title: Heart Failure Associated Changes in Alternative Splicing of Sarcomere Genes

city: Boston

first: Sek Won

last: Kong

state: MA

address: 300 Longwood Avenue

department: Informatics Program

summary:
Alternative mRNA splicing is an important mechanism for regulation of gene expression. Changes in gene expression contribute to the pathogenesis of heart failure. However, changes in mRNA splicing have not been systematically examined in heart disease. We hypothesized that mRNA splicing is changed in diseased hearts.
We used the Affymetrix exon array, which separately measures expression of each known and computationally predicted exon, to globally evaluate changes in mRNA splicing in left ventricular myocardial RNA from control and ischemic cardiomyopathy (ICM) patients. We found that mRNA splicing is systematically changed in heart failure. RTPCR  validated 9 previously unreported alternative splicing events. Furthermore, we demonstrated that the splicing of four key sarcomere genes, cardiac troponin T (TNNT2), cardiac troponin I (TNNI3), myosin heavy chain 7 (MYH7), and filamin C (FLNC), was significantly altered in ICM. Altered splicing of these genes in heart disease was confirmed in independent ICM samples, and in dilated cardiomyopathy and aortic stenosis. The minor variant fraction of these five genes was sufficient to classify samples into control or disease groups with 95% accuracy.
Our data indicate that alternative splicing is systematically altered in human heart disease, suggesting that disease-associated perturbation of RNA splicing may contribute to the pathogenesis and development of heart failure. Disease-related changes in splicing of sarcomere genes may directly impact cardiomyocyte function.

overall_design: 15 ischemic heart failure samples and 15 age and sex matched control heart samples were collected. Left ventricular myocardial samples, remote from infarcted areas, were obtained from explanted ischemic cardiomyopathy hearts at the time of transplantation, and from unused transplant donor hearts. Diseased hearts had ejection fraction < 40% and/or New York State Heart Association class III or class IV heart failure.

first: Sek

middle: W

first: William

last: Pu


title: Multi-component epigenetic control of pro-invasive genes in cancer cells

status: Public on Jan 05 2010

city: La Jolla

first: Andrei

last: Chernov

state: CA

address: 9500 Gilman Dr

department: Anesthesiology

country: USA

institute: University of California San Diego

type: Genome binding/occupancy profiling by genome tiling array

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

overall_design: Refer to individual Series


title: miR-140 deficiency effect on the chondrocytes

status: Public on Jan 01 2010

city: Setagaya

first: Hiroshi

last: Asahara

state: Tokyo

department: Department of Systems BioMedicine

country: Japan

institute: National Research Institute for Child Health and Development

summary:
Analysis of mouse chondrocytes lacking the microRNA-140. MicroRNAs are genomically encoded small RNAs to regulate the gene expression. miR-140 shows high expression in cartilage. Results provide insight into the molecular mechanisms underlying miR-140 function in chondrocytes.

Keywords: Expression profiling by array

overall_design: DNA microarray analysis was performed using Affymetrix mouse genome 430 2.0 array. RNA samples collected from cultured rib chondrocytes of wild-type and miR-140-/- to identify potential mRNA targets of miR-140. 2 µg of total RNA was reverse transcribed with SuperScript II and second strand cDNA was synthesized. Biotinylated antisense cRNAs was amplified and transcribed using the GeneChip expression 3’-Amplification reagent (Affymetrix). Finally, 10 µg of cRNAs were fragmented and hybridized to GeneChip (R) Mouse Genome 430 2.0 array (Affymetrix). Microarray data were summarized by Robust Multichip Average (RMA) method and statistical analysis was performed using NIA Array Analysis (http://Igusun.grc.nia.nih.gov/ANOVA/).

first: Shigeru

last: Miyaki

first: Tempei

last: Sato


title: T.F. Glis3: a novel critical player in the regulation of pancreatic beta-cell development and insulin gene expression

city: RTP

first: NIEHS

last: Microarray Core

state: NC

address: 111 T.W. Alexander Drive

department: DIR

institute: NIEHS

summary: Glis3 mutant mice (Glis3zf/zf) die within the first week after birth due to overt diabetes, evidenced by hyperglycemia and hypoinsulinemia. Histopathological analysis showed that Glis3zf/zf mice develop a pancreatic phenotype with a dramatic loss of beta- (insulin) and delta- (somatostatin) cells contrasting a smaller relative loss of alpha- (glucagon), PP- (pancreatic polypeptide), and epsilon- (ghrelin) cells. Glis3zf/zf mice develop ductal cysts with decreased number of primary cilia, while the acini are not significantly affected. Gene expression profiling by microarray analysis demonstrated that the expression of terminal hormonal genes and several transcription factors important in endocrine development were significantly deregulated in Glis3zf/zf mice. During pancreatic development, Glis3 mRNA expression is induced during the secondary transition, a stage of cell lineage specification and extensive patterning. Changes in pancreatic development of Glis3zf/zf mice are noted during and after this stage. The population of pancreatic progenitors appears not to be greatly affected in Glis3zf/zf mice; however, the number of neurogenin 3 (Ngn3) positive, endocrine progenitors is significantly reduced. Our study indicates that Glis3 plays a key role in cell lineage specification, particularly the development of mature pancreatic beta-cells. In addition, we identified evidence that Glis3 regulates insulin gene expression through two Glis-binding sites in its proximal promoter indicating that Glis3 is a regulator of insulin gene expression.

overall_design:
For E15.5 microarray, RNAs were purified from 3 of WT and 4 of Glis3zf/zf pancreas and applied on Affymetrix chip.
For postnatal day 3 (PND3) analysis RNA samples from 2 pups of for each WT or Glis3zf/zf pups were pooled, then analyzed.

last: Kang

last: Beak

last: Kim

last: Jetten


title: Multi-component epigenetic control of pro-invasive genes in cancer cells (Illumina)

summary: To identify the epigenetic signature that controls cancer cell migration, we performed integrated gene expression, miRNA and epigenetic profiling of 486 selected invasion-associated genes in non-migratory MCF-7 breast carcinoma and highly migratory U251 glioma cells. We used a custom-built chromatin immunoprecipitation (ChIP)-on-Chip microarray that included complimentary oligonucleotide probes for the genes that were functionally linked to proteolysis, migration and tumorigenesis such as extracellular matrix proteins, cellular proteinases and their inhibitors, growth factors and cytokines, and adhesion and signaling receptors. As a result, we determined the role histone H3 modifications [(Lys-4 dimethylation (H3K4me2), Lys-27 trimethylation (H3K27me3) and acetylation (H3ac)] play in transcriptional regulation of the multiple invasion-associated genes. Predominantly, transcriptional silencing of the pro-invasive genes in MCF-7 cells involved the repressive H3K27me3 mark and, frequently, the presence of the stem cell-like bivalent epigenetic mark (enrichment in both H3K27me3 and H3K4me2). In turn, pro-invasive genes in U251 cells were epigenetically stimulated by a gain in H3K4me2 and histone H3 hyperacetylation, and by a global reduction of H3K27me3. Intriguingly, the expression of multiple collagen genes was highly enhanced in glioma cells, thus suggesting that gliomas themselves deposit a specialized, invasion-promoting matrix.

overall_design: Gene Expression Microarrays to complement the ChIP-on-Chip experiment, MCF7 vs.U251 cells. Biological replicates: 3-10 control intra-array replicates

middle: V

first: Alex

last: YStrongin


title: Expression data from E10 cells with miR-129 over-expression

city: BoSTON

first: jining

last: lu

address: 715 Albany street R304

institute: Boston University

summary:
miRNAs are known to regulate gene expression by suppressing translation, but there is also a wealth of data showing that they can act as critical regulators of mRNA stability of their targets. In this experiment, we analyzed the mRNA expression profiles of E10 with high expression of miR-129 as compared to control cells to identify miR-129 targets.
E10 cells infected with miR-129 over-expressing lentivirus or the control lentivirus were cultured for 48 hours. More than 80% of cells were infected. Total RNA samples were isolated using Trizol (invitrogen), and subjected to labeling, fragmentation and hybridization, according to manufacturer’s protocols. Mouse Genome 430 2.0 Array (Affymetrix) was used for mRNA expression profiling.

overall_design: We compared the mRNA expression profiles between cells infected with miR-129 expressing lentivirus and the cells infected with control lentivirus

first: Jining

last: Lu

first: Junjie

last: Wu


title: Female sex and oestrogen receptor β attenuate cardiac remodelling and apoptosis in pressure overload

status: Public on Jan 20 2010

city: Berlin

first: Henning

last: Witt

address: Ihnestrasse 65

department: Hans Lehrach

country: Germany

institute: Max Planck Institute for Molecular Genetics

summary: Aims: We investigate sex differences and the role of oestrogen receptor beta (ERbeta) in a mouse model of pressure overload-induced myocardial hypertrophy. Methods and results: We performed transverse aortic constriction (TAC) or sham surgery in male and female wild-type (WT) and ERbeta knockout (ERbeta-/-) C57Bl6 mice. All mice were characterised by echocardiography and haemodynamic measurements and were sacrificed nine weeks after surgery. Left ventricular (LV) samples were analysed by microarray profiling, real-time RT-PCR and histology. After nine weeks, WT males showed more hypertrophy and heart failure signs than WT females. Notably, WT females developed a concentric form of hypertrophy, while males developed eccentric hypertrophy. These sex differences were abolished in ERbeta-/- mice. ERbeta deletion augmented the TAC-induced increase in cardiomyocyte diameter in both sexes. Gene expression profiling revealed that male WT hearts had a stronger induction of matrix-related genes and a stronger repression of mitochondrial genes than female hearts. ERbeta-/- mice exhibited a different transcriptome. Induction of pro-apoptotic genes after TAC occurred in ERbeta-/- mice of both sexes with a stronger expression in ERbeta-/- males. Histological analysis revealed, that cardiac fibrosis was more pronounced in male WT TAC than in female mice. This was abolished in ERbeta-/- mice. Apoptosis was significantly induced in both sexes of ERbeta-/- TAC mice, but it was most prominent in males. Conclusion: Female sex offers protection against ventricular chamber dilation in the TAC model. Both the female sex and ERbeta attenuate the development of fibrosis and apoptosis; thus slowing the progression to heart failure.

overall_design: The influence of sex (male/female) and estrogen receptor beta expression (ERbeta knockout/wildtype) on cardiac hypertrophy (transverse aortic constriction/sham operated) was investigated. The left ventricular transcriptome of four individual mice for each combination of the three factors (sex, genotype, surgery) was detected with Affymetrix RAE 430 2.0 GeneChip arrays.

first: Daniela

last: Fliegner

first: Patricia

last: Ruiz Noppinger

first: Vera

last: Regitz Zagrosek


title: MYC Transactome Mapped by Global Array-based Nuclear Run-on (ANRO - Affymetrix)

city: baltimore

first: chris

last: cheadle

state: MD

address: 5200 Eastern Ave

department: SOM

institute: JHU

summary:
We describe and illustrate the use of a method to measure nascent nuclear gene transcription with an Array-based Nuclear Run-On (ANRO) assay using commercial microarray platforms.
ANRO measurements in an inducible c-Myc expressing human P493-6 B cell model was performed following 48 hours with or without MYC gene induction.  Samples were prepared from either nuclear run-on or  total RNA and were applied  to Affymetrix Exon arrays and similarly regulated, full length transcripts were demonstrated from each preparation type.

