title: Analysis of temporal mRNA expression changes in cultured keratinocytes from Casp-8F/–K5-Cre and Casp-8F/+K5-Cre mice

status: Public on Jul 29 2009

city: Hannover

first: Oliver

last: Dittrich-Breiholz

address: Carl-Neuberg-Str. 1

department: Research Core Unit Genomics

institute: Medical School Hannover

summary: Expression of enzymatically inactive caspase-8, or deletion of caspase-8 from basal epidermal keratinocytes, triggers chronic skin inflammation in mice. Unlike similar inflammation resulting from arrest of NF-kB activation in the epidermal cells, the effect induced by caspase-8 deficiency did not depend on TNF, IL1, dermal macrophage function, or expression of the Toll-like receptor adapter proteins MyD88 or TRIF. Both interferon regulatory factor (IRF)3 and TANK-binding kinase were constitutively phosphorylated in the caspase-8-deficient epidermis, and knockdown of IRF3 in the epidermis-derived cells from these mice abolished the expression of upregulated genes. Temporal and spatial analyses of the alterations in gene expression that result from caspase-8 deficiency reveal that the changes are initiated before birth, around the time that cornification develops, and occur mainly in the suprabasal layer. Finally, we found that caspase-8-deficient keratinocytes display an enhanced response to gene activation by transfected DNA. Our findings suggest that an enhanced response to endogenous activators of IRF3 in the epidermis, presumably generated in association with keratinocyte differentiation, contributes to the skin inflammatory process triggered by caspase-8 deficiency.

overall_design: Epidermal keratinocytes were isolated from the skin of Casp-8F/–K5-Cre or Casp-8F/+K5-Cre mice. Keratinocyte samples from two mice of each genotype were isolated and subsequently cultured. Total RNA was extracted at the first and the third passage of cultivation (8 RNA samples originated in total). The appropriate pairs of RNA samples suited for a direct comparison of the two different genotypes under examination were differently labeled and subsequently co-hybridized onto one microarray (dual color design).

first: Andrew

last: Kovalenko

first: Jin-Chul

last: Kim

first: Tae-Bong

last: Kang

first: Akhil

last: Rajput

first: Konstantin

last: Bogdanov

first: Michael

last: Kracht

first: Ori

last: Brenner

first: David

last: Wallach


title: Gene expression profiling of Stat3flx/flx/NIC breast tumors compared to wild type NIC tumors.

status: Public on Sep 01 2009

city: Montreal

first: Solmaz

last: Shahalizadeh

state: Quebec

address: 3649 Prom. Sir-William-Osler, Room 435

department: McGill Centre for Bioinformatics

country: Canada

institute: McGill University

summary:
A Stat3-dependent transcription regulatory network involved in inflammation and metastasis is identified.
Analyses of the gene expression data revealed that Stat3flx/flx/NIC tumors exhibited a significant reduction in the expression of factors involved in both tumor angiogenesis (fibronectin, von willebrand factor, annexin a3, thrombopoietin, fibulin 5) and in the acute phase inflammatory response (cebpd, osmr, saa1, saa2)

overall_design: Common reference design. 8 samples including RNA extracted from 3 pools of Stat3wt/wt/NIC (WT) tumor tissues (5 individual tumor samples per pool) and 5 individual Stat3flx/flx/NIC (Homo) tumor tissue samples.

first: Jill

middle: J

last: Ranger

middle: E

last: Levy

middle: T

last: Hallett

first: William

last: Muller


title: Wild-type p53 enhances efficiency of simian virus 40 large-T-antigen-induced cellular transformation

status: Public on Jul 18 2009

city: Hamburg

first: Genrich

last: Tolstonog

department: Department of Tumor Virology

country: Germany

institute: Heinrich-Pette-Institute, Leibniz Institute for Experimental Virology

summary: To measure on a global scale the SV40 large T antigen-mediated changes in gene transcription in mouse embryo fibroblasts differing in the expression of p53.

overall_design: Samples of total RNA from 3T3 (wt p53) and 10-1 (p53-null) mouse embryo fibroblasts stably transfected with SV40 large T-antigen expressing pMYcLT vector (3T3 LT and 10-1 LT cells) or empty pMYsIG vector (3T3 IG and 10-1 IG cells) were subjected to gene expression analysis.

middle: V


title: Influence of MLL/ENL expression on murine bone marrow cells with a conditional Mef2c knockout or a Mef2c rescue

status: Public on Jul 22 2009

first: Carol

last: Stocking

address: Martinistrasse 52

institute: Heinrich-Pette-Institut

summary: Acute myelogenous leukemia (AML) is driven by leukemic stem cells (LSC) generated by mutations that confer (or maintain) self-renewal potential coupled to an aberrant differentiation program. Using retroviral mutagenesis, we identified genes that generate LSC in collaboration with genetic disruption of the gene encoding interferon response factor 8 (Irf8), which induces a myeloproliferation in vivo.  Amongst the targeted genes, we identified Mef2c, encoding a MADS transcription factor, and confirmed that over-expression induced a myelomonocytic leukemia in cooperation with Irf8 deficiency.  Strikingly, several of the genes identified in our screen have been reported to be upregulated in the mixed-lineage leukemia (MLL) subtype.  High MEF2C expression levels were confirmed in AML patient samples with MLL gene disruptions, prompting an investigation of the causal interplay.  Using a conditional mouse strain, we demonstrated that Mef2c deficiency does not impair the establishment nor maintenance of LSC generated in vitro by MLL/ENL fusion proteins – however, its loss led to compromised homing and invasiveness of the tumor cells. Mef2c-dependent targets included several genes encoding matrix metalloproteinases and chemokine ligands and receptors, providing a mechanistic link to increased homing and motility. Thus an early event in LSC generation may be responsible for the aggressive nature of this leukemia subtype.

overall_design: For gene expression profiling of M/E cells, RNA was isolated from M/E-Mef2c del/- cells infected with MYs-iPAC (empty vector) or MYs-pMef2cASR after puromycin selection at three different time points, pooled, and hybridized against the Agilent Whole Mouse Genome Microarray 4x44K using the one-color service of Miltenyi. Transcript levels were verified by real-time RT-PCR using the SYBRGreen Reaction Mix (Roche Mannheim) in a Roche Light-Cycler. cDNA levels were normalized against Hprt transcript levels. Primers and amplification conditions are available upon request.

first: Andrea

last: Schüler


title: Parasite strain-specific pathogenesis in murine infections with Trypanosoma brucei

status: Public on Jul 11 2009

city: Glasgow

first: Liam

last: Morrison

address: 120 University Avenue

department: Wellcome Centre for Molecular Parasitology

country: United Kingdom

institute: University of Glasgow

summary:
Different strains of T. brucei induce different degrees of pathology in infected animals, and TREU927-infected mice display greater splenomegaly and anaemia than 247-infected mice. The analysis of differential host gene expression in infected spleens has allowed the identification of which pathways or processes are crucial in determining the progression of disease, for example IL10, LXR/RXR activation and alternative macrophage activation.
We used microarray analysis to examine host gene expression between uninfected and infected mice, and between mice infected with the two trypanosome strains.

overall_design: Mouse spleens were dissected from infected or uninfected mice 10 days post infection, when the differences in pathology criteria (hepatomegaly, red blood cell numbers, reticulocyte percentage, IL10, IFNg and Il12 levels, and splenomegaly) were the greatest. This allowed a three-way comparison, uninfected vs 247-infected, uninfected vs 927-infected, and 247-infected vs 927-infected, allowing us to analyse genes that are differentially expressed between infected and uninfected spleens, but also crucially allows the differentiation between host gene expression with pathogenic (927) and less pathogenic (247) trypanosome strains.

first: Mike

last: Turner

first: Annette

last: MacLeod

first: Andy

last: Tait


title: Apoptosis genes specifically modulated by NFAT in LPS-activated dendritic cells

status: Public on Jun 17 2009

city: Milan

first: Francesca

last: Granucci

address: Piazza della Scienza 2

country: Italy

institute: University of Milano-Bicocca

summary: Dendritic cells (DCs) are a special class of leukocytes able to activate both innate and adaptive immune responses. They interact with microbes through germline-encoded pattern-recognition receptors (PRRs), which recognize molecular patterns expressed by various microorganisms. Upon antigen binding, PRRs instruct DCs for the appropriate priming of natural killer cells, followed by specific T-cell responses. Once completed the effector phase, DCs reach the terminal differentiation stage and eventually die by apoptosis. We have observed that following lipopolysaccharide (LPS)-stimulation the initiation of the apoptotic pathway in DCs is due the activation of NFAT proteins. Indeed, LPS induces Src-family kinase and phospholipase C (PLC)γ2 activation, influx of extracellular Ca2+ and calcineurin-dependent nuclear NFAT translocation. The initiation of this pathway is independent of TLR4 engagement, and dependent exclusively on CD14. According with this observation CD14-deficient DCs do not die following LPS stimulation. Nevertheless, CD14-deficient DC death following LPS activation can be restored by co-stimulating DCs with LPS and thapsigargin. Thapsigargin empties the intracellular calcium stores by blocking calcium pumping into the sarcoplasmic and endoplasmic reticulum and thereby activates plasma membrane calcium channels. This, in turn, allows an influx of calcium into the cytosol and NFAT activation. To identify the NFAT controlled apoptosis genes in LPS activated DCs we have performed a kinetic microarray analysis (0, 48 and 60 h) in conditions allowing or inhibiting NFAT activation. Four genes have been selected: Nur77, Gadd45g, Ddit3/Gadd153/Chop-10 and Tia1.

overall_design: To identify apoptosis genes selectively modulated by NFAT, a comparative kinetic (time points 0, 48 and 60 h) microarray analysis was performed in the following conditions: 1) wild type bone marrow derived DCs (wtBMDCs) stimulated with LPS; 2) CD14-deficient BMDCs stimulated with LPS; 3) wtBMDCs stimulated with LPS in presence of thapsigargin; 4) CD14-deficient BMDCs stimulated with LPS in presence of thapsigargin.

first: Ivan

last: Zanoni

first: Renato

last: Ostuni


title: Expression data from retinas of wildtype and Nhlh2 knockout mice

status: Public on Jun 25 2009

city: Belfast

middle: Arthur

last: Simpson

state: N. Ireland

address: The Wellcome – Wolfson Institute for Experimental Medicine, 97 Lisburn Road

department: Wellcome-Wolfson Institite for Experimental Medicine

institute: Queen's University Belfast

summary: Nhlh2 is a neuronal helix-loop-helix transcription factor. The goal of this study was to determine the pattern of gene expression in wildtype mouse retina and to compare it to that in the retinas of mice in which the nhlh2 gene had been knocked out.

overall_design: RNA was extracted from three pairs of littermates, each comprising one wildtype and one knockout sample. The littermate samples are: retina_wt_rep1 & retina_nhlh2_rep1; retina_wt_rep2 and retina_nhlh2_rep2; retina_wt_rep3 & retina_nhlh2_rep3.

middle: A

first: Tiziana

last: Cogliati


title: Generation of induced pluripotent stem cells by efficient reprogramming of adult bone marrow cells

status: Public on Jul 02 2009

city: Machida-shi

first: Kenji

last: Nagao

state: Tokyo

address: 3-6-6, Asahi-machi,

department: Innovative Drug Research Laboratories

country: Japan

institute: Kyowa Hakko Kirin Co., Ltd.

