title: Affymetrix gene expression of Transitional Type-1 B-cells from Wild-type (CBA), Xid and Btk KO mice

status: Public on Jan 10 2014

city: Solna

first: Jessica

middle: Margareta

last: Lindvall

address: Tomtebodavägen 23A

department: NBIS

institute: SciLifeLab. Stockholm University

summary:
Splenic Transitional Type-1 B-cells from CBA wild-type mice, X-linked immunodeficiency mice and Bruton's tyrosine kinase knock-out mice. Two replicates where run on Affymetrix 420 2.0 arrays for CBA wild-type,  Xid samples and the Btk KO samples.
Bruton's tyrosine kinase (Btk) is a cytoplasmic tyrosine kinase important for B-lymphocyte maturation. Mutations in Btk give rise to the primary immunodeficiency disease X-linked agammaglobulinemia (XLA) in man and X-linked immunodeficiency (Xid) in mice. Recent studies have subdivided the mouse immature, or transitional, B-cells into two distinct subsets according to their respective surface markers. Transitional type 1 (T1) and transitional type 2 (T2) cells are also located in distinct anatomic locations. Based on a limited number of markers it has previously been reported that the earliest phenotypic sign of Btk deficiency is manifested at the T2 stage in mice. Here, we report on distinct genome-wide transcriptomic signature differences found in T1 B-lymphocytes from Btk-defective compared to normal mice and demonstrate that Btk deficiency is visible already at this stage.

overall_design: 2 replicates of T1 B-cells from CBA (WT), Xid samples and the Btk KO samples

middle: M

first: K

last: Blomberg

first: Anna

last: Berglöf

first: C

last: Edvard Smith


title: Identification of Ccr4-Not complex as a regulator of transition from partial to genuine iPS cells

status: Public on Jan 07 2014

city: Hidaka

first: Akihiko

last: Okuda

state: Saitama

address: 1397-1 Yamane

department: Research Center for Genomic Medicine

country: Japan

institute: Saitama Medical University

summary: Partial induced pluripotent cells (iPSCs) are cell lines strayed from normal route from somatic cells to iPSCs and are immortalized. Mouse partial iPSCs are able to convert to real iPSCs by the exposure to 2i condition using MAPK and GSK3? inhibitors. However, the molecular mechanisms of this conversion are totally not known. Our piggyback vector mediated genome-wide screen revealed that Cnot2, one of core components of Ccr4-Not complex participates in this conversion. Subsequent analyses revealed other core components, i.e., Cnot1 and Cnot3 and Trim28 which is known to extensively share genomic binding sites with Cnot3 contribute to this conversion as well. Our bioinformatics analyses indicate that the major role of these factors in the conversion is the down-regulation of developmental genes in partial iPSCs.

overall_design: Two partial iPSC clones (2B1 and 5C5) cultured under conventional culture condition with leukemia inhibitory factor (LIF) and serum and those converted to iPSCs by the exposure to 2i condition were used for RNA source. Partial iPSCs (2B1) cultured under conventional condition in which either one of Cnot1, Cnot2, Cnot3 and Trim28 cDNA or these factors were combinatorially incorporated after retrovirus infection and those in which empty vector or Nanog were stably integrated were also used for RNA source. In addition, embryonic fibroblasts and embryonic stem cells (ESCs) from 13.5 dpc embryos and blastocysts, respectively, from Nanog-GFP transgenic mice and wild-type ESC line (EBRTcH3) were used for RNA source.

first: Masayoshi

last: Kamon

first: Ayumu

last: Suzuki

first: Masataka

last: Hirasaki

first: Yutaka

last: Nakachi

first: Yosuke

last: Mizuno

first: Yasushi

last: Okazaki


title: Gene expression profiles in the liver of AIM+/+ and AIM-/- mice fed a high-fat diet

city: Osaka

first: Toshihiro

last: Kai

state: Osaka

address: 3-1-98 Kasugade-naka, Konohana-ku

department: Genomics Research

institute: Dainippon Sumitomo Pharma Co., Ltd.

summary: Expression of genes related to fibrosis was assessed in the liver of AIM+/+ and AM-/- mice fed a high-fat diet (HFD) for various period. Overall, there was no significant difference in the magnitude of expression of fibrosis-related genes during the steatosis progression.

overall_design: AIM+/+ and AIM-/- mice were fed an HFD for 0, 12 or 20 weeks. Liver samples were homogenized with Trizol, and total RNA was extracted according to the manufacturer's instructions. Microarray experiments were performed using Mouse Genome 430 2.0 Arrays (Affymetrix).

first: Natsumi

last: Maehara

first: Satoko

last: Arai

first: Mayumi

last: Mori

first: Yoshihiro

last: Iwamura

first: Jun

last: Kurokawa

first: Shunsuke

last: Kusunoki

first: Kaori

last: Taniguchi

first: Toru

last: Miyazaki


title: Gene expression analysis in liver collected from mice administered non-toxic, toxic, or severely toxic LNA sequences

status: Public on Jan 08 2014

city: groton

first: Petra

last: Koza-Taylor

state: CT

address: Eastern Point Road

country: USA

institute: Pfizer

summary: Development of LNA gapmers, antisense oligonucleotides used for efficient inhibition of target RNA expression, is limited by non-target mediated hepatotoxicity issues. In the present study, we investigated hepatic transcription profiles of mice receiving non-toxic and toxic LNA gapmers after a single and repeat administration.

overall_design: To understand the mechanism of LNA gapmer-induced heptotoxicity in mice, we investigated the transcription profiles of liver RNA isolated from mice receiving non-toxic sequence (NTS-1), toxic sequence (TS-2), or severely toxic sequence (HTS-3) of LNA gapmers at 25 mg/kg (dose volume of 10 mL/kg) at 8, 16, or 72 hrs after a single administration (by subcutaneous injection ) using microarray analysis. We also investigated the transcription profiles of liver RNA isolated from mice receiving non-toxic sequence (NTS-1) or toxic sequence (TS-2) of LNA gapmers at 25 mg/kg (dose volume of 10 mL/kg) at 2 weeks after repeated administration (by subcutaneous injection ) using microarray analysis.

last: Kakiuchi-Kiyota

first: Nagappan

last: Mathialagan


title: Expression data from bone marrow (BM) neutrophils

status: Public on Jan 06 2014

city: Toledo

first: Akira

last: Takashima

state: OH

address: 3000 Arlington Ave.

department: Medical Microbiology and Immunology

institute: University of Toledo

summary: We employed GeneChip analysis to investigate the global gene expression profiles of neutrophils from BM

overall_design: Gr-1high/CD48– neutrophils were sorted from the BM of C57BL/6 mice by FACS in two independent experiments

first: Hironori

last: Matsushima


title: Expression changes in the absence of miR-128 in striatal D1-receptor positive neurons

city: San Francisco

first: Chan Lek

last: Tan

state: California

address: 1550 Fourth St. Room 346

department: Physiology

institute: University of California

summary:
MicroRNA regulates protein expression of cells by repressing translation of specific target messenger transcripts. Loss of the neuron specific microRNA miR-128 in Dopamine D1-receptor expressing neurons in the murine striatum (D1-MSNs) lead to increased neuronal excitability, locomotor hyperactivity and fatal epilepsy.
To examine expression changes in the absence of miR-128 in D1-MSNs, we used mice expressing EGFP-tagged ribosomes in D1-MSNs with either D1-MSN-specific homozygous deletion of miR-128-2 locus or no deletion. Transcripts co-immunoprecipitated with tagged ribosomes were analyzed by microarray.

overall_design: 9 mutant animals ( D1-MSN-tagged ribosome; D1-MSN specific miR-128-2 homozygous deletion) and 7 age matched littermate control animals (D1-MSN-tagged ribosome only).

first: Chan

middle: L

first: Anne

last: Schaefer


title: Expression data from Gdap1 knock-out (deletion of exon 5) mice

status: Public on Jan 03 2014

city: Zurich

first: Axel

last: Niemann

address: Otto-Stern-Weg 7

department: Biology

country: Switzerland

institute: ETH Zurich

summary:
GDAP1 is a mitochondrial fission factor and mutations in GDAP1 cause Charcot-Marie-Tooth disease. Gdap1 knockout mice, mimicking genetic alterations of patients suffering from severe CMT forms, develop an age-related, hypomyelinating peripheral neuropathy.
We used microarrays to determine changes in the expression profiles in the peripheral nervous system before a phenotype was detectable in the animal model (2 month of age).

overall_design: To seek changes in gene expression patterns of Gdap1-/- mice, we isolated motoneurons by laser dissection and took sciatic nerve lysates of two-month-old mice and purified RNA of five mice. Based on the amount and quality of the isolated RNA we selected three samples per tissue (sciatic nerve lysate and motoneruons) and genotype (GDAP1-/- or wild type). Note: the probe sets for Gdap1 lie within exon 4 and exon 6, thus no apparent loss of Gdap1 mRNA expression is present in Gdap1-/- animals.

first: A

first: H

last: Halfter

first: P

last: Young

first: U

last: Suter


title: Generation of highly tumorigenic cells from N-RAS61K-induced senescent cells

status: Public on Jan 20 2014

city: Wuerzburg

first: Susanne

middle: Elma

last: Kneitz

address: Biozentrum, Am Hubland

department: Physiologigcal Chemistry

country: Germany

institute: University of Wuerzburg

summary: Activation of oncogene signaling in primary cells generally results in cellular senescence. This process is not only considered to be  tumor-protective, but also irreversible. However, if senescence induction can be circumvented, e.g. by additional genetic or epigenetic changes, tumor progression occurs. An in-vivo example for oncogene-induced senescence are human nevus cells, most of which bear oncogenic mutations in RAS/RAF/MAPK pathway genes. Here, we show that expression of the human melanoma oncogene N-RAS61K in cultured pigment cells initially induces OIS characterized by a highly multinucleated phenotype. Surprisingly, after prolonged periods of oncogene expression, mononucleated cells emerge from the multinucleated cells. They are highly proliferative, anoikis-resistent and induce fast growing and metastatic melanoma upon transplantation into nude mice. During long-term oncogene expression and the corresponding development of anoikis iresistance, expression of melanocyte-specific genes is lost. Our data demonstrate that the induction of oncogene-induced senescence is not just a failsafe escape mechanism, but also provides a source for highly aggressive tumor cells.

overall_design: total samples analysed are 4

first: Claudia

last: Leikam

first: Anita

last: Hufnagel

first: Christoph

last: Otto

first: Daniel

last: Murphy

first: Manfred

last: Schartl

first: Svenja

last: Meierjohann


title: p38a-dependent gene expression in keratinocytes

status: Public on Jan 01 2014

city: Charlestown

first: Jin Mo

last: Park

state: MA

address: 149 Thirteenth Street

department: Cutaneous Biology Research Center

institute: Massachusetts General Hospital

summary:
Gene expression in wild-type and p38a-knockout keratinocytes were compared. Keratinocytes were isolated from newborn mice, and left unirradiated (0 h) and irradiated (4 h) with ultraviolet-B (UVB).
C57BL/6 wild-type mice, and keratinocyte-specific p38a-knockout mice on a C57BL/6 background were used for isolation of primary keratinocytes.

overall_design: Gene expression in keratinocytes was analyzed 0 and 4 h after UVB irradiation (75 mJ/cm2).

first: Yasuyo

last: Sano

first: Jin


title: Effect of Lead on Genome-Wide Expression in Developing Mouse Brain during Synaptogenesis

city: London

first: Shiva

last: Singh

address: Western Science Centre

country: Canada

institute: University of Western Ontario

summary:
Lead exposure causes a variety of health effects, especially in children, that may include cognitive and behavioural problems. This study explores the mechanisms associated with this relationship by assessing alterations in gene expression of C57BL/6J pups treated with 50mg/kg lead compared to controls.
In addition this study also analyzed brain gene expression differences in Metallothionein I and II (Mt-I and Mt-II) knockout mice treated with lead.

