title: Expression data from wild type and Ctip2-/- (Bcl11b) mutant mouse striatum at P0

first: Bradley

last: Molyneaux

department: MGH-HMS Center For Nervous System Repair

summary:
Striatal medium spiny neurons (MSN) are critically involved in motor control, and their degeneration is a principal component of Huntington’s disease. We find that the transcription factor Ctip2 (also known as Bcl11b) is central to MSN differentiation and striatal development. Within the striatum, it is expressed by all MSN, while it is excluded from essentially all striatal interneurons. In the absence of Ctip2, MSN do not fully differentiate, as demonstrated by dramatically reduced expression of a large number of MSN markers, including DARPP-32, FOXP1, Chrm4, Reelin, MOR1, GluR1, and Plexin-D1. Furthermore, MSN fail to aggregate into patches, resulting in severely disrupted patch-matrix organization within the striatum. Finally, heterotopic cellular aggregates invade the Ctip2-/- striatum suggesting a failure by MSN to repel these cells in the absence of Ctip2.   In order to investigate the molecular mechanisms that underlie Ctip2-dependent differentiation of MSN and that underlie the patch-matrix disorganization in the mutant striatum, we directly compared gene expression between wild type and mutant striatum at P0. Because CTIP2-expressing MSN constitute 90-95% of the neurons within the striatum, we reasoned that we should be able to detect changes in medium spiny neuron gene expression in Ctip2 null mutants. We microdissected out small regions of striatum at matched locations in wild type and Ctip2-/- mutant littermates at P0 and investigated gene expression with Affymetrix microarrays. We selected the 153 most significant genes and further analyzed them to identify a smaller set of genes of potentially high biological relevance. In order to verify the microarray data and define the distribution of the identified genes in the striatum, we performed in situ hybridization or immunohistochemistry for 12 selected genes: Plexin-D1, Ngef, Nectin-3, Kcnip2, Pcp4L1, Neto1, Basonuclin 2, Fidgetin, Semaphorin 3e, Secretagogin, Unc5d, and Neurotensin. We find that all these genes are either specifically downregulated (Plexin-D1, Ngef, Nectin-3 Kcnip2, Pcp4L1, Neto1), or upregulated (Basonuclin 2, Fidgetin, Semaphorin 3e, Secretagogin, Unc5d, Neurotensin), in the Ctip2-/- striatum, confirming and extending the microarray results. Together, these data indicate that Ctip2 is a critical regulator of MSN differentiation, striatal patch development, and the establishment of the cellular architecture of the striatum.
Keywords: mutant analysis

overall_design: Matched regions of striatum from wild type and Ctip2-/- mice were obtained via 500 µm diameter punch biopsies performed in the center of the developing striatum in acutely sectioned 300 µm coronal slices of the brain at postnatal day 0 (P0). Sections were matched rostro-caudally between wild type and null mutant tissue, and fiduciary landmarks were used to assure reproducible microdissection of comparable regions. RNA was extracted using the StrataPrep Total RNA Mini Kit (Stratagene, La Jolla, CA), and RNA quality was assayed using a bioanalyzer (Agilent Technologies, Paola Alto, CA). To ensure reproducibility and biological significance, microarrays were performed with RNA samples from three independent wild type, one heterozygote, and four Ctip2-/- mice (biological replicates). Microarray data were normalized using the RMA function within Bioconductor (Irizarry et al., 2003).  Statistical significance of gene expression differences between wild type and knockout was determined using Statistical Analysis of Micrarrays (SAM) (Tusher et al., 2001). Using a SAM d-score cutoff of > 2 or < -2, we selected the 153 most significant genes and further analyzed them to identify a smaller set of genes of potentially high biological relevance.

first: Paola

last: Arlotta

first: Jeffrey

last: Macklis


title: Activin-deficient granulosa cells

status: Public on Dec 28 2007

city: Houston

first: Martin

last: Matzuk

state: TX

address: One Baylor Plaza

country: USA

institute: Baylor College of Medicine

summary:
Compares activin deficient granulosa cells (Inhba flox/-; Inhbb-/-; Amhr2cre/+) to wild type granulosa cells
Keywords: Genetic Modificaton

overall_design: Three replicate wild type granulosa cell samples compared to 2 activin-deficient granulosa cell samples.  Each replicate is derived from 2-3 females.

middle: M

first: Stephanie

middle: A

last: Pangas

first: Carolina

middle: J

last: Jorgez

first: Chester

middle: W

last: Brown

first: Rajendra

last: Kumar


title: Expression data from immature pDC and pDC activated with CpG 1826 and influenza virus PR8

status: Public on Dec 13 2007

city: Philadelphia

first: Amaya

middle: I

last: Wolf

state: PA

address: 3601 Spruce street

institute: Wistar Institute

summary:
CpG 1826 binds to Toll-like receptor (TLR)9, whereas influenza virus PR8 activates pDC via TLR7. Differential stimulation of pDCs is expected to result in unique activation mechanism(s) leading to a different phenotypically and functionally matured pDC
We used microarrays to detail the global programme of gene expression underlying the maturation process of pDC activated with CpG 1826 and influenza virus PR8. We identified a distinct expression profile of upregulated immunomediators.
Keywords: time course

overall_design: Sorted pDCs were cultured for 1h and 4hs in medium control or with 5 µg/ml CpG 1826 or 300 HAU/ml purified influenza A/PR/8 virus. The first experiment (e1) included pDC in media and stimulated with CpG for 4h. In two other independent experimental batches (e2 and e3), we obtained samples of sorted pDC cultured in medium alone (med), and with CpG or PR8 (flu) for 1h and 4h. RNA extraction was performed using the RNeasy Kit (Qiagen) and hybridization on Affymetrix microarrays was performed using standard protocols. We sought to obtain homogeneous populations of pDCs at different time points under defined activation conditions in order to decipher the temporal resolution of expression profiles during the process of their maturation.

first: Wolfgang

last: Weninger

last: Iparraguirre

first: John

last: Tobias


title: Regulation of Liver Regeneration and Hepatocarcinogenesis by Suppressor of Cytokine Signaling 3

status: Public on Dec 12 2007

city: Seattle

first: James

middle: William

last: MacDonald

state: WA

address: 4225 Roosevelt Way NE

department: Environmental and Occupational Health Sciences

institute: University of Washington

summary:
Suppressor of cytokine signaling 3 (SOCS3) down-regulates several signaling pathways in multiple cell types, and previous data suggest that SOCS3 may shut off cytokine activation at the early stages of liver regeneration. We developed hepatocyte-specific Socs3 knockout (Socs3 h-KO) mice to directly study the role of SOCS3 during liver regeneration after 2/3 partial hepatectomy (PH). Socs3 h-KO mice demonstrate marked enhancement of DNA replication and liver weight restoration after 2/3 PH in comparison with littermate controls. Without SOCS3, signal transducer and activator of transcription 3 (STAT3) phosphorylation is prolonged, and activation of the mitogenic kinases extracellular signal-regulated kinase 1/2 (ERK1/2) is enhanced after PH. In vitro, we show that SOCS3 deficiency enhances hepatocyte proliferation in association with enhanced STAT3 and ERK activation after epidermal growth factor (EGF) or interleukin 6 (IL-6) stimulation. Microarray analyses show that SOCS3 modulates a distinct set of genes after PH, which fall into diverse physiologic categories. Using a model of chemical-induced carcinogenesis, we found that Socs3 h-KO mice develop hepatocellular carcinoma (HCC) at an accelerated rate. By acting on cytokines and multiple proliferative pathways, SOCS3 modulates both physiologic and neoplastic proliferative processes in the liver, and may act as a tumor suppressor.
Keywords: SOCS3, liver regeneration

overall_design: Hepatocyte-specific excision of the Socs3 gene was achieved by breeding Socs3 fl/fl mice with mice expressing the Cre recombinase transgene under control of the albumin promoter (Alb-Cre+), yielding Socs3 h-KO mice. Socs3 fl/fl, Alb-Cre- littermates were used as controls for all experiments, and are henceforth referred to as littermates. All mice (C57BL/6) were free of Helicobacter species, housed in a specific pathogen free facility with 12-h light/dark cycles with free access to standard food and water. 2/3 PH and sham operations were performed as previously described (15, 50) (n=3-6 mice per genotype per time point). Liver remnants were weighed after removal of necrotic stumps and sutures, and compared to post-operative body weight. For HCC experiments, a single i.p. injection of DEN (5mg/kg, Sigma) was performed 12-14 d after birth. For short time points, a single injection of DEN (100mg/kg) (31) was given to 4 wk old mice. At indicated time points, mice were sacrificed by CO2 inhalation. All animal studies were carried out under approved IACUC protocols at the University of Washington.

first: Richard

middle: P

last: Beyer


title: Expression data from olfactory epithelium of Lip-C-treated mice compared to Lip-O-treated control mice

status: Public on Dec 14 2007

city: Lexington

first: Marilyn

middle: L.

last: Getchell

state: KY

address: 800 South Limestone St.

department: Anatomy and Neurobiology

institute: University of Kentucky

summary:
Microarray analysis of gene expression in the olfactory epithelium of macrophage depleted mice to study the role of macrophages in regulating neurodegeneration, neuroprotection, and neurogenesis of olfactory sensory neurons
Keywords: comparison of gene expression level in sham and 48 hr OBX Lip-O mice versus Lip-C mice

overall_design: Olfactory epithelium from LIp-C-treated and Lip-O-treated mice was microdissected for RNA extraction and hybridization on Affymetrix microarrays. We compared levels of gene expression in macrophage-depleted and non-depleted sham and 48 hr OBX mice using a 2x2 ANOVA and pairwise comparisons to identify molecular mechanisms of macrophage-mediated neurodegeneration, neuroprotection, and neurogenesis and to validate the gene expression patterns using real-time RT-PCR and immunohistochemistry

first: Aaron

middle: S

last: Borders

first: Matthew

last: Hersh

middle: L

first: Nico

last: vanRooijen

first: Donald

last: Cohen

first: Arnold

last: Stromberg

first: Thomas

middle: V


title: The effect of dominant negative c-Jun, TAM67, on tumorigenesis of ETV6-NTRK3 transduced Eph4 cells

city: Boston

first: Zhe

last: Li

state: MA

department: Division of Hematology/Oncology

institute: Children's Hospital Boston

summary:
We report a mouse model that recapitulates expression of the ETV6-NTRK3 (EN) fusion oncoprotein, the product of the t(12;15)(p13;q25) translocation characteristic of human secretory breast carcinoma. Activation of EN expression in mammary tissues by Whey acidic protein (Wap) promoter-driven Cre leads to fully penetrant, multifocal malignant breast cancer with short latency. We provide genetic evidence that committed bipotent or CD61+ luminal alveolar progenitors, are targets of tumorigenesis. Furthermore, EN transforms these otherwise transient progenitors through activation of the AP1 complex. Given increasing relevance of chromosomal translocations in epithelial cancers, such mice serve as a paradigm for the study of their genetic pathogenesis and cellular origins, and generation of novel preclinical models.
We showed that forced expression of a dominant negative version of c-Jun (TAM67) in EN-transduced Eph4 mammary epithelial cells impairs their ability to form tumors in immunodeficient nude mice, thus provided validation that EN-initiated mammary tumorigenesis is largely mediated through the AP1 complex.
Keywords: genetic modification, cell type comparison

overall_design: To validate that EN-initiated mammary tumorigenesis is largely mediated through the AP1 complex, we generated EN-transduced Eph4 (EN-Eph4) mammary epithelial cells as well as EN-Eph4 cells co-expressing a dominant negative version of c-Jun (TAM67), and transplanted them into nude mice. We then isolated total RNAs from resulted tumors and collected their expression profiles using Affymetrix mouse MOE 430.2 chips.

