title: Distinct Early Molecular Responses to Mutations Causing vLINCL and JNCL Presage ATP Synthase Subunit c Accumulation in Cerebellar Cells

city: Boston

first: Susan

last: Cotman

address: 185 Cambridge Street

institute: MGH

summary: Variant late-infantile (vLINCL) and juvenile neuronal ceroid lipofuscinosis (JNCL) share clinical and pathological features, including lysosomal accumulation of mitochondrial ATP synthase subunit c, but the unrelated CLN6 and CLN3 genes may initiate disease via similar or distinct cellular processes. To gain insight into the NCL pathways, we established murine wild-type and vLINCL CbCln6nclf cerebellar cells and compared them to wild-type and JNCL CbCln3∆ex7/8 cerebellar cells. CbCln6nclf/nclf cells and CbCln3∆ex7/8/∆ex7/8 cells both displayed abnormally elongated mitochondria and reduced cellular ATP levels and, as cells aged to confluence, exhibited accumulation of subunit c protein in Lamp 1-positive organelles. However, at sub-confluence, endoplasmic reticulum PDI immunostain was decreased only in CbCln6nclf/nclf cells, while fluid-phase endocytosis and LysoTracker labeled vesicles were decreased in both CbCln6nclf/nclf and CbCln3∆ex7/8/∆ex7/8 cells, though only the latter cells exhibited abnormal vesicle subcellular distribution. Furthermore, unbiased gene expression analyses revealed only partial overlap in the cerebellar cell genes and pathways that were altered by the Cln3∆ex7/8 and Cln6nclf mutations. Thus, these data support the hypothesis that vLINCL and JNCL mutations trigger distinct processes that converge on a shared pathway, which is responsible for proper subunit c protein turnover and neuronal cell survival.

overall_design: Genotype comparison. 3 replicates each of CD1 wild-type cells, CD1 Cln3 mutant cells, C57BL6 wild-type cells, and C57BL6 Cln6 mutant cells.


title: Conversion of murine extraembryonic trophoblast stem cells into induced pluripotent stem cells

status: Public on Feb 01 2011

city: Bonn

first: Peter

last: Kuckenberg

address: Sigmund Freud Str. 25

department: Institut of Pathology

country: Germany

institute: University Medical School Bonn

summary: Extraembryonic trophoblast stem cells (TSC) can be converted to induced pluripotent stem cells (TSC-iPSCs) by overexpressing Oct4, Sox2, Klf4 and cMyc.

overall_design: TSC lines were derived from mice harboring a doxycycline inducible Oct4 allele and an Oct4-GFP reporter that has been demonstrated to be activated in cells upon acquisition of pluripotency. Oct4-GFP-positive blastocysts were collected at 3.5 dpc and transduced with lentiviruses encoding doxycycline inducible Sox2, Klf4 and cMyc transgenes (4FTSC). 4FTSC lines were passaged 10 times to establish a population of constantly growing, self-renewing TSCs in the presence of FGF4 and fibroblast conditioned media. To induce lineage conversion, 4FTSCs were cultured under ESC/Lif conditions and doxycycline. After 28 days, several colonies displaying ESC-characteristic dome-shaped colony morphology and bright Oct4-GFP fluorescence could be detected. The 4FTSC-derived colonies were isolated mechanically, dissociated by trypsinization, and plated onto MEFs in ESC medium without doxycycline demonstrating the independence of exogenous factors. They will be called TSC-iPSCs (Trophoblast stem cell derived induced pluripotent stem cells). To examine if the extraembryonic lineage-specific mRNA profile was overcome, the gene-expression profiles of TSC-iPSCs and their parental 4FTSCs were analyzed by microarray analyses and compared to control ESCs.

first: Hubert

last: Schorle


title: Comprehensive proteomic and transcriptomic characterization of hepatic expression signatures affected in p14 liver conditional knockout mice

city: Bolzano

first: Johannes

last: Rainer

address: Via A. Volta 21

department: Institute for Biomedicine

country: Italy

institute: Eurac Researc

summary:
Scaffold proteins regulate intracellular MAP kinase signaling by providing critical spatial and temporal specificity. We have shown previously that the scaffold protein MEK1 partner (MP1) is localized to late endosomes by the adaptor protein p14. Using conditional gene disruption of p14 in livers of mice we analysed protein and transcript signatures in tissue samples. Further biological network analysis predicted that the differentially expressed transcripts and proteins are involved in cell cycle progression and regulation of cellular proliferation. Although some of the here identified signatures were previously linked to phospho-ERK activity, most of them were novel targets of late endosomal p14/MP1/MEK/ERK signaling module. Finally, the proliferation defect was confirmed in a chemically induced liver regeneration model in p14 liver knock-out mice.
Conditional liver p14 KO mice were generated by mating p14 f/f mice with mice expressing Cre recombinase under control of Alb promoter and alpha-fetoprotein enhancer. The obtained p14 floxed/floxed;AlfpCre(p14 liver KO) mice were used in experiments as KO mice. To prevent the influence of AlfpCre transgene we used p14 +/+;AlfpCre mice as a control. All mice were derived in a C57BL/6 background and were six weeks old.

overall_design: Expression profiles of KO mouse samples were compared to expression profiles of corresponding control mice and differentially expressed genes were identified.

first: Ivan

last: Prokudin

first: Taras

last: Stasyk

first: Guenther

middle: K

last: Bonn

first: Reinhard

last: Kofler

first: Lukas

middle: A

last: Huber


title: Expression data from murine cell line transduced with epitope tagged forms of Hoxa9

city: Ann Arbor

first: Jay

last: Hess

state: MI

address: 1301 Catherine

department: Pathology

country: USA

institute: University of Michigan

summary:
Importantly increasing evidence shows that Hox genes such as Hoxa9 are key regulators of stem cell self-renewal and hematopoiesis. Hoxa9 is expressed in early hematopoietic progenitor cells and promotes stem cell expansion. In contrast Hoxa9 down regulation is associated with hematopoietic differentiation. In addition to its role in development, HOXA9 has been intensively studied because of its central role in human acute leukemias. Despite their obvious biomedical importance, the mechanisms through which Hoxa9 and its partner proteins exert their downstream functions are poorly understood.
Using whole-genome gene expression profiling, we identified direct targets of Hoxa9 in murine MHPs after 4-OHT withdraw, resulting in cell differentiation.

overall_design: Bone marrow cells were harvested from 5-Fluorouracil treated female 6-8 week old C57BL/6 mice and transduced with an MSCV-based retrovirus expressing Hoxa9 fused to a modified estrogen receptor ligand binding domain (Hoxa9-ER).  Hoxa9-ER cells were washed 3x and resuspended in IL-3+ media with/without 100 nM 4-OHT (Sigma).  At selected intervals, cells were removed for flow cytometric analysis using anti-Gr1 and anti-Mac1 antibodies (BD biosciences), morphologic assessment by cytocentrifugation and staining with Diff-Quick reagents (Intl. Med. Equip.), and RNA collection.  For RNA, Pellets were lysed in Trizol reagent (Invitrogen) and RNA was extracted following manufacturer's instructions until phase separation, after which RNeasy columns (Qiagen) were employed for further purification. cRNA probes were synthesized at the University of Michigan microarray core.  Probes were hybridized to Affymetrix Mouse 430 2.0 array.


title: Identification and validation of gene expression changes upon removal of Dicer in the murine limb mesenchyme

status: Public on Jan 31 2011

city: Gainesville

first: M Cecilia

last: Lopez

state: FL

address: 1376 Mowry Road

department: Molecular Genetics and Microbiology

institute: University of Florida

summary:
Wild type and Dicer null embryonic mouse limbs were analaysed using Affymetrix arrays to identify gene expression changes. Genes that were up-regulated in Dicer-null limbs were canidates for being miRNA targets.
Potential miRNA target genes were validated using qRTPCR.

overall_design: Mice carrying a heterozygous Dicer floxed allele and the prxcre driver allele were crossed to homozygous Dicer Floxed mice. Embryos were harvested from pregent moms and genotyped to determine heterozygous, Wild type and mutant limb buds. These limb buds were used to prepare RNA for array analysis.

first: Danielle

middle: M

last: Maatouk

first: Roger

middle: B

last: Gaskins III

first: Jason

middle: R

last: O'Rourke

first: Maurice

middle: S

last: Swanson

first: M

middle: C

first: Michael

middle: T

last: McManus

first: Henry

middle: V

last: Baker

first: Brian

middle: D

last: Harfe


title: lin-35(n745) mutants vs. wild type

status: Public on Jan 25 2011

city: Santa Cruz

first: Susan

last: Strome

state: CA

address: 1156 High St

department: MCD Biology

institute: UC Santa Cruz

summary: Transcriptional profiling of C. elegans first larval stage whole animals comparing lin-35(n745) mutants and N2 (wild type) at 26 degrees.

overall_design: One-condition experiment, mutant (lin-35) vs. WT.  Biological replicates 4 mutant, 4 wildtype harvested indepedently.  One lin-35 replicate and one WT replicate per array.

first: Wenchao

last: Wang

first: Lisa

middle: N

last: Petrella

first: Caroline

last: Spike

first: Andreas

last: Rechsteiner

first: Valerie

last: Reinke


title: Comparative transcriptomic analysis of BA- or BL-

status: Public on Jan 27 2011

city: Tsuruoka

first: Shinji

last: Fukuda

state: Yamagata

address: 246-2 Mizukami, Kakuganji

department: Institute for Advanced Biosciences

country: Japan

institute: Keio University

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

overall_design: Refer to individual Series


title: Comparative gene expression of mouse Pancreatic specific transcription factor 1a (Ptf1a/p48) in pancreatic progenitor cells

status: Public on Jan 24 2011

city: Copenhagen N

first: Anne

last: Grapin-Botton

address: Blegdamsvej3 B

department: DanStem

country: Denmark

institute: University of Copenhagen

summary:
Ptf1a was identified as the essential transcription factor which controls pancreatic exocrine enzyme expression. With lineage tracing eperiments Ptf1a was recognized as an important pancreatic progenitor transcription factor and Ptf1a null mice do not develop a pancreas.
We used gene expression arrays to determine the global differeences in expression levels when pancreatic progenitor cells are expanding in Ptf1a heterozygote versus null mutants at E10.5.

overall_design: Ptf1a E10.5 dorsal pancreas total RNA from pools of 3 embryos was twice linear amplified and hybridized to Affymetrix GeneChip Mouse Genome 430 2.0 in triplicate for the Ptf1a KO and in duplicate for the Ptf1a heterozygote

first: Nancy

last: Thompson


title: Direct Cell Conversion of Human Fibroblasts to Monocytic phagocytes by Forced Expression of Monocytic Regulatory Network Elements

status: Public on Feb 15 2011

city: Yokohama

first: Takahiro

last: Suzuki

state: Kanagawa

address: 1-7-22 Suehiro-cho, Tsurumi-ku

department: Center for Integrative Medical Sciences

institute: RIKEN

summary: Direct cell conversion is now expected to apply to therapeutic purposes. Although that has been succeeded in several cell types, the mechanism or general way to identify the key transcription factors are still unclear. In addition, most of the cases are not completely identical with the target cells. In previous work, we suggested that cell status is maintained by a homeostatic network of limited number of TFs and no single transcription factor is both necessary and sufficient to drive the differentiation process. Here, identifying the key TFs of human monocyte by combining comparative gene expression analysis and literature based text-mining, we mimicked the monocytic regulatory network in human dermal fibroblasts to induce direct cell conversion of the fibroblasts to monocytes. We suggested that although it is a primary master TF, single TF is not sufficient to induce the direct cell conversion and orchestrated TF regulation is necessary to complete the cell conversion.

