title: ENCODE cell phenotype retrospective study

status: Public on Sep 16 2008

city: Rensselaer

first: Sridar

middle: V

last: Chittur

state: NY

address: One Discovery Drive, CRC 342G

department: Center for Functional Genomics

institute: SUNY-University at Albany

summary:
These samples are part of the ENCODE consortium’s proposed time-limited Pilot Study for confirmation of the utility of RNA abundance measurements as a standard reference phenotyping tool.

Keywords: cell type comparison

For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and  http://www.genome.gov/Pages/Research/ENCODE/ENCODEDataReleasePolicyFinal2008.pdf

overall_design: Each of the 7 ENCODE laboratories submitted at least one of the two Tier1 cell lines. These were processed on Affymetrix Exon 1.0 ST arrays to obtain retrospective phenotyping data for each cell line.


title: Lymphatic endothelium of metastatic tumours has a distinct transcription profile.

status: Public on Sep 22 2008

city: Oxford

first: Dilair

last: Baban

address: Roosevelt Drive

department: Wellcome Trust Centre Human Genetics

country: United Kingdom

institute: University of Oxford

summary:
Invasion of lymphatic vessels is a key step in the metastasis of primary tumour cells to draining lymph nodes. Recent evidence indicates that such metastasis can be facilitated by tumour lymphangiogenesis, although it remains unclear whether this is a consequence of increased lymphatic vessel numbers or alteration in the properties of the vessels themselves. Here we have addressed this important question by comparing the RNA profile of normal dermal lymphatic endothelial cells (LEC) with those isolated from tumours of murine T-241/VEGF-C metastatic fibrosarcoma. Our findings reveal significant changes in the expression of some 792 genes in tumour lymphatics (≥ 2 fold up/downregulation, p ≤ 0.05), involving particularly transcripts associated with junctional adhesion, immunomodulation, extracellular matrix and vessel growth/patterning, several of which we have confirmed by RT-PCR and/or immunohistochemistry. Interestingly, this altered phenotype could not be attributed solely to VEGF-C induced lymphoproliferation, as no similar change in gene expression was reported when human LEC were cultured with VEGF-C in vitro. Moreover, we show that a key protein upregulated in the mouse model, namely the tight junction protein Endothelial Cell Specific Adhesion Molecule (ESAM), is similarly upregulated in tumour lymphatic vessels from 2/2 patients with head and neck squamous cell carcinoma and 4/4 patients with aggressive bladder carcinoma. These findings demonstrate a previously unrecognized influence of tumour environment on lymphatic gene expression and identify candidate tumour specific vessel markers that may prove valuable for either prognosis or therapy.
Keywords: Tumor, Metastasis, Lymphatic endothelium, comparative transcriptional profiling

overall_design: Here we have investigated the invasion of lymphatic vessels as a key step in the metastasis of primary tumour cells to draining lymph nodes by comparing the gene expression profile of normal dermal lymphatic endothelial cells (LEC) with those isolated from tumours of murine  T241/VEGF-C/GFP metastatic fibrosarcoma. Three biological replicates were analyzed from each group.

first: Steven

last: Clasper

first: Yihai

last: Cao

first: Stephan

last: Ewers

first: Stefan

last: Butz

first: Dietmar

last: Vestweber

first: David

middle: G

last: Jackson


title: Expression data from liver of adult mice that differ in expression of Regulator of sex-limitation genes.

status: Public on Sep 10 2008

city: Ann Arbor

first: Christopher

middle: J

last: Krebs

state: MI

address: 1241 E. Catherine St

department: Human Genetics

country: USA

institute: University of Michigan Medical School

summary:
Regulator of sex-limitation (rsl) is a recessive mouse phenotype in which the otherwise male-specific sex-limited protein (Slp) gene is expressed in females. Positional cloning in rsl mice led to the identification of mutations in two neighboring KRAB zinc finger transcriptional repressors, Rsl1 and Rsl2, and BAC transgenic rescue experiements verified their ability to repress male-specific genes in the liver.
Microarrays were used here to expand the list of Rsl-target genes in mouse liver. Enrichment of genes involved in intermediary metabolism among those responsive to Rsl suggest a role for Rsl1/2 in metabolic homeostasis in the mouse.

Keywords: sex comparison and genetic modification

overall_design: Total RNA was extracted from livers of adult male and female wild type, rsl-null and transgenic mice that overexpress Rsl1 or Rsl2, specifically in the liver. Equivalent amounts of RNA were pooled from five or more mice per sex and genotype. Two pools per sex and genotype were hybridized to the Affymetrix Mouse Genome 430 2.0 array.

first: Diane

middle: M

last: Robins


title: Gene-level summary data from Affymetrix Human Exon 1.0 ST array

status: Public on Sep 15 2008

city: Pittsburgh

first: Rakesh

last: Sindhi

state: PA

address: 3705 Fifth Avenue

department: Hillman Center for Pediatric Transplantation

institute: Children’s Hospital of Pittsburgh

summary:
The Affymetrix Human Exon 1.0 ST array was used to measure differential splicing patterns in archived RNA isolated from 26 of 80 children (11 Rejectors and 15 Non-Rejectors). The gene-level probe summaries reported in this series were computed using the Affymetrix Power Tools (APT) software and 'rma-sketch' normalization method.
Keywords: Affymetrix 1.0 ST exon array; gene-level analysis

overall_design: The gene-level normalized intensities (NI) were computed with the MiDAS algorithm and both the splicing index (SI) and Student's t-test p-values (two-sided) were computed on the NI values in R.  To remove low expressed gene-level probes, those with values less than 3.5 (log2 scale) in >50% of the samples in either group were filtered out leaving 17,242 of the original 22,011 probes. Those gene-level probes that were highly differentially expressed between groups were also removed using a fold change threshold of log2. This step accounts for the tendency for the genelevel probe set intensities in each group to be "disproportionately affected by background noise or saturation" (Affymetrix Technical notes).

first: Brandon

middle: W

last: Higgs


title: Early Gene expression changes after axonal injury

status: Public on Sep 01 2008

city: Chicago

first: Thomas

last: Lukas

state: IL

address: 303 E. Chicago Ave

department: MPBC

institute: Northwestern University

summary:
We used optic nerve injury as a model to study early signaling events in the neuronal soma following axonal injury. Optic nerve injury results in the selective death of retinal ganglion cells (RGCs). The time course of cell death takes place over a period of days with the earliest detection of RGC death at about 48 hr post injury. We hypothesized that in the period immediately following axonal injury, there are changes in the soma that signal surrounding glia and neurons and that start programmed cell death.  In the current study, we investigated early changes in cellular signaling and gene expression that occur within the first 6 hrs post optic nerve injury.  We detected differences in phosphoproteins and gene expression within this time period that we used to interpret temporal events.  Our studies revealed that the entire retina has been signaled by the RGC soma within 30 min after optic nerve injury and that pathways that modulate cell death are likely to be active in RGCs within 6 hrs following axonal injury

Keywords: Stress Response

overall_design: In the treated animals, axons of the optic nerve were crushed with fine forceps for 10 sec, 1 mm posterior to the globe, under direct visualization, within an intact meningeal sheath. Controls were contralateral eyes from the same animals in each group that had not been injured. After 6 hr eyes were enucleated and processed for tissue sectionin


title: The TLR2/NOD2/RICK signaling axis regulates stimulus-specific IL-10 production

city: Memphis

last: Finkelstein

state: TN

address: 332 N. Lauderdale St.

department: Computational Biology

institute: St Jude Children's Research Hospital

summary:
Recognition and response to gram-positive bacteria by macrophages and dendritic cells is mediated in part through TLR2. We found that that Streptococcus pneumoniae cell wall fragments, containing primarily peptidoglycan and teichoic acids, induced prodigious secretion of IL-10 from macrophages and dendritic cells and was dependent on TLR2 and NOD2, a cytoplasmic CARD-NACHT-LRR protein encoded by Card15. IL-10 secretion in response to cell walls was also dependent on RICK/RIP2, a kinase associated with NOD2, and MYD88 but independent of the ERK/p38 pathway. The reduction of IL-10 secretion by cell wall-activated NOD2-deficient myeloid–derived cells translated into downstream effects on IL-10 target gene expression and elevations in subsets of pro-inflammatory cytokine expression normally restrained by autocrine/paracrine effects of IL-10. Since NOD2 is linked to aberrant immune responses in Crohn’s Disease patients bearing mutations in CARD15, the temporal and quantitative effects of the TLR2/NOD/RICK pathway on IL-10 secretion may affect homeostatic control of immune responses to gram-positive bacteria.
Keywords: immune response simulated pathogen response

overall_design: KO mice were treated with a cel wall extract and evaluated for immune response 1 hr and 4 hrs after treatment

first: Lilian

last: Moreira

first: Karim

middle: C

last: El Kasmi

first: Amber

last: Smith

first: Sophie

last: Fillon

first: Elaine

last: Tuomanen

first: Genhong

last: Cheng

first: Gabriel

last: Nunez

first: Peter

last: Murray


title: A profile of murine thymocytes from mice hypomorphic for Atg16l1

city: Boston

first: Ramnik

last: Xavier

state: MA

address: 185 Cambridge Street, 7th Floor

institute: Massachusetts General Hospital

summary: The aim of this study is to survey global gene expression of total thymocytes from wild-type mice and Atg16l1 mutant (hypomorph) mice.

overall_design:
Total RNA was extracted from total thymocytes from the following samples and analyzed:

Atg16l1 hypomorph: 2 mice (7 weeks), 1 male and 1 female
Control: 2 mice (7 weeks), 1 male and 1 female

Global gene expression profiling was performed using Affymetrix technology.  The animals used were independent of each other.


title: Expression data from WT and E2A-KO bone marrow stem and progenitor cell subfractions.

status: Public on Aug 31 2008

city: Lund

first: Robert

last: Månsson

address: Klinikgatan 26, BMC B12

department: Hemapotoietic stem cell biology

country: Sweden

institute: Lund University

summary: Expression profiling of WT and E2A-KO LSK FLT3- and LMPP protenitor cells.

overall_design: LSK FLT3- and LMPP stem/progenitor cells from WT and E2A-KO mice were FACS sorted. Subsequently RNA was extracted, labelled and hybridized to Affymetrix microarrays. Goal of experiment was to investigate expression changes between WT and KO LMPP cells.

first: Sheila

last: Dias

first: Sandeep

last: Gurbuxani

first: Sigvardsson

last: Mikael

first: Barbara

last: Kee


title: The Creb1 coactivator Crtc1 is required for energy balance and fertility

status: Public on Sep 04 2008

city: San Diego

first: Marc

last: Montminy

state: CA

address: 10010 N. Torrey Pines Rd

department: PBL

institute: Salk Institute

summary: The adipocyte-derived hormone leptin maintains energy balance by acting on hypothalamic leptin receptors (Leprs) that trigger the signal transducer and activator of transcription 3 (Stat3). Although disruption of Lepr-Stat3 signaling promotes obesity in mice, other features of Lepr function, such as fertility, seem normal, pointing to the involvement of additional regulators. Here we show that the cyclic AMP responsive element–binding protein-1 (Creb1)-regulated transcription coactivator-1 (Crtc1) is required for energy balance and reproduction—Crtc1-/- mice are hyperphagic, obese and infertile. Hypothalamic Crtc1 was phosphorylated and inactive in leptin-deficient ob/ob mice; leptin administration increased amounts of dephosphorylated nuclear Crtc1. Dephosphorylated Crtc1 stimulated expression of the Cartpt and Kiss1 genes, which encode hypothalamic neuropeptides that mediate leptin’s effects on satiety and fertility. Crtc1 overexpression in hypothalamic cells increased Cartpt and Kiss1 gene expression, whereas Crtc1 depletion decreased it. Indeed, leptin enhanced Crtc1 activity over the Cartpt and Kiss1 promoters in cells overexpressing Lepr and these effects were disrupted by expression of a dominant-negative Creb1 polypeptide. As leptin administration increased recruitment of hypothalamic Crtc1 to Cartpt and Kiss1 promoters, our results indicate that the Creb1-Crtc1 pathway mediates the central effects of hormones and nutrients on energy balance and fertility.

