title: SMRT-RID mutation linked to Type I Pneumocyte Associated Respiratory Distress Syndrome via TR repression

status: Public on Oct 14 2011

first: Ruth

last: Yu

summary: We show that knock-in mutations of the nuclear corepressor SMRT in C57Bl6 mice (SMRTmRID) produces a novel respiratory distress syndrome (RDS) due to prematurity of the type I pneumocyte.  Treatment with the anti-thyroid hormone drug, propylthiouracil (PTU), completely rescues the SMRT-induced RDS, suggesting an unrecognized and essential role for the thyroid hormone receptor (TR) in lung development.  We show that TR and SMRT control type I pneumocyte differentiation through Klf2, which in turn appears to directly activate the type I pneumocyte gene program.  Conversely, mice without lung Klf2 lack mature type I pneumocytes and die shortly after birth, closely recapitulating the SMRTmRID phenotype.  These results identify a second nuclear receptor, the TR, in type I pneumocyte differentiation and suggest a new type of therapeutic option in the treatment of glucocorticoid non-responsive RDS.

overall_design: Total RNA was obtained from WT and SMRT-RID E18.5 lungs of embryos from mothers treated with Diet containing 0.15% PTU or control chow for 2 days (from E16.5).

first: Liming

last: Pei

first: Ronald

last: Evans


title: Identification of TDP-43 and FUS mRNA targets and pathways in the cytoplasmic compartment of motoneuronal NSC-34 cells

status: Public on Oct 22 2011

city: Cusano milanino

first: Claudia

last: Colombrita

address: Via Zucchi, 18

country: Italy

institute: IRCCS Istituto Auxologico Italiano

summary: We performed RNA immunoprecipitation (IP) and microarray (RIP-chip) analyses to identify and compare the biological mRNA targets of two RNA-binding proteins (RBP), TDP-43 and FUS, associated to cytoplasmic ribonucleoprotein (RNP) complexes of motoneuronal NSC-34 cells with the final aim to unravel their role in mRNA transport, stability, and translation in neuronal cells.

overall_design: To identify the transcripts contained and bound in the isolated RNP complexes, a chip analysis was performed using the recovered mRNAs from triplicate experimantal RIP samples (TDP-43-IP samples, the FUS-IP samples and the control IgG-IP sample).

first: Antonia

last: Ratti

first: Elisa

last: Onesto


title: Total gene expression analysis of LMP2A/λ-MYC and λ-MYC tumors

status: Public on Oct 26 2011

city: Chicago

first: Kathryn

last: Bieging

state: IL

address: 303 East Chicago Ave

department: Microbiology-Immunology

country: USA

institute: Northwestern University

summary: We have developed a transgenic mouse model for Epstein-Barr virus-associated Burkitt's lymphoma.  Transgenic mice that express LMP2A and MYC in B cells develop spontaneous lymph node tumors at different rates.  Tumor onset occurs at approximately 40-60 days in  LMP2A/λ-MYC mice and at 100-200 days in λ-MYC mice.  This study compared total gene expression in the tumor cells from each genotype, as well as in B cells isolated from 3 week old mice prior to tumor onset.  Comparison of total gene expression in tumor cells from LMP2A/λ-MYC and λ-MYC transgenic mice identified a short list of differentially expressed genes.  Comparison of gene expression in B cells from the spleens of 3 week old mice, in contrast, identified a 10-fold increase in the number of differentially expressed genes.

overall_design: B cells from the spleens of 3 week old LMP2A/λ-MYC (n=5), λ-MYC (n=5), LMP2A (n=3), and WT (n=3) transgenic mice were purified using magnetic-activated cell sorting (MACS) beads purchased from Miltenyi for CD19 positive selection.  Total RNA was isolated from these purified B cells, as well as from cervical lymph node tumor cells that developed in LMP2A/λ-MYC (n=7) and λ-MYC (n=5) transgenic mice using RNeasy RNA extraction kit from QIAGEN.   Cervical lymph node tumor cells were >90% positive for the B cell marker B220, and were not further purified.  Total gene expression was assessed in each sample, along with heart and brain reference samples using MouseRef-8 v2.0 Expression Bead Chips purchased from Illumina.  GeneSpring analysis software was used to analyze the expression data and identify significantly differentially expressed genes (fold change >1.5-fold and false discovery rate< 0.05).

middle: T

first: Richard

last: Longnecker


title: Reprogramming is achieved within a single cell cycle after mouse nuclear transfer

status: Public on Oct 04 2011

city: New York

first: Dieter

middle: M

last: Egli

state: NY

address: 1150 St. Nicholas Avenue, room 607B, New York NY 10032

institute: Columbia University

summary: Although nuclear transfer allows the reprogramming of somatic cells to totipotency, little is known concerning the kinetics by which it takes place or the minimum requirements for its success. Here, we demonstrate that reprogramming can be achieved within a few hours and a single cell-cycle as long as two key constraints on reprogramming are satisfied.  First, the recipient cell chromosomes must be removed during mitosis. Second, the nuclear envelope of the donor cell must be broken down and its chromosomes condensed, allowing an embryonic nucleus to be constructed around the incoming chromosomes. If these requirements are not met, then reprogramming fails and embryonic development arrests. These results point to a central role for processes intimately linked to cell division in mediating efficient transitions between transcriptional programs.

overall_design: tail tip skin fibroblasts were transferred into mitotic mouse zygotes, blastomeres or oocytes.

first: Kevin

last: Eggan


title: Gene expression profiles of T cell fraction enriched for donor antigen-reactive T cells in skin allografted recipient mice (I)

status: Public on Oct 13 2011

city: Seoul

first: Dong-Gyun

last: Lim

address: 245 Eulji-ro, Jung-gu

country: South Korea

institute: National Medical Center, Research Institute

summary: Measurement of specific gene expression in clinical samples is a promising approach for monitoring the recipient immune status to the graft in organ transplantation. Identification of biomarker genes closely associated with tolerance or rejection is critical for this monitoring protocol. Unlike previous studies, our microarray analysis focused on donor antigen-reactive T cells, which were prepared by collecting CD69+ T cells from cocultures of recipient peripheral T cells and donor antigen-presenting cells. A comparison of different recipient groups enabled us to identify several tolerance- and rejection-correlated biomarker genes, including previously unknown genes. By measuring biomarker gene expression in the CD69+ T cell fraction using quantitative reverse-transcription polymerase chain reaction, we were able to precisely detect the immune status of recipients relative to their graft.

overall_design: Full-thickness donor (BDF1; C57BL/6 x DBA/2) tail skin was grafted onto recipient (C57BL/6) mice. Tolerance to the graft was induced by donor specific transfusion combined with administration of anti-CD40L Ab (MR-1). Total T lymphocytes were prepared from spleen and lymph nodes of tolerant recipient mice on day 21 and 100 after skin transplantation, untreated recipient mice on day 7, and ungrafted, healthy C57BL/6 mice and used as early tolerant, tolerant, rejecting and naïve T lymphocyte samples, respectively. In order to isolate alloantigen-reactive cells, T lymphocytes were cocultured with donor BM-DCs for 20-21 hours and then separated into two subpopulations based on CD69 expression using fluorescence cell sorter. Total RNA was extracted from these CD69+ and CD69- T cells and subjected to microarray using Illunima MouseRef-8 Expression BeadChip. All data analysis and visualization of differentially expressed genes was conducted using Illumina BeadStudio v3.1.3 (Gene Expression Module v3.3.8), Array Assist 5.5.1 (Stratagene) and R 2.4.1(www.r-project.org).  Candidate tolerance genes were defined as the common genes satisfying the following criteria; 1) 1.5 fold or higher expression in CD69+ T cells isolated from tolerant recipients than those from naïve mice, 2) 1.5 fold or higher expression in CD69+ T cells than CD69- T cells from tolerant mice, 3) 500 or higher average signal measured in CD69+ T cells from tolerant mice. The criteria for candidate rejection genes were 1) 1.5 fold or higher expression in CD69+ T cells isolated from rejecting recipients than those from tolerant mice, 2) 1.5 fold or higher expression in CD69+ T cells than CD69- T cells from rejecting mice, 3) 500 or higher average signal measured in CD69+ T cells from rejecting mice.

first: Youn-Hee

last: Park

first: Sung-Eun

last: Kim

first: Eun-Jung

last: Jung

first: Seong-Hee

last: Jeong

first: Su-Jin

last: Shin

first: Chan-Sik

first: Duck-Jong

last: Han

first: Song-Cheol


title: Cannabinoid Receptor 1 Dependent Effects of Isopropoyl dodeycl fluorophosphonate on Hepatic Gene Expression

status: Public on Oct 01 2011

city: OAKLAND

first: Max

last: Ruby

state: CA

address: 5700 Martin Luther King Jr. Way

institute: Children's Hospital Oakland Reserach Institue

summary: We tested the effects of isopropoyl dodecyl fluorophosphonate (IDFP) (10 mg/kg, i.p.), a pharmacological inhibitor of endocannabinoid degradation, on hepatic gene expression in mice. To determine if increased cannabinoid receptor 1 signaling is responsible for IDFP induced effects a subset of mice were pretreated with the cannabinoid receptor 1 antagonist (AM251) (10 mg/kg, i.p.).

overall_design: Total RNA obtained from liver of mice treated with DMSO (n=6), IDFP (n=8), or AM251/IDFP (n=5) (all 10 mg/kg i.p.) for 4 hours.

middle: A

first: Ronald

last: Krauss


title: Gene Expression Study in Progranulin-Deficient Mice

status: Public on Sep 01 2011

city: Los Angeles

first: Giovanni

last: Coppola

address: 1524 Gonda, 695 Charles Young Drive South

department: Psychiatry and Neurology

institute: UCLA

summary: Study of brain regions from GRN KO, Heterozygous and WT mice at different time points (2-6-9 months)

overall_design: Cortex, cerebellum and hippocampus were dissected and studied at 2-6-9 months from KO (-/-), Het (-/+), and WT (+/+) animals

first: Lauren

last: Herl

first: Fuying

last: Gao

first: Daniel

middle: H

last: Geschwind

first: Robert

middle: V

last: Farese


title: Gene expression analysis of OX40-triggered mouse Treg

status: Public on Sep 26 2011

city: Milan

first: Paola

last: Pittoni

state: Italy

address: Via Amadeo, 42

department: Dept. Experimental Oncology

institute: IRCCS Istituto Nazionale dei Tumori

summary: Regulatory T (Treg) maintain the tumor microenvironment in an immunosuppressive state preventing effective anti-tumor immune response. A possible strategy to overcome Treg cell suppression focuses on OX40, a costimulatory molecule expressed constitutively by Treg cells while induced in activated effector T (Teff) cells. OX40 stimulation by the agonist mAb OX86 inhibits Treg cell suppression and boosts Teff cell activation. Here we uncover the mechanisms underlying the therapeutic activity of OX86 treatment dissecting its distinct effects on Treg and on effector memory T (Tem) cells, which are the most abundant CD4+ populations strongly expressing OX40 at the tumor site. In response to OX86, tumor-infiltrating Treg cells produced significantly less interleukin 10 (IL-10), possibly in relation to a decrease in the transcription factor IRF1. Tem cells responded to OX86 by upregulating surface CD40L expression, providing a licensing signal to dendritic cells (DCs). The CD40L/CD40 axis was required for Tem cell-mediated in vitro DC maturation and in vivo DC migration. Accordingly, OX86 treatment was no longer therapeutic in CD40 KO mice. In conclusion, following OX40 stimulation, blockade of Treg cell suppression and enhancement of the Tem cell adjuvant effect both concurred to free DCs from immunosuppression and to activate the immune response against the tumor.

overall_design: Total RNA obtained from sorted mouse FoxP3-GFP+ Treg activated in vitro with anti-CD3 in the presence of an OX40-agonist mAb (OX86) or isotype control.

