title: Altered gene expression is associated with age-dependent memory impairment

status: Public on Apr 19 2010

summary: The mechanisms underlying age-associated memory impairment are  not well understood.  We have shown that the onset of memory disturbances in the aging brain is associated with altered hippocampal chromatin plasticity. During learning, aged mice display a specific deregulation of histone H4 lysine 12 (H4K12) acetylation. To analyze if deregulated H4K12 acetylation impacts on learning-induced gene-expression required for memory consolidation we performed a high-density oligonucleotide microarray to compare the entire hippocampal gene-expression profile of 3 and 16-month-old mice during memory consolidation.

overall_design: In order to identify genes differentially regulated between 3- and 16-month old mice upon fear conditioning we subjected 3- and 16-month old mice  to fear conditioning (4 mice each group, total 8 mice) . Mice of the same age that were handled but not subjected to any of the employed behavior paradigms served as control  (4 mice 3-month old and 4 mice 16-month old, total 8 mice). During fear conditioning mice are subjected to a novel context  followed by a mild electric foot-shock (context-shock exposure). In order to identify genes that are differentially regulated upon fear conditioning and are specific to associative learning we also tested the hippocampal gene-expression profile of  3-month old mice subjected to the same context-exposure that is not followed by a foot-shock (Context-exposure) (4 mice) or receive an immediate foot shock once they are placed in the context and only afterwards are allowed to explore the context (shock-context exposure) (4 mice). In order to identify genes that are regulated upon fear conditioning and are specific to associative learning we compared the hippocampal gene-expression profile of mice subjected to fear conditioning (context-shock), context or shock-context exposure regarding to their age-matched control mice (3 month old) mentioned above (control). Hippocampi from each mice were tested resulting to 24 samples which were separately hybridized (OneColor Array Design).

first: Lennart

last: Opitz

last: Salinas-Riester

first: Shahaf

last: Peleg

first: Farahnaz

last: Sananbenesi

first: Athanasios

last: Zovoilis

first: Andre

last: Fischer


title: Gene expression data of interleukin-7-dependent and BCR-ABL1-transformed pre-B cells

status: Public on May 10 2010

city: Los Angeles

first: Markus

last: Müschen

state: CA

address: 4650 Sunset Blvd

department: Childrens Hospital Los Angeles

country: USA

institute: University of Southern California

summary:
This analysis focused on identifying factors that protect pre-B cells against DNA double strand break (DSB)-mediated DNA damage stress during pre-B cell differentiation. Differentiation of pre-B cells including  immunoglobulin light chain gene recombination were performed by withdrawal of interleukin-7 (IL-7) from IL-7-dependent murine pre-B cells or by inhibition of the BCR-ABL1 kinase activity in BCR-ABL1-transformed pre-B cells.
The BCR-ABL1 kinase inhibitor STI571 (Imatinib) was used for the inhibition of BCR-ABL1.

overall_design: IL-7-dependent murine pre-B cells were either cultured in IL-7 (10 ng/ml) or induced to differentiate by withdrawal of IL-7. BCR-ABL1-transformed pre-B cells were either treated with 10 µM STI571 (in absence or presence of 10 ng/ml IL-7) for 16 hours or cultured without STI571. Three samples for each condition were processed.

first: Cihangir

last: Duy

first: Jessica

middle: J

last: Yu

first: Rahul

last: Nahar

first: Srividya

last: Swaminathan

first: Soo-mi

last: Kweon

first: Jose

middle: M

last: Polo

first: Ester

last: Valls

first: Lars

last: Klemm

first: Seyedmehdi

last: Shojaee

first: Leandro

last: Cerchietti

first: Wolfgang

last: Schuh

first: Hans-Martin

last: Jäck

first: Christian

last: Hurtz

first: Parham

last: Ramezani-Rad

first: Sebastian

last: Herzog

first: Hassan

last: Jumaa

first: Phillip

middle: H

last: Koeffler

first: Ignacio

last: de Alborán

first: Ari

last: Melnick

first: Hilda

middle: B

last: Ye


title: FL5.12 Bfl-1DC/p53DD-derived splenic tumors compared to the parental FL5.12 Bfl-1DC/p53DD cell line

status: Public on Mar 23 2010

city: Worcester

first: Matthew

last: Simmons

state: MA

address: 364 Plantation St

department: Cancer Biology

institute: UMASS Medical School

summary: The antiapoptotic Bcl-2 family member Bfl-1 is upregulated in many human tumors in which NF-kB is implicated, and contributes significantly to tumor cell survival and chemoresistance. We previously found that NF-kB induces transcription of bfl-1, and that the Bfl-1 protein is also regulated by the ubiquitin-proteasome. However little is known of the role that dysregulation of Bfl-1 turnover plays in cancer. We found that ubiquitination-resistant mutants of Bfl-1 display increased stability and greatly accelerate tumor formation in a mouse model of leukemia/lymphoma. Gene expression profiling revealed that tyrosine kinase Lck is highly upregulated and activated in these tumors compared to the parental cells, as were several genes in the RANK signaling pathway, and leads to activation of the IKK, Akt and Erk signaling pathways, which are key mediators in cancer. Tumor assays with cells coexpressing constitutively active Lck with Bfl-1, or with tumor-derived cells following shRNA-mediated Lck knockdown, unveiled functional cooperation between Bfl-1 and Lck in leukemia/lymphomagenesis. These data demonstrate that ubiquitination is a critical mechanism for regulating Bfl-1 function, and suggest that mutations in bfl-1 or in the signaling pathways that control its ubiquitination may predispose to cancer. Additionally since bfl-1 is upregulated in many human hematopoietic tumors, these data suggest that strategies to promote Bfl-1 ubiquitination may improve therapy in drug-resistant tumors.

overall_design: FL5.12 pro-B cells were stably transfected with Bfl-1DC and p53DD (Parental - P) and injected i.v. into nude mice.  The spleens were harvested from three independent mice that developed leukemia/lymphoma (T1, T2, and T3).  To identify the changes in gene expression that occurred during tumorigenesis, RNA was isolated from the parental cell line (P) and from  three independent splenic tumors (T) and hybridized to Affymetrix Mouse Genome 430A_2.0 arrays.  The analysis was performed in duplicate.

first: Céline

last: Gélinas

first: Gaofeng

last: Fan

first: Jui

last: Dutta-Simmons

first: Jérôme

middle: F

last: Kucharczak

first: Yacov

last: Ron

first: David

last: Weissmann

first: Chiann-Chyi

last: Chen

first: Chandreyee

last: Mukherjee

first: Eileen

last: White


title: Comparison of naïve, postmitotic (CD44-lo/CD62L-hi) and effector (CD44-hi/CD62L-lo) CD8+ Tcells during BMT in GVHD mice

status: Public on May 21 2010

city: Ann Arbor

first: Rork

last: Kuick

state: MI

address: University of Michigan, SPH II, 1415 Washington Heights, Room M2533

institute: University of Michigan

summary:
Naïve CD44-lo/CD62L-hi/CD8+ T cells from C3H.SW mice were compared to CD44-hi/CD82L-lo/CD8+ effector memory T cells and CD44-lo/CD62L-hi/CD8+ postmitotic T cells, using 3 biological replicates of each type of sample.  The later two cells types were highly purified at day 14 after transplantation from GVHD B6/SJL mice receiving donor C3H.SW mouse-derived naive CD44-lo/CD62L-hi/CD8+ T cells and T cell-depleted bone marrow. Recipient mice had first been lethally irradiated at a dose of 10Gy in two fractions. This is a MHC-identical minor histocompatibility antigen-mismatched mouse GVHD model of human allogeneic hematopoietic stem cell transplantation. Naive T cell samples were from pools of 2 mice each, while effector memory and postmitotic T cell samples were purified from pools of T cells from 4 mice each.  After RNA  extraction and cleanup, biotin labeled cRNA was prepared from 600 ng total RNA, using two rounds of in vitro transcription, and hybridized to Affymetrix Mouse Genome 430A 2.0 arrays using standard techniques.

Keywords: Cell type comparison

overall_design: 9 samples were analyzed on 9 Affymetrix microarrays to assay mRNA levels.  There were 3 biological replicates of each of 3 different cell types.

first: Koji

last: Kato

first: Shuaiyang

last: Cui

first: Shin

last: Mineishi

first: Jina

last: Wang

first: Elizabeth

last: Bacon

first: Jian

last: Huang

first: Peter

last: Klein

last: Hexner

first: Jiu

last: Jiang

first: Pavan

last: Reddy

first: James

middle: L

last: Ferrara

first: Stephan

middle: G

last: Emerson

first: Yi

last: Zhang


title: Mthfd1 is a modifier of intestinal carcinogenesis

status: Public on Mar 20 2010

city: Ithaca

first: David

last: Lin

state: NY

address: T2 006A VRT

institute: Cornell University

summary:
The metabolic pathways that underlie the association between folate deficiency and increased risk for colorectal cancer (CRC) remain unclear. We have studied the effect of C1THF synthase (encoded by the Mthfd1 gene) and dietary folate and choline on intestinal tumor development in Apcmin/+ mice and azoxymethane (AOM)-induced colon cancer in mice. Mthfd1 deficiency did not alter tumor number or load in Apcmin/+ mice, but did result in a decreased incidence of colon tumors. Conversely, Mthfd1 deficiency increased tumor number 3.5-fold and tumor load 2-fold in AOM-treated mice. Here we tested colons isolated from wildtype and Mthfd1-deficient animals for alterations in gene expression.

Keywords: genetic modification

overall_design: RNA was isolated from proximal colons of MTHFD heterozygous and wild-type mice raised on a control diet. Three colon samples were isolated from each genotype to provide biological replication.

first: Patrick

last: Stover

first: Amanda

last: MacFarlane

first: Cheryll

last: Perry

first: Michael

last: McEntee


title: Liver gene expression from chromogranin A knockout mice (Mahapatra et al. 2005) vs. wild-type mice

status: Public on Mar 03 2010

city: La Jolla

first: Ryan

last: Friese

institute: University of California San Diego

summary: The objective of the experiment is to determine the genes differentially expressed in the liver of the chromogranin A knockout mouse (Mahapatra et al., 2005).

overall_design: Liver from chromogranin A knockout mice (n=3) and wild-type control mice (n=3).

middle: S


title: Heterogeneity in MYC-Induced Mammary Tumors Determines Outcomes Following Loss of Myc Activity

status: Public on Jun 18 2010

city: Durham

first: Janet

middle: Y.

last: Leung

state: NC

address: 101 Science Dr.

institute: Duke University

summary: We used microarrays to compare gene expression profiles between mouse mammary tumors initiated by Myc to those that have escaped Myc oncogene dependence.

overall_design: We collected tumor biopsies of Myc-initiated tumors and samples of tumors that persisted or recurred after Myc withdrawal.  RNA was extracted from these tumors and hybridized to microarrays.

middle: Y


title: Transactivation of the dopamine receptor 3 gene results in development of B-cell lymphoma in mice

status: Public on Mar 08 2010

city: Setagaya-ku

first: MASAFUMI

last: ONODERA

state: Tokyo

department: Department of Genetics

country: Japan

institute: National Research Institute for Child Health and Development

summary:
Transactivation of the dopamine receptor 3 gene by a single provirus integration results in development of B-cell lymphoma in transgenic mice generated from retrovirally transduced embryonic stem cells.