overall_design: Mice were fasted overnight for 18h and refed for 6h.  Hypothalami were obtained from 3 wild-type and 3 Crtc1 knockout mice.  Total RNA was isolated from each sample and equal amounts from each sample were pooled for the microarray.

first: Judith

middle: Y

last: Altarejos

first: Naomi

last: Goebel

first: Michael

middle: D

last: Conkright

first: Hiroshi

last: Inoue

first: Jianxin

last: Xie

first: Carlos

last: Arias

first: Paul

middle: E

last: Sawchenko


title: Transcription factor Arx null brains (fulp-affy-mouse-364520)

status: Public on Aug 30 2008

city: Phoenix

first: Winnie

last: Liang

state: AZ

address: 445 N. Fifth Street

institute: Translational Genomics

summary:
Arx is a paired-box homeodomain transcription factor and the vertebrate ortholog to the Drosophila aristaless (al) gene.  Mutations in Arx are associated with a variety of human diseases, including X-linked infantile spasm syndrome (OMIM: 308350), X-linked myoclonic epilepsy with mental retardation and spasticity (OMIM: 300432), X-linked lissencephaly with ambiguous genitalia (OMIM: 300215), X-linked mental retardation 54 (OMIM: 300419), and agenesis of the corpus callosum with abnormal genitalia (OMIM: 300004).  Arx-deficient mice exhibit a complex, pleiotrophic phenotype, including decreased proliferation of neuroepithelial cells of the cortex, dysgenesis of the thalamus and olfactory bulbs, and abnormal nonradial migration of GABAergic interneurons.  It has been suggested that deficits in interneuron specification, migration, or function lead to loss of inhibitory neurotransmission, which then fails to control excitatory activity and leads to epilepsy or spasticities.  Given that Arx mutations are associated with developmental disorders in which epilepsy and spasticity predominate and that Arx-deficient mice exhibit deficits in interneuron migration, understanding the function of Arx in interneuron migration will prove crucial to understanding the pathology underlying interneuronopathies.  Yet, downstream transcriptional targets of Arx, to date, remain unidentified.
The aim of this project is to identify bona fide transcriptional targets for the Arx, a transcription factor required for normal migration of interneurons from the ganglionic eminences to the cortex, and to investigate the functions of these genes in the Arx-dependent pathway regulating nonradial neuronal migration.
We hypothesize that the genes regulated by the Arx transcription factor will play a critical role in the nonradial migration of interneurons and that the results of this study will provide novel insights into the molecular mechanisms of nonradial neuronal migration, in particular, and possibly the molecular and biochemical pathogenesis underlying epilepsy, mental retardation, infantile spasm syndromes, and other so-called interneuronopathies;
We have recently generated a transgenic mouse with a floxed Arx allele (Arxflox).  We have generated conditional knockouts in which Arx is removed specifically from the brain by mating Arxflox mice with transgenic mice expressing Cre behind the neural tube-specific transcriptional regulatory elements of the POU domain, class 3, transcription factor 4 promoter.  Preliminary analyses of these mice suggest that conditional knockout mice recapitulate the nonradial migration defects associated with conventional knockout mice.  We will compare the gene expression profiles of ganglion eminences (GEs; the anatomical source for nonradially migrating interneurons) from male Arxflox mice that express Pou3f-Cre to those from male mice without Arxflox allele.  Animals will be prepared and sacrificed following our institutional protocol.  Tissue will be rapidly dissected from E14.5 (the temporal peak of interneuron migration) GEs (MGE and LGE from both left and right hemispheres).  Preliminary experiments suggest that the amounts of RNA that can be isolated from a pair of GEs is in the range of 2000-3500 ng, which should be sufficient for microarray analysis following linear amplification of RNA.  The GEs from each animal will be combined, snap frozen in liquid nitrogen, and stored at -80 C until RNA is extracted.  Total RNA will be extracted using Trizol followed by RNA purification with the RNeasy cleanup kit.  We will be providing total RNA samples from four wildtype and four transgenic animals (true biological replicates) from three separate litters to mitigate any expression differences resulting from mouse to mouse or litter to litter variation.

first: Carl

middle: T

last: Fulp


title: Diabetes and the retina (eldre-affy-mouse-319092)

summary:
Diabetes is a disease now affecting more than 20 million people in the United States alone.  When left untreated it has numerous debilitating effects including diabetic retinopathy, which is characterized by the death of retinal neurons as well as a breakdown of the retinal vascularization.  This leads to nearly 24,000 cases of blindness each year among diabetic patients.  Studies have shown the importance of both nitric oxide and the gene VEGF in retinopathy, however little is known about the condition's progression.  This study would determine which genes are affected early in diabetes and more generally, give insite into how neural degeneration occurs in the retina.
We aim to show the gene-level changes in the diabetic mouse retina five weeks after induction of diabetes.  Our laboratory's primary focus is on NO production through nNOS, iNOS and endothelial (eNOS).  We hope to be able to correlate some of the transcript level changes with genes known to be involved in the NO signalling pathways.
Previous data by our lab and others have shown that neuronal nitric oxide synthase (nNOS) and inducible NOS (iNOS) are upregulated under diabetic conditions in the retina.  Additional work in our lab has shown that the lack of  nitric oxide (NO) produced by nNOS may affect neurotransmitter production, particularly with GABA.  We have also shown that mice with induced diabetes show neurochemical changes in the retina after only one to three weeks.  Thus, we expect to see gene level changes associated with the retina before psysological changes in newly diabetic mice.
Adult CD1 mice of random sexes are injected with the drug streptozotocin on three successive days while fasting 8 hours before the injection.  This drug selectivley destroys  the beta-islet cells of the pancrease.  Their blood sugar levels are then tested after a resting period.  Mice with glucose levels above 250mg/dL are considered diabetic from the date of the last injection.
Mice are then sacrificed after the waiting period by breif isoflourine inhalation followed by decapitation.  Retinas are immediately removed in cold HBSS and RNA is extracted using Trizol extraction.  To get adequate amounts of RNA, we will pool four retinas (2 animals) together.

Keywords: dose response

first: William

last: Eldred


title: Expression data from transgenic Aire expressing pancreatic islets

status: Public on Aug 20 2008

first: CBDM

last: Lab

address: 77 Avenue Louis Pasteur

department: Microbiology and Immunobiology

institute: Harvard Medical School

summary:
The aim of this study was to determine the effect of transgenic Aire expression on the transcriptional profile of a tissue that normally does not express Aire: pancreatic islets. The transcriptional profile of transgenic RIP-Aire27 islets was compared to non-transgenic littermate islets as well as to archival NOD thymic medullary epithelial cells (MEC) data. All data were from non-obese diabetic (NOD) mice

Keywords: RIP-Aire transgenic vs non-transgenic comparison

overall_design: 3-wk-old individual male RIP-Aire27 or non-transgenic littermates islets were isolated by gradient purification followed by hanpicking under a microscope for subsequent RNA purification, labeling and hybridization to Affymetrix arrays.

first: Mireia

last: Guerau-de-Arellano

first: Diane

last: Mathis

first: Christophe

last: Benoist


title: Microarray of Trex1 WT and Trex1 KO hearts on RAG2KO background

status: Public on Aug 22 2008

city: New Haven

first: Daniel

middle: B

last: Stetson

state: CT

address: 300 Cedar Street

department: Immunobiology

institute: Yale University

summary: Heart ventricle tissue was harvested from Trex1/RAG2 DKO mice and from Trex1WT/RAG2KO littermate controls.  RNA was extracted, and an Affymetrix Mouse 430 2.0 gene chip analysis was performed.

overall_design: Three pairs of littermates are included: 779/780, 4184/4185, and 4192/4193.

first: Ruslan

last: Medzhitov


title: Gene expression profiles of age-associated clonal expansions of CD8 memory T cells

status: Public on Aug 15 2008

city: Denver

first: Eric

last: Clambey

state: CO

address: 1400 Jackson Street, Goodman Bldg, Rm K519

department: Immunology

institute: National Jewish Research & Medical Center

summary:
Many aged individuals develop monoclonal expansions of CD8 T cells.  These expansions are derived from a CD8 memory T cell that outcompetes neighboring CD8 T cells.  The molecular alterations within clonal expansions that confer this competitive advantage relative to other CD8 T cells remains unknown.  These microarray experiments were designed to identify genes differentially expressed in age-associated expansions of CD8 memory T cells relative to polyclonal CD8 memory T cells found in the same aged mice.
Subsequent analysis of these data identified two major types of clonal expansions, distinguished by expression level of integrin a4 mRNA and protein.  Based on this classification, Expansion_rep1 belongs to the integrin a4 high subtype of clonal expansions.  In contrast, reps 2, 4, and 5 belong to the integrin a4 low subtype of clonal expansions.  Given the divergent biological properties of these two subtypes of clonal expansions, we have focused genes differentially expressed between Expansion_rep 2, 4, and 5 and their paired PolyclonalAged samples.

Keywords: Cell type comparison of gene expression

overall_design: A total of 8 samples were analyzed for gene expression using the Affymetrix mouse genome 430 2.0 microarray platform.  The experimental samples of interest were age-associated clonal expansions of CD8 memory T cells.  We purified four clonal expansions from four independent, aged mice (indicated as "Expansion" rep1 2, 3, 4).  For each clonal expansion of CD8 memory T cells that was purified, there was a paired control in which polyclonal CD8 memory T cells were harvested from the same aged mouse (denoted as "PolyclonalAged" rep1, 2, 3, 4).  These paired samples allow one to consider gene expression changes from mice which have undergone the same age-associated changes in biology.  The predominant comparison this study focused on was changes in gene expression between age-associated clonal expansions of CD8 memory T cells and their paired, polyclonal CD8 memory T cells.  A total of 4 of these pairs were collected.

first: Philippa

last: Marrack


title: Expression data from Mouse Lymphoma

status: Public on Aug 09 2008

city: Singapore

first: Seiichi

last: Mori

state: Singapore

address: Centre for Life Sciences #02-07, 28 Medical Drive

department: Cancer Science Institute Singapore

country: Singapore

institute: National University of Singapore

summary:
We have made use of the Eμ-myc transgenic mouse, a model for the study of B-cell lymphoma development that is initiated through a defined genetic alteration, to explore the contributions of additional somatic alterations that contribute to the heterogeneity of the resulting tumors.  As one example of such heterogeneity, we have focused on the observation that lymphomas develop in Eμ-myc mice with a variable time of onset.  Twenty-five early-onset, 25 late-onset lymphomas and 10 normal samples were each assayed on an Affymetrix Mouse Genome 430 2.0 array.
Keywords: Myc induced lymphomas with various time-of-onset

overall_design: To focus on events that might distinguish early and late onset tumors, we performed genome-wide expression analyses of early- and late-onset lymphomas from Eµ-myc transgenic mice using expression microarray techniques.  Total RNA was prepared from 25 early-onset (32-76 days, 62.6+/-11.0 days, median 65 days), 25 late-onset tumors (253-649 days, 391.5+/-101.8 days, median 398 days) and 10 normal tissues (lymph nodes or spleen, 38-438 days, 181.0+/-175.2 days, median 62.5 days) and subjected to Affymetrix GeneChip analyses.