first: Alessia

last: Burocchi


title: S100A4+ Stromal Cells from Normal Lung vs. Metastatic Lung

status: Public on Aug 30 2011

city: Boston

first: Joyce

middle: Tse

last: O'Connell

state: MA

address: 330 Brookline Avenue

department: Division of Matrix Biology, Department of Medicine

institute: Beth Israel Deaconess Medical Center and Harvard Medical School

summary: Analysis of S100A4+ stromal cells at the gene expression level in physiological setting versus metastatic setting.

overall_design: Total RNA was isolated from FACS-sorted S100A4+ stromal cells from normal lung of S100A4-GFP transgenic mice compared to FACS-sorted S100A4+ stromal cells from metastatic lung of 4T1 tumor-bearing S100A4-GFP transgenic mice.

first: Raghu

last: Kalluri


title: Direct lineage conversion of terminally differentiated hepatocytes to functional neurons

status: Public on Aug 31 2011

city: Stanford

first: Miao-Chih

last: Tsai

address: 269 Campus Drive, CCSR 2140

institute: Stanford University

summary:
Mouse fibroblasts and hepatocyte can be directly reprogrammed to induced neuronal (iN) cells.  Genome-wide expression analysis showed that Hep-iN cells had not only induced a neuronal transcriptional program but also effectively silenced the hepatocyte transcriptome suggesting that the reprogramming factors lead to a binary lineage switch decision rather than an induction of hybrid phenotypes. Similarly, the fibroblast-specific transcriptional program was downregulated in fibroblast-derived iN cells.
BAM = infection with the 3 factors (Ascl1 - Brn2 - Myt1l) .
ATT = Hepatocytes_derived_induced_neurons derived from TauGFP-AlbCre-R26-lsl-tomato

overall_design: Total RNA obtained from MEFs subjected to 21 days lentivirus infection for neuronal induction compared to uninfected MEFs.

first: Howard

last: Chang

first: Samuele

last: Marro

first: Marius

last: Wernig


title: Genome-wide identification of Bcl11b gene targets

status: Public on Aug 02 2011

city: La Jolla

first: Elizabeth

middle: A.

last: Thomas

address: 10550 N. Torrey Pines Rd

department: Molecular Biology

institute: The Scripps Research Institute

summary: B-cell leukemia/lymphoma 11B (Bcl11b) is a transcription factor showing predominant expression in the striatum.  To date, there are no known gene targets of Bcl11b in the nervous system.  Here, we define targets for Bcl11b in striatal cells by performing genome-wide expression profiling.  Transcriptome-wide analysis revealed that 694 genes were significantly altered in striatal cells over-expressing Bcl11b, including genes showing striatal-enriched expression similar to Bcl11b.  Functional analysis on the gene target list identified significant association of Bcl11b to brain-derived neurotrophic factor/neurotrophin signaling.  These data implicate Bcl11b as a novel regulator of the BDNF signaling pathway, which is disrupted in many neurological disorders.

overall_design: n=4 wt STHdh striatal cells  and n=4 Bcl11b-transfected STHdh striatal cells

first: Bin

last: Tang

first: Lana

last: Schaffer

first: Steven

middle: R

last: Head


title: The expression profiles of genes using genetically modified parthenogenetic mouse embryonic stem cells

status: Public on Jul 30 2011

city: Seu-gu

first: Jaeku

last: Kang

state: Daejeon

address: 685, Gasuwon-dong

department: Department of Pharmacology

institute: College of Medicine, Konyang University

summary: Embryonic stem (ES) cells are used in cell therapy and tissue engineering due to their ability to produce different cells types. However, studies of ES cells that are derived from fertilized embryos have raised concerns about the limitations imposed by ethical and political considerations. Therefore, many studies of ES cells use the ES cells that are derived from unfertilized oocytes and adult tissue. Although parthenogenetic embryonic stem (ESP) cells also avoided ethical and political dilemmas and can be used in cell-based therapy, the ESP cells exhibit growth retardation problems. Therefore, to investigate the potential for muscle growth from genetically modified ESP cells, we established four ES cell types, including normal embryonic stem (ESN) cells, ESP cells, ESP cells that overexpress the Igf2 gene (ESI) and ESP cells with down-regulated H19 gene expression (ESH). Using these cells, we examined the expression profiles of genes that were related to imprinting and muscle using microarrays.

overall_design: Total RNA obtained from isolated genetically modified parthenogenetic mouse embryonic stem cells compared to parthenogenetic mouse embryonic stem cells. 2 Biological Replication.


title: Regulation of Mammalian Cell Growth and Survival By an RNA Polymerase II-Pausing Factor (Gene expression)

status: Public on Aug 17 2011

first: Jianlong

last: Sun

address: 1 Blackfan Street

department: Hematology/Oncology

institute: Boston Children's Hospital

summary: Many mammalian genes are occupied by paused RNA polymerase II (pol II) at promoter-proximal regions on both sides of transcription start sites (TSSs).  However, the consequences of pol II pausing on gene expression and cell biology are not fully understood.  Here we report that genetic ablation of the b subunit of mouse negative elongation factor (Nelf-b), a key pol II-pausing factor, results in slower progression at multiple cell cycle stages and increased apoptosis.  Consistently, a whole-genome analysis indicates that growth and cell death-related genes are highly enriched among the direct target genes of Nelf-b.  In particular, Nelf-b deletion increases pol II density in the promoter-distal region of stress response genes and their overall expression levels in the absence of any external stress signals.  In addition, our work also reveals a previously unappreciated role of Nelf-b role in curbing TSS-upstream transcription of many mammalian genes.  We suggest that Nelf-mediated pol II pausing balances the cellular needs for growth/survival and stress response by preventing excessive basal transcription of stress-induced genes.

overall_design: Immortalized mouse embryonic fibroblasts derived from a Nelf-b flox/- embryo were infected with control or Cre-epxressing retrovirus.  Gene expression profile of control and knockout MEF at 7 days after virus infection were compared by using Illumina's mouse whole-genome gene expression BeadChIPs.  There are two replicates for both control and knockout MEF samples.

first: Rong

last: Li


title: VillinCre-Blimpflox mice postpartum day 7

status: Public on Jul 18 2011

city: Amsterdam

first: Jarom

last: Heijmans

address: Meibergdreef 69-71

department: Tytgat Institute for liver and intestinal research

country: Netherlands

institute: Academic Medical Center

summary: In many mammalian species, the intestinal epithelium is immature at birth. During the suckling to weaning transition, the intestine matures. This developmental transition is the result of a genetic program that is intrinsic to the gut and independent of luminal content, but its regulators have not been identified. We investigated the function of the transcriptional repressor Blimp-1 using mice with intestine-specific ablation of Blimp-1. Deletion of Blimp-1 results in growth retardation and excess neonatal mortality. Mutant mice lack all typical epithelial features of the suckling period and are born with features of adult-like intestine.

overall_design: To assess the function of the gene Prdm1 (Blimp) on postnatal day 7 intestinal epithelium, VillinCre-Blimpflox and control (VillinCre-Blimpwt or Cre-Blimpflox) mice were generated. Mice were sacrificed at day 7 postnatal, and pieces of whole mid-intestine were taken for analysis.

first: Vanesa

last: Muncan


title: Global gene expression analysis of three different types of mouse motor neurons

status: Public on Aug 18 2011

city: Cambridge

first: Esther

middle: Yesde

last: Son

address: 7 Divinity Avenue

department: Stem Cells and Regenerative Biology

institute: Harvard University

summary: Analysis of gene expression differences in three types of mouse motor neurons: (1) those harvested from E13.5 mouse embryos; (2) those derived from embryonic stem cells by directed differentiation; and (3) those made from mouse embryonic fibroblasts by transcription factor reprogramming.

overall_design: Hb9::GFP+ mouse motor neurons were obtained by three methods [(1) dissection of Hb9::GFP-transgenic E13.5 mouse embryo spinal cord; (2) directed differentiation of an Hb9::GFP-transgenic mouse embryonic stem cell line, V6.5; (3) reprogramming of Hb9::GFP-transgenic mouse embryonic fibroblasts by overexpression of 10 transcription factors]. Each type of motor neuron was purified by FACS and harvested in Trizol. Total RNA was purified and prepared for hybridization onto Illumina MouseRef-8.

middle: Y

first: Justin

middle: K

last: Ichida

first: Kevin

last: Eggan


title: Mast cell targeting hampers prostate adenocarcinoma development but promotes the occurrence of highly malignant neuroendocrine cancers.

status: Public on Jun 15 2011

first: Paola

last: Pittoni

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

overall_design: Refer to individual Series

first: Giorgio

last: Mauri


title: Gene expression analysis of prostate tumors arisen in TRAMP mice in which mast cells are pharmacologically stabilized or genetically ablated.

summary: Analysis of gene expression of prostate tumors arisen in TRAMP mice in which mast cells are pharmacologically stabilized or genetically ablated.The hypothesis tested in the present study was that mast cells inhibition or absence impacted prostate tumor development and histotype. Results demonstrate that prostate tumors arisen in TRAMP mice in which mast cells are pharmacologically stabilized or genetically ablated have a neuroendocrine signature.

overall_design: Total RNA obtained from prostate tumors from 24 wks old TRAMP mice chronically treated with sodium chromoglycate (cromolyn) since 8 wks of age, and from 24 wks old TRAMP KitW-sh mice, compared to untreated 30 wks old TRAMP mice and to non tumoral prostates


title: PTEN intact and NULL prostates in intact and castrate mice.

status: Public on May 19 2011

first: Yu

last: Chen

address: 1275 York Ave, Box 20

department: Human Oncology and Pathogenesis Program

institute: Memorial Sloan Kettering Cancer Center

summary: We performed expression profiling of prostates of 3 month wild-type and PTEN NULL mice and assessed the response to 3 days of castration.

overall_design: Seven three month old WT and PbCre x PTEN f/f (PTEN NULL) mice were used. They are in the C57B6 background. Three mice in each group were castrated. Three days after castration, the prostate were harvested and RNA isolated by standard protocols and analyzed by expression profiling.

first: Brett

last: Carver

first: Charles

middle: L

last: Sawyers


title: Gene expression of primary MMTV-Neu tumors compared to secondary tumors generated from lin- and single tumor initiating cell (TIC) transplantation

status: Public on May 30 2011

city: Toronto

first: Jeff

last: Liu

state: Ontario

address: 101 College Street, RM 4-601

department: Princess Margaret Cancer Center

country: Canada

institute: University Health Network

summary: Most solid tumors seem to be organized in a hierarchy in which only a fraction of cells, termed tumor-initiating cells (TICs), is capable of disseminating new tumors after transplantation into recipient mice. However, whether a single TIC can induce a tumor or whether it requires additional TICs or non-TICs for tumor initiation is not known. Here we show that injections of single CD24+:Jag1- cells from Her2/Neu+ mammary tumors into recipient mammary glands induced tumors at a frequency of 1/22.  Single cell-derived secondary tumors exhibited histology, flow cytometry and global expression profiles that were indistinguishable from primary tumors. Thus, a single TIC can act cell autonomously to induce a tumor and therefore complete eradication of all TICs would be required to cure cancer.