overall_design: Total RNA obtained from human dermal fibroblasts(FIB), human CD14+ monocytes(MON), mock lentivirus vector transduced fibroblasts (FIB-mock), SPI1 transduced fibroblasts (FIB-SPI1), and SPI1, CEBPA, MNDA, IRF8 transduced fibroblasts(FIB-4Fs). The fold change was computed compared with fibroblasts or FIB-mock.

first: Mika

last: Nakano-Ikegaya

first: Haruka

last: Yabukami-Okuda

first: Ayumi

last: Ogawa

first: Harukazu

first: Yoshihide

last: Hayashizaki


title: lin-15B(n744) mutants vs. wild type

summary: Transcriptional profiling of C. elegans first larval stage whole animals comparing lin-15B(n744) mutants and N2 (wild type) at 26 degrees.

overall_design: One-condition experiment, mutant (lin-15B) vs. WT.  Biological replicates 4 mutant, 4 wildtype harvested indepedently.  One lin-35 replicate and one WT replicate per array.


title: Transcriptomic response of murine liver to severe injury and hemorrhagic shock

city: Pittsburgh

first: Joyeeta

last: Dutta-Moscato

state: PA

address: 450 Technology Drive, Suite 300

department: Surgery

institute: University of Pittsburgh

first: Rebecca

last: Edmonds

first: Yoram

last: Vodovotz

first: Claudio

last: Lagoa

first: Yawching

last: Yang

first: Mitchell

middle: P

last: Fink

first: Ryan

last: Levy

first: Jose

last: Prince

first: David

middle: J

last: Kaczorowski

first: George

last: Tseng

first: Timothy

last: Billiar


title: [E-TABM-482] DNA methylome of human spermatozoa

status: Public on Feb 05 2011

city: Hinxton

first: ArrayExpress

last: EBI

state: Cambridgeshire

address: Wellcome Trust Genome Campus

country: United Kingdom

institute: European Bioinformatics Institute

type: Methylation profiling by high throughput sequencing

summary:
Genome-wide DNA methylation profile of human spermatozoa using the meDIP technique and massively parallel sequencing.
DNA methylation is an indispensible epigenetic modification required for regulating the expression of mammalian genomes. Immunoprecipitation-based methods for DNA methylome analysis are rapidly shifting the bottleneck in this field from data generation to data analysis, necessitating the development of better analytical tools. In particular, an inability to estimate absolute methylation levels remains a major analytical difficulty associated with immunoprecipitation-based DNA methylation profiling. To address this issue, we developed a cross-platform algorithm-Bayesian tool for methylation analysis (Batman)-for analyzing methylated DNA immunoprecipitation (MeDIP) profiles generated using oligonucleotide arrays (MeDIP-chip) or next-generation sequencing (MeDIP-seq). We developed the latter approach to provide a high-resolution whole-genome DNA methylation profile (DNA methylome) of a mammalian genome. Strong correlation of our data, obtained using mature human spermatozoa, with those obtained using bisulfite sequencing suggest that combining MeDIP-seq or MeDIP-chip with Batman provides a robust, quantitative and cost-effective functional genomic strategy for elucidating the function of DNA methylation.

ArrayExpress Release Date: 2008-06-10

Publication Title: A Bayesian deconvolution strategy for immunoprecipitation-based DNA methylome analysis
Publication Author List: Thomas A Down; Vardhman K Rakyan; Daniel J Turner; Paul Flicek; Heng Li; Eugene Kulesha; Stefan GrÃ¤f; Nathan Johnson; Javier Herrero; Eleni M Tomazou; Natalie P Thorne; Liselotte BÃ¤ckdahl; Marlis Herberth; Kevin L Howe; David K Jackson; Marcos M Miretti; John C Marioni; Ewan Birney; Tim J P Hubbard; Richard Durbin; Simon TavarÃ©; Stephan Beck

Person Roles: submitter; investigator
Person Last Name: Flicek
Person First Name: Paul
Person Mid Initial
Person Email: flicek@ebi.ac.uk
Person Address: Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SD, UK
Person Affiliation: European Bioinformatics Institute

overall_design:
Experimental Design: high_throughput_sequencing_design
Experimental Factor Name: CELLTYPE
Experimental Factor Type: cell_type


title: Comparative transcriptomic analysis of BA- or BL- associated murine colonic epithelium

first: Shinji

last: Fukuda

summary: A huge number of microorganisms are colonized in human gut and the balance of their composition is closely related to human health. Recently, many probiotics such as bifidobacteria or lactobacilli have been introduced in our life as effective agents. However, we have not well understood their beneficial mechanisms including host-bacterial crosstalk To analyze the differences of gene expression between BA- or BL-associated murine colonic epithelium, we performed comparative transcriptomic analysis.

overall_design:
Bifidobacterium adolescentis (BA)-associated mice and Bifidobacterium longum (BL)-associated mice were used. Colonic epithelium was isolated and gene expression profile was analyzed.
Each 3 samples were analyzed.

first: Kikuji

last: Itoh

first: Hiroshi

last: Ohno


title: Development of gene expression signatures for breast cancer stem cells (SP cells)

status: Public on Jan 19 2011

city: shanghai

first: m

middle: jing

last: zi

address: libing Rd

country: China

institute: southgene

summary: To further compare gene expression profile between breast cancer stem cells (SP cells) and non-SP cells, we have employed illumina GEX microarray as a discovery platform to identify gene differential expression between SP with non-SP cells.

overall_design: SP analysis and sorting were done using a FACSVantage SE.The breast cancer cells were sorted into SP and non-SP cells.Total RNA was isolated from the FACS-sorted SP or non-SP cells, and gene expression signiture was detected by microarray.

first: Hongxia

last: Wang

first: Fengchun

last: Zhang

first: Mingzhu

last: Huang


title: Expression data from primary mammary epithelial cells expressing ectopic p190B RhoGAP

status: Public on Jan 22 2011

city: South Bend

first: Tracy

last: Vargo-Gogola

state: IN

address: 1234 Notre Dame Avenue

department: Biochemistry and Molecular Biology

institute: Indiana University School of Medicine

summary: P190B RhoGAP is required for mammary gland development, and its overexpression disrupts mammary gland branching morphogenesis.  To better understand the mechanisms by which p190B regulates mammary gland development we performed gene expression microarray analysis on mammary epithelial cells isolated from p190B overexpressing transgenic mice compared to control mice.

overall_design: The mice used in this study were previously developed to inducibly overexpress p190B selectively in the mammary gland (Vargo-Gogola 2006). FVB/N mice carrying the MMTV-rtTA and TetO-p190B-IRES-luciferase transgenes or the MMTV-rtTA transgene only (Gunther EJ, FASEB) were fed doxycycline (Dox) chow (2 g/kg) for 7 d prior to removal of mammary glands and isolation of primary mammary epithelial cells at 6 weeks of age.

first: Peter

last: McHenry


title: Transcriptomic response of murine liver to severe injury and hemorrhagic shock: Affymetrix portion of dual platform

first: Joyeeta

last: Dutta-Moscato

summary: A dual platform microarray analysis was used to characterize the temporal transcriptomic response in the mouse liver following trauma and hemmorhagic shock

overall_design: Mice were divided into five groups, anesthetized and surgically treated to simulate a time course and trauma severity model: non-manipulated animals (C), minor trauma (MT), 1.5 hour of hemorrhagic shock and severe trauma (HS/T), 1.5 hour HS/T followed by 1 hour resuscitation (HS/T+1.0R), 1.5 hour HS/T followed by 4.5 hours resuscitation (HS/T+4.5R)

first: Rebecca

last: Edmonds

first: Yoram

last: Vodovotz

first: Claudio

last: Lagoa

first: Yawching

last: Yang


title: Key roles for SRF in embryonic epidermal differentiation

status: Public on Jan 20 2011

city: New York

first: Agnes

last: Viale

state: NY

address: 1275 York Avenue

department: Molecular Biology

institute: Memorial Sloan Kettering Cancer Center

summary: During development, a polarized sheet of epidermal cells undergoes stratification and differentiation to produce the skin barrier. Through mechanisms poorly understood, the process involves adhesion and Notch signaling. To elucidate how epidermal embryogenesis is governed, we conditionally targeted transcription factor serum response factor (SRF), which has been shown to be essential for proper epidermal differentiation in vitro and in vivo. Seeking mechanism, we identified actomyosin-related genes as well-known SRF targets downregulated shortly after ablation. We show that this results in a diminished cortical actomyosin network which fails to regulate the transition of cells from the basal proliferative layer to the suprabasal differentiating layer resulting in an inability of cells to properly execute stratification and differentiation.

overall_design: FACS purification of basal epidermal cells from E16.5 SRF fl/fl ROSA26 YFP fl/fl  K14-Cre (cKO) or SRF fl/+ ROSA26 YFP fl/fl  K14-Cre (WT) was performed on a FACS Vantage SE system equipped with FACS DiVa software (BD Biosciences). Cells were gated for single events and viability and then sorted according to α6 integrin-PE expression and YFP.

first: Chen

last: Luxemburg

first: Amalia

last: Pasolli

first: Scott

last: Williams

first: Elaine

last: Fuchs


title: Selenium toxicity but not deficient or super-nutritional selenium status vastly alters the transcriptome in rodents

city: Madison

first: Roger

last: Sunde

state: WI

address: 1415 Linden Dr

department: Nutritional Sciences

institute: University of Wisconsin

summary:
Protein and mRNA levels for several selenoproteins, such as glutathione peroxidase-1 (Gpx1), are down-regulated dramatically by selenium (Se) deficiency.
Selenoprotein levels in rats increase sigmoidally with increasing dietary Se and reach defined plateaus at the Se requirement, making them sensitive biomarkers for Se deficiency, but not high for Se status.  Biomarkers for high Se status are needed as super-nutritional Se intakes are associated with beneficial and adverse health outcomes, but conventional biomarkers are not especially useful above the Se requirement.  To characterize Se regulation of the transcriptome, we conducted 3 microarray experiments in weanling mice and rats fed Se-deficient diets supplemented with levels of Se up to 5 µg Se/g diet.

sample_organism:
Mus musculus
Rattus norvegicus

platform_organism:
Mus musculus
Rattus norvegicus

overall_design: Rats or mice were fed Se-deficient diets supplemented with sodium selenite up to 5 ug Se/g diet for 28 or 35 days.  Affymetrix Rat 230 2.0 and Mouse 430 2.0 Genome Arrays were used to analyze gene expression in liver in all studies plus kidney in the mouse study.

first: Anna

last: Raines


title: Transcriptomic profiling of Cop1-deficient embryos

status: Public on Jan 13 2011

city: Leuven

first: Rekin's

last: Janky

address: Herestraat 49 Box 816

department: Nucleomics Core

country: Belgium

institute: VIB

summary: In order to assess the physiological role of Cop1 in vivo we generated mice that do no longer express the protein. Cop1KO mice die at around E10.5 of embryonic development. In order to gain insights into the molecular mechanisms that cause the embryonic death we compared the genome-wide gene expression profile of E9.5 wild-tytpe and Cop1-null embryos. The data do not support a role for Cop1 in the regulation of the p53 pathway in vivo and highlight a role for Cop1 in cardiovascular development and/or angiogenesis. The abstract of the associated publication is as follows:Biochemical data have suggested conflicting roles for the E3 ubiquitin ligase Cop1 in tumourigenesis. Here we present the first in vivo investigation of the role of Cop1 in cancer aetiology. We used an innovative genetic approach to generate an allelic series of Cop1 and show that Cop1 hypomorphic mice spontaneously develop malignancy at a high frequency in their first year of life and are highly susceptible to radiation-induced lymphomagenesis. Biochemically, we show that Cop1 regulates c-Jun oncoprotein stability and modulates c-Jun/AP1 transcriptional activity in vivo. Cop1-deficiency stimulates cell proliferation in a c-Jun-dependent manner. We conclude that Cop1 is a tumour suppressor that antagonizes c-Jun oncogenic activity in vivo.