first: Rachel

last: Rempel

first: Joseph

middle: R

last: Nevins


title: Expression data from single cells from mouse primordial germ cell lineage (E6.25-E8.25, wild type and Blimp1KO)

city: Nara

first: Kazuki

last: Kurimoto

address: 840 Shijo-Cho, Kashihara

department: School of medicine

country: Japan

institute: Nara Medical University

summary:
Specification of germ cell fate is fundamental in development.  With a highly representative single-cell microarray and rigorous quantitative-PCR analysis, we defined the genome-wide transcription dynamics that create primordial germ cells (PGCs) from the epiblast, a process that exclusively segregates them from their somatic neighbors.  We also analyzed the effect of the loss of Blimp1, a key transcriptional regulator, on these dynamics.  Our analysis revealed that PGC specification involves complex, yet highly ordered regulation of a large number of genes, proceeding under the strong influence of mesoderm induction with active repression of specific programs such as epithelial-mesenchymal transition, Hox gene activation, cell-cycle progression and DNA methyltransferase machinery.  Remarkably, Blimp1 is essential for repressing nearly all the genes normally down-regulated in PGCs relative to their somatic neighbors, whereas it is dispensable for the activation of approximately half of the genes up-regulated in PGCs.
Keywords: single cell analysis, time course, Blimp1 knocked out

overall_design: Embryo isolation, dissection, and single cell cDNA amplification were performed as described (Kurimot et al., 2006, Nucleic Acids Res 34: e42; Kurimoto et al., 2007, Nature protocols, 2007, 2:739-52).  Randomly picked cells were screened with gene-specific primers for Blimp1 and fragilis to select Blimp1-positive embryonic cells (which marks lineage-restricted PGC precursors or PGCs).  For Blimp1 KO embryos, non-functional transcript from the Blimp1null allele was detected with the same primer set.

first: Yukihiro

last: Yabuta

first: Yasuhide

last: Ohinata

first: Mayo

last: Shigeta

first: Kaori

last: Yamanaka

first: Mitinori

last: Saitou


title: Deletional Tolerance Mediated by Extrathymic Aire-Expressing Cells

status: Public on Aug 08 2008

city: Stanford

first: David

last: Wong

address: 269 Campus Drive

institute: Stanford University

summary:
The prevention of autoimmunity requires elimination of self-reactive T cells during their development and maturation. Expression of diverse self-antigens by stromal cells in the thymus is essential to this process, and depends, in part, on the activity of the Autoimmune Regulator (Aire) gene. Here we report the identification of extrathymic Aire-expressing cells (eTACs) resident within the secondary lymphoid organs. These stromally-derived eTACs express a diverse array of unique self-antigens and are capable of interacting with and deleting naive autoreactive T cells. Using two-photon microscopy we observe stable, antigen-specific interactions between eTACs and autoreactive T cells. We propose that such a secondary network of self-antigen-expressing stromal cells may help reinforce immune tolerance by preventing the maturation of autoreactive T cells that escape thymic negative selection.
A genetic modification design type is where an organism(s) has had genetic material removed, rearranged, mutagenized or added, such as knock out.
Keywords: genetic_modification_design

overall_design: 8 samples

first: James

last: Gardner

first: Howard

last: Chang

first: Mark

last: Anderson


title: Transcriptomic analysis of PPARalpha-dependent alterations during cardiac hypertrophy

status: Public on Aug 06 2008

city: Maastricht

first: Marc

last: van Bilsen

address: PO BOX 616

country: Netherlands

institute: Universiteit Maastricht

summary:
Findings suggest that PPARalpha plays a decisive role in the development of hypertrophy, affecting the functional outcome of the heart. Unfortunately, information on the nature of PPARalpha-dependent processes in cardiac hypertrophy is fragmentary and incomplete.
The primary aim of this study was to identify the processes and signaling pathways regulated by PPARalpha in hearts challenged by a chronic pressure overload by means of whole genome transcriptomic analysis. Second, we wanted to gain insight how PPARalpha modulates the identified processes, e.g. by trans-activation or by trans-repression.

Keywords: 28 days of TAC

overall_design: Wild-type and PPARalpha-/- mice were sham-operated or subjected to TAC for 28 days. Left ventricular gene expression profile was determined using Affymetrix 430 2.0 arrays containing over 45,000 probe sets (covering over 34,000 mouse genes) to detect PPARalpha-related differences in cardiac gene expression under basal conditions and after imposition of a sustained hemodynamic stress.

first: Pascal

last: Smeets

first: Heleen

last: Vogels-van den Bosch

first: Peter

last: Willemsen

first: Alphons

last: Stassen

first: Torik

last: Ayoubi

first: Ger

last: van der Vusse


title: Genetic variants in Major Histocompatibility Complex-linked genes Associate with Pediatric Liver Transplant Rejection

first: Rakesh

last: Sindhi

summary:
Limited access to large samples and independent replication cohorts precludes genome-wide association (GWA) studies of rare but complex traits. To localize candidate genes in an on-going study utilizing family-based GWA, a novel exploratory analysis was first tested on 1,774 major histocompatibility complex single nucleotide polymorphisms (SNPs) in 240 DNA samples from 80 children with primary liver transplantation (LTx), and their biological parents. Genotyping was performed using the Illumina HumHap550k SNP BeadArray; the genotype calls for the 1813 SNPs in the MHC region are provided in the genotype_data.zip supplementary file linked to this series (see README file in the zip archive for more information).

The Affymetrix Human Exon 1.0 ST array was used to measure differential splicing patterns in archived RNA isolated from 26 of 80 children for genes found near associated SNPs.

This SuperSeries is composed of the SubSeries listed below.

overall_design: DNA from LTx rejector children were compared against LTx non-rejector children to identify associated SNPs in a two-level analysis approach.  Those SNPs that were found to be most associated were then identified for splice variant influence using the Affymetrix Exon 1.0 ST Array.

first: Brandon

last: Higgs


title: Expression data from mouse lung

status: Public on Aug 01 2008

city: Hanover

first: Thomas

middle: H

last: Hampton

state: NH

address: North College Street

department: Microbiology Immunology

institute: Geisel School of Medicine at Dartmouth

summary:
Exposure to high levels of arsenic in drinking water is associated with several types of cancers including lung, bladder and skin, as well as vascular disease and diabetes. Drinking water standards are based primarily on epidemiology and extrapolation from higher dose experiments, rather than measurements of phenotypic changes associated with chronic exposure to levels of arsenic similar to the current standard of 10ppb, and little is known about the difference between arsenic in food as opposed to arsenic in water. Measurement of phenotypic changes at low doses may be confounded by the effect of laboratory diet, in part because of trace amounts of arsenic in standard laboratory chows, but also because of broad metabolic changes in response to the chow itself. Finally, this series contrasts 8hr, 1mg/kg injected arsenic with the various chronic exposures, and also contrasts the acute effects of arsenic, dexamethasone or their combination. Male C57BL/6 mice were fed on two commercially available laboratory diets (LRD-5001 and AIN-76A) were chronically exposed, through drinking water or food, to environmentally relevant concentrations of sodium arsenite, or acutely exposed to dexamethasone.
Keywords: dose response

overall_design: Male C57BL/6 mice, fed on two commercially available laboratory diets (LRD-5001 and AIN-76A), were chronically exposed through drinking water or food, to environmentally relevant concentrations of sodium arsenite. Another group animals, fed on the AIN 76A diet, was  IP injected with dexamethasone (1 mg/kg), sodium arsenite (1mg/kg), both dexamethosone and arsenite, or saline alone.

first: Michael

middle: A

last: Ihnat

first: Joshua

last: Hamilton


title: Genome-wide coactivation screen identifies BAF60a as a regulator of lipid metabolism through PGC-1alpha

first: Siming

last: Li

address: 210 Washtenaw Ave

institute: University of Michigan

summary:
Impaired mitochondrial function has been implicated in the pathogenesis of type 2 diabetes, heart failure and neurodegeneration as well as during aging.  Studies with the PGC-1 transcriptional coactivators have demonstrated that these factors are key components of the regulatory network that controls mitochondrial function in mammalian cells.  Here we describe a genome-wide coactivation assay to globally identify the transcriptional partners for PGC-1α. These analyses revealed a molecular signature of the PGC-1α transcriptional network, and identified BAF60a (Smarcd1), a subunit of the SWI/SNF chromatin-remodeling complex, as a critical regulator of lipid homeostasis.  Adenoviral-mediated expression of BAF60a stimulates fatty acid β-oxidation in cultured hepatocytes and reduces hepatic triglyceride levels in diet-induced obese mice.  BAF60a physically interacts with PGC-1α and is recruited to PPARα target genes in the fasted liver.  Liver-specific RNAi knockdown of BAF60a impairs fatty acid oxidation and results in severe hepatic steatosis following starvation.  These results define a role for the SWI/SNF complexes in the regulation of hepatic lipid metabolism, and reveal a potential target for therapeutic intervention.
Keywords: Adenoviral transduction.

overall_design: Primary hepatocytes were isolated from C57/Bl6J mice (10 weeks old) and transduced with recombinant adenoviruses expressing GFP or BAF60a for 40 hrs.  Total RNA was isolated for array analysis.

first: Chang

last: Liu

first: Tong

last: Hao

first: Ting

last: Han

last: Hill

last: Vidal

first: Jiandie

last: Lin


title: Gene expression profiles of E15.5 developing podocytes in the developing kidney isolated from MafB-GFP transgenic mice using FACS on 430 2.0 Array chip. (GUDMAP Series ID: 22)

status: Public on Aug 04 2008

city: Edinburgh

first: GUDMAP

last: Developers

address: Crewe Road

institute: IGMM MRC Human Genetics Unit

summary:
The long term objective is to create an encyclopedia of the expression levels of all genes in multiple components of the developing kidney. The central thesis is straightforward. The combination of fluorescent activated cell sorting (FACS) plus microarray analysis offers a powerful, efficient and effective method for the creation of a global gene expression atlas of the developing kidney. Microarrays with essentially complete genome coverage can be used to quantitate expression levels of every gene in FACS isolated components of the developing kidney. The ensuing rapid read-out provides an expression atlas that is more sensitive, more economical and more complete than would be possible by in situ hybridizations alone.