overall_design: Gene expression is compared at a global level after 48 hours with and without tetracycline as measured for both nuclear run-on and total RNA using the Affymetrix Exon microarray platform.

first: Jinshui

last: Fan

first: Chris

last: Cheadle


title: identification of TGCT genes involved in initiation and maintenance of transformed germ cells.

status: Public on Dec 31 2009

city: Houston

first: Rui

last: Zhu

state: TX

address: 1515 Holcombe Blvd.

department: Genetics

institute: UT MD Anderson Cancer Center

summary:
Initially, we had compared gene expression differences in the embryonic gonads (E13.5) of the 129 and M19 strains by performing microarray analysis.  These studies allowed us to identify downregulation of expression of the D19Bwg1357e, Zfp162 and Cox15 genes in the M19 strain.
We next decided to examine gene expression profile changes in the embryonic gonads of 129 and M19 at additional stages so as to identify other TGCT genes from M19 that are also involved in initiation and maintenance of transformed germ cells.  For this we isolated E13.5, E15.5 and E17.5 genital ridges from male embryos.

overall_design:
Microarray analysis of E13.5, E15.5 and E17.5 genital ridges from male embryos of M19 and 129.
Total RNA prepared from the embryonic gonads were analyzed on 12 Affymetrix mouse 430_2 arrays. The objective of the analysis is to determine the differentially expressed genes for the following comparisons:
1.	Comparisons of the two strains at each stage, specifically:
1a. 129-E13-GR vs. M19-E13-GR
1b. 129-E15-GR vs. M19-E15-GR
1c. 129-E17-GR vs. M19-E17-GR
2.	Comparisons of the different stage in strain 129, specifically:
2a. 129-E13-GR vs. 129-E15-GR
2b. 129-E15-GR vs. 129-E17-GR
3.	Comparisons of the different stage in strain CSS, specifically:
3a. M19-E13-GR vs. M19-E15-GR
3b. M19-E15-GR vs. M19-E17-GR
After data process and quality assessment, 38069 out of 45101 probe sets proceeded for further analysis to identify differentially expressed genes. Hierarchical cluster analysis shows that samples of two strains from the same stage were grouped together and separated from the other stages (Fig.8). The initial analysis indicates a number of trends in gene expression patterns.  Moreover, downregulation of expression of D19Bwg1357e, Zfp162 and Cox15 genes in M19 was also verified in this analysis.  These data are currently being analyzed with the help of Dr. Y. Ji and L. Xiao from the Department of Bioinformatics and Computational Biology and Department of Biostatistics at M.D. Anderson Cancer Center.  The results are unpublished.


title: FoxOs cooperatively regulate diverse pathways governing neural stem cell homeostasis

first: Haoqiang

last: Ying

address: 44 Binney St.

department: Medical Oncology

institute: Dana-Farber Cancer Institute

overall_design: expression profile between six independant neural stem cell lines (three FoxO null and three wild type) were compared


title: VTA neurons show an adaptive transcriptional response to MPTP which differs from SN neurons

city: Philadelphia

first: Sudarshan

last: Phani

state: PA

address: 900 Walnut Street, JHN Suite 462

department: Farber Institute for Neurosciences

institute: Thomas Jefferson University

summary:
Implications for neuroprotection in Parkinson's disease

Parkinson’s disease and its characteristic symptoms are thought to arise from the progressive degeneration of specific midbrain dopamine (DA) neurons.  In humans, DA neurons of the substantia nigra (SN) and their projections to the striatum show selective vulnerability, while neighboring DA neurons of the ventral tegmental area (VTA) are relatively spared from degeneration.  This pattern of cell loss is mimicked in humans, primates, and certain rodents by the neurotoxin MPTP.  In this study, we aimed to test the hypothesis that there are factors in the VTA that are potentially neuroprotective against MPTP and that these factors change over time.  We have found a differential transcriptional response within the cells of the SN and VTA to sustained exposure to a low dose of MPTP.  Specifically, the VTA has increased expression of 148 genes as an early response to MPTP and 113 genes as a late response to MPTP toxicity.  This response encompasses many areas of cellular function, including protein regulation (Phf6) and ion/metal regulation (PANK2, Car4).  Notably, these responses were largely absent from the cells of the SN.  Our data show a clear dynamic response in maintaining the homeostasis and viability of the neurons in the VTA that is lacking in the SN after neurotoxin challenge.

We used microarrays to analyze the differential response of the substantia nigra (SN) and ventral tegmental area (VTA) to a chronic low dose of the neurotoxin MPTP.

overall_design: Transgenic hTH-GFP mice were treated with MPTP (4mg/kg) for either 2 or 10 days.  Control mice were given an equal volume of saline for 10 days.  Dopamine neurons from the substantia nigra and ventral tegmental areas of control and MPTP treated animals were laser captured.  The RNA was isolated and processed for microarray hybridization.  Each group had three biological replicates, for a total of 18 samples.  Three each in the following: Control SN, Control VTA, 2 day MPTP SN, 2 day MPTP VTA, 10 day MPTP SN, 10 day MPTP VTA.  Samples were log2 transformed and RMA normalized using Agilent Genespring 10.0 GX.

first: Gregory

last: Gonye

first: Lorraine

last: Iacovitti


title: Design of a novel highly efficient peptide-based siRNA-delivery vector, PepFect6

city: Tartu

first: Jonas

last: Hälldin

address: Riia st 23

department: Biotech Department

country: Estonia

institute: Tartu University

summary: While small interfering RNAs (siRNAs) have been rapidly appreciated to induce gene silencing, efficient vectors for primary cells and for systemic in vivo delivery are lacking. We here present a novel chemically modified cell-penetrating peptide named PepFect6 (PF6) for efficient delivery of siRNAs into various types of cells including e.g. lymphocyte suspension cells and primary embryonic stem cells. Stable PF6/siRNA nano- particles rapidly enter entire cell populations resulting in strong and persistent RNAi responses, without associated transcriptomic or proteomic changes. In contrast to the majority of chemical reagents, PF6-mediated delivery is independent of cell confluence and, in most cases, not significantly hampered by the presence of serum. Finally, strong RNAi responses are observed in two different in vivo models following systemic delivery of PF6/siRNA in mice. Taken together, PF6 is an efficient siRNA delivery vector with superior delivery properties as compared to other tested transfection reagents.

overall_design: PepFec6 is a cell penetrating peptide (CPP). We have used it for bringing cargo into cells. In this study we compare PepFec6 to Lipofectamine 2000. In the actual experiments here, we have compared gene expression in HeLa cells treated with SiRNA corresponding to the gene HPRT1 with either Lipofectamine 2000 or PepFect6 as the carrier into the cells. For our submitted manuscript, we are using two M/A plots based on the microarray results to demonstrate the gene expression with cells treated with Lipo-SiRNA compared to untreated controls and PepFect-SiRNA compared to untreated cells.

first: Samir

last: El Andaloussi

first: Katri

last: Rosenthal-Aizman

first: Taavi

last: Lehto

first: Imre

last: Mäger

first: Iulian

middle: I

last: Oprea

first: Helena

last: Sork

first: Dana

middle: M

last: Copolovici

first: Kaido

last: Kurrikoff

first: Kariem

last: Ezzat

first: Peter

last: Guterstam

first: Henrik

last: Johansson

first: Joana

middle: R

last: Viola

first: Eman

last: Zaghloul

first: Julia

last: Suhorutsenko

last: Hälldin

first: Oscar

middle: E

last: Simonson

first: Pedro

last: Moreno

first: Nikita

last: Oskolkov

first: Ulf

last: Tedebark

first: Andres

last: Metspalu

first: Janne

last: Lehtio

first: C

last: Smith

first: Ülo

last: Langel


title: shGFP- and shQk-transduced Ink4a/Arf-/- Pten-/- primary mouse astrocytes

status: Public on Dec 30 2009

first: Hailei

last: Zhang

address: 44 Binney Street

summary: Identify potential QK-regulated mRNAs and linked pathways by comparing the transcriptional profiles of shGFP- and shQK-transduced Ink4a/Arf-/- Pten-/- primary mouse astrocytes

overall_design: Ink4a/Arf-/- Pten-/- primary mouse astrocytes infected with shQk-1, shQk-2 and infected with shGFP as control

first: An-Jou

last: Chen

first: Yonghong

last: Xiao

first: Haile

last: i Zhang


title: QK-knockdown Ink4a/Arf-/- Pten-/- mouse astrocytes transduced with miR-20a or scrambled non-targeting microRNA (miR-NT)

summary: Identify potential miR-20a regulated mRNAs and linked pathways in the setting of QK knockdown by comparing the transcriptional profiles of shQK-transduced primary mouse Ink4a/Arf-/- Pten-/- astrocytes together with miR-20a or a scrambled miRNA control (miR-NT)

overall_design: QK-knockdown Ink4a/Arf-/- Pten-/- mouse astrocytes transduced with miR-20a or a scrambled non-targeting microRNA (miR-NT)


title: Gene-level expression data in melanocytes and in melanoma cell lines WM1552C and A375 over-expressing miR211

city: Savannah

first: ranjan

middle: joseph

last: perera

state: GA

address: 4700 Waters Ave

department: DLOR

institute: Anderson Cancer Center

summary: MicroRNAs (miRNAs) influence cancer development through post-transcriptional negative regulation of both tumor suppressors and oncogenes.  We subjected melanoma cell lines, normal melanocytes, and keratinocytes to array based miRNA profiling, and identified several distinct miRNAs with differential expression.  Specifically, miR-211 levels were depleted in all eight melanoma cell lines examined, and also in 23 of 30 distinct patient melanoma samples (graded as primary in situ, regional metastatic, distant metastatic and nodal metastatic).  Putative target genes of miR-211 were identified, and their anticipated increased expression levels were confirmed in melanoma cell lines, which were reduced in two melanoma cell lines that artificially over-expressed miR-211.  Four such target genes (TCF12, RAB22A, KCNMA1 and SLC37A3) were confirmed by a target cleavage assay.  Stable over-expression of miR-211 in two melanoma cell lines caused significant growth inhibition and reduced invasiveness.  The differential expression of miR-211 in a variety of melanoma cell lines and clinical samples, consistent inverse correlation between miR-211 and its target mRNA levels, and growth retardation and reduced invasiveness of melanoma cell lines by miR-211 are all consistent with the idea that the depletion of miR-211 is a key step in melanoma development and/or progression

overall_design: The 15 Samples in this submission represent gene-level expression profiling of isolated total RNA from WM1552C, WM1552+miRNA211, A375, A375+miRNA211 and melanocytes hybridized to Affymetrix exon ararys.

