title: Examining efficiency of enrichment of kidney pericyte-specific messages by TRAP (Translating Ribosome Affinity Purification)

city: Edinburgh

first: GUDMAP

last: Developers

address: Crewe Road

institute: IGMM MRC Human Genetics Unit

summary: The long term goal is to define the transcriptional changes that accompany pericyte-to-myofibroblast transition in fibrotic kidney disease. Medullary pericytes are identified by their expression of a eGFPL10a fusion protein whose expression is driven by a Col1a1 promoter.  Pericyte-specific RNA is generated by eGFP-affinity purification of polysomes from medullary lysates and then subject to microarray analysis.

overall_design: Col1a1-eGFPL10a mice were subject to Sham or unilateral ureteral obstruction surgery. Sham kidneys were collected at day 0, and UUO kidneys were collected at day 2 or day 5 for TRAP.

first: Ben

last: Humphreys


title: Toxoplasma RH and Mock Infection of macrophages

status: Public on Feb 25 2014

city: Stanford

first: Anjali

last: Shastri

state: CA

address: D305 Farichild Building; 299 Campus Drive

department: Microbiology & Biology

country: USA

institute: Stanford University

summary:
Infection of RAW264.7 cells with RHΔku80 parasites or mock-infection for 24 hours
To measure changes in gene expression induced in macropahges upon Toxoplasma infection, we infected RAW 264.7 macrophages in cell culture with RHΔku80 parasites or syringe-lysed human foreskin fibroblast monolayers (mock-infected). RNA was harvested 24 hours post infection.

overall_design: Cells were infected with Toxoplasma or mock-infected in vitro, in duplicate

first: Magdalena

last: Franco


title: Expression data from adult mouse normal and damaged retina from B6 and 129 mouse strains

status: Public on Mar 06 2014

city: Kobe

first: Masayo

last: Takahashi

state: Hyogo

address: 2-2-3 Minamimachi, Minatojima, Chu-o-ku

country: Japan

institute: RIKEN CDB

summary:
Retinal damage causes proliferation of Muller glia, but the degree of proliferation depends on mouse strains. Muller glial proliferation was significantly promoted by the addition of GSK3 inhibitor in 129, but not in B6. We used retinal explant culture as a model for retinal damage which caused preferential photoreceptor death in a few days.
We used microarrays to detail the global programme of gene expression regulating the proliferative potential of Muller glia after retinal damage.

overall_design: Total RNA from intact whole retina, retinal tissue cultured for three days, and retinal tissue cultured with chir99021 for three days was used. Retinal tissues from 10 weeks old mice were used.

first: Akiko

last: Suga


title: Divergent immunity and energetic programs in the gills of migratory and resident Oncorhynchus mykiss

status: Public on Mar 04 2014

city: Victoria

middle: F

last: Koop

state: BC

address: PO Box 3020 STN CSC

department: Biology

country: Canada

institute: The University of Victoria

summary: To identify gene expression differences between Oncorhynchus mykiss that migrate and those that reside in freshwater, we compared gill transcriptomes of fish prior to release from a hatchery with those of fish recaptured eight days post-release while all fish were still in freshwater, but some were captured next to the hatchery (non-migrants) and others were captured moving toward the ocean (migrants). The in-hatchery sampling method represents a highly similar environment for all the fish, and allows for the determination of activated genes predictive of smolting programs prior to release into streams. Morphological (e.g. color) and physiological (gill NaCl-ATPase activity) data were also obtained and correlated to gene expression differences to aid in predictions.

overall_design: Gill tissue was sampled for transcriptome profiling 13 days prior to two different releases from the hatchery (total sampled within hatchery n = 19). Samples were also taken eight days after the two releases near-hatchery (total in-creek n = 20) or migrating towards the ocean but still in freshwater (second release only n = 20). Finally, 48 days after the second release a final set of resident fish were sampled near the hatchery (n =10). In terms of time after release, the most parallel comparison is the second 8 day post release sample in-creek and migrating. Although all samples were obtained in freshwater, the samples with the most similar local environment are the pre-release samples.

middle: G

last: Sutherland

first: Kyle

middle: C

last: Hanson

first: Johanna

middle: R

last: Jantzen

first: Christian

middle: T

last: Smith


title: Host Responses to Sepsis Vary in Different Low-Lethality Murine Models

status: Public on Feb 21 2014

city: Gainesville

first: M Cecilia

last: Lopez

state: FL

address: 1376 Mowry Road

department: Molecular Genetics and Microbiology

institute: University of Florida

summary: The CS and CLP murine models of intra-abdominal sepsis have unique transcriptomic respones 2 hrs, 1 and 3 days after sepsis

overall_design:
We used mouse microarrays to detail the molecular profile of the events that occur following infection in two different sepsis models
Infection protocol: Used the Cecal Ligation and Puncture (CLP) model and Cecal Slurry (CS) method in young mice.

first: Lori

last: Gentile

first: Dina

last: Nacionales

first: M. Cecilia

first: Erin

last: Vanzant

first: Angela

last: Cuenca

first: Benjamin

middle: E

last: Szpila

first: Alex

first: Anna

last: Joseph

first: Frederick

middle: A

last: Moore

first: C

last: Leeuwenburgh

first: Henry

middle: V

last: Baker

first: Lyle

middle: L

last: Moldawer


title: Expression data of NIH3T3 in G0 and G1 phases

city: Boston

first: Toshihiko

last: Oki

state: MA

address: 185 Cambridge Street

department: Center for Regenerative Medicine

institute: Massachusetts General Hospital

summary:
NIH3T3 in the middle of G0 to G1 transion consists of the cells which is still staying G0 phase and the cells which enters G1. Monitoring the expressions of p27 and Cdt1 enables to distinguish these two; p27+/Cdt1+ cells as the cells in G0 phase and p27-Cdt1+ cells as G1 phase
We sorted  p27+Cdt1+ (G0) NIH3T3 cells and p27-Cdt1+ (G1) NIH3T3 cells in the middle of G0-G1 transition, 5 hours after serum addition following the serum addition using mVenus-p27K- and mCherry-hCdt1(30/120) .
We compared the expression profiles of these NIH3T3 cells in G0 and G1 phases and identified the genes upregulated in G0 or G1 phases.

overall_design: The p27+Cdt1+ (G0) NIH3T3 cells and p27-Cdt1+ (G1) NIH3T3 cells were sorted by FACS for RNA extraction and hybridization on Affymetrix microarrays.

first: Koutarou

last: Nishimura

first: Jiro

last: Kitaura

first: Katsuhiro

last: Togami

first: Akie

last: Maehara

first: Kumi

last: Izawa

first: Asako

last: Sakaue-Sawano

first: Atsushi

last: Niida

first: Satoru

last: Miyano

first: Hiroyuki

last: Aburatani

last: Miyawaki

first: Toshio

last: Kitamura


title: Expression data during plantaris muscle hypertrophy with/without satellite cells induced by synergist ablation in young adult Pax7-DTA mice

status: Public on Feb 20 2014

city: Lexington

first: Christopher

last: Fry

state: KY

address: 900 South Limestone

institute: University of Kentucky

summary:
Global gene expression patterns were determined from microarray results from sham surgery or following 1 week of plantaris muscle hypertrophy induced by synergist ablation in young adult Pax7-DTA mice (4 months).
Vehicle treated mice have their full complement of satellite cells; tamoxifen treated mice have had their satellite cells genetically depleted through Cre-loxP technology

overall_design: After sham surgery or 1 week of overload, Affymetrix chips (mouse430_2.0) were used with 1 µg of total RNA derived from a pooled sample of the right and left plantaris muscles from 11 animals.

middle: S

first: Janna

last: Jackson

first: Tyler

middle: J

last: Kirby

first: John

last: McCarthy

first: Charlotte

last: Peterson


title: Age-related changes in the cellular composition and epithelial organization of the mouse trachea

city: Durham

first: Brigid

last: Hogan

state: North Carolina

address: 388 Nanaline Duke Bldg PO Box 3709

department: Cell Biology

institute: Duke University Medical Center

summary: We report here senescent changes in the structure and organization of the mucociliary pseudostratified epithelium of the mouse trachea and the main stem bronchi. We confirm previous reports of the graduate appearance of age-related, gland-like structures (ARGLS) in the submucosa, espeically in the intercartilage regions and carina. Immunohistochemistry shows these structures contain ciliated and secretory cells and Krt5+ basal cells, but not the myoepithelial cells or ciliated ducts typical of normal submucosal glands. Data suggests they arise de novo by budding from teh surface epithelium rather than by delayted growth of small or cryptic submucosal glands. In old mice the surface epithelium contains fewer cells per unit length than in young mice and the proportion of Krt5+, p63+ basal cells is reduced in both males and females. However, there appears to be no significant difference in the ability of basal stem cells isolated from individual young and old mice to form clonal tracheospheres in culture or in the ability of the pithelium to repair after damage by inhaled sulfur dioxide. Gene expression analysis by Affymetrix microarray and quantitative PCR, as well as immunohistochemistry and flow sorting studies, are consistent with low-grade chronic inflammation in the tracheas of old versus young mice. The significance of these changes for ARGL formation are not clear since several treatments that induce acute inflammation in young mice did not result in budding of the surface epithelium.

overall_design: Total RNA from distal tracheas and carinas of four young (2 month) and four older (14 month) C57Bl/6 female mice was extracted using QIAshredder and RNeasy Micro Kits (QIAGEN). The quality was checked with a 2100 Bioanalyzer (Agilent Technologies). Total RNA was processed using Ambion MessageAmpTM Premier by the Duke Microarray Facility. Standard Affymetrix protocols and Affymetrix GeneChip® Mouse Genome 430 2.0 Array chips were used to generate .cel files.

first: Carolien

last: Wansleeben


title: Differentially activated CD8 T cells in liver and gut

city: Berlin

first: Pawel

last: Durek

address: Charitéplatz 1

country: Germany

institute: Deutsches Rheuma-Forschungszentrum

summary: Naïve, liver- and gut-activated CD8 OT-I T cells show differential migration behaviour. To analyze which genes could be responsible for different migration patterns, naïve, liver-activated and gut-activated CD8 T cells were isolated and compared for their gene expression profile.

overall_design:
Gene expression profiles of naïve CD8 OT-I T cells  versus liver-activated T cells and gut-activated T cells, respectively. Naïve CD8 OT-I T cells were isolated from lymph nodes and spleens of OT-I mice. CD8 OT-I T cells activated by liver-derived and gut-derived antigen for three days in vivo, positive for CFSE were sorted from livers of TF-OVA mice or from mesenteric lymph nodes of iFABP-OVA mice.
After total RNA extraction, reverse transcription, cDNA extraction, the biotinylated cRNA was transcribed, fragmented, and 15 µg cRNA hybridized in duplicates for each of the three groups to the GeneChip arrays. Group1: naïve, Group2: liver-activated Group3: gut-activated. Lists of differentially regulated genes were created using High Performance Chip Data Analysis (HPCDA) with Bioretis database (http://www.bioretis-analysis.de). Worldwide data sharing is possible via Bioretis, please ask the authors.

first: Ira

last: Eickmeier

first: Daniel

last: Seidel

first: Joachim

last: Grün

first: Anja

last: Kühl

first: Alf

last: Hamann

first: Bertram

last: Wiedenmann

first: Eckart

last: Schott


title: Expression profiling by array in livers of Nrf2 null mice administered CDDO-IM

status: Public on Feb 18 2014

city: Baltimore

first: Thomas

last: Kensler

state: MD

address: 615 N. Wolfe St.