overall_design: RNA from 6 different control embryos (+/+ or +/-) were mixed and subdivided into control pool 1 and pool 2. RNA from 6 different Cop-null embryos were mixed and subdivided into KO pool 1 and pool 2.

first: William

last: Skarnes


title: The role of SphK1 in hTNFα induced inflammation

status: Public on Jan 15 2011

city: Charleston

first: DeAnna

last: Baker

state: SC

address: 114 Doughty Street STB #416

department: Medicine

institute: Medical University of South Carolina

summary:
The study analyzes analyzes gene expression changes in the ankle joint in mouse TNFa overexpression models with or without sphingosine kinase 1 activity.
SphK1 is a sphingolipid enzyme that converts sphingosine to bioactive sphingosine-1-phosphate (S1P).  Recent data suggest a potential relationship between SphK1 and TNFα and have implicated SphK1/S1P in the development and progression of inflammation.  Here we further study the relationship of TNFα and SphK1 using an in vivo model.  Transgenic hTNFα mice, which develop a spontaneous arthritis (limited to paws) at 20 weeks, were crossed with SphK1 activity null mice (SphK1-/-) to study the development of inflammatory arthritis in the functional absence of SphK1.  Results show that hTNF/SphK1-/- have significantly less severity and progression of arthritis and bone erosions as measured through micro-CT images.  Additionally, less COX-2 protein, mTNFα transcript levels and fewer Th 17 cells were detected in the joints of hTNF/SphK1-/- compared to hTNF/SphK1+/+ mice.  Microarray analysis of the ankle joint showed that hTNF/SphK1-/- mice have increased transcript levels of IL-6 and SOCS3 compared to hTNF/SphK1+/+ mice.  Finally, fewer mature osteoclasts were detected in the ankle joints of hTNF/SphK1-/- mice compared to hTNF/SphK1+/+ mice.  These data show that SphK1 plays a role in hTNFα induced inflammatory arthritis, potentially through a novel pathway involving IL-6 and SOCS3.

overall_design: Two wild-type replicates; three replicates of human TNFa transgene overexpression and normal sphingosine kinase 1; three replicates of human TNFa transgene overexpression and sphingosine kinase 1 null.

first: Gary

last: Gilkeson


title: Circulating miRNAs as biomarkers and potential functional mediators of early stage breast cancer

status: Public on Jan 16 2011

city: Buffalo

first: hua

last: zhao

address: Elm and Carlton Streets

institute: Roswell Park Cancer Institute

summary: Analysis of the levels of circulating miRNAs from women with early stage breast cancer and matched healthy controls.

overall_design: miRNAs in plasma samples from 20 women with early stage breast cancer (10 Caucasian American and 10 African American) compared with 20 matched healthy controls (10 Caucasian American and 10 African American).

first: H

last: Zhao

first: J

last: Shen

first: L

last: Medico

first: D

last: Wang

first: C

last: Ambrosone

first: S

last: Liu


status: Public on Jan 12 2011

city: Baltimore

first: Luis

middle: Andres

last: Garza

state: MD

address: 1550 Orleans St. Suite 204 CRBII Koch

department: Dermatology

institute: Johns Hopkins School of Medicine

summary:
Mouse back skin was disassociated to single cells, sorted by cell surface markers and tested by microarrray
To compare the gene expression of mouse bulge (CD34+CD200+CD49+) versus secondary hair germ (CD34-CD200+CD49+) versus interfollicular epidermis (CD34-CD200-CD49+)
xx
Bald scalp retains hair follicle stem cells but lacks CD200-rich and CD34-positive hair follicle progenitor cells
Androgenetic alopecia (AGA) or common baldness results from a marked decrease in hair follicle size. This miniaturization may be related to loss of hair follicle stem or progenitor cells. To test this hypothesis, we analyzed bald and non-bald scalp from the same individuals for the presence of hair follicle stem and progenitor cells using flow cytometry to quantitate cells expressing CYTOKERATIN 15 (KRT15), CD200, CD34 and ALPHA-6-INTEGRIN (ITGA6). High levels of KRT15 expression correlated with stem cell properties of small cell size and quiescence. Cells with the highest level of KRT15 expression were maintained in bald scalp; however, distinct populations of CD200high ITGA6high cells and CD34-positive cells were markedly diminished. Consistent with a progenitor cell phenotype, the diminished populations localized closely to the stem-cell rich bulge area but were larger and more proliferative than the bulge stem cells. In functional assays, analogous CD200 high /Itga6 high cells from murine hair follicles were multipotent and generated new hair follicles in skin reconstitution assays. These findings suggest that a defect in stem cell activation plays a role in the pathogenesis of AGA.

overall_design: 4 independent biologic replicates  (each pooled from 3 distinct mice) were sorted for Mouse bulge (CD34+CD200+CD49+) versus secondary hair germ (CD34-CD200+CD49+) versus interfollicular epidermis (CD34-CD200-CD49+)

first: Tailun

last: Zhou

first: Hanz

last: Blat

first: Michelle

last: Lee

first: Hellen

last: He

first: David

last: Stanton

first: Lee

last: Carrasco

first: John

last: Tobias

first: Chao

last: Yang

first: George

last: Cotsarelis


title: Deletion of Scap in Alveolar Type II Cells Influences Lung Lipid Homeostasis and Identifies a Compensatory Role for Pulmonary Lipofibroblasts

status: Public on Jan 08 2011

city: Cincinnati

first: Yan

last: Xu

state: OH

address: 3333 Burnet Ave

institute: Cincinnati Children's Hospital Medical Center

summary: Pulmonary function after birth is dependent upon surfactant lipids that reduce surface tension in the alveoli. The sterol-responsive element-binding proteins (SREBPs) are transcription factors regulating expression of genes controlling lipid homeostasis in many tissues. To identify the role of SREBPs in the lung, we conditionally deleted the SREBP cleavage-activating protein gene, Scap, in respiratory epithelial cells (Scap∆/∆) in vivo. Prior to birth (E18.5), deletion of Scap decreased the expression of both SREBPs and a number of genes regulating fatty acid and cholesterol metabolism. Nevertheless, Scap∆/∆ mice survived postnatally, surfactant and lung tissue lipids being substantially normalized in adult Scap∆/∆ mice. Although phospholipid synthesis was decreased in type II cells from adult Scap∆/∆ mice, lipid storage, synthesis, and transfer by lung lipofibroblasts were increased. mRNA microarray data indicated that SCAP influenced two major gene networks, one regulating lipid metabolism and the other stress-related responses. Deletion of the SCAP/SREBP pathway in respiratory epithelial cells altered lung lipid homeostasis and induced compensatory lipid accumulation and synthesis in lung lipofibroblasts.

overall_design: To identify the role of SREBPs in the lung, we conditionally deleted the SREBP cleavage-activating protein gene, Scap, in respiratory epithelial cells (Scap∆/∆) in vivo.Lung cRNA was hybridized to the murine genome MOE430 V2 chips.

first: Valerie

last: Besnard

first: Susan

middle: E

last: Wert

first: Mildred

last: Stahlman

first: Anthony

last: Postle

first: Machiko

last: Ikegami

first: Jeffrey

last: Whitsett


title: Fibroblast-specific focal adhesion kinase links mechanical force to fibrosis via chemokine-mediated inflammatory pathways

status: Public on Jan 14 2011

city: Stanford

first: Michael

last: Januszyk

address: 257 Campus Dr.

institute: Stanford University

summary: Hypertrophic scar (HTS) formation is characterized by exuberant fibroproliferation for reasons that remain poorly understood1. One important but often overlooked component of wound repair is mechanical force, which regulates reciprocal cell-matrix interactions through focal adhesion components including focal adhesion kinase (FAK)1,2. Here we report that FAK is activated following cutaneous injury and that this activation is potentiated by mechanical loading. Transgenic mice lacking fibroblast-specific FAK exhibit significantly less fibrosis in a preclinical model of HTS formation. Inflammatory pathways involving monocyte chemoattractant protein-1 (MCP-1), a chemokine highly implicated in human skin fibrosis3, are triggered following FAK activation, mechanistically linking physical force to fibrosis. Further, small molecule inhibition of FAK effectively abrogates fibroproliferative mechanisms in human cells and significantly reduces scar formation in vivo. Collectively, these findings establish a molecular basis for HTS formation based on the mechanical activation of fibroblast-specific FAK and demonstrate the therapeutic potential of targeted mechanomodulatory strategies.

overall_design: Wildtype murine tissue was harvested at either day 6 or 14 post-injury following 48 hours or 10 days of mechanical loading, respectively (n=4 mice per group per time point). Murine RNA was isolated, labeled, and hybridized to the GeneChip microarray according to the manufacturer’s protocols (Affymetrix, Santa Clara, CA, USA). Each gene in the microarray was represented by 20 oligonucleotide pairs, with each pair consisting of an oligonucleotide perfectly matched to the cDNA sequence, and a second oligonucleotide containing a single base mismatch. Raw microarray data (sample intensity files) were processed using GeneSpring GX 11.0 (Agilent Technologies Inc., Santa Clara, CA, USA).

first: Victor

middle: W

last: Wong

first: Josemaria

last: Paterno

last: Longaker

first: Geoffrey

last: Gurtner


title: Exosomes mediate protective messages during oxidative stress; role of exosomal shuttle RNA

status: Public on Jan 07 2011

city: Gothenburg

first: Hadi

last: Valadi

address: Guldhedsgatan 10A

department: Dept. of Rheumatology and Inflammation Research

country: Sweden

institute: University of Gothenburg

summary: Exosomes are small extracellular nano-vesicles of endocytic origin that mediate different signals between cells, by surface interactions and by shuttling of functional RNA from one cell to another. In this study, we show that exosomes, produced by mouse mast cells exposed to oxidative stress, change their mRNA content and also that these exosomes can influence the response of other cells to oxidative stress by providing recipient cells with a resistance against oxidative stress. Finally, we also show that UV-light affect the biological functions associated with exosomes released under oxidative stress. These results argue that exosomal shuttle of RNA is involved in cell-to-cell communication, by influencing the response of recipient cells to an external stimulus.

overall_design: We used microarrays to detail to examine the gene expression underlying the effect of H2O2 on the exosomal RNA and how exosomes isolated from oxidative stress influence the growth of recipient cells during oxidative stress. The mRNA content of the exosomes from normal conditions (MC9 Exo_norm) were compared to that from exosomes from H2O2 conditions (MC9 Exo_H2O2). The mRNA content of recipient cells MC9 were identified before (MC9 cells_norm) and after (MC9 cells_H2O2) addition of exosomes that were isolated from normal and H2O2 conditions.

first: Maria

last: Eldh

first: Karin

last: Ekström

first: Margareta

last: Sjöstrand

first: Bob

last: Olsson

last: Jernås

first: Jan

last: Lötvall


title: Nonalcoholic fatty liver disease in AxB mice

status: Public on Jan 05 2011

city: Chapel Hill

first: Arlin

last: Rogers

state: NC

address: Campus Box 7431

department: Lineberger Comprehensive Cancer Center

institute: University of North Carolina

summary:
Spontaneous insulin resistance and NAFLD emerged in AxB F1 male mice with parent-of-origin effects such that AB6F1 (AJ dam x B6 sire) were susceptible whereas B6AF1 (B6 dam x AJ sire) were resistant.
We used microarrays to correlate gene expression with the NAFLD phenotype in 9-month-old male AB6F1 (affected) versus B6AF1 (unaffected) mice.

overall_design: Whole liver slices from two 9-month-old AB6F1 and B6AF1 males were collected for RNA extraction and hybridization on Affymetrix microarrays.


title: Transcription factors expressed in olfactory bulb local progenitor cells revealed by genome-wide transcriptome profiling

status: Public on Jan 04 2011

city: Berkeley

first: Grodon

middle: Ross Orion

last: Campbell

state: California

address: 265 Life Science Addition

department: Molecular and Cell Biology

institute: University of California, Berkeley

summary: We used transcriptional profiling to monitor gene expression of whole olfactory bulbs at daily intervals from embryonic day 11 through birth, generating a compendium of gene expression encompassing the major developmental events of this tissue.

overall_design: OBs from CD1 mice (Charles River Laboratories, Wilmington, MA), were isolated from embryos daily between E11 and postnatal day zero (P0), for a total of nine time points. RNA was purified with TRIzol reagent (Invitrogen, Carlsbad, CA), subjected to two rounds of amplification, labeled, and hybridized to Affymetrix Mouse Genome 430.2 GeneChip microarrays (Affymetrix Inc., Santa Clara, CA, USA) using Affymetrix reagents and protocols (http://www.affymetrix.com). One microarray for each time point using RNA from the OBs of one individual embryo.

first: Gordon

first: John

last: Ngai


title: Smooth muscle IL-4 receptor activation induces airway hyper-responsiveness

first: Bruce

last: Aronow

summary:
Selective stimulation of IL-4 receptor on smooth muscle induces airway hyper-responsiveness in mice.

