title: Mouse HCC model

city: Stanford

first: Julien

last: Sage

state: CA

address: 265 Campus Drive, SIM1 G2078

department: Pediatrics

institute: Stanford University

summary: A mouse model of HCC has been developed based on the reported inactivation of the RB pathway in the majority of human HCC. This mouse model harbors floxed alleles of Rb and p130 genes, as well as germline mutation of the p107 gene. Various strategies to activate the activity of a Cre recombinase leads to the efficient deletion of the three genes in the liver of adult mice (TKO mice). Disruption of the RB pathway induces the rapid development of HCC. These HCCs share many similar features of human HCC.

overall_design: The goal of this array is to assess genome wide expression of TKO HCCs. Gene expression of control livers (n=4) or TKO HCCs (n=5) was measured using the Affymetrix GeneChip Mouse Genome 430-2.0 arrays

last: Viatour


title: Effects of prostate cancer cells on osteoblasts

status: Public on Jul 01 2010

city: Hamburg

first: Thomas

last: Streichert

address: Martinistr. 52, Campus Forschung N27, 2. OG

department: Institute For Clinical Chemistry / Central Laboratories

country: Germany

institute: University Medical Center Hamburg-Eppendorf

summary:
Primary murine osteoblasts were isolated form the calvariae of newborn mice.  10 days after the addition of ascorbic acid (50 µg/ml) and ß-glycerophosphate (10 mM),  cells were serum-starved over night and then incubated for 6 hours with condtioned medium of MDA-PCa2b cells or conditioned medium of PC-3 cells

Keywords: expression profiling by array

overall_design: The aim of the experiment was to identify transcriptional changes in osteoblasts caused by factors derived from two different prostate cancer cell lines

first: J

last: Schulze

last: Albers

first: A

last: Baranowsky

last: Keller

first: T

last: Zustin

first: M

last: Amling

last: Schinke


title: Microarray analysis of iris gene expression in mice with mutations influencing pigmentation

city: Iowa City

first: Markus

middle: H

last: Kuehn

state: IA

address: 375 Newton Road

department: Ophthalmology and Visual Sciences

country: USA

institute: University of Iowa

summary: Several ocular diseases involve the iris, notably including oculocutaneous albinism, pigment dispersion syndrome, and exfoliation syndrome. To screen for candidate genes that may be active in these diseases, genome-wide iris gene expression patterns were comparatively analyzed from mouse models of these conditions.

overall_design: Irides were obtained from healthy C57Bl/6J, B6-Lystbg-J/J which carry a mutation in the Lyst gene, B6(Cg)-TyrC-2J/J which carry a mutation in the tyr gene, and B6.D2-Tryp1bGpnmbR150X/Sj with mutations in both Tryp1 and Gpnmb.  Four eyes from two mice were pooled for one sample.  Three samples were prepared for each strain.

first: Colleen

middle: M

last: Trantow

first: Tryphena

middle: L

last: Cuffy

first: John

last: Fingert

first: Michael

middle: G

last: Anderson


title: Gene expression in the Efferent duct, Epididymis, and Vas deferens during Embryonic Development

status: Public on Jun 30 2010

city: Pullman

first: Elizabeth

last: Snyder

state: WA

department: School of Molecular Biosciences

institute: Washington State University

summary: The tissues of the male reproductive tract are characterized by distinct morphologies, ranging from highly coiled to un-coiled.  Global gene expression profiles of the efferent ducts, epididymis, and vas deferens were generated from embryonic day 14.5 to postnatal day 1, the period when gross morphological changes are initiated and tissue-specific morphologies emerge.  Expression profiles of homeobox genes, as potential regionalization factors, were examined.  Tissue transcriptome comparison identified two expression profiles of interest: genes similar between the epididymis and vas deferens early in development but dissimilar later and genes dissimilar between the epididymis and efferent duct early but similar later.  Ontology analysis demonstrated cell adhesion-associated genes to be highly enriched in both comparisons.  This work identified several potential regulators of cell adhesion along the tract and indicates cell adhesion may be modulated in a tissue-specific manner, playing an important role in the establishment of each tissue’s final morphology.

overall_design:
Efferent duct, epididymis, and vas deferens samples at E14.5, E16.5, E18.5, and P1 in duplicate
Developmental time course, tissue to tissue comparison, microarray study


title: Transcriptome analysis of miR-144/451-null bone marrow erythroid cells

status: Public on Jul 15 2010

city: Philadelphia

first: Duonan

last: Yu

state: PA

address: 3615 Civic center Blvd, ARC Rm315F

department: hematology

institute: The children's hospital of philadelphia

summary: microRNA miR-144/451 is highly expressed during erythropoiesis. We deleted the miR-144/451 gene locus in mice and compared the transcriptomes of miR-144/451-null bone marrow erythroid precursors to stage-matched wild-type control cells.

overall_design: Ter119+/CD71+/FSC-high bone marrow erythroblasts were sorted directly into Trizol LS reagent. Total RNAs extracted from three miR-144/451 knock-out and three wide type mice were analyzed using  Affymetrix Mouse Genome 430 2.0 Arrays.

first: Mitchell

middle: J

last: Weiss


title: Dmrt1 (doublesex and mab-3 related transcription factor 1) knockout expression analyses in E13.5 testes in S6 background

city: Minneapolis

first: Aaron

last: Sarver

state: MN

address: 425 East River Road

department: Masonic Cancer Center

institute: University of Minnesota

summary: Dmrt1 (doublesex and mab-3 related transcription factor 1) is a conserved transcriptional regulator of male differentiation required for testicular development in vertebrates. In mice of the 129Sv strain, loss of Dmrt1 causes a high incidence of teratomas.  Mutant 129Sv germ cells undergo apparently normal differentiation up to embryonic day 13.5 (E13.5), but some cells fail to arrest mitosis and ectopically express pluripotency markers. Expression analysis and chromatin immunoprecipitation identified DMRT1 target genes whose misexpression may underly teratoma formation.

overall_design: Comparison of E13.5 testes gene expression between Dmrt1(+/-) and Dmrt1(-,-) animals that show high incidence of teratoma formation.


title: Genome-Wide Maps of WT and DBDmut Estrogen Receptor in Human Breast Cancer Cells

city: La Jolla

first: Joshua

middle: D

last: Stender

address: 9500 Gillman

institute: University of California at San Diego

type: Genome binding/occupancy profiling by high throughput sequencing

summary: We wanted to explore the relative contributions of DNA binding and tethering regulation modes by the estrogen receptor in human breast cancer cells

overall_design: We defined the genome-wide localization of WT and DBDmut estrogen receptors in human breast cancer cells

first: Chris

last: Benner

first: Benita

last: Katzenellenbogen

first: Christopher

last: Glass


title: Genome-Wide Analysis of Estrogen Receptor-α DNA Binding and Tethering Mechanisms

summary:
The nuclear receptor, estrogen receptor alpha (ERα), controls the expression of hundreds of genes responsible for target cell phenotypic properties, but the relative importance of direct vs. tethering mechanisms of DNA binding has not been established.  In this first report, we examine the genome-wide chromatin localization of an altered-specificity mutant ER with a DNA-binding domain deficient in binding to estrogen response element (ERE)-containing DNA (DBDmut ER) vs. wild type ERα. Using high-throughput sequencing of ER chromatin immunoprecipitations (ChIP-Seq) and mRNA transcriptional profiling, we show that direct ERE binding is required for most (75%) estrogen-dependent gene regulation and 90% of hormone-dependent recruitment of ER to genomic binding sites.  De novo motif analysis of the chromatin binding regions in MDA-MB-231 human breast cancer cells defined unique transcription factor profiles responsible for genes regulated through tethering vs. direct DNA (ERE) binding, with Runx motifs enriched in ER-tethered sites.  We confirmed a role for Runx1 in mediating ERa genomic recruitment and regulation of tethering genes.  Our findings delineate the contributions of ERE binding vs. binding through response elements for other transcription factors in chromatin localization and ER-dependent gene regulation, paradigms likely to underlie the gene regulatory actions of other nuclear receptors as well.

This SuperSeries is composed of the SubSeries listed below.

overall_design: Refer to individual Series


title: Unacylated Ghrelin Rapidly Modulates Lipogenic and Insulin Signaling Pathway Gene Expression in Metabolically Active Tissues of GHSR Deleted Mice

status: Public on Jun 26 2010

city: Rotterdam

first: Patric

last: Delhanty

address: Dr Molewaterplein 50

department: Internal Medicine

country: Netherlands

institute: Erasmus MC

summary: Background: There is increasing evidence that unacylated ghrelin (UAG) improves insulin sensitivity and glucose homeostasis; however, the mechanism for this activity is not fully understood since a UAG receptor has not been discovered. Methodology/Principal Findings: To assess potential mechanisms of UAG action in vivo, we examined rapid effects of UAG on genome-wide expression patterns in fat, muscle and liver of growth hormone secretagogue receptor (GHSR)-ablated mice using microarrays. Expression data were analyzed using Ingenuity Pathways Analysis and Gene Set Enrichment Analysis. Regulation of subsets of these genes was verified by quantitative PCR in an independent experiment. UAG acutely regulated clusters of genes involved in glucose and lipid metabolism in all three tissues, consistent with enhancement of insulin sensitivity. Conclusions/Significance: Fat, muscle and liver are central to the control of lipid and glucose homeostasis. UAG rapidly modulates the expression of metabolically important genes in these tissues in GHSR-deleted mice indicating a direct, GHSR-independent, action of UAG to improve insulin sensitivity and metabolic profile.

overall_design: White adipose tissue (gonadal), muscle and liver collected from female GHSR knockout mice 6 hours after ip. injection with saline or unacylated ghrelin (20 nmol/kg). Two replicates.

first: Yuxiang

last: Sun

first: Jenny

middle: A

last: Visser

first: Anke

last: van Kerkwijk

first: Martin

last: Huisman

first: Wilfred

middle: F

last: van IJcken

first: Sigrid

last: Swagemakers

first: Roy

last: Smith

first: Axel

middle: P

last: Themmen

first: Aart-Jan

last: van der Lely


title: Expression profile of cell lines overexpressing miR-520g

city: Toronto

first: David

middle: J. H.

last: Shih

state: ON

address: 686 Bay St

department: Developmental and Stem Cell Biology

country: Canada

institute: Hospital for Sick Children

summary:
Primitive neuro-ectodermal tumours (PNET) of the supratentorial region are rare, highly malignant embryonal brain tumours affecting young children. We recently highlighted the importance of a microRNA cluster housing miR-520g. We utilized the Illumina HumanWG-6 v3 R2 and HumanHT-12 v3 R2 Expression BeadChip platforms to profile the effects of miR-520g on gene expression.

Keywords: gene expression, pediatric brain tumour, microRNA

overall_design:
We stably transfected human neural stem cells with miR-520g or pcDNA plasmid. They were cultured under differentiating conditions and subsequently harvested for microarray analysis. We performed two independent experiments with at least two technical replicates each.