first: Edward

last: Meister

first: Ranjan

last: Perera


title: Comparison of gene expression pattern between Wild-type and Hypb knockout embryo yolk sacs

status: Public on Dec 28 2009

city: Shanghai

first: Ming

last: Hu

address: 197 Ruijin Road II

country: China

institute: Shanghai Institute of Hematology

summary:
This study aimed at exploring the physiological function of mammalian HYPB by means of knockout mouse model. Homogenous disruption of mouse Hypb gene leads to embryonic lethality at E10.5-E11.5. Severe vascular defects were observed in the Hypb-/- embryos, yolk sac and placenta.In the mutant embryo and yolk sac, disorganized and abnormally dilated capillaries cannot be remodeled into large blood vessels or intricate networks. Thus, our results suggest that the mammalian HYPB HMT plays an important role in embryonic vascularization.
Keywords: knockout, mouse embryo development, angiogenesis, yolk sac, E9.0, E10.5

overall_design: To systematically examine and compare gene expression patterns between Hypb+/+ and Hypb-/- embryos at the global genome-level, we use the Affymetrix GeneChip® mouse genome 430 2.0 arrays. We choose to use E9.0 and E10.5 yolk sacs for analysis because at E9.0 this early stage Hypb-/- embryos did not show severe visible mutant phenotype, and at E10.5 this antemortem stage Hypb-/- embryos show mang lethal mutant phenotypes. For comparison, four independently derived yolk sacs were pooled for each genotype of the two development stages, and three biological repeats were performed.

first: Xiaojian

last: Sun

first: Yuanliang

first: Qiuhua

last: Huang

first: Saijuan

first: Zhu


title: Estradiol or Testosterone treated efferent duct and caput epididymis

city: Pullman

first: Elizabeth

last: Snyder

state: WA

address: BioLife Science Building Rm 202

department: School of Molecular Biosciences

institute: Washington State University

summary: The role of estrogen and testosterone in the regulation of gene expression in the proximal reproductive tract is not completely understood.  To address this question, mice were treated with testosterone or estradiol and RNA from the efferent ducts and caput epididymis was processed and hybridized to Affymetrix MOE 430 2.0 microarrays.  Analysis of array output identified probe sets in each tissue with altered levels in hormone treated versus control animals.  Hormone treatment efficacy was confirmed by determination of serum hormone levels pre- and post-treatment and observed changes in transcript levels of previously reported hormone-responsive genes.  Tissue-specific hormone sensitivity was observed with 2867 and 3197 probe sets changing significantly in the efferent ducts after estrogen and testosterone treatment, respectively.  In the caput epididymis, 117 and 268 probe sets changed after estrogen and testosterone treatment, respectively, demonstrating a greater response to hormone in the efferent ducts than the caput epididymis. Transcripts sharing similar profiles in the intact and hormone-treated animals compared with castrated controls were also identified. Ontological analysis of probe sets revealed a significant number of hormone-regulated transcripts encode proteins associated with lipid metabolism, transcription and steroid metabolism in both tissues.  Real-time RT-PCR was employed to confirm array data and investigate other potential hormone-responsive regulators of proximal reproductive tract function.  The results of this work reveal previously unknown responses to estrogen in the caput epididymis and to testosterone in the efferent ducts as well as tissue specific hormone sensitivity in the proximal reproductive tract.

overall_design: Adult animals were castrated or sham-castrated, allowed to recover for 14 days, and then treated with 0.015 mg estradiol (castrated), 0.015 mg testosterone propionate (castrated), or vehicle (castrated and sham-castrated as biological controls) in duplicate.  Efferent duct and caput epididymis was collected from each sample and analyzed.  Duplicates are included in the provided data and numbered 1 or 2 for each treatment regimen.

first: Christopher

middle: L

last: Small

first: Ying

last: Li

first: Michael

middle: D

last: Griswold


title: Chronic hyperglycemia impairs metabolic switching of human myotubes

status: Public on Dec 24 2009

city: Oslo

first: Hege

last: Thoresen

address: Sem Sælandsvei 3

department: School of Pharmacy

country: Norway

institute: University of Oslo

summary: Skeletal muscle of insulin resistant individuals is characterized by lower fasting lipid oxidation and reduced ability to switch between lipid and glucose oxidation. The purpose of the present study was to examine if impaired metabolic switching could be induced by chronic hyperglycemia. Human myotubes were treated with or without chronic hyperglycemia (HG) (20 mmol/l glucose for 4 days), and the metabolism of [14C]oleic acid (OA) and [14C]glucose was studied. Acute glucose (5mmol/l) suppressed OA oxidation by 50% in normoglycemic (NG) (5.5 mmol/l glucose) cells. Myotubes exposed to chronic hyperglycemia showed a significantly reduced OA uptake and oxidation to CO2, whereas acid-soluble metabolites were increased. Glucose suppressibility, the ability of acute glucose to suppress lipid oxidation, was significantly reduced to 21%, while adaptability, the capacity to increase lipid oxidation with increasing fatty acid availability, was unaffected. Glucose uptake and oxidation was significantly reduced by about 40%. Substrate oxidation in presence of mitochondrial uncouplers showed that net and maximal oxidative capacities were significantly reduced after hyperglycemia, and the concentration of ATP was reduced by 25%. However, none of the measured mitochondrial genes were downregulated nor was mitochondrial content. Microarray showed that no genes were significantly regulated by chronic hyperglycemia. Addition of chronic lactate reduced both glucose and OA oxidation to the same extent as hyperglycemia, and this effect was specific for lactate. In conclusions, chronic hyperglycemia reduced substrate oxidation in skeletal muscle cells and impaired the metabolic switching. The effect is most likely due to an induced mitochondrial dysfunction.

overall_design: Cell experiment, paired observations treated vs control, cells from 3 different donors

first: Vigdis

last: Aas

first: Nina

middle: P

last: Hessvik

first: Marianne

last: Wettergreen

first: Andreas

last: Wensaas

first: Stefan

last: Hallén

first: G

middle: H

first: Arild

middle: C

last: Rustan


title: Expression data from 20-week-old mice proximal tubules

city: Montreal

first: Nicolas

last: Godin

state: QC

address: 3850 St-Urbain

country: Canada

institute: Université de Montréal

summary: dB/dB mice develop different kidney pathologies resulting from high body weight. We seek to better understand the mechanisms of this kidney damage in proximal tubules. We isolated RNA from proximal tubules of different groups of mice, and we seek to understand how the anti-oxidant enzyme catalase may regulate kidney damage in this model.

overall_design: Proximal tubules were isolated from 4 groups of 20-week-old mice: wild type, catalase-transgenic, dB/dB, and dB/dB catalase-transgenic. RNA was then extracted from these tubules to use in the microarrays. Triplicates were performed for each group.

first: John

middle: S

last: Chan

first: Marie-Luise

last: Brezniceau


title: Jumonji modulates Polycomb activity and self-renewal versus differentiation of stem cells

status: Public on Dec 29 2009

first: Xiaohua

last: Shen

department: Pediatric Oncology

institute: Dana Farber Cancer Institute

type: Genome variation profiling by genome tiling array

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

overall_design: Refer to individual Series


title: Sustained L-type Calcium Channel Blockade Alters Gene Regulation in the Adult Mouse Ventricle

city: Lexington

middle: Anne

last: Schroder

state: KY

address: 800 Rose Street, MS508

department: Physiology

institute: University of Kentucky

summary:
Objective: L-type calcium channels (LTCC) homeostatically regulate calcium on a beat by beat basis, but also provide Ca that over long time scales may contribute to transcriptional regulation.  We previously showed that sustained LTCC blockade (CCB) elicits LTCC remodeling in ventricular cardiac myocytes (CM).  Here we hypothesize that sustained CCB has broad effects on the expression of genes involved in calcium handling.  Methods and Results: Therefore, we subjected adult mice to sustained CCB for 24 hours and performed gene expression profiling.  In comparison to vehicle-only control animals, 231 genes were up-regulated, and 111 genes were down-regulated by sustained LTCC blockade (p <0.01).  Gene ontology analysis suggested that the CaMKIIdelta signaling pathway was up-regulated in these cells.  Unexpectedly, phosphorylation of phospholamban (PLN) at threonine17 (Thr17), an index of CaMKIIdelta activity, was not changed by sustained CCB; however, the degree of phosphorylation of the neighboring PLN-Ser16 substrate site for PKA was significantly reduced by sustained CCB compared to control.  Gene expression profiling suggested no change in PKA, but it showed that protein phosphatase 2A (PP2A) mRNA increased, and immunoblots demonstrated that PP2Ac-alpha protein was significantly increased by sustained CCB.  Consistent with elevated PP2Ac-alpha protein expression LTCC exhibited decreased phosphorylation of the C-terminal Ser1928 PKA substrate site.  Conclusions: We conclude that sustained CCB elicits a spectrum of transcriptional events, including compensatory up-regulation of LTCC and PP2Ac-alpha.  Although this study is restricted to mouse, these results suggest the new hypothesis that clinically-relevant sustained LTCC blockade in humans results in changes in gene regulation in the heart.
Keywords: L-type calcium channel, calcium channel blockade, verapamil

overall_design:
Female and male ICR mice (12-14 weeks age) weighing between 25 and 30 grams were anesthetized with a ketamine/xylazine mixture ( i.p.) allowing the subcutaneous implantation of miniosmotic pumps (Alzet, model 2001).  The pumps were filled with either verapamil or vehicle (0.02% ascorbic acid).  Control animals carried mini-pumps with vehicle and control animals were investigated in parallel with each set of experimental animals.  Mini pumps delivered verapamil at 3.6 mg/kg/day for 24 (RNA)-48 (protein) hours.  After treatment animals were anesthetized and weighed.  Hearts were excised, rinsed, blotted dry, weighed, and then frozen on dry ice and the stored at -80oC until studied.    Animals were anesthetized and euthanized according to animal protocols approved by the University of Kentucky Institutional Animal Care and Use Committee.  This investigation conforms with the Guide for the Care and Use of Laboratory Animals published by the US National Institutes of Health (NIH Publication NO. 85-23, revised 1996).

Left ventricular free wall from female mice was rapidly excised and either snap frozen at -80oC or used immediately for RNA isolation.  Three VER treated mice and 3 vehicle treated mice were used to generate RNA for microarray.  Total RNA was isolated using the RNAqueous -4PCR kit (Ambion) and quantitated spectrophotometrically at 260nm.  Contaminating genomic DNA was eliminated by DNase treatment (Ambion).  RNA quality was assessed using the Agilent 2100 Bioanalyzer.   Microarray data was obtained using the Affymetrix 430 V2 GeneChip (representing 45,101 probe sets), in accordance with the manufacturer’s specifications.

middle: A

first: Jonathan

last: Satin


title: TgFVB vs FVB 6 and 8 week kidneys

status: Public on Dec 25 2009

city: Seattle

first: Neal

last: Paragas

address: 850 Republican St

institute: University of Washington

summary: Human Immunodeficiency Virus (HIV) associated nephropathy (HIVAN) is characterized clinically by both nephrosis and by rapidly progressive kidney dysfunction. HIVAN is characterized histologically by both collapsing focal segmental glomerulosclerosis and prominent tubular damage. Neutrophil Gelatinase Associated Lipocalin (NGAL) is known to be rapidly expressed in distal segments of the nephron at the onset of different types of acute kidney injury, but few studies have examined NGAL in chronic kidney disease models. We found that urinary NGAL (uNGAL) was highly expressed by patients with biopsy proven HIVAN, whereas HIV+ patients without HIVAN demonstrated lower levels. uNGAL was also highly expressed in the TgFVB mouse model of HIVAN, which demonstrated NGAL gene expression in dilated, microcystic segments of the nephron. These data show that NGAL is markedly upregulated in the setting of HIVAN, and suggest that uNGAL levels may provide a non-invasive screening test to detect HIVAN related tubular disease.

overall_design: Microarray data revealed that NGAL was one of the most highly upregulated gene the TgFVB mouse.