overall_design: Total RNA obtained from primary MMTV-Neu tumors, secondary tumors generated by lin- cell transplantation, and secondary tumors generated by a single TIC, were used for microarray analysis to determine differentially regulated genes in the secondary tumors.  Cluster analysis based on gene expression were then performed to assess tumor similarity

first: Tao

last: Deng

first: Sean

middle: E

last: Egan

first: Eldad

last: Zacksenhaus


title: Expression data from mouse neonatal ovarian DMBA and BaP culture experiments

status: Public on May 13 2011

city: Newcastle

first: Alexander

middle: Peter

last: Sobinoff

state: NSW

address: University Drive

department: Science and IT

country: Australia

institute: University of Newcastle Australia

summary: Mammalian females are born with a finite number of non-renewing primordial follicles, the majority of which remain in a quiescent state for many years. Due to their non-renewing nature, these “resting” oocytes are particularly vulnerable to xenobiotic insult, resulting in premature ovarian senescence and the formation of dysfunctional oocytes.  In this study we characterised the mechanisms of ovotoxicity for the ovotoxic agent 7,12-dimethylbenz-[a]anthracene (DMBA), which targets immature follicles. Neonatal mouse ovaries (PND3-4) were cultured in the presence of DMBA (50nM) or BaP (1uM) for 96 hours to observe their effects on the ovarian transcriptome. This was done in the hopes of gaining a better understanding of the mechanisms underpinning xenobiotic induced pre-antral ovotoxicity.

overall_design: Ovaries from day 3-4 Swiss neonatal mice were cultured in DMBA or BaP containing media for 96 hours. The ovaries were then collected for RNA extraction and hybridization on an Illumina Sentrix Mouse ref-8 v2 Beadchip

middle: P

first: Eileen

last: McLaughlin


title: Gene expression profile of mouse developmentally competent and incompetent (NSN) 2-cell embryos.

city: Berlin

first: Alessandro

last: Prigione

state: Berlin

address: Robert-Roessle-Str. 10

country: Germany

institute: Max Delbrueck Center for Molecular Medicine

summary: Microarray analysis of gene expression in 2-cell embryos obtained from developmentally competent MII oocytes or developmentally incompetent MII (NSN) oocytes.

overall_design: In this study we have compared the expression profile of 2-cell embryos obtained after  following in vitro fertilisation of  developmentally competent (control) or incompetent (NSN) MII oocytes with the aim of identifying the gene expression networks that operate at this specific stage of development.

first: Maurizio

last: Zuccotti

first: Valeria

last: Merico

first: Michele

last: Bellone

first: Francesca

last: Mulas

first: Lucia

last: Sacchi

last: Rebuzzini

first: Carlo

last: Redi

first: Riccardo

last: Bellazzi

first: James

last: Adjaye

first: Silvia

last: Garagna


title: Dynamic Chromatin Localization of Sirt6 Shapes Stress- and Aging- Related Transcriptional Networks (Illumina)

status: Public on May 11 2011

first: Kun

last: Qu

address: 269 Campus Dr. CCSR 2150

department: Dermatology

summary:
Sirtuins (Sirt) are a family of enzymes that modify chromatin and other proteins to affect gene activity. Loss of Sirt6 leads to a progeria-like phenotype in mice, but the target of SIRT6 action has been elusive. Here we show that Sirt6 binds to thousands of gene promoters in a stress-inducible fashion, guided by the stress-responsive transcription factor NF-κB.
Chromatin profiling by ChIP-chip analysis of Sirt6 and NF-KB component RelA combined with expression array data of wildtype, Sirt6 knockout and Sirt6 RelA double knockout cells demonstrates that RelA recruits Sirt6 to NF-KB targets in response to TNF-a induction and that many of these targets are important for senescence and aging.

overall_design: comparison of wild type,  Sirt6-/- and Sirt6-/- RelA-/- MEF cells

first: Kawahara

last: Tiara L

first: Rapicavoli

last: Nicole A

first: Wu

last: Angela R

first: Qu

last: Kun

first: Quake

last: Stephan R

first: Chang

last: Howard Y


title: Gene expression microarray for mouse ES cells vs. mouse ES cells treated with 48 hr N2B27

status: Public on May 03 2011

first: Matt

last: Thomson

address: 52 Oxford Street 368

department: MCB

summary: Core circuits of transcription factors stabilize stem and progenitor cells by suppressing genes required for differentiation.  We do not know how such core circuits are reorganized during cell fate transitions to allow differentiation and lineage choice to proceed. Here, we asked how the pluripotency circuit, a core transcriptional circuit that maintains mouse embryonic stem (ES) cells in a pluripotent state, is dismantled as ES cells differentiate and choose between the neural ectodermal and mesendodermal progenitor cell fates. When ES cells are recultured from pluripotency maintaining conditions to the basal media N2B27, the expression of the pluripotency circuit genes begins to change. At 48 hours post N2B27 addition, the ES cells are competent to respond to differentiation signals. Here, our microarray analysis compares the gene expression profile of ES cells vs. the gene expression profile of cells that have been treated with N2B27 for 48 hours, reaching the competent state.

overall_design: 2 x mouse ES cells in pluripotency maintaining conditions. 3 x mouse ES cells after 48 hr of N2B27 culture

first: Siyuan

middle: J

last: Liu

first: Sharad

last: Ramanathan


title: Wdr5 mediates self-renewal and reprogramming via the embryonic stem cell core transcriptional network (2)

status: Public on Apr 08 2011

first: Jonathan

last: Monk

address: One Gustave L. Levy Place

department: Gene and Cell Medicine

institute: Mt. Sinai School of Medicine

summary:
The embryonic stem (ES) cell transcriptional and epigenetic networks are critical for the maintenance of ES cell self-renewal. It remains unclear whether interactions. Here we show that a core member of the Set/MLL complex, WDrepeat protein-5 (Wdr5), is a novel regulator of self-renewal and partners with Oct4 to maintain an intact transcriptional network and for efficient formation of induced pluripotent stem (iPS) cells. Moreover, we provide evidence that Oct4 interacts with chromatin components and is indispensible for epigenetic regulation.  These findings suggest an integrated transcriptional and epigenetic model, mediated through Wdr5, for the maintenance of ES cell self-renewal and somatic cell reprogramming.

Differential gene expressions upon down-regulation of Wdr5 was analysed by comparing Wdr5R4 –dox (triplicate) and LucR +dox (duplicate) RNA samples

Gene expression changes upon down-regulation of Oct4 was analysed by comparing Oct4 shRNA (duplicate) and GFP shRNA (duplicate) after 4day transfection

overall_design:
Wdr5: 5 samples are analyzed: Luciferase (Luc, 2 replicates) and Wdr5 with no dox (minusDox, 3 replicates)
Oct4-GFP: 4 samples are analyzed: Oct4 shRNA (Oct4, 2 replicates) and GFP shRNA (GFP, 2 replicates)

first: Yen-Sin

last: Ang

first: Su-Yi

last: Tsai

first: Dung-Fang

last: Lee

first: Jie

last: Su

first: Kajan

last: Ratnakumar

first: Henia

last: Darr

first: Betty

last: Chang

first: Michael

last: Rendl

first: Christoph

last: Schaniel

first: Emily

last: Bernstein

first: Ihor

last: Lemischka


title: Mouse gene expression profiling in ventilator-induced lung injury

status: Public on Jun 14 2011

city: Philadelphia

first: Tamas

last: Dolinay

state: PA

address: 220 S. 33rd St., Towne building, Room 390

department: Bioengineering

institute: University of Pennsylvania

summary: In this model of ventilator-induced lung injury (VILI), we compared the gene expression profile of whole lungs extracted from sponaneously breathing mice (control, c) or mouse submitted to 8 hours mechanical venitlation with 12 ml/kg tidal volume 2cmH2O of positive end expiratory pressure (PEEP) (ventilation, v). Spontaneously breathing NOD/shi mice were randomized to control (n=3) or ventilation (n=5) condition. In brief, mice were anesthetized with the injection of ketamine (65 mg/kg, ip), acepromazine (2 mg/kg, ip) and xylazine (13 mg/kg, ip)(Henry Schein Inc., Melville, NY). Once deep sedation was achieved, a tracheostomy was performed and a PE-10 cannula was inserted in the trachea and stabilized with silk ligature. Control animals were immediately sacrificied with a supra-physiological dose of ketamine (300 mg/kg, ip). For ventilated mice, the cannula was connected to a custom built Voltek rodent ventilator (Voltek Enterprises, Toronto, CA). We ventilated mice for 8 hours using 2cmH2O positive end expiratory pressure (PEEP), inflating the lungs every hour to 20 cmH2O pressure as we have previously described.  (16). The chest muscle was paralyzed with the injection of pancurorium (1mg/kg, ip)(Sigma-Aldrich) in ventilated mice to avoid spontaneous breathing. Heart rate and respiratory rate was continuously monitored and additional anesthesia was provided if a >15% increase in these parameters was detected. The animal protocol was approved by the BWH Institutional Animal Care and Use Committee (protocol #04477). Ventilated animals At the end of the each experiment, the animals were sacrificed with a supra-physiological dose of ketamine (300 mg/kg, ip). Subsequently, the chest cavity was opened, and the right lung was isolated and ligated at the main bronchus.Lungs were harvested and snap frozen in liquid nitrogen for total RNA extraction.

overall_design: Total RNA was extracted from lungs of controls (n=3) and mice submitted to ventilation (n=5) and there gene expression profiles were compared.

first: Dolinay

last: Tamas

first: Gowrisankar

last: Sivakumar

first: Zandinejad

last: Keivan

first: Landazury

last: Roberto

first: Gazourian

first: Choi

last: Augustine M.K


title: Genome-wide analysis of REST knockdown responsive gene expression in mouse ES cells

status: Public on Apr 01 2011

city: Singapore

first: hongbing

last: yu

address: 60 biopolis street, #02-01, genome

department: stem cell and development

country: Singapore

institute: genome institute of singapore

summary: Analysis of gene expression profiling upon REST shRNA knockdown in mouse ES cells for 72 hours,

overall_design: Total RNA obtained from pSuper vector control and REST shRNA treatment for 72 hours using Invitrogen RNA extraction kit.

first: Hong-Bing

last: Yu


title: The specifcity of innate immune response is enforced by repression of interferon-response elements by NFkB p50

status: Public on Mar 01 2011

first: Alexander

last: Hoffmann

address: UCSD m/c 0375, NSB 3318 9500, Gilman Dr

department: Chemistry and Biochemistry

institute: UCSD

summary: The specific binding of transcription factors to cognate sequence elements is thought to be critical for the generation of specific gene expression programs. The transcription factors nuclear factor kB (NF-kB) and the interferon (IFN) regulatory factors (IRFs) bind to the kB site and the interferon response element (IRE), respectively, of target genes, and they are activated in macrophages after exposure to pathogens. However, how these factors produce pathogen-specific inflammatory and immune responses remains poorly understood. Combining top-down and bottom-up systems biology approaches, we have identified the NF-kB p50 homodimer (p50:p50) as a regulator of IRF responses. First, unbiased genome-wide expression analysis revealed that p50 repressed a subset of IFN-inducible genes through a previously uncharacterized subclass of guanine-rich IRE (G-IRE) sequences, which was substantiated by biochemical and structural analyses. Second, mathematical modeling predicted that p50:p50 might enforce the stimulus-specificity of composite promoters. Indeed, the production of the antiviral regulator IFN-b was rendered stimulus-specific by the binding of p50:p50 to the G-IRE–containing IFNb enhancer to suppress cytotoxic IFN signaling. Specifically, a deficiency in p50 resulted in the inappropriate production of IFN-b in response to bacterial DNA sensed by Toll-like receptor 9. This role for NF-kB p50 in enforcing the specificity of the cellular response to pathogens by binding to a previously uncharacterized subset of IRE sequences alters our understanding of how the NF-kB and IRF signaling systems cooperate to regulate antimicrobial immunity.

