title: Mig-6 plays a critical role in the regulation of cholesterol homeostasis and bile acid synthesis.

status: Public on Aug 31 2011

city: Grand Rapids

first: TaeHoon

last: Kim

state: Michigan

address: 333 Bostwick Avenue NE

department: Department of Obstetrics, Gynecology & Reproductive Biology

institute: Michigan State University College of Human Medicine

summary: The disruption of cholesterol homeostasis leads to an increase in cholesterol levels which results in the development of cardiovascular disease. Mitogen Inducible Gene 6 (Mig-6) is an immediate early response gene that can be induced by various mitogens, stresses, and hormones. To identify the metabolic role of Mig-6 in the liver, we conditionally ablated Mig-6 in the liver using the Albumin-Cre mouse model (Albcre/+Mig-6f/f; Mig-6d/d). Mig-6d/d mice exhibit hepatomegaly and fatty liver. Serum levels of total, LDL, and HDL cholesterol and hepatic lipid were significantly increased in the Mig-6d/d mice. The daily excretion of fecal bile acids was significantly decreased in the Mig-6d/d mice. DNA microarray analysis of mRNA isolated from the livers of these mice showed alterations in genes that regulate lipid metabolism, bile acid, and cholesterol synthesis, while the expression of genes that regulate biliary excretion of bile acid and triglyceride synthesis showed no difference in the Mig-6d/d mice compared to Mig-6f/f controls. These results indicate that Mig-6 plays an important role in cholesterol homeostasis and bile acid synthesis. Mice with liver specific conditional ablation of Mig-6 develop hepatomegaly and increased intrahepatic lipid and provide a novel model system to investigate the genetic and molecular events involved in the regulation of cholesterol homeostasis and bile acid synthesis. Defining the molecular mechanisms by which Mig-6 regulates cholesterol homeostasis will provide new insights into the development of more effective ways for the treatment and prevention of cardiovascular disease.

overall_design: Eight week old Mig-6f/f vs Mig-6d/d male mice after undergoing a 24 hour fast

first: Bon

last: Ku

first: Tae

middle: H

first: Lisa

middle: D

last: White

first: Robert

last: Stevens

first: Francesco

last: DeMayo

first: Jae-wook

last: Jeong


title: Expression data from primary hepatocytes knocking down or overexpressing IRE1a

city: Shanghai

first: Ting

last: Mao

address: 294 Taiyuan Road

country: China

institute: INS, SIBS, CAS

summary:
The ER-resident protein kinase/endoribonuclease IRE1 is activated through trans-autophosphorylation in response to protein folding overload in the ER lumen and maintains ER homeostasis by triggering a key branch of the unfolded protein response. Here we show that mammalian IRE1a in liver cells is also phosphorylated by a kinase other than itself in response to metabolic stimuli. Glucagon stimulated protein kinase PKA, which in turn phosphorylated IRE1a at Ser724, a highly conserved site within the kinase activation domain. Blocking Ser724 phosphorylation impaired the ability of IRE1a to augment the upregulation by glucagon signaling of the expression of gluconeogenic genes. Moreover, hepatic IRE1a was highly phosphorylated at Ser724 by PKA in mice with obesity, and silencing hepatic IRE1a markedly reduced hyperglycemia and glucose intolerance. Hence, these results suggest that IRE1a integrates signals from both the ER lumen and the cytoplasm in the liver and is coupled to the glucagon signaling in the regulation of glucose metabolism.
We used DNA microarray to analyze the transcriptomic change upon IRE1a overexpression or IRE1a depletion in primary hepatocytes, to study the changes related to IRE1a

overall_design: Primary hepatocytes were infected with the desired adenoviruses (Ad-EGFP, Ad-WT, Ad-S724A, Ad-shCON, Ad-shIRE1a#2) or treated with glucagon. Total cellular RNA was isolated with TRIzol (Invitrogen) and subjected to analysis by Affymetrix Mouse Genome 430 2.0 Arrays. Three experiments were independently conducted.

first: Jialiang

last: Huang

first: Yong

last: Liu


title: Comparison of Flk-1+/Etv2- vs Flk-1+/Etv2+ populations

city: Kobe

first: Hiroshi

last: Kataoka

state: Hyogo

department: Stem Cell Biology

country: Japan

institute: RIKEN CDB

summary:
Screening for genes up in Etv2+ cells within Flk-1+ ES derived mesoderm
Microarray analysis performed to screen for the candidate genes regulated by Etv2. Differentiated Flk-1+ mesoderm can be devided into Etv2+ or-. Etv2+ cells are assumed to be committed to hemato/endothelial cells. Comparison of two populations can reveal genes relevant in this commitment.

overall_design: Extract RNA from sorted  Flk-1+/Etv2- vs Flk-1+/Etv2+ populations.Etv2-Venus KI ES cells were differentiated on OP9 for 4-5 days and Flk-1+ population was separated into Etv2-Venus+ or- cells. Total RNA was purified from each population for analysis.

first: Misato

last: Hayashi

first: Shin-Ichi

last: Nishikawa

first: Martin

middle: L

last: Jakt

first: Takaya

last: Kasukawa


title: Comparison of Flk-1+/PDGFRa+(Flk-1PRa+(DP)) population from Etv2Het vs Etv2KO ES cells

summary: Screening for genes regulated by Etv2 within Flk-1+/PDGFRa+ ES derived mesoderm.Microarray analysis performed to screen for the candidate genes regulated by Etv2.  TT2 ES cells differentiated on OP9 feeder cells were sorted using Flk-1 and PDGFRa antibodies.Gene expressions from these two populations were compared.

overall_design: Extract RNA from sorted  Flk-1+/PDGFRa+ populations from Etv2Het vs KO cells. To obtain primitive mesoderm cells TT2 ES cells of corresponding genotypes were differentiated on OP9 cells for 4 days.  Flk-1+/PDGFRa+ populations were sorted from Etv2 Het vs. KO cells for RNA extraction.


title: CD4+ T cell gene expression in B6 vs B6.Sle1c2 mice

status: Public on Aug 30 2011

city: Gainesville

first: Laurence

middle: M

last: Morel

state: FL

department: Pathology, Immunology and Laboratory Medicine

country: USA

institute: University of Florida

summary:
Sle1c is a sublocus of the NZM2410-derived Sle1 major susceptibility locus.  We have previously shown that Sle1c contributes to lupus pathogenesis by conferring CD4+ T cell-intrinsic hyperactivation and increased susceptibility to chronic graft-versus-host disease (cGVHD) that mapped to the centromeric portion of the locus.  In this study, we have refined the centromeric sublocus to a 675Kb interval, termed Sle1c2.  Recombinant congenic strains expressing Sle1c2 exhibited a T cell-intrinsic CD4+ T cell hyperactivation and cGVHD susceptibility, similar to mice with the parental Sle1c.
We performed a microarray analysis on CD4+ T cells to gain insights into the transcriptional programs that regulate the hyperactivation conferred by Sle1c2.

overall_design: CD4+ T cell cDNA was prepared from spenocytes from 5 mice from each strain and B6.Sle1c2 gene expression was compared to B6 gene expresion.

first: Daniel

middle: J

last: Perry

first: Henry

middle: V

last: Baker

first: Igor

last: Dozmorov


title: Role of Cofilin 1 pathway and actin dynamics in nuclear retinoid receptor function

status: Public on Aug 26 2011

city: Frederick

first: Jun

last: Yang

state: MD

address: P. O. Box B

institute: SAIC-Frederick, Inc

summary: We have investigated the role of actin dynamics and the effect of actin cytoskeleton modifying agents on retinoid receptor-mediated transactivation. Using Nef, an actin modifying HIV-1 protein, the role of LMK1/CFL1-mediated actin dynamics in receptor function was studied. The effect of Nef expression on transcriptome was investigated following transfection of HEK293 cells with Nef-expressing plasmid. The array data identified Nef-induced inhibition of a number of genes that contain retinoid receptor binding sites in their promoters.

overall_design: The experiment was designed to study the effect of expression of HIV-1 Nef protein on gene expression levels in HEK293 cells. Cells were transfected in three different experiments (each time in duplicate) with Nef expressing plasmid and a plasmid that contained a non-expressing Nef construct (Nef/Stop) as control. The cells were harvested after 36 of transfection and processed for gene array.

first: Mohammad

last: Ishaq

first: Ven

last: Natarajan


title: Miz-1 is required to coordinate the pre-TCR-dependent transitional step in DN3/DN4 thymocytes

status: Public on Aug 24 2011

city: Montréal

first: Lothar

last: Vassen

state: Quebec

address: 110, avenue des Pins Ouest

department: Hematopoiesis and Cancer

country: Canada

institute: IRCM

summary:
Lineage negative, CD44 negative, CD25 positive thymocytes were isolated from wt mice or  Miz1 POZ-domain knockout mice to analyze the effect of loss of Miz1 in the DN3 population of T-cells
We used the mouse Affymetrix MOE430-2 microarray to characterize global gene expression changes of DN3 thymocytes from Miz1 knockout mice.

overall_design: We performed microarray based gene expression profiling to determine the effect of loss of Miz1 activity on the gene expression pattern of mouse DN3 thymocytes from wt and Miz1-delta-POZ mice.

first: Ingrid

last: Saba

first: Christian

last: Kosan

first: Tarik

last: Moroy


title: Differential pre-mRNA processing in Crebbp+/- mice

status: Public on Aug 25 2011

city: Plantagenet

first: Madeleine

middle: E.

last: Lemieux

state: ON

address: 275 Main St., Suite 252

institute: Bioinfo

summary: The presence of unspliced transcripts in hematopoietic stem cells (HSCs) and the proposed association of CREBBP with the constitutive production of unspliced RNA and with pre-mRNA processing prompted us to examine more closely an anomaly we had noted in microarray-based gene expression studies but had previously attributed to experimental noise. We noticed that more than half of the probe sets down-regulated in Crebbp+/- fetal liver HSCs (FLHSCs) relative to wild-type (WT) mapped entirely within introns, rather than detecting exonic or spliced sequences. We therefore set out to test whether this might be evidence that reduced CREBBP levels selectively alter the generation of full-length, unspliced pre-mRNA. We also asked whether this process might be associated with differentiation since self-renewal and lineage commitment are the both responses for which HSCs are primed.

overall_design:
Total RNA from wild-type, Crebbp+/-, Ep300+/-, Cdkn1a-/- FLHSCs and from wild type and Crebbp+/- mouse embryonic fibroblasts (MEFs) was isolated and hybridized to Affymetrix Mouse 430 2.0 expression microarrays. Fetal liver HSC RNA was amplified using the Ovation kit prior to hybridization.
cell type comparison

middle: E


title: The consequences of n-3 polyunsaturated fatty acids (PUFA) depletion on hepatic lipid metabolism in mice

city: Brussels

first: Jean-Baptiste

last: Demoulin

address: av Hippocrate 75, B1.74.05

department: de Duve Institute

country: Belgium

institute: Université catholique de Louvain

summary: In the present study, we investigated the consequences of n-3 polyunsaturated fatty acids (PUFA) depletion on hepatic lipid metabolism in mice fed during three months with a diet presenting a high n-6/n-3 PUFA ratio to induce n-3 PUFA depletion. Microarray analyses were performed to identify the molecular targets involved in the development of hepatic steatosis associated with n-3 PUFA depletion.