Non-normalized data for Samples GSM425301-GSM425312 are available in the supplementary file 'GSE16988_GPL6884_non-normalized_data.txt'; non-normalized data for Samples GSM425313-GSM425318 are available in the supplementary file 'GSE16988_GPL6947_non-normalized_data.txt'.

first: Mei

last: Li

first: Kyle

last: Lee

first: Yun

middle: T

last: Lu

first: Ian

last: Clarke

first: Daniel

last: Picard

first: Limei

last: Zhou

first: Charles

last: Eberhart

first: Tim

last: Van Meter

first: Ching

last: Lau

first: Scott

last: Pomeroy

first: Peter

last: Collins

first: Piergiorgio

last: Modena

first: Amar

last: Gajjar

first: Michael

last: Taylor

first: Eric

last: Bouffet

first: James

last: Rutka

middle: B

last: Dirks

first: Cynthia

middle: E

last: Hawkins

first: Annie

last: Huang


title: Gene expression profiling in murine Smad-deficient CD4+ T cells stimulated with TGF-b

status: Public on Jun 22 2010

city: Shinjyuku-ku

first: Tomohito

last: Takimoto

state: Tokyo

address: 35 Shinanomachi

department: Microbiology and Immunology

country: Japan

institute: Keio University School of Medicine

summary:
TGF-b is an important pleiotropic cytokine with potent immunoregulatory properties. Although many previous reports have been proposed for the immunoregulatory functions of TGF-b on T cells, such as the suppression of cell proliferation, cytokine production and cytokine signaling, as well as the induction of apoptosis, it is not well elucidated whether the each effect of TGF-b on T cells is dependent on Smad signaling or Smad-independent other signaling pathways.
The aim of the study was to clarify the involvement of Smad signaling and to investigate the redundancy of Smad2 and Smad3 on various TGF-b-mediated regulation of gene expression in CD4+ T cells. We used microarrays to detail the global program of gene expression regulated by TGF-b in CD4+ T cells, and identified distinct classes of up/down-regulated genes which are dependent on or independent of TGF-b-Smad signaling. Most of genes regulated by TGF-b were redundantly dependent on Smad2 and Smad3, including Foxp3 and IL-2. In addition, some genes were sufficiently regulated via Smad2 or Smad3 signaling alone. In contrast, TGF-b-mediated RORgt induction was independent of Smad signaling.

overall_design: CD4+CD25-CD44loCD62Lhi T cells (naive) were isolated from the spleens in wild-type (WT), T cell-specific Smad2 conditional knockout (Smad2KO or Smad2del/del), Smad3 knockout (Smad3KO or Smad3-/-) or Smad2del/delSmad3+/- mice by using a BD FACS ariaTM cell sorter (BD Bioscience) (purity: >98%). Freshly purified cells were then stimulated with anti-TCR stimuli in the absence or presence of TGF-b for 24 hr, respectively. A complete and precise experimental procedure is given in the "treatment protocol". It was very difficult to obtain the enough number of CD4+CD25-CD44loCD62Lhi naive T cells from Smad2del/delSmad3-/- mice because alomost all of CD4+ T cells were activated in Smad2del/delSmad3-/- mice. We confirmed that the several known Smad-regulated genes were almost out of control in Smad2del/delSmad3+/- CD4+ T cells by using quantitative RT-PCR. Furthermore, previous studies have reported the similar results in other cell types deficit in two alleles of Smad2 and one allele of Smad3. For these reasons, we substituted Smad2del/delSmad3+/- naive T cells for Smad2/3-deficient naive T cells. Cells were quickly collected 24 hr after culture for RNA extraction and hybridization on Affymetrix microarrays.

first: Akihiko

last: Yoshimura


title: Anti-CD3 therapy permits regulatory T cells to surmount T cell receptor-specified peripheral niche constraints

status: Public on Jun 23 2010

city: Boston

first: CBDM

last: Lab

state: MA

address: 77 Avenue Louis Pasteur

department: Microbiology and Immunobiology

institute: Harvard Medical School

summary:
Treatment with anti-CD3 is a promising therapeutic approach for autoimmune diabetes, but its mechanism of action remains unclear. Foxp3+ regulatory T (Treg) cells may be involved, but the evidence has been conflicting, and there is great uncertainty as to possible mechanistic connections. We investigated this issue in mice derived from the NOD model, which were engineered mice in which Treg populations were perturbed, or could be manipulated by acute ablation or transfer. The data highlighted the involvement of Foxp3+ cells in anti-CD3 action. Rather than a generic influence on all Treg cells, the therapeutic effect seemed to involve an striking expansion of previously constrained Treg cell populations; this expansion occurred not through conversion from Foxp3- Tconv cells but from a dramatic proliferative expansion. We found that Treg cells are normally constrained by TCR-specific niches in secondary lymphoid organs, and that intraclonal competition restrains their possibility for conversion and expansion in the spleen and lymph nodes, much as niche competition limits their selection in the thymus. The strong perturbations induced by anti-CD3 overcame these niche limitations, in a process dependent on receptors for trophic cytokines, interleukin-2 receptor (IL-2R) and IL-7R.
Keywords: Treatment response

overall_design: All gene expression profiles were obtained from highly purified T cell populations sorted by flow cytometry. RNA from 5 - 50 x 104 cells was amplified, labeled, and hybridized to Affymetrix M430v2. Raw data were preprocessed with the RMA algorithm in GenePattern, and averaged expression values were used for analysis.

first: Junko

last: Nishio

first: Markus

last: Feuerer

first: Jamie

last: Wong

first: Diane

last: Mathis

first: Christophe

last: Benoist


title: MyD88-mediated signaling prevents development of adenocarcinomas of the colon via interleukin-18

status: Public on Jun 24 2010

city: Frederick

first: Rosalba

last: Salcedo

state: MD

address: 1050 Boyles Street, Bldg. 567

institute: SAIC-NCI

summary: Inflammation has pleiotropic effects on carcinogenesis and tumor progression. Signaling through the adaptor protein MyD88 promotes carcinogenesis in several chemically induced cancer models. Interestingly, we observed a protective role for MyD88 in the development of AOM/DSS colitis-associated cancer. The inability of Myd88-/- mice to heal ulcers generated upon injury creates an inflammatory environment that increases the frequency of mutations and results in a dramatic increase in adenoma formation and cancer progression. Susceptibility to colitis development and enhanced polyp formation were also observed in Il18-/- mice upon AOM/DSS treatment, suggesting that the phenotype of MyD88 knockouts is in part due to their inability to signal through the IL-18 receptor. This study revealed a previously unknown level of complexity surrounding MyD88 activities downstream of different receptors that differentially impact tissue homeostasis and carcinogenesis.

overall_design: The Myd88 knockout mice were backcrossed to obtain at least 98% congenicity to B6NCr background. As control groups, wild type mice of identical background were used. Ten biological repeats were performed for the treated wild type and Myd88 samples. Six biological repeats were performed for the untreated wild type and Myd88 samples.


title: Immunoregulatory actions of T cell PPAR g at the colonic mucosa

status: Public on Jun 21 2010

city: blacksburg

first: Saroj

middle: K

last: Mohapatra

state: VA

address: washington Street

department: VBI

institute: Virginia Tech

summary:
BACKGROUND: Peroxisome proliferator-activated receptor g (PPAR g) is a nuclear receptor whose activation has been shown to modulate macrophage and epithelial cell-mediated inflammation.  The objective of this study was to use a systems approach for investigating the mechanism by which the deletion of PPAR g in T cells modulates the severity of dextran-sodium sulfate (DSS)-induced colitis, immune cell distribution and global gene expression.
METHODS: Wild-type (WT) or PPAR g flfl; CD4 Cre+ (CD4cre) mice in a C57BL/6 background were challenged with 2.5% DSS in their drinking water for 0, 2, or 7 days.  Mice were scored on disease severity both clinically and histopathologically. Flow cytometry was used to assess lymphocyte and macrophage populations in the blood, spleen, and mesenteric lymph nodes (MLN).  Global gene expression in colonic mucosa was profiled using Affymetrix microarrays.
RESULTS: Both disease severity and inflammation-related body weight loss were accelerated by the deficiency of PPAR g in T cells.  Examination of colon histopathology revealed significantly greater epithelial erosion, leukocyte infiltration, and mucosal thickening in the CD4cre mice on day 7.  CD4cre mice had more CD8+ T cells than wt mice and fewer CD4+FoxP3+ regulatory T cells (Treg) and IL10+CD4+ T cells in blood and MLN, respectively.  Transcriptomic profiling revealed around 3000 genes being transcriptionally altered as a result of DSS challenge in CD4cre mice. These included up-regulated adhesion molecules on day 7 and proinflammatory cytokines interleukin-6 (IL-6) and IL-1b, and suppressor of cytokine signaling 3 (SOCS-3) mRNA expression.
CONCLUSIONS: These findings suggest that T cell PPAR g down-regulates inflammation during DSS colitis by inhibiting colonic expression of inflammatory mediators and increasing MLN Treg.

overall_design: Colonic mucosa from wt and CD4cre mice were sampled at 0 (no DSS), 2, and 7 days of DSS-induced experimental colitis

first: Amir

last: Guri

first: William

last: Horne

first: Raquel

last: Hontecillas

first: Josep

last: Bassaganya-Riera


title: Expression data from Evi1-transduced primary bone marrow cells

status: Public on Jun 18 2010

city: Tokyo

first: Akihide

last: Yoshimi

address: 7-3-1 Hongo, Bunkyo-ku

department: Department of Hematology & Oncology

institute: Tokyo University

summary: Evi1 is essential for proliferation of hematopoietic stem cells and implicated in the development of myeloid disorders. Particularly, high Evi1 expression defines one of the largest clusters in acute myeloid leukemia and is significantly associated with extremely poor prognosis. Improvement of the therapeutic outcome of leukemia with activated Evi1 is one of the most challenging issues. However, mechanistic basis of Evi1-mediated leukemogenesis has not been fully elucidated. Here we show that Evi1 directly represses PTEN transcription in the murine bone marrow, which leads to activation of AKT/mTOR signaling. In a murine bone marrow transplantation model, Evi1 leukemia showed remarkable sensitivity to an mTOR inihibitor rapamycin. Furthermore, we found that Evi1 binds to several polycomb group proteins and recruits polycomb repressive complexes for PTEN downregulation, which reveals a novel epigenetic mechanism of AKT/mTOR activation in leukemia. Expression analyses and chromatin immunoprecipitation assays using human samples indicate that our findings in mice models are recapitulated in human leukemic cells. Dependence of Evi1-expressing leukemic cells on AKT/mTOR signaling provides the first example of targeted therapeutic modalities that suppress the leukemogenic activity of Evi1. The PTEN/AKT/mTOR signaling pathway and the Evi1-polycomb interaction can be promising therapeutic targets for leukemia with activated Evi1.

overall_design:
Gene expression analysis for the purpose of identifying the target genes of Evi1 in primary bone marrow.
5-FU-primed mononuclear bone marrow cells harvested from C57/B6 mice were retrovirally transduced with Evi1-GFP or GFP. GFP positive cells were sorted and analyzed by Affymetrix® Mouse Genome 430 2.0 Array® for gene expression. Four independent experiments were performed.

first: Susumu

last: Goyama

first: Naoko

last: Watanabe-Okochi

first: Yumiko

last: Yoshiki

first: Yasuhito

last: Nannya

first: Eriko

last: Nitta

first: Shunya

last: Arai

first: Tomohiko

last: Sato

first: Munetake

last: Shimabe

first: Masahiro

last: Nakagawa

first: Yoichi

last: Imai

first: Toshio

last: Kitamura

first: Mineo

last: Kurokawa


title: Comparison of gene expression between wild type, Notch1-activated, and RBPJ loss-of-function embryonic mouse yolk sac tissue at E9.5

city: Kansas City

first: Jay

last: Vivian

state: KS

address: 3901 Rainbow Blvd.

department: Pathology

institute: University of Kansas Medical Center

summary: The signaling cascades that direct the morphological differentiation of the vascular system during early embryogenesis are not well defined.  To further understand the role of Notch signaling during endothelial differentiation, this study uses both an in vivo gain-of-function and an in vivo loss-of-function approach.  At embryonic day 9.5, embryos with activated Notch1 signaling in the endothelia display a variety of growth and cardiovascular defects, and die soon after E10.5.  Most notably, the extra-embryonic vasculature of the yolk sac displays remodeling differentiation defects.  In the wild-type yolk sac, the primary vascular network has begun to reorganize, forming the large primary vessels and the smaller capillaries.  In the activated Notch1 embryos, remodeling is defective; the vasculature have an enlarged surface with decreased inter-vessel space.  Embryos with ablated Notch signaling also display growth and vascular defects at E9.5 similar to the activated Notch1 embryos, however they exhibit a lack of vascular remodeling in the yolk sac, retaining the simple vascular plexus seen at E8.5.  These results indicate that Notch signaling plays a critical role in the remodeling of the vasculature in the early embryo, particularly in the extra-embryonic region.