summary: Reprogramming of somatic cells provides potential for the generation of specific cell types, which could be a key step in the study and treatment of human diseases. In vitro reprogramming of somatic cells into a pluripotent embryonic stem (ES) cell–like state has been reported by retroviral transduction of murine fibroblasts using four embryonic transcription factors or through cell fusion of somatic and pluripotent stem cells. The generation of reprogrammed pluripotent cells using a somatic cell donor source such as bone marrow (BM) or peripheral blood is of particular therapeutic interest because of the relative ease of harvesting these cell types. Here we show that mouse adult BM mononuclear cells（BM MNCs）are competent as donor cells and can be reprogrammed into pluripotent ES cell-like cells. We isolated BM MNCs and embryonic fibroblasts (MEFs) from Oct4-EGFP transgenic mice, fused them with ES cells and infected them with retroviruses expressing Oct4, Sox2, Klf4, and c-Myc. Fused BM cells formed more ES-like colonies than did MEFs. Infected BM cells gave rise to iPS cells, although transduction efficiencies were not high. It was more efficient to pick up iPS colonies as compared with MEFs. BM-derived iPS (BM iPS) cells expressed embryonic stem cell markers, formed teratomas, and contributed to chimera mice with germline development. Clonal analysis revealed that BM iPS clones had diversity, although some clones were found to be genetically identical with different phenotypes. Here we demonstrate, for the first time, the induction of pluripotent cells directly from hematopoietic tissue.

overall_design: Gene expression profiling was performed in mouse BMMNCs, ES and BMMNC derived iPS cell lines.

first: Atsushi

last: Kunisato

first: Mariko

last: Wakatsuki

first: Yuuki

last: Kodama

first: Haruna

last: Shinba

first: Isao

last: Ishida


title: NFAT-mediated gene expression response to LPS in murine dendritic cells and macrophages

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

overall_design: Refer to individual Series


title: IKKα Is Required to Maintain Skin Homeostasis and Prevent Skin Cancer

status: Public on Jul 14 2009

city: Smithville

first: Yinling

last: Hu

state: TX

address: 1808 Park Road 1C

department: Carcinogenesis

country: USA

institute: UT M.D.Andreson Cancer Center

summary: It has long been known that excessive mitotic activity due to H-Ras can block keratinocyte differentiation and cause skin cancer. It is not clear, however, whether there are any innate surveillants that ensure keratinocytes undergoing terminal differentiation, preventing the disease. IKKα induces keratinocyte terminal differentiation and its reduction promotes skin tumor development. However, its nature function in skin cancer is unknown. Here we found that mice with IKKα deletion in keratinocytes or in hair follicle keratinocytes developed a thickened epidermis and spontaneous squamous cell-like carcinomas. Inactivation of epidermal growth factor receptor (EGFR) or reintroduction of IKKα inhibited excessive mitosis, induced terminal differentiation, and prevented skin cancer through an EGFR-driven autocrine loop in mice. Thus, IKKα serves as an innate surveillant.

overall_design: The differences in gene expression profiles of CHUK deleted mouse keratinocytes compared to wild type mouse keratinocytes were analyzed using two dual-channel agilent microarrays in duplicates.

first: Bigang

last: Liu

first: Xiaojun

last: Xia

first: Feng

last: Zhu

first: Eunmai

last: Park

first: Steve

last: Carbaj

first: Kaoru

last: Kiguchi

first: John

last: DiGiovanni

first: Susan

last: Fischer


title: Gene expression in macrophages stimulated with LPS in conditions allowing or inhibiting NFAT activation

first: Francesca

last: Granucci

summary:
Macrophages and dendritic cells (DCs) differently contribute to the generation of coordinated immune system responses against infectious agents. They interact with microbes through germline-encoded pattern-recognition receptors (PRRs), which recognize molecular patterns expressed by various microorganisms. Upon antigen binding, PRRs instruct DCs for the appropriate priming of natural killer cells, followed by specific T-cell responses. Once completed the effector phase, DCs reach the terminal differentiation stage and eventually die by apoptosis. By contrast, following antigen recognition, macrophages initiate first the inflammatory process and then switch to an anti-inflammatory phenotype for the restoration of tissue homeostasis. Following lipopolysaccharide (LPS)-stimulation the initiation of the apoptotic pathway in DCs is due the activation of NFAT proteins. DC stimulation with lipopolysaccharide (LPS) induces Src-family kinase and phospholipase C (PLC)γ2 activation, influx of extracellular Ca2+ and calcineurin-dependent nuclear NFAT translocation. The initiation of this pathway is independent of TLR4 engagement, and dependent exclusively on CD14. We asked whether macrophage survival after LPS encounter was due to their inability to activate the Ca2+ pathway.

As matter of fact, bone marrow-derived macrophages were unable to mobilize Ca2+ and to translocate NFAT to the. To further investigate whether the Ca2+-NFAT pathway played any role in LPS-stimulated macrophages, we performed a comparative kinetic microarray analysis in conditions allowing or inhibiting NFAT activation. We show here that no modulation of gene expression can be attributed to NFAT.

overall_design: Gene expression analyses were performed using Affymetrix GeneChips in the following groups of murine macrophaghes: 1) CD14-deficient macrophages stimulated with LPS; 2) wt macrophages stimulated with LPS in presence of EGTA; 3) wt macrophages stimulated with LPS. The following kinetic time points were examined: 0, 6 and 24 hours following LPS activation. This experimental setting allowed us to select for effects due to Ca2+ fluxes and exclude the effects due to other causes, particularly the block of TRIF recruitment in CD14-deficient cells and the EGTA effects unrelated to Ca2+ chelation.

first: Ivan

last: Zanoni

first: Renato

last: Ostuni


title: Gene expression in dendritic cells stimulated with LPS in conditions allowing or inhibiting NFAT activation

summary: Interleukin-2 (IL-2) is one of the molecules produced by mouse dendritic cells (DCs) after stimulation by Toll like receptor (TLR) agonists. By analogy with the events following T-cell receptor (TCR) engagement leading to IL-2 production we have observed that DC stimulation with lipopolysaccharide (LPS) induces Src-family kinase and phospholipase C (PLC)γ2 activation, influx of extracellular Ca2+ and calcineurin-dependent nuclear NFAT translocation. We have also observed that the initiation of this pathway is independent of TLR4 engagement, and dependent exclusively on CD14. To determine the role of NFAT in LPS activated dendritic cells we have performed microarray analysis in conditions allowing or inhibiting NFAT activation. We show here that LPS-induced NFAT activation via CD14 is necessary to cause death of terminally differentiated DCs, an event that is essential for maintaining self-tolerance and preventing autoimmunity. Consequently, blocking this pathway in vivo causes prolonged DC survival and an increase in T cell priming capability.

overall_design: Gene expression analyses were performed using Affymetrix GeneChips in the following groups of murine bone marrow-derived dendritic cells: 1) CD14-deficient BMDCs stimulated with LPS; 2) wtBMDCs stimulated with LPS in presence of EGTA; 3) wtBMDCs stimulated with LPS. This experimental setting allowed us to select for effects due to Ca2+ fluxes and exclude the effects due to other causes, particularly the block of TRIF recruitment in CD14-deficient cells and the EGTA effects unrelated to Ca2+ chelation.


title: Expression of autotaxin and lysophosphatidic acid receptors increases mammary tumorigenesis, invasion, and metastases

status: Public on Jun 11 2009

city: Chapel Hill

first: Charles

middle: M.

last: Perou

state: NC

address: 12-044 Lineberger Comprehensive Cancer Center CB# 7295

department: Professor of Genetics, and Pathology & Laboratory Medicine; Lineberger Comprehensive Cancer Center

institute: University of North Carolina at Chapel Hill

summary: Lysophosphatidic acid (LPA) acts through high-affinity G protein-coupled receptors to mediate a plethora of physiological and pathological activities associated with tumorigenesis. LPA receptors and autotaxin (ATX/LysoPLD), the primary enzyme producing LPA, are aberrantly expressed in multiple cancer lineages. However, the role of ATX and LPA receptors in the initiation and progression of breast cancer has not been evaluated. We demonstrate that expression of ATX or each edg family LPA receptor in mammary epithelium of transgenic mice is sufficient to induce a high frequency of late-onset, estrogen receptor (ER)-positive, invasive, and metastatic mammary cancer. Thus, ATX and LPA receptors can contribute to the initiation and progression of breast cancer.

overall_design: referenceXsample

first: Shuying


title: ALS mice muscle gene expression data

status: Public on Jun 02 2009

city: Cusano Milanino

first: Antonia

last: Ratti

state: Milan

address: Via Zucchi, 18

department: Dept. Neurological Sciences

institute: IRCCS Istituto Auxologico Italiano, University of Milan


title: Gene expression profiling of muscles from transgenic humanSODG93A mice at presymptomatic stage

summary:
The transgenic mice expressing the human mutated form (G93A) of the SOD1 gene represent a valuable model of Amyotrophic Lateral Sclerosis (ALS). SOD1 is one of the main causative genes of familial ALS which accounts for 10% of cases. These transgenic animals develop a motorneuronal pathology that recapitulates well the neuropathological features occuring in ALS patients, and the progression of the disease can be monitored by a series of motor tests. Gastrocnemius is the first and most affected muscle in the disease, while triceps is relatively spared.

Gene expression data of degenerating motor neurons at different disease stages are already available, while gene expression data on the muscle tissue are missing. Our aim is to define the role of muscle in motor neuron degeneration in ALS.

Keywords: Single stage analysis (presymptomatic stage, 7 week-old mice)

overall_design: We considered two sets of muscle at presymptomatic stage (7 weeks): gastrocnemius and triceps from 4 transgenic SOD1G93A and 4 non-transgenic mice (NTg).

first: Stefano

last: Calza

first: Manuela

last: Volta


title: Gene expression profiling of muscles from transgenic humanSODG93A mice at symptomatic stage

summary:
The transgenic mice expressing the human mutated form (G93A) of the SOD1 gene represent a valuable model of Amyotrophic Lateral Sclerosis (ALS). SOD1 is one of the main causative genes of familial ALS which accounts for 10% of cases. These transgenic animals develop a motorneuronal pathology that recapitulates well the neuropatological features occuring in ALS patients, and the progression of the disease can be monitored by a series of motor tests. Gastrocnemius is first and most affected muscle in the disease, while triceps is relatively spared.

Gene expression data of degenerating motor neurons at different disease stages are already available, while gene expression data on the muscle tissue are missing. Our aim is to define the role of muscle in motor neuron degeneration in ALS.