Abstract: Production of the cytokines IL-4 and IL-13 is increased in both human asthma and mouse asthma models and Stat6 activation by the common IL-4/IL-13R drives most mouse model pathophysiology, including airway hyperresponsiveness (AHR). However, the precise cellular mechanisms through which IL-4Rα induces AHR remain unclear. Overzealous bronchial smooth muscle constriction is thought to underlie AHR in human asthma, but the smooth muscle contribution to AHR has never been directly assessed. Furthermore, differences in mouse vs. human airway anatomy and observations that selective IL-13 stimulation of Stat6 in airway epithelium induces murine AHR raise questions about the importance of direct IL-4R effects on smooth muscle in murine asthma models and relevance of these models to human asthma. Using transgenic mice in which smooth muscle is the only cell type that expresses or fails to express IL-4Rα, we demonstrate that direct smooth muscle activation by IL-4, IL-13, or allergen is sufficient, but not necessary, to induce AHR and show that 5 genes known to promote smooth muscle migration, proliferation and contractility are activated by IL-13 in smooth muscle in vivo.  These observations demonstrate that IL-4Rα promotes AHR through multiple mechanisms and provide a model for testing smooth muscle-directed asthma therapeutics.

overall_design:
For the microarray aspect of of the study, there were three groups of mice:
1.   IL4R gene knockout (KO) mice
2.   WT mice
3.  IL4R KO mice that were also transgenic for a gene construct that expressed IL4R under the control  of the smooth muscle-specific promoter from the SMP8 gene

All mice were subjected to intratracheal IL13 exposure for 7 days, and whole lung RNA was prepared for microarray analysis 24 hours after the last instillation.

Per treatment and genotype: Two RNA pools were made from four mice each.  These were labeled and hybridized to make a total of 6 microarrays.  RNA was labeled with the standard Affymetrix 3' labeling protocol to make cDNA that was hybridized to Mouse MOE 430 plus 2.0 GeneChips.

Gene transcripts were identified that differed in their relative expression  as a function of IL4R expression on the smooth muscle cells.

first: Noriko

last: Yanase

first: Charles

last: Perkins

first: Marsha

last: Wills-Karp

first: Fred

last: Finkelman


title: Smad1 and its target gene Wif1 coordinate BMP and Wnt signaling activities to regulate lung development

city: Los Angeles

first: Wei

last: Shi

address: 4650 Sunset Boulevard

institute: Children's Hospital Los Angeles

summary: Bone morphogenetic protein 4 (BMP4) is essential for lung development. To define its intracellular signaling mechanisms by which BMP4 regulates lung development, BMP-specific Smad1 or Smad5 was selectively knocked out in fetal mouse lung epithelial cells. Abrogation of lung epithelial-specific Smad1, but not Smad5, resulted in retardation of lung branching morphogenesis and reduced sacculation, accompanied by altered distal lung epithelial cell proliferation and differentiation, and consequently severe neonatal respiratory failure. By combining cDNA microarray with ChIP-chip analyses, Wnt inhibitory factor-1 (Wif1) was identified as a novel target gene of Smad1 in the developing mouse lung epithelial cells. Loss of Smad1 transcriptional activation of Wif1 expression was associated with reduced Wif1 expression and increased Wnt/beta-catenin signaling activity in lung epithelia, resulting in specific fetal lung abnormalities. Therefore, a novel regulatory loop of BMP4-Smad1-Wif1-Wnt/beta-catenin in coordinating BMP and Wnt pathways to control fetal lung development is suggested.

overall_design: mRNA profiling: Total RNA was isolated from left lobe lungs of three pair of E18.5 wild type and Smad1 lung epithelium-specific conditional knockout mice

first: Bing

last: Xu


title: Comparative transcriptomic analysis of BA- or BL- associated murine colonic epithelium after O157 infection

city: Tsuruoka

first: Shinji

last: Fukuda

address: 246-2 Mizukami, Kakuganji

institute: Keio University

summary: A huge number of microorganisms are colonized in human gut and the balance of their composition is closely related to human health. Recently, many probiotics such as bifidobacteria or lactobacilli have been introduced in our life as effective agents. However, we have not well understood their beneficial mechanisms including host-bacterial crosstalk. Accordingly, we took advantage of the protective mechanisms of probiotics against lethal infection of enterohemorrhagic Escherichia coli O157:H7 in murine gnotobiote model system

overall_design:
Germ free (GF) mice was used as control.
E means O157-monoassociated mice.
BAE means B. adolescentis and O157-associated mice.
BLE means B. longum and O157-associated mice.
Numbers indicate the days after O157 infection.

first: Kikuji

last: Itoh

first: Hiroshi

last: Ohno


title: Specific MicroRNAs Are Preferentially Expressed by Skin Stem Cells To Balance Self-Renewal and Early Lineage Commitment

city: Boulder

first: liang

last: zhang

state: CO

address: University of Colorado at Boulder, Han lab, Department of MCD Biology, Campus box 0347

institute: university of colorado at boulder

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

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

platform_organism:
Homo sapiens
Mus musculus
Rattus norvegicus
Human alphaherpesvirus 1
Human betaherpesvirus 5
Murid betaherpesvirus 1
human gammaherpesvirus 4
JC polyomavirus
Human immunodeficiency virus 1
Murid gammaherpesvirus 4
Human gammaherpesvirus 8
Betapolyomavirus hominis
Betapolyomavirus macacae

overall_design: Refer to individual Series


title: Expression data of P4 stage hair follicle early bulge and non-bulge ORS cells

summary:
Increasing evidence suggests that microRNAs may play important roles in regulating self-renewal and differentiation in mammalian stem cells (SCs). Here, we explore this issue in skin. We first characterize microRNA expression profiles of skin SCs versus their committed proliferative progenies and identify a microRNA subset associating with “stemness”. Of these, miR-125b is dramatically downregulated in early SC-progeny. We engineer an inducible mice system and show that when miR-125b is sustained in SC-progenies, tissue balance is reversibly skewed towards stemness at the expense of epidermal, oil-gland and HF differentiation. Using gain-and-loss of function in vitro, we further implicate miR-125b as a repressor of SC differentiation. In vivo, transcripts repressed upon miR-125b induction are enriched >700% for predicted miR-125b targets normally downregulated upon SC-lineage commitment. We verify some of these miR-125b targets, and show that Blimp1 and VDR in particular can account for many tissue imbalances we see when miR-125b is deregulated.

We used microarrays to compare the global gene expression profile of early bulge stem cells and non bulge ORS cells.

overall_design: Hair follicle cells were isolated from P4 Backskin of K14-RFP/Sox9-EGFP double transgenic mice as following: interfollicular epidermis sheet was pealed from hair follicle & dermis after dispase treatment. The hair follicle & dermis were first digested by collagenase (Sigma). Intact hair follicles were separated from dermal cells by low speed spinning (20g). The hair follicles were then digested by Trypsin and filtered by 40 µm cell strainers.   The isolated hair follicle cells were FACS sorted. Dead cells and large differentiated cells were excluded based on DAPI and side scattering. Early bulge cells were gated as GFPHi,RFPHi. Non-bulge ORS cells were gated as GFP-, RFPHi.

first: Zhang

last: Liang

first: Stokes

last: Nicole

first: Polak

last: Lisa

first: Rose

last: Jason

first: Nowak

last: Jonathan

first: Fuchs

last: Elaine


title: Gene therapy of Mpl -/- mouse LSK cells

status: Public on Jan 03 2011

city: Leiden

first: Martijn

last: Brugman

address: PO Box 9600

department: Immunohematology and Bloodtransfusion

country: Netherlands

institute: LUMC

summary: Comparison of Mpl-/- mouse LSK cells, either treated with control (GFP) or Mpl lentivirus. Lineage negative bone marrow cells were isolated and transduced and transplanted into Mpl-/- recipient mice. After transplantation and follow up mice were sacrificed and LSK (lineage negative, Sca-1 positive, cKit positive) cells were isolated by FACS. RNA was isolated using RNeasy Micro Kit (Qiagen GmbH, Hilden, Germany) and RNA was amplified for microarray hybridization using the Nugen Ovation system (Nugen Technologies, AC Bemmel, Netherlands). The resulting material was hybridized to Affymetrix Mouse 430 2.0 arrays. RMA normalization and summarization was performed in R 2.10 using Bioconductor packages.  The aim was to show the normalization of Mpl associated gene expression.

overall_design: 3 control (GFP transduced) samples of Mpl -/- mouse LSK cells and 3 treatment (Mpl transduced) samples of Mpl -/- mouse LSK cells.

first: Dirk

last: Heckl

middle: H

first: Ute

last: Modlich

first: Christopher

last: Baum


title: Gene Expression data of P4 stage hair follicle ORS cells from DTG (K14-rtTA,TRE-miR-125b) and control littermates

summary:
Increasing evidence suggests that microRNAs may play important roles in regulating self-renewal and differentiation in mammalian stem cells (SCs). Here, we explore this issue in skin. We first characterize microRNA expression profiles of skin SCs versus their committed proliferative progenies and identify a microRNA subset associating with “stemness”. Of these, miR-125b is dramatically downregulated in early SC-progeny. We engineer an inducible mice system and show that when miR-125b is sustained in SC-progenies, tissue balance is reversibly skewed towards stemness at the expense of epidermal, oil-gland and HF differentiation. Using gain-and-loss of function in vitro, we further implicate miR-125b as a repressor of SC differentiation. In vivo, transcripts repressed upon miR-125b induction are enriched >700% for predicted miR-125b targets normally downregulated upon SC-lineage commitment. We verify some of these miR-125b targets, and show that Blimp1 and VDR in particular can account for many tissue imbalances we see when miR-125b is deregulated.