overall_design: A conditional transgenic system was used in this study to activate Notch signaling. The ubiquitous ROSA26Notch transgene with a Neo/stop cassette flanked by loxP sites, followed by the N1-ICD cDNA, was recombined with a Tie2-CRE mouse, resulting in the removal of the STOP cassette and the subsequent activation of the Notch1 intracellular domain.  This allowed for the overexpression and expansion of Notch signaling in all endothelial cells.  Male Tie2-Cre mice were mated with female ROSA26Notch mice and the resulting embryos were dissected at embryonic day 9.5.  To ablate Notch signaling, Tie2-Cre mice were used in a two-generation cross to obtain Tie2-Cre; Rbpj flox/flox embryos.  These embryos lack RBPJ binding activity in the endothelia.  In both instances, embryos were used for genotyping and the yolk sac were separated and used to isolate total RNA with an RNeasy mini kit. The RNA was analyzed with the Mouse Genome 430A Array from Affymetrix.  Samples were performed in duplicate, and RNA from wild type yolk sac tissues was compared to activated Notch and RBPJ loss-of-function yolk sac tissues.

first: Jessica

middle: N

last: Copeland


title: Discrete Roles of STAT4 and STAT6 Transcription Factors in Tuning Epigenetic Modifications and Transcription during Helper T Cell Differentiation (gene expression)

city: Bethesda

first: Golnaz

last: Vahedi

address: 9000 Rockville Pike Bldg 10 Rm 13C101A

department: NIAMS

institute: National Institutes of Health

summary: Signal transducer and activator of transcription 4 (STAT4) and STAT6 are key factors in the specification of helper T cells; however, their direct roles in driving differentiation are not well understood.  Using chromatin immunoprecipitation and massive parallel sequencing, we quantitated the full complement of STAT-bound genes, concurrently assessing global STAT-dependent epigenetic modifications and gene transcription using cells from cognate STAT-deficient mice. STAT4 and STAT6 each bound over 4000 genes with distinct binding motifs.  Both played critical roles in maintaining chromatin configuration and transcription of a core subset of genes through the combination of different epigenetic patterns. Globally, STAT4 had a more dominant role in promoting active epigenetic marks, whereas STAT6 had a more prominent role in antagonizing repressive marks. Clusters of genes negatively regulated by STATs were also identified, highlighting previously unappreciated repressive roles. Therefore, STAT4 and STAT6 play wide regulatory roles in T helper specification.

overall_design: The roles of STAT proteins to shape T helper cell phenotype was investigated by comparing DNA binding profiles of STAT4 and STAT6 in Th1 and Th2 conditions. The functional outcome of STAT bindings was further evaluated by profiling histone epigenetic marks and gene expression changes between WT and STAT-deficient T cells in Th1 and Th2 conditions. Affymetrix Mouse Genome 430 2.0 Arrays were used to evaluate global gene expression.

first: Lai

last: Wei

first: Hong-Wei

last: Sun

first: Wendy

last: Watford

first: Hiroaki

last: Takatori

first: Haydee

last: Ramos

first: Hayato

last: Takahashi

first: Jonathan

last: Liang

first: Gustavo

last: Gutierrez-Cruz

first: Chongzhi

last: Zang

first: Weiqun

last: Peng

first: John

last: O'Shea

first: Yuka

last: Kanno


title: Immunoregulatory actions of epithelial cell PPAR g at the colonic mucosa

first: Saroj

last: Mohapatra

summary:
BACKGROUND: Peroxisome proliferator-activated receptor g (PPAR g) is a nuclear receptor whose activation has been shown to modulate macrophage and epithelial cell-mediated inflammation.  The objective of this study was to use a systems approach for investigating the mechanism by which the deletion of PPAR g in epithelial cells modulates the severity of dextran-sodium sulfate (DSS)-induced colitis, immune cell distribution and global gene expression.
RESULTS: The deficiency of PPAR g in epithelial cells does not significantly affect disease activity or body weight but worsens colon histopathlogy. WT mice have greater CD4+IL10+ T cells and fewer MHC II+ macrophages in mesenteric lymph nodes. Global gene expression analysis reveals greater changes after 7 days of DSS challenge (compared to 2 days).

overall_design: Colonic mucosa from VC- (WT) and VC+ (PPARg knock-out in epithelial cells) mice were sampled at 0 (no DSS), 2, and 7 days of DSS-induced experimental colitis

first: Amir

last: Guri

first: Montse

middle: C

last: Salarich

first: William

last: Horne

first: Raquel

last: Hontecillas

first: Josep

last: Bassaganya-Riera


title: EWS-FLI1 reactivates a neural crest stem cell program in human neural crest-derived mesenchymal stem cells

status: Public on Jun 15 2010

city: Ann Arbor

first: Elizabeth

middle: R

last: Lawlor

state: MI

address: 1600 Huron Parkway, NCRC Bldg 520

institute: University of Michigan

summary:
Ewing sarcoma family of tumors (ESFT) are aggressive bone and soft tissue tumors of unknown cellular origin. Most ESFT express EWS-FLI1, a chimeric protein which functions as a growth-promoting oncogene in ESFT but is toxic to most normal cells. A major difficulty in understanding EWS-FLI1 function has been the lack of an adequate model in which to study EWS-FLI1-induced transformation. Although the cell of origin of ESFT remains elusive, both mesenchymal (MSC) and neural crest (NCSC) have been implicated. We recently developed the tools to generate NCSC from human embryonic stem cells (hNCSC). In the current study we used this model to test the hypothesis that neural crest-derived stem cells are the cells of origin of ESFT and to evaluate the consequences of EWS-FLI1 expression on human neural crest biology.
hNCSC transduced with an EWS-FLI1 lentivirus tolerated expression of the oncoprotein. Moreover, EWS-FLI1-transduced hNCSC continued to proliferate and maintain EWS-FLI1 expression in culture for several weeks after transduction. Affymetrix HuEx 1.0 expression profiling of hNCSC cells five days post-transduction with EWS-FLI1 demonstrated the expected induction and repression of well-established EWS-FLI1 targets and also identified numerous other novel EWS-FLI1-regulated genes that are likely to be cell-type and situation specific. In particular, the EWS-FLI1 repressive signature was found to be highly context dependent. Moreover, while control vector transduced cells displayed an MSC-like phenotype, EWS-FLI1-transduced cells maintained a NCSC-like phenotype and genetic profiling revealed reprogramming towards a more pluriopotent, neuroectodermal state. Finally, EWS-FLI1 expressing cells upregulated expression of the polycomb proteins BMI-1 and EZH2. These data implicate neural crest-derived cells in the origin of ESFT and suggest that EWS-FLI1 enables malignant transformation by inducing maintenance of a multipotent, NCSC-state through deregulation of polycomb genes.

overall_design: 3 replicate samples for 4 different stem cell populations were analyzed by HuEx arrays. The 4 sample types were adult human bone marrow-derived mesenchymal stem cells, human embryonic stem cell-derived nueral crest stem cells (hNCSC), control vector-transduced hNCSC-derived mesenchymal stem cells (NC-MSC), and EWS-FLI1-transduced hNCSC-derived mesenchymal stem cells (NC-MSC EF).  Control and EWS-FLI1 transduced NC-MSC were isolated 5 days after lentiviral transduction.  Transcript level expression data was compared among the different populations to determine differences and similarities between NCSC, BM-MSC and NC-MSC with/without EWS-FLI1 expression. These data were used to identify EWS-FLI1 targets in NC-MSC and to characterize the genetic changes that occur in NCSC as they generate NC-MSC progeny.


title: Expression data from (bezafibrate treated-wild type, Clock mutant, and PPARalpha-null) mouse liver

city: Ibaraki

first: Katsutaka

last: Oishi

address: Tsukuba

institute: AIST

summary:
A functional interaction between peroxisome proliferator-activated receptor alpha (PPARalpha) and components of the circadian clock has been suggested; however, it remains to be clarified whether those transcriptional factors interact with each other to regulate the expression of their target genes.
In this study, we used a ligand of PPARalpha, bezafibrate, to search the PPARalpha-regulated genes that express in a CLOCK-dependent circadian manner. Microarrays analyses using hepatic RNA isolated from bezafibrate treated-wild type, Clock mutant (Clk/Clk), and PPARalpha-null mice revealed that 136 genes are transcriptionally regulated by PPARalpha in a CLOCK-dependent manner.

overall_design:
Clk/Clk mutant mice with Jcl:ICR background, wild-type mice with the same strain, and PPARalpha-null mice aged 6-12 weeks were housed under a 12 h light-12 h dark cycle [LD 12:12; lights on at Zeitgeber time (ZT) 0]. For chronic treatment of bezafibrate, mice were provided with either a normal diet or the same diet containing 0.5% w/w bezafibrate for 5 days. A white fluorescent lamp provided light (300 - 500 lux at cage level) during the day. To examine the transient effect of bezafibrate injection on hepatic gene expression, bezafibrate was dissolved in warm (~40 C) sterile corn oil (Sigma) at a concentration of 10 mg/ml and administered intraperitoneally (i.p.) in a single dose of 100 mg/kg body weight at ZT2.
To examine the PPARalpha-regulated genes that express in a CLOCK-dependent manner in mice, we performed oligonucleotide microarray analysis at ZT14, when CLOCK/BMAL1 transcriptional activity is maximal, using RNA isolated from wild-type (n = 3), Clock mutant (n = 3), and PPARalpha-null mice (n = 3) treated with bezafibrate for 5 days, and control wild-type mice (n = 3). Livers were collected and frozen in liquid nitrogen. Total RNA (250 ng) was extracted using RNAiso.

first: Satoru

last: Koyanagi

first: Naoya

last: Matsunaga

first: Koji

last: Kadota

first: Eriko

last: Ikeda

last: Hayashida

first: Yukako

last: Kuramoto

first: Shigehiro

last: Ohdo

first: Hiroshi

last: Shimeno

first: Shinji

last: Soeda


title: BTG1 regulates glucocorticoid receptor autoinduction in acute lymphoblastic leukemia

city: Nijmegen

first: Joost

last: van Galen

institute: Radboud University Nijmegen Medical Centre

summary:
RNAi mediated knockdown of BTG1 in the acute lymphoblastic cell line RS4;11 causes this cell line to become resistant to prednisolone treatment when compared to control cells.
In this experiment we treated BTG1 knockdown RS4;11 cells and control RS4;11 cells either with prednisolone or a vehicle control and compared the gene expression patterns of these cell lines.

overall_design: 8 samples were analyzed: we treated RS4;11 control or RS4;11 shRNA BTG1 cells with either prednisolone or vehicle control, the experiment was performed in duplicate. Genes with a > 2-fold change in expression after prednisolone treatment when compared to vehicle treatment were selected. Expression changes in BTG1 knockdown cells were compared to those in control vector transduced cells.

