title: Comparative gene expression profile of Hes1-overexpressing cultured hippocampal neurons vs the corresponding control populations (neurons expressing GFP)

status: Public on Dec 30 2014

city: Seville

first: Pedro

middle: Jose

last: Chacon

state: Seville

address: Americo Vespucio s/n

department: Cell Signaling

country: Spain

institute: Andalusian Center of Molecular Biology and Regenerative Medicine (CABIMER).

summary: Homologue of Enhancer-of-split 1 (Hes1) is a transcription factor that regulates neuronal plasticity, promoting the growth of dendrites and increasing the GABAergic input. A higher expression of Hes1 also results in neuronal resistance against the noxious activity of amyloid beta, the main agent in the advent and progression of the Alzheimer's disease. As a transcription factor, Hes1 controls de expression of many genes. Using the microarray technology we have detected that the expression of one secreted synaptic protein, cerebellin 4 (Cbln4) was particularly increased upon overexpression of Hes1. We also present evidence that Cbln4 plays an essential role in the formation and maintenance of inhibitory GABAergic connections and that either overexpression of Cbln4 in cultured hippocampal neurons or the application of recombinant Cbln4 to the cultures increased the number of GABAergic varicosities and rescued neurons from amyloid beta induced cell death.

overall_design: 6 DIV cultured hippocampal neurons were transduced with Sindbis virus overexpressing myc-tagged Hes1 and EGFP under different promoters or GFP alone as control. Cells were lysed and total RNA was extracted. Gene expression profiles were obtained for each sample and compared.

middle: J

first: Alfredo

last: Rodriguez-Tébar


title: Ring1A and Ring1B in thymocytes

status: Public on Dec 26 2014

city: Yokohama

first: Takaho

middle: A.

last: Endo

state: Kanagawa

address: 1-7-22 Suehiro, Tsurumi

department: IMS

country: Japan

institute: RIKEN

type: Genome binding/occupancy profiling by array

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

overall_design: Refer to individual Series


title: Gene expression profiling of murine incisor pulp following resection of the inferior alveolar nerve

city: Oklahoma City

first: Richard

last: Pelikan

state: Oklahoma

address: 825 NE 13th St

department: Genes & Human Disease Research Program

country: USA

institute: Oklahoma Medical Research Foundation

summary: The overall goal of this project is to investigate the contribution of the inferior alveolar nerve (IAN) towards cellular mechanisms required for regeneration of the murine incisor. Here, we conducted gene expression profiling of adult murine incisor dental mesenchyme tissue following two weeks after unilateral resection of the IAN from both the denerved and contralateral incisor of five wild-type mice.

overall_design: To investigate the mechanism of murine incisor regeneration dependent on innervation, we analyzed incisor dental mesenchyme of adult wild-type mice two weeks after unilateral resection of the IAN. We performed microarray analyses of incisor dental mesenchyme of wild-type mice from both the denerved and contralateral lower incisor at postnatal day P60 (n=5 mice) to examine the genes potentially regulated by factors contributed to the incisor mesenchyme by innervation.

first: Hu

last: Zhao

middle: C

first: Yang

last: Chai


title: Microarray analysis of DN thymocytes in LckCreCdkn2a-/-Ring1A-/-Ring1Bfl/fl mice

summary: During ontogeny, totipotent progenitors undergo stepwise lineage-determination to give rise to progenitors with narrower potential and eventually to unipotent progenitors. Status of the progenitors with restricted potential is determined by transcription factors, and by epigenetic mechanisms. It is generally conceived that transcription factors primarily determine the commitment status of progenitors and epigenetic mechanisms follow to fix the status. In line with this idea is that, whereas many cases are known where the loss or over-expression of a certain single transcription factor bring about the cell fate conversion, no cases have ever been reported where alteration of epigenetic status solely leads to convert the determined cell lineage. Here we provide such a case where the inactivation of polycomb-medicated epigenetic regulation resulted in conversion of T lineage progenitors to B cell fate. In mice in which epigenetic repressor Ring1A and B are conditionally deleted in T cell lineage, T cell development was severely blocked at around T cell lineage determination step. Such developmental block was partially rescued by the additional deletion of Cdkn2a, one of cell cycle inhibitors, allowing the generation of T cell lineage progenitors that bear rearranged TCRβ chain gene. We found that these T cell progenitors co-express B cell lineage associated genes, and furthermore, these T cell progenitors were able to give rise to IgM+ mature B cells with normal function upon transfer to immuno-deficient mouse. These results indicate that T and B cell lineages are asymmetric in requirement of epigenetic regulation for the maintenance of respective lineages.

overall_design: RNA samples from LckCre(-)Cdkn2a-/-Ring1A-/-Ring1Bfl/fl (DKO) and LckCre(+)Cdkn2a-/-Ring1A-/-Ring1Bfl/fl (TKO)

first: Tomokatsu

last: Ikawa

middle: A


title: Gene expression in liver of wild-type and Mtap heterozygous mice

status: Public on Dec 31 2014

city: Philadelphia

first: warren

last: kruger

state: PA

address: 333 Cottman Ave.

institute: Fox Chase Cancer Center

summary: The study was designed to identify differentially expressed transcripts between wild type and Mtap heterozygous mice

overall_design: four mice of each genotype were used.  All mice were male.  Mice were between 92 and 101 days of age.

first: Warren

last: Kruger


title: Yap1 activation enables bypass of oncogenic Kras addiction in pancreatic cancer (part 1)

city: Houston

first: Avnish

last: Kapoor

state: Texas

address: 1901 East Rd

institute: MD Anderson Cancer Center

summary: Activating mutations in KRAS are among the most frequent events in diverse human carcinomas  and are particularly prominent in human pancreatic ductal adenocarcinoma (PDAC). An  inducible KrasG12D-driven mouse model of PDAC has established a critical role for sustained  KrasG12D expression in tumor maintenance, providing a model to determine the potential for, and  underlying mechanisms of, KrasG12D–independent PDAC recurrence. Here we show that some  tumors undergo spontaneous relapse and are devoid of KrasG12D expression and downstream  canonical MAPK signaling and instead acquired amplification and overexpression of the  transcriptional co-activator Yap1. Functional studies established the role of Yap1 and the  transcriptional factor Tead2 in driving KrasG12D–independent tumor maintenance. The  Yap1/Tead2 complex acts cooperatively with E2F transcription factors to activate a cell cycle  and DNA replication program. Our studies, along with corroborating evidence from human  PDAC models, portend a novel mechanism of escape from oncogenic Kras addiction in PDAC.

overall_design: To evaluate the potential for recurrence mechanisms following KrasG12D extinction in p48Cre tetO_LKrasG12D ROSA_rtTAL+ p53L+ mice, we utilized MRI imaging to monitor regression of advanced pancreatic tumors measuring at least 8 mm in diameter at time of doxycycline withdrawal. Primary relapsed pancreatic tumor lines were established from eight independent tumors. These lines (E1-E16)  were cultured in the absence of doxycycline for 24 hours and total cellular RNA was prepared. For control samples, two iKras lines (described in Ying et al., 2012) were cultured in the presence of doxycycline and total cellular RNA was prepared.


title: Endogenous Wnt proteins induce differentiation and loss of pluripotency in EpiSCs

status: Public on Dec 24 2014

city: Rotterdam

first: Dorota

last: Kurek

address: Dr Molewaterplein 50

country: Netherlands

institute: ErasmusMC

summary: We compared the transcriptomes of EpiSCs maintained in the presence or absence of Wnt pathway inhibitor IWP2. We screened also our gene expression data for potential markers for genuine EpiSCs, maintained in the presence of Wnt inhibition and compared with ESC expression data. We compared the transcriptomes of EpiSCs maintained in the presence or absence of IWP2. The high level of Wnt-induced differentiation occurring in conventional EpiSC cultures may have interfered with the analysis of their characteristics. By applying Wnt inhibitors we are now able to establish the properties of genuine EpiSCs.

overall_design: We compared the gene expression profiles of conventional EpiSCs, genuine EpiSCs, and ESCs using Affymetrix Genechip analysis. This revealed a set of genes that is expressed lower in genuine EpiSCs compared to conventional EpiSCs.

first: Derk

last: ten Berge


title: Whole-genome hypothalamic transcriptome data collected from wild-type and ob/ob Pdyn-eGFP-RPL10a mice using BAC TRAP procedure

status: Public on Dec 25 2014

city: New York

first: Zhiying

last: Li

state: NY

address: 1230 York ave.

institute: Rockefeller University

summary:
Prodynorphine-expressing neurons were targeted by eGFP-RPL10a, a transgene that is expressed under the control of the Pdyn promoter in a BAC containing the Pdyn backbone.
Trangenic mice were made with FvB embryos via pro-nuclear injection. Transgene-positive progenies were bred to C57BL/6J for more than five generations before being used in the current experiment.
Triplicates of 6-8 hypothalami were collected per sample from wild-type and ob/ob adult mice. Polysomal IP RNA and total Input RNA were purified from each sample.

overall_design: Affymetrix GeneChip Mouse 430 2.0 arrays (900495) were used to identify transcripts that are specifically expressed in Pdyn neurons with a fold change (IP vs. Input) of >=2 in wild-type mice.  The same microarrays were also used to identify Pdyn-specific transcripts that are differentially regulated transcriptionally by leptin deficiency with a fold change (ob IP vs. wt IP) of >=1.5.

first: Jeffrey

middle: M

last: Friedman

first: Myriam

last: Heiman

first: Paul

last: Greengard


title: Transcriptional responses of mouse adipocytes during insulin resistance

status: Public on Dec 23 2014

city: Boston

first: Evan

last: Rosen

state: MA

address: 3 Blackfan Cir

department: Endocrinology

institute: Beth Israel Deconess Medical Center

summary:
Insulin resistance is a sine qua non of Type 2 diabetes (T2D) and a frequent complication of multiple clinical conditions, including obesity, aging, and steroid use, among others. How such a panoply of insults can result in a common phenotype is incompletely understood. Furthermore, very little is known about the transcriptional and epigenetic basis of this disorder, despite evidence that such pathways are likely to play a fundamental role. Here, we compare cell autonomous models of insulin resistance induced by the cytokine tumor necrosis factor-a (TNF) or by the steroid dexamethasone (Dex) to construct detailed transcriptional profiles associated with cellular insulin resistance.
Gene expression data from mouse adipocyte, with TNF or Dex treatments at different time points.

overall_design: Murine 3T3-L1 adipocytes were treated separately with dexamethasone (Dex; 20nM) or tumor necrosis factor-alpha. To comprehensively assess gene expression changes caused by Dex and TNF in a time-dependent manner, we profiled cells at early (2 hours), intermediate (24 hours), and late (6 days) points in the development of insulin resistance.


title: Yap1 activation enables bypass of oncogenic Kras addiction in pancreatic cancer (part 2)

overall_design: To evaluate the mechanism of Yap1 mediated bypass of tumor regression upon KrasG12D extinction


title: Yap1 activation enables bypass of oncogenic Kras addiction in pancreatic cancer


title: Expression Data from PtenF341V and Null Mouse Embryonic Fibroblasts

status: Public on Dec 19 2014

city: COlumbus

first: Onur

last: Egriboz

state: OH

address: 460 W 12th Ave

department: Molecular Genetics

institute: The Ohio State University

summary: PTEN imparts tumor suppression in mice by cell autonomous and non-autonomous mechanisms. Whether these two tumor suppressor mechanisms are mediated through similar or distinct signaling pathways is not known. Here we generated and analyzed knockin mice that express a series of human cancer-derived mutant alleles of PTEN that differentially alter the Akt axis in either stromal or tumor cell compartments of mammary glands. We find that cell non-autonomous tumor suppression by Pten in stromal fibroblasts strictly requires activation of P-Akt signaling, whereas cell autonomous tumor suppression in epithelial tumor cells is independent of overt canonical pathway activation. These findings expose distinct Akt-dependent and independent tumor suppressor functions of PTEN in stromal fibroblasts and tumor cells, respectively, that can be used to guide clinical care of breast cancer patients

overall_design: Wild type, Pten null and PtenF341V primary mouse embryonic fibroblasts isolated from 13.5 day old embryos (E13.5) were cultured, RNA was extracted and Affymetrix gene expression arrays were performed.