overall_design: Male C57Bl/6J mice (9 weeks old) were housed in groups of four mice per cage at 22°C in a 12h light/dark cycle and given free access to diet and water.  After an acclimatization period of 1 week, the mice were fed a control (CT) or an n-3 PUFA-depleted diet (DEF) for 3 months. At the end of the study period, mice (CT, n=6; DEF, n=7) were anesthetized after a 6h period of fasting. Some mice (CT: n=4 et DEF: n=7) were anesthetized without being starved. A fraction of the main liver lobe was fixed-frozen in isopentane and kept at -80°C for histological analysis. The excess tissue material was immediately clamped in liquid N2 and kept at -80°C. All mice experiments were approved by the local animal ethics committee, and the housing conditions were as specified by the Belgian Law of November 14, 1993 on the protection of laboratory animals (agreement n° LA 1230314).

first: Barbara

last: Pachikian

first: Ahmed

last: Essaghir

first: Nathalie

last: Delzenne


title: Gene expression data of BCR-ABL1 transformed myeloid cells from BCL6 wild-type and BCL6 knockout mice treated with and without Imatinib and RI-BPI

city: Los Angeles

first: Markus

last: Müschen

state: CA

address: 4650 Sunset Blvd

department: Childrens Hospital Los Angeles

institute: University of Southern California

summary: To identify differences in the gene regulation between BCL6+/+ and BCL6-/- CML cells a gene expression analysis has been performed. We investigated the gene expression pattern in BCL6+/+ cells in the presence or absence of Imatinib and a combination of Imatinib and RI-BPI (a novel retro-inverso BCL6 peptide inhibitor). In BCL6-/- CML cells, we investigated the gene expression pattern in the presence or absence of Imatinib.

overall_design: BCR-ABL1 transformed myeloid cells from BCL6+/+ mice were cultured in the presence or absence of 10µM Imatinib or 10µM Imatinib and 20µM RI-BPI for 16 hours. BCR-ABL1 transformed myeloid cells from BCL6-/- mice were cultured in the presence or absence of 10µM Imatinib. Two samples for each condition were processed.

last: Hurtz


title: Genome-wide analysis of Ollier disease: Is it all in the genes?

city: Leiden

first: Twinkal

middle: Chandubhai

last: Pansuriya

state: Zuid-Holland

address: Albinusdreef 2

department: Pathology

country: Netherlands

institute: LUMC

type:
Expression profiling by array
Genome variation profiling by SNP array

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

overall_design: Refer to individual Series


title: Gene Expression Data Following Chronic Vehicle or Fluoxetine Treatment in Thirty Mouse Inbred Lines

city: Chapel Hill

first: Cristina

last: Santos

address: 120 Mason Farm Road

department: Pharmacy (DPET)

institute: UNC-CH

summary: In order to understand how biochemical and genetic differences correlate with treatment response, we measured depressive-like behavior, gene expression and the levels of thirty-six neurobiochemical analytes across a panel of genetically-diverse mouse inbred lines after chronic treatment with vehicle or fluoxetine. Neurobiochemical markers were chosen based on their putative molecular function within pathways proposed to underlie depression, which include neuronal transmission, HPA-axis regulation, and neuroimmune processes. The goal of this study is to establish genetic and biochemical biomarkers that can predict treatment response and to propose a molecular pathway that is critical in mediating anti-depressant response.

overall_design: Thirty mouse inbred strains (129S1/SvImJ, A/J, AKR/J, BALB/cJ, BTBRT T(+) tf/J, BUB/BnJ, C3H/HeJ, C57BL/6J, C57BLKS/J, C57BR/cdJ, C58/J, CBA/J, CE/J, DBA/2J, FVB/NJ, I/LnJ, LG/J, LP/J, MA/MyJ, MRL/MpJ, NOD/LtJ, NOR/LtJ, NZB/BlNJ, NZW/LacJ, P/J, PL/J, RIIIS/J, SJL/J, SM/J, and SWR/J)  aged 5-6 weeks old were obtained from The Jackson Laboratory (Bar Harbor, ME). Male mice were kept in polycarbonate cages on a 12-hour light/dark cycle (lights on at 0700h) with access to food and water ad libitum. Following one week of habituation, mice were randomized to either control or treatment group (n=12 male mice per strain per treatment group). Mean water intake for each strain was determined previously by measuring daily water consumption for three weeks (n=12 mice per strain). This information, along with average weight measurements for each strain, was used to determine the amount of fluoxetine required to provide a daily oral dose of 0 or 18 mg/kg per mouse. After chronic administration of 0 or 18 mg/kg of fluoxetine for 21 days, mice aged 9-10 weeks were tested in a tail-suspension and open field apparatus. Upon completion of the study, mice were sacrificed by cervical dislocation and decapitation between 0900h and 1300h. Trunk blood was quickly collected and allowed to clot on ice. Following centrifugation, serum samples were collected and stored at -20C for determination of fluoxetine and norfluoxetine levels using liquid chromatography-mass spectrometry/mass spectrometry (LC-MS/MS). Micro-dissections of individual regions were performed on serial coronal brain sections (approximately 10 µm) that were placed on a cold metal block. Cortex was taken from the same section for each animal and immediately snaps frozen on dry ice. Samples were stored at -80C until analysis.


title: Dap12-deficient mouse brain (1 month)

city: Uppsala

first: Anna

last: Kiialainen

address: University Hospital, Entrance 70

department: Deapartment of Medical Sciences

country: Sweden

institute: Uppsala University

summary:
Polycystic lipomembranous osteodysplasia with sclerosing leukoencephalopathy (PLOSL) is an inherited brain and bone disease. It manifests as dementia and bone fractures. The PLOSL phenotype is caused by loss-of-function mutations in one of the two genes encoding the components of the DAP12/TREM2 receptor complex. The DAP12/TREM2 complex is expressed in cells of the myeloid lineage, including microglia in the central nervous system (CNS). The molecular mechanisms producing the CNS phenotype of PLOSL remain largely unknown. To gain insight into dysfunctional CNS pathways behind PLOSL, we performed genome-wide expression analysis of Dap12 (Tyrobp)-deficient mouse brain. In Dap12-deficient mice, we observed alterations in several pathways involved in synaptic function. In agreement with the myelin loss in PLOSL patients, we also saw changes in transcript levels of genes encoding myelin components.
Keywords: knockout response

overall_design: Transcript profiles of the midbrain (diencephalon and basal ganglia) of three Dap12-knockout and three heterozygous mice were analyzed.

first: Henna

last: Linturi

first: Juha

last: Saharinen

first: Lewis

last: Lanier

first: Outi

last: Kopra

first: Leena

last: Peltonen


title: Expression data from a new FACS approach isolated hESC derived endoderm cells using transcription factors

city: Stanford

first: Yuqiong

last: Pan

address: 300 Pasteur Drive, Alway Bldg. Rm M313

department: Depts of Statistics and Genetics

institute: Stanford University

summary:
We show that high quality microarray gene expression profiles can be obtained following FACS sorting of cells using combinations of transcription factors. We use this transcription factor FACS (tfFACS) methodology to perform a genomic analysis of hESC-derived endodermal lineages marked by combinations of SOX17, GATA4, and CXCR4, and find that triple positive cells have a much stronger definitive endoderm signature than other combinations of these markers.
Additionally, SOX17+GATA4+ cells can be obtained at a much earlier stage of differentiation, prior to expression of CXCR4+ cells, providing an important new tool to isolate this earlier definitive endoderm subtype. Overall, tfFACS represents an advancement in FACS technology which broadly crosses multiple disciplines, most notably in regenerative medicine to redefine cellular populations.

overall_design: 21 Total samples were analyzed. Samples collected after 5 days of hESC differentiation included SOX17+GATA4+ CXCR4+ cells, unfixed CXCR4+ cells, and unsorted fixed cells. Samples collected after 3 days of differentiation included SOX17+GATA4+ cells, SOX17-GATA- cells, and unsorted fixed cells. As controls, we analyzed both unfixed hESCs and fixed hESCs. All samples contained biological duplicates, triplicates or quadriplicates. We performed hierarchical clustering to demonstrate whether cellular fixation alone could change gene expression. We based this analysis on 1647 transcript clusters with coefficient of variation > 0.5 across the samples and expression values >= 500 in at least 2 out of the 21 samples. We found that fixation and staining steps did not cause distortions in gene expression measurements. This is supported by the fact that fixed and unfixed cells cluster together based upon differentiation stage, not based upon degree of fixation. Furthermore, using GSEA analysis, we found that the SOX17+GATA4+CXCR4+ day 5 cells and day 3 SOX17+GATA4+ were more enriched for compiled gold-standard endodermal genes than the CXCR4+ day 5 population.

first: Zhengqing

last: Ouyang

first: Wing

last: Wong

first: Julie

last: Baker


title: Comparison of enchondromas with controls (growth plate and cartilage)

summary: Ollier disease is a rare, non-hereditary disorder which is characterized by the presence of multiple enchondromas (EC), benign cartilaginous neoplasms arising within the medulla of the bone, with an asymmetric distribution. The risk of malignant transformation towards central chondrosarcoma (CS) is increased up to 35%. The etiology of Ollier disease is unknown. We therefore undertook genome-wide expression profiling using Illumina Beadarray v3.0 for 7 enchondromas of 6 patients and compared them with controls in order to find differentially expressed genes in these benign tumors.

overall_design: The goal of this study was to find differentially expressed genes between enchondromas, a benign cartilage forming tumor occuring in the metaphyses of bone, and controls. We have used samples of normal growth plate and articular cartilage as the controls. Seven enchondromas were compared to two growth plate and four cartilage samples.

middle: C


title: Genome-wide expression analysis of Dap12 (Tyrobp)-deficient mouse brain and microglial cells


title: Primary and secondary CD8 T cells during acute and chronic LCMV infection

status: Public on Aug 23 2011

city: Atlanta

first: Erin

last: West

state: GA

address: 1510 Clifton Rd NE RRC room G211

institute: Emory University

summary: Understanding the response of memory CD8 T cells to persistent antigen re-stimulation and the role of CD4 T cell help is critical to the design of successful vaccines for chronic diseases. However, studies comparing the protective abilities and qualities of memory and naïve cells have been mostly performed in acute infections, and little is known about their roles during chronic infections. Herein, we show that memory cells dominate over naïve cells and are protective when present in large enough numbers to quickly reduce infection.  In contrast, when infection is not rapidly reduced, memory cells are quickly lost, unlike naïve cells.  This loss of memory cells is due to (i) an early block in cell proliferation, (ii) selective regulation by the inhibitory receptor 2B4,  and (iii) increased reliance on CD4 T cell help.  These findings have important implications towards the design of T cell vaccines against chronic infections and tumors.

overall_design: 16 samples are analyzed: 3 replicates of secondary effector CD8 P14 T cells at day 8 post-acute lymphocytic choriomeningitis virus (LCMV) infection; 4 replicates of secondary effector CD8 P14 T cells at day 8 post-chronic LCMV infection; 4 replicates of primary effector CD8 P14 T cells at day 8 post-acute LCMV infection; and 5 replicates of primary effector CD8 P14 T cells at day 8 post-chronic LCMV infection.

first: Ben

last: Youngblood

first: Wendy

middle: G

last: Tan

first: Hyun-Tak

last: Jin

first: Koichi

last: Araki

first: Gabriela

last: Alexe

first: Bogumila

middle: T

last: Konieczny

first: Slivia

last: Calpe

first: Gordon

last: Freeman

first: Cox

last: Terhorst

first: W

middle: N

last: Haining

first: Rafi

last: Ahmed


title: Effects of benfotiamine in cultured human myotubes exposed to both normal and high glucose cencentrations

status: Public on Aug 22 2011

city: Oslo

first: Hege

last: Thoresen

address: Sem Sælandsvei 3

department: School of Pharmacy

country: Norway

institute: University of Oslo

summary:
The aim of the present work was to study the effects of benfotiamine (S-benzoylthiamine O-monophosphate) upon glucose and lipid metabolism and gene expression in differentiated human skeletal muscle cells (myotubes) incubated for 4 days under normal (5.5 mM glucose) and hyperglycemic (20 mM glucose) conditions.
Myotubes established from lean, healthy volunteers were treated with benfotiamine for 4 days. Glucose and lipid metabolism were studied with labeled precursors. Gene expression was measured using real time polymerase chain reaction (qPCR) and microarray technology.