first: Roland

last: Kuiper

first: Liesbeth

last: van Emst

first: Marloes

last: Levers

first: Esther

last: Tijchon

first: Blanca

last: Scheijen

first: Esmé

last: Waanders

first: Simon

middle: V

last: van Reijmersdal

first: Christian

last: Gilissen

first: Ad

last: Geurts van Kessel

first: Peter

last: Hoogerbrugge

first: Frank

last: van Leeuwen


title: Pre-B cell leukemia homeobox protein Pbx1 is associated with lupus susceptibility in mice and humans

status: Public on Jun 16 2010

city: Oklahoma City

first: Igor

middle: M

last: Dozmorov

state: OK

address: 825 NE 13th Street

department: Arthritis & Immunology

institute: OMRF

summary: Sle1a.1 is part of the Sle1a lupus susceptibility locus which results in the production of activated and autoreactive CD4+ T cells as well as a reduction in the peripheral regulatory T cell (Treg) pool.  Sle1a.1 CD4+ T cells showed a defective response to retinoic acid (RA) expansion of TGFβ-induced Tregs.  At the molecular level, Sle1a.1 corresponds to an increased expression of a novel splice isoform of Pbx1, Pbx1-d. Pbx1-d over-expression is sufficient to induce an activated/inflammatory phenotype in Jurkat T cells, and to decrease their apoptotic response to RA.  PBX1-d is expressed more frequently in lupus patients than in healthy controls, and its presence correlates with an increased memory T cell population.  These findings indicate that Pbx1 is a novel lupus susceptibility gene that regulates T cell activation and tolerance.

overall_design: Total RNA from CD4+ T cells from C57BL/6 (B6) and B6.Sle1a.1 (Sle) mice was isolated, with 4 biological replicates each. Gene expression data from C57BL/6 mice were compared with data from B6.Sle2c1 mice.

first: Carla

last: Cuda

first: Shiwu

last: Li

first: Hari

middle: H

last: Potula

first: Zhiwei

last: Xu

first: Ed

last: Butfiloski

first: Lung-Ji

last: Chang

first: Eric

middle: S

last: Sobel

first: Laurence

last: Morel


title: Listeria monocytogenes induces T cell receptor unresponsiveness via its pore-forming toxin listeriolysin O

status: Public on Jun 29 2010

city: Braunschweig

first: Robert

last: Geffers

address: Inhoffenstr. 7

department: Dep. Molecular Bacteriology

institute: HCI - Helmholtz Centre for Infection Research

summary:
The success of many pathogens relies on their ability to circumvent the innate and adaptive immune defenses. How bacterial pathogens subvert host responses is not clear. Cholesterol-dependent cytolysins (CDCs) represent an expansive family of homologous pore-forming toxins produced by more than 20 Gram-positive bacterial species. Here we show that listeriolysin O (LLO), a prototype CDC produced by Listeria monocytogenes, inhibits antigen receptor-induced T cell proliferation. In vivo proliferation of OT II T cells was highly diminished in the presence of wild type but not the LLO-deficient bacteria. T cells pre-exposed to LLO ex vivo were also impaired in proliferation upon TCR activation in vivo and in vitro. Our results suggest that LLO-induced T cell unresponsiveness is due to the sub-threshold activation of T cells via the induction of a calcium-NFAT dependent transcriptional program that drives the expression of negative regulators of TCR signaling.

Keywords: Listerilysin O, Ionomycin, 3 hours stimulation

overall_design: Pooled primary CD4+ T cells isolated from spleen and mesenteric lymph nodes were incubated in either control (Ctrl) medium or medium containing 0.25 ug/ml listeriolysin O (LLO) or 1 uM Ionomycin (Iono) for 3 hours. Thereafter, cells were washed and RNA was prepared.

first: R

first: N

last: Gekara

first: S

last: Weiss


title: LEOPARD Syndrome iPS, BJ iPS and Fibroblasts

status: Public on Jun 10 2010

city: New York

first: Yongchao

last: Ge

state: NY

address: One Gustave L Levy Place #1137

department: Neurology

institute: Mount Sinai School of Medicine

summary: Expression data from LEOPARD Syndrome-iPS clones, BJ-iPS cells and parental Fibroblasts

overall_design: 9 samples in total are analyzed. Among 22011 genes in expression data,  there are 3657 genes with at least 2 fold expression change between the average of the three fibroblast lines versus all of the iPS lines/HES samples. A heatmap can be generated for the expression levels for the 3657 genes and 9 samples.

first: X

last: Carvajal-Vergara

last: Rozov

first: Y

first: B

last: Gelb

first: I

last: Lemischka


title: Myocardial expression data from ketogenic diet-fed mice

status: Public on Jun 07 2010

city: St. Louis

first: Peter

last: Crawford

state: MO

address: 660 S. Euclid Ave.

institute: Washington University School of Medicine

summary:
Specific pathogen free wild-type C57Bl/6 male mice fed ketogenic diet (Bio-Serv AIN-76-A) for 4 weeks

Keywords: RNA Expression Array

overall_design: Hearts from 12 week-old mice that were maintained on a standard polysacchardide-rich chow until the age of 8 weeks, at which time they were switched to a ketogenic diet (ad libitum) and maintained for 4 additional weeks prior to collection of tissues


title: Arthritic KRN T cells and wild type T cells from germ free and specific pathogen free mice

status: Public on Jun 05 2010

first: CBDM

last: Lab

summary: A general defect of GF K/BxN T cell proliferation response toward antigen motivated us to look for the impairment in GF K/BxN T cells that might leads to the low Ab production and reduced disease phenotype seen in GF K/BxN mice. To find the difference between GF and SPF K/BxN T cells in a broad and non-biased fashion, we performed gene-expression profiling of these cells using microarrays.

overall_design: All gene expression profiles were obtained from highly purified T cell populations sorted by flow cytometry. To reduce variability, cells from multiple mice were pooled for sorting, and triplicates or quadruplates were generated for all groups. Raw data were preprocessed with the RMA algorithm in GenePattern, and averaged expression values were used for analysis.

first: Hsin-Jung

last: Wu

first: Diane

last: Mathis

first: Christophe

last: Benoist


title: Expression data from lenses triply deficient for E2F1, E2F2, and E2F3 transcription factors

first: Pamela

middle: L.

last: Wenzel

address: 300 Longwood Ave

department: Hematology/Oncology

institute: Children's Hospital Boston

summary:
The E2F family consists of transcriptional repressors and activators that control cell proliferation.  In the classic paradigm of cell cycle regulation, the three activators, E2F1, E2F2 and E2F3, are invariably depicted as the final components of a CDK/Rb signaling cascade that executes the transcriptional program necessary to commit cells to enter S phase.
Unexpectedly, we find through analysis of Affymetrix expression array data that mature lens epithelial cells deficient for E2F1-3 fail to repress cell cycle-regulated genes (and other targets of E2F) and that this corresponds with subsequent apoptosis and cellular collapse in the lens.

overall_design: Murine lenses were collected at two stages of development for RNA extraction and hybridization on Affymetrix microarrays. Our aim was to determine key events that lead to cellular collapse of lenses triply deficient for E2F1, E2F2, and E2F3 in neonates.

middle: L

first: Gustavo

last: Leone


title: PLAGL2 regulates Wnt signaling to impede differentiation in neural stem cells and glioma

status: Public on Jun 14 2010

first: Haoqiang

last: Ying

address: 44 Binney St.

department: Medical Oncology

institute: Dana-Farber Cancer Institute

summary: A hallmark feature of glioblastoma (GBM) cells is its strong self-renewal potential and immature differentiation state -- stem cell-like properties which may contribute to the plasticity and intense therapeutic resistance of GBM.  The molecular basis of the immature differentiation profile remains an area of active investigation. Here, integrated genomic and biological analyses identified PLAGL2 as a potent proto-oncogene targeted for amplification/gain in malignant gliomas as well as in colorectal cancers. High level of PLAGL2 expression strongly suppresses neural stem cell (NSC) and glioma-initiating cell (GIC) differentiation while promoting their proliferation and self-renewal capacity under differentiation induction conditions. On the mechanistic level, the PLAGL2 transcriptome analysis revealed that these differentiation suppressive activities are attributable in part to PLAGL2 modulation of Wnt/beta-catenin signaling via up-regulation of Wnt6 ligand as well as Fzd9 and Fzd2 receptor expression. Correspondingly, inhibition of Wnt signaling in PLAGL2-expressing NSC partially restores their differentiation capacity. The identification of PLAGL2 as a glioma oncogene highlights the importance of a growing class of cancer genes functioning to impart stem cell-like characteristics on malignant cells.

overall_design: p53-null mouse NSCs are infected with retrovirus expressing either control vector or PlagL2. Total RNA were collected upon differentiation in 1% FBS for 24 hr. 3 replicates each.


title: Expression profiling of splenic dendritic cells

city: SÃO PAULO

first: Helder

middle: I.

last: Nakaya

state: SÃO PAULO

address: AVENIDA PROFESSOR LINEU PRESTES, 580, Block 17

country: Brazil

institute: Universidade de São Paulo

summary:
Dendritic cells (DCs) play a vital role in innate immunity. Transcriptome of DCs isolated from mouse spleen was obtained and deposited here.
Keywords: Spleen, DCs

overall_design: We sought to determine the expression profile of splenic CD11c+ cells. RNA was extracted from DCs sorted from mouse spleen (CD11c+ cells) and hybridized on Affymetrix microarrays.

first: Santhakumar

last: Manicassamy

middle: I

first: Bali

last: Pulendran


title: Mouse pancreatic islets during pregnancy

status: Public on Jun 04 2010

city: Bunkyo-Ku

first: Hirotaka

last: Watada

address: 2-1-1 Hongo

department: Medicine, Metabolism and Endocrinology

institute: Juntendo University

summary:
During pregnancy, pancreatic islets undergo structural and functional changes that lead to enhance insulin release in response to increased insulin demand, which is rapidly reversed at parturition. One of the most important changes is expansion of pancreatic β-cell mass mainly by increased proliferation of β cells.
We used microarrays to detail the global programme of gene expression and identified distinct up- or down-regulated genes during pregnancy.

overall_design: Maternal islet were isolated from mice at dpc 0 and 12.5 dpc of pregnancy for RNA extraction and hybridization on Affymetrix microarrays. We sought to identify the responsible factors for the proliferation of islets during pregnancy.

first: Yukiko

last: Toyofuku

first: Toyoyoshi

last: Uchida

first: Yoshio

last: Fujitani


title: Comprehensive expression profiling across primary fetal liver terminal erythroid differentiation

city: Cambridge

first: Shilpa

middle: Manohar

last: Hattangadi

address: 9 Cambridge Center

department: Lodish Lab

institute: Whitehead Institute (WIBR)

summary: Primary murine fetal liver cells were freshly isolated from day e14.5 livers and then sorted for successive differentiation stages by Ter119 and CD71 surface expression (ranging from double-negative CFU-Es to Ter-119 positive enucleated erythrocytes) [Zhang, et al. Blood. 2003 Dec 1; 102(12):3938-46]. RNA isolated from each freshly isolated, stage-sorted population was reverse-transcribed, labelled, and then hybridized onto 3' oligo Affymetrix arrays.  Important erythroid specific genes as well as the proteins that regulate them were elucidated through this profiling based on coexpression and differential expression patterns as well as by extracting specific GO categories of genes (such as DNA-binding proteins).

overall_design:
Abstract (submitted paper): rationale for expression profiling
Gene-targeting experiments report that the homeodomain-interacting protein kinases 1 and 2, Hipk1 and Hipk2, are essential but redundant in hematopoietic development—because Hipk1/Hipk2 double-deficient animals exhibit severe defects in hematopoiesis and vasculogenesis while the single knockouts do not. These serine-threonine kinases phosphorylate, and consequently modify the functions of, several important hematopoietic transcription factors and cofactors.  Here we show that Hipk2 knockdown alone plays a significant role in terminal fetal liver erythroid differentiation.  Hipk1 and Hipk2 are highly induced during primary mouse fetal liver erythropoiesis.  Specific knockdown of Hipk2 inhibits terminal erythroid cell proliferation—explained in part by impaired cell cycle progression as well as increased apoptosis—and terminal enucleation as well as the accumulation of hemoglobin.  Hipk2 knockdown also reduces the transcription of many genes involved in proliferation and apoptosis as well as important, erythroid-specific genes involved in hemoglobin biosynthesis—such as alpha-globin and mitoferrin 1—demonstrating that Hipk2 plays an important role in some but not all aspects of normal terminal erythroid differentiation.