Keywords: Single stage analysis (early symptomatic stage, 14 weeks-old mice)

overall_design: We considered two sets of muscle at symptomatic stage (14 weeks): gastrocnemius and triceps from 4 transgenic SOD1G93A and 4 non-transgenic mice (NTg). Gastrocnemius from 4 nerve-crushed mice were also considered as controls for the denervation process


title: Analysis of mRNA expression differences in the skin of Casp-8F/–K5-Cre and Casp-8F/+K5-Cre mice

first: Oliver

last: Dittrich-Breiholz


title: Accelerated Postnatal Growth Increases Lipogenic Gene Expression and Adipocyte Size in Low-Birth Weight Mice

status: Public on May 14 2009

city: Boston

first: Mary Elizabeth

last: Patti

state: MA

address: 1 Joslin Place

department: Research Division

institute: Joslin Diabetes Center

summary:
OBJECTIVE: To characterize the hormonal milieu and adipose gene expression in response to catch-up growth (CUG), a growth pattern associated with obesity and diabetes risk, in a mouse model of low birth weight (LBW). RESEARCH DESIGN AND METHODS: ICR mice were food restricted by 50% from gestational days 12.5-18.5, reducing offspring birth weight by 25%. During the suckling period, dams were either fed ad libitum, permitting CUG in offspring, or food restricted, preventing CUG. Offspring were killed at age 3 weeks, and gonadal fat was removed for RNA extraction, array analysis, RT-PCR, and evaluation of cell size and number. Serum insulin, thyroxine (T4), corticosterone, and adipokines were measured.
RESULTS: At age 3 weeks, LBW mice with CUG (designated U-C) had body weight comparable with controls (designated C-C); weight was reduced by 49% in LBW mice without CUG (designated U-U). Adiposity was altered by postnatal nutrition, with gonadal fat increased by 50% in U-C and decreased by 58% in U-U mice (P < 0.05 vs. C-C mice). Adipose expression of the lipogenic genes Fasn, AccI, Lpin1, and Srebf1 was significantly increased in U-C compared with both C-C and U-U mice (P < 0.05). Mitochondrial DNA copy number was reduced by >50% in U-C versus U-U mice (P = 0.014). Although cell numbers did not differ, mean adipocyte diameter was increased in U-C and reduced in U-U mice (P < 0.01). CONCLUSIONS: CUG results in increased adipose tissue lipogenic gene expression and adipocyte diameter but not increased cellularity, suggesting that catch-up fat is primarily associated with lipogenesis rather than adipogenesis in this murine model.

overall_design: Epididymal fat samples were obtained at age 3 weeks from 5 control mice (CC), 5 mice exposed to in utero undernutrition (UC), and 4 mice exposed to undernutrition in utero and during suckling (UU).

first: Elvira

last: Isganaitis

first: Josep

last: Jimenez-Chillaron

first: Melissa

last: Woo

first: Alice

last: Chow

first: Jennifer

last: DeCoste

first: Martha

last: Vokes

first: Manway

first: Simon

last: Kasif

first: Ann-Marie

last: Zavacki

first: Rebecca

middle: L

last: Leshan

first: Martin

middle: G

last: Myers

first: Mary-Elizabeth


title: PKGI KO vs. WT brown adipocytes and brown adipose tissues

status: Public on May 16 2009

city: Bonn

first: Peter

last: Mayer

address: Kurt-Georg-Kiesinger-Allee

institute: Fed. Inst. for Drugs and Med. Devices

summary: Gene expression in brown adipose tissue and in primary adipocytes derived thereof from PKGI-/- mice was studied in comparison to wild type mice.

overall_design: Experiments were performed in triplicate, i.e three PKGI-/- mice and matching wt littermates were used for brown adipocyte preparation; another three mouse pairs were used for tissue preparation.

first: Bodo

last: Haas

first: Alexander

last: Pfeifer


title: IL-3 coordination of myeloblast function by modulating mRNA stability

status: Public on Jun 01 2009

city: Pittsburgh

first: Richard

last: Steinman

state: PA

address: 5117 Centre Avenue

department: Medicine

institute: University of Pittsburgh

summary: The growth factor interleukin-3 (IL-3) promotes the survival and growth of multipotent hematopoietic progenitors and stimulates myelopoiesis.  It has also been reported to oppose terminal granulopoiesis and to support leukemic cell growth through autocrine or paracrine mechanisms.  We used kinetic microarray, Northern Blotting and bioinformatics analysis of IL-3 dependent myeloblasts to determine whether IL-3 acts in part by regulating the rate of turnover of mRNA transcripts in specific functional pathways.  Our results indicate that exposure of myeloblasts to IL-3 causes immediate early stabilization of hundreds of transcripts in pathways relevant to myeloblast function.  Examples include transcripts associated with proliferation and leukemic transformation (pik3cd, myb, pim-1), hematopoietic development (cited2), differentiation control (cdkn1a) and RNA processing (BRF1, BRF2).  A domain in the 3’-utr of IL-6 that mediates IL-3 responsiveness contains AU-rich elements that bind proteins known to modulate mRNA stability, however a known destabilizing protein (AUF1) is shown not to mediate degradation in the absence of IL-3.    These findings support a model of IL-3 action through mRNA stability control and suggest that aberrant stabilization of this network of transcripts could contribute to growth patterns observed in leukemia.

overall_design: Cells were exposed to actinomycin D to block transcription for 0, 2 or 4 hours. The cytokine IL-3 was added after actinomycin D either at a high (1 ng/ml) or low (10 pg/ml) concentration.  The effect of cytokine on transcript decay rates was therefore determined.  There were five determinations per experiment (0 hour, and 2 hr and 4 hours, the latter two time points at both high and at low IL3); two independent experiments are represented (10 microarray analyses in total).

first: Jason

last: Ernst

first: Louis

last: Ghanem

first: Ziv

last: Bar-Joseph

first: Michael

last: McNamara


title: Metastable pluripotent states in NOD mouse derived ES cells

status: Public on Apr 09 2009

city: Cambridge

first: Albert

middle: W

last: Cheng

address: Room 453, 9 Cambridge Center

institute: Whitehead Institute

summary: Embryonic stem (ES) cells are isolated from the inner cell mass (ICM) of developing blastocysts, whereas epiblast stem cells (EpiSCs) are derived from the post-implantation epiblast and are characterized by a restricted developmental potential. Although certain mouse strains, such as the non-obese diabetic (NOD) mice, are considered “non-permissive” for ES cell derivation, they retain the capacity to generate EpiSCs. Using the NOD strain as a model, we characterized the stability of pluripotent states in cells generated by ICM explantation or direct in vitro reprogramming. We find that ES-like NOD stem cells can be captured in both approaches by providing exogenous constitutive expression of Klf4 or c-Myc transcription factors or small molecules that can replace these factors during in vitro reprogramming. The fully pluripotent NOD ES and iPS cells appear “metastable”, as the cells acquire an alternative EpiSC-like identity after removal of the exogenous factors, while reintroduction of these factors converts the cells back to ICM-like pluripotency. Our findings suggest that stem cells from different genetic backgrounds can assume distinct states of pluripotency in vitro, the stability of which is regulated by endogenous genetic determinants and can be modified by the continuous presence of defined exogenous factors.

overall_design: Gene expression profiling was performed in mouse ES, EpiSC and EpiSC-like cell lines.

first: Jacob

last: Hanna

first: Styliani

last: Markoulaki

first: Maisam

last: Mitalipova

first: John

middle: P

last: Cassady

first: Judith

last: Staerk

first: Bryce

last: Carey

first: Ruth

last: Foreman

first: Christopher

last: Lengner

last: Love

first: Qing

last: Gao

first: Rudolf

last: Jaenisch


title: Role of SRF in activity-regulated  transcription in the striatum of the brain

status: Public on Apr 30 2009

city: Heidelberg

first: Jan

last: Rodriguez Parkitna

address: Im Neuenheimer Feld 581

institute: German Cancer Research Center

summary:
Ablation of the Srf  gene in dopaminoceptive neurons of the brain was performed using the Cre/loxP system, with the recombinase expressed from a BAC-derived Drd1a promoter.
Our goal was to analyze how loss of SRF will affect acitivity-regulated transcription induced by strong stimulation, i.e. cocaine.
Keywords: Treatment x Genotype

overall_design: Animals were injected i.p. with either 25 mg/kg cocaine or saline and sacrificed after one hour by cervical dislocation. Expression profiling was performed using total RNA isolated from the striatum.


title: Infection of the larval airway epithelium by Erwinia carotovora

status: Public on May 11 2009

city: Kiel

first: Christina

last: Wagner

address: Am Botanischen Garten 1-9

department: Zoophysiology

institute: Zoological Institute

summary:
The unsurpassed simplicity of the fruitfly’s airway epithelium, that is made of homogenous epithelial cells only, favours its use as a model to study general features and response characteristics of airway epithelia in general. All epithelial cells are able to launch an immune response as characterized by the expression of antimicrobial peptide genes. Infection induces a complex change in the expression profile of these epithelial cells. Outstanding are a priming of the immune system and the launch of a survival program, presumably to counteract infection induced apoptotic signals, which comprises the concurrent expression of known longevity genes such as dFoxo, and dThor. In regions of the airway epithelium with strong immune reactions, a complex remodelling of the airways can be observed, which is characterized by metaplasia and presumably also by hyperplasia of the affected epithelial cells. At the transcriptional level, this reorganization of the airway epithelium is mirrored by a recapitulation of genetic programs that are characteristic for early phases of airway development. Taken together, the response characteristics of the fly’s airway epithelium towards infections discloses features that are known from inflammatory diseases of the human lung, thus opening the opportunity to study fundamental aspects of these diseases in the fly.

Keywords:infection, Erwinia c., third instar larva, airway epithelium, two-colour microarray

overall_design:
Infection of the airway epithelium by the gram-negativ bacteria Erwinia carotovora. For the infection experiments third instar larvae of the GFP-reporter strain YW DD1 were used and only isolated when the whole epithelium of the airway epithelium showed GFP expression. Uninfected larvae were used as controls. In general, four replicates were performed including dye-swaps.
A table of significantly-regulated genes from the SAM-output and GeneTraffic-output has been linked as a supplementary file at the foot of this record.

first: Thomas

last: Roeder


title: Larval airway epithelium response to infection


title: Gene expression profiles of primary tumors with radiotherapy and lung metastases in mouse squamous cell carcinoma model.

status: Public on Apr 23 2009

city: Chiba

first: Kaori

last: Imadome

state: Chiba

address: Anagawa 4-9-1

department: Research Center of Charged Particle Therapy

institute: National institute of radiological sciences

summary:
To examine whether the local carbon ion radiotherapy affects the characteristics of the metastatic tumors, the expression profiles of the primary tumors and the lung metastases were studied in a mouse squamous cell carcinoma model by applying local radiotherapy with no irradiation (negative control), gamma-ray irradiation (reference beam), and carbon-ion irradiation.
Keywords: mouse, squamous cell carcinoma, primary tumor, lung metastases, radiotherapy, carbon ion, gamma ray

overall_design: A highly metastatic mouse squamous cell carcinoma NR-S1 was implanted into the hind leg of synergetic C3H/HeNrs mice and irradiated with 5 Gy of carbon ion beam. 8 Gy of gamma ray was used as a reference beam. At 2 weeks after the irradiation, the lung tissue was sampled. In order to collect samples of primary tumors, the tumors were implanted in other mice and irradiated in the same manner, and the primary tumors were collected at 1 week after the irradiation. The tumor cells of the primary and metastatic tumors were collected by laser microdissection, and oligonucleotide microarray analysis of the irradiated primary tumors and the metastatic tumors were all performed in comparison to the non-irradiated primary tumor by two-color methods.

first: Tomoaki

last: Tamaki

first: Mayumi

last: Iwakawa


title: Met induces mammary tumors with diverse histologies and is associated with poor outcome and human basal breast cancer

status: Public on Mar 30 2009

city: St. Louis

first: Robert

last: Lesurf

state: MO

address: 4444 Forest Park Ave

department: McDonnell Genome Institute

institute: Washington University in St. Louis

summary:
Elevated Met receptor tyrosine kinase (RTK) expression correlates with poor outcome in breast cancer, yet a causal role for Met in the development of breast cancer has not been directly established. To examine this question, we generated a transgenic mouse model that targets expression of an oncogenic Met receptor (MetMut) to the mammary epithelium. We show that MetMut induces mammary tumors with a variety of histopathologies that exhibit gene expression profiles sharing similarities with human basal and luminal breast tumor subtypes. Among all breast cancers, we further demonstrate that the Met receptor is primarily overexpressed in human basal and HER2 positive breast cancers, and that a Met associated gene expression signature identifies patients with poor prognosis.
Keywords: Met, mammary, poor outcome, EMT, basal breast cancer

overall_design: Common reference design. 26 samples (including 20 normal tissue and 32 tumor tissue samples) replicated twice as dye swaps, generating a total of 52 arrays.

first: Marisa

last: Ponzo

first: Stephanie

last: Petkiewicz

first: Frances

last: O’Malley

first: Dushanthi

last: Pinnaduwage

first: Irene

last: Andrulis

first: Shelley

middle: B

last: Bull

first: Naila

last: Chughtai

first: Dongmei

last: Zuo

first: Margarita

last: Souleimanova

first: David

last: Germain

first: Atilla

last: Omeroglu

middle: D

last: Cardiff

first: Michael

last: Hallett

first: Morag

last: Park


title: Comparison of ATG5-/- Bcl-2 tumors expressing p62-GFP versus those expressing EGFP

status: Public on Mar 12 2009

city: New Brunswick

first: Robin

last: Mathew

state: NJ

address: 195 Little Albany Street

department: CINJ

institute: Cancer Institute of New Jersey

summary:
Autophagy is a starvation response that facilitates cell survival under metabolic stress and yet defects in autophagy promote tumorigenesis.  While the role of understarvation is relatively clearer, its mechanistic role in tumorigenesis is poorly understood. We show that defective autophagy promotes protein damage and accumulation of p62, a marker for protein damage accumulation that is cleared through autophagy pathway.  The failure to eliminate p62  in autophagy-defective cells, leads to deregulation of cell signalling and gene expression and ultimately promotes tumorigenesis.  Thus defective-autophagy is a mechanism for p62 accumulation commonly observed in human tumors.