title: Wnt & LIF signalling in mESC

city: Sevilla

first: Patricia

last: Ruiz-Ontañón

address: Av Américo Vespucio

department: TErapia CElular y Medicina Regenerativa

country: Spain

institute: CABIMER

summary:
The molecular processes underlying the properties of ESC are yet unknown even when it's well established that LIF/STAT3 is neccesary for the maintenance of pluripotency. Other pathways as Wnt are may be implicated in the regulation of the biological mechanisms in mESC. Work model: D3-ES cultivated with or without LIF and treated with chronic (7 days) low doses (50nM) of GSK3 β inhibitor (lithium).
We used microarrays to detail the global profile of gene expression to identified different groups of up and down-regulated genes in the work model.

overall_design: mESC cultivated as it has been defined in the work model were prepared for RNA extraction and hybridization on Affymetrix microarrays. We analyzed 3 independent experiments per replicate, and we did three replicates per sample.

last: Ruiz-Ontañon

first: Eloisa

last: Andujar

first: Bernat

last: Soria

first: Karim

last: Hmadcha


title: Identification of inflammatory genes suppressed by heat shock

status: Public on Dec 21 2009

city: Ube

first: Akira

last: Nakai

state: Yamaguchi Prefecture

address: Minami-Kogushi 1-1-1

department: Graduate School of Medicine

institute: Yamaguchi University

summary: To clarify inflammatory genes whose expression is suppressed at high temperatures, we performed comprehensive analysis of gene expression by using a DNA microarray. Two independent primary cultures of mouse embryo fibroblasts (MEF1 and MEF2) were treated with LPS for 4 hours, or treated with LPS for 4 hours after the pretreatment with heat shock at 42˚C for 1 hour, and we identified 100 genes that undergo more than a 3-fold increase with LPS treatment. Remarkably, 86 genes (86%) underwent less than a 2-fold increase after combined treatments with heat shock and LPS in MEF1 and MEF2 cells.

overall_design: Total RNAs were prepared from two primary cultures of mouse embryo fibroblasts (MEF) derived from two independent embryos at embryonic day 15.5 (ICR mice). Cells were maintained at 37˚C (Control), treated with lipopolysaccharide (LPS, E. coli 0127:B8, Sigma, 1 μg/ml) for 4 hours, or treated with LPS for 4 hours after the pretreatment of heat shock at 42˚C for 1 hour. Gene expression was analyzed by using GeneChip Mouse Genome 430 2.0 Array (Affymetrix, Santa Clara, CA).

first: Sachiye

last: Inouye

first: Hitoshi

last: Ichikawa

first: Ryosuke

last: Takii

first: Mitsuaki

last: Fujimoto


title: Development of a three dimensional in vitro teratoma assay for pluripotent human embryonic stem cells

city: Singapore

first: Woon-Khiong

email: dbscwk@nus.edu.sg, g0500139@nus.edu.sg

address: S2-05-19, 14 Science Drive 4

department: Biological Sciences

country: Singapore

institute: National University of Singapore

summary:
The best assay for confirmation of pluripotency for mouse embryonic stem cells (ESCs) is blastocyst chimerism and for human ESCs the production of teratomas in immunodeficient mice that contain lineages from all three primordial germ layers. However, the latter assay has been interpreted by some as one type of human-animal chimera and studies involving human-animal chimerism present a wide range of ethical issues with restrictive legislation in some countries. The need for teratoma assays is compelling because unproven differentiation may suggest a dangerously flawed cell resource for use in future therapies. We find that a three dimensional anchorage independent growth protocol for hESCs using methylcellulose and matrigel encourages prolonged growth of embryoid bodies (EBs) leading onto formation of teratomas in vitro. Our late EBs are a miniature form of teratomas containing lineages from all three germ layers, do not show embryonal carcinoma cells and allows integration of microinjected cancer cells (HepG2-GFP).

Additional data files are linked below as supplementary files:
[1] Beadstudio_Controls_non-normalized.txt: Control Probe Profile intensity data exported from Beadstudio.
[2] Beadstudio_background_removed_non-normalized.txt: Background corrected intensity data exported from Beadstudio using the default Beadstudio background correction setting. No normalization carried out on the data.
[3] VST_quantile_filterp0.01_normalized.txt: Data after VST transformation, quantile normalized and filtered with detection p-value 0.01. This data set was used for analysis in the accompanying publication.

overall_design: Total RNA obtained from embryoid bodies grown in different culture conditions (EB: embryoid body medium, BCM: bulk conditioned medium, MAT: matrigel) and harvested at several time points (7day, 14 day, 30 day, 60 day, 90day).

first: Chui

middle: Y

last: Fong

first: Li

last: Chak

first: Arjunan

last: Subramanian

first: Jee

last: Tan

first: Kalamegam

last: Gauthaman

first: Mahesh

last: Choolani

first: Woon

middle: K

first: Ariff

last: Bongso


title: Mast cells in response to some pathogens elicit a transcriptional program devoid of type I IFN response

city: Braunschweig

first: Robert

last: Geffers

address: Inhoffenstr. 7

department: Dep. Molecular Bacteriology

institute: HCI - Helmholtz Centre for Infection Research

summary:
Although mast cells elicit proinflammatory and type I IFN responses upon VSV infection, in response to  L.monocytogenes (L.m) or S. Typhimurium (S.t), such cells elicit a transcriptional program devoid of type I IFN response.

Balanced induction of proinflamatory and type I interferon (IFN) responses upon activation of Toll like receptors (TLRs) determines the outcome of microbial infections and the pathogenesis of autoimmune and other inflammatory diseases. Mast cells, key components of the innate immune system, are known for their debilitating role in allergy and autoimmune syndromes. However, their potential role in anti-microbial host defenses is increasingly being acknowledged. How mast cells interact with microbes and the nature of responses triggered thereof is not well characterized. Here we show that in response to TLR activation by Gram-positive and negative bacteria or their components like LPS, unlike macrophages, mast cells elicit pro-inflammatory but not type I IFN responses. We demonstrate that in mast cells, the bound bacteria and TLR ligands remain trapped at the cell surface and do not undergo internalization - a prerequisite for type I IFN induction. Such cells could, however, elicit type I IFNs in response to vesicular stomatitis virus (VSV), which accesses the cytosolic RIG-I receptor. Although important for anti-viral immunity, a strong type I IFN response is known to contribute to pathogenesis during bacterial infection. Thus, while endowed with the capacity to elicit type I IFNs in response to viral infection, the fact that mast cells only elicit pro-inflammatory responses upon bacterial infection illustrates that mast cells, key effector cells of the innate immune system, are well adjusted for optimal anti-bacterial and anti-viral responses.

overall_design:
Wild type control (cntr) or interferon receptor (IFNAR)-deficient mast cells (MC) or macrophages (MAC) were infected with L.m. and S.t. (MOIs 50 and 5 for MC and MAC, respectively). MC and MAC were exposed to VSV-AV2 (MOI: 2). Samples were analyzed after 6 hours. Uninfected/unstimulated cells were used as reference samples for calculating fold change in gene expression.

Gene Expression levels were determined by the Affymetrix MOE 430 2.0 GeneChips. Signal Intensities were calculated using the RMA algorithm and for statistical analysis we applied GeneSpring GX 10 software suite (Agilent Technologies, Waldbronn, Germany).  MultiExperiment Viewer (MEV) software version 4.4 of the Institute for Genomic Research was used for clustering algorithm data analysis and visualization.

first: R

first: N

last: Gekara

last: Dietrich


title: Expression data from E12.5 ePet-EYFP rostral and caudal serotonin (5HT) neurons purified by flow cytometry

status: Public on Dec 16 2009

city: Cleveland

first: Evan

middle: S.

last: Deneris

state: OH

address: 2109 Adlebert Road

department: Neurosciences

institute: Case Western Reserve University

summary: The 5HT system is organized into rostral and caudal populations with discrete anatomical locations and opposite axonal trajectories in the developing hindbrain. 5HT neuron cell bodies in the rostral subdivision migrate to the midbrain and pons and extend ascending projections throughout the forebrain.  5HT cell bodies in the caudal subdivision migrate to the ventral medulla and caudal half of the pons and provide descending projections to the brainstem and spinal cord.

overall_design: We used microarrays to determine genes expressed by both rostral and caudal 5HT neurons as well as genes that are differentially expressed between rostral and caudal 5HT neurons at E12.5 when axon pathfinding and cell migration are underway. E12.5 neural tubes were isolated from ePet-EYFP embryos and dissected into a rostral domain (mesecephalic flexure to pontine flexure) and a caudal domain (pontine flexure to spinal cord). After cell dissociation (details under growth protocol), cells were subjected to fluorescent activated cell sorting (FACS) to obtain 4 cell populations. R+ = rostral ePetEYFP positive 5HT neurons; R- = YFP negative non-serotonergic cells in the rostral neural tube; C+ = caudal ePetEYFP positive 5HT neurons; C- = YFP negative non-serotonergic cells in the caudal neural tube. 200,000 cells for each of the 4 cell types (R+, R-, C+, C-) were collected for RNA extraction and hybridization to Affymetrix Mouse 430 2.0 arrays.

first: Christi

middle: J

last: Wylie


title: Analysis of changes in gene expression in epidermal stem cells upon loss of Polycomb silencing

status: Public on Dec 18 2009

city: New York

first: Elena

last: Ezhkova

state: NY

address: 1428 Madison Avenue, Atran Building, AB7-10B

department: DRB

institute: MSSM

summary: Although in vitro studies of embryonic stem cells have identified Polycomb repressor complexes (PRCs) as key regulators of differentiation, it remains unclear as to how PRC-mediated mechanisms control fates of multipotent progenitors in developing tissues. Here, we show that an essential PRC component, Ezh2, is expressed in epidermal progenitors, but diminishes concomitant with embryonic differentiation and with postnatal decline in proliferative activity. We show that Ezh2 controls proliferative potential of basal progenitors by repressing the Ink4A-Ink4B locus, and tempers the developmental rate of differentiation by preventing premature recruitment of AP1 transcriptional activator to the structural genes that are required for epidermal differentiation. Together, our studies reveal that PRCs control epigenetic modifications temporally and spatially in tissue-restricted stem cells by maintaining their proliferative potential and globally repressing undesirable differentiation programs, while selectively establishing a specific terminal differentiation program in a step-wise fashion.

overall_design: RNAs from FACS-purified WT and Ezh2 cKO basal cells were provided to the Genomics Core Facility of the Memorial Sloan-Kettering Cancer Center (MSKCC) for quality control, quantification, reverse transcription, labeling and hybridization to MOE430A 2.0 microarray chips (Affymetrix). Arrays were scanned per the manufacturer’s specifications for the Affymetrix MOE430v2 chip.