institute: The Johns Hopkins University

summary: Nrf2 null mice administered CDDO-IM

overall_design: Nrf2 null mice treated with CDDO-IM

first: Melinda

last: Yates


title: The role of Rif1 in ES cells

status: Public on Feb 19 2014

city: New Haven

first: Andrew

middle: Zhuo

last: Xiao

state: CT

address: 10 Amistad St

department: Genetics

institute: Yale Stem Cell Center

summary:
Purpose:The goals of this study are to understand the mechanisms underlying reduced self-renewal and loss of pluripotency by depletion of Rif1.
Methods: We performed global gene expression analysis of Rif1 knockdown ES cell lines using Affymetrix 430 2.0 arrays, compared to shRNA controls.

overall_design: J1 ES cells were transfected with Control shRNA and Rif1 shRNA using lipofectamine 2000. Forty-eight hours after transfection, cells were collected for global gene expression analysis using Affymetrix mouse genome 430 2.0 array. Stable F1 Rif1 knockdown ES cells at passage 16 were used for long-term gene expression chip microarray using Affymetrix mouse genome 430 2.0 array.

first: Lin

last: Liu


title: Effect of Graded Nrf2 Activation on Phase-I and -II Drug Metabolizing Enzymes and Transporters in Mouse Liver

city: Kansas City

first: Curtis

last: Klaassen

state: KS

address: 3901 Rainbow Boulevard

institute: University of Kansas Medical Center

summary:
Nuclear factor erythroid 2-related factor 2 (Nrf2) is a transcription factor that induces a battery of cytoprotective genes in response to oxidative/electrophilic stress. Kelch-like ECH associating protein 1 (Keap1) sequesters Nrf2 in the cytosol. The purpose of this study was to investigate the role of Nrf2 in regulating the mRNA of genes encoding drug metabolizing enzymes and xenobiotic transporters. Microarray analysis was performed in livers of Nrf2-null, wild-type, Keap1-knockdown mice with increased Nrf2 activation, and Keap1-hepatocyte knockout mice with maximum Nrf2 activation. In general, Nrf2 did not have a marked effect on uptake transporters, but the mRNAs of organic anion transporting polypeptide 1a1, sodium taurocholate cotransporting polypeptide, and organic anion transporter 2 were decreased with Nrf2 activation. The effect of Nrf2 on cytochrome P450 (Cyp) genes was minimal, with only Cyp2a5, Cyp2c50, Cyp2c54, and Cyp2g1 increased, and Cyp2u1 decreased with enhanced Nrf2 activation. However, Nrf2 increased mRNA of many other phase-I enzymes, such as aldo-keto reductases, carbonyl reductases, and aldehyde dehydrogenase 1. Many genes involved in phase-II drug metabolism were induced by Nrf2, including glutathione S -transferases, UDP- glucuronosyltransferases, and UDP-glucuronic acid synthesis enzymes. Efflux transporters, such as multidrug resistance-associated proteins, breast cancer resistant protein, as well as ATP-binding cassette g5 and g8 were induced by Nrf2. In conclusion, Nrf2 markedly alters hepatic mRNA of a large number of drug metabolizing enzymes and xenobiotic transporters, and thus Nrf2 plays a central role in xenobiotic metabolism and detoxification.
We used microarrays to detail the global programme of gene expression in response to Nrf2 activation and identified distinct classes of up- and down-regulated genes. process.

overall_design: Gene expression in livers of Nrf2-null, WT, Keap1-KD, and Keap1-HKO mice was determined using Affymetrix Mouse 430.20 arrays by the KUMC Microarray Core Facility. Biological cRNA replicates (n=3) of each genotype were hybridized to an individual array.

middle: D


title: Gene expression changes associated with prognosis of Merkel cell carcinoma

city: Royal Oak

first: Bryan

last: Thibodeau

state: MI

address: 3811 West 13 Mile Road

department: BioBank

institute: Beaumont Research Institute

summary:
Purpose: Due to the rarity of Merkel Cell Carcinoma (MCC), prospective clinical trials have not been practical. This study seeks to identify biomarkers to differentiate between patients with a good and poor prognosis.

Methods: Patients were stratified into good, moderate or poor prognosis. Merkel cell carcinoma (MCC) patients were stratified into one of three groups based upon status 24 months following treatment. Poor prognosis patients either presented with or progressed to distant metastasis. Patients with favorable prognosis had local disease presentation with no subsequent recurrence or nodal disease at presentation with no progression during follow-up of longer than 24 months. Moderate prognosis had recurrent local disease, development of nodal metastasis, or nodal disease at presentation with no progression during follow-up of fewer than 24 months. Using ArcturusXT Laser Capture Microdissection (Molecular Devices), tumor cells were isolated from the specific areas of interest. The captured tumor tissue was subjected to RNA extraction using the Invitrogen PureLink™ FFPE RNA Isolation Kit. The extracted RNA was analyzed for integrity with the Agilent Bioanalyzer then amplified and hybridized to Affymetrix GeneChip Human Exon 1.0 ST arrays using the NuGEN WT- Ovation™ FFPE System.

Results: A total of 191 genes showed significant differential expression (p≤0.05 and 1.5-fold cutoff) between the different between the good and poor prognosis groups. Keratin 20 (KRT20) and Neurofilament protein (NEFM) have been identified in previous studies as proteins of interest in MCC. Our study showed these genes to be significantly upregulated in patients with a poor prognosis. Of interest, phospholipase A2, group X was upregulated in poor responders. Phospholipases liberate arachidonic acid from cellular membranes which can be metabolized to eicosanoids through three major pathways: the cyclooxygenase (COX), the lipoxygenase (LOX) and the cytochrome P450 monooxygenase pathways. This pathway has been implicated in several cancers.

Conclusions: The study identified genes with a previous association with MCC as well as some novel genes. These genes provide the basis for further research into possible biomarkers that will enable the differentiation between patients with a good and poor prognosis.

overall_design: Using laser capture microdissection, tumor cells of patients with a good (n=5), moderate (n=3), and poor prognosis (n=7) were isolated from paraffin embedded archival tissue of 15 patients with Merkel cell carcinoma. Affymetrix Human Exon 1.0ST microarrays were utilized to compare gene expression signatures from good and poor prognosis patients.

first: Loren

last: Masterson

first: Laura

last: Fortier

first: Timothy

last: Geddes

first: Barbara

last: Pruetz

first: Richard

last: Keidan

first: George

last: Wilson


title: Expression data from Mammospheres

first: Jane

last: Holland

address: Robert-Roessle-Str. 10

department: Signal Transduction, Invasion and Metastasis of Epithelial Cells

institute: Max Delbrück Center for Molecular Medicine

summary: The combined activation of Wnt/ß-catenin and MET/HGF is required for mammary cancer stem cell (MaCSC) maintenance. We generated mammospheres derived from tumors of mice harboring Wnt/Met signaling mutations on which we performed microarray analysis to evaluate gene expression signatures controlled by Wnt and MET pathways. We used the gene expression profiles to dissect the role and the functions of these pathways in MaCSCs.

overall_design: We treated mammospheres with Wnt and MET pathway inhibitors alone or in combination. Samples treated with DMSO were used as vehicle control.

first: Walter

last: Birchmeier


title: Microarry datasets for RAW cells stimulated with R848 in the absence or presence of apilimod or API09

city: Cambridge

first: Xinming

last: Cai

address: 250 Massachusetts Avenue

institute: Novartis Institutes for Biomedical Research

summary: Apilimod is a reported TLR pathway antagonist in clinical trial. To understand the mode of action of apilimod, we applied global microarray analysis to explore the effect of apilimod on gene expression of RAW cell in the absence of presence of R848 (TLR7 ligand).

overall_design: RAW cells were stimulated with R848 in the absence or presence of apilimod (1μM).  mRNAs were extracted at 0h, 1h,3h, 7h, and 22h for affymetrix analysis. The inactive analog of apilimod (API09) was included as a control.

first: Yongyao

last: Xu

first: Qian

last: Huang

first: Nicole

last: Hartmann


title: Expression data of WHV/c-myc transgenic mice at preneoplastic and neoplastic stages

status: Public on Mar 01 2014

city: Shanghai

first: wang

last: feng

address: 320 Yue Yang Road

country: China

institute: Institute of Biochemistry and Cell Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences

summary:
The WHV/c-myc transgenic mouse is an animal model of hepatocarcinogenesis that can exquisitely mimic the cancer staging in human Hepatocellular carcinoma (HCC), in which the c-myc oncogene is activated by adjacent woodchuck hepatitis virus (WHV) DNA sequences. Compared to other models of c-myc transgenic mice, WHV/c-myc mice stably develop HCC with a relatively short latent period of 8 to 12 months, with a high (near 100%) tumor incidence.
The aim of this study was to discover new HCC biomarkers and analyze expression patterns of selected candidate biomarkers prior to liver tumor onset by employing WHV/c-myc transgenic mice.

overall_design: Using Affymetrix Mouse Genome 430 2.0 Expression Arrays, we studied hepatic gene expression profiles of WHV/c-myc transgenic mice at 5 months and 11 months, age-matched wild-type C57/BL6 mice were used as controls. At 5 months, the livers of transgenic mice exhibited mild to moderate hepatocyte dysplasia, this time point represents the preneoplastic stage. At 11 months, the tumors were visualized in WHV/c-myc transgenic mice and consisted mainly of well-differentiated, trabecular-type HCCs, and this time point was considered as neoplastic stage.

first: Feng

last: Wang

first: Liang

last: Da

first: Zhen

last: Xing

first: Chengfu

last: Sun

first: Pierre

last: Tiollais

first: Mujun

last: Zhao


title: Transcription array by profiling in WT and SRC-2 null mouse liver

status: Public on Feb 14 2014

city: East Lansing

first: Jae-Wook

last: Jeong

state: Michigan

address: 965 Fee Road

department: Department of Obstetrics, Gynecology and Reproductive Biology

institute: Michigan State University

summary: The molecular targets of SRC-2 regulation in the murine liver stimulate fatty acid degradation and glycolytic pathway while fatty acid, cholesterol, and steroid biosynthetic pathways are down-regulated.

overall_design: A genomic approach using microarray analysis was employed to identify the subsets of genes that are altered in the liver of  SRC-2-/- mice.

first: Inseok

last: Kwak

first: Kevin

middle: Y

last: Lee

first: Lisa

last: White

first: Xiao-Ping

first: F

last: Brunicardi

first: Bert

middle: W

last: O'Malley

first: Francesco

last: DeMayo


title: FoxA1 directs the lineage and immunosuppressive properties of FoxA1+ regulatory T cells in EAE and MS

status: Public on Feb 16 2014

city: Lund

first: Robert

last: Carlsson

address: Sölvegatan 17

department: IKVL

country: Sweden

institute: Lund University

summary: Affymetrix gene expression analysis was carried out to investigate the differences in gene profile of MBP89-101-reactive encephalitogenic T cells before and after co-culture with cerebellar granular neurons (CGNs). Co-culture of MBP89-101-reactive encephalitogenic T cells with CGNs leads to generation of T cells with regulatory T cells phenotype (CD4+CD25+membrane bound TGF-b+ T cells) or a new regulatory phenotype (CD4highPD-L1high T cells). CGN-induced CD4+CD25+membrane bound TGF-b+ T regulatory cells, CD4highPD-L1high T cells were purified by FACSAria. IFN-beta induced T lymphocytes (CD4highPD-L1high T cells) were also FACSAria purified. All these populations were compared to  MBP89-101-reactive encephalitogenic T cells. Samples were prepared from biological triplicates for each FACSAria sorted population.

overall_design: There are four different cell types, as determined by cell surface markers, in triplicate in the experiment.

first: Yawei

last: Liu

first: Michael

last: Kosicki

first: JunYang


title: Gene expression in thymi of Tcf1 -/-, Tcf +/- or Tcf1 -/- mice with tumor.