first: Enrico

last: Caserta

first: Thierry

last: Pecot

first: Melissa

last: Mountel

first: Gustavo

last: Leone

first: Michael

last: Ostrowski


title: Expression Data from Pten mutant epithelial cells

summary:
PTEN imparts tumor suppression in mice by cell autonomous and non-autonomous mechanisms. Whether these two tumor suppressor roles are mediated through similar or distinct signaling pathways is not known. Here we generated and analyzed knockin mice that express a series of human cancer-derived mutant alleles of PTEN in either stromal or tumor cell compartments of mammary glands. We find that cell non-autonomous tumor suppression by Pten in stromal fibroblasts strictly requires activation of P-Akt signaling, whereas cell autonomous tumor suppression in epithelial tumor cells is independent of overt canonical pathway activation
These findings expose distinct Akt-dependent and independent tumor suppressor functions of PTEN in stromal fibroblasts and tumor cells, respectively, that can be used to guide clinical care of breast cancer patients

overall_design: Wild type. PtenF341V, PtenWT/null, and  Pten null CDH1 positive epithelials cells of mammary ducts from 8 week old female mice were isolated by FACS, RNA was extracted and Affymetrix gene expression arrays were performed.

first: Yu

last: Lianbo

first: Julie

last: Wallace


title: Expression data from the spleen of tumor bearing mice

city: Shanghai

first: Han

last: yanmei

address: 800 Xiangyin Road

country: China

institute: Second Military Medical University

summary:
We identify a new cell subset Ter119+CD45- small cells that promotes tumor metastasis in hepatocellular carcinoma (HCC)-bearing mice.
We used microarrays to detail the gene expression of Ter119+CD45- cells comparing with CD45- cells in the spleen of hepatocellular carcinoma (HCC)-bearing mice.

overall_design: Ter119+CD45- cells in the spleen of hepatocellular carcinoma (HCC)-bearing mice, being sorted by a MoFlo high-speed cell sorter, were prepared for RNA extraction and hybridization on Affymetrix microarrays. The CD45+ cells from the same tumor bearing mice were prepared as control.

first: Yanmei

last: Han

first: Zhubo

last: Chen


title: Gene expression characterization of HPV positive head and neck cancer to predict response to Chemoradiation

city: Royal Oak

first: Bryan

last: Thibodeau

state: MI

address: 3811 West 13 Mile Road

department: BioBank

institute: Beaumont Research Institute

summary:
Background: Human papillomavirus has been shown to have a causal role in the development of head and neck squamous cell carcinoma and represents a distinct and well-defined pathology. While HPV-positive HNSCC is associated with a better response to treatment and prognosis, a subset of patients do not respond favorably to current standard of care thus suffering unnecessary morbidity and delay to receive effective therapy.
Methods: RNA from nineteen patients with HPV-positive HNSCC was subjected to gene expression analysis using Affymetrix microarrays. HPV-status was confirmed by detection of HPV16 E7 with RT-PCR.
Results: In addition to specific genetic biomarkers (including LCE3D, KRTDAP, HMOX1, KRT19, MDK, TSPAN1), differentially expressed genes were highly represented in the cell processes of genomic stability, cell cycle, and DNA damage.
Conclusions: This pilot study suggests possible biomarkers that predict response to chemoradiation therapy. These data can potentially lead to an assay that can be used clinically to predict HPV-positive HNSCC patients that will not benefit from chemoradiation, thus helping clinicians to lower morbidity and get selected patients to surgery faster.

overall_design: HPV-positive head and neck squamous cell carcinoma (HNSCC) has a good prognosis with a large percentage of patients responding to therapy. However, a certain percentage of patients do not respond. Gene expression data from Affymetrix Human Exon 1.0ST microarrays was utilized to compare patients that responded to therapy with those that did not respond.

first: Timothy

last: Geddes

first: Samreen

last: Ahmed

first: Laura

middle: E

last: Fortier

first: Barbara

middle: L

last: Pruetz

first: Jessica

last: Wobb

first: George

middle: D

last: Wilson

first: Jan

last: Akervall


title: Gene expression changes in hepatic stellate cells in response to fibrogenic agents.

first: Robert

middle: F.

last: Schwabe

address: 1150 St. Nicholas Ave.

department: Medicine- Division of Digestive Diseases

institute: Columbia University

summary:
Gene expression of hepatic stellate cells exposed to fetal bovine serum (FBS)
(cultured alone and in the presence of Kupffer cells)
activated and CCl4 exposure and Bile-duct ligation is characterized.
Affymetrix Mouse 430 2.0 gene expression measurements were
used to characterize the transcriptomic basis of the effects of the above treatments and
genotypes on firbrogenesis.

overall_design:
Gene expression of mouse hepatic stellate cells was characterized under the following conditions:
A. Quiescent (n=5).
B. Activated by FBS (n=3).
C. Cocultured with Kupffer cells and activated by FBS (n=3).
D. Activate by bile-duct ligation (n=3).
E. Activated by CCl4 (n=3).

first: Jean-Philippe

last: Pradere

first: Johannes

last: Kluwe

first: Samuele

last: DeMinicis

first: Geum-Youn

last: Gwak

first: Dianne

middle: H

last: Dapito

first: Myoung-Kuk

last: Jiang

first: Nina

last: Günter

first: Ingmar

last: Mederacke

first: Richard

last: Friedman

middle: F


title: Pax2 Dependent Expression in the Intermediate Mesoderm at E11.5

status: Public on Dec 13 2014

city: Ann Arbor

first: Greg

last: Dressler

address: 109 Zina Pitcher Drive

department: Pathology

institute: University of Michigan

summary:
Heterozygous and homozygous Pax2 E11.5 embryos were collected and the intermediate mesoderm was dissected and dispersed into single cells.
The Pax2 positive cells also expressed EGFP, which was knocked into the Pax2 locus.  EGFP positive cells were sorted by FACS and RNA isolated.

overall_design: We compared RNA expression levels in EGFP positive cells from Pax2 null and Pax2 heterozygote embryos.

first: Egon

last: Ranghini


title: Improved antitumor activity of immunotherapy combined with BRAF and MEK inhibitors in BRAFV600E mutant melanoma

status: Public on Dec 12 2014

city: Los Angeles

first: Jennifer

last: Tsoi

state: CA

address: 570 Westwood Blvd, CNSI 4338

department: University of California, Los Angeles

institute: UCLA

summary: The first clinical trial testing the combination of targeted therapy with a BRAF inhibitor vemurafenib and immunotherapy with a CTLA-4 antibody ipilimumab was terminated early due to significant liver toxicities, possibly due to paradoxical activation of the MAPK pathway by BRAF inhibitors in tumors with wild type BRAF. MEK inhibitors can potentiate the MAPK inhibition in tumor, while potentially alleviating the unwanted paradoxical MAPK activation. With a mouse model of syngeneic BRAFV600E driven melanoma (SM1), we tested whether the addition of the MEK inhibitor trametinib would enhance the immunosensitization effects of the BRAF inhibitor dabrafenib. Combination of dabrafenib and trametinib with pmel-1 adoptive cell transfer (ACT) showed complete tumor regression. Bioluminescent imaging and tumor infiltrating lymphocyte (TIL) phenotyping showed increased effector infiltration to tumors with dabrafenib, trametinib or dabrafenib plus trametinib with pmel-1 ACT combination. Intracellular IFN gamma staining of the TILs and in vivo cytotoxicity studies showed trametinib was not detrimental to the effector functions in vivo. Dabrafenib increased tumor associated macrophages and T regulatory cells (Tregs) in the tumors, which can be overcome by addition of trametinib. Microarray analysis revealed increased melanoma antigen, MHC expression, and global immune-related gene upregulation with the triple combination therapy. Given the up-regulation of PD-L1 seen with dabrafenib and/or trametinib combined with antigen specific ACT, we tested the triple combination of dabrafenib, trametinib with anti-PD1 therapy, and observed superior anti-tumor effect to SM1 tumors. Our findings support the testing of these combinations in patients with BRAFV600E mutant metastatic melanoma.

overall_design: SM1 tumors were implanted into C57BL/6 mice. Mice were treated by ACT of pmel-1 splenocytes or C57BL/6 splenocytes as control. Pmel-1 treated mice were additionally treated with either vehicle, dabrafenib, trametinib, or combination of both drugs and control mice were treated with vehicle or combination of both drugs.

first: Siwen

last: Hu-Lieskovan

first: Stephen

last: Mok

first: Blanca

last: Moreno

first: Lidia

last: Robert

first: Lucas

last: Goedert

last: Koya

first: Thomas

middle: G

last: Graeber

first: Begonya

last: Comin-Anduix

first: Antoni

last: Ribas


title: Hepatic expression data between C57BL/6J and DBA/2J mice

status: Public on Dec 14 2014

city: shanghai

first: Mingzhe

last: Zhu

address: south chongqing Road

institute: hsc

summary:
C57BL/6J (B6) and DBA/2J (D2) mice were fed a high-fat/high-cholesterol diet in order to investigate the responses to that diet over time and their underlying genetic factors. We observed distinctly diverse responses between B6 and D2 mice, including dynamic distribution of cholesterol in serum and bile, hepatic apoptosis and dynamic formation of gallstones and atherosclerosis.
Hepatic microarray analysis revealed distinctly different gene expression patterns in functional pathway groups including lipid metabolism, oxidative stress, immune/inflammation response and apoptosis, which might account for the different responses.This might provide us not only new insights into gallstones formation and atherosclerosis, but also opportunities to identify candidate genes for high-fat/high-cholesterol related diseases.

overall_design: C57BL/6J (B6) and DBA/2J (D2) mice were fed a high-fat/high-cholesterol diet in 0,1,4 12,21 weeks,respectively. Liver tissues of mice from each time-point were removed for RNA extraction.  Equal amounts of RNA samples from five mice of each strain at each time-point were pooled and then used to generate biotinylated cRNA targets for Affymetrix GeneChip Mouse Genome 430 2.0 Array.


title: Effects of O-GlcNAc modification on gene expression using O-GlcNAcase deleted Mouse Embryonic Fibroblast cells.

status: Public on Dec 29 2014

city: Bethesda

first: Chithra

middle: N

last: Keembiyehetty

state: MD

address: 8 Center Dr.

department: NIDDK

institute: NIH

summary:
Single O-GlcNAc modification orchestrate by O-GlcNAc Transferase (OGT) and O-GlcNAcase (OGA alias MGEA5) enzymes, affects signal transduction and gene expression by chromatin modulation. We developed Oga deleted MEF (mouse embryonic fibroblast) cells to investigate effects of O-GlcNAc modification in mice. RNA isolated from Mouse Embryonic Fibroblast cells generated from Oga Knock out (KO) Heterozygous (Het) and wild type (WT) cells and subjected to microarray analysis.
Results provide insight into regulatory pattern of O-GlcNAc modification, and associated signaling pathways

overall_design: Conditionally deleted Oga heterozygous mice (Oga +/-) were derived by crossing Oga floxed male mouse (Oga floxed/+  in genetic background C57B1/6)  with the MMTV-cre female mouse (B6129-Tgn(MMTV-Cre)1Mam. Resultant Oga heterozygous mice cross bred and collected MEF cells (mouse embryonic fibroblast) from wild type (WT), Heterozygous (het) and Knock out (KO) embryos at E12.5 dpc. RNA extracted from female MEF cell lines and conducted microarray  analysis in 3 technical replicates.

