title: Digoxin and its derivatives suppress Th17 cell differentiation by antagonizing RORγt activity

first: Jun

last: Huh

address: 540 1st avenue

institute: NYU medical school

summary: CD4+ T helper lymphocytes that express interleukin-17 (Th17 cells) have critical roles in mouse models of autoimmunity, and there is mounting evidence that they also influence inflammatory processes in humans.  Genome-wide association studies in humans have linked genes involved in Th17 cell differentiation and function with susceptibility to Crohn’s disease, rheumatoid arthritis, and psoriasis1-3. Thus, the pathway towards differentiation of Th17 cells and, perhaps, of related innate lymphoid cells with similar effector functions4, 5, is an attractive target for therapeutic applications. Mouse and human Th17 cells are distinguished by expression of the retinoic acid receptor-related orphan nuclear receptor RORγt, which is required for induction of IL-17 transcription and for the manifestation of Th17-dependent autoimmune disease in mice6. By performing a chemical screen with an insect cell-based reporter system, we identified the cardiac glycoside digoxin as a specific inhibitor of RORγt transcriptional activity. Digoxin inhibited murine Th17 cell differentiation without affecting differentiation of other T cell lineages and was effective in delaying the onset and reducing the severity of autoimmune disease in mice.  At high concentrations, digoxin is toxic for human cells, but non-toxic synthetic derivatives, 20,22-dihydrodigoxin-21,23-diol (Dig(dhd)) and digoxin-21-salicylidene (Dig(sal)), specifically inhibited induction of IL-17 in human CD4+ T cells.  Using these small molecule compounds, we demonstrated that RORγt is imporant for the maintenance of IL-17 expression in mouse and human effector T cells. These data suggest that derivatives of digoxin can be used as chemical probes for development of RORγt-targeted therapeutic agents that attenuate inflammatory lymphocyte function and autoimmune disease.

overall_design: We performed gene expression profiling with total RNA samples isolated from DMSO- or digoxin-treated wildtype or RORγt-deficient cells cultured in Th17 conditions. Total RNA was extracted with TRIzol. RNA was labeled and hybridized to GeneChip Mouse Genome 430 2.0 arrays following the Affymetrix protocols. Data were analyzed in GeneSpring GX11.5.

first: Monica

middle: W

last: Leung

first: Pengxiang

last: Huang

first: Daniel

last: Ryan

first: Michael

last: Krout

first: Raghu

last: Malapaka

first: Jonathan

last: Chow

first: Nicolas

last: Manel

first: Maria

last: Ciofani

first: Sangwon

last: Kim

first: A

last: Cuesta

first: Fabio

last: Santori

first: Juan

last: Lafaille

first: H

middle: E

last: Xu

first: David

last: Gin

first: Fraydoon

last: Rastinejad

first: Dan

last: Littman


title: T cell dependent immune responses: B cell activation and differentiation Group1 Fo, Group2 GC1, Group3 GC2

status: Public on Mar 29 2011

city: Berlin

first: Pawel

last: Durek

address: Charitéplatz 1

country: Germany

institute: Deutsches Rheuma-Forschungszentrum

summary: Upon immunization with a T cell dependent antigen naive follicular B cells (Fo) are activated and a germinal center reaction is induced. Within the next 2 weeks large germinal centers develop where the process of affinity maturation takes place. To analyze the gene expression profile of resting and activated B cells, follicular B cells (Fo), B cells from early (GC1) and late germinal centers (GC2) were isolated and their gene expression profile compared.

overall_design:
Gene expression profiles of Fo versus GC1 and GC2 B cells, respectively. Naïve Fo B cells were isolated from non-immunized BALB/c mice. Germinal center B cells sorted from spleen cell suspensions of BALB/-c mice immunized with the T cell dependent antigen 2-phenyl Oxazolone. GC1 B cells were isolated 7 days after primary immunization. GC2 cells were isolated 15 days after primary immunization.
After total RNA extraction, reverse transcription, cDNA extraction, the biotinylated cRNA was transcribed, fragmented, and 15 µg cRNA hybridized in duplicates for each of the three groups to the GeneChip arrays. Group1: Fo, Group2: GC1, Group3: GC2. Lists of differentially regulated genes were created using High Performance Chip Data Analysis (HPCDA) with Bioretis database (http://www.bioretis-analysis.de). Worldwide data sharing is possible via Bioretis, please ask the authors.

first: Gordon

last: Wilke

first: Gudrun

last: Steinhauser

first: Joachim

middle: R

last: Grün

first: Claudia

last: Berek


title: Accelerated leukemogenesis by truncated CBFb-SMMHC defective in high-affinity binding with RUNX1

city: Bethesda

first: Christopher

last: Pan

state: MD

address: Rm 5228, Bldg 50, South Dr.

department: NHGRI

country: USA

institute: NIH

summary:
Dominant RUNX1 inhibition has been proposed as a common pathway for CBF-leukemia.  CBFb-SMMHC, a fusion protein in human acute myeloid leukemia (AML), dominantly inhibits RUNX1 largely through its RUNX1 high-affinity binding domain (HABD). We generated knock-in mice expressing CBFb-SMMHC with a HABD deletion, CBFb-SMMHCd179-221. These mice developed leukemia highly efficiently, even though hematopoietic defects associated with Runx1-inhibition were partially rescued.
To identify changes in gene expression with the deletion of the HABD, we compared the gene expression profile in leukemia samples from mice expressing CBFb-SMMHCd179-221 with those from mice expressing full length CBFb-SMMHC.

overall_design: Spleen cells were isolated from leukemic knock-in mice with full length CBFb-SMMHC at 2 months after ENU treatment and 2 leukemic CBFb-SMMHCd179-221 expressing chimeric mice at 3 weeks after birth. For each genotype, we performed two independent experiments with 4 Affymetrix GeneChip 430 chips.

first: Yasuhiko

last: Kamikubo

first: Ling

last: Zhao

first: Mark

last: Wunderlich

first: Takeshi

last: Corpora

first: R

middle: K

last: Hyde

first: Thomas

last: Paul

first: Mondira

last: Kundu

first: Lisa

last: Garrett-Beal

first: Sheila

last: Compton

first: Gang

last: Huang

first: Linda

last: Wolff

first: Yoshiaki

last: Ito

first: John

last: Bushweller

first: James

middle: C

last: Mulloy

first: P

middle: P

last: Liu


title: Gene expression of the whole mouse eye

status: Public on Mar 20 2011

first: Lai

last: Wei

address: 10 Center Dr. Room 2B47

institute: NIH/NEI/NCCAM

summary:
Background
Age-related macular degeneration (AMD) is the leading cause of irreversible blindness in the elderly population worldwide. Recent studies have demonstrated strong genetic associations between AMD and single nucleotide polymorphisms (SNPs) within genes such as CFH and HTRA1. However, we have identified monozygotic twins discordant for AMD phenotypes (one with disease, the other without disease), suggesting that an epigenetic mechanism may also contribute to the pathogenesis of AMD.

Methods
We identified two twin pairs with phenotypic discordance of AMD. We obtained genomic DNA from their peripheral blood mononuclear cells (PBMCs) and subjected them to DNA methylation-chip analysis (MeDIP-chip) that profiled genome-wide DNA methylation patterns on promoters of all genes and microRNAs. We next utilized the Methyl-Profiler DNA methylation assays to detect the methylation status of selected promoters. Flow cytometry and quantitative real-time PCR were used to detect the expression of the selected gene in peripheral blood cells, as well as in retinal and choroidal tissues of AMD patients and non-AMD controls.

Results
Our MeDIP-chip analysis identified 256 genes with hypo-methylated promoters only in the twins with AMD and 744 genes with hyper-methylated promoters only in the twins with AMD. Importantly, the promoter region of IL17RC was associated with hypo-methylated CpG sites only in the twins with AMD but not in the twins without AMD. We also found the association of the hypo-methylated IL17RC promoter with AMD in 7 pairs of siblings with discordant AMD pathology (P=0.003), as well as an independent patient cohort (95 neovascular wet and 107 geographic atrophy dry AMD patients as well as 96 non-AMD controls (95% CI, 0.01-0.10, P=9.8x10-8 for wet AMD vs. control; 95% CI, 0.05-0.32, P=2.2x10-5 for dry AMD vs. control)). Interestingly, we did not find an association between the levels of methylation on the IL17RC promoter with the previously identified genetic risk alleles in CFH, HTRA1, and ARMS2. We demonstrated an elevated expression of the IL-17RC protein in CD14+ monocytes in the peripheral blood of AMD patients as compared to non-AMD controls. These IL-17RC+ monocytes have elevated expression of CXCR1, CXCR2, and CXCR4. In addition, IL17RC was expressed only in the retinal and choroidal tissues from AMD patients but not from age-matched controls.

Conclusions
We show an association of the hypo-methylated IL17RC promoter with AMD, which resulted in the elevated expression of IL-17RC in peripheral blood cells as well as the retinal and choroidal tissues of AMD patients. Our study suggests that the hypo-methylated IL17RC promoter and elevated expression of IL-17RC can potentially serve as biomarkers for the diagnosis of AMD, while IL-17RC can be a new therapeutic target for AMD. In addition, our results strongly suggest an epigenetic control mechanism of AMD pathogenesis.

overall_design: The Affymetrix MOE430 2.0 GeneChip was used to detect gene expression patterns within the whole eye of C57B/6 normal mice.

first: Sagarika

last: Chakrabarty


title: Microarray gene expression profiling of heart failure induced in apolipoprotein E-deficient mice by treatment with rosiglitazone

status: Public on Mar 18 2011

city: Zurich

first: Ursula

last: Quitterer

address: Winterthurerstrasse 190

department: Molecular Pharmacology

country: Switzerland

institute: ETH Zurich

summary: The anti-diabetic drug and agonist of the peroxisome proliferator-activated receptor gamma (Pparg), rosiglitazone, was recently withdrawn in many countries because the drug use was associated with an increased risk of heart failure. To investigate underlying pathomechanisms, we chose 6-month-old apolipoprotein E (apoE)-deficient mice, which are prone to atherosclerosis and insulin resistance, and thereby mimic the risk profile of patients with cardiovascular disease. After 8 weeks of rosiglitazone treatment (30 mg/kg/day), echocardiography and histology analyses demonstrated that rosiglitazone had induced heart failure with cardiac dilation. Concomitantly, cardiac lipid overload and lipid-induced cardiomyocyte death developed. The microarray gene expression study of heart tissue from rosiglitazone-treated apoE-deficient mice relative to untreated apoE-deficient mice and non-transgenic B6 mice identified cardiac Pparg-dependent lipid metabolism genes in rosiglitazone-treated mice, which seem to trigger a major heart failure promoting pathway.

overall_design: Microarray gene expression profiling was performed with heart tissue isolated from three study groups: (i) rosiglitazone-treated 8-month-old apolipoprotein (apoE)-deficient mice with symptoms of heart failure, (ii) untreated 8-month-old apoE-deficient mice, and (iii) age-matched, untreated, non-transgenic B6 control mice.

first: Joshua

last: Abd Alla


title: Crosstalk between gene body DNA methylation, H3K9me3 and H3K36me3 chromatin marks and transcription

status: Public on Mar 31 2011

city: Duarte

first: Xiwei

last: Wu

state: CA

address: 1500 E. Duarte Rd.