first: Elaine

last: Fuchs


title: Dysregulation of the Wnt pathway inhibits timely myelination and remyelination in the mammalian CNS

status: Public on Dec 10 2009

city: SAN FRANCISCO

first: David

last: Rowitch

address: 513 Parnassus Ave, Medical Science Building

department: Neurology

institute: University of California San Francisco

summary: The progressive loss of CNS myelin in patients with multiple sclerosis (MS) has been proposed to result from the combined effects of damage to oligodendrocytes and failure of remyelination. A common feature of demyelinated lesions is the presence of oligodendrocyte precursors (OLPs) blocked at a premyelinating stage. However, the mechanistic basis for inhibition of myelin repair is incompletely understood. To identify novel regulators of OLP differentiation, potentially dysregulated during repair, we performed a genome-wide screen of 1040 transcription factor-encoding genes expressed in remyelinating rodent lesions. We report that ∼50 transcription factor-encoding genes show dynamic expression during repair and that expression of the Wnt pathway mediator Tcf4 (aka Tcf7l2) within OLPs is specific to lesioned—but not normal—adult white matter. We report that β-catenin signaling is active during oligodendrocyte development and remyelination in vivo. Moreover, we observed similar regulation of Tcf4 in the developing human CNS and lesions of MS. Data mining revealed elevated levels of Wnt pathway mRNA transcripts and proteins within MS lesions, indicating activation of the pathway in this pathological context. We show that dysregulation of Wnt–β-catenin signaling in OLPs results in profound delay of both developmental myelination and remyelination, based on (1) conditional activation of β-catenin in the oligodendrocyte lineage in vivo and (2) findings from APCMin mice, which lack one functional copy of the endogenous Wnt pathway inhibitor APC. Together, our findings indicate that dysregulated Wnt–β-catenin signaling inhibits myelination/remyelination in the mammalian CNS. Evidence of Wnt pathway activity in human MS lesions suggests that its dysregulation might contribute to inefficient myelin repair in human neurological disorders.

overall_design: 12 samples total. Two variables in the experiment: genotype (wild type or Olig2cre/DA-Cat) and Developmental stage (Day 4 or Day 15). 4 phenotypes in total with 3 biological replicates for each phenotype.


title: Differential gene expression in wild-type versus Yaa mutant mouse spleen cells

status: Public on Dec 15 2009

city: Oklahoma City

first: Bart

last: Frank

state: OK

institute: OMRF

summary:
T cells from many patients with systemic lupus erythematosus are hypoproliferative in response to TCR ligation. This defect is mediated, at least in part, through down regulation of the TCR zeta chain. Investigation of this phenomenon in lupus-prone mice revealed that the hypoproliferative T cell phenotype apparent in BXSB males is mediated
in part by the Yaa locus. The BXSB model of lupus is a recombinant inbred strain that was originally derived from a cross between a male SB/LE mouse and a female C57BL/6 mouse. BXSB is unique among lupus-prone mouse strains, in that males carry an autoimmune accelerating factor on the Y chromosome, termed Yaa, which accelerates disease onset in male BXSB mice so that fatal glomerulonephritis occurs around 6 months of age. It was recently reported that the Yaa locus is a translocation of a short stretch of genes including that encoding Toll-like
receptor 7 (Tlr-7) from the X to the Y chromosome, leading to a two-fold over expression of a subset of these genes, including Tlr-7, and hypersensitivity of Yaa+ cells to TLR-7 agonists.

To more fully understand the functional significance of the Yaa gene and how it plays a part in the modulation of CD4+ T cell responses, we performed microarray analysis using Affymetrix 430 2.0 arrays on spleens from B6 male B6.Yaa male samples.  The analysis revealed an enhanced signature of innate immunity, including increased expression not only of Tlr7 and Tlr8, in line with reports that the Yaa locus leads to a duplication of the murine Tlr7 and Tlr8 genes , but also of Tlr2, Tlr5, Cd14, Lbp, C2, C3 and genes for several heat-shock proteins. T cells from B6.Yaa mice also displayed decreased TCRζ expression. Interestingly, cell surface levels of the inhibitory molecule B7-H1 were increased on B6.Yaa B cells and monocytes/macrophages. In line with increased TLR-7 expression reported in B6.Yaa mice, the TLR-7 agonist imiquimod increased B7-H1 expression on normal B cells. Restoration of proliferation in co-cultures of B6 T cells and B6.Yaa APC with B7-H1 blocking Ab demonstrated a mechanistic contribution of B7-H1 up-regulation to Yaa-mediated APC-dependent T cell hypoproliferation. In addition, T cell hypoproliferation was induced in normal B6 T cells in vitro by the application of imiquimod. However, this defect was not mediated by B7-H1 or secreted factors but was independent of APC and mediated through direct imiquimod stimulation of T cells themselves. We postulate that excessive TLR-7 stimulation in Yaa+ mice mediates T cell hypoproliferation in part through up-regulation of B7-H1 and possibly also through direct T cell-mediated effects.
Keywords: differential gene expression, RNA, spleen, C57Bl/6J, B6.SB-Yaa/J, male, wild type, Yaa

overall_design:
Control mice: four C57Bl/6J male spleens
Experimental mice: three B6.SB-Yaa/J male spleens and one pool of two B6.Yaa male spleens for the third Yaa sample (GSM236622)
All mice were obtained from the Jackson Laboratories between March and December 2005.

Spleen cell suspensions were prepared by teasing spleen tissue through 70 micron nylon screens and lysing red cells with ammonium chloride.
All mice were 8 weeks of age at the time of the experiment.

RNA was separately extracted, labeled, and hybridized from each animal.

first: Philip

last: Mudd

first: Brittany

middle: N

last: Teague

first: Mark

middle: B

first: Igor

last: Dozmorov

first: Richard

last: Cadwell

first: Munim

last: Deen

first: William

last: Rodgers

first: Michael

last: Centola

first: Darise

last: Farris


title: Expression data with mouse osteoblast cell from wild-type and retinoblastoma tumor suppressor(Rb) knock-out.

status: Public on Dec 04 2009

city: Tampa

first: Douglas

last: Cress

state: FL

address: 12902 Magnolia Drive

department: Molecular Oncology

institute: Moffitt Cancer Institute

summary:
Here we report the characterization of a novel role for the retinoblastoma protein (pRb) as a regulator of osteoblast adhesion. Abrogation of pRb in osteoblasts resulted in aberrant cadherin expression and loss of adherens junctions. This produced defects suggestive of a transformed phenotype such as impaired cell-to-cell adhesion, loss of contact-dependent growth arrest, and the capacity to evade anoikis. This also resulted in profound abnormalities in bone structure. Consistent with this, microarray analyses showed that pRb regulates a wide repertoire of osteoblast cell adhesion genes. In addition, pRb loss also resulted in altered expression and function of several known regulators of cellular adhesion and adherens junction assembly, such as the Rho GTPase Rac1 and the merlin tumor suppressor. Taken together, our results show that pRb controls cell adhesion by regulating the expression and adherens junction components and by regulating the function of molecules involved in adherens junction assembly and stability.
Microarray results helped us to portrait the overall influence on cell adhesion via both individual genes and pathway analysis.

overall_design: MC3T3 cells were obtained from immortalizing primary cultured mouse osteoblast cells by using 3T3 protocol. There are 3 biological replicates for each group, 6 samples in total were analyzed.

first: Bernadette

last: Sosa-García

first: Volkan

last: Gunduz

first: Viviana

last: Vázquez-Rivera

first: Gabriela

last: Wright

first: Haikuo

last: Bian

last: W. Hinds

first: Pedro

last: G. Santiago-Cardona


title: Expression data from oil or ICI 182,780 treated COUP-TFII mutant mice

city: Houston

first: Dong-Kee

last: Lee

address: One Baylor Plaza

department: Molecular and Cellular Biology

institute: Baylor College of Medicine

summary: Synchrony between embryo competency and uterine receptivity is essential for a successful implantation. Mice with ablation of COUP-TFII in the uterus (PRCre/+;COUP-TFIIflox/flox), exhibit implantation defects and increased ER activity in the luminal epithelium, suggesting the high ER activity may disrupt the window of uterine receptivity. In order to determine if the increased ER activity in PRCre/+;COUP-TFIIflox/flox mutant is the cause of the defective implantation, we inhibited of ER activity in order to  rescue the implantation defect in mutant mice. ICI 182,780 (ICI), a pure ER antagonist, was administered to PRCre/+;COUP-TFIIflox/flox mutant and COUP-TFIIflox/flox control mice during receptive period and the number of implantation sites were examined. COUP-TFIIflox/flox control mice treated with oil or ICI showed the normal number of implantation sites. As expected no implantation sites were observed in PRCre/+;COUP-TFIIflox/flox mutant mice treated with oil, consistent with previous observation. However, implantation sites were detected, albeit at a reduced number in comparison to the control in PRCre/+;COUP-TFIIflox/flox mutant mice upon ICI treatment.. ICI treatment was also able to rescue the expression of WNT4 and BMP2, genes important for endometrial decidualization in the PRCre/+;COUP-TFIIflox/flox mutant mice. To ensure the rescue of embryo attachment and decidualization is a consequence of a reduction of estrogen receptor activity with ICI treatment of the mutants, we examined the expression of ER target gene, such as lactoferrin, in PRCre/+;COUP-TFIIflox/flox mutant mice. Having shown that ICI could rescue the implantation and decidualization defects of the PRCre/+;COUP-TFIIflox/flox mutant mice, the ability of ICI treatment to rescue pregnancy in these mice was assayed. While mice were born in COUP-TFIIflox/flox control mice given ICI, no pups were born in the PRCre/+;COUP-TFIIflox/flox mutant mice, with the loss in pregnancy in the PRCre/+;COUP-TFIIflox/flox mutant mice treated with ICI being due to defects in placentation. These results demonstrate that during the peri implantation period,  COUP-TFII’s role in regulating embryo attachment and decidualiton is through the reduction of ER activity. However COUP-TFII expression is still required in the post implantation period to facilitate placentation.

overall_design: Murine uteri were isolated at 6 hour after oil or ICI 182,780 injection for RNA extraction and hybridization on Affymetrix microarrays. To do this mice were ovariectomized and treated hormones (estrogen and progesterone) to mimic the early pregnant condition.

first: Isao

last: Kurihara

first: Jae-Wook

last: Jeong

first: John

last: Lydon

first: Francesco

last: Demayo

first: Ming-Jer

last: Tsai

first: Sophia


title: Gene expression data from small intestines

status: Public on Dec 17 2009

city: Columbus

first: Gustavo

last: Leone

address: 640 west 12th avenue

department: 840A Biomedical Research Tower

institute: The Ohio State University

summary:
Rb and E2F are thought to play antagonistic roles in celll proliferation.  However, this model is based mostly from in vitro cell culture systems.  We used small intestines to test this model in vivo.
We found that deletion of E2f1-3 in the small intestine of mice suppressed the ectopic expression of E2F targets and cell proliferation caused by Rb-deficiency.  Surprisingly, E2f1-3 deletion failed to arrest the proliferation of intestinal cells containing an intact Rb gene, and instead led to E2F target derepression and apoptosis.

overall_design: Total RNA of crypts and villi from wild-type, Rb-/-, E2f1-/-, E2f2-/-, E2f3-/-, E2f1-/-, E2f2-/-, and E2f3-/- small intestines.  Small intestines were harvested 7 days after mice were injected intraperitoneally with beta-napthoflavone.

first: Jim

last: Pipas


title: Comparison of gene expression profiles between human and mouse monocyte subsets [mouse data]

first: Gwendalyn

last: Randolph

address: 1425 Madison Ave

department: Gene and Cell Medicine

institute: Mount Sinai School of Medicine

summary: Human and mouse blood each contain two monocyte subsets. Here, we investigated the extent of their similarity using a microarray approach. Approximately 300 genes in human and 550 genes in mouse were differentially expressed between subsets. More than 130 of these gene expression differences were conserved between mouse and human monocyte subsets. We confirmed numerous differences at the cell surface protein level. Despite overall conservation, some molecules were conversely expressed between the two species’ subsets, including CD36, CD9, and TREM-1. Furthermore, other differences existed, including a prominent PPARγ signature in mouse monocytes absent in human. Overall, human and mouse monocyte subsets are far more broadly conserved than currently recognized. Thus, studies in mice may indeed yield relevant information regarding the biology of human monocyte subsets. However, differences between the species deserve consideration in models of human disease studied in the mouse.