Keywords: Comparison of kidney components.

overall_design: At different developmental time points we isolate discrete elements of the kidney by using fluorescent activated cell sorting (FACS) and then define their gene expression profiles with microarrays.

first: Steve

last: Potter

first: Eric

last: Brunskill


title: TfRc Dependent Gene Expression in Embryonic Renal Cells

city: New York

first: Jonathan

last: Barasch

address: 630 West 168th St

institute: Columbia University

summary:
We investigated the ability of transferrin receptor1 (TfRc) knockout cells to populate different domains of the developing kidney by using a chimeric approach. The TfRc cells developed into all segments of the developing nephron, but there was a relative exclusion from the ureteric bud and a positive bias towards the stromal compartment. Here we conducted a microarray analysis of differential gene expression between TfRc deficient and wild type (wt) cells in chimeric embryonic kidneys derived from embryos created by blastocyst injection of wt blastocysts with TfRc-/- green fluorescent protein-expressing (GFP+) embryonic stem cells.
Keywords: cell type comparison, genetic modification, iron signaling

overall_design: Following blastocyst injection of 3-5 TfRc-/- GFP+ embryonic stem cells in wt blstocysts, we harvested the chimeric kidney at day E15.5 and separated the TfRc-/- GFP+ cell population from wt GFP- cell population by using fluorescence activated cell sorting. Biotinlyated cRNA was prepared from the isolated cells and hybridized to Mouse Genome 430 2.0 Arrays (Affymetrix) according to standard protocols.

first: JauYi

first: Neal

last: Paragas

first: Kai

last: Schmidt-Ott

first: Xia

last: Chen


title: Global gene expression analysis between Gfi1+/+ and Gfi1-/- splenic B cells

status: Public on Aug 26 2008

city: Braunschweig

first: Robert

last: Geffers

address: Inhoffenstr. 7

department: Dep. Molecular Bacteriology

country: Germany

institute: HCI - Helmholtz Centre for Infection Research

summary: The zinc finger transcription factor growth-factor-independent-1 (Gfi1) has been involved in various cellular differentiation processes. Gfi1 acts as a transcriptional repressor and splicing control factor upon binding to cognate binding sites in regulatory elements of its target genes. Here, we report that Gfi1-deficient mice develop autoimmunity. Gfi1-deficient peripheral B-cells show a hyperproliferative phenotype, leading to expansion of plasma cells, increased levels of nuclear autoantibodies, and immunoglobulin deposition in brain and kidneys. Dysregulation of multiple transcription factors and cell-cycle control elements may contribute to B-cell dependent autoimmunity. Gfi1 thus emerges as a novel master-regulator restricting autoimmunity.

overall_design: Splenic B220+CD19+ CD138- B cells of 4 week old Gfi1+/+ and Gfi1-/- mice were isolated and RNA was extracted from one sample per group and microarray analysis was performed.

first: R

first: C

last: Rathinam

last: Klein


title: Wild-type cultured neutrophils versus miR-223 null cultured neutrophils

status: Public on Jul 31 2008

city: Cambridge

first: Whitehead

last: Institute

address: 9 Cambridge Center

department: Genome Technology Core

institute: Whitehead Institute

summary: This array analysis is to study the regulation of target messages’ expression in in vitro cultured murine neutrophils versus miR-223 null neutrophils.  Culture media was SILAC-IMDM for MS analysis.

first: Daehyun

last: Baek

first: Judit

last: Villén

first: Chanseok

last: Shin

first: Fernando

last: Camargo

first: Steven

last: Gygi

first: David

last: Bartel


title: Wild-type neutrophils and miR-223 null neutrophils

summary: This array analysis is to study the regulation of target messages’ expression in murine neutrophils versus miR-223 null neutrophils.

overall_design: Three arrays for wild-type neutrophils and miR-223 null neutrophils


title: Analysis of Aire effects on individual mice of different genetic backgrounds

status: Public on Jul 22 2008

first: CBDM

last: Lab

summary:
We compared gene expression profiles of aire-deficient and wild-type littermate thymic medullary epithelial cells. This was done in order to determine whether Aire's effects differed among strains, and also among individuals of the same strain.
Keywords: genetic modification

overall_design: Individual thymi were digested with collagenase, dispase and DNAse, and meduallary epithelial cells with the phenotype CD45-G8.8+Ly51intMHCclasssIIhi were isolated by FACS.

first: Emily

middle: S

last: Venanzi

first: Christophe

last: Benoist

first: Diane

last: Mathis


title: BMI-1 promotes Ewing sarcoma tumorigenicity independent of CDKN2a-repression

status: Public on Jul 18 2008

city: Ann Arbor

first: Elizabeth

last: Lawlor

address: 1600 Huron Parkway, NCRC Bldg 520

summary:
Over-expression of the polycomb group gene BMI-1 is implicated in the pathogenesis of many human cancers.  In this study, we investigate the role of BMI-1 as a functional oncogene in the Ewing’s Sarcoma Family of Tumors (ESFT), a highly aggressive group of bone and soft tissue tumors. Our data show that BMI-1 is highly expressed by the majority of primary ESFT and ESFT cell lines. However, in contrast to previous reports in other human cancer cell types, knockdown of BMI-1 in ESFT cell lines has no effect on cell survival.  Instead, gain and loss of function studies in vitro and in vivo demonstrate that BMI-1 promotes the anchorage independent growth and tumorigenicity of ESFT. Importantly, we also find that modulation of BMI-1 alters the tumorigenicity of both p16-wild type and p16-null cell lines and that BMI-1-mediated effects on growth promotion are independent of CDKN2a repression. Gene expression profiling of ESFT cells following BMI-1 modulation reveals novel downstream effectors of BMI-1 function including key developmental, cell:cell and cell:matrix adhesion pathways. These data support a central role for BMI-1 in the pathogenesis of ESFT and reveal that p16-independent functions of BMI-1 are largely responsible for its oncogenic function in this tumor family.

Keywords: Modification of BMI-1 expression in ESFT cell lines

overall_design: 6 samples, 2 conditions, 3 replicates per condition


title: Microarray analysis identifies distinct subpopulations of arthritic mice deficient for interleukin 1 receptor antagonist

city: Memphis

first: Jian

last: Yan

address: 956 Court Ave

department: Orthopedics Surgery

institute: University of Tennessee Health Science Center

summary:
Rheumatoid arthritis (RA) is a heterogeneous disease with clinical and biological polymorphisms. However, little is known about baseline molecular variations among individual RA patients. The purpose of this study was to address this issue using F2 intercross mice generated from arthritis-prone BALB/c and arthritis-resistant DBA/1 mice deficient for interleukin 1 receptor antagonist (Il1rn). Two distinct subpopulations of arthritic mice were identified in the 38 mice studied. One subgroup of diseased mice was characterized by myeloid cell dominant inflammation, whereas the other was mainly associated with increased anti-apoptotic activities of inflammatory cells.
Keywords: disease state analysis

overall_design: Thirteen F2 mice, 18 with arthritis and 18 without, were included in this study. Total RNAs were extracted from individual spleens for Affymmetrix mouse genome array analysis. Normalized data were hierarchically clustered to identify subpopulations of arthritic mice.

first: Yan

last: Jiao

first: John

last: Stuart

first: Weikuan

last: Gu


title: Ctr9 knockdown in mouse ES cells

city: Dresden

first: Li

last: Ding

address: Pfotenhauerstr. 108

institute: MPI-CBG

summary: To monitor global transcript changes after Paf1C depletion we transfected ESCs with esiRNA targeting Ctr9 and control esiRNA (Luc).

overall_design: 4 replicates of esiRNA tranfection controls (luciferase esiRNA) and 4 replicates of Ctr9 esiRNA tranfection samples


title: Expression profile from doxorubicine treated B16 melanoma cells

city: Charlestown

first: Chun

last: Kim

address: Bldg 149, 13th Street

department: Cutaneous Biology Research Center

institute: Massachusetts General Hospital

summary:
Tumor resistance to anti-cancer drugs is a major huddle in chemotherapy. To identify cancer genes that contribute to chemoresistance, B16 mouse melanoma cells were used as a model.
We used microarrays to decipher the specific gene regulation in doxorubicine treated B16 mouse melanoma cells.

Keywords: Time course

overall_design: B16 cells were treated with 1 microgram/ml of doxorubicine and the RNAs were purified at 0, 2, and 4h after the treatment.

first: Jin

last: Park


title: 4 days cultured progenitors and 8 days cultured mature neutrophils from WT vs miR-223 null neutrophils

status: Public on Jul 30 2008

first: Whitehead

last: Institute

summary: This array analysis is to study developmental time course of the regulation of target messages’ expression during culture of murine neutrophils versus miR-223 null neutrophils.  Culture media was SILAC-IMDM for MS analysis.

overall_design: Two arrays of each for 4 days cultured progenitors and 8 days cultured mature neutrophils from wild-type cultured neutrophils versus miR-223 null cultured neutrophils

first: Daehyun

last: Baek

first: Judit

last: Villén


title: Shared gene expression profiles in developmental heart valve remodeling and osteoblast progenitor cells

status: Public on Jul 11 2008

city: Cinicnnati

first: Katherine

last: Yutzey

state: OH

address: 240 Albert Sabin Way

department: Divison of Molecular Cardiovascular Biology

institute: Cinicnnati Children's Hospital Medical Center

summary:
E12.5 AV cushion and E17.5 AV valve from wild-type FVB/N mice and in vitro cultured MC3T3 cells

In the study we demonstrated shared gene expression in embryonic heart valve development and Osteoblast progenitor cells.

The atrioventricular (AV) valves of the heart develop from undifferentiated mesenchymal endocardial cushions, that later remodel into stratified valves with diversified extracellular matrix (ECM). Because the mature valves express genes associated with osteogenesis and exhibit disease-associated calcification, we hypothesized the existence of shared regulatory pathways active in the remodeling AV valves and in bone progenitor cells. In order to define gene regulatory programs of valvulogenesis relative to osteoblast progenitors, we undertook Affymetrix gene expression profiling analysis of murine embryonic day (E)12.5 AV cushions compared to E17.5 remodeled AV valves (mitral and tri-cuspid) and to pre-osteoblast MC3T3-E1 (subclone4) cells. Overall MC3T3 cells were significantly more similar to E17.5 valves than to E12.5 cushions, supporting the hypothesis that valve remodeling involves the expression of many genes also expressed in osteoblasts. Several transcription factors characteristic of mesenchymal and osteoblast precursor cells, including Twist1 are predominant in E12.5 cushion. Valve remodeling also includes differential regulation of matrix metalloproteinases and their inhibitors as well as characteristic collagen isoform switching. Among the most highly enriched genes during valvulogenesis were members of the small leucine-rich proteoglycan (SLRP) family including Asporin, a known negative regulator of osteoblast differentiation and mineralization.  Together, these data support shared gene expression profiles of the remodeling valves and osteoblast bone precursor cells in normal valve development and homeostasis with potential functions in calcific valve disease.
Keywords: Embryonic valve development time point

overall_design: In the study, we hybridized RNA from E12.5 AV cushion and E17.5 AV valve from wild-type FVB/N mice and in vitro cultured MC3T3 cells to Affymetrix MOE430 2 GeneChip® arrays.

first: Santanu

last: Chakraborty

first: Jonathan

last: Cheek

first: Bhuvaneswari

last: Sakthivel

first: Bruce

last: Aronow


title: Role of epithelial to mesenchymal transition (EMT) in spontaneous breast cancer metastasis

city: Vancouver

first: Shoukat

last: Dedhar

state: British Columbia

address: 675 West 10th Avenue

country: Canada

institute: BC Cancer Research Centre

summary:
Epithelial-mesenchymal transition (EMT) has been linked to cancer progression and metastatic propensity. The 4T1 tumor is a clinically relevant model of spontaneous breast cancer metastasis. Here we characterize 4T1-derived cell lines for EMT, in vitro invasiveness and in vivo metastatic ability. Contrary to expectations, the 67NR cells, which form primary tumors but fail to metastasize, express vimentin and N-cadherin, but not E-cadherin. 4T1 cells, however, express E-cadherin, are highly migratory and invasive, and metastasize to multiple sites. The 66cl4 metastatic cells display mixed epithelial and mesenchymal markers, but are less migratory and invasive than 67NR cells. These findings demonstrate that the metastatic ability of breast cancer cells does not correlate with genotypic and phenotypic properties of EMT per se, and suggest that other processes may govern metastatic capability. Gene expression analysis also has not identified differences in EMT markers, but has identified several candidate genes that may influence metastatic ability.
Keywords: cell type comparison

overall_design: Female BALB/c mice were injected with 1x10^6 viable cells (3 mice with 4T1/CMVLUC, 3 mice with 66cl4/CMVLUC, and 3 mice with 67NR/CMVLUC) into the right fourth mammary gland. 15 days after injection primary tumors were excised, and total RNA for microarray hybridization was isolated from the tumor part of laser capture microdissected sections.