first: Cristina

middle: E

last: Tognon

first: Poul

middle: H

last: Sorensen

first: Stuart

last: Orkin


title: Molecular correlates of sleep deprivation in the brain of three inbred mouse strains in an around-the-clock experiment

status: Public on Dec 07 2007

city: Lausanne

first: Mehdi

last: Tafti

address: Genopode

department: CIG

country: Switzerland

institute: University of Lausanne

summary:
These studies adress differential changes in gene expression between sleep deprived and control mice. We profiled gene expression at four time points across the 24H Light/Dark cycle to take into account circadian influences and used three different inbred strains to understand the influence of genetic background.
Keywords: brain, circadian, genetic background, sleep deprivation

overall_design: Experiments were performed on male mice ( AKR/J (A), C57BL/6J (B), DBA/2J (D)), 12-13 weeks of age, purchased from Jackson Laboratory. Animals were housed in a light/dark cycle of 24 hrs with water and food available ad libitum. Mice of the 3 inbred strains were sleep deprived for 6h starting at light onset (ZT0), at the middle of the light (ZT6), at the beginning of the dark (ZT12), or at the middle of the dark (ZT18) period, and sacrificed together with their home-cage controls (n=9 / strain =3 / time =4 / condition =2; total =216 mice).

first: Stéphane

last: Dorsaz

first: Brice

last: Petit

first: Sylvain

last: Pradervand

first: Paul

last: Franken


title: The effect of sleep deprivation on gene expression in the brain and the liver of three inbred mouse strains

summary:
These studies adress differential changes in gene expression between 6h sleep deprived and control mice in the brain and the liver. We profiled gene expression in three different inbred strains to understand the influence of genetic background.
Keywords: brain, genetic background, sleep deprivation

overall_design: Experiments were performed on male mice (C57BL/6J (B6), AKR/J (AK), DBA/2J (D2)), 12-13 weeks of aged, purchased from Jackson Laboratory. Animals were housed in a light/dark cycle of 24 hrs with water and food available ad libitum. Mice of the 3 inbred strains were sleep deprived for 6h starting at light onset (ZT0) and sacrificed together with their home-cage controls at ZT6 (n=9 / strain =3 / condition =2 / tissues =2; total = 108 mice).

first: Didier

last: Chollet


title: Gene expression in brain Homer1a-expressing cells after sleep deprivation

summary:
To gain insight into the molecular changes of sleep need, this study addresses gene expression changes in a subpopulation of neurons selectively activated by sleep deprivation. Whole brain expression analyses after 6h sleep deprivation clearly indicate that Homer1a is the best index of sleep need, consistently in all mouse strains analyzed. Transgenic mice expressing a FLAG-tagged poly(A)-binding protein (PABP) under the control of Homer1a promoter were generated. Because PABP binds the poly(A) tails of mRNA, affinity purification of FLAG-tagged PABP proteins from whole brain lysates, is expected to co-precipitate all mRNAs from neurons expressing Homer1a. Three other activity-induced genes (Ptgs2, Jph3, and Nptx2) were identified by this technique to be over-expressed after sleep loss. All four genes play a role in recovery from glutamate-induced neuronal hyperactivity. The consistent activation of Homer1a suggests a role for sleep in intracellular calcium homeostasis for protecting and recovering from the neuronal activation imposed by wakefulness.
Keywords: sleep deprivation, neuronal subpopulation transcriptome

overall_design: Experiments were performed on male mice, 12 weeks of age +/- 1 week. Animals were housed in polycarbonate cages (31x18x18cm) in an experimental room with an ambient temperature varying from 23° to 25°C under a 12:12 hrs light/dark cycle. Food and water were available ad libitum. At light onset mice were either sleep deprived by gentle handling (n=10) or left undisturbed (n=10) for 6 hrs. Animals were then randomly sacrificed by cervical dislocation. Total RNA from the whole brain was isolated for control (n=4) and sleep deprived (n=4)  using a commercial RNA extraction kit (RNeasy Lipid Tissue Kit, Quiagen). Specific Homer1a-expressing cells polyA RNAs were immunoprecipitated following the total brain crosslinking (1% formaldehyde perfusion)  for sleep deprived (n=6) and control (n=6) animals. The total RNA from the pull-down supernatants were also harvested (n=4). To test for transcriptional changes after sleep deprivation Homer1a-expressing cells, we proceeded in 2 steps: (1) identify probe sets enriched in the pull-down extracts, (2) among those probe sets compare sleep deprivation to control condition in both pull-down (6 vs. 6 chip comparison) and whole-brain (4 vs. 4 chip comparison) extracts. 4728 probe sets were significantly enriched at 5% FDR when pull-downs were compared to both supernatant and whole-brain extracts.

first: Stéphanie

last: Maret

first: Laure

last: Gurcel

first: Otto

last: Hagenbuchle

first: Alexandra

last: Paillusson


title: Expression data from olfactory epithelium of Harlequin mutant mice compared to littermate controls

status: Public on Dec 06 2007

first: Marilyn

last: Getchell

summary:
Microarray analysis of gene expression in the olfactory epithelium of Harlequin mouse as a model of oxidative-stress induced neurodegeneration of olfactory sensory neurons
Keywords: comparison of gene expression level in unperturbed tissue of mutant vs. control mouse

overall_design: Olfactory epithelium from Harlequin mutant mice and littermate control mice was microdissected for RNA extraction and hybridization on Affymetrix microarrays. We compared levels of gene expression in 6-month old mice to begin to identify mechanisms of oxidative-stress induced neurodegeneration and to correlate the cellular changes that we observed in the olfactory epithelium by using histology and immunohistochemistry with gene expression changes.

first: Radhika

last: Vaishnav

first: Liping

last: Huang

first: Matthew

last: Hersh


title: Transformed glial progenitor cells (prosc-affy-mouse-450860)

status: Public on Dec 04 2007

city: Phoenix

first: Winnie

last: Liang

state: AZ

address: 445 N. Fifth Street

institute: Translational Genomics

summary:
The goals of this research are three-fold:  (i) One is to identify genetic changes associated with tumorgenesis that interfere with the ability of transformed glial cells to differentiate.  This is connected with (ii) our analysis of the regulation of differentiation in normal glial progentor cells, as only by understanding this in normal cells can we understand what is occurring when differentiation fails in transformed versions of the same cells.  (iii) The third is to identify the molecular basis for the greater resistance of transformed glial progenitor cells to chemotherapeutic agents as compared with normal glial progenitor cells. Thus, analysis of the populations provided will yield data crucial to two of our central areas of research, as awarded by NINDS in "Oligodendrocytes & precursors: toxicity of chemotherapy" (5R01NS044701), and "Low-level toxicant perturbation of neural cell function" (1R01ES012708).
Our ability to work with essentially unlimited numbers of primary progenitor cells and transformed derivatives of these cells offers one of the few systems in which side-by-side comparison of normal and transformed cells at both the biochemical and molecular levels is possible. Using defined cell populations, expression profiles will be compared to reveal changes in cell type specific markers and regulatory factors associated with transformation.  In addition, retention of markers despite transformation may enable identification of new markers useful in the diagnosis of glial tumors.
Transformation of glial progenitor cells is associated both with loss of the proteins required for normal differentiation and with an inability to normally activate proteins that function in differentiation control.  By side-by-side analysis of gene expression in normal and transformed glial progenitor cells, and analysis of the response to inducers of differentiation in each these populations, we will identify candidate regulators critical in the control of normal differentiation. Identification of these regulators will also provide clues as to overcome the blockade of differentiation that occurs in glial cancers (which represent the majority of adult brain tumors).
RNA will be isolated from two separate preparations of glial progenitors. Preparation of purified populations has been described in multiple of our previous publications (Mayer, M. et al. (1994) Development 120, 142-153; Mayer-Pröschel, M. et al. (1997) Neuron 19, 773-785; Rao, M. and Mayer-Pröschel, M. (1997) Dev. Biology 188, 48-63). Total RNA from purified cell cultures will be extracted in a two step process. RNA will first be extracted by dounce homogenization in phenol/guanidine isothiocyonate solution (Trizol, Invitrogen, California) followed by isopropanol precipitation. Contaminating traces of DNA and protein will then be removed by silica-based affinity chromatography and Dnase treatment (NucleoSpin RNA Purification system, Clontech, California). Depending on the cell type, 5x105 cells will typically yield 5-15µg of high quality RNA (OD260/280=2.1 at pH7.5). In order to determine purity and molecular weight distribution, samples will be routinely tested on a Agilent Bioanalyzer. cDNA will be generated from total RNA and then be submitted to one round of amplification and labeling using the messageAmp system (Ambion). Probes are then hybridized to the Affymerix Rat 230 (A/B or 2.0) GeneChip expression array. Array data will be processed using the Micro Array Suite 5.0 (MAS, Affymetrix). .Cel files containing normalized, relative expression data for all genes tested will be used for downstream statistical analysis.
Keywords: other

first: Christoph

last: Proschel


title: Expression data of early skin development mice

status: Public on Dec 05 2007

city: Shanghai

first: jing

last: zhang

address: No 411 Hefei Road

country: China

institute: Institute of Health Sciences,Shanghai Institutes for Biological Sciences (SIBS), Chinese Academy of Sciences (CAS)

summary:
Mice with the spontaneous uncv mutation are hairless.  We utilize the uncv null mouse to investigate the underlying mechanisms giving rise to the relevant phenotypes and reveal significant changes in certain signaling pathways by microarray.
Keywords: RNA expression study

overall_design: Dorsal skins were taken from 4-day-old uncv null mice and wild type mice (as control), and they are sisters-german.  The parent is uncv heterozygosis(uncv +/-), and their children has 3 genotype: wild(uncv +/+), heterozygosis(uncv +/-) and null (uncv -/-).  We can easily distinguish them by their beard length and shape or identify their genotype by PCR using specific primers.  HR 02 is a wild mouse sample and uncv null mice expresses as HR 03 and HR 04.  RNA isolation was performed with the QIAGEN RNeasy mini kit (QIAGEN, Valencia, CA, USA) following standard instructions.

first: Jing

last: Zhang

first: Han

middle: C

last: Zheng


status: Public on Dec 01 2007

city: Charlottesville

first: Yong

state: VA

address: 1340 Jefferson Park Ave

department: Medicine

institute: University of Viginia

summary:
Murine Pulmonary Responses to Ambient Baltimore Particulate Matter: Genomic Analysis and Contribution to Airway Hyperresponsiveness