Keywords: Autophagy, p62, Signal transduction, NF-kB, tumorigenesis.

overall_design: Gene expression profile were performed on total mRNA isolated from tumors from atg5-/- Bcl-2 immortalized mouse epithelial (iBMK) cells expressing p62-EGFP (2 tumors) and EGFP (2 tumors) proteins using GeneChip Mouse Genome 430A 2.0 array (Affymetrix, Santa Clara, CA) repressing 22,629 full-length genes and ESTs.  The two parallel tumors derived from isogenic iBMK cell lines expressing p62-EGFP were defined as replicates and were compared to two EGFP-expressing tumors that were also defined as replicates. Affymetrix raw data set of approximately 14,000 genes were further refined using Genes@Work USE-Fold feature selection algorithm to identify a set of 893 genes differentially expressed in p62-EGFP tumors compared to EGFP tumors at a significance level of p=0.05.  The differentially expressed genes were then subjected to Gene Set Enrichment Analysis (GSEA) to identify pathways that are differentially regulated in the dataset (p=0.05).  These genes were also independently analyzed and mapped to canonical pathways using Ingenuity Pathway Analysis (IPA) (Ingenuity Systems, Redwood City, CA; www.ingenuity.com).  The significance of association between the data set and the canonical pathways were calculated based on the ratio of the number of genes from the data set that map to the canonical pathway to the total number of genes in the pathway and expressed as negative log p value using Fisher’s exact test (www.ingenuity.com).

first: Cristina

last: Karp


title: Gene Expression Changes Induced by Bacterial Superantigen, Staphylococcal Enterotoxin B

city: Jacksonville

first: Yan

middle: W.

last: Asmann

state: FL

address: 4500 San Pablo Road South

institute: Mayo Clinic

summary: Toxic shock syndrome (TSS) is an acute, serious systemic illness caused by bacterial superantigens (BSAg). We characterized the early molecular events underlying TSS using our HLA-DR3 transgenic mouse model and studied gene expression profiling using DNA microarrays.

overall_design: HLA-DR3 transgenic mice were intraperitoneally treated with either PBS or bortezomib on days -1 and 0. On day 0, each treatment group was further divided in to two groups, one received 10 μg of endotoxin-reduced highly purified SEB and the other PBS alone thus making a total of 4 groups (i.e., PBS+PBS, bortezomib+PBS, PBS+SEB, bortezomib+SEB). Three hours later, mice were euthanized by CO2 asphyxiation, spleens were immediately collected and frozen in liquid nitrogen. Once all the animals had been sacrificed, total RNA from spleens was extracted

first: Govindarajan

last: Rajagopalan

first: Ashenafi

middle: Y

last: Tilahun

first: Chella

middle: S

last: David


title: Expression data from sorted follicle populations in the 2nd telogen to anagen transition.

city: New York

last: Rendl

state: NY

address: 1428 Madison Avenue

institute: Mount Sinai School of Medicine

summary:
Hair Follicle regeneration relies on both epithelial components (bulge and hair germ cells) and a mesenchymal one (dermal papilla cells).
We used microarrays to detail the global programme of gene expression underlying organ regeneration at the transition between quiescent stages (early and middle telogen) and the initiation of a new growth (late telogen).

overall_design: These microarray at the 3 different stages were designed to identify signals released by the mesenchymal dermal papilla cells to activate epithelial growth, their target genes in the hair germ and bulge compartments, and to get at gene signature differences and similarities between hair germ and bulge cells.

first: Valentina

last: Greco

first: Elaine

last: Fuchs


title: Phosphorylation of MeCP2 at Serine 80 regulates its chromatin association and neurological function

status: Public on Feb 10 2009

city: Los Angeles

first: Yi

last: Sun

state: CA

address: 635, Charles E. Young Dr. South

department: Molecular and Medical Pharmacology

institute: UCLA

summary: Mutations of MECP2 (Methyl-CpG Binding Protein 2) cause Rett Syndrome. As a chromatin associated multifunctional protein, how MeCP2 integrates external signals and regulates neuronal function remain unclear. While neuronal activity-induced phosphorylation of MeCP2 at serine 421 (S421) has been reported, the full spectrum of MeCP2 phosphorylation together with the in vivo function of such modifications are yet to be revealed. Here we report the identification of several novel MeCP2 phosphorylation sites in normal and epileptic brains from multiple species. We demonstrate that serine 80 (S80) phosphorylation of MeCP2 is critical as its mutation into alanine (S80A) in transgenic knock-in mice leads to locomotor deficits. S80A mutation attenuates MeCP2 chromatin association at several gene promoters in resting neurons and leads to transcription changes of a small number of genes. Calcium influx in neurons causes dephosphorylation at S80, potentially contributing to its dissociation from the chromatin. We postulate that phosphorylation of MeCP2 modulates its dynamic function in neurons transiting between resting and active states within neural circuits that underlie behaviors.

overall_design: E 15.5 Mecp2 -/y cortical neurons were infected with lentivirus expressing wild-type and S80A mutant MeCP2 at similar protein expression level. 2 biological independent samples and dye swap were used for this set (GSM367413) and replicate 2 set (GSM367414).

first: Jifang

last: Tao

first: Keping

last: Hu

first: Qiang

last: Chang

first: Hao

last: Wu

first: Nicholas

last: Sherman

first: Keri

last: Martinowich

first: Robert

last: Klose

first: Carolyn

last: Shanen

first: Rudolf

last: Jaenisch

first: Weidong

last: Wang


title: Role of p53 in mouse iPS cell generation

status: Public on Mar 01 2009

city: Kyoto

first: Shinya

last: Yamanaka

address: 53 Kawahara-machi, Shogoin, Sakyo-ku

institute: Center for iPS Cell Research and Applicaton (CiRA), Kyoto University

summary: We observed a marked increase in efficiency of iPS cell generation when p53 is deleted.

overall_design:
Gene expression patterns were compared between p53 wt MEF and p53-null MEF cells.
Gene expression patterns were also compared between ES cells and MEF.


title: Expression data from adipocytes and white adipose tissue of mice maintained on normal chow or high fat diet

status: Public on Mar 03 2009

city: La Jolla

first: Marc

last: Montminy

address: 10010 N. Torrey Pines Rd.

institute: The Salk Institute

summary:
We studied the role of the cAMP responsive factor CREB in promoting insulin resistance following its activation in adipose under obese conditions
We identified genes that were upregulated in primary cultures of mouse adipocytes following exposure to forskolin; and we characterized genes that are also induced in white adipose tissue in mice maintained on a  high fat diet.
Keywords: signaling study

overall_design: Primary cultures of mouse adipocytes,harvested from visceral adipose tissue,  were exposed to forskolin (10uM) or vehicle control (DMSO) for 2 hours.  White adipose tissue (epididymal fat pads) were collected from mice maintained on a 60% high fat diet  for 12 weeks and from control mice on normal chow.

first: Ling

last: Qi


title: Transcription factor Achaete scute-like 2 (Ascl2) controls intestinal stem cell fate

status: Public on Mar 13 2009

city: Dresden

first: Daniel

middle: E.

last: Stange

address: Fetscherstr. 74

institute: University Clinic Dresden

summary:
The small intestinal epithelium is the most rapidly self-renewing tissue of mammals. Proliferative cells are confined to crypts, while differentiated cell types predominantly occupy the villi. We recently demonstrated the existence of a long-lived pool of cycling stem cells defined by Lgr5 expression and intermingled with post-mitotic Paneth cells at crypt bottoms. We have now determined a gene signature for these so called Crypt Base Columnar (CBC) cells. One of the genes within this stem cell signature is the Wnt target Ascl2. Transgenic expression of the Ascl2 transcription factor throughout the intestinal epithelium induces crypt hyperplasia and de novo crypt formation on villi. Induced deletion of the Ascl2 gene in adult small intestine leads to disappearance of the CBC stem cells within days. The combined results from these gain- and loss-of-function experiments imply that Ascl2 controls intestinal stem cell fate.

Keywords: expression profiling

overall_design: For the stem cell signature we used cell fractions of intestines from Lgr5-EGFP-ires-CreERT2 mice, expressing GFP under the control of the Lgr5 promoter. RNA was isolated from two FACS sorted cell populations, one expressing GFP at high levels (GFPhi) and the other expressing GFP at low levels (GFPlo). For the analysis of Ascl2 target genes RNA was isolated from intestinal epithelial cells of Ah-Cre/Ascl2floxed/floxed animals and Ah-Cre/Ascl2floxed/wt control animals 3 and 5 days post induction. Differentially labelled cRNA from GFPhi and GFPlo cells from two different sorts (each combining three different mice) were hybridised on 4X44K Agilent Whole Mouse Genome dual colour Microarrays (G4122F) in two dye swap experiments, resulting in four individual arrays. For the Ascl2 target gene analysis we analyzed the 3 and 5 days PI experiments in two dye swap experiments, resulting in four individual arrays.

first: Laurens

last: van der Flier

last: van de Wetering

first: Hans

last: Clevers


title: Brd7, a novel PBAF-specific SWI/SNF subunit, is required for gene activation and repression in embryonic stem cells

status: Public on Apr 01 2009

first: Matthias

last: Kaeser

address: 10010 North Torrey Pines Road

department: RBIO-E

summary: The composition of chromatin remodeling complexes dictates how these enzymes control transcriptional programs and cellular identity. Here, we investigate the composition of SWI/SNF complexes in embryonic stem cells (ESCs). In contrast to differentiated cells, ESCs have a biased incorporation of certain paralogous SWI/SNF subunits, with low levels of Brm, BAF170 and ARID1B. Upon differentiation, the expression of these subunits increases, resulting in a higher diversity of compositionally distinct SWI/SNF enzymes. We also identify Brd7 as a novel component of the PBAF complex in both ESCs and differentiated cells. Using shRNA-mediated depletion of Brg1, we show that SWI/SNF can function as both a repressor and an activator in pluripotent cells, regulating expression of developmental modifiers and signaling components such as Nodal, ADAMTS1, Bmi-1, CRABP1 and TRH. Knock-down studies of PBAF-specific Brd7 and of a signature subunit within the BAF complex, ARID1A, show that these two sub-complexes affect SWI/SNF target genes differentially, in some cases even antagonistically. This may be due to their different biochemical properties. Finally, we examine the role of SWI/SNF in regulating its target genes during differentiation. We find that SWI/SNF affects recruitment of components of the pre-initiation complex in a promoter-specific manner, to modulate transcription positively or negatively. Taken together, our results provide insight into the function of compositionally diverse SWI/SNF enzymes that underlie their inherent gene-specific mode of action.

