clones as assessed by Southern Blot Analysis (3 clones for EML-HOXB4 and 3 clones for control EML-GFP cells).   RNA was isolated from the KLS (c-Kit+, Lin-, Sca-1+) fraction of each single cell clone population and processed for hybridization to array chips using established lab protocols.  Chip-Chip analysis of the three HOXB4 overexpressing clones was performed to identify HOXB4 bound promoters.

first: H

middle: M

last: Lee

last: Zhang

first: V

first: D

last: Tuck

first: B

middle: G

last: Forget


title: Dynamic single-cell imaging of direct reprogramming reveals an early specifying event

status: Public on Apr 16 2010

first: Richard

last: Koche

address: 185 Cambridge St.

institute: Broad Institute of Harvard and MIT

summary: The study of induced pluripotency often relies on experimental approaches that average measurements across a large population of cells, the majority of which do not become pluripotent. Here we used high-resolution, time-lapse imaging to trace the reprogramming process over 2 weeks from single mouse embryonic fibroblasts (MEFs) to pluripotency factor-positive colonies. This enabled us to calculate a normalized cell-of-origin reprogramming efficiency that takes into account only the initial MEFs that respond to form reprogrammed colonies rather than the larger number of final colonies. Furthermore, this retrospective analysis revealed that successfully reprogramming cells undergo a rapid shift in their proliferative rate that corresponds to a reduction in cellular area. This event occurs as early as the first cell division and with similar kinetics in all cells that form induced pluripotent stem (iPS) cell colonies. These data contribute to the theoretical modeling of reprogramming and suggest that certain parts of the reprogramming process follow defined rather than stochastic steps.

overall_design: Gene expression profiling: Mouse E13.5 fibroblasts were generated by blastocyst injection with doxycycline inducible Oct4, Sox2, Klf4, and c-Myc primary iPS cells as previously described.  Cells were serum starved with 0.5% FBS containing medium, followed by either continued serum starvation for 96 hours, or by 96 hours of factor induction through medium supplemented with 2 ug/ml doxycycline (Sigma). Two biological replicates of each sample (SerumStarveControl and 96hrInduction) were collected and RNA was isolated in preparation for analysis on Affymetrix Mouse Genome 430 2.0 Arrays as previously described.

first: Zachary

middle: D

last: Smith

first: Alexander

last: Meissner


title: Expression Data from WT and Sh2d1a-/- in vivo follicular helper CD4 T cells (TFH) versus non follicular helper CD4 T cells (non-TFH)

city: San Diego

first: Shane

last: Crotty

state: CA

address: 9420 Athena Circle

department: Vaccine Discovery

institute: La Jolla Institute for Allergy and Immunology

summary: CD4 T cell help is critical for both the generation and maintenance of germinal centers, and T follicular helper (TFH) cells are the CD4 T cell subset required for this process. SAP (SH2D1A) expression in CD4 T cells is essential for germinal center development. However, SAP-deficient mice have only a moderate defect in TFH differentiation as defined by common TFH surface markers. CXCR5+ TFH cells are found within the germinal center as well as along the boundary regions of T/B cell zones. Here we show that germinal center associated T cells (GC TFH) can be identified by their co-expression of CXCR5 and the GL7 epitope, allowing for phenotypic and functional analysis of TFH and GC TFH populations. Here we show GC TFH are a functionally discrete subset of further polarized TFH cells, with enhanced B cell help capacity and a specialized ability to produce IL-4 in a TH2-independent manner. Strikingly, SAP-deficient mice have an absence of the GC TFH subset and SAP- TFH are defective in IL-4 and IL-21 production. We further demonstrate that SLAM (Slamf1, CD150), a surface receptor that utilizes SAP signaling, is specifically required for IL-4 production by GC TFH. GC TFH cells require IL-4 and IL-21 production for optimal help to B cells. These data illustrate complexities of SAP-dependent SLAM family receptor signaling, revealing a prominent role for SLAM receptor ligation in IL-4 production by germinal center CD4 T cells but not in TFH and GC TFH differentiation.

overall_design: Analysis of in vivo antigen-specific (LCMV-specific, SMARTA TCR transgenic) WT and Sh2d1a-/- follicular helper CD4 T cells (CXCR5high),versus non-follicular helper CD4 T cells (CXCR5low), eight days after viral infection.


title: Expression Data from in vivo Tfh vs GC Tfh vs non-Tfh

overall_design:
Analysis of in vivo polyclonal GC Tfh vs Tfh vs Non-Tfh eight days after LCMV viral infection.
Analysis of in vivo follicular helper CD4 T cells (CXCR5high GL7low), versus germinal center follicular helper CD4 T cells (CXCR5hi GL7hi), versus non-follicular helper CD4 T cells (CXCR5low) eight days after viral infection.


title: Expression data from mouse ES and iPS cells

status: Public on May 13 2010

city: Beijing

first: Qi

last: Zhou

address: No.1 Beichen West Road

country: China

institute: Institute of Zoology, Chinese Academy of Sciences

summary: Induced pluripotent stem (iPS) cells were produced from reprogramming of somatic cells, and they are shown to possess pluripotent properties similar to embryonic stem (ES) cells. Here we used microarrays to detail the global expression pattern among the ES cells and iPS cells, as well as the original mouse embryo fibroblast (MEF), to identify important players involved in the reprogramming process.

overall_design: Mouse ES cell cultures, as well as selected iPS cell lines and the original MEF cells they were derived from, were used for RNA extraction and hybridization on Affymetrix microarrays. Three biological replicates for each sample were processed. GeneChips were processed and data were analyzed using the RMA package of Bioconductor.

first: Xiu-Jie

last: Wang


title: Expression analysis data from large T antigen-immortalized murine embryonic fibroblasts (MEFs)

status: Public on Apr 17 2010

address: 9500 Gilman Drive

institute: UCSD

summary:
Microarrays were used to examine the genome-wide expression in FIH null, VHL null and VHL/FIH double null MEFs.
We used these data to analyze how deletion of FIH or VHL alone affects gene expression and if VHL and FIH have synergistic effects and differential selectivity on regulating gene expression.

overall_design: To assess how deletion of FIH, VHL or both VHL and FIH affect gene expression genome-wide, we generated FIH null, VHL null and VHL/FIH double null MEFs after adeno-cre virus infection on large T-immortalized FIHdf, VHLdf, and VHLdf/FIHdf MEFs. These MEFs were cultured under normoxia (21% O2) with complete culture medium before RNA extraction. Total RNA were isolated by using the Qiagen RNeasy kit and treated with on-column DNase digestion. Affymetrix GeneChip Mouse Genome 430 2.0 Array was used.

first: Randall

last: Johnson


title: Expression data from Transgenic mice skin expressing deltaNp63alpha

city: BUFFALO

first: SATRAJIT

last: SINHA

address: 701 ELLICOTT STREET

institute: SUNY AT BUFFALO

summary: We developed a Tet-inducible system to express deltaNp63alpha isoform under the control of keratin 5 promoter. Transgenic mice, which were Bigenic (BG) developed a severe skin phenotype with abnormal keratinocyte differentiation and defects in hair follicle development and cycling. Skin samples from transgenic animals and wild type animals were analyzed for global transcriptome changes.

overall_design: We used microarrays to performing transcriptional profiling of deltaNp63alpha transgenic and control dorsal skin at P16.

first: Rose-Anne

last: Romano

first: Kirsten

last: Smalley

first: Song

last: Liu

first: Satrajit

last: Sinha


title: Gene expression data of BCR-ABL1 transformed B cell precursors from BCL6 wild-type and BCL6 knockout mice

status: Public on May 10 2010

city: Los Angeles

first: Markus

last: Müschen

address: 4650 Sunset Blvd

department: Childrens Hospital Los Angeles

institute: University of Southern California

summary: To elucidate the mechanism of BCL6-mediated pre-B cell survival signaling, we investigated the gene expression pattern in BCR-ABL1-transformed BCL6+/+ and BCL6-/- B cell precursors. Pharmacological inhibition of BCR-ABL1 was performed with the BCR-ABL1 kinase inhibitor STI571 (Imatinib).

overall_design: BCR-ABL1 transformed B cell precursors of BCL6 wildtype and BCL6 knockout mice were either treated with 10µM STI571 (Imatinib) for 16 hours or cultured in absence of STI571. Three samples for each condition were processed.

first: Cihangir

last: Duy

first: Jessica

middle: J

last: Yu

first: Rahul

last: Nahar

first: Srividya

last: Swaminathan

first: Soo-mi

last: Kweon

first: Jose

last: Polo

first: Ester

last: Valls

first: Lars

last: Klemm

first: Seyedmehdi

last: Shojaee

first: Leandro

last: Cerchietti

first: Wolfgang

last: Schuh

first: Hans-Martin

last: Jäck

first: Christian

last: Hurtz

first: Parham

last: Ramezani-Rad

first: Sebastian

last: Herzog

first: Hassan

last: Jumaa

first: Phillip

last: Koeffler

first: Ignacio

last: de Alborán

first: Ari

last: Melnick

first: Hilda

middle: B

last: Ye


title: Germinal center T follicular helper cell IL-4 production is dependent on SLAM receptor (CD150)

first: Shane

last: Crotty

summary:
CD4 T cell help is critical for both the generation and maintenance of germinal centers, and T follicular helper (TFH) cells are the CD4 T cell subset required for this process. SAP (SH2D1A) expression in CD4 T cells is essential for germinal center development. However, SAP-deficient mice have only a moderate defect in TFH differentiation as defined by common TFH surface markers. CXCR5+ TFH cells are found within the germinal center as well as along the boundary regions of T/B cell zones. Here we show that germinal center associated T cells (GC TFH) can be identified by their co-expression of CXCR5 and the GL7 epitope, allowing for phenotypic and functional analysis of TFH and GC TFH populations. Here we show GC TFH are a functionally discrete subset of further polarized TFH cells, with enhanced B cell help capacity and a specialized ability to produce IL-4 in a TH2-independent manner. Strikingly, SAP-deficient mice have an absence of the GC TFH subset and SAP- TFH are defective in IL-4 and IL-21 production. We further demonstrate that SLAM (Slamf1, CD150), a surface receptor that utilizes SAP signaling, is specifically required for IL-4 production by GC TFH. GC TFH cells require IL-4 and IL-21 production for optimal help to B cells. These data illustrate complexities of SAP-dependent SLAM family receptor signaling, revealing a prominent role for SLAM receptor ligation in IL-4 production by germinal center CD4 T cells but not in TFH and GC TFH differentiation.