We used microarrays to compare the global gene expression profile of P4 stage hair follicle ORS cells from DTG (K14-rtTA,TRE-miR-125b) and control littermates.


title: Modulation of calcium activated potassium channels induces cardiogenesis of pluripotent stem cells and enrichment of pacemaker- like cells

city: Aachen

first: Martin

last: Zenke

state: NRW

address: Universitatsklinikum Aachen, RWTH

department: Cell Biology

institute: Institute for Biomedical Engineering

summary:
Background: Ion channels are key determinants for the function of excitable cells but little is known about their role and involvement during cardiac development. Earlier work identified Ca2+-activated potassium channels of small and intermediate conductance (SKCas) as important regulators of neural stem cell fate. Here, we have investigated their impact on the differentiation of pluripotent cells towards the cardiac lineage. Methods and Results: We have applied the SKCa-activator EBIO on embryonic stem cells and identified this particular ion channel family as a new critical target involved in the generation of cardiac pacemaker-like cells: SKCa-activation led to rapid remodeling of the actin cytoskeleton, inhibition of proliferation, induction of differentiation and diminished teratoma formation. Time-restricted SKCa-activation induced cardiac mesoderm and commitment to the cardiac lineage as shown by gene regulation, protein and functional electrophysiological studies. In addition, the differentiation into cardiomyocytes was modulated in a qualitative fashion, resulting in a strong enrichment of pacemaker-like cells. This was accompanied by induction of the sino-atrial gene program and in parallel by a loss of the chamber-specific myocardium. In addition, SKCa activity induced activation of the Ras-Mek-Erk signaling cascade, a signaling pathway involved in the EBIO-induced effects.
Conclusions: SKCa-activation drives the fate of pluripotent cells towards the cardiac lineage and preferentially into pacemaker-like cardiomyocytes. This provides a novel strategy for the enrichment of cardiomyocytes and in particular, the generation of a specific subtype of cardiomyocytes, pacemaker-like cells, without genetic modification.

overall_design:
Untreated ES cells in three independent experiments:
- Untreated control ES cells sample 1 (Con_1)
- Untreated control ES cells sample 2 (Con_2)
- Untreated control ES cells sample 3 (Con_3)

EBIO-treated ES cells in three independent experiments:
- EBIO-treated ES cells sample 1 (EBIO_1)
- EBIO-treated ES cells sample 2 (EBIO_2)
- EBIO-treated ES cells sample 3 (EBIO_3)

Untreated differentiated ES cells in two independent experiments:
- Untreated control differentiated ES cells sample 1 (Con_day5+10_1)
- Untreated control differentiated ES cells sample 2 (Con_day5+10_2)

EBIO-treated differentiated ES cells in two independent experiments:
- EBIO-treated differentiated ES cells sample 1 (EBIO_day5+10_1)
- EBIO-treated differentiated ES cells sample 2 (EBIO_day5+10_2)

first: A

last: Kleger

first: T

last: Seufferlein

first: D

last: Malan

first: M

last: Tischendorf

last: Storch

last: Wolheim

first: S

last: Latz

last: Protze

last: Porzner

first: C

last: Proepper

last: Brunner

middle: F

last: Katz

first: G

last: Pusapati

first: L

last: Bullinger

first: R

last: Koehntop

first: K

last: Giehl

last: Spyrantis

first: O

last: Wittekindt

first: Q

last: Lin

first: B

middle: K

last: Fleischmann

last: Wartenberg

middle: M

last: Wobus

last: Boeckers

last: Liebau


title: Expression data from early and late born Atoh1 lineages within the E14.5 rhombomere 1 and isthmus

status: Public on Jan 01 2011

first: Rob

last: Machold

address: 522 First Avenue

department: Otolaryngology

institute: NYU School of Medicine

summary: Following neural tube closure at around E9.5, the rhombic lip within the rhombomere 1/isthmus region ("upper rhombic lip") produces a sequence of neuronal lineages that populate the brainstem and cerebellum. The transcription factor Atoh1 (Math1) is required for this specialized neurogenesis, although the genetic programs that delineate the temporal cell fate changes downstream of Atoh1 are not well characterized. We examined the gene expresion changes that take place within Atoh1 lineages

overall_design: We purified early (E10.5) and late (E13.5) born Atoh1 expressing cells from E14.5 embryos using a transgenic labeling strategy, and analyzed differences in gene expression across the two populations using the microarray data shown below.

last: Klein

last: Fishell


title: Widespread targeted chromatin remodeling during the initial phase of somatic cell reprogramming [expression]

city: Boston

first: Richard

last: Koche

state: MA

address: 185 Cambridge St.

institute: Broad Institute of Harvard and MIT

summary: Despite rapid progress in characterizing transcription factor-driven reprogramming of somatic cells to an induced pluripotent stem (iPS) cell state, many mechanistic questions still remain. To gain insight into the earliest events in the reprogramming process, we systematically analyzed the transcriptional and epigenetic changes that occur during early factor induction after discrete numbers of divisions. We observed rapid, genome-wide changes in the euchromatic histone modification, H3K4me2, at more than a thousand loci including large subsets of pluripotency or developmentally related gene promoters and enhancers. In contrast, patterns of the repressive H3K27me3 modification remained largely unchanged except for focused depletion specifically at positions where H3K4 methylation is gained. These chromatin regulatory events precede transcriptional changes within the corresponding loci. Our data provide evidence for an early, organized, and population-wide epigenetic response to ectopic reprogramming factors that clarify the temporal order through which somatic identity is reset during reprogramming.

overall_design: Gene expression was measured by Affymetric microarrays during the initial phase of the reprogramming of mouse embryonic fibroblasts.

first: Zachary

last: Smith

first: Alexander

last: Meissner


title: Background analysis using yeast RNA on the Mouse 430 2.0 array

city: Atlanta

first: Michael

last: Zilliox

state: GA

address: 1510 Clifton Road

department: Microbiology and Immunology

institute: Emory University School of Medicine

summary: We hybridized yeast RNA to the mouse 430 2.0 array to estimate the background binding for each probe.

overall_design: We used yeast RNA to estimate background binding for probes on the mouse chip.

first: Matthew

last: McCall

first: Rafael

middle: A

last: Irizarry


title: Differentiation of Mammary Tumors by SKI-606 (bostutinib) (gene expression)

city: La Jolla

first: Roy

last: Williams

state: CA

address: 3030 Science Park Road

department: Regenerative Medicine

institute: The Scripps Research Institute

summary: While c-Src is infrequently mutated in human cancers, it mediates oncogenic signals of many activated growth factor receptors and thus remains a key potential target of cancer therapy. However, the widespread function of Src in many cell types and processes requires evaluation of Src-targeted therapeutics within a normal developmental and immune competent environment. In an effort to direct clinical use of Src inhibitors, we tested the effectiveness of one of the four Src inhibitors in clinical testing, SKI-606 (bosutinib), in the MMTV-PyVmT transgenic mouse model of breast cancer. Tumor formation in this model is dependent on the presence of Src, but the necessity of Src kinase activity for tumor formation has not been determined. Furthermore, Src inhibitors have not been examined in an autochthonous tumor model. Here we show that oral administration of the Src inhibitor SKI-606 inhibited the phosphorylation of Src in mammary tumors, and caused a rapid decrease in the Ezh2 Polycomb group histone H3K27 methyltransferase and an increase in epithelial organization.  SKI-606 prevented the appearance of palpable tumors in more than half of the animals treated from puberty and stopped tumor growth in older animals with preexisting tumors.  These antitumor effects were accompanied by decreased cellular proliferation, altered tumor blood vessel organization and dramatically increased differentiation to lactational and epidermal cell fates. SKI-606 controls the development of mammary tumors in this model by inducing differentiation.

first: Robert

last: Oshima

first: Lionel

last: Hebbard


title: Microarray expression data from the Mus musculus intestine

status: Public on Jan 06 2011

city: Kiel

last: Haesler

address: Schittenhelmstr. 12

department: IKMB / 1st Dept. of Medicine

institute: University Clinic of Schleswig Holstein

summary:
Genome wide expression profiling to determine the overlap of Affymetrix-signals with SOLID sequencing
RNA was extracted using the Qiagen RNeasy kit following the manufacturers guidelines, arrays were prepared and hybridized following the Affymetrix protocol.

overall_design: Mus musculus samples from small intestine and colon, to be compared to transcript data aquired with other techniques

last: Häsler

first: U

last: Klostermeier


title: Genome-wide analysis of lung myeloid dendritic cells gene expression from healthy or emphysema subjects

city: Houston

first: Farrah

last: Kheradmand

address: One Baylor Plaza

institute: Baylor College of Medicine

summary: Lung myeloid dendritic cells isolated from emphysema but not healthy subjects induce Th1 and Th17 cells differentiation. The goal of this study is to identify the genes differentially expressed by lung myeloid dendritic cells from healthy or emphysema subjects. These genes may play crucial roles in directing Th1 and Th17 cells differentiation.

overall_design: Total mRNA was extracted from lung myeloid dendritic cells isolated from lungs of three healthy controls and three emphysema patients.

first: Ming

last: Shan


title: Hepatocyte-nuclear-factor-4a promotes gut neoplasia in mice and protects against the production of reactive oxygen species

city: Sherbrooke

first: Francois

last: Boudreau

state: Quebec

address: 3001 12e ave Nord

department: Anatomy and Cell Biology

country: Canada

institute: University of Sherbrooke

summary: Hepatocyte-nuclear-factor-4α (Hnf4α) is a transcription factor that controls epithelial cell polarity and maturation during embryogenesis.   Hnf4α conditional deletion during post-natal development results in minor consequences on intestinal epithelium integrity but promotes activation of the Wnt/β-catenin pathway. Here we show that Hnf4α does not act as a tumor suppressor gene but is crucial to promote gut tumorigenesis in mice.  Polyp multiplicity in ApcMin mice that lacks Hnf4α is suppressed in comparison to littermate ApcMin controls. Analysis of microarray gene expression profiles from mice lacking Hnf4α in the intestinal epithelium identifies its novel function in regulating the expression of reactive oxygen species (ROS) detoxifying genes.   This role is supported with the demonstration that HNF4α is functionally involved in the protection against spontaneous and 5-fluorouracil chemotherapy-induced production of intracellular ROS in colorectal cancer cell lines.  The analysis of a colorectal cancer patient cohort establishes that HNF4α is significantly up-regulated at both gene transcript and protein levels in tumors relative to adjacent benign epithelial resections. Several genes involved in ROS neutralization are also up-regulated in correlation with HNF4α expression.  All together, the findings point to the nuclear receptor HNF4α as a potential therapeutic target to eradicate aberrant epithelial cell resistance to ROS production during intestinal tumorigenesis.

overall_design: HNF4alpha was conditionally knockout in the mouse epithelial intestine with the 12.4-kb VillinCRE. A total of 3 control and 3 mutant littermates individuals were sacrificed at 7 months of age. The distal jejunum was harvested and Total RNA was isolated from each individuals. Each RNA sample was independently used to generate probes to screen affymetrix chips.

first: Mathieu

last: Darsigny

first: Jean-Philippe

last: Babeu

first: Julie

last: Carrier

first: Ernest

middle: G

last: Seidman

first: Fernand-Pierre

last: Gendron

first: E

last: Lévy

first: Nathalie

last: Perreault

first: François


title: Loss of Hepatocyte-Nuclear-Factor-1α Impacts on Adult Mouse Intestinal Epithelial Cell Growth and Cell Lineages Differentiation

summary:
Although hepatocyte-nuclear-factor-1α (Hnf1α) is crucial for pancreas and liver functions, it is believed to play a limited functional role for intestinal epithelial functions.  The aim of this study was to assess the consequences of abrogating Hnf1α on the maintenance of adult small intestinal epithelial functions.

Methodology/Principal Findings
An Hnf1α knockout mouse model was used. Assessment of histological abnormalities, crypt epithelial cell proliferation, epithelial barrier, glucose transport and signalling pathways were measured in these animals.  Changes in global gene expression were also analyzed. Mice lacking Hnf1α displayed increased crypt proliferation and intestinalomegaly as well as a disturbance of intestinal epithelial cell lineages production during adult life.   This phenotype was associated with a decrease of the mucosal barrier function and lumen-to-blood glucose delivery. The mammalian target of rapamycin (mTOR) signalling pathway was found to be overly activated in the small intestine of adult Hnf1α mutant mice.  The intestinal epithelium of Hnf1α null mice displayed a reduction of the enteroendocrine cell population.  An impact was also observed on proper Paneth cell differentiation with abnormalities in the granule exocytosis pathway.