overall_design: Pups of three genotypes (C57BL/6J, Mt-KO with a C57BL/6J background and Heterozygote Mt-KO) were injected with lead acetate during synaptogenesis and weight-matched controls were injected with saline at the same time points. Whole brains were harvested and RNA extracted and pooled from 5 pups and hybridized to Mouse Genome 430 2.0 Arrays. In total 6 arrays were used, one for each genotype and treatment.

first: Priya

last: Verma


title: A Molecular Portrait of the Homologous Recombination DNA Repair via Genome-wide Transcriptome Profiling

status: Public on Jan 24 2014

city: Houston

first: Chun-Jen

middle: Curtis

last: Lin

state: Texas

address: 7345 Fannin Street

department: Systems Biology

institute: University of Texas MD Anderson Cancer Center

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

overall_design: Refer to individual Series

first: Guang

last: Peng

first: Curtis

middle: C

first: Wei

last: Mo

first: Hui

last: Dai

first: Yun-Yong

first: Soo-Mi

last: Kim

first: Qianxing

first: Yang

first: Stefan

last: Siwko

first: Ruozhen

last: Hu

first: Ju-Seog

last: Lee

first: Bryan

last: Hennessy

first: Gordon

middle: B

last: Mills

first: Shiaw-Yih


title: Analysis of impact of Toxoplasma effector MAF1 during Type II infection in WT MEFs and during Type I  infection in WT and MAVS KO MEFs

status: Public on Jan 23 2014

city: Stanford

first: John

last: Boothroyd

state: CA

address: 299 Campus Drive

department: Microbiology and Immunology

institute: Stanford University

summary:
The goals of the microarray experiment were to determine the role of MAF1, the Toxoplasma gondii mediator of host mitochondrial association, on host cell gene expression by comparing infection of WT cells with Type II and Type II:MAF1 parasites. We also explored the role of MAF1 on host cell gene expression by comparing profiles of WT and MAVS KO MEFs infected with Type I and Type Imaf1KO parasites.
We used microarrays to detail the global programme of gene expression underlying cellularisation and identified distinct classes of up-regulated genes during this process.

overall_design: WT MEFs were infected with Type II and Type II:MAF1 parasites at an MOI of 5. At 8 hpi RNA was harvested using TriZol. The Affymetrix IVT (16h) express kit was used for cDNA synthesis and labeling.

first: Lena

middle: F

last: Pernas

first: Yaw

middle: A

last: Ankomah

first: Anjali

middle: J

last: Shastri

first: Sarah

middle: E

last: Ewald

first: Moritz

last: Treeck


title: Dmrt1 (doublesex and mab-3 related transcription factor 1) conditional knockout expression analysis of E15.5 ovaries.

city: Minneapolis

first: Aaron

last: Sarver

state: MN

address: 425 East River Road

department: Masonic Cancer Center

institute: University of Minnesota

summary: Dmrt1 (doublesex and mab-3 related transcription factor 1) is a conserved transcriptional regulator of male differentiation required for testicular development in vertebrates.  This study examines the result of conditional removal of Dmrt1 in E15.5 ovaries.


title: Gene expression profiling of #483 T-ALL clone FACS sorted from BM and spleen

city: Hannover

first: Adrian

last: Schwarzer

address: Carl-Neuberg-Str. 1

department: Experimental Hematology

institute: Hannover Medical School

type:
Expression profiling by array
Third-party reanalysis

summary:
#483 T-ALL cells were transplanted into C57BL6/J mice. Engraftment was monitored by FACS analysis of peripheral blood obtained by retroorbital blood collection. 20 days after transplantation EGFP+ T-ALL cells were sorted from the bone marrow and spleen of three individual mice. Total RNA was prepared using the RNeasy Micro Kit (Qiagen GmbH, Hilden, Germany) and quality of RNA was assessed using the Agilent 2100 Bioanalyzer. RNA was reverse transcribed and amplified using the Affy GeneChip 3' IVT Express Kit. Fragmented and labeled cDNA was hybridized to Affymetrix Mouse Genome 430 2.0 GeneChip arrays. We compared the global gene expression profile of the #483 T-ALL to normal, CD4+CD8+ thymocytes from published dataset that shared the same mouse strain (C57BL6/J), RNA isolation and amplification technology and microarray platform (Li et al., 2008, GSE12948). The .CEL files from the Microarray experiments obtained from GEO were preprocessed together with the .CEL files from the #483 T-ALL clone using RMA.

The complete dataset representing the #483 T-ALL and the CD4+CD8+ double positive thymocytes from Series GSE12948 (re-processed using RMA), is linked below as a supplementary file.

overall_design: #483 T-ALL cells were transplanted into 3 sublethally (7.5 Gy) irradiated C57BL6/J mice. 20 days after Tx EGFP+ T-ALL cells were isolated and subjected to Microarray Analysis. Each mouse serves as a biological replicate.


title: Peripheral circulating mRNA profiling in predicting the pathological response to neoadjuvant chemoradiation for esophageal squamous cell carcinoma

city: Taipei

first: Feng-Ming

last: Hsu

address: No.7, Chung Shan S. Rd.

department: Department of Oncology

country: Taiwan

institute: National Taiwan University Hospital

summary: Analysis of peripheral circulating mRNA expression levels in patients undergoing neoadjuvant chemoradiation for esophageal squamous cell carcinoma. The hypothesis test was that chemoradiation alters the circulating mRNA expression profiles and the profiling is predictive of pathological response. Results provide information on the response of circulating mRNAs to chemoradiation and identify novel biomarkers or targets in esophageal squamous cell carcinoma.

overall_design: Total RNA obtained from peripheral whole blood before and after neoadjuvant chemoradiation in patients with esophageal squamous cell carcinoma. 21 patients with 42 samples were analyzed. The expression profiles from pathological complete responders were compared to non-complete responders.

first: Jason

last: Cheng

first: Eric

middle: Y

last: Chuang

first: Jang-Ming


title: Gene expression after type-I interferon treatment in primary neurons, primary fibroblasts and L929 cells

city: Brussels

first: Michiels

last: Thomas

address: avenue Hippocrate, 74 (B1.74.07)

department: de Duve

country: Belgium

institute: Université Catholique de Louvain

summary: Microarray expression profilling of mouse primary mixed cortical/hippocampal neurons, primary fibroblasts and L929 cells to compare ISGs signature in disctinct cell types

overall_design: Primary mixed cortical/hippocampal neurons, primary fibroblasts (MEFs) and L929 cells were mock-treated or treated with 5U/mL of IFN-beta and RNA was harvested after 24 hours. For neurons and fibroblast, 2 samples were analyzed for each condition.

first: M

last: Kreit

first: S

last: Paul

first: L

last: Knoops

first: A

last: De Cock

first: F

last: Sorgeloos

first: T

last: Michiels


title: Reversible and irreversible differentiation of cardiac fibroblasts

city: Leuven

first: Rekin's

last: Janky

address: Herestraat 49 Box 816

department: Nucleomics Core

institute: VIB

summary: Aim: Differentiation of cardiac fibroblasts (Fb) into myofibroblasts (MyoFb) is responsible for connective tissue buildup in myocardial remodeling. We examined reversibility of MyoFb differentiation. Methods and Results: Adult rat cardiac Fb were cultured on a plastic substratum providing mechanical stress, with conditions to obtain different Fb phenotypes. Fb spontaneously differentiated to proliferating MyoFb (p-MyoFb) with stress fiber formation decorated with alpha-smooth muscle actin (α-SMA). Transforming growth factor-β1 (TGF-β1) promoted terminal differentiation into α-SMA positive MyoFb showing near absence of proliferation i.e. non-p-MyoFb (2-fold increase in cell number after 12 days vs 11-fold for p-MyoFb). SD-208, a TGF-β-receptor-I kinase blocker, inhibited p-MyoFb differentiation as shown by stress fiber absence, low levels of α-SMA protein expression, and high levels of proliferation (32-fold increase after 12 days). Fb seeded in collagen matrices induced no contraction, whereas p-MyoFb and non-p-MyoFb induced 2.5- and 4-fold contraction. Fb produced low levels of collagen and secreted high levels of IL-10. Non-p-MyoFb showed high collagen production and high MCP-1 and TIMP-1 secretion. Transcriptome analysis indicated differential gene expression between all phenotypes. Dedifferentiation of p-MyoFb, but not of non-p-MyoFb, was induced by SD-208 despite maintained stress, shown by stress fiber de-polymerization in 30% of p-MyoFb vs in 8% of non-p-MyoFb. Stress fiber de-polymerization could be induced by mechanical strain release in p-MyoFb and non-p-MyoFb (2 day culture in unrestrained 3-D collagen matrices). Only p-MyoFb showed true dedifferentiation after long-term 3-D culture. Conclusions: Both reduction in mechanical strain and TGF-β-receptor-I kinase inhibition can reverse p-MyoFb differentiation but not in non-p-MyoFb.

overall_design: Fibroblasts isolated from each rat heart (n= 4) were cultured in specific conditions to obtain different fibroblast phenotypes: 1) spontaneously differentiation into proliferating myofibroblasts (code RC), 2) terminal differentiation into non-proliferating myofibroblasts with TGF-β1 (code RT) and 3) inhibition of myofibroblast differentiation with SD-208, a TGF-β-receptor-I kinase blocker (code RS).  RNA concentration and purity from a total of 12 samples were determined spectrophotometrically using the Nanodrop ND-1000 (Nanodrop Technologies) and RNA integrity was assessed using a Bioanalyser 2100 (Agilent). Using the Ambion WT Expression Kit, per sample, an amount of 100 ng of total RNA spiked with bacterial poly-A RNA positive controls (Affymetrix) was converted to double stranded cDNA in a reverse transcription reaction. Next the sample was converted and amplified to antisense cRNA in an in vitro transcription reaction which was subsequently converted to single stranded sense cDNA. Finally, samples were fragmented and labeled with biotin in a terminal labeling reaction according to the Affymetrix WT Terminal Labeling Kit. A mixture of fragmented biotinylated cDNA and hybridisation controls (Affymetrix) was hybridised on Affymetrix GeneChip® Rat Gene 2.0 ST array  followed by staining and washing in a GeneChip® fluidics station 450 (Affymetrix) according to the manufacturer’s procedures. To assess the raw probe signal intensities, chips were scanned using a GeneChip® scanner 3000 (Affymetrix).

first: Ronald

last: Driesen

first: Joelle

last: Abi-Char

first: Chandan

middle: K

last: Nagaraju

first: Tamara

last: Coenen

first: Paul

last: Lijnen

first: Robert

middle: H

last: Fagard

first: Karin

middle: R

last: Sipido

first: Victor

middle: V

last: Petrov


title: Gene expression profiling in the developing neural tube

city: Beer Sheva

first: Tamar

last: Harel

address: POB 653

department: Genetics

country: Israel

institute: Ben-Gurion University

summary: At an incidence of approximately 1/1000 births, neural tube defects (NTDs) comprise one of the most common and devastating congenital disorders. In an attempt to enhance and expand our understanding of neural tube closure, we undertook a high-throughput gene expression analysis of the neural tube as it was forming in the mouse embryo. Open and closed sections of the developing neural tube were micro-dissected from mouse embryos, and hybridized to Affymetrix mouse expression arrays. Clustering of genes differentially regulated in open and closed sections of the developing neural tube highlighted molecular processes previously recognized to be involved in neural tube closure and neurogenesis. Analysis of the genes in these categories identified potential candidates underlying neural tube closure. In addition, we identified approximately 25 novel genes, of unknown function, that were significantly up-regulated in the closed neural tube. Based on their expression patterns in the developing neural tube, five novel genes are proposed as interesting candidates for involvement in neurogenesis. The high-throughput expression analysis of the neural tube as it forms allows for better characterization of pathways involved in neural tube closure and neurogenesis, and hopefully will strengthen the foundation for further research along the pathways dictating neural tube development.