Asthma is a complex disease characterized by airway hyperresponsiveness (AHR) and chronic airway inflammation. Environmental factors such as ambient particulate matter (PM), a major air pollutant, has been demonstrated in epidemiological studies to contribute to asthma exacerbation and increased asthma prevalence. OBJECTIVE: We investigated the genomic and pathophysiological effects of Baltimore PM (median diameter 1.78 µm) in a murine model of asthma to identify potential biomarkers. METHODS: A/J mice with ovalbumin (OVA) –induced AHR were exposed to PM (20 mg/kg, intratracheal), and both AHR and bronchoalveolar lavage (BAL) were assayed on days 1, 4, and 7 post exposure. Lung gene expression profiling (Affymetrix Mouse430_ 2.0) by PM (20 mg/kg, intratracheal) were assayed on OVA- and / or PM--challenged mice. RESULTS: Significant increases of airway responsiveness in OVA-treated mice were observed, indicating an asthmatic phenotype. Ambient PM exposure induced significant changes in AHR in both naive mice and OVA-induced asthmatic mice. In both naive and OVA challenged asthmatic mice, PM induced eosinophil and neutrophil infiltration into airways, elevated BAL protein content, and stimulated secretion of TH1 cytokines (IFN-g, IL-6, and TNF-a) and TH2 cytokines (IL-4, IL-5, and eotaxin) into BAL. Consistent with these results, PM induced expression of genes of innate immune response, chemotaxis and complementary system. CONCLUSION: These studies, consistent with epidemiological data, indicate that PM increases AHR and lung inflammation in naïve mice and exacerbates the asthma phenotype of increased AHR and gene expression pattern changes correlated with acute lung inflammation and airway damage.
We used microarrays to detail the global programme of gene expression induced by rhPBEF treatment and VALI.
Keywords: gene expression

overall_design: animals were treated by PBS, Oval albumin, PM, or both OVA/PM

first: Ting

last: Wang

first: Lilianna

last: Moreno-Vinasco

first: Yves

last: Lussier

first: Viswanathan

last: Natarajan

first: Joe

middle: G

last: Garcia


title: Sleep deprivation and the brain

first: Mehdi

last: Tafti

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

overall_design: Refer to individual Series


title: CLL in Em-TCL1 mice provides a biologically relevant model to unravel and reverse immune deficiency in human cancer.

first: Gullu

last: Gorgun

address: 44 Binney Street

department: Medical Oncology

institute: Dana-Farber Cancer Institute

summary:
Immune deficiency is common in cancer, but the biological basis for this and ways to reverse it remains elusive. Here we present a mouse model of B cell chronic lymphocytic leukemia (CLL) that recapitulates changes in the non-malignant circulating T cells seen in patients with this illness.1 To validate this model, we examined changes in T cell gene expression, protein expression and function in Em-TCL1 transgenic mice as they developed CLL 2,3 and demonstrate that development of CLL in these transgenic mice is associated with changes in impaired T cell function and in gene expression in CD4 and CD8 T cells similar to those observed in patients with this disease. Infusion of CLL cells into non-leukemia bearing Em-TCL1 mice rapidly induces these changes, demonstrating a causal relationship between leukemia and the induction of T cell changes. This model allows dissection of the molecular changes induced in CD4 and CD8 T cells by interaction with leukemia cells and further supports the concept that cancer results in complex abnormalities in the immune microenvironment.
Gene expression profiling was performed to determine whether Em-TCL1 murine model of chronic lymphocytic leukemia (CLL) mimics T cell defects induced by CLL cells in patients with CLL.
Keywords: comparative gene expression profiling analysis.

overall_design: CD4 T cells and CD8 T cells were obtained from spleens of B6C3 and Em-TCL1 transgenic murine model of CLL or from peripheral blood mononuclear cells of previously untreated patients with CLL and healthy individuals (Pubmed ID: 15965501). Gene expression profiling was performed using total RNA and the data were analysed to compare gene expression profile of CLL to healthy within or between the species.

first: Güllü

last: Görgün

first: Tobias

last: Holderried

first: Alan

last: Ramsay

first: David

last: Zahrieh

first: Fenglong

last: Liu

first: John

last: Quackenbush

first: Carlo

last: Croce

last: Gribben


title: Sequential responses to high-fat feeding in an obese mouse model

city: Singapore

first: Mei Yen

last: Chan

state: Singapore

address: 5 Lower Kent Ridge Road

department: Pediatrics

country: Singapore

institute: Yong Loo Lin School of Medicine, National University of Singapore

summary:
We examined the effects of high-fat diet on feeding behaviour, body weight regulation and common biomarkers associated with weight gain in the C57BL/6J mice over a period of 10 weeks, making measurements at weeks 2, 4 and 10. We examined the transcriptomic profile of hepatic genes involved in the major lipid metabolic pathways, validating the key genes with quantitative real-time reverse-transcription PCR (qRT-PCR) and their gene products with western blots.
Keywords: Lipogenesis, Hyperphagia, Fat Oxidation, Energy Regulation, Body Weight

overall_design: C57BL/6J mice were randomly assigned to consume either the control (C) or HFC diet. Body weights and food intake were measured weekly and other measurements at weeks 2, 4 and 10. Microarrays were used to screen the transcriptional response of the livers at the 3 time-points. Genes, encoding enzymes regulating key steps of lipid metabolism, were then selected from the microarray data for validation by qRT-PCR and their protein expression by western blot assays.

first: Mei-Yen

first: Yulan

last: Zhao

first: Chew-Kiat

last: Heng


title: Diarrhea as a Cause of Mortality in a Mouse Model of Infectious Colitis

city: Chapel Hill

first: Rebecca

middle: Catherine

last: Fry

address: 1213 MHRC

department: Environmental Sciences and Engineering

institute: UNC-Chapel Hill

summary:
Examination of host genome-wide changes upon encounters with pathogens provides insight into the pathogenesis of infection and disease. When performed comparatively, it may shed light on the mechanisms underlying host susceptibility. In this study, gene expression in the mouse colon was investigated in two cognate lines of mice that differ in their response to Citrobacter rodentium infection; susceptible inbred FVB/N (FVB) and resistant outbred Swiss Webster (SW) mice. Gene expression in the distal colon was investigated prior to infection and at 4 and 9 days post-inoculation using a whole mouse genome Affymetrix array. Computational analysis identified 462 (1%) probe sets differentially expressed by more than 2-fold between uninoculated SW and FVB mice. In response to C. rodentium infection, 5,123 probe sets (11.4%) were significantly modulated in one or both lines of mice. Microarray data were validated by quantitative real time RT-PCR on 35 selected genes (r = 0.87, p < 0.001) and were found to have a 94% concordance. Transcripts represented by 1,547 probe sets (3.4%), were differentially expressed between FVB and SW mice regardless of infection status (host effect). Genes associated with transport were over-represented to a greater extent than immune response-related genes (25% vs. 11% of enrichment, respectively). Electrolyte analysis revealed hypochloremia and hyponatremia in susceptible animals. The results support the hypothesis that mortality in C. rodentium-infected FVB mice is associated with impaired ion transport and development of fatal hypovolemia. These studies contribute to our understanding of the pathogenesis of C. rodentium and suggest novel strategies for the prevention and treatment of diarrhea associated with bacterial infections of the intestinal tract.
Keywords: temporal change (post infection)

overall_design: Global gene expression analysis was performed on the distal colon with 2-3 mice per group. Because no difference for any parameters was observed in uninfected mice at 4 or 9 dpi, the animals were pooled into an uninoculated control groups for each line of mouse. The selection of representative samples for microarray analysis was based on known infection status and colonic lesions. The final number of biological replicates for each condition was n = 5 for uninoculated FVB mice (“Fp” group), n = 4 for uninoculated SW mice (“Sp” group), and n = 3 for infected animals from each line at each time point (“Fi4”, “Si4”, “Fi9”, and “Si9” respectively).

first: Diana

last: Borenshtein

first: Elizabeth

middle: B

last: Groff

first: Prashant

middle: R

last: Nambiar

first: Vincent

last: Carey

first: James

last: Fox

last: Schauer


title: Transcriptional expression of ICC-DMP and ICC-MY in murine small intestine

status: Public on Nov 29 2007

city: Reno

first: Hui

last: Chen

state: NV

address: 1664 N Virginia St

department: Physiology and Cell Biology

institute: University of Nevada, Reno

summary:
Interstitial cells of Cajal (ICC) have important functions in regulation of motor activity in the gastrointestinal tract.  In murine small intestine ICC are gathered in the region of the myenteric plexus (ICC-MY) and within the deep-muscular plexus near the submucosal surface of the circular muscle layer (ICC-DMP).  These two classes of ICC have different physiological functions.
ICC-MY are pacemaker cells and generate the slow wave electrical rhythmicity of gastrointestinal organs.  ICC-DMP form synaptic connections with the varicose nerve terminals of enteric motor neurons and are involved in reception and transduction of motor neurotransmission.  In the present study we used recently developed highly selective techniques to isolate the two classes of ICC from enzymatically dispersed intestinal muscles by fluorescence-activated cell sorting.  Transcriptional expression of the two functional classes was investigated using DNA microarray analysis.
Keywords: comparative transcriptional profiling

overall_design: ICC-DMP and ICC-MY cells were isolated from the murine small intestinal tissues and their transcriptional expression was compared with that of the tunica muscularis tissues. Transcriptional expression profiles of ICC-DMP and ICC-MY were compared to each other also.

last: Young

first: Kenton

middle: M

last: Sanders


title: mTOR pathway controls mitochondrial gene expression and respiration through the YY1/PGC-1alpha transcriptional complex

first: Pere

last: Puigserver

address: 1 Jimmy Fund Way

department: Cancer Biology

summary:
Mitochondrial oxidative function is tightly controlled to maintain energy homeostasis in response to nutrient and hormonal signals. An important cellular component in the energy sensing response is the target of rapamycin (TOR) kinase pathway; however whether and how mTOR controls mitochondrial oxidative activity is unknown. Here, we show that mTOR kinase activity stimulates mitochondrial gene expression and oxidative function.  In skeletal muscle cells and TSC2-/- MEFs, the mTOR inhibitor rapamycin largely decreased gene expression of mitochondrial transcriptional regulators such as PGC-1alpha and the transcription factors ERRalpha and NRFs. As a consequence, mitochondrial gene expression and oxygen consumption were reduced upon mTOR inhibition. Using computational genomics, we identified the transcription factor YY1 as a common target of mTOR and PGC-1alpha that controls mitochondrial gene expression. Inhibition of mTOR resulted in a failure of YY1 to interact and be coactivated by PGC-1alpha. Notably, knock-down of YY1 in skeletal muscle cells caused a significant decrease in mRNAs of mitochondrial regulators and mitochondrial genes that resulted in a decrease in respiration. Moreover, YY1 was required for rapamycin-dependent repression of mitochondrial genes. Thus, we have identified a novel mechanism in which a nutrient sensor (mTOR) balances energy metabolism via transcriptional control of mitochondrial oxidative function. These results have important implications for our understanding of how these pathways might be altered in metabolic diseases and cancer.
Keywords: comparative genomics, drug treatment response

overall_design:
Using Affymetrix MOE430 v2 gene chips, biological triplicates of each condition were analyzed: vehicle-treated, rapamycin-treated, gfp-infected, and pgc-1alpha-infected resulting in a total of 12 samples.