Gene transfer vectors based on retroviruses are commonly used in gene therapy applications because of their unique ability to integrate efficiently into host genomes. This ability also forms the basis of a transformation event that can be induced in transduced cells by transactivation of proto-oncogenes near the vector integration sites. Here, we report on the development of lymphoma in mice generated from embryonic stem cells transduced with an enhanced green fluorescent protein. The cells expressed B220, CD5, Mac1, and IgM on their surfaces and expressed transcription factors characteristic of B cell lymphoma. Importantly, each mouse had a single copy of the provirus in its genome; the copy was integrated into the second intron of the dopamine receptor 3 (D3) gene, and high-level expression of D3 was detected only in the lymphoma cells. Ectopic expression of D3 in murine marrow cells resulted in preferential proliferation of cells at the pre-B-cell stage in response to a D3-specific agonist, but this proliferation was not observed in vivo. Cells co-transduced with D3 and Bcl-xL genes had a phenotype similar to that of lymphoma in vivo, suggesting that the leukemogenesis induced by retroviral integration required “second hit” mutations of additional genes.

overall_design: Two independently establisehd lymphoma cell lines and  two control splenocyte samples were subjected to expression array analysis.

first: Yumi

last: Hirata

first: Sanae

last: Hamanaka

first: Masafumi

last: Onodera


title: Gene expression from chromogranin A knockout mice vs. wild-type mice

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

overall_design: Refer to individual Series


title: Expression data from mouse lung treated with MACA, BSA or HBSS

status: Public on Mar 01 2010

city: Research Triangle Park

first: Cherie

middle: M.

last: Pucheu-Haston

address: 109 T.W. Alexander Drive

department: NHEERL

institute: U.S. Environmental Protection Agency

summary:
We hypothesize that there is a set of differentially-expressed gene “biomarkers” that distinguishes the immune response associated with the induction of allergic sensitization from non-allergic immune responsiveness following a single exposure. The goal of this preliminary study was to identify potential biomarkers that differentiate the response to allergens vs non-allergens following an acute exposure in naïve individuals.
We evaluated the gene transcriptional responses of mouse lungs following a single exposure to agents of high or low allergenicity or vehicle control.

overall_design: Female BALB/c mice received a single intratracheal aspiration exposure to Metarhizium anisopliae crude antigen (MACA) or bovine serum albumin (BSA) in Hank’s Balanced Salt Solution (HBSS) or HBSS alone.  RNA was isolated from lung tissue of 3-4 biological replicates from each treatment group at 3h and 12h post-treatment.

first: Marsha

middle: D

last: Ward


title: Murine Fgf3-/-;Fgf10-/- vs. Fgf3+/-;Fgf10+/- otic placode profiling

city: Salt Lake City

first: Suzanne

middle: L.

last: Mansour

state: UT

address: 15 North 2030 East

department: Human Genetics

institute: University of Utah

summary: Transcriptional profiling of mouse 4-8 somite microdissected otic placodes from Fgf3/Fgf10 double heterozygotes (controls) compared to Fgf3/Fgf10 double null mutants.  The purpose was to determine the effectors that are induced (or repressed) by Fgf3 and Fgf10 in the course of otic placode induction.

overall_design: Two condition experiment, double heterozygote vs. double null placodes.  Biological replicas:  3 Fgf3+/-;Fgf10+/- and 3 Fgf3-/-;Fgf10-/- pools of ten placodes each.

first: Lisa

last: Urness


title: Comparison of gene expression in mouse placentas with different combination of MT1-MMP and MT2-MMP alleles

city: Bethesda

first: Kenn

last: Holmbeck

state: MD

address: 30 Convent Drive

institute: NIDCR

summary: MT1-MMP and MT2-MMP double deficiency in mice leads to development of a placental defect resulting in embryonic death after E10.5. The protein substrate for these two proteases in placenta is unknown, which poses an obstacle in uncovering of molecular mechanism behind the observed placental defect. In search for a potential substrate for these two proteases in placenta we have employed whole genome microarray expression profiling as a discovery platform to identify genes, expression of which might be affected by double MMP deficiency.

overall_design: Fetal parts of mouse placentas were isolated from E10.5 placentas of different genotypes for MT1- and MT2-MMP.

first: Ludmila

last: Szabova


title: PARP1 and Salmonella

status: Public on May 01 2010

city: Zurich

first: Hubert

last: Rehrauer

address: Winterthurerstr. 190

department: FGCZ

country: Switzerland

institute: ETH Zurich / University of Zurich

summary:
BACKGROUND & AIMS: The immune system comprises an innate and an adaptive immune response to combat pathogenic agents. The human enteropathogen Salmonella enterica serovar Typhimurium invades the intestinal mucosa and triggers an early innate pro-inflammatory host gene response, which results in diarrheal disease.  Several host factors are involved in the acute early response to Salmonella infection. Transcription factors and transcription co-regulators have an especially important function, because they are required for the expression and synthesis of pro-inflammatory cytokines, chemokines and adhesion molecules. A central transcription factor involved in inflammation is NF-κB, which requires the nuclear protein PARP1 as co-factor for the expression of some of its target genes. Here, we investigated the role of PARP1 during Salmonella infection using a mouse model for Salmonella-induced colitis.
METHODS: To study enterocolitis by Salmonella Typhimurium, an established mouse model system, which relies on streptomycin-pretreatment prior to Salmonella infection, was employed. Histopathologic signs of inflammation and cecum colonization at various time-points after infection of wild type and PARP1 knockout mice were analyzed. PARP1 expression in the gut mucosa was studied by quantitative RT-PCR, Western blot and immunofluorescence. Gene expression profiles of infected and control infected mice in the wild type or PARP1 knockout background were obtained by whole mouse genome arrays and confirmed by quantitative RT-PCR.

overall_design: 2 genotypes (wildtype, PARP1 knockout), 2 treatments (Salmonella SB300 infection, Salmonella SB161 control infection), 2 time-points (6h, 10h). 2-3 replicates/condition.

first: M

last: Altmeyer

last: Barthel

last: Eberhard

first: H

first: W

last: Hardt

last: Hottiger


status: Public on Mar 15 2010

city: Boston

first: Amit

last: Sinha

address: 44 Binney St

department: Pediatric Oncology

institute: Dana-Farber Cancer Institute

summary:
Activation or maintenance of a leukemia stem cell self-renewal pathway in downstream myeloid cells is an important component of AML development
We generated either MLL-AF9 mediated murine leukemias that originate from committed progenitor (GMP) cells or Hoxa9/Meis1a mediated murine leukemias that originate from hematopoietic stem cells (HSC). The leukemia stem cell fraction in these two type of leukemias shared a common self-renewal pathway with normal hematopoietic stem cells.

Keywords: Cell type comparison

overall_design: Total RNA from HSC (KLS), CMP, and GMP, and from leukemia stem cells (LGMP)  was isolated and hybridized to Affymetrix expresison microarrays.

first: Yingzi

last: Wang

first: Andrei

middle: V

last: Krivtsov

first: Scott

middle: A

last: Armstrong


title: Merlin/NF2 Suppresses Tumorigenesis by Inhibiting the E3 Ubiquitin Ligase CRL4DCAF1 in the Nucleus

status: Public on Feb 25 2010

city: New York

first: Wei

last: Li

address: 430 East 67th street

department: Cell Biology

institute: Memorial Sloan-Kettering Cancer Center

summary: Current models imply that the FERM domain protein Merlin, encoded by the tumor suppressor NF2, inhibits mitogenic signaling at or near the plasma membrane. Here, we show that the closed, growth inhibitory form of Merlin accumulates in the nucleus, binds to the E3 ubiquitin ligase CRL4DCAF1, and suppresses its activity. Depletion of DCAF1 blocks the promitogenic effect of inactivation of Merlin. Conversely, enforced expression of a Merlin-insensitive mutant of DCAF1 counteracts the antimitogenic effect of Merlin. Re-expression of Merlin and silencing of DCAF1 induce a similar, tumor-suppressive program of gene expression. Tumor-derived mutations invariably disrupt Merlin’s ability to interact with or inhibit CRL4DCAF1. Finally, depletion of DCAF1 inhibits the hyperproliferation of Schwannoma cells from NF2 patients and suppresses the oncogenic potential of Merlin-deficient tumor cell lines. We propose that Merlin suppresses tumorigenesis by translocating to the nucleus to inhibit CRL4DCAF1.

overall_design: To examine if Merlin controls gene expression through inhibition of CRL4DCAF1, and define the general function of this ligase, we compared the gene expression program activated by expression of Merlin or by depletion of DCAF1 in Merlin-null FC-1801 mouse Schwannoma cells

first: Liru

last: You

first: Jonathan

last: Cooper

first: Gaia

last: Schiavon

first: Angela

last: Pepe-Caprio

first: Lu

last: Zhou

first: Ryohei

last: Ishii

first: Marco

last: Giovannini

first: Oliver

last: Hanemann

first: Stephen

last: Long

first: Hediye

last: Erdjument-Bromage

first: Pengbo

first: Paul

last: Tempst

first: Filippo

last: Giancotti


title: Blood Gene Expression Signatures Predict Invasive Candidiasis

first: Hamza

last: Aziz

address: 101 Science Drive

department: Institute of Genomic Science and Policy

summary: Focusing on host response to infection, we utilized a murine model to develop a  blood gene expression signature that accurately classified mice with candidemia and distinguished candidemia from S. aureus bacteremia.  Validation of the signature was achieved in an independent cohort of mice.

overall_design: BALB/c male mice were injected with either normal saline, C.albicans, or S.aureus and sacrificed at pre-set time points of 24, 48, 72-96 hrs (Infection Duration).  Blood was placed in RNA Later (R) for RNA expression analysis and the right kidney collected for analysis of pathogen burden.

first: Aimee

middle: K

last: Zaas

first: Joseph

last: Lucas

first: John

middle: R

last: Perfect

first: Geoffery

last: Ginsburg


title: Gene expression signatures for mESC treated by RNAi strategy on down regulation of gene  Mtf2

status: Public on Feb 20 2010

city: Urbana

first: Dan

last: Xie

state: IL

address: 3215 Digital Computer Lab, MC-278, 1304 W. Springfield Ave

department: Bioengineering

institute: University of Illinois at Urbana and Champaign

summary: To further explore the function of Mtf2, the homolog of Drosophila Polycomb group gene PCL, we have employed the mouse whole genome microarray expression profiling as a discovery platform to identify genes mediated by Mtf2. Oligos of 2 different RNAi target sites on gene Mtf2 were cloned into RNAi Vector pSuper and transfected individually into Mouse Embryonic Stem Cell line E14. Empty Vector pSuper and plasmid containing RNAi target against gene Luciferase (Firefly) were performed in the same way as negative controls. The down regulation effect of gene Mtf2 was quantified by real-time PCR in the same RNA samples subjected to microarray analysis.

overall_design: mESC was transfected by RNAi plasmids with resistence of puromycin and selected by Puromycin(1mg/ml) for 2 days. 4 independent experiments were performed for vector pSuper, plasimd pSuper-Luci-RNAi, pSuper-Mtf2-RNAi-1, pSuper-Mtf2-RNAi-3.


title: Active Lgr5 Positive Stem Cells Drive Self-Renewal in the Pyloric Stomach and Efficiently Build Pyloric Units In-vitro

status: Public on Feb 01 2010

city: Dresden

first: Daniel

middle: E.

last: Stange

address: Fetscherstr. 74

country: Germany

institute: University Clinic Dresden

summary: The Wnt target gene Lgr5 marks cycling stem cells in the small intestine, colon and hair-follicle. In the adult stomach, Lgr5 expression is confined to 3-4 proliferating cells at the gland base throughout the pylorus and limited numbers of corpus-type glands adjacent to the esophagus and squamous forestomach. In-vivo lineage tracing reveals that the pyloric Lgr5+ve cells rapidly generate all the major cell-types present in the gastric epithelium and maintain this multipotent stem cell activity over at least 20 months. In-vitro, single adult Lgr5+ve cells efficiently generate gastric units closely resembling mature pyloric glands. We conclude that Lgr5 is marking an active stem cell population at the base of the pyloric glands contributing to the long-term renewal of the adult gastric epithelium. The transcriptome of the adult Lgr5+ve stem cells harbors multiple Wnt target genes, implying a role for Wnt signaling in regulating pyloric stem cell function in-vivo. Conditional deletion of APC in these Lgr5+ve stem cells rapidly initiates tumor formation, supporting a potential role for aberrant Wnt signaling activity in gastric cancer.