city: Leiden

first: Martijn

middle: H

last: Brugman

address: Albinusdreef 2

department: IHB

country: Netherlands

institute: LUMC

summary:
The HMG-box factor Tcf1 is required during T-cell development in the thymus and mediates the nuclear response to Wnt signals. Tcf1−/− mice have previously been characterized and show developmental blocks at the CD4−CD8− double negative (DN) to CD4+CD8+ double positive transition. Due to the blocks in T-cell development, Tcf1−/− mice normally have a very small thymus. Unexpectedly, a large proportion of Tcf1−/− mice spontaneously develop thymic lymphomas with 50% of mice developing a thymic lymphoma/leukemia at the age of 16 wk. These lymphomas are clonal, highly metastatic, and paradoxically show high Wnt signaling when crossed with Wnt reporter mice and have high expression of Wnt target genes Lef1 and Axin2. In wild-type thymocytes, Tcf1 is higher expressed than Lef1, with a predominance of Wnt inhibitory isoforms. Loss of Tcf1 as repressor of Lef1 leads to high Wnt activity and is the initiating event in lymphoma development, which is exacerbated by activating Notch1 mutations. Thus, Notch1 and loss of Tcf1 functionally act as collaborating oncogenic events. Tcf1 deficiency predisposes to the development of thymic lymphomas by ectopic up-regulation of Lef1 due to lack of Tcf1 repressive isoforms and frequently by cooperating activating mutations in Notch1. Tcf1 therefore functions as a T-cell–specific tumor suppressor gene, besides its established role as a Wnt responsive transcription factor. Thus, Tcf1 acts as a molecular switch between proliferative and repressive signals during T-lymphocyte development in the thymus.
Using the Tcf1−/− ΔVII/ΔVII knockout mouse (Verbeek et al. Nature 1995), thymocytes of 17 mice (5 control Tcf+/-, 4 Tcf-/- and 8 Tcf-/- with thymic lymphoma) were homogenized for RNA isolation using Qiagen RNeasy minicolumns. The quantity and quality of total RNA was determined using spectrophotometry (Nanodrop) and an Agilent Bioanalyzer. One µg of RNA was used to generate cRNA using Affymetrix One cycle cDNA synthesis kit (Affymetrix, Santa Clara, CA, USA), after which the samples were biotinylated using an Affymetrix IVT labeling kit (Affymetrix). The samples were hybridized overnight at 42°C to GeneChip mouse genome 430 2.0 Arrays (Affymetrix). Washing and staining steps were performed on a Fluidics station 450, and the Genechips were scanned using a GeneChip scanner 3000 (Affymetrix) at the Department of Immunology, Erasmus Medical Center. Raw data were normalized and summarized using Robust Multichip Average (RMA) method.

overall_design: The experiment consists of 5 control Tcf+/- thymi,  4 Tcf-/- thymi and 8 Tcf-/- thymus samples with thymic lymphoma.

first: Machteld

middle: M

last: Tiemessen

first: Miranda

last: Baert

first: Tom

last: Schonewille

first: Farbod

last: Famili

first: Daniela

last: Salvatori

first: Jules

middle: P

last: Meijerink

first: Ugur

last: Ozbek

first: Hans

last: Clevers

first: Jaques

last: van Dongen

first: Frank

last: Staal


title: Phenotypes of Th lineages generated by the commonly used activation with anti-CD3/CD28 antibodies differ from those generated by the physiological activation with the specific antigen

status: Public on Feb 13 2014

city: Bethesda

first: Lai

last: Wei

address: 10 Center Dr. Room 2B47

institute: NIH/NEI/NCCAM

summary: T-helper (Th) lineages have been generated in vitro by activating CD4 cells with anti-CD3/CD28 antibodies during polarization. Physiologically, however, the generation of Th lineages is by activation with the specific antigen presented by antigen-presenting cells (APC). Here, we used TCR-transgenic mice to compare the phenotypes of Th1, Th9 and Th17 lineages when generated by either one of the two activation modes. Lineage Th cells specific against hen egg lysozyme (HEL), were adoptively transferred into recipient mice transgenically expressing HEL in their lens. Remarkable differences were found between lineages of Th1, Th9, or Th17, generated by either one of the two modes in their capacities to migrate to and proliferate in the recipient spleen and, importantly, to induce inflammation in the recipient mouse eyes. Substantial differences were also observed between the lineage pairs in their transcript expression profiles of certain chemokines and chemokine receptors. Surprisingly, however, close similarities were observed between the transcript expression profiles of lineages of the three phenotypes, activated by the same mode. Furthermore, Th cell lineages generated by the two activation modes differed considerably in their pattern of gene expression, as monitored by microarray analysis, but exhibited commonality with lineages of other phenotypes generated by the same activation mode. This study thus shows that (i) Th lineages generated by activation with anti-CD3/CD28 antibodies differ from lineages generated by antigen/APC and (ii) the mode of activation determines to a large extent the expression profile of major transcripts

overall_design: Naïve CD4+ T cells purified from spleen and lymph node cells of 3A9 mice were activated and polarized toward Th1, Th9, and Th17 lineages, under either plate bound anti-CD3/anti-CD28 (PBAB) or APC presented HEL protein (HA).

first: Cuiyan

last: Tan

first: Igal

last: Gery


title: Susceptibility to photo-oxidative damage of mice lacking the Rod derived Cone Viability Factor gene Nxnl1

status: Public on Feb 12 2014

city: Paris

first: Frederic

last: Blond

address: 17 rue Moreau

country: France

institute: Institut de la Vision

summary: Rod-derived Cone Viability Factor is a trophic factor of the thioredoxins family that promotes the survival of cone photoreceptors. It is encoded by the nucleoredoxin-like gene 1 Nxnl1 which also encodes by alternative splicing for RdCVFL, for a thioredoxin enzyme that interacts with the protein TAU. The role of thioredoxins in the defense mechanism against oxidation led us to examine the retinal phenotype of the Nxnl1-/- mouse after photo-oxidative stress.

overall_design: In total 16 samples were analyzed, they represent two different genotypes (wt/wt, ko/ko) both on pure BALB/c background and two doses of light that were tested in triplicate each.

first: Irene

last: Lee-Rivera

first: Ghizlane

last: Elachouri

first: Naomi

last: Berdugo

first: Emmanuelle

last: Clérin

first: Hawa

last: Camara

first: Wolfgang

last: Raffelsberger

first: Jun

last: Wan

first: Najate

last: Ait-Ali

first: Melissa

last: Desrosiers

first: Marie-Laure

last: Niépon

first: Frédéric

first: Raymond

last: Ripp

first: Olivier

last: Poch

first: José-Alain

last: Sahel

first: Don

last: Zack

first: Thierry

last: Léveillard


title: Metabolic programs orchestrated by the activated Ha-ras and β-catenin oncoproteins in mouse liver tumors [mRNA]

status: Public on Feb 10 2014

city: Basel

first: Jonathan

last: Moggs

address: Fabrikstrasse 2

country: Switzerland

institute: Novartis

summary: The process of hepatocarcinogenesis in the diethylnitrosamine (DEN) initiation/phenobarbital (PB) promotion mouse model involves the selective clonal outgrowth of cells harboring oncogene mutations in Ha-ras, B-raf, or Ctnnb1. Here, we have characterized mouse liver tumors harboring either Ctnnb1 or Ha-ras mutations via integrated molecular profiling at the transcriptional and translational and post-translational levels. In addition, metabolites of the intermediary metabolism were quantified by high resultion 1H magic angle nuclear magnetic resonance (HR-MAS NMR). We have identified tumor characteristic genotype-specific differences in mRNA and miRNA expression, protein levels, and post-translational modifications and in metabolite levels that facilitate the molecular and biochemical stratification of tumor phenotypes. Bioinformatic integration of these data at the pathway level led to novel insights into tumor genotype-specific aberrant cell signaling and in particular to a better understanding of alterations in pathways of the cell intermediary metabolism, which are driven by the constitutive activation of the β-Catenin and Ha-ras oncoproteins in tumors of the two genotypes.

overall_design: Male C3H/HeJ mice received a single i.p. injection of DEN (10 or 90µg/g body weight) at 2, or 6 weeks of age. After a treatment-free interval of 2 weeks, the C3H/HeJ mice were either kept on a diet containing 0.05% PB or on a PB-free control diet for 28 to 36 weeks before they were sacrificed. Ha-ras- or Ctnnb1-mutated tumors and control tissues were isolated and either flash frozen in liquid nitrogen and stored at -80°C, or prepared for immunohistochemistry.

first: Elif

middle: B

last: Unterberger

first: Michael

last: Schwarz

first: Johannes

last: Eichner

last: Römer


title: Integrated analysis of microRNA and mRNA expression and association with HIF binding in MCF-7 cells under hypoxia [mRNA]

city: Oxford

first: Carme

last: Camps

address: Roosevelt Drive

country: United Kingdom

institute: Wellcome Trust Centre for Human Genetics/ U. of Oxford

summary:
Purpose: We aimed to investigate in depth the regulation of microRNA expression by hypoxia in the breast cancer cell line MCF-7, establish the relationship between microRNA expression and HIF binding sites, pri-miRNA transcription and microRNA processing gene expression.
Methods: microRNA sequencing data and gene expression microarray data were generated from MCF-7 cells submitted to an hypoxia timecourse (16h, 32h and 48h at 1% Oxygen). Data was integrated to 500 published high-stringency HIF binding sites identified in MCF-7 cells.
Results: We identified 41 microRNAs significantly up- and 28 down- regulated, of which 38 mature and 20 star forms are reported in conjunction with hypoxia for the first time. HIF-1α and HIF-2α binding sites within 50kb distance of microRNA loci were found by integration of HIF ChIP-seq data, showing overall association between binding sites and up-regulation. Gene expression profiling analysis showed no full coordination between pri-miRNA and microRNA expression, pointing towards additional levels of regulation. Several transcripts playing a role in microRNA processing were found regulated by hypoxia, of which two were HIF dependent.
Conclusions: The data support the hypothesis that microRNA expression under hypoxia is regulated at transcriptional and post-transcriptional level. HIF is involved at both levels, regulating the transcription of certain microRNAs and also the expression of key elements of the microRNA processing pathway.

overall_design: Gene expression profiles of MCF-7 exposed to hypoxia (1% Oxygen) for 16h (3 replicates), 32h (3 replicates) and 48h (3 replicates) and to normoxia (3 replicates) were generated using Illumina microarrays.

first: Jiannis

last: Ragoussis


title: Metabolic programs orchestrated by the activated Ha-ras and β-catenin oncoproteins in mouse liver tumors

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

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

overall_design: Refer to individual Series


title: Selective nuclear export of specific classes of mRNA from mammalian nuclei is promoted by GANP

first: Vihandha

last: Wickramasinghe

address: Hills Road

institute: MRC Cancer Unit, Hutchison/MRC Research Centre

summary: The nuclear phase of the gene expression pathway culminates in the export of mature mRNAs to the cytoplasm through nuclear pore complexes (NPCs). GANP (Germinal-centre Associated Nuclear Protein) promotes the transfer to NPCs of mRNAs bound to the transport factor NXF1. Here, we demonstrate that GANP, subunit of the TREX-2 mRNA export complex, promotes selective nuclear export of a specific subset of mRNAs whose transport depends on NXF1. Genome-wide gene expression profiling showed that half of the transcripts whose nuclear export was impaired following NXF1 depletion also showed reduced export when GANP was depleted. GANP-dependent transcripts were highly expressed, yet short-lived, and were highly enriched in those encoding central components of the gene expression machinery such as RNA synthesis and processing factors. After injection into Xenopus oocyte nuclei, representative GANP-dependent transcripts showed faster nuclear export kinetics than representative transcripts that were not influenced by GANP depletion. We propose that GANP promotes the nuclear export of specific classes of mRNAs that may facilitate rapid changes in gene expression.