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

first: Vigdis

last: Aas

first: Nina

middle: P

last: Hessvik

first: Marianne

last: Wettergreen

first: Andreas

last: Wensaas

first: Stefan

last: Hallén

first: G

first: Arild

last: Rustan


title: Gene expression profiles of striatum and cerebellum from knock-in mouse model of Huntington's disease

city: Boston

first: Jong-Min

last: Lee

state: MA

address: 185 Cambridge Street

department: Center for Human Genetic Reseaarch

institute: Massachusetts General Hospital

summary: Huntington’s disease (HD) involves marked early neurodegeneration in the striatum whereas the cerebellum is relatively spared despite the ubiquitous expression of full-length mutant huntingtin, implying that inherent tissue-specific differences determine susceptibility to the HD CAG mutation. To understand this tissue specificity, we compared early mutant huntingtin-induced gene expression changes in striatum to those in cerebellum in young Hdh CAG knock-in mice, prior to onset of evident pathological alterations. Endogenous levels of full-length mutant huntingtin caused qualitatively similar, but quantitatively different gene expression changes in the two brain regions. Importantly, the quantitatively different responses in striatum and cerebellum in mutant mice were well accounted for by the intrinsic molecular differences in gene expression between striatum and cerebellum in wild-type animals. Tissue-specific gene expression changes in response to the HD mutation, therefore, appear to reflect the different inherent capacities of these tissues to buffer qualitatively similar effects of mutant huntingtin. These findings highlight a role for intrinsic quantitative tissue differences in contributing to HD pathogenesis, and likely to other neurodegenerative disorders exhibiting tissue-specificity, thereby guiding the search for effective therapeutic interventions.

overall_design: Total RNA was isolated from striatum and cerebellum of Hdh CAG knock-in mice (HdhQ111/HdhQ111) and wild-type mice (Hdh+/Hdh+, 3~10 weeks) for gene expression profiling using Affymetrix MG430 2.0 arrays.


title: Identification of genes regulated by the RANK IVVY motif in macrophages

status: Public on Aug 20 2011

city: Birmingham

first: Dongquan

last: Chen

state: AL

address: 1717 11th Ave South

department: Medicine

institute: Univ of Alabama at Birmingham

summary: Identification of genes regulated by RANK RVVY motif in macrophages by gene expression analysis of TNFR1-/-R2-/- BMMs expressing a chimeric receptor consisting of the external domain of mouse TNFR1 linked to the transmembrane and intracellular domain of mouse RANK (WT) and NFR1-/-R2-/- BMMs expressing a chimeric receptor consisting of the external domain of mouse TNFR1 linked to the transmembrane and intracellular domain of mouse RANK bearing inactivating mutations in the IVVY motif (Mu).

overall_design:
two groups: mutant (mu) and wildtype (wt)
three replicates: rep1, rep2, and rep3

first: Xu

last: Feng


title: Expression data from mouse EMT-induced and non-induced cells

status: Public on Aug 13 2011

city: Setagaya-ku

first: Akihiro

last: Umezawa

state: Tokyo

department: Center for Regenerative Medicine

institute: National Center for Child Health and Development

summary: The conversion of an epithelial cell to a mesenchymal cell is critical to vertebrate embryogenesis and a defining structural feature of organ development, such as forming fibroblasts in injured tissues, or in initiating metastases in epithelial cancer. From a general perspective, EMT is about disaggregating epithelial units and reshaping epithelia for movement.   This phenotypic conversion requires the molecular reprogramming of epithelia with new biochemical instructions. It is known that commonly used molecular markers for EMT include increased expression of N-cadherin and vimentin, nuclear localization of beta-catenin, and increased production of the transcription factors such as Snail, Twist, and SIP1/ZEB2. Much of this conversion, however, has been studied during experiments that expose new transduction and signaling pathways in epithelia, and more recently in fibrogenic tissues. It is not yet clear whether the fibroblast transition of EMT is an expected middle phase of transdifferentiating epithelia, or whether EMT producing fibroblasts is an arrested form of transdifferentiation.   EMT is easily engaged by a combination of cytokines associated with proteolytic digestion of basement membranes upon which epithelia reside. We analyzed PCA and hierarchical clustering method of the gene expression pattern of the renal tubular cells and mammary gland cells. We then identified the genes which discriminate between the renal tubular and the mammary gland epithelial cells (PC1), or EMT-induced and non-induced cells (PC3). Undergoing EMT identifies the genes that discriminate between the renal tubular and the mammary gland epithelial cells(PC1), or EMT-induced and non-induced cells (PC3).

overall_design: Affymetrix GeneChip Mouse Genome 430 2.0 Array was used to transcriptionally profile to compare mouse EMT-induced cells and non-induced cells.

first: M

last: Toyoda

first: T

last: Hamatani

first: H

last: Okada

first: K

last: Matsumoto

last: Saito

first: A


title: Dap12 microglia

first: Anna

last: Kiialainen

summary:
Polycystic lipomembranous osteodysplasia with sclerosing leukoencephalopathy (PLOSL) is an inherited brain and bone disease. It manifests as dementia and bone fractures. The PLOSL phenotype is caused by loss-of-function mutations in one of the two genes encoding the components of the DAP12/TREM2 receptor complex. The DAP12/TREM2 complex is expressed in cells of the myeloid lineage, including microglia in the central nervous system (CNS). The molecular mechanisms producing the CNS phenotype of PLOSL remain largely unknown. To gain insight into dysfunctional CNS pathways behind PLOSL, we performed genome-wide expression analysis of Dap12 (Tyrobp)-deficient mouse microglial cells.
Keywords: knock-out response

overall_design: Transcript profiles of three wild type and three Dap12-deficient primary microglial cultures were analyzed.

first: Henna

last: Linturi

first: Juha

last: Saharinen

first: Lewis

last: Lanier

first: Outi

last: Kopra

first: Leena

last: Peltonen


title: HuR (ELAVL1) RIP-chip and knockdown exon array

status: Public on Aug 19 2011

city: Durham

first: Neelanjan

last: Mukherjee

state: NC

address: 101 Science Drive

department: Institute for Genome Sciences & Policy

institute: Duke University

type:
Expression profiling by array
Other

summary:
Integrative regulatory mapping indicates that the RNA-binding protein HuR (ELAVL1) couples pre-mRNA processing and mRNA stability
In this dataset, we employed two distinct experiments. 1) HuR RIP-chip to identify mRNA targets of HuR. 2) HuR knockdown to identify mRNAs whose expression are dependent on HuR.

overall_design: All 12 samples were normalized with PLIER using Affymetrix power tools. To identify RNA targets of HuR, HuR RIP samples were compared to Mock RIP samples. To identify RNA regulated by HuR, HuR knockdown samples were compared to mock knockdown samples.

first: Jack

last: Keene


title: The Polycomb Group Protein Suz12 Is Required for Embryonic Stem Cell Differentiation

status: Public on Aug 12 2011

city: Milano

first: Diego

last: Pasini

address: Via Adamello, 16

department: Experimental Oncology

country: Italy

institute: European Institute of Oncology

summary: Polycomb group (PcG) proteins form multiprotein complexes, called Polycomb repressive complexes (PRCs). PRC2 contains the PcG proteins EZH2, SUZ12, and EED and represses transcription through methylation of lysine (K) 27 of histone H3 (H3). Suz12 is essential for PRC2 activity and its inactivation results in early lethality of mouse embryos.

overall_design: Total RNA was extracted independently from three WT and three Suz12 KO ES cell clones. RNA was quantified, and equal amounts fromthe three Suz12 WT and the three Suz12 KO samples were pooled into one sample to reduce the experimental variation. Targets for microarray hybridization were synthesized according to the supplier’s instructions (Affymetrix). Hybridization, washing, staining, scanning, and data analysis were performed at the Affymetrix microarray unit at the Institute of Molecular Oncology of the Italian Foundation for Cancer Research-European Institute of Oncology campus, Milan, Italy, according to the manufacturer’s instructions.

first: Kristian

last: Helin


title: Down-regulation of cholesterol biosynthesis in forebrains of ERCC1-deficient mice

status: Public on Aug 16 2011

city: Louisville

first: Scott

middle: Carl

last: Smith

state: KY

address: 511 S. Floyd St.

department: Neurosurgery

institute: Kentucky Spinal Cord Injury Research Center

summary:
Background: Several genetic defects of the nucleotide excision repair (NER) pathway, including deficiency of the Excision Repair Cross-Complementing rodent repair deficiency, complementation group 1 (ERCC1), result in pre-mature aging, impaired growth, microcephaly and delayed development of the cerebellum. Such a phenotype also occurs in ERCC1-knockout mice which survive for up to 4 weeks after birth. Therefore, we analyzed cerebellar and hippocamapal transcriptomes of these animals at 3 weeks of age to identify the candidate mechanisms underlying brain consequences of reduced ERCC1 activity.
Results: In the cerebellum, the most prominent change was upregulation of genes that are associated with gliosis. Although Purkinje cell degeneration has been reported in some mouse strains with NER impairment, Purkinje cell transcriptome was mostly unaffected by the ERCC1 knockout. In the hippocampus, the gliosis response was minimal. Instead, there was an extensive downregulation of genes related to lipid metabolism including several enzymes of the cholesterol biosynthesis pathway as well as lipoproteins and plasma membrane proteins. Reduced expression of the cholesterol biosynthesis pathway genes was also present in the neocortex of adult mice whose ERCC1 gene was replaced by a mutant allele with a partial activity.
Conclusions: Downregulation of forebrain cholesterol biosynthesis genes is a newly identified consequence of ERCC1 deficiency. Its presence in adult mice suggests that it is not a secondary consequence of brain growth impairment. Instead, reduced cholesterol biosynthesis may contribute to such an impairment as well as affect function of mature synapses.

overall_design: We analyzed the hippocampus and cerebellum from three Ercc1-/- and three WT littermates using the Affymetrix Mouse Genome 430_2.0. Data was analyzed using the dChip DNA-Chip analyzer software .

first: Andria

middle: R

last: Robinson

first: Jing-Juan

last: Zheng

first: Laura

last: Niedernhofer

first: Michal

last: Hetman


title: Delineation of Two Clinically and Molecularly Distinct Subgroups of Posterior Fossa Ependymoma

status: Public on Aug 15 2011

city: Houston

first: Stephen

middle: Mack

last: Christopher

state: TX

address: 1102 Bates Avenue C1030.02

department: Pediatrics

institute: Baylor College of Medicine

summary:
Gene expression (mRNA) profiling of human ependymomas
Despite the histological similarity of ependymomas from throughout the neuraxis, the disease likely comprises multiple independent entities, each with a distinct molecular pathogenesis. Transcriptional profiling of two large independent cohorts of ependymoma reveals the existence of two demographically, transcriptionally, genetically, and clinically distinct groups of posterior fossa (PF) ependymoma. Group-A patients are younger, have laterally located tumors with a balanced genome, and are much more likely to exhibit recurrence, secondary metastasis, and death as compared to Group-B patients. Identification and optimization of immunohistochemical markers for PF ependymoma subgroups allowed validation of our findings on a third independent group of tumors using a human ependymoma tissue microarray, and provides a tool for prospective prognostication and stratification of PF ependymoma patients.