Data were analyzed by RMA (with default settings) in BioConductor 1.2 -- one batch for the Rapamycin vs. Vehicle, and another batch for the PGC vs GFP.

middle: T

last: Cunningham

first: Dan

last: Arlow

first: Francisca

last: Vazquez

first: Vamsi

middle: K

last: Mootha


title: Expression data from spontaneous liver tumors of Trim24/TIF1a-null mice.

status: Public on Nov 19 2007

city: ILLKIRCH CEDEX

first: Régine

last: Losson

address: 1 rue Laurent Fries

country: France

institute: IGBMC

summary:
The transcriptional coregulator Trim24 (formerly known as TIF1a) functions in mice as a liver-specific tumor suppressor. Mice carrying a null mutation in the Trim24 gene all develop hepatocellular carcinoma (HCC).
We used microarrays to identify the alterations in gene expression patterns associated with loss of Trim24 and consequent HCC development.
Keywords: normal-tumor comparison

overall_design: Five independent liver tumor  (HCC) samples taken from five Trim24 knockout (KO) mice and five normal liver tissue samples taken from wild-type (WT) littermate controls  were used for RNA extraction and hybridization on Affymetrix  microarrays.

first: Konstantin

last: Khetchoumian

first: Johan

last: Tisserand


title: Microarray expression profiles of mammary tumors developed in Wap-Cre;Etv6-NTRK3 mice

first: Zhe

last: Li

summary:
We report a mouse model that recapitulates expression of the ETV6-NTRK3 (EN) fusion oncoprotein, the product of the t(12;15)(p13;q25) translocation characteristic of human secretory breast carcinoma. Activation of EN expression in mammary tissues by Whey acidic protein (Wap) promoter-driven Cre leads to fully penetrant, multifocal malignant breast cancer with short latency. We provide genetic evidence that committed bipotent or CD61+ luminal alveolar progenitors, are targets of tumorigenesis. Furthermore, EN transforms these otherwise transient progenitors through activation of the AP1 complex. Given increasing relevance of chromosomal translocations in epithelial cancers, such mice serve as a paradigm for the study of their genetic pathogenesis and cellular origins, and generation of novel preclinical models.
In this study, we generated microarray expression profiling data from both genetically marked, FACS-sorted tumor epithelial cells and from unfractionated mammary tumors and normal mammary glands. By using gene set enrichment analysis (GSEA) on these data, we have identified the AP1 transcriptional complex as the major downstream effector of the ETV6-NTRK3 signaling.
Keywords: genetic modification, cell type comparison

overall_design: Take the advantage of the Cre-lox system and a floxed lacZ reporter at the Rosa26 locus (Rosa-Stop-lacZ), we genetically marked mammary epithelial cells in which the conditional Etv6-NTRK3 knockin allele were turned on, and followed them to the hyperplasia and tumor stages. We then sorted lacZ+ hyperplastic mammary epithelial cells and lacZ+ tumor epithelial cells and collected their expression profiles by Affymetrix mouse whole genome MOE430.2 chips. We also collected expression profiles from unfractionated mammary tumors (unsorted tumors) derived from the same mouse model and mammary glands from normal mice.

first: Stuart

last: Orkin


title: Gene expression data after acute withdrawal of TERT in mouse skin

city: Stanford

first: Jinkuk

last: Choi

state: CA

address: 269 Campus Dr. CCSR Rm. 1150

institute: Stanford University

summary:
TERT is an essential protein component of telomerase, a ribonuclearprotein complex that protects chromosomal ends. Ectopic expression of TERT in mouse skin activates hair follicle stem cells and induces active growth phase of hair cycles, called anagen. This activity of TERT is independent of its reverse transcriptase function, indicating that this is a non-telomeric function of TERT.
We performed time-course microarray analysis using conditional bi-transgenic mice (iK5-TERT) to understand the mechanism of this novel non-telomeric function of TERT.
Keywords: Time course, 2 cohorts (control, experimental)

overall_design: Hair follicles of iK5-TERT mice at postnatal day 60 is in TERT-induced anagen. To those mice, we injected either PBS, to maintain TERT transgene expression, or doxycycline, to rapidly extinguish transgene expression. We then took time-course dorsal skin biopsies (0,6,12,24 hr) of these mice and analyzed differential gene expressions using Affymetrix Genechips and various bioinformatic tools, including SAM, to discover TERT-regulated genes.

first: Lucinda

last: Southworth

first: Kavita

middle: Y

last: Sarin

first: Andrew

last: Venteicher

first: Wenxiu

last: Ma

first: Woody

last: Chang

first: Peggie

last: Cheung

first: Sohee

last: Jun

first: Maja

last: Artandi

first: Naman

last: Shah

last: Kim

first: Steven


title: Expression data from mouse liver

status: Public on Nov 17 2007

city: Hanover

first: Thomas

last: Hampton

state: NH

address: North College Street

department: Microbiology Immunology

institute: Geisel School of Medicine at Dartmouth

summary:
Exposure to high levels of arsenic in drinking water is associated with several types of cancers including lung, bladder and skin, as well as vascular disease and diabetes. Drinking water standards are based primarily on epidemiology and extrapolation from higher dose experiments, rather than measurements of phenotypic changes associated with chronic exposure to levels of arsenic similar to the current standard of 10ppb, and little is known about the difference between arsenic in food as opposed to arsenic in water. Measurement of phenotypic changes at low doses may be confounded by the effect of laboratory diet, in part because of trace amounts of arsenic in standard laboratory chows, but also because of broad metabolic changes in response to the chow itself. Finally, this series contrasts 8hr, 1mg/kg injected arsenic with the various chronic exposures, and also contrasts the acute effects of arsenic, dexamethasone or their combination. Male C57BL/6 mice were fed on two commercially available laboratory diets (LRD-5001 and AIN-76A) were chronically exposed, through drinking water or food, to environmentally relevant concentrations of sodium arsenite, or acutely exposed to dexamethasone.
Keywords: dose response

overall_design:
Male C57BL/6 mice, fed on two commercially available laboratory diets (LRD-5001 and AIN-76A), were chronically exposed through drinking water or food, to environmentally relevant concentrations of sodium arsenite.
Another group animals, fed on the AIN 76A diet, was  IP injected with dexamethasone (1 mg/kg), sodium arsenite (1mg/kg), both dexamethosone and arsenite, or saline alone.

first: Michael

middle: A

last: Ihnat

first: Joshua

middle: W

last: Hamilton


title: Gene expression program of AM-14 B cells stimulated through the B cell receptor (BCR) and/or Toll-like receptors (TLR)

city: Minneapolis

first: Jason

last: Bauer

state: MN

address: 420 Deleware St SE MMC108

institute: University of Minnesota

summary:
We have previously shown that rheumatoid factors (RF) produced by Fas-deficient autoimmune-prone mice typically bind autologous IgG2a with remarkably low affinity. Nevertheless, B cells representative of this RF population proliferate vigorously in response IgG2a/chromatin immune complexes through a mechanism dependent on the sequential engagement of the BCR and Toll-like receptor 9 (TLR9). To more precisely address the role of both receptors in this response, we analyzed the signaling pathways activated in AM14 B cells stimulated with these complexes. We found that the BCR not only serves to direct the chromatin complex to an internal compartment where it can engage TLR9 but also transmits a suboptimal signal that in combination with the signals emanating from TLR9 leads to NF?B activation and proliferation. Importantly, engagement of both receptors leads to the upregulation of a group of gene products, not induced by the BCR or TLR9 alone, that include IL-2. These data indicate that autoreactive B cells, stimulated by a combination of BCR and TLR9 ligands, acquire functional properties that may contribute to the activation of additional cells involved in the autoimmune disease process.
Keywords: cell stimulation

overall_design: 15 Samples, 3 replicates for each treatment


title: Expression data from side-population sorted putative intestinal stem cells.

status: Public on Nov 12 2007

first: Ajay

last: Gulati

state: NC

address: 130 Mason Farm Road, CD#7220

department: Pediatric Gastroenterology

institute: University of North Carolina at Chapel Hill

summary:
While the existence of intestinal epithelial stem cells (IESCs) has been well established, their study has been limited due to the inability to isolate them.  Previous work has utilized side population (SP) sorting of the murine small intestinal mucosa to isolate a viable fraction of cells enriched for putative IESCs.  We have used microarray analyses to characterize the molecular features of this potential stem cell population.
Keywords: Comparitive gene expression analysis

overall_design: Fluorescence activated cell sorting of cells stained with Hoechst 33342 and FITC labeled anti-CD45 antibody was used to isolate CD45-/SP and CD45-/nSP cell fractions from mucosal specimens pooled from 3 mice.  Intact jejunum specimens were collected prior to sorting.  4 sorts were completed.  Therefore, 3 experimental groups were defined: CD45-/SP, CD45-/nSP and intact jejunum, each with 4 biological replicates.  Total RNA was extracted from each experiment group for each sort, resulting in 12 specimens submitted for analysis using Affymetrix 430 2.0 Gene Chips.

first: Scott

last: Ochsner

first: Susan

middle: J

last: Henning


title: Embryonic stem cells with expanded CAG repeats (lorin-affy-mouse-501743)

first: Winnie

last: Liang

summary:
Huntingtons disease (HD) is a devastating neurodegenerative disease, with out effective treatment.  Despite significant advances, our understanding of how an expanded CAG repeat in the amino terminus of the large ubiquitously expressed HD gene product remains incomplete.  Augmented adult neurogenesis in response to acute and chronic injury, including Huntingtons disease, has been demonstrated, but its role development, disease, and recovery is largely unknown, as are the factors controlling it.  The HD gene product, huntingtin (htt) is know to interact with a number of transcription factors which subsequently influence gene expression.  Understanding the factors involved in controlling neurogenesis in response to disease would bridge a significant knowledge gap and have tremendous therapeutic potential.
We propose to identify transcripts responsible for CAG repeat facilitated neurogenesis.
Our hypothesis is that expanded CAG repeats in the Huntingtons disease gene facilitates neurogenesis by altering transcription of genes critical in neurogenesis.
We have developed a model in which mouse embryonic stem cells (ESC) with expanded CAG repeats have facilitated neurogenesis.  In this model more ESC with expanded CAG repeats transition to neuronal precursors and then develop into mature neurons more rapidly than control ESC.  We propose to compare the gene expression profiles between ESC with expanded CAG repeats and control ESCs on days 4 and 6 of neuronal differentiation.  Initial studies indicate that key transcriptional differences are occurring at these time points.  Control ECS and a an ESC line with150 CAG repeats will be differentiated in triplicate, and RNA isolated form each replicate.  It is anticipated that comparison of gene expression between the control and CAG repeat lines at each time point will identify transcripts involved in CAG repeat facilitated neurogenesis.  Observed differences at day 4 may be more relevant to the transition from ESC to neuronal precursor whereas differences at day 6 may be more relevant to the neuronal precursor to neuron transition.
Keywords: time-course

first: Matt

last: Lorincz


title: Mouse lung with recombinant human soluble PBEFtreatment and ventilator-induced lung injury: age 8-12wks

status: Public on Nov 01 2007

first: Yong

last: Huang

summary:
We have previously demonstrated that pre-B-cell colony enhancing factor (PBEF) ais a biomarker in sepsis and sepsis-induced acute lung injury (ALI) with genetic variants conferring ALI susceptibility118. In the current study, we explored the mechanistic participation of PBEF in ALI and ventilator-induced associated lung injury (VIALI). Initial in vitro studies and demonstrated rhPBEF aas a direct rat neutrophil chemotactic factor in vitro producing marked in vivo increases in BAL leukocytes (PMNs) in vivo following (intratracheal injection (,IT) in C57B6 mice. These latter changes were accompanied by increased BAL levels of the PMN chemoattractants (, KC and MIP2), and modest changes in lung vascular and but were not associated with significant increasesin alveolar permeability. We next explored the potential synergism between rhPBEF administration (IT) and a mechanical ventilation model of modest VILI lung injury (4 hours, 30 ml/kg tidal volume). We and observed dramatic synergistic increases in BAL PMNs, and both BAL protein and cytokine levels (IL-6, TNF-?, KC). Gene expression profiling Microarray analysis further supported a major role for PBEF in the induction of gene modules associated with ALI and VALI (NFkB pathway, leukocyte extravasation, apoptosis, toll receptor signaling). Finally, we exposed wild type and heterozygous PBEF+/- mice (targeted deletion of a single PBEF allele deletion) to a model of severe VILImechanical ventilation-induced lung injury (4 hours, 40 ml/kg tidal volume). PBEF+/- mice were significantly protected from VIALI-associated increases in BAL protein and BAL IL-6 levels and exhibited significantly reduced expression of ALI-associated gene expression modules. Together, these results indicate that PBEF is a key inflammatory mediator intimately involved in both the development and severity of ventilator-induced ALI.
We used microarrays to detail the global programme of gene expression induced by rhPBEF treatment and VALI.
Keywords: response to treatment and/or stress

overall_design: animals were treated by PBS, rhPBEF (IT administration), VILI (4 hours, 30 ml/kg tidal volume), or both.