overall_design: We used gene expression profiling to compare the abundance of cytoplasmic RNAs after GANP or NXF1 depletion

first: Ron

last: Laskey


title: The acetylome regulators Hdac1 and Hdac2 differently modulate intestinal epithelial cell dependent homeostatic responses in experimental colitis

status: Public on Feb 08 2014

city: Sherbrooke

first: Martin

last: Lessard

state: Qc

address: 2000 College

department: Sherbrooke Research Centre

institute: Agriculture and AgriFood Canada

summary: Histone deacetylases (Hdac) remove acetyl groups from proteins, influencing global and specific gene expression. Hdacs control inflammation, as shown by Hdac inhibitor-dependent protection from DSS-induced murine colitis. While tissue-specific Hdac knockouts show redundant and specific functions, little is known of their intestinal epithelial cell (IEC) role. We have shown previously that dual Hdac1/Hdac2 IEC-specific loss disrupts cell proliferation and determination, with decreased secretory cell numbers and altered barrier function. We thus investigated how compound Hdac1/Hdac2 or Hdac2 IEC-specific deficiency alters the inflammatory response. Floxed Hdac1 and Hdac2 and villin-Cre mice were interbred. Compound Hdac1/Hdac2 IEC-deficient mice showed chronic basal inflammation, with increased basal Disease Activity Index (DAI) and deregulated Reg gene colonic expression. DSS-treated dual Hdac1/Hdac2 IEC-deficient mice displayed increased DAI, histological score, intestinal permeability and inflammatory gene expression. In contrast to double knockouts, Hdac2 IEC-specific loss did not affect IEC determination and growth, nor result in chronic inflammation. However, Hdac2 disruption protected against DSS colitis, as shown by decreased DAI, intestinal permeability and caspase-3 cleavage. Hdac2 IEC-specific deficient mice displayed increased expression of IEC gene subsets, such as colonic antimicrobial Reg3b and Reg3g mRNAs, and decreased expression of immune cell function-related genes. Our data show that Hdac1 and Hdac2 are essential IEC homeostasis regulators. IEC-specific Hdac1 and Hdac2 may act as epigenetic sensors and transmitters of environmental cues and regulate IEC-mediated mucosal homeostatic and inflammatory responses. Different levels of IEC Hdac activity may lead to positive or negative outcomes on intestinal homeostasis during inflammation

overall_design: Total RNAs from the colon of three control and three Hdac2 IEC-specific knockout mix background (CD-1/129/C57BL/6) mice were isolated with the Rneasy kit (Qiagen, Mississauga, ON, Canada).

first: Naomie

last: Turgeon

first: Julie

last: Gagné

first: Mylène

last: Blais

first: Fernand-Pierre

last: Gendron

first: François

last: Boudreau

first: Claude

last: Asselin


title: Gene expression of murine B cells activated via TLR4 or TLR4 + CD40: Group1 naïve B cells, Group2 LPS activated B cells 24h, Group3 LPS + anti-CD40 activated B cells 24h, Group4 LPS activated B cells 72h, and Group5 LPS + anti-CD40 activated B cells 72h.

status: Public on Feb 24 2014

first: Pawel

last: Durek

address: Charitéplatz 1

institute: Deutsches Rheuma-Forschungszentrum

summary: Murine B cells can be activated via the surface receptors TLR4 and CD40. For a global assessment of differences in gene expression between these two different modes of B cell activation a genome wide transcriptome analysis was performed. In order to dissect different gene expression profiles of B cells, activation was induced by LPS or LPS + anti-CD40 for 24h and 72h. Both activation states were compared to each other but also to naïve B cells.

overall_design:
Gene expression profiles of naïve B cells, B cells activated with LPS and B cells activated with LPS + anti-CD40. Affymetrix MG 430 2.0 whole genome arrays were performed in quadruplicates for naïve B cells, B cells activated via TLR4 for 24 h and 72 h, and B cells activated via TLR4 + CD40 for 24 h and 72 h (20 arrays in total). To obtain genes significantly regulated upon stimulation with LPS, the expression profiles of naïve B cells, B cells activated with LPS for 24 h, and B cells activated with LPS for 72 h were compared to each other.
After total RNA extraction, reverse transcription, cDNA extraction, the biotinylated cRNA was transcribed, fragmented, and 15 µg cRNA hybridized in quadruplicates for each of the five groups to the 20 GeneChip arrays: Group1 naïve B cells, Group2 LPS activated B cells 24h, Group3 LPS + anti-CD40 activated B cells 24h, Group4 LPS activated B cells 72h, and Group5 LPS + anti-CD40 activated B cells 72h.
All chips were imported into BioRetis (http://www.bioretis-analysis.de) and are open to the community now. If you want to obtain one or more lists of HPCDA significant genes you should click on a link of single chips (e.g. GSM879034) to get a description how to manage this.

first: Ping

last: Shen

first: Toralf

last: Roch

first: Vicky

last: Lampropoulou

first: Richard

last: O’Connor

first: Ulrik

last: Stervbo

first: Ellen

last: Hilgenberg

first: Stefanie

last: Ries

first: Van-Duc

last: Dang

first: Yarúa

last: Jaimes

first: Capucine

last: Daridon

first: Rui

last: Li

first: Luc

last: Jouneau

first: Pierre

last: Boudinot

first: Siska

last: Wilantri

first: Imme

last: Sakwa

first: Yusei

last: Miyazaki

first: Melanie

last: Leech

first: Rhoanne

middle: C

last: McPherson

first: Stefan

last: Wirtz

first: Markus

last: Neurath

first: Kai

last: Hoehlig

first: Edgar

last: Meinl

first: Andreas

last: Grützkau

first: Joachim

last: Grün

first: Katharina

last: Horn

first: Anja

last: Kühl

first: Thomas

last: Dörner

first: Amit

last: Bar-Or

last: Kaufmann

first: Stephen

last: Anderton

first: Simon

last: Fillatreau


title: Expression data from mouse bone marrow cells expressing renin driven expression of green fluorescent protein.

status: Public on Feb 17 2014

city: St. Catharines

first: Ping

last: Liang

state: Ontario

address: 500 Glenridge Ave

department: Department of Biological Sciences

institute: Brock University

summary:
Local renin antiotensin systems have been identified for many extra-renal sites. Bone marrow has been proposed as one such site, although the nature of the renin-expressing cell type(s) has not been established.
Affymetrix microarrays were used to characterize the expression profile of renin-expressing GFP positive cells.

overall_design: Green fluorescent protein positive cells were sorted from whole bone marrow collected from adult transgenic mice. Bone marrow from several mice was collected and pooled on the day of a FACS sort. A portion of this was reserved for RNA extraction while the remainder was sorted. RNA was prepared with Trizol. Bone marrow collection and sorting was performed 3 times so that microarrays could be run in triplicate.

first: Craig

last: Jones

first: Li

last: Pan

first: Kenneth

last: Gross


title: Comparative transcriptomics of Atlantic Salmo salar, chum Onchorhynchus keta and pink salmon O. gorbuscha responding to salmon lice Lepeophtheirus salmonis infections

city: Victoria

first: Ben

middle: F

last: Koop

address: PO Box 3020 STN CSC

institute: The University of Victoria

summary: The present work characterizes the response of co-habited Atlantic (Salmo salar), chum (Oncorhynchus keta) and pink salmon (Oncorhynchus gorbuscha) to sea lice infections. Atlantic and pink salmon anterior kidney samples were profiled at three time points over nine days after the start of an experimental infection. Chum salmon anterior kidney was profiled at day six post infection only. All three species  were also profiled at six days post exposure for skin responses of the pectoral fin, typically associated with lice infection.

sample_organism:
Oncorhynchus gorbuscha
Oncorhynchus keta
Salmo salar

overall_design: Anterior kidney was profiled at day 3, 6, 9 post exposure to lice infection in Atlantic and pink salmon, but only at 6 days post exposure in chum salmon (for each day/species n = 10 for control, 10 for infected). Controls were treated exactly as experimental, but with the addition of seawater only (no lice). Time-matched controls were used for analysis. Please note that each tissue/species combination was normalized separately and then indirectly compared.

last: Sutherland

first: Kim

last: Koczka

first: Motoshige

last: Yasuike

first: Ryosuke

last: Yazawa

middle: R


title: G9a influences neuronal subtype specification in striatum

status: Public on Feb 05 2014

city: New York

last: Shen

state: NY

address: 1425 Madison Ave

department: Neuroscience

institute: Icahn School of Medicine at Mount Sinai

summary: Cocaine-mediated repression of the histone methyltransferase (HMT) G9a has recently been implicated in transcriptional, morphological, and behavioral responses to chronic cocaine administration. Here, using a ribosomal affinity purification approach, we find that G9a repression by cocaine occurs in both Drd1 (striatonigral)- and Drd2 (striatopallidal)-expressing medium spiny neurons (MSNs). Conditional knockout and overexpression of G9a within these distinct cell types, however, reveals divergent behavioral phenotypes in response to repeated cocaine treatment. Our studies further indicate that such developmental deletion of G9a selectively in Drd2 neurons results in the unsilencing of transcriptional programs normally specific to striatonigral neurons, and the acquisition of Drd1-associated projection and electrophysiological properties. This partial striatopallidal to striatonigral ‘switching’ phenotype in mice indicates a novel role for G9a in contributing to neuronal subtype identity, and suggests a critical function for cell-type specific histone methylation patterns in the regulation of behavioral responses to environmental stimuli.

overall_design: Polyribosome associated mRNAs from 2-5 month old, age and sex matched Drd1-Cre; Drd1-TRAP; G9afl/fl and Drd1-TRAP; G9afl/fl, Drd2-Cre; Drd2-TRAP; G9afl/fl and Drd2-TRAP; G9afl/fl mice (n = 2-4 mice/genotype/drug treatment, 2 hours after the last of eight repeated cocaine injections of 20 mg/kg/day) were obtained as previously described. EGFP labeled ribosomes and associated mRNAs were immunoprecipitated using a mix of two monoclonal anti-GFP antibodies (50 μg of clones #19C8 and #19F7 for each IP, available at Sloan-Kettering Monoclonal Antibody Facility). Purified mRNA was amplified and processed for microarray and qPCR analysis using the Affymetrix two-cycle cDNA Synthesis kit (Affymetrix) as previously described. Affymetrix Mouse Genome 430 2.0 arrays were used in all experiments. Information regarding the array design and features can be found at www.affymetrix.com. Mouse Genome 430 2.0 arrays were scanned using the GeneChip Scanner 3000 (Affymetrix) and globally scaled to 150 using the Affymetrix GeneChip Operating Software (GCOS v1.4).

first: Ian

last: Maze

first: Eric

last: Nestler


title: Nuclear receptor-mediated alleviation of alcoholic fatty liver by polyphenols contained in alcoholic beverages

status: Public on Feb 01 2014

city: kawasaki

first: Akihito

last: Yasuoka

state: kanagawa

address: kawasaki-ku, tonomachi 3-25-13

department: project of health and anti-aging

institute: kanagawa academy of science and technology

summary: To elucidate the effect of the polyphenols contained in alcoholic beverages on the metabolic stress induced by ethanol consumption, four groups of mice were fed for five weeks on Lieber's diet with or without ethanol, with ethanol plus ellagic acid, and with ethanol plus trans-resveratrol. Alcoholic fatty liver was observed in the group fed the ethanol diet but not in those fed the ethanol plus polyphenol diets. Liver transcriptome analysis revealed that the addition of the polyphenols suppressed the expression of the genes related to cell stress that were up-regulated by ethanol alone. Conversely, the polyphenols up-regulated the genes involved in bile acid synthesis, unsaturated fatty acid elongation, and tetrahydrofolate synthesis that were down-regulated by ethanol alone. Because parts of these genes were known to be regulated by the constitutive androstane receptor (CAR), we performed the same experiment in the CAR-deficient mice. As a result, fatty liver was observed not only in the ethanol group but also with the ethanol plus polyphenol groups. In addition, there was no segregation of the gene expression profiles among these groups. These results provide a molecular basis for the prevention of alcohol-induced stress by the polyphenols in alcoholic beverages.