overall_design: We analyzed 102 primary ependymomas on the Affymetrix Exon 1.0ST platform (Gene Level).

last: Mack

first: Hendrik

last: Witt

first: Michael

last: Taylor

first: Stefan

last: Pfister


title: Healthy volunteers gene expression study of CD4 and NK lymphocytes

city: Ljubljana

first: Kristina

last: Gruden

address: Vecna pot 111

department: Department of Biotechnology and Systems Biology

country: Slovenia

institute: National Institute of Biology

summary: Sixteen volunteers, that were age, gender and BMI matched, were included in the study. Blood samples were taken one per each volunteer on three different days to also assess variability of gene expression markers in one individual. In all datasets variability between volunteers was higher than variability of measurables in samples collected from the same volunteer on different days. We have identified genes in individuals that are highly stable during one month period and are thus suitable as markers of individual disease/therapy progress. A list of genes with low overall variability is also available. Interestingly, data show that important components of immune response are down-regulated with BMI in T helper and NK cells. This paper also gives the first insight into the gene expression profile of T helper and NK cells in healthy population.

overall_design: CD4 and NK lymphocytes were isolated with positive selection using magnetic nanoparticle based kits from StemCell Inc. (Canada) and frozen to -80°C until total RNA extraction.

first: Ana

last: Herman

first: Matjaž

last: Hren

first: Primož

last: Rožman

first: Miomir

last: Kneževič

first: Neža

last: Turnšek

first: Maja

last: Ravnikar

last: Jeras


title: Expression profile of adult mouse 51 CNS regions

city: Kobe, Hyogo

first: Hiroki

last: Ueda

address: 2-2-3, Minatojima-minamimachi, Chuo-ku

department: Center for Developmental Biology

institute: RIKEN

summary: The adult mammalian brain is composed of distinct regions that have specialized roles. To dissect molecularly this complex structure, we conducted a project, named the BrainStars (B*) project, in which we sampled ~50 small brain regions, including sensory centers and centers for motion, time, memory, fear, and feeding.  To avoid confusion from temporal differences in gene expression, we sampled each region every 4 hours for 24 hours, and pooled the sample sets for DNA-microarray assays. Therefore, we focused only on spatial differences in gene expression. We then used informatics to identify candidates for (1) genes with high or low expression in specific regions, (2) switch-like genes with bimodal or multimodal expression patterns, and (3) genes with a uni-modal expression pattern that exhibit stable or variable levels of expression across brain regions. We used our findings to develop an integrated database (http://brainstars.org/) for exploring genome-wide expression in the adult mouse brain.

overall_design: For 51 CNS regions, slices (0.5-mm thick) of mouse brain were cut on a Mouse Brain Matrix, frozen, and the specific regions were punched out bilaterally with a microdissecting needle (gauge 0.5 mm) under a stereomicroscope. For each region, we took samples every 4 hours, starting at ZT0 (Zeitgaber time 0; the time of lights on), for 24 hours (6 time-point samples for each region), and we pooled the samples from the different time points.  We independently sampled each region twice (n=2).

first: Takeya

last: Kasukawa

first: Koh-hei

last: Masumoto

first: Itoshi

last: Nikaido

first: Mamoru

last: Nagano

first: Kenichiro

last: Uno

first: Kaori

last: Tsujino

first: Carina

last: Hanashima

first: Yasufumi

last: Shigeyoshi


title: Transcript level in F9 teratocarcinoma WT and RARalpha knockout in presence and absence of all-trans retinoic acid

status: Public on Aug 10 2011

city: New York

first: Kristian

middle: Bruun

last: Laursen

address: 1300 York Avenue

department: Pharmacology

institute: Weill Cornell Medical College

summary:
Retinoic acid receptors (RARs) α, β and γ are key regulators of embryonic development. Hematopoietic differentiation is regulated by RARα, and several types of leukemia show aberrant RARα activity. We demonstrate that RARα plays an important role in cellular memory and imprinting by regulating the CpG methylation status of specific promoter regions.
We used microarrays to identify genes, which display differential expression in F9 RARalpha knockout (RARaKO) cells relative to F9 wt cells.

overall_design: F9 teratocarcinoma cells (WT and RARaKO) were treated for 8 hours with either vehicle (EtOH) or all-trans Retinoic Acid (atRA) in the presence of the protein synthesis inhibitor Cycloheximide

middle: B

first: Lorraine

last: Gudas


title: Expression data of MED12 full-length and domain deleted construct overexpression and RNAi knockdown in HEK293 cells.

status: Public on Aug 11 2011

city: Iowa City

first: Pamela

last: Wernett

state: IA

address: 500 Newton Rd., MEB

department: Psychiatry

institute: University of Iowa

summary:
MED12 is an X-chromosome member of the Mediator complex that is a key regulator of tissue specific gene expression and moderates intracellular signaling via multiple developmental pathways.  Sequence variations in the carboxy-terminus of MED12, which contains a PQL and Opa domain, are associated with X-linked mental retardation behavioral syndromes and schizophrenia.  Unfortunately, the mechanism(s) through which MED12 sequence variation in the carboxy-terminus could alter vulnerability to neurodevelomental and neuropsychiatric illnesses is yet unclear.
In order to elucidate a better understanding of this process, we examined the role of the MED12 carboxy-terminus in cell cycle and gene expression with full-length and domain deleted overexpression constructs and RNA interference in HEK293 cells.  Our microarray data show a set of genes differentially expressed in the experimental conditions versus the GFP control.  The top 50 most differentially expressed genes in the experimental conditions versus the GFP control also show that MED12 expression level differentially affects stress response and transcriptional regulation pathways.
These results are consistent with prior studies showing that MED12 has a key role in determining neuronal cell fate and our theoretical understanding of the biological basis of psychosis.  They also lend further insight upon the pathways through which MED12 exerts its effects upon differentiation and disease pathogenesis, which may one day lead to new approaches to the treatment of MED12-related disorders.

overall_design: 12 samples were analyzed, being comprised of four conditions with three biological replicates.  Comparisons were made between the GFP control to experimental condition (i.e. GFP vs MED12 FL; GFP vs MED12 PQL/Opa; and GFP vs MED12 shRNA 5)

first: Robert

middle: A

last: Philibert


title: Chemokines regulate small leucine-rich proteoglycans in the extracellular matrix of the pressure-overloaded right ventricle

first: Ståle

last: Nygård

address: Institute for Experimental Medical Research, Oslo University Hospital - Ulleval

summary: Chemokines have been suggested to play a role during development of left ventricular failure, but little is known about their role during right ventricular (RV) remodeling and dysfunction. The first aim of this study was to identify chemokines which are regulated during RV pressure overload. We then hypothesized that these chemokines regulate SLRPs (small leucine-rich proteoglycans)

overall_design: A microarray study was performed on  5 pulmonary banded and sham operated wildype mice.

first: Anne

last: Wæhre

first: Geir

last: Christensen


title: Gene expression analysis of thymocyte subsets

city: Saint Louis

first: Takeshi

last: Egawa

state: MO

address: 660 South Euclid

department: Pathology and Immunology

institute: Washington University School of Medicine

summary:
Mouse thymocytes can be classified into four major subsets based on expression of CD4 and CD8 co-receptors. CD4-CD8- (double negative, DN) cells become CD4+CD8+ (double positive, DP) cells following productive T cell receptor (TCR) beta chain rearrangement. A small proportion of DP cells are selected through interaction of clonal TCRalpha/beta and MHC self peptide complex expressed on thymic stromal cells. DP cell expressing MHC class I-restricted TCR become CD4-CD8+ cells, which will finally differentiate into cytotoxic T cells, while MHC class II restricted selection generates CD4+CD8- helper lineage T cells.
We used microarrays to identify genes important for thymocyte differentiation and lineage determination by profiling gene expression in different thymocyte subsets.

overall_design: Mouse thymocytes were divided into four subsets based on CD4, CD8a, and TCRb expression and purified by flw cytometry. FACS purified DN (CD4-CD8a-TCRb-), DP (CD4+CD8a+), CD4SP (CD4+CD8a-TCRbhi) and CD8SP (CD4-CD8a+TCRbhi) populations were lysed in Trizol, and provided to the Genomics Core Facility of the Memorial Sloan-Kettering Cancer Center (MSKCC) for quality control, quantification, reverse transcription, labeling and hybridization to MOE430A 2.0 microarray chips (Affymetrix). Arrays were scanned per the manufacturer’s specifications for the Affymetrix MOE430v2 chip.

first: Dan

last: Littman


title: Expression data from murine Tet-off MLL-AF9/Ras acute myeloid leukemia cell lines following withdrawal of MLL-AF9

status: Public on Aug 05 2011

city: Vienna

first: Johannes

last: Zuber

state: Vienna

address: Dr. Bohr-Gasse 7

country: Austria

institute: Research Institute for Molecular Pathology (IMP)

summary:
To explore oncogene addiction programs in a genetically defined leukemia context we developed an AML mouse model driven by a conditional MLL-AF9 allele together with oncogenic Ras, which enabled us to examine the consequences of MLL-AF9 inhibition in established disease. In order to produce a tightly regulated system that was easy to monitor, we constructed two retroviral vectors containing dsRed-linked MLL-AF9 under control of a tetracycline response element promoter, and KrasG12D or NrasG12D linked to the “Tet-off” tet-transactivator, which activates TRE expression in a doxycycline repressible manner. Leukemias were generated by retroviral cotransduction of both vectors into hematopoietic stem and progenitor cells, which were transplanted into syngeneic mice. Cells harboring both constructs induced aggressive myelomonocytic leukemia. Five independent primary leukemia cell lines were established from bone marrow of terminal mice. Treatment of these lines with doxycycline rapidly turned off MLL-AF9 expression, and induced terminal myeloid differentiation and complete disease remission in vivo.
To identify molecular mechanisms underlying addiction to MLL-AF9, we analyzed global gene expression changes following doxycycline-induced suppression of MLL-AF9.

overall_design: Independent primary acute myeloid leukemia lines induced by cotransduction of Tet-off MLL-AF9 together with either KrasG12D or NrasG12D were grown in culture and treated with doxycycline for 6 days to inactivate MLL-AF9 expression. In addition, primary acute myeloid leukemia lines with constitutive MLL-AF9 and KrasG12D were included to control for the effects of doxycycline. Untreated and treated cells were harvested for RNA extraction and hybridization to Affymetrix arrays.

first: Amy

last: Rappaport


title: AML mouse models

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

overall_design: Refer to individual Series

first: Scott

middle: W

last: Lowe


title: Patterns of gene expression associated with temporal phases of S. aureus infection

status: Public on Aug 03 2011

city: Braunschweig

last: Geffers

address: Inhoffenstr. 7

department: Dep. Molecular Bacteriology

country: Germany

institute: HCI - Helmholtz Centre for Infection Research

summary:
To acquire more information regarding the local immune events during the different phases of S. aureus infection, gene profiling using microarray technology was used to identify host genes whose expression is substantively altered in the kidneys during the acute (T2) and persistent phase of infection (T28). Genes associated with the distinct transcript profiles were identified by comparing the relative abundance of transcripts at 2 days (acute) and 28 days (persistent) of infection to their abundance in the kidneys of uninfected control animals (CTL).