first: John

last: Hanover

first: Dona

last: Love


title: Vaccine-Elicited CD4 T Cells Induce Immunopathology Following Chronic LCMV Infection

status: Public on Dec 04 2014

city: Oxford

first: Nicholas

last: Provine

state: Oxfordshire

address: John Radcliffe Hospital

department: NDM - Experimental Medicine

country: United Kingdom

institute: University of Oxford

summary:
CD4 T cells promote innate and adaptive immune responses, but how vaccine-elicited CD4 T cells contribute to immune protection remains unclear.
Here we evaluated whether induction of virus-specific CD4 T cells by vaccination would protect mice against infection with chronic lymphocytic choriomeningitis virus (LCMV).
Immunization with vaccines that selectively induced CD4 T cell responses resulted in catastrophic inflammation and mortality following challenge with a persistent form of LCMV.
Immunopathology required antigen-specific CD4 T cells and was associated with a cytokine storm, generalized inflammation, and multi-organ system failure. Virus-specific CD8 T cells or antibodies abrogated the pathology.
These data demonstrate that vaccine-elicited CD4 T cells in the absence of effective antiviral immune responses can trigger lethal immunopathology.

overall_design: Splenic GP66-specific CD4 T cells from mice immunized with either a LMwt vaccine (sham) or LMgp61 vaccine (CD4 vaccine) were purified by FACS on day 8 post-infection with LCMV clone 13

first: Pablo

last: Penaloza-MacMaster

first: Dan

last: Barouch


title: Rsk2 controls synovial fibroblast hyperplasia and the course of arthritis.

city: Berlin

first: Pawel

last: Durek

address: Charitéplatz 1

country: Germany

institute: Deutsches Rheuma-Forschungszentrum

summary: To understand differences in the pathogenesis of synovial hyperplasia during TNF-induced arthritis, we compared the global gene expression of hTNFtg and hTNFtg;Rsk2-/y primary synovial fibroblasts.

overall_design: Murine fibroblast-like synoviocytes (FLS) were isolated from the hind paws of hTNFtg and hTNFtg;Rsk2-/y (background: C57BL/6) 6-9 week-old mice via collagenase digestion. The cells of two mice were pooled and cultivated for at least 3 passages before usage. For characterization, the cells were tested for the surface expression of CD90.2 and VCAM1 by flow cytometric analysis, whereas CD11b as a monocytic marker had to be absent. Total RNA was extracted using the RNeasy Mini kit (Qiagen). The integrity and amount of isolated RNA was assessed for each sample using an Agilent 2100 Bioanalyzer (Agilent, Waldbronn, Germany) and a NanoDrop ND-1000 spectrophotometer (NanoDrop Technologies, Wilmington, DE). Double-stranded complementary RNA was synthesized from 1 µg total RNA using Message AmpII Biotin (Ambion, USA). Fifteen micrograms of fragmented cRNA of each sample were hybridized to six MG_U430_2 GeneChips (Affymetrix). Hybridization was performed in a Hybridization Oven 640, and chips were washed and stained in the Fluidics Station 450 (both Affymetrix). Finally, the arrays were scanned with a GeneChip Scanner 3000 using the GCOS software, version 1.4, both Affymetrix. All relevant GCOS data of quality checked microarrays were analyzed with High Performance Chip Data Analysis (HPCDA, unpublished), using the BioRetis database (www.bioretis-analysis.de), as described and validated previously.

first: Anja

last: Derer

first: Christina

last: Böhm

first: Bettina

last: Grötsch

first: Joachim

middle: R

last: Grün

first: Andreas

last: Grützkau

first: Michael

last: Stock

first: Kirsten

last: Neubert

first: Sybille

last: Sehnert

first: Georg

last: Schett

first: Axel

last: Hueber

first: Jean-Pierre

last: David


title: Transcriptional and post-transcriptional analysis of CD4+ T cell clones deriving from HTLV-1 infected individuals

status: Public on Dec 03 2014

city: lyon

first: franck

last: mortreux

address: 46 allee d'Italie

country: France

institute: oncovirology and Biotherapies, UMR5239, LBMC

summary: T-cell clones were obtained by limiting dilution culture of PBMC of HTLV-1 carriers. Exon expression profiling was performed using Affymetrix exon array (Affymetrix Human Exon 1.0 ST Array) according to the manufacturer's instructions.

overall_design: The main objectives were to assess whether transcriptional and post-transcriptional modifications associate with HTLV-1 infection in vivo. To this end, T-cell clones, infected or not by HTLV-1, were obtained by limiting dilution culture of PBMC derived from HTLV-1 carriers. Exon expression profiles of cloned T cells was analyzed using Affymetrix exon array (Affymetrix Human Exon 1.0 ST Array) according to the manufacturer's instructions.

first: Morgan

last: Thenoz

first: Céline

last: VERNIN

first: Franck

last: MORTREUX

first: Séverine

last: CROZE

first: Catherine

last: LEGRAS-LACHUER

first: Nicolas

last: NAZARET


title: Transcriptomic responses of Atlantic salmon (Salmo salar) to environmental enrichment during juvenile rearing

status: Public on Dec 10 2014

city: Newport

first: Melissa

last: Evans

state: OR

address: 2030 SE Marine Science Dr.

institute: Oregon State University

summary: Captive rearing programs (hatcheries) are often used in conservation and management efforts for at-risk salmonid fish populations. However, hatcheries typically rear juveniles in environments that contrast starkly with natural conditions, which may lead to phenotypic and/or genetic changes that adversely affect the performance of juveniles upon their release to the wild. Environmental enrichment has been proposed as a mechanism to improve the efficacy of population restoration efforts from captive-rearing programs: in this study, we examine the influence of environmental enrichment during embryo and yolk-sac larval rearing at the level of the transcriptome in Atlantic salmon (Salmo salar). Full siblings were reared in either a “simple” environment devoid of structure or a “complex” environment enriched with gravel substrate. At the end of endogenous feeding by juveniles, we examined patterns of gene transcription in head tissues using the cGRASP-designed Agilent 4×44K microarray. Significance analysis of microarrays (SAM) indicated that 808 genes were differentially transcribed between rearing environments and a total of 184 gene ontological (GO) terms were over- or under-represented, several of which are associated with mitosis/cell cycle and muscle and heart development. However, there were also pronounced differences among families in gene transcriptional response to rearing environment, with the number of genes significantly differentially transcribed by juveniles in our independent analyses of each family ranging from zero to 3445 (FDR of 5%). Overall, our results suggest that rearing environment enrichment can profoundly change patterns of gene transcription during salmon development, but that the degree of response depends on genetic background.

overall_design: This was a two-condition experiment in which a total of 30 RNA samples isolated from the heads of developing salmon were analysed: 15 juveniles reared in a traditional hatchery environment and 15 reared in a hatchery environment enriched with gravel substrate.

first: Tiago

middle: S

last: Hori

first: Matthew

last: Rise

first: Ian

last: Fleming


title: Effects of pregnancy on hepatic gene expression in CYP2D6-humanized mice

city: Chicago

first: Wei

last: Zhang

state: Illinois

address: 840 S. Wood Street

department: Pediatrics & Institute of Human Genetics

institute: University of Illinois

summary: Hepatic drug metabolism plays a key role in determining drug response and safety. Studies of drug metabolism generate valuable information about regulation of genes encoding drug-metabolizing enzymes and enzyme functions that are critical in developing dosing guideline. However, current knowledge is insufficient to support dosing guideline for pregnant women. Specifically, substrates of a major drug-metabolizing enzyme CYP2D6 show increased elimination during pregnancy, but the underlying mechanisms are completely unknown largely due to a lack of experimental models. Here, we introduce CYP2D6-humanized (Tg-CYP2D6) mice as an animal model where hepatic CYP2D6 expression is increased during pregnancy, recapitulating the clinically reported changes in CYP2D6-mediated drug metabolism. In these mice, pregnancy had minimal effects on the expression of hepatocyte nuclear factor (HNF) 4a, the transcription factor controlling basal CYP2D6 expression. Krüppel-like factor (KLF) 9 and small heterodimer partner (SHP) were found up- and down-regulated in Tg-CYP2D6 mouse livers during pregnancy, respectively. KLF9 enhanced HNF4a-mediated transactivation of the CYP2D6 promoter whereas SHP repressed it. Retinoic acid (RA), an endogenous compound that induces SHP, exhibited decreased hepatic levels during pregnancy. These results indicate that interplay among hepatic transcription factors HNF4a, SHP, and KLF9 underlies CYP2D6 induction during pregnancy, and that retinoic acid is a potential trigger. This is the first report on the mechanisms underlying CYP2D6 induction and illustrates the utility of humanized mice as an in vivo model to study altered drug disposition during pregnancy.

overall_design: Livers collected at pre-pregnancy, 21 days of pregnancy, and 7 days postpartum from CYP2D6-humanized mice.

first: Hyunyoung

last: Jeong


title: Subcellular transcriptome alterations in a cell culture model of spinal muscular atrophy point to widespread defects in axonal growth and presynaptic differentiation

status: Public on Dec 01 2014

city: Wuerzburg

first: Susanne

middle: Elma

last: Kneitz

address: Biozentrum, Am Hubland

department: Physiologigcal Chemistry

institute: University of Wuerzburg

summary: Neuronal function critically depends on coordinated subcellular distribution of mRNAs. Disturbed mRNA processing and axonal transport has been found in spinal muscular atrophy and could be causative for dysfunction and degeneration of motoneurons. Despite the advances made in characterizing the transport mechanisms of several axonal mRNAs, an unbiased approach to identify the axonal repertoire of mRNAs in healthy and degenerating motoneurons has been lacking. Here we used compartmentalized microfluidic chambers to investigate the somatodendritic and axonal mRNA content of cultured motoneurons by microarray analysis. In axons, transcripts related to protein synthesis and energy production were enriched relative to the somatodendritic compartment. Knockdown of Smn, the protein deficient in spinal muscular atrophy, produced a large number of transcript alterations in both compartments. Transcripts related to immune functions, including MHC class I genes, and with roles in RNA splicing were upregulated in the somatodendritic compartment. On the axonal side, transcripts associated with axon growth and synaptic activity were downregulated. These alterations provide evidence that subcellular localization of transcripts with axonal functions as well as regulation of specific transcripts with nonautonomous functions is disturbed in Smn-deficient motoneurons, most likely contributing to the pathophysiology of spinal muscular atrophy.