overall_design: The pyloric region of 20 stomachs was isolated from 20 Lgr5-EGFP-ires-CreERT2 knock-in mice, tissue trypsinized to single cells and FACS sorted. Two populations were isolated, one expressing GFP at high levels and one expressing GFP at low levels. RNA from these cell populations was isolated, differentially labeled and hybridized on two microarrays in a colourswitch experiment.

first: Nick

last: Barker

middle: E

first: Marc

last: van de Wetering

first: Hans

last: Clevers


title: Sex-specific early growth hormone responses in mouse liver (Mus musculus)

status: Public on Jan 27 2010

first: David

middle: J.

last: Waxman

address: 5 Cummington Mall

department: Department of Biology and Bioinformatics Program

institute: Boston University

summary: Sex differences in liver gene expression are dictated by sex-differences in circulating growth hormone (GH) profiles.  Presently, the pituitary hormone dependence of mouse liver gene expression was investigated on a global scale to discover sex-specific early GH response genes that might contribute to sex-specific regulation of downstream GH targets and to ascertain whether intrinsic sex-differences characterize hepatic responses to plasma GH stimulation.  RNA expression analysis using 41,000-feature microarrays revealed two distinct classes of sex-specific mouse liver genes:  genes subject to positive regulation (class-I) and genes subject to negative regulation by pituitary hormones (class-II).  Genes activated or repressed in hypophysectomized (Hypox) mouse liver within 30-90min of GH pulse treatment at a physiological dose were identified as direct targets of GH action (early response genes).  Intrinsic sex-differences in the GH responsiveness of a subset of these early response genes were observed.  Notably, 45 male-specific genes, including five encoding transcriptional regulators that may mediate downstream sex-specific transcriptional responses, were rapidly induced by GH (within 30min) in Hypox male but not Hypox female mouse liver.  The early GH response genes were enriched in 29 male-specific targets of the transcription factor Mef2, whose activation in hepatic stellate cells is associated with liver fibrosis leading to hepatocellular carcinoma, a male-predominant disease.  Thus, the rapid activation by GH pulses of certain sex-specific genes is modulated by intrinsic sex-specific factors, which may be associated with prior hormone exposure (epigenetic mechanisms) or genetic factors that are pituitary-independent, and could contribute to sex-differences in predisposition to liver cancer or other hepatic pathophysiologies.

overall_design: Liver RNA isolated from the following ten groups of mice was used in the present study:  Sham surgery-treated and vehicle-injected male and female mice (M-Sham (n = 7) and F-Sham (n = 8), respectively); male and female mice hypophysectomized at adulthood (M-Hypox, n = 6; F-Hypox, n = 7); M-Hypox and F-Hypox mice treated with a single GH injection and killed 30 min later (M-Hypox + GH (30), n = 7; and F-Hypox + GH (30), n = 7); M-Hypox and F-Hypox mice treated with a single GH injection and killed 90 min later (M-Hypox + GH (90), n = 7; F-Hypox + GH (90), n = 7); M-Hypox and F-Hypox mice treated with two GH injections spaced 4 hr apart and killed 30 min after the second GH injection (M-Hypox + 2 GH, n = 8; and F-Hypox + 2 GH, n = 6). These RNA pools were used in eleven separate sets of competitive hybridization experiments in a loop design: 1) M-Sham vs. F-Sham; 2) M-Hypox vs. M-Sham; 3) M-Hypox + GH (30) vs. M-Hypox; 4) M-Hypox + GH (90) vs. M-Hypox; 5) M-Hypox + 2 GH vs. M-Hypox; 6) F-Hypox vs. F-Sham; 7) F-Hypox + GH (30) vs. F-Hypox; 8) F-Hypox + GH (90) vs. F-Hypox; 9) F-Hypox + 2 GH vs. M-Hypox; 10) M-Hypox vs. F-Hypox; and 11) M-Hypox + GH (30) vs. F-Hypox + GH (30).  Fluorescent labeling of RNA and hybridization of the Alexa 555-labeled and Alexa 647-labeled aRNA samples to Agilent Whole Mouse Genome oligonucleotide microarrays (4 x 44K format; Agilent Technology, Palo Alto, CA; catalog # G4122F) were carried out, with dye swapping for each of the eleven hybridization experiments to eliminate dye bias.  Two microarrays, one for each mixed cDNA sample, were hybridized for each of the eleven fluorescent reverse pairs, giving a total of 22 microarrays.

first: Valerie

last: Wauthier

first: Aarathi

last: Sugathan

first: Alan

last: Dombkowski

middle: J


title: Genome-wide RNAi screen identifies miR-19 targets in Notch-induced acute T-cell leukaemia (T-ALL)

status: Public on Jan 30 2010

first: Andrew

last: Wolfe

address: 1275 York Ave

department: Cancer Biology and Genetics

summary: MicroRNAs (miRNAs) have emerged as novel cancer genes. In particular, the 17~92 cluster of miRNAs is highly expressed in haematopoietic cancers and promotes lymphomagenesis in vivo1,2. Clinical use of these findings hinges on isolating the oncogenic activity within the 17~92 cluster and defining its relevant target genes. Here we show that miR-19 is sufficient to promote leukaemogenesis in Notch1 induced T-cell lymphoblastic leukaemia (T-ALL) in vivo. Consistent with the pathogenic importance of this interaction, we report a novel translocation targeting the 17~92 miRNA cluster coinciding with a second rearrangement that activates Notch1 in T-ALL. To identify the miR-19 targets responsible for its oncogenic action, we conducted a large-scale short-hairpin RNA (shRNA) screen for genes whose knockdown could phenocopy miR-19. Strikingly, the results of this screen were enriched for miR-19 target genes, and included Bim (Bcl2L11)1,3, AMP-activated kinase (Prkaa1), and the tumour suppressor phosphatases Pten and PP2A (Ppp2r5e). Hence, an unbiased, functional genomics approach reveals a coordinate clamp down on several regulators of PI3K-related survival signals by the leukaemogenic miR-19.

overall_design: Gene expression data revealing differences in gene expression between parental FL5-12 cells transduced with Vector and miR-19 expressing FL5-12 cells

first: Konstantinos

last: Mavrakis

first: Hans-Guido

last: Wendel


title: Bone-marrow derived macrophages response to the Whipple's disease agent, Tropheryma whipplei

status: Public on Jan 19 2010

city: Marseille

first: Benoit

last: Desnues

address: 27 boulevard Jean Moulin

department: URMITE UMR CNRS 6236

country: France

institute: Faculté de Médecine de la Timone

summary: We have employed whole genome microarray expression profiling to identify differently expressed genes following infection of bone-marrow derived macrophages with T. whipplei. Macrophages were infected with T. whipplei (MOI 50:1) for 6 hours and a signature was identified that distinguished between infected and control samples. Expression of several genes from this signature was quantified in the same RNA samples by real-time PCR, confirming the predicted macrophage response pattern.

overall_design: Gene expression in macrophages was measured at 6 hours after infection.  Three independent experiments were performed.


title: An Ets2-specific transcriptional program in tumor-associated macrophages promotes metastasis

status: Public on Jan 05 2010

city: Columbus

first: Michael

last: Ostrowski

state: OH

address: 460 W 12th Ave

institute: Ohio State University

summary:
Macrophages have been implicated in breast cancer progression and metastasis, but relatively little is known about the genes and pathways that are involved.  Using a conditional allele of Ets2 in the mouse, we have identified Ets2 as a critical gene in tumor associated macrophages (TAMs) that specifically promotes mammary tumor metastasis.  Loss of Ets2 in TAMs decreased the frequency and size of lung metastases without impacting primary tumor burden.  Expression profiling of isolated tumor macrophages established that Ets2 deficiency resulted in the de-repression of a defined set of anti-angiogenic genes.
Activation of this transcriptional program correlated with decreased angiogenesis in metastatic tumors and decreased metastatic growth.  Comparison of this Ets2-specific TAM expression profile with human breast cancer profiles revealed a macrophage gene expression signature that could predict overall survival of estrogen receptor negative patients.  In summary, we have identified a critical factor, Ets2, in TAMs that represses a transcriptional program to promote the growth of mammary tumor metastases in the lung.

overall_design: Breast TAMs were isolated from early-stage PyMT-induced mammary tumors expressing Ets2 and also from the tumors with Ets2-deficient TAMs. Since macrophages have also been implicated in normal mammary gland remodeling, normal remeodeling macrophages were also purified from females expressing Ets2 and the ones where Ets2 is deleted in the macrophages. One RNA sample was extracted from each genetic group for gene-expression profiling.

first: Tahera

last: Zabuawala

last: Taffany

first: Sudarshana

middle: M

last: Sharma

first: Anand

last: Merchant

first: Brett

last: Adair

first: Ruchika

last: Srinivasan

first: Thomas

last: Rosol

first: Soledad

last: Fernandez

first: Kun

last: Huang

first: Gustavo

last: Leone

middle: C


title: Identification of the Early VIP Transriptome and its Associated Interactome in Activated Murine CD4 T Cells

status: Public on Jan 09 2010

city: Huntington

first: Yulia

last: Dementieva

state: WV

address: One John Marshall Drive

department: Mathematics

institute: Marshall University

summary:
Identification of the Early Vasoactive Intestinal Peptide (VIP) Transriptome and its Associated Interactome in Activated Murine CD4 T Cells
In an attempt to understand  the biological role of this neuropeptide in the immune system, we choose CD4 T cells  as a cellular system for identifying a VIP-induced transcriptome.
Murine CD4 T cells were isolated and used to identify changes in gene expression in the presence of  PMA/ionomycin (activated) for five hours with and without 10-7 M VIP.

overall_design: Balanced-block design, 6 biological replicates. PMA/ionomycin (activated) mouse CD4 T spleenocytes with VIP ligand (sample) vs. PMA/ionomycin (activated) mouse CD4 T spleenocytes without VIP ligand (control), dye-swaps.

first: Sheri

middle: T

last: Dorsam

first: Emilie

last: Vomhof-Dekrey

first: Rebecca

last: Hermann

first: Jodie

last: Haring

first: Travis

last: van der Steen

first: Erich

last: Wilkerson

first: Goran

last: Boskovic

first: James

last: Denvir

first: Donald

last: Primerano

first: Glenn

middle: P


title: Expression data from motor nerve-stimulated and the contralateral control tabialis anterior muscles in mice

status: Public on Jan 07 2010

city: Charlottesville

first: Zhen

last: Yan

state: VA

address: 409 Lane Rd

department: Medicine

institute: University of Virginia

summary:
Exercise induces skeletal muscle adaptation, and the p38 mitogen-activated protein kinase signaling pathway is thought to play an important role in the adaptive processes. We have obtained new evidence that the gamma isoform of p38 is required for exercise-induced metabolic adaptation in skeletal muscle; however,  the neuromuscular activity-dependent target genes of p38gamma remain to be defined.
We used microarrays to detail the global programme of gene expression underlying the skeletal muscle genetic reprogramming in response to increased contractile activity and identified distinct classes of up-regulated genes during this process that are dependent on the functional activity of the p38gamma isoform.

