title: Expression data from wild type and calreticulin deficient murine embryonic stem cells

status: Public on Dec 02 2009

city: Rochester

first: Randolph

last: Faustino

state: MN

address: 200 First Street SW

institute: Mayo Clinic

summary:
Primordial genomic challenge compromises embryonic development and survival, and surveillance of deployed transcriptional programs may provide an early opportunity to forecast phenotype abnormalities. Here, comparisons between wild-type and calreticulin-ablated embryonic stem cells revealed transcriptome shifts precipitated by calreticulin loss. Bioinformatic analysis identified down and up-regulation in 1187 and 418 genes, respectively. Cardiovascular development precedes other organogenic programs, and examination of cardiogenic genes revealed a map of calreticulin-calibrated expression profiles that encompass the developmental regulators, Ccnd1, Ccnd2 and Notch1. Interrogation of primary function in the resolved network forecasted abnormalities during myocardial development. Whole embryo magnetic resonance imaging, verified by pathoanatomical analysis, diagnosed prominent ventricular septal defect. Correlation clustering and network resolution of probesets associated with protein folding/chaperoning and calcium handling demonstrated 14 and 19 genes, respectively, modulated by calreticulin deficiency. Calreticulin deletion provoked ontological re-prioritization of gene expression, molecular transport and protein trafficking that translated into multiple subcellular functional outcomes. Individual stem cell-derived cardiomyocytes lacking calreticulin demonstrated a disorganized contractile apparatus with mitochondrial paucity and architectural aberrations. Thus, bioinformatic deconvolution of primordial embryonic stem cell transcriptomes enables predictive phenotyping of defective developmental networks that coalesce from complex systems biology hierarchies.

Keywords: Comparison of embryonic stem cell genomes between wild type and calreticulin knockouts

overall_design: Stem cells cultured in triplicate (or more) were pooled to provide raw material per sample. Each sample represents  material collected from three technical replicates or more. In this manner, two wild type samples, and five derived from calreticulin knockout samples, were obtained. Although sample content contains material from three or more technical replicates harvested contemporaneously, each sample is a distinct biological replicate.  Total RNA was extracted from each of the samples and RNA pools were profiled on Affymetrix Mouse 430 2.0 Arrays to identify global gene expression changes invoked by genomic ablation of calreticulin.

middle: S

first: Anca

last: Chriac

first: Nicolas

last: Niederlander

first: Timothy

last: Nelson

first: Atta

last: Behfar

first: Prasanna

last: Mishra

first: Slobodan

last: Macura

first: Marek

last: Michalak

first: Andre

last: Terzic

first: Carmen

last: Perez-Terzic


title: Feeding schedule and the circadian clock shape rhythms in hepatic gene expression

status: Public on Nov 12 2009

city: La Jolla

first: Christopher

last: Vollmers

state: CA

address: 10010 North Torrey Pines Road

department: Regulatory Biology Laboratory

country: USA

institute: The Salk Institute for Biological Studies

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

overall_design: Refer to individual Series


title: Retinal gene expression in Egr-1 knock-out mice during development (p30 and p42)

status: Public on Nov 30 2009

city: Tuebingen

first: Marita

middle: Pauline

last: Feldkaemper

address: Calwerstrasse 7/1

department: Section of Neurobiology of the Eye

country: Germany

institute: University Eye Hospital Tuebingen, Institute for Ophthalmic Research