overall_design:
[BMDM]: Total RNA extracted from wt, p50-/- or ifnar-/- bone marrow derived macrophages (BMDMs) were subjected to stimulation with LPS, CpG or IFNb
[MEF]: Total RNA extracted from wt or p50KO primary mouse embryonic fibroblasts were subjected to stimulation with LPS or IFNb

first: Christine

middle: S

last: Cheng


title: Mouse Models of Alveolar/Embryonal Rhabdomyosarcoma & Spindle Cell Sarcomas

status: Public on Feb 17 2011

city: San Antonio

first: Yidong

last: Chen

state: Texas

address: 8403 Floyd Curl Drive, MSC 7784

department: Population Health Sciences

institute: UT Health Science Center at San Antonio

summary: A series of conditional mouse models of embryonal rhabdomyosarcoma, alveolar rhabdomyosarcoma and spindle cell sarcoma were generated and validated for relavence to corresponding human cancers.

overall_design: Conditional mouse models of embryonal rhabdomyosarcoma, alveolar rhabdomyosarcoma and spindle cell sarcoma were created by activation or deletion of Pax3:Fkhr, p53, Ptch1 or Rb1 genes.

first: Brian

last: Rubin

first: Koichi

last: Nishijo

first: Hung-I

first: Sean

last: Davis

first: Paul

last: Meltzer

first: Charles

last: Keller


title: Reduced levels of two modifiers of epigenetic gene silencing, Dnmt3a and Trim28, cause increased phenotypic noise.

status: Public on Nov 15 2010

city: Herston

first: Suyinn

last: Chong

state: Queensland

address: 300 Herston Rd

department: Division of Genetics and Population Health

institute: Queensland Institute of Medical Research

summary: Inbred individuals reared in controlled environments display considerable variance in many complex traits. The underlying cause of this variability has been an enigma, hence the term intangible variation. Here we show that two modifiers of epigenetic gene silencing play a critical role in the process. Inbred mice heterozygous for a null mutation in DNA methyltransferase 3a (Dnmt3a) or tripartite motif protein 28 (Trim28), show greater coefficients of variance in body weight than their wildtype littermates. Inbred mice carrying a mutation in Trim28 develop metabolic syndrome and abnormal behaviour with incomplete penetrance. These studies provide a molecular explanation of developmental noise in whole organisms and suggest that faithful epigenetic control of transcription is central to suppressing deleterious levels of phenotypic variation. These findings have broad implications for understanding the mechanisms underlying sporadic and complex disease in humans.

overall_design: Liver gene expression in Trim28MommeD9 heterozygotes compared to wildtype littermates.


title: Programming of marginal zone B cell fate by basic krüppel-like factor (BKLF/KLF3)

status: Public on Jan 29 2011

city: Montréal

first: Jean-Philippe

last: Goulet

state: Québec

address: C.P. 6128, succursale Centre-ville

institute: Université de Montréal

summary:
Gene expression analysis of splenic follicular B cells and marginal zone B cells from B6 and CD19:KLF3 transgenic mice
Comparing KLF3-transgenic and non-transgenic follicular B cells by RNA-microarray revealed that KLF3 regulates a subset of genes that was similarly up-/downregulated upon normal MZ B cell differentiation. Indeed, KLF3 expression overcame the lack of MZ B cells caused by different genetic alterations, such as CD19-deficiency or blockade of B-cell activating factor (BAFF)-receptor signaling, indicating that KLF3 may complement alternative NF-κB signaling. Thus, KLF3 is a driving force towards MZ B cell maturation.

overall_design: RNA of splenic follicular B cells and marginal zone B cells were obtained from 4 different mice per group (B6 and CD19:KLF3 mice). 16 samples = 8 individual mice x 2 B cell subsets.

first: Fabien

last: Agenès

first: Jean-Baptiste

last: Loubert

first: Jorg

last: Kirberg


title: Gene networks associated with conditional fear in mice identified using a systems genetics approach

status: Public on Mar 15 2011

first: Christopher

last: Park

address: 23-151 CHS, 650 Charles E. Young Drive

department: Molecular and Medical Pharmacology

institute: UCLA

summary: To uncover genetic networks governing the biology of conditional fear, we used a systems genetics approach to analyze a hybrid mouse diversity panel (HMDP) with high mapping resolution.  By integrating fear phenotypes, transcript profiling data from hippocampus and striatum and genotype information, two gene co-expression networks correlated with context-dependent immobility were identified.  We prioritized the key markers and genes in these pathways using intramodular connectivity measures and structural equation modeling.  We mapped 27 behavioral quantitative trait loci with a false discovery rate of 5%.  We also identified two gene co-expression networks correlated with context-dependent immobility. Highly connected genes in the context fear modules included Psmd6, Ube2a and Usp33, suggesting an important role for ubiquitination in learning and memory.  We surveyed the architecture of brain transcript regulation and showed preservation of gene co-expression modules in hippocampus and striatum while also highlighting important differences.  Rps15a, Kif3a, Stard7, 6330503K22RIK, and Plvap were among the individual genes whose transcript abundance associated strongly with fear phenotypes.

overall_design: Total mRNA islolated from hippocampus and striatum of strains from Hybrid Mouse Diversity Panel and gene expression quantified using Illumina MouseRef-8 v2.0 microarrays.  Submission includes gene expression data from 100 strains of HMDP for hippocampus (n=1 for each strain) and 98 strains of HMDP for striatum (n=1 for each strain).

middle: C

first: Greg

middle: D

last: Gale

first: Simone

last: de Jong

first: Anatole

last: Ghazalpour

last: Bennett

last: Farber

first: Peter

last: Langfelder

first: Andy

last: Lin

first: Arshad

last: Khan

first: Eleazar

last: Eskin

first: Steve

last: Horvath

first: Aldons

last: Lusis

first: Roel

last: Ophoff

first: Desmond

last: Smith


title: TRANSCRIPTOMIC PROFILING OF ASTROCYTES TREATED WITH THE RHO KINASE INHIBITOR FASUDIL REVEALS CYTOSKELETAL AND PRO-SURVIVAL RESPONSESTRANSFORMATION INDUCED BY THE RHO KINASE INHIBITOR FASUDIL.

status: Public on May 10 2011

city: Melbourne

first: Victoria

middle: Mary

last: Perreau

state: Victoria

address: Parkville

department: Center for Neuroscience

institute: University of Melbourne

summary: Analysis of genome wide gene expression changes over a time course of 24 hours induced by the Rho kinase inhibitor Fasudil in primary mouse astrocyte cultures.

overall_design: Total RNA was extracted from primary astrocyte cultures prepared from mouse forebrain from 1.5 day old mice and treated with Fasudil or vehicle control for 2, 6, 12 or 24 hours.

first: Chew

last: Lau

middle: M

first: Minghui

last: Chen

first: Holly

last: Cate

first: Nam

last: Cheung

first: Ross

last: O'Shea

first: Philip

last: Beart


title: Gene expression analysis of murine day 6 embryoid bodies (EBs ) with or without Notch1 (ICN1) induction.

status: Public on Nov 14 2010

first: Il-Ho

last: Jang

address: Karp Bld, rm 7004, 1 Blackfan circle

institute: Children's Hospital Boston

summary: Analysis of CD41 single positive, VE-cadherin single positive, double positive, and double negatvie populations among 7AAD-CD45- cells from day 6 EBs

overall_design: Doxycline-inducible ICN1 ES cells were differentiated into EBs and ICN1 was induced from day 3-5. Non-induced or induced day 6 EBs were dissociated and subjected to FACS sorting and RNA extraction.

first: Il

middle: H

first: Pamela

last: Wenzel

first: Tsutomu

last: Kume

first: Sumon

last: Datta

first: Mounia

last: Lagha

first: Thorsten

last: Schlaeger

first: Leonard

middle: I

last: Zon

first: Long

last: Zhao

first: Caroline

last: Burns

first: George

middle: Q

last: Daley


title: In vivo cell-autonomous transcriptional abnormalities revealed in mice expressing mutant huntingtin in striatal but not cortical neurons

status: Public on Jan 01 2011

first: Elizabeth

middle: A.

last: Thomas

address: 10550 N. Torrey Pines Rd

department: Molecular Biology

institute: The Scripps Research Institute

summary: Huntington’s disease (HD), caused by a CAG repeat expansion in the huntingtin (HTT) gene, is characterized by abnormal protein aggregates and motor and cognitive dysfunction.  Htt protein is ubiquitously expressed, but the striatal medium spiny neuron (MSN) is most susceptible to neuronal dysfunction and death.  Abnormal gene expression represents a core pathogenic feature of HD, but the relative roles of cell-autonomous and non-cell-autonomous effects on transcription remain unclear. To determine the extent of cell-autonomous dysregulation in the striatum in vivo, we examined genome-wide RNA expression in symptomatic D9-N171-98Q (a.k.a. DE5) transgenic mice in which the forebrain expression of the first 171 amino acids of human Htt with a 98Q repeat expansion is limited to MSNs. Microarray data generated from these mice were compared to those generated on the identical array platform from a pan-neuronal HD mouse model, R6/2, carrying two different CAG repeat lengths, and a relatively high degree of overlap of changes in gene expression was revealed. We further focused on known canonical pathways associated with excitotoxicity, oxidative stress, mitochondrial dysfunction, dopamine signaling and trophic support, among others.   While genes related to excitotoxicity, dopamine signaling and  trophic support, were altered in both DE5 and R6/2 transgenic mice, which may be either cell-autonomous or non-cell-autonomous,,  genes related to mitochondrial dysfunction, oxidative stress and the peroxisome proliferator-activated receptor are primarily affected in DE5 transgenic mice, indicating  cell autonomous mechanisms Overall, our results demonstrate that HD-induced dysregulation of the striatal transcriptome can be largely attributed to intrinsic effects of mutant Htt,,such that mutant Htt-induced effects in cortical neurons is not necessary for striatal dysfunction/degeneration.

overall_design: Striatum from DE5 transgenic mice vs. wt littermate controls

first: Michelle

last: Ehrlich

first: Soong-Ho

last: Kim

first: Timothy

middle: B

last: Brown

first: Giovanni

last: Coppola

middle: A

first: Daniel

last: Geschwind


title: Global transcriptomic profiling of ischemic/reperfusion injury in an in vivo mouse model.

status: Public on Jan 10 2011

city: Hobart

first: Minghui Jessica

last: Chen

state: Tasmania

address: Menzies Research Institute, University of Tasmania, Private Bag 24

department: Neuroscience group

institute: Menzies Research Institute

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

overall_design: Refer to individual Series


title: Global transcriptomic profiling of ischemic/reperfusion injury in an in vivo Gpx1 -/- transgenic mouse model.

summary: Glutathione peroxidase (Gpx) is a selenium-containing enzyme that catalyses the reduction of a variety of biological peroxides at the expense of reduced glutathione (GSH). Gpx1 is the most abundant isoform and its role has been implicated in neurodegenerative disorders such as Parkinson’s disease (PD), dementia with Lewy bodies tissue (DLB) (Power and Blumbergs, 2009) and traumatic brain injury (Tsuru-Aoyagi et al., 2009). Due to its high abundance, mutation of the Gpx1 allele would lower overall Gpx activity in the brain significantly. Gpx1 knockout (Gpx1-/-) mice do not show overt phenotypic differences, but all indications suggest that these mice are in a chronic “pro-oxidant” state (Cheng et al. 1999; de Haan et al. 2004). Indeed, a recent study from our laboratory illustrated that the absence of Gpx1 exacerbated stroke injury via increased ROS production and vascular permeability (Wong et al. 2008). Furthermore, Gpx1-/- mice demonstrated an increase in caspase-3 activation and greater infarct volume (Crack et al. 2001)

overall_design: Microarray analysis was performed on the right striatum and cortex(corresponded to infarct area) of post-I/R injured brain tissues of Gpx1 -/- brains using Illumina mouse Ref8 V2 genechips. Suture-induced middle cerebral artery occlusion was induced for 2h followed by reperfusion, with tissue extraction taking place 2h, 8h and 24h post-reperfusion (n=4 respectively). Sham controls were included in this study too (n=4 respectively).