first: Yuanmei

last: Lou

first: Olena

last: Preobrazhenska

first: Ulrich

last: auf dem Keller

first: Margaret

last: Sutcliffe

first: Lorena

last: Barclay

first: Paul

last: McDonald

first: Calvin

last: Roskelley

first: Christopher

last: Overall


title: Expression comparison between wild-type and transgenic mouse lenses

city: Göteborg

first: Henrik

last: Landgren

address: Medicinaregatan 9E

department: Cell and molecularbiology

institute: Goteborg university

summary:
The vertebrate ocular lens consists of two basic cell types: the lens fibers, highly specialized cells that make up the bulk of the lens and are the basis for its unique optical characteristics, and the epithelial cells that cover the anterior hemisphere and acts as a stem cell population for progenitors of new fibers. The forkhead transcription factor FoxE3 is essential for maintenance, proliferation and survival of the epithelial cells, and silencing of the FoxE3 gene coincides with the cell cycle arrest that marks initiation of fiber cell differentiation. Here we have used transgenic ectopic expression of murine Foxe3 in fiber cells to investigate the consequences of persistent Foxe3 expression during fiber differentiation. Microarray transcript profiling showed that ectopic Foxe3 caused a general increase in mRNAs which are normally enriched in epithelial cells, consistent with an epithelialization of the transgenic fibers.
Keywords: Genetic modification

overall_design: Whole lenses from P2 animals were dissected and genotyped. 12 lenses from each genotype were used for RNA extraction and hybridization to Affymetrix arrays. Total of 3 replicates/genotype.

first: Peter

last: Carlsson


title: Expression and neurobehavioral analyses in prosaposin deficient mice: Molecular alterations precede neuronal deficits

city: Cincinnati

first: nupur

last: dasgupta

address: 3333 Burnet Ave.

institute: Cincinnati Children's Hopital Medical Center

summary:
Prosaposin encodes, in tandem, four small acidic activator proteins (saposins) with specificities for glycosphingolipids hydrolases in lysosomes. To explore the molecular mechanism(s) of disease progression, temporal transcriptome microarray analyses of cerebrum and cerebellum tissues were conducted using mRNA from three prosaposin deficiency mouse models: PS-NA (hypomorphic prosaposin deficiency), PS-/- (prosaposin null) and 4L/PS-NA (a V394L/V394L glucocerebrosidase mutation and PS-NA) mice. Our results indicate that regionally specific gene expression abnormalities preceded the histological and behavioral changes and CEBPD is a candidate regulator of brain disease in prosaposin deficiency. The alterations of gene expression are detected at birth and are more profound in cerebellum than cerebrum.
Keywords: disease-state analysis

overall_design: In order to increase the temporal resolution of expression profile in brain, the disease progression in those models were inverstigated in two regions of brains (cerebellum and cerebrum) at three or four time points according to the genotypes. PS-/-: new born (0d), 10 days (10d), 20 days (20d), 25 days (25d); PS-NA: new born, 4 weeks (4w), 12 weeks (12w), 18 weeks (18w);  4L/PS-NA: 4 weeks (4w), 12 weeks (12w), 18 weeks (18w). The data from those models were analyzed relative to the corresponding wild type at same time point (0d, 10d, 20d, 4w, 12w, 18w).


title: Deaf-1 regulated genes in the mouse mammary gland

status: Public on Aug 21 2008

city: Parkville

first: Jane

last: Visvader

state: Vic

address: 1G Royal Pde

department: Victorian Breast Cancer Research Consortium

country: Australia

institute: Walter and Eliza Hall Institute of Medical Research

summary: Microarray analysis was used to compare the gene expression profiles of Deaf-1-transduced mouse mammary epithelial cells (MECs) relative to Deaf-1-deficient MECs.

overall_design:
To investigate potential target genes of Deaf-1, primary mammary epithelial cells (MECs) were isolated from a Deaf-1-null mouse and immortalised by transduction with a retrovirus encoding the human papilloma virus (HPV16) E6/E7 proteins.  Two clones were selected and transduced with either an empty retrovirus or one encoding Deaf-1. RNA was subsequently isolated from cells at 24 and 48 hours after transduction for Affymetrix analysis.  High levels of Deaf-1 expression were demonstrated in cells transduced with the Deaf-1 retrovirus relative to controls following a 48 hour selection in puromycin.  This time-point was therefore selected for further analysis.

To compare the gene expression profiles of Deaf-1-transduced MECs relative to Deaf-1-deficient MECs, Affymetrix analysis was performed using the GeneChip® Mouse Expression Set 430 2.0 array which comprises 39,000 transcripts on a single array.  Total RNA was harvested from two independent clones (C1 and E1) infected with either control or Deaf-1-expressing retrovirus making 4 samples in total.  Clones C1 and E1 were treated as biological replicates in the subsequent analysis.

first: Holly

last: Barker

first: Gordon

middle: K

last: Smyth

first: James

last: Wettenhall

first: Teresa

last: Ward

first: Mary

middle: L

last: Bath

first: Geoffrey

last: Lindeman


title: Gene expression analysis of embryo-derived stromal cell lines

status: Public on Jul 07 2008

city: Muenchen

first: Robert

last: Oostendorp

address: Ismaningerstrasse 22

department: Klinikum rechts der Isar

institute: Technische Universitaet Muenchen

summary:
Hematopoiesis occurs in a microenviroenment in which stromal cells are prominent. Stromal cells have been shown to maintain stem cell behaviour of hematopoietic stem cells. We derived several different stromal cell lines from midgestation embryos which will, or will not maintain hemetopoietic stem cells in cultures.
We used microarrays to detail the global programme of gene expression underlying maintenance and emergence of hematopoietic stem cells in cocultures with embryo-derived stromal cells.

Keywords: Comparison
CEL files will become available on November 29, 2008

overall_design: Embryo-derived stromal cell lines were grown to confluence and irradiated as described earlier (Oostendorp et al., Stem Cells. 2005;23:842:50). Normalized Gene expression of the three different cell lines was compared.

first: Jonas

last: Renström

first: Jörg

last: Mages

first: Martin

last: Judex

first: Roland

last: Lang


title: Murine embryonic stem cell-derived astrocytes

status: Public on Jul 06 2008

first: Tarjei

last: Mikkelsen

address: 7 Cambridge Center

institute: Broad Institute

summary: Expression profiles for Gfap-positive astrocytes obtained by in vitro differentiation of 129SvJae x C57BL/6 murine embryonic stem (ES) cells. Generated to examine the relationship between expression levels and DNA methylation patterns.

overall_design: 3 replicates of ES-derived astrocytes.

first: Marius

last: Wernig

first: Rudolph

last: Jaenisch

first: Eric

last: Lander

first: Alexander

last: Meissner


title: XBP1 links ER stress to intestinal inflammation

status: Public on Jul 10 2008

city: Boston

first: Ann-Hwee

last: Lee

address: 651 Huntington Ave, FXB/205

institute: Harvard School of public health

summary: XBP1 is the transcriptino factor that is activated by the ER stress. XBP1 is known to induce the ER dexpansion and increase the expression of the ER chaperone genes to prtect the cell from the ER stress. We generated a mouse strain that lacked XBP1 specifically in the mouse intestine by breeding the XBP1flox mice with Villin-cre mice. Here we examined genes that are differentially expressed between WT and XBP1 KO mouse intestine to identify genes that are downstream of XBP1.

overall_design: Total RNAs were pooled from three mice of indicated genotypes. Microarray experiments were performed by using Affymetrix GeneChip® Mouse Genome 430 2.0 Array in Biopolymers Facility at Harvard Medical School.

first: Arthur

last: Kaser

first: Ann

first: Laurie

last: Glimcher

first: Richard

last: Blumberg


title: Expression data from laminin alpha 2 chain deficient mice vs wild type

city: LUND

first: Mattias

middle: Carl

last: Häger

state: M

address: BMC, B12

department: Expreimental Biology

institute: Lunds University

summary:
Mutations in the gene encoding laminin a2 chain cause congenital muscular dystrophy, MDC1A. In skeletal muscle, laminin a2 chain binds at least two receptor complexes; the dystrophin-glycoprotein complex and integrin a7b1. To gain insight into the molecular mechanisms underlying this disorder, we performed gene expression profiling of laminin a2 chain deficient mouse limb muscle. One of the down-regulated genes encodes a protein called calcium and integrin binding protein 2 (Cib2) whose expression and function is unknown. However, the closely related Cib1 has been reported to bind integrin aIIb and may be involved in outside-in-signaling in platelets. Since Cib2 might be a novel integrin a7b1 binding protein in muscle, we have studied Cib2 expression in the developing and adult mouse. Cib2 mRNA is mainly expressed in the developing central nervous system and in developing and adult skeletal muscle. In skeletal muscle Cib2 colocalizes with integrin a7B subunit at the sarcolemma and at the neuromuscular- and myotendinous junctions. Finally, we demonstrate that Cib2 is a calcium binding protein that interacts with integrin a7Bb1D. Thus, our data suggest a role for Cib2 as a cytoplasmic effector of integrin a7Bb1D signaling in skeletal muscle

Keywords: disese state analysis

overall_design: Skeletal muscle (all hind limb skeletal muscle) from 4-weeks old laminin alpha 2 chain deficient mice and 4-weeks old wild type mice were isolated individually and RNA were extracted and hybridized on Affiymetrix microarrys. Three biological replicates from each group were analyzed.

last: Hager

first: Maria

last: Bigotti

first: Renat

last: Meszaros

first: Virginie

last: Carmignac

first: Johan

last: Holmberg

first: Valérie

last: Allamand

first: Mikael

last: Åkerlund

first: Sebastian

last: Kalamajski

first: Andrea

last: Brancaccio

first: Ulrike

last: Mayer

first: Madeleine

last: Durbeej


title: Identifying alternative hyper-splicing signatures in MG-thymoma by exon arrays

status: Public on Jul 03 2008

city: London

first: Lilach

last: Soreq

address: Queen Square

department: Molecular  Neuroscience

institute: UCL

summary:
Background: The vast majority of human genes (.70%) are alternatively spliced. Although alternative pre-mRNA  processing is modified in multiple tumors, alternative hyper-splicing signatures specific to particular tumor types are still  lacking. Here, we report the use of Affymetrix Human Exon Arrays to spot hyper-splicing events characteristic of myasthenia  gravis (MG)-thymoma, thymic tumors which develop in patients with MG and discriminate them from colon cancer changes.  Methodology/Principal Findings: We combined GO term to parent threshold-based and threshold-independent ad-hoc  functional statistics with in-depth analysis of key modified transcripts to highlight various exon-specific changes. These  denote alternative splicing in MG-thymoma tumors compared to healthy human thymus and to in-house and Affymetrix  datasets from colon cancer and healthy tissues. By using both global and specific, term-to-parent Gene Ontology (GO)  statistical comparisons, our functional integrative ad-hoc method allowed the detection of disease-relevant splicing events.  Conclusions/Significance: Hyper-spliced transcripts spanned several categories, including the tumorogenic ERBB4 tyrosine  kinase receptor and the connective tissue growth factor CTGF, as well as the immune function-related histocompatability  gene HLA-DRB1 and interleukin (IL)19, two muscle-specific collagens and one myosin heavy chain gene; intriguingly, a  putative new exon was discovered in the MG-involved acetylcholinesterase ACHE gene. Corresponding changes in  spliceosome composition were indicated by co-decreases in the splicing factors ASF/SF2 and SC35. Parallel tumor-associated  changes occurred in colon cancer as well, but the majority of the apparent hyper-splicing events were particular to MGthymoma  and could be validated by Fluorescent In-Situ Hybridization (FISH), Reverse Transcription–Polymerase Chain  Reaction (RT-PCR) and mass spectrometry (MS) followed by peptide sequencing. Our findings demonstrate a particular  alternative hyper-splicing signature for transcripts over-expressed in MG-thymoma, supporting the hypothesis that  alternative hyper-splicing contributes to shaping the biological functions of these and other specialized tumors and  opening new venues for the development of diagnosis and treatment approaches