overall_design: Skeletal muscle-specific p38gamma knockout mice and the wild type littermates are subject to motor nerve stimulation of one of the tibialis anterior muscles followed by microarray analysis of both the stimulated and the contralateral control muscles.

first: Andrew

last: Pogozelski

first: Xinhe

last: Yin

first: Jen-Tsan

last: Chi


title: Chronic liver inflammation-induced double strand DNA breaks enhance hepatocarcinogenesis

status: Public on Jan 03 2010

city: Jerusalem

first: Reba

last: Condiotti

department: Goldyne Savad Institute of Gene Therapy

country: Israel

institute: Hadassah Medical Center

summary:
Surgical resection is the preferred treatment for Hepatocellular carcinoma; however, it induces tumor recurrence. Our objective was to understand the molecular mechanisms linking liver regeneration under chronic-inflammation to tumorigenesis. Mdr2-knockout mice, a model of inflammation-associated cancer, underwent partial-hepatectomy which led to enhanced hepatocarcinogenesis. Yet, liver regeneration in these mice was severely attenuated. We demonstrate the activation of the DNA damage response machinery and altered genomic instability during early liver inflammatory stages resulting in hepatocyte apoptosis and cell-cycle arrest, and suggest their involvement in tumor recurrence subsequent to partial hepatectomy. We propose that under the regenerative proliferative stress induced by liver resection, the genomic unstable hepatocytes generated during chronic-inflammation, escape apoptosis and reenter the cell-cycle, triggering the enhanced tumorigenesis
At present, there is a great organ shortage worldwide, thus the main treatment for Hepatocellular carcinoma (HCC) is liver resection. However, liver resection induces recurrence and mortality. In our study, we decipher, for the first time, the contribution of the DNA damage response in HCC development and recurrence, the immediate and long term effect. This is an important finding regarding the association between carcinogenesis and DNA damage response. Additionally, we demonstrate yet another link between inflammation, inducing DNA damage and genome instability, and carcinogenesis that has not been explored in the past. These results may assist in developing treatments that will reduce tumor recurrence and additionally, new prophylactic therapies during early inflammatory stages.

Keywords: time course, regeneration

overall_design: RNA was isolated from liver samples of 9-month-old Mdr2-/- and control mice obtained on days 0 (the removed lobe), 2 and 6 following PHx. Samples of d0 were obtained from the same mice that were sacrificed on later days. As we were concerned by the variability in the KO group 6 samples were obtained for d0. All other time points and groups contained 3 samples each.

first: Hila

last: Barash

first: Eitan

last: Gross

first: Ariel

last: Israel

first: Irit

last: Cohen

first: Nathalie

last: Corchia

first: Tehila

last: Ben-Moshe

first: Yifat

last: Edrei

first: Orit

last: Pappo

first: Eli

last: Pikarsky

first: Daniel

last: Goldenberg

first: Israel

last: Vlodavsky

first: Yosef

last: Shiloh

first: Eithan

last: Galun

first: Rinat

last: Abramovitch


title: Identification of the Early VIP Transriptome and its Associated Interactome in Resting and Activated Murine CD4 T Cells

first: Yulia

last: Dementieva

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

overall_design: Refer to individual Series


title: Down-regulation of JunB by RNAi in mouse muscles in vivo

status: Public on Jan 01 2010

city: Padova

first: Gerolamo

last: Lanfranchi

address: Via U. Bassi, 58/B

department: CRIBI - Biotechnology Center and Biology Department

country: Italy

institute: University of Padova

summary: The size of skeletal muscles, like that of all cells, is precisely regulated by intracellular signaling networks that determine the balance between overall rates of protein synthesis and degradation. Muscle fiber growth and protein synthesis are stimulated by the IGF1/Akt/mTOR pathway, and muscle wasting, as occurs with disuse, denervation, fasting, and various systemic diseases (e.g. cancer, sepsis) results from excessive protein breakdown in muscle and induction of a set of atrophy-related genes by the FoxO transcription factors. Here we show that the transcription factor JunB is also a major regulator of growth and atrophy of adult (post mitotic) muscle cells. We found that in atrophying myotubes, JunB protein was excluded from the nucleus and that decreasing JunB expression by RNAi in muscles of adults reduced fiber size. Furthermore, in normal muscles of adult mice JunB over-expression increased fiber diameter dramatically (up to 40% in 7 days), and stimulated protein synthesis, but unlike IGF-1 or insulin, JunB did not activate the Akt/mTOR pathway. Importantly, when JunB was transfected into denervated muscles to maintain its level high, fiber atrophy was prevented, and the induction of the critical atrophy-associated ubiquitin-ligases, atrogin-1 and MuRF-1, was greatly reduced. JunB inhibited their induction by impairing FoxO3 binding to their promoters and thus reduced the stimulation of protein breakdown by FoxO3. Thus JunB is important, not only in dividing populations, but also in mature skeletal muscle where it is required for the maintenance of muscle size and can induce rapid hypertrophy and block atrophy.

overall_design: Mouse adult tibialis anterior muscles were transfected with vectors expressing shRNA against JunB or scramble. 4 muscles were used for each condition. Mice were sacrificed 12 days later and total RNA was extracted. 1 μg of total RNA was amplified with the One Color Microarray Based Gene Expression kit (Agilent) following the manufacturer’s instructions. 1.6 μg of labeled target was hybridized on Agilent Whole Mouse Genome (4 × 44k) Oligo Microarray at 42° C. Data have been extracted with Agilent Future Extraction Software and normalized between experiments with the quantile method. Genes without positive and significant values on at least six experiments were filtered out. Data set of differentially expressed genes has been searched matching to the template profile based on Pearson correlation between dataset and template.

first: Anna

last: Raffaello

first: Giulia

last: Milan

first: Eva

last: Masiero

first: Silvia

last: Carnio

first: Donghoon

last: Lee

first: Alfred

middle: L

last: Goldberg

first: Marco

last: Sandri


title: Age-related para-inflammation in the neuroretina of the mouse

city: Aberdeen

first: Heping

last: Xu

address: Forresterhill

department: Ophthalmology

country: United Kingdom

institute: Univeristy of Aberdeen

summary: To understand the age-related retinal gene changes, gene transcription profiles of neural retinal tissues from young adult (3-month) mice and old (20-month) mice were investigated by microarray. With age, 632 genes were up-regulated and 429 genes were down-regulated in the retina. Functional annotation showed that genes linked to immune responses and to tissue stress/injury responses were most modified by old age. Significant numbers of gene involved in the innate immune response including leukocyte activation, chemotaxis, endocytosis, complement activation, phagocytosis and myeloid cell differentiation were up-regulated and only a few were down-regulated. Increased microglial and complement activation in the aging retina was further confirmed by confocal microscopy of retinal tissues. The results suggest that retinal aging is accompanied with activation of a number of local inflammatory responses. A modified form of low-grade chronic inflammation (para-inflammation) characterizes these aging changes and involves mainly the innate immune system. Para-inflammation per se may be beneficial to normal retinal physiology in aging by promoting retinal homeostasis; conversely, dysreulation of the para-inflammation response may contribute to the pathogenesis of age-related retinal degeneration.

overall_design: Six young (3-month) and six old (20-month) mice were used for microarray study. Total RNA from each sample were extracted and undergone quality control analysis. RNA from 3 mice of the same group were then pooled together for gene array experiment.

first: Mei

last: Chen


title: Murine Back Skin: Control vs. Cyclosporin A-treated

status: Public on Dec 24 2009

city: Yokohama

first: Yumiko

last: Tsuji

address: 2-12-1, Fukuura, Kanazawa-ku

institute: Shiseido

summary:
We analyzed the gene expression at the onset of hair growth induced by cyclosporin A (CsA), a well-known hair growth inducer,  with DNA microarray, and unveiled the step-by-step progression of hair growth.

KEYWORDS: Cyclosporin A, Cyclosporine A, Ciclosporin A

overall_design: Ethanol-treated vs. cyclosporin A-treated mice back skin. Biological replicates: 2 control replicates, 2 cyclosporin A-treated replicates. Two, 4, and 7 days after application

last: Ishimatsu-Tsuji

first: Tsutomu

last: Soma

first: Jiro

last: Kishimoto


title: Expression data from 17 day old testes of wild type and UBR2-/- mice

status: Public on Dec 31 2009

city: Pittsburgh

first: Jee Young

last: An

state: PA

address: 3501 Terrace St. Salk 647D

institute: University of Pittsburgh

summary: Ubiquitylation of histones provides an important mechanism regulating chromatin remodeling and gene expression. Recent studies have revealed ubiquitin ligases involved in histone ubiquitylation, yet the responsible enzymes and the function of histone ubiquitination in spermatogenesis remain unclear. Here we show that the ubiquitin ligase UBR2, one of the recognition E3 components of the N-end rule proteolytic pathway, localizes to meiotic chromatin regions, including unsynapsed axial elements linked to chromatin inactivation, and mediates, in combination with the ubiquitin-conjugating enzyme HR6B, the ubiquitination of histone H2A. UBR2 interacts with HR6B and H2A and promotes the HR6B-H2A interaction and the HR6B-to-H2A transfer of ubiquitin. UBR2 and ubiquitinated H2A (uH2A) spatiotemporally mark meiotic chromatin regions subject to transcriptional silencing, and UBR2-deficient spermatocytes fail to induce the ubiquitination of H2A during meiosis. UBR2-deficient spermatocytes are profoundly impaired in transcriptional silencing of genes linked to unsynapsed axes of the X and Y chromosomes. We propose a model, in which UBR2 on axial elements of the X-Y pair enables HR6B on the linked chromatin domain to repeat histone ubiquitination cycles while scanning a string of nucleosomes. Our results suggest that histone ubiquitination in germ cells may be mediated by E3-E2 pairs distinct from those in somatic cells, providing a new insight into chromatin remodeling and gene expression regulation.

overall_design: For each genotype, 2 testes were collected from different individual in same litter at 17 days old. Biotinylated cRNA was produced and hybridized on Affimetrix mouse genome 430A 2.0 array.

first: Jee-Young

first: Yong-Tae

last: Kwon


title: CTL differentiation: WT vs. IL-2Ra deficient CTL

status: Public on Dec 23 2009

first: Matthew

last: Williams

address: 15 N. Medical Dr. E.

department: Pathology

institute: University of Utah

summary: Gene expression analysis of WT and IL-2Ra-deficient CTL (P14) isolated 8 days after inffection with LCMV.  The goals of the study are to assess the impact of IL-2 signals on effector and memory CTL differentiation.

overall_design: This is a 2-condition experiement comparing WT P14 Tg T cells eight days after LCMV infection to IL-2Ra-deficient P14 Tg T cells isolated at the same time from the same host.  Cells are isolated via FACS-sorting form the spleen.


title: Expression data from Balb/c mice kidney samples

status: Public on Dec 01 2009

city: Bronx

first: Han

last: Si

address: 1300 Morris Park

department: Medicine/Nephrology

institute: AECOM

summary:
Males are 50% more likely to develop end stage kidney failure compared to women. As a model of the human condition we analyzed gene expression changes in healthy and diseased mouse kidneys.
Interestingly, the set of gender biased genes in healthy kidneys were different from those in diseased kidneys indicating not only baseline gene expression differences but also that the male and female kidney respond differently to disease condition.