first: Karly

last: Burke

first: Harvey

last: Lodish


title: Expression data from MRTFA-B double knockout brain

city: Dallas

first: Mayssa

middle: H.

last: Mokalled

state: TX

address: 5323 Harry Hines Blvd.

department: Molecular Biology

institute: UT Southwestern Medical Center at Dallas

summary: We used microarrays to detail the global pattern of gene expression in the cortical regional of MRTF-A/-B double knockout mice at Postnatal day 0 (P0).

overall_design: RNA samples were collected from the cortical regions of control and MRTF-A/-B double knockout mice at P0.  Three control MRTFA-/-;MRTF-BFlox/Flox and three MRTF-A-/-;MRTF-BF/F;GFAP-Cre RNA samples were collected and pooled for hybridization on Affymetrix microarrays.

first: Eric

last: Olson


title: Down-regulated Genes in Mouse Dental Papillae and Pulp

city: Chiba

first: Takashi

last: Muramatsu

address: 1-2-2, Masago, Mihama-ku

institute: Tokyo Dental College

summary:
Goal of experiment: Identify genes down-regulated between pre- and post-natal stages in mouse dental papillae.
Epithelial-mesenchymal interaction is very important during tooth development, and many genes are associated with odontogenesis.  The capacity for odontogenesis in mouse dental papillae disappears between the pre- and post-natal stages.  We hypothesized that genes involved in odontogenesis were down-regulated in dental papillae between these stages.  To test this hypothesis, we investigated and compared gene profiles in pre- and post-natal stage dental papillae with the GeneChip® Mouse Genome 430 2.0 Array.

overall_design: Experimental factors: tooth development (odontogenesis)


title: Expression Data from chemical induced tumors obtained from NDR1+/+, NDR1+/- and NDR1-/- mice

city: Basel

first: Brian

middle: Arthur

last: Hemmings

address: Maulbeerstrasse 66

department: Growth Control

country: Switzerland

institute: Friedrich-Miescher Institute

summary: Loss and heterozygosity for NDR1 predisposes mice to T-cell lymphoma development. To analyze mechanisms of tumor development in these mice chemically (ENU)-induced tumors were collected and RNA was extracted.

overall_design: Tumors were collected from mice upon tumor development or 9 months after ENU treatment. Tumors were flash frozen and parts of the tumors were analyzed for RNA, proteins and histology.

first: Hauke

last: Cornils

middle: A


title: The role of Ternary Complex factors in T-cell Positive Selection

status: Public on Jun 01 2010

city: London

first: Robert

middle: Harris

last: Nicolas

address: 44 Lincoln's Inn feilds

department: Transcription

country: United Kingdom

institute: LRI Cancer research UK

summary: Removal of the transcription factor SAP1a member of the Ternary Complex Factor (TCF) group of transcription factors which in conjunction with Serum Response Factor (SRF) has been shown to have a profound effect on positive selection in the thymus. When another TCF Elk1 is knocked out in mice there is no effect on positive selection unless it is on a Sap1a KO background where the phenotype is very severe. We have stimulated isolated double positive T cells (DPs) with anti-CD3 to mimic positive selection and compared basal and stimulated transcription across the four genotypes to discover the downstream targets of Sap1a involved in positive selection.

overall_design: The Affymetrix mouse Chip Mouse430_2 arrays were used to define gene expression profiles in purified DPs with and with out CD3 treatment from 3 mice for each genotype (Wt,SapKO, ElkKO and SAP/Elk double KO)

first: Rob

first: Patrick

last: Costello


title: Testis samples from Alkbh1 wild-type and KO mice

status: Public on Jun 02 2010

city: Oslo

first: Anja

last: Nilsen

address: Sognsvannsveien 20

country: Norway

institute: University of Oslo

summary:
The aim of the study was to elucidate the role of Alkbh1 by targeted deletion in C57/BL6 mice.
Alkb deficiency results in sex-ratio distortion of offspring and apoptosis in adult testes, most likely caused by defects in the pachytene stage during spermatogenesis.
Due to the pivotal role of Alkbh1 in mouse survival and potentially in germ cells, we searched for Alkbh1-regulated genes in adult testes.

overall_design: Testes from 12 week old mice were selected for RNA extraction and hybridization on Affymetrix microarrays. We used testes from 3 wild type mice and 3 KO mice

first: Line

last: Nordstrand

first: Jessica

last: Svärd

first: Elisabeth

last: Larsen

first: Rune

last: Ougland

first: Kari

last: Furu

first: Guro

middle: F

last: Lien

first: Torbjørn

last: Rognes

first: Satoshi

last: Namekawa

first: Jeannie

middle: T

last: Lee

first: Arne

last: Klungland


title: Mouse small cell lung cancer model

city: Stanford

first: Julien

last: Sage

state: CA

address: 265 Campus Drive, SIM1 G2078

department: Pediatrics

institute: Stanford University

summary: A mouse model for human small cell lung carcinoma (SCLC) has been developed based on evidence in human tumors that the tumor suppressor functions of RB and p53 are defective in more than 90% of SCLC cases. We also developed another mouse model also combines loss of p130 (Rbl2), an RB-related gene, with deletion of RB and p53. These two mouse tumors were shown to closely resemble human SCLC.

overall_design: The goal of this array experiment is to assess genome-wide gene expression of those mouse tumors and determine the similarity of the mouse models to human SCLC. Gene expression from Mouse Rb/p53 ( n=10 ) and Rb/p53/p130 primary tumors ( n=3 ) as well as tumor-free adult mouse lungs ( n=2 ) was measured using the Affymetrix GeneChip Mouse Genome 430-2.0 arrays.

first: Kwon-Sik

last: Park


title: DNA microarrays of SKOM transduced MEFs with added Tgfb1 or co-expressing Snail

city: Guangzhou

first: Duanqing

last: Pei

state: Guangdong

address: Room 301, International Business Incubator, Guangzhou science park

department: Center for Molecular Medicine

country: China

institute: Guangzhou Institute of Biomedicine and Health, Chinese Academy of Sciences(GIBH.CAS)

summary:
The Tgf-b signaling pathway plays an important role in both embryonic development and epithelial to mesenchymal transition (EMT), but the influence of this pathway and its relationship with EMT in fibroblast reprogramming is not defined.
Using Affymetrix mouse genome array and mouse embryonic fibroblast cells (MEFs), we analyzed the expression profiles of Tgf-b1 and one of its important mediators in EMT, Snail, regulated genes at Day 10 during the process of reprogramming. A total of 535 genes were differentially expressed (2-fold change) in cells activated by Tgf-b1 and 970 genes were differentially expressed in cells over-expressing Snail. Among them, 170 genes were shared in both categories. The differentially expressed genes involve in many biological processes, including Tgf-b signaling pathway, cell communication, ECM-receptor interaction, cell adhesion, focal adhersion, and Hedgehog signaling pathway

overall_design: MEFs derived from a OG2 mouse is a typical kind of fibroblast cells used in most reprogramming studies. Cells were cultured in MEF medium in an incubator with 5% CO2 at 37oC before retrovirus infection and the medium was changed into ES medium after infection of the reprogramming cocktail (Sox2, Klf4, Oct4 and cMyc).  At Day 10 after infection, cells were collected and total RNA were extracted from the cells and was hybridized on Affymetrix GeneChip Mouse Genome 430 2.0 Array.

first: Jialiang

last: Liang

first: Wenzhi

last: He


title: wild type mouse lung control vs. high fat diet

city: Durham

first: Yuh-Chin

middle: Tony

last: Huang

state: NC

address: Erwin Rd

department: Medicine

institute: Duke University Medical Center

summary: To study the effects of a high fat diet on the mouse lung transcrptional profile.

overall_design: 6 samples were analyzed.  3 wild type mice on a control diet (lung samples) vs. 3 wild type mice on a high fat diet (lung samples).

first: Edward

middle: D

last: Karoly


title: Human Exon Array Profiling of Ewing sarcoma

city: Ann Arbor

first: Elizabeth

middle: R

last: Lawlor

address: 1600 Huron Parkway, NCRC Bldg 520

institute: University of Michigan

summary: Ewing sarcoma family tumors (ESFTs) are aggressive tumors of putative stem cell origin for which prognostic biomarkers and novel treatments are needed. We have previously shown that the polycomb gene BMI-1 functions as an oncogene in ESFT. In several human cancers, high expression of BMI-1 is associated with poor outcome. For the current study, we evaluated the significance of variable BMI-1 expression levels in a large cohort of primary ESFT. Immunohistochemical staining of 130 tumors revealed that BMI-1 is over-expressed by the vast majority of ESFT. However, in 20% of cases, BMI-1 levels are low to undetectable. Significantly, although clinical presentation and outcome were found to be similar between BMI-1-high and BMI-1-low tumors, gene expression profiling studies showed marked differences in their respective gene expression profiles. Gene specific enrichment analysis identified that several cancer-associated canonical biologic pathways, including IGF1, mTOR and WNT, are significantly down-regulated in BMI-1-low compared to BMI-1-high tumors. Consistent with these in vivo data, in vitro studies of IGF1-R inhibition showed that the growth inhibitory effects of IGF1-R blockade are diminished in BMI-1-low ESFT cells. ESFT that do not over-express BMI-1 represent a novel subclass with a distinct molecular profile and altered activation of cancer-associated pathways.

overall_design: Affy HuEx 1.0 array profiling of 10 primary ESFT samples obtained from patients with newly diagnosed ESFT. 5 confirmed BMI-1 low and 5 confirmed BMI-1 high expressers by immunostaining.


title: Ascorbate effect on serum free cultured hESC

city: St Lucia

first: Sean

last: Grimmond

state: Q

address: Services Rd

department: Institute for Molecular Bioscience

country: Australia

institute: University of Queensland

summary:
Ascorbate activates CD30 expression and causes widespread specific demethylation of the epigenome of serum free cultured hESC.