department: Computational and Quantitative Medicine

institute: City of Hope National Medical Center

type: Genome binding/occupancy profiling by genome tiling array

type: Methylation profiling by genome tiling array

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

overall_design: Refer to individual Series


title: ChIP-seq analysis reveals distinct H3K27me3 profiles associated with gene regulation

status: Public on Mar 21 2011

city: Parkville

first: Matthew

middle: Daniel

last: Young

state: Victoria

address: 1G Royal Parade

department: Bioinformatics

country: Australia

institute: Walter & Eliza Hall Institute of Medical Research

type: Genome binding/occupancy profiling by high throughput sequencing


title: mRNA and microRNA expression profile in mouse lung development

city: Rochester

first: Jie

last: Dong

state: MN

address: 200 1st SW

department: Thoracic Surgery

institute: Mayo Clinic

type:
Expression profiling by array
Other
Non-coding RNA profiling by array


title: Gene expression profiling of pregnant and virgin mouse lung and liver

status: Public on Mar 19 2011

city: Torino

first: Paolo

last: Provero

address: Via Nizza 52

department: Molecular Biotechnology and Health Sciences

country: Italy

institute: University of Turin

summary: Metastasis depends on the ability of tumor cells to establish a relationship with the newly seeded host tissue that is conducive to their survival and proliferation. Recent evidence suggests that tumor cells regulate their own dissemination by preparing permissive “metastatic niches” within host tissues. However, the factors that are implicated in rendering tissues permissive for metastatic tumor growth have yet to be fully elucidated. Breast tumors arising during pregnancy display highly aggressive behaviour and early metastatic proclivity, raising the possibility that pregnancy may constitute a physiological condition of permissiveness for tumor dissemination. We show that during murine gestation, both the rate and degree of metastatic tumor growth are enhanced irrespective of tumor type and that decreased natural killer (NK) cell activity is responsible for the observed increase in experimental metastasis. We identify gene expression changes in pregnant mouse lung and liver that bear striking similarity with  reported pre-metastatic niche signatures and several of the up-regulated genes are indicative of myeloid-cell infiltration. We provide evidence, that CD11b+ Gr-1+ myeloid-derived suppressor cells accumulate in pregnant mice and exert an inhibitory effect on NK cell activity, thereby enhancing metastatic tumor growth. MDSC have never been evoked in the context of pregnancy and our observations suggest that they may represent a further shared mechanism of immune suppression occurring during gestation and tumor growth.

overall_design: Three chips were done per organ (liver/lung) and per condition (virgin/pregnant), with equal amounts of RNA from two mice pooled for one chip.

first: Laetitia

last: Mauti

first: Marie-Aude

last: LeBitoux

first: Karine

last: Baumer

first: Jean-Christophe

last: Stehle

first: Dela

last: Golshayan

first: Qin

last: Yu

first: Ivan

last: Stamenkovic


title: Comparative transcriptome profiling of Amyloid Precursor Protein APP family members in the adult cortex

city: Heidelberg

first: Ulrike

last: Müller

address: Im Neuenheimer Feld 364

department: Bioinformatics and Functional Genomics

institute: Institute of Pharmacy and Molecular Biotechnology, University of Heidelberg

summary: The β-amyloid precursor protein APP and the related APLPs, undergo complex proteolytic processing giving rise to several fragments. Whereas it is well established that Aβ accumulation is a central trigger for Alzheimer disease (AD), the physiological role of APP family members and their diverse proteolytic products is still largely unknown. The secreted APPsα ectodomain has been shown to be involved in neuroprotection and synaptic plasticity. The γ-secretase generated APP intracellular domain AICD, functions as a transciptional regulator in heterologous reporter assays, although its role for endogenous gene regulation has remained controversial.  To gain further insight into the molecular changes associated with knockout phenotypes and to elucidate the physiological functions of APP family members including their proposed role as transcriptional regulators we performed a DNA microarray transcriptome profiling of the frontal cortex of adult wild type, APP-/-, APLP2-/- and APPsα knockin (KI) mice, APPα/α, expressing solely the secreted APPsα ectodomain. Biological pathways affected by the lack of APP family members included regulation of neurogenesis, regulation of transcription and regulation of neuron projection development. Comparative analysis of transcriptome changes and qPCR validation identified co-regulated gene sets. Interestingly, these included heat shock proteins and plasticity related genes that were down-regulated in knock-out cortices. In contrast, we failed to detect significant differences in expression of previously proposed AICD target genes including Bace1, Kai1, Gsk3b, p53, Tip60 and Vglut2. Only Egfr was slightly up-regulated in APLP2-/- mice. Comparison of APP-/- and APPα/α with wild-type mice revealed a high proportion of co-regulated genes indicating an important role of the C-terminus for cellular signaling. Finally, comparison of APLP2-/- on different genetic backgrounds revealed that background related transcriptome changes may dominate over changes due to the knockout of a single gene.   Shared transcriptome profiles corroborated closely related physiological functions of APP family members in the adult central nervous system. As expression of proposed AICD target genes was not altered in adult cortex, this may indicate that these genes are not affected by lack of APP under resting conditions or only in a small subset of cells.

overall_design: Prefrontal cortices of adult male mice (24 - 28 weeks) of the following genotypes were analyzed: WT (n=3), APP-/-  (n=3), APPα/α (n=3), APLP2-/- (n=3), APLP2(R1)-/- (n=3). WT, APP-/-, APPα/α, APLP2-/- had been backcrossed for six generations to C57BL/6 mice. APLP2(R1)-/- harbors the identical knockout allele as APLP2-/- but was back-crossed only once.

first: Dorothee

last: Aydin

first: Mikhail

last: Filippov

first: Norbert

last: Gretz

first: Roland

last: Eils

first: Benedikt

last: Brors


title: ChIP-seq analysis reveals distinct H3K27me3 profiles associated with gene regulation [mRNA profiling]

type:
Expression profiling by array
Third-party reanalysis

summary: Transcriptional control is dependent on a vast network of epigenetic modifications.  One epigenetic mark of particular interest is tri-methylation of lysine 27 on histone H3 (H3K27me3), which is catalyzed and maintained by the Polycomb Repressor Complex (PRC2).  Although this histone mark is studied widely, the precise relationship between its local pattern of enrichment and regulation of gene expression is currently unclear.  We have used ChIP-seq to generate genome wide maps of H3K27me3 enrichment, and have identified three enrichment profiles with distinct regulatory consequences. First, a broad domain of H3K27me3 enrichment across the body of genes corresponds to the canonical view of H3K27me3 as inhibitory to transcription.  Second, a peak of enrichment around the transcription start site is commonly associated with “bivalent” genes, where H3K4me3 also marks the TSS.  Finally and most surprisingly, we identified an enrichment profile with a peak in the promoter of genes that is associated with active transcription. Genes with each of these three profiles were found in different proportions in each of the cell types studied.  The data analysis techniques developed here will be useful for the identification of common enrichment profiles for other histone modifications that have important consequences for transcriptional regulation.

overall_design:
Expression profiling of Gata1 null Megakaryocyte Erythroid cells (G1ME cells)

Supplementary file: Comprehensive matrix representing the entire gene expression dataset (i.e., GSM691834 and GSM691835, plus the re-analyzed Samples from Series GSE8024).

middle: D


title: A Molecular Signature Associated with Human Melanoma Brain Metastasis and Spontaneous Micrometastasis

status: Public on Mar 17 2011

city: Tel Aviv

first: Metsada

last: Pasmanik-Chor

address: Ramat Aviv

department: Biology

country: Israel

institute: Tel Aviv University

summary:
We established a model of human melanoma metastasis to identify differentially expressed genes in brain metastasis, compared to cutaneous melanoma from which they were developed. Such genes may control brain metastasis. The identification and characterization of these genes would advance the understanding of the metastatic process and may lead to new diagnostics and therapeutic approach.
Brain metastases occur in almost 40% of melanoma patients. The median survival of such patients does not exceed a few months. Very little information is available on mechanisms underlying the progression of melanoma towards brain metastasis. The function, and significance of the various factors involved in melanoma progression must be deciphered using relevant models. Currently, most human melanoma brain metastasis models consist of xenografted cells inoculated into immune-deficient mice mainly by intracarotid or intra-cardiac administration.  We generated a reproducible melanoma brain metastasis model, consisting of brain-metastasizing variants and local, sub-dermal variants that originate from the same melanomas thus sharing a common genetic background. The brain metastasizing variants were obtained by intra-cardiac inoculation. One of the brain metastasizing variants when inoculated sub-dermally yielded spontaneous brain dormant micrometastasis. Cells from the spontaneous brain micrometastasis when removed from the brain microenvironment proliferate very well in vitro and generate tumors in the skin being the orthotopic organ site. The brain metastasis and micro-metastasis cells expressed higher levels of ANGPTL4, COX-2, MMP1, MMP2 and PRAME and lower levels of CLDN1, CYR61 and IL-6R than the cutaneous variants. These gene products may be involved in melanoma brain metastasis and may serve as novel brain metastasis biomarkers and targets for therapy.

overall_design: 8 Samples (arrays) were analyzed. We generated pairwise comparisons between cutaneous and brain metastatic variants of the same genetic background, using Partek Genomics Suite, in the three melanoma models. Genes with p≤5% and a fold-change difference of ≥1.25 or <-1.25 were selected.

first: Sivan

last: Izraely

first: Orit

last: Sagi-Assif

first: Anat

last: Klein

first: Tsipi

last: Meshel

first: Galia

last: Tsarfaty

first: Clara

last: Nahmias

first: PierreOlivier

last: Couraud

first: Eugene

last: Ateh

first: Joseph

last: L. Bryant

first: Dave

middle: S

last: Hoon

first: Isaac

last: Witz


title: Preclinical Models for Neuroblastoma: Establishing a Baseline for Treatment

city: Memphis

first: David

last: Finkelstein

state: TN

address: 332 N. Lauderdale St.

department: Computational Biology

institute: St Jude Children's Research Hospital

summary: Here we characterize and optimize both systems to increase their utility for preclinical studies. We show that TH-MYCN mice develop tumors in the paraspinal ganglia, but not in the adrenal, with cellular and gene expression patterns similar to human NB. In addition, we present a new ultrasound guided, non-invasive orthotopic xenograft method. This injection technique is rapid, provides accurate targeting of the injected cells and leads to efficient engraftment. We also demonstrate that tumors can be detected, monitored and quantified prior to visualization using ultrasound, MRI and bioluminescence. Finally we develop and test a “standard of care” chemotherapy regimen. This protocol, which is based on current treatments for neuroblastoma, provides a baseline for comparison of new therapeutic agents.

overall_design: A total of 17 samples are provided reprsenting TH-MYCN tumors derived from mice

first: Tal

last: Teitz

first: Jennifer

last: Stanke

first: Sara

last: Federico

first: Cori

middle: L

last: Bradley

first: Rachel

last: Brennan

first: Jiakun

last: Zhang

first: Melissa

last: Johnson

first: Jan

last: Sedlacik

first: Madoka

last: Inoue

first: Ziwei

middle: M

first: Sharon

last: Frase

first: Jerold

last: Rehg

first: Claudia

last: Hillenbrand

first: Christopher

last: Calabrese

first: Michael

middle: A

last: Dyer

first: Jill

last: Lahti


title: Expression data from from the E9.25 hearts of mouse embryos

status: Public on Mar 26 2011

city: Shinjuku-ku

first: Keiko

last: Uchida

state: Tokyo

address: 35 Shinanomachi

country: Japan

institute: Keio University School of Medicine

summary: Congenital heart defects (CHDs) occur in 0.5–1% of live births, yet the underlying genetic etiology remains mostly unknown. Recently, a new source of myocardial cells, namely the second heart field (SHF), was discovered in the splanchnic mesoderm. Abnormal development of the SHF leads to a spectrum of outflow tract defects, such as persistent truncus arteriosus and tetralogy of Fallot. Intracellular Ca2+ signaling is known to be essential formany aspects of heart biology including heart development, but its role in the SHF is uncertain. Here, we analyzed mice deficient for genes encoding inositol 1,4,5-trisphosphate receptors (IP3Rs), which are intracellular Ca2+ release channels on the endo/sarcoplasmic reticulum that mediate Ca2+ mobilization. Mouse embryos that are double mutant for IP3R type 1 and type 3 (IP3R1−/−IP3R3−/−) show hypoplasia of the outflow tract and the right ventricle, reduced expression of specific molecular markers and enhanced apoptosis ofmesodermal cells in the SHF. Gene expression analyses suggest that IP3R-mediated Ca2+ signalingmay involve, at least in part, theMef2C–Smyd1 pathway, a transcriptional cascade essential for the SHF. These data reveal that IP3R type 1 and type 3 may play a redundant role in the development of the SHF.