Keywords: Gender difference

overall_design: We used AffymetrixM430A2.0 microarrays to determine global gene expression differences in kidneys of 10-week old healthy Balb/c male and female mice. In order to identify gene expression differences under disease conditions, animals were injected with doxorubicin, a substance that is known to induce albuminuria and glomerulosclerosis in Balb/c mice as it is directly toxic to podocytes.

first: Katalin

last: Susztak


title: Genes induced by IL-9 in the colon of transgenic mice

status: Public on Dec 25 2009

city: Brussels

first: Jean-Christophe

last: Renauld

address: Avenue Hippocrate, 74

country: Belgium

institute: Ludwig Institute for Cancer Research

summary:
The aim of this work was to identify genes induced by IL-9 in the colon of IL-9-tarnsgenic mice (Tg5). Therefore, we performed a comprehensive study of the genes expressed in the colon of IL-9 transgenic and wild type FVB mice, taking advantage of the affymetrix microarray technology.

Keywords: cytokine-induced response

overall_design: RNA was extracted from a piece of the distal colon from IL-9 transgenic or wild type TVB mice. RNA samples from 4 different mice were pooled for each group before  hybridization on Affymetrix microarrays.

first: Valérie

last: Steenwinckel

first: Jamila

last: Louahed


title: The Ets domain transcription factor Spdef drives maturation of Goblet and Paneth cells in the intestinal epithelium

status: Public on Feb 10 2010

first: Daniel

last: Stange

summary:
BACKGROUND & AIMS: Stems cells within the intestinal epithelium generate daughter cells which undergo lineage commitment and maturation through the concerted action of the Wnt and Notch signalling cascades. Both pathways, in turn, regulate transcription factor networks which further define differentiation towards either enterocytes or one of three secretory cell lineages (Paneth, goblet or enteroendocrine cells). In this manuscript, we identified the Ets domain transcription factor, Spdef, as a novel lineage maker of goblet and Paneth cells. METHODS: To address the function of Spdef in vivo, we inactivated the Spdef gene and analysed the intestinal phenotype using a range of histological techniques and DNA microarray profiling. RESULTS: In accordance with the expression data we found that loss of Spdef severely impaired the maturation of goblet and Paneth cells and conversely lead to an accumulation of immature secretory progenitors. Moreover, we provide evidence suggesting that Spdef positively and negatively regulates a specific subset of goblet and Paneth cell genes including Cryptdins, Mmp7, Ang4, Kallikreins, and Muc2. CONCLUSION: We propose a model whereby Spdef acts downstream of Math1 to promote terminal differentiation of a secretory progenitor pool towards Paneth and goblet cells.

Keywords: expression profiling

overall_design: To compare wild-type versus Spdef-/- intestinal or colonic tissue samples, pooled total RNA from 2-3 littermates were utilized for each experiment. In addition, tissue samples from both adult (P30) or E18.5 fetal mice were compared. Overall, we carried out 3 dye swap experiments for E18.5 small intestine and P30 colon resulting in 6 arrays each, and 2 dye swap experiments for E18.5 colon and P30 small intestine resulting in 4 arrays each.

first: Alex

last: Gregorieff

first: Hans

last: Clevers


title: Hepatic transcriptome of KK/H1J diabetic mice treated with bisphosphatase deficient PFK-2 adenovirus

city: Minneapolis

first: Salmaan

last: Khan

state: MN

address: 420 Washington Ave, 7-162 MCB Building

department: BMBB

institute: University of Minnesota

summary: In an effort to reduce hepatic glucose production and lower plasma glucose levels that are characteristics of diabetes, we have devised a treatment whereby we enhance glycolysis in the liver of a type 2 diabetic mouse model (KK/H1J).  We achieve this by raising the levels of a potent regulator of glucose metabolism, fructose-2,6-bisphosphate (F26BP). Treating the mice in this way, we have demonstrated amelioration of the diabetic phenotype in terms of lowering plasma glucose and insulin levels. These treated mice also display reduced weight gain, reduced adiposity, and normalized plasma and hepatic lipid levels.  These latter metabolic changes brought about by raising F26BP levels are counterintuitive.  A concurrent increase in glycolysis and lipogenesis is expected, however, we observe an increase in glycolysis with a concurrent decrease in lipogenesis.  Preliminary analysis of gene expression in these mice has revealed alterations in gene expression of several genes that support the therapeutic effect of raising F26BP levels.  To further profile F26BP effects on hepatic gene expression, we have applied a comprehensive approach to identify sets of genes and thereby biological pathways that are differentially regulated when hepatic glycolysis is accelerated in diabetic mice.  Comparing diabetic and treated animals, we hope to further clarify the molecular and genetic signature of type 2 diabetes and obesity and elucidate how this signature is affected by raising F26BP levels.  Our study examining gene array as well as the hepatic proteome has identified multiple gene and protein expression changes.  Of particular relevance, we note that fatty acid metabolism and cholesterol metabolism pathways are significantly down-regulated in diabetic mice treated with a PFK-2 mutant engineered to raise F26BP levels, which underlie the changes we see in the metabolic parameters.

overall_design: 6 KK/H1J mice, a polygenic model of type 2 diabetes and obesity, weighing approximately 35g were used in this study. 3 mice were injected with GFP control adenovirus and 3 mice were injected with bisphosphatase deficient PFK-2 adenovirus (BPD).  Mice were followed for 7 days before livers were extracted. Total cellular RNA was extracted from each mouse and analyzed by microarray separately.

first: Chaodong

last: Wu

first: BhanuChandra

last: Mulukutla

first: Wei-Shou

last: Hu

last: Lange


title: Identification of the Early VIP Transriptome and its Associated Interactome in Resting Murine CD4 T Cells

first: Yulia

last: Dementieva

summary:
Identification of the Early Vasoactive Intestinal Peptide (VIP) Transriptome and its Associated Interactome in Resting Murine CD4 T Cells
In an attempt to understand  the biological role of this neuropeptide in the immune system, we choose CD4 T cells  as a cellular system for identifying a VIP-induced transcriptome.
Murine CD4 T cells were isolated and used to identify changes in gene expression in the absence of  PMA/ionomycin (resting)  with and without 10-7 M VIP.

overall_design: Balanced-block design, 6 biological replicates. Naïve mouse CD4 T spleenocytes with VIP ligand (sample) vs. naïve mouse CD4 T spleenocytes without VIP ligand (control), dye-swaps.

first: Sheri

last: Dorsam

first: Emilie

last: Vomhof-Dekrey

first: Rebecca

last: Hermann

first: Jodie

last: Haring

first: Travis

last: van der Steen

first: Erich

last: Wilkerson

first: Goran

last: Boskovic

first: James

last: Denvir

first: Donald

last: Primerano

first: Glenn


title: Tumor-specific CD4+ T cells eradicate established melanoma

status: Public on Jan 15 2010

city: Baltimore

first: Paul

middle: Andrew

last: Antony

address: 10 South Pine Street

department: Program in Molecular Microbiology and Immunology

institute: University of Maryland School of Medicine

summary:
Adoptive transfer of CD4+ T cells (TRP-1 CD4+ T cells) specific for tyrp-1 (tyrosinase-related protein 1) eradicate established tumors (melanoma) in lymphopenic RAG-/- hosts.
In vitro differentiated CD8+ T cells have been the primary focus of immunotherapy of cancer with little focus on CD4+ T cells. Immunotherapy involving in vitro differentiated T cells given after lymphodepleting regimens significantly augments antitumor immunity in animals and human patients with cancer. However, the mechanisms by which lymphopenia augments adoptive cell therapy and the means of properly differentiating T cells in vitro are still emerging. We demonstrate that naïve tumor/self-specific CD4+ T cells naturally differentiated into T helper type 1 (Th1) cytotoxic T cells in vivo and caused the regression of established tumors and depigmentation in lymphopenic hosts. Therapy was independent of vaccination, exogenous cytokine support, CD8+-, B-, NK and NK-T cells. Proper activation of CD4+ T cells in vivo was important for tumor clearance as naïve tumor-specific CD4+ T cells could not completely treat tumor in lymphopenic common gamma chain-deficient (gc-/-) hosts. gc signaling in the tumor-bearing host was important for survival and proper differentiation of adoptively transferred tumor-specific CD4+ T cells. Thus, these data provide a platform for designing immunotherapies that incorporate tumor/self-reactive CD4+ T cells.

overall_design: 2 x 10^5 sorted TRP-1 CD4+ T cells were transferred i.v. into tumor-bearing RAG-/- hosts on day 7-10 after tumor challenge, and ~1 x 10^6 CD4+ T cells were isolated 1 week later by flow sorting from pooled lymph nodes (LN) or spleens. Dye-swaps were performed.


title: P19 cells+LIN28_RA-differentiated_Day 4

city: Stratford

first: Eric

middle: G

last: Moss

state: NJ

address: UMDNJ-SOM/GSBS

department: Molecular Biology

institute: UMDNJ

summary: LIN28 is an RNA-binding protein expressed in many developing tissues. It can block let-7 microRNA processing and help promote pluripotency. We observe LIN28 expression in the developing neural tube, colocalizing with SOX2, suggesting a role in neural development. To better understand its normal developmental function, we investigated LIN28 activity during neurogliogenesis in vitro where the succession of neuronal to glial cell fates occurs as it does in vivo. LIN28 expression was high in undifferentiated cells, and was down-regulated rapidly upon differentiation. Constitutive LIN28 expression caused a complete block of gliogenesis and an increase in neurogenesis. LIN28 expression was compatible with neuronal differentiation and did not increase proliferation. LIN28 caused significant changes in gene expression prior to any effect on let-7, notably on Igf2. Furthermore, a mutant LIN28 that permitted let-7 accumulation was still able to completely block gliogenesis. Thus, at least two biological activities of LIN28 are genetically separable and may involve distinct mechanisms. LIN28 can differentially promote and inhibit specific fates and does not function exclusively by blocking let-7 family miRNAs. Importantly, LIN28’s role in cell fate succession in vertebrate cells is analogous to its activity as a developmental timing regulator in C. elegans.

overall_design: Two repeats of two cell lines induced to differentiate with retinoic acid/aggregation for four days. Control cells: unmodified mouse P19 embryonal carcinoma cells. Experimental cells: P19 cells constitutively expressing human LIN28A.

first: Erica

last: Balzer

first: Christian

last: Heine

first: Qiang

last: Jiang

first: Vivian

last: Lee


title: Undifferentiated Pleomorphic Sarcoma Model

status: Public on Nov 21 2009

city: Durham

first: Jeffrey

last: Mito

institute: Duke University Medical Center

summary: Analysis of undifferentiated pleomorphic sarcoma/malignant fibrous histiocytoma-like tumors from LSL-KrasG12D, p53Fl/Fl mouse model of soft tissue sarcoma.

overall_design: Murine soft tissue sarcomas (n = 17) were compared to normal muscle (n = 4).  Tumors were isolated surgically from soft tissue sarcomas generated by conditional Kras and p53 alleles.  Tumors were induced using an adenovirus expressing Cre recombinase.  Normal muscle samples were isolated from mice of the same genotype without tumor induction.

first: Richard

middle: F

last: Riedel

first: Leslie

last: Dodd

first: Guy

last: Lahat

first: Alexander

last: Lazar

middle: D

first: Lars

last: Stangenberg

first: William

last: Eward

first: Sam

middle: S

last: Yoon

first: Brian

last: Brigman

first: Tyler

last: Jacks

first: Dina

last: Lev

first: Sayan

last: Mukherjee

first: David

last: Kirsch


title: Profiling gene expression in Vax2 knockout compared with wild type mice

city: Naples

first: Vincenzo

middle: Alessandro

last: Gennarino

state: Italy

address: Via Pietro Castellino,111

department: TIGEM

institute: Telethon

summary:
Total RNA samples from Vax2 knockout mouse eyes (at least two  biological replicates) were profiled by gene expression. As control we used total RNA from  wild type  eyes. The analysis was carried out at five different developmental stages: E10.5, E12.5, E16.5, P8, and P60.