first: Sang-Bum

last: Hong

first: Saad

last: Sammani

first: Lilianna

last: Moreno-Vinasco

first: Yves

last: Lussier

first: Joe

last: Garcia


title: Thy1+ 2dpp gonocytes RA regulation

status: Public on Nov 07 2007

city: Pullman

first: Lizhong

last: Yang

address: 531 Fulmer Hall/POB 644660

department: School of Molecular Biosciences

institute: Washington State University

summary:
to investigate the RA regulated genes in 2 dpp thy1+ gonocytes
Keywords: RA effects on gonocytes

overall_design: gonocytes were isolated from 2 dpp mouse testes by THY1+ MACS sorting and cultured without serum, growth factors and feeder cells for 8hr, with either vehicle ethanol or RA (100 nM). Two control and two RA treated samples were included.

first: qing

last: zhou

middle: D

last: griswold


title: Expression data from mouse lung with recombinant human soluble PBEFtreatment and ventilator-induced lung injury

summary:
We have previously demonstrated that pre-B-cell colony enhancing factor (PBEF) ais a biomarker in sepsis and sepsis-induced acute lung injury (ALI) with genetic variants conferring ALI susceptibility118. In the current study, we explored the mechanistic participation of PBEF in ALI and ventilator-induced associated lung injury (VIALI). Initial in vitro studies and demonstrated rhPBEF aas a direct rat neutrophil chemotactic factor in vitro producing marked in vivo increases in BAL leukocytes (PMNs) in vivo following (intratracheal injection (,IT) in C57B6 mice. These latter changes were accompanied by increased BAL levels of the PMN chemoattractants (, KC and MIP2), and modest changes in lung vascular and but were not associated with significant increasesin alveolar permeability. We next explored the potential synergism between rhPBEF administration (IT) and a mechanical ventilation model of modest VILI lung injury (4 hours, 30 ml/kg tidal volume). We and observed dramatic synergistic increases in BAL PMNs, and both BAL protein and cytokine levels (IL-6, TNF-?, KC). Gene expression profiling Microarray analysis further supported a major role for PBEF in the induction of gene modules associated with ALI and VALI (NFkB pathway, leukocyte extravasation, apoptosis, toll receptor signaling). Finally, we exposed wild type and heterozygous PBEF+/- mice (targeted deletion of a single PBEF allele deletion) to a model of severe VILImechanical ventilation-induced lung injury (4 hours, 40 ml/kg tidal volume). PBEF+/- mice were significantly protected from VIALI-associated increases in BAL protein and BAL IL-6 levels and exhibited significantly reduced expression of ALI-associated gene expression modules. Together, these results indicate that PBEF is a key inflammatory mediator intimately involved in both the development and severity of ventilator-induced ALI.
Keywords: We used microarrays to detail the global programme of gene expression induced by rhPBEF treatment and VALI.


title: H. hepaticus infection and liver cancer

first: Rebecca

last: Fry

summary:
We are investigating the transcriptional response of mice infected with Helicobacter hepaticus and links to liver cancer
We used microarrays to detail the global programme of gene expression underlying H. hepaticus induced liver cancer
Keywords: disease model

overall_design: Mice with tumors were compared to mice with infection only (comparison 2) and mice infected were compared to control mice (comparison 1)

first: Alexis

first: Melanie

last: Ihrig

first: Yan

last: Feng

first: Sandy

last: Xu

first: Samuel

last: Boutin

first: Arlin

last: Rogers

first: Leona

last: Samson

first: James

last: Fox


title: Isolation and molecular characterization of cancer stem cells in MMTVWnt-1 murine breast tumors

city: Redwood City

first: Xinhao

last: Wang

address: 800 Chesapeake

institute: OncoMed Pharmaceuticals Inc

summary:
In human breast cancers, a phenotypically distinct minority population of tumorigenic cancer (TG) cells (sometimes referred to as cancer stem cells) drives tumor growth when transplanted into immunodeficient mice. Our objective was to identify a mouse model of breast cancer stem cells that could have relevance to studying human breast cancer. To do so, we utilized breast tumors of the MMTVWnt-1 mice. MMTV-Wnt-1 breast tumors were harvested, dissociated into single cell suspensions, and FACS sorted on Thy1, CD24, and CD45. FACS sorted cells were then injected into recipient background FBV/NJ female mice. Thy1+CD24+ cancer cells, which constitute approximately 1-4% of tumor cells were highly enriched for cells capable of regenerating new tumors when compared to cells of the tumor that did not fit this profile (“Not Thy1+CD24+”). Resultant tumors were of the same phenotypic diversity as the original tumor and behaved in a similar manner when passaged. Microarray analysis comparing Thy1+CD24+ tumor cells to “Not Thy1+CD24+” cells identified a list of differentially expressed genes. Orthologs of these differentially expressed genes predicted survival of human breast cancer patients from two different study groups. These studies suggest that there is a cancer stem cell compartment in the MMTV-Wnt-1 murine breast tumor and that there is a clinical utility of this model for the study of cancer stem cells.
Keywords: cell type comparison

overall_design: Expression profling were performed on 3 tumorigenic and 3 non tumorigenic samples of MMTV-Wnt-1 breast tumors. A gene signature was derived by comparing the gene expressions of 3 tumorigenic samples with 3 nontumorigenic samples

first: R

last: Cho

first: X

first: M

last: Diehn

first: K

last: Shedden

first: G

last: Chen

last: Sherlock

first: A

last: Gurney

first: J

last: Lewicki

middle: F

last: Clarke


title: Liver fenofibrate feeding mouse

status: Public on Nov 16 2007

city: Bronx

first: David

middle: L

last: Silver

state: NY

address: 1300 Morris Park Ave.

department: Biochemistry

institute: Albert Einstein College of Medicine

summary:
To identify novel PPARalpha target genes involved in lipid metabolism
Keywords: gene expression changes, drug treatment, fibrates, liver

overall_design: 8 week old male 129SvEJ mice (wild-type and pparalpha -/-) mice were fed a chow diet of 0.2% fenofibrate for 7 days. Liver RNA was isolated and pooled from 3 mice from each genotype and used for Affymetrix gene array analysis


title: Gene expression profiling of E12.5 wildtype- and Sp3 null hearts

city: Rotterdam

first: Sjaak

last: Philipsen

address: Dr. Molewaterplein 50

department: Cell Biology

country: Netherlands

institute: Erasmus MC

summary:
Mice lacking the zinc finger transcription factor Specificity protein 3 (Sp3) die prenatally in the C57Bl/6 background. To elucidate the cause of mortality we analyzed the potential role of Sp3 in embryonic heart development. Sp3 null hearts display defective looping at E10.5, and at E14.5 the Sp3 null mutants have developed a range of severe cardiac malformations. In an attempt to position Sp3 in the cardiac developmental hierarchy, we analysed the expression patterns of >15 marker genes in Sp3 null hearts. Expression of Cardiac ankyrin repeat protein (Carp) was downregulated prematurely after E12.5, while expression of the other marker genes was not affected. ChIP analysis revealed that Sp3 is bound to the Carp promoter region in vivo. Microarray analysis indicates that small molecule metabolism and cell-cell interactions are the most significantly affected biological processes in E12.5 Sp3 null myocardium. Since the epicardium showed distension from the myocardium, we studied expression of Wt1, a marker for epicardial cells. Wt1 expression was diminished in epicardium-derived cells in the myocardium of Sp3 null hearts. We conclude that Sp3 is required for normal cardiac development, and suggest that it has a crucial role in myocardial differentiation. (
Keywords: Transcription factors, Sp3, knockout mice, cardiac malformations, E12.5

overall_design: Hearts were dissected from E12.5 wildtype (n=3) and Sp3 knockout (n=3) fetuses. Total RNA was isolated from individual hearts; 5μg was used for labelling and hybridization to 430 2.0 Gene Chips (a total of 6).

first: Pieter-Fokko

last: van Loo

first: Edris

last: Mahtab

first: Lambertus

last: Wisse

first: Jun

last: Hou

first: Frank

last: Grosveld

first: Guntram

last: Suske

first: Adriana

last: Gittenberger-de Groot


title: Contribution of Foxp3 to the Treg signature

first: CBDM

last: Lab

address: 77 Avenue Louis Pasteur

department: Microbiology and Immunobiology

institute: Harvard Medical School

summary:
The transcription factor Foxp3 is usually considered the master regulator for the CD4+CD25+ "Treg" lineage, which plays a key role in controlling immune and autoimmune responses, and is characterized by a unique transcriptional signature. We have performed a meta-analysis of this signature in Treg cells in several conditions to delineate the elements that can be ascribed to T cell activation, TGFbeta signaling, or Foxp3 itself. We find that these influences synergize to activate many of the signature’s components. Foxp3 and TGFbeta signaling have interconnected relationships, as Foxp3 is induced by TGFbeta while enhancing TGFbeta’s positive feedback loop.  Much of the Treg signature cannot be ascribed to Foxp3, as it contains gene clusters that are co-regulated, but cannot be transactivated, by Foxp3.  This suggests that the Treg lineage is specified at a higher level of regulation, upstream of Foxp3, which does control some of the lineage’s essential immunoregulatory attributes.
Keywords: Cell population comparison

overall_design: All gene expression profiles were obtained from highly purified T cell populations sorted by flow cytometry.  To reduce variability, cells from multiple mice were pooled for sorting, and three replicates were generated for essentially all groups. RNA from 0.5-2.5 x 105 cells was amplified, labeled, and hybridized to Affymetrix M430v2 microarrays. Raw data were preprocessed with the RMA algorithm in GenePattern, and averaged expression values were used for analysis.

first: Jonathan

last: Hill

first: Markus

last: Feuerer

first: Sokol

last: Haxhinasto

first: Kaley

last: Tash

first: Diane

last: Mathis

first: Christophe

last: Benoist


title: Lymphtoxin pathway effects on thymic medullary epithelial cells

status: Public on Oct 23 2007

summary:
We compared gene expression profiles of lymphotoxin alpha- and lymphtoxin beta receptor-deficient thymic medullary epithelial cells with their wild-type littermates, as well as with Aire-deficient and wild-type littermates. This was done in order to determine whether there was overlap in the effects of lymphotoxin and aire.
Keywords: genetic modification

overall_design: Individual thymi were digested with collagenase, dispase and DNAse, and meduallary epithelial cells with the phenotype CD45-G8.8+Ly51intMHCclasssIIhi were isolated by FACS.

first: Emily

middle: S

last: Venanzi


title: Gene Expression in Transgenic Mice Expressing CD30L on T Cells

status: Public on Oct 30 2007

city: Seattle

first: John

last: Gosink

address: 1201 Amgen Court West

institute: Amgen

summary:
CD30L and CD30 are cell-surface glycoproteins in the TNF and TNFR superfamilies,  respectively. Their expression is limited to immune cells and is tightly regulated. Cell surface expression of CD30 is restricted to subpopulations of activated T and B cells.  CD30L is expressed primarily on activated T cells and subpopulations of B cells. The significance of CD30/CD30L interactions in immune regulation is not fully understood.  Reported activities of CD30/CD30L in immune responses imply roles in regulation of secondary memory and antibody responses. Depending on the experimental system, both positive and negative regulation of immunoglobulin class switching and antibody production have been reported. Additionally, the biological activity of CD30/CD30L in animals has been difficult to assess due to the restricted and tightly regulated expression of this receptor-ligand pair. We generated transgenic mice with constitutive T cell specific overexpression of CD30L as a tool to help unravel the consequences of CD30/CD30L interactions in vivo. CD30L transgenic mice displayed a phenotype and responses to antigen challenge supporting a role for CD30/CD30L in promoting immunoglobulin class switching and antibody production. CD30L transgenic mice had increased numbers of germinal centers, elevated class-switched immunoglobulin  isotypes, increased germinal center B cells and plasma cells, upregulation of genes indicative of B-cell activity, and exaggerated antibody responses to immune challenge.  Interestingly, despite the heightened B-cell activity in CD30L transgenic mice, CD30L overexpression on T cells did not result in overt autoimmunity. Our results demonstrate that overexpression of CD30L on T cells promotes T cell-dependent B cell responses characterized by secondary antibody responses.
Keywords: Transgenic vs. wild-type

overall_design: Spleen, thymus, mesenteric lymph nodes and peripheral lymph nodes where samples from both CD30L transgenic and non-transgenic littermates (4 mice per group.)