overall_design: The two major subsets of monocytes (Ly-6C+ and Ly-6Clo) from 12-week old C57Bl/6 mice were sorted and the RNA extracted and hybridized to Affymetrix GeneChip® 430 2.0 arrays. We pooled leukocytes from 5 mice for each sort and sorted 4 separate times for 4 biological replicates. The two major monocyte subsets (CD16- and CD16+) were isolated from venous heparinized blood from apparently healthy human volunteers using MACS technology with all reagents and tools from Miltenyi Biotec. Three separate donors were hybridized three different times to Affymetrix U133 Plus 2.0 array.

first: Molly

last: Ingersoll

first: Rainer

last: Spanbroek

first: Claudio

last: Lottaz

first: Marion

last: Frankenberger

first: Reinhard

last: Hoffmann

first: Jörg

last: Mages

first: Roland

last: Lang

first: Matthew

last: Collin

first: Frank

last: Tacke

first: Andreas

last: Habenicht

first: Loems

last: Ziegler-Heitbrock


title: Microarray profiling analysis in Jmj-Fl/Fl and Jmj-null ESCs.

city: Boston

first: Xiaohua

last: Shen

address: 44 Binney Street

summary:
We used microarrays to detail the role of JMJ in ES cell function.

Keywords: cell type and time course

overall_design: Cells were harvested for RNA extraction and hybridization on Affymetrix microarrays.

first: Stuart

last: Orkin


title: colonic vs bone marrow MSC

status: Public on Dec 03 2009

city: St. Louis

first: Thaddeus

last: Stappenbeck

state: MO

address: 660 S. Euclid Avenue, Box 8118

department: Pathology and Immunology

institute: Washington University in St. Louis

summary: We found that mesenchymal stem cells isolated from colonic tissue express significantly increased expression of Ptgs2 or cox-2 compared to that of mesenchymal stem cells isolated from the bone marrow, one of the most common tissues from which this cell type is derived.  We hypothesized that the localization of these cells in the colon exposes them to specific environmental factors that induce and/or maintain increased constitutive levels of cox-2 uniquely in this cell type.  In order to identify possible candidate molecules regulating cox-2 in these cells, we decided to compare the transcriptomes of colonic mesenchymal stem cells and bone marrow-derived mesenchymal stem cells.

overall_design: Mesenchymal stem cells were isolated by fast plastic adherence after collagenase type I-mediated dissociation of the tissue of origin.  Cells were maintained in culture in low glucose DMEM with 10mM HEPES and 10% FBS.  Cells were passaged at 90-100% confluency.  Approximately 4 million cells from four MSC lines, two from colon and two from bone marrow, were lysed between passages 5 and 10.  Total RNA was isolated, amplified, and hybridized to Affymetrix MOE230.2 chips.

first: Monica

middle: R

last: Walker


title: Microarray gene expression profiling of aorta genes of APOE-deficient mice receiving the ACE inhibitor captopril

city: Zurich

first: Ursula

last: Quitterer

address: Winterthurerstrasse 190

department: Molecular Pharmacology

country: Switzerland

institute: ETH Zurich

summary:
Microarray gene expression profiling of aorta genes of APOE-deficient mice receiving atherosclerosis treatment with the ACE inhibitor captopril.
Hypercholesterolemic APOE-deficient mice were used as a standard model of atherosclerosis to study gene expression changes during atherosclerosis treatment with the ACE inhibitor captopril. Microarray analysis was performed of whole aortas isolated from captopril-treated APOE-deficient mice relative to untreated APOE-deficient mice with overt atherosclerosis, and nontransgenic control mice. Microarray gene expression profiling revealed that captopril-mediated atherosclerosis prevention involved inhibition of aorta-infiltrating immune cells such as pro-atherogenic T lymphocytes and macrophages.

overall_design: Microarray gene expression profiling was performed of whole aortas isolated from APOE-deficient mice with atherosclerosis relative to captopril-treated APOE-deficient mice, and nontransgenic control mice. Three study groups were analyzed, i.e. 8-months-old untreated APOE-deficient mice with overt atherosclerosis, age-matched APOE-deficient mice treated for 7 months with the angiotensin-converting enzyme (ACE) inhibitor, captopril (20 mg/kg in drinking water), and nontransgenic control C57BL/6J mice. Two biological replicates were made of each group, and total RNA of three aortas was pooled for one gene chip.

first: Joshua

last: Abd Alla


title: Gene expression before HAART initiation predicts HIV-infected individuals at risk of poor CD4+ T cell recovery.

city: La Jolla

first: Christopher

last: Woelk

address: 9500 Gilman Dr.

department: Medicine

institute: University of California San Diego

summary:
Analysis of peripheral blood mononuclear cells (PBMCs) taken from 24 HIV-infected male participants before the start of highly active antiretroviral therapy (HAART).
Results identify biomarkers for the identification of HIV-infected participants that progress to good versus poor CD4+ T cell recovery after 48 weeks of HAART.

overall_design: This retrospective study evaluated PBMC gene expression in cells taken within 2 weeks before intitiation of HAART from 24 recently HIV-infected individuals to identify genes whose expression is predictive of CD4+ T cell recovery after 48 weeks of HAART.

first: Nadejda

last: Beliakova-Bethell


title: Expression data from wild type, Ring1B-/-, Eed-/-, and Ring1B/Eed double deficient mouse ES cells

status: Public on Dec 01 2009

city: Vienna

first: Moritz

middle: M

last: Gaidt

address: Campus-Vienna-Biocenter 1

country: Austria

institute: IMP

summary: Polycomb complexes establish chromatin modifications for maintaining gene repression and are essential for embryonic development in mice. Here we use pluripotent embryonic stem (ES) cells to demonstrate an unexpected redundancy between Polycomb repressive complex 1 (PRC1) and PRC2 during the formation of differentiated cells. ES cells lacking the function of either PRC1 or PRC2 can differentiate into cells of the three germ layers, whereas simultaneous loss of PRC1 and PRC2 abrogates differentiation. On the molecular level the differentiation defect is caused by the derepression of a set of genes that is redundantly repressed by PRC1 and PRC2 in ES cells. Furthermore, we find that genomic repeats are Polycomb targets and show that in the absence of Polycomb complexes endogenous MLV elements can mobilize. This indicates a contribution of the PcG system to the defense against parasitic DNA and a potential role of genomic repeats in Polycomb mediated gene regulation.

overall_design: RNA from wt and PcG mutant ES cells was extracted using Trizol and hybridized to an Affymetrix Mouse 430_2.0 chip. Labeling, hybridization and primary data analysis were performed by a commercial provider (Atlas Biolabs, Berlin). Before RNA extraction, the undifferentiated ES cell state was confirmed by colony morphology. All genotypes were hybridized in biological triplicates.

first: Martin

last: Leeb

first: Diego

last: Pasini

first: Maria

last: Novatchkova

first: Markus

last: Jaritz

first: Kristian

last: Helin

first: Anton

last: Wutz


title: Expression profiling of sox11-expressing glioma-initiating cell-like cells

city: Sapporo

first: Toru

last: Kondo

address: Kita-15, Nishi-7, Kita-ku,

department: Institute for Genetic Medicine

institute: Hokkaido University

summary: To identify factors involved in tumorigenicity of glioma-initiating cells (GICs), we compared gene expression in GIC-like cells with and without sox11 expression.

overall_design: We established sox11-expressing mouse glioma-initiating cell (GIC)-like cell line (NSCL61s), NSCL61s-sox11, which lost tumorigenicity when transplanted in vivo. We think that genes, which are differently expressed between NSCL61s and NSCL61s-sox11, would be new targets for glioma therapy.


title: Expression profiles of mouse glioma-initiating cell-like subclones

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

overall_design: Refer to individual Series


title: Expression profiling of mouse glioma-initiating cell-like cells (GICs) and non-GICs

summary: To identify factors involved in glioma-initiating cells (GICs), we compared gene expression between GIC-like cells and non-GICs.

overall_design: Neural stem cells (NSCs) were transfected with pCMS-EGFP-HRasL61 and pBabe-neo by electroporation and cultured in 0.5 mg/ml neomycin. The GFP-positive stable NSCs (NSCL61s) were purified by flow cytometry. Total RNA was prepared using RNeasy Mini Kit (QIAGEN).


title: Expression data from EGFR mutant transgenic mice

city: Nashville

first: William

last: Pao

state: TN

address: 2220 Pierce Avenue, 777 Prestion Research Building

institute: Vanderbilt University

summary: We performed mRNA expression profiling of lung tumors from C/L858R, C/T790M, and C/L+T mice and from corresponding normal lung tissue.

overall_design: mRNA was extracted from pulverized lung samples using Trizol (Invitrogen) and then hybridized to MOE 430 2.0 chips (Affymetrix) using standard hybridization techniques.

first: Lucia

last: Regales


title: Knockout of the selenocysteine tRNA (Trsp) gene in mouse macrophage

status: Public on Dec 22 2009

city: Bethesda

first: Bradley

last: Carlson

address: 9000 Rockville Pike

institute: National Cancer Institute

summary:
Comparative analysis of gene expression in bone marrow-derived macrophages (BMDM) from trsp knockout mice  (Trspfl/fl-LysM-Cre+/-) and Control (Trspfl/fl-LysM-Cre-/-) mice.