overall_design: Five-week-old C3H/HeN female mice (CLEA, Japan) were acclimated to the maintenance condition (25°C, 8:00-20:00 day / 20:00-8:00 night cycle and 35~40 % humidity), fed a CE-2 diet (CLEA, Japan), and given water ad libitum for one week. Each group of mice (n=4 for wild type mice analysis and n=3 for CAR decficient mice analysis) was fed Lieber's isocaloric diet (Oriental yeast, Japan) containing water, containing ethanol, containing ethanol and ellagic acid (Fluka Biochemika, Switzerland), or containing ethanol and trans-resveratrol (Sigma, USA) (Supplementary Table 1) for one week at 10:00 ad libitum. Then, the mice were fed each diet at 12 g / day for four weeks (Supplementary Fig. 1A). The approximate intake of each polyphenol was 50 mg / kg body weight / day. At 10:00 of the final day of the experimental period, the animals were anesthetized by diethyl ether, sacrificed by cervial fracture, and the heart blood, and the liver were collected.


title: Exposure to Propylthiouracil in Pregnant Mice Potentiates the Transcriptional Response to Thyroid Hormone in the Fetal Cerebral Cortex

status: Public on Feb 04 2014

city: ottawa

first: hongyan

last: dong

address: 50 colombine Dr.

institute: health canada

summary: Although the effects of thyroid hormones (TH) on the brain development have been extensively studied perinatally, effects of TH of maternal origin on the fetal brain development have been largely unexplored. We applied a high throughput study on the mouse models with aberrant TH levels on gestation day (GD) 16, before the onset of fetal thyroid function. Although 3 day treatment with methimazole (MMI) and perchlorate significantly decreased TH levels in fetal cerebral cortex, few changes in the abundance of mRNA were revealed by the microarray analysis. Injection TH to dams 12 hours before sacrifice on GD 16 induced 161 genes significantly changed in fetal cortex. Nine out of 10 selected genes were confirmed with RT-PCR, including known TH responsive gene Klf9 and other novel TH responsive genes such as Appbp2, Ppap2b and Fgfr1op2. TH regulation of the expression of these genes was also confirmed with cultured N2aβ cells. Thyroid responsive elements (TREs) in the promoters of these genes were identified using electrophoresis mobility shift assay. TH effect on microRNA (miRNA) expression in developing cortex on GD 16 and postnatal day (PND) 15 was investigated with microarray and RT-PCR. Some of  miRNAs and precursors decreased in fetal cortex from the dams injected with TH on GD 16, including miR-16 and miR-106. Using 3’ untranslate region reporter vector, we identified Klf9 is one of the target genes of miR-106, while Ppap2b is the target of miR-16. These results indicated that TH regulation on gene expression could through TR-TRE interaction and through regulating target miRNA expression. This study is the first report to identify TH responsive genes and miRNAs genome wide in the early fetal brain; it provides evidence to further understand the mechanism of TH effect on brain development.

overall_design:
Timed-pregnant C57BL/6 mice (n=20; Harlan, Indianapolis, IN) arrived on gestational day (GD) 11 and were housed individually in plastic cages under a 12:12 light cycle (0600 h–1800 h) with food available ad libitum. Mice were divided randomly into one of 4 groups (control, hypo, hypo+ and hyper; 5 per group) . Mice in the control and hyper groups were provided with fresh drinking water containing 2% sucrose from GD 13 to GD 16 until sacrifice. Mice in hypo and hypo+ were provided with fresh drinking water daily containing 1% Perchlorate (Per) and 0.025% Methimazole (MMI) supplemented with 2% sucrose (to mask bitterness) from GD 13 to sacrifice on GD 16. Twelve hours prior to sacrifice on GD 16 all mice received a single subcutaneous injection. Control and hypo mice received vehicle (0.9% saline in 100 µl volume); the hypo+ group received 25.0 µg/100g body weight thyroxine (T4) with 2.5 µg/100g body weight T3 to restore a physiological level of TH; the hyper group received 100.0 µg/100g body weight T4 with 10.0 µg/100g body weight T3 to model hyperthyroidism. Dams were killed by exposure to CO2. Fetuses were dissected from the uterine horn and embryonic membranes then frozen on pulverized dry ice. Tissue samples were taken from the fetuses to determine sex using PCR for SRY (Yang J and RT Zoeller, 2002). Fetal cerebral cortices were removed from each mouse and used for microarray and RT-PCR analysis.
Total RNA was extracted from half cortices of individual female fetuses using RNeasy Lipid tissue Mini kits (Qiagen, Germantown, MD) according to the manufacturer's instructions.  The quality of total RNA was evaluated by A260/A280 ratio (found to be at least 1.8 for each sample) and by electrophoresis on the Agilent Bioanalyzer.  The Yale Center for the Neuroscience Microarray Consortium carried out the Affymetrix microarray analysis using The GeneChip Rat Genome 230 2.0 Array.  Preparation of labeled cRNA for hybridization onto Affymetrix GeneChips followed the recommended Affymetrix protocol.  Control versus each of the three treatment groups: hyper, hypo, and hypo+.
1 of 20 samples removed due to poor quality.

first: Hongyan

last: Dong

first: Seo-Hee

last: You

first: Andrew

last: Williams

first: Mike

last: Wade

first: Carole

last: Yauk

first: R

middle: T

last: Zoeller


title: Aged Mice are Unable to Mount an Effective Myeloid Response to Sepsis

city: Gainesville

first: M Cecilia

last: Lopez

address: 1376 Mowry Road

institute: University of Florida

summary: Old C57BL/6 mice cannot mount an effective innate immune response

overall_design: We used mouse microarrays to detail the molecular profile of the events that occur following infection

first: Dina

last: Nacionales

first: Lori

last: Gentile

first: Erin

last: Vanzant

first: M

first: Angela

last: Cuenca

first: Alex

middle: G

first: Ricardo

last: Ungaro

first: Yi

last: Li

first: Tezcan

middle: O

last: Baslanti

first: Azra

last: Bihorac

first: Frederick

middle: A

last: Moore

first: Henry

last: Baker

first: Christiaan

last: Leeuwenburgh

first: Lyle

last: Moldawer

first: Philip

last: Efron


title: Whole genome expression data from pre-auricular and post-auricular skin tissues

status: Public on Feb 07 2014

city: Beijing

first: lili

last: zhang

address: No.7 Beitucheng West Road, Chaoyang District

institute: Beijing Institute of Genomics, Chinese Academy of Sciences

summary: Photoaging is cumulative damage that is caused by chronic, repeated solar radiation exposure to skin. Its molecular mechanisms are poorly understood at the level of global gene expression.This study set out to uncover genes and functional modules involved in photoaging at the level of transcription, with the use of skin samples from Chinese women.Using the Illumina microarray platform, we compared the genome-wide expression profiles of 21 pairs of sun-exposed pre-auricular and sun-protected post-auricular skin samples from northern Chinese women.In total, 1,621 significantly regulated genes were identified from skin due to photoaging by microarray analysis. These genes were subjected to functional enrichment analyses with both the Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) annotation databases. As revealed by the functional analyses, the up-regulated functional modules in sun-exposed pre-auricular skin were related to various cellular activities in regulation of the skin homeostasis (e.g., the KEGG pathways TGF-beta signaling pathway and ECM-receptor interaction ), whereas the down-regulated functional modules were mostly metabolic-related. Additionally, five selected genes (HOXA5, LEPR, CLDN5, LAMC3, and CGA) identified as differentially-expressed were further confirmed on their expression by quantitative real-time PCR (Q-RT-PCR). Our findings suggest that damage from skin homeostasis and down-regulation of skin metabolism may play important roles in the process of photoaging.

overall_design: We compared the genome-wide expression profiles of 21 pairs of sun-exposed pre-auricular and sun-protected post-auricular skin samples from northern Chinese women by using the Illumina microarray platform.

first: Wei

last: Yan

first: Lili

last: Zhang

first: Yan

first: Feng

first: Ningbei

last: Yin

first: Hongbin

last: Lin

first: Chenyu

last: Huang

first: Lei

last: Wang

first: Duen-Mei

first: Zhenmin

last: Zhao


title: Induction of interferon-stimulated genes on the IL-4 response axis by Epstein-Barr virus infected human B cells; relevance to cellular transformation.

status: Public on Feb 03 2014

city: Durham

first: Wenbin

last: Wei

address: Stockton Road

department: Biosciences

institute: Durham University

summary:
Epstein-Barr virus (EBV) is an oncogenic virus that is associated with the pathogenesis of several human lymphoid malignancies, including Hodgkin's lymphoma. Infection of normal resting B cells with EBV results in activation to lymphoblasts that are phenotypically similar to those generated by physiological stimulation with CD40L plus IL-4. One important difference is that infection leads to the establishment of permanently growing lymphoblastoid cell lines, whereas CD40L/IL-4 blasts have finite proliferation life-spans. To identify early events which might later determine why EBV infected blasts go on to establish transformed cell lines, we performed global transcriptome analyses on resting B cells and on EBV and CD40L/IL-4 blasts after 7 days culture. As anticipated, there was considerable overlap in the transcriptomes of the two types of lymphoblasts when compared to the original resting B cells, reflecting common changes associated with lymphocyte activation and proliferation.
Of interest to us was a subset of 225 genes that were differentially expressed between EBV and CD40/IL4- blasts. Genes which were more highly expressed in EBV blasts were substantially and significantly enriched for a set of interferon-stimulated genes which on further in silico analyses were found to be repressed by IL-4 in other cell contexts and to be up-regulated in micro-dissected malignant cells from Hodgkin's lymphoma biopsies when compared to their normal germinal center cell counter parts. We hypothesized that EBV and IL-4 were targeting and discordantly regulating a common set of genes. This was supported experimentally in our model where IL-4 stimulation partially reversed transcriptional changes which follow EBV infection and it impaired the efficiency of EBV-induced B cell transformation. Taken together, these data suggest that discordant regulation of interferon and IL-4 pathway genes by EBV that occurs early following infection of B cells has relevance to the development or maintenance of an EBV-associated malignancy.

overall_design: 9 samples were analysed and these included 3 biological replicates of the following samples: primary B cells isolated by positive selection using CD19+ Dynabeads and harvested immediately for RNA and primary B cells infected with EBV or stimulated with CD40L and IL4 and harvested 7 days post-infection/ cytokine stimulation. All biological replicates represent B cells which were pooled from 3 or 4 different buffy coat donors.

first: Nikki

last: Smith

first: Rosemary

last: Tierney

first: Martina

last: Vockerodt

first: Paul

last: Murray

first: Ciaran

last: Woodman

first: Martin

last: Rowe


title: Dose-response modeling of early molecular and cellular key events in CAR-mediated hepatocarcinogenesis pathway

city: RTP

first: Susan

last: Hester

state: NC

address: 109 TW Alexander Dr

institute: US EPA

summary:
Male and female CD-1 mice were administered dietary Phenobarbital for 2 or 7 days. In-life, enzyme activity, cell proliferation, genomic analysis, and Bench-mark dose modeling was carried out.
The goal was to exmaine low-dose PB effects on early key events in CAR-mediated hepatocarcinogenesis.