overall_design: R1 ESCs were infected in duplicates with shRNA targeting Brg1 or GLUT4 (as a control). Knockdown of Brg1 mRNA affected Brg1 protein levels efficiently. RNA was isolated 67 hours post-infection and analyzed using microarrays.

first: Aaron

last: Aslanian

first: Meng-Qiu

last: Dong

first: John

middle: R

last: Yates

first: Beverly

middle: M

last: Emerson


title: R1 mESC Exposed to Butyrate

status: Public on Mar 05 2009

city: Seattle

first: Brig

last: Mecham

state: WA

address: 1100 Fairview Ave N

institute: University of Washington

summary: To assess the effect of sodium butyrate exposure on mouse ESC grown without self-renewal support (I.e. without feeders or LIF) - these cells were compared to cells grown without sodium buytrate, but with added mouse LIF via Agilent whole mouse genome array

overall_design: R1 mESC were grown under 2 conditions, with mLIF on gelatin or without LIF on gelatin for 15 passages to compare change in the RNA profile

first: Carol

last: Ware

first: Anthony

last: Blau

first: Brigham


title: Effect of DEHP on adult mouse Sertoli cells rich areas (SCRA)

status: Public on Feb 19 2009

city: Villenave d'Ornon

first: Pascal

middle: GP

last: Martin

address: 71 avenue Edouard Bourlaux

department: UMR1332 BFP

country: France

institute: INRAE

summary:
BACKGROUND: Phthalates are manmade industrial additives used mostly as plasticizers. In addition to their deleterious effects on male genital development, population studies have recently documented correlations between phthalates exposure and subtle impacts on reproductive tract development and on the metabolic syndrome in male adults. In mature rodents liver di-(2-ethylhexyl)-phthalate (DEHP) activates the peroxisome proliferators-activated receptor (PPARalpha), a member of the nuclear receptor (NR) superfamily.  OBJECTIVES: Using a systems biology approach, we aimed at defining potential mechanisms underlying the impacts of DEHP on adult mouse liver and testis.  METHODS: Thus, we performed a parallel analysis of transcript and metabolic profiles in the liver from adult mice exposed to varying DEHP doses. Moreover, we obtained pangenomic mRNA profiles of laser-captured Leydig and Sertoli cells from mature animals exposed to DEHP.  RESULTS: Hepatic genes modulated by DEHP are predominantly PPARalpha targets. However, the induction of some prototypic cytochrome P450 genes strongly supports the activation of additional NR pathways. Integration of hepatic transcriptomic and metabonomic profiles further revealed a correlation between the impacts of DEHP on a cluster of genes and metabolites linked to heme synthesis and on a cluster of Rev-erbalpha target genes related to metabolic and circadian clock pathways. Cell-specific effects of DEHP were investigated in the adult testis and a noticeable impact of DEHP was observed on Leydig cells transcriptome.  CONCLUSIONS: We report a detailed analysis of DEHP interference with hepatic Constitutive Androstane Receptor (CAR) and Rev-erbalpha pathways and a novel transcriptional impact of DEHP on adult endocrine cells of the testis.

Keywords: Treatment effect

overall_design: two condition experiment, Sertoli cells-rich areas from DEHP-treated mice vs. Sertoli cells-rich areas from vehicle-treated mice. Biological replicates: 4 DEHP-treated samples and 4 vehicle-treated samples. Dye-swap design. N=4 DEHP-treated vs vehicle-treated x 2 microarrays (dye-swap)=8 microarrays

first: Alexandre

last: Eveillard

first: Frédéric

last: Lasserre

first: Thierry

last: Pineau


title: Effect of DEHP on adult mouse

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

overall_design: Refer to individual Series


title: Effect of DEHP on adult mouse Leydig cells

overall_design: two condition experiment, Leydig cells from DEHP-treated mice vs. Leydig cells from vehicle-treated mice. Biological replicates: 2 DEHP-treated samples and 3 vehicle-treated samples. Each treated sample has been hybridized against each vehicle-treated sample in a dye-swap design. N=2 DEHP-treated x 3 vehicle-treated x 2 microarrays=12 microarrays


title: Effect of p53 on iPS cell generation

first: Shinya

last: Yamanaka

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus


title: Cell autonomous roles for AP-2alpha in lens vesicle separation and maintenance of the lens epithelial cell phenotype.

status: Public on Jan 24 2009

city: LYON

first: Jiri

last: ZAVADIL

state: Other

address: 150 COURS ALBERT THOMAS

institute: IARC WHO

summary:
This is a comparative microarray analysis of LE-AP-2a mutants vs. wild-type P0 littermate lenses.
This analysis revealed differential gene expression of 415 mRNAs, including reduced expression of genes important for maintaining lens epithelial cell phenotype, such as E-cadherin.

Keywords: Differential gene expression

overall_design: Biological triplicates of mouse lenses were analyzed (three wild-type lens samples and three Le-AP-2 mutant samples)

first: Giuseppe

middle: F

last: Pontoriero

first: Paula

last: Deschamps

first: Ruth

last: Ashery-Padan

first: Ryan

last: Wong

first: Ying

last: Yang

last: Zavadil

first: Ales

last: Cvekl

first: Shelley

last: Sullivan

first: Trevor

last: Williams

first: Judith

last: West-Mays


title: ESC Exposed to Butyrate

first: Brig

last: Mecham


title: Effects of psychological stress on gene expression in the mouse rectum.

status: Public on Feb 14 2009

city: Tokushima

first: Tomoko

last: Kawai

address: 3-18-15 Kuramoto-cho

department: Stress Science

institute: Institue for Health Biosciences, The University of Tokushima Graduate School

summary: Using isolation stress model, we showed that goblet cell-dependent mucosal barrier functions in the mouse rectum was more vulnerable to stress than the colon. We also found that isolation stress specifically stimulated IL-18 production only in the rectum. Furthermore, the crucial role of IL-18 in the stress response of the mouse rectum was confirmed using IL-18 knockout mice. Microarray analysis was used to assess the stress response and to identify responsible genes for the vulnerability of the mouse rectum to isolation stress.

overall_design: Total RNA was prepared from the colon and the rectum of wild-type and IL-18 knockout mice before isolation and 8 days after starting isolation. The one GSM sample of microarray analysis was made by pooling an equal amount of total RNA 5 mice of each group. Agilent whole mouse genome oligonucleotide microarray was used to measure gene expression in these samples according to the manufacture’s protocol.

first: Kensei

last: Nishida

first: Mai

last: Kamizato

first: Keiko

last: Takeo

first: Kiyoshi

last: Masuda

first: Shigetada

last: Teshima-Kondo

first: Atsuo

last: Sekiyama

first: Kazuhito

last: Rokutan


title: Lacrimal Gland Gene expression in Aromatase Knockout Mice and Wild Type Controls

status: Public on Feb 01 2009

city: Boston

first: David

address: 20 Staniford Street

institute: Schepens Eye Research Institute

summary:
The Effect of Aromatase Knockout on Gene Expression in the Mouse Lacrimal and Meibomoan Gland.
Keywords: Aromatase Knockout vs Wild Type Control

overall_design: Lacrimal and meibomian glands were harvested from homozygous male and female aromatase knockout mice and age matched wild type controls. Tissues were pooled into 3 biological replicates and were hybridized to separate microarrays.  Each cRNA prep was hybridized to a GE Healthcare/Amersham Biosciences CodeLink UniSet Mouse 20K I Bioarray and a Affymetrix GeneChip Mouse Expression Array 430A.

first: T

last: Suzuki

first: S

last: Richards

first: R

middle: V

last: Jensen

first: D


title: Microarray Analysis of Hepatic Genes Differentially Expressed in the Presence of the Maslinic Acid in Olive Oil

status: Public on Jan 20 2009

city: Zaragoza

first: Jesus

last: Osada

address: Miguel Servet, 177

country: Spain

institute: Universidad de Zaragoza

summary:
Two olive oils only differing in the presence of maslinic acid were prepared. Using DNA microarrays, hepatic gene expression was analysed in apoE-deficient mice with a C57BL/6J genetic background
Keywords: diet study

overall_design:
The experimental animals were 12, two-month old, female, homozygous apoE KO mice with a C57BL/6J genetic background.
Two study groups were established: a) one received a chow diet (Teklad Mouse/Rat Diet no. 2014, Harlan Teklad, Harlan Ibérica, Barcelona, Spain) supplemented with 10% (w/w) olive oil (diet OO) (n=6), and b) the other received the same chow diet but supplemented with 10% (w/w) maslinic acid- enriched olive oil (diet MAOO; n= 6 and).

first: Natalia

last: Guillen

first: Sergio

last: Acín

first: Joaquín

middle: C

last: Surra

first: Andrés

last: García-Granados

first: Valentina

last: Ruiz-Gutiérrez

first: Jesús


title: Impact of IL-10 pulmonary gene expression in mouse M. tuberculosis infection

status: Public on Jan 08 2009

city: Erlangen

first: Roland

last: Lang

address: Wasserturmstr. 3-5

institute: University Hospital Erlangen

summary:
The cytokine IL-10 deactivates macrophages and has been shown to impair resistance to mycobacterial infection. We have infected transgenic mice overexpressing IL-10 under control of the macrophage-specific CD68 promoter (macIL-10tg mice) with Mycobacterium tuberculosis by aerosol and found increased bacterial loads in the lungs of macIL-10tg mice.
To identify programs of genes regulated by IL-10 and associated with increased mycobacterial replication, genome-wide expression analysis was performed.

Keywords: Effect of infection; effect of genotype; timecourse

first: Christoph

last: Hölscher


title: Comparison of CpG and TDB induced activation patterns in macrophages.

city: Munich

first: Joerg

last: Mages

address: Trogerstrasse 30

department: Institute of Medical Microbiology, Immunology and Hygiene

institute: Technical University Munich

summary:
Bone marrow derived macrophages 1 µM CpG or 20 µg/ml TDB, an analogon to the mycobacterial cord factor TDM for 8h, 24h, 48h and 72h respectively.
Keywords: CpG, TDB, macrophage, time series

overall_design: time series; 8h, 24h, 48h and 72h CpG or TDB

first: Jörg

first: Anna

last: Babiak

first: Angela

last: Servatius


title: Gene expression profiling of peripheral blood and alveolar recruited mononuclear phagocytes in Pam3CSK4 treated mice

status: Public on Jan 01 2009

city: Giessen

first: Jochen

last: Wilhelm

address: Gaffkystrasse 10

department: ECCPS Microarray Unit

institute: Uniklinikum Giessen

summary: Aim of this project was to examine the global gene expression profiles of mononuclear phagocytes recruited from peripheral blood to the alveolar space following alveolar deposition of the TLR2-ligand Pam3CSK4 in transgenic CX3CR1+/GFP mice.

overall_design: Alveolar macrophages (AM) and peripheral blood monocytes (PBM) were isolated from broncho-alveolar lavages and from blood, respectively, using FACS. Expression profiles from AM and PBM of the same mice were compared on the same slides. Each labeled RNA sample contained RNA pooled from six individuals. Four pairs of RNA from corresponding AM and PBM pools were hybridized, giving a total amount of 24 individual mice analyzed. Two hybridizations were performed with AM labeled with Cy3 and PBM with Cy5, two hybridizations were performed with swaped dyes.