overall_design: In total 4 samples were analyzed, they represent two different genotypes (wt, double ko) that were tested in duplicate each.


title: Inflammation driven by tumor-specific Th1 cells protects against B-cell cancer

status: Public on Mar 15 2011

city: Oslo

first: Alexandre

last: Corthay

address: Rikshospitalet

department: Department of Biosciences

country: Norway

institute: University of Oslo

summary: The immune system can both promote and suppress cancer. Chronic inflammation and proinflammatory cytokines such as interleukin (IL)-1 and IL-6 are considered tumor-promoting. In contrast, the exact nature of protective antitumor immunity remains obscure. In this study, we have quantified locally secreted cytokines during primary immune responses against myeloma and B-cell lymphoma in mice. Strikingly, successful cancer immunosurveillance mediated by tumor-specific CD4+ T cells was consistently associated with elevated local levels of both proinflammatory (IL-1aplha, IL-1beta, and IL-6) and T helper 1 (Th1)-associated cytokines (interferon-alpha, IL-2, IL-12). Cancer eradication was achieved by a collaboration between tumor-specific Th1 cells and tumor-infiltrating, antigen-presenting macrophages. Th1 cells induced secretion of IL-1? and IL-6 by macrophages. Th1-derived interferon-? was shown to render macrophages directly cytotoxic to cancer cells, and to induce macrophages to secrete the angiostatic chemokines CXCL9/MIG and CXCL10/IP-10. Thus, inflammation, when driven by tumor-specific Th1 cells, may prevent rather than promote cancer.

overall_design: Tumoricidal macrophages were isolated from Idiotype-specific TCR-transgenic SCID mice injected with MOPC315-containing Matrigel. Control macrophages were obtained from TCR-transgenic SCID mice injected with Matrigel containing antigen-loss MOPC315.

first: Ole-Audun

last: Haabeth

first: Kristina

middle: B

last: Lorvik

first: Clara

last: Hammarström

first: Ian

last: Donaldson

first: Guttorm

last: Haraldsen

first: Bjarne

last: Bogen


title: HL-1 cardiomyocyte response to hypoxia

status: Public on Mar 16 2011

city: Gothenburg

first: Jeanna

last: Perman

address: Bruna Stråket 16

country: Sweden

institute: Wallenberg Laboratory for cardiovascular research

summary: Expression profiling of cultured HL-1 cardiomyocytes subjected to hypoxia for 8 hours.

overall_design: Three samples from each condition were analyzed

first: Daniel

last: Hägg

first: Per-Arne

last: Svensson


title: Geminin-regulated genes during neural fate acquisition of mouse embryonic stem cells

city: Saint Louis

first: Kristen

last: Kroll

state: MO

address: 320 McDonnell Sciences/660 S. Euclid Ave.

department: Developmental Biology

institute: Washington University School of Medicine

summary: Formation of the complex vertebrate nervous system begins when pluripotent cells of the early embryo are directed to acquire a neural fate.  Although cell intrinsic controls play an important role in this process, the molecular nature of this regulation is not well defined.  Here we assessed the role for Geminin, a nuclear protein expressed in embryonic cells, in neural fate acquisition from mouse embryonic stem (ES) cells. While Geminin knockdown does not affect the ability of ES cells to maintain or exit pluripotency, we found that it significantly impairs their ability to acquire a neural fate. Conversely, Geminin overexpression promotes neural gene expression, even in the presence of growth factor signaling that antagonizes neural transcriptional responses. These data demonstrate that Geminin’s activity contributes to mammalian neural cell fate acquisition. We investigated the mechanistic basis of this phenomenon and found that Geminin maintains a hyperacetylated and open chromatin conformation at neural genes. Interestingly, recombinant Geminin protein also rapidly alters chromatin acetylation and accessibility even when Geminin is combined with nuclear extract and chromatin in vitro. These findings define a novel activity for Geminin in regulation of chromatin structure. Together, these data support a role for Geminin as a cell intrinsic regulator of neural fate acquisition that promotes expression of neural genes by regulating chromatin accessibility and histone acetylation.

overall_design: Mouse embryonic stem cells were differentiated for two days in N2B27 medium, with or without Doxycycline-inducible shRNAmir knockdown of Geminin and compared by microarray. Three independent experiments were conducted, using two different mouse embryonic stem cell lines for Doxycycline-inducible knockdown of Geminin. The two ES lines express unique shRNAmir sequences targeting Geminin (shRNAmir #9 and #11) to control for off-target effects.

first: Dan

last: Yellajoshyula

first: Ethan

last: Patterson

first: Matthew

last: Elitt


title: The intestinal stem cell signature identifies colorectal cancer stem cells and predicts disease relapse

status: Public on Mar 14 2011

city: Barcelona

first: Eduard

last: Batlle

address: Baldiri i Reixach 10

country: Spain

institute: Institute for Research in Biomedicine

summary:
Using EphB2 or the ISC marker Lgr5, we have FACS-purified and profiled intestinal stem cells (ISCs), crypt proliferative progenitors and late transient amplifying cells to define a gene expression program specific for normal ISCs.
A frequent complication in colorectal cancer (CRC) is regeneration of the tumor after therapy. The intestinal stem cell signature predicts disease relapse in CRC and identifies a stem cell-like population that displays robust tumor- initiating capacity in immunodeficient mice as well as long-term self-renewal potential.

overall_design: We FACS purified mouse intestinal crypt cells according to their EphB2 or Lgr5 contents. We used Affymetrix chips to hybridize 2 samples from EphB2 high, 2 samples from EphB2 medium and 2 samples from EphB2 low cells (one sample from each group in a first hybridization on February 2009 plus an additional sample from each group on March 2009). Additionally, we hybridized one sample from Lgr5-EGFP high and one sample from Lgr5-EGFP low cells, obtained from Lgr5-EGFP knock-in mice (Barker et al., 2007).

first: Anna

last: Merlos


title: Expression data from mouse oral keratinocyte

city: Guangzhou

first: Tong

last: Wu

state: Guangdong

address: Zhongshaner Road

country: China

institute: Sun Yat-sen University

summary:
Keratinocytes are the major constituent of epithelial cells at mucosal surfaces and skin, which cover organs, internal cavities and the body. Traditionally, keratinocytes have been considered as an inert component of the multilayered epithelium to protect the subepithelial compartments from the pathogenic microorganisms, toxic stimuli and physical trauma. However, accumulated researches of the airway, gastrointestinal tract and skin have demonstrated that keratinocytes function in the development of the immune system, promotion of pathologic inflammation and even impose diverse decisions on immune cells.
We used microarrays to detail the global gene expression of oral keratinocyte during oral adaptive immune response.

overall_design: Oral keratinocyte were collected at three time points (control, 48h and 96h) in oral adaptive immune response for RNA extraction and hybridization on Affymetrix microarrays

first: Bin

last: Cheng


title: Expression data from granulocytic MDSC (G-MDSC) and neutrophils

status: Public on Mar 10 2011

city: Tampa

first: Je-In

last: Youn

state: FL

address: 12902 Magnolia Drive

institute: H. Lee. Moffitt Cancer Center

summary:
Myeloid derived suppressor cells (MDSC) playing the immune suppressive roles in tumor bearing host consists of two major subsets of granulocytic and monocytic cells. Granulocytic MDSC (G-MDSC) express CD11b+ Gr-1high Ly6G+ Ly6Clow and produce high level of reactive oxygen species (ROS). Interestingly, neutrophils are well known ROS producing cells during immune defensive process and share same surface markers with G-MDSC. These similar features always brought the fundamental questions what’s the difference between G-MDSC and neutrophils but it’s not yet proven clearly.
In this study, we examined the gene expression of G-MDSC and neutrophils using Affymetrix microarray

overall_design: G-MDSC (CD11b+Ly6G+Ly6Clow) were purifed from splenocytes in EL4 lymphoma tumor bearing mice by positive selection of Ly6G using microbeads isolation. Neutrophils were purified from ascitic fluids induced after injection of milk protein, casein by negative selection of F4/80 and positive selection of Ly6G using microbeads isolation. Their RNA was extracted and gene expression was analyzed using Affymetrix microarray.

first: Dmitry

middle: I

last: Gabrilovich


title: Expression data from P14 TCR cytotoxic T cells overexpressing HDAC7 phosphorylation deficient mutant

status: Public on Mar 13 2011

city: DUNDEE

first: Maria

middle: N

last: Navarro

address: Dow Street

department: Cell Signallig and Immunology

country: United Kingdom

institute: University of Dundee

summary: The present study reports an unbiased analysis of the cytotoxic T cell serine-threonine phosphoproteome using high resolution mass spectrometry. Approximately 2,000 phosphorylations were identified in CTLs of which approximately 450 were controlled by TCR signaling. A significantly overrepresented group of molecules identified in the phosphoproteomic screen were transcription activators, co-repressors and chromatin regulators. A focus on the chromatin regulators revealed that CTLs have high expression of the histone deacetylase HDAC7 but continually phosphorylate and export this transcriptional repressor from the nucleus. HDAC7 dephosphorylation results in its nuclear accumulation and suppressed expression of genes encoding key cytokines, cytokine receptors and adhesion molecules that determine CTL function. The screening of the CTL phosphoproteome thus reveals intrinsic pathways of serine-threonine phosphorylation that target chromatin regulators in CTLs and determine the  CTL functional program. We used Affymetrix microarray analysis to explore the molecular basis for the role of HDAC7 in CTLs and the impact of GFP-HDAC7 phosphorylation deficient mutant expression on the CTL transcriptional profile.

overall_design: In vitro generated P14 TCR cytotoxic T cells were retrovirally infected with a construct encoding GFP-HDAC7 phosphorylation deficient mutant, sorted in base of GFP expression (GFP positive and GFP negative) and processed for microarray analysis in three biological replicas.

first: Carmen

last: Feijoo-Carnero


title: Gene expression analysis of mouse ear samples treated with chemical allergen

city: Toledo

first: masaaki

last: miyazawa

state: OH

address: 3000 Arlington Ave

department: Medical Microbiology and Immunology

institute: University of Toledo College of Medicine

summary:
Identification of chemical allergen inducible genes in mouse skin.
Ear samples were isolated from CL57BL/6 mice 6 hours after topical application of a prototypic chemical allergen, a skin irritant or vehicle alone.

overall_design: Total RNA were extracted from ear skin samples treated with a chemical allergen, a skin irritant, or vehicle alone for 6 hours.