This SuperSeries is composed of the SubSeries listed below.


title: Gene expression profiling of constitutive activation of Smoothened in the mouse uterus

status: Public on Apr 13 2010

city: Houston

first: Chad

last: Creighton

state: TX

address: One Baylor Plaza, Mail Stop: BCM305

department: Biostatistics, Ducan Cancer Center

institute: Baylor College of Medicine

summary:
In order to gain a better understanding of Ihh action during embryo implantation, we constitutively activated Smo in the murine uterus using the PRcre mouse model (PRcre/+SmoM2+; SmoM2).  Female SmoM2 mice were infertile. They exhibited normal serum progesterone levels and normal ovulation, but ova failed to be fertilized in vivo and the uterus failed to undergo the artificially induced decidual response.  SmoM2 mice exhibited uterine hypertrophy.  The endometrium had a reduced number of uterine glands and the endometrial stroma lost its normal morphologic characteristics.  Microarray analysis of 3 month old SmoM2 uteri demonstrated a chondrocytic signature and confirmed that constitutive activation of SmoM2 increased extracellular matrix production.  Thus, constitutive activation of Smo in the mouse uterus alters the extracellular matrix which interferes with early pregnancy.

Keywords: two group comparison

overall_design: We constitutively activated Hh signaling in the uterus by the expression of a mutant SmoM2 allele. We crossed these mice to the PRcre mouse model to constitutively activate Smo in the murine uterus (PRcre/+SmoM2+; SmoM2). High density DNA microarray analysis was performed on 3 month old control and SmoM2 uteri.

first: Franco

last: Demayo

first: Heather

last: Franco


title: Global gene expression profile of human placental pericytes

status: Public on Apr 14 2010

first: Cheryl

middle: L.

last: Maier

address: 10 Amistad St.

department: Immunobiology

summary:
The objective of this array was to determine the global gene expression profile of human placental pericytes for comparison with other publicly available arrays of pericytes and mesenchymal stromal cells isolated from various human tissues.

Pericytes are critical cellular components of the microvasculature that play a major role in vascular development and pathologies, yet their study has been hindered by lack of a standardized method for their isolation and growth.  Here we report a method for culturing human pericytes from a readily available tissue source, placenta, and provide a thorough characterization of resultant cell populations. We developed an optimized protocol for obtaining pericytes by outgrowth from microvessel fragments recovered after enzymatic digestion of human placental tissue. We characterized outgrowth populations by immunostaining, by gene expression analysis, and by functional evaluation of cells implanted in vivo. Our approach yields human pericytes that may be serially expanded in culture and that uniformly express the cellular markers NG2, CD90, CD146, α-SMA, and PDGFR-β, but lack markers of smooth muscle cells, endothelial cells, and leukocytes. When co-implanted with human endothelial cells into C.B-17 SCID/bg mice, human pericytes invest and stabilize developing human endothelial cell-lined microvessels. We conclude that our method for culturing pericytes from human placenta results in the expansion of functional pericytes that may be used to study a variety of questions related to vascular biology.

overall_design: Total RNA from three different pericyte isolations at subculture 1 was collected and examined for relative gene expression.

first: Benjamin

last: Shepherd

first: Jordan

last: Pober


title: Differential gene expression patterns in lung carcinogenesis mediated by loss of mouse tumor supressor Gprc5a

first: Humam

last: Kadara

address: 2130 W. Holcombe Blvd

institute: University of Texas MD Anderson Cancer Center

summary: Increasing the understanding of the impact of changes in oncogenes and tumor suppressor genes is essential for improving the management of lung cancer. Recently, we identified a new mouse lung-specific tumor suppressor - the G-protein coupled receptor 5A (Gprc5a). We sought to understand the molecular consequences of Gprc5a loss and towards this we performed microarray analysis of the transcriptomes of lung epithelial cells cultured from normal tracheas of Gprc5a knockout and wild-type mice to define a loss-of-Gprc5a gene signature. Moreover, we analyzed differential gene expression patterns between Gprc5a knockout normal lung epithelial cells as well as lung adenocarcinoma cells isolated and cultured from tumors of NNK-exposed Gprc5a knockout mice.

overall_design: Gprc5a wild type cells (WT-NLE) and Gprc5a knockout cells (NULL-NLE) were isolated and cultured from trachea of three week old Gprc5a wild type and knockout mice, respectively. MDA-F471 mouse lung adenocarcinoma cells were derived de novo from an adenocarcinoma that was found in the lung of a female Gprc5a-knockout mouse sacrificed 16 months after NNK tobacco carcinogen i.p. injection based on a protocol approved by the M.D. Anderson Cancer Center Institutional Animal Care and Use Committee. Following RNA extraction and purification, the transcriptome of the Gprc5a wild type and knockout cells were analyzed by microarray analysis using the Affymetrix MG-430 2.0 murine array platform.

first: Junya

last: Fujimoto

first: Taoyan

last: Men

first: Xiaofeng

first: Dafna

last: Lotan

first: Ju-Seog

last: Lee

first: Reuben


title: Differential gene expression between ERRa KO and WT mouse kidneys

status: Public on Apr 11 2010

city: Montreal

first: Vincent

last: Giguere

state: Quebec

address: 1160 Pine avenue West

department: Biochemistry

country: Canada

institute: McGill University

summary: Estrogen-related receptor (ERR) alpha is an orphan nuclear receptor highly expressed in the kidneys. ERRalpha is implicated in renal sodium and potassium homeostasis and blood pressure regulation. We used microarray analysis to identify differentially expressed genes in ERR alpha knockout mice kidneys versus wild-type. The results provide insight on the roles of ERRalpha in the kidney.

overall_design: Three biological replicates of WT and ERRaKO were performed, for a total of 6 samples. 2-3 month old males of each genotype were used.

first: Annie

last: Tremblay


title: POU4F1 is associated with t(8;21) AML and contributes directly to its unique transcriptional signature

status: Public on Apr 09 2010

city: Baltimore

first: Patrick

last: Cahan

state: MD

address: 733 North Broadway, MRB 653

department: ICE and Biomedical Engineering

institute: Johns Hopkins University School of Medicine

summary: POU4F1 is associated with t(8;21) acute myeloid leukemia (AML) and contributes directly to its unique transcriptional signature

overall_design: To identify targets of POU4F1, we performed gene expression profiling, comparing Pou4f1+/+ or Pou4f1-/- fetal liver cells to cells overexpressing POU4F1 and identified 140 differentially expressed genes.

first: Julie

last: Fortier

first: Timothy

middle: A

last: Graubert


title: Pediatric mastocytosis-associated KIT extracellular domain mutations exhibit different functional and signaling properties compared with KITphosphotransferase domain mutations.

status: Public on Apr 10 2010

city: Marseille

first: Pascal

last: FINETTI

state: BdR

address: 232 Bd Ste Marguerite

department: Centre de cancérologie de Marseille

country: France

institute: Institut Paoli-Calmettes

summary: Most adult patients have a D816V mutation in phosphotransferase domain (PTD), we have described that half of the children carry mutations in extracellular domain (ECD). KIT-ECD versus IT-PTD-mutants were introduced into rodent Ba/F3, EML, Rat2 and human TF1 cells to investigate their biological effect. ECD- and PTD-mutants also displayed distinct whole-genome transcriptional profiles in EML cells. We observed differences in their signaling properties: they both activated STAT pathways, whereas AKT pathway was only activated by ECD-mutants. Consistently, AKT inhibitor suppressed ECD-mutant-dependent proliferation, clonogenicity and erythroid differentiation. Expression of myristoylated AKT restored erythroid differentiation in EMLPTD cells, suggesting the differential role of AKT in those mutants. Overall, our study implied different pathogenesis of pediatric versus adult mastocytosis, which might explain their diverse phenotypes.

overall_design: Each EML cell line (Del417-419insY mutant and D816V mutant) was cultured with or without 250 ng/mL SCF for 48h. Gene expression profile analysis was performed using whole-genome microarrays. RNA expression profiling of cell lines was done with Affymetrix M430 2.0 mouse oligonucleotide microarrays containing 45.101 probe sets, representing 21.408 transcripts and variants including 17.482 well-characterized mouse genes. Preparation of cRNA, hybridizations, washes, detection and quantification were done as recommended by the supplier. For each sample, synthesis of the first-strand cDNA was done from 3 μg total RNA by T7-oligo(dT) priming, followed by second-strand cDNA synthesis. After purification, in vitro transcription associated with amplification generated cRNA-containing biotinylated pseudouridine. Biotinylated cRNA was purified, quantified and chemically fragmented (95°C for 35 min), then hybridized to microarrays in 200 μL hybridization buffer at 45°C for 16 h. Automated washes and staining with streptavidin-phycoerythrin were done as recommended. Signal amplification was done by biotinylated antistreptavidin antibody with goat-IgG blocking antibody. Scanning was done with Affymetrix GeneArray scanner and quantification with Affymetrix GCOS software.