first: Nam

last: Cheung

first: Minghui

first: Peter

last: Crack

first: Jayapal

last: Manikandan


title: Dynamic Chromatin Localization of Sirt6 Shapes Stress- and Aging- Related Transcriptional Networks

first: Kun

last: Qu

institute: Stanford University

type: Genome binding/occupancy profiling by genome tiling array


title: Global transcriptomic profiling of ischemic/reperfusion injury in an in vivo wild-type mouse model.

summary: Ischemic stroke triggers severe focal hypoperfusion accompanied with deprivation of oxygen and glucose to the cerebral tissue, together with loss of ATP, depolorization of neurons, elevated extracellular potassium concentration, and subsequently leads to excitotoxicity as well as increased oxidative stress promoting microvascular injury, blood-brain-barrier deregulation, post-ischemic inflammation and eventually the consequential neurological deficit. Although reperfusion of ischemic brain tissue is critical for restoring normal function, it can paradoxically result in secondary damage, called ischemia/reperfusion (I/R) injury.

overall_design: Microarray analysis was performed on the right striatum and cortex (corresponded to infarct area) of post-I/R injured brain tissues of wild-type (WT-MCAO) using Illumina mouse Ref8 V2 genechips. Suture-induced middle cerebral artery occlusion was induced for 2h followed by reperfusion, with tissue extraction taking place 2h, 8h and 24h post-reperfusion (n=4 respectively). Sham controls were included in this study too (n=4 respectively).


title: Regulation of male germ cell cycle arrest and differentiation by DND1 is modulated by genetic background

status: Public on Dec 22 2010

city: Bar Harbor

first: Steven

last: Munger

state: ME

address: 600 Main Street

institute: The Jackson Laboratory

summary: Transcriptional profiling of E14.5 XY germ cells (marked with Oct4-EGFP transgene) from two strain backgrounds (C57BL/6J and 129S1/SvImJ) that differ in their susceptibility to testicular teratomas.

overall_design: Two condition experiment. For each sample, Oct4-EGFP+ germ cells from all XY embyos within a litter were pooled. For the C57BL/6J background, n=3 pooled biological replicates were profiled, and n=2 replicates were obtained and profiled for 129S1/SvImJ.

first: Matthew

last: Cook

first: Blanche

last: Capel


title: IL-1β-driven neutrophil biogenesis and survival preserve anti-bacterial defense in IKKβ deficiency

status: Public on Nov 12 2010

city: Taipei

first: Liang-Chuan

last: Lai

state: Taiwan

address: 1 Jen-Ai Road, Sec 1

department: Physiology

country: Taiwan

institute: National Taiwan University

summary: IKKβ-dependent NF-κB activation is associated with inflammation and tumorigenesis and is critical for innate immunity. Despite risk of immune suppression, pharmacological blockade of IKKβ/NF-κB has been considered as an attractive strategy for treatment of inflammatory diseases and cancer. Unexpectedly, treatment with IKKβ inhibitors caused neutrophilia, which also occurs in mice with inducible IKKβ deletion, termed IkkβΔ mice. IkkβΔ mice show hyperproliferation of granulocyte progenitors and increased neutrophil lifespan. Deletion of IL-1 receptor 1 in IkkβΔ mice restored normal blood cellularity and prevented neutrophil-driven inflammation. However, IkkβΔ/Il-1r1-/- mice, in contrast to IkkβΔ mice, are highly susceptible to bacterial infections indicating that either IKKβ/NF-κB or IL-1R signaling are sufficient for maintaining anti-microbial defenses, but inactivation of both pathways severely compromises innate immunity.

overall_design: Thioglycollate-elicited peritoneal neutrophils were purified from IkkβF/F and IkkβΔ mice using anti-Ly-6G magnetic beads and cultured. Ly-6G+ neutrophils were collected and total RNA was extracted with TRIzol® (Invitrogen) and was purified by RNA micro cleanup Kit (Qiagen). Biotinylated cRNA was synthesized using an RNA Amplification Kit (Ambion) following manufacturer's directions. Biotin-labeled cRNA was hybridized to Illumina Mouse-Ref8 BeadChips (Illumina) and the results were analyzed using BeadStudio v3.1 software. Data analysis and quality control were carried out using Partek® software.

first: Li-Chung

last: Hsu

first: Thomas

last: Enzler

first: Jun

last: Seita

first: Anjuli

last: Timmer

first: Chih-Yuan

last: Lee

first: Ting-Yu

first: Guann-Yi

last: Yu

first: Vlad

last: Temkin

first: Victor

last: Nizet

first: Irving

last: Weissman

first: Michael

last: Karin


title: Conversion of Epiblast Stem Cells to Embryonic Stem Cells by Small Molecules

status: Public on Oct 30 2010

first: Hongyan

last: Zhou

address: 10550 North Torrey Pines Road

institute: the scripps research institute

summary: Recently, (in vitro) pluripotent EpiSCs were derived from the post-implantation egg cylinder stage epiblasts of mouse and rat. These EpiSCs resemble and correspond very closely to the conventional human embryonic stem cells (hESCs) in the colony morphology and culture/signaling requirements for maintaining pluripotency, but exhibit a range of significant phenotypic and signaling response differences from the conventional mouse ES cells (mESCs). These observations strongly support the notion that EpiSCs and hESCs are intrinsically similar, and raise an attractive hypothesis: as mESCs and EpiSCs/hESCs represent two distinct pluripotency states: the mESC-like state representing the ICM of pre-implantation blastcyst and the EpiSC-like state representing the post-implantation epiblasts, whether the epiblast state (including conventional hESCs) can be converted back to the ICM state.   Despite  studies providing evidence that epiblast-like cells exist and transition back and forth within colony of conventional mESCs; mESCs and EpiSCs share substantial set of pluripotency transcriptional factors, including Oct4, Sox2 and Nanog; and mESCs are more stable in culture, in the present study we found that EpiSCs differentiated rapidly  under mESC culture conditions and no “spontaneously” converted mESC could be readily identified and isolated over serial passages at the population or clonal level. Remarkably, we found that blockage of the TGFβ pathway or inhibition of the H3K4 demethylase LSD1 with small molecule inhibitors induced dramatic morphological changes of EpiSCs towards mESC phenotypes with activation of some ICM-specific gene expression. However, full conversion of EpiSCs to a mESC-like state with competence to chimeric contribution can only be readily generated with a combination of inhibitors of LSD1 and ALK. These observations underscore a powerful and direct induction of reprogramming from the developmentally later-stage EpiSCs to a mESC-like stage by a synergy of signaling and direct epigenetic modulations. It also highlights a significant role for TGFβ pathway inhibition in promoting reprogramming to and sustaining true pluripotency, which further supports our recent studies in generating chimerism-competent rat pluripotent cells. Collectively, our studies provide a proof-of-concept demonstration that pluripotency-restricted EpiSCs can be readily converted to a mESC-like state in the absence of any genetic manipulation by precise pharmacological control of signaling pathways that distinguish the two pluripotency states and an epigenetic target simultaneously, and offer a convenient experimental system to further study the mechanism. Such method and concept may also provide an avenue for generating a new type of mESC-like human pluripotent cell.

overall_design: Global gene-expression analyses of the parnate/mAMFGi cells

first: Jin

middle: Y

last: Joo

first: Jeong

middle: T

last: Do

first: Saiyong

last: Zhu

first: Wenlin

last: Li

first: Wen

last: Xiong

last: Kim

first: Kang

last: Zhang

first: Hans

middle: R

last: Schöler

first: Sheng

last: Ding


title: Specific functions for ERK/MAPK signaling during PNS development

status: Public on Oct 16 2010

city: Los Angeles

first: Giovanni

last: Coppola

address: 1524 Gonda, 695 Charles Young Drive South

department: Psychiatry and Neurology

summary: We have established functions of the stimulus dependent MAPKs, ERK1/2 and ERK5 in DRG, motor neuron, and Schwann cell development. Surprisingly, many aspects of early DRG and motor neuron development were found to be ERK1/2 independent and Erk5 deletion had no obvious effect on embryonic PNS. In contrast, Erk1/2 deletion in developing neural crest resulted in peripheral nerves that were devoid of Schwann cell progenitors, and deletion of Erk1/2 in Schwann cell precursors caused disrupted differentiation and marked hypomyelination of axons. The Schwann cell phenotypes are similar to those reported in neuregulin-1 and ErbB mutant mice and neuregulin effects could not be elicited in glial precursors lacking Erk1/2. ERK/MAPK regulation of myelination was specific to Schwann cells, as deletion in oligodendrocyte precursors did not impair myelin formation, but reduced precursor proliferation. Our data suggest a tight linkage between developmental functions of ERK/MAPK signaling and biological actions of specific RTK-activating factors.

overall_design: Microarray analysis on RNA extracts derived from E12.5 Erk1/2CKO(Wnt1) and wildtype DRGs

first: Jason

last: Newbern

first: Xiaoyan

first: Sarah

middle: E

last: Shoemaker

first: Jiang

first: Jian

last: Zhong

first: Yaohong

last: Wu

first: Daniel

last: Bonder

first: Steven

last: Hollenback

last: Geschwind

first: Gary

last: Landreth

first: William

last: Snider


title: To determine the global gene expression response in murine LPS-induced macrophages treated with a bromodomain inhibitor.

status: Public on Nov 10 2010

city: Stevenage

first: Paul

last: Wilson

state: Hertfordshire

address: GlaxoSmithKline Medicine Research Centre

department: Target Sciences

country: United Kingdom

institute: GSK

summary:
Bone marrow-derived macrophages, Unstimulated DMSO Bone marrow-derived macrophages, Unstimulated + I-BET (GSK525762A) Bone marrow-derived macrophages, LPS 1h DMSO Bone marrow-derived macrophages, LPS 1h + I-BET (GSK525762A) Bone marrow-derived macrophages, LPS 2h DMSO Bone marrow-derived macrophages, LPS 2h + I-BET (GSK525762A) Bone marrow-derived macrophages, LPS 4h DMSO Bone marrow-derived macrophages, LPS 4h + I-BET (GSK525762A)
LPS (100 ng/mL) was purchased from Sigma. Bone Marrow-derived macrophages (BMDMs) were differentiated from C57BL/6 bone marrow using 5 ng/mL each of recombinant M-CSF and IL-3 (Peprotech) for 7 days as described (Jeffrey et al, Nature Immunology, 2006). 2 x10^6 BMDMs were treated with DMSO or 1  μM of I-BET for 30 minutes before the addition of LPS (100 ng/mL) for 1, 2 or 4h. Unstimulated control samples were incubated with I-BET only for 1 hour. 500 ng of total RNA from 3 independent samples per group was used to prepare biotin-labeled RNA using Ambion Illumina TotalPrep RNA Amplification Kit (Applied Biosystems) and hybridized to Illumina MouseRef-8 v2.0 expression BeadChip kits. The chips were scanned using Illumina BeadArray Reader.

overall_design: 3 biological replicates and 4 timepoints

first: Kate

last: Jeffrey

first: Alexander

last: Tarakhovsky


title: CpG B and R848 induced gene expression in IRAK2 wildtype and deficient mouse macrophages

status: Public on Sep 23 2010

city: Cleveland

first: Youzhong

last: Wan

state: OH

address: 9500 Euclid Avenue, NE20

department: Immunology

institute: Cleveland Clinic Foundation

summary:
Compared to wildtype macrophages, IRAK2 deficient macrophages show higher induced gene expression in responsse to CpG B, but not R848
Manuscipt title: The dual function of IRAK2 in TLR9-mediated interfereon and proinflammatory cytokine production

overall_design: Bone marrow derived macrophages from wildtype and IRAK2 knockout mouse were stimulated with CpG B or R848 for 2 hours, or untreated.

first: Xiaoxia

last: Li

first: Pieter

middle: W

last: Faber


title: Hepatic gene expression profiling reveals key pathways involved in leptin mediated weight loss in ob/ob mice.

city: Augusta

first: Jin-Xiong

last: She

state: GA

department: Center for Biotechnology and Genomic Medicine

institute: Medical College of Georgia

summary:
The purpose of this study was to identify leptin target genes and subsequent pathways correlated with leptin-mediated weight loss. We utilized the microarray technology to compare two types of leptin administration: one involving a direct stimulatory effect when administered peripherally (subcutaneous: SQ) and another that is indirect, involving a hypothalamic relay that suppresses food intake when leptin is administered centrally (intracerebroventricular: ICV). We report here the impact of central and peripheral administration of leptin on food intake, body weight and body fat composition in ob/ob mice. We also report hepatic gene expression changes caused by central versus peripheral leptin administration.