overall_design: PB at 0, 0.15, 1.5, 15, 75, or 150 mg/kg-day for 2 or 7 days to characterize multiple apical and molecular endpoints.

first: David

last: Geter

first: Virunya

last: Bhat

first: B

last: Gollapudi

first: Radhakrishna

last: Sura


title: Oxidative stress induces mitochondrial dysfunction and a protective unfolded protein response in RPE cells

status: Public on Jan 30 2014

city: Baltimore

first: Marisol

last: Cano

state: Maryland

address: 400 N Broadway

department: Ophthalmology

institute: Johns Hopkins University

summary: How retinal pigmented epithelial (RPE) cells degenerate from oxidative stress in age-related macular degeneration (AMD) is incompletely understood. The study's intent was to identify key cytoprotective pathways activated by oxidative stress, and to determine the extent of their protection. Immunohistochemistry was used to identify the unfolded protein response (UPR) and mitochondria in the RPE of AMD samples. Maculas with early AMD had prominent IRE1α, but minimal mitochondrial TOM20 immunolabeling in mildly degenerated RPE. RPE cells treated with cigarette smoke extract (CSE), by microarray analysis, had over-represented genes involved in the antioxidant and unfolded protein response, and mitochondrial location. CSE induced the UPR sensors IRE1α, p-PERK, and ATP6, which activated CHOP. CHOP knockdown compromised cell viability after CSE exposure. At the same CSE doses, mitochondria generated superoxide anion and produced less ATP. In mice given intravitreal CSE, the RPE had increased IRE1α and decreased ATP, which elicited RPE epithelial-mesenchymal transition, as suggested by altered ZO1 immunolabeling of RPE flatmounts. Our experiments indicate that RPE cells exposed to oxidative stress respond with a cytoprotective antioxidant and unfolded protein response, but develop mitochondrial impairment that contributed to epithelial mesenchymal transition. With similar responses in the RPE of early AMD samples, these results suggest that mitochondria are vulnerable to oxidative stress while the ER elicits a protective response during early AMD.

overall_design: A total of 9 samples were analyzed: 3 control samples, 3 samples treated with 100ug/ml of Cigarette Smoke Condensate, and 3 samples treated with 250ug/ml of Cigarettes Smoke Condensate.

first: Brad

last: Barnett

first: Katayoon

last: Ebrahimi

first: Jun

last: Wan

first: Jiang

last: Qian

first: James

last: Handa


title: Genome-wide expression profile on hiPSCs and hiPSC-derived CD33+ myeloid cells

status: Public on Jan 31 2014

city: Badajoz

first: Angel

middle: Carlos

last: Roman

address: Avda. de Elvas s/n

department: Bioquimica y Biologia Molecular y Genetica

country: Spain

institute: Universidad de Extremadura

summary: To gain insights into which pathways might be dysregulated in JMML, we compared the transcriptome profiles among hiPSC and sorted CD33+ myeloid cells from control and patient samples. NS/JMML-derived CD33+ myeloid cells showed dysregulation in major biological processes. Moreover, a consistent expression pattern among sets of genes related to pluripotency and myeloid regulation was observed in the control, NS and NS/JMML CD33+ myeloid cells further supporting generally successful myelopoiesis.

overall_design: Total RNA obtained from hiPSC and sorted CD33+ myeloid  cells (at day 14 of differentiation) from control and patient samples

first: Sonia

last: Mulero-Navarro

first: Ana

last: Sevilla

first: Dung-Fang

last: Lee

first: Sunita

last: D'Souza

first: Sherly

last: Pardo

first: Ilan

last: Riess

first: Jie

last: Su

first: Ninette

last: Cohen

first: Christoph

last: Schaniel

first: Alessia

last: Baccarini

first: Brian

last: Brown

first: Hélène

last: Cavé

first: Aurélie

last: Caye

first: Marion

last: Strullu

first: Christopher

last: Park

first: Safak

last: Yalcin

first: Perundurai

middle: S

last: Dhandapany

first: Ge

last: Yongchao

first: Lisa

last: Edelmann

first: Sawsan

last: Bahieg

first: Patrick

last: Raynal

first: Elisabetta

last: Flex

first: Marco

last: Tartaglia

first: Kateri

last: Moore

first: Ihor

last: Lemischka

first: Bruce

last: Gelb


title: Gene expression alterations in the cerebellum and granule neurons of Cstb-/- mouse are associated with early synaptic changes and inflammation

status: Public on Mar 03 2014

city: Helsinki

first: Tarja

middle: Hannele

last: Joensuu

address: Haartmaninkatu 8 (PO Box 63)

department: Folkhälsan Institute of Genetics

country: Finland

institute: Folkhälsan Research Center

summary: Progressive myoclonus epilepsy of Unverricht-Lundborg type (EPM1) is an inherited neurodegenerative disease with myoclonus, seizures and ataxia, caused by the mutations in cystatin B (CSTB) gene. In an approach towards understanding the molecular basis of pathogenic events in EPM1 we have utilized the cystatin B  deficient mice (Cstb-/-), a model for the disease. We have characterized the gene expression changes from the cerebellum of Cstb-/- mouse at postnatal day 7 (P7) and P30 as well as in cultured cerebellar granule cells using a pathway-based approach. A marked upregulation of immune response genes was seen at P30, reflecting the ongoing neuropathology, however, the observed alterations in complement cascade genes could also imply defects in synaptic plasticity. Differentially expressed genes in pre-symptomatic Cstb-/- animals at P7 were connected to synaptic function and plasticity and in cultured cerebellar granule cells to cellular biogenesis, cytoskeleton and intracellular transport. Especially GABAergic pathways were affected.

overall_design: The sample preparation and hybridzation of each cRNAs on GeneChip® Mouse Genome 430 2.0 arrays (Affymetrix, Santa Clara, CA, USA) were performed in Helsinki Biomedicum Biochip Center (Finland).

first: Saara

last: Tegelberg

first: Eva

last: Reinmaa

first: Mikael

last: Segestråle

first: Paula

last: Hakala

first: Heidi

last: Pehkonen

first: Esa

last: Korpi

first: Jaana

last: Tyynelä

first: Tomi

last: Taira

first: Iiris

last: Hovatta

first: Outi

last: Kopra

first: Anna-Elina

last: Lehesjoki


title: Characterize the unique transcriptional changes in the embryonic trachea of knockout mice

city: iowa city

first: xinchang

last: zhou

state: IA

address: 200 Hawkins Dr

department: Otolaryngology

institute: university of iowa

summary:
To further identify the transcriptional changes underlying congenital tracheal malformation in a1H knockout mice, the differential gene expression panel was examined by Affymetrix microarray.
To investigate the roles of a1H-regulated genes in tracheal development, we characterize the unique transcriptional changes of early trachea in kockout mice, and compare the expression profiles of knock out trachea with those of wild type trachea.
We used microarrays to detail the global programme of gene expression underlying cellularisation and identified distinct classes of up or down-regulated genes during this process.

overall_design: Mouse embryos trachea were collected at embryo day 16 (E16) for RNA extraction and hybridization on Affymetrix microarrays. We sought to obtain homozygous mouse embryos trachea in order to compare with gene expression profile of wild type mouse tracheal.

first: Jose

last: Manaligod

first: Rong

last: Fan

first: Xinchang

last: Zhou


title: Expression data from testes of the mouse X-chromosome substitution strains

city: Tokyo

first: Ayako

last: Oka

address: Hulic Kamiyacho Building 2F, Toranomon 4-3-13, Minato-ku

institute: Transdisciplinary Research Integration Center

summary: To investigate the evolutionary divergence of transcriptional regulation between the mouse subspecies, we performed transcriptome analysis by microarray on testes from the X-chromosome substitution strain, which carries different subspecies-derived X chromosome on the host subspecies genome. Transcription profiling showed that large-scale aberrations in gene expression were occurred on the introgressed X chromosome. This improper expression was restored by introducing chromosome 1 from the same donor strain as the X chromosome, suggesting that the genetic incompatibility between trans-acting regulatory gene(s) on chromosome 1 and X-linked downstream genes might be a cause of the misregulation.

overall_design: Testes were collected from 5- and 7-day-old males for RNA extraction and the microarray experiments were performed by using Affymetrix microarrays. Testes from three different males for each strain were tested independently. Tested males are from control C57BL/6J (B6) strain, MSM strain, X-chromosome substitution strain (B6-ChrXMSM), partial X-chromosome substitution strain 1 (B6-ChrXTMSM), partial X-chromosome substitution strain 2 (XS39-tel), and restored (B6-ChrXTMSM X B6-Chr1MSM) F1.


title: compare the difference of gene expression between wild type ESCs and Mll2 Knockdown ESCs

status: Public on Jan 25 2014

city: Shanghai

first: Xiaoling

last: WAN

address: 320 Yue-yang road, Shanghai

institute: Institut pasteur of Shanghai, Chinese Academy of Sciences

summary:
Mll2 (ALR) is a histone 3 lysine 4 trimethyltransferase to function as gene activation.In our study, we found that Mll2 is vital for proper control of proliferation and lineage differentiation of mouse ESCs, particularly towards the cardiac-specific lineages.
We used microarrays to detail the global programme of gene expression to compare the difference after Mll2 knockdown in E14 cell lines.

overall_design: E14 cells were infected with lentiviruses expressing short hairpin RNA (shRNA) for Mll2  for 24 hours, and then puromycin was added at 2mg/ml to select for 5 days. Then collet samples of control and Mll2 knockdown E14 cells for RNA extraction and hybridization on Affymetrix microarrays.

last: Wan

first: Yan

last: Zhang


title: Effect of Mirn378 overexpression on gene expression during C2C12 myogenic and BMP2-induced osteogenic differentiation

status: Public on Jan 28 2014

city: Nijmegen

first: Marlinda

last: Hupkes

address: Heyendaalseweg 135

department: Cell and Applied Biology

institute: Radboud University Nijmegen

summary:
Background: MicroRNAs (miRNAs) are a family of small, non-coding single-stranded RNA molecules involved in post-transcriptional regulation of gene expression. As such, they are believed to play a role in regulating the step-wise changes in gene expression patterns that occur during cell fate specification of multipotent stem cells. Here, we have studied whether terminal differentiation of C2C12 myoblasts is indeed controlled by lineage-specific changes in miRNA expression.
Results: Using a previously generated RNA polymerase II (Pol-II) ChIP-on-chip dataset, we show differential Pol-II occupancy at the promoter regions of six miRNAs during C2C12 myogenic versus BMP2-induced osteogenic differentiation. Overexpression of one of these miRNAs, miR-378, enhances Alp activity, calcium deposition and mRNA expression of osteogenic marker genes in the presence of BMP2.
Conclusions: Our results demonstrate a previously unknown role for miR-378 in promoting BMP2-induced osteogenic differentiation.

overall_design: Stable C2C12 cell lines C2C12-pMirn0 and C2C12-pMirn378 were generated by lentiviral transduction of C2C12 myoblasts with a Mirn378-overexpression construct and its parent vector, respectively. C2C12-pMirn0 and C2C12-pMirn378 cells were plated at 2.5 x 10^4 cells/cm2 (day -1), cultured for 1 day in DMEM 10%NCS, then (d0) treated with or without 300 ng/ml bone morphogenetic protein 2 (BMP2) for 6 days. RNA was extracted on d0, d3 and d6 and hybridized to GeneChip Mouse Genome 430 2.0 array (Affymetrix).