first: Maciej

last: Cabanski

first: Mirko

last: Steinmüller

first: Ludger

last: Fink

first: Werner

last: Seeger

first: Jürgen

last: Lohmeyer


title: Lung Trafficking of Macrophages

summary: Trafficking of monocytes into lung tissue and their differentiation into lung resident macrophages and dendritic cells is supposed to be regulated by the expression of specific gene clusters, which promote cell-cell interaction, migration and matrix degradation and the acquisition of tissue specific cellular phenotypes. Traffic related gene clusters include chemokines, integrins, and tissue-degrading matrix metallopeptidases, for all of which members have been shown to be functionally important. A complete picture, however, of the gene clusters that are regulated during in vivo migration and differentiation of peripheral blood monocytes under non-inflammatory conditions has not been obtained yet. Currently, adaptive changes of cellular phenotypes cannot be directly assessed by cell fate mapping during the slow trafficking of mononuclear phagocytes to lung tissue under steady-state conditions. Therefore, as an alternative approach to gain a better insight into the genetic programs that drive the mononuclear phagocyte migration and differentiation processes, the transcriptomes of circulating monocytes were compared with their lung tissue mononuclear phagocyte progeny.

overall_design: A total of 32 animals were used in this study. From each Animal, Monocytes, Macrophages and dendritic cells were isolated. Cells were sorted from blood-free lungs and peripheral blood. In order to get enough RNA for a labeling reaction, RNA of each 4 of these animals was pooled (same amount of RNA per animal). The different pools were subjected to microarray analysis comparing Monocytes, Macrophages and Dendritic Cells in a ring design with 4 hybridizations per comparison. There were 8 different pools per cell type, 4 of which were labeled with Cy3 and the other 4 were labelled with Cy5 (balanced dye-swap). Each possible combination of cell types was compared with 4 hybridizations, resulting in a total number of 12 hybridizations. Each hybridization used RNA from different animals. In each of these comparisons, each cell type was labelled twice with Cy3 and twice with Cy5.

first: Zbigniew

last: Zasłona

first: Lidija

last: Cakarova

first: Leigh

last: Marsh

last: von Wulffen


title: PKGI WT vs KO BAT

status: Public on Dec 31 2008

city: Bonn

first: Peter

last: Mayer

address: Kurt-Georg-Kiesinger-Allee

institute: Fed. Inst. for Drugs and Med. Devices

summary: Brown adipose tissue (BAT) and brown adipocytes differentiated in vitro from preadipocytes of PKGI-/- mice vs. WT were compared on a whole genome DNA array

overall_design:
Two dual-channel chip hybridization experiments were performed, one comparing BAT tissue from a PKGI-/- mouse with BAT tissue from a wild type littermate, and the other comparing brown adipocytes derived from preadipocytes of a PKGI-/- and a WT littermate mouse.
Biological replicates were included in the experiments but were not hybridized on a chip. Instead, chip results were verified by quantitative Real-Time PCR in all biological replicates.

first: Bodo

last: Haas

first: Katja

last: Jenissen

first: Wilhelm

last: Bloch

first: Stefan

last: Herzig

first: Reinhard

last: Fässler

first: Alexander

last: Pfeifer


title: IL-6 induced changes in gene expression in activated mouse CD4+ T cells

status: Public on Jan 17 2009

city: Burlington

first: Mercedes

last: Rincon

state: VT

address: 89 Beaumont Ave., Given D305

department: Medicine/Immunobiology program

institute: University of Vermont

summary:
IL-6, a proinflammtory cytokine produced by antigen presenting cells and non-hematopoietic cells in response to external stimuli, acts as an important bridge between the innate and adaptive immune responses. IL-6 together with IL-4 can promote Th2 polarization, while in combination with TGFbeta mediates Th17 differentiation. We examined early changes in gene expression in mouse CD4+ T cells induced by IL-6.
Keywords: adaptive immune response

overall_design: Cells from spleen and lymph nodes of B10.BR wild type mice (Jackson Laboratory, Bar Harbor, Maine) were purified by negative selection to deplete CD8+, MHC II+, NK1.1+ and CD11b+ cells. Further purification was done by FACS-sorting into a NK1.1-CD4+ T cell population (>99% purity). Cells from three independent preparations (from 2 mice each) were split in half, activated with plate-bound anti-CD3 (5 ug/ml) and soluble anti-CD28 (1 ug/ml) in the absence or presence of recombinant mIL-6 (100 ng/ml; R&D Systems). After 16 h, total RNA was prepared using the RNAeasy Mini Kit (Qiagen) including a DNaseI-digestion step according to the manufacturer's protocol.

first: Oliver

last: Dienz

first: Jeffrey

last: Bond

first: Sheri

last: Eaton

first: Eva

last: Briso de Montiano

first: David

last: Moquin

first: Colette

last: Charland

first: Warren

middle: J

last: Leonard

first: Laura

last: Haynes


title: Transcription profile of CD103- vs CD103+ dendritic cells derived from CX3CR1+c-kit+- bone marrow cells (M1993 M2067)

status: Public on Dec 17 2008

city: Hannover

last: Dittrich-Breiholz

address: Carl-Neuberg-Str. 1

department: Research Core Unit Genomics

institute: Medical School Hannover

summary:
We hypothesize that under homeostatic as well as inflammatory conditions circulating monocytes and/or their bone marrow-derived progenitors might contribute to the replenishment of CD103+ and CD103- DC in lymphoid and non-lymphoid compartments. To that end, bone marrow cells from CX3CR1+/gfp C57BL/6 mice were sorted as follows: lineage negative (CD3, CD19, NK1.1, Ter119, Ly6G and CD11c) CX3CR1+c-kit+. Sorted cells were further cultured in vitro under the continuous presence of GM-CSF. lin-CX3CR1+c-kit+ bone marrow cells gave rise to CD103+ and CD103- DC in vitro. To test whether CD103 might be a suitable marker that allows the differentiation of functionally distinct DC subsets generated in vitro, CD11c+CD103+ and CD11c+CD103- DC were sorted from day 5 cultures of lin-CX3CR1+c-kit+ cells and analyzed by whole mouse genome microarrays from Agilent technologies. Compared to CD103+ DC, CD103- DC displayed a strong up-regulation of transcripts for genes involved in innate immunity, whereas those involved in costimulation were down-modulated. Our data suggest distinct functional activity of these two DC subsets.
Keywords: Transcriptional profiling-Cell type comparison

overall_design: We compared the transcriptional profile of CD11c+CD103+ and CD11c+CD103- dendritic cells by use of Agilent Whole Mouse Genome Microarrays. Two sets of samples were generated independently as real biological replicates. The microarray analysis was performed as a dual-color experiment, including a dye-swap.

first: Maria

middle: L

last: del Rio

first: Jose-Ignacio

last: Rodriguez-Barbosa

first: Jasmin

last: Bölter

first: Matthias

last: Ballmaier

first: Michael

last: Kracht

first: Steffen

last: Jung

first: Reinhold

last: Förster


title: AhR activation by TCDD in the ET, cortical epithelial cell line

city: Duesseldorf

first: Markus

last: Frericks

address: Auf'm Hennekamp 50

department: Immunology

institute: Institute for Environmental Research

summary:
Over activation of the aryl hydrocarbon receptor (AhR) by TCDD results ampng other phenotypes in severe thymic atrophy accompanied by immunosuppression. The link between thymic atrophy, skewed thymocyte differntiation and immunosuppression is still not fully resolved. This study investigates the TCDD elicted exprssion changes in the ET, cortical thymus epithelial cell line.
Keywords: TCDD, AhR, thymic epithelial cells, thymic involution, thymus atrophy

overall_design: ET cells were grown to 80-90% confluence and treated with 5nM TCDD or solvent control (1,4-Dioxane, 0,05%V). 2h,4h and 6h after treatment, RNA was isolated using TRIzol and gene expression measured. All experiments wer done in biological duplicates.

first: Lyle

last: Burgoon

first: Tim

last: Zacharewski

first: Charlotte

last: Esser


title: Expression profiling of thymic lymphomas from p53 mutant (R270H) mice with varying HIF levels

status: Public on Jan 12 2009

city: Philadelphia

first: M. Celeste

last: Simon

address: 421 Curie Blvd.

institute: University of Pennsylvania

summary:
Expression profiling of thymic lymphomas derived from HIF1a+/+, p53R270H/R270H; HIF1a+/-, p53R270H/R270H; and HIF1aKI/+, p53R270H/R270H mice.

HIF1a and HIF2a share a high degree of sequence homology, but recent work has shown that the two a subunits can have contrasting and tissue-specific effects on tumor growth. To directly compare the role of each HIFa subunit in spontaneous tumorigenesis, we bred a mouse model of expanded HIF2a expression and Hif1a+/- mice to homozygotes for the R270H mutation in p53.  Heterozygosity for Hif1a significantly reduced the incidence of thymic lymphomas observed in this model. Moreover, reduced Hif1a levels correlated with decreased stabilization of activated Notch1 and expression of the Notch target genes, Dtx1 and Nrarp.

Keywords: genetic modification, disease state analysis

overall_design: Thymic lymphoma tissue was preserved at the time mice were sacrificed. 4-5 samples from each of 3 genotypes (HIF1a+/-, p53R270H/R270H, HIF1aKI/+; p53R270H/R270H; and HIF1a+/+, p53R270H/R270H) were then used for microarray analysis to identify differences in gene expression that could account for changes in tumor onset and incidence.

first: Simon

last: M. Celeste


title: Macrophage response to silica nanoparticles

status: Public on Dec 11 2008

city: Richland

first: Katrina

last: Waters

address: 902 Battelle Blvd; MSIN J4-18

department: Biological Sciences Division

institute: Pacific Northwest National Laboratory

summary:
Using a macrophage cell line, we demonstrate the ability of amorphous silica particles to stimulate inflammatory protein secretion and induce cytotoxicity.  Whole genome microarray analysis of early gene expression changes induced by 10nm and 500nm particles showed that the magnitude of change for the majority of genes correlated more tightly with particle surface area than either particle mass or number.  Gene expression changes that were size-specific were also identified, however the overall biological processes represented by all gene expression changes were nearly identical, irrespective of particle diameter.  Our results suggest that on an equivalent nominal surface area basis, common biological modes of action are expected for nano- and supranano-sized silica particles.

Keywords: Dose-response study

overall_design: RAW 264.7 mouse macrophage cells were treated with two sizes of amorphous silica particles at three doses each for 2 hours.  Cells were exposed to 10nm silica at 5 (low), 20 (mid), or 50 (high) ug/ml or 500nm silica at 250 (low), 500 (mid), or 1000 (high) ug/ml in serum-free medium.

first: Brian

last: Thrall


title: Expression profiling of normal murine lymphoid progenitors and MLL-AF4 leukemic lymphoblasts

status: Public on Nov 04 2008

city: Plantagenet

first: Madeleine

last: Lemieux

state: ON

address: 275 Main St., Suite 252

institute: Bioinfo

summary:
We created a mouse model where conditional expression of physiologic levels of an Mll-AF4 fusion oncogene induces development of acute lymphoblastic (ALL) or acute myeloid leukemias (AML). Immunophenotypic and gene expression analysis of the ALL cells demonstrated bone marrow replacement with B-precursor cells which express a gene expression profile that has significant overlap with profiles in human MLL-rearranged ALL.

Keywords: Cell type comparison

overall_design: Total RNA from normal pro-B, pre-B, immature B and mature B lymphocytes, and from leukemic pre-B cells was isolated and hybridized to Affymetrix expresison microarrays.

middle: E


title: Gene Expression in MEFs Trisomic for Chromosomes 1, 13, 16 and 19

status: Public on Nov 05 2008

city: Cambridge

first: Charles

middle: Arthur

last: Whittaker

institute: Koch Institute

summary:
Aneuploidy, an incorrect chromosome number, is the leading cause of miscarriages and mental retardation in humans and is a hallmark of cancer. We examined the effects of aneuploidy on primary mouse cells by generating a series of cell lines that carry an extra copy of one of four mouse chromosomes. In all four trisomic lines proliferation was impaired and metabolic properties were altered. Immortalization, the acquisition of the ability to proliferate indefinitely, was also affected by the presence of an additional chromosome, with some chromosomes inhibiting immortalization while others accelerating the process. Our data indicate that aneuploidy decreases not only organismal but also cellular fitness and elicits traits that are shared between different aneuploid cells.