overall_design: Embryos were dissected at days E8.5 and E9.5, and the neuroepithelium/ neural tube were mechanically detached from underlying tissues, and then separated into two regions: 1) “open neuroepithelium”: neuroepithelial tissue caudal to the open/closed junction, and 2) “closed neural tube”, extending from a somite’s breadth rostral to the open/closed junction, up to the level of the fifth- or sixth-to-last somite. Samples consisted of biological triplicates of RNA extract from the above tissues (pooled by litter, and representing a total of 111 embryos): E8.5 open neuroepithelium, E8.5 closed neural tube, E9.5 open neuroepithelium, and E9.5 closed neural tube. Thus, a total of 12 samples (representing 111 embryos) were hybridized to the GeneChip Mouse Genome 430 2.0 Array (Affymetrix Inc., Santa Clara, CA, USA). One of the samples (06, closed E8.5) deviated significantly from the others in quality assessment and was therefore removed from subsequent analysis and not submitted to GEO.

first: Ohad

middle: S

last: Birk


title: Trip12 deficiency effect on embryonic stem cell line

city: Tsukuba science city

first: masashi

last: kajiro

state: Ibaraki

institute: University of Tsukuba

summary:
Analysis of E14 embryonic stem cells lacking Trip12 ubiquitin ligase activity.
We used microarrays to detail the global gene expression profiles affected by Trip12 ubiquitin ligase activity in mouse embryonic stem cell.

overall_design: Total RNA was extracted from wild-type and Trip12 mutant mouse embryonic stem cells and hybridized on Affymetrix microarrays.

first: Masashi

last: Kajiro


title: Differential neuronal targeting of a new and 2 known calcium channel β4 subunit splice variants correlates with their regulation of gene expression

status: Public on Dec 31 2013

city: Innsbruck

first: Daniel

last: Bindreither

state: Tirol

address: Innrain 82

department: Division of Molecular Pathophysiology

country: Austria

institute: Medical University Innsbruck

summary:
The β subunits of voltage-gated calcium channels regulate surface expression and gating of CaV1 and CaV2 α1 subunits, and thus contribute to neuronal excitability, neurotransmitter release and calcium-induced gene regulation. In addition certain β subunits are targeted into the nucleus, where they directly interact with the epigenetic machinery. Whereas their involvement in this multitude of functions is reflected by a great molecular heterogeneity of β isoforms derived from four genes and abundant alternative splicing, little is known about the roles of individual β variants in specific neuronal functions. In the present study, an alternatively spliced β4 subunit lacking the variable N-terminus (β4e) is identified. It is highly expressed in mouse cerebellum and cultured cerebellar granule cells (CGC) and modulates P/Q-type calcium currents in tsA cells and CaV2.1 surface expression in neurons. Compared to the other two known full-length β4 variants (β4a, β4b) β4e is most abundantly expressed in the distal axon, but lacks nuclear targeting properties. To examine the importance of nuclear targeting of β4 subunits for transcriptional regulation, we performed whole genome expression profiling of CGCs from lethargic mice individually reconstituted with β4a, β4b, and β4e. Notably, the number of genes regulated by each β4 splice variant correlated with the rank order of their nuclear targeting properties (β4b> β4a> β4e). Together these findings support isoform-specific functions of β4 splice variant in neurons, with β4b playing a dual role in channel modulation and gene regulation, while the newly detected β4e variant serves exclusively in calcium channel-dependent functions.
We used microarrays to identify gene expression changes caused by β4 splice variants (β4a, β4b and β4e) of the voltage gated calcium channel in cultured cerebellar granule cells of lethargic mice

overall_design: Cultured cerebellar granule cells from lethargic (129/SvJ background) mice reconstituted with the β4 splice variants (β4a, β4b and β4e) were compared to eGFP transfected controls

first: Solmaz

last: Etemad

first: Gerald

last: Obermair

first: Ariane

last: Benedetti

first: Ruslan

last: Stanika

first: Valentina

last: Di Biase

first: Verena

last: Burtscher

first: Alexandra

last: Koschak

first: Reinhard

last: Kofler

first: Stephan

last: Geley

last: Wille

last: Lusser

first: Veit

last: Flockerzi

first: Bernhard

last: Flucher


title: Endothelin2 signaling in the neural retina promotes the endothelial tip cell state and inhibits angiogenesis

city: Baltimore

first: Amir

last: Rattner

state: MD

address: 725 North Wolfe St., PCTB Room 805

department: Molecular Biology and Genetics

institute: Johns Hopkins University

summary: Endothelin signaling is required for neural crest migration and homeostatic regulation of blood pressure.  Here we report that constitutive over-expression of Endothelin-2 (Edn2) in the mouse retina perturbs vascular development by inhibiting endothelial cell (EC) migration across the retinal surface and subsequent EC invasion into the retina. Developing endothelial cells exist in one of two states: tip cells at the growing front, and stalk cells in the vascular plexus behind the front.  This division of endothelial cell states is one of the central organizing principle of angiogenesis.  In the developing retina, Edn2 over-expression leads to over-production of endothelial tip cells by both morphologic and molecular criteria.  Spatially localized over-expression of Edn2 produces a correspondingly localized endothelial response.  Edn2 over-expression in the early embryo inhibits vascular development at mid-gestation, but Edn2 over-expression in developing skin and brain has no discernable effect on vascular structure.  Inhibition of retinal angiogenesis by Edn2 requires expression of Endothelin receptor A (Ednra) but not Ednrb in the neural retina.  Taken together, these observations imply that the neural retina responds to Edn2 by synthesizing one or more factors that promote the endothelial tip cell state and inhibit angiogenesis.  The response to Edn2 is sufficiently potent that it over-rides the activities of other homeostatic regulators of angiogenesis, such as vascular endothelial growth factor.

overall_design: Z/Edn2 females were crossed to Six3-Cre; Six3-Cre males. Postnatal P8 pups were genotyped for the Z/Edn2 allele by detection of Laz-Z activity in tail clips. Retinas from 2 - 3 pups were pooled for each data point.

first: Jeremy

last: Nathans


title: Visceral obesity in murine pregnancy

city: Edinburgh

first: Donald

last: Dunbar

address: 47 Little France Crescent

department: Centre for Cardiovascular Science

country: United Kingdom

institute: University of Edinburgh

summary:
Maternal obesity is linked with increased adverse outcomes for mother and fetus. However, the metabolic impact of excessive fat accumulation within the altered hormonal context of pregnancy is not well understood. We used a murine model of obesity, the high fat diet-fed C57BL/6J mouse to determine adipose tissue-mediated molecular mechanisms driving metabolic dysfunction throughout pregnancy. Remarkably, obese mice exhibited a normalization of visceral fat accumulation at late-stage pregnancy (-53%, P<0.001 E18.5) to achieve levels comparable in mass (per gram of body weight) to that of non pregnant, control diet fed mice. Moreover, whilst obese pregnant mice showed a marked glucose intolerance and apparent insulin resistance at mid-stage pregnancy (E14.5), glucose homeostasis converged with that of lean pregnant mice at late-stage pregnancy, suggesting an unexpected amelioration of the worsening metabolic dysfunction in obese pregnant mice.
Transcriptomic analysis of the late-stage visceral fat indicated reduced de novo lipogenic drive (Me1, Fasn, Scd1, Dgat2), retinol metabolism (Rdh11, Rbp4) and inflammation (Mcp1, Tnfα) in obese pregnant mice that was confirmed functionally by their lower adipose proinflammatory macrophage density. Elevated expression of estrogen receptor a (ERα) in visceral adipose tissue was identified as potential unifying mechanism for the transcriptional changes and reduced adiposity of late stage obese pregnancy. Support for a role for ERα was provided by experiments showing that the ERα selective agonist PPT suppressed lipogenesis in primary mouse adipocytes and suppressed Me1, Fasn, SCD1 and Dgat2 mRNA levels in mature female human ChubS7 clonal fat cells. Our data reveal a novel role for elevated visceral adipocyte estrogen signaling as a protective mechanism against visceral fat hypertrophy and inflammation in late pregnancy.

overall_design: Pregnant high fat, pregnant control fat, non pregnant high fat, non pregnant control fat. Five biologial replictes each (20 samples).


title: Analysis of TBR1 downnstream target genes in embryonic forebrains

first: Yi-Ping

last: Hsueh

address: 128 Academia Road, Section 2, Nankang

department: Institute of Molecular Biology

institute: Academia Sinica

summary:
TBR1 is a forebrain specific T-box transcription factor. Tbr1-/- mice have been characterized by defective axonal projections from cerebral cortex and abnormal neuronal migration of cerebral cortex and amygdala.
To investigate how TBR1 regulates neural development, the gene expression profile of Tbr1-/- brains was compared with WT littermates.

overall_design: Total RNAs purified from forebrains at embryonic day 16.5 were hybridized on Affymetrix microarrays

first: Wen-His

last: Chou


title: Gene expression data from murine mDC and pDC

city: Philadelphia

first: Amaya

middle: I

last: Wolf

state: PA

address: 3601 Spruce street

institute: Wistar Institute

summary: mDC and pDC exhibit distinct TLR expression pattern and differ in their responses to various TLR ligands. The goal of this study was to identify genes, that were differentally expressed between mDC and pDC as a means to determine how TLR signaling pathways operate. Suprisingly, expression of TLR-assoociated signaling proteins were found to be present at equivalent levels between mDC and pDC, despite differential expression of TLRs, and thus revealing insight into use of adaptor proteins that function as general regulators of TLR signaling pathways in both cell types.

overall_design: mDC and pDC were sorted from spleens of mice in 2 independent experiments: The first experiment included 2 replicates of pDC that were cultured in medium for 1h prior to RNA extraction and 1 replicate of mDC that were directly processed for RNA extraction after the sort. In a second experiment we obtained 2 more replicates of mDC that were processed for RNA extraction directly after the sort and run on a seperate microarray for gene expression analysis.

first: Wolfgang

last: Weninger


title: Comparison of gene change in lymphoma cells after co-culture with endothelial cells

city: New York

first: Bisen

last: Ding

state: NY

address: 1300 York Avenue

institute: Cornell Medical College

summary: Mouse lymphoma cells were co-cultured with endothelial cells in serum/cytokine-free condition. To identify specific genetic changes, we compared lymphoma cells cultured in medium containing 10% fetal bovine serum with lymphoma cells co-cultured with endothelial cells.

overall_design: The experiment compared genetic change in lymphoma cells caused by co-culture with endothelial cells.