overall_design: total samples analysed are 18

first: Michael

last: Briese

first: Lena

last: Saal

last: Glinka

last: Sendtner


title: Effect of loss of PKC theta and p50+cRel on gene expression post T-cell stimulation

city: Tampa

first: Amer

last: Beg

state: FL

address: 12902 Magnolia Drive

institute: Moffitt Cancer Center

summary: OT-1 Transgenic CD8 T-cells were isolated from spleens of WT, PKCθ theta KO, and p50 cRel DKO mice.  The T-cells were either cultured with non-pulsed DC (WT only and signified as "WT - UN") or with BMDCs pulsed with the OVA peptide SIINFEKL (N4)  (WT, PKCθ theta KO, and p50 cRel DKO and signified as 'genotype - N4') at a ratio of 1:10 (DC:T-cell) for 18 hours. DCs then were depleted from the culture and RNA was made from the T-cells to measure gene expression at the early / late stage of T-cell activation

first: Crystina

last: Bronk

first: Sean

last: Yoder


title: Malignant-like transformation of normal stem and progenitor cells by myeloid leukemia

city: Singapore

first: Henry

last: Yang

address: 28 Medical Drive

country: Singapore

institute: Cancer Science Institute of Singapore

summary: It has long been known that leukemic cells disrupt normal patterns of blood cell formation, but little is understood about mechanisms. It has generally been assumed that normal hematopoietic stem and progenitor cells (HSPC) are simply out-competed for space by malignant cells. We designed a strategy to determine if leukemic cells alter intrinsic properties and functions of normal HSPCs. Chimeric mice were generated by transplantation of normal marrow and marrow from an inducible transgenic model of chronic myelogenous leukemia (CML). With induction of CML, the composition of the marrow changed dramatically, and normal HSPCs divided more readily and lost their ability to produce lymphocytes. In contrast, only modest changes were recorded in numbers of normal hematopoietic stem cells (HSCs). However, these stem cells were not unscathed, and had reduced reconstitution and self-renewal potential upon transplantation. Interestingly, the normal bystander cells acquired gene expression patterns resembling their neighboring malignant counterparts. This suggested that much of the leukemia signature is mediated by extrinsic factors in the environment.

overall_design: Leukemic mice were generated by transplanting equal numbers of CD45.2+ BCR-ABL x SCL-tTA transgenic murine bone marrow along with CD45.1+ bone marrow into CD45.1+ hosts. After induction of the leukemic cells by removal of Tet water, 4 weeks later the CD45.1+ LT-HSC (CD150+ CD48- KSL) were sorted from controls or leukemic mice intro Trizol. Samples were prepared for microarray analysis after RNA isolation using the Nugen kit (Ovation Pico WTA System V2).

first: Robert

last: Welner

first: Giovanni

last: Amabile

first: Deepak

last: Bararia

first: Akos

last: Czibere

first: Hong

first: Lorena

last: de Figueiredo-Pontes

first: Min

last: Ye

first: Elena

last: Levantini

first: Annalisa

last: DiRuscio

last: Martinelli

first: Daniel

last: Tenen


title: Interferon response genes as immunopathogenic correlates of SARS coronavirus infection in mice (129/S6/SvEv)

status: Public on Nov 30 2014

city: Toronto

first: Longsi

last: Ran

state: ON

address: 101 College Street

department: Division of Experimental Therapeutics

country: Canada

institute: Toronto General Research Institute

summary:
To further identify and understand the molecular and immunological correlates of pathology for SARS-CoV infection, we infected 129/S6/SvEv or B129 mice with the TOR2 strain of SARS-CoV.  SARS-CoV was detected in the lung and nasal turbinates of infected mice peaking at 1 day post infection (DPI) in both tissues before decreasing rapidly to levels below detection at 7 DPI and 3 DPI, respectively.  Pulmonary lesions in virus-infected animals included bronchiolar, peribronchiolar, and perivascular foci of mild to moderate subacute inflammation. Chronic inflammation included inflammatory macrophages, lymphocytes, and plasma cells. Neutralizing antibodies appeared on 5 DPI (IgM); converting to IgG on 7 DPI.  Despite the prevailing notion that SARS-CoV interferes with the induction of interferon (IFN) signaling, mice infected with SARS-CoV in vivo demonstrated significantly increased expression of innate antiviral interferon (IFN) response genes (IRGs) in the lungs during the first week of acute infection.  By the end of the second week of infection, coordinated expression of MHC class I / II and antigen presentation genes occurred in correlation with declining viral titres.  Collectively, the mouse data suggests that robust IFN-driven innate immune responses and a critical shift from innate to adaptive immune responses is necessary for clearance and recovery from SARS-CoV infection.

Keywords: time course

overall_design: In this study, we present the characterization of a 4- to 6-week old mouse (129/S6/SvEv) model for SARS-CoV (TOR-2) in conjunction with a functional genomics analysis of the lungs.  The study design is a time course (0, 1, 2, 3, 5, 14, 28 days post-infection) examination of the natural history and IFN-mediated host responses in SARS-CoV-infected mice.  Three mice are included at each time point for a total of 21 datasets.  The Affymetrix Genechip Mouse Genome 430 2.0 Array oligonucleotide array representing approx. 39,000 murine genes was chosen as the microarray platform.

first: David

last: Kelvin


title: Isoform-specific regulation of NCAM1 gene expression in ischemic cardiomyopathy

first: Ellen

last: Leich

department: Institute of Pathology

summary: Although ischemic cardiomyopathy (ICM) is the leading cause of chronic heart failure, one of the most common diseases overall, many aspects of the molecular pathogenesis of ICM still remain to be clarified. It has been We have previously shown that the neural cell adhesion molecule (NCAM1, CD56) is upregulated in ischemic cardiomyopathy by novel isoforms of the transcription factor RUNX1 (AML1) and, in the current study, we show that this upregulation is attributed exclusively to the NCAM1 isoform CD56-140kD. Moreover, we show that the upregulation of CD56-140kD has proapoptotic and antiproliferative effects on cardiomyocytes in vitro as well as inducing mitochondrial damage and reducing the capacity for Ca2+-uptake. As loss of cells and negative inotropy have previously been identified as major components in the development of ischemic cardiomyopathy, these data suggest that the upregulation of CD56-140kD may play a relevant role in the pathogenesis of ICM and therapeutic strategies targeting this molecule may prove to be valuable tools in the management of this very common and often fatal disease in the future.

overall_design: Overall analysis of four samples: Two replicate experiments, each with one sample of CD56-140kd transfected HL-1 cells and one sample of mock transfected HL-1 cells.

first: Benjamin

last: Etschmann

first: Mehmet

middle: K

last: Tur

first: Alexander

last: Benz

first: Christiane

last: Waller

first: Kai

last: Schuh

first: Andreas

last: Rosenwald

first: Christian

last: Hamm

first: Georg

last: Ertl

last: Bräuninger

first: Stefan

last: Gattenlöhner


title: Identification of Gene Regulation Pattern from Lung Cancer Human Tissues

city: Gainesville

first: Xin

last: Qi

address: 1600 SW Archer Rd

department: Medicinal Chemistry

institute: University of Florida

summary: To identify individual genes with potential diagnostic and therapeutic utilities in lung cancer, we performed gene expression profiling out of a broad coverage of human transcriptome using clinical patient tissues. Six RNA samples extracted from five cancerous tissues and one normal control were subjected to Affymetrix gene array analysis using Human Exon 1.0 ST Array. Data were further processed using Expression Console and Transcriptome Analysis Console softwares. Both core-gene expression analysis and extended-gene expression analysis were performed to discover significantly regulated genes associated with lung cancer progression.

overall_design: We used five human lung cancer samples (three primary cancer samples and two metastatic cancer samples) and one normal control to perform microarray gene expression profiling. One cancer sample (C688) was tested with matched normal control (N687), while others are unmatched samples.

first: Junjie

last: Fu


title: Effect of somatostatin knockout on sexually dimorphic hepatic gene expression

first: Malcolm

last: Low

address: 1000 Wall Street

summary:
The liver is one of the most sexually dimorphic organs as measured by gene expression differences. About 80% of the sexually dimorphic genes are known to be regulated by growth hormone (GH). Somatostatin (SST) inhibits the release of GH.
We generated a SST-knockout mouse and analyzed the hepatic gene expression changes in both sexes.

overall_design: We used liver samples from three mice of both sexes and somatostatin genotypes. Mouse background was C57BL/6.

first: Jessica

last: Adams

middle: J


title: Genome-wide Mapping of ARRB1 Reveals its Role as a HIF1A Transcriptional Co-regulator and Regulator of Cellular Metabolism [expression array]

status: Public on Nov 26 2014

city: Cambridge

first: Chandra

last: Chilamakuri

address: Robinson Way

institute: Cancer Research UK Cambridge Institute

summary: Beta-arrestin 1 (ARRB1) has been implicated in transcriptional regulation as part of protein complexes bound to chromatin. Here we investigate its effect on transcription and its potential impact on prostate cancer. We report the first genome-wide mapping of chromatin binding for ARRB1 and combine it with expression array data to define its transcriptome. We identify Hypoxia Inducible Factor 1A (HIF1A) as a nuclear binding partner that recruits ARRB1 to promoter regions of HIF1A targets. We show that ARRB1 modulates HIF1A-dependent transcription and promotes a shift in cellular metabolism from oxidative phosphorylation to aerobic glycolysis. In addition, we show that ARRB1 plays an important role in neoplastic transformation, cell growth and resistance to hypoxic stress. This is the first example of an endocytic adaptor protein regulating metabolic pathways and implicates ARRB1 as a tumour promoter.

overall_design: Gene expression of C4-2 cells stably overexpressing ARRB1-GFP or nuclear ARRB1-GFP fusion proteins  were compared with the GFP empty vector control or parental C4-2 cell lines using the illumina expression array platform. There were three biological replicates for the control groups and two for each of the ARRB1 groups.

first: Vincent

last: Zecchini

last: Neal

first: Ian

last: Mills

first: Roslin

last: Russell


title: Gene expression in human lymphoblastoid cell-line GM12878 in response to doxorubicin treatment

status: Public on Nov 14 2014

city: Research Triangle Park

first: Xuting

last: Wang

state: NC

address: 111 TW Alexander Dr

institute: NIEHS/NIH

summary:
To determine if induced p53 binding is associated with gene expression in genome-wide. We examined mRNA levels with the Affymetrix Human Exon 1.0 ST platform in human lymphoblastoid GM12878 cells treated with doxorubicin to activate p53.
In response to various cellular stresses, the tumor suppressor gene p53 induces activation or repression of more than a thousand human genes. Selective binding and transactivation of a large potential pool of p53 response elements (REs) is believed to regulate the variation in stress response across stress types and between cell types. To elucidate how the human genome is targeted by p53 at the chromatin level, we mapped the genome-wide localization of p53 and H3K4me3 from Doxo-treated human lymphoblastoid cells, and examined the relationships among p53 occupancy, gene expression, H3K4me3, chromatin accessibility (DNase 1 Hypersensitivity, DHS), ENCODE chromatin states, RE sequence specificity and evolutionary conservation.

overall_design: Human lymphoblastoid (GM 12878) cells at a density of 900,000 cells/ml were prepared in triplicate for each time point and treated with 0.5 µM doxorubicin (Calbiochem) for  4, 18 hr or no treatment (at 0 time). Total RNA will be extracted from each culture (9 RNA samples) using the Qiagen RNeasy kit with DNase digestion. RNA was quantified using RiboGreen (Invitrogen), check for quality by OD and Bioanalyzer and stored at -80°C.  Expression analysis was conducted at at NIEHS Microarray Core using Affymetrix Human Exon 1.0 ST arrays following the Affymetrix hybridization protocols. Exon expression data were analyzed through Affymetrix Expression Console using gene-level RMA summarization and sketch-quantile normalization methods.

first: Dan

last: Su

first: Douglas

last: Bell


title: Expression data from conditionally immortalized MLL-AF9 and MLL-ENL hematopoietic progenitor cells following loss of MLL-fusion oncogene

city: London

first: Owen

last: Williams

address: 30 Guilford Street

department: Cancer section

institute: UCL GOS ICH

summary: Chromosomal translocations encoding the MLL-AF9 and MLL-ENL fusion transcription factors are prevalent in infant acute leukaemia and therapy-related leukaemia. In order to conditionally express the MLL-fusion oncogene in primary haematopoietic progenitor cells (HPC), retroviral delivery of the Tet-off expression system was used (Horton et al., Cancer Res, 2005). Treatment of the conditional cells with Doxycycline caused a decrease in MLL-AF9/ENL mRNA and protein expression, and resulted in terminal differentiation of the cells. By analysing global changes in gene expression after treatment of cells with Doxycycline we were able to identify a number of potential transcriptional target genes of the MLL-AF9 and MLL-ENL fusion oncogenes.