Keywords: cell type comparison

overall_design: The mRNAs from 9 different mouse embryo fibroblast (MEF) lines with a normal complement of chromosomes were compared to mRNAs from 1 MEF line with three copies of chromosome 1, 4 MEF lines with three copies of chrmosome 13, 3 MEF lines with three copies of chromosome 16 and 1 MEF line with three copies of chromosome 19.

first: Bret

last: Williams

first: Vineet

last: Prabhu

first: Karen

last: Hunter

first: Christina

last: Glazier

middle: A

first: David

last: Housman

first: Angelika

last: Amon


title: Rb1 deficient Apc1638N cecal tumors vs duodenal tumors

status: Public on Oct 24 2008

first: Dmitriy

last: Sonkin

address: 250 Massachusetts Avenue

institute: Novartis Institutes for BioMedical Research

summary: To examine the role of Rb1 in gastrointestinal (GI) tumors we generated mice with an Apc1638N allele, Rbtm2brn floxed alleles, and a villlin-cre transgene (RBVCA). These mice had reduced median survival due to an increase in tumor incidence and multiplicity in the cecum and the proximal colon; they differed from murine intestinal tumors of the Apc1638N type which normally arise solely in the small intestine. We have examined by micro-array analysis three cecal tumors from these mice (probable adenomas), and compared them to three duodenal tumors (probable adenocarcinomas). Expression profiles of duodenal and cecal tumors relative to each other show unique gene subsets up and down regulated. The two tumor types were subsequently shown to differentially regulate distinct sets of genes over expressed in a majority of human colorectal carcinomas.

overall_design: We have compared 3 cecal tumors with 3 duodenal tumors from Rb1 deficient Apc1638N mice.

first: Melanie

last: Kucherlapati

first: Kan

last: Yang

first: Kunhua

last: Fan

first: Mari

last: Kuraguchi

first: Andrew

last: Rosulek

first: Martin

last: Lipkin

first: Roderick

middle: T

last: Bronson

first: Bruce

last: Aronow

first: Raju


title: Identification of Pax6-dependent gene regulatory networks in the mouse lens

status: Public on Oct 17 2008

first: Jiri

last: ZAVADIL

summary:
This is an integrative genome-wide approach to identify downstream networks controlled by Pax6 during mouse lens and forebrain development.
Differential gene expression was analyzed in Pax6 mouse heterozygous and wildtype newborn mouse lenses, with subsequent comparison of  this data  with Pax6 forebrain expression data (Holm et al., 2007).

Keywords: Differential gene expression

overall_design: Three biological replicate experiments were performed from wildtype and heterozygote mice.

first: Louise

last: Wolf

first: Ying

first: Jinhua

last: Wang

first: Qing

last: Xie

first: Barbara

last: Braunger

first: Ernst

last: Tamm

last: Zavadil

first: Ales

last: Cvekl


title: PDGF-B induces a homogeneous class of oligodendrogliomas from embryonic neural progenitors

status: Public on Nov 28 2008

city: Genoa

first: Paolo

last: Malatesta

address: Largo Rosanna Benzi 10

institute: IRCCS Ospedale Policlinico San Martino

summary: We analyzed the generation of mouse gliomas following the overexpression of PDGF-B in embryonic neural progenitors. Comparison of our microarray data, with published gene expression data sets for many different murine neural cell types, revealed a closest relationship between our tumor cells and oligodendrocyte progenitor cells, confirming definitively that PDGF-B-induced gliomas are pure oligodendrogliomas.

overall_design:
Sorted cultures of GFP-positive cells from 3 independent tumors were harvested with Trizol (Invitrogen) and used for further processing. RNA extraction and microarray hybridization procedure were performed at the “Consorzio Genopolis” (University of Milano-Bicocca, Dept. of Biotechnology and Bioscience) using the Affymetrix GeneChip Mouse Genome 430A 2.0 Array. Files containing the raw data from the study published by Cahoy and collegues 28, using the Affymetrix GeneChip Mouse Genome 430 2.0 Array, were retrieved at the NCBI GEO DataSets online repository (GSE9566 record). Data were analyzed using the R software and BioConductor version 2.2 29. Only the probesets common to both platforms were used for the comparison. Expression values were extracted from both our and public raw data files using the RMA method built in the affy 1.18.2 package without prior normalization and collected in a single data set. Probe level quantile normalization method provided by the affyPLM 1.16.0 package was then used to normalize the dataset. The probesets where then ranked based on the variance of their expression level across the different cell types and the uppermost 5% (1135 probesets with highest variance) were selected and used to produce a hierarchical clustering of the samples. Hierarchical clustering was obtained using hclust method with complete linkage and euclidean distance in R.

The following Sample from GSE9566 were analyzed:
GSM241889 OLs (GC_b)
GSM241890 Myelin OLs (MOG_b)
GSM241891 OLs (GC_a3)
GSM241892 OLs (GC_c)
GSM241893 Myelin OLs (MOG_a2)
GSM241894 Myelin OLs (MOG_c)
GSM241895 OPCs (PDGF)
GSM241896 Neurons P16 (10d)
GSM241897 Neurons P16n (11d)
GSM241898 Astros P7 (5a)
GSM241899 Neurons P7 (5b)
GSM241900 Astros P7 (6a)
GSM241901 Neurons P7 (6b)
GSM241902 Astros P8 (7a)
GSM241903 Neurons P7 (8b)
GSM241904 Neurons P16 (13b)
GSM241912 Astros P17 (22a)
GSM241914 Astros P17 (24a)
GSM241915 Astros P17g (25g)
GSM241916 OPCs (30o)
GSM241917 OLs (30p)
GSM241918 Myelin OLs (30q)
GSM241919 Astros P30 (33a)
GSM241920 Astros P1 (34a)
GSM241922 Neurons P7n (38B)
GSM241925 Astros P17g (36g)
GSM241926 Astros P17 (32a)


title: Tlx (nr2e1)-dependent gene expression in adult neural stem cells

status: Public on Dec 01 2008

city: Dallas

first: Chun-Li

last: Zhang

address: 6000 Harry Hines Blvd

institute: UT Southwestern

summary:
Tlx (nr2e1) is an orphan nuclear receptor that is highly expressed in proliferating neural stem cells (NSCs) in the adult mouse forebrain. The goal was to identify Tlx-regulated genes in this specific cell population. Two populations of Tlx-positive neural stem cells were isolated from 2-month-old male mice based on a LacZ marker that was knocked into the Tlx locus. The first population, Tlx(f/Z;CreER), contains a floxed allele of Tlx (f), the LacZ marker (Z), and a CreER fusion transgene. Addition of tamoxifen (4OH-tamoxifen) into this NSC population leads to Cre-mediated deletion of the floxed allele of Tlx. The second NSC population, Tlx(f/Z), does not contain a CreER transgene; thus it does not respond to tamoxifen treatment and was used as a control.
Keywords: Nuclear receptor-dependent gene expression

overall_design: Total RNA samples from two biological replicates were collected at 36 hr or at 60 hr after tamoxifen or vehicle treatment. Total of 16 samples were used to analyze the global gene expression changes using Affymetrix chips.

first: Yuhua

last: Zou

first: Ronald

last: Evans

first: Fred

middle: H

last: Gage


title: Regulation of lymphoid versus myeloid fate choice by Mef2c

status: Public on Nov 21 2008

first: Fernando

last: Camargo

address: 9 Cambridge Center

institute: Whitehead Institute

summary: Despite recent advances in the identification of lymphoid-restricted progenitors, the transcription factors essential for their generation remain to be identified. Here we describe an unexpected role for the myeloid oncogene Mef2c in multipotent progenitors (MPPs), where it is required for pan-lymphoid differentiation. Mef2c deficiency was associated with profound defects in B, T, NK cell and common lymphoid progenitor production and an enhanced myeloid output. Mef2c deficiency in MPPs leads to downregulation of several key lymphoid regulators and the upregulation of the myeloid factor C/EBPa. Our studies also show that Mef2c is a critical transcriptional target of PU.1 during lymphopoiesis. Thus, Mef2c is a crucial component of the transcriptional network that regulates lymphoid specification and cell fate choice in MPPs.

overall_design: Expression profiles of multipotent progenitor cells (MPPs) from Mef2c deficient (Mx1-Cre Mef2cf/f  ) mice where compared to MPPs from control (Mef2cf/f  ) mice in triplicate.

first: Sandra

last: Stehling-Sun

middle: D


title: Gene expression profiling of IL-18 stimulated, in vitro differentiated mouse mucosal mast cells (MMC)

status: Public on Sep 26 2008

city: Budapest

first: Zoltan

last: Wiener

address: Nagyvarad ter 4.

department: Dept of Genetics, Cell- and Immunobiology

country: Hungary

institute: Semmelweis University

summary:
The aim of the present study was to clarify the role of IL-18 in mouse mast cell functions. Mouse mucosal mast cells (Balb/c) were differentiated in the presence of IL-3 (5 ng/ml), SCF (40 ng/ml), IL-9 (10 ng/ml) and human TGFbetaI (2 ng/ml) for >4 weeks. Cells were then stimulated by 100 ng/ml IL-18 for 2 hours to monitor the direct effect of IL-18. Treated samples were compared to the untreated ones in a paired experimental setting.

Keywords: expression microarray, mast cell, IL-18

overall_design: Four biological replicates were included. IL-18 stimulated samples were labelled by Cy5 and the control ones by Cy3. We used the paired experimental setting: each treated sample was compared to its appropriate control.

first: Andras

last: Falus

first: Eva

last: Gorbe


title: Effects of CaMKIV loss on cocaine-induced gene expression in the striatum

status: Public on Sep 10 2008

city: Heidelberg

first: Jan

last: Rodriguez Parkitna

address: Im Neuenheimer Feld 581

institute: German Cancer Research Center

summary:
Ablation of the Camk4 gene in dopaminoceptive neurons of the brain was performed using the Cre/loxP system, with the recombinase expressed from a BAC-derived Drd1a promoter.
Our goal was to analyze how loss of CaMKIV will affect acitivity-regulated transcription induced by strong stimulation, i.e. cocaine.
Keywords: Treatment x Genotype

overall_design: Animals were injected i.p. with either 25 mg/kg cocaine or saline and sacrificed after one hour by cervical dislocation. Expression profiling was performed using total RNA isolated from the striatum.


title: H3K79 methylation profiles define murine and human MLL-AF4 leukemias

first: Madeleine

last: Lemieux

type: Genome binding/occupancy profiling by genome tiling array

summary:
We created a mouse model where conditional expression of physiologic levels of an Mll-AF4 fusion oncogene induces development of acute lymphoblastic (ALL) or acute myeloid leukemias (AML). Immunophenotypic and gene expression analysis of the ALL cells demonstrated bone marrow replacement with B-precursor cells which express a gene expression profile that has significant overlap with profiles in human MLL-rearranged ALL.