Selenium, a micronutrient whose deficiency in the diet causes immune dysfunction and inflammatory disorders, exerts its physiological effects partly in the form of selenium-containing proteins (selenoproteins). Incorporation of selenium into the amino acid selenocysteine (Sec), and subsequently into selenoproteins, is mediated by Sec tRNA[Ser]Sec. To identify macrophage-specific selenoprotein function, we generated mice with the Sec tRNA[Ser]Sec gene specifically deleted in myeloid cells. These mutant mice were devoid of the selenoproteome in macrophages, yet exhibited largely normal inflammatory responses. However, selenoprotein deficiency led to aberrant expression of extracellular matrix-related genes, and diminished migration of macrophages in a protein gel matrix. Therefore, selenium status may affect immune defense and tissue homeostasis through its effect on selenoprotein expression and the trafficking of tissue macrophages.

overall_design: We have generated mice in which we have selectively removed the selenocysteine tRNA gene (trsp) in macrophages under the control of LysM-Cre promoter. Microarray analysis was performed on RNA samples taken from bone marrow-derived macrophages in knockout and control mice. 1. Control unstimulated 2. Knockout unstimulated 3. Control lipopolysaccharide (LPS) stimulated (4h) 4. Knockout LPS stimulated (4h). Three replicates for each condition. Thus, a total of 12 samples.

first: Min-Hyuk

last: Yoo

first: Yasuyo

last: Sano

first: Aniruddha

last: Sengupta

first: Jin

last: Kim

first: Robert

last: Irons

first: Vadim

last: Gladyshev

first: Dolph

last: Hatfield

last: Park


title: Mouse aorta smooth muscle cells differentiate into lymphoid tissue organizers upon combined TNFR1/LTBR NF-kB signaling

status: Public on Nov 25 2009

city: Munich

first: Andreas

middle: Johann Richard

last: Habenicht

state: Bavaria

address: Pettenkoferstraße 9a

institute: Ludwig Maximilians Universität München

summary: Cultured mouse aorta endothelial cells (from 8-12 weeks old C57BL/6J mice, passage 2-3) were exposed to phosphate buffered saline (control) or a combination of TNFalpha plus agonistic alpha-LTßR antibody for 24 hours as described in Lötzer et al. 2009. Arterioscler. Thromb. Vasc. Biol., in press. Total RNA was extracted and microarrays were prepared.

overall_design: Mouse aorta endothelial cells in tissue culture were stimulated with agonists and subsequently microarray, RT-PCR, and protein assays / analyses were performed.

first: Katharina

last: Loetzer

first: Michael

last: Beer


title: Gene expression profiles in Elastin (Eln+/-) mouse aorta and aortic valve tissue

status: Public on Nov 30 2009

city: Cincinnati

middle: Bruce

last: Hinton

address: 3333 Burnet Ave

department: Dept Of Pediatrics

institute: Cincinnati Children's Hospital Medical Center

summary: Elastin wild type Eln+/+ and Eln+/- mouse aorta and aortic valve tissue.  In the study, we demonstrated differential gene expression in juvenile elastin deficient mouse valve tissue.

overall_design: In the study, we hybridized RNA from Elastin wild type (Eln+/+) aorta tissue, elastin wild type (Eln+/+) aortic valve tissue, elastin (Eln+/-) aorta tissue and elastin (Eln+/-) aortic valve tissue to Affymetrix GeneChip Mouse Genome 430 2.0 Array

first: Jennifer

last: Adelman-Brown

first: Sandra

last: Witt

first: Bruce

last: Aronow

first: Varun

last: Krishnamurthy

first: Matthew

last: Gruber

first: Hanna

last: Osinska

first: Bhuvaneswari

last: Sakthivel

first: Daria

last: Narmoneva

last: Mecham

first: D

middle: W

last: Benson


title: The anti-angiogenic and anti-tumor cell signaling networks of the kringle 1 domain of hepatocyte growth factor (HGFK1)

city: Hong Kong

first: Wing-Sze

last: Leung

address: 8S03, Kadoorie Biological Sciences Building, The University of Hong Kong

department: Computer Science

country: Hong Kong

institute: The University of Hong Kong

summary:
Previously, we have demonstrated that the recombinant adeno-associated virus carrying the kringle domain 1 of hepatocyte growth factor (rAAV-HGFK1) gene is a potential anti-angiogenic approach for the treatment of hepatocellular carcinoma (HCC) and exerts direct inhibition effects on tumor cells. Here, using genome-wide expression profiling technology, coupled with RT-PCR validation, we investigated the differentially expressed genes and proposed the mechanisms involved in HGFK1 anti-angiogenic and anti-tumor cell signaling networks.
Keywords: HGFK1, anti-angiogenic signaling network, anti-tumor cell signaling network

sample_organism:
Mus musculus
Rattus norvegicus

platform_organism:
Mus musculus
Rattus norvegicus

overall_design: Microarray probe sets which were at least 2-fold changed upon rAAV-HGFK1 treatment when compared to rAAV-EGFP (baseline control) treatment on the cells are considered as differentially expressed genes (DEGs). The differentially expressed genes were analyzed using two software tools, namely PathwayArchitect (version 1.0.0) (www.strategene.com) and Ingenity Pathways Analysis (version 5.0) (http://www.ingenuity.com/index.html). They are designed to assist microarray data analysis and provide visualization of biological pathways, gene regulation networks and protein-protein interactions to users. The signaling networks proposed above were manually determined and created based on the relevant findings in literature provided by the software tools.

first: Wing

first: Zan

last: Shen

first: Hsiang

middle: F

last: Kung

first: Marie

last: Lin


title: Gene expression rates in a mouse model for Potocki-Lupski Syndrome

city: Lausanne

first: Alexandre

last: Reymond

address: Genopode building

department: Center for Integrative Genomics

institute: University of Lausanne

summary:
To identify gene(s) that are modified in their relative expression levels in the Potocki-Lupski Syndrome mouse model and map to the rearranged region, i.e. possible candidate genes at the source of the PTLS-like phenotypes shown by the PTLS mouse, we comp
Keywords: disease model, expression profiling

overall_design: We profiled the hippocampi of three Dp(11)17/+ and three wild type males, all six in a pure C57BL/6-Tyr c-Brd genetic background.

first: Jacqueline

last: Chrast

first: Katherina

last: Walz

first: Jessica

last: Molina


title: Role of FoxO3 in adult neural stem cell maintenance in mice

status: Public on Nov 29 2009

city: Stanford

first: Alex

last: Morgan

state: CA

address: 251 Campus Drive, MSOB X-215

department: Biomedical Informatics

institute: Stanford Medical School

summary: In the nervous system, neural stem cells (NSC) are necessary for the generation of new neurons and for cognitive function. Here we show that FoxO3, a member of a transcription factor family known to extend lifespan in invertebrates, regulates the NSC pool. We find that adult FoxO3-/- mice have fewer NSC in vivo than wild type counterparts. NSC isolated from adult FoxO3-/- mice have decreased self-renewal and an impaired ability to generate different neural lineages. Identification of the FoxO3-dependent gene expression profile in NSC suggests that FoxO3 regulates the NSC pool by inducing a program of genes that preserves quiescence, prevents premature differentiation, and controls oxygen metabolism. The ability of FoxO3 to prevent the premature depletion of NSC might have important implications for counteracting brain aging in long-lived species.

overall_design: mRNA expression from secondary neurospheres cultured from cells taken from mouse forebrains was compared between FoxO3+/+ (wildtype) and FoxO3-/- (null mutant) mice from the FVB/N background.

first: Valerie

last: Renault

first: Anne

last: Brunet


title: Single cell analysis of the Common Lymphoid Progenitor compartment reveals functional and molecular heterogeneity

status: Public on Nov 24 2009

city: Toronto

first: Sasan

last: Zandi

state: Ontario

address: 101 college St

institute: UHN

summary: In order to investigate molecular events involved in the regulation of lymphoid lineage commitment, we crossed lamda5 reporter transgenic mice to mice where the GFP gene is inserted into the Rag1 locus. This allowed us to sub-fractionate common lymphoid progenitors (CLPs) and pre-pro-B cells into lamda5-Rag1low, lamda5-Rag1high and lamda5+Rag1high cells. Clonal in vitro differentiation analysis demonstrated that Rag1low cells gave rise to B/T and NK cells. Rag1high cells displayed reduced NK-cell potential with preserved capacity to generate B- and T-lineage cells while the lamda5+ cells were B-lineage restricted. Ebf1 and Pax5 expression was largely confined to the Rag1high populations. These cells also expressed a higher level of the surface protein LY6D providing an additional tool for the analysis of early lymphoid development. These data suggest that the classical CLP compartment composes a mixture of cells with more or less restricted lineage potentials opening new possibilities to investigate early hematopoiesis.

overall_design: Two newly identified subpopulations of common lymphoid progenitors (CLP), hereafter called CLP_RAGhigh and CLP_RAGlow, have been sorted in 2 replicates. RNA was extracted from 2,000 purified adult BM cells using the RNAeasy microkit. RNA was labeled and amplified by dual amplification and hybridized to Affymetrix microarray MOE430_2, according to AffymetrixTM GeneChip Expression Analysis Technical Manual. Probe level expression values were calculated using the RMA algorithm.

first: Robert

last: Mansson

first: Eva

last: Welinder

first: David

last: Bryder

first: Mikael

last: Sigvardsson


title: Normal Colon Epithelial Cells

city: Augusta

first: Lesleyann

last: Hawthorn

institute: Medical College of Georgia Cancer Center

summary:
Provides a set of enriched normal colon epithelial cells to use as a baseline for disease of the colon

We present a dependable expression reference data set for non-neoplastic colonic epithelial cells. An enriched population of fresh colon epithelial cells were obtained from non-neoplastic, colectomy specimens and analyzed using Affymetrix GeneChip Exon 1.0 ST arrays. The findings from this study represent the first comprehensive expression profile for non-neoplastic colonic epithelial cells reported.  For demonstration purposes, we have compared the data derived from these cells to a publically available set of tumor and normal matched colon data.  This analysis allowed an assessment of global gene expression alterations and demonstrated that adjacent normal tissues, with a high degree of cellular heterogeneity, are not always representative of normal cells for comparison to tumors which arise from the colon epithelium. We also examined alternative splicing events in tumors compared to normal colon epithelial cells. Our analysis of splice variants on a genome-wide scale illustrate that this is a very labor intensive procedure, requiring vigilant examination of the data. It is projected that the contribution of this set of data derived from pure colonic epithelial cells will enhance studies in colon-related disease and offer a vital baseline for studies aimed at elucidating the mechanisms of alternative splicing.

overall_design: Colon epithelial cells were isolated and enriched and hybridized to Exon 1.0 ST arrays


title: Novel Regulators of Fgf23 Expression and Mineralization in Hyp Bone

city: Memphis

first: Darryl

last: Quarles

address: 920 Madison Ave

institute: University of Tennessee Health Science Center (UTHSC)

summary: We used gene array analysis of cortical bone to identify Phex-dependent gene transcripts regulating Fgf23 production and mineralization in Hyp mice. We discovered that activation of Fgf receptor- and Wnt-pathways contribute to increased Ffg23 gene transcription in Hyp bone. We found evidence in Hyp bone for increased expression of Fgf1, Fgf7, and Egr2 in the Fgf-signaling pathway and decrements in Sost and Cpz and increments in Sfrp1 and 4 in the Wnt-signaling pathway. Moreover, activation of Fgf and Wnt-signaling stimulated, whereas Tgf β inhibited Fgf23 promoter activity in osteoblasts. We also observed reductions in Bmp1, a metalloproteinase that metabolizes the Fgf23 regulatory extracellular matrix protein Dmp1. These findings suggest that elevation of Fgf23 expression in osteocytes is regulated by interactions between cell surface expression of Phex, extracellular matrix proteins and paracrine effects of Fgf and Wnt. Alterations were also found in enzymes regulating the posttranslational processing and stability of Fgf23, including decrements in the glycosyltransferase Galnt3 and the proprotein convertase Pcsk5. In addition, we found that the Pcsk5 and the glycosyltransferase Galnt3 were decreased in Hyp bone, suggesting that reduced post-translational processing of FGF23 may also contribute to increased Fgf23 levels in Hyp mice. With regards to mineralization, we identified additional candidates to explain the intrinsic mineralization defect in Hyp osteoblasts, including increases in the mineralization inhibitors Mgp and Thbs4, as well as increases in local pH altering factors, carbonic anhydrase 12 (Car12) and 3 (Car3) and the sodium-dependent citrate transporter (Slc13a5). These studies demonstrate the complexity of gene expression alterations in bone that accompanies inactivating Phex mutations and identify novel pathways that may coordinate Fgf23 expression and mineralization of extracellular matrix in Hyp bone.