Keywords: Disease analysis, Tumor type comparison analysis

overall_design:
4 samples, 2 MG-Thymoma and 2 healthy Thymus are given, male and female in each.
CEL files were analyzed to generate both exon-level (probe set) and transcript-level data


title: Gene expression in TFH cells

city: Houston

first: Chen

last: Dong

state: TX

address: 7455 Fannin

institute: MD Anderson Cancer Center

summary:
After activation, CD4+ helper T (Th) cells differentiate
into distinct effector subsets. Although chemokine
(C-X-C motif) receptor 5-expressing T follicular
helper (Tfh) cells are important in humoral immunity,
their developmental regulation is unclear. Here we
show that Tfh cells had a distinct gene expression
profile and developed in vivo independently of the
Th1 or Th2 cell lineages. Tfh cell generation was regulated
by ICOS ligand (ICOSL) expressed on B cells
and was dependent on interleukin-21 (IL-21), IL-6,
and signal transducer and activator of transcription
3. However, unlike Th17 cells, differentiation of Tfh
cells did not require transforming growth factor
b (TGF-b) or Th17-specific orphan nuclear receptors
RORa and RORg in vivo. Finally, naive T cells activated
in vitro in the presence of IL-21 but not
TGF-b signaling preferentially acquired Tfh gene
expression and promoted germinal-center reactions
in vivo. This study thus demonstrates that Tfh is a
distinct Th cell lineage.

overall_design: Splenic CD4+CXCR5+ T cells were isolated from KLH-immunized mice and restimulated with anti-CD3 for 4 hours before total RNA preparation. Affymetrix gene chips were used to analyze their gene expression. Tfh, Th1, Th2, and Th17 examined

first: Roza

last: Nurieva

first: Qiang

last: Tian


title: Gene expression changes in primary aortic endothelial cells during expression of dominant negative PPAR gamma (V290M).

status: Public on Jul 23 2008

city: Iowa City

first: Henry

last: Keen

state: IA

department: Pharmacology

institute: University of Iowa

summary: Ligand-mediated activation of the nuclear hormone receptor PPAR gamma lowers blood pressure and improves glucose tolerance in humans.  Two naturally occurring mutations (P467L, V290M) in the ligand binding domain of PPAR gamma have been described in humans that lead to severe insulin resistance and hypertension.  Experimental evidence suggests that these mutant versions of PPAR gamma act in a dominant negative fashion.  To better understand the molecular mechanisms underlying PPAR gamma action in the vasculature, we determined the global gene expression profile in primary aortic endothelial cells in response to endothelial cell specific expression of a dominant negative isoform of PPAR gamma (V290M).

overall_design: We generated transgenic mice specifically targeting expression of dominant negative human PPAR gamma to the endothelium using an endothelial-specific promoter (vascular endothelial cadherin or CDH5). Primary aortic endothelial cells were isolated from 10 non-transgenic and 10 EC-DN mice by Dominion Pharmakine (http://www.pharmakine.com/).  For each group, 5 cultures of cells were established. Each culture was derived from 2 mice and remained separate from the other cultures. Cellular RNA was prepared using conventional methods and quality was assessed using the Bioanalyzer 2100 (Agilent Technologies). For the microarray hybridizations, RNA from 3 of the cultures in each group was used.  All the microarray procedures were conducted at the University of Iowa DNA Core facility using standard Affymetrix protocols. In brief, approximately 50 ng of total RNA was used as input to a two-step amplification procedure (NuGen, http://www.nugeninc.com/) to generate biotin-labeled RNA fragments for hybridization to the Affymetrix GeneChip Mouse Genome 430 2.0 array.

first: Curt

last: Sigmund

first: Andreas

last: Beyer

first: Carmen

last: Halabi

first: Willem

last: de Lange

first: Frank

last: Faraci


title: Identification of genes that restrict astrocyte differentiation of midgestational neural precursor cells

city: Ikoma

first: Tsukasa

last: Sanosaka

state: Nara

department: bioscience

institute: NAIST

summary:
During development of the mammalian central nervous system (CNS), neurons and glial cells (astrocytes and oligodendrocytes) are generated from common neural precursor cells (NPCs). However, neurogenesis precedes gliogenesis, which normally commences at later stages of fetal telencephalic development. Astrocyte differentiation of mouse NPCs at embryonic day (E) 14.5 (relatively late gestation) is induced by activation of the transcription factor STAT3, whereas at E11.5 (mid-gestation) NPCs do not differentiate into astrocytes even when stimulated by STAT3-activating cytokines such as leukemia inhibitory factor (LIF). This can be explained in part by the fact that astrocyte-specific gene promoters are highly methylated in NPCs at E11.5, but other mechanisms are also likely to play a role. We therefore sought to identify genes involved in the inhibition of astrocyte differentiation of NPCs at midgestation. We first examined gene expression profiles in E11.5 and E14.5 NPCs, using Affymetrix GeneChip analysis, applying the Percellome method to normalize gene expression level. We then conducted in situ hybridization analysis for selected genes found to be highly expressed in NPCs at midgestation. Among these genes, we found that N-myc and high mobility group AT-hook 2 (Hmga2) were highly expressed in the E11.5 but not the E14.5 ventricular zone of mouse brain, where NPCs reside. Transduction of N-myc and Hmga2 by retroviruses into E14.5 NPCs, which normally differentiate into astrocytes in response to LIF, resulted in suppression of astrocyte differentiation. However, sustained expression of N-myc and Hmga2 in E11.5 NPCs failed to maintain the hypermethylated status of an astrocyte-specific gene promoter. Taken together, our data suggest that astrocyte differentiation of NPCs is regulated not only by DNA methylation but also by genes whose expression is controlled spatio-temporally during brain development.
Keywords: Cell type comparison

overall_design: Neuroepithelial cells(NPCs) were prepared from telencephalons of E11.5 and E14.5 mice and cultured in N2-supplemented Dulbecco's Modified Eagle's Medium with F12 (GIBCO) containing 10 ng/ml basic FGF (R&D Systems) (N2/DMEM/F12/bFGF) on culture dishes (Nunc) or chamber slide (Nunc) which had been precoated with poly-L-ornithine (Sigma) and fibronectin (Sigma). E11.5 NPCs were cultured for one day and E14.5 NPCs were for four days.

first: Masakazu

last: Namihira

first: Hirotsugu

last: Asano

first: Jun

last: Kohyama

first: Ken-ichi

last: Aisaki

first: Katsuhide

last: Igarashi

last: Kanno

first: Kinichi

last: Nakashima


title: GATA4 conditional knockout in the small intestine

status: Public on Sep 01 2008

city: Charleston

first: Stephen

last: Duncan

state: SC

address: 173 Ashley Avenue, BSB 6th Floor, Room 657A

department: Regenerative Medicine and Cell Biology

institute: Medical University South Carolina

summary:
Background and Aims: Although the zinc finger transcription factor GATA4 has been implicated in regulating jejunal gene expression, the contribution of GATA4 in controlling jejunal physiology has not been addressed. Methods: We generated mice in which the Gata4 gene was specifically deleted in the small intestinal epithelium.  Measurements of plasma cholesterol and phospholipids, intestinal absorption of dietary fat and cholesterol, and gene expression were performed on these animals. Results: Mice lacking GATA4 in the intestine displayed a dramatic block in their ability to absorb cholesterol and dietary fat. Comparison of the global gene expression profiles of control jejunum, control ileum, and GATA4 null jejunum by gene array analysis demonstrated that GATA4 null jejunum lost expression of 53% of the jejunal-specific gene set and gained expression of 47% of the set of genes unique to the ileum. These alterations in gene expression included a decrease in mRNAs encoding lipid and cholesterol transporters as well as an increase in mRNAs encoding proteins involved in bile acid absorption. Conclusion: Our data demonstrate that GATA4 is essential for jejunal function including fat and cholesterol absorption and confirm that GATA4 plays a pivotal role in determining jejunal versus ileal identity.
Keywords: genetic modification

overall_design:
Total RNA was harvested from the following sources and used to Affymetrix array analysis following manufacturer defined protocols:
control jejunum (Gata4loxP/+VilCre), 3 male mice, adult (6-8 wk)
mutant jejunum (Gata4loxP/-VilCre), 3 male mice, adult (6-8 wk)
control ileum (Gata4loxP/+VilCre), 3 male mice, adult (6-8 wk).

A total of nine Mouse Genome 430_2.0 arrays were hybridized for this study.

Jejunum was defined as 10 cm from the pyloric sphincter, and ileum was defined as 1 cm from the cecum.  The animals used to harvest control jejunum and ileum were independent of each other.

first: Michele

last: Battle

first: Benjamin

last: Bondow

first: Moriah

last: Iverson

first: Scott

last: Adams

first: Ronald

last: Jandacek

first: Patrick

last: Tso


title: GADD45a in ventilator-induced lung injury: role of Akt signaling

status: Public on Jul 01 2008

city: Charlottesville

first: Yong

last: Huang

state: VA

address: 1340 Jefferson Park Ave

department: Medicine

institute: University of Viginia

summary: We explored the mechanistic involvement of the growth arrest and DNA damageinducible gene, GADD45a, in LPS- and ventilator-induced inflammatory lung injury (VILI). Multiple biochemical and genomic parameters of inflammatory lung injury indicated GADD45a-/- mice to be modestly susceptible to intratracheal LPS-induced lung injury and profoundly susceptible to high tidal volume ventilation-induced lung injury (VILI) with increases in microvascular permeability and levels of inflammatory cytokines in bronchoalveolar lavage. Expression profiling of lung tissues from GADD45a-/- mice revealed strong dysregulation in the B cell receptor signaling pathway suggesting involvement of PI3 kinase/Akt signaling components while the wild type controls depicted no observable changes. Western blot analyses of lung homogenates confirmed ~50% reduction in Akt protein levels in GADD45a-/- mice accompanied by marked increases in Akt ubiquitination. Electrical resistance measurements across human lung endothelial cell monolayers with either reduced GADD45a or Akt expression (siRNAs) revealed significant potentiation of LPS-induced human lung endothelial barrier dysfunction which was attenuated by overexpression of a constitutively active Akt1 transgene. These studies validate GADD45a as a novel candidate gene in inflammatory lung injury and a significant participant in vascular barrier regulation via effects on Akt-mediated endothelial signaling

overall_design: 4 experimental groups, each with 3 mouses. Wild type control group, VILI group, GADD-/- group, GADD-/- and VILI group.