first: Cynthia

last: Willis


title: Semilunar valve phenotype of Cxcr7-/- neonates

city: Darlinghurst

first: Christine

last: Biben

state: NSW

address: 384 Victoria Street

department: Developmental Biology

country: Australia

institute: Victor Chang Institute

summary:
Cxcr7-/- mice die a few hours after birth. All of them display semilunar valves abnormalities, including bicuspid aortic or pulmonary valves. Those defects only become obvious before birth.
Keywords: genetic modification

overall_design: Biological replicates of pools of 3 mutant samples (2 valves with 2-3 leaflets each, so 4-6 leaflets/mutant) and 3 wildtype littermates (6 leaflets/wildtype).

last: Biben*

first: Frederic

last: Sierro*

first: Blanche

last: Woehl

first: Fabienne

last: MacKay

first: Charles


title: Transcriptional changes in Lhx8 Null newborn mouse ovaries

status: Public on Oct 31 2007

city: Houston

first: Aleksandar

last: Rajkovic

address: One Baylor Plaza

institute: Baylor College of Medicine

summary:
Lhx8 is a homeobox gene expressed in oocytes and critical in oogenesis. Lhx8 deficiency leads to rapid loss of postnatal oocytes. Early oocyte differentiation is poorly understood. We hypothesized that lack of Lhx8 perturbs global expression of genes preferentially expressed in oocytes.  We compared Lhx8 knockout and wild type ovaries using Affymetrix 430 2.0 microarray platform.
Keywords: Genetic Modification

overall_design: Each array was hybridized with cRNA produced from pooled total RNA from at least 25 specimens.  The experiment was performed with 3 replicates.  The results from these three arrays was compared to arrays hybridized with cRNA produced from pooled total RNA from at least 25 wild type specimens of the same genetic background.

first: Youngsok

last: Choi

first: Daniel

last: Ballow

first: Amy

last: Xin


title: Expression in Kir6.1-deficient heart following LPS challenge

city: La Jolla

first: Yu

last: Xia

address: 10550, N. Torrey Pines Rd.

department: Genetics

institute: The Scripps Research Institute

summary:
KATP opposes depolarization of cells in the heart, smooth muscle, and other tissues by permitting the efflux of potassium ions and this efflux is evidently required to prevent unopposed vasoconstriction and insufficiency of coronary artery blood flow triggered by one or more cytokines induced in response to LPS.   The cytokine(s) involved must elicit a dysfunctional response in the Kir6.1-deficient environment, and to gain further insight into the effects of the mutation, we examined the transcriptional status of whole heart, isolated from normal C57BL/6J mice or KcnJ8Md/Md mice, before and after injection of 1 μg of LPS
Keywords: Time course, stress response, disease state analysis, genetic modification

overall_design: 3 mice per genotype were injected with 0.5 ug LPS in PBS or with PBS alone and hearts were collected after 30 min or 3 h.

first: Ben

last: Croker

first: Bruce

last: Beutler


title: Diurnally regulated gene expression in the prefrontal cortex of C57Bl/6J mice at Zeitgeber Time (ZT) 3, 9, 15, and 21.

city: Philadelphia

first: Maja

last: Bucan

address: 415 Curie Blvd

institute: UPENN

summary:
Background: The prefrontal cortex is important in regulating sleep and mood. Diurnally regulated genes in the prefrontal cortex may be controlled by the circadian system, by the sleep-wake states, or by cellular metabolism or environmental responses. Bioinformatics analysis of these genes will provide insights into a wide-range of pathways that are involved in the pathophysiology of sleep disorders and psychiatric disorders with sleep disturbances. Results: We examined gene expression in the mouse prefrontal cortex at four time points during the 24-hour (12-hour light:12-hour dark) cycle by microarrays, and identified 3,890 transcripts corresponding to 2,927 genes with diurnally regulated expression patterns. We show that 16% of the genes identified in our study are orthologs of identified clock, clock controlled or sleep/wakefulness induced genes in the mouse liver and SCN, rat cortex and cerebellum, or Drosophila head. The diurnal expression patterns were confirmed in 16 out of 18 genes in an independent set of RNA samples. The diurnal genes fall into eight temporal categories with distinct functional attributes, as assessed by the Gene Ontology classification and by the analysis of enriched transcription factor binding sites. Conclusions: Our analysis demonstrates that ~10% of transcripts have diurnally regulated expression patterns in the mouse prefrontal cortex.  Functional annotation of these genes will be important for the selection of candidate genes for behavioural mutants in the mouse and for genetic studies of disorders associated with anomalies in the sleep:wake cycle and circadian rhythms.
Keywords: diurnally-regulated gene expression

overall_design: Prefrontal cortex from 3 biological replicates of C57BL/6J mice at four Zeitgeber Times (ZT 3, 9, 15, and 21) were analyzed

first: Shuzhang

last: Yang

first: Kai

last: Wang

first: Otto

last: Valladares

first: Sridhar

last: Hannenhalli


title: Microarray Analyses of Newborn Mouse Ovaries Lacking Nobox

summary:
Nobox is a homeobox gene expressed in oocytes and critical in oogenesis. Nobox deficiency leads to rapid loss of postnatal oocytes. Early oocyte differentiation is poorly understood. We hypothesized that lack of Nobox perturbs global expression of genes preferentially expressed in oocytes as well as microRNAs.  We compared Nobox knockout and wild type ovaries using Affymetrix 430 2.0 microarray platform. We discovered that 28 out of 38 (74%) of the genes down-regulated more than five fold in the absence of Nobox were preferentially expressed in oocytes, while only 5 out of 33 (15%) of genes up-regulated more than five fold in the absence of Nobox, were preferentially expressed in oocytes. Protein binding microarray helped identify nucleotide motifs that NOBOX binds, and that several down-regulated genes contain within putative promoter regions. MicroRNA population in newborn ovaries deficient of Nobox, was largely unaffected. Genes whose proteins are predicted to be secreted, but previously unknown to be significantly expressed in early oogenesis, were down regulated in Nobox knockouts and included astacin-like metalloendopeptidase (Astl), Jagged 1 (Jag1), oocyte secreted protein 1 (Oosp1), fetuin beta (Fetub) and R-spondin 2 (Rspo2). In addition, pluripotency associated genes, Pou5f1 and Sall4 are drastically down-regulated in Nobox deficient ovaries, while testes determining gene Dmrt1 is over-expressed. Our findings indicate that Nobox is likely an activator of oocyte-specific gene expression, and suggest that oocyte plays an important role in suppressing expression of male determining genes such as Dmrt1.
Keywords: Genetic Modification

overall_design: Newborn ovaries were pooled separately from wild type and Nobox -/- animals and total RNA isolated using RNeasy mini kit (Qiagen, CA). Newborn ovaries were collected within 12 hours of delivery. Animal experimentation was approved by the  Institutional Animal Care and Use Committee of Baylor College of Medicine. Three independently pooled RNA samples from wild type and Nobox -/- newborn ovaries were used to generate biotinylated cRNA. Biotinylated cRNA was hybridized to GeneChip Mouse Expression Set 430 2.0 (Affymetrix, Inc.). Since three independent experiments were performed from three independent pools of wild type and Nobox -/- RNA, signal intensities for particular genes were averaged between the three chips and ratio of the wild type over knockout signal calculated. Signal less than 100 was considered background. The raw data in the Affymetrix CEL files were normalized by the RMA method (robust multi-array analysis) [15, 16]. Then the null hypothesis was tested that there is no significant changes in gene expression between the treatment pairs. This was done by LIMMA [17] and the pooled local error (LPE) method [18]. The raw pvalues were adjusted by the Benjamini-Hochberg method for the false discovery rate of 5% [19]. We used DAVID database [20] to aid in functional annotation of genes affected by Nobox deficiency

first: Younsok

first: Yingying

last: Qin

first: Michael

last: Berger

first: Martha

last: Bulyk


title: Estrogen receptors alpha and beta mediation of gene expression in mouse vascular tissue

status: Public on Oct 19 2007

city: Boston

first: Ulla

last: Hansen

address: 5 Cummington St

department: Biology

institute: Boston University

summary:
Estrogen plays an important role in the regulation of vascular tone and in the pathophysiology of cardiovascular disease. Physiological effects of estrogen are mediated through estrogen receptors alpha (ERalpha) and beta (ERbeta), which are both expressed in vascular smooth muscle and endothelial cells. However, the molecular pathways mediating estrogen effects in blood vessels are not well defined. We have performed gene expression profiling in the mouse aorta to identify comprehensive gene sets the expression of which is regulated by long-term (1 wk) estrogen treatment. The ER subtype dependence of the alterations in gene expression was characterized by parallel gene expression profiling experiments in ERalpha-deficient [ERalpha knockout (ERalphaKO)] and ERbeta-deficient (ERbetaKO) mice.
Importantly, these data revealed that ERalpha- and ERbeta-dependent pathways regulate distinct and largely nonoverlapping sets of genes. Whereas ERalpha is essential for most of the estrogen-mediated increase in gene expression in wild-type aortas, ERbeta mediates the large majority of estrogen-mediated decreases in gene expression.  Biological functions of the estrogen-regulated genes include extracellular matrix synthesis, in addition to electron transport in the mitochondrion and reactive oxygen species pathways. Of note, the estrogen/ERbeta pathway mediates down-regulation of mRNAs for nuclear-encoded subunits in each of the major complexes of the mitochondrial respiratory chain. Several estrogen-regulated genes also encode transcription factors. Overall, these findings provide a foundation for understanding the molecular basis for estrogen effects on vasculature gene expression.
Keywords: estrogen, estrogen receptor knockout, gene expression, mouse aorta

overall_design: Six estrogen receptor alpha knockout (ERaKO) and six estrogen receptor beta knockout (ERbKO) mice and ten of their wild-type littermates (all female, 2.5-4.5 months of age) were ovarioectomized.  Half the mice from each genotype were implanted with 17beta-estradiol pellets, the other half with placebo pellets.   After 7-8 days of estrogen/placebo treatment, aortas were harvested, total RNAs were purified for Affymetrix GeneChip microarray analysis, without pooling. This experiment consists of 6 groups with 3 (ERaKO and ERbKO) or 5 (WT) biological replicates per group, for a total of 22 samples.

first: Raegan

last: O'Lone

first: Katrin

last: Knorr

first: Iris

middle: Z

last: Jaffe

middle: E

last: Schaffer

first: Paolo

last: Martini

first: Richard

middle: H

last: Karas

first: Jadwiga

last: Bienkowska

last: Mendelsohn


title: Identification and characterization of the changed transcripts in cumulus cells of Bmp15-/- and Bmp15-/-Gdf9+/--DM mice.