Keywords: gene expression array-based (RNA / in situ oligonucleotide)

overall_design: Vax2 knockout mouse animal model analyzed at various developmental stages.

first: Giovanna

last: Alfano

first: Sandro

last: Banfi

middle: A


title: Murine 3T3-L1 adipocytes vs. adipocyte-derived microvesicles (ADMs)

status: Public on Nov 17 2009

city: Tsu

first: Naohito

last: Aoki

address: 1577 Kurimamachiya-cho

department: Graduate School of Bioresources

institute: Mie University

summary: mRNA profiles of adipocyte-derived microvesicles (ADMs) and their donor 3T3-L1 adipoyctes (Day 11) were compared.  ADMs included RNA without typical 28S and 18S ribosomal RNA.

overall_design: ADMs  vs. donor 3T3-L1 adipocytes. Biological replicates: 2 ADMs replicates, 2 donor cells.


title: Expression analysis on Mll1+/+ and Mll1-/- MEFs

status: Public on Oct 20 2009

city: Kansas City

first: Pengfei

last: Wang

state: MO

address: 1000 E. 50th Street

institute: Stowers Institute

summary:
Global analysis of H3K4 methylation defines MLL family member targets and points to a role for MLL1-mediated H3K4 methylation in the regulation of transcriptional initiation by RNA polymerase II

A common landmark of activated genes is the presence of trimethylation on lysine 4 of histone H3 (H3K4) at promoter regions.  The Set1/COMPASS was the founding member and the only H3K4 methylases in S. cerevisiae, however, in mammals at least six H3K4 methylases Set1A/B and MLL1-4 are found in COMPASS-like complexes capable of methylating H3K4. To gain further insight into the different roles and functional targets for the H3K4 methylases, we have undertaken a genome-wide analysis of H3K4 methylation pattern in wild-type Mll1+/+ and Mll1-/- mouse fibroblasts (MEFs).  We found that Mll1 is required for the H3K4 trimethylation of less than 5% of promoters   carrying this modification.  Many of these genes, which include developmental regulators such as Hox genes show decreased levels of RNA polymerase II recruitment and   expression concomitant with the loss of H3K4 methylation. Although Mll1 is only required for the methylation of a subset of Hox genes, Menin, a component of the Mll1   and Mll2 complexes, is required for the overwhelming majority of H3K4 methylation at Hox loci.  However, the loss of MLL3/4 and/or the Set1 complexes have little to no effect   on the Hox loci H3K4 methylation or expression levels in these MEFs.  Together these data provide insight into redundancy and specialization of COMPASS-like complexes in   mammals and provide evidence on a possible role for Mll1-mediated H3K4 methylation in the regulation of transcriptional initiation.

overall_design: Expression arrays were done with Mll1+/+ and Mll1-/- mouse embryonic fibroblasts. Four replicates were done (dyes were swapped). DNA was hybridized to Agilent Mouse Whole Genome Expression Arrays (4x44k).

first: Chengqi

last: Lin

first: Edwin

middle: R

last: Smith

first: Hong

last: Guo

middle: W

last: Sanderson

first: Min

last: Wu

first: Madelaine

last: Gogol

first: Tara

last: Alexander

first: Christopher

last: Seidel

first: Leanne

last: Wiedemann

first: Kai

last: Ge

first: Robb

last: Krumlauf

first: Ali

last: Shilatifard


title: Strain differences in e11.5 XY gonad transcriptome suggest a mechanism for the sensitivity of C57BL/6J to sex reversal

status: Public on Oct 30 2009

city: Bar Harbor

first: Steven

last: Munger

state: ME

address: 600 Main Street

institute: The Jackson Laboratory

summary: Transcriptional profiling of individual mouse embryonic (e11.5) XY gonads comparing inbred strains that are sensitive (C57BL/6J) and resistant (129S1/SvImJ) to XY sex reversal, and their reciprocal F1 hybrids.

overall_design: Two-color Agilent microarray profiles of 20 individual pairs of e11.5 XY gonads, including 5- C57BL/6J, 5- 129S1/SvImJ, 5- (B6x129S1)F1, and 5- (129S1xB6)F1 samples. Within each strain, samples were collected from multiple litters to account for potential litter biases. All samples were processed following the same protocol.

first: Blanche

last: Capel


title: Expression data for conditional Dnmt1knockout hematopoietic stem and progenitor cells

city: Boston

first: Jennifer

last: Trowbridge

state: MA

address: 44 Binney St., Mayer 652

department: Pediatric Oncology

institute: Dana-Farber Cancer Institute

summary:
DNA methylation is essential for mammalian development and plays crucial roles in a variety of biological processes. The DNA methyltransferase Dnmt1 serves to maintain parental cell methylation patterns on daughter DNA strands in mitotic cells, however, the precise role of Dnmt1 in regulation of quiescent adult stem cells is not known.
To examine the role of Dnmt1 in adult hematopoietic stem cells (HSCs), we conditionally disrupted Dnmt1 in the hematopoietic system. We used microarrays to profile the global gene expression program in hematopoietic stem and progenitor cells following deletion of Dnmt1.

overall_design: Dnmt1 was conditionally deleted in the hematopoietic system by injections of poly(I)poly(C) to induce Cre expression from the Mx-Cre transgene. Control mice were also injected with poly(I)poly(C) but do not carry the Mx-Cre transgene. Four days after completion of poly(I)poly(C) injections, bone marrow was harvested from the mice, antibody-mediated magnetic bead selection was used to remove cells expressing mature lineage markers, and the resulting lineage-depleted cells were stained with fluorochrome-conjugated antibodies against the surface receptors c-Kit, Sca-1 and CD34. Populations of LT-HSCs, MPPs and myeloid progenitors were FACS sorted, RNA was extracted and amplified from these sorted populations and hybridized to Affymetrix microarrays to compare changes in gene expression induced by conditional knockout of Dnmt1 compared to control in each of the three cell populations. There are 2 biological replicates for the LT-HSCs and MPPs and 3 biological replicates for the myeloid progenitors.

first: Stuart

middle: H

last: Orkin


title: Cdx and Hox genes differentially regulate posterior axial growth in mammalian embryos

status: Public on Oct 19 2009

city: Utrecht

first: Jacqueline

last: Deschamps

address: Uppsalalaan 8

country: Netherlands

institute: Hubrecht Institute

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

overall_design: Refer to individual Series


title: Testosterone-induced persistent dysregulations and transdifferentiation to exocrine pancreas in the female liver

status: Public on Oct 28 2009

city: Düsseldorf

first: Jürgen

last: Krücken

state: NRW

address: Universitätsstr. 1

department: Division of Molecular Parasitology

institute: Heinrich-Heine-University Düsseldorf

summary: Androgenic steroids are increasingly used for hormone therapy of postmenopausal women and abused as life style drugs and for doping purposes, though knowledge about associated health risks in females is very limited. In order to understand more about short- and long-term androgen effects on a molecular level, we have analyzed hepatic gene expression in female C57BL/6 mice immediately after subcutaneous treatment with testosterone for 3 weeks and after 12 weeks hormone withdrawal using Affymetrix array technology and quantitative real-time RT-PCR. Among about 14,000 genes examined, 48 were up- and 65 genes were downregulated by testosterone after 3-weeks treatment and about 50% of these changes persisted even 12 weeks after testostrone withdrawal.  In addition to obvious risks such as induction of hepatocellular carcinomas and virilization of liver metabolism, testosterone induced a series of changes, as e.g. dysregulation of hepatic gene expression due to incomplete conversion of female to male phenotype – in particular downregulation of cytochrom P450 isoforms and sulfotransferases. As a long-term testosterone effect, transcripts emerged in the liver that are normally specific for the exocine pancreas including amylase 2, ribonuclease 1, and several trypsin-, chymotrypsin-, and elastase-like proteases. This transdifferentiation of hepatic to exocrine pancreatic tissue indicates that testosterone can initiate long-lasting differentiation programs, which – once induced – progress even after androgen withdrawal. This may have far-reaching consequences difficult to foresee implying long-term hazards of testosterone-treatment for female health that have not been taken into account yet.

overall_design: Mice were treated with testosterone or sesame oil (vehicle) for three weeks twice a week. Gene expression in the liver was analyzed either directly after treatment or after three weeks of hormone/vehicle withdrawal. For each of these four groups, three individual mice were used as biological replicates.

first: Denis

last: Delić

first: Christina

last: Weiland

first: Hans-Werner

last: Vohr

first: Frank

last: Wunderlich


title: Cdx and Hox genes differentially regulate posterior axial growth in mammalian embryos - 5/6 somites embryonic stage

summary: Hox and Cdx transcription factors regulate embryonic positional identities. Cdx mutant mice display posterior body truncations of the axial skeleton, neuraxis, and caudal uro-rectal structures. We show that trunk Hox genes stimulate axial extension as they can largely rescue these Cdx mutant phenotypes. Conversely, posterior  (paralog group 13) Hox genes can prematurely arrest posterior axial growth when precociously expressed. Our data suggest that the transition from trunk to tail Hox gene expression successively regulates construction and termination of axial structures in the mouse embryo. Thus, Hox genes seem to differentially orchestrate posterior expansion of embryonic tissues during axial morphogenesis as an integral part of their function in specifying head-to-tail identity. In addition, we present evidence that Cdx and Hox transcription factors exert these effects by controlling Wnt signaling. Concomitant regulation of Cyp26a1 expression, restraining retinoic acid signaling in the posterior growth zone, may likewise play a role in timing the trunk-tail transition.

overall_design: A micro-array screen of down regulated and upregulated genes in Cdx2+/-Cdx4-/-  mutant embryos versus wildtype embryos was performed at the embryonic stage of 5/6 somites. RNA was isolated from the posterior part of the embryos dissected at the same axial level using the last somite boundary as a landmark.  Posterior tissues from pools of 10 embryos of each genotype were pooled. The labeled cRNAs were hybridized on 4X44K Agilent Whole Mouse Genome dual colour Microarrays (G4122F) in two dye swap experiments, resulting in four individual microarrays.

first: Cesca

last: van de Ven


title: Global analysis of H3K4 methylation

first: Pengfei

last: Wang

type: Genome binding/occupancy profiling by array

first: Chengqi

last: Lin

first: Edwin

last: Smith

first: Hong

last: Guo

first: Brian

last: Sanderson

first: Min

last: Wu

first: Madelaine

last: Gogol

first: Tara

last: Alexander


title: Gene expression data of cSHMT mutant, heterozygous, and wild-type mouse colons

status: Public on Oct 01 2009

city: Ithaca

first: David

state: NY

address: T2 006A VRT

institute: Cornell University

summary:
Folate-mediated one-carbon metabolism is required for purine, thymidylate, and S-adenosylmethionine synthesis. Impairments in folate metabolism diminish cellular methylation potential and genome stability. Cytoplasmic serine hydroxymethyl transferase (cSHMT) regulates partitioning between thymidylate and SAM biosynthesis. These experiments were designed to determine if mutations in cSHMT led to alterations in gene expression.