Keywords: gene expression

overall_design: identification of host genes whose expression is substantively altered in the kidneys during the acute (T2) and persistent phase of infection (T28) compared to uninfected control (CTL).

first: C

last: Ziegler

first: R

first: E

last: Medina


title: Expression data from control or CCR4b/CNOT6L-depleted cells

city: San Antonio

first: Masahiro

last: Morita

state: Texas

address: 4939 Charles Katz Drive

department: Department of Molecular Medicine

institute: University of Texas Health Science Center at San Antonio

summary:
The stability of mRNA influences the abundance of cellular transcripts and proteins. Deadenylases play critical roles in mRNA turnover and thus are important for the regulation of arious biological events. Here, we report the identification and characterization of CCR4b/CNOT6L, which is homologous to yeast CCR4 mRNA deadenylase.
We compared the expression profiles of the cellular genes between control and CCR4b/CNOT6L-depleted cells by microarray analysis

overall_design: Total RNAs were extracted from control or CCR4b-depleted cells. Following the isolation of RNA, all subsequent technical procedures, including quality control of RNA, labeling, hybridization, and scanning of the arrays, were performed in BIO MATRIX Research, Inc., cDNA, and biotinlabeled cRNA was synthesized according to protocols for Affymetrix array analysis. Biotin-labeled cRNAs (15  g) were hybridized to the GeneChip Mouse Genome 430 2.0 Array (Affymetrix, Santa Clara, CA). To determine the average differences for each probe set, changes were calculated by a global normalization method using Affymetrix GCOS (GeneChipOperating Software) software.

first: Tadashi

last: Yamamoto


title: Notch1 mediates cell fate decisions in the mouse uterus and is critical for complete decidualization

status: Public on Aug 09 2011

city: Basel

first: Damian

last: Roqueiro

address: Mattenstrasse 26

department: Biosystems Science and Engineering

country: Switzerland

institute: ETH Zurich

summary:
Uterine receptivity implies a dialogue between the hormonally primed maternal endometrium and the free-floating blastocyst. Endometrial stromal cells proliferate, avert apoptosis, and undergo decidualization in preparation for implantation; however, the molecular mechanisms that underlie differentiation into the decidual phenotype remain largely undefined. The Notch family of transmembrane receptors transduce extracellular signals responsible for cell survival, cell-to-cell communication, and trans-differentiation, all fundamental processes for decidualization and pregnancy. Using a murine artificial decidualization model, pharmacological inhibition of Notch signaling by gamma-secretase inhibition resulted in significantly decreased deciduoma. Furthermore, a progesterone receptor (PR)-Cre Notch1 bigenic (Notch1d/d) confirmed a Notch1-dependant hypomorphic decidual phenotype.
Microarray and pathway analysis, following Notch1 ablation, demonstrated significantly altered signaling repertoire. Concomitantly, hierarchical clustering demonstrated Notch1-dependent differences in gene expression. Uteri deprived of Notch1 signaling demonstrated decreased cellular proliferation; namely, reduced proliferation-specific antigen, Ki67, altered p21, cdk6, and cyclinD activity, and increased apoptotic-profile, augmented cleaved caspase-3, Bad, and attenuated Bcl2. Demonstrated here, the pre-implantation uterus relies on Notch signaling to inhibit apoptosis of stromal fibroblasts  and regulate cell cycle progression, which together promotes successful decidualization. In summary, Notch1 signaling modulates multiple signaling mechanisms crucial for decidualization and we provide greater perspective to the coordination of multiple signaling modalities required during decidualization

overall_design: RNA samples from 3-5 separate mice were extracted. All mRNA quantities were normalized against 18S gene expression. Gene expression levels were measured by real-time RT-PCR SYBR Green analysis using the ABI Prism 7700 Sequence Detector System according to manufacturer’s instructions (Applied Biosystems).

first: Asgerally

last: Fazleabas

first: Yalda

last: Afshar


title: Negative regulation of the IFN/STAT signaling pathway by the Trim24 tumor suppressor protein through Rara inhibition

status: Public on Aug 02 2011

city: Illkirch

first: Doulaye

last: Dembele

address: 1 rue Laurent Fries

department: Biopuces

country: France

institute: IGBMC

summary:
Recent genetic studies in mice have established a key role for the nuclear receptor coregulator Trim24 in liver tumor suppression and provided evidence that Trim24 suppresses hepatocarcinogenesis by inhibiting retinoic acid receptor alpha (Rara)-dependent transcription and cell proliferation. However, it is unknown which downstream targets of Rara regulated by Trim24 are critical for tumorigenesis. We report here that loss of Trim24 results in the overexpression of interferon (IFN)/STAT pathway genes in the liver, a process that occurs early in tumorigenesis and is more pronounced in tumors, despite the enhanced expression, late in the disease, of negative regulators such as Usp18, Socs1 and Socs2.
Remarkably, Rara haplodeficiency, which was previously shown to suppress tumor development in Trim24-/- mice, also suppresses overexpression of the IFN/STAT pathway,  thus providing evidence for a cross-pathway control that may be relevant to the transformation process. Biochemical studies revealed that Trim24 binds to the retinoic acid (RA)-responsive element in the Stat1 promoter in a RA-dependent manner and represses RA-induced transcription from this promoter. Together, these results identify Trim24 as a novel regulator of the IFN/STAT pathway and indicate that Trim24-mediated repression of the IFN/STAT signaling through Rara inhibition may play a critical role in preventing liver cancer.

overall_design:
Generation of Trim24-/- mice has been described previously (Khetchoumian et al., 2007) by gene disruption. To generate compound mutant mice with a single allele of Rara deleted in the Trim24 -/-  mutant background, we crossed Trim24 -/-  mice with Rara+/-  mice. The resulting Trim24+/- Rara+/-  mice were generated in the hybrid (C57BL/6 (60%), 129/Sv (40%)) genetic background. These double heterozygous Trim24+/- Rara+/-  mice were intercrossed to generate Trim24 -/-, Trim24 -/- Rara+/- and wild-type mice.
Transcriptional profiling of mice at 5-weeks and 14-weeks of age.

first: Johan

last: Tisserand

first: Régine

last: Losson


title: esBAF facilitates pluripotency by conditioning the genome for LIF/STAT3 signaling and by regulating Polycomb function

status: Public on Aug 01 2011

city: RTP

first: Raja

last: Jothi

address: 111 TW Alexander Drive; A314

department: National Institute of Environmental Health Sciences

institute: National Institutes of Health

type: Genome binding/occupancy profiling by high throughput sequencing

summary: Signaling by the cytokine LIF and its downstream transcription factor, STAT3, prevents differentiation of pluripotent embryonic stem cells (ESCs) by opposing MAP kinase signaling.  This contrasts with most cell types where STAT3 signaling induces differentiation.  We find that STAT3 binding across the pluripotent genome is dependent upon Brg, the ATPase subunit of a specialized chromatin remodeling complex (esBAF) found in ESCs.  Brg is required to establish chromatin accessibility at STAT3 binding targets, in essence preparing these sites to respond to LIF signaling. Moreover, Brg deletion leads to rapid Polycomb (PcG) binding and H3K27me3-mediated silencing of many Brg-activated targets genome-wide, including the target genes of the LIF signaling pathway.  Hence, one crucial role of Brg in ESCs involves its ability to potentiate LIF signaling by opposing PcG. Contrary to expectations, Brg also facilitates PcG function at classical PcG target including all four Hox loci, reinforcing their repression in ESCs.  These findings reveal that esBAF does not simply antagonize PcG, but rather, the two chromatin regulators act both antagonistically and synergistically with the common goal of supporting pluripotency.

overall_design:
Brg conditional embryonic stem cell (ESC) line was prepared from Brg(lox/lox);Actin-CreER mice that allow conditional deletion of Brg upon addition of 4-hydroxytamoxifen (4OHT, Sigma). Brg conditional ESCs were treated with 4-OHT for 72 hours to delete Brg. Brg protein levels completely abolished only at 48 hours (Brg-KO). RNA from Brg conditional ESCs (WT), Brg-KO ESCs, Brg conditional ESCs starved of LIF (Lif-WD) for 48 hours were extracted using Trizol reagent (Invitrogen), followed by RNeasy kit with DNaseI digestion to eliminate genomic DNA. Purified RNA was processed and hybridized onto Affymetrix Mouse MOE 4.0 3’ expression arrays according to the manufacturer's instructions.

ChIP-Seq was used to detect and measure STAT3 occupancy and levels of H3K27me3 in the genome before and after the removal of the SWI/SNF ATPase Brg in mouse ESCs. Total of 4 samples (WT and KO STAT3; WT and KO H3K27me3). Input DNA was sequenced as control.

first: Gerald

last: Crabtree

first: Lena

last: Ho


title: Twist1 Directly Regulates Genes That Promote Cell Proliferation and Migration in Developing Heart Valves

status: Public on Jul 28 2011

city: Cinicnnati

first: Katherine

last: Yutzey

state: OH

address: 240 Albert Sabin Way

department: Divison of Molecular Cardiovascular Biology

institute: Cinicnnati Children's Hospital Medical Center

summary: Twist1, a basic helix-loop-helix transcription factor, is expressed in mesenchymal precursor populations during embryogenesis and in metastatic cancer cells.  In the developing heart, Twist1 is highly expressed in endocardial cushion (ECC) valve mesenchymal cells and is down regulated during valve differentiation and remodeling.  Previous studies demonstrated that Twist1 promotes cell proliferation, migration, and expression of primitive ECM molecules in ECC mesenchymal cells. Furthermore, Twist1 expression is induced in human pediatric and adult diseased heart valves.  However, the Twist1 downstream target genes that mediate increased cell proliferation and migration during early heart valve development remain largely unknown.  Candidate gene and global gene profiling approaches were used to identify direct transcriptional targets of Twist1 during heart valve development.  Candidate target genes were analyzed for evolutionarily conserved regions (ECRs) containing E-box consensus sequences that are potential Twist1 binding sequences.   ECRs containing conserved E-box sequences were identified for Twist1 responsive genes Tbx20, Cdh11, Sema3C, Rab39b, and Gadd45a.  Twist1 binding to these sequences in vivo was determined by chromatin immunoprecipitation assays, and binding was detected in ECCs but not late stage remodeling valves.  In addition identified Twist1 target genes are highly expressed in ECCs and have reduced expression during heart valve remodeling in vivo which is consistent with the expression pattern of Twist1. Together these analyses identify multiple new genes involved in cell proliferation and migration that are differentially expressed in the developing heart valves, are responsive to Twist1 transcriptional function, and contain Twist1 responsive regulatory sequences.

overall_design: Murine MC3T3-E1 preosteoblast cells were treated with siScrambled control or siTwist1 to achieve knockdown of Twist1. Both siScr and siTwist1 were performed in triplicate.  Isolated RNA was analyzed with Affymetrix muring MOE 430 2.0 gene chip microarray.

first: Mary

last: Lee


title: Gene expression profiling of human CD8+ CD161hi and CD161lo memory and naïve T cell subsets

city: Seattle

first: Cameron

last: Turtle

state: WA

address: 1100 Fairview Ave N

institute: Fred Hutchinson Cancer Research Center

summary:
Gene expression profiling of human CD8+ CD161hi and CD161lo central and effector memory and naïve T cell subsets.