first: Ying

last: Yang

first: S

last: Letard

first: L

last: Borge

first: A

last: Chaix

first: K

last: Hanssens

last: Lopez

first: M

last: Vita

first: P

last: Finetti

last: Birnbaum

first: F

last: Bertucci

last: Gomez

last: de Sepulveda

last: Dubreuil


title: Molecular Profiling of the Developing Axial Skeleton: A role for Tgfbr2 in the Development of the Intervertebral Disc.

city: Birmingham

first: Rosa

last: Serra

state: AL

address: 1918 University Blvd. 660 MCLM

department: Cell Biology

institute: University of Alabama at Birmingham

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

overall_design: Refer to individual Series


title: PI3K pathway activity in the normal airway of smokers with lung cancer, and in smokers with airway dysplasia

status: Public on Apr 12 2010

first: Adam

last: Gustafson

address: 44 Cummington St

institute: Boston University

summary: Cytologically normal airway epithelial samples were collected during bronchoscopy of current and former smokers. Subjects enrolled in this study were either under suspicion of having lung cancer, had dysplasia in their airway, or were a healthy current, former or never smoker. We supplemented existing GEO series (GSE4115 and GSE7895) with the samples in this study to explore PI3K pathway activity in the these cohorts.

overall_design: This study contains: 2 arrays from smokers with COPD (no lung cancer), 1 array from smoker without COPD (no lung cancer); 2 samples from patients with lung cancer, 2 samples from patients without lung cancer; 20 samples from 10 matched individuals with airway dysplasia before and after treatment with myo-inositol, 6 additional samples from individuals with airway dysplasia; 27 samples from mammary epithelial cells used in oncogenic pathway analysis that have either the PI3K pathway activated, the Np63 pathway activated, or are a GFP control.

first: Avrum

last: Spira


title: Gene expression in embryonic intervertebral disc and vertebrae.

summary: Very little is known about how intervertebral disc (IVD) is formed or maintained. Members of the TGF-ß superfamily are secreted signaling proteins that regulate many aspects of development including cellular differentiation. We recently showed that deletion of Tgfbr2 in Col2a expressing tissue results in alterations in development of IVD annulus fibrosus. The results suggested TGF-ß has an important role in regulating development of the axial skeleton, however, the mechanistic basis of TGF-ß action in these specialized joints is not known.  One of the hurdles to understanding development of IVD is a lack of known markers. To identify genes that are enriched in the developing IVD and to begin to understand the mechanism of TGF-ß action in IVD development, we undertook a global analysis of gene expression comparing gene expression profiles in developing vertebrae and IVD.  We also compared expression profiles in tissues from wild type and Tgfbr2 mutant mice.  Lists of IVD and vertebrae enriched genes were generated. Expression patterns for several genes were verified either through in situ hybridization or literature/ database searches resulting in a list of genes that can be used as markers of IVD.  Cluster analysis using genes listed under the Gene Ontology terms multicellular organism development and pattern specification indicated that mutant IVD more closely resembled vertebrae than wild type IVD. We propose TGF-ß has two functions in IVD development: 1) to prevent chondrocyte differentiation in the presumptive IVD and 2) to promote differentiation of annulus fibrosus from sclerotome. We have identified genes that are enriched in the IVD and regulated by TGF-ß that warrant further investigation as regulators of IVD development.

overall_design: Thirteen samples were analyzed.  This includes three biological replicates of laser captured IVD from E13.5 day control mice, three biological replicates of laser captured vertebrae from the same E13.5 day control mice, three biological relicates of laser captured vertebrae from E13.5 day Col2aCre;Tgfbr2lox/lox mice, and four biological replicates of laser captured IVD from E13.5 day Col2aCre;Tgfbr2lox/lox mice.


title: TGF-beta and BMP mediated gene expression in cultured sclerotome.

summary: Very little is known about how intervertebral disc (IVD) is formed or maintained. Members of the TGF-ß superfamily are secreted signaling proteins that regulate many aspects of development including cellular differentiation. We recently showed that deletion of Tgfbr2 in Col2a expressing tissue results in alterations in development of IVD annulus fibrosus. The results suggested TGF-ß has an important role in regulating development of the axial skeleton, however, the mechanistic basis of TGF-ß action in these specialized joints is not known.  To understand the mechanism of TGF-ß action in IVD development, we undertook a global analysis of gene expression comparing gene expression profiles in sclerotome cultures treated with TGF-ß or BMP4. As expected, treatment with BMP4 resulted in up-regulation of cartilage marker genes including Acan, Sox 5, Sox6, and Sox9.  In contrast, treatment with TGF-ß1 did not regulate expression of cartilage markers but instead resulted in up-regulation of many IVD markers including Fmod and Adamtsl2. We propose TGF-ß has two functions in IVD development: 1) to prevent chondrocyte differentiation in the presumptive IVD and 2) to promote differentiation of annulus fibrosus from sclerotome. We have identified genes that are enriched in the IVD and regulated by TGF-ß that warrant further investigation as regulators of IVD development.

overall_design: Nine samples were analyzed.  Three biological replicates of untreated sclerotome grown in micromass culture.  Three biological replicates of cells treated with 50 ng/ml BMP4 for 8 hours and three biological replicates of cells treated with 5 ng/ ml TGF-ß1 for 8 hours.


title: The miR-17/92 Polycistron Is Up-regulated in Sonic Hedgehog-Driven Medulloblastomas and Induced by N-myc in Sonic Hedgehog–Treated Cerebellar Neural Precursors

status: Public on Apr 02 2010

city: HEIDELBERG

first: Paul

middle: A.

last: Northcott

address: Im Neuenheimer Feld 280

institute: German Cancer Research Center (DKFZ)

summary: Medulloblastoma is the most common malignant pediatric brain tumor, and mechanisms underlying its development are poorly understood. We identified recurrent amplification of the miR-17/92 polycistron proto-oncogene in 6% of pediatric medulloblastomas by high-resolution single-nucleotide polymorphism genotyping arrays and subsequent interphase fluorescence in situ hybridization on a human medulloblastoma tissue microarray. Profiling the expression of 427 mature microRNAs (miRNA) in a series of 90 primary human medulloblastomas revealed that components of the miR-17/92 polycistron are the most highly up-regulated miRNAs in medulloblastoma. Expression of miR-17/92 was highest in the subgroup of medulloblastomas associated with activation of the sonic hedgehog (Shh) signaling pathway compared with other subgroups of medulloblastoma. Medulloblastomas in which miR-17/92 was up-regulated also had elevated levels of MYC/MYCN expression. Consistent with its regulation by Shh, we observed that Shh treatment of primary cerebellar granule neuron precursors (CGNP), proposed cells of origin for the Shh-associated medulloblastomas, resulted in increased miR-17/92 expression. In CGNPs, the Shh effector N-myc, but not Gli1, induced miR-17/92 expression. Ectopic miR-17/92 expression in CGNPs synergized with exogenous Shh to increase proliferation and also enabled them to proliferate in the absence of Shh. We conclude that miR-17/92 is a positive effector of Shh-mediated proliferation and that aberrant expression/amplification of this miR confers a growth advantage to medulloblastomas.

overall_design: A total of 90 primary medulloblastoma specimens were profiled by Affymetrix exon array and gene-level analysis was performed.

first: Africa

last: Fernandez-L

first: John

last: Hagan

first: David

middle: W

last: Ellison

first: Wesia

last: Grajkowska

first: Yancey

last: Gillespie

first: Richard

last: Grundy

last: Van Meter

first: James

middle: T

last: Rutka

first: Carlo

last: Croce

first: Anna

last: Kenney

first: Michael

last: Taylor


title: Expression data from rostral forebrains of wild-type and Fezf1-/- Fezf2-/- mice

city: Nagoya

first: Masahiko

last: Hibi

state: Aichi

address: Furocho, Chikusaku

department: Bioscience and Biotechnology Center

country: Japan

institute: Nagoya University

summary:
Zinc-finger genes Fezf1 and Fezf2 encode transcriptional repressors. Fezf1 and Fezf2 are expressed in the early neural stem/progenitor cells and control neuronal differentiation in mouse dorsal telencephalon.
We compared gene expression profiles of rostral forebrains, which contain the telencephalon and the rostral part of the diencephalon, from embryonic day (E) 9.5, E10.5, and E12.5 wild-type control and Fezf1-/- Fezf2 -/- mouse embryos.

overall_design: The forebrain rostral to the caudal limit of the lateral ventricles was isolated manually from E9.5, E10.5, and E12.5 wild-type and Fezf1-/- Fezf2-/- mice. Total RNAs were isolated by Separsol-RNA I and were used for microarray analyses.

first: Takeshi

last: Shimizu

first: Masato

last: Nakazawa


title: Regulation of chondrogenesis in early murine limb mesenchyme by BMP signals

status: Public on Apr 01 2010

city: Vancouver

first: Tully

middle: Michael

last: Underhill

state: British Columbia

address: 2222 Health Sciences Mall

department: Biomedical Research Centre

institute: University of British Columbia

summary: Numerous studies have established a critical role for BMP signaling in skeletal development.  In the developing axial skeleton, sequential SHH and BMP signals are required for specification of a chondrogenic fate in somitic tissue.  A similar paradigm is thought to operate in the limb, but the signals involved are unclear.  To investigate the nature of these signals we examined BMP action in mesenchymal populations derived from the early murine limb bud (~ E10.5).  These populations exhibited a graded response to BMPs, in which early limb mesenchymal (EL) cells (from the distal hind limb) displayed an anti-chondrogenic response, whereas BMPs promoted chondrogenesis in older cell populations. To better understand the molecular basis of disparate BMP action in these various populations, gene expression profiling with Affymetrix microarrays was employed to identify BMP-regulated genes.  These analyses showed that BMPs induced a distinct gene expression pattern in the EL cultures versus later mesenchymal limb populations (IM and LT).