title: Protocol Dependence of Sequencing-based Gene Expression Measurements

status: Public on Mar 24 2011

city: Cambridge

first: John

middle: F

last: Thompson

state: MA

address: One Kendall Square

department: Genomic Sciences

institute: Helicos BioSciences

type: Expression profiling by high throughput sequencing

type: Non-coding RNA profiling by high throughput sequencing

summary: RNA samples from human tissues (brain and liver) and cell lines (K562 and HL60) were used to assess RNA fragmentation, RNA fractionation, cDNA synthesis, and single versus multiple tag counting.  Technical replicates and different cDNA synthesis protocols were compared.  Though protocols employing polyA RNA selection generate the highest number of non-ribosomal reads and the most precise measurements for coding transcripts, such protocols were found to detect only a fraction of the non-ribosomal RNA in human cells.  PolyA RNA excludes thousands of annotated and even more unannotated transcripts, resulting in an incomplete view of the transcriptome.  Ribosomal-depleted RNA provides a more cost-effective method for generating complete transcriptome coverage.  Expression measurements using single tag counting provided advantages for assessing gene expression and for detecting short RNAs relative to multi-read protocols.  Detection of short RNAs was also hampered by RNA fragmentation.

overall_design: 69 different sequencing channels from a HeliScope Genetic Analysis System and 2 channels from an Illumina machine are included.  Some samples were sequenced on multiple channels and some samples include technical replicates.

first: Tal

last: Raz

first: Philip

last: Kapranov

first: Doron

last: Lipson

first: Stan

last: Letovsky

first: Patrice

last: Milos


title: Reactive oxygen species induced gene expression changes on dendritic cells

summary:
Identification of ROS induced genes on dendritic cells
Dendritic cells were incubated for 15 min with or without a ROS inhibitor (DPI), washed extensively and incubated for 30 min with a chemical allergen (DNFB), hydrogen peroxide, and vehicle alone in HBSS containing DPI or vehicle. After washed extensively, the samples were post-incubated for 5.5 h with DNFB, hydrogen peroxide, or vehicle in complete culture medium containing DPI or vehicle.

overall_design: Total RNA was extracted from cells treated with a chemical allergen, hydrogen peroxide, and vehicle alone in the presence or absence of a ROS inhibitor.

first: Masaaki

last: Miyazawa

first: Akira

last: Takashima


title: Gene expression from bronchial and nasal epithelial cell samples of healthy current and never smokers.

city: Bosotn

first: Xiaoling

last: Zhang

address: 715 Albany Street

department: Pulmonary

institute: Boston University

summary: mRNA expression was assayed from bronchial epithelial cells collected via bronchoscopy and nasal epithelial cells collected by brushing the inferior turbinate  from healthy current and never smoker volunteers in order to determine the relationship between smoking-related gene expression changes in bronchial and nasal epithelium within the same individual.

overall_design: Bronchial epithelial cells were collected from current and never smokers via bronchoscopy, and nasal epithelial cells were collected by brushing the inferior turbinate during the same clinic visit. 1ug of RNA was isolated and hybridized to Affymetrix Human Exon 1.0 ST microarrays to obtain mRNA expression. The genome build upon which transcript assignments are based is hg18 (HuEx-1_0-st-v2.na27.hg18.transcript.csv).

first: Avrum

last: Spira


title: Expression data from affected skin from psoriasis mouse models and normal skin from control mice

status: Public on Mar 03 2011

city: Boston

first: William

last: Swindell

address: 77 Avenue Louis Pasteur

department: Genetics

institute: Harvard University

summary:
Development of a suitable mouse model would facilitate the investigation of pathomechanisms underlying human psoriasis and would also assist in development of therapeutic treatments.   However, while many psoriasis mouse models have been proposed, no single model recapitulates all features of the human disease, and standardized validation criteria for psoriasis mouse models have not been widely applied. In this study, whole-genome transcriptional profiling is used to compare gene expression patterns manifested by human psoriatic skin lesions with those that occur in five psoriasis mouse models (K5-Tie2, imiquimod, K14-AREG, K5-Stat3C and K5-TGFbeta1). While the cutaneous gene expression profiles associated with each mouse phenotype exhibited statistically significant similarity to the expression profile of psoriasis in humans, each model displayed distinctive sets of similarities and differences in comparison to human psoriasis. For all five models, correspondence to the human disease was strong with respect to genes involved in epidermal development and keratinization. Immune and inflammation-associated gene expression, in contrast, was more variable between models as compared to the human disease. These findings support the value of all five models as research tools, each with identifiable areas of convergence to and divergence from the human disease. Additionally, the approach used in this paper provides an objective and quantitative method for evaluation of proposed mouse models of psoriasis, which can be strategically applied in future studies to score strengths of mouse phenotypes relative to specific aspects of human psoriasis.
Global transcriptional profiling was utilized to evaluate the similarity between human psoriasis and the psoriasis-like phenotypes that develop in five mouse models (K5-Tie2, IMQ, K14-AREG, K5-Stat3C, K5-TGFbeta1)

overall_design: Expression patterns associated with mouse phenotypes were evaluated by comparing lesional skin from transgenic or IMQ-treated mice (n = 2-3) with normal skin obtained from control mice (n = 2-3).

first: Andrew

last: Johnston

first: Johann

last: Gudjonsson


title: Alternatively Spliced Variants of Interleukin-4 Promote Inflammation Differentially

status: Public on Mar 07 2011

city: Baltimore

first: Sergei

last: Atamas

address: 10 S. Pine St., MSTF 834

department: Department of Medicine

institute: University of Maryland School of Medicine

summary:
IL-4d2 is a natural splice variant of IL-4 which lacks the region encoded by the second exon. Numerous recent reports suggested that the expression levels of IL-4d2 change in various diseases, especially those with pulmonary involvement, but the effects of IL-4d2 on the lungs in vivo have never been studied. Replication-deficient adenovirus-mediated gene delivery of mouse IL-4d2 to mouse lungs in vivo was used, and the effects compared with similar adenoviral delivery of mouse IL-4 or with infection with a NULL viral construct.
The objective was to determine whether full-length wild-type Interleukin-4 encoded by exons 1-4 (IL-4) and alternatively spliced variant econded by exons 1,3, and 4 (IL-4d2) differentially affect gene expression in the lungs in vivo. The results show that IL-4d2 and IL-4 affected global gene expression differentially.

Keywords: Comparative analysis of gene delivery of alternative splice variants in vivo

overall_design: There were three mice overexpressing mouse IL-4 in their lungs, three mice overexpressing mouse IL-4d2 in their lungs, and three mice similarly infected with control AdV-NULL virus not encoding a cytokine.


title: Expression analysis of mouse embryonic stem cell (mESC) derived neuronal cell-types

status: Public on Mar 04 2011

city: Stockholm

first: Lia

last: Panman

address: Nobelsvag 3

institute: LICR

summary:
The generation of specific types of neurons from stem cells offers important opportunities in regenerative medicine. However, future applications and proper verification of cell identities will require stringent ways to generate homogenous neuronal cultures. Here we show that under permissive culturing conditions individual transcription factors can induce a desired neuronal lineage from virtually all expressing cells by a mechanism resembling developmental binary cell fate switching. Such efficient selection of cell fate resulted in remarkable cellular enrichment that enabled global gene expression validation of generated neurons and identification of novel features in the studied cell lineages. Several sources of stem cells have a limited competence to differentiate into e.g. dopamine neurons. However, we show that the combination of factors that normally promote either regional or dedicated neuronal specification can overcome limitations in cellular competence and promote efficient reprogramming also in more remote neural contexts, including human neural progenitor cells.
We used microarray analysis to verify the identity of several mESC derived neuronal cell types. By genome-wide gene expression comparisons we  gained novel insights into  molecular properties of several clinical relevant neuronal cell types.

overall_design: Total RNA was extracted from wild-type and transcription-factor induced mESC derived post-mitotic neurons and hybridized on Affymetrix arrays. In total triplicates of 9 different samples were analyzed. Wild-type samples served as control samples.

first: Thomas

last: Perlmann


title: NFATc1 controls the survival, function and suppressive capacity of B lymphocytes upon B cell receptor stimulation

city: Wuerzburg

first: Ellen

last: Leich

department: Institute of Pathology

institute: University of Wuerzburg

summary: Triggering of B cell receptors (BCR) induces a massive synthesis of NFATc1 in splenic B cells. By inactivating the Nfatc1 gene and re-expressing NFATc1 we show that NFATc1 levels are critical for the survival of splenic B cells upon BCR stimulation. NFATc1 ablation led to decreased BCR-induced Ca++ flux and proliferation of splenic B cells, increased apoptosis and suppressed germinal centre formation and immunoglobulin class switch by T cell-independent antigens. By controlling IL-10 synthesis in B cells, NFATc1 supported the proliferation and IL-2 synthesis of T cells in vitro and appeared to contribute to the mild clinical course of Experimental Autoimmune Encephalomyelitis in mice bearing NFATc1-/- B cells. These data indicate NFATc1 as a key factor controlling B cell function.

overall_design: Splenic mice cells were isolated from mice bearing NFATc1 deficient B-cells and from control mice, stimulated with anti-IgM for 0h, 3h, 8h and 16h, respectively and isolated using Milteny beads to enrich the B cell population. This experiment was performed in 3 biological replicates.

first: Sankar

last: Bhattacharyya

first: Jolly

last: Deb

first: Amiya

last: Patra

first: Duong

last: Pham

first: Chen

last: Wen

last: Benkert

first: Martin

last: Vaeth

first: Friederike

last: Berberich-Siebelt

first: Stefan

last: Klein-Hessling

last: Müller

first: Julia

last: Jellusova

first: Astrid

last: Schweizer

first: Lars

last: Nitschke

first: Andreas

last: Rosenwald

first: Swen

last: Engelmann

first: Ursula

last: Bommhardt

first: Andris

last: Avots

first: Anjana

last: Rao

first: Eisaku

last: Kondo

first: Edgar

last: Serfling


title: Supplementary dietary calcium stimulates faecal fat and bile acid excretion, but does not protect against obesity and insulin resistance in C57BL/6J mice

city: Wageningen

first: Guido

last: Hooiveld

address: HELIX, Stippeneng 4

department: Div. Human Nutrition & Health

country: Netherlands

institute: Wageningen University

summary:
There is increased interest in the potential protective role of dietary Ca in the development of metabolic disorders related to the metabolic syndrome. Ca-induced intestinal precipitation of fatty acids and bile acids as well as systemic metabolic effects of Ca on adipose tissue is proposed to play a causal role. In this experiment, we have studied all these aspects to validate the suggested protective effect of Ca supplementation, independent of other dietary changes, on the development of diet-induced obesity and insulin resistance. In our diet intervention study, C57BL/6J mice were fed high-fat diets differing in Ca concentrations (50 v. 150 mmol/kg). Faecal excretion analyses showed an elevated precipitation of intestinal fatty acids (2·3-fold; P < 0·01) and bile acids (2-fold; P < 0·01) on the high-Ca diet. However, this only led to a slight reduction in fat absorption (from 98 to 95 %; P < 0·01), mainly in the distal small intestine as indicated by gene expression changes. We found no effect on body-weight gain. Lipolysis and lipogenesis-related parameters in adipose tissue also showed no significant changes on the high-Ca diet, indicating no systemic effects of dietary Ca on adiposity. Furthermore, early gene expression changes of intestinal signaling molecules predicted no protective effect of dietary Ca on the development of insulin resistance, which was confirmed by equal values for insulin sensitivity on both diets. Taken together, our data do not support the proposed protective effect of dietary Ca on the development of obesity and/or insulin resistance, despite a significant increase in fecal excretion of fatty acids and bile acids.