Keywords: comparison

overall_design:
Leptin deficient (ob/ob) mice were continuously administered leptin over 12-days using central (intracerebroventricular) or peripheral (subcutaneous) route of administration. Liver RNA was extracted and hybridized to Illumina microarrays and gene expression data was analyzed. The global gene expression profiles were compared after the central and peripheral leptin treatments in ob/ob mice and C57BL6 mice were used for the baseline gene expression. The groups are as below:
Liver_B6: C57BL6 mice
Liver_VEH_SQ: ob/ob mice with vehicle subcutaneous treatment
Liver_LEP_SQ: ob/ob mice with leptin subcutaneous treatment
Liver_VEH_ICV: ob/ob mice with vehicle intracerebroventricular treatment,
Liver_LEP_ICV: ob/ob mice with leptin intracerebroventricular treatment,
Liver_LEP_ICVN:  represents four animals from LEP_ICV group in which treatment failed or the cannula may not have been in place. While analyzing the phenotype data, we found that there was no weight loss in these four animals. Sectioning of the brain could not confirm placement of the cannula in these animals. The expression of these animals is very similar to the vehicle treated animals.

first: Ashok

last: Sharma

first: Shoshana

last: Bartell

first: Clifton

last: Baile

first: Bo

last: Chen

first: Robert

last: Podolsky

first: Richard

last: McIndoe


title: Downregulation of Myc is essential for terminal erythroid maturation

status: Public on Oct 13 2010

first: Senthil Raja

last: Jayapal

address: #08-01, Genome, 60 Biopolis Street

department: Stem cell and developmental biology

institute: Genome Institute of singapore

summary: Terminal differentiation of mammalian erythroid progenitors involves 4-5 cell divisions and induction of many erythroid important genes, followed by chromatin and nuclear condensation and enucleation. The protein levels of c-myc (Myc) are reduced dramatically during late stage erythroid maturation, coinciding with cell cycle arrest in G1-phase and enucleation, suggesting possible roles for c-myc in either or both of these processes. Here we demonstrate that ectopic Myc expression affects terminal erythroid maturation in a dose-dependent manner. Expression of Myc at physiological levels did not affect erythroid differentiation or cell cycle shutdown, but specifically blocked erythroid nuclear condensation and enucleation. Myc prevented deacetylation of several lysine residues in histones H3 and H4 that are normally deacetylated during erythroid maturation. When over-expressed at levels higher than the physiological range, Myc blocked erythroid differentiation and the cells continued to proliferate in cytokine-free, serum-containing culture medium with an early erythroblast morphology. These studies reveal an important dose-dependent function of Myc in regulating terminal maturation in mammalian erythroid cells. Our findings further support the emerging notion that Myc regulates chromatin structure by regulating global histone acetylation states.

overall_design: Five groups with three biological replicates in each.

first: Senthil

first: Kian

middle: L

last: Lee

first: Peng

last: Ji

first: Philipp

last: Kaldis

first: Harvey

middle: F

last: Lodish

first: Bing

last: Lim


title: Gene expression profiling in the submandibular gland, stomach, and duodenum of CAVI-deficient mice

status: Public on Oct 02 2010

city: Tampere

first: Pei-wen

last: Pan

address: Biokatu 6

country: Finland

institute: Institute of Medical Technology, University of Tampere

summary: In order to explore the functions of carbonic anhydrase VI (CAVI) more fully, we examined the transcriptomic responses to CAVI deficiency in the submandibular gland, stomach, and duodenum of Car6-/- mice by cDNA microarray. 94, 56, and 127 genes were up- or down-regulated in the above-mentioned tissues of Car6-/- mice, respectively. The functional clustering of differentially expressed genes revealed a number of altered biological processes. In the duodenum, the significantly affected biological pathways included immune system process and retinol metabolic process. Response to oxidative stress and brown fat cell differentiation changed remarkably in the submandibular gland. Notably, the submandibular gland, stomach, and duodenum shared one prominent transcriptional susceptibility pathway-catabolic process.

overall_design: Submandibular gland, stomach, and duodenum samples were collected from three wild-type and three Car6-/- female mice, respectively, at the age of two months. Total RNAs were purified and used for cDNA microarray.

first: Katri

last: Käyrä

first: Jukka

last: Leinonen

first: Marja

last: Nissinen

first: Seppo

last: Parkkila

first: Hannu

last: Rajaniemi


title: Vascular gene expression in mice overexpressing human endothelin-1 targeted to the endothelium

status: Public on Sep 01 2010

city: Montreal

first: Stefania

last: Simeone

state: Quebec

address: 3755 Côte Ste-Catherine Road

department: Hypertension and Vascular Research Unit

institute: Lady Davis Institute for Medical Research

summary: Endothelin-1 (ET-1), an endothelium-derived vasoconstrictor peptide, plays a role in the pathophysiology of cardiovascular disease. Transgenic mice that overexpress human preproET-1 selectively in the endothelium (eET-1) exhibit endothelial dysfunction, hypertrophic remodeling and vascular inflammation of resistance-size arteries in the absence of blood pressure elevation. To understand the mechanisms whereby ET-1 induces vascular damage, vascular gene expression using DNA microarrays was employed. RNA from mesenteric arteries of female and male young (6-7 weeks) and mature (6-8 months) eET-1 and wild type (WT) mice was isolated and changes in gene expression were determined by genome-wide expression profiling using Illumina microarray. This study revealed a set of genes potentially regulated by ET-1, which might be implicated in ET-1 induced-vascular damage.

overall_design:
Samples 1-8: Total RNA obtained from the entire mesenteric arterial tree of young (6-7 weeks) female preproendothelin-1 overexpressing mice compared to age and sex matched wild type littermate controls.

Samples 9-16: Total RNA obtained from the entire mesenteric arterial tree of mature (6-8 months) female preproendothelin-1 overexpressing mice compared to age and sex matched wild type littermate controls.

Samples 17-24: Total RNA obtained from the entire mesenteric arterial tree of young (6-7 weeks) male  preproendothelin-1 overexpressing mice compared to age and sex matched wild type littermate controls.

Samples 25-32: Total RNA obtained from the entire mesenteric arterial tree of mature (6-8 months) male preproendothelin-1 overexpressing mice compared to age and sex matched wild type littermate controls.

first: Pierre

last: Paradis

first: Ernesto

last: Schiffrin


title: Benefits of a 6 week supplementation of sebacic acid on a mouse model of type 2 diabetes (db/db mice)

status: Public on Oct 29 2010

city: Lausanne

first: Frederic

last: Raymond

address: Campus EPFL - Quartier de l'Innovation

department: Functional Genomics

country: Switzerland

institute: Nestle Institute of Health Sciences

summary: This study aimed at investigating the impact of chronic ingestion of sebacic acid (SA), a 10 carbons medium-chain dicarboxylic acid, on glycemic control in a mouse model of type 2 diabetes (db/db mice). Three groups of 15 mice were fed for 6 weeks either a chow diet (Ctrl), or a chow diet supplemented with 1.5% or 15% (SA1.5% and SA15% resp.) energy from SA. Fasting glycemia was measured once a week and HbA1c before and after supplementation. An oral glucose tolerance test (OGTT) was performed at the end of the supplementation. Gene expression was determined by transcriptomic analysis on the liver of the Ctrl and SA15% groups. Results-After 42 days of supplementation, fasting glycemia and HbA1c were ~70% and ~25% lower in the SA15% group compared to other groups showing a beneficial effect of SA on hyperglycemia. During OGTT, blood glucose area under the curve (AUC) was reduced after SA15% compared to other groups. This effect was associated with a tendency for an improved insulin response. In the liver, Pck1 and FBP mRNA were statistically decreased in the SA15% compared to Ctrl suggesting a reduced hepatic glucose output induced by SA.   Conclusions-Dietary supplementation of SA largely improves glycemic control in a mouse model of type 2 diabetes. This beneficial effect may be due (1) to a reduced hepatic glucose output resulting from transcriptional down regulation of key gluconeogenesis genes and (2) to an improved glucose induced-insulin secretion.

overall_design:
Microarray analysis of 6-8 wk old male BKS.Cg-m+/+Leprdb/J 000642 db/db mice. 2 groups. n=15/group:
1) Control group.
2) Sebacic acid high dose group - 15% (77.6g/kg food, ≈9g/kg body weight per day).

first: Christophe

last: Binnert

first: Mathieu

last: Membrez

first: Sylviane

last: Metairon


title: Epithelial-to-Mesenchymal Transition of Murine PTEN-/- Liver Tumor Cells Promotes Tumor Growth and Invasion

status: Public on May 12 2010

city: Hershey

first: Wei

last: Ding

address: 500 University Drive

department: Pediatrics

institute: Pennsylvania State University College of Medicine

summary:
Background: Epithelial-to-Mesenchymal Transition (EMT) is predicted to play a critical role in tumor progression and metastasis in Hepatocellular Carcinoma. Our goal was to elucidate a mechanism of tumor proliferation and metastasis using a novel murine model of EMT.

Methods: 2×106 liver cells isolated from Ptenloxp/loxp;Alb-Cre+ mice, expanded from a single CD133+CD45- cell clone, Passage 0 (P0), were sequentially transplanted to obtain two passages of tumor cells, Passage 1 and 2 (P1 & P2) . Cells were analyzed for gene expression using microarray and real-time PCR. Functional analysis included cell proliferation, migration, and invasion in-vitro and orthotopic tumor growth and metastasis assays in-vivo.

Results: Although P0, P1, and P2 each formed tumors consistent with mixed liver epithelium, within the P2 cells, two distinct cell types were clearly visible: cells with epithelial morphology similar to the P0 cells, and cells with fibroblastoid morphology. The P2 mesenchymal cells demonstrated increased locomotion on wound healing, increased cell invasion on Matrigel basement membrane, increased EMT associated gene Snail1, Zeb1, and Zeb2 expression, and down-regulated E-cadherin. P2 mesenchymal cells demonstrated significantly faster tumor growth compared to P2 Epithelial counterparts, with peritoneal seeding and invasion of intestine, pancreas, spleen, and lymph nodes. Furthermore, P2 mesenchymal cells secreted high levels of Hepatocyte Growth Factor (HGF), which acted in paracrine fashion to drive epithelial cells to undergo EMT.