The genetic and epigenetic integrity of human Embryonic Stem cells (hESCs) is critical to their future applications in research and medicine. hESC cultured in serum free media can accumulate point mutations, aneuploidy and progressive epigenetic changes over prolonged culture in vitro. We have identified ascorbate as the only molecule in the very widely used Knock-out serum replacement medium that is sufficient to induce expression of CD30, a biomarker for aneuploidy in hESCs. In fact, we show that hESC cultured in the presence of ascorbate for 20 passages not only display demethylation of the CD30 locus, but exhibit widespread and remarkably specific and consistent demethylation of 1,847 genes in both HES2 and HES3 cells. The specific ascorbate induced demethylation changes in the hESC epigenome, of which 86% are shared between the two lines, identify a subset of genes in hESC, including CD30, that are sensitive to serum free culture medium induced epigenetic changes.
Experiment. HES2 cells were maintained on 20% Fetal calf serum on mouse embryonic fibroblast feeder layers with mechanical dissection.  Using HES2 after 99 mechanical passages (P99), hESC were grown for 17-20 (+17 - +20) passages in the presence of 20% Knock-Out Serum Replacement (Invitrogen) either with (+ASC) or without (-ASC) Ascorbate with enzymatic culturing.

overall_design: RNA (FACs sorted for the presence of the pluripotent stem marker TG30) from three passages (17, 19 and 20) (replicates) for both +ASC and –ASC samples were arrayed.

first: Gabriel

last: Kolle


title: Expression data from bone marrow derived- and tumor induced- CD11b+ MDSC

status: Public on Jun 03 2010

city: Padova

first: Silvio

last: Bicciato

address: via U. Bassi 59/b

department: Molecular Medicine

country: Italy

institute: University of Padova

summary:
Tumor growth is associated with a profound alteration of myelopoiesis, leading to recruitment of immunosuppressive cells known as myeloid-derived suppressor cells (MDSCs). Analyzing the cytokines affecting myelo-monocytic differentiation produced by various experimental tumors, we found that  GM-CSF, G-CSF, and IL-6 allowed a rapid generation of MDSCs from precursors present in mouse and human bone marrow (BM). BM-MDSCs induced by GM-CSF+IL-6 possessed the highest tolerogenic activity, as revealed by the ability to impair the priming of IFN- -producing CD8+ T cells upon in vivo adoptive transfer. Moreover, adoptive transfer of syngeneic, GM-CSF+IL-6-conditioned MDSCs to diabetic mice transplanted with allogeneic pancreatic islets resulted in long term acceptance of the allograft and correction of the diabetic status. Cytokines inducing MDSCs acted on a common molecular pathway. Immunoregulatory activity of both tumor-induced and BM-derived MDSCs was entirely dependent on C/EBP  transcription factor, a key component of the emergency myelopoiesis triggered by stress and inflammation. Adoptive transfer of tumor antigen-specific CD8+ T lymphocytes resulted in therapy of established tumors only in mice lacking C/EBP  in myeloid compartment. These data unveil another link between inflammation and cancer and identify a novel molecular target to control tumor-induced immune suppression.
We used gene expression analysis to identify those factors, secreted by tumor-infiltrating MDSC, which could drive emathopoiesis. Moreover we compare gene expression profile of tumor-induced MDSC, obtained from either the spleen and the tumor infiltrate of tumor bearing mice,  and in vitro bone marrow-derived MDSC.

overall_design: CD11b+ cells were immunomagnetically enriched from various murine tissue and experimental conditions, and cRNA samples were prepared accordingly to Expression Analysis: Technical Manual. 701021 Rev. 5. Santa Clara, CA, Affymetrix; 2004, and hybridized to the Affymetrix GeneChip MOE430 2.0 array which contains more than 45,000 probe sets, representing more than 34,000 genes. CD11b+ cells obtained from the spleen of healthy BALB/c and C57BL/6 mice were used as reference sample for tumor induced CD11b+ MDSC, enriched from either the spleen and the tumor infiltrate of tumor-bearing mice. Moreover CD11b+ cells enriched from fresh bone marrow were used as reference sample for in vitro bone marrow-differentiated MDSC, obtained with either GM-CSF+IL-6 and GM-CSF+G-CSF 4 days cytokine cocktail treatment.

first: Ilaria

last: Marigo

first: Luigi

last: Dolcetti

first: Stefano

last: Ugel

first: Nada

last: Sonda

first: Paola

last: Zanovello

first: Susanna

last: Mandruzzato

first: Vincenzo

last: Bronte


title: Expression data of hepatocellular carcinoma and adjacent liver tissues

city: Tokyo

first: satow

last: reiko

address: 5-1-1 Tsukiji, Chuo-ku

institute: National Cancer Center Research Institute

summary:
To identify therapeutic targets with high specificity to HCC, we searched for genes significantly up-regulated in HCC over corresponding non-tumor liver using high-density microarrays

Keywords: disease state analysis

overall_design: HCC and surrounding non-tumor liver tissue samples were collected from 10 cases who underwent liver resection for HCC at National Cancer Center Hospital (Tokyo, Japan). One µg of total RNA was converted to end-labeled cRNA using the Whole Transcript Sense Target Labeling kit (Affymetrix, Santa Clara, CA). The fluorescent cRNA probes were hybridized to Human Exon 1.0 ST arrays (Affymetrix), as instructed by the supplier.

first: Tesshi

last: Yamada


title: MicroRNAs dynamically remodel gastric smooth muscle cells

city: Reno

first: Seungil

last: Ro

state: NV

address: 1664 N. Virginia St.

department: Physiology and Cell biology

institute: University of Nevada School of Medicine

summary:
Smooth muscle cells (SMCs) display dynamic plasticity by changing phenotype under various pathophysiological conditions. Uncovering how SMCs regulate their phenotype is a key to understanding the molecular mechanisms of a number of gastrointestinal diseases. MicroRNAs (miRNAs), generated in cells by Dicer, have been identified as regulators of the differentiation state of SMCs. The goal of this study was to investigate the role of miRNAs during the development of gastrointestinal SMCs in a transgenic animal model. We generated SMC-specific Dicer (smDicer) null animals that express the reporter, green fluorescence protein (eGFP), in a SMC-specific manner. eGFP labeled SMCs were used for morphological, cytometric and genetic studies of smDicer null mutant and wild type control mice. The structure of the bowel wall was examined by confocal microscopy, and function was evaluated by recording spontaneous and evoked contractions. SMCs were purified with fluorescence-activated cell sorting and SM specific gene expression studies were performed with genechip arrays, PCR and quantitative PCR. Bioinformatic analyses were used to characterize the interaction between miRNAs and target genes. SMC-specific knockout of Dicer prevented SMC miRNA biogenesis, causing dramatic changes in phenotype, function, and global gene expression in SMCs. Profiling and bioinformatic analyses showed SMC phenotype is regulated by a complex network of positive and negative feedback by SM miRNAs, serum response factor (SRF), and other transcriptional factors. SM miRNAs play an important role in growth, development and survival of SMCs. Phenotypic changes of SMCs may be regulated through multiple pathways in an interaction network of SM miRNAs, SRF, and additional transcriptional factors.
We used microarrays to identify genetic changes during the development of gastric smooth muscle cells in the smDicer null mice.

overall_design: Mouse mRNA microarrays were performed on GeneChip® Mouse Genome 430 2.0 Arrays (Affymetrix). Total RNAs isolated from the jejunal muscularis of the smDicer knockout (KO) and the wild type (WT) control mice at the ages of ~3 weeks were used for the arrays. The cDNA synthesis, hybridization, cDNA labeling, and scanning were performed. Gene expression between the smDicer KO and the WT controls were compared.

first: Chanjae

last: Park


title: Expression data from exercised-trained, myog-deleted adult mice

status: Public on May 29 2010

city: HOUSTON

first: JAMES

middle: ERIC

last: MEADOWS

address: 1515 HOLCOMBE BLVD

department: BIOCHEMISTRY

institute: MD ANDERSON CANCER CENTER

summary:
Although skeletal muscle metabolism is a well-studied physiological process, little is known about how it is regulated at the transcriptional level. The myogenic transcription factor myogenin is required for skeletal muscle development during embryonic and fetal life, but myogenin’s role in adult skeletal muscle is unclear. We sought to determine myogenin’s function in adult muscle metabolism. A Myog conditional allele and Cre-ER transgene were used to delete Myog in adult mice. Mice were analyzed for exercise capacity by involuntary treadmill running. To assess oxidative and glycolytic metabolism, we monitored blood glucose and lactate levels and performed histochemical analysis on muscle fibers. Surprisingly, we found that Myog-deleted mice performed significantly better than controls in high- and low-intensity treadmill running. This enhanced exercise capacity was due to more efficient oxidative metabolism during low-intensity exercise and more efficient glycolytic metabolism during high-intensity exercise. Furthermore, Myog-deleted mice had an enhanced response to long-term voluntary exercise training on running wheels. We identified several candidate genes whose expression was altered in exercise-stressed muscle of mice lacking myogenin. The results suggest that myogenin plays a critical role as a high-level transcriptional regulator to control the energy balance between aerobic and anaerobic metabolism in adult skeletal muscle.
We used microarrays to detail the global program of gene expression underlying enhanced exercise endurance associated with myog-deletion and long-term exercise training.

overall_design: Mouse gastrocnemius muscles were selected after 6 months of myog-deletion and exercise training for RNA extraction and hybridization on Affymetrix microarrays. We chose 3 wild type and 3 myog-deleted mice that best represented the average of each larger group that was tested during our mouse exercise studies.

first: Eric

last: Meadows

first: Jesse

last: Flynn

first: William

last: Klein


title: Diverse Targets of the Transcription Factor STAT3 Contribute to T Cell Pathogenicity and Homeostasis [Affymetrix Expression]

status: Public on May 30 2010

city: Bethesda

first: Golnaz

last: Vahedi

address: 9000 Rockville Pike Bldg 10 Rm 13C101A

department: NIAMS

institute: National Institutes of Health

summary: STAT3, an essential transcription factor with pleiotropic functions, plays critical roles in the pathogenesis of autoimmunity. Despite recent data linking STAT3 with inflammatory bowel disease, exactly how it contributes to chronic intestinal inflammation is not known. Using a T cell transfer model of colitis we found that STAT3 expression in T cells was essential for the induction of both colitis and systemic inflammation. STAT3 was critical in modulating the balance of T helper 17 (Th17) and regulatory T (Treg) cells, as well as in promoting CD4+ T cell proliferation. We used chromatin immunoprecipitation and massive parallel sequencing (ChIP-Seq) to define the genome-wide targets of STAT3 in CD4+ T cells. We found that STAT3 bound to multiple genes involved in Th17 cell differentiation, cell activation, proliferation and survival, regulating both expression and epigenetic modifications.  Thus, STAT3 orchestrates multiple critical aspects of T cell function in inflammation and homeostasis.

overall_design: WT and STAT3-deficient CD4+  T cells were activated with anti-CD3 and anti-CD28, in the presence of cytokines (interleukin (IL)-6 and TGFb) or medium alone for three days. RNA was extracted and hybridized to Affymetrix microarray chips.

first: Lydia

last: Durant

first: Wendy

last: Watford

first: Haydeé

last: Ramos

first: Arian

last: Laurence

first: Lai

last: Wei

first: Hayato

last: Takahashi

first: Hong-Wei

last: Sun

first: Yuka

last: Kanno

first: Fiona

last: Powrie

first: John

middle: J

last: O’Shea


title: Atoh1 inhibits neuronal differentiation and collaborates with Gli1 to generate medulloblastoma-initiating cells

city: Memphis

first: Chunxu

last: Qu

state: TN

address: 262 Danny Thomas Pl

department: Pathology

institute: St Jude Children's Research Institute

summary:
The morphogen and mitogen, Sonic Hedgehog, activates a Gli1-dependent transcription program that drives proliferation of granule neuron progenitors (GNPs) within the external germinal layer of the postnatally developing cerebellum.  Medulloblastomas with mutations activating the Sonic Hedgehog signaling pathway preferentially arise within the external germinal layer, and the tumor cells closely resemble GNPs.  Atoh1/Math1, a basic helix-loop-helix transcription factor essential for GNP histogenesis, does not induce medulloblastomas when expressed in primary mouse GNPs that are explanted from the early postnatal cerebellum and transplanted back into the brains of naïve mice.  However, enforced expression of Atoh1 in primary GNPs enhances the oncogenicity of cells overexpressing Gli1 by almost three orders of magnitude.  Unlike Gli1, Atoh1 cannot support GNP proliferation in the absence of Sonic Hedgehog signaling and does not govern expression of canonical cell cycle genes.  Instead, Atoh1 maintains GNPs in a Sonic Hedgehog-responsive state by regulating genes that trigger neuronal differentiation, including many expressed in response to bone morphogenic protein-4.  Therefore, by targeting multiple genes regulating the differentiation state of GNPs, Atoh1 collaborates with the pro-proliferative Gli1-dependent transcriptional program to influence medulloblastoma development.