Keywords: Diet intervention study

overall_design: Nine-week-old mice were fed a high fat purified diet with a low calcium concentration of  50mmol/kg (LCa diet) or a high calcium concentration of 150mmol/kg (HCa diet) for 8 weeks. Body weight was recorded weekly and after 7 weeks of diet intervention an oral glucose tolerance test was performed. For microarray analysis, after 2 weeks of diet intervention, 6 mice per diet group were anaesthetized with a mixture of isofluorane (1.5%), nitrous oxide (70%) and oxygen (30%) and the small intestines were excised. Adhering fat and pancreatic tissue were carefully removed. The small intestines were divided in three equal parts along the proximal to distal axis (SI 1, SI 2 and SI 3) and microarray analysis was performed on pooled mucosal scrapings.

first: Nicole

last: de Wit

first: Els

last: Oosterink

first: Hanneke

last: Bosch-Vermeulen

first: Michael

last: Muller

first: Roelof

last: van der Meer


title: Expression data from non-metastatic and metastatic osteosarcoma cells

city: Tokyo

first: Takeshi

middle: G

last: Kashima

address: Hongo 7-3-1

department: Pathology

institute: University of Tokyo

summary:
Osteosarcoma (OS) is the malignant bone tumor with a high tendency to metastasize to the lung, where the molecular mechanisms are unclear. The mouse OS cell line LM8 has been isolated originally from the Dunn OS cell line by in vivo selection as a subline with a high metastatic potential to the lung.
We used gene chip-based global gene expression analysis of differential screening between parental Dunn and LM8 cells in order to reveal genes predominantly expressed in LM8 cells, which correlate with high metastatic potential.

overall_design: 2 cell lines

first: Masahiko

last: Fujiwara

first: Daisuke

last: Komura


title: FoxOs are lineage-restricted redundant tumor suppressors and regulate endothelial cell homeostasis.

first: Yonghong

last: Xiao

address: 450 Brookline Ave., HIM218A

institute: Dana-Farber Cancer Institute

summary: Activated phosphoinositide 3-kinase (PI3K)-AKT signaling appears to be an obligate event in the development of cancer. The highly related members of the mammalian FoxO transcription factor family, FoxO1, FoxO3, and FoxO4, represent one of several effector arms of PI3K-AKT signaling, prompting genetic analysis of the role of FoxOs in the neoplastic phenotypes linked to PI3K-AKT activation. While germline or somatic deletion of up to five FoxO alleles produced remarkably modest neoplastic phenotypes, broad somatic deletion of all FoxOs engendered a progressive cancer-prone condition characterized by thymic lymphomas and hemangiomas, demonstrating that the mammalian FoxOs are indeed bona fide tumor suppressors. Transcriptome and promoter analyses of differentially affected endothelium identified direct FoxO targets and revealed that FoxO regulation of these targets in vivo is highly context-specific, even in the same cell type. Functional studies validated Sprouty2 and PBX1, among others, as FoxO-regulated mediators of endothelial cell morphogenesis and vascular homeostasis.

overall_design: Mice were engineered with negative control (MxCre- Fk1 L/L Fk2 L/L Afx L/L) and experimental (MxCre+ Fk1 L/L Fk2 L/L Afx L/L) genotypes. RNAs were isolated from Lung endothelial cells (2 negative controls, 2 experimental), liver sinusoidal endothelial cells (3 negative controls, 3 experimental) and thymus cells (2 negative controls, 2 experimental), and profiled on Affymetrix Mouse Genome 430 2.0 Array.

first: Ji-Hye

last: Paik

first: Ramya

last: Kollipara

first: Gerald

last: Chu

first: Hongkai

last: Ji

first: Zhihu

last: Ding

first: Lili

last: Miao

first: Zuzana

last: Tothova

first: James

middle: W

last: Horner

first: Daniel

last: Carrasco

first: Shan

last: Jiang

first: Gary

last: Gilliland

first: Lynda

last: Chin

first: Wing

middle: H

last: Wong

first: Diego

last: Castrillon

first: Ronald

last: DePinho


title: Expression data from mouse ovarian surface epithelium cells at different stages of malignancy

city: Blacksburg

first: Eva

last: Schmelz

state: VA

address: Virginia Tech

department: HNFE

institute: Virginia Tech

summary:
Ovarian cancer is one of the most deadly cancers accounting for only 3% of diagnosed cancers, but is the fifth leading cause of cancer deaths among woman; however, the progression of ovarian cancer is poorly understood.  To study and further understand the early events that lead to epithelial derived ovarian cancer, we previously developed a cell model of progressive ovarian cancer. Mouse ovarian surface epithelial (MOSE) cells have undergone spontaneous transformation in cell culture and represent pre-neoplastic, non-tumorigenic to an aggressive malignant phenotype.
Microarray analysis was performed with RNA isolated from different stages of MOSE cells to examine changes in gene expression as MOSE cells transition from a pre-neoplastic to a malignant state.

overall_design: RNA was isolated from MOSE early cell representing a pre-neoplastic, non-malignant stage, MOSE Intermediate cells representing a noeplastic, pre-invasive state, and MOSE Late cells representing a malignant, invasive stage.  Three biological replicates were used to take into account variations within the heterogeneous cultures.

first: Amy

last: Creekmore


title: SIRT3 opposes metabolic reprogramming of cancer cells through HIF1a destabilization

first: Marcia

last: Haigis

address: 77 Ave Louis Pasteur

institute: Harvard Medical School

summary: Tumor cells exhibit aberrant metabolism characterized by high glycolysis even in the presence of oxygen. This metabolic reprogramming, known as the Warburg effect, provides tumor cells with the substrates and redox potential required for the generation of biomass. Here, we show that the mitochondrial NAD-dependent deacetylase SIRT3 is a crucial regulator of the Warburg effect. SIRT3 loss promotes a metabolic profile consistent with high glycolysis required for anabolic processes in vivo and in vitro. Mechanistically, SIRT3 mediates metabolic reprogramming independently of mitochondrial oxidative metabolism and through HIF1a, a transcription factor that controls expression of key glycolytic enzymes. SIRT3 loss increases reactive oxygen species production, resulting in enhanced HIF1a stabilization. Strikingly, SIRT3 is deleted in 40% of human breast cancers, and its loss correlates with the upregulation of HIF1a target genes. Finally, we find that SIRT3 overexpression directly represses the Warburg effect in breast cancer cells. In sum, we identify SIRT3 as a regulator of HIF1a and a suppressor of the Warburg effect.

overall_design: RNA isolated from brown adipose tissue of SIRT3 WT and KO mice. 5 wild-type samples and 5 SIRT3 KO samples

first: Lydia

last: Finley

first: Arkaitz

last: Carracedo

first: Jaewon

last: Lee

first: Amanda

last: Souza

first: Ainara

last: Egia

first: Jiangwen

last: Zheng

first: Julie

last: Teruya-Feldstein

first: Paula

last: Moreira

first: Sandra

last: Cardoso

first: Clary

last: Clish

first: Pier

last: Pandolfi


title: Prognostic Gene Expression Signature of Carcinoma Associated Fibroblasts in Non-Small Cell Lung Cancer [expression profiling_NSCLC stroma]

status: Public on Apr 08 2011

city: Toronto

first: Ming-Sound

last: Tsao

country: Canada

institute: Ontario Cancer Institute/ Princess Margaret Hospital

summary: The tumor microenvironment strongly influences cancer development, progression and metastasis. The role of carcinoma-associated fibroblasts (CAFs) in these processes and their clinical impact has not been studied systematically in non-small cell lung carcinoma (NSCLC). We established primary cultures of CAFs and matched normal fibroblasts (NFs) from 15 resected NSCLC. We demonstrate that CAFs have greater ability than NFs to enhance the tumorigenicity of lung cancer cell lines. Microarray gene expression analysis of the 15 matched CAF and NF cell lines identified 46 differentially expressed genes, encoding for proteins that are significantly enriched for extracellular proteins regulated by the TGF-beta signaling pathway. We have identified a subset of 11 genes that formed a prognostic gene expression signature, which was validated in multiple independent NSCLC microarray datasets. Functional annotation using protein-protein interaction analyses of these and published cancer stroma-associated gene expression changes revealed prominent involvement of the focal adhesion and MAPK signalling pathways. Fourteen (30%) of the 46 genes also were differentially expressed in laser-capture micro-dissected corresponding primary tumor stroma compared to the matched normal lung. Six of these 14 genes could be induced by TGF-beta1 in NF. The results establish the prognostic impact of CAF-associated gene expression changes in NSCLC patients.

overall_design: 30 samples: 15 primary lung tumor stroma, 15 normal lung parenchyma

first: Roya

last: Navab

first: Dan

last: Strumpf


title: Expression data from murine PBCs from mice with advanced mammary tumors and their tumor-free counterparts.

status: Public on Mar 01 2011

city: Durham

first: Erich

last: Huang

state: NC

address: 101 Science Drive

department: Institute for Genome Sciences and Policy

institute: Duke University

summary: Female MMTV/c-MYC transgenic mice expressed the c-MYC proto-oncogene or a more stable point mutation variant (T58A) of the gene under the control of the hormone-responsive MMTV long terminal repeat (LTR) in an FVB/NJ background (Jackson Laboratories, Bar Harbor, ME). The hormones released during pregnancy and lactation have been shown to enhance expression of the oncogene. Thus, the mice were maintained in a continuous breeding program. Mice were monitored twice weekly for tumor development by palpation and tumors were measured twice weekly. Once the tumors reached 3cm3 the animals were sacrificed and tissue was obtained to confirm the tumors by histological analysis. As a control, female mice of the same age and background strain were maintained in the same facility and under the same breeding conditions as their transgenic counterparts.

overall_design: Blood (50-250 µL, based on weight of the mouse) was collected from MMTV/c-MYC female mice and controls at regular intervals (approximately once per month) and again prior to euthanization (average age 431 days).

first: Heather

last: LaBreche

first: Joseph

middle: R

last: Nevins


title: Expression data from WT, Crebbp+/- and Ep300+/- bone marrow stroma

city: San Antonio

first: Vivienne

last: Rebel

state: TX

address: 8403 Floyd Curl Drive

institute: UTHSCSA

summary: We found that the bone marrow microenvironment of Crebbp+/- mice was unable to properly maintain the immature stem - and progenitor pools. Instead, it stimulates myeloid differentiation that progresses into a myeloproliferative-like disease. Since CREBBP is a transcriptional co-activator, we used gene expression analysis to globally assess functional deficiencies in Crebbp+/- bone marrow stroma cells at a molecular level. Ep300 encodes a protein which is highly similar in structure and function to CREBBP; nevertheless, Ep300+/- mice suffer neither excessive myeloid differentiation nor loss of HSCs. Therefore, to identify expression changes specifically related to Crebbp heterozygosity, we focused on genes that showed significant differences in expression levels between Crebbp+/- and wild-type bone marrow stroma but no difference between Ep300+/- and wild-type.

overall_design: Bone marrow stroma was established from wild-type, Crebbp+/- and Ep300+/- mice that were 3-4 months old for RNA extraction and hybridization on Affymetrix microarrays. There are 4 biological replicates for each genotype used.