The mechanisms by which IL-17 secreting cells are regulated have not been completely elucidated. We previously identified a population of rhodamine-effluxing memory CD8+ T cells with high expression of CD161 that contributes to immune reconstitution after lymphopenia-inducing chemotherapy. Here we find that CD161hi CD8+ T cells share transcriptional programming with Th17 cells, but most do not secrete IL-17 or proliferate to stimulation through the T cell receptor (TCR). Transcriptional analysis of subsets identified by expression of CD161 and CD62L revealed a novel mechanism of TCR signaling pathway regulation in CD161hi CD8+ T cells that is distinct from that described in anergic or tolerant cells and renders them functionally dependent on costimulation through innate cytokine receptors or CD28. CD161hi CD8+ T cells, induced to proliferate by a TCR signal delivered with costimulation, demonstrated plasticity that was dependent on the nature of costimulation and resulted in expansion of IL-17 secreting cells that could not proliferate to a TCR signal alone or differentiation to Tc1-like cells that proliferated to TCR stimulation in the absence of costimulation. The data show an association between TCR signaling pathway downregulation and type 17 programming in CD161hi CD8+ T cells, whose dysregulation could mediate IL-17 dependent inflammatory diseases.

overall_design:
T cell subsets were sort-purified from healthy adults and analyzed by gene expression profiling.

Isolation:
Effluxing CD161hi and non-effluxing CD161lo CD8+ TCM and TEM subsets were purified using magnetic bead separation and cell sorting to achieve >98% purity, as previously described (35). CD8+ T cells were positively selected using CD8 Microbeads (Miltenyi Biotec, Germany), loaded with Rh123 (Sigma, St. Louis, MO) and cultured for 30 min to allow Rh123 efflux, then labeled with fluorochrome-conjugated antibodies to CD4, CD16, TCRγδ, Vα24, CD8, CD95, CD62L and CD161. CD161hi and CD161lo TCM and TEM subsets were sort-purified on a FACS ARIA equipped with 405 nm, 488 nm and 633 nm lasers (BD Biosciences). CD161hi TCM and TEM subsets were identified as CD62L+/Rh123lo/CD161hi and CD62L-/Rh123lo/CD161hi events, respectively, in the CD4-/CD16-/TcRγδ-/Vα24-/CD8+/CD95+ population.  CD161lo TCM and TEM subsets were identified as CD62L+/Rh123hi/CD161int/neg and CD62L-/Rh123hi/CD161int/neg events, respectively, in the CD4-/CD16-/TcRγδ-/Vα24-/CD8+/CD95+ population.

Gene expression profiling:
RNA was extracted from sort-purified subsets from 6 healthy individuals using the RNeasy Plus Minikit (Qiagen, Valencia, CA) and biotinylated, followed by generation of amplified cRNA for array hybridization using the Illumina TotalPrep RNA Amplification Kit (Applied Biosystems, Foster City, CA). Amplified biotinylated cRNA was then purified before quality control to ensure high quality cRNA was available for hybridization. Labeled cRNA was hybridized to Illumina WG-6 Expression BeadChips v3.0 (Illumina, San Diego, CA), which quantitate expression of 48,802 transcripts derived from the NCBI RefSeq (Build 36.2, Release 22) and UniGene databases (Build 199). BeadChips were washed before reading and image extraction, and then scanned on an Illumina BeadArray Reader. The resulting TIFF images were processed using GenomeStudio Gene Expression Module (GEM) software. Data quality was assessed using the Control Summary feature in GenomeStudio GEM. For a given analysis set, a GenomeStudio Probe-level Final Report was generated by combining the Sample Probe Profile and Control Probe Profile tables. The Final Report comprising the full dataset was initially processed using the Bioconductor package lumi by employing a background correction estimate and quantile normalization.  A small adjustment (i.e. 20 counts) was made to the entire dataset to make all intensity signals non-negative and these values were log2-transformed. The dataset was initially filtered using the ‘shorth’ function of the Bioconductor package genefilter, resulting in retention of 31,084 of 48,802 original probes. Each pairwise comparison was further filtered by discarding probes whose signal intensity was less than a defined signal “noise floor” across all arrays in the data subset. This was achieved by calculating the median of the ‘negative control’ probe signals for each array, averaging these values, and setting the noise floor as 3 times this average. Differential gene expression was then determined using the Bioconductor package limma, and a false discovery rate (FDR) method applied to correct for multiple testing. Significant differential gene expression was defined by a log2 ratio > 0.585 (± 1.5-fold) and FDR (adjusted p value) < 0.05.

middle: J

first: Jeff

last: Delrow

first: Ryan

last: Basom

first: Stanley

last: Riddell


title: Comparison of gene expression profiles of normal human bronchial epithelial cells in 2D and 3D cultural conditions

status: Public on Jul 27 2011

city: Dallas

first: Lianghao

last: Ding

address: 5323 Harry Hines Blvd

institute: UT Southwestern Medical Center

summary: The experiment is part of a project to study DNA repair process after ionizing radiation  in organotypic 3-dimentional human bronchial epithlial cell culture.

overall_design: Human bronchial epithelial cells were grown in tissue culture flask (2D) or in matrics gel (3D). Three independent cultures were done for each condition.

first: Aroumougame

last: Asaithamby

first: Burong

last: Hu

first: Oliver

last: Delgado

first: Michael

middle: D

last: Story

first: John

last: Minna

first: Jerry

last: Shay

first: David

last: Chen


title: Dmrt1 (doublesex and mab-3 related transcription factor 1) conditional knockout expression analysis of P28 testes

status: Public on Jul 29 2011

city: Minneapolis

first: Aaron

last: Sarver

state: MN

address: 425 East River Road

department: Masonic Cancer Center

institute: University of Minnesota

summary: Dmrt1 (doublesex and mab-3 related transcription factor 1) is a conserved transcriptional regulator of male differentiation required for testicular development in vertebrates.  This study examines the result of conditional removal of Dmrt1 from Sertoli cells in P28 testis tissue.

overall_design: Testes from P28 Dmrt1 flox/flox mice were compared to testes from P28 Dmrt1 flox/flox mice with the Sertoli cell-specific Sf1 (Nr5a1; MGI:1346833) or Dhh (MGI:94891) promoters driving Cre expression.


title: Effects of caspase-8 deletion in the intestinal epithelium

status: Public on Jul 23 2011

city: Erlangen

first: Christoph

last: Becker

address: Hartmannstrasse 14

institute: University of Erlangen-Nuremberg

summary:
Caspase-8 is a cystein protease involved in regulating apoptosis. The function of caspase-8 was studied in the intestinal epithelium, using mice with an intestinal epithelial cell specific deletion of caspase-8.
We used microarrays to investigate the difference of the global programme of gene expression in intestinal epithelial cells of control and caspase-8 deficient mice.

overall_design: Intestinal epithelial cells were isolated from 3 control mice and 3 mice with a conditional deletion of caspase-8 in the intestinal epithelium. RNA was isolated and subjected to Affymetrix gene chip analysis.

first: Claudia

last: Günther


title: Pathways identified by toxicogenomics analysis reveal the size and dose independency of silica particles-induced toxicity in mice.

city: Hangzhou

first: Xiaoyan

last: Lu

address: Yuhang Road 866

institute: Zhejiang University

summary:
Understanding the interactions of nanostructures with biological systems is essential to nanotoxicological research.
Using a microarray-based toxicogenomics approach at early stage, this study investigated the relationship between particle size and toxicity of silica particles (SP) with diameters of 30, 70, and 300 nm (SP30, SP70, and SP300) as well as the mechanism of injury in mice.

overall_design: Two experiments with SiO2 particles of different sizes were considered in mice. One was aimed to investigate the dose-response relationship of SP70 toxicity at a dose of 10, 20, or 40 mg/kg (experiment 1), and the other set to study the size-response relationship of SP-induced toxicity using SP30, SP70, or SP300 (experiment 2). In experiment 2, two dosages each of SP30, SP70, and SP300 were performed. One was 10 mg/kg at three particle sizes, and the other was toxic doses of the three particle sizes, i.e., 10 mg/kg for SP30, 40 mg/kg for SP70, and 200 mg/kg for SP300. The toxic doses of the three particle sizes of SP were decided on the basis of the results of histopathological examinations and serum biochemical analysis in our previous study.n = 5

first: Tingting

last: Jin

first: Yu

last: Tian

first: Yachao

first: Bin

first: Huasheng

last: Xiao

first: Xiaohui

last: Fan


title: Expression and CGH analysis of haploid ES cells

first: Martin

last: Leeb

address: Dr.-Bohr-Gasse 9/3

department: Max Perutz Labs

institute: University of Vienna

type: Genome variation profiling by genome tiling array


title: Reconstitution of the mouse germ-cell specification pathway in culture by pluripotent stem cells

city: Nara

first: Kazuki

last: Kurimoto

address: 840 Shijo-Cho, Kashihara

department: School of medicine

institute: Nara Medical University

summary: The generation of properly functioning gametes in vitro, a key goal in developmental/reproductive biology, requires multi-step reconstitutions of complex germ cell development. Based on the logic of primordial germ cell (PGC)-specification, we demonstrate here the generation of PGC-like cells (PGCLCs) in mice with robust capacity for spermatogenesis from embryonic stem cells (ESCs) and induced pluripotent stem cells (iPSCs) through epiblast-like cells (EpiLCs), a cellular state highly similar to pre-gastrulating epiblasts, but distinct from epiblast stem cells (EpiSCs). The global transcription profiles, epigenetic reprogramming, and cellular dynamics during PGCLC induction from EpiLCs are a meticulous capture of those associated with PGC specification from the epiblasts. Furthermore, we identify Integrin-beta 3 and SSEA1 as markers that purify PGCLCs with spermatogenic capacity free from tumorigenic undifferentiated cells. With the reconstitution of PGC specification pathway from the naive inner cell mass state, our study defines a paradigm for the essential step of in vitro gametogenesis.

overall_design: We performed this analysis to reveal the characters of the cells that we created in this study, epiblast-like cells (EpiLCs) and primordial germ cells-like cells (PGCLCs).  Because EpiLCs were induced from embryonic stem cells (ESCs), and equivalent to pre-gastrulating epiblast (embryonic day [E] 5.5-6.0) in vivo (embryo), ESCs and epiblast were included in this analysis.  Epiblast stem cells (EpiSCs) are a culture cell type derived from  epiblast, and were also included.  PGCLCs were supposed to be equivalent to E9.5 PGCs based on reporter fluorescent transgene expressions and epigenetic properties, and therefore E9.5 PGCs were also inckuded in this analysis.  Because epiblast and E9.5 PGCs are of a small number of cells in embryos (a few hundred to thousand cells), cDNAs were amplified with a quantitative global PCR method (Kurimoto et al., 2006, Nucleic Acids Research) for microarray analyses.  We took two biological replicate for each cell type.

first: Katsuhiko

last: Hayashi

first: Hiroshi

last: Ohta

first: Mitinori

last: Saitou


title: Influence of C/EBPβ 3'UTR on RasV12 induced gene expression

city: Frederick

first: Peter

middle: F

last: Johnson

state: MD

address: Bldg 539, rm 122, 1050 Boyles St., NCI-Frederick

department: Center for Cancer Research

institute: NCI

summary: C/EBPb is an auto-repressed protein that becomes posttranslationally activated by Ras-MEK-ERK signalling. C/EBPb is required for oncogene-induced senescence (OIS) of primary fibroblasts, but also displays pro-oncogenic functions in many tumour cells. Here, we show that C/EBPb activation by H-RasV12 is suppressed in immortalized/transformed cells, but not in primary cells, by its 30 untranslated region (30UTR). 30UTR sequences inhibited Ras-induced cytostatic activity of C/EBPb, DNA binding, transactivation, phosphorylation, and homodimerization, without significantly affecting protein expression. The 30UTR suppressed induction of senescence-associated C/EBPb target genes, while promoting expression of genes linked to cancers and TGFb signalling. An AU-rich element (ARE) and its cognate RNA-binding protein, HuR, were required for 30UTR inhibition. These components also excluded the Cebpb mRNA from a perinuclear cytoplasmic region that contains activated ERK1/2, indicating that the site of C/EBPb translation controls de-repression by Ras signalling. Notably, 30UTR inhibition and Cebpb mRNA compartmentalization were absent in primary fibroblasts, allowing Ras-induced C/EBPb activation and OIS to proceed. Our findings reveal a novel mechanism whereby non-coding mRNA sequences selectively regulate C/EBPb activity and suppress its anti-oncogenic functions.