Keywords: disease state analysis

overall_design: 14 samples, 1 time series, 2 engineered Medulloblastoma tumors

first: Olivier

last: Ayrault

first: Haotian

last: Zhao

first: Frederique

last: Zindy

first: Charles

last: Sherr

first: Martine

last: Roussel


title: The transcriptome of nonpolypoid and polypoid preinvasive lesions of the human large intestine

status: Public on May 27 2010

city: Zurich

first: Giancarlo

last: Marra

address: Winterthurerstrasse 190

department: Molecular Cancer Research

institute: University of Zurich

summary: The aim was to analyze the transcriptome of different types of preneoplastic colorectal lesions in comparison with that of the corresponding normal mucosa.

overall_design: Ninety-two samples were analyzed. Forty-two precancerous colorectal lesions (25 nonpolypoid, 17 polypoid) and 4 colorectal cancers, and the corresponding normal mucosa from the same colonic segment where the lesion was taken.

first: Endre

last: Laczko


title: Hepatic acute phase proteins control innate immune responses during infection by promoting myeloid derived suppressor cell function

city: Wageningen

first: Guido

last: Hooiveld

address: HELIX, Stippeneng 4

department: Div. Human Nutrition & Health

institute: Wageningen University

summary: Acute phase proteins (APPs) are an evolutionarily conserved family of proteins produced mainly in the liver in response to infection and inflammation. Despite vast pro- and anti-inflammatory properties ascribed to individual APPs, their collective function during infections remains poorly defined. Using a murine model for polymicrobial sepsis we show here that abrogation of APP production by hepatocyte-specific gp130 deletion, the signaling receptor shared by IL-6-family cytokines, dramatically increased mortality despite normal bacterial clearance. Hepatic gp130 signaling through signal transducer and activator of transcription (Stat)3 was required to control systemic inflammation. Notably, hepatic gp130/Stat3 activation was also a prerequisite to facilitate mobilization and tissue accumulation of myeloid-derived suppressor cells (MDSCs), a cell population mainly known for anti-inflammatory properties in cancer. We show that MDSCs were critical to regulate innate inflammation and their adoptive transfer efficiently protected gp130-deficient mice from sepsis-associated mortality. We identified serum amyloid A and Cxcl-1/KC as hepatic acute phase genes that cooperatively promoted MDSC mobilization, accumulation and survival. Administration of these proteins efficiently elevated MDSC numbers and reversed dysregulated inflammation and restored survival of gp130-deficient mice. Thus, gp130-dependent communication between the liver and MDSCs through acute phase proteins critically controls inflammatory responses during infection.

overall_design: Control [gp130f/f] and liver-specific Gp130 knockout [gp130delta(hepa)] mice were subjected to polymicrobial sepsis. Twelve hours after induction of sepsis mice were sacrificed and livers were removed. For control treatment mice were sacrified without any prior treatment. Total RNA was isolated and subjected to gene expression profiling.

first: Leif

middle: E

last: Sander

first: Sara

last: Dutton Sackett

first: Uta

last: Dierssen

first: Naiara

last: Beraza

first: Reinhold

middle: P

last: Linke

first: Michael

last: Müller

first: Julie

last: Magarian Blander

first: Frank

last: Tacke

first: Christian

last: Trautwein


title: Distinct signature of altered homeostasis in aging rod photoreceptors: Implications for retinal diseases

city: Rockville

first: Radu

last: Cojocaru

address: 5635 Fishers Lane, Suite 510

institute: Elsevier

summary: To better understand the mechanistic basis of aging and its relationship with retinal degeneration, we examined gene expression changes in aging rod photoreceptors. Rod photoreceptor cell death is a feature of normal retinal aging and is accelerated in many retinal degenerative diseases, including AMD, the leading cause of untreatable adult blindness in the United States and other western countries.  To our knowledge, the examination of age-related gene expression changes in a specific neuronal cell-type is novel, and it has allowed us to identify significant age-related changes with better resolution than is possible with whole retina samples.  We used flow cytometry and a transgenic mouse with GFP-tagged rod photoreceptors to purify this specific cell population, and gene expression changes were evaluated at three time points using microarrays and quantitative RT-PCR.  Our results suggest that aging is progressive, beginning even in young adult mice.  Although rod photoreceptors are highly specialized neurons, our analyses revealed changes in consensus pathways of aging, including oxidative phosphorylation and stress responses affecting transcription and inflammation.  In addition, we identified stress response processes that may be especially relevant for the aging retina and retinal diseases, such as angiogenesis and nuclear receptor signaling pathways that affect retinoid and lipid metabolism.

first: Sunil

last: Parapuram

first: Jessica

last: Chang

first: Ritu

last: Khanna

first: Matthew

last: Brooks

first: Mohammad

last: Othman

first: Sepideh

last: Zareparsi

first: Naheed

last: Khan

first: Tiziana

last: Cogliati

first: Anand

last: Swaroop


title: Physiological Jak2V617F expression causes a lethal myeloproliferative neoplasm with differential effects on hematopoietic stem and progenitor cells

status: Public on May 15 2010

city: Cambridge

first: Fatima

last: Al-Shahrour

address: 7 Cambridge Center

department: Cancer program

institute: Broad Institute of MIT and Harvard

summary: We report a Jak2V617F knock-in mouse myeloproliferative neoplasm (MPN) model resembling human polycythemia vera (PV). The MPN is serially transplantable and we demonstrate that the hematopoietic stem cell (HSC) compartment has the unique capacity for disease initiation but does not have a selective competitive advantage over wild type HSCs. In contrast, myeloid progenitor populations are expanded and skewed towards the erythroid lineage, but cannot transplant the disease. Treatment with a JAK2 kinase inhibitor ameliorated the MPN phenotype, but did not eliminate the disease-initiating population. These findings provide insights into the consequences of JAK2 activation on HSC differentiation and function and have the potential to inform therapeutic approaches to JAK2V617F positive MPN.

overall_design: LKS cells were isolated from wild type (n=4) and JAK2V617F mutant mice (n=4). RNA was extracted using Qiagen RNeasy Micro Kit according to manufacturers instruction and amplified using NUGEN amplification kit. cDNA was fragmented and biotinylated before hybridization onto Affymetrix Mouse Expression Array 430 2.0.

first: Ann

last: Mullally

first: Steven

middle: W

last: Lane

first: Brian

last: Ball

first: Christine

last: Megerdichian

first: Rachel

last: Okabe

first: Mahnaz

last: Paktinat

first: Erika

last: Haydu

first: Elizabeth

last: Housman

first: Allegra

middle: M

last: Lord

first: Gerlinde

last: Werning

middle: G

last: Kharas

first: Thomas

last: Mercher

first: Jeffery

middle: L

last: Kutok

first: D

last: Gilliland

first: Benjamin

last: Ebert


title: Expression data from LPS-stimulated RAW 264.7 mouse macrophages treated with Hypericum perforatum fraction and bioactive constituents

city: Ames

first: Diane

last: Birt

state: IA

address: 215 Mackay Iowa State University

department: Food Science and Human Nutrition

institute: Iowa State University

summary:
Hypericum perforatum extracts have been used as dietary supplements to treat conditions including mild-moderate depression and inflammation. A group of four bioactive constituents were identified from an active fraction of the extract.
In order to identify the mechanism for the potential anti-inflammatory activity of the identified compounds, we used Affymatrix microarray to study the gene expression profile impacteded by these compounds, as well as the active fraction in LPS-stimulated mouse macrophages.

overall_design: We treated RAW264.7 mouse macrophages with DMSO control, active fraction from Hypericum perforaum extract, and a combination of the 4 putative bioactive compounds, called the 4-component system, all with and without LPS induction. A total of six treatment combinations were included in the final gene expression analysis using microarray.

first: K

last: Hammer

first: M

middle: Y

last: Yum

first: P

last: Dixon


title: Nkx2.5 regulates Jarid2 during outflow tract morphogenesis

status: Public on May 17 2010

city: Charleston

first: Jeremy

last: Barth

state: SC

address: 173 Ashley Ave, BSB 627

institute: MUSC

summary:
The transcription factor Nkx2.5 is required for specification of pharyngeal arch second heart field (SHF) progenitors that contribute to outflow tract (OFT) and right ventricle (RV) formation. Multiple sets of microarray data were analyzed to identify genes that are candidate targets of Nkx2.5 in the second heart field. These sets are: 1) publicly available data for cardiothoracic tissue from E9.5 Nkx2.5 wild-type, heterozygous and homozygous embryos; 2) an analysis of mouse E10.5 pharyngeal arch tissue; 3) an analysis of mouse E12.5 heart tissue; and 4) a temporal analysis of the cardiogenic cell line P19CL6. This combined analysis identified 11 genes (Lrrn1, Elovl2, Safb, Slc39a6, Khdrbs1, Hoxb4, Fez1, Ccdc117, Jarid2, Nrcam, and Enpp3) expressed in SHF-containing pharyngeal arch tissue whose regulation is dependent on Nkx2.5 expression.

This SuperSeries is composed of the SubSeries listed below.

overall_design: Refer to individual Series


title: Gene expression in Lineage negative bone marrow cells of C57B/L6 and B.D(Chr5) mice

status: Public on May 21 2010

city: Richmond

first: Amanda

last: Waterstrat

state: KY

address: 521 Lancaster Ave

department: Biological Sciences

institute: Eastern Kentucky University

summary:
These mouse strains differ in absolute numbers of hematopoietic stem cells but differ genetically only at the Chr 5 congenic locus.
We used microarray analysis to identify candidate regulators of hematopoietic stem cells based on differential gene expression patterns.

overall_design: Triplicate RNA samples were isolated from 500,00-800,000 Lineage negative bone marrow cells from each strain.  Each of the six samples were analyzed on 6 separate MG 430 2.0 Affymetrix Microarray Chips.

first: Ying

last: Liang

first: Gary

last: Van Zant


title: Comparison of GFP- and Nurr1-infected ES-cell derived neurons

city: Stockholm

first: Nikolaos

last: Volakakis

address: Nobels vag 3

country: Sweden

institute: LICR

summary: ES cell-derived neurons of forebrain identity were isolated by magnetic sorting, cultured for 7 days and transduced with either Nurr1 or eGFP lentivirus. After an additional 12 h in culture, mRNA was isolated and subjected to microarray analysis.

overall_design:
The raw data have been provided in CEL format

The processed data have been provided in CHP format

ES-cell derived forebrain neurons were plated in 10cm dishes and infected with either GFP or Nurr1 lentivirus at a MOI of 10. 18h after infection, RNA was prepped by the Qiagen mini kit and submitted to labeling and hybridization.

Microarray experiments were carried out using GeneChip 430A 2.0 arrays (Affymetrix). Data was normalized and expression values were computed using the gcrma method. Statistical analysis was performed by empirical Bayes inference for linear models using the limma package. The inclusion criteria fold-change was > 1.6 and P < 0.001

first: Banafsheh

last: Kadkhodaei

first: Eliza

last: Joodmardi

first: Karin

last: Wallis

first: Lia

last: Panman

first: Jessica

last: Silvaggi

first: Bruce

last: Spiegelman

last: Perlmann


title: Prednisolone-induced differential gene expression in liver of mice carrying the wild type or a dimerization-defective glucocorticoid receptor

status: Public on May 20 2010

city: Nijmegen

first: Raoul

last: Frijters

address: Geert Grooteplein Zuid 26-28

department: Centre for Molecular and Biomolecular Informatics

institute: Radboud University Nijmegen Medical Centre

summary:
Glucocorticoids control expression of a large number of genes after binding to the glucocorticoid receptor (GR). Transcription may be regulated either by binding of the GR dimer to DNA regulatory elements or by protein-protein interactions of GR monomers with other transcription factors. Although the type of regulation for a number of individual target genes is known, the relative contribution of both mechanisms to the regulation of the entire transcriptional program remains elusive.
To study the importance of GR dimerization in regulation of gene expression, we performed gene expression profiling in liver of prednisolone-treated wild type (WT) and genetically engineered mice that have lost the ability to form GR-dimers (GRdim).

overall_design: Mice carrying a wild type (WT) glucocorticoid receptor or a dimerization-defective glucocorticoid receptor (GRdim) were treated subcutaneous with vehicle or prednisolone (1mg/kg) and sacrificed 150 minutes later. From the livers of these mice total RNA was extracted, processed and hybridized on Affymetrix microarrays. In total 24 mice (6 vehicle-treated WT mice, 6 prednisolone-treated WT mice, 6 vehicle-treated GRdim mice and 6 prednisolone-treated GRdim mice) were included in the study.

first: Wynand

last: Alkema


title: The ubiquitin-conjugating enzyme HR6B is required for maintenance of X chromosome silencing in mouse spermatocytes and spermatids

status: Public on May 08 2010

city: Rotterdam

first: Eskeatnaf

last: Mulugeta Achame

state: Rotterdam

address: Dr Molewaterplein 50

department: Reproduction and Development

institute: Erasmusmc

summary:
Background: The ubiquitin-conjugating enzyme HR6B is required for spermatogenesis in mouse. Loss of HR6B results in aberrant histone modification patterns on the trancriptionally silenced X and Y chromosomes (XY body) and on centromeric chromatin in meiotic prophase. We studied the relationship between these chromatin modifications and their effects on global gene expression patterns, in spermatocytes and spermatids.