title: HP1gamma Knock Down  in Human cells

status: Public on Feb 27 2011

city: Paris

first: Violaine

last: Saint-André

address: 26 rue d'Ulm

country: France

institute: Institut Curie

summary:
Study of HP1 Knock Down on gene expression and splicing regulation in Human HeLa cells
Maturation of pre-mRNAs is initiated co-transcriptionally. It is therefore conceivable that chromatin-borne information participates in alternative splicing. Here, we find that elevated levels of tri-methylation of histone H3 on lysine 9 (H3K9me3) are a characteristic of the alternative exons of several genes including CD44. On this gene, the chromodomain protein HP1gamma, frequently defined as a transcriptional repressor, facilitates inclusion of the alternative exons via a mechanism involving decreased RNA polymerase II elongation rate. In addition, accumulation of HP1gamma on the variant region of the CD44 gene stabilizes association of the pre-mRNA with the chromatin. Altogether, our data provide evidence for localized histone modifications impacting alternative splicing. They further implicate HP1gamma as a possible bridging molecule between the chromatin and the maturating mRNA, with a general impact on splicing decisions.

overall_design: Transcriptome analysis of siRNA anti-HP1gamma transfected HeLa cells on GeneChip® Human Exon 1.0 ST Arrays (Affymetrix). Control HeLa cells have been transfected with the same concentration of siRNA anti-GAPDH. Experiment has been done in experimental triplicates.

first: Eric

last: Batsché

first: Christian

last: Muchardt


title: Effects of HMGN variants on cellular transcription profile

status: Public on Feb 28 2011

city: Rostock

first: Leila

last: Taher

address: Ernst-Heydemann-Str. 8

institute: University of Rostock

summary:
HMGN (high mobility group N) is a family of intrinsically disordered nuclear proteins that binds to nucleosomes, alters the structure of chromatin and affects transcription. A major unresolved question is the extent of functional specificity, or redundancy, between  the various members of the HMGN protein family.
Here we analyze the transcriptional profile of cells in which the expression of various HMGN proteins has been either deleted or doubled. The results reveal an HMGN-variant specific effect on the fidelity of the cellular transcription profile, indicating that functionally, the various HMGN subtypes are not fully redundant.

overall_design: RNA was collected from either primary knock-out MEFs or SV40-transformed MEFs and MIN6 cells over expressing various HMGN proteins and mutants and hybridized to Affymetrix arrays. We obtained a double ammount of HMGN proteins in MEFs and MIN6 cells by retroviral infection and subsequent selection procedure. We collected all infected cells (pools, not clones) in order to eliminate the effect of viral integration in the genome.

first: Mark

last: Rochman


title: Identification of Metastasis-prone Lung Adenocarcinoma Cell Population That Is Sensitive to Notch Inhibition

status: Public on Feb 24 2011

city: Houston

first: Chad

last: Creighton

address: One Baylor Plaza, Mail Stop: BCM305

department: Biostatistics, Ducan Cancer Center

institute: Baylor College of Medicine

summary:
Tumor cells that give rise to metastatic disease are a primary cause of cancer-related death and have not been fully elucidated in patients with lung cancer. Here, we addressed this question by using tissues from a mouse that develops metastatic lung adenocarcinoma owing to expression of mutant K-ras and p53. We identified a metastasis-prone population of tumor cells that differed from those with low metastatic capacity on the basis of having sphere-forming capacity in Matrigel cultures, increased expression of CD133 and Notch ligands, and relatively low tumorigenicity in syngeneic mice. Knockdown of jagged1 or pharmacologic inhibition of its downstream mediator phosphatidylinositol 3-kinase abrogated the metastatic but not the tumorigenic activity of these cells. We conclude from these studies on a mouse model of lung adenocarcinoma that CD133 and Notch ligands mark a population of metastasis-prone tumor cells and that the efficacy of Notch inhibitors in metastasis prevention should be explored.

Keywords: two group comparison

overall_design: 344SQ subcutaneous tumors (from a lung adenocarcinoma cell line derived from a KrasLA1/+; p53R172HdelG/+ mouse that metastasizes widely following subcutaneous injection into syngeneic mice) were sorted by flow cytometry into CD133high and CD133low fractions.  RNA samples from these fractions were processed and analyzed on Affymetrix Mouse Expression Array 430A 2.0 chips.

first: Jon

last: Kurie

first: Yanan

last: Yang

first: Don

last: Gibbons

first: Wei

last: Lin


title: Wnt and Tcf3-mediated regulation of gene expression in mouse embryonic stem cells

city: Chicago

first: Bradley

last: Merrill

address: 900 S. Ashland Ave

institute: University of Illinois at Chicago

summary:
The observation that Tcf3 (MGI name: Tcf7l1) bound the same genes as core stem cell transcription factors, Oct4 (MGI name:Pou5f1), Sox2 and Nanog, revealed a potentially important aspect of the poorly understood mechanism whereby Wnts stimulate self renewal of pluripotent mouse embryonic stem (ES) cells.  Although the conventional view of Tcf proteins as the β-catenin-binding effectors of Wnt signaling suggested Tcf3 should activate target genes in response to Wnts, here we show that Wnt3a and Tcf3 effectively antagonize each other’s effects on gene expression. Genetic ablation of Tcf3 caused similar effects as treating cells with recombinant Wnt3a.
Moreover, Tcf3 was not necessary for Wnt3a-stimulation of gene expression as the majority of Wnt3a-stimulated genes exhibited a greater increase in Tcf3-/- ES cells than in Tcf3+/+ ES cells. These expression data, together with genetic experiments, show that Wnt3a stimulates ES cell self renewal by inhibiting Tcf3.

overall_design: Tcf3+/+ and Tcf3-/- mouse embryonic stem cells were cultured in self renewal conditions containing recombinant Wnt3a for RNA extraction and hybridization on Affymetrix microarrays.

first: Fei

last: Yi

middle: J


title: Transcriptome analysis on gastric cancer

city: Athens

first: Juan

last: Cui

address: 120 Green Street

department: Biochemistry and Molecular Biology

institute: University of Georgia

summary: Reliable identification of cancer markers can have substantial implications to early detection of cancer. We report here an integrated computational and experimental study on identification of gastric cancer markers in patients’ tissue and sera based on (i) genome-scale transcriptomic analyses on 80 paired gastric cancer/reference tissues, with the aim of identifying abnormally expressed genes at various subtypes/stages of gastric carcinoma (ii) a computational identification of differentially expressed genes that may have their proteins secreted into blood circulation, followed by experimental validations.

overall_design: 160 Total samples were analyzed on paried tumor and adjacent normal tissues from 80 gastric cancer patients.  Differential analysis identified genes with a fold-change  over 1.5.

first: Ying

last: Xu


title: ERK5 Regulates Muscle Cell Fusion through Klf Transcription Factors

status: Public on Feb 21 2011

city: Kyoto

first: Eisuke

last: Nishida

address: Kitashirakawa, Sakyo-ku

department: Department of Cell and Developmental Biology

institute: Graduate School of Biostudies, Kyoto University

summary: In skeletal muscle differentiation, muscle-specific genes are regulated by two groups of transcription factors, the MyoD and MEF2 families, which work together to drive the differentiation process. Here we show that ERK5 regulates muscle cell fusion through Klf transcription factors. The inhibition of ERK5 activity suppresses muscle cell fusion with minimal effects on the expression of MyoD, MEF2, and their target genes. Promoter analysis coupled to microarray assay reveals that Klf-binding motifs are highly enriched in the promoter regions of ERK5-dependent upregulated genes. Remarkably, Klf2 and Klf4 expression are also upregulated during differentiation in an ERK5-dependent manner, and knockdown of Klf2 or Klf4 specifically suppresses muscle cell fusion. Moreover, we show that the Sp1 transcription factor links ERK5 to Klf2/4, and that nephronectin, a Klf transcriptional target, is involved in muscle cell fusion. Therefore, an ERK5/Sp1/Klf module plays a key role in the fusion process during skeletal muscle differentiation.

overall_design: To identify those genes whose expression levels are regulated by the ERK5 pathway in differentiating C2C12 cells, we performed genome-wide analysis by using Affymetrix GeneChip oligonucleotide microarrays. We performed two independent experiments. For each experiment, we used five samples: cells in growth medium (0 day), lacZ-infected cells at two time points (2.5 days and 4.5 days of differentiation) and dnMEK5-infected cells at two time points (2.5 days and 4.5 days of differentiation). Each virus was infected at 1 day of differentiation. Total RNA was prepared using the RNeasy Mini Kit (Qiagen) according to the manufacturer’s instructions. The total RNA of each condition was obtained from two independent experiments. Synthesis of cDNA in vitro transcription and biotin labeling cRNA, and hybridization to the Mouse Genome 430 2.0 array (Affymetrix) were performed according to Affymetrix protocols. Hybridized arrays were scanned using an Affymetrix GeneChip Scanner. Scanned Chip images were analyzed with GeneChip operating Software v.1.4 (GCOS) and GeneSpring GX 11.0.2. (Agilent technologies).

first: Kazunori

last: Sunadome

first: Takuya

last: Yamamoto


title: Expression data at 24 hours after the blocking of Shh signaling in tooth germs at embryonic day 14

status: Public on Feb 22 2011

city: Seoul

first: Sung-Won

last: Cho

address: Seongsanno 250, Seodaemun-gu

department: Oral Biology

country: South Korea

institute: Yonsei University College of Dentistry

summary:
The genetic mechanism governing the spatial patterning of teeth still remains to be elucidated. Sonic hedgehog (Shh) is one of key signaling molecules involved in the spatial patterning of teeth. By utilizing maternal transfer of 5E1 (an IgG1 monoclonal antibody against Shh protein) through the placenta to block Shh signaling, we investigated the changes in tooth patterning and in gene expression.
We used microarrays to detect specific genes related with Shh signaling in tooth germs and identified some specific genes up- or down-regulated after blocking of Shh signaling activity.

overall_design: Gene-chip expression analysis was performed with RNA from mandibular tooth germs from embryos of pregnant mice at one day after injection of 5E1 (an IgG1 monoclonal antibody against Shh protein; number of replicates =2), 40-1a (an IgG1 monoclonal antibody against β-galactosidase; number of replicates=2), cyclopamine (a specific Smo antagonist; number of replicates=2) or PBS (Phosphate buffered saline; number of replicates=2), using a Affymetrix mouse gene microarray.

first: Sung

first: Sungwook

last: Kwak

first: Han

last: Park

first: Min

last: Lee

first: Eun

last: Kim

first: Kyoung

first: Jong

first: Jeong

middle: O

last: Shin

first: Gi

first: Hyuk

last: Kwon

first: Liwen

last: Li

first: Jinglei

last: Cai

first: Eizo

last: Nakagawa

last: Jung


title: Ubb Knockout Mouse Testis

city: Pullman

first: Ryan

last: Evanoff

state: WA

department: School of Molecular Biosciences

institute: Washington State University

summary: Analysis of Ubb knockout mouse testes at 7, 4, 21, and 28 dpp.  Ubiquitin (Ub) is an essential protein found in all eukaryotic cells and plays important roles in a variety of cellular functions including germ cell development.  Targeted disruption of the polyubiquitin gene Ubb results in male and female infertility in mice with germ cells arrested at meiotic prophase I.

overall_design: Whole testes from wild-type (WT) and Ubb−/− (KO) mice were harvested at 7, 14, 21, and 28 days postpartum.  Total RNA was extracted and hybridized to Affymetrix Mouse Genome 430 2.0 arrays.