Conclusions/Significance
Together, these results unravel a functional role for Hnf1α in regulating adult intestinal growth and sustaining the functions of intestinal epithelial cell lineages.

overall_design: HNF1alpha was knocked out. A total of 3 control and 3 mutant littermate individuals were sacrificed at 4 months of age. The jejunum was harvested and total RNA was isolated from each individual. Each RNA sample was independently used to generate probes to screen Affymetrix chips.

first: Carine

middle: R

last: Lussier

last: Brial

first: Sebastien

last: Roy

first: Marie-josee

last: Langlois

first: Elena

last: Verdu

last: Rivard


title: Comparison of granulosa cells from WT and Inha KO mice following gonadotropin stimulation

status: Public on Feb 01 2011

first: Martin

last: Matzuk

state: TX

summary: Inhibin α knockout (Inha-/-) female mice develop sex cord-stromal ovarian cancer with complete penetrance and previous studies demonstrate that the pituitary gonadotropins [follicle stimulating hormone (FSH) and luteinizing hormone (LH)] are influential modifiers of granulosa cell tumor development and progression in inhibin-deficient females. Recent studies have demonstrated that Inha-/- ovarian follicles develop precociously to the early antral stage in prepubertal mice without any increase in serum FSH and these studies suggested that in the absence of inhibins, granulosa cells differentiate abnormally, and thus at sexual maturity may undergo an abnormal response to gonadotropin signaling. To test this hypothesis, we stimulated immature WT and Inha-/- female mice prior to gross tumor formation with gonadotropin analogs, and subsequently examined post-gonadotropin induced ovarian follicle development, as well as preovulatory and hCG-induced gene expression changes in granulosa cells.  We find that at three weeks of age, inhibin-deficient ovaries do not show further antral development nor undergo cumulus expansion.  Widespread alterations in the transcriptome of gonadotropin-treated Inha-/- granulosa cells suggest that gonadotropins initiate an improper program of cell differentiation in Inha-/- cells. Overall, our experiments reveal that inhibins are essential for the normal gonadotropin-dependent response of granulosa cells.

overall_design: (2) Genotypes (WT, Inh KO) collected from 2 preovulatory granulosa cells with and without hCG, in triplicate independent samples

first: Stephanie

last: Pangas


title: The effects of aging vs. alpha7 nAChR subunit deficiency on the mouse brain transcriptome

city: Tel Aviv

first: Merav

last: Kedmi

address: 6 Weizmann street

country: Israel

institute: Tel Aviv Sourasky Medical Center

summary: Aging is accompanied by expression changes in multiple genes and the brain is one of the tissues most vulnerable to aging. Since the alpha7 nicotinic acetylcholine receptor (nAChR) subunit has been associated with neurodevelopmental disorders and cognitive decline during aging, we hypothesized that its absence might affect gene expression profiles in aged brains. To study whether transcriptional changes occur due to aging, alpha7 deficiency or both, we analyzed whole brain transcriptomes of young (8 week) and aged (2 year) alpha7 deficient and wild-type control mice, using Mouse Genome 430 2.0 microarray. Highly significant expression changes were detected in 47 and 1543 genes (after Bonferroni and FDR correction) in the brains of aged mice compared to young mice, regardless of their genotype. These included genes involved in immune system function and ribosome structure, as well as genes that were previously demonstrated as differentially expressed in aging human brains. Genotype-dependent changes were detected in only 3 genes, Chrna7 which encodes the alpha7 nAChR subunit, and two closely linked genes, likely due to a mouse background effect. Expression changes dependent on age-genotype interaction were detected in 207 genes (with a low significance threshold). Age-dependent differential expression levels were approved in all nine genes that were chosen for validation by real-time RT-PCR. Our results suggest that the robust effect of aging on brain transcription clearly overcomes the almost negligible effect of alpha7 nAChR subunit deletion, and that germline deficiency of this subunit has a minor effect on brain expression profile in aged mice.

overall_design: Total of 20 samples. 10 from young adult mice (8 weeks) and 10 from aged mice (2 years). In each age group, 5 were wild-type control mice and 5 alpha7 nAChR subunit defecient mice

first: Avi

last: Orr-Urtreger


title: The soluble intracellular domain of megalin does not affect renal proximal tubular function in vivo

city: Berlin

first: Thomas

last: Willnow

state: Berlin

address: Robert-Rössle-Str. 10

institute: Max Delbrück Center for Molecular Medicine (MDC)

summary:
The endocytic receptor megalin constitutes the main pathway for clearance of plasma proteins from the glomerular filtrate in the proximal tubules. However, little is know about the mechanisms that control receptor activity. A widely discussed hypothesis states that the intracellular domain (ICD) of megalin, released upon ligand binding, acts as a transcription regulator to suppress receptor expression - a mechanism proposed to safeguard the proximal tubules from protein overload. Here, we have put this hypothesis to the test by generating a mouse model co-expressing the soluble ICD and the full-length receptor. Despite pronounced expression in the proximal tubules, the ICD failed to exert any effects on renal proximal tubular function such as megalin expression, protein retrieval, or renal gene transcription. Thus, our data argue that the ICD does not play a role in regulation of megalin activity in vivo in the proximal tubules.
We used microarrays to compare gene expression profile in adult kidney from a new mouse model expressing the intracellular domain of megalin with wildtype.

overall_design: 10 week old mice were collected for RNA extraction and hybridization on Affymetrix microarrays. Three individuals for each genotype were analyzed comparing heterozygous animals for the intracellular domain of megalin with littermates controls.

first: Annabel

last: Christ

first: Sara

last: Terryn

first: Erik

middle: I

last: Christensen

first: Matthew

last: Huska

first: Miguel

last: Andrade-Navarro

first: Norbert

last: Hübner

first: Olivier

last: Devuyst

first: Annette

last: Hammes


title: Global gene expression profiles in skeletal muscle of monozygotic female twins discordant for hormone replacement therapy

city: Jyväskylä

first: Paula

last: Ronkainen

address: PO Box 35

country: Finland

institute: University of Jyväskylä

summary:
Analysis of gene expression profiles in skeletal muscle tissue after long-term use of HRT. Networks of enriched processes in skeletal muscle responding to long-term use of estrogen-based HRT in comparison with women without any HRT in a genetically controlled setting were contructed.
The association between the expression of specific biological processes and muscle composition or performance was tested. The hypothesis was that the differences in gene expression profiles reflect the known differences in muscle composition and performance.

overall_design: Total RNA obtained from muscle biopsies (vastus lateralis) from genetically identical female twin pairs (n=11 pairs) of which one sister is a user of postmenopausal, estrogen-based HRT (n=11), while the other is a never-user (n=11).

first: Vuokko

last: Kovanen


title: Expression data in mouse liver exposed to low dose-rate radiation

city: Sendai

first: Yoshihiko

last: Uehara

state: Miyagi

address: 2-1 Seiryo-machi, Aoba-ku

institute: Tohoku Univ. Sch. Med.

summary:
Expression profiles in mouse liver exposed to long-term gamma-irradiation were examined to assess in vivo effects of low dose-rate radiation. Three groups of male C57BL/6J mice were exposed to whole body irradiation at dose-rates of 17-20 mGy/day, 0.86-1.0 mGy/day or 0.042-0.050 mGy/day for 401-485 days (cumulative doses were approximately 8 Gy, 0.4 Gy or 0.02 Gy, respectively).
Expression profiles were produced for RNA isolated from irradiated individual animals and for pooled RNA from sham-irradiated 3 animals for control. The expression levels of 6 irradiated animals for each dose were compared individually with those of 2 pooled controls (3 irradiated samples to one pooled control in first and second experiments).

overall_design: The experiments were conducted twice at similar dose-rates. In the first experiment, three groups of 8 weeks old male C57BL/6J mice were exposed to whole body irradiation at dose-rates of either 16.6 mGy/day (H1), 0.858 mGy/day (M1) or 0.042 mGy/day (L1) for 485 days (cumulative doses were 8030 mGy, 416 mGy or 20.6 mGy, respectively). In the second experiment, the doe-rates were slightly elevated as 20.0 mGy/day (H2), 1.000 mGy/day (M2) or 0.050 mGy/day (L2) for 401 days (doses were 8015 mGy, 401 mGy or 20 mGy, respectively). A group of control unirradiated mice were set for each experiment (C1, C2).


title: Expression data from Th2 cell of ECM1 KO mice vs WT mice

status: Public on Dec 31 2010

city: Shanghai

first: Yuan

last: Zhang

address: Yueyang St. 320#

institute: Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences

summary:
CD4+ helper T cells are critical for immunological response. Th2 cells, a subset of CD4+ helper T cells, are responsible for asthma and other immune diseases. We found a Th2 secreted protein, ExtraCellular Matrix protein 1 (ECM1), which is highly induced by classic IL-4 signaling pathway during helper T cells differentiation.
We used microarrays to clarify the global programme of gene expression difference underlying fully developed Th2 cells from WT and ECM1 KO mice and identified distinct classes of up and down regulated genes by ECM1.

overall_design: Naïve CD4+ T cells are seperated from WT and ECM1 mice, cultured and harveseted for RNA extraction and hybridization on Affymetrix microarrays.

first: Zhenhu

last: Li


title: Mammalian stem cells respond to terahertz radiation with changes in gene expression

status: Public on Dec 28 2010

city: Los Alamos

first: Boian

middle: S

last: Alexandrov

state: NM

address: Bikini Atoll Road

department: Theoretical Division

institute: LANL

summary: We report that extended exposure to broad-spectrum terahertz radiation results in specific changes in cellular functions that are closely related to DNA-directed gene transcription. Our gene chip survey of gene expression shows that whereas 89% of the protein coding genes in mouse stem cells do not respond to the applied teraherz radiation, certain genes are activated, while other are repressed. RT-PCR experiments with selected gene probes corresponding to transcripts in the three groups of genes detail the gene specific effect. The response was not only gene specific but also irradiation conditions dependent. Our findings suggest that the applied terahertz irradiation accelerates cell differentiation toward adipose phenotype by activating the transcription factor peroxisome proliferator-activated receptor gamma (PPARG). Finally, our molecular dynamics computer simulations indicate that the local breathing dynamics of the PPARG promoter DNA coincides with the gene specific response to the THz radiation. We propose that THz radiation is a potential tool for cellular reprogramming.

overall_design: Growing in petri dish mouse mesenchymal stem cell culture is irradiated with THz radiation for 9 hours. Nonirradiated cells are used as a control. Immediately after irradiation total RNA is isolated from both THz treated and untreated cells. We used miroarrays to identify genes that are changing cellular level in response to THz radiation.