status: Public on Oct 22 2007

city: Bar Harbor

first: You-Qiang

last: Su

state: ME

address: 600 Main Street

institute: The Jackson Laboratory

summary:
Mouse oocytes control cumulus cell metabolic processes that are deficient in the oocytes themselves and this delegation is necessary for oocyte development.  Oocyte-derived bone morphogenetic factor 15 (BMP15) and growth differentiation factor 9 (GDF9) appear to be key regulators of follicular development. The effect of these factors on cumulus cell function before the preovulatory surge of luteinizing hormone (LH) was assessed by analysis of the transcriptomes of cumulus cells from wildtype (WT), Bmp15-/-, and Bmp15-/- Gdf9+/- double mutant (DM) mice using microarray analysis.  The biological themes associated with the most highly-affected transcripts were identified using bioinformatic approaches, IPA and GenMAPP/MAPPFinder. There were 5,332, 7,640, and 2,651 transcripts identified to be significantly changed in the comparisons of Bmp15-/- vs. WT, DM vs. WT, and DM vs. Bmp15-/- respectively by the criteria of FC (fold change) p <0.01.  Among theses changed transcripts, 744 were commonly changed in all three pair-wise comparisons, and hence were considered to be the most highly affected transcripts by mutation of Bmp15 and Gdf9.  IPA Analyses revealed that metabolism was the major theme associated with the most highly-changed transcripts: glycolysis and sterol biosynthesis were the two most significantly affected pathways.  Most of the transcripts encoding enzymes for sterol biosynthesis were down-regulated in both mutant cumulus cells and in WT cumulus cell after oocytectomy.  Similarly, there was a reduction of de novo-synthesized cholesterol in these cumulus cells.  This suggests that oocytes regulate cumulus cell metabolism, particularly sterol biosynthesis, by promoting the expression of corresponding transcripts.  Furthermore, in WT-mice, Mvk, Pmvk, Fdps, Sqle, Cyp51, Sc4mol, and Ebp, which encode enzymes in the sterol biosynthetic pathway, were found to be expressed robustly in cumulus cells, but expression was barely detectable in oocytes.  Levels of de novo-synthesized cholesterol were significantly higher in cumulus–enclosed oocytes than denuded oocytes.  These results indicate that mouse oocytes are deficient in their ability to synthesize cholesterol and require cumulus cells to provide them with products of the sterol biosynthetic pathway.  Oocyte-derived BMP15 and GDF9 may promote this metabolic pathway in cumulus cells as compensation for their own deficiencies.
Keywords:  Gdf9, Bmp15, cumulus cells, transcriptome, metabolism, sterol biosynthesis, genotype comparison, microarray, ingenuity pathways analyses.

first: Koji

last: Sugiura

first: Karen

last: Wigglesworth

first: Marilyn

last: O'Brien

first: Jason

middle: P

last: Affourtit

first: Stephanie

last: Pangas

first: Martin

last: Matzuk

first: John

last: Eppig


title: Unique Molecular Signature of Multipotent Adult Progenitor Cells (Affy)

status: Public on Oct 11 2007

city: Leuven

first: Fernando

last: Ulloa Montoya

address: Herestraat 49 bus 804

country: Belgium

institute: Katholieke Universiteit Leuven

summary:
We compare the transcriptome of embryonic stem cells (ESCs), adult stem cells with apparent greater differentiation potential such as multipotent adult progenitor cells (MAPCs), mesenchymal stem cells (MSCs) and neurospheres (NS). Mouse and rat MAPCs were used in this study and two different array platforms (Affymetrix and NIA) were used for mouse samples.
Keywords: mRNA expression profiling, oligonucleotide microarrays, stem cells

sample_organism:
Mus musculus
Rattus norvegicus

platform_organism:
Mus musculus
Rattus norvegicus

overall_design: Three mRNA samples (biological replicates) per cell type taken at different passage number were compared. Cell types include mouse ESCs, mouse MSCs and three clones isolated using mouse MAPC culture condition: mMAPC-1, mMAPC-2 and mClone-3.  mMAPC-1 and mClone-3 were obtained from same bone marrow isolation, mMAPC-2 was obtained in a different bone marrow isolation. Two clones derived from same rat bone marrow using rat MAPC culture conditions were compared. Three mRNA samples (biological replicates) per clone were taken at different passage numbers

first: Wei-Shou

last: Hu

first: Catherine

last: Verfaillie


title: Gene Microarray analysis of Th17 cells

status: Public on Oct 17 2007

city: Kyoto

first: Shimon

last: Sakaguchi

address: 53 Shogoin Kawahara-cho,

country: Japan

institute: Institute for Frontier Medical Sciences Kyoto University

summary:
Th17 cells are enriched by sorting FR4-CD4+ T cells from SKG mice. A large number of Th17 cells also develop spontaneously when CD4+ T cells from IFN-g-deficient (IFN-g-/-) BALB/c mice are transferred to T cell-deficient RAG2-deficient (RAG2-/-) mice and subjected to homeostatic proliferation, whereas they fail to develop in similar transfer of IL-6-deficient (IL-6-/-) CD4+ T cells to IL-6-/- RAG2-/- mice.
To explore the functional molecules specifically expressed by Th17 cells, we conducted Gene Microarray analysis between 10-month-old SKG FR4-CD4+ cells and age-matched BALB/c FR4-CD4+ cells, and between IFN-g-/- CD4+ cells transferred to RAG2-/- mice and IL-6-/- CD4+ T cells transferred to IL-6-/- RAG2-/- mice. The analysis revealed that 1,556 and 115 genes were up-regulated in 10-month-old SKG FR4-CD4+ and IFN-g-/- CD4+ T cells after homeostatic proliferation, respectively, with 29 genes shared by the two groups of genes. The 29 genes included those encoding cytokines, chemokines, and their receptors, such as IL-1 receptor type1 (IL-1R1), IL-17, IL-22, IL-21, CCR6, and CCL20.
Keywords: cell type comparison

overall_design: We conducted Gene Microarray analysis between 10-month-old SKG FR4-CD4+ cells and age-matched BALB/c FR4-CD4+ cells, and between IFN-g-/- CD4+ cells transferred to RAG2-/- mice and IL-6-/- CD4+ T cells transferred to IL-6-/- RAG2-/- mice using GeneChip Mouse Genome 430 2.0 Array (Affymetrix). Each gruop has three replicates.

first: Keiji

last: Hirota

first: Hiroyuki

last: Yoshitomi

first: Motomu

last: Hashimoto

first: Shinji

last: Maeda

first: Shin

last: Teradaira

first: Naoshi

last: Sugimoto

first: Tomoyuki

last: Yamaguchi

first: Takashi

last: Nomura

first: Hiromu

last: Ito

last: Nakamura

first: Noriko


title: Distinct pathways of pathogenesis in mice with experimental cerebral malaria following P. berghei ANKA infection.

city: Brisbane

first: Christian

last: Engwerda

state: Queensland

address: 300 Herston Road, Herston

institute: Queensland Institute of Medical Research

summary:
Cerebral malaria (CM) is a severe complication of Plasmodium falciparum infection, predominantly experienced by children and non-immune adults, which results in great mortality and long-term sequelae. Recent reports based on histology of post-mortem brain tissue suggest that CM may be the common end point for a range of syndromes. Here, we have analysed the gene expression profiles in brain tissue taken from experimental CM (ECM)-susceptible, Plasmodium berghei ANKA (PbA)-infected C57BL/6 (B6) and CBA/CaH (CBA) mice with ECM. Gene expression profiles were largely heterogeneous between the two ECM-susceptible strains. These results, combined with experimental data, support the existence of distinct pathogenic pathways in CM.
Keywords: disease state analysis

overall_design: C57BL/6 and CBA/CaH mice were infected with 10e5 Plasmodium berghei ANKA-infected RBCs and monitored for ECM development. At onset of ECM symptoms, infected mice and naive controls were culled, perfused (in order to remove non-adherent circulating cells), and brains were removed. Total RNA was extracted from these brains and pooled (n=6 mice/ group). Pooled RNA samples were converted to cDNA and antisense cRNA, labelled and hybridized to GeneChip Mouse Genome 430 2.0 Arrays (Affymetrix, Surrey Hills, Australia). Arrays were scanned using the GeneChip Scanner 3000 (Affymetrix) and GeneChip Operating Software v1.1.1 (Affymetrix). Normalisation and initial analyses were carried out in GeneSpring v7 (Agilent Technologies). Values below 0.01 were set to 0.01. Each measurement was divided by the 50th percentile of all measurements in that sample. The data was filtered for genes flagged as present, which had at least an expression level of 50. Following this, a threshold of 2.5 fold up-regulation or down-regulation of genes differentially expressed during ECM was set.

first: Louise

last: Randall

first: Glen

last: Boyle


title: Pineal gland gene expression of 129 Wt P0 mice versus NeuroD1 pineal gene expression at P0

status: Public on Oct 13 2007

city: Bethesda

first: Michael

last: Bailey

state: MD

address: 9000 Rockville Pike, Bldg 49, Rm 6A71

department: NICHD

institute: National Institutes of Health

summary:
This study determines pineal gland gene expression levels in the NeuroD1 knockout mouse at postnatal day zero.
Comparison was performed against pineal gland gene expression levels in 129 wildtype mice also disected at P0.
Keywords: Comparison of wildtype versus transgenic pineal gland gene expression

overall_design:
Wildype 129 mice served as the reference in comparing the levels of gene expression in the NeuroD1 transgenic animals.
3 pineal glands were disected at P0 during the daytime and pooled for each sample.
3 separate biological samplings were performed.
Triplicate arrays were run for wildtype and the homozygous animals.

first: Estella

last: Munoz

first: Rath

last: Martin

first: Qiong

last: Shi

first: Fabrice

last: Morin

first: Steven

last: Coon

first: Morten

last: Moller

first: David

middle: C

last: Klein


title: Expression data from Pseudomonas aeruginosa exposed airway epithelium from C57Bl6 and MMP-7 and MMP-10 deficient mice.

status: Public on Oct 08 2007

first: Sean

last: Kassim

address: 815 Mercer St

department: Medicine, PCCM

institute: University of Washington

summary:
Airway epithelium is the initial point of host-pathogen interaction in Pseudomonas aeruginosa infection, an important pathogen in cystic fibrosis and nosocomial pneumonia. We used global gene expression analysis to determine airway epithelial transcriptional responses dependent on matrilysin (MMP-7) and stromelysin-2 (MMP-10), two matrix metalloproteinases induced by acute P. aeruginosa pulmonary infection. Extraction of Differential Gene Expression (EDGE) analysis of gene expression changes in P. aeruginosa infected organotypic tracheal epithelial cell cultures from wildtype, Mmp7-/-, and Mmp10-/- mice identified 2,089 matrilysin-dependent and 1,628 stromelysin-2-dependent genes that were differentially expressed. Key node network analysis showed that these MMPs controlled distinct gene expression programs involved in proliferation, cell death, immune responses, and signal transduction, among other host defense processes. Our results demonstrate discrete roles for these MMPs in regulating epithelial responses to pseudomonas infection and show that a global genomics strategy can be used to assess MMP function.
Keywords: time course

overall_design: C57Bl6, Mmp7-/- and Mmp10-/- mouse epithelium at an organotypic air liquid interface culture was exposed to Pseudomonas aeruginosa for 1 and 24 h. RNA was collected from these samples as well as uninfected 0 h and assessed for expression changes using Affymetrix Mouse 430 2.0 Arrays. Triplicate samples were processed for each genotype at each time point.