overall_design: Mouse embryos at gestational age E10.5 were collected and various portions of the limb were micro-dissected.  These led to the generation of three populations of cells, early (EL) limb mesenchymal cells from the distal half of the hind limb, an intermediate (IM) population derived from the distal 1/3 of the fore limb, and a later (LT) population from the proximal 2/3 of the fore limb.  Mesenchymal cells were isolated and cultured with and without BMP4 treatment.  RNA was extracted from cultures at either Day 0,1 or 2, labelled and hybridized to Affymetrix 430 2.0 microarrays.  For each time point, RNA was collected from two biological replicates for each treatment condition.

first: T


title: Visualization of cancer initiating cell in the vascular niche utilized with transcriptional activity of PSF1

status: Public on Mar 31 2010

city: Suita

first: Nobuyuki

last: Takakura

state: Osaka

address: Yamada-oka 3-1

department: Signal Transduction

institute: The Research Institute for Microbial Disease, Osaka university

summary: Identification of cancer stem/initiating cells (CSCs/CICs) by a specific marker is useful for diagnosis and therapy of cancer. We have determined that PSF1 which plays a role in DNA replication in lower species is strongly expressed in wide range of normal stem cell population. Here, utilizing the transcriptional activity of PSF1 promoter in tumor cell xenograft model, we show that PSF1high cancer cells display malignant features including high proliferating activity, serial transplantation potential, and metastatic ability those are used for criteria of CSCs/CICs. PSF1high cancer cells localize in perivascular region and genetically display ES cell like signature. Silencing of PSF1 by RNAi inhibited growth of cancer cells mediated by disruption of DNA synthesis and chromosomal segregation. These suggested that PSF1 is a possible maker and a molecular target of CSCs/CICs.

overall_design: We have cloned the mouse PSF1 promoter gene and established  lung carcinoma (lewis lung carcinoma: LLC) and colon cancer (colon26) cell lines stably expressing enhanced green fluorescent protein (EGFP) under the transcriptional control of PSF1 promoter (LLC- and colon-PSF1P-EGFP, respectively). Mouse xenograft tumor cells were dissociated and sorted into PSF1 low and high expression cells by FACS. We sought whether PSF1 high expression cells possess embryonic stem cells-like signature.

first: Yumi

last: Nagahama

first: Takashi

last: Minami


title: Differential gene expression in CD11b+ splenocytes from mice subject to social threat vs. control

first: Steve

last: Cole

address: 11-934 Factor Bldg, UCLA

institute: UCLA School of Medicine

summary:
Gene expression profiling was carried out on splenocyte mRNA samples collected from 10 animals subject to repeated social threat (pooled into 2 groups of 5) and 10 animals subject to non-threatening control conditions (pooled into 2 groups of 5).  The primary research question is whether gene expression differs in CD11b+ splenocytes from animals exposed to social threat vs non-threatening control conditions.

Keywords: Risk prediction

overall_design: RNA from 5 mice/sample was pooled to generate 4 total samples: 2 from mice subject to repeated social threat, and 2 from control mice.


title: Differential gene expression in prefrontal cortex from mice subject to social threat vs. control

summary:
Gene expression profiling was carried out on prefrontal cortex mRNA samples collected from 10 animals subject to repeated social threat (pooled into 2 groups of 5) and 10 animals subject to non-threatening control conditions (pooled into 2 groups of 5).  The primary research question is whether gene expression differs in prefrontal cortex tissue from animals exposed to social threat vs non-threatening control conditions.

Keywords: Risk prediction


title: Expression data from lung of mice bearing mutations of FGFR3 and FGFR4

city: Rochester

first: Soumyaroop

last: Bhattacharya

state: NY

address: 601 Elmwood Avenue Box 850

department: Pediatrics

institute: University of Rochester Medical Center

summary:
Gene expression profiling of newborn lung tissue revealed few changes in compound FGFR3/FGFR4 deficient mice, consistent with their normal lung morphology at birth, suggesting the sequence of events leading to the phenotype initiates after birth in this model.
Profiling of 4 week-old lung tissues revealed an induction of genes related to elastic fiber assembly in compound mutants.

overall_design: Lung RNA isolated from three animals of each genotype-age group were pooled for each Affymetrix chip (n=3 chips for each, except n=2 for wild type at 4 weeks.

first: Sorachai

last: Srisuma


title: H3K27 Methyltransferase PRC2 Represses Wnt Genes to Facilitate Adipogenesis

status: Public on Mar 19 2010

city: Bethesda

first: Lifeng

last: Wang

address: 9000 Rockville Pike

department: NIDDK

institute: NIH

summary: The Wnt/b-catenin signaling inhibits adipogenesis. Genome-wide profiling studies have revealed the enrichment of histone H3K27 methyltransferase PRC2 on Wnt genes. However, the functional significance of such a direct link between the two types of developmental regulators in mammalian cells, and the role of PRC2 in adipogenesis, remain unclear. Here we show PRC2 and its H3K27 methyltransferase activity are required for adipogenesis. PRC2 directly represses Wnt1, 6, 10a and 10b genes in preadipocytes and during adipogenesis. Deletion of the enzymatic Ezh2 subunit of PRC2 eliminates H3K27me3 on Wnt promoters and de-represses Wnt expression, which leads to activation of Wnt/b-catenin signaling and inhibition of adipogenesis. Ectopic expression of the wild type Ezh2, but not the enzymatically inactive F667I mutant, prevents the loss of H3K27me3 and the defects in adipogenesis in Ezh2-/- preadipocytes. The adipogenesis defects in Ezh2-/- cells can be rescued by expression of adipogenic transcription factors PPARa, C/EBPb, or inhibitors of Wnt/b-catenin signaling. Interestingly, Ezh2-/- cells show marked increase of H3K27 acetylation globally as well as on Wnt promoters. These results indicate that H3K27 methyltransferase PRC2 directly represses Wnt genes to facilitate adipogenesis, and suggest that acetylation and trimethylation on H3K27 play opposing roles in regulating Wnt expression.

overall_design: To identify additional PRC2-regulated genes in preadipocytes, we performed microarray analysis in Ezh2flox/flox preadipocytes infected with retroviruses expressing Cre or vector alone.

first: Qihuang

last: Jin

first: Ji-Eun

last: Lee

first: I-hsin

last: Su

first: Kai

last: Ge


title: Expression data from effector CD4 T cells isolated from MRL/Faslpr mice.

status: Public on Mar 18 2010

first: Amanda

last: Poholek

address: 300 Cedar St. TAC S530

institute: Yale University

summary:
MRL/Faslpr mice is a lupus prone strain that exhibits lupus disease features at 12-16 weeks of age, including high-titer circulating anti-DNA antibodies, splenomegaly, lymphadnopathy, skin lesions, and IgG deposits in the kidney. At 16-24 weeks of age, CD4+ B220- CD44+ T cells were sorted into three populations based on the expression of two cell surface molecules, CD62L and PSGL1. CD62Lhi PSGL1hi, CD62Llo PSGL1hi, and CD62Llo PSGL1lo CD4+ T cells were isolated directly ex vivo. There was no treatment given to the animals. Naive (CD62Lhi CD44lo) CD4+ B220- T cells were isolated from young 6-8 week old female mice for comparison.
We used a microarray to identify unique features of the CD62Llo PSGL1lo population in comparison to naïve CD4+ T cells and other activated CD4+ T cells.

overall_design: Cells were isolated from the spleens of aged (16-24 weeks) female MRL/Faslpr mice directy ex vivo, and immediatley sorted into 3 populations; CD62Lhi PSGL1hi, CD62Llo PSGL1hi, and CD62Llo PSGL1lo. All 3 populations of cells were previously gated on TCRb+, CD4+, B220-, CD44+. Naive CD4 T cells were isolated  directly ex vivo from the spleens of young (6-8 weeks) female MRL/Faslpr mice, and immediately sorted by gating on TCRb+, CD4+, B220-, CD62Lhi, CD44lo. Three indepedent sorts were performed. RNA was isolated using Qiagen's RNAeasy kit and total RNA was submitted to the W.M. Keck Foundation Biotechnology Resource Laboratory at Yale for amplification and hybridization to Affymetrix Mouse Genome 430 2.0 GeneChips.

middle: C

first: Joe

last: Craft


title: Comparative transcriptional profiling of tumor-associated and normal lymphatic endothelial cells

city: Zurich

first: milica

last: Nikolic

department: DCHAB

country: Switzerland

institute: ETH

summary:
In the past decade, the relevance of tumor-induced lymphangiogenesis for the metastatic spread of tumor cells has been demonstrated, thus indicating the potential of targeting tumor lymphangiogenesis to treat cancer. Whereas numerous preclinical studies demonstrated that blocking angiogenesis or lymphangiogenesis could inhibit tumor metastasis, the scarcity of highly selective targeting candidates hampers their translation to the clinic.
We employed a new approach consisting of immuno-laser capture microdissection (i-LCM) and transcriptional profiling by means of microarrays in order to identify novel tumor-specific endothelial markers.