first: Zhongwei

last: Cao

first: Bi-Sen

first: Jason

middle: M

last: Butler

first: Peipei

last: Guo

first: Sharrell

last: Lee

first: Koji

last: Shido

first: Shahin

last: Rafii

first: Joseph

last: Scandura


title: Deficiency in tumor suppressor p53 is required for doxorubicin induced transcriptional upregulation of NF-kB target genes in human breast cancer

city: Barcelona

first: Alba

last: Dalmases

address: Dr.Aiguader 88

country: Spain

institute: IMIM

summary:
NF-kB has been linked to doxorubicin-based chemotherapy resistance in breast cancer patients. NF-kB nuclear translocation and DNA binding in doxorubicin treated-breast cancer cells have been extensively examined, however its functional consequences in terms the spectrum of NF-kB -dependent genes expressed and, thus, the impact on tumour cell behaviour are unclear.
We hypothesized that NF-kB gene expression profile induced by doxorubicin might be different among breast cancer cells and tumors. Doxorubicin treatment in the p53-mutated MDA-MB-231 cells resulted in NF-kB driven-gene transcription demonstrated by gene expression microarrays. Selected genes (ICAM-1, CXCL1, IL8) related with invasion, metastasis and chemoresistance expression were confirmed by RT-PCR in a subset of additional doxorubicin-treated cells and fresh primary human breast tumors. In both systems, p53-deficient background correlated with the activation of these NF-kB targeted genes. Overexpression of p53WT in the mutant p53 MDA-MB-231 cells impaired NF-kB driven transcription induced by doxorubicin. Moreover, tumors with a p53 deficient background and nuclear NF-kB /p65 expression correlated with reduced disease free-survival. This study supports that tumor molecular profiles for doxorubicin driven NF-kB-response are likely to exist. A link between p53 deficiency and the presence of active transcriptionally NF-kB could favour an aggressive behaviour and might have implications for doxorubicin-based chemotherapy in breast tumors exhibiting aberrant p53 activity

overall_design: 12 samples were analyzed: controls (n=3); Doxorubicin treated (n=3);  MLN120B treated  (n=3);  MLN120B + Doxorubicin treated  (n=3)

first: Ana

last: Rovira


title: hCAF1/CNOT7 regulates interferon signaling by targeting STAT1

city: Paris

first: Pierre

last: de la Grange

address: 29, rue du Faubourg Saint-Jacques

department: Paris Biotech Santé

country: France

institute: GenoSplice technology

summary: Stringent regulation of the interferon signaling pathway is essential for maintaining the immune response to pathogens and tumors. The transcription factor STAT1 is a crucial mediator of this response. Here we show that hCAF1/CNOT7 regulates class I and II interferon pathways at different crucial steps. In resting cells hCAF1 can control STAT1 trafficking by interacting with the latent form of STAT1 in the cytoplasm. IFN treatment induces STAT1 release, suggesting that hCAF1 may shield cytoplasmic STAT1 from undesirable stimulation. Consistent, hCAF1 silencing enhances STAT1 basal promoter occupancy associated with increased expression of a subset of STAT1-regulated genes. Consequently, hCAF1 knockdown cells exhibit an increased protection against viral infection and reduced viral replication. Furthermore, hCAF1 participates in the extinction of the IFN signal, through its deadenylase activity, by speeding up the degradation of some STAT1-regulated mRNAs. Since abnormal and unbalanced JAK/STAT activation is associated with immune disorders and cancer, hCAF1 could play a major role in innate immunity and oncogenesis, contributing to tumor escape.

overall_design: mRNAs from cells expressing the siRNA siRNA duplexes targeting hCAF1, corresponding to the coding region 941-961 (kd) (hCAF1 NCBI Reference Sequence: NM_013354.5) and one non-targeting control siRNA (mock).

first: Clément

last: Chapat

first: Chloé

last: Kolytcheff

first: Muriel

last: Le Romancer

first: Didier

last: Auboeuf

first: Kamel

last: Chettab

first: Stéphanie

last: Sentis

first: Laura

last: Corbo


title: Dmrt1 (doublesex and mab-3 related transcription factor 1) conditional knockout expression analysis of E15.5 testes and ovaries

first: Aaron

last: Sarver

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


title: Cooperation of estrogen and oocytes on gene expression in mouse cumulus cells

city: Bar Harbor

first: Timothy

middle: Michael

last: Stearns

state: ME

address: 600 Main Street

department: Computational Sciences

institute: The Jackson Laboratory

summary: Oocyte-derived paracrine factors and estrogens cooperate to regulate the function and development of mouse cumulus cells.

overall_design: Cumulus oocyte complexes (COCs) were isolated from ovaries of mice. Oocytes were removed from some complexes (OOX). Groups were cultured with/without oocytes with/without estrogen and then cumulus cell transcriptome analyzed by microarrays.

last: Sugiura

first: John

last: Eppig


title: HIF knockdowns in human hematopoietic stem cells

city: London

first: Richard

middle: James

last: Mitter

state: LONDON

address: 1 Midland Road

department: Bioinformatics & Biostatistics

institute: The Francis Crick Institute

summary: Hematopoietic stem cells (HSCs), which reside in bone marrow niches, are exposed to low levels of oxygen and follow an oxygen gradient throughout their differentiation. Hypoxia-inducible factors (HIFs) are the main factors regulating the cell response to oxygen variation. Recent studies using conditional knockout mouse models have unveiled a major role of HIF-1a in the maintenance of murine HSCs, however the role of HIF-2a is still unclear. Here, we show that knockdown of HIF-2a and to a much lower extent, HIF-1a impedes the long-term repopulating ability of human CD34+ umbilical cord blood derived cells. The defects observed in hematopoietic stem and progenitor cell (HSPC) function after HIF-2a knockdown was due to an increase in the production of reactive oxygen species (ROS), which increases the endoplasmic reticulum (ER) stress in HSPCs and triggers apoptosis by the activation of the unfolded-protein-response (UPR) pathway. Importantly, HIF-2a deregulation also resulted in a significant decrease of engraftment of human acute myeloid leukemia (AML) cells. Overall, our data demonstrates a key role of HIF-2a in the maintenance of human HSPCs and in the survival of primary AML cells.

overall_design: 2 controls and 2 shHIF2 CD34+ cell samples sorted from mice after 6 weeks of engraftment

first: Kevin

last: Rouault-Pierre

first: Lourdes

last: Lopez-Onieva

first: Katie

last: Foster

first: Fernando

last: Anjos-Afonso

first: Isabelle

last: Lamrissi-Garcia

first: Martin

last: Serrano-Sanchez

first: Zoran

last: Ivanovic

first: Hubert

last: de Verneuil

last: Gribben

first: David

last: Taussig

first: Hamid

last: Rezvani

first: Frédéric

last: Mazurier

first: Mitter

last: Richard

first: Dominique

last: Bonnet


title: Fluoxetine resistance in mice is associated with attenuated progression of a stereotyped dentate gyrus gene expression program

first: mark

last: alter

address: 125 S. 31st Street

department: Center for Neurobiology and Behvior

institute: University of Pennsylvania

summary: Selective serotonin reuptake inhibitors (SSRIs) such as fluoxetine are the most common treatment for major depression. However, approximately 50% of depressed patients fail to achieve an effective treatment response. Understanding how gene expression systems relate to treatment responses may be critical for understanding antidepressant resistance. Transcriptome profiling allows for the simultaneous measurement of expression levels for thousands of genes and the opportunity to utilize this information to determine mechanisms underlying antidepressant treatment responses. However, the best way to relate this immense amount of information to treatment resistance remains unclear. We take a novel approach to this question by examining dentate gyrus transcriptomes from the perspective of a stereotyped fluoxetine-induced gene expression program. Expression programs usually represent stereotyped changes in expression levels that occur as cells transition phenotypes. Fluoxetine will shift transcriptomes so they lie somewhere between a baseline state and a full-response at the end of the program. The position along this fluoxetine-induced gene expression program (program status) was measured using principal components analysis (PCA). The same expression program was initiated in treatment-responsive and resistant mice but treatment response was associated with further progression along the fluoxetine-induced gene expression program. The study of treatment-related differences in gene expression program status represents a novel way to conceptualize differences in treatment responses at a transcriptome level. Understanding how antidepressant-induced gene expression program progression is modulated represents an important area for future research and could guide efforts to develop novel augmentation strategies for antidepressant treatment resistant individuals.

overall_design: 38 samples, 2 dentate regions (dorsal/ventral), 3 groups (control, antidepressant resistant (4 mice), antidepressant responsive (7 mice), untreated (8 mice).


title: E12.5 CD9+ Mouse Placental Trophoblast Microarray, Wild-type vs c-Met KO

city: LOS ANGELES

first: Hanna

last: Mikkola

address: 621, Charles E. Young Drive South

department: MCDB

institute: UCLA

summary:
The placenta serves as the structural interface for nutrient and waste exchange for proper fetal development. Although defects in placental function result in various placental disorders, molecular mechanisms orchestrating placental development and function are poorly understood. Gene targeting studies have shown that Hgf or c-Met KO embryos exhibit growth retardation and markedly smaller size of the placenta, and die by E14.5. Stem/progenitor cells in various tissues express c-Met and they participate in morphogenesis and tissue repair. Thus, we hypothesized that the HGF/c-Met signaling pathway is essential for the emergence, proliferation, and/or differentiation of putative stem/precursor cells of labyrinth trophoblasts at the midgestation stage.
To examine the downstream mechanisms of HGF/c-Met signaling pathway that regulate placental labyrinth development, we performed microarray analysis and compared the transcriptional profiles of wild-type and c-Met g-KO placentas. The highly enriched gene ontology categories among the transcripts that were down-regulated in the mutant placentas were related to cell cycle, transcription, and placenta development. Surprisingly, the most highly enriched GO category among the up-regulated genes was immune response. Furthermore, genes classified as “unsaturated fatty acid metabolic process” were also significantly enriched among the up-regulated genes. This expression data suggested that HGF/c-Met signaling pathway positively regulates progression of cell cycle and transcription of placenta specific genes, and negatively regulates inflammatory reaction and fatty acids synthesis in the trophoblasts, thereby coordinating many critical cellular processes in the placenta.

overall_design: Freshly harvested mouse placental trophoblast was enriched for CD9 from wild -type and c-Met KO placenta with 2 independent biological replicates

first: Masaya

last: Ueno


title: Dmrt1 (doublesex and mab-3 related transcription factor 1) conditional knockout expression analysis of E15.5 testes.

city: Minneapolis

first: Aaron

last: Sarver

address: 425 East River Road

institute: University of Minnesota

summary: Dmrt1 (doublesex and mab-3 related transcription factor 1) is a conserved transcriptional regulator of male differentiation required for testicular development in vertebrates.  This study examines the result of conditional removal of Dmrt1 in E15.5 testes tissue in B6 and 129Sv strains.


title: Gene expression profiling of mammary epithelial cells isolated from Cuzd1-null and heterozygous mice on day 18 of pregnancy

city: Urbana

first: Quanxi

last: Li

state: IL

address: 2001 S lincoln Avenue

department: Comparative Bioscience

institute: Universit of Illinois at Urbana-Champaign

summary:
Our study revealed that CUZD1 (CUB and zona pellucida-like domain containing protein-1) is a novel target of estrogen regulation in the mouse mammary epithelium. Mice lacking Cuzd1 exhibit delayed ductal outgrowth during puberty and a striking impairment in ductal branching and alveolar development during pregnancy. Ablation of Cuzd1  led to a marked reduction in steroid-induced proliferation of mammary ductal and alveolar epithelium.
To identify the downstream targets of Cuzd1 in mammary gland development, we performed gene expression profling of mammary epithlial cells  isolated from Cuzd1-null and its heterozygous litteremates  on day 18 of pregnancy. The microarray results revealed downregulation of mRNAs corresponding to several members of the epidermal growth factor family in mammary epithelial cells of Cuzd1-null mice. Consequently, the activation of the ERBB receptors, ERBB1 and ERBB4, and their downstream target STAT5, was disrupted in Cuzd1-null mammary tissue. Collectively, these findings support a unique role for CUZD1 as a critical mediator of the steroid-induced proliferation and differentiation of ductal epithelium during pregnancy and lactation.

overall_design: To investigate the functional role of Cuzd1, we created Cuzd1-null mice by homologous recombination using mouse embryonic stem cells. As severe defect was observed in alveolargenesis and lactation of Cuzd1 null mammary gland, we purified mammary epithlial cells from day18 pregnant mice (n=5 for each genotype), purified total RNA from these cells, pooled these samples and then hybridized to high density affymetrix microarrays.