first: Nuala

last: Meyer

first: Saad

last: Sammani

last: Singleton

first: Liliana

last: Moreno-Vinasco

first: Jaideep

last: Moitra

first: Carrie

last: Evenoski

first: Aliya

middle: N

last: Hussain

first: Jeffrey

last: Jacobson

first: Yves

last: Lussier

first: Joe

middle: G

last: Garcia


title: Changes in gene expression following Protocadherin 12 knockout

status: Public on Jun 30 2008

city: GRENOBLE

first: Philippe

last: HUBER

address: 17, Rue des martyrs

department: iRTSV

country: France

institute: Inserm-CEA

summary:
Protocadherin 12 (Pcdh12) is a transmembrane adhesive protein with homophilic adhesive properties and expressed in endothelial cells, the glycogen trophoblast cells of the placenta, and the mesangial cells of kidney glomeruli. Pcdh12-deficient mice are alive although they show alterations in placenta development.
To reveal Pcdh12-associated pathways, 45,000 - Affymetrix probe arrays were used on Pcdh12 knockout and control placentas.
Keywords: Comparative gene knockout results

overall_design: To identify genes whos expression was modified by Pcdh12 deficiency, we examined global gene expression profiles of whole E12.5 knockout placentas (Pcdh12 -l-) and their wild-type (WT – Pcdh12+l+ ) littermates, using the Affymetrix Murine Genome 430 2.0 microarrays. Gestation day 12 was chosen as it is the period at which placentas already formed distinct layers, but organogenesis is still very active. Total RNA was extracted from five Pcdh12 knockout embryos and five normal placentas. RNA were tested for integrity on Agilent 2100 BioAnalyzer, prior to cRNA synthesis and chip hybridization (performed by the Institute of Genetics and Molecular and Cellular Biology, Strasbourg, France).

first: Christine

last: Rampon

first: Stéphanie

last: Bouillot

first: Adriana

last: Climescu-Haulica

first: Marie-Hélène

last: Prandini

first: Francine

last: Cand

last: Vandenbrouck

last: Huber


title: Expression data from bone marrow CLP and B-cell progenitor subfractions.

status: Public on Jun 29 2008

city: Lund

first: Robert

last: Månsson

address: Klinikgatan 26, BMC B12

department: Hemapotoietic stem cell biology

institute: Lund University

summary:
Expression profiling of CLP subfractions (with different potential to develop into T-cells) and B-cell progenitors.
Keywords: cell type comparison, B-cell progenitor, common lymphoid progenitor cells (CLP)

overall_design: CLP and B-cell progenitor subpopulations were FACS sorted. Subsequently RNA was extracted, labelled and hybridized to Affymetrix microarrays. The CLP subfractions were the target of investigation (B-cell progenitors subpopulations served as references of expression levels for B-cell related transcripts) as we sought to identify expression changes potentially explaining difference in function between the hCD25 positiv and negativ subsets.

first: Sigvardsson

last: Mikael


title: Gene expression analysis of embryonic stem cells expressing VE-cadherin (CD144) during endothelial differentiation

status: Public on Jul 14 2008

first: Peter

last: Oettgen

address: Harvard Institutes of Medicine, 4 Blackfan Circle

department: Department of Medicine

institute: Beth Israel Deaconess Medical Center

summary:
Endothelial differentiation occurs during normal vascular development in the developing embryo. Mouse embryonic stem (ES) cells were used to further define the molecular mechanisms of endothelial differentiation. By flow cytometry a population of VEGF-R2 positive cells was identified as early as 2.5 days after differentiation of ES cells, and a subset of VEGF-R2 + cells, that were CD41+ positive at 3.5 days.  A separate population of VEGF-R2+ stem cells expressing the endothelial-specific marker CD144 (VE-cadherin) was also identified at this same time point. Microarray analysis of >45,000 transcripts was performed on RNA obtained from cells expressing VEGF-R2, CD41, and CD144.
Keywords: expression analysis

overall_design: We identified four populations of cells; cells expressing VEGF-R2 (day 2.5), CD41 expressing cells (day 3.5), cells expressing CD144 (VE-Cadherin, day 3.5), and cells expressing CD144 (day 6.5). In addition to this, we have also obtained the negative control cells at each time such as VEGF-R2 (day 2.5) negative, CD41 negative (day 3.5), CD144 negative (VE-Cadherin, day 3.5), and negative CD144 (day 6.5). RNA for the microarray experiments were obtained in duplicate from two separately conducted experiments using the murine embryonic stem cells..

first: Vesna

last: Nikolova-Krstevski

first: Manoj

last: Bhasin

first: Hasan

last: Out

first: Towia

last: Libermann


title: Murine embryonic lung development: time course (C57BL/6J)

status: Public on Jul 15 2008

city: Charlestown

first: Kamila

last: Naxerova

address: 149 13th Street

department: Center For Systems Biology

institute: Massachusetts General Hospital / Harvard Medical School

summary:
We generated gene expression profiles of 5 time points in murine lung development (E11.5, E13.5, E14.5, E16.5 and P5). The goal of this study was to establish a reference data set for exploration of large-scale similarities between transcriptomes in development and cancer.
Keywords: time course

overall_design: Whole lung expression profiles from C57BL/6J mice at E11.5 (pooled sample), E13.5, E14.5, E16.5 and P5.

first: Carol

middle: J

last: Bult

first: Anne

last: Peaston

first: Karen

last: Fancher

first: Barbara

last: Knowles

first: Simon

last: Kasif

first: Isaac

last: Kohane


title: pool of thyroids from wild type, E7 and RET-PTC tg mice at 2, 6 and 10 months

city: Brussels

first: Vincent

last: Detours

address: 808 Route de Lennik

department: School of Medicine

country: Belgium

institute: Free University of Brussels

summary:
The RET/PTC3 (RP3) fusion gene is the most frequent mutation found in radiation-induced papillary thyroid cancers (PTC). Several studies suggest that the RET/PTC rearrangement is an initiating event in tumorigenesis. E7 is an oncoprotein derived from the Human Papilllomavirus 16 (HPV16) responsible for most cervical carcinoma in women. We studied here the sequence of events leading to thyroid cancer in Tg-RP3 and Tg-E7 mice expressing the transgene exclusively in the thyroid under the control of thyroglobulin (Tg) promoter. Both transgenic mice develop thyroid hyperplasia followed by solid differentiated carcinoma in older animals. To understand the different steps leading to carcinoma, we analyzed thyroid gene expression in both strains at different ages (2, 6, 10 months) by microarray technology. Important biological processes were differentially regulated in the two tumor types. In E7 thyroids cell cycle was the most upregulated process; observation consistent with the huge size of these tumors. In RP3 thyroids immunity was the most significantly regulated process, as previously observed in microarray data on human PTC. Interestingly, other human PTC characteristics were also observed in RP3 but not in E7 mouse tumors: similar regulation of several human PTC markers, upregulation of many EGF-like growth factors and finally significant regulation of angiogenesis and extracellular matrix remodeling-related genes. In summary we showed that RP3 contrary to E7 mouse tumors share several important genotypic characteristics with human PTC, observation reinforcing the validity of this model to study human thyroid tumorigenesis.
Keywords: time course, genetic modification, disease state, cancer

overall_design: collection of 3*3=9 microarrays hybridized with pools of thyroids from wild type, E7 and and RET-PTC mice, harvested at 2, 6 and 10 months.

first: Agnes

last: Burnia


title: Mesp1-induced gene expression changes

city: Saint Louis

first: Coleman

last: Lindsley

state: MO

address: BOX 8118, 660 S. Euclid Ave.

department: Pathology and Immunology

institute: Washington University School of Medicine

summary:
During gastrulation, cells of the prospective mesoderm ingress through the primitive streak and acquire fates based on complex spatial and temporal cues.  Progenitors of the cardiogenic mesoderm are first found at E6.5 in the posterior lateral epiblast and subsequently  migrate laterally and anteriorly to form the cardiac crescent at E7.5, when regionalized cell fates are first delineated .  Lineage tracing and heterotopic transplantation studies suggest that precursors in the earliest heart field possess potential to generate myocardium, endocardium, and pericardium.  The mechanisms by which inductive signals in the primitive streak effect the development of this pancardiac progenitor field, however, remain poorly understood
In mice, the earliest restricted progenitors of the cardiovascular system are marked by expression of the basic helix-loop-helix transcription factor, Mesp1.  We therefore use microarray analysis to determine the early and intermediate effects of transiently forced Mesp1 expression during ES cell differentiation.
Keywords: time course

overall_design: ES cells bearing a targeted, doxycycline inducible Mesp1 transgene were differentiated in the absence or presence of DKK1 from day 0-4, either with or without transient doxycycline treatment from day 2-4.

first: R

first: K

middle: M

last: Murphy


title: Mouse mammary tumor-initiating cells

status: Public on Jun 27 2008

first: Mei

last: Zhang

address: One Baylor Plaza

institute: Baylor College of Medicine

summary:
Using a syngeneic p53 null mouse mammary gland tumor model that closely mimics human breast cancer, we have identified by limiting dilution transplantation as well as in vitro mammosphere and clonogenic assays a Lin-CD29HighCD24High subpopulation of tumor-initiating cells.  Differentially expressed genes in the Lin-CD29HighCD24High mouse mammary gland tumor-initiating cell population include those involved in DNA damage response and repair, as well as genes involved in epigenetic regulation previously shown to be critical for stem cell self-renewal.
Keywords: tumor-initiating cells

overall_design:
The cells were labeled (for FACS sorting) with CD29 and CD24 antibodies, and 4 subpopulations were collected (CD29HighCD24High, CD29HighCD24Low,CD29LowCD24High, and CD29LowCD24Low) to do either in vivo transplantation or to isolate RNA from each of them for array to correlate the in vivo data.

12 samples (RNA of 4 subpopulations based on expression of CD29 and CD24 for each tumor of 3) were included in the identification of differentially expressed genes of tumor-initiating cells. 5 samples (RNA of subpopulations based on expression of CD29 and CD24  of normal mammary epithelial cells ) were included in the normal group analysis. Reference RNA was used to normalize all samples.


title: The effect of dietary CLA on mammary tumorigenesis

status: Public on Nov 19 2008

city: Santa Monica

first: Margaret

last: Flowers

address: 2200 Santa Monica Blvd.

department: Dept of Experimental Therapeutics

institute: John Wayne Cancer Institute

summary: Conjugated linoleic acid (CLA), a class of fatty acids found in beef and dairy products, has been shown to inhibit tumorigenesis in a variety of cancer model systems. Based on previously well-documented anti-tumor activity of CLA in rodent models of breast cancer, a pilot study was initiated to examine the effect of dietary CLA in a well-established transgenic model of breast cancer.  Western blots were performed for the detection of AKT, c-Src, ERK1/2, and Cdc24. CLA significantly increased tumor burden (p<0.1) independent of an increase in oncogenic signaling. Mammary gland whole mounts indicated a loss of mammary adipose and extensive epithelial expansion in CLA-treated animals. Microarray analysis indicated a significant reduction in cytoskeletal related genes with at least a two-fold decrease in five out of six CLA-fed animals compared to untreated controls. Reduction of Cdc42, a key regulator of cell adhesion and cytoskeletal arrangements, was confirmed at the protein level by western blot (p<0.01). These findings suggest that dietary CLA may advance the malignant phenotype by promoting a loss of cell polarity and adhesion in the mammary gland epithelium. This action may have serious clinical implications for a subset high-risk population and warrants further investigation.

overall_design: Virgin, four-week-old PyV-mT mice were administered a diet of a mixed-isomer CLA formulation (1% wt/wt) (N=6) or control AIN96G diet (N=5) for four weeks. Measurements of food disappearance, weights and palpations were recorded weekly. All animals were euthanized at eight weeks of age.  Formalin-fixed, paraffin-embedded mammary gland tissue was used for H&E and trichrome staining and immunohistochemistry for Ki67. Tissue levels of CLA were measured by gas chromatography. Thoracic mammary glands were fixed in glacial acetic acid:ethanol and carmine stained. cDNA microarray was performed on RNA from 6 CLA-fed mice and 4 control mice using the Affymetrix 430 2.0 mouse genome chips.