Conclusion: EMT is associated with a high rate of liver tumor proliferation, invasion, and metastasis in-vivo, which is driven by HGF in a feed-forward mechanism.

overall_design: Total RNA isolated from subcutaneously transplanted tumors with PTENloxp/loxp;Alb-Cre+ genetic background

first: Hanning

last: You

first: Francis

last: LeBlanc

first: Hien

last: Dang

first: C

last: Rountree


title: Control of intestinal homeostasis, colitis and colitis-associated colorectal cancer by the inflammatory caspases

status: Public on Jul 01 2010

first: Garabet

last: Yeretssian

state: QC

address: 3649 Promenade Sir-William Osler

department: Medicine

institute: McGill

summary: Inflammatory caspases are essential effectors of inflammation and cell death. Here, we investigated their roles in colitis and colorectal cancer and report a bimodal regulation of intestinal homeostasis, inflammation and tumorigenesis by caspases-1 and -12. Casp1-/- mice exhibited defects in mucosal tissue repair and succumbed rapidly after dextran sulfate sodium (DSS) administration. This phenotype was rescued by administration of exogenous interleukin-18 and was partially reproduced in mice deficient in the inflammasome adaptor ASC. Casp12-/- mice, in which the inflammasome is derepressed, were resistant to acute colitis and showed signs of enhanced repair. Together with their increased inflammatory response, the enhanced repair response of Casp12-/- mice rendered them more susceptible to colorectal cancer induced by azoxymethane (AOM)+DSS. Taken together, our results indicate that the inflammatory caspases are critical in the induction of inflammation in the gut following injury, which is necessary for tissue repair and maintenance of immune tolerance.

overall_design: Total RNA obtained from isolated tumors or normal colon tissue from wild type and caspase-12 deficient mice were compared.

first: Maya

last: Saleh


title: Comparison of 2 ADAMTS metalloproteases in closure of mouse palate - versican proteolysis in regulating palatal mesenchyme proliferation

first: Courtney

last: Nelson

address: 9500 Euclid Avenue

department: Department of Biomedical Engineering

institute: Cleveland Clinic

summary: We identify a role for two evolutionarily related, secreted metalloproteases of the ADAMTS family (A disintegrin-like and metalloprotease domain with thrombospondin type-1 motif), ADAMTS20 and ADAMTS9, in palatogenesis. Adamts20 mutations cause the mouse white spotting mutant belted (bt), whereas Adamts9 is essential for survival beyond 7.5 days of gestation (E7.5). Functional overlap of Adamts9 with Adamts20 was established in bt/bt:Adamts9+/- mice, which have increased white spotting relative to bt mice, as previously reported, and a fully penetrant cleft palate. Palatal closure was delayed, although eventually completed, in both bt/+;Adamts9+/- and bt/bt mice, demonstrating a cooperative role of these related genes. Adamts9 and Adamts20 are both expressed in palatal mesenchyme, with Adamts9 expressed exclusively in microvascular endothelial cells. Palatal shelves from bt/bt:Adamts9+/- mice fused in culture, suggesting an intact TGFbeta signaling pathway in palatal epithelium, and indicating a temporally specific delay in palatal shelf elevation and growth toward the midline. Palatal shelf mesenchymal cells showed a statistically significant decrease of cell proliferation at E13.5 and E14.5, as well as decreased processing of versican, an ADAMTS substrate, at these stages. Vcan haploinsufficiency led to a greater penetrance of cleft palate in bt mice, and impaired proliferation was also seen in palatal mesenchymal cells of these mice, suggesting a role for ADAMTS-mediated versican proteolysis in palatal closure. In a parallel with recent work identifying a role for a bioactive ADAMTS-generated versican fragment in regulating apoptosis during interdigital web regression, we propose that versican proteolysis may influence palatal mesenchymal cell proliferation.

overall_design: Palatal shelves were dissected from four E13.75 Adamts9+/-:bt/bt embyos (correspond to the 4 samples: Palate_Adamts9+/-:bt/bt_Rep1, Palate_Adamts9+/-:bt/bt_Rep2, Palate_Adamts9+/-:bt/bt_Rep3 and Palate_Adamts9+/-:bt/bt_Rep4) and age-matched 3 wild-type C57Bl/6 embryos (correspond to the 3 samples: Palate_WT_Rep1, Palate_WT_Rep2, and Palate_WT_Rep3) that were used as the controls

first: Hiroyuki

last: Enomoto

first: Robert

last: Somerville

first: Katrina

last: Mielke

first: Laura

last: Dixon

first: Banu

last: Gopalan

first: Kimerly

last: Powell

first: Suneel

middle: S

last: Apte


title: Organogenesis relies on the SoxC transcription factors for the survival of neural and mesenchymal progenitors

status: Public on Apr 15 2010

first: Pallavi

last: Bhattaram

summary:
During organogenesis, neural and mesenchymal progenitor cells give rise to many cell lineages, but their molecular requirements for self-renewal and lineage decisions are incompletely understood. Here we show that their survival critically relies on the redundantly acting SoxC transcription factors Sox4, Sox11 and Sox12. The more SoxC alleles are deleted in mouse embryos, the more severe and widespread organ hypoplasia is. SoxC triple-null embryos die at mid-gestation unturned and tiny, with normal patterning and lineage specification, but with massively dying neural and mesenchymal progenitor cells. Specific inactivation of SoxC genes in neural and mesenchymal cells leads to selective apoptosis of these cells, suggesting SoxC cell-autonomous roles. Tead2 functionally interacts with the SoxC genes in embryonic development, and is a direct target of the SoxC proteins. The SoxC genes therefore ensure neural and mesenchymal progenitor cell survival and act in part by activating this transcriptional mediator of the Hippo signaling pathway.
During organogenesis, neural and mesenchymal progenitor cells give rise to many cell lineages, but their molecular requirements for self-renewal and lineage decisions are incompletely understood. Here we show that their survival critically relies on the redundantly acting SoxC transcription factors Sox4, Sox11 and Sox12. The more SoxC alleles are deleted in mouse embryos, the more severe and widespread organ hypoplasia is. SoxC triple-null embryos die at mid-gestation unturned and tiny, with normal patterning and lineage specification, but with massively dying neural and mesenchymal progenitor cells. Specific inactivation of SoxC genes in neural and mesenchymal cells leads to selective apoptosis of these cells, suggesting SoxC cell-autonomous roles. Tead2 functionally interacts with the SoxC genes in embryonic development, and is a direct target of the SoxC proteins. The SoxC genes therefore ensure neural and mesenchymal progenitor cell survival and act in part by activating this transcriptional mediator of the Hippo signaling pathway.

overall_design: Total RNA isolated from limb bud cells in culture treated with Cre recombinase expressing adenovirus to inactivate floxed SoxC genes was compared to total RNA isolated from cells treated with LacZ expressing adenovirus as well as untreated cells as controls.

first: Alfredo

last: Penzo-Mendez

first: Veronique

last: Lefebvre


title: Gene Expression Analysis of Sox17-induced Mouse Embryonic Stem Cells

status: Public on Mar 31 2010

city: Cambridge

first: Kathy

last: Niakan

state: MA

address: 7 Divinity Ave

department: Stem Cell and Regenerative Biology

institute: Harvard University

summary: To determine the effect of Sox17 overexpression in mouse embryonic stem (ES) cells, we performed gain-of-function analysis by generating ES cell lines carrying a doxycycline inducible FLAG-tagged Sox17 transgene. We treated Sox17-inducible ES cells with doxycycline, collected RNA and performed genome-wide transcriptional analysis. We found that genes invovled in adhesion function and basement membrane establishment were transcriptionally upregulated in ES cells upon induction of Sox17. We also observed downregulation in the transcription of genes involved in pathways known to be functionally important for ES cell pluripotency and self-renewal. However, Sox17 expression was not sufficient to rapidly down-regulate Sox2, Nanog, and Oct4.

overall_design: Two independent doxycycline inducible Sox17-overexpressing mouse embryonic stem cells were derived. The genes expression changes in the Sox17-induced cells were compared to untreated (no doxycycline) controls and to control cells treated with or without doxycycline. The total RNA from these samples were amplified using Ambion Illumina TotalPrep RNA Amplification kit and arrayed on Illumina MouseRef8 v2 chips.

middle: K

first: Richard

last: Sherwood


title: Alternate protein kinase A activity identifies a unique population of stromal cells in adult bone

status: Public on Mar 21 2010

city: Bethesda

first: Kitman

last: Tsang

state: MD

address: 10 Center Drive, 10-CRC, Rm1E-3216

institute: SEGEN/PDEGEN/NICHD/NIH

summary: We investigated the Prkar1a+/- mice when bred with Prkaca+/- genetic backgrounds. Prkar1a+/-Prkaca+/- mice not only continued to develop bone lesions but also demonstrated a significant increase in both the number and the severity of the lesions, as well as a reduction in the age of first appearance of any bone abnormality.  Histological analysis of bone from Prkar1a+/-Prkaca+/- mice showed that lesions had similarity to tumors from humans with CNC and some resemblance (but also differences) from humans and mice with fibrous dysplasia (FD). Prkar1a+/- and Prkar1a+/-Prkaca+/- mouse lesions always involved a particular sub-population of cells that could be identified as belonging to the osteoblastic lineage, that were initially located on the endosteal surface of the periosteum and nearby trabecular bone proximal to the growth plate of the long bones and vertebrae, and resembled bone stromal cells (BSCs). The bone lesions expressed high level of mesenchymal proteins like n-cadherin, vimentin, snail1, twist1, mmp2 and mmp9 when compared to WT bone. On top of this, bone lesions from  Prkar1a+/-Prkaca+/- mice also showed an increased expression of keratin related genes, which are involved in hair follicle and epithelial differentiation, when compared to lesions from Prkar1a+/- mice.

overall_design: Total RNA obtained from bone lesions from Prkar1a+/- and Prkar1a+/-Prkaca+/- mice were compared to those obtained from WT and Prkaca+/- mice.

first: K

first: M

last: Nesterova

last: Stratakis

last: Cheadle

first: T

last: Watkins


title: Effect of hIAPP aggregation on gene expression by mouse bone marrow-derived macrophages after 12 hours

status: Public on Aug 11 2010

city: Vancouver

first: Clara

last: Westwell-Roper

state: BC

address: 950 West 28th Ave

department: Pathology and Laboratory Medicine

institute: Child and Family Research Institute, University of British Columbia

summary: The purpose of this experiment was to determine changes in gene expression by bone marrow-derived macrophages (BMDMs) treated with synthetic human vs. rodent islet amyloid polypeptide (IAPP). Synthetic human IAPP at 15 uM aggregates to form fibrils in vitro, whereas rodent IAPP is non-amyloidogenic. We hypothesized that interaction of macrophages with human IAPP aggregates can activate pro-inflammatory signalling pathways in macrophages, as described for other amyloidogenic peptides.

overall_design: This array includes eight samples from one experiment, with two groups of four replicates each. Each replicate represents BMDMs from one well of a 24-well plate. The control group was treated with 15 uM rat IAPP for 12 hours prior to total RNA extraction; the experimental group was treated with 15 uM human IAPP.

first: C

last: Verchere


title: eIF4E phosphorylation promotes tumorigenesis and is associated with prostate cancer progression

status: Public on Aug 17 2010

city: Stockholm

first: Ola

last: Larsson

department: Department of oncology-pathology

country: Sweden

institute: Karolinska Institutet

summary: Translational regulation plays a critical role in cell growth and proliferation, and its dysregulation results in cancer. Aberrant expression of the mRNA 5’cap-binding protein, eIF4E, has been implicated in cancer development and progression. eIF4E activity is promoted by phosphorylation. Here we show that “knock-in” mice in which eIF4E cannot be phosphorylated are resistant to tumorigenesis in a prostate cancer model. We identify multiple candidate genes involved in the resistance to oncogenic transformation. Importantly, phosphorylation of eIF4E is increased in hormone-refractory prostate cancer, the deadliest stage of the disease. Our results highlight eIF4E phosphorylation as a critical event in tumorigenesis.