Keywords: genetic modification

overall_design: RNA was isolated from proximal colons of cSHMT mutant, heterozygous, and wild-type mice raised on a folate-deficient diet. Three colon samples were isolated from each genotype to provide biological replication.  Mutant and heterozygous data were then compared pair-wise against wild-type expression data.

first: Patrick

last: Stover

first: Amanda

last: MacFarlane

first: Cheryll

last: Perry

first: Michael

last: McEntee


title: TIS21/BTG2/PC3 and cyclin D1 are key determinants of nuclear diacylglycerol kinase-zeta-dependent cell cycle arrest

status: Public on Sep 30 2009

city: Bologna

first: Alberto

middle: Maria

last: Martelli

address: via Irnerio 48

department: Department of Human Anatomy

institute: University of Bologna

summary: In addition to lipid second messengers derived from the plasma membrane, increasing evidence supports the existence of nuclear lipid-dependent signaling networks. Diacylglycerol is a key second messenger, generated at the nuclear level, which is metabolized by diacylglycerol kinases (DGKs). It has been demonstrated that nuclear DGK-ζ negatively regulates cell cycle progression. The aim of this study was to identify key determinants of nuclear DGK-ζ-dependent cell cycle arrest in C2C12 mouse myoblasts. Using DNA microarrays, Real-Time RT-PCR and western blot, we demonstrated that nuclear DGK-ζ downregulated the expression of cyclin D1 and increased the expression of TIS21/BTG2/PC3, a transcriptional regulator of cyclin D1 with a strong anti-proliferative function. Overexpression of TIS21/BTG2/PC3 blocked the cells in G1 phase of the cell cycle and decreased the levels of Ser807/811 phosphorylated retinoblastoma protein, similarly to overexpression of DGK-ζ. Moreover, during myogenic differentiation of C2C12 cells, we showed an increase of TIS21/BTG2/PC3 expression and a decrease in cyclin D1 levels. siRNA downregulation of TIS21/BTG2/PC3 impaired myogenic differentiation by opposing cell cycle arrest. In summary, these data identify TIS21/BTG2/PC3 and cyclin D1 as downstream effectors of the nuclear DGK-ζ and highlight the importance of this DGK isoform in the regulation of myoblast proliferation and differentiation.

overall_design: single time point analysis of gene expression changes induced by DGK-zeta transfection in C2C12 cells. DGK-zeta-transfected cells are compared to untreated control cells and to EGFP-transfected cells.

first: Camilla

last: Evangelisti

first: Annalisa

last: Astolfi

first: Gian

last: Gaboardi

first: Pierluigi

last: Tazzari

first: Andrea

last: Pession

first: Kaoru

last: Goto


title: Abdominal Aortic Aneurysm in the ApoE Knockout Mouse: Time Course of Control vs. Angiotensin II

city: Stanford

first: Joshua

middle: M.

last: Spin

state: CA

address: 300 Pasteur Drive

institute: Stanford University

summary:
Transcriptional profiling of suprarenal aorta from ApoE-/- mice  (12-14 weeks old, C57BL/6J background)  treated by subcutaneous pump with angiotensin II or saline for 7d, 14d and 28d. Includes Ang II-treated samples at 7d found to have dissected aneurysms.
Goal was to examine gene expression in developing AAA in this model over time.

overall_design: Two condition experiment, one suprarenal aorta per array. Saline vs. angiotensin II at 3 time points, with inclusion of 3 Ang II-treated dissected. Total 35 arrays: 6 saline 7d, 6 saline 14d, 5 saline 28d, 4 Ang II 7d, 5 Ang II 14d, 6 Ang II 28d, 3 Ang II-dissected 7d.


title: Caloric restriction modified anxiety- and depressive-like behavior and gene expression change in the mouse amygdala

status: Public on Sep 15 2009

city: Tokushima

first: Yuta

last: Yamamoto

address: 3-18-15 Kuramoto-cho

department: Stress Science

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

summary: Moderate caloric restriction (CR) and weight loss are beneficial for the promotion of health; however, there is controversy regarding the effects of dieting regimens on behavior. In this study, we investigated two different dieting regimens: repeated fasting and refeeding (RFR) and daily feeding of half the amount of food consumed by RFR mice (CR). Mice in both regimens were subjected to 20% reduction in food intake and transiently reduced their body weights during the first 12 days of the study. Open field, light-dark transition, elevated plus maze, and forced swimming tests indicated that CR, but not RFR, reduced anxiety- and depressive-like behaviors, with a peak on day 8. Using a mouse whole genome microarray, we analyzed gene expression in the prefrontal cortex, amygdala, and hypothalamus. In addition to the caloric restriction-responsive genes commonly modified by RFR and CR, each regimen differentially changed the expression of distinct genes in each region. The most profound change was observed in the amygdala of CR mice: 884 genes were specifically up-regulated. Ingenuity pathway analysis showed that these 884 genes significantly modified 9 canonical pathways in the amygdala. alpha-adrenergic and dopamine receptor signaling were the two top-scoring pathways. Quantitative real-time RT-PCR confirmed the up-regulation of 6 genes in these pathways. Ppp1r1b encoded Darpp-32 including dopamine receptor signaling, and the increased protein was specific for CR mice. Our results suggest that moderate CR may modify anxiety- and depressive-like behaviors and alter gene expression especially in the mouse amygdala.

overall_design: We tested three feeding regimens. One group of mice had ad libitum (AD) access to food, and was used as a control group. The repeated fasting and refeeding (RFR) group of mice were fasted on day 0 and allowed to feed ad libitum on day 1. Amounts of food consumed by the three mice on day 1 were measured. The half amount of food consumed by the RFR mice was given to three mice in another cage for two days (days 0 and 1) (CR group). The fasting followed by refeeding (RFR) and the restriction of food (CR) were repeated up to day 16. Body weights and consumed chow were measured at 20:00 every day, and then the fasting or feeding period was started. In RFR mice, fasting was started on day 0.Total RNA was prepared from the prefrontal cortex, hypothalamus, and amygdala in the mice of each group on day 8. An equal amount of RNA from 4 mice in each group was pooled and used for microarray analysis.

first: Toshihito

last: Tanahashi

first: Tomoko

last: Kawai

first: Sakurako

last: Katsuura

first: Sachiko

last: Chikahisa

first: Kensei

last: Nishida

first: Sigetada

last: Teshima-Kondo

first: Hiroyoshi

last: Sei

first: Kazuhito

last: Rokutan


title: Eos mediates Foxp3-dependent gene silencing in CD4+ regulatory T cells

status: Public on Sep 01 2009

first: Fan

last: Pan

address: 1650 Orleans St CRB I Room 424

department: Oncology

institute: Johns Hopkins Medical Institions, School of Medicine

summary:
Eos expression in Treg cells have been documented by several microarrays including ours. We hypothesized that Eos facilitates Foxp3- dependent gene repression in Regulatory T cells. In order to investigate the role of Eos in mediating the Foxp3-dependent gene silencing program,  we utilized lentiviral shRNA knockdown of Eos in natural Tregs isolated from the periphery of Balb/C mice. A renilla luciferase (RL) gene specific shRNA lentivirus was used as a control for the transduction of cells. The transcriptional profile of naive  T cells, natural Tregs, Eos knockdown Tregs, and control shRNA knockdown Tregs was compared using Agilent 4x 44K whole mouse genome array.
The goal of this microarray is to document the global effect of  the loss of Eos expression on the transcriptional profile of natrual Treg cells.

overall_design: Eos knock-down (si-Eos) was mediated by Lentivirus expressing GFP as a reporter of transduction and sorting marker.  Renilla luciferase specific shRNA lentiviral transduction was carried out in parallel as a control. Naïve (CD4+CD25-CD62Lhi) T cells and nTreg cells were freshly isolated from Balb/C mice.

first: Drew

last: Pardoll


title: Unexpected expression of alpha- and beta-globin in mesencephalic dopaminergic neurons and glial cells

status: Public on Aug 04 2009

city: Trieste

first: Paola

last: Roncaglia

state: TS

address: via Bonomea 265

department: Neurobiology

institute: SISSA/ISAS (International School for Advanced Studies)

summary: The mesencephalic dopaminergic (mDA) cell system is composed by two major groups of projecting cells in the Substantia Nigra (A9 neurons) and the Ventral Tegmental Area (A10 cells). A9 neurons form the nigrostriatal pathway and are involved in regulating voluntary movements and postural reflexes. Their selective degeneration leads to Parkinson’s disease (PD). We used cDNA microarrays and nanoCAGE technology coupled with Laser Capture Microdissection (LCM) to characterize the intrinsic physiological properties of A9 DA neurons. Surprisingly, we found that these cells express alpha- and beta- chains of haemoglobin.   Here we report that globin-immunoreactivity decorates the majority of A9 DA neurons, a subpopulation of cortical and hippocampal astrocytes as well as mature oligodendrocytes. This pattern of expression was confirmed in different mouse strains, in rat and human. This is the first report showing that haemoglobin is expressed in the Substantia Nigra of human post mortem brain.  Our data suggest that the most famed oxygen-carrying globin is not exclusively restricted to the blood, but it may play a role in the normal physiology of the brain as well as in neurodegenerative disorders.

overall_design: To investigate the biological effects of globin expression, alpha- and beta- chains of mouse hemoglobin were overexpressed in MN9D dopaminergic neuroblastoma cell lines. RNA from 4 replicates each of over-expressing cells and of control samples, for a total of 8 samples, were hybridized on Affymetrix GeneChip Mouse Genome 430A 2.0 Arrays. Hybridization of one of the control samples did not pass quality assessment and the sample was therefore excluded from further analysis.


title: Uterine gene profiles from WT, KIKO (DNA-binding deficient ERα) and aERKO mice treated with estradiol or xenoestrogens

city: RTP

first: NIEHS

last: Microarray Core

state: NC

address: 111 T.W. Alexander Drive

department: DIR

institute: NIEHS

summary: Ovariectomized WT, KIKO (DNA-binding deficient ERα) or αERKO female mice were injected (ip) with saline (vehicle), estradiol (E2; 250 ng), bisphenol A (BPA; 750 µg) or 2,2-bis(p-hydroxyphenyl)-1,1,1-trichloroethane (HPTE; 750 µg) and uteri were collected after 2 or 24 hours. Uterine profiles were compared and indicated the early (2 hour) responses to E2 were highly correlated to the BPA and HPTE profiles. KIKO patterns included overlap with WT but also included distinct responses. Later (24 hour) responses in the KIKO were weaker, indicating DNA binding is needed to maintain the estrogenic response. BPA and HPTE also showed a weakened late response in the WT, suggesting they are impeded estrogens.

overall_design: Three WT, KIKO or αERKO ovariectomized mice per treatment group were injected with vehicle, E2, BPA or HPTE and uterine tissue was collected after 2 or 24 hour and frozen in liquid nitrogen. RNA was isolated from a pool of the three uteri using Trizol reagent and then cleaned with a Qiagen RNA easy mini kit. RNA quality was validated with the Agilent 2100 Bioanalyzer in the microarray facility.  RNA samples were then analyzed by 2-color Agilent Whole Mouse arrays with fluor flips.  Each array was co hybridized with vehicle and treated RNA within the genotype (WT, KIKO or aERKO).

first: S

last: Hewitt

first: K

last: Korach

first: J

last: Jameson

last: O'Brien


title: Expression data from mNSc after 48 hour of treatment with CD95L-T4

status: Public on Sep 28 2009

city: Heidelberg

first: sachin

last: kumar

state: Baden-Württemberg

address: Molecular Neurobiology; German Cancer Research Center; INF 581;

institute: DKFZ

summary: In neural stem cells, stimulation of the “death receptor” CD95 does not trigger apoptosis but resulted in increased stem cell survival and neuronal specification via activation of the Src /PI3K /AKT/mTOR signalling pathway. To further characterize CD95-dependent neural stem cell survival and differentiation we used conventional gene expression profiling combined with translation state array analysis. Mouse neural stem cells grown in neurosphere cultures were stimulated with a trimerized CD95L construct (CD95L-T4) and total as well as polysomal bound RNA was isolated 48 hours after stimulation and analysed by microarrays. CD95L-T4 treatment induced a global increase in ribosome-bound mRNA and protein translation as well as changes on genes involved in neurogenesis, protein synthesis and transcription factors.

overall_design: Mouse neural stem cells grown in neurosphere cultures were stimulated with a trimerized CD95L construct (CD95L-T4) and total as well as polysomal bound RNA was isolated 48 hours after stimulation and hybridized on affymetrix microarrays.