first: Indrani

last: Bagchi


title: Gene expression profiles from mammary tissue of control mice, small K5ΔNβcat hyperplasia, large K5ΔNβcat hyperplasia and K5ΔNβcat tumor

first: charles

last: decraene

address: 26 rue d'ULM

institute: Institut Curie

summary: Basal-like breast cancer is a heterogeneous disease characterised by the expression of basal cell markers, no oestrogen or progesterone receptor expression and a lack of HER2 overexpression. Recent studies have linked activation of the Wnt/beta-catenin pathway to basal-like breast cancer. Transgenic mice expressing N-terminally truncated stabilised beta-catenin in the mammary basal/myoepithelial cell layer (K5deltaNbetacat strain) develop mammary hyperplasias that progress to invasive carcinomas. Histological and microarray analyses of these lesions have revealed their high similarity to a subset of basal-like human breast tumours with squamous differentiation. As in human basal-like carcinomas, the Myc pathway was found to be activated in the mammary lesions of K5deltaNbetacat mice. Mammosphere and transplantation assays showed that a basal cell population with stem/progenitor characteristics was amplified in K5deltaNbetacat mouse preneoplastic glands. Myc deletion from the mammary basal layer of K5deltaNbetacat mice abolished both basal cell regenerative capacity and tumorigenesis. These results show that Myc is essential for beta-catenin-induced stem cell amplification and tumorigenesis and that basal stem/progenitor cells may be at the origin of a subset of basal-like breast tumours.

overall_design: mammary tissue from K5ΔNβcat mice were dissected at successive stages of development (small hyperplasia (n=5), large hyperplasia (n=5), tumor (n=11) and control (n=4)) for RNA extraction and hybridization on Affymetrix microarrays

first: Mejdi

last: Moumen

first: Aurélie

last: Chiche

first: Charles

last: Decraene

first: Valérie

last: Petit

first: Alberto

last: Gandarillas

first: Marie-Ange

last: Deugnier

first: Marina

last: Glukhova

first: Marisa

last: Faraldo


title: Salinomycin induces cell death and differentiation in head and neck squamous cell carcinoma stem cells despite activation of EMT and Akt

city: La Jolla

first: Alan

last: Kiang

address: 9500 Gilman Drive

institute: University of California, San Diego

summary: Cancer stem cells are believed to play a crucial role in cancer recurrence due to their resistance to conventional chemotherapy and capacity for self-renewal. Recent studies have reported that salinomycin, a livestock antibiotic, selectively targets breast cancer stem cells 100-fold more effectively than paclitaxel. In our study we sought to determine the effects of salinomycin on head and neck squamous cell carcinoma (HNSCC) stem cells. We show that salinomycin is able to decrease cell viability and induce apoptosis. In combination with the chemotherapeutic agents cisplatin and paclitaxel, salinomycin synergistically killed HNSCC cancer stem cells more effectively than either drug alone. Furthermore, we observed that salinomycin decreases stem cell properties as shown by a significant reduction in sphere formation and a decrease of both CD44 and BMI-1. Contrary to expectations, salinomycin caused an induction of EMT as shown by an increase in Snail and Vimentin, and a decrease in E-cadherin expression. Even though EMT was induced, salinomycin caused a decrease in invasion through a membrane. In search of a possible mechanism, the effects on the Akt pathway were explored. Interestingly, salinomycin also induced phosphorylation of Akt. Activation of EMT and Akt are both tightly associated with an increase in stemness, which brings to question the relationship between CSCs and these two fundamental pathways. Taken together, our findings indicate that salinomycin shows promise as a novel treatment for HNSCC despite an activation of EMT and Akt.

overall_design: MicroRNA obtained from JLO-1 cells treated for 48 hours in varying doses of salinomycin. Changes in microRNA expression are analyzed by normalizing expression values with the control sample.

first: Weg

last: Ongkeko


title: Enhanced cisplatin therapy for ovarian cancer cell lines

city: Torino

first: Raffaele

last: Calogero

state: To

address: Via Nizza 52

department: Molecular Biotechnology Center

country: Italy

institute: University of Torino

overall_design: Refer to individual Series


title: LSD1 knockdown in 3T3-L1 preadipocytes

first: Marcelina

last: Parrizas

address: CEK, Rosello, 153, pl.5

department: Endocrinology

institute: IDIBAPS

summary: Obesity is often associated with a low-grade systemic inflammation state that contributes to the development of insulin resistance and atherosclerotic complications. This is usually coupled with increased macrophage infiltration in the adipose tissue and a defect in adipocyte differentiation that results in accumulation of hypertrophic fat cells characterized by a deregulated pattern of adipokine expression. Here we show that knockdown of histone demethylase lsd1 in 3T3-L1 preadipocytes results in defective adipogenesis and derepression of an inflammatory program in these cells.

overall_design:
The dataset consists of four sample groups: [1] 3T3-L1 preadipocytes (passage 19) transfected with a control scrambled siRNA at 24h after transfection (siC.24h), [2] 3T3-L1 preadipocytes (p.19) transfected with a siRNA directed against LSD1 at 24h after transfection (siLsd1.24h), [3] 3T3-L1 preadipocytes (p.21) transfected with a control scrambled siRNA at 48h after transfection (siC.48h), and [4] 3T3-L1 preadipocytes (p.21) transfected with a siRNA directed against LSD1 at 48h after transfection (siLsd1.48h).
The 24h sample groups (siC.24h and siLsd1.24h) consist of two biological replicate samples; the 48h sample groups (siC.48h and siLsd1.48h) consist of three biological replicate samples. Each sample was hybridized to a separate array, for a total of ten arrays.

first: Felicia

last: Hanzu

first: Melina

last: Musri

first: Alvaro

last: Sánchez-Herrero

first: Marc

last: Claret

first: Yaiza

last: Esteban

first: Perla

last: Kaliman

first: Ramon

last: Gomis

last: Párrizas


title: Expression profiles of CSE1L silenced ovarian cancer cell lines

summary: Knocking down of CSE1L made ovarian cancer cells, but not other cancer and normal cell lines, sensitized to cisplatin and triggered apoptosis. The nuclear localization in ovarian cancer cells suggested that CSE1L might primarily regulate transcription. .

overall_design: Using microarrays, we evaluated the expression profiles of CSE1L silenced SK-OV-3 and TOV-21G cells

first: Annalisa

last: Lorenzato

first: Cosimo

last: Martino

first: Martina

last: Olivero

first: Yvonne

last: Oligshlager

first: Anna

last: Ferrero

first: Nicoletta

last: Biglia

first: MariaFlavia

last: DiRenzo


title: PPARd target genes in MEFs

city: Bethesda

first: Qihuang

last: Jin

address: 9000 Rockville Pike

department: NIDDK

institute: NIH

summary: The PPAR (Peroxisome proliferator-activated receptor) family of nuclear receptors has three members: PPARg, PPARa and PPARd. Although they share similar structures, their biological functions are distinct. PPARg controls lipid storage and adipogenesis, while PPARd is associated with fat burning. The highly specific synthetic ligand for PPARd, GW501516, is a promising drug candidate for obesity and diabetes. Here we use Affymetrix microarray to analyze gene expression profile in mouse embryo fibroblasts treated with 100 nM GW501516 for 0, 2, 8 and 24 hours. These data may provide new clues into the molecular mechanism by which GW501516 ameliorates obesity and diabetes.

overall_design: Wild type mouse embryonic fibroblasts (MEFs) stably infected with retroviruses MSCVpuro expressing PPARd were plated at 0.5 million per 10 cm dish. After overnight incubation, cells were treated with 100nM GW501516 for 0h, 2h, 8h and 48h. Cells were collected at subconfluent condition. Total RNAs were sequentially purified with Trizol (Invitrogen) and RNeasy kit (Qiagen) and analyzed in triplicate on Mouse Genome 430 2.0 Array (Affymetrix) at NIDDK Microarray Core Facility following standard protocols.

first: SunHwa

last: Hong

first: Kai

last: Ge


title: Epigenetic analysis of men with low birth weight following a control and high-fat overfeeding diet

city: Copenhagen N

first: Stine

last: Jacobsen

address: Tagensvej 20, sec. 7652

department: Diabetes and Metabolism

country: Denmark

institute: Rigshospitalet

summary: Genome-wide DNA methylation profiling of  young men born with low birth weight following a control and high-fat overfeeding diet using Illumina's Infinium 27k Human DNA methylation Beadchip v. 1.2. DNA methylation profiles were obtained for 27,578 CpG sites in human skeletal muscle.

overall_design: Randomized cross-over desgin, where all subjects receieved both treatments (control and high-fat overfeeding diet). Biopsies were obtained from 17 different individuals amounting to 16 samples following the control diet and 15 samples following the high-fat overfeeding diet (paired n=14). Bisulphite converted DNA from the 31 samples were hybridised to the Illumina Infinium 27k Human Methylation Beadchip.

first: Allan

last: Vaag

first: Mario

last: Fraga


title: Genome-wide screening and identification of long noncoding RNAs and their interaction with protein coding RNAs in bladder urothelial cell carcinoma

city: Nanjing

first: Wen

last: Cheng

address: 305 Zhong Shan Dong Lu

department: Department of Urology

country: China

institute: Jinling Hospital

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

summary: To understand the role of long non-coding RNAs and interaction with coding RNAs in bladder urothelial cell carcinoma (BUCC), we performed genome-wide screening long non-coding RNAs and coding RNAs expression on primary BUCC tissues and  normal tissues using long non-coding RNA array (Agilent  plateform (GPL13825). By comparing these two groups,  significantly differentially expressed lncRNAs  and coding RNAs  were identified. We further identifed a subset of long noncoding RNAs and their correlation with neighboring coding genes using bioinformatic tools. This analysis provides foundamental understaning of transcriptomic landscape changing during bladder carcinogenesis.

overall_design: 12 BUCC primary tumors and 3 normal tissues were used for long noncoding RNA array experiments which including long non-coding RNAs and coding RNAs. The differential expression of subset of long noncoding RNAs and their interaction with coding RNAs in BUCC compared with normal tissue will be identified with comtational analysis.


title: Prevention of mammary tumor progression by silencing HoxA1  via intraductal injection of nanoparticle-formulated siRNA

city: Rochester

first: Hu

last: Li

address: 200 First Street, Gonda Building G19-408

department: Molecular Pharmacology & Experimental Therapeutics

institute: Mayo Clinic

summary: Silencing HoxA1 in vivo by intraductal delivery of nanoparticle-formulated siRNA reduced mammary tumor incidence by 75% , reduced cell proliferation, and prevented loss of ER and PR expression.

overall_design: 8 week wild type FVB mouse whole mammary gland and 8week to 20 week transgenic FVB C3(1)-SV40Tag mouse whole mammary gland

first: A

last: Brock


title: PCAF/GCN5-regulated genes in MEFs

summary: Histone acetyltransferases (HATs) GCN5/PCAF and CBP/p300 are transcription coactivators. However, how these HATs regulate ligand-induced nuclear receptor target gene expression remains unclear. Here we show in mouse embryonic fibroblasts (MEFs), deletion of GCN5/PCAF specifically eliminates acetylation on H3K9 (H3K9Ac) while deletion of CBP/p300 selectively reduces acetylation on H3K18 and H3K27 (H3K18/27Ac). Treating MEFs with a specific ligand for nuclear receptor PPARdelta induces sequential increases of H3K18/27Ac and H3K9Ac on the promoter of PPARdelta target gene Angptl4, which correlates with a robust ligand-induced Angptl4 expression. Inhibiting transcription elongation blocks ligand-induced H3K9Ac but not H3K18/27Ac on Angptl4 promoter. Finally, we show CBP/p300 and their HAT activities are required, while GCN5/PCAF and H3K9Ac are dispensable, for ligand-induced PPARdelta target gene expression in MEFs. These results highlight the substrate and site specificities of HATs in cells, and suggest that GCN5/PCAF- and CBP/p300-mediated histone acetylations play distinct roles in regulating ligand-induced nuclear receptor target gene expression.