first: Ana

last: Sotoca

last: M. Hendriks

first: Everardus

middle: J

last: van Zoelen

first: Koen

last: Dechering


title: Akt signalling leads to stem cell activation and promotes tumour development in epidermis.

status: Public on Jan 26 2014

city: Madrid

first: Ramon

last: Garcia-Escudero

state: Madrid

address: Avda Complutense 40, Ed 70A

department: Biomedical Innovation

institute: CIEMAT

summary: A permantly active form of the oncogene Akt was expressed in the keratinocytes of the basal proliferative layer of the epidermis. Stem cells of the hair follicle expressing the cell surface marker CD34 were isolated. RNA form the CD34(+) and CD34(-) keratinocytes was extracted and and hybridized to Mouse Genome 430 2.0 Affymetrix arrays.

overall_design: Gene expression was compared between CD34(+) hair follicle stem cells and CD34(-) cells isolates from the back skin of K5-myrAkt transgenic mice.

first: Corina

last: Lorz

first: Carmen

last: Segrelles

first: Maria

middle: I

last: Garin

first: Jesus

last: Paramio


title: Expression data from colon and livers of mice

status: Public on Jan 24 2014

first: Kato

last: Hisanori

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

institute: The University of Tokyo

summary:
Here we describe our unprecedented approach in proposing parsley (PAR) as a nutraceutical intervention in inflammatory bowel disease (IBD) using a mouse model of dextran sodium sulphate (DSS)-induced colitis, following a multi-integrated-omics analysis. PAR supplementation (n=7) significantly improved colon shortening and increased the disease activity index compared to the DSS group (n=7). The colonic transcriptome revealed the down-regulation of inflammatory cytokines, and the hepatic transcriptome and metabolome revealed the up-regulation of fatty acid synthesis genes, thereby improving body weight loss. Down-regulated cancer markers were observed in the hepatic transcriptome and proteome. A global plasma metabolite analysis indicated shifts in the citric cycle and urea cycle, implicating improved impaired glycolysis and oxidative stress. Our integration of three omics analyses highlighted the involvement of the methionine-recycling pathway and PAR’s role in decreasing the risk of IBD. This pioneering use of multi-integrated-omics in the evaluation of nutrients’ effects on physiology is expected to be widely useful and informative, shaping the future of nutritional research.
Here we describe our unprecedented approach in proposing parsley (PAR) as a nutraceutical intervention in inflammatory bowel disease (IBD) using a mouse model of dextran sodium sulphate (DSS)-induced colitis, following a multi-integrated-omics analysis. PAR supplementation (n=7) significantly improved colon shortening and increased the disease activity index compared to the DSS group (n=7). The colonic transcriptome revealed the down-regulation of inflammatory cytokines, and the hepatic transcriptome and metabolome revealed the up-regulation of fatty acid synthesis genes, thereby improving body weight loss. Down-regulated cancer markers were observed in the hepatic transcriptome and proteome. A global plasma metabolite analysis indicated shifts in the citric cycle and urea cycle, implicating improved impaired glycolysis and oxidative stress. Our integration of three omics analyses highlighted the involvement of the methionine-recycling pathway and PAR’s role in decreasing the risk of IBD. This pioneering use of multi-integrated-omics in the evaluation of nutrients’ effects on physiology is expected to be widely useful and informative, shaping the future of nutritional research.

overall_design: Total hepatic and colonic RNA from each respective group were pooled (n=7). The microarray analysis was carried as out as described by Jia et al. 8 Mouse Genome 430 2.0 Array GeneChips (Affymetrix, Santa Clara, CA) containing over 30,000 gene probe sets were used for genome-wide expression profiling.

first: Huijuan

last: Jia

first: Wanping

last: Aw

first: Manaka

last: Hanate

first: Saito

last: Kenji

first: Hiroshi

last: Tanaka

first: Hisanori

last: Kato


title: A novel class of alternative 3’-terminal exons is involved in cell-cycle regulation by topoisomerase inhibitors

city: ORSAY

first: Martin

last: Dutertre

address: Rue Henri Becquerel

institute: INSERM

summary: Alternative 3’-terminal exons, which use intronic polyadenylation sites, are generally unconserved and lowly expressed, while the main gene products end in the last exon of genes. In this study, we discover a class of human genes, where the last exon appeared recently during evolution, and the major gene product uses an alternative 3’-terminal exon corresponding to the ancestral last exon of the gene. This novel class of alternative 3’-terminal exons are down-regulated on a large scale by doxorubicin, a cytostatic drug targeting topoisomerase II, and play a role in cell cycle regulation, including centromere-kinetochore assembly. The RNA-binding protein, HuR/ELAVL1 is a major regulator of this specific set of alternative 3’-terminal exons. HuR binding to the alternative 3’-terminal exon in the pre-messenger RNA promotes its splicing, and is reduced by topoisomerase inhibitors. These findings provide new insights into the evolution, function and molecular regulation of alternative 3’-terminal exons.

overall_design: 6 samples of MCF7 cells exposed to different treatments were analyzed: 3 x control_6 hours; 3 x doxorubicin_6 hours.

first: Fatima

last: Zahra Chakrama

first: Emmanuel

last: Combe

first: François-Olivier

last: Desmet

first: Hussein

last: Mortada

first: Micaela

last: Polay Espinoza

first: Lise

last: Gratadou

first: Didier

last: Auboeuf


title: Expression data from induced pluripotent stem cell-derived endothelial cells from healthy and diet-induced obesity mice

city: Stanford

first: Nicholas

last: Mordwinkin

state: CA

address: 265 Campus Drive, G1105

institute: Stanford University

summary:
Little is known about the function of induced pluripotent stem cell-derived endothelial cells (iPSC-ECs) generated from diabetics, as this could potentially limit subsequent therapeutic use in this patient population.
Here, we demonstrate that iPSC-ECs derived from diet-induced obesity (DIO) mice exhibit evidence of endothelial dysfunction. We also observed that mice receiving intramuscular (IM) injections of DIO iPSC-ECs had significantly decreased reperfusion following hindlimb ischemia compared to mice administered with iPSC-ECs from control mice. Hindlimb sections revealed increased muscle atrophy and presence of inflammatory cells in mice receiving iPSC-ECs from DIO mice. When pravastatin was administered to mice receiving DIO iPSC-ECs, a significant increase in reperfusion was observed, which was blunted by co-administration of L-NAME. This study is the first to provide evidence that iPSC-ECs from pre-diabetic mice exhibit signs of endothelial function, and suggest that pravastatin administration may be needed for diabetic patients receiving autologous iPSC-ECs therapy in the clinic.

overall_design: Four samples were analyzed, two from the healthy (control) group and two from the diet-induced obesity group

first: Joseph

last: Wu


title: Suppression of molecular inflammatory pathways by Toll-like Receptor 7, 8, and 9 antagonists in a model of IL-23-induced skin inflammation

status: Public on Jan 21 2014

city: New York

first: Mayte

last: Suarez-Farinas

address: 1425 Madison Ave, L2-70C, Box 1077,

institute: Mount SinaiSchool of Medicine

summary: Psoriasis is a complex inflammatory disease resulting from the activation of T helper (Th) 1 and Th17 cells.  Recent evidence suggests that abnormal activation of Toll-like receptors (TLRs) 7, 8 and 9 contributes to the initiation and maintenance of psoriasis.  We have evaluated the effects of TLR antagonists on the gene expression profile in an IL-23-induced skin inflammation model in mice.  Psoriasis-like skin lesions were induced in C57BL/6 mice by intradermal injection of IL-23 in the dorsum.  Two TLR antagonists were compared: IMO-3100, an antagonist of TLRs 7 and 9, and IMO-8400, an antagonist of TLRs 7, 8 and 9, both of which previously have been shown to reduce epidermal hyperplasia in this model.  Skin gene expression profiles of IL-23-induced inflammation were compared with or without TLR antagonist treatment.  IL-23 injection resulted in alteration of 5100 gene probes (fold change ≥ 2, FDR < 0.05) including IL-17 pathways that are up-regulated in psoriasis vulgaris.   Targeting TLRs 7, 8 and 9 with IMO-8400 resulted in modulation of more than 2300 mRNAs while targeting TLRs 7 and 9 with IMO-3100 resulted in modulation of more than 1900 mRNAs.  Both agents strongly decreased IL-17A expression (>12-fold reduction), normalized IL-17 induced genes such as beta-defensin and CXCL1, and normalized aberrant expression of keratin 16 (indicating epidermal hyperplasia). These results suggest that IL-23-driven inflammation in mouse skin may be dependent on signaling mediated by TLRs 7, 8, and 9 and that these receptors represent novel therapeutic targets in psoriasis vulgaris and other diseases with similar pathophysiology.

overall_design: Expression profiles for  mice with IL23-induced phenotype (psoriasisform) at baseline and after treatment with two doses of TLR7/8/9 antagonist and saline. Samples for nomal mice are also available

first: James

last: Krueger

last: Suárez-Fariñas

first: Robert

last: Arbeit


title: Expression data from MYCN transgenic mice

city: Nagoya

first: Yuko

last: Murakami-Tonami

address: 1-1 Kanokoden, Chikusa-ku

institute: Aichi Cancer Center

summary:
TH-MYCN transgenic (Tg) mice are the model for neuroblastoma. One of the sympathetic ganglia is the origin of neuroblastoma in those mice. The tumor incidences of homozygotes and hemizygotes are 100% and 70-80%, respectively.
The involvement of midkine (Mdk), a tumor-related growth factor, was also examined by knockout mice.

overall_design: Ganglia and tumor tissues were dissected from several genotypes of mice (MYCN Tg homozygote and hemizygote, knockout (KO) of Mdk gene). In some of cases, we cultured neurosphere and tumorsphere. The mRNA extracted from those samples were subjected to Affymetrix microarrays.

first: Hitoshi

last: Ichikawa

first: Satoshi

last: Kishida


title: Gene expression data of postnatal Pitx2 deficient heart

city: Houston

first: Min

last: Zhang

state: Texas

address: One Baylor Plaza Room 504E

department: Department of Molecular Physiology

institute: Baylor College of Medicine

summary:
Pitx2 is the homeobox gene located in proximity to the human 4q25 familial atrial fibrillation locus. Pitx2 haploinsufficient mice are prone to pacing induced atrial fibrillation indicating that reduced Pitx2 promotes an arrhythmogenic substrate within the atrium. Here, we inactivated Pitx2 in postnatal heart and discovered that unstressed adult Pitx2 mutant mice had sinus node dysfunction with impaired atrial conduction, an arrhythmia closely associated with atrial fibrillation.
A genome-wide search for Pitx2 transcriptional targets using ChIP-sequencing and RNA expression profiling shows that Pitx2 represses target genes encoding cell junction proteins, ion channels, and critical transcriptional regulators many of which have been implicated in human atrial fibrillation by genome wide association studies.

overall_design: Pitx2 control and mutant hearts were collected from 3-, 6- and 12-week-old mice. At each time point, three cotrols and three mutants were collected as biological replicates. cDNA microarray analysis was performed using Affymetrix GeneChip Mouse Genome 430 2.0 Array (Affymetrix, Santa Clara, CA).

first: M

first: J

last: Martin


title: Expression data of BRCA1 shRNA and PTEN shRNA single knockdown, BRCA1_PTEN shRNA double knockdowns and control shRNA in MCF-10A cells

first: Chun-Jen

middle: Curtis

last: Lin

address: 7345 Fannin Street

department: Systems Biology

institute: University of Texas MD Anderson Cancer Center

summary: Homologous recombination-mediated DNA repair deficiency (HRD) predisposes to cancer development, but also provides therapeutic opportunities. Here, we identified an HRD gene signature that robustly predicted HRD status. Unexpectedly, concurrent loss of PTEN in BRCA1-deficient cells might extensively rewire the HR repair network and confer resistance to PARP inhibitor, partially through over-expression of TTK. We used the HRD gene signature as a drug discovery tool and found several PARP-inhibitor-synergizing agents through the connectivity map. Thus gene expression profiling can be used to define the functional status of the HR repair network providing prognostic and therapeutic information.

overall_design:
Various shRNAs that target genes involved in homologous recombination (HR) were transfected in MCF-10A non-transformed breast cells lines. Stable HR gene knockdown MCF-10A cells were seeded 200000 at 10 cm plate. Cells were harvested after 48 hours culturing and used for gene expression profiling.