overall_design: Lineage negative progenitors were purified from murine bone marrow and co-transduced with MSCV-TRE-MLL-AF9 or MSCV-TRE-MLL-ENL and MSCV-tTA retroviral supernatants. Six independent cell lines (MA1, MA3, MA4, ME4, ME5, ME7) with conditional expression of the MLL-AF9 or MLL-ENL oncogene and two independent cell lines (cMA3, cME3) with constitutive MLL-fusion oncogene expression were generated. The immortalised cell lines were characterised to determine their tTA dependent MLL-fusion oncogene expression, morphology, immunophenotype, and cytokine requirements. Total RNA was extracted, using TRIzol reagent, from the cell lines, each of them cultured without or with 2µg/ml Doxycycline for 48 hours and used for hybridisation on Affymetrix microarrays.

first: Vanessa

last: Walf-Vorderwuelbecke

first: Sarah

last: Horton

first: Jasper

last: de Boer


title: NRASG12V mediates leukemia self renewal [Microarray]

status: Public on Nov 16 2014

city: Minneapolis

first: Rebecca

last: LaRue

state: MN

address: 117 Pleasant St SE

department: Department of Lab medicine and Pathology

institute: University of Minnesota

summary: Mutant RAS oncoproteins activate signaling molecules that drive oncogenesis in multiple human tumors including acute myelogenous leukemia (AML). However, the specific function of these pathways in AML is unclear. To elucidate the downstream functions of activated NRAS in AML, we employed a murine model of AML harboring Mll-AF9 and NRASG12V. We found that NRASG12V enforced leukemia self-renewal gene expression signatures and was required to maintain an MLL-AF9 and MYB-dependent gene expression program. In a multiplexed analysis of RAS-dependent signaling intermediates, the leukemia stem cell compartment was preferentially sensitive to RAS withdrawal. Use of RAS-pathway inhibitors showed that NRASG12V maintained leukemia self-renewal through mTOR and MEK pathway activation, implicating these pathways as potential targets for cancer stem cell-specific therapies.

overall_design: Mice harboring NRASG12V/Mll-AF9 AML were treated with doxycyline to abolish NRASG12V expression.  Leukemia samples were harvested at 12 hour intervals after doxycyline treatment.  RNA was extracted from these samples and submitted for gene expression microarray analysis

first: Zohar

last: Sachs

first: Hanh

middle: T

last: Nguyen

first: Karen

first: Nurul

last: Hassan

first: Ernesto

last: Diaz-Flores

first: Susan

last: Rathe

first: Aaron

last: Sarver

first: Sean

last: Bendall

first: Ngoc

last: Ha

first: Miechaleen

last: Diers

first: Gary

middle: P

last: Nolan

first: Kevin

last: Shannon

first: David

last: Largaespada


title: An EphB-Abl signaling pathway important for intestinal tumor initiation and growth

status: Public on Nov 13 2014

city: Stockholm

first: Maria

last: Genander

address: Tomtebodavägen 16

department: Department of Cell and Molecular Biology

country: Sweden

institute: Karolinska Institutet

summary:
EphB receptors regulate the proliferation and positioning of intestinal stem and progenitor cells. In addition, they can act as tumor promoters for adenoma development, but suppress progression to invasive carcinoma. Here we used imatinib to abrogate Abl kinase activity in ApcMin/+ mice and in mice with LGR5+ stem cells genetically targeted for APC. This treatment inhibited the tumor-promoting effects of EphB signaling without attenuating EphB-mediated tumor suppression, demonstrating the role of EphB signaling in intestinal tumor initiation. The investigated treatment regimen extended the lifespan of ApcMin/+ mice, and reduced cell proliferation in cultured slices of adenomas from FAP patients. These findings connect the EphB signaling pathway to the regulation of intestinal adenoma initiation via Abl kinase. Our findings may have clinical implications for pharmacological therapy against adenoma formation and cancer progression in patients predisposed to develop colon cancer.
We used microarray to assess the short term (3h and 12h) effects on gene expression in colon stem and progenitor cells after administration of Imatinib.

overall_design: Colon samples were obtained at different timepoints after injection of Imatinib and processes for RNA extraction and hybridization for Affymetrix array.

first: Jonas

last: Frisén


title: Oncogenic Ras inhibits IRF1 to promote viral oncolysis

city: St. John's

first: Sherri

last: Christian

state: Newfoundland

address: 232 Elizabeth Ave

department: Biochemistry

institute: Memorial University of Newfoundland

summary: Oncolytic viruses exploit common molecular changes in cancer cells, which are not present in normal cells, to target and kill cancer cells. Ras transformation and defects in type I interferon (IFN)-mediated antiviral responses are known to be the major mechanisms underlying viral oncolysis. Previously, we demonstrated that oncogenic RAS/Mitogen-activated protein kinase kinase (Ras/MEK) activation suppresses the transcription of many IFN-inducible genes in human cancer cells, suggesting that Ras transformation underlies type I IFN defects in cancer cells. Here, we investigated how Ras/MEK downregulates IFN-induced transcription. By conducting promoter deletion analysis of IFN-inducible genes, namely guanylate-binding protein 2 and IFN gamma inducible protein 47 (Ifi47), we identified the IFN regulatory factor 1 (IRF1) binding site as the promoter region responsible for the regulation of transcription by MEK. MEK inhibition promoted transcription of the IFN-inducible genes in wild type mouse embryonic fibroblasts (MEFs), but not in IRF1−/− MEFs, showing that IRF1 is involved in MEK-mediated downregulation of IFN-inducible genes. Furthermore, IRF1 protein expression was lower in RasV12 cells compared with vector control NIH3T3 cells, but was restored to equivalent levels by inhibition of MEK. Similarly, the restoration of IRF1 expression by MEK inhibition was observed in human cancer cells. IRF1 re-expression in human cancer cells caused cells to become resistant to infection by the oncolytic vesicular stomatitis virus strain. Together, this work demonstrates that Ras/MEK activation in cancer cells downregulates transcription of IFN-inducible genes by targeting IRF1 expression, resulting in increased susceptibility to viral oncolysis.

overall_design: RNA was isolated from RasV12 transformed NIH/3T3 cells (RasV12 cells) treated with 20μM U0126 or 500U/ml IFN-α, or left untreated, for 6 hours, triplicate biological samples (9 samples).

first: Yumiko

last: Komatsu

first: Nhu

last: Ho

first: Theerawat

last: Pongnopparat

last: Licursi

first: Kensuke

last: Hirasawa


title: Microarray expression profiling study of Runx1-null and wild type luminal mammary epithelial cells

city: Boston

first: Zhe

last: Li

address: 77 Avenue Louis Pasteur, Room 466

department: Medicine, Genetics Division

institute: Brigham and Women's Hospital

summary: RUNX1 encodes a RUNX family transcription factor (TF) and was recently identified as a novel mutated gene in human luminal breast cancers. We found that Runx1 is expressed in all subpopulations of murine mammary epithelial cells (MECs) except the secretory alveolar luminal cells. Conditional knockout of Runx1 in MECs by MMTV-Cre led to a decrease in luminal MECs, largely due to a profound reduction in the estrogen receptor (ER)-positive mature luminal subpopulation, a phenotype that could be rescued by loss of either Trp53 or Rb1. Mechanistically RUNX1 represses Elf5, a master regulatory TF gene for alveolar cells, and activates Foxa1, a key mature luminal TF gene involved in the ER program. Collectively, our data identified a key regulator of the ER+ luminal lineage whose disruption may contribute to development of ER+ luminal breast cancer when under the background of either TP53 or RB1 loss.

overall_design: Thoracic and inguinal mammary glands from 3 MMTV-Cre;Runx1L/L;R26Y and 3 MMTV-Cre;Runx1+/+;R26Y adult virgin females were dissected out, minced and digested to single cell suspension. Runx1L is the floxed conditional knockout allele of Runx1. R26Y is a conditional YFP reporter that would be turned on upon Cre-mediated recombination. FACSaria machine was used to sort out the YFP-marked luminal epithelial cell population of each of these 6 mice. Total RNA was isolated with Qiagen RNeasy kit and subsequently amplified by Nugen V2 and applied to Affymetrix mouse genome 430 2.0 arrays.

first: Maaike

last: van Bragt


title: Twist1 in skin tumorigenesis

city: Brussels

first: benjamin

last: beck

address: route de Lennik 808

country: Belgium

institute: ULB

summary: This study was designed to investigate the transcripts that are regulated by Twist1 in skin tymor epithelial cells in a p53-dependent and independent manner. To this aim, Tumor epithelial cells from primary mouse skin tumors of different genotypes were FACS sorted and analyzed by microarray.

overall_design:
Tumor bearing mice of different genotypes (CTRL, K14CreER:Twist1fl/fl, K14CreER:Twist1fl/fl:p53fl/fl) were treated with tamoxifen for 5 days to induce the deletion of Twist1 with or without p53 and. Tumors were disected and digested to harvest tumor epithelial cells. Tumor cells were FACS sorted using a combination of Epcam/CD45/CD31/CD140a and DAPI ti isolate tumor epithelial cells. These cells were harvested in lysis buffer and RNA was extracted using the Qiagen RNA purification microkit to perform microarrayprofilling.
All the mice used for this study are all littermates from mixed background strains (up to 6 transgenes combined). The details relative to these mice are described in Cell Stem Cell article (in press).

first: Benjamin

last: Beck

first: Cédric

last: Blanpain


title: Expression data from bone marrow neutrophils with or without LPS stimulation in wild type and miR-125a deficient mice

status: Public on Dec 02 2014

city: shanghai

last: Shen

address: 145 Shan Dong Middle Road

institute: Shanghai Institute of Rheumatology

summary:
Neutrophil activation plays a critical role in the inflammatory response to gram-negative bacterial infections. Lipopolysaccharide (LPS) from gram-negative bacterial has been shown to be a major mediator of neutrophil activation to produce pro-inflammatory cytokines, chemokines and ROS which are important to tissue damage in LPS induced septic shock.
We used microarrays to detail the global gene expression of neutrophils from miR-125a+/+ and miR-125a-/- mice after LPS stimulation.

overall_design: Bone marrow neutrophils from miR-125a deficient and wild type mice were enriched by magnetic beads, then stimulated without or with LPS for 3 hours and harvested in Trizol . Extracted RNAs from three independent experiments were pooled for hybridization on Affymetrix microarrays.

first: Yihong

last: Yao

first: Yuting

last: Qin

first: Lingling

last: Wu


title: Gene Expression Profiling of Ewing Sarcoma Tumors Reveals the Prognostic Importance of Tumor-Stromal Interactions [EuroEwing]

status: Public on Nov 11 2014

city: Ann Arbor

first: Elizabeth

middle: R.