overall_design: By using short immunostainings prior to microdissection, specific identification of lymphatic (LECs) and blood (BECs) endothelial cells was allowed. For the subsequent gene expression profiling, a single round of the Ribo-Spia amplification method in combination with the Affymterix microarray platform was used. Comparison of gene expression profiles of tumor-associated and normal LECs resulted in the identification of differentially expressed genes in tumor-associated lymphatic vasculature.

first: Michael

last: Detmar

first: Milica


title: Mouse primary megakaryocytes, wild type & NF-E2p45-deficient

status: Public on Mar 22 2010

city: Sendai

first: Hozumi

last: Motohashi

state: Miyagi

address: 2-1 Seiryo-machi, Aoba-ku

department: Center for Radioisotope Science

institute: Tohoku University Graduate School of Medicine

summary: To identify p45 target genes, we conducted gene expression profiling with p45-null megakaryocytes cultured from E14.5 fetal liver. Many genes encoding membrane proteins and enzymes related to platelet function, including Txas, Glycoprotein 6 (Gp6) and Selectin P (Selp), were repressed in the absence of p45. Considering the similar DNA binding specificity of p45 and Nrf2 in vitro, we expected p45 to activate cytoprotective genes that are established Nrf2 targets. However, the expression of numerous detoxifying enzymes and stress-responsive genes, including NAD(P)H:quinone oxidoreductase (Nqo1), were increased in the absence of p45.

overall_design: To obtain wild type and p45-null fetal livers, p45+/- mice were crossed.  Whole livers were recovered from mouse fetuses at E14.5 and single cell suspensions were prepared by successive passage through 25-gauge needles. Fetal liver cells were maintained in RPMI1640 (Wako) supplemented with 20% charcoal-stripped fetal bovine serum, 50 units/ml penicillin, 50 µg/ml streptomycin, and 50 ng/ml of recombinant human thrombopoietin.  CD41+ cells were selected from a 4 day primary culture of E14.5 fetal liver cells using a MACS magnetic system (Miltenyi Biotec). The fetal liver culture with TPO described above was incubated with FITC-conjugated anti-CD41 antibody (BD Pharmingen, clone MWReg30) followed by incubation with anti-FITC microbeads. Subsequently, the microbeads were selected magnetically through MACS large cell columns (Miltenyi Biotec). Total RNA was extracted from the CD41+ cells using Isogen (Nippon Gene).

first: Momoko

last: Kimura

first: Hiroyuki

last: Aburatani

first: Masayuki

last: Yamamoto


title: Expression data from ES cell-derived motoneuron

status: Public on Mar 16 2010

city: Sinjhuang

first: Chi-Chung

address: No. 510, Jhongjheng Rd.,

country: Taiwan

institute: Fu Jen Catholic University

summary:
Neural formation from ES cells provides a novel system for studying axonogenesis in projection neurons.
We used microarrays to clarify the global gene expression patterns of ES-derived motoneurons and compared with the parental undifferentiated ES cells.

overall_design: HB9-GFP ES cells on day 7 were mechanically pipetted into small cell clumps and concentrated to a density of approximately 1×104 cells/μl in neural differentiation medium. The animals received total laminectomy from T8 to T10. Total RNA was extracted from the undifferentiated ES cells (1531), the sorted HB9-GFP+ cells (1557), the sorted sox1 neural stem cells (1602) and the mouse cerebellar granule cells (1532) on postnatal day 6 and performed hybridization on Affymetrix microarrays.

first: Hong-Lin

first: Hung-Chuan

last: Pan

first: Ya-Ting

last: Wu


title: mRNA and microRNA microarray analysis on human Jurkat T cells exposed to silver nanoparticles and silver ions

status: Public on Mar 10 2010

city: seoul

first: jinhee

last: choi

address: 90 Jeonnong-dong, Dongdaemun-gu

department: College of Urban Science

country: South Korea

institute: University of Seoul

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

summary: To identify genes and pathways involved in AgNPs and Ag ion toxicity, mRNA microarray analysis was conducted on human Jurkat T cells. The results indicate that more DEGs were induced by AgNPs than by Ag ion and AgNPs induced gene expression were not clustered with control and Ag ion induced ones. DEG analysis indicated that metallothionein (MT) 2A, 1H, 1F, and 1A and endonucleases G like 1 (ENDOGL1) were upregulated by AgNPs exposure more than 2 folds compared to control.

overall_design:
Jurkat T cells were exposed to 0.2 mg/L of AgNPs and Ag ions for 24 h. After treatment, total RNA was extracted and mRNA microarray was conducted on control, AgNPs treated and Ag ion treated Jurktat T cells. Microarray analysis were performed in triplicate.
Jurkat T cells were exposed to 0.2 mg/L of AgNPs and Ag ions for 24 h. After treatment, total RNA was extracted and miRNA microarray was conducted on control, AgNPs treated and Ag ion treated Jurktat T cells.

first: Jinhee

last: Choi


title: Cbfb/Runx1-repression independent blockage of differentiation and accumulation of Csf2rb expressing cells by Cbfb-MYH11

first: Christopher

address: Rm 5228, Bldg 50, South Dr.

department: NHGRI

summary:
It is known that CBFB-MYH11, the fusion gene generated by inversion of chromosome 16 in human acute myeloid leukemia, is causative for oncogenic transformation. However, the mechanism by which CBFB-MYH11 initiates leukemogenesis is not clear. Previously published reports showed that CBFB-MYH11 dominantly inhibits RUNX1 and CBFB, and such inhibition has been suggested as the mechanism for leukemogenesis. However, knockin mice expressing Cbfb-MYH11 (Cbfb+/MYH11) showed defects in primitive hematopoiesis not seen in Cbfb null (Cbfb-/-) embryos indicating that Cbfb-MYH11 has repression independent activities as well.
To identify gene expression changes associated with this novel activity, we compared the gene expression profile in the blood cells of Cbfb+/MYH11 and Cbfb-/- embryonic day 12.5 (E12.5) embryos with that of their wildtype littermates.

overall_design: Cbfb-MYH11 chimeras were mated to C57/Bl6 females to generate Cbfb+/MYH11 (Cbfb+/MYH11) and Cbfb+/+ (WT) embryos. Cbfb+/- x Cbfb+/- matings were used to generate Cbfb+/+ (Cbfb+/+) and Cbfb-/- (Cbfb-/-) embryos. Blood from 8-10 E12.5 embryos of the same genotype was pooled, and RNA was isolated, labeled, and hybridized to Affymetrix Genechip mouse microarray (430 2.0) chips. 4 chips were used for both the Cbfb+/MYH11 and littermate control samples. 3 chips were used for the Cbfb-/- samples and littermate control samples.

first: R

middle: K

last: Hyde

first: Yasuhiko

last: Kamikubo

first: Stacie

last: Anderson

first: Martha

last: Kirby

first: Lemlem

last: Alemu

first: Ling

last: Zhao

first: P

middle: P

last: Liu


title: Gene expression profiling of temporal lobes of wfs1 deficient mice

status: Public on Mar 09 2010

city: Perth

first: Sulev

last: Koks

state: Western Australia

address: 90 South Street

department: Centre for Molecular Medicine and Innovative Therapeutics

country: Australia

institute: Murdoch University

summary: Aim of present study was to describe the changes induced deletion of the Wfs1 gene in the temporal lobe of mice. Mutant mice were backcrossed to two different genomic backgrounds in order to exclude confounding foreign genomic background influence. Samples from temporal lobes were analyzed by using Affymetrix Genechips, expression profiles were functionally annotated by using GSEA and Ingenuity Pathway Analysis. We found that Wfs1 mutant mice are significantly smaller (20.9 ± 1.6 g) than their wild-type counterparts (31.0 ± 0.6g, p < 0.0001). Interestingly, genechip analysis identified growth hormone transcripts up-regulated and functional analysis found appropriate pathways activated. Moreover, we found significant increase in the level of IGF1 in the plasma of wfs1 mutant mice. Taken together, wfs1 mutation induces growth retardation whereas the growth hormone pathway is activated. Further studies are needed to describe biochemical and molecular details of the growth hormone axis in the wfs1 mutant mice.

overall_design: 37 samples, two genotypes (wild type and mutant), in two different genetic background (C57B6 and 129S6)

first: Ursel

last: Soomets

first: Jose

last: Paya-Cano

first: Cethy

last: Fernandes

first: Hendrik

last: Luuk

first: Mario

last: Plaas

first: Anton

last: Terasmaa

first: Valo

last: Tillmann

first: Klari

last: Noormets

first: Eero

last: Vasar

first: Leo

last: Schalkwyk


title: Expression data from P2 mouse hippocampus

status: Public on Mar 08 2010

city: Shanghai

first: Weiping

last: Zhang

address: 800 Xiangyin Road

department: Pathophysiology

institute: Second Military Medical University

summary:
Zinc finger protein ZBTB20 plays a critical role in mouse hippocampal development by orchestrating gene expression profile of hippocampal neurons.
We used microarrays to investigate the target gene of ZBTB20 in mouse hippocampal development.

overall_design: Mouse hippocampi were harvested at postnatal day 2 for RNA extraction and hybridization on Affymetrix microarrays. We sought to identify the target genes of transcription factor ZBTB20 in hippocampal development. To that end, we isolated the hippocampi from ZBTB20 knockout and their littermate control mice.

first: Zhifang

last: Xie


title: The difference of gene expression in mouse OPCs in normothermic and hypothermic culture

status: Public on Mar 06 2010

city: Shinjuku

first: Masahiro

last: Yamamoto

state: Tokyo

address: 35 Shinano-machi

department: Department of Kampo Medicine

institute: Keio University School of Medicine

summary:
We have found that the cell yield of oligodendrocyte precursor cells (OPCs) are higher in 31.5 ℃ than in 37 ℃ not by suppression of apoptosis but by enhancement of proliferation.
Here, we performed transcriptome analysis using Affymetrix GeneChip on the primary cultured oligodendrocyte precursor cells prepared from the brain of ICR mice.