first: Sina

last: Gharib

first: Brigham

last: Mecham

first: Timothy

last: Birkland

first: William

last: Parks

first: John

last: McGuire


title: Global gene expression profile of interspecies pregnant implantation sites between rat and mouse

status: Public on Dec 01 2007

city: Beijing

first: Xiujun

last: Fan

address: No25 Beishihuan Xilu

institute: Institute of Zoology

summary:
In present, interspecies cloning and interspecies-pregnancy were studied for endangered species rescue. However, the low implantation and survival ratio, spontaneous abortion, and unknown reason embryos absorption are the common and difficult problems of interspecies-pregnancy. In order to discover the mechanism of interspecies-pregnant failure and find ways to overcome the xeon-pregnant obstacles, we chosen the rat embryos pregnant in mouse uterus as a interspecies-pregnancy model. Three groups were set, mouse embryos to mouse recipients (MM) as control group, rat embryos to mouse recipients (RM), and rat and mouse embryos to mouse recipients together (RMM) as experiment groups. The former studies showed that rat embryos live no longer than day 7 of mouse pregnancy (D7). Our results showed that rat embryos survived to D7, and still existed to day 9 of mouse pregnancy (D9) in RM group. Surprisingly, the rat embryos survived to day 13 of the mouse gestation (D13) in RMM group. Microarray analysis was used to detect the global-gene expression profile changes of the whole implantation sites among the three groups at D7 and D9. By this way, we screened out the genes promoting the implanted rat embryos development in a mouse uterus which helped the rat embryos survive to D13 in RMM group compared with RM group, and the genes hindering the rat embryos development in a mouse uterus which prevented rat embryos living longer than D7 in RM group and D13 in RMM group compared with MM group. These findings provide insights into the mechanism of interspecies pregnant failure and new idea for interspecies pregnant studies.
Keywords: time course, pregnancy day

overall_design:
microarray was use to screen the genes among the day 7 and day 9 implantation sites of rat embryos implantation sites in a mouse uterus between rat embryos transfer to mouse recipients and rat embryos transfer to mouse recipients with mouse embryos. The mouse day7 and day 9 embryos implantation sites were use as control.
totally 6 samples were analyzed, each samples two replications (one of them had three replications).

first: Jing

last: Li

first: Enkui

last: Duan


title: Effect of histone deacetylase inhibitors on osteoblast gene expression

status: Public on Oct 06 2007

city: Rochester

first: Jennifer

last: Westendorf

address: 200 First Street SW

institute: Mayo Clinic

summary:
Background:
Osteoblast differentiation requires the coordinated stepwise expression of multiple genes.  Histone deacetylase inhibitors (HDIs) accelerate the osteoblast differentiation process by blocking the activity of histone deacetylases (HDACs), which alter gene expression by modifying chromatin structure.  We previously demonstrated that HDIs and HDAC3 shRNAs accelerate matrix mineralization and the expression of osteoblast maturation genes (e.g. alkaline phosphatase, osteocalcin).  Identifying other genes that are differentially regulated by HDIs might identify new pathways that contribute to osteoblast differentiation.

Results:
To identify other osteoblast genes that are altered early by HDIs, we incubated MC3T3-E1 preosteoblasts with HDIs (trichostatin A, MS-275, or valproic acid) for 18 hours in osteogenic conditions.  The promotion of osteoblast differentiation by HDIs in this experiment was confirmed by osteogenic assays.  Gene expression profiles relative to vehicle-treated cells were assessed by microarray analysis with Affymetrix GeneChip 430 2.0 arrays. The regulation of several genes by HDIs in MC3T3-E1 cells and primary osteoblasts was verified by quantitative real-time PCR.  Nine genes were differentially regulated by at least two-fold after exposure to each of the three HDIs and six were verified by PCR in osteoblasts. Four of the verified genes (solute carrier family 9 isoform 3 regulator 1 (Slc9a3r1), sorbitol dehydrogenase 1, a kinase anchor protein, and glutathione S-transferase alpha 4) were induced.  Two genes (proteasome subunit, beta type 10 and adaptor-related protein complex AP-4 sigma 1) were suppressed.  We also identified eight growth factors and growth factor receptor genes that are significantly altered by each of the HDIs, including Frizzled related proteins 1 and 4, which modulate the Wnt signaling pathway.

Conclusions: This study identifies osteoblast genes that are regulated early by HDIs and indicates pathways that might promote osteoblast maturation following HDI exposure. One gene whose upregulation following HDI treatment is consistent with this notion is Slc9a3r1.  Also known as NHERF1, Slc9a3r1 is required for optimal bone density.  Similarly, the regulation of Wnt receptor genes indicates that this crucial pathway in osteoblast development is also affected by HDIs.  These data support the hypothesis that HDIs regulate the expression of genes that promote osteoblast differentiation and maturation.
Keywords: gene expression

overall_design: To identify other osteoblast genes that are altered early by HDIs, we incubated MC3T3-E1 preosteoblasts with HDIs (trichostatin A, MS-275, or valproic acid) or the vehicle control (DMSO) for 18 hours in osteogenic conditions.  Gene expression profiles relative to vehicle-treated cells were assessed in triplicate (in some cases quadruplicate) samples by microarray analysis with Affymetrix GeneChip 430 2.0 arrays.

first: Tania

last: Schroeder

first: Aswathy

last: Nair

first: Rodney

last: Staggs

first: Anne-Francoise

last: Lamblin


title: Hepatocellular carcinoma follows loss of liver-gender specificity in mice

city: Chapel Hill

first: Rebecca

middle: Catherine

last: Fry

address: 1213 MHRC

institute: UNC-Chapel Hill

summary:
We are investigating hepatic transcriptional responses associated with castration and tumorigenic hepatitis induced by Helicobacter hepaticus infection in mature male A/JCr mice
Microarray data demonstrated a global loss of gender-dimorphic gene expression regulation in mice with chronic hepatitis and liver cancer
Keywords: dose

overall_design: Male A/JCr mice were inoculated with H. hepaticus or vehicle at 4 weeks; some underwent castration at 1 year, and all were necropsied at 21 months

first: Arlin

middle: B

last: Rogers

first: Elizabeth

last: Theve

first: Yan

last: Feng

first: Kristen

last: Clapp

first: Kathleen

last: Cormier

first: James

middle: G

last: Fox


title: Expression data from Dicer knockout MEF

status: Public on Oct 05 2007

city: Cambridge

first: Noam

last: Shomron

address: 77 Massachusetts Ave 68-217

institute: Massachusetts Institute of Technology

summary:
A functional part of the Dicer gene was knocked out from MEF using a conditional knockout strain
Expression of miRNA target genes were evaluated to gain better understanding of regulation by miRNAs
Keywords: Wild-type and knockout

overall_design: MEF_CDKO+Tamoxifen (2 concentrations and 2 replicates each = 4 arrays) were compared to MEF_CDKO No Treatment / MEF_WT+Tamoxifen / MEF_WT No Treatment (2 replicates each = 6 arrays)

first: Rickard

last: Sandberg

first: Cydney

last: Neilsen

first: E

last: Hornstein

first: Christopher

last: Burge


title: Expression profile from anthrax edema toxin (ET) treated murine bone marrow derived macrophages (BMDM)

status: Public on Sep 28 2007

city: Charlestown

first: Chun

last: Kim

address: Bldg 149, 13th Street

department: Cutaneous Biology Research Center

institute: Massachusetts General Hospital

summary:
Bacillus anthracis, the causative agent of anthrax, secretes three toxin proteins: protective antigen (PA), lethal factor (LF), and edema factor (EF). PA is a transporter of LF and EF into host cells by receptor-mediated endocytosis. LF is a metalloprotease that cleaves mitogen-activated protein kinase (MAPK) kinases (MKK), while EF is an adenylate cyclase, which converts ATP to cAMP.
We used microarrays to decipher the specific gene regulation in edema toxin (ET), the complex of EF and PA, treated mouse bone marrow derived macrophages.
Keywords: Time course

overall_design: BMDM were treated with 1 mg/ml of ET and the RNAs were purified at 0, 2, and 4h after toxin treatment.

first: Jin

middle: M

last: Park


title: Differential expression of BMP4-regulated genes associated with commitment of C3H10T1/2 cells into adipocytes

status: Public on Sep 26 2007

city: Baltimore

first: M.

middle: Daniel

last: Lane

address: 725 N. Wolfe St

institute: Johns Hopkins University

summary:
C3H10T1/2 stem cells are committed to the adipocyte lineage by treatment with BMP-4 and grown to postconfluence.  When subjected to our standard differentiation protocol, the committed cells differentiate into adipocytes in a manner indistinguishable from that of 3T3-L1 preadipocytes.  In contrast, C3H10T1/2 cells not committed with BMP-4 remain undifferentiated despite treatment with differentiation inducers.  The molecular basis of the commitment process, however, has not been elucidated.  Since postconfluent uncommitted and committed C3H10T1/2 cells respond differently to the differentiation inducers, it was reasoned that the two cell types differed at the gene expression level.  Therefore, we undertook microarray gene expression profiling to detect changes between the two cell populations at postconfluence to identify expressed genes that may be responsible for the dramatic change in phenotype.
Keywords: control vs treated

overall_design: C3H10T1/2 cells were plated and treated with 50 ng/ml BMP4 and grown to postconfluence.  Control samples were treated in the same manner were not given BMP4.  Total RNA was collected at postconfluence.  There were 3 replicates each for control and treated cells.

first: Tamara

last: Otto

first: Robert

middle: R

last: Bowers

first: Daniel


title: Deletion of PKBalpha/Akt1 affects thymic development

status: Public on Oct 03 2007

city: Basel

first: Brian

middle: A

last: Hemmings

address: Maulbeerstrasse 66

institute: Friedrich Miescher Institute

summary:
The thymus constitutes the primary lymphoid organ for the majority of T cells. The phosphatidyl-inositol 3 kinase (PI3K) signaling pathway is involved in lymphoid development. Defects in single components of this pathway prevent thymocytes from progressing beyond early T cell developmental stages. Protein kinase B (PKB) is the main effector of the PI3K pathway. To determine whether PKB mediates PI3K signaling in early T cell development, we characterized PKB knockout thymi. Our results reveal a significant thymic hypocellularity in PKBalpha-/- neonates and an accumulation of early thymocyte subsets in PKBalpha-/- adult mice. The latter finding is specifically attributed to the lack of PKBalpha within the lymphoid component of the thymus. Microarray analyses show that the absence of PKBalpha in early thymocyte subsets modifies the expression of genes known to be involved in pre-TCR signaling, in T cell activation, and in the transduction of interferon-mediated signals. This report highlights the specific requirements of PKBalpha for thymic development.
Keywords: Genetic modification

overall_design: Early thymocyte subsets (DN3 and ISP8) were sorted by FACS from 4 PKBalpha-/- / PKBalpha+/+ mouse littermate pairs. The same number of DN3 or ISP8 cells was sorted (7 000 to 25 000 cells) within a PKBalpha-/- / PKBalpha+/+ pair. Four replicates per condition were then analysed (4xPKBalpha-/- DN3, 4xPKBalpha+/+ DN3, 4xPKBalpha-/- ISP8, 4xPKBalpha+/+ ISP8). Total RNA was extracted using PicoPureTM RNA isolation kit (Arcturus, Sunnyvale, CA, USA) and RNA quality was controlled using the 2100 Bioanalyser (Agilent Technologies, Santa Clara, CA, USA). Total RNA was amplified and labeled using the Affymetrix 2-cycle 3’ labelling kit according to manufacturer’s instructions. After fragmentation, 10 ug cRNA was hybridised to mouse genome 430 2.0 GeneChips (Affymetrix, Santa Clara, CA). The supplementary file represents the expression values estimated using the GC-RMA function provided by Refiner 3.1 (Genedata, Basel, Switzerland) for each of the samples.

first: Elisabeth

last: Fayard

first: Jason

last: Gill

first: Magdalena

last: Paolino

first: Debby

last: Hynx

first: Georg

last: Hollander