last: Lawlor

address: 1600 Huron Parkway

department: Pediatrics

institute: University of Michigan

summary: For the current study we performed whole genome expression profiling on two independent cohorts of clinically annotated, localized Ewing sarcoma (ES) tumors in an effort to identify and validate prognostic gene signatures. ES specimens were obtained from the Children’s Oncology Group (COG) and whole genome expression profiling performed using Affymetrix Human Exon 1.0 ST arrays. Lists of differentially expressed genes between survivors and non-survivors were used to identify prognostic gene signatures

overall_design: 46 samples obtained from the COG Biorepository in Columbus, Ohio (Cooperative Human Tissue Network - CHTN) were prospectively acquired from patients on clinical trials INT-0154 (CCG-7942, POG-9354) and AEWS0031, the two most recent COG clinical protocols for patients with localized Ewing sarcoma (ES). An independent set of 39 tumors samples was obtained from the EuroEwing tumor biorepository in Muenster, Germany and were prospectively acquired from patients registered on EICESS 92 (European Intergroup Cooperative Ewing's Sarcoma Study) and EuroEwing 99.  Gene expression was compared between between survivors and non-survivors, and differentially expressed genes used to identify prognostic gene signatures

first: Samuel

last: Volchenboum

first: Jorge

last: Andrade

first: Lei

last: Huang

first: Donald

middle: A

last: Barkauskas

first: Mark

last: Krailo

first: Richard

middle: B

last: Womer

first: Andreas

last: Ranft

first: Jenny

last: Potratz

first: Uta

last: Dirksen

first: Timothy

last: Triche


title: Expression data from adult Onecut2 WT and KO animals

city: Ames

first: Jeffrey

middle: M

last: Trimarchi

state: IA

address: 3188 Molecular Biology Building

department: GDCB

institute: Iowa State University

summary: In this study, we examine the consequences of the loss of two related factors, Onecut1 and Onecut2, during mouse retinal development and maturation.

overall_design: To investigate potential phenotypes in Onecut2-KO retinas, microarrays were performed on retinas isolated from mature OC2-KO mice and WT littermates.

first: Jillian

last: Goetz

first: Greg

last: Martin


title: Gene expression and alternative splicing in pancreatic ductal adenocarcinoma (PDAC) [gene level]

status: Public on Nov 10 2014

first: Jun

last: Wang

address: Charterhouse Square

institute: Barts Cancer Institute, Queen Mary, London

summary:
Alternative splicing is a key event to human transcriptome and proteome diversity and complexity. Recent evidence suggests that pancreatic cancer might possess particular patterns of splice variation that influence the function of individual genes contributing to tumour progression in this disease. The identification of new pancreatic cancer-associated splice variants would offer opportunities for novel diagnostics and potentially also represent novel therapeutic targets.
In this dataset, we investigated the alterations in the splicing machinery in pancreatic adenocarcinoma (PDAC) specimens with full clinicopathological details, in comparisons to adjacent pancreatic tissues and normal tissues from donors.

overall_design:
We extracted total RNA from 28 PDAC specimens, 4 adjacent tissues and 2 normal pancreatic tissues from donors, and hybridized them to Affymetrix exon arrays. Affymetrix GeneChip® Human Exon 1.0 ST Arrays (Affymetrix, Santa Clara, CA, USA) were used for gene expression and alternative splicing analysis. Labelling and hybridization were performed according to the manufacturer's instructions. After scanning, .CEL files were checked for quality and analysed following the pipeline based on aroma.affymetrix R package, to produce transcript, probeset and probe-level intensities. This was followed by intensity filtering as recommended by Affymetrix.

This submission includes the gene-level analysis.

first: Syed

last: Haider

first: Claude

last: Chelala

first: Tatjana

last: Crnogorac-Jurcevic

first: Aldo

last: Scapra

first: Nick

last: Lemoine


title: BMSC gene expression in co-culture with endothelial cells

status: Public on Nov 08 2014

city: Bergen

first: Ying

last: Xue

address: Årstadveien 19

department: Department of Dentistry

country: Norway

institute: University of Bergen

summary:
In this experiment human Bone Marrow Stem Cells (hBMSCs) are grown in co-culture with Human Umbilical Vein Endothelial Cells (HUVECs) for 5 days, HUVECs are removed by trypsination before call harvest. In parallel hBMSCs are grown in monoculture as a control for 5 days, and a sham trypsination performed before harvesting of the cells.
The aim for the project is to analyze the gene expression alteration in hBMSCs resulting from BMSCs being co-cultured with HUVECs.

overall_design: The microarray platform chosen is Illumina, which is a one-channel system, and this experiment uses HumanWG-6 v3.0 Expression BeadChips. The 1-channel nature of the platform yields the simple design of 1 sample hybridized to 1 array on a microarray slide. This particular chip has 6 arrays on each slide.  At each time points there were 6 samples in the co-culture (T) group and 6 samples in the control (C) group, all together 12 samples. Samples came from 6 different donors denoted D1-D6, and the sample from donor X in the co-culture group is paired with the sample from donor X in the control group.

first: Kamal

last: Mustafa


title: Expression data from 45 paired of gastric cancer tissues and gastric normal tissues

city: Changchun

first: XiaoTian

last: Zhang

state: Jilin

address: No.126 of Xinmin street, College of Basic Medicine, Jilin University.

institute: Jilin University

summary: In this dataset, we include the expression data obtained from gastric cancer tissues and gastric normal tissues to determine the differentially expressed genes in gastric cancer tissues.

overall_design: 90 tissues (45 paired of gastric cancer vs.normal tissues) were analysed. We generated the same number as pairwise comparisons. Genes with a fold-change >1.5 were selected

first: Xiaotian


title: Expression data from 2-3 month old brain-specific IκBα conditional knockout mice

status: Public on Nov 06 2014

city: Houston

first: Hui

last: Zheng

state: TEXAS

address: one baylor plaza

department: Huffington Center on Aging

institute: Baylor College of Medicine

summary:
The activation of NFkB pathway is commonly observed in many neurodegenerative disease and contributes to the disease pathogenesis. However, with hundreds of target genes expressed in the brain, the mechanism of NFkB signaling transduction pathway is bearly understood.
We were interested in revealing the downstream mediators of NFkB in the brain and chose the IkBa-dificient model as our tool. IkBa is the essential negative regulator of NFkB activity and deletioon of IkBa induced NFkB hyperactivation. We used Nestin-Cre to conditionally knockout IkBa in the brain cells of neural lineage and performed the microarray to give us candidate genes.

overall_design: Mouse hippocampi were dissected from 3 pairs of 2-3 month old IkBa brain-specific knockout animals and their littermate controls and used for RNA extraction and subsequent microarray assay

first: Hong

last: Lian

first: Baiping

first: David

last: Shim


title: SPR509: Lung metastasis

city: South San Francisco

first: Josh

last: Kaminker

address: 1 DNA Way

department: Bioinformatics and Computational Biology

institute: Genentech

summary:
Determine gene expression differences between normal, metastatic and non-metastatic mouse lung tissue.
Priming of the organ-specific premetastatic sites is thought to be an important yet incompletely understood step during metastasis. In this study, we show that the metastatic tumors we examined overexpress granulocyte-colony stimulating factor (G-CSF), which expands and mobilizes Ly6G+Ly6C+ granulocytes and facilitates their subsequent homing at distant organs even before the arrival of tumor cells. Moreover, G-CSF-mobilized Ly6G+Ly6C+ cells produce the Bv8 protein, which has been implicated in angiogenesis and mobilization of myeloid cells. Anti-G-CSF or anti-Bv8 antibodies significantly reduced lung metastasis. Transplantation of Bv8 null fetal liver cells into lethally irradiated hosts also reduced metastasis. We identified an unexpected role for Bv8: the ability to stimulate tumor cell migration through activation of one of the Bv8 receptors, prokineticin receptor (PKR)-1. Finally, we show that administration of recombinant G-CSF is sufficient to increase the numbers of Ly6G+Ly6C+ cells in organ-specific metastatic sites and results in enhanced metastatic ability of several tumors.

overall_design: 67NR and 4T1mouse breast carcinoma cell lines were injected into fourth mammary fat pad; lung tissue was collected when tumor reached volume of 50mm3. RNA was extracted using Qiagen kit.

first: Napoleone

last: Ferrara

first: Marcin

last: Kowanetz

first: Joshua

first: Zora

last: Modrusan


title: Chromatin de-compaction by the nucleosomal binding protein HMGN5 impairs nuclear sturdiness.

status: Public on Nov 22 2014

city: Rostock

first: Leila

last: Taher

address: Ernst-Heydemann-Str. 8

institute: University of Rostock

summary: In most metazoan nuclei, heterochromatin is located at the nuclear periphery in contact with the nuclear lamina, which provides mechanical stability to the nucleus. We show that in cultured cells, chromatin de-compaction by the nucleosome binding protein HMGN5 decreases the sturdiness, elasticity, and rigidity of the nucleus. Mice overexpressing HMGN5, either globally or only in the heart, are normal at birth but develop hypertrophic heart with large cardiomyoctyes, deformed nuclei and disrupted lamina, and die of cardiac malfunction. Chromatin de-compaction is seen in cardiomyocytes of newborn mice but misshaped nuclei with disrupted lamina are seen only in adult cardiomyocytes, suggesting that loss of heterochromatin diminishes the ability of the nucleus to withstand the mechanical forces of the contracting heart. Thus, heterochromatin enhances the ability of the nuclear lamina to maintain the sturdiness and shape of the eukaryotic nucleus; a structural role for chromatin that is distinct from its genetic functions.

overall_design: The full length mouse Hmgn5 cDNA, containing the entire 5’ UTR and FLAG tag on the 3’ end was amplified by PCR and inserted between BglII and XhoI sites of the pCALL vector (Novak et al., 2000). This vector contains a floxed LacZ cDNA driven by the CAG (a hybrid CMV enhancer and chicken beta–actin) promoter which is highly active in early mouse embryos. The vector was linearized by NotI digestion and injected into fertilized oocytes of C57BL/6 mice. Total embryonic excision of LacZ sequence was done by breeding floxed HMGN5-TG mice with SoxCre mice (Hayashi et al., 2002). Heart-specific excision was performed by breeding floxed HMGN5-TG mice with alphaMHC-cre mice (Oka et al., 2006).Total RNA from the left ventricle of newborn and adult Hmgn5-hTG mice which overexpress HMGN5 only in the heart  as well as control mice was collected from biological triplicates (duplicates, in the case of newborn wild-type mice) and analyzed by Affymetrix expression arrays.

first: Takashi

last: Furusawa

first: Mark

last: Rochman

first: Michael

last: Bustin


title: Expression data from study on IL33 signaling in Dusp5 deficient eosinophils

first: Derek

last: Holmes

institute: Genentech Inc

summary: Dusp5 regulates ERK phosporylation following IL-33 receptor ligation in cultured eosinophils. Dusp5 deficient eosinophils show increased ERK phosphorylation, and as a result are less apoptotic. Since ERK stimulation results in downstream activation of transcription factors, we are utilizing a microarray approach to find alterations in gene expression to uncover potential mechanisms for increased cell survival.

overall_design: Day 12 bone marrow derived eosinophils from Dusp5+/+ and Dusp5-/- mice (5 mice per genotype) were left untreated (media only) or IL-33 (25ng/ml) stimulated for 4 hours. Treated cells were washed with ice cold PBS and cell pellets were directly lysed in RLT buffer (Qiagen) followed by immediate RNA isolation (RNEasy plus mini kit with genomic DNA eliminator columns). Sample group names: Group 1- Dusp5+/+ Untreated (N=5) Group 2- Dusp5-/- Untreated (N=5) Group 3- Dusp5+/+ IL-33 4hrs (N=5) Group 4- Dusp5-/- IL-33 4hrs (N=5) Sample Names: Group 1- BM Eos unstimulated WT-1....WT-5 Group 2- BM Eos unstimulated Dusp5-/- -1......Dusp5-/- -5 Group 3- BM Eos IL-33 4hrs WT-1....WT-5 Group 4- BM Eos IL-33 4hrs Dusp5-/- -1......Dusp5-/- -5

first: Jung-Hua

last: Yeh

first: Donghong

last: Yan

first: Min

last: Xu

first: Andrew

middle: C

last: Chan


title: Expression data from GNMT and MAT1A knockout models that develop all the stages of non-alcoholic fatty liver disease including hepatocellular carcinoma [GNMT_MAT1A_3&8_months]

status: Public on Nov 07 2014

city: Alnarp

first: Itziar

last: Frades

address: Sundsvägen 14

department: Plant Protection Biology

institute: Swedish University of Agricultural Sciences

summary: Liver global gene expression patterns of 9 GNMT-knockout mice histopathologically determined to have non-alcoholic steatohepatitis (NASH) and hepatocellular carcinoma (HCC) together with 10 MAT1A-knockout mice histopathologically determined to have steatosis and NASH. All these have their respective wild type patterns. These were analyzed to define signatures to study the pathogenesis of NAFLD-derived HCC, explore which subtypes of cancers can be investigated using mouse models and define a signature of HCC differential survival that can be used to characterize HCC subtypes of different survival derived from mixed etiologies.