first: Kwon

middle: Y

last: Ryu

first: Shamim

last: Sinnar


title: Expression data from Bmi1-null c-Kit+Sca-1+Lineage marker- (KSL) hematopoietic stem/progenitor cells

city: Chiba

first: ATSUSHI

last: IWAMA

address: 1-8-1 Inohana, Chuo-ku

department: Department of Cellular and Molecular Medicine

institute: Graduate School of Medicine, Chiba University

summary: Bmi1 is a component of polycomb repressive complex 1 and its role in the inheritance of the stemness of adult somatic stem cells has been well characterized.  Bmi1 maintains the self-renewal capacity of adult stem cells, at least partially, by repressing the Ink4a/Arf locus that encodes a cyclin-dependent kinase inhibitor, p16Ink4a, and a tumor suppressor, p19Arf 14.  Deletion of both Ink4a and Arf in Bmi1-deficient mice substantially restored the defective self-renewal capacity of HSCs and neural stem cells.

overall_design: Purified KSL cells from BM of wild-type, Bmi1-/-, Ink4a-/-Arf-/-, and  Bmi1-/- Ink4a-/-Arf-/- mice were subjected to RNA extraction and hybridization on Affymetrix microarrays.

first: Atsushi

last: Iwama

first: Hideyuki

last: Oguro

first: Hitoshi

last: Ichikawa


title: Gene expression profiles using microarrays in mdx and mdx/MMP-2-/- mice at 1 and 3 months of age

status: Public on Feb 19 2011

city: Matsumoto

first: daigo

last: miyazaki

address: 3-1-1 Asahi

department: Department of Medicine (Neurology and Rheumatology)

institute: Shinshu University School of Medicine

summary: Matrix metalloprotease (MMP) -2 has been reported to be up-regulated in skeletal muscle in the lethal X-linked muscle disorder Duchenne muscular dystrophy (DMD), which is caused by loss of dystrophin. However, the role of MMP-2 in dystrophin-deficient muscle is not well known. The aim of this study was to verify the role of MMP-2 in dystrophin-deficient muscle by using mdx mice with genetic ablation of MMP-2 (mdx/MMP-2-/-). Gene expression profiles were analyzed in the skeletal muscle of mdx and mdx/MMP-2-/- mice at 1 and 3 months of age.

overall_design:
Tibialis anterior muscle was isolated from four groups of mice (mdx and mdx/MMP-2-/- mice at 1 and 3 months of age). Total RNA was purified and prepared for hybridization to Affymetrix Mouse Genome 430 2.0 arrays (Affymetrix Inc., Santa Clara, CA, USA) using Affymetrix reagents and protocols.
The mRNA levels of differentially expressed genes from gene chip analysis were confirmed by quantitative real-time PCR assay.

first: Daigo

last: Miyazaki

first: Akinori

last: Nakamura

first: Kazuhiro

last: Fukushima

first: Kunihiro

last: Yoshida

first: Shin’ichi

last: Takeda

first: Shu-ichi

last: Ikeda


title: Gene expression in E14 TG2a cells grown with or without LIF and sorted for 5T4 expression

status: Public on Feb 15 2011

city: Manchester

first: Crispin

last: Miller

address: Wilmslow Road

department: Applied computational Biology

institute: Paterson Institute for Cancer Research

summary: E14 TG2a cells grown with LIF were disaggregated and FACS sorted for cell surface 5T4 negativity versus E14 TG2a cells grown without LIF for 3 days  and sorted for 5T4 positivity.

overall_design: Two samples in triplicate. 5T4- vs. 5T4+

first: Peter

last: Stern


title: Differential Expression of Ove26(Diabetic) vs FVB(Nondiabetic) mice

city: New York

first: Ann

middle: Marie

last: Schmidt

state: NY

department: Department of Surgery

institute: Columbia University

summary:
Objective – Previous studies showed that genetic deletion or pharmacological blockade of the Receptor for Advanced Glycation Endproducts (RAGE) prevents the early structural changes in the glomerulus associated with diabetic nephropathy (DN).  To overcome limitations of mouse models that lack the progressive glomerulosclerosis observed in humans, we studied the contribution of RAGE to DN in the OVE26 type 1 mouse, a model of progressive glomerulosclerosis and decline of renal function.

Research Design and Methods – We bred OVE26 mice with homozygous RAGE knock out (RKO) mice and examined structural changes associated with DN and used inulin clearance studies and albumin:creatinine measurements to assess renal function. Affymetrix Mouse 430.2 microarrays were used to measure the differential expression of OVE26vsFVB(WT) mice.   Transcriptional changes in the TGF-β1 and Plasminogen activator inhibitor 1 gene products were measured by pcr to investigate mechanisms underlying accumulation of mesangial matrix in OVE26 mice.

Results - Deletion of RAGE in OVE26 mice reduced nephromegaly, mesangial sclerosis, cast formation, glomerular basement membrane thickening, podocyte effacement, and albuminuria. The significant 29% reduction in glomerular filtration rate observed in OVE26 mice was completely prevented by deletion of RAGE.  Increased transcription of the genes for Plasminogen activator inhibitor 1, TGF-β1, TGF-β induced, α1- (IV) collagen observed in OVE26 renal cortex significantly reduced in OVE26 RKO kidney cortex.  ROCK1 activity was significantly lower in OVE26 RKO compared to OVE26 kidney cortex.

Conclusions - These data provide compelling evidence for critical roles for RAGE in the pathogenesis of DN and suggest that strategies targeting RAGE in long-term diabetes may prevent loss of renal function.

overall_design: The differential gene expression of OVE26 (diabetics) vs FVB (nodiabetic WT) mice was measured using Affymetrix Mouse 430.2 arrays.

first: Nina

last: Reiniger

first: Kai

last: Lau

first: Daren

last: McCalla

first: Bonnie

last: Eby

first: Bin

last: Cheng

first: Yan

last: Lu

first: Wu

last: Qu

first: Nosirudeen

last: Quadri

first: Radha

last: Ananthakrishnan

first: Maryana

last: Furmansky

first: Rosa

last: Rosario

first: Fei

last: Song

first: Vivek

last: Rai

first: Alan

last: Weinberg

first: Richard

last: Friedman

first: Ravichandran

last: Ramasamy

first: Vivette

last: D'Agati

first: AnnMarie


title: Expression data from MMTV-PDK1 transgenic mice

status: Public on Feb 05 2011

city: Washington

first: Robert

last: Glazer

state: DC

address: 3970 Reservoir Rd, NW

department: Oncology

institute: Georgetown University

summary:
The role of PDK1 on mammary tumorigenesis and its interaction with PPARdelta, was assessed. Transgenic mice were generated in which PDK1 was expressed in the mammary epithelium.
We used microarrays to analyse global gene expression changes in MMTV-PDK1 transgenic mice versus wild-type mice and determine any differential responses to GW501516 treatment.

overall_design: RNA was isolated (RNeasy Mini Kit, Qiagen) from mammary gland tissue from nulliparious transgenic and wild-type mice maintained on normal rodent chow or a diet supplemented with GW501516 for 1 week.

first: Claire

last: Pollock


title: T cell genes regulated by retinoic acid

status: Public on Feb 14 2011

city: West Lafayette

first: Chang

last: Kim

state: IN

address: 725 Harrison St

department: Comparative Pathobiology

institute: Purdue

summary: This is to determine the T cell genes regulated by retinoic acid.

overall_design:
3 groups of CD4+ T cells (control, RA and Ro)
2 arrays were used for each group

first: Benjamin

last: Ulrich

first: Seung

last: Kang

first: Ann

last: Feil


title: [E-MTAB-131] Estrogen Receptor alpha estrogen-responsive binding sites in MCF-7

city: Hinxton

first: ArrayExpress

last: EBI

state: Cambridgeshire

address: Wellcome Trust Genome Campus

institute: European Bioinformatics Institute

summary:
We performed chromatin immunoprecipitation (ChIP) with two polyclonal anti-ERalpha antibodies directed against the N- and C-terminus of the protein, with or without estrogen treatment for 45 minutes of MCF-7 cells, and the immunoprecipitated DNA was sequenced with the Illumina/Solexa Genome Analyzer.

ArrayExpress Release Date: 2009-07-27

Publication Title: Estrogen receptor alpha controls a gene network in luminal-like breast cancer cells comprising multiple transcription factors and microRNAs.
Publication Author List: Cicatiello L, Mutarelli M, Grober OM, Paris O, Ferraro L, Ravo M, Tarallo R, Luo S, Schroth GP, Seifert M, Zinser C, Chiusano ML, Traini A, De Bortoli M, Weisz A.

Person Roles: submitter
Person Last Name: Mutarelli
Person First Name: Margherita
Person Mid Initials:
Person Email: mutarelli@tigem.it
Person Phone:
Person Address:
Person Affiliation:

Person Roles: investigator
Person Last Name: Weisz
Person First Name: Alessandro
Person Mid Initials:
Person Email: alessandro.weisz@unina2.it
Person Phone:
Person Address:
Person Affiliation:

overall_design:
Experimental Design: compound_treatment_design
Experimental Design: in_vivo_design
Experimental Design: binding_site_identification_design
Experimental Design: high_throughput_sequencing_design
Experimental Design: ChIP-seq
Experimental Factor Name:COMPOUND
Experimental Factor Name:TIME
Experimental Factor Name:IMMUNOPRECIPITATE
Experimental Factor Type: compound
Experimental Factor Type: time
Experimental Factor Type: immunoprecipitate
Quality Control Type: real_time_PCR_quality_control
Quality Control Type: technical_replicate


title: Prolyl hydroxylase PHD3 is essential for hypoxic regulation of neutrophilic inflammation in humans and mice

status: Public on Feb 08 2011

city: Sheffield

first: Sarah

middle: Ruth

last: Walmsley

address: Department of Infection and Immunity, The Medical School, Beech Hill Road

institute: University of Sheffield

summary:
Neutrophils were isolated form peripheral blood of wildtype and Phd3 null mice, cultured for 4 hours in hypoxia (3% O2) and micro array analysis performed
The aim of the present study is to identify the mechanism by which phd3 is required for the hypoxia mediated survival of neutrophils

overall_design: Murine peripheral blood neutrophils were isolated from wildtype and phd3 null mice, cultured for 4 hours in hypoxia (3% O2) and micro array analysis performed

first: Edwin

last: Chilvers

first: Alfred

last: Thompson

first: Kathryn

last: Vaughan

first: Helen

last: Marriott

first: Lisa

middle: C

last: Parker

first: Gary

last: Shaw

first: Selina

last: Parmar

first: Martin

last: Schneider

first: Ian

last: Sabroe

first: David

last: Dockrell

first: Marta

last: Milo

first: Cormac

middle: T

last: Taylor

first: Randall

last: Johnson

first: Christopher

last: Pugh

first: Peter

last: Ratcliffe

first: Patrick

last: Maxwell

first: Paeter

last: Carmeliet

first: Moira

middle: K

last: Whyte


title: Chronic Cigarette Smoke Exposure Results in Coordinated Methylation and Gene Expression Changes in Human Alveolar Macrophages

status: Public on Feb 03 2011

city: Iowa City

first: Thomas

last: Bair

state: IA

address: 335 EMRB

institute: University of Iowa

summary: Cigarette smoking is the leading cause of emphysema in the United States. Alveolar macrophages play a critical role in the inflammation-mediated remodeling of the lung parenchyma in emphysema. However, the exact gene pathways and the role of DNA methylation in moderating this pathological transformation are not known. In order to more exactly understand this process, we compared genome-wide expression and methylation signatures of alveolar macrophages isolated from heavy smokers with those isolated from non-smoking controls. We found enrichment of differential methylation in genes from immune system and inflammatory pathways as determined by standard pathway analysis. Consistent with recent findings, significant methylation changes were particularly enriched in the areas flanking CpG islands (CpG shores). Analysis of matching gene expression data demonstrated a parallel enrichment for changes in immune system and inflammatory pathways. We conclude that alveolar macrophages from the lungs of smokers demonstrate coordinated changes in DNA methylation and gene expression that link to inflammation pathways. We suggest that further studies of DNA methylation in immune and inflammation-related gene expression are needed to understand the pathogenesis of emphysema and other smoking-related diseases.

overall_design:
Expression analysis of 13 smokers vs. 10 non-smokers on the Affymetrix Exon Array.