overall_design: We isolated total RNAs from long bones of both WT and Hyp mice at 12 days of age. Since the RNA yields from the long bones are very low, we combined 2 bone samples with same genotype (WT or Hyp) for one RNA extraction. We will compare the difference of the gene expressions between Hyp and WT. We will use 4 samples in each animal condition.

first: Shiguang

last: Liu

first: Wen

last: Tang

first: Jianwen

last: Fang

first: Hua

last: Li

first: L.

middle: D


title: Age Dependent Gene Expression Responses to Inhaled Lipopolysaccharide Combined with Mechanical Ventilation

status: Public on Nov 23 2009

city: Seattle

first: Lincoln

last: Smith

address: 1660 S. Columbian Wy, 151L

department: Pediatrics

institute: University of WA

summary: Children have a lower incidence and mortality from acute lung injury than adults, and infections are the most common event associated with acute lung injury (ALI).  To study the effects of age on susceptibility to ALI, we investigated the responses to microbial products combined with mechanical ventilation in juvenile (21 day) and adult (16 week-old) mice.  We hypothesized that the increased incidence and severity of lung injury associated with increasing age is due in large part to acquired changes in the way in which inflammatory responses are activated in the lungs in response to microbial products and mechanical ventilation.

overall_design: Juvenile (21 day) and adult (16 week) C57BL/6 mice were treated with an aerosol of E. coli 0111:B4 lipopolysaccharide (LPS) (20 mL of 0.1 mg/mL) for 30 minutes in a sealed aerosol chamber, immediately followed by mechanical ventilation (LPS+MV) using tidal volume = 15 mL/kg, rate = 80 breaths/min, FiO2 = 30% and positive end expiratory pressure = 2 cm H2O for the duration of the study period time = 2 hours.  Comparison groups included mice treated with LPS or mechanical ventilation (MV) alone, and untreated age-matched controls. There were N = 4 animals per group except the juvenile mice treated with MV alone and LPS+MV where there were N = 3.  Each sample was an individual animal, therefore there were 30 samples.  Mice treated with LPS alone were placed into a sealed aerosol chamber as stated above, and then allowed to breath spontaneously with free access to food and water for the duration of the study period time = 2 hours.  Mice treated with MV alone were treated with the mechanical ventilation protocol stated above for the duration of the study period time = 2 hours.  At the end of the study period, the mice were euthanized, and the lungs were immediately removed and placed into RNAlater (Ambion, Austin, TX) for at least 24 hr prior to isolation of total lung mRNA.

first: Sina

last: Gharib


title: Reprogramming of a B cell line into macrophages

city: Barcelona

first: Thomas

last: GRAF

address: Dr.Aiguader, 88

institute: Center for Genomic Regulation (CRG)

summary: Transcription factor induced reprogramming of one specialized cell type into another is a promising approach for regenerative medicine. However, the process still remains poorly understood, in large part because of the lack of adequate experimental models. Here we describe a robust cell reprogramming system consisting of a B cell line with an inducible form of C/EBPa that can be converted into macrophages with essentially 100% efficiency in only 2 to 3 days. The conversion involves reciprocal changes in cell surface antigen expression, increase in cell granularity and size, alterations in cellular structures, formation of membrane extensions, acquisition of phagocytic capacity and an increased inflammatory responsiveness as well as migratory activity. Analysis of the transcriptome shows complex reciprocal regulation of B cell and macrophage genes, including transcription factors required for the formation of the two lineages. The fact that the cells become irreversibly committed to a macrophage fate within 1 to 2 days after activation of C/EBPa show that they are truly reprogrammed. The system should be useful to study epigenetic and cell biological mechanisms of transcription factor induced cell reprogramming.

overall_design:
time course analysis.
6 duplicated conditions: 12 samples.
control: HAFTL cells
time points: vehicle control, 3h, 12h, 24h, 48h.

first: Lars

last: Bussmann

first: Alexis

last: Schubert

first: Thien-Phong

last: Vu Manh

first: Luisa

last: De Andres

first: Sabrina

last: Desbordes

first: Maribell

last: Parra

first: Timo

last: Zimmermann

first: Francesca

last: Rapino

last: Graf


title: Effects of extensive fasting on hepatic transcription

first: Christopher

last: Vollmers

address: 10010 North Torrey Pines Road

department: Regulatory Biology Laboratory

institute: The Salk Institute for Biological Studies

summary: Temporally restricted feeding has a profound effect on the hepatic circadian clock. While the circadian clock is largely unaffected by by extensive fasting, many transcripts are known to be affected by a fasting paradigm. This dataset shows the effect of extensive fasting on dynamic gene expression in the liver

overall_design: C57/B6 mice were entrained to ad libitum feeding schedule for two weeks. They were then released into constant were food was withdrawn at CT16. On the second day in constant darkness tissue was collected at the indicated timepoints. Total RNA was extracted and 5ug of total RNA was used for the standard Affymetrix protocol of amplification, labeling and hybridization

first: Shubroz

last: Gill

first: Luciano

last: DiTacchio

first: Hiep

last: Le

first: Sandyarani

last: Pulivarthy

first: Satchidananda

last: Panda


first: Andreas

last: Habenicht

summary: Mouse aorta smooth muscle cells (SMCs) express TNF receptor superfamily member 1A (TNFR1) and lymphotoxin ß receptor (LTßR). Circumstantial evidence has linked the SMC LTßR to tertiary lymphoid organogenesis in diseased aortae of hyperlipidemic mice. Here, we explored potential roles of TNFR1 and LTßR activation in cultured SMCs. TNFR1 signaling by TNF activated the classical RelA NF-κB pathway, whereas LTßR signaling by agonistic anti LTßR antibody activated both the classical RelA and alternative RelB NF-κB pathways. Addition of both agonists synergized to enhance p100 inhibitor processing to the p52 subunit of NF-κB and promoted its nuclear translocation suggesting RelA-RelB cross-talk in transcription regulation. Correspondingly, microarrays showed that simultaneous TNFR1 and LTßR activation when compared to activation of single receptors was followed by markedly elevated levels of mRNAs encoding leukocyte homeostatic chemokines CCL2, CCL5, CXCL1, and CX3CL1. Furthermore, SMCs acquired prototypical features of mesenchymal cells known as lymphoid tissue organizers (LTOs), which control tertiary lymphoid organogenesis in autoimmune diseases, through hyperinduction of CCL7, CCL9, CXCL13, CCL19, CXCL16, VCAM-1, and ICAM-1. Experiments with ltbr-/- SMCs suggested that the LTßR-RelB activation component of NF-κB signaling was obligatory to generate the LTO phenotype. TNFR1-LTßR crosstalk also resulted in augmented synthesis and prolonged secretion of lymphorganogenic chemokine proteins into the culture medium. Thus, combined TNFR1-LTßR signaling triggers SMC transdifferentiation into a phenotype that strikingly resembles LTOs. LTO-like SMCs may adopt a thus far unrecognized role in diseased arteries, i.e. to coordinate tertiary lymphoid organogenesis in atherosclerosis, aortic aneurysm, and transplant vasculopathy.

overall_design: Smooth muscle cells in tissue culture were stimulated with agonists and subsequently microarray, RT-PCR, and protein assays / analyses were performed

first: Katharina

last: Lötzer

first: Michael

last: Beer


title: The effects of temporally restricted feeding on hepatic gene expression

summary: Temporally restricted feeding is known to impact the circadian clock. This dataset shows the effects of temporally restricted feeding on the hepatic transcriptome.

overall_design: C57/B6 mice were entrained for two weeks to a temporally restricted feeding schedule. Food was made available only between ZT(CT)1 and ZT(CT)9. Mice were then released into constant darkness while food availability was still restricted and liver tissue was collected at the indicated timepoints on the second day in constant darkness. Total RNA was extracted and 5ug were submitted to the standard Affymetrix protocol for amplification, labeling and hybridization.


title: The effects of temporally restricted feeding on hepatic gene expression of Cry1, Cry2 double KO mice

summary: Restricted feeding impacts the hepatic circadian clock of WT mice. Cry1, Cry2 double KO mice lack a circadian clock and are thus expected to show rhythmical gene expression in the liver. Imposing a temporally restricted feeding schedule on these mice  shows how the hepatic circadian clock and rhythmic food intake regulate rhythmic transcription in parallel

overall_design: Cry1, Cry2 double KO mice were entrained either to ad libitum or temporally restricted feeding (tRF) schedules. Food was made available to mice under the tRF regimen only between ZT(CT)1 and ZT(CT)9. Mice were then released into constant darkness while the respective feeding schedules were still maintained. Liver tissue was collected on the second day of constant darkness at the indicated timepoints. Total RNA was extracted and 5ug of RNA was used in the standard Affymetrix protocol for amplification, labeling and hybridization


title: Expression data from AID-silenced mouse plasmacytoma J558 (BALB/c, H-2Ld)cell lines

status: Public on Nov 20 2009

city: Columbus

first: Yi

last: Xiao

address: 1640 Neil Ave

department: Pathology

institute: Ohio State University

summary: To determine the potential mechanisms by which AID-elimination facilitate better J558 tumor rejection by P1CTL, we performed cDNA microarray analysis to compare AID-silenced J558 cells and their relative controls.

overall_design: The mouse Affymetrix Mouse Genechips 430-2.0 arrays were hybridized to RNA derived from control and AID-silenced J558 cells according to manufacturer’s directions. Two different pairs of cells (C4 vs AID 2.27 (a) and C5 vs AID 2.13 (b)) were used for RNA extraction and hybridization on Affymetrix microarrays.

first: Xue-Feng

last: Bai

first: Jin-Qing

last: Liu


title: Expression profile of isolated lymphoblasts from mice treated with vehicle or SAHM1

status: Public on Nov 12 2009

city: Cambridge

first: Raymond

last: Moellering

state: MA

address: 12 Oxford Street

department: Chemistry and Chemical Biology

institute: Harvard University

summary:
NOTCH proteins regulate signaling pathways involved in cellular differentiation, proliferation and death. Overactive Notch signaling as been observed in numerous cancers and has been extensively studied in the context of T-cell acute lymphoblastic leukemia (T-ALL) where more than 50% of pateints harbour mutant NOTCH1. Small molecule modulators of these proteins would be important for understanding the role of NOTCH proteins in malignant and normal biological processes.
We were interested to measure the global gene expression changes in leukemic cells isolated from mice harbouring a NOTCH1-driven genetically engineered T-cell leukemia after treatment with SAHM1, a synthetically stabilized α-helical peptide derived from the MAML1 co-activator protein.

overall_design: A genetically engineered murine model of NOTCH1-driven T-ALL was developed by retroviral transduction of murine bone marrow with a mutant NOTCH1 allele commonly observed in human T-ALL patients. Transplantation of transduced cells gave  rise to T-ALL that was quantifiable by bio-luminescence in our model. After established leukemia was evident by continually increased tumor burden (luminescence) mice were either treated with vehicle alone (5% DMSO in Hank's buffered saline solution) or SAHM1 (30 mg/kg, twice daily, intraperitoneal injection). After five days of treatment, mice receiving SAHM1 had a significant decrease in tumor growth. To measure a pharmacodynamic effect on Notch signaling, circulating lymphoblasts were collected from vehicle- (n=3) and SAHM1-treated (n=3) mice and gene expression profiles were generated.

first: Melanie

last: Cornejo

first: D

middle: G

last: Gilliland

first: Tina

last: Davis

first: Andrew

middle: L

last: Kung