overall_design: Oligodendrocyte precursor cells were prepared from primary mixed cell cultures of embryonic mouse cerebral hemispheres. The cerebral hemispheres from 15-day-old mouse embryos were enzymatically dissociated, seeded and cultured for 5 days in D-MEM containing 10% FBS. The cells were passaged to serum-free basal medium and cultured for further 48 hr at 37 ℃ and 31.5 ℃.

first: Sinya

last: Imada


title: Gene Expression Profiling of Blastocysts Reveals Early Differences Associated with Parthenogenetic Embryos

city: Tampa

first: Sean

last: Yoder

state: FL

address: 12902 Magnolia Dr.

department: Molecular Genomics Core Facility

institute: Moffitt Cancer Center & Research Institute

summary:
The goal of this experiment is to test the differences between parthenogenetic and normal fertilized embryos at the blastocyst stage.
Keywords: gene expression assay for comparison purposes

overall_design: 30 embryos were pooled to generate each sample.  One sample for each condition was processed per array.  The tetraploid embryos were used as a pseudoreplicate for the diploid embryos.  parthenotes were compared to the fertilized embryos.

first: Lin

first: Chao

last: Wu

first: Steven

last: Enkemann

first: Ping

last: Liang

first: Remko

last: Hermus

first: Claudia

last: Zanazzi

first: Leedert

last: Looijenga


title: Time-series of IL-6 stimulated primary mouse hepatocytes

status: Public on Mar 24 2010

city: Munich

first: Andreas

last: Roller

address: Max-Lebsche-Platz 31

institute: Munich Leukemia Laboratory

summary: External stimulations of cells by hormones, growth factors or cytokines activate signal transduction pathways that subsequently induce a rearrangement of cellular gene expression. The representation and analysis of changes in the gene response is complicated, and essentially consists of multiple layered temporal responses. In such situations, matrix factorization techniques may provide efficient tools for the detailed temporal analysis. Related methods applied in bioinformatics intentionally do not take prior knowledge into account. In signal processing, factorization techniques incorporating data properties like second-order spatial and temporal structures have shown a robust performance. However, large-scale biological data rarely imply a natural order that allows the definition of an autocorrelation function. We therefore develop the concept of graph-autocorrelation. We encode prior knowledge like transcriptional regulation, protein interactions or metabolic pathways as a weighted directed graph. By linking features along this underlying graph, we introduce a partial ordering of the samples to define an autocorrelation function. Using this framework as constraint to the matrix factorization task allows us to set up the fast and robust graph decorrelation (GraDe) algorithm. To analyze the alterations in the gene response in IL-6 stimulated primary mouse hepatocytes by GraDe, a time-course microarray experiment was performed. Extracted gene expression profiles show that IL-6 activates genes involved in cell cycle progression and cell division in a time-resolved manner. On the contrary, genes linked to metabolic and apoptotic processes are down-regulated indicating that IL-6 mediated priming rendered hepatocytes more responsive towards cell proliferation and reduces expenses for the energy household.

overall_design: Primary mouse hepatocytes were used in the analysis comprising stimulations with 1 nM IL-6 for 1 h, 2 h, 4 h and an unstimulated control (0 h), each performed in triplicate.

last: Kowarsch

first: Florian

last: Blöchl

first: Sebastian

last: Bohl

first: Maria

last: Saile

first: Nobert

last: Gretz

first: Ursula

last: Klingmüller

first: Fabian

last: Theis


title: Expression data from OVE26 diabetic mouse kidney

city: Louisville

first: lu

last: yang

state: KY

address: 570 S Preston Str

institute: University of Louisville

summary:
OVE26 mouse was chosen to study the progressive changes in renal gene expression because it displays the most advanced albuminuria mouse models that assembles advanced human diabetic nephropathy.
OVE26 mice induce inflammatory gene expression changes consistent with advanced renal disease, associated with severe albuminuria and not reported in any other diabetic models. They provide the first opportunity in a model of diabetic nephropathy to assess the effect of induction of inflammatory proteins that have been implicated in renal injury.

overall_design: Microarray expression was performed on whole kidney from control and diabetic mice at 2, 4 and 8 months of age and validated by rtPCR, in situ hybridization or immunohistochemistry.

first: Lu

last: Yang

first: Paul

middle: N

last: Epstein


title: Gene profiling of pathological cardiac hypertrophy vs physiological hypertrophy

city: Sydney

first: Ruby

middle: CY

last: Lin

state: NSW

address: 176 Hawkesbury Road, Westmead

institute: The Westmead Institute for Medical Research

summary:
Cardiac hypertrophy can lead to heart failure, and is induced either by physiological stimuli eg postnatal development, chronic exercise training or pathological stimuli eg pressure or volume overload. Majority of new therapies for heart failure has mixed outcomes. A combined mouse model and oligo-array approach are used to examine whether phosphoinositide 3-kinase (p110-alpha isoform) activity is critical for maintenance of cardiac function and long-term survival in a setting of heart failure. The significance and expected outcome are to recognise genes involved in models of heart failure ie pathological- vs physiology-hypertrophy, and examine the molecular mechanisms responsible for such activity.
Growth of the heart can be induced by physiological stimuli e.g., postnatal development, chronic exercise training, or pathological stimuli e.g., pressure or volume overload. Physiological hypertrophy (“good”) is characterised by a normal organisation of cardiac structure, and normal or enhanced cardiac function. In comparison, pathological hypertrophy (”bad”) is associated with fibrosis, cardiac dysfunction, and increased morbidity and mortality. The mechanistic process which allows the heart to enlarge in response to physiological stimuli while maintaining normal or enhanced function is of great clinical relevance because one potential therapeutic strategy is to inhibit the pathological growth process while augmenting the physiological growth process. One of the major process that regulate heart size is by phosphoinositide 3-kinase (PI3K). Thus the end goal of this project is to determine whether the p110 alpha isoform of PI3K could be a potential tool for augmenting physiological growth and improving cardiac function of the failing diseased heart, and to examine the underlying mechanisms responsible.
Keywords: Disease progression analysis

overall_design:
Ntg (nontransgenic), dnPI3K (cardiac-specific transgenic model with reduced PI3K activity) and caPI3K (transgenic mice with increased PI3K activity) mice were used. Mice were divided into MI (myocardial infarction) group and sham (control operation) groups, resulting in 6 experimental groups. 4 arrays were included in each group, each assigned an array number as follows:

Ntg sham: 415, 416, 1184. 1185

Ntg MI: 140, 1127, 1174, 1190

dnPI3K sham: 417, 418, 1191, 1181

dnPI3K MI: 228, 1117, 87, 927

caPI3K sham: 1416, 1413, 1417, 1410

caPI3K MI: 257, 261, 1123, 987

The following comparisons were studied:
-Ntg sham compared to Ntg MI
-caPI3K sham compared to caPI3K MI
-dnPI3K sham compared to dnPI3K MI
-(Ntg MI-Ntg sham) to (caPI3K MI-caPI3K sham) to (dnPI3K MI-dnPI3K   sham)

Multiple comparison normalised to Ntg sham.

first: Julie

middle: R

last: McMullen


title: Transcriptional alterations in cycling neural stem cells underlying alcohol use disorders

city: Syracuse

first: Frank

last: Middleton

address: 505 Irving Avenue

department: Neuroscience and Physiology

institute: SUNY Upstate Medical Univ

summary: Ethanol inhibits the proliferation of neural stem cells in the fetal, adolescent, and adult brain.  The consequences are cognitive deficits associated with fetal alcohol spectrum disorder and alcohol use disorder.  We tested the hypothesis that ethanol affects progression through cell cycle checkpoints by differentially modifying transcriptional processes.  Monolayer cultures of NS-5 neural stem cells were treated for 48 hr with the mitogenic agent FGF2 or the anti-mitogenic TGFβ1 in the absence or presence of ethanol.  Cell cycle elongation was induced by a global down-regulation of genes involved in cell cycle progression, including the cyclin E system.  Checkpoint regulation occurred downstream of p21 and Jun-oncogene signaling cascades.  Thus, ethanol can affect cell cycle progression by altering transcript expression of strategic genes downstream of the G1/S checkpoint.

overall_design: NS5 neural stem cells were grown in Euromed Media supplemented with N2 and glutamine.  Cells were plated on poly-ornathine and laminin in the presence of FGF2 (10 ng/ul) and EGF (10 ng/ul) for 24 hrs.  Media was removed, cells were rinsed, and placed in growth factor free conditions for 4 hrs.  NS5 cells were then exposed to one of four treatment for 48 hrs: FGF2 (10 ng/ul) only, FGF2 (10 ng/ul) and ethanol (400 mg/dl), TGF-beta1 (10 ng/ul) only, or TGF-beta1 (10 ng/ul) and ethanol (400 mg/dl). Total RNA was collected immediately following treatment.

first: Steven

last: Hicks

first: Michael

last: Miller


title: Gene profile of PTIP deletion in adult murine cardiac tissue

status: Public on Mar 02 2010

city: Ann Arbor

first: Adam

middle: B.