overall_design: NIH-3T3 cells were retrovirally infected and selected with appropriate antiobiotics.  Equal number of cells were plated and collected 48-72 hours later.

first: Christopher

last: Huggins


title: Molecular Determinants of Dorsal Spinal Cord Interneurons Specified by Atoh1 (Math1)

first: Helen

last: Lai

address: 6000 Harry Hines Blvd, NA4.146

summary: Neural basic helix-loop-helix (bHLH) transcription factors are important for the differentiation and cell type specification of neurons.  They are thought to share direct downstream targets in their common role as neuronal differentiation factors, but have distinct targets with respect to their cell type specific roles.  Little is known about distinct cell-type specific bHLH targets as previous work did not distinguish these from common targets.  Based on previous genetic evidence, we hypothesize that bHLH transcription factors have unique targets for their function in regulating neuronal sub-type specification.  Atoh1 (Math1) is a bHLH transcription factor that specifies different cell types of the proprioceptive pathway in mammals such as the dorsal interneuron 1 population of the developing neural tube.  Using microarray analyses of neighboring specific bHLH sorted populations from developing mouse neural tubes, we determine transcripts unique to the Atoh1-derived population and not those common to bHLH transcription factors in related neural progenitor populations.  Chromatin immunoprecipitation followed by sequencing (ChIP-seq) experiments of native tissue followed by enhancer reporter analyses identified five direct cell-type specific targets of Atoh1 in vivo: Klf7, Rab15, Rassf4, Selm, and Smad7, along with their Atoh1-responsive enhancers.  These Atoh1 targets were found from native tissue in the appropriate developmental context and have diverse functions that range from transcription factors to regulators of endocytosis and signaling pathways. Only Rab15 and Selm are expressed across several different Atoh1-specified cell types including external granule cells (EGL) in the developing cerebellum, hair cells of the inner ear, and Merkel cells, demonstrating that even within Atoh1 lineages, not all Atoh1 specific targets are shared.  Our work establishes on a molecular level that the neuronal differentiation bHLH transcription factors also have distinct targets for their roles in neuronal sub-type specification. From this work, we can begin to address how bHLH transcription factors are able to specify unique cell types and initiate programs that organize neuronal diversity.

overall_design:
Gene expression analysis: Two samples, Atoh1-GFP and dNeurog1-GFP, were analyzed.  Two biological replicates of each.  Atoh1-GFP transgenics are mice with GFP inserted into a BAC that drives GFP to the Atoh1-derived population of the developing neural tube marking the dorsal interneuron 1 population (Raft et al. Development 2007).  dNeurog1-GFP  transgenics are mice with a Neurog1 enhancer that drives GFP to the dorsal part of the developing neural tube marking the dorsal interneuron 2 population (Nakada et al. Dev Bio 2004).

Chip-seq analysis: Series GSE22111

first: Jane

middle: E


title: Gene expression of polyoma middle T antigen induced mammary tumors [NZB x PyMT]

status: Public on Jul 22 2011

city: Rockville

first: Ying

last: Hu

email: yhu@mail.nih.gov, hunterk@mail.nih.gov

address: 9609 Medical Center Dr.

department: NCI/CCR

institute: NIH

summary: Mouse genetic crosses were established between the PyMT model of metastatic breast cancer and NZB strain.  Tumors were harvested from the animals for gene expression analysis to identify genes and network modules associated with progression to distant metastatic disease.

overall_design: Gene expression of 68 samples from the NZB crosses were assayed on Affymetrix chips

first: Kent

last: Hunter


title: Differential effects of krill oil and fish oil on the hepatic transcriptome in mice

city: Madison

first: Jamie

last: Barger

state: WI

address: 510 Charmany Drive, Suite 263

institute: LifeGen Technologies, LLC

summary: Dietary supplementation with ω-3 polyunsaturated fatty acids (ω-3 PUFAs), specifically the fatty acids docosahexaenoic acid (DHA; 22:6 ω-3) and eicosapentaenoic acid (EPA; 20:5 ω-3), is known to have beneficial health effects including improvements in glucose and lipid homeostasis and modulation of inflammation. To evaluate the efficacy of two different sources of ω-3 PUFAs, we performed gene expression profiling in the liver of mice fed diets supplemented with either fish oil or krill oil. We found that ω-3 PUFA supplements derived from a phospholipid krill fraction (krill oil) downregulated the activity of pathways involved in hepatic glucose production as well as lipid and cholesterol synthesis. The data also suggested that krill oil-supplementation increases the activity of the mitochondrial respiratory chain. Surprisingly, an equimolar dose of EPA and DHA derived from fish oil modulated fewer pathways than a krill oil-supplemented diet and did not modulate key metabolic pathways regulated by krill oil, including glucose metabolism, lipid metabolism and the mitochondrial respiratory chain. Moreover, fish oil upregulated the cholesterol synthesis pathway, which was the opposite effect of krill supplementation. Neither diet elicited changes in plasma levels of lipids, glucose or insulin, probably because the mice used in this study were young and were fed a low fat diet. Further studies of krill oil supplementation using animal models of metabolic disorders and/or diets with a higher level of fat may be required to observe these effects.

overall_design: Twenty-one microarrays: three diets (CO, FO, KO) x seven mice per diet x one microarray per mouse

middle: L


title: Comparison of total and polyribosome-associated mRNA levels in male Fmr1 KO mice and male WT littermates

status: Public on Jul 21 2011

city: New York

first: Chaolin

last: Zhang

state: NY

address: 1230 York Ave

department: Molecular Neuro-Oncology

institute: Rockefeller University

summary:
The Fragile X Mental Retardation Protein, FMRP, is thought to regulate the translation of a specific set of neuronal mRNAs on polyribosomes.  Therefore, we prepared polyribosomes on sucrose gradients and purified mRNA specifically from these fractions, as well as the total mRNA levels, to determine whether a set of mRNAs might be changed in its % association with polyribosomes in the absence of FMRP in the KO mouse model.
No significant differences were found, other than the Fmr1 transcript itself, in total mRNA levels or % polyribosome association that withstood multiple test correction, in P7 Fmr1 KO mouse cerebral cortex compared with WT littermates..

overall_design: We prepared polyribosomes on sucrose gradients from 6 littermate pairs of Fmr1 KO and WT littermates (FVB background, P7 males, cerebral cortex) and purified RNA from both polyribosomal fractions and input to the gradient, reflecting total mRNA levels for comparison.

first: Robert

last: Darnell

first: Jennifer

middle: C

first: Claire

last: Fraser


title: Expression data from Rbp2f/f and Rbp2-/- ES cells before and after differentiation

status: Public on Jul 20 2011

city: New Haven

first: Qin

last: Yan

state: CT

address: Department of Pathology, PO Box 208023

institute: Yale School of Medicine

summary: Aberrations in epigenetic processes, such as histone methylation, can lead to cancer. Retinoblastoma Binding Protein 2 (RBP2)(also called JARID1A or KDM5A) can demethylate tri- and di-methylated lysine 4 in histone H3, which are epigenetic marks for transcriptionally active chromatin, whereas the MEN1 tumor suppressor promotes H3K4 methylation.  Previous studies suggested that inhibition of RBP2 contributed to tumor suppression by pRB. Here we show RBP2 loss promotes cellular differentiation in vitro.  We use mouse expression array 430 2.0 array to profile gene expression patterns of Rbp2f/f and Rbp2-/- ES cells in ES cell medium and after 6 days in ES cell medium without LIF.

overall_design: Subconfluent Rbp2f/f and Rbp2-/- ES cells in ES cell medium and after 6 days in ES cell medium without LIF were harvested for RNA isolation using RNeasy mini kit with on-column DNase digestion (Qiagen). Gene expression profiling was performed using Affymetrix GeneChip mouse genome 430 2.0 arrays. Duplicate samples were used

first: William

middle: G

last: Kaelin


title: Effect of ablation of Max gene expression on ES cells cultured under conventional or 2i/Nam condition.

city: Hidaka

first: Akihiko

last: Okuda

state: Saitama

address: 1397-1 Yamane

department: Research Center for Genomic Medicine

institute: Saitama Medical University

summary: c-Myc is one of key players that are crucially involved in maintaining the undifferentiated state and the self-renewal of ESCs. To understand the mechanism by which c-Myc helps preserve these prominent characteristics of ESCs, we generated null-ES cells for the Max gene, which encodes the best characterized partner protein for all Myc family proteins. Although Myc/Max complexes have been widely regarded as crucial regulators of the ESC status, our data reveal that ESCs do not absolutely require these complexes in so-called ground state or related conditons and that this requirement is restricted to conventional ES culture conditions without using a MAPK inhibitor.

overall_design: Simply Dox-treated or Nanog (WT or D67G mutant)-rescued Max-null ESCs which were cultured under conventional culture condition and 2i/Nam-treated completely Max-null ES cells from which Dox-regulatable cDNA was removed were used for RNA source. Samples from Dox-untreated Max-null ESCs cultured under conventional culture condition were used as reference samples for Dox-treated cells and Nanog-rescued cells, while a sample from wild-type ESCs cultured under 2i/Nam condition was used as a reference sample for completely Max-null ES cells cultured with 2i/Nam.

first: Tomoaki

last: Hishida

first: Yuriko

last: Nozaki

first: Yutaka

last: Nakachi

first: Yosuke

last: Mizuno

first: Yasushi

last: Okazaki


title: Expression data from murine acute myeloid leukemia (AML) cells following shRNA-mediated suppression of Myb

city: Vienna

first: Johannes

last: Zuber

address: Dr. Bohr-Gasse 7

institute: Research Institute for Molecular Pathology (IMP)

summary:
Using an integrative approach combining a Tet-off conditional AML mouse model, global expression profiling following suppression of the driving MLL-AF9 oncogene, and a new Tet-on conditional shRNA expression system we have identified Myb as critical mediator of addiction to MLL-AF9. Suppression of Myb in established AML in vivo terminates aberrant self-renewal and triggers a terminal myeloid differentiation program that precisely phenocopies the effects of suppressing MLL-AF9. Remarkably, suppressing Myb effectively eradicates aggressive and chemotherapy resistant AML.
To further investigate Myb dependent transcriptional programs involved in mediating aberrant self-renewal in leukemia, we globally surveyed gene expression changes following acute shRNA-induced suppression of Myb in an established Tet-on competent model of MLL-AF9;NrasG12D-induced AML.

overall_design: To enable regulatable suppression of Myb in AML, we retrovirally transduced established Tet-on competent MLL-AF9;NrasG12D induced AML cells with TRMPV-Neo vectors (Zuber et al., Nature Biotech, 2010) harboring shRNAs targeting Myb (shMyb.2572 and shMyb.2652), a control shRNA targeting Renilla Luciferase (shRen.713), or an empty miR30 cassette of the recipient cloning vector (Rec). Following drug selection, shRNA expression was induced by doxycycline treatment and total RNA was isolated from sorted shRNA expressing (Venus+/dsRed+) leukemia cells after 3 days of dox treatment, and subjected to Affymetrix microarray expression analysis. Expression profiles following expression of two independent Myb shRNAs were compared to those observed after induction in shRen.713- and Rec-expressing control samples (each in 3 biological replicates).