overall_design: PCAF and GCN5 have some redundant function. To identify PCAF/GCN5-regulated genes, immortalized MEFs with PCAF knockout and GCN5 conditional knockout were infected with retroviruses expressing either Cre recombinase or vector alone. We prepared duplicated RNAs from either vector or Cre infected cells (PCAF-/-;GCN5+/- or PCAF-/-;GCN5+/-) and RNAs from either Vector or Cre infected the other independently immortalized cells for 6 affymetrix microarray.

first: Zhijing

last: Zhang

first: Lawryn

last: H. Kasper

first: Lifeng

last: Wang

first: Chaochen

first: Paul

last: K. Brindle

first: Sharon

last: Dent


title: Recombinant human lactoferrin activates human dendritic cells via Toll-like receptors-2 and -4

status: Public on Dec 30 2013

first: Raffaele

last: Calogero

summary: Talactoferrin alfa (TLF) is a unique recombinant version of human lactoferrin, an important immunomodulatory protein present in exocrine secretions and in the secondary granules of neutrophils.  Talactoferrin has demonstrated anti-cancer activity in preclinical studies and in Phase III clinical trials in patients with Renal Cell Cancer and non-small cell lung cancer. We have shown that TLF induces the maturation of human DCs derived from monocytes, suggesting that the linkage of the innate and adaptive immunity through DC maturation is a key immune function mediated by TLF. In this study we used genome-wide expression analysis to explore the mechanisms by which TLF leads to the functional maturation of DC. We show that GMP level recombinant TLF activates human DCs in a Toll-like receptor (TLR) -2 and -4 dependent manner.

overall_design: Human peripheral blood mononuclear cells (PBMCs) were obtained from buffy coats of healthy donors. CD14+ cells were isolated from fresh PBMCs by positive immunoselection with magnetic beads. Immature dendritic cells (i-DC) from four donors were generated using granulocyte-macrophage colony-stimulating factor (GM-CSF) and IL-4.  On day 6, cells were harvested in order to have iDC or mDC (conventionally matured DC) by addition of Tumor Necrosis Factor (TNF) -alfa and IL-1beta  or TLF-DC  (Talactoferrin matured DC) adding Food and Drug Administration-approved, GMP level recombinant TLF generated in eukaryotic cells.  After 24 hour culture, cells were harvested and analyzed with Illumina arrays.

first: Michela

last: Spadaro

first: Monica

last: Montone

first: Daniela

last: Cantarella

first: Guido

last: Forni

first: Federica

last: Pericle

first: Steve

last: Pascolo

first: Maddalena

last: Arigoni

last: Cavallo


status: Public on Dec 22 2013

city: Dunedin

first: Christopher

last: Brown

address: 710 Cumberland St

department: Biochemistry

country: New Zealand

institute: University of Otago

summary:
RAW264.7 macrophages infected with MNV-1 and mock infected gene expression measured by microarray.
To be published in Waugh, E. Chen, A. Baird, M. Fleming, S. Brown, C.M. and V K. Ward (2014) Characterization of the chemokine response of RAW264.7 cells to infection by murine norovirus. Virus Genes

overall_design: Four Samples, two mock and two MNV-1 infected.

first: Emily

last: Waugh

first: Chris


title: Dietary fat disturbance of of gut microbial diurnal patterns uncouples host metabolic networks.

status: Public on Dec 24 2013

city: Charlottesville

first: Yong

last: Huang

state: VA

address: 1340 Jefferson Park Ave

department: Medicine

institute: University of Viginia

summary: Diet-induced obesity (DIO) is rapidly becoming a global health problem, particularly as Westernization of emerging nations continues. Currently, one third of adult Americans are considered obese and, if current trends continue, >90% of US citizens are predicted to be affected by 2050. However, efforts to fight this epidemic have not yet produced sound solutions for prevention or treatment. Our studies reveal a balanced and chronobiological relationship between food consumption, daily variation in gut microbial evenness and function, basomedial hypothalamic circadian clock (CC) gene expression, and key hepatic metabolic regulatory networks , including CC and nuclear receptors (NR), that is are essential for metabolic homeostasis. “Western” diets high in saturated fats dramatically alter diurnal variation in microbial composition and function, which in turn lead to uncoupling of the hepatic CC and NR networks from central CC control in ways that offset the timing and types of regulatory factors directing metabolic function. These signals include microbial metabolites such as short chain fatty acids (SCFAs) and hydrogen sulfide (H2S) that can directly regulate or disrupt metabolic networks of the hepatocyte. Our study therefore provides insights into the complex and dynamic relationships between diet, gut microbes, and the host that are critical for maintenance of health. Perturbations of this constellation of processes, in this case by diet-induced dysbiosis and its metabolomic signaling, can potentially promote metabolic imbalances and disease. This knowledge opens up many possibilities for novel therapeutic and interventional strategies to treat and prevent DIO, ranging from the manipulation of gut microbial function to pharmacological targeting of host pathways to restore metabolic balance.

overall_design: Mice were raised under germ-free or specific pathogen-free condition, or germ-free followed by conventionization. Liver tissues were harvested for total RNA isolation and hybridization on Affymetrix microarrays

first: Vanessa

last: Leone

first: Sean

last: Gibbons

first: Jack

last: Gilbert

first: Eugene

last: Chang


title: Global expression of mouse hepatocytes cultured as monolayers or as three-dimensional aggregates

status: Public on Dec 23 2013

city: San Francisco

first: Tammy

middle: T

address: 513 Parnassus Ave., HSW 1601

department: Surgery

institute: University of California, San Francisco

summary: Three-dimensional (3D) culture of hepatocytes leads to improved and prolonged synthetic and metabolic functions, but the underlying molecular mechanisms were unknown.  In order to investigate the molecular mechanisms underlying 3D cell-cell interactions in maintaining hepatocyte differentiated functions ex vivo, microarray analyses were performed on primary mouse hepatocytes cultured either as monolayers on tissue culture dishes (TCD) or as 3D aggregates in rotating wall vessel (RWV) bioreactors.

overall_design: Primary hepatocytes were isolated from mice and cultured on TCDs or within RWVs for 4 hours or 24 hours.  Freshly isolated hepatocytes (t0) were used as baseline controls.  Each experimental condition has three independent biological replicates.


title: Expression data of mouse hematopoietic cells, Nr4a1/3 wild type and double mutant

city: Houston

first: Orla

last: Conneely

state: TX

address: One Baylor Plaza

institute: Baylor College of Medicine

summary: We investigate the cellular and molecular mechanisms of tumor suppression by NR4A1 and NR4A3, and show a cell intrinsic essential function in maintenance of hematopoietic stem cell (HSC) homeostasis. In the absence of Nr4a1/3, HSC lost quiescence, became highly proliferative leukemia-stem cell (LSC) that transplanted AML to recipient mice. We further revealed that loss of NR4A1/3 leads to deregulated expression of the key cell cycle regulator Cdkn1c (P57), c-Myc oncogene, and glucose metabolic genes leading to enhanced aerobic glycolysis or ‘Warburg effect’ in LSCs. Reintroduction of Nr4a1 in LSCs restored HSC quiescence, and reversed Nr4a1/3 deficiency induced P57 suppression and c-Myc overexpression. Collectively, we identify an essential role of Nr4a1/3 in coordinately regulating cell cycle entry and glucose metabolism to prevent uncontrolled stem cell proliferation and AML transformation. These results have major implications for designing therapeutic strategies in AML.

overall_design: To identify NR4A-dependent molecular signaling pathways that may control HSC homeostasis, we performed genome-wide transcript profiling of Lin-Sca1+ (LS) cells from WT and DKO mice. For Affymetrix analysis, we generated three independent pools of RNA from sorted LS cells from 10-20 WT or DKO (2- to 3-week-old) mice per sample.

first: Shuo

last: Zhang

first: Liguo

last: Wang

first: Seth

last: Boudreaux

first: Wei

last: Li


title: Expression data from C2C12 myotubes infected with RML prions

city: Edmonton

first: Allen

last: Herbst

state: AB

address: 114C BARB

institute: University of Alberta

summary: Prion infection in animals results in neurodegeneration and eventually death. To examine the cellular impact of Prion disease, we profiled non-proliferative fully differentiated C2C12 cells, which can replicate prions to high levels. Results suggest that accumulation of high levels of PrPSc in C2C12 myotubes does not cause any overt cellular dysfunction or molecular pathology.

overall_design: C2C12 cells were differentiated into confluent myotubes. Cells were infected or not with 100ul of 10% brain homogenate obtained from a C57BL/6 mouse clinically affected with RML prions. 16 days after infection, cells were collected by scraping and RML was purified.

first: Debbie

last: McKenzie


title: Expression data from Th17 cells of different origins

status: Public on Dec 21 2013

city: Tokyo

first: Noriko

last: Komatsu

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

department: Immunology

institute: the Univ of Tokyo

summary:
Foxp3 is indispensable for Treg suppressive function, but the stability of Foxp3 has been controversial. In autoimmune arthritis, Th17 cells play a critically important pathological role, but the origin of Th17 cells remains unknown
We used microarrays to detail the global programme of gene expression of Th17 cells originated from Foxp3+T cells compared to conventional naive CD4+T cells derived Th17 cells. We also take samples of Treg cells and Th0 cells for the experimetnatl control.

overall_design: Each T cell subset after the culture was subjected to RNA extraction and hybridization on Affymetrix microarrays.


title: Expression data from c-Src inhibited osteoblasts

status: Public on Dec 20 2013

city: L'Aquila

first: Barbara

last: Peruzzi

address: Via Vetoio

institute: University of L'Aquila

summary: The tyrosine kinase c-Src has a crucial role in maintaining osteoblast in a less differentiated status, as already described in the literature. We used microarrays to detail the global programme of gene expression in osteoblasts treated with a well known c-Src inhibitor (PP1).

overall_design: Osteoblast primary cultures were isolated from calvaria of 7 days-old CD1 mice. These cell were starved and treated with vehicle (DMSO) or 2 micromolar PP1 for 24 hours. Then RNA was extracted and hybridizated on Affymetrix microarray.

first: Mattia

last: Capulli

first: Nadia

last: Rucci

first: Anna

last: Teti


title: IQGAP2 knockout model of hepatocellular carcinoma

status: Public on Dec 13 2013

city: Stony Brook

first: Dmitri

last: GNATENKO

address: T15/053 HSC SUNY

institute: Stony Brook University

summary: Whole body knockout mice lacking IQ-motif containing GTPase-activating protein 2 (IQGAP2) develop spontaneous hepatocellular carcinoma (HCC) at the age of 12 months and older (Schmidt et al., 2008). Hepatic transcript expression profiles were obtained for IQGAP2 knockout and wild-type control mice of two age groups, 6- and 24-month-old. Liver samples from 24-month-old IQGAP2 knockout mice were HCC tumors, livers from all other groups were tumor-free. Results provide insights into the potential role of IQGAP2 as a liver-specific tumor suppressor.

overall_design: Transcript profiles of four groups of mouse livers (N = 3 in each group) were compared using Affymetrix GeneChip® Mouse Genome 430 2.0 Array. The groups included livers from 6- and 24-month-old wild-type (WT) mice and 6- and 24-month-old (KO) Iqgap2-/- mice.

last: Gnatenko

first: Xiao

last: Xu

last: Zhu

first: Valentina

last: Schmidt


title: Expression data from Tg4510 and Wild-type mice after AAVTFEB injection

status: Public on Dec 19 2013

first: Horatiu

last: Voicu

summary: We used microarrays to detail the global programme of gene expression after 4 months of TFEB overexpression in the brain.