overall_design: GNMT- and MAT1A-knockout mice liver samples having steatosis, non-alcoholic steatohepatitis and hepatocellular carcinoma were selected for RNA extraction and hybridization on Affymetrix microarrays.


title: Gene Expression Profiling of Ewing Sarcoma Tumors Reveals the Prognostic Importance of Tumor-Stromal Interactions: A Report from the Children's Oncology Group

first: Elizabeth

last: Lawlor

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

overall_design: Refer to individual Series


title: Human monocyte derived macrophage microarray analysis

status: Public on Nov 05 2014

first: Tony

last: Segal

address: 5 University Street

department: Medicine

institute: UCL

summary:
Microarray data was acquired from human primary monocyte-derived macrophages in order to test the validity of a graphical software package (z-score outlier detection (ZODET))
Complex human diseases can show significant heterogeneity between patients with the same phenotypic disorder. An outlier detection strategy was developed to identify variants at the level of gene transcription that are of potential biological and phenotypic importance.   Here we describe a graphical software package (z-score outlier detection (ZODET)) that enables identification and visualisation of gross abnormalities in gene expression (outliers) in individuals, using whole genome microarray data. Mean and standard deviation of expression in a healthy control cohort is used to detect both over and under-expressed probes in individual test subjects. We compared the potential of ZODET to detect outlier genes in gene expression datasets with a previously described statistical method, gene tissue index (GTI), using a simulated expression dataset and a publicly available monocyte-derived macrophage microarray dataset. Taken together, these results support ZODET as a novel approach to identify outlier genes of potential pathogenic relevance in complex human diseases. The algorithm is implemented using R packages and java.

overall_design: 40 volunteer were bled and primary monocyte derived macrophages were cultured. These samples were then randomised into two equal sized groups (control - A1-20 and experimental - B1-20) and run on the ZODET software.

first: Anthony

middle: W

last: Smith

first: Adam

last: Levine

first: Gavin

last: Sewell

first: Daniel

middle: L

last: Roden

first: Anna

last: Lobley


title: Generation of CNS neural stem cells and PNS derivatives from neural crest derived peripheral stem cells

status: Public on Nov 01 2014

city: Innsbruck

first: Galina

last: Apostolova

address: Innrain 66

department: Institute for Neuroscience

country: Austria

institute: Medical University Innsbruck


title: Gene Expression Profiling of Ewing Sarcoma Tumors Reveals the Prognostic Importance of Tumor-Stromal Interactions [COG]

first: Samuel

last: Volchenboum

first: Jorge

last: Andrade

first: Lei

last: Huang

first: Donald

last: Barkauskas

last: Krailo

first: Richard

last: Womer

first: Andreas

last: Ranft

first: Jenny

last: Potratz

first: Uta

last: Dirksen

first: Timothy

last: Triche


title: Generation of CNS neural stem cells and PNS derivatives from neural crest derived peripheral stem cells [Dataset 1]

summary: Neural crest-derived neural stem cells (NCSCs) from the embryonic PNS can be reprogrammed in neurosphere culture (NS) to rNCSCs that produce CNS progeny, including myelinating oligodendrocytes. Using global gene expression analysis we now demonstrate that rNCSCs completely lose their previous PNS characteristics and acquire the identity of neural stem cells derived from embryonic spinal cord (SCSCs). Reprogramming proceeds rapidly and results in a homogenous population of Olig2-, Sox3- and Lex-positive CNS stem cells. Low-level expression of pluripotency inducing genes Oct4, Nanog and Klf4 argues against a transient pluripotent state during reprogramming. The acquisition of CNS properties is prevented in the presence of BMP4 (BMP NCSCs) as shown by marker gene expression and the potential to produce PNS neurons and glia. In addition, genes characteristic for mesenchymal and perivascular progenitors are expressed, which suggests that BMP NCSCs are directed towards a pericyte progenitor/mesenchymal stem cell (MSC) fate. Adult NCSCs from mouse palate, an easily accessible source of adult NCSCs, display strikingly similar properties. They do not generate cells with CNS characteristics but lose the neural crest markers Sox10 and p75 and produce MSCs. These findings show that embryonic NCSCs acquire a full CNS identity in neurosphere culture. In contrast, MSCs are generated from adult pNCSCs and BMP NCSCs, which reveals that postmigratory NCSCs are a source for MSCs up to the adult stage.

overall_design: Affymetrix Mouse 430_2 arrays were used to compare the gene expression profiles of  E12.5 mouse spinal cord-derived neurospheres (SCSCs) and E12.5 DRG-derived neurospheres, cultured in the absence (rNCSCs) or in the presence of BMP4 (BMP NCSCs).

first: Marlen

last: Weber

first: Darius

last: Widera

first: Michel

last: Mittelbronn

first: Georg

last: Dechant

first: Barbara

last: Kaltschmidt

first: Hermann

last: Rohrer


title: Gene expression analysis of choroid plexus tumors

city: Toronto

first: Diana

last: Merino

state: Ontario

address: 686 Bay St.

department: Genetics and Genome Biology

institute: The Hospital for Sick Children

summary: Gene expression was assessed in a cohort of 40 choroid plexus tumors isolated from fresh-frozen tissue. We investigated unique expression patterns among tumor subgroups and refined the classification of choroid plexus tumors according to gene expression intensities.

overall_design: Forty choroid plexus tumors (16 choroid plexus carcinomas, 16 choroid plexus papillomas and 8 atypical choroid plexus papillomas) were analyzed. No replicates were used.

first: Adam

last: Shlien

first: Anita

last: Villani

first: Margaret

last: Pienkowska

first: Stephen

last: Mack

first: Vijay

last: Ramaswamy

first: David

last: Shih

first: Ruth

last: Tatevossian

first: Ana

last: Novokmet

first: Sanaa

last: Choufani

first: Rina

last: Dvir

first: Myran

last: Ben-Arush

first: Brent

last: Harris

first: Eugene

middle: I

last: Hwang

first: Rishi

last: Lulla

first: Stefan

last: Pfister

first: Maria

last: Achatz

first: Nada

last: Jabado

first: Jonathan

last: Finlay

first: Rosanna

last: Weksberg

first: Cynthia

last: Hawkins

first: Michael

middle: D

last: Taylor

first: Uri

last: Tabori

last: Ellison

last: Gilbertson

last: Malkin


title: Gene expression profiling of murine WT and DNR Tregs

city: Hefei

first: Yin-Hu

last: Wang

state: Anhui

address: Huangshan Road 443, Western Campus of USTC

department: School of Life Sciences and Institution of Immunology

institute: University of Science and Technology of China

summary:
Donminant negative transform growth factor receptor II (DNR) mice were served as a murine primary biliary cirrhrosis model. CD4+Foxp3+ Regulatory T cells (Tregs) play a critical role in self-tolerance and in regulating PBC.
In order to determine whether DNR mice derived Tregs processed  defective function compared with WT Tregs, CD4+Foxp3+ Treg cells were sorted from DNR and WT mice, respectively, then gene expression analysis was performed by using the Affymetrix GeneChip Mouse Genome 430 2.0 arrays

overall_design: CD4+Foxp3+ Tregs were sorted from the spleen of 10-week-old DNR mice and B6 wild-type mice, respectively. RNA of each sample was then extracted and hybridized on Affymetrix microarrays to detail differences between DNR Tregs and WT Tregs in gene expression.

first: Wei

last: Yang

first: Zhe-Xiong

last: Lian


title: Functional cooperativity between Myc and PI3K signaling for indefinite self-renewal property of embryonic stem cells

status: Public on Oct 30 2014

city: Hidaka

first: Akihiko

last: Okuda

state: Saitama

address: 1397-1 Yamane

department: Research Center for Genomic Medicine

institute: Saitama Medical University

summary: We explored the relationship between Myc activity and PI3K signaling in ESCs. Our data demonstrate that Myc and PI3K signaling function cooperatively for supporting pluripotent property of ESCs. Moreover, our data demonstrate that exposure of ESCs to 2i condition render both Myc and PI3K dispensable for preserving ESC status.

overall_design: Effect of PI3K inhibitor, LY4294002 on EBRTcH3 ESCs or their derivatives overexpressing c-Myc (wild-type or T58A mutant) was examined. Effect of LY4294002 on EBRTcH3 ESCs under 2i conditions was also examined. Furthermore, effect of Max expression ablation was compared between ESCs and those overexpressing p110 alpha.

first: Tomoaki

last: Hishida

first: Miyuki

last: Katano

first: Yutaka

last: Nakachi

first: Yosuke

last: Mizuno

first: Yasushi

last: Okazaki

first: Juan

last: Belmonte


title: GENE EXPRESSION CHANGES WITHIN MÜLLER GLIAL CELLS DURING RETINITIS PIGMENTOSA

status: Public on Oct 31 2014

first: Karin

last: Roesch

state: MA

address: 77 Avenue Louis Pasteur

institute: Harvard Medical School

summary: Retinitis Pigmentosa (RP) is a progressive retinal degeneration in which the retina loses nearly all of its photoreceptor cells and undergoes major structural changes. Little is known regarding the role the resident glia, the Müller glia, play in the progression of the disease. Here we define gene expression changes in Müller glial cells (MGCs) from two different mouse models of RP, the retinal degeneration 1 (rd1) and rhodopsin knock-out (Rhod-ko) models. The RNA repertoire of 28 single MGCs was comprehensively profiled, and a comparison was made between MGC from wild type (WT) and mutant retinas. Two time points were chosen for analysis, one at the peak of rod photoreceptor death and one during the period of cone photoreceptor death.   MGCs have been shown to respond to retinal degeneration by undergoing gliosis, a process marked by the upregulation of GFAP. In this data, many additional transcripts were found to change. These can be placed into functional clusters, such as retinal remodeling, stress response, and immune related response. It is noteworthy that a high degree of heterogeneity among the individual cells was observed, possibly due to their different spatial proximities to dying cells, and/or inherent heterogeneity among MGCs.

overall_design: Retinas were dissociated and single Muller Glial Cells were picked under a dissecting microscope using a micropipette based on their distinct morphological shape. Single cell cDNAs were generated and genome wide profiles were obtained by hybridization to Affymetrix 430 2.0 microarrays. Data was normalized using MAS5.0 software. A total of 28 Muller Glial Cells were analyzed and confirmed post hoc by expression of known marker genes.