This submission represents the expression component of the study.

first: Rory

middle: A

last: Sears

first: Linda

middle: S

last: Powers

first: Alicia

last: Gerke

last: Gross

first: Robert

last: Philibert

first: Martha

middle: M

last: Monick


title: [E-MTAB-115] ChIP-seq for FOXA2 HNF4a and NRF2 / GABP in HepG2

first: ArrayExpress

last: EBI

summary:
In each cell type the expression of genes is regulated by the action of a large number of transcription factors, but so far we have only a rudimentary knowledge of the location of the gene regulatory elements where they bind. This can now be addressed with genome-wide ChIP experiments. In a previous ChIP-chip study of USF1 and USF2 we found evidence also of binding of GABP, FOXA2 and HNF4a within the enriched regions. Here we have applied ChIP-seq for these transcription factors and identified 3064 peaks of enrichment for GABP, 7266 for FOXA2 and 18783 for HNF4a. HNF4a and FOXA2 binding was found in at least half of the regions previously identified as bound by USF2 but not USF1, showing that they frequently bind the same regulatory elements. GABP peaks were found at transcription start sites whereas 94 % of FOXA2 and 90 % of HNF4a peaks were located at other positions. We developed a method based on the high resolution achieved by ChIP-seq to accurately define TFBS within peaks, and found the predicted sites to have an elevated conservation level compared to peak centers; however the majority of bindings were not evolutionary conserved. An unexpected interaction between HNF4a and GABP was seen at TSS, with as many as 1/3 of the HNF4a positive promoters being bound also by GABP, and co-immunoprecipitations show that these factors are in the same complex in the nucleus.

ArrayExpress Release Date: 2009-06-10

Publication Title: Molecular interactions between HNF4a, FOXA2 and GABP identified at regulatory DNA elements through ChIP-sequencing
Publication Author List: Ola Wallerman, Mehdi Motallebipour, Stefan Enroth, Kalicharan Patra, MadhuSudan Reddy Bysani,  Jan Komorowski, Claes Wadelius

Person Roles: submitter
Person Last Name: Wallerman
Person First Name: Ola
Person Mid Initials:
Person Email: ola.wallerman@genpat.uu.se
Person Phone:
Person Address: IGP, Rudbecklab
Person Affiliation: Uppsala University

overall_design:
Experimental Design: high_throughput_sequencing_design
Experimental Design: binding_site_identification_design
Experimental Design: transcription profiling by high throughput sequencing
Experimental Factor Name: IMMUNOPRECIPITATE
Experimental Factor Name: LIBRARY_FRAGMENT_SIZE
Experimental Factor Type: immunoprecipitate
Experimental Factor Type: protocol


title: Functions of HDAC1 and HDAC2 in Schwann cells during postnatal

status: Public on Feb 25 2011

city: Zurich

first: Ueli

last: Suter

address: Schafmattstrasse 18

department: Cell Biology

institute: ETH Zurich

summary: The aim of our study is to determine the functions of histone deacetylases (HDACs) 1 and 2 in Schwann cells during postnatal development of the peripheral nervous system (PNS). Schwann cells are the myelinating glial cells of the PNS. At birth, mouse sciatic nerves mature in 2 subsequent phases: 1/ big caliber axons get sorted into a 1 to 1 relationship with Schwann cells, 2/ Schwann cells build a myelin sheath around sorted axons. In mice where both HDAC1 & HDAC2 have been specifically knocked out in Schwann cells, both phases are impaired. HDACs are chromatin remodeling enzymes, they can thus alter gene expression directly. We want to identify which genes controlled by HDAC1 and HDAC2 in Schwann cells are necessary for the maturation of sciatic nerves. Because HDAC1 and HDAC2 can compensate for each other loss to some extend, we will first analyze changes of gene expression in HDAC1/HDAC2 double KO animals. We expect to gain critical insights into the molecular mechanisms controlling Schwann cell differentiation and myelination. This knowledge is of key importance for the success of regenerative medicine in peripheral neuropathies, nerve tumors, and transplantation paradigms in non-regenerative CNS lesions and in large PNS injuries.

overall_design: 3 double knockout mutants for HDAC1 and HDAC2 and 3 control littermates were analyzed. Tissues analyzed: sciatic nerves of 2 day-old mouse pups

first: Claire

last: Jacob

first: Christian

last: Somandin


title: Expression data from control and Phospholipid dependent kinase 1 (PDK1) null cytotoxic T-lymphocytes (CTL) and from control and Akt inhibitor treated CTL

status: Public on Feb 01 2011

city: Dundee

first: maria

middle: carmen

last: feijoo

address: Dow Street

department: Cell biology and immunology

institute: University of Dundee

summary:
In cytotoxic T cells (CTL), Protein Kinase B /Akt is activated by the T cell antigen receptor (TCR) and the cytokine Interleukin 2 (IL2), in part by phosophorylation of Akt by Phospholipid dependent kinase 1 (PDK1).
The role of PDK1 and Akt in CTL has however not been fully defined.
In order to explore the relative roles of these kinases in CTL we used microarrays to profile the gene expression of control and PDK1 null CTL.
In separate experiments we compared the gene expression profiles of control and Akt inhibitor treated CTL.

overall_design:
CTL were generated from 3 mice each carrying two loxP flanked PDK1 alleles plus a tamoxifen inducible Cre transgene.
PDK1 was then deleted from these CTL by tamoxifen treatment and the gene expression pattern determined by microarray.
Tamoxifen treated PDK1wt/wt TamoxCre+ CTL generated from 3 PDK1wt/wt TamocCre+ mice were used as a control.
In separate experiments CTL were were generated from 3 wild-type mice and then half the CTL generated from each mouse were treated with the Akt inhibitor AktI-1/2.
The gene expression patterns of the AktI treated and the untreated CTL were then compared by microarray.

first: Andrew

last: Macintyre

first: David

last: Finlay

first: Gavin

last: Preston

last: Sinclair

first: Caryll

last: Waugh

last: Tamas

first: Carmen

last: Feijoo

first: Klaus

last: Okkenhaug

first: Doreen

last: Cantrell


title: Gene expression differences in mouse islets after isolation at different time points (0-48hr)

city: montreal

first: bing

last: han

state: qc

address: 2099 alexandre deseve

department: medicine

institute: university of montreal

summary: TGFbi (transforming growth factor-beta-induced) is a secreted protein and is capable of binding to both extracellular matrix (ECM) and cells. It thus acts as a bifunctional molecule enhancing ECM and cell interactions, a lack of which results in dysfunction of many cell types. In this study, we investigated the role of TGFbi in the function and survival of islets. Based on DNA microarray analysis followed by qPCR confirmation, the TGFbi gene showed drastic increases in expression in islets after culture. We demonstrated that recombinant TGFbi could preserve the integrity and enhance the function of cultured islets. Such a beneficial effect was mediated via signalling through FAK. Exogenous TGFbi was capable of sustaining high-level FAK phosphorylation in isolated islets, and FAK knockdown by siRNA in islets resulted in compromised islet function. TGFbi Tg islets showed better integrity and insulin release after in vitro culture. In vivo, b-cell proliferation was detectable in Tg but not wild type pancreata. At age above 12 months, Tg pancreata contained giant islets. Tg mice displayed better glucose tolerance than the controls. Tg islets were more potent in lowering blood glucose when transplanted into syngeneic mice with streptozotocin-induced diabetes, and these transplanted islets also underwent regeneration. Our results indicate that TGFbi is a vital trophic factor promoting islet survival, function and regeneration. At least some of its beneficial effect was mediated by signalling through FAK.

overall_design:
Six independent batches of islets were isolated. For each batch, islets from 4 C57BL/6 mice were pooled, and were divided into 3 groups, which were harvested at 0 h, 24 h and 48 h after culture. Total RNA was extracted from the islets with QIAGEN RNeasy Micro Kits. After reverse transcription, cDNA served as a template for PCR-based cRNA amplification. It was then reverse-transcribed to produce second-generation cDNA, which was employed to generate biotin-labelled cRNA probes. The probes were hybridized on GeneChip Mouse Genome 430 2.0 Array (Affymetrix, Santa Clara, CA), which contains 39,000 transcripts. DNA microarray analysis was performed at the McGill University Genome Quebec Innovation Centre.

For each time point, 6 chips were hybridized with cRNA from the 6 batches of isolated islets. For samples collected at 24 and 48 hours (6 batches for each time point), if the mean signal strength of a gene had above 4-fold difference over that of the 0 h samples, it was selected for reverse polymerase chain reaction (PCR) confirmation. Details of the experimental protocols and data analysis procedure can be found in http://www.affymetrix.com/support/downloads/manuals/expression_analysis_technical_manual.pdf .

Batch 1: YF050524MOT01, YF050524MOT07, YF050524MOT13
Batch 2: YF050524MOT02, YF050524MOT08, YF050524MOT14
Batch 3: YF050524MOT03, YF050524MOT09, YF050524MOT15
Batch 4: YF050524MOT04, YF050524MOT10, YF050524MOT16
Batch 5: YF050524MOT11, YF050524MOT17
Batch 6: YF050524MOT06, YF050524MOT12, YF050524MOT18


title: Expression data of alloantigen stimulated splenocytes treated with leukocyte costimulatory blockade antibodies or no treatment

city: Stanford

first: Kitchener

middle: D.

last: Wilson

state: CA

address: S140 Grant Bldg

institute: Stanford University

summary: To elucidate the gene expression “footprint” of antigenically challenged T-cells which had been treated with anti-LFA-1, CTLA4Ig, anti-CD40-ligand antibodies, we performed microarray gene expression analysis comparing the expression profile of costimulatory blockade treated and untreated responder T-cells.

overall_design: Allogeneic murine splenocytes were co-cultured in an vitro set-up for a mixed lymphocyte reaction. For the experimental/treated group, the leuckocyte costimulatory blocking antibodies anti-LFA-1, CTLA4Ig, anti-CD40-ligand were added to the media, the control group did not have any antiodies added to the media. After 5 days of incubation the responder CD4 and CD8 T cells were isolated by FACS and the gene expression was analyzed using affymetrix microarray platforms.

first: Jeremy

middle: I

last: Pearl

first: Zhumur

last: Ghosh


title: Expression data from the Ire1α null and control murine livers in the absence or presence of ER stress

city: ANN Arbor

first: wenbo

last: xu

state: MI

address: MSR BILD II

institute: university of michigan

summary:
Ire1α conditional null or control mice of 3-months old were injected intraperitoneally with TM or vehicle.
At 8 hours after the injection, total RNA was isolated from murine liver tissue and subjected to Affymetrix microarray analysis.

overall_design: We used microarrays to profile the global programme of gene expression in the livers of Ire1α null and control mice in the absence or presence of ER stress.

first: Kezhong

last: Zhang

first: Randal

last: Kaufman