first: Anny

last: Usheva

first: Ludmil

middle: B

first: Jonathan

last: Bock

first: Yayoi

last: Fukuyo

first: Sona

last: Kang

first: M

middle: L

last: Phipps

first: Kim

middle: O

last: Rasmussen

first: Alan

last: Bishop

first: Evan

middle: D

last: Rosen

first: Jennifer

last: Martinez

first: Hou-Tong

last: Chen

first: George

last: Rodriguez


title: Stroke-brain infiltrating stem cells - mouse

city: Shreveport

last: Alexander

state: LA

address: 1501 Kings Highway

department: Physiology

institute: LSUHSC-Shreveport

summary:
Genes upregulated in stroke infiltrating stem cells were compared against the parent non-infiltrated mouse stem cell line derived from immortomouseTM.
Abstract
Background and Purpose- Although the therapeutic potential of bone marrow-derived stem cells (SC) has been addressed in different experimental models of ischemic stroke, it is still unclear how SC induce neuroprotection following stroke. In this study, we describe a novel method for recovering SC infiltrating post-stroke brain tissue allowing the determination of  genes which become persistently activated / or depressed (compared to their naïve counterparts) during SC-mediated neuroprotection.
Methods- Ischemic stroke was induced in C57BL/6 mice by middle cerebral artery occlusion for 1 h, followed by reperfusion. SC were isolated from H-2Kb-tsA58 (immortomouseTM) mice, and were administered (i.v.) 24 h after reperfusion. At the onset of therapeutic improvement (14 days after ischemia), infarcted brain tissue was isolated and infarct-infiltratng SC cultured at 33°C. Microarray analysis and RT-PCR were performed to compare persistent differential gene expression between naïve  and infiltrating SC populations.
Results- Z-scoring revealed dramatic changes in extracellular genes of analyzed cells. Pair-wise analysis detected 80 extracellular factor genes that were up-regulated (  2 fold, P<0.05, Benjamini-Hochberg correction) between naïve and infiltrated SC. Although several conventional neuroregenerative, nerve guidance and angiogenic factors (bFGF, bone morphogenetic protein, angiopoietins, neural growth factors were among the expressed genes detected  we identified Cytokine receptor-like factor 1 (Crlf1), Fgf7, family with sequence similarity 19, member A5 (Fam19a5), Glypican 1 (Gpc1), Dickkopf homolog 2 (Dkk2), Endothelial cell-specific molecule 1, Osteopontin (OPN)35, Tissue factor pathway inhibitor 2, Masp3 mRNA for MBL-associated serine protease-3, Glial cell line derived neurotrophic factor (Gdnf), Bone morphogenetic protein 2 (Bmp2), Olfactomedin 1, Sushi-repeat-containing protein, X-linked 2 (Srpx2).
Conclusions- SC infiltrating the post-i  schemic brain assume a persistently altered pattern of expressed extracellular genes compared to naïve SC that contributes to neuroprotection, regeneration and angiogenesis in infarcts.

Keywords: Gene activation / suppression study

overall_design: Comparison of persistent stem cell gene expression induced by stroke-infarct infiltration

first: J

first: D

middle: N

last: Granger

first: G

last: Yilmaz

first: C

last: Erkuran-Yilmaz


title: Effect of H11 Kinase/Hsp22 deletion in response to cardiac stress

city: Seoul

first: Jiyeon

last: Park

address: 222, Banpo-daero

department: Catholic Center for Precision Medicine Research

country: South Korea

institute: The Catholic University of Korea

summary: The expression of the small molecular weight heat shock protein (Hsp) H11 kinase/Hsp22 (Hsp22) is restricted to a limited number of tissues, including the heart and skeletal muscle, both in rodents and in humans. We generated a mouse knockout (KO) model, and investigated the role of Hsp22 in regulating cardiac hypertrophy in response to pressure overload. We compared gene expression profiles between WT and KO mice in basal condition and three days pressure overload after transverse aortic constriction (TAC). These data illustrated a novel mechanism of Hsp22-related gene expression in response to cardiac stress.

overall_design: We used microarray to examine differential gene expression by Hsp22 deletion at baseline and 3-day pressure overload. Left ventricles from wild type and Hsp22 knockout mice were selected from basal condition (each, n=3) and TAC surgery (each, n=4).

first: Hongyu

last: Qiu

first: Paulo

last: Lizano

first: Lydie

last: Laure

first: Xiangzhen

last: Sui

first: Eman

last: Rashed

first: Ji

middle: Y

first: Chull

last: Hong

first: Shumin

last: Gao

first: Eric

last: Holle

first: Didier

last: Morin

first: Sunil

last: Dhar

first: Thomas

last: Wagner

first: Alain

last: Berdeaux

first: Bin

last: Tian

first: Stephen

last: Vatner

first: Christophe

last: Depre


title: Expression data from macroH2A shRNA lines

status: Public on Dec 23 2010

city: New York

first: Emily

last: Bernstein

state: NY

address: 1470 Madison Avenue, 6th floor Rm 302

department: Oncological Sciences

institute: Mount Sinai School of Medicine

summary:
Cancer is a disease of both genetic and epigenetic changes. While increasing evidence demonstrates that oncogenic progression entails chromatin-mediated changes such as DNA methylation, the role of histone variants in cancer initiation and progression currently remains unexplored. Here, we report that the histone variant macroH2A (mH2A) suppresses tumour progression of malignant melanoma.
We hypothesized that loss of mH2A could contribute to melanoma progression by relieving repression of cell cycle- and metastasis-related genes. To gain insight into the transcriptional state of mH2A1 and mH2A2-deficient cells, we examined their gene expression profiles using Affymetrix microarrays.

overall_design: Murine B16-F1 cells with lentiviral shRNAs against mH2A1 and mH2A2 were generated along with control shRNA (against GFP) and used for the microarray analysis. Two independent biological replicates were used.

first: Avnish

last: Kapoor


title: CCAAT/Enhancer Binding Proteins (C/EBP)-α and -β are Essential for Ovulation, Luteinization and the Expression of Key Target Genes

first: JoAnne

last: Richards

department: Molecular and Cellular Biology

summary: Luteinizing hormone (LH) activation of the EGF receptor/RAS/ERK1/2 pathway is essential for ovulation and luteinization because granulosa cell depletion of Erk1/2 (Erk1/2gc-/- mice) renders mice completely infertile. Because of their potential as  mediators of ERK1/2-dependent granulosa cell differentiation, we disrupted genes encoding the CCAAT/enhancer-binding proteins, (C/EBP) a and C/EBPb.  Female Cebpbgc-/- mutant mice but not Cebpagc-/- mice were subfertile whereas Cebpa/bgc-/- double mutant females were sterile. Follicles failed to ovulate, ovaries were devoid of corpora lutea, luteal cell marker genes (Lhcgr, Prlr, Ptgfr, Cyp11a1 and Star) were absent and serum progesterone levels were low. Microarray analyses identified numerous C/EBPa/b target genes in eCG-hCG treated mice. At 4h post-hCG, a subset (19%) of genes altered in the Cebpa/b depleted cells was also altered in Erk1/2 depleted cells; hence they are common effectors of ERK1/2. Additional genes down-regulated in the Cebpa/b depleted cells at 8 and 24h post-hCG include known (Akr1b7, Runx2, Star, Saa3) and novel (Abcb1b, Apln, Igfbp4, Prlr, Ptgfr Timp4) C/EBP target genes including effectors of vascular cell development.  Bhmt, a gene controlling methionine metabolism and expressed exclusively in liver and kidney, was high in WT luteal cells but totally absent in Cebpa/b mutant cells. Because numerous genes potentially associated with vascular development were suppressed in the mutant cells, C/EBPa/b appear to dictate the luteinization process by also controlling genes that regulate the formation of the extensive vascular network required to sustain luteal cells. Thus, C/EBPa/b mediate several aspects of granulosa cell differentiation as well as the complex process of luteinization.

overall_design:
Five granulosa cell treatments were included:
CEBPα/β conditional KO ovary, eCG-treated 48h, hCG 4h
wild type ovary, eCG-treated 48h, hCG 8h
CEBPα/β conditional KO ovary, eCG-treated 48h, hCG 8h
wild type ovary, eCG-treated 48h,  hCG 24h
CEBPα/β conditional KO ovary, eCG-treated 48h, hCG 24h

first: Heng-Yu

last: Fan

first: Zhilin

last: Liu

first: Peter

last: Johnson


title: Expression data from mouse liver on multisetp-exposure to ethylbenzene

status: Public on Dec 25 2010

city: Abiko

first: Minori

last: Dateki

state: Chiba

department: Environmental Science Laboratory

institute: Central Research Institute of Electric Power Industry

summary:
The processes involved in the adaptation of animals to environmental factors such as chemicals have not yet been fully elucidated. We focused on the adaptive potential of the mouse liver against hepatotoxic chemical-induced injury.
We used microarrays to determine genes with adaptive transcriptional regulation against ethylbenzene, hepatotoxic chemical, on multistep-exposure.

overall_design: Four animal groups received the following treatments: phosphate-buffered saline (PBS) followed by PBS (P+P), ethylbenzene followed by PBS (E+P), PBS followed by ethylbenzene (P+E), and ethylbenzene followed by ethylbenzene (E+E).  For the first exposure, ethylbenzene (7 mmol kg-1) or PBS (equivalent volume to ethylbenzene) was intraperitoneally injected twice at a 24 h interval. After 7 days of normal feeding, each animal group was treated with ethylbenzene (7 mmol kg-1) or PBS as the secondary exposure. The mice were sacrificed 5 h after the secondary exposure for RNA extraction and hybridization on Affymetrix. The number of mice of each group is as follows, P+P, E+P = 3. P+E, E+E = 5. Specimens from mice of each group were pooled, and 10 μg RNA from each pool was used for cRNA synthesis.


title: Gene expression data from wild-type and Nlrc5 knockout GM-CSF induced bone marrow dendritic cells infected with Newcastle Disease virus.

status: Public on Dec 22 2010

city: Tsukuba

first: Yutaro

last: Kumagai

state: Ibaraki

address: Central 5-41, Higashi 1-1-1

department: BRD

institute: AIST

summary: Nlrc5 is encoding a Nod-like receptor protein NLRC5/NOD27. To check the involvement of Nlrc5 in antiviral response, we examined gene expression profile in wild-type and Nlrc5 knockout GM-CSF bone marrow macrophage with using microarrays.

overall_design: Bone marrow cells were cultured with GM-CSF and harvested on day 6. The induced dendritic cells were then stimulated with NDV at moi 1, collected at 0, 2, and 4 hours after infection. Total RNA was extracted and subjected to microarray experiment according to manufactures' instructions.

first: Himanshu

last: Kumar

first: Taro

last: Kawai

first: Shizuo

last: Akira


title: Expression data from PDK4 overexpressing (Ad-PDK4 infected) and control (Ad-control infected) mouse liver

summary:
We identified PDK4 as a gene with adaptive transcriptional response to chemical stress. Although PDK4 is an energy resource regulator induced by starvation, expression of other fasting-inducible genes was unaffected, indicating additional physiological role of PDK4 for liver adaptation to the chemical stress.
We used microarrays to determine genes with altered transcriptional level by PDK4 overexpression.

overall_design: Mice were infected with Ad-control (empty adenovirus vector) or Ad-PDK4 (PDK4 overexpressing adenovirus vector) at a dose of 10^9 PFU/mouse by tail vein injection. 3 days after the infection, mice were sacrificed for RNA preparation from the liver. Ad-control infected = 4, Ad-PDK4 infected = 3. Specimens from mice of each group were pooled, and 10 ug RNA from each pool was used for cRNA synthesis.


title: Genome-wide gene expression analysis for target genes to differentiate patients with intestinal tuberculosis and Crohn’s disease

city: New Delhi

first: Vineet

last: Ahuja

state: delhi

address: Department of Gastroenterology, All India Institute of Medical Sciences

country: India

institute: AIIMS

summary: This study aimed at genome-wide gene expression analysis of colonic biopsies from confirmed cases of intestinal tuberculosis (ITB) and Crohn's disease (CD) in comparison to controls. Further, to evaluate the role of T regulatory cells, Foxp3 mRNA expression was quantified in serum as well as colonic biopsies of patients with intestinal tuberculosis, Crohn's disease and controls.

overall_design: Paired samples, i.e. serum and colonic biopsies, were taken from 33 study subjects, which included patients with ITB and CD, and controls. RNA extraction was done and stringent quality checks performed. Human whole genome gene expression microarray analysis was performed on the Illumina HumanWG-6 Bead Chip with six total RNA samples of the 3 groups in duplicates. Real-time PCR for FOXP3 mRNA expression was analyzed in serum samples (4-CD, 5-ITB, 4-controls) and colonic biopsy samples (4-CD, 5-ITB, 4-controls).