overall_design: Groups of Tg4510 and Wild-type mice were injected at P0 in the brain. Those groups of mice and the respectively controls were sacrificed and analyzed after 4 months from the injection. RNA extraction from the hippocampus and hybridization on Affymetrix microarrays was done.

first: V

last: Polito

first: B

first: M

last: Sardiello


title: Expression data from miR-92 over-expressing R26MER/MER mouse embryonic fibroblast (MEFs)

status: Public on Dec 11 2013

city: Berkeley

first: Lin

last: He

address: 535 LSA, UC-Berkeley

institute: UC-Berkeley

summary:
miR-92 enhances c-Myc induced apoptosis. In the R26MER/MER mouse embryonic fibroblasts (MEFs), a switchable variant of Myc, MycERT2, was knocked into the genomic region downstream of the constitutive Rosa26 promoter, allowing acute activation of c-Myc by 4-OHT-induced nuclear translocation. This in vitro system nicely recapitulates c-Myc-induced apoptosis, as activated MycERT2 induces strong p53-dependent apoptosis in response to serum starvation. Enforced miR-92 expression in three independent R26MER/MER MEF lines significantly enhanced Myc-induced apoptosis.
We used microarrays to investigate the molecular mechanism underlying miR-92 functions.

overall_design: Three independent R26MER/MER MEF lines were infected by MSCV vector alone or by MSCV vector encoding miR-92. These MEFs were serum starved and 4-OHT treated to trigger strong Myc-induced apoptosis.

first: Virginie

last: Olive

first: Zhenyu

last: Xuan


title: Expression data from mouse adipose tissue macrophage

status: Public on Dec 18 2013

city: NEW YORK

first: Xiaoyuan

address: 1150 St Nicholas Ave.

institute: Columbia University

summary:
In mammals, expansion of adipose tissue mass induces accumulation of adipose tissue macrophages (ATMs). We isolated CD11c- (FB) and CD11c+ (FBC) perigonadal ATMs from SVCs of lean (C57BL/6J Lep +/+) and obese leptin-deficient (C57BL/6J Lep ob/ob) mice.
We used expression microarrays to generate transcription profiles of perigonadal ATMs from lean (C57BL/6J Lep +/+) and obese (C57BL/6J Lep ob/ob) mice. Profiling purified FBs and FBCs, we identified 521 transcripts whose expression was differentially (nominal p-value < 0.01) expressed between FBs from lean and obese mice and 1509 genes whose expression was differentially (nominal p-value <0.01) expressed between FBC from lean and obese mice

overall_design: RNA was isolated from sorted FBC (F4/80+, CD11b+, CD11c+) cells and FB ( F4/80+, CD11b+, CD11c-) cells and using RNeasy micro-kits (Qiagen), using a PicoPure RNA isolation kit then amplified two-rounds. Labeled cRNA Mouse Genome 430 2.0 arrays (purified FB and FBC adipose tissue macrophages.  There was a total of sixteen samples. FB and FBC populations were isolated from 4 lean and 4 obese mice.

first: Anthony

middle: W

last: Ferrante


title: A Mesodermal Factor, T (BRACHYURY), specifies mouse germ cell fate by directly activating germline determinants.

city: Nara

first: Kazuki

last: Kurimoto

address: 840 Shijo-Cho, Kashihara

department: School of medicine

institute: Nara Medical University

summary: The germ cell lineage ensures reproduction and heredity in metazoans. Primordial germ cells (PGCs) in mice are induced in pluripotent epiblast cells by BMP4 and WNT3, yet their mechanism of action remains elusive. Here, using in vitro PGC specification system, we show that WNT3, but not BMP4, induces many transcription factors associated with mesoderm in epiblast-like cells (EpiLCs) through beta-CATENIN. Among these, T (BRACHYURY), a classical and conserved mesodermal factor, was essential for robust activation of Blimp1 and Prdm14, two of the germline determinants. T, but not SMAD1 or beta-CATENIN/TCF1, binds distinct regulatory elements of both Blimp1 and Prdm14, and directly up-regulates these genes without BMP4 and WNT3. Without BMP4, a program induced by WNT3 prevents T from activating Blimp1 and Prdm14, demonstrating that BMP4 is permissive for PGC specification. These findings establish a fundamental role of a mesodermal gene in PGC specification, a potentially evolutionarily conserved mechanism across metazoans.

overall_design: Wnt3 (+/+) and Wnt3 (-/-) mouse embryonic stem cells (mESCs) bearing the BV transgenes expressing membrane-targeted Venus under the control of Blimp1 regulatory elements (Blimp1-mVenus: BV;  PMID 18583473) were established and maintained. Epiblast-like cells (EpiLCs) were then induced from the established ES lines, followed by the cytokine stimulation (No cytokines [negative control], BMP4, Wnt3a, BMP4+Wnt3a) for different periods (0h, 12h, 24h, 36h).

first: Shinya

last: Aramaki

first: Katsuhiko

last: Hayashi

first: Hiroshi

last: Ohta

first: Yukihiro

last: Yabuta

first: Hiroko

last: Iwanari

first: Yasuhiro

last: Mochizuki

first: Takao

last: Hamakubo

last: Shirahige

first: Mitinori

last: Saitou


title: Expression data from control (F/F) and Snai1 knockout (KO) embryoid body (EB) and teratoma ™

status: Public on Dec 10 2013

first: Yongshun

last: Lin

address: 10 Center Dr.

institute: National Heart, Lung, and Blood Institute

summary:
Snai1 is a master factor of epithelial to mesenchymal transitioin (EMT), however, its role in embryonic stem cell (ESC) differentiation and lineage commitment remains undefined.
We used microarrays to compare the global programme of gene expression between control and Snai1 knockout ESCs-derived EB and teratoma.

overall_design: For EBs, control and Snai1 knockout ESCs were cultured as embryoid bodies in spotaneous differentiation media, RNA of 5 days EBs were collected for Affymetrix microarrays. For teratomas, control and Snai1 knockout ESCs were injected into nude mice to form teratomas. RNA of 6 weeks were collected for Affymetrix microarrays.

first: Stephen

last: Weiss


title: Gene Expression Profiles Distinguish Children with Inactive Polyarticular Juvenile Idiopathic Arthritis (JIA) with a Predilection to Flare

status: Public on Dec 14 2013

city: Oklahoma City

first: Bart

last: Frank

state: OK

institute: OMRF

summary:
Gene expression profiles were obtained from 17 children with rheumatoid factor negative (RF-) polyarticular juvenile idiopathic arthritis (JIA). The disease was inactive in all patients at visit 1. Thee disease remained inactive at visit 2 for 9 patients, while the other 8 patients were experiencing a disease flare at visit 2. The goal of the study was to better understand the underlying molecular biology of flares in JIA
Total RNA was obtained from PBMC at two different times in the course of disease

overall_design: 2 samples from each of 17 patients were collected and analyzed different times in the course of the disease

first: Mark

middle: B

first: Nicholas

last: Knowlton

last: Armstrong

first: Jeanette

last: Osban

first: Kaiyu

last: Jiang

first: Kathleen

last: O’Neil

first: Michael

last: Centola

first: Yanmin

last: Chen

first: Jenny

first: James

middle: N

last: Jarvis


title: Expression data from Dmp1-GFP sorted osteocytes

status: Public on Dec 12 2013

city: Toon

first: Yuuki

last: Imai

state: Ehime

address: Shitsukawa

department: Proteo-Science Center

institute: Ehime University

summary: Estrogens are well known steroid hormones necessary to maintain bone health. In addition, mechanical loading, which estrogen signaling may intersect with the Wnt/β-catenin pathway, is also essential for bone health. As osteocytes are known as the major mechanosensory cells embedded in mineralized bone matrix, osteocyte ERα deletion mice (ERαΔOcy/ΔOcy) were generated by mating ERα floxed mice with Dmp1-Cre mice to determine functions of ERα in osteocytes. Trabecular bone mineral density of female, but not male ERαΔOcy/ΔOcy mice was significantly decreased. Bone formation parameters in ERαΔOcy/ΔOcy were significantly decreased while osteoclast parameters were unchanged. This suggests that ERα in osteocytes exerts osteoprotective function by positively controlling bone formation. To identify potential targets of ERα, gene array analysis of Dmp1-GFP osteocytes FACS sorted from ERαΔOcy/ΔOcy and control mice was performed. Expression of Mdk and Sostdc1, both known inhibitors of Wnt, were significantly increased without alteration of the mature osteocyte marker Sost or β-catenin. Hindlimb unloading exacerbated the trabecular bone loss, but surprisingly cortical bone was resistant. These studies show that ERα in osteocytes has osteoprotective effects in trabecular bone through regulating expression of Wnt antagonists, but conversely plays a negative role in cortical bone loss due to unloading.

overall_design: Wild type and osteocyte-specific Estrogen Receptor alpha knock-out mice were generated. The number of both genotypes of mice was three. Calvarial osteocytes of both genotypes harboring Dmp1-GFP were extracted by sequential enzymatic digestion, followed by FACS Aria sorting and total RNAs were purified for Affymetix GeneChip microarray analysis without pooling.

first: Shino

last: Kondoh

first: Katsuhide

last: Igarashi


title: Expression data from mouse B Cells with mir-155 KO and WT

status: Public on Dec 03 2013

city: Seoul

first: Jin-Wu

last: Nam

address: 222 Wangsimni Seongdong-gu

country: South Korea

institute: Hanyang University

summary: We used microarrays to investigate the global changes of gene expression in B cells of mir-155 Knockout mice.

overall_design: Analysis of mir-155 knockout cultured and activated B Cells versus wild-type cultured and activated B Cells, by microarray profiling

first: C

last: Shin

first: D

last: Baek

last: Bartel


title: Genome wide analysis of transcriptome and microRNAs in early stage of Alzheimer’s disease (mRNA)

status: Public on Dec 01 2013

city: Ansan

first: Hyemyung

last: Seo

address: Hanyang University

summary:
We addressed the integrated analysis of mRNA and miRNA expression levels of Tg6799 AD model mice at 4 month and 8 months of age. Total 8 gene cluster modules for co-expression network were predicted from transcriptome data and 6 modules were show relation  with AD or aging. We constructed early stage AD network using data integration between mRNA and miRNA profiles and predicted miRNAs strongly involved in module regulation. We found that ARRDC3 showed AD mutation dependent changes of expression and was related metabolic dysfunction in early stage AD.
These results demonstrate that candidate genes on the simultaneous profiling of mRNA and miRNA expressions in genome wide can be used for the understanding of non-coding RNA related gene expression in early stage AD. We suggested that our results could be future candidate to be developed as early biomarkers in progressive AD pathology.  This result can be used for the further application in neurodegenerative diseases.

overall_design: Tg6799 transgenic mice were purchased from The Jackson Laboratory (USA) and were housed under a 12h light-dark cycle with free access to food and water. Female Tg6799 mice are maintained until 4 months and 8 months of age (for littermate control: LM and mutant subjects: MT). RNA samples were isolated from hippocampus of mice using TRI-Reagent (Sigma-Aldrich, St. Louis, MO) according to the manufacturer’s instructions. Gene expression was analyzed with GeneChip® Mouse Genome 430 2.0 Arrays (Affymetrix, Santa Clara, CA), which is comprised of over 45,000 probe sets representing approximately 28,700 well-characterized mouse genes. The  Ion Total RNA-Seq Kit v2 (Lifetechnologies, USA) was used for the preparation of micro RNA libraries according to the manufacturer's instructions. Total numbers of subject used are as followed: 1) LM 4 months : MT 4 months : LM 8 months : MT 8 months (2:4:2:4) for screening mRMA and miRNA, 2) LM 4 months : MT 4 months : LM 8 months : MT 8 months (4:4:4:4) for expression verification.         Tg6799 transgenic mice were purchased from The Jackson Laboratory (USA) and were housed under a 12h light-dark cycle with free access to food and water. Female Tg6799 mice are maintained until 4 months and 8 months of age (for littermate control: LM and mutant subjects: MT). RNA samples were isolated from hippocampus of mice using TRI-Reagent (Sigma-Aldrich, St. Louis, MO) according to the manufacturer’s instructions. Gene expression was analyzed with GeneChip® Mouse Genome 430 2.0 Arrays (Affymetrix, Santa Clara, CA), which is comprised of over 45,000 probe sets representing approximately 28,700 well-characterized mouse genes. The  Ion Total RNA-Seq Kit v2 (Lifetechnologies, USA) was used for the preparation of micro RNA libraries according to the manufacturer's instructions. Total numbers of subject used are as followed: 1) LM 4 months : MT 4 months : LM 8 months : MT 8 months (2:4:2:4) for screening mRMA and miRNA, 2) LM 4 months : MT 4 months : LM 8 months : MT 8 months (4:4:4:4) for expression verification.