first: Amy

last: Rappaport

first: Scott

last: Lowe


title: FMRP Associates with Polyribosomes

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

overall_design: Refer to individual Series


title: Genome-wide analysis distinguishes hyperglycemia regulated epigenetic signatures of primary vascular cells (gene expression)

city: Melbourne

first: Assam

last: El-Osta

address: 75 Commercial Road

country: Australia

institute: Baker Heart and Diabetes Institute

summary: We report that hyperglycemia-mediated induction of genes and pathways associated to endothelial dysfunction occur through modulation of acetylated H3K9/K14 inversely correlated with methyl-CpG content.

overall_design:
Examination of H3K9/K14 histone acetylation and DNA methylation in hyperglycemic conditions.
see GSE29251 for histone acetylation and DNA methylation

first: Luciano

last: Pirola

first: Aneta

last: Balcerczyk

first: Richard

last: Tothill

first: Izhak

last: Haviv

first: Antony

last: Kaspi

first: Sebastian

last: Lunke

first: Tom

last: Karagiannis

first: Stephen

last: Tonna

first: Adam

last: Kowalczyk

first: Bryan

last: Beresford-Smith

first: Mark

last: Zieman

first: Ma

last: Kelong

first: Zhang

last: Hongyu

first: Sun

last: Jinfeng

first: Jingde

last: Zhu


title: Gene expression profiles of mouse sentinel lymph nodes (SLNs) in xenotransplanted and non tumor bearing CB17 SCID.

status: Public on Jul 15 2011

first: Andreas

last: Bracher

address: Lazarettgasse 14, Floor 4, Lab 6

department: General Dermatology

institute: Medical University of Vienna

summary: Cutaneous melanoma first metastasizes into sentinel lymph nodes that control the lymphatic drain from the area of the primary tumor. This observation is used clinically for melanoma patients with primary melanomas thicker than 1mm (tumor stage ≥T2a), for these patients sentinel lymph node biopsy has become an important and routinely performed diagnostic procedure. The importance of sentinel node analysis is reflected by a significant better prognosis of melanoma patients with tumor free sentinel nodes compared to patients with metastatic sentinel nodes. Although intensively studied, not much is known about mechanisms responsible for the development of melanoma metastasis.To analyze gene expression in mouse SLNs of M24met tumor bearing animals as compared to tumor free control animals, SLNs were taken at different time points and analyzed for the presence of human M24met to classify SLNs into control, negative, macro metastatic SLN. After categorized SLNs were subjected to microarray analysis.

overall_design: To analyze gene expression in mouse SLNs of human M24met tumor bearing animals as compared to tumor free control animals, SLNs were taken at different time points and analyzed for the presence of human M24met to classify SLNs into control, negative, macro metastatic SLN. Briefly, explanted SLNs were stored in RNA later (Ambion, Austin, TX) and DNA as well as RNA was extracted using AllPrep DNA/RNA Mini Kit and RNeasy Micro Kit (Qiagen, Valencia, CA) according to manufacturer’s instructions. To detect human cells in mouse SLNs we used a polymerase chain reaction method for the detection of a human-specific 850-bp fragment of the alpha-satellite DNA on human chromosome 17. For analysis of gene expression RNA from control SLN from tumor free animals (control), RNA from tumor negative SLN (negative), and RNA from macro metastatic SLN (positive) from tumor bearing animals was used to analyze gene expression on Mouse Genome 430A 2.0 Arrays (Affymetrix, Santa Clara, CA)

first: Stefanie

last: Tauber

first: Martin

last: Bilban

first: Silvia

last: Steele

first: Robert

last: Loewe


title: A Regenerative Trait in Mice with a Point Mutation in TGFBR1

status: Public on Jul 11 2011

city: San Diego

first: John

last: Walker

state: CA

address: 10675 John Jay Hopkins

institute: Genomics Institute of the Novartis Research Foundation

summary:
Regeneration of differentiated tissue in mammals is rare.  In an effort to identify genes that affect the healing process, we screened G3 mice containing germline point mutations for closure of an ear punch wound.  One particular line was identified with a heritable hole closure phenotype containing differentiated tissue. Mapping and sequencing efforts revealed that the mutant mice harbor a R244Q point mutation coded by the TGFBR1 gene which leads to enhanced signaling activity in a reporter gene assay.  Although there was no obvious effect on the immune system, bone marrow stromal cells from the mutant mice revealed accelerated chondrogenesis, mimicking the in vivo development of cartilage islands in the regenerated ears. This genetically well-defined mouse model should help to further dissect the role of TGF-beta signaling in vertebrate healing and regeneration.

Keywords: treatment and time course in wt and mutant samples

overall_design: TGFb or vehicle treatment at different time points in mouse embryonic fibroblasts from wildtype and TGFb1 mutant (heterozygous and homozygous) mice.  Mutant is constitutively active.

first: Jun

last: Liu

first: Kristen

last: Johnson

first: Jie

last: Li

first: Victoria

last: Piamonte

first: Brian

middle: M

last: Steffy

first: Mindy

last: Hsieh

first: Jay

last: Zhang

first: Xu

last: Wu

first: Sheng

last: Ding

first: Richard

last: Glynne

first: Peter

last: Schultz


title: Retinoic acid (RA) induction time-course to profile gene expression during mES cell differentiation.

status: Public on Jul 19 2011

city: Kansas CIty

first: Alexander

middle: (Garrett)

last: Garruss

state: Missouri

address: 1000 East 50th Street

institute: Stowers Institute for Medical Research

summary: Murine ES cell gene expression before RA induction are used to compare gene expression for time-points of 2, 4, 6hrs post-induction.

overall_design: KH2 ES Cell RA Differentiation Time-course

first: Bony

last: De Kumar

middle: S

last: Garrett

first: Robb

last: Krumlauf


title: Expression array using Maffucci tumours

city: Leiden

first: Twinkal

middle: Chandubhai

last: Pansuriya

state: Zuid-Holland

address: Albinusdreef 2

department: Pathology

institute: LUMC

summary: We did whole genome analysis of enchondromas and chondrosarcomas of Maffucci patients. Since the disease is very rare, we had only three frozen tumour samples were available to continue with the expression array. Enchondromas of Maffucci syndrome did not show any loss of heterozygosity (LOH) or common copy number alterations (CNA) and we looked at the differentially expressed genes between Ollier high grade and Maffucci high grade tumours. There were no significant differentially expressed genes were found between these two groups. This might be due to the small sample size.

overall_design: We used Affymetrix SNP 6.0 array on enchondromas (n=4) and chondrosarcomas (n=2) and compared the results to a previously studied cohort of patients with Ollier disease (n = 37). We used Illumina expression array v3 chip on enchondroma (n=1) and chondrosarcomas (n=2) from Maffucci patients.

first: Judith

last: Bovee

first: Jan

last: Oosting


title: Developmental profiling of spiral ganglion neurons reveals insights into auditory circuit assembly

city: Boston

first: Lisa

last: Goodrich

state: MA

address: 220 Longwood Avenue

department: Neurobiology

institute: Harvard Medical School

summary:
The sense of hearing depends on the faithful transmission of sound information from the ear to the brain by spiral ganglion (SG) neurons.  However, how SG neurons develop the connections and properties that underlie auditory processing is largely unknown.
We catalogued gene expression in mouse SG neurons at six developmental stages, ranging from embryonic day 12 (E12), when SG neurons first extend projections, up until postnatal day 15 (P15), after the onset of hearing.  For comparison, we also analyzed the closely-related vestibular ganglion (VG) at the same time points.

overall_design: To identify genes involved in SG axon guidance and branching, target selection, synaptogenesis, synaptic refinement, and synaptic function, we collected SG at E12 and E13, E16, P0, P6, and P15.  We also collected VG at the same time points.  For E12 and E13 time points, SG and VG were microdissected from Rnx-cre; Z/EG embryos, which express GFP in the VG.  E16-P15 VG was also isolated by microdissection from Rnx-cre; Z/EG animals.  E16-P15 SG neurons were isolated by FACS sorting dissociated cochlea from Mafb-GFP animals.

first: Cindy

last: Lu


title: Protection from obesity and diabetes by blockade of TGF-beta/Smad3 signaling

status: Public on Jul 13 2011

city: Bethesda

first: WeiPing

last: Chen

address: Bldg 8, Room 1A11, NIDDK/NIH

department: GCL

institute: NIDDK/NIH

summary: Imbalances in glucose and energy homeostasis are at the core of the worldwide epidemic of obesity and diabetes. Here, we illustrate an important role of the TGF-beta/Smad3 signaling pathway in regulating glucose and energy homeostasis. Smad3 deficient mice are protected from diet-induced obesity and diabetes. Interestingly, the metabolic protection is accompanied by Smad3-/- white adipose tissue acquiring the bioenergetic and gene expression profile of brown fat/skeletal muscle. Smad3-/- adipocytes demonstrate a marked increase in mitochondrial biogenesis, with a corresponding increase in basal respiration, and Smad3 acts as a repressor of PGC-alpha1 expression. We observe significant correlation between TGF-beta1 levels and adiposity in rodents and humans. Further, systemic blockade of TGF-beta1 signaling protects mice from obesity, diabetes and hepatic steatosis. Together, these results demonstrate that TGF-beta signaling regulates glucose tolerance and energy homeostasis and suggest that modulation of TGF-beta1 activity might be an effective treatment strategy for obesity and diabetes.

overall_design: Smad3-/- and WT mice were fed with regular diet (RD) and high fat diet (HFD), and diet induced obese (DIO) mice were treated with IgG and anti-TGF-b1 antibody

first: Hariom

last: Yadav

first: Celia

last: Quijano

first: Anil

middle: K

last: Kamaraju

first: Oksana

last: Gavrilova

first: Rana

last: Malek

first: Weiping

first: Patricia

last: Zerfas

first: Duan

last: Zhigang

first: Elizabeth

last: Wright

first: Christina

last: Steulten

last: Sun

first: Scott

last: Lonning

first: Monica

last: Skarulis

first: Anne

last: Sumner

first: Toren

last: Finke

first: Sushil

last: Rane


title: Expression analysis of haploid and diploid ES cells in 2i medium

first: Martin

last: Leeb

address: Dr.-Bohr-Gasse 9/3

summary: gene expression differences were analysed between haploid and diploid ES cells

overall_design: biological triplicates of haploid and diploid ES cell lines were analysed on an Affymetrix GeneChip 430 array

first: Anton

last: Wutz


title: Expression data from targeting of NOS2 in glioma stem cells

status: Public on Jul 08 2011

city: Cleveland

first: Jeremy

last: Rich

address: NE3-30 Lerner Reseach Institute, 9500 Euclid Avenue

department: Stem Cell Biology and Regenerative Medicine

institute: Cleveland Clinic

summary: Analysis of the effects of targeting NOS2 at the gene expression level. Our studies demonstrated a role for NOS2 in glioma biology through the maintenance of the glioma stem cell phenotype. Microarray results provide novel targets of NOS2 and suggest mechanisms through which NOS2 contributes to glioma stem cell biology.

overall_design: Glioma stem cells isolated from two different human glioma xenografts were infected with a non-targeting control shRNA or two different shRNAs directed against NOS2 (each treatment in each tumor performed in technical duplicates).

middle: N

first: Christine

last: Eyler

first: Anita

last: Hjelmeland