first: Swati

last: Subodh

first: Amit

last: Tuteja

first: Veena

last: Tiwari

first: Sushil

first: Krishnamoorthy

last: Narayanasamy

first: Govind

last: Makharia

first: S

last: Acharya


title: Network Analysis of Skin Tumor Progression Identifies a Rewired Genetic Architecture Affecting Inflammation and Tumor Susceptibility (papillomas)

city: San Francisco

first: David

last: Quigley

address: 1450 Third St. Room 207

department: Helen Diller Comprehensive Cancer Center

institute: UCSF

summary: Germline polymorphisms influence gene expression networks in normal mammalian tissues. Analysis of this genetic architecture can identify single genes and whole pathways that influence to complex traits including inflammation and cancer susceptibility. Changes in the genetic architecture during the development of benign and malignant tumours have not been investigated. Here, we document major changes in germline control of gene expression during skin tumour development as a consequence of cell selection, somatic genetic events, and changes in tumour microenvironment. Immune response genes such as Interleukin 18 and Granzyme E are under germline control in tumours but not in normal skin. Gene expression networks linked to tumour susceptibility and hair follicle stem cell markers in normal skin undergo significant reorganization during tumour progression. Our data highlight opposing roles of Interleukin-1 signaling networks in tumour susceptibility and tumour progression and have implications for the development of chemopreventive strategies to reduce cancer incidence.

overall_design: Skin tumors were induced on dorsal back skin from a Mus spretus / Mus musculus backcross ([SPRET/Ei X FVB/N] X FVB/N) mice by treatment of dorsal back skin with dimethyl benzanthracene (DMBA) and tetradecanoyl-phorbol acetate (TPA). This treatment induced multiple benign papillomas as well as malignant squamous cell carcinomas (SCC) and spindle cell carcinomas. Gene expression analysis was performed on mRNA extracted from 68 papillomas: two papillomas from each of 31 FVBBX mice and a single papilloma from six additional FVBBX mice. Papillomas were harvested when mice were sacrificed due to presence of a carcinoma or termination of the experiment.

first: Minh

last: To

first: Il-Jin

last: Kim

first: Kevin

last: Lin

first: Donna

last: Albertson

first: Jonas

last: Sjolund

first: Jesús

last: Pérez-Losada

first: Allan

last: Balmain


title: Dysregulated expression and alternative splicing of genes controlling neuritogenesis and axon guidance revealed by exon-sensitive microarrays in models of neurodegeneration

city: Torino

first: Raffaele

last: Calogero

state: To

address: Via Nizza 52

department: Molecular Biotechnology Center

institute: University of Torino

summary:
Mitochondrial dysfunction has been directly or indirectly implicated in the pathogenesis of a number of neurodegenerative disorders including Parkinson's disease, Alzheimer's disease and Amyotrophic Lateral Sclerosis (ALS).  We used exon-sentive microarrays to characterize the responses to different mitochondrial perturbations in cellular models. We examined human SH-SY5Y neuroblastoma cells treated with paraquat, a neurotoxic herbicide which both catalyzes the formation of reactive oxygen species (ROS) and induces mitochondrial damage in animal models, and SH-SY5Y cells stably expressing the mutant SOD1(G93A) protein, one of the genetic causes of ALS. We identified a common set of genes that have a deregulated transcription and alternative splicing in both models. Noticeably, pathway analysis revealed that the expression of a subset of genes involved in neuritogenesis and axon guidance is perturbed, suggesting that alterations of axonal function may descend directly from mitochondrial damage and be responsible for neurodegenerative conditions.

This SuperSeries is composed of the SubSeries listed below.

overall_design:
Paraquat treatment on cell lines derived from human neuroblastoma SH-SY5Y and the same cell line stably transfected with cDNAs coding for wild type SOD1 or ALS mutant SOD1 G93A was carried out as described in  (Maracchioni et al. J Neurochem 2007, 100, 142-153). Human neuroblastoma SH-SY5Y untransfected or stably transfected with cDNAs coding for wild type SOD1 or the mutant SOD1(G93A) , were cultured  in D-MEM/F-12 media  with GlutaMAX™ (Gibco, Invitrogen, UK), 10% FBS,  100 Units/ml penicillin G, 100µg/ml streptomycin/ penicillin (Euroclone, Milano, Italy). Stably transfected cells were also maintained in the presence of 400µg/ml Geneticin (G418 sulphate, Euroclone). Cells were fed every 2–3 days and passed once a week. For the microarray experiment, after an initial amplification of each cell type [(SH-SY5Y; SOD1(WT), SOD1(G93A)], cells were aliquoted and cryopreservated in liquid nitrogen. For every experiment an aliquot of each cell line was thawed and seeded. After having reached confluence, cells were reseeded at 3x106cells in 100mm dish. Paraquat (N,N’-dimethyl-4,4’-bipyridinium dichloride, Sigma-Aldrich) treatment was carried out as described in (Maracchioni et al. J Neurochem 2007, 100, 142-153).

Total RNA was extracted using TRIzol® Reagent (Invitrogen), and subsequently purified using silica membrane spin columns from RNeasy Mini kit (Qiagen). RNA quantity and purity were assessed using a NanoDrop® instrument (Thermo Fisher Scientific Inc.). Total RNA integrity was assessed by using a 2100 Bioanalyzer (Agilent Technologies) and the RNA Integrity Number (RIN) was calculated.

Each condition was replicated 5 times. After extraction and quality check 1.5 µg of total RNA was subjected to removal of ribosomal RNA following the procedure suggested by the manufacturer (Affymetrix). The resulting total RNA was then used to created the biotin-labeled library to be hybridized on GeneChip® Exon 1.0 ST human microarrays following the procedure described by the manufacturer (Affymetrix).

The CEL files resulting from the hybridization were analyzed using oneChannelGUI 1.6.5 (Sanges et al. Bioinformatics 2007, 23, 3406-3408).

Exon and gene-level probeset summarization was done by mean of RMA and sketch quantile normalization.

Gene-level differential expression: to assess differential expression at gene-level, we used an empirical Bayes method together with a false discovery rate (FDR) correction of the p-value  Thus, the list of differentially expressed genes was generated using an FDR ≤ 0.05 together with an absolute log2(fold-change) threshold of 1.

Exon-level analysis: an intensity filter was subsequently applied at gene-level to remove not expressed and low expressed genes, i.e. genes were retained for exon-level analysis if in all biological replication gene-level signal was greater than 5. Subsequently, only genes characterized to have at least two RNA isoforms annotated in Ensembl database were retained for further analysis.  The Splicing Index value was calculated by taking the log2 ratio of the normalized exon intensity (NI) in Sample 1 and the NI in Sample 2. The normalized exon intensity (NI) is the ratio of the probe set intensity to the gene intensity.

Alternative splicing events (ASEs) were detected as described in (Della Beffa et al. BMC Genomics 2008, 9, 571).

first: Silvia

last: Lenzken

first: Valentina

last: Romeo

first: Francesca

last: Zolezzi

last: Cordero

first: Giuseppe

last: Lamorte

first: Davide

last: Bonanno

first: Donatella

last: Biancolini

first: Mauro

last: Cozzolino

first: Alessia

last: Maracchioni

first: Remo

last: Sanges

first: Tilmann

last: Achsel

first: Mariateresa

last: Carrì

last: Barabino


title: Network Analysis of Skin Tumor Progression Identifies a Rewired Genetic Architecture Affecting Inflammation and Tumor Susceptibility (carcinomas)

first: David

last: Quigley

overall_design: Skin tumors were induced on dorsal back skin from a Mus spretus / Mus musculus backcross ([SPRET/Ei X FVB/N] X FVB/N) mice by treatment of dorsal back skin with dimethyl benzanthracene (DMBA) and tetradecanoyl-phorbol acetate (TPA). This treatment induced multiple benign papillomas as well as malignant squamous cell carcinomas (SCC) and spindle cell carcinomas. 60 carcinomas were harvested from 55 mice; five mice provided two carcinomas each.

first: Minh

last: To

first: Il-Jin

last: Kim

first: Kevin

last: Lin

last: Albertson

last: Sjolund


title: Gene expression in retina and LGN of wild type and Chrnb2-/- mice

city: Davis

first: Carol

middle: Marie

last: Rubin

address: One Shields Avenue

department: Neurobiology Physiology and Behavior

institute: University of California, Davis

summary:
Mice lacking the beta 2 subunit (Chrnb2) of the neuronal nicotinic acetylcholine receptor display altered retinal waves and disorganized projections of the retinal ganglion cells to the lateral geniculate nucleus (LGN).  mRNA populations from retinas and LGN from Chrnb2-/-and wild type (C57BL/6J)  mice  were compared at 4 days postnatal, when RGC segregation to the LGN begins in WT mice.  Retinal mRNAs were also compared at adulthood.
Using microarray hybridization, we identified transcripts which are differentially expressed between Chrnb2-/- and wild type animals in these two tissues at these two ages.

overall_design: mRNA was isolated from retina and LGN of three male littermates each of WT and Chrnb2-/- mice at P4.  mRNA from retinas of two adult male littermates of each type was also examined.


title: Expression data of cystic renal epithelial tissue from mice deficient for fumarate hydratase.

city: london

first: Patrick

middle: J

last: Pollard

address: POBOX 123

institute: Cancer Research UK

summary:
Fumarate hydratase (FH) mutations cause hereditary leiomyomatosis and renal cell cancer (HLRCC). We have conditionally inactivated the murine ortholog (Fh1) in renal tubular epithelial cells in order to generate an in vivo model of HLRCC. Fh1 knockout mice recapitulates important aspects of HLRCC including the development of renal cysts that overexpress hypoxia inducible factor alpha (Hifa) and Hif-target genes.
We used microarrays to detail the global programme of gene  expression underlying cyst development in Fh1 knockout mice and identified distinct classes of up-regulated genes during this process.
Keywords: gene expression, comparison (wild-type n=3 vs knockout n=3)

overall_design: Renal epithelial tissue was macro-dissected from Fh1 knockout mice and sex-matched litter mate control disease-free animals for RNA extraction and hybridization on Affymetrix microarrays.

first: Ian

middle: P

last: Tomlinson


title: Inflammation and tumor susceptibility in skin cancer

type: Genome variation profiling by genome tiling array

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

sample_organism:
Mus musculus
Mus spretus
Mus musculus x Mus spretus

overall_design: Refer to individual Series


title: Profiling neuroblastoma SH-SY5Y with Paraquat treatment

first: Raffaele

last: Calogero

summary: Human SH-SY5Y neuroblastoma cells treated with paraquat, a neurotoxic herbicide which both catalyzes the formation of reactive oxygen species (ROS) and induces mitochondrial damage in animal models was profiled using Affimetrix Exon 1.0 ST GeneChips®

overall_design: Human SH-SY5Y neuroblastoma cells was compared with respect to Human SH-SY5Y neuroblastoma cells treated with Paraquat. Parqaut treatment was done as described by Maracchioni, A., Totaro, A., Angelini, D.F., Di Penta, A., Bernardi, G., Carri, M.T., and Achsel, T. (2007) J Neurochem 100, 142-153

first: Silvia

middle: C

last: Lenzken

first: Valentina

last: Romeo

last: Zolezzi

last: Cordero

last: Lamorte

last: Bonanno

first: MariaTeresa


title: Profiling wt SOD versus ALS SOD1(G93A) mutant

summary: Whole-genome profiling of SH-SY5Y cells was done on neuroblastoma SH-SY5Y stably transfected with cDNAs coding for SOD1WT or the mutant SOD1(G93A) protein.

overall_design: Five wt SOD versus five mutant SOD

first: Francesca

first: Giuseppe

first: Davide

first: Donatella

last: Biancolini

last: Cozzolino

last: Maracchioni

last: Sanges

last: Achsel

last: Carrì

first: R

last: Barabino