This SuperSeries is composed of the SubSeries listed below.

overall_design: Refer to individual Series


title: Attenuated upregulation of GABAergic markers in response to BDNF in neurons lacking Xbp1

status: Public on Sep 25 2008

city: Wako

first: Kazuya

last: Iwamoto

address: 2-1 Hirosawa

department: Brain Science Institute

institute: RIKEN

summary:
XBP1 is a transcription factor that is induced by unconventional splicing associated with endoplasmic reticulum stress and plays a role in development of liver and plasma cells. We previously reported that brain derived neurotrophic factor (BDNF) leads to splicing of XBP1 mRNA in neurites, and that XBP1 is required for BDNF-induced neurite extension and branching. To search for the molecular mechanisms of how XBP1 plays a role in neural development, comprehensive gene expression analysis was performed in primary telencephalic neurons obtained from Xbp1 knockout mice at embryonic day 12.5. By searching for the genes induced by BDNF in wild type neurons but this induction was reduced in Xbp1 knockout mice, we found that upregulation of three GABAergic markers, somatostatin (Sst), neuropeptide Y (Npy), and calbindin (Calb1), were compromised in Xbp1 knockout neurons. Attenuated induction of Npy and Calb1 was confirmed by quantitative RT-PCR. In neurons lacking in Xbp1, upregulation of GABAergic markers was attenuated.  Impaired BDNF-induced neurite extension in Xbp1 knockout neurons might be mediated by disturbed BDNF-induced differentiation of GABAergic interneurons.
Keywords: time-cource, genetic modification

overall_design:
Brain derived neurotrophic factor (BDNF) effect examined in telencephalon primary cultures from Xbp1 knockouts and wild-type controls.
Two female Xbp1 +/- mice were mated with male Xbp1 +/- mice, and at embryonic day 12.5 (E12.5) the embryos were dissected. Among the 25 embryos obtained from the 2 pregnant female mice, 6 were genotyped as Xbp1 -/- and 4 were Xbp1 +/+ by a rapid PCR assay using Z-Taq. Telencephalon was dissected from each embryo, and treated with collagenase and trypsin. Six Xbp1 -/- telencephalon samples and 4 Xbp1 +/+ samples were collected together, respectively. Each sample was divided into 15 aliquots, and the cells were subject to low density culture on plastic culture dishes. The neurons were maintained in a serum-free medium (Neurobasal medium supplemented with 0.5 mM glutamine and B27 supplement [Invitrogen]). On the third day in vitro (3 DIV) , neurons in 10 of 15 dishes in each group were stimulated with BDNF (100 ng/ml). On 4 DIV, neurons in 5 dishes stimulated with BDNF (24 hours BDNF treatment) and 5 dishes with no stimulation (0 hour) were lysed to extract total RNA. On 5 DIV, neurons in 5 dishes stimulated with BDNF (48 hours BDNF treatment) were lysed.
Total RNA was extracted using RNAeasy Micro Kit (Qiagen, Hilden, Germany) according to the protocol provided by the manufacturer. The quantity and quality of RNA were measured using NanoDrop ND-1000. Biotin-labeled cRNA for DNA microarray analysis was synthesized using Two Cycle cDNA Synthesis and IVT labeling Kit. The integrity of the cRNA samples was verified using Test3 Array. Each biotin-labeled cRNA sample from one dish was hybridized to a single Affymetrix GeneChip Mouse Genome 430A 2.0 Array, and totally 30 arrays were used. The hybridization signal on the chip was scanned using an HP GeneArray scanner and processed by MAS5. After imported into GeneSpring software, data normalization was performed by dividing each microarray data set by its median value. Probes called as present in at least half of the 30 samples were selected.

first: Akiko

last: Hayashi

first: Takaoki

last: Kasahara

first: Mizue

last: Kametani

first: Tadafumi

last: Kato


title: Cardiac samples from OTT1 null/null and OTT1 null/wt embryonic mice

status: Public on Oct 01 2008

first: Jonathan

middle: Lee

last: Jesneck

address: 7 Cambridge Center

department: Cancer Program

institute: Broad Institute

summary: The infant leukemia-associated gene, Ott1(Rbm15), has broad regulatory effects within the murine hematopoiesis. However, germline Ott1 deletion  results in fetal demise prior to E10.5, indicating additional developmental requirements for Ott1. The spen gene family, to which Ott1 belongs, has a transcriptional activation/repression domain and RNA recognition motifs, and in Drosophila has a significant role in the development of the head and thorax. Early Ott1-deficient embryos show growth retardation and incomplete closure of the notochord. Further analysis demonstrated placental defects in the spongiotrophoblast and syncytiotrophoblast layers, resulting in an arrest of vascular branching morphogenesis. Rescue of the placental defect using a conditional allele with a trophoblast-sparing cre transgene allowed embryos to form a normal placenta and survive gestation. This result shows that the process of vascular branching morphogenesis in Ott1-deficient animals is regulated by the trophoblast compartment rather than the fetal vasculature. Mice surviving to term manifested hyposplenia and abnormal cardiac development. Analysis of global gene expression of Ott1-deficient embryonic hearts shows enrichment of hypoxia-related genes and significant alteration of several candidate genes critical for cardiac development. Thus, Ott1-dependent pathways in addition to being implicated in leukemogenesis, may also be important in the pathogenesis of placental insufficiency and cardiac malformations.

overall_design:
We generated in triplicate mice containing the Ott1flox and Ott1null alleles. Tg-Sox2-cre animals were obtained from Jackson labs (Bar Harbor, ME). Genotyping was performed by PCR analysis of murine or embryonic tissue [Raffel, 2007 #218]. Timed matings were determined by presence of a vaginal plug at E0.5.

RNA was extracted from 3 hearts each from  either Ott1null/nullSox2-cre or Ott1null/wtSox2-cre E18.5 embryos using the RNeasy Micro kit (Qiagen, Valencia, CA) and treated with RNAse-free DNAse (Qiagen, Valencia, CA). 50 ng of purified total RNA was linearly amplified using the Ovation RNA amplification system V2 (Nugen, San Carlos, CA) and biotinylated with the FL-Ovation Biotin Module V2 (Nugen, San Carlos, CA) per the supplied protocol. cDNA was then hybridized to Affymetrix Mouse expression array 430A2.0 chips by the Dana Farber Microarray Core Facility (Boston, MA).  The raw gene expression values were preprocessed with robust multi-array analysis (RMA) algorithm using BioConductor software.

first: Glen

last: Raffel

first: Gerald

last: Chu

first: Dana

last: Cullen

first: Roderick

last: Bronson

first: Olivier

last: Bernard

first: D.

middle: G

last: Gilliland


title: Effect of acute muscle unloading on soleus and gastrocnemius muscle gene expression

city: Sharnbrook

first: Fei Ling

last: Lim

state: Bedfordshire

address: Colworth Science Park

institute: Unilever

summary:
Gene expression changes induced by acute skeletal muscle unloading, which leads to physiological changes including muscle atrophy, fibre-type switching, and loss of ability to transition between lipid and glucose as energy source (metabolic inflexibility), was investigated by hind-limb suspension (HLS) treatment of Male ICR mice (28–32 g body wt; Harlan, Indianapolis, IN). Agilent Whole Mouse Genome Oligo Microarrays were utilised to examine the effects of HLS on mRNA expression profiles of the soleus muscle and the gastrocnemius muscle in the hindlimbs of freely ambulating control and 24h HLS treated mice.
Keywords: treatment vs control, tissue type comparison

overall_design: Five independent biological replicates of this experiment (Control and HLS) were carried out.

first: Dawn

last: Mazzatti

first: Melissa

last: Smith

first: Radu

last: Oita

first: Andrew

last: White

first: Michael

middle: B

last: Reid


title: Gene expression profile of cervical and skin tissues from HPV 16 E6 transgenic mice

status: Public on Sep 01 2008

city: Mexico City

first: Alfredo

last: Hidalgo-Miranda

address: Periferico Sur 4124, Torre Zafiro II, piso 6

country: Mexico

institute: National Institute of Genomic Medicine

summary:
Background
The in vivo properties of HR-HPV E6 and E7 oncoproteins have been previously evaluated through the generation and characterization of HPV transgenic mouse strains. Although K14E6 transgenic mice develop spontaneous tumors of the skin epithelium, no spontaneous reproductive tract malignancies arise, unless the transgenic mice were treated chronically with 17β-estradiol. Taken together, these findings suggest that E6 performs critical functions in normal adult cervix and skin, highlighting the need to define E6-controlled transcriptional programs in these tissues. We evaluated the different expression profile of 14,000 genes in skin or cervix from young K14E6 transgenic mice compared with corresponding tissues from non-transgenic (FVB) mice.

Result
Microarray analysis identified a total of 676 and 1154 genes that were significantly up and down-regulated, respectively, in skin from K14E6 transgenic mice. On the other hand, in cervix from K14E6 transgenic mice we found that only 97 and 252 genes were significantly up and down-regulated, respectively. One of the most affected processes in the skin from K14E6 transgenic mice was the cell cycle. We also found that skin from transgenic mice showed down-regulation in pro-apoptotic genes expression, particularly in those related to the extrinsic apoptotic pathway. In contrast, we observed up-regulation of anti-apoptotic genes. Another pathway that was severely affected in skin was the immune response. In cervix from transgenic mice, we could not find affected any gene related to the cell cycle and apoptosis pathways. Interestingly, we observed alterations in the expression of immune response genes in cervix from K14E6 transgenic mice. Pathways such as angiogenesis, cell junction, cytoskeleton, keratinocyte differentiation and epidermis development, showed different gene expression in skin or cervix from K14E6 transgenic mice.

Conclusion
Alterations in gene expression identified in the current study might partially explain why our K14E6 transgenic mice present a more aggressive phenotype in the skin than in the cervix. Expression of the HPV16 E6 oncoprotein alters expression of genes that fell into several functional groups providing insights into pathways by which E6 deregulate cell cycle progression, apoptosis and the host resistance to infection and immune function, providing new opportunities for early diagnostic markers and therapeutic drug targets.
Keywords: Human_papillomavirus, transgenic mice, expression profile

overall_design: We compared the expression paterns in the skin and cervix of K14E6 transgenic mice against the same tissues from non-transgenic FVB mice. For each tissue, we pooled total RNA from three different 6 week virgin mice. Total RNA from the cervix and lower reproductive tract and dorsal skin were obtained from fresh frozen tissue using Trizol. Total RNA was processed an hybridized onto Affymetrix Mouse Genome 430A 2.0 Arrays. For each sample, a technical replica was included.

first: Daniel

last: Mendoza-Villanueva

first: Jose

last: Diaz-Chavez

first: Laura

last: Uribe-Figueroa

first: Claudia

last: Rangel-Escareño

first: Santiago

last: March-Mifsut

first: Gerardo

last: Jimenez-Sanchez

first: Paul

last: Lambert

first: Patricio

last: Gariglio


title: Lung transcriptome from M. avium infected WT, IFNg-/- and IRF1-/- mice

city: Erlangen

first: Roland

last: Lang

address: Wasserturmstr. 3-5

institute: University Hospital Erlangen

summary:
Mycobacterium avium infection in mice induces granuloma necrosis in the lung which is dependent on IFNg. IRF1 is a transcription factor activated by IFNg signaling. The effect of IFNg and IRF1 on immunopathology and transcriptional changes in the lung were analysed using gene-deficient mice.
The data from the Ifng-/- experiment have been described (Aly et al. 2007. J Pathol 212:295).

Keywords: Infection, Genotype comparison

overall_design: In two independent blocks of experiments, Ifng-/- and Irf1-/- mice on a C57Bl/6 background and their respective controls were infected with Mycobacterium avium via aerosol. After 14 weeks, mice were sacrificed and the lung RNA prepared using TriFast FL (Peqlab). Total RNA (1µg) was labeled and hybridized to Affymetrix mouse MOE430A 2.0 GeneChips according to the manufacturer’s recommendations. For each condition three biological replicates (except Ifng-/-, no infection) were used. Total of 23 Samples.

first: Stefan

last: Ehlers

first: Sahar

last: Aly

first: Jörg

last: Mages