last: Stein

state: MI

address: 108 Zina Pitcher Dr

department: Medicine

institute: University of Michigan

summary: Methylation of histone H3 lysine 4 (H3K4me) at actively expressed, cell type-specific genes is established during development by the Trithorax group of epigenetic regulators.  In mammals, the Trithorax family includes KMT2A-D (MLL1-4), a family of SET domain proteins that function in large complexes to impart mono-, di-, and trimethylation at H3K4.  Individual KMT2s and their co-factors are essential for embryonic development and the establishment of correct gene expression patterns, presumably by demarcating the active and accessible regions of the genome in a cell specific and heritable manner.  Despite the importance of H3K4me marks in development, little is known about the importance of histone methylation in maintaining gene expression patterns in fully differentiated and non-dividing cell types. In this report, we utilized an inducible cardiac-specific Cre driver to delete the PTIP protein, a key component of a H3K4me complex, and ask whether this activity is still required to maintain the phenotype of terminally differentiated cardiomyocytes.  Our results demonstrate that reducing the H3K4me3 marks is sufficient to alter gene expression patterns and significantly augment systolic heart function.  These results clearly show that maintenance of H3K4me3 marks is necessary for the stability of the transcriptional program in differentiated cells. The array we performed allowed us to identify genes that are regulated by PTIP and histone methylation.

overall_design: 8-week-old littermate mice on a mixed C57B6 and B6129 background were utilized. Three mice were on a background with a PTIP floxed allele and a wild type PTIP allele (PTIP+1, PTIP+2, PTIP+3). Three mice had a transgene that expresses a modified estrogen receptor -Cre recombinase fusion protein under the control of a cardiac-specific driver (alpha myosin heavy chain, Jackson Lab stock #005650) and a floxed PTIP allele and a null PTIP (PTIPKO1, PTIPKO2, PTIPKO3). Both groups of mice were injected with tamoxifen at 8 weeks of age. Tamoxifen deletes the floxed PTIP allele in the PTIPKO mice. 5 days after tamoxifen injection, RNA was harvested from left ventricle (LV) apices in both groups. RNA was then sent to the University of Michigan microarray facility core for analysis.


title: Coenzyme Q10-dependent gene expression in SAMP1 mice tissues

status: Public on Mar 05 2010

city: Kiel

last: Döring

address: Heinrich-Hecht-Platz 10

department: Human Nutrition and Food Science

institute: Christian-Albrechts-University Kiel

summary: Our present study reveals significant decelerating effects on senescence processes in middle-aged SAMP1 mice supplemented for 6 or 14 months with the reduced form (QH2, 500 mg/ kg BW/ day) of coenzyme Q10 (CoQ10). To unravel molecular mechanisms of these CoQ10 effects, a genome-wide transcript profiling in liver, heart, brain and kidney of SAMP1 mice supplemented with the reduced (QH2) or oxidized form of CoQ10 (Q10) was performed. Liver seems to be the main target tissue of CoQ10 intervention, followed by kidney, heart and brain. Stringent evaluation of the resulting data revealed that QH2 has a stronger impact on gene expression than Q10, which was primarily due to differences in the bioavailability. Indeed, we found that QH2 supplementation was more effective than Q10 to increase levels of CoQ10 in the liver of SAMP1 mice (54.92-fold and 30.36-fold, respectively). To identify functional and regulatory connections of the “top 50” (p < 0.05) up- and down-regulated QH2-sensitive transcripts in liver (fold changes ranging from 21.24 to -6.12), text mining analysis (Genomatix BiblioSphere, GFG level B3) was used. Hereby, we identified 11 QH2-sensitive genes which are regulated by PPAR-α and are primarily involved in cholesterol synthesis (e.g. HMGCS1, HMGCL, HMGCR), fat assimilation (FABP5), lipoprotein metabolism (PLTP) and inflammation (STAT-1). Thus, we provide evidence that QH2 is involved in the reduction of fat and cholesterol synthesis via modulation of the PPAR-α signalling pathway. These data may explain, at least in part, the observed effects on decelerated age-dependent degeneration processes in QH2-supplemented SAMP1 mice.

overall_design: Whole genome expression profiles were analysed from liver, heart, brain and kidney (each analyzed separately) of SAMP1 mice supplemented with QH2, Q10 or a control diet. From every experimental group, three mice each were sacrificed 6 or 14 months after supplementation, resulting in a total of 72 microarrays.

first: Constance

last: Schmelzer

first: Hiroshi

last: Kubo

first: Keiichi

last: Higuchi


title: A Functional Role of RB-Dependent Pathway in the Control of Quiescence in Adult Epidermal Stem Cells Revealed by Genomic Profiling

status: Public on Mar 20 2010

city: Madrid

first: Ramon

last: Garcia-Escudero

state: Madrid

address: Avda Complutense 40, Ed 70A

department: Biomedical Innovation

country: Spain

institute: CIEMAT

summary: Continuous cell renewal in mouse epidermis is at the expense of a pool of pluripotent cells that lie in a well defined niche in the hair follicle known as the bulge. To identify mechanisms controlling hair follicle stem cell homeostasis, we developed a strategy to isolate adult bulge stem cells in mice and to define their transcriptional profile. We observed that a large number of transcripts are underexpressed in hair follicle stem cells when compared to non-stem cells. Importantly, the majority of these downregulated genes are involved in cell cycle. Using bioinformatics tools, we identified the E2F transcription factor family as a potential element involved in the regulation of these transcripts. To determine their functional role, we used engineered mice lacking Rb gene in epidermis, which showed increased expression of most E2F family members and increased E2F transcriptional activity. Experiments designed to analyze epidermal stem cell functionality (i.e.: hair regrowth and wound healing) imply a role of the Rb-E2F axis in the control of stem cell quiescence in epidermis.

overall_design: Total RNA was prepared from CD34+ and CD34- keratinocytes obtained from pools of at least six mice per MACS isolation procedure. A total of three isolation procedures were performed. RNA extracted from each fraction (CD34+ / CD34-) was assessed for its quality using Agilent 2100 Bioanalyzer (Agilent Technologies) and hybridized to two Affymetrix Mouse 430 2.0 arrays, to ensure reproducibility of the process. This resulted in a total of 12 chips (6 CD34+ / 6 CD34-).

first: Corina

last: Lorz

first: Carmen

last: Segrelles

first: Marina

middle: I

last: Garin

first: Jose

middle: M

last: Ariza

first: Mirentxu

last: Santos

first: Sergio

last: Ruiz

middle: F

last: Lara

first: Ana

last: Martinez-Cruz

first: Clotilde

last: Costa

first: Agueda

last: Buitrago-Perez

first: Cristina

last: Saiz-Ladera

first: Marta

last: Dueñas

first: Jesus

last: Paramio


title: Genomic definition of multiple ex vivo Treg sub-phenotypes

city: Boston

first: CBDM

last: Lab

state: MA

address: 77 Avenue Louis Pasteur

department: Microbiology and Immunobiology

institute: Harvard Medical School

summary: Regulatory T (Treg) cells that express the FoxP3 transcription factor are essential for lymphoid homeostasis and immune tolerance to self. Other non-immunological functions of Treg cells, such as controlling metabolic function in adipose tissue, are also emerging. Treg cells originate primarily in the thymus, but can also be elicited from conventional T cells by in vivo exposure to low-dose antigen or homeostatic expansion, or by activation in the presence of TGFβ in vitro. Treg cells are characterized by a distinct transcriptional signature controlled in part, but not solely, by FoxP3. For a better perspective on transcriptional control in Treg cells, we compared gene expression profiles of a broad panel of Treg cells from various origins or anatomical locations. Treg cells generated by different means form different sub-phenotypes identifiable by particular combinations of transcripts, none of which fully encompass the entire Treg signature. Molecules involved in Treg effector function, chemokine receptors, and the transcription factors that control them are differentially represented in these subphenotypes. Treg cells from the gut proved dissimilar to cells elicited by exposure to TGFβ, but instead they resembled a CD103+Klrg1+ subphenotype preferentially generated in response to lymphopenia.

overall_design: All gene expression profiles were obtained from highly purified T cell populations sorted by flow cytometry. To reduce variability, cells from multiple mice were pooled for sorting, and replicates or triplicates were generated for all groups. RNA from 1-5 x 104 cells was amplified, labeled, and hybridized to Affymetrix M430v2 microarrays. Raw data were preprocessed with the RMA algorithm in GenePattern, and averaged expression values were used for analysis.

first: Markus

last: Feuerer

first: Jonathan

last: Hill

first: Karsten

last: Kretschmer

first: Harald

last: von Boehmer

first: Diane

last: Mathis

first: Christophe

last: Benoist


title: Gene expression data of BBB and BCB two-cell embryos

city: Philadelphia

first: Zhiming

last: Han

state: PA

address: 3307 North Broad Street, AHB 561

department: Fels Institute for Cancer Research and Molecular Biology

institute: Temple University

summary:
We constructed one-cell stage embryos by maternal pronuclear (mPN) transfer having B6 ooplasm, B6 paternal PN (pPN), and either B6 or C3H mPN (BBB and BCB, respectively). We collected embryos of each type that were either treated (BBB+a, BCB+a) or untreated with α-amanitin (BBB, BCB) at the two-cell stage for microarray analysis.
Comparison of the transcriptomes of these different kinds of embryos revealed genes for which expression differs according to maternal PN strain of origin, and the α-amanitin data revealed which of these differences is due to gene transcription, as opposed to any transcription-independent differences attributable to ooplasm-derived maternal mRNA pools.

overall_design: There are 4 replicates for each kind/treatment two-cell embryos (BBB, BCB, BBB+a, BCB+a).

first: Namdori

last: Mtango

first: Zhisheng

last: Zhong

first: Rita

last: Vassena

first: Keith

middle: E

last: Latham


title: Gene expression profile of Dicer-deficient oocytes

city: Research Triangle Park

first: Paula

last: Stein

state: NC

address: 111 T.W. A;exander Dr.