first: Cynthia

last: Thomson

first: Joyce

last: Schroeder

first: David

last: Besselsen

first: Ritu

last: Pandey

first: Patricia

last: Thompson


title: GATA4 is a direct activator of Cyclin D2 and is required for proliferation in 2nd heart field-derived myocardium

first: Sek Won

last: Kong

state: MA

address: 300 Longwood Avenue

department: Informatics Program

institute: Boston Children's Hospital

summary:
The second heart field (SHF) comprises a population of mesodermal progenitor cells that are added to the nascent linear heart to give rise to the majority of the right ventricle, interventricular septum, and outflow tract of mammals and birds. The zinc finger transcription factor GATA4 functions as an integral member of the cardiac transcription factor network in the SHF and its derivatives. In addition to its role in cardiac differentiation, GATA4 is also required for cardiomyocyte replication, although the transcriptional targets of GATA4 required for proliferation have not been previously identified. In the present study, we disrupted Gata4 function exclusively in the SHF and its derivatives. Gata4 SHF knockout mice die by embryonic day 13.5 and exhibit hypoplasia of the right ventricular myocardium and interventricular septum and display profound ventricular septal defects. Loss of Gata4 function in the SHF results in decreased myocyte proliferation in the right ventricle, and we identify numerous cell cycle genes that are dependent on Gata4 by microarray analysis. We show that Gata4 is required for Cyclin D2 expression in the right ventricle and that the Cyclin D2 promoter is bound and activated by GATA4 via three consensus GATA binding sites. These findings establish Cyclin D2 as a direct transcriptional target of GATA4 and support a model in which GATA4 controls cardiomyocyte proliferation by coordinately regulating numerous cell cycle genes.
Keywords: genetic modification

overall_design:
Onewat ANOVA with post-hoc was done with 3 genotypes with replicates. Three genetypes are Gata4flox/+; Nkx2-5+/+ (control, n=3), Gata4flox/+; Nkx2-5Cre/+ (Gata4; Nkx2-5 double heterozygous,
170 n=3), and Gata4flox/flox; Nkx2-5Cre/+ (Gata4 CKONkx, n=5).

first: Anabel

last: Rojas

first: SekWon

first: William

last: Pu

first: Brian

last: Black


title: Expression data from primary mesangial cells stimulated with DNA and RNA ligands

city: munich

first: Ramanjaneyulu

last: Allam

address: Schillerstr. 42

department: Medizinische Poliklinik-Innenstadt

institute: Klinikum der Universität München

summary:
Extrarenal viral infections commonly trigger glomerulonephritis mostly in association with immune complex disease. The immunoglobulin component of immune complexes can activate glomerular cell Fc receptors but whether complexed viral nucleic acids contribute to glomerular inflammation remains unknown. Glomerular mesangial cells express TLR3 but lack TLR7-9, hence, it is unclear whether mesangial cells can recognize and respond to viral ssRNA or DNA. Here we studied the immune responses activated by 3P-RNA (5'Triphosphate RNA) and Non-CpG DNA (Double stranded DNA) in primary mesangial cells (PMC).
We used microarrays to detail the global programme of gene expression that induced by 3P-RNA and Non-CpG DNA.

Keywords: diffrent ligands

overall_design: PMC were stimulated with 3P-RNA and Non-CpG DNA for 6 hours and then total RNA was isolated for hybridization to MOE430_2 arrays.

first: Allam

last: Ramanjaneyulu

first: Anders

last: Hans-Joachim


title: C-terminal diversity within the p53 family accounts for differences in DNA binding and transcriptional activity

status: Public on Aug 01 2008

city: Wuerzburg

first: Christof

last: Burek

address: Josef-schneider-Str. 2

department: Pathologie

institute: Universitaet Wuerzburg

summary:
The p53 family is known as a family of transcription factors with functions in tumor suppression and development. Whereas the central DNA binding domain is highly conserved among the three family members p53, p63 and p73, the C-terminal domains (CTDs) are diverse and subject to alternative splicing and post-translational modification. Here we demonstrate that the CTDs strongly influence DNA binding and transcriptional activity. While p53 and the p73 isoform p73gamma have basic CTDs and form weak sequence-specific protein-DNA complexes, the major p73 isoforms alpha, beta and delta have neutral CTDs and bind DNA strongly. A basic CTD has been previously shown to enable sliding along the DNA backbone and to facilitate the search for binding sites in the complex genome. Our experiments, however, reveal that a basic CTD also reduces protein-DNA complex stability, intranuclear mobility, promoter occupancy in vivo, transgene activation and induction of cell cycle arrest or apoptosis. A basic CTD in p53 and p73gamma therefore provides both positive and negative regulatory functions presumably to enable rapid switching of protein activity in response to stress. In contrast, most p73 isoforms exhibit constitutive DNA binding activity consistent with a predominant role in developmental control.
Keywords: Adenoviros, p73 / p53

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus

overall_design: Infection of H1299 cell with different p73/p53 constructs by adenoviral system

first: Markus

last: Sauer

first: Anne

middle: C

last: Bretz

first: Rasa

last: Beinoraviciute-Kellner

first: Michaela

last: Beitzinger

first: Andreas

last: Rosenwald

first: Gregory

last: Harms

first: Thorsten

last: Stiewe


title: Pluripotent stem cells induced from adult neural stem cells by reprogramming with two factors

status: Public on Jun 28 2008

city: Aachen

first: Martin

last: Zenke

state: NRW

address: Universitatsklinikum Aachen, RWTH

department: Cell Biology

institute: Institute for Biomedical Engineering

summary: Reprogramming of somatic cells is a valuable tool to understand the mechanisms of regaining pluripotency and further opens up the possibility of generating patient-specific pluripotent stem cells. Reprogramming of mouse and human somatic cells into pluripotent stem cells, designated as induced pluripotent stem (iPS) cells, has been possible with the expression of the transcription factor quartet Oct4 (also known as Pou5f1), Sox2, c-Myc, and Klf4. Considering that ectopic expression of c-Myc causes tumourigenicity in offspring and retroviruses themselves can cause insertional mutagenesis, the generation of iPS cells with a minimal number of factors may hasten the clinical application of this approach. Here, we show that adult mouse neural stem cells express higher endogenous levels of Sox2 and c-Myc than embryonic stem cells, and that exogenous Oct4 together with either Klf4 or c-Myc are sufficient to generate iPS cells from neural stem cells. These two-factor (2F) iPS cells are similar to embryonic stem cells at the molecular level, contribute to development of the germ line, and form chimeras. We propose that, in inducing pluripotency, the number of reprogramming factors can be reduced when using somatic cells that endogenously express appropriate levels of complementing factors.

overall_design:
8 hybridizations in total.
NSC derived iPS cells by 2 factors (Oct4 and Klf4) in triplicate:
- iPS cell_2F_1
- iPS cell_2F_2
- iPS cell_2F_3
Embryonic Stem cells (ESC) in triplicate:
- ESC_1
- ESC_2
- ESC_3
NSC cultures in duplicates:
- NSC_2
- NSC_3
NSC derived iPS cells by 4 factors (Oct4, Sox2, c-Myc and Klf4) in triplicate:
- iPS cell_4F_1
- iPS cell_4F_2
- iPS cell_4F_3

first: Jeong-Beom

last: Kim

first: Holm

last: Zaehres

first: Guangming

last: Wu

first: Luca

last: Gentile

first: Vittorio

last: Sebastiano

first: Kinarm

last: Ko

first: Marcos

last: Araúzo-Bravo

first: Dong-Wook

last: Han

first: David

last: Ruau

first: Hans

last: Schöler


title: Lim Homeobox Gene, LHX8, Is Essential for Mouse Oocyte Differentiation and Survival

status: Public on Jun 26 2008

first: Aleksandar

last: Rajkovic

summary:
Lhx8 is a member of the LIM-homeobox transcription factor family and preferentially expressed in oocytes and germ cells within the mouse ovary. We discovered that Lhx8 knockout females lose oocytes within 7 days after birth. At the time of birth, histological examination shows that Lhx8 deficient (Lhx8(-/-)) ovaries are grossly similar to the newborn wild type ovaries. Lhx8(-/-) ovaries fail to maintain the primordial follicles and the transition from primordial to growing follicles does not occur. Lhx8(-/-) ovaries misexpress oocyte-specific genes such as Gdf9, Pou5f1, and Nobox. Very rapid loss of oocytes may partly be due to drastic the down-regulation of Kit and Kitl in Lhx8(-/-) ovaries. We compared Lhx8(-/-) and wild-type ovaries using Affymetrix 430 2.0 microarray platform. Eighty (44%) of 180 of the genes down-regulated more than 5-fold in Lhx8(-/-) ovaries were preferentially expressed in oocytes, whereas only 3 (2%) of 146 genes up-regulated more than 5-fold in the absence of Lhx8 were preferentially expressed in oocytes. In addition, the comparison of genes regulated in Lhx8(-/-) and Nobox(-/-) newborn ovaries discovered a common set of 34 genes whose expression level is affected in both Lhx8 and Nobox deficient mice. Our findings show that Lhx8 is a critical factor for maintenance and differentiation of the oocyte during early oogenesis and it acts in part by down-regulating the Nobox pathway.

This SuperSeries is composed of the SubSeries listed below.

overall_design: Refer to individual Series


title: Pharmacological regulation of skeletal muscle gene expression

status: Public on Jun 18 2008

city: La Jolla

first: Ruth

last: Yu

state: CA

address: 10010 N Torrey Pines Rd

department: Gene Expression Lab

institute: Salk Institute

summary:
Exercise activates serine/threonine kinase AMPK and transcriptional factor PPARdelta that re-model metabolism and endurance capacity of skeletal muscle.  Whether and how synthetic activation of these molecules regulated muscle gene signature is unknown.
We have conducted skeletal muscle microarrays from mice treated with AMPK agoinst (AICAR), PPARdelta agonist (GW1516) or the combination of the two drugs to investigate the individual and interactive effects of the two on muscle genes.

Keywords: Pharmacology study

overall_design: C57Bl/6J mice were treated with Vehicle, AICAR, GW1516 and the combination of two drugs for 6 days, followed by collection of quadriceps for gene expression analysis.

first: Vihang

last: Narkar

first: Ron

last: Evans


title: Acquisition of granule neuron precursor identity and Hedgehog-induced medulloblastoma in mice.

status: Public on Jun 24 2008

city: Boston

first: Alvin

middle: T.

last: Kho

address: 320 Longwood Avenue

summary:
Origins of the brain tumor, medulloblastoma, from stem cells or restricted pro-genitor cells are unclear. To investigate this, we activated oncogenic Hedgehog signaling in multipotent and lineage-restricted CNS progenitors. We observed that normal unipo-tent cerebellar granule neuron precursors (CGNP) derive from hGFAP+ and Olig2+ rhombic lip progenitors. Hedgehog activation in a spectrum of early and late stage CNS progenitors generated similar medulloblastomas, but not other brain cancers, indicating that acquisition of CGNP identity is essential for tumorigenesis. We show in human and mouse medulloblastoma that cells expressing the glia-associated markers Gfap and Olig2 are neoplastic and that they retain features of embryonic-type granule lineage progenitors. Thus, oncogenic Hedgehog signaling promotes medulloblastoma from lineage-restricted granule cell progenitors.
Gene expression profiling of cerebellar tumors generated from various early and late stage CNS progenitor cells.

overall_design: Group comparisons with biological replicates

first: Keith

last: Ligon

last: Rowitch