overall_design: Comaparison of total RNA and polysomal RNA from mouse embryo fibroblasts derived from WT and eIF4E-KI (non phosphorylatable eIF4E) mice

first: Nahum

last: Sonenberg


title: Global gene expression profiles of mouse ESCs, disease-specific iPSCs, and gene-corrected iPSCs

status: Public on Apr 16 2010

city: Münster

first: Boris

last: Greber

address: Röntgenstraße 20

department: Cell and Developmental Biology

institute: Max Planck Institute for Molecular Biomedicine

summary: The use of patient-derived induced pluripotent stem (iPS) cells as treatment for genetic diseases entails genetic repair or transfer of genetic information as a prerequisite. We have chosen the murine model of tyrosinemia type 1 (fumarylacetoacetate hydrolase deficiency; FAH(-/-) mice) as a paradigm for hereditary metabolic liver disorders and evaluated fibroblast-derived FAH(-/-)-iPS cell lines as targets for gene correction. By aggregating FAH(-/-)-iPS cells with tetraploid embryos, we obtained FAH-/--iPS cell–derived mice, which exhibited the phenotype of the founding FAH(-/-)-mice. We then rescued the diseased phenotype by lentiviral transduction of FAH-cDNA and performed embryo aggregation with these gene-corrected FAHgc-iPS cells to obtain viable healthy mice. Our results demonstrate that iPS cell technology is a valid approach to establish mouse disease models directly from somatic cells bearing genetic defects. Furthermore, established iPS cell lines can be genetically manipulated without loss of pluripotency for treatment of genetic diseases.

overall_design: 6 samples: 1 MEF, 1ESC, 4 iPSCs


title: Expression profiles of ES cells, epiblast stem cells, and epiblast stem cells reverted to an ES-like state

status: Public on Feb 21 2010

summary: This analysis compares the expression profiles of CGR8 ES cells, E3 epiblast stem cells, and E3R cells (E3 EpiSCs reverted to an ES-like state).

overall_design: All three lines were grown under their respective standard conditions.


title: 12h pathway stimulation / inhibition experiment in mouse ES cells

summary: This experiment records the transcriptional responses of mES cells (line OG2) to FGF/ERK stimulation in the presence of LIF, to LIF/STAT3 inhibition in the presence of an FGF/ERK inhibitor, and to combined FGF/ERK stimulation / LIF/STAT3 inhibition.

overall_design: ES cells were grown feeder-free on gelatin in KSR medium containing an FGF/ERK inhibitor and LIF and were then treated for 12h as indicated for the individual samples.


title: 3h pathway stimulation / inhibition experiment in epiblast stem cells

summary: This experiment records the transcriptional responses of EpiSCs (line E3) to FGF/ERK inhibition, GSK3ß inhibition, LIF/STAT3 activation, as well as combined treatment for 3 hours each.

overall_design: EpiSCs were grown in KSR medium on low-density feeders. At semiconfluency, media were changed as detailed for the individual samples. Cells were harvested for RNA isolation 3 hours later.


title: Prkar1a haploinsufficiency leads to an overall increase in tumors caused by other genetic defects or chemical induction

status: Public on Dec 24 2009

first: Madson

last: Almeida

address: 10 Center Drive, MSC 1103

department: Section on Genetics and Endocrinology / NICHD

institute: NIH

summary:
[original title] Prkar1a haploinsufficiency in mice leads to an overall increase in tumors caused by other genetic defects or chemical induction

We investigated the Prkar1a+/- mice when bred within the Rb1+/- or Trp53+/- genetic backgrounds, or treated with a 2-step skin carcinogenesis protocol. Prkar1a+/-Trp53+/- mice developed more bone sarcomas than Trp53+/- mice (p<0.05) and Prkar1a+/-Rb1+/- mice grew more and larger pituitary and thyroid tumors than Rb1+/- mice. All mice with double heterozygosity had significantly reduced life-spans compared with their single-heterozygous counterparts. Finally, Prkar1a+/- mice developed more papillomas than wild-type animals when treated with a 2-step skin carcinogenesis protocol. A whole-genome transcriptome profiling of tumors produced by all three models identified Wnt signaling as the main pathway activated by abnormal cAMP signaling in these tissues, along with (expected) cell cycle gene abnormalities, all confirmed by qRT-PCR array and immunohistochemical analyses.

overall_design:
Total RNA obtained from skin papillomas from Prkar1a+/- mice were compared to those obtained from WT mice.
Total RNA obtained from pituitary and thyroid tumors from Rb1+/- mice were compared to those samples obtained from Prkar1a+/- Rb1+/- mice. Total RNA obtained from sarcomas from Tp53+/- mice were compared to those samples obtained from Prkar1a+/- Tp53+/- mice.


title: Expression profiles of two epiblast stem cell lines and one ES cell line

summary: This analysis compares the expression profiles of E3 epiblast stem cells (hybrid background), T9 EpiSCs (129 inbred background), and OG2 ES cells.


title: Transcriptomic Comparison in the Retinas of Two Mouse Models of Diabetes

status: Public on Jan 30 2010

first: Penn State

last: COM

department: Genome Sciences Facility

institute: Penn State College of Medicine

summary: Mouse models of type I diabetes offer the potential to combine genetic approaches with other pharmacological or physiological manipulations to investigate the pathophysiology and treatment of diabetic retinopathy.  Type I diabetes is induced in mice through chemical toxins or may arise spontaneously from genetic mutations.  Both models are associated with retinal vascular and neuronal changes.  Retinal transcriptomic responses in C57BL/6J mice treated with strepotozotocin and Ins2Akita were compared after 3 months of hyperglycemia.  Specific gene expression changes suggest a neurovascular inflammatory response in diabetic retinopathy.  Genes common to the two models may represent the response of the retina to hyperglycemia; while changes unique to each model may represent time-dependent disease progression differences in the various models.  Further investigation of the commonalities and differences between mouse models of type I diabetes may define cause and effect events in early diabetic retinopathy disease progression.

overall_design: To compare two mouse models of type I diabetes, ie, STZ-induced and Ins2Akita, a gene expression analysis was conducted examining whole retinas collected after 3 months of hyperglycemia.

first: Willard

last: Freeman

first: Georgina

middle: V

last: Bixler

first: Robert

last: Brucklacher

first: Erin

last: Walsh

first: Scot

last: Kimball

first: Leonard

last: Jefferson

first: Sarah

last: Bronson


title: Expression profiles of epiblast stem cells and embryonic stem cells

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

overall_design: Refer to individual Series


title: Specificity for the Nature of Inflammation in Lung Cancer Promotion in Mice

status: Public on Dec 23 2009

city: Houston

first: Scott

last: Evans

state: TX

address: 1400 Holcombe Blvd

department: Pulmonary Medicine - Unit 1462

institute: University of Texas-M.D. Anderson Cancer Center

summary:
A large amount of epidemiologic data supports a role for chronic inflammation in epithelial carcinogenesis. In the lung, several studies have found that smokers with chronic obstructive pulmonary disease (COPD), an inflammatory disease of the airways and alveoli, have an increased risk of lung cancer (1.3 to 4.9 fold) compared to smokers without COPD. We have also shown that COPD-like airway inflammation induced by an aerosolized lysate of non-typeable Hemophilus influenzae (NTHi) promotes lung cancer in a Clara cell-targeted K-ras mutant mouse model (CC-LR) of lung cancer. In contrast, existing epidemiologic data suggest that allergic inflammation of the airways may be protective against lung cancer. We tested this association in a mouse model of allergic airway inflammation. CC-LR mice were sensitized to ovalbumin by intraperitoneal injection weekly for two weeks, then challenged for 30 min to an aerosol of ovalbumin in 0.9% saline weekly for eight weeks. This resulted in eosinophilic lung inflammation associated with increased levels of T helper 2 (Th2) cytokines and mucous metaplasia of airway epithelium, similar to what is seen in asthma patients. However, consistent with epidemiologic data, this type of inflammation did not result in any significant differences in lung surface tumor number (22 ± 3 in OVA exposed vs 26 ± 6 in control mice). We conclude that asthma-like (Th2) inflammation does not promote lung carcinogenesis in a Ras-initiated background, and demonstrate a clear specificity for the nature of inflammation in lung cancer promotion. These findings will assist in determination of the essential cells and signaling events in lung cancer promotion by inflammation.

Keywords: lung, chonic inflammation, microarray

overall_design: Wildtype or CC-LR (a Clara cell-targeted K-ras mutant mouse model of lung cancer) mice were either challenged with an aerosol of an NTHi lysate or to an aerosol of ovalbumin for eight weeks, and microarray analysis was performed on whole lung homogenates from mice on the first day after the 8th exposure.

first: Seyed

middle: J

last: Moghaddam


title: Analysis of altered gene expressions in valproate-treated Disc1-L100P mutant mice

status: Public on Nov 24 2009

city: Toronto

first: Paul

middle: C

last: Boutros

state: Ontario

address: 101 College Street, Suite 800

institute: Ontario Institute for Cancer Research

summary:
Microarray analysis revealed that changes in genes expressions are brain region-dependent; expression of several genes are affected by point mutation L100P, which was verified by RT-PCR (Lcn2, Cyr61, Slc6a12, Slc40a1, Egr2), a few genes are affected by genotype and valproate (Dusp1 and Purb), suggesting their role in valproate-induced benificial effect on sensorimotor gaiting in Disc1-L100P mutant mice. The final conclusion will be drawn after series of RT-PCR confirmation.

Keywords: drug response and genetic modification

overall_design: Unequal two-factor, two-level experiment with drug/control and genetic-variation/wild-type as the factors. 4 datasets of 4 different tissues

first: Tatiana

last: Lipina

first: F

middle: N

last: Haque

first: Albert

middle: H

last: Wong

first: John

last: Roder


title: 12h pathway stimulation / inhibition experiment in epiblast stem cells

first: Boris

last: Greber

summary: This experiment records the transcriptional responses of EpiSCs (line E3) to FGF/ERK inhibition, GSK3ß inhibition, LIF/STAT3 activation, as well as combined treatment for 12 hours each.

overall_design: EpiSCs were grown in KSR medium on low-density feeders. At semiconfluency, media were changed as detailed for the individual samples. Cells were harvested for RNA isolation 12 hours later.


title: Heparan Sulfation Dependent FGF Signalling Maintains ES Cells Primed for Differentiation in a Heterogeneous State

status: Public on Nov 13 2009

city: Singapore

first: Kian Leong

last: LEE

state: Singapore

address: #07-21, 8 College Road

department: Duke-NUS Medical School

institute: National University of Singapore (NUS)

summary: Embryonic stem (ES) cells continuously decide whether to maintain pluripotency or differentiate. While exogenous LIF and BMP4 perpetuate a pluripotent state, less is known about factors initiating differentiation. We show that heparan sulfate (HS) proteoglycans are critical co-receptors for signals inducing ES cell differentiation. Genetic targeting of NDST1 and 2, two enzymes required for N-sulfation of proteoglycans, blocked differentiation. This phenotype was rescued by HS presented in trans or by soluble heparin. NaClO3-, which reduces sulfation of proteoglycans, potently blocked differentiation of wild type cells. Mechanistically, N-sulfation was identified to be critical for functional autocrine FGF4 signalling. Micro array analysis identified the pluripotency maintaining transcription factors Nanog, KLF2/4/8, Tbx3 and Tcf3 to be negatively regulated, whereas markers of differentiation such as Gbx2, Dnmt3b, FGF5 and Brachyury were induced by sulfation-dependent-FGFR signalling. We show that several of these genes are heterogeneously expressed in ES cells and targeting of heparan sulfation or FGFR-signalling facilitated a homogenous Nanog/KLF4/Tbx3 positive ES cell state. This finding suggests that the recently discovered heterogeneous state of ES cells is regulated by HS-dependent FGFR signalling. Similarly, culturing blastocysts with NaClO3- eliminated GATA6 positive primitive endoderm progenitors generating a homogenous Nanog positive inner cell mass. Functionally, reduction of sulfation robustly improved de novo ES cell derivation efficiency. We conclude that N-sulfated HS is required for FGF4 signalling to maintain ES cells primed for differentiation in a heterogeneous state. Inhibiting this pathway facilitates a more naïve ground state.

overall_design: Four groups with three biological replicates and a technical duplicate in each

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