The shRNAs that target PTEN or BRCA1 genes were transfected in MCF-10A non-transformed breast cell line by lentiviral particles to generate either single gene knockdown or double gene knockdown. Stable BRCA1, PTEN, and BRCA1_PTEN MCF-10A cells were selected. Scrambled control shRNA-transfected MCF-10A cells were applying as control.  All knockdown and control MCF-10A cells were seeded with 2 x 10^5 cells at 10 cm culture plate. Cells were cultured in MCF-10A medium and harvested after 48 hours culturing.  mRNA was extracted from collected cells and performing gene expression profiling. Three or four biological replicates were applied. Four biological replicates were applied.

first: Guang

last: Peng

first: Curtis

first: Wei

last: Mo

first: Hui

last: Dai

first: Yun-Yong

last: Park

first: Soo-Mi

last: Kim

first: Qianxing

first: Yang

first: Stefan

last: Siwko

first: Ruozhen

last: Hu

first: Ju-Seog

last: Lee

first: Bryan

last: Hennessy

first: Samir

last: Hanash

first: Gordon

last: Mills

first: Shiaw-Yih


title: Mouse model of severe asthma: ovalbumin challenge

status: Public on Feb 02 2014

first: Alex

last: Morgan

address: 251 Campus Drive, MSOB X-215

department: Biomedical Informatics

institute: Stanford Medical School

summary: Mouse lung samples from mice challenged with OVA or PBS control.  Wildtype (B6) mice were tested, as well as mast cell deficient mice with engraftment of normal mast cells and mast cells deficient in IgE or Ifn-gamma signaling.

overall_design: Treatment/Control

first: Alexander


title: Effects of sodium tungstate administration in Irs2 -/- mice

status: Public on Jan 19 2014

city: BArcelona

first: Joana

last: Oliveira

address: Rosselló

institute: Idibaps

summary: Relative beta cell deficit and increased beta cell apoptosis are hallmarks of type 2 diabetes (T2D). The Insulin/Insulin Growth Factor (Igf) signaling pathway is an established regulator of beta cell survival and is found downregulated in human T2D islets. The Insulin Receptor Substrate 2 (Irs2) plays a central role in the coordination of this pathway in beta cells. Thus, Irs2 knockout mice (Irs2 -/-) exhibit increased beta cell apoptosis that leads to a progressive decline of beta cell mass and hyperglycaemia. In this study, we sought to determine whether the anti-diabetic compound sodium tungstate could prevent the onset of diabetes in Irs2 -/- mice. Oral administration of tungstate resulted in an overall improvement in whole-body glucose tolerance in Irs2 -/- mice which correlated with increased beta cell mass. Enhanced beta cell mass was due to a dramatic reduction of beta cell apoptosis without changes in proliferation. Whole genome gene profiling analysis of islets isolated from treated Irs2 -/- mice confirmed a broad impact of tungstate on cell death pathways. Mechanistically, tungstate induced Erk1/2 phosphorylation in islets in vitro and, in agreement, treated Irs2 -/- islets exhibited increased basal Erk1/2 phosphorylation. Tungstate also downregulated expression of apoptosis-related genes in Irs2-/- islets in vitro, uncovering a direct effect of this compound in islets. All together, our data demonstrate that tungstate can restore beta cell mass and glucose homeostasis in a context of deficient Insulin/Igf signaling. This study underscores the importance of developing strategies specifically designed to arrest beta cell apoptosis as a means to prevent progressive beta cell failure in diabetes.

overall_design: 10-week old WT and Irs2 -/- mice were randomly divided into two treatment group, in a total of 4 experimental groups. For 21 days one group received distilled water as drinking water (untreated group) whilst the other received ad libitum a solution of 2mg/ml of sodium tungstate in distilled water (treated group). For each experimental group 2 independent samples were analysed, in a total of 8 samples.

first: Sandra

last: Rebuffat

first: Gomis

last: Ramon

first: Gasa

last: Rosa


title: Expression data from mouse limb tendon cells during development.

status: Public on Jan 18 2014

city: Paris

first: Delphine

last: Duprez

address: 9, Quai Saint Bernard

institute: CNRS/UPMC

summary:
We have undertaken a screen of mouse limb tendon cells in order to identify molecular pathways involved in tendon development. Mouse limb tendon cells were isolated based on Scleraxis (Scx) expression at different stages of development: E11.5, E12.5 and E14.5
Microarray comparisons were carried out between tendon progenitor and differentiated stages.

overall_design: Forelimbs from E11.5, E12.5 and E14.5 Scx-GFP embryos were collected and dissociated with trypsin to obtain cell suspensions. Scx-positive tendon cells were isolated by FACS. RNA was extracted and Fragmented biotin-labelled cRNA samples were hybridized on Affymetrix Gene Chip Mouse Genome 430 2.0 arrays.

first: Séverine

last: Croze

first: Joël

last: Lachuer

first: Nicolas

last: Nazaret


title: Expression data from Sin3Bp+/-KRaspG12D and Sin3Bp-/-KRaspG12D pancreata and from cultured primary pancreatic duct epithelial cells (PDEC) of the same genotype.

city: New York City

first: Richard

last: Graveline

address: 550 1st ave - Medical Science Building, Room 417

department: Biochemistry and molecular Pharmacology

institute: NYU Langone Medical center

summary:
Pancreatic ductal adenocarcinoma (PDAC) is strikingly resistant to conventional approaches. In this study, we report that the histone deacetylase associated SIN3B protein is required for activated KRAS-induced senescence in vivo using a mouse model of pancreatic cancer.
We used microarray data to determine if SIN3B regulates KRAS-induced expression of the inflammatory response.

overall_design: Total RNA from Sin3Bp+/-KRaspG12D and Sin3Bp-/-KRaspG12D pancreas (two pancreata for each genotype) or PDEC (one for each genotype) was extracted and hybridized on Affymtrix microarrays.

first: Gregory

last: David


title: Expression data from primary osteoblasts isolated from calvaria of Gnptab(c.3082insC) knock-in mice compared with osteoblasts isolated from wild-type littermates

status: Public on Jan 29 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:
Mucolipidosis type II (MLII) is a severe inherited multisystemic disorder caused by mutations in the GNPTAB gene. Skeletal abnormalities are a predominant feature of MLII. Here we investigate the gene expression in a knock-in mouse model for mucolipidosis type II, generated by the insertion of a cytosine in the murine Gnptab gene (c.3082insC) that is homologous to a homozygous mutation in an MLII patient.
Since osteoblasts are critically involved in regulating bone development and remodeling, a genome-wide expression analysis was performed  with RNA isolated from primary cultures of osteoblasts originating from MLII knock-in mice (KI) compared to RNA from wild-type (WT) osteoblasts to identify dysregulated genes involved in pathogenic mechanisms.

overall_design: Primary osteoblasts were isolated from calvaria of 5-day-old wild-type (WT) and MLII knock-in littermates (KI). RNA was extracted at day 10 of differentiation induced by ascorbic acid and beta-glycerophosphate and hybridization on Affymetrix microarrays. We used preparations of RNA from two individual primary cultures of osteoblasts for every genotype (WT_OB_I, WT_OB_II, KI_OB_I, KI_OB_II) and compared WT vs KI samples.

first: Katrin

last: Kollmann

first: Jan

last: Pestka

first: Kristin

last: Klätsche

first: Benjamin

last: Otto

last: Braulke

first: Thorsten

last: Schinke


title: High Runx1 levels promote a reversible more differentiated cell-state in hair follicle stem cells during quiescence

status: Public on Jan 15 2014

city: Ithaca

first: Tudorita

last: Tumbar

address: 260 Biotechnology Building

department: Molecular Biology & Genetics

institute: Cornell University

summary: Quiescent hair follicle (HF) bulge stem cells (SCs) differentiate to early progenitor (EP) hair germ (HG) cells, which divide to produce transit-amplifying (TA) matrix cells. EPs can revert to SCs upon injury, but whether this de-differentiation occurs in normal HF homeostasis (hair cycle), and the mechanisms regulating both differentiation and de-differentiation are unclear. Here we use lineage tracing, gain of function, transcriptional profiling, and functional assays to examine the role of observed endogenous Runx1 level changes in the hair cycle. We find that forced Runx1 expression implements hair degeneration (catagen) and simultaneously promotes changes in the quiescent bulge SC transcriptome towards a cell-state resembling the EP HG fate. This cell-state transition is functionally reversible. We propose that SC differentiation and de-differentiation are likely to occur during normal HF degeneration and niche restructuring in response to changes in endogenous Runx1 levels associated with SC location with respect to the niche.

overall_design: Freshly isolated skin cells were FACS sorted based on K15-GFP+/a6-integrin+/CD34- as hair germ and K15-GFP+/a6-integrin+/CD34+ bulge cells. Duplicate samlpes from mice at PD20 that showed telogen morphology throughout skin were used for RNA prepartion and Affymetrix analysis. Wild and transgenic samples after 1-day of doxycycline treatement were compared.

first: Song

middle: E

last: Lee

first: Aiko

last: Sada


title: Lsd1 coordinates trophoblast development by retaining stem cells in their niche and directing cell fate

status: Public on Jan 17 2014

city: Freiburg

last: Günther

address: Breisacherstr. 66

department: Central Clinical Research

institute: Freiburg University Medical Center

summary:
Stem cells reside in specific niches providing stemness-maintaining environments. Thus, the regulated migration from these niches is associated with differentiation onset. However, mechanisms retaining stem cells in their niche remain poorly understood. Here, we show that the epigenetic regulator lysine-specific demethylase 1 (Lsd1) organises the trophoblast niche of the early mouse embryo by coordinating migration and invasion of trophoblast stem cells (TSCs). Lsd1 deficiency leads to the depletion of the stem cell pool resulting from precocious migration of TSCs.

Migration is induced by premature expression of the transcription factor Ovol2 that is repressed by Lsd1 in undifferentiated wild-type TSCs. Increasing Ovol2 levels suffices to recapitulate the migration phenotype. Furthermore, Lsd1-deficient TSCs exhibit a developmental bias towards cells of the syncytiotrophoblast and impaired spongiotrophoblast and trophoblast giant cell differentiation. In summary, we describe that the epigenetic modifier Lsd1 coordinates placental development by retaining TSCs in their niche and directing trophoblast differentiation.

overall_design: Mouse trophoblast stem cells (TSCs) were isoloated from a single conditional Lsd1-deficient mouse (Lsd1tm1Schüle). Deletion of Lsd1 was induced eight days before the collection of RNA by addition of 0.2 µM 4OH-tamoxife. Cells were isolated at successive stages of differentiation for total RNA extraction and hybridization on Affymetrix microarrays. To that end, we harvested cells at three time-points: before induction of differentiation (d0), two days after induction of differentiation (d2), and four days after induction of differentiation (d4). Three replicates (1, 2, 3) for control (-) and Lsd1-deficeint (+) cells were included for each differentiation stage.

first: Stefanie

last: Hölz

first: Roland

last: Schüle