first: H


title: Expression data from control and Snai1 knockout embryonic stem cells (ESCs)

city: Bethesda

first: Yongshun

last: Lin

summary:
Snail1 is a master epithelial-mesenchymal trisition (EMT) factor but its role in ESC maintenance is unknown.
We used microarrays to compare the global gene expression  between control and Snai1 knockout ESCs.

overall_design: RNA extracted from control and Snai1 knockout ESCs were hybridizated on Affymetrix microarrays.

first: Stephen

last: Weiss


title: Expression data from livers of C57BL/6J mice fed a high-fat diet and coffee

first: Shoko

last: Takahashi

address: 1-1-1 Yayoi, Bunkyo-ku

department: aDepartment of Applied Biological Chemistry, Graduate School of Agricultural and Life Sciences

country: Japan

institute: The University of Tokyo

summary:
The present study was conducted to evaluate the effects of  the intake of three types of coffee (caffeinated, decaffeinated,  and green unroasted coffee) on the livers of C57BL/6J mice fed  a high-fat diet, and to extensively elucidate the physiological  responses to coffee intake by analysing the findings obtained  from a comprehensive transcriptomic analysis using DNA  microarrays.
The present study was conducted to evaluate the effects of  the intake of three types of coffee (caffeinated, decaffeinated,  and green unroasted coffee) on the livers of C57BL/6J mice fed  a high-fat diet, and to extensively elucidate the physiological  responses to coffee intake by analysing the findings obtained  from a comprehensive transcriptomic analysis using DNA  microarrays.

overall_design: Briefly, 7-week-old male C57BL/6J mice purchased from Charles River Laboratories Japan (Yokohama) were divided into the following five groups. The normal diet group (ND group) was fed D12450B (10 kcal% fat, Research Diets, New Brunswick, NJ, USA). The high-fat diet group (HF group) was fed D12492 (60 kcal% fat, Research Diets, New Brunswick, NJ, USA). The caffeinated coffee group (HFCC group) was fed a high-fat diet containing 2% caffeinated freeze-dried coffee. The decaffeinated coffee group (HFDC group) was fed a high-fat diet containing 2% decaffeinated freeze-dried coffee. The green unroasted coffee group (HFGC group) was fed a high-fat diet containing 2% unroasted caffeinated freeze-dried coffee. The mice had ad libitum access to their diets and drinking water. After 9 weeks, mice were sacrificed and the livers were subjected to the Affymrtix DNA microarray experiment.

first: Hisanori

last: Kato


title: Progressive loss of PGC-1alpha expression in aging muscle potentiates glucose intolerance and systemic inflammation

status: Public on Dec 05 2013

city: Toronto

first: Benjamin

last: Haibe-Kains

state: Ontario

address: 610 University Avenue

department: Princess Margaret Research

institute: Princess Margaret Cancer Centre

summary: Decreased mitochondrial mass and function in muscle of diabetic patients is associated with low PGC-1alpha, a transcriptional coactivator of the mitochondrial gene program. To investigate whether reduced PGC-1alpha and oxidative capacity in muscle directly contributes to age-related glucose intolerance, we compared the genetic signatures and metabolic profiles of aging mice lacking muscle PGC-1alpha. Microarray analysis revealed that a significant proportion of PGC-1alpha-dependent changes in gene expression overlapped with age-associated effects, and aging muscle and muscle lacking PGC-1alpha shared gene signatures of impaired electron transport chain activity and TGFbeta signalling.

overall_design: Gastrocnemius muscle mRNA from young (10 week old) and old (24 month old) wild-type and knock-out (muscle-specific PGC-1alpha, myogenin-cre) C57Bl/6N/6J/129 mice

first: S

last: Sczelecki

first: Aurèle

last: Besse-Patin

first: A

last: Abboud

first: Sandra

last: Kleiner

last: Laznik-Bogoslavski

middle: D

last: Wrann

first: J

middle: L

last: Ruas

first: B

last: Estall


title: BRAF Mutation, NRAS Mutation, and the Absence of an Immune-Related Expressed Gene Profile Predict Poor Outcome in Patients with Stage III Melanoma

city: North Sydney

first: Graham

middle: J.

last: Mann

state: NSW

address: Poche Centre, 40 Rocklands Road

country: Australia

institute: Melanoma Institute Australia

summary: Prediction of outcome for melanoma patients with surgically-resected macroscopic nodal metastases is very imprecise. We performed a comprehensive clinicopathologic assessment of fresh-frozen macroscopic nodal metastases and the preceding primary melanoma, somatic mutation profiling and gene expression profiling to identify determinants of outcome in 79 melanoma patients.  In addition to disease stage <II at initial presentation, the following clinical and pathologic factors were independent predictors of improved outcome (ORs for survival >4yr, 90%CI): presence of a nodular component in the primary melanoma (6.8, 0.6-76.0), and small cell size (11.1, 0.8-100.0) or low pigmentation (3.0, 0.8-100.0) in the nodal metastases. Absence of BRAF mutation (20.0, 1.0-1000.0) or NRAS mutation (16.7, 0.6-1000.0) were both favourable prognostic factors. A 46-gene expression signature with strong over-representation of immune response genes was predictive of better survival (10.9, 0.4-325.6); in the full cohort median survival was >100 months in those with the signature, but 10 months in those without. This relationship was validated in two previously published independent stage III melanoma datasets. We conclude that the presence of BRAF mutation, NRAS mutation and absence of an immune-related expressed gene profile predict poor outcome in melanoma patients with macroscopic stage III disease.

overall_design: Samples eligible for this study (n=79) were obtained from lymph node specimens (Melanoma Institute Australia (MIA) Biospecimen Bank) in which macroscopic tumor was observed, obtained from patients believed to be without distant metastases at the time of tumor banking based on clinical examination and computerised axial tomographic scanning of the brain, chest, abdomen and pelvis. Specimens were macro-dissected at time of banking and subsequently reviewed to meet minimum criteria for tumor cell content (>80%) and amount of necrosis (<30%). Linked clinical and pathologic data were obtained from the MIA research database. Total RNA was extracted from 20-30mg of fresh frozen tissue. Tissue samples were homogenized using a high-speed agitation polytron blender (Kinematica, Luzern, Switzerland) in the presence of Trizol. The RNA was isolated and purified with an RNeasy purification kit (Qiagen RNeasy purification kit- Qiagen Pty Ltd., Clifton Hill, Victoria, Australia) with DNAse I digestion on the column. The quality of the RNA preparations was assessed using the Agilent 2100 Bioanalyser (Agilent Technologies, Palo Alto, CA, USA). RNA integrity scores were >8 for all samples analyzed. cRNA amplification and labelling with biotin were performed using Illumina TotalPrep RNA amplification kit according to the manufacturer’s directions (Ambion, Inc., Austin, TX, USA) with 250ng total RNA as input material. Gene expression analysis was performed using the Sentrix Human-6 v3 Expression BeadChips (Illumina, Inc., San Diego, CA, USA), and BeadStation system from Illumina as per manufacturer’s instructions. Expression BeadChip using array annotation based on R-2.11.0 and illuminaHumanv3.db. Quality control was performed on all chips using R/Bioconductor and the lumi package (www.bioconductor.org). Data normalization was performed using a variance-stabilizing transform (VST) and quantile normalization as implemented in the lumi package for R/Bioconductor.

middle: J

first: Gulietta

last: Pupo

first: Anna

middle: E

last: Campain

first: Candace

last: Carter

first: Sarah-Jane

last: Schramm

first: Svetlana

last: Pianova

first: Sebastien

last: Gerega

first: Chitra

last: De Silva

first: Kenneth

last: Lai

first: James

last: Wilmott

first: Maria

last: Synnott

first: Peter

last: Hersey

first: Richard

middle: F

last: Kefford

first: John

last: Thompson

first: Yee

last: Yang

middle: A

last: Scolyer


title: Expression Data from Normal or ErbB2 Tumor Fibroblasts With or Without Ets2

city: Columbus

first: Julie

last: Wallace

state: OH

address: 460 W. 12th Ave 840 BRT

country: USA

institute: OSUCCC

summary:
The mechanisms involved in epithelium-stroma interactions remain poorly understood, despite the importance of the microenvironment during tumorigenesis.  Here, we studied the role of Ets2 transcrpiton factor in tumor associated fibroblasts in the MMTV-ErbB2 mammary tumor model.  Inactivation of Ets2 specifically in fibroblasts using Fsp-cre significantly reduced tumor growth, in contrast to Ets2 inactivation in epithelium in which no differences in tumor growth were observed.
Microarray analysis on isolated fibroblasts demonstrated the important role of Ets2 in remodeling of the extracellular matrix and angiogenesis in these cells.  Tumors lacking Ets2 in fibroblats had diminished blood vessels.  Our tumor specific gene signature was also represented in the stroma of human breast cancer patients.  Collectively, our results suggest Ets2 uniquely contributes to angiogenesis from fribroblasts in the tumor microenvironment.

overall_design: Primary mammary fibroblasts were isolated from mice with no oncogene with or without Ets2 and with the ErbB2 oncogene with or without Ets2, RNA was extracted and samples were submitted for Affymetrix gene expression arrays

first: Subhasree

last: Balakrishnan

first: Lianbo

last: Yu

first: Michael

middle: C

last: Ostrowski


title: Expression Data from Endothelial Cells as a Consequence of Ets2 Signaling in PyMT Tumor Associated Fibroblasts

summary:
Tumor associated fibroblasts are known to play an important role in angiogenesis, however the specific signaling pathways playing an important role in this cross talk remain ill defined.  Here, we studied how Ets2 transcrpiton factor signaling in tumor associated fibroblasts effected gene expression in surrounding endothelial cells in the MMTV-PyMT mammary tumor model.
Inactivation of Ets2 specifically in fibroblasts using Fsp-cre significantly reduced tumor associated angiogenesis, and was indicated to effect ECM remodeling, cell adhesion and cell chemotaxis processes in neighboring endothelial cells.  We have identified Ets2 in fibroblasts as a key signaling molecule to induce tumor associated angiogenesis.  Additionally, this function does not rely on the presence of tumor cells, indicating a memory in fibroblasts to induce angiogenesis.

overall_design: Primary mammary endothelial cells were isolated from mice with or without fibroblast Ets2 in the presence of the PyMT oncogene through sorting with a CD31 antibody. RNA was extracted and samples were submitted for Affymetrix gene expression arrays


title: Differentiation defective phenotypes revealed by large scale analyses of human pluripotent stem cells

city: Kyoto

first: Shinya

last: Yamanaka

address: 53 Kawahara-machi, Shogoin, Sakyo-ku

institute: Center for iPS Cell Research and Applicaton (CiRA), Kyoto University

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

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

overall_design: Refer to individual Series