Results: HR6B is enriched on the XY body and on centromeric regions in pachytene spermatocytes. Global gene expression analyses revealed that spermatid-specific single- and multicopy X-linked genes are prematurely expressed in Hr6b knockout spermatocytes. Very few other differences in gene expression were observed in these cells, except for upregulation of major satellite repeat transcription. In contrast, in Hr6b knockout spermatids, 7298 genes were differentially expressed; 65% of these genes was downregulated, but we observed a global upregulation of gene transcription from the X chromosome. In wildtype spermatids, approximately 20% of the single-copy X-linked genes reach an average expression level that is similar to the average expression from autosomes.

Conclusions: Spermatids maintain an enrichment of repressive chromatin marks on the X chromosome, originating from meiotic prophase, but this does not interfere with transcription of the single-copy X-linked genes that are reactivated or specifically activated in spermatids. HR6B represses major satellite repeat transcription in spermatocytes, and functions in the maintenance of X chromosome silencing in spermatocytes and spermatids. It is discussed that these functions involve modification of chromatin structure, possibly including H2B ubiquitylation.

overall_design: 8 Affymetrix microarrays were generated: 4 from wildtype and HR6B knockout spermatocytes (2 replicates each), and 4 from wildtype and HR6B knockout spermatids (2 replicates each).

last: Achame

first: Evelyne

last: Wassenaar

first: Jos

last: Hoogerbrugge

first: Esther

last: Sleddens-Linkels

first: Marja

last: Ooms

first: Zu-Wen

last: Sun

first: Wilfred

last: van IJcken

first: J

last: Grootegoed

first: Willy

last: Baarends


title: LAPC cells, treated versus untreated

status: Public on May 31 2010

city: Toronto

first: carl

last: virtanen

state: Ontario

address: 101 College St

department: Princess Margaret Genomics Centre

institute: University Health Network

summary: Comparison of LAPC cells isolated from naive PBS treated and influenza treated mice.

overall_design: LAPC cells from treated and untreated mice. No replicates. Comparison of expression signatures of LAPC cells with other immune system cells.

first: Jae-Kwang

last: Yoo

first: Carole

last: Galligan

first: Carl

last: Virtanen

first: Eleanor

middle: N

last: Fish


title: Genome wide expression analysis of ER alpha and beta with or without  E2 treatment in U2OS cell line.

status: Public on May 12 2010

city: Emeryville

first: Xiaoyue

last: Zhao

address: 5858 Horton St

institute: Bionovo Inc.

summary: Estrogen receptor beta (ERbeta) has potent anti-proliferative and anti-inflammatory properties, suggesting that ER beta-selective agonists might be a new class of therapeutic and chemopreventative agents. To understand how ER beta regulates genes, we identified genes regulated by the unliganded and liganded forms of ER alpha and ER beta in U2OS cells. Microarray data demonstrated that virtually no gene regulation occurred with unliganded ER alpha, whereas many genes were regulated by estradiol (E2). These results demonstrate ER alpha requires a ligand to regulate a single class of genes. In contrast, ER beta regulated three classes of genes. Class I genes were regulated primarily by unliganded ER beta. Class II genes were regulated only with E2, whereas Class III genes were regulated by both unliganded ER beta and E2. There were 453 Class I genes, 258 Class II genes and 83 Class III genes. To explore the mechanism whereby ER beta regulates different classes of genes ChIP-seq was performed to identify ER beta binding sites and adjacent transcription factor motifs in regulated genes. AP1 binding sites were more enriched in Class I genes, whereas ERE, NFKB1 and SP1 sites were more enriched in class II genes. ER beta bound to all three classes of genes demonstrating that ER beta binding is not responsible for differential regulation of genes by unliganded and liganded ER beta. The coactivator, NCOA2 was differentially recruited to several target genes. Our findings indicate that the unliganded and liganded forms of ER beta regulate three classes of genes by interacting with different transcription factors and coactivators.

overall_design: U2OS cell lines are stably transfected with a doxycycline-inducible ER alpha or beta. 18 samples are analyzed with triplicate for each of the 6 conditions. The 6 conditions include ER alpha transfected without doxycycline added, ER alpha transfected with doxycycline added, ER alpha transfected with doxycycline added and E2 treatment, ER beta transfected without doxycycline added, ER beta transfected with doxycycline added, and ER beta transfected with doxycycline added and E2 treatment.


title: Expression data from white adipose tissue of Perilipin A transgenic mice

status: Public on May 13 2010

city: Sapporo

first: Hideaki

last: Miyoshi

state: Hokkaido

address: Kita-15, Nishi-7, Kita-ku

department: Internal Medicine II

institute: Hokkaido University Graduate School of Medicine

summary: Perilipin A (PeriA) exclusively locates on adipocyte lipid droplets and is essential for lipid storage and lipolysis. Adipocyte specific overexpression of PeriA caused resistance to diet-induced obesity and resulted in improved insulin sensitivity. In order to better understand the biological basis for this observed phenotype we performed DNA microarray analysis on white adipose tissue (WAT) from PeriA transgenic (Tg) and control wildtype (WT) mice.

overall_design: We generated transgenic mice that overexpressed human PeriA using the adipocyte specific aP2 promoter/enhancer (Miyoshi, et al. J Lipid Res 2010). All PeriA Tg mice used for the study were female, and heterozygous for the transgene. Littermates that lacked the transgene were used as controls (WT). All mice were housed at room temperature, maintained on a 12 h light/dark cycle, given free access to water, and fed a high-fat diet (HFD) until the age of 30 weeks. On the day prior to tissue harvest at 30 weeks, WAT from perigonadal were rapidly dissected out, extracted total RNA, and hybridized on Affymetrix microarrays.

first: Takashi

last: Sawada


title: Insulin receptor signaling in osteoblasts regulates postnatal bone acquisition and body composition

status: Public on May 07 2010

city: Birmingham

first: Dongquan

last: Chen

state: AL

address: 1717 11th Ave South

institute: Univ of Alabama at Birmingham

summary:
Global energy balance in mammals is controlled by the actions of circulating hormones that coordinate fuel production and utilization in metabolically active tissues.  Bone-derived osteocalcin, in its undercarboxylated, hormonal form, regulates fat deposition and is a potent insulin secretagogue.  Here, we show that insulin receptor (IR) signaling in osteoblasts controls osteoblast development and osteocalcin expression by suppressing the Runx2 inhibitor Twist-2.  Mice lacking IR in osteoblasts have low circulating undercarboxylated osteocalcin and reduced bone acquisition due to decreased bone formation and deficient numbers of osteoblasts.  With age, these mice develop marked peripheral adiposity and hyperglycemia accompanied by severe glucose intolerance and insulin resistance.  The metabolic abnormalities in these mice are improved by infusion of exogenous under-carboxylated osteocalcin.  These results indicate the existence of a bone-pancreas endocrine loop through which insulin signaling in the osteoblast ensures osteoblast differentiation and stimulates osteocalcin production, which in turn regulates insulin sensitivity and pancreatic insulin secretion to control glucose homeostasis.
We used microarrays to detail the global gene expression changes in response to insulin acting through insulin receptor in osteoblasts and identified distinct genes specifically involved in bone remodeling process.

overall_design: 4 groups and 3 time points (0h as a control, 6h, 12h, and 24h)

first: Thomas

last: Clemens


title: Effect of cholera toxin or forskolin on mouse bone marrow-derived dendritic cells

city: La Jolla

first: Nick

last: Webster

address: 9500 Gilman Drive

institute: UCSD

summary: Bone marrow-derived dendritic cells from C57BL/6 mice were treated with 1 ug/ml cholera toxin, 10 uM forskolin or control medium for 2 h.

overall_design: drug treatment groups

first: Sandip

last: Datta

first: Eyal

last: Raz


title: A genomic atlas of mouse hypothalamic development

status: Public on May 04 2010

city: Baltimore

first: Seth

last: Blackshaw

state: MD

address: 733 N. Broadway, Suite 351

department: Neuroscience

institute: The Johns Hopkins University

summary: The hypothalamus is a central regulator of many behaviors essential for survival such as temperature regulation, food intake and circadian rhythms. However, the molecular pathways that mediate hypothalamic development are largely unknown.  To identify genes expressed in developing mouse hypothalamus, microarray analysis at 12 different developmental time points was performed.  Developmental in situ hybridization was conducted for 1,045 genes dynamically expressed by microarray analysis.  In this way, we identified markers that stably labeled each major hypothalamic nucleus over the entire course of neurogenesis, and thus constructed a detailed molecular atlas of the developing hypothalamus.  As proof of concept for the utility of this data, we used these markers to analyze the phenotype of mice where Sonic Hedgehog (Shh) was selectively deleted from hypothalamic neuroepithelium, demonstrating an essential role for Shh in anterior hypothalamic patterning.  Our results serve as a resource for functional investigations of hypothalamic development, connectivity, physiology, and dysfunction.

overall_design: Affymetrix MOE430 microarrays were used to analyze the expression patterns of mouse hypothalamic and preoptic area tissues.  The results were compared across the variables of Strain, Sex and Age.

first: Tomomi

last: Shimogori

first: Daniel

middle: A

last: Lee

first: Ana

last: Miranda-Angulo

first: Yaqin

last: Yang

first: Hong

last: Wang

first: Lizhi

last: Jiang

first: Aya

middle: C

last: Yoshida

first: Hiromi

last: Mashiko

first: Ayane

last: Kataoka

first: Marina

last: Avetisyan

first: Lixin

last: Qi

first: Jiang

last: Qian


title: The influence of Snail expression on mRNA transcription levels in II-18 cells

status: Public on May 03 2010

city: Fukuoka

first: Yuta

last: Shirogane

state: Fukuoka

address: 3-1-1 Maidashi, Higashi-ku

department: Faculty of Medicine

institute: Kyushu University

summary: Snail is a transcriptional repressor, which induces epithelial-mesenchymal transition. However, overall functions of Snail remain to be elucidated. This microarray was performed to investigate the influence of Snail expression on mRNA transcription levels in a lung adenocarcinoma cell line, II-18.

overall_design: II-18 cells were infected by retrovirus vectors expressing Snail or control vectors at a multiplicity of infection of 50-100.  After 5 days postinfection, total RNA was obtained from II-18 cells expressing Snail (3 samples) or control II-18 cells (3 samples).

first: Makoto

last: Takeda

first: Maino

last: Tahara

first: Satoshi

last: Ikegame

first: Takanori

last: Nakamura

first: Yusuke

last: Yanagi