first: Jeffrey

last: Trimarchi

first: Constance

last: Cepko


title: Gene Expression Profiling of Fibroblasts in Actute Kidney Injury

status: Public on Oct 28 2014

city: Göttingen

last: Zeisberg

address: Robert-Koch-Street 40

department: Nephrology/Rheumatology

institute: University Medical Center Göttingen

summary:
Fibroblasts are present in every organ. While the role fibroblasts in chronic diseases such as fibrosis or tumor expression has been extensively explored, little is known about their physiological role. The kidney possesses a unique capacity to recover from even severe acute injury. We study molecular mechanisms of this intrinsic repair capacity in the mouse model of ischemia-reperfusion (IR). In this model, the renal artery and vein are clamped for 45 min, leading to acute kidney injury. The kidney spontaneously recovers from such IR injury within 14 days. IR kidney injury is associated with a transient accumulation of fibroblasts in the diseased tissue. We hypothesized that fibroblasts aid the repair of acute IR injury in the kidney. To elucidate how FSP1+ fibroblasts may contribute to the repair of kidney injury, we undertook a global unbiased approach to compare gene expression profiles of fibroblasts isolated from kidneys post-IRI and from control kidneys by FACS sorting.
To investigate the role fibroblasts may play in the repair of kidney inhury, we performed ischemia reperfusion injury surgery on transgenic mice in which the FSP-1 promoter drives EGFP expression. Kidney injury peaks at day 3 post-IRI, followed by spontaneous regeration that restores nearly perfect kidney architecture and health by day 10. Fibroblasts are thought to possibly play a role in this process, as they are normally rare in the healthy kidney, acute kidney injury is associated with a transient accumulation of interstitial fibroblasts, but whether they may help repair the acute kidney injury or in fact could contribute to the damage is not known. To compare the  gene expression profiles of normal fibroblasts and those from post-ischemic kidneys, we sacrificed control FSP1-GFP mice and the FSP1-GFP mice three days post-IRI. We generated single-cell suspensions from both the post-IRI and control kidneys, and then isolated FSP1-GFP+ cells by FACS sorting that, when cultured on plastic, displayed typical fibroblast morphology.  Total RNA was immediately extracted from the sorted cells and amplified to produce enough for a array. We biotinylated five of the samples from post-ischemic kidneys and three of the control (non-ischemic) kidneys and used Affymetrix 3' Arrays to examine differences in gene expression profiles between the two groups that may she some light on what role, if any, fibroblasts play in the spontaneous healing of the kidney after acute kidney injury.

overall_design:
We performed ischemia reperfusion surgery in FSP1-GFP mice, and at day 3, we sacrificed the mice, isolated FSP1-GFP positive cells from both IR and normal control kidneys by FACS sorting, extracted total RNA from the isolated FSP1-GFP cells and used Affymetrix Mouse Expression Array 430 2.0 microarrays to perform gene expression profiling of the samples. All told, we performed the FACS Sorting, RNA extration, and hybridization with 5 ischemic kidneys and 3 normal kidneys.
Fibroblasts, acute kidney injury, repair, comparative gene expression profiling, microarrays, FACS sorting, role in healing

first: Scott

last: McGoohan


title: Expression data from E14.5 Onecut1 WT and KO animals

summary: In this study, we examine the consequences of the loss of two related factors, Onecut1 and Onecut2, during mouse retinal development.

overall_design: To investigate potential phenotypes in Onecut1-KO retinas, microarrays were performed on retinas isolated from E14.5 mice

first: Jillian

last: Goetz

first: Greg

last: Martin


title: Regulation of gene expressions in vivo by anti-VEGF therapy [Mouse430_2]

status: Public on Nov 09 2014

city: Oxford

first: Francesca

last: Buffa

address: The Weatherall Institute of Molecular Medicine

institute: University of Oxford

summary: U87-EV human glioblastoma xenograft tumours is therapeutically treated by bevacizumab, a humanized anti-human VEGF mAb, when tumour is established in BALB/c SCID mice. At the end point, collect tumour samples and extracted total RNA for microarray to investigate the gene profile changes compared to control. These include the genes from human tumour cells and mouse host stroma cells.

overall_design: 3 control samples versus 3-bevacizumab treated samples

first: Adrian

last: Harris


title: Gene expression and alternative splicing in pancreatic ductal adenocarcinoma (PDAC)

city: London

first: Jun

last: Wang


title: Expression data from CCRF_CEM cell line treated with 7-(2-Thienyl)-7-deazaadenosine  (AB61), tubercidin and actinomycin D

status: Public on Oct 22 2014

city: Olomouc

first: Petr

last: Dzubak

address: Hnevotinska 5

department: Institute of Molecular and Translational Medicine

country: Czech Republic

institute: Palacky University, Faculty of Medicine and Dentistry

summary:
CCRF_CEM cell line was treated by AB61 which is potent cytotoxic compound, as the positive controls were used tubercidin and actinomycin D.
To assay the biological activity of the AB61 more broadly we performed transcriptional microarray analysis. .

overall_design: CCRF_CEM cell line was treated by AB61, tubercidin and actinomycin D at 5xIC50 for 3 hours. Total RNA was extracted and hybridized on Affymetrix microarrays. We sought to obtain expressional profile to get differential expression of genes following the drug treatment.

first: Pavla

last: Perlikova


title: Expression data in antigen-specific CD8 T cells in the absence of ATG7

status: Public on Oct 26 2014

city: Atlanta

first: Xiaojin

last: Xu

state: Georgia

address: 1510 Clifton Road

department: Emory Vaccine Center and Department of Microbiology and Immunology

institute: Emory University School of Medicine

summary:
Autophagy genes play an important role in the T cell activation and proliferation. We examined the role of ATG7 during the process of CD8 T cell memory formation. In the absence of ATG7, antigen-specific CD8 T cells failed to survive past the contraction phase and failed to give rise to memory cells.
We used microarrays to examine the global programme of gene expression underlying changes introduced in the absence of the ATG7 gene and identified distinct classes genes varied their expression during this time-point.

overall_design: Mouse LCMV-specific CD8 T cells were isolated at day 8 post LCMV infection for RNA extraction and hybridization on Affymetrix microarrays. We sought to compare the gene expression profiles in wild-type cells and cells lacking the ATG7 gene during the peak of their expansion.

first: Xu

last: Xiaojin

first: Araki

last: Koichi

first: Ahmed

last: Rafi


title: Generation of CNS neural stem cells and PNS derivatives from neural crest derived peripheral stem cells [Dataset 2]

first: Galina

last: Apostolova

overall_design: Affymetrix Mouse 430_2 arrays were used to compare the gene expression profiles of embryonic DRG-derived reprogrammed NCSCs and adult NCSCs from mouse palate.

first: Marlen

last: Weber

first: Darius

last: Widera

first: Michel

last: Mittelbronn

first: Georg

last: Dechant

first: Barbara

last: Kaltschmidt

first: Hermann

last: Rohrer


title: Calcitonin controls bone formation by inhibiting the release of sphingosine 1-phosphate from osteoclasts

status: Public on Oct 19 2014

city: Hamburg

first: Thomas

last: Streichert

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

department: Institute For Clinical Chemistry / Central Laboratories

institute: University Medical Center Hamburg-Eppendorf

summary: The hormone calcitonin (CT) is primarily known for its pharmacologic action as an inhibitor of bone resorption, yet CT-deficient mice display increased bone formation. These findings raised the question about the underlying cellular and molecular mechanism of CT action. Here we show that either ubiquitous or osteoclast-specific inactivation of the murine CT receptor (CTR) causes increased bone formation. CT negatively regulates the osteoclast expression of Spns2 gene, which encodes a transporter for the signaling lipid sphingosine 1-phosphate (S1P). CTR-deficient mice show increased S1P levels, and their skeletal phenotype is normalized by deletion of the S1P receptor S1P3. Finally, pharmacologic treatment with the non-selective S1P receptor agonist FTY720 causes increased bone formation in wildtype, but not in S1P3-deficient mice. This study redefines the role of CT in skeletal biology, confirms that S1P acts as an osteoanabolic molecule in vivo, and provides evidence for a pharmacologically exploitable crosstalk between osteoclasts and osteoblasts.

overall_design: Osteoclasts of wildtype and Calcr-/- C57Bl/6 mice were treated with Calcitonin and compared to the non-treated osteoclasts of wildtype or Calcr-/- mice, respectively.

first: Thorsten

last: Schinke


title: Parkinson Phenotype in Aged PINK1-Deficient Mice Is Accompanied by Progressive Mitochondrial Dysfunction in Absence of Neurodegeneration

status: Public on Nov 04 2014

city: Tuebingen

first: Michael

middle: H.

last: Walter

address: Calwer Str. 7

department: Department of Medical Genetics

institute: University of Tuebingen

summary: Parkinson's disease (PD) is an adult-onset movement disorder of largely unknown etiology. We have previously shown that loss-of-function mutations of the mitochondrial protein kinase PINK1 (PTEN induced putative kinase 1) cause the recessive PARK6 variant of PD. Now we generated a PINK1 deficient mouse and observed several novel phenotypes: A progressive reduction of weight and of locomotor activity selectively for spontaneous movements occurred at old age. As in PD, abnormal dopamine levels in the aged nigrostriatal projection accompanied the reduced movements. Possibly in line with the PARK6 syndrome but in contrast to sporadic PD, a reduced lifespan, dysfunction of brainstem and sympathetic nerves, visible aggregates of α-synuclein within Lewy bodies or nigrostriatal neurodegeneration were not present in aged PINK1-deficient mice. However, we demonstrate PINK1 mutant mice to exhibit a progressive reduction in mitochondrial preprotein import correlating with defects of core mitochondrial functions like ATP-generation and respiration. In contrast to the strong effect of PINK1 on mitochondrial dynamics in Drosophila melanogaster and in spite of reduced expression of fission factor Mtp18, we show reduced fission and increased aggregation of mitochondria only under stress in PINK1-deficient mouse neurons. Thus, aging Pink1−/− mice show increasing mitochondrial dysfunction resulting in impaired neural activity similar to PD, in absence of overt neuronal death. Transcriptome microarray data of Pink1-/- mouse brains in absence of a stressor, even at old age, show remarkably sparse dysregulations. See Gispert-S et al 2009 PLOS ONE.

overall_design: Factorial design comparing Pink1 knock-out mice with wild type littermates in three different tissues (striatum, midbrain, cerebellum at four different timepoints (6, 12, 14 weeks, and 18 month)

first: Alexander

last: Kurz

last: Auburger

first: Suzana

last: Gispert


title: Continuous T cell receptor signals maintain a functional regulatory T cell pool

status: Public on Oct 21 2014

city: Martinsried

first: Marc

last: Schmidt-Supprian

state: Bavaria

address: Am Klopferspitz 18

department: Molecular Immunology

institute: Max Planck Institute of Biochemistry

summary:
During development, thymocytes bearing a moderately self-reactive T cell receptor (TCR) can be selected to become regulatory T  (Treg) cells. Several observations suggest that also in the periphery mature Treg cells continuously receive self-reactive TCR signals. However, the importance of this inherent autoreactivity for Treg cell biology remains poorly defined.
To address this open question, we genetically ablated the TCR of mature Treg cells in vivo. These experiments revealed that TCR-induced Treg lineage-defining FoxP3 expression and gene hypomethylation were uncoupled from TCR input in mature Treg cells. However, Treg cell homeostasis, cell-type-specific gene expression and suppressive function critically depend on continuous triggering of their TCR.

overall_design: TCRpos (FoxP3+ CD4+ CD25high cells from CαF/F FoxP3 I eGFP mice) and TCRneg (FoxP3+ TCR– CD4+ CD25high cells from Mx-Cre CαF/F FoxP3 I eGFP mice) Treg cells were FACS sorted 6 weeks after poly(I:C) injection. Cells from 3-5 mice were pooled for sorting, and 4 replicates for the controls (TCRpos) as well as 5 replicates for the Mx-Cre (TCRneg) mice were generated. mRNA from 3-5 x 105 cells was purified with a RNeasy Micro kit (Qiagen), amplified, labeled and hybridized to Affymetrix M430 V2 microarrays

first: J

last: Vahl

first: Sonja

last: Schallenberg

last: Buch

first: Karsten

last: Kretschmer