department: Reproductive and Developmental Biology Laboratory

institute: NIEHS

summary: Small RNAs, such as miRNAs and siRNAs, are involved in gene regulation in a variety of systems, including mouse oocytes. Dicer is a ribonuclease III enzyme essential for miRNA and siRNA biosynthesis. In an effort to uncover the function of small RNAs during oocyte growth, we specifically deleted Dicer in growing oocytes and analyzed the global pattern of gene expression in these Dicer-deficient oocytes.

overall_design: Germinal vesicle-intact, fully grown oocytes were collected from eCG-primed wild-type or Dicer-deficient female mice and freed of attached cumulus cells by pipetting. Twenty oocytes per mouse were used for RNA extraction and hybridization on the MOE430 v2 Affymetrix microarray platform. Oocytes from four wild-type and four Dicer-knockout mice were analyzed.

first: Francesca

last: Duncan

first: Elizabeth

last: Murchison

first: Gregory

middle: J

last: Hannon

first: Richard

last: Schultz


title: Molecular analysis of endothelial progenitor cell (EPC) subtypes

status: Public on Mar 01 2010

city: Belfast

first: Christina

middle: L

last: O'Neill

state: Northern Ireland

address: Centre for Vision & Vascular Science   Institute of Clinical Sciences A Grosvenor Road Royal Victoria Hospital

department: Centre for Vision and Vascular Science

country: United Kingdom

institute: Queens University Belfast

summary: Genome -wide analysis of EPC subtypes obtained from both umbilical cord and peripheral blood. This experiment sought to compare the expression levels of eEPCs and OECs against monocytes and human dermal microvascular cells (HDMECs) in order to establish if these cells are linked to a monocytic or endothelial lineage. This is very important as the term EPC is currently used to describe cell populations which are quite dissimilar in terms of biological properties.

overall_design: Total RNA was isolated from 7 day old eEPCs, early passage OECs, freshly isolated CD14+ monocytes and early passage DMECs using RNAqueous kit. Three biological replicates per EPC subtype from peripheral blood was used for trancriptome analysis using Illumina Human WG-6 v3.9 beadchip.

first: Reinhold

last: Medina

first: Mark

last: Sweeney

first: Jasenka

last: Guduric-Fuchs

first: Tom

middle: A

last: Gardiner

first: David

last: Simpson

first: Alan

last: Stitt


title: Effect of BMP4 and noggin on gene expression in murine R1 ES cells

city: Beijing

first: Bing

last: Zhou

address: Datun Road

department: Center for Molecular Systems Biology

institute: Institute of Genetics and Developmental Biology, Chinese Academy of Sciences

summary: To confirm that the SMAD1/5- and SMAD4-associated genes are direct transcriptional regulators in mESCs in response to BMP, we treated undifferentiated R1 ES cells with BMP4 or with the BMP4 antagonist noggin, which can inhibit BMP signaling effectively for 4 h.

overall_design: Undifferentiated R1 ES cells were treated for 4 h with BMP4 or with the BMP4 antagonist noggin, which can inhibit BMP signaling effectively. Untreated R1 ES cells served as the control.

first: Teng

last: Fei

first: Kai

last: Xia

first: Zhongwei

last: Li

first: Shanshan

last: Zhu

first: Hua

last: Chen

first: Jianping

last: Zhang

first: Zhang

first: Huasheng

last: Xiao

first: Jing-Dong

last: Han

first: Ye-Guang


title: Expression  data from K5-IKKbeta transgenic mouse skin

first: Manuel

last: Navarro

address: Av. Complutense 40

department: Molecular Oncology

summary: IKKbeta is a subunit of the IkB kinase (IKK) complex required for NF-kB activation in response to pro-inflammatory signals. NF-kB regulates the expression of many genes involved in inflammation, immunity and apoptosis, and also controls cell proliferation and differentiation in different tissues; however, its function in skin physiopathology remains controversial. We here report the alterations caused by increased IKKbeta activity in basal cells of the skin of transgenic mice.

overall_design: Transgenic mice which express the IKKbeta gene under the control of the keratin K5 regulatory elements were generated. We analyzed back skins from wildtype and transgenic animals. Each individual array has RNA from three different mice of the same genotype.

first: Angel

last: Ramirez


title: Gene expression profiling of conditional ablation of Indian hedgehog in the mouse uterus

city: Houston

first: Heather

last: Franco

state: TX

address: 1 Baylor Plaza

department: Molecular and Cellular Biology

institute: Baylor College of Medicine

summary:
Conditional ablation of Indian hedgehog (Ihh) in the murine uterus results in mice that are sterile due to defects in embryo implantation.  We performed microarray analysis on these mice at the time point at which the Ihh target genes are induced by the administration of exogenous hormone to mimic day 3.5 of pregnancy.  This analysis identified 863 genes altered by the conditional ablation of Ihh.  Of these, genes that regulated the cell cycle were overrepresented.  In addition, genes involved in epidermal growth factor (EGF) and estrogen (E2) signaling were found to be deregulated upon Ihh ablation.  Furthermore, upon conditional ablation of Ihh, 15 month old mice exhibited hallmarks of estrogenized uteri such as cystically dilated glands and hyalinized stroma. Thus, Ihh regulates embryo implantation by impacting the cell cycle, EGF signaling, and E2 signaling.

Keywords: two group comparison

overall_design: We conditionally ablated Indian hedgehog in the mouse uterus using the PRcre mouse model  (PRcre/+Ihhf/f; Ihhd/d). High density DNA microarray analysis was performed on Day -1 of the artificial decidual response on Ihhf/f and Ihhd/d uteri.

first: Franco

last: Demayo


title: Hematopoietic Stem Cell Differentiation Regulated by a Single Ubiquitin Ligase: Substrate Complex

city: LYON

first: Jiri

last: ZAVADIL

state: Other

address: 150 COURS ALBERT THOMAS

institute: IARC WHO

summary: Hematopoietic stem cell (HSC) differentiation is regulated by cell-intrinsic and extrinsic cues. In addition to transcriptional regulation, post-translational regulation may also control HSC differentiation. To test this hypothesis, we visualized ubiquitin-regulated protein stability of a single transcription factor, c-Myc. The stability of c-Myc protein was instructive of HSC quiescence and c-Myc protein abundance was controlled by the ubiquitin ligase Fbw7. Fine changes in stability of c-Myc protein regulated the HSC “gene expression signature”. Using whole genome genomic approaches, we identified specific regulators of HSC function that are directly controlled by c-Myc binding, however adult HSCs and embryonic stem cells sense and interpret distinctly c-Myc regulated gene expression. These studies show a ubiquitin ligase–substrate pair can orchestrate the molecular program of HSC differentiation.

overall_design: Gene expression profiles from c-Myc-High and c-Myc-Low expressing Lineage negative, c-Kit and Sca1 positive (LSKs) were compared using genome wide mRNA expression profiling by Affymetrix genechip arrays (Mouse 430 2.0) and key targets were validated by chromatin immunoprecipitation experiments.

first: Linsey

last: Reavie

first: Guisy

last: Della Gata

first: Kelly

last: Crusio

first: Beatriz

last: Aranda-Orgilles

first: Shannon

last: Buckley

first: Benjamin

last: Thompson

first: Eugine

last: Lee

first: Jie

last: Gao

first: Andrea

last: Bredemeyer

first: Beth

last: Helmink

last: Zavadil

first: Barry

last: Sleckman

first: Teresa

last: Palomero

first: Adolfo

last: Ferrando

first: Iannis

last: Aifantis


title: Temporal profiling of gene expression in cochleae of wild type and alpha9 null mice

first: Douglas

last: Vetter

address: 136 Harrison Ave.

department: Dept. Neuroscience

institute: Tufts Univ. Sch. Med.

summary: Efferent inhibition of cochlear outer hair cells is mediated by nicotinic cholinergic receptors containing alpha9 (a9)  and alpha10 subunits. Mice lacking a9 nicotinic subunits fail to exhibit classic olivocochlear responses and are characterized by abnormal synaptic morphology at the base of outer hair cells. To detail molecular changes induced upon the loss of a9 subunit, we sampled cochlear RNA from wild type and a9 null mice at postnatal (P) days spanning periods of  synapse formation and maturation (P3, P7, P13 and P60). Our findings point to a delay in cochlear maturation starting at the onset of hearing (P13), as well as an up-regulation of various GABA receptor subunits in adult mice lacking the a9 nicotinic subunit.

overall_design: Cochleae were removed at postnatal ages P3, P7, P13 and P60. Cochlear tissues from 3-5 mice were pooled per replicate; biological triplicates were performed for each age and genotype.

first: Sevin

last: Turcan


title: Gene Expression Analysis of Ara-C Resistance in AML

city: Minneapolis

first: David

middle: A.

last: Largaespada

state: MN

address: 2231 6th Street SE

department: Dept. of Genetics, Cell Biology and Development, Cancer Center

institute: The University of Minnesota

summary: Using two independently derived murine BXH2 cell lines, Ara-C resistant derivatives were developed by exposure to increasing concentrations of Ara-C.  Microarray analysis comparing the Ara-C resistant cells to their Ara-C sensitive parental cell lines identified potential genes involved in Ara-C resistance.

overall_design: Two highly Ara-C-resistant cell lines, B117H and B140H, were derived from Ara-C-sensitive parental cell lines, B117P and B140P.  Variations in gene expression between these Ara-C-resistant and -sensitive sets were studied. Three replicates per cell line.

first: Susan

last: Rathe