first: Nina

last: Corsini

first: Ana

last: Martin-Villalba

first: Nobert

last: Gretz

first: Sachin

last: Kumar


title: Gene expression profiling in liver of mice with a mutant Wrn protein treated with/without vitamin C compared to WT mice.

status: Public on Sep 08 2009

city: Lausanne

first: Eric

last: Paquet

state: Vaud

address: Station 15  CH - 1015

department: Life sciences

institute: EPFL

summary: Werner syndrome (WS) is a rare disorder characterized by the premature onset of a number of age-related diseases. The gene responsible for WS is believed to be involved in different aspects of transcription, replication, and/or DNA repair. We generated a mouse model with a deletion in the helicase domain of the murine WRN homologue that recapitulates most of the WS phenotypes including an abnormal hyaluronic acid excretion, higher reactive oxygen species (ROS) levels, increased genomic instability and cancer incidence resulting in a 10-15% decreased life span expectancy. In addition, WS patients and Wrn mutant mice show hallmarks of a metabolic syndrome including premature visceral obesity, hypertriglyceridemia, insulin-resistant diabetes type 2 and associated cardiovascular diseases. In this study, we compared the expression profile of liver tissues from 9 months old Wrn mutant and wild type animals. Gene set enrichment analysis of the microarray data indicated that Wrn mutant mice exhibited down-regulation of genes normally decreased in several transgenic mouse models of hepatoma and during caloric restriction. Wrn mutant mice also altered the expression of genes involved in inflammation as well as in glutathione and xenobiotic metabolisms. These results indicate that Wrn mutant mice respond to the observed oxidative stress by altering the necessary pathways to survive. Vitamin C supplementation rescued the life span expectancy of Wrn mutant mice and reversed several age-related abnormalities in adipose, cardiac, and liver tissues, genomic integrity and inflammatory status. Finally, gene set enrichment analyses revealed that vitamin C decreased genes normally up regulated in human WS fibroblasts and cancers and it increased genes involved in tissue injury response and adipocyte dedifferentiation in obese mice.

overall_design: Microarray analyses were performed on the liver tissues of 9 months old mice. Four independent biological replicates of this experiment (wild type vs Wrn mutant or wild type vs vitamin C treated mutant mice) were carried out with a dye swap on two replicates of each genotype.

first: Laurent

last: Massip

first: Chantal

last: Garand

first: Victoria

last: Cogger

first: Jennifer

middle: N

last: O’Reilly

first: Leslee

last: Tworek

first: Avril

last: Hatherell

first: Carla

last: Taylor

last: Thorin

first: Peter

last: Zahradka

first: David

last: Le Couteur

first: Michel

last: Lebel


title: Murine Embryonic Fibroblasts: Wild-type Stmn1 versus null Stmn1 Cells

status: Public on Jul 31 2009

city: Bethlehem

first: Danielle

middle: N.

last: Ringhoff

address: 111 Research Drive

department: Biological Sciences

institute: Lehigh University

summary:
Background: Stathmin (STMN1) protein functions to regulate assembly of the microtubule cytoskeleton by destabilizing microtubule polymers. Stathmin over-expression has been correlated with cancer stage progression, while stathmin depletion leads to death of some cancer cell lines in culture. In contrast, stathmin-null mice are viable with minor axonopathies and loss of innate fear response. Several stathmin binding partners, in addition to tubulin, have been shown to affect cell motility in culture. To expand our understanding of stathmin function in normal cells, we compared gene expression profiles, measured by microarray and qRT-PCR, of mouse embryo fibroblasts isolated from STMN1+/+ and STMN1-/- mice to determine the transcriptome level changes present in the genetic knock-out of stathmin.  Results: Microarray analysis of STMN1 loss at a fold change threshold of 2.0 revealed expression changes for 437 genes, of which 269 were up-regulated and 168 were down-regulated.  Microarray data and qRT-PCR analysis of mRNA expression demonstrated changes in the message levels for STMN4, encoding RB3, a protein related to stathmin, and in alterations to many tubulin isotype mRNAs.  KEGG Pathway analysis of the microarray data indicated changes to cell motility-related genes, and qRT-PCR plates specific for focal adhesion and ECM proteins generally confirmed the microarray data.  Several microtubule assembly regulators and motors were also differentially regulated in STMN1-/- cells, but these changes should not compensate for loss of stathmin.  Conclusions: Approximately 50% of genes up or down regulated (at a fold change of ≥ 2) in STMN1-/- mouse embryo fibroblasts function broadly in cell adhesion and motility. These results support models indicating a role for stathmin in regulating cell locomotion, but also suggest that this functional activity may involve changes to the cohort of proteins expressed in the cell, rather than as a direct consequence of stathmin-dependent regulation of the microtubule cytoskeleton.
Gene expression of mouse embryo fibroblasts lacking stathmin reveal changes in genes contributing to cell motility

overall_design: Two-color Agilent 4x44k chips with dye-swap on 2 of 4 arrays.  Replicate data presented.

first: Lynne

last: Cassimeris


title: The effect of TIM-3 stimulation on the gene expression profile of B16-F10 melanoma cells

city: Budapest

first: Zoltan

last: Wiener

address: Nagyvarad ter 4.

department: Dept of Genetics, Cell- and Immunobiology

country: Hungary

institute: Semmelweis University

summary: The effect of TIM-3 stimulation was studied on B16F10 mouse melanoma cells, in vitro.

overall_design:
Cy3: B16F10 mouse melanoma cells, treated by unspecific goat IgG (control) for 2 hours.
Cy5: B16F10 mouse melanoma cells, in vitro, treated by an agonist goat polyclonal anti-mouse TIM3 antibody (RnD Systems) for 2 hours.
Four biological replicates were used (in this study, biological replicate means different passage numbers of the same cell line). In each case, the treated sample (Cy5) was compared to its control one (Cy3) in Agilent dual-color microarray experiments.

first: Anna

last: Gilicze

last: Pocza

first: Viktor

last: Molnar

first: Edit

last: Buzas

first: Andras

last: Falus


title: Expression data from C2C12 myoblasts transduced with PRDM16 or vector

first: Shingo

last: Kajimura

address: 44 Binney Street

department: Department of Cell Biology

institute: Harvard Medical School

summary:
PRDM16 is a 140 kDa transcriptional coregulatory protein. PRDM16 has been shown to function as a bi-directional switch in brown fat cell fate by stimulating the development of brown fat cells from myf-5 positive myoblastic precursors.
We used microarrays to detail the global programme of gene expression underlying the myoblasts-brown fat conversion induced by PRDM16.

overall_design: undifferentiated C2C12 myoblasts were stably expressed with retroviral PRDM16 or vector control.  Total RNAs were isolated by Trizol, and subjected to Affymetrix microarrays.

first: Bruce

middle: M

last: Spiegelman


title: Comparison of immature BMDC to BMDC after nkt cell modulation

status: Public on Oct 17 2009

city: Milan

first: simone

last: caielli

address: Via olgettina, 60

institute: San Raffaele Scientific Institute

summary: Analyze the gene expression profile of BMDC before and after nkt cell modulation.

overall_design: Total RNA was extracted from CD11c cells with TRIzol Reagent, purified with RNeasy Kit (Qiagen) and subsequently amplificated  using the one cycle target labeling kit according to the AffymetrixGeneChip® Expression Analysis Technical Manual (Affimetrix). Fragmented cRNAs were probed to AffymetrixGeneChip® Mouse Genome 430 2.0 arrays for 16 hours at 45°C in the AffymetrixHybridization Oven 640. The arrays were then washed and stained with streptavidin-phycoerythrin using the AffymetrixFluidic Station 450/250 and scanned using the AffymetrixGeneChip® Scanner 3000. The images were analyzed using GCOC® Software and comparison analyses carried out according to the instructions provided by Affymetrix. Each experiment was performed in triplicates and repeated two times. Data handling was mainly done using Bioconductor Software. The probe set-based summary data were log transformed and normalized for probe set intensity-dependent biases. The identification of differentially expressed genes was addressed using linear modeling approach and empirical Bayer methods together with false discovery rate correction of the p-value. We considered a gene to be differentially increased in nkt-DCs only if its expression intensity was significantly changed (p<0.001) compared to Untr-DCs.

first: Simone

last: Caielli

first: Cristina

last: Conforti-Andreoni

first: Ester

last: Badami

first: Denis

last: Baev

first: Marialuisa

last: Malosio

first: Marika

last: Falcone


title: The effect of TIM-3 stimulation on the gene expression profile of IgE/antigen-activated mouse mast cells

summary: TIM-3 is known to be expressed on dendritic cells, monocytes, melanoma cells, mast cells and on activated Th1 cells. In activated Th1 cells, stimulating TIM-3 by one of its ligands, galectin-9, leads to apoptosis and thus it plays a central role in terminating Th1-type immune responses. Interestingly, in IgE/antigen-activated mast cells TIM-3 enhances the production of IL-13 and IL-4. To get a more complete picture about the gene expression changes induced by TIM-3 in mast cells, in vitro differentiated mouse immature mast cells were stimulated by an agonist anti-TIM-3 antibody and IgE-sensitized mouse immature mast cells were activated by antigen and an agonist anti-TIM-3 antibody for 2 or 16 hours (overnight).

overall_design: Bone marrow cells were differentiated in RPMI + 10% FCS + 5 ng/ml mouse IL-3 + 40 ng/ml mouse SCF for >4 weeks. The purity of the cell cultures was >90% at this time point (FcERIa+/c-kit+ cells). These in vitro-differentiated immature mast cells were then treated by either control goat IgG or an agonist anti-mouse TIM-3 antibody (RnD Systems, 15 ug/ml for 2 or 16 hours). For the IgE/antigen-activated mouse mast cells, these in vitro-differentiated immature mast cells were sensitized by 5 ug/ml anti-DNP IgE (Sigma) for 1 hour and then treated with 100 ng/ml DNP-HSA (antigen, Sigma) and either control goat IgG or an agonist anti-mouse TIM-3 antibody (RnD Systems, 15 ug/ml) for 2 or 16 hours. The anti-TIM-3 samples were labeled by Cy5 and they were compared to the Cy3-labeled, goat IgG controls in a dual-color, paired experimental setup. The Agilent Whole Mouse Genome 4x44K expression microarray kit and Dual-Color Protocol version 5.5 were used in the experiments.


title: Expression profile of splenocytes with glucose-6-phosphate isomerase (GPI) induced arthritis

status: Public on Jul 24 2009

city: Tsukuba

first: Isao

last: Matsumoto

department: Clinical Immunology

institute: University of Tsukuba

summary: To explore TNF-related genes in GPI-induced arthritis, we performed GeneChip analysis using arthritic splenocytes and control-immunized splenocytes. Among the arrayed TNFalpha-related genes, TIARP mRNA was highly expressed in arthritic splenocytes, with levels exceeding more than 20-times the control splenocytes

overall_design: The spleens of three GPI-GST (MW=89 kD) (300 µg) -immunized DBA/1 mice were harvested on day 10. As a control, the spleens of three GST (MW=26 kd) (100 µg) -immunized DBA/1 mice were used. Total RNA was extracted from the splenocytes using Isogen (Nippon gene), then 15 ug of RNA was utilized for cDNA synthesis by reverse transcription followed by synthesis of biotinylated cRNA through in vitro transcription. After cRNA fragmentation, hybridization with mouse 430A2.0 GeneChip (Affymetrix, Santa Clara, CA) with probes for 43,000 mouse genes ESTs was performed according to the protocol provided by the manufacturer. Analysis was performed by gene expression software

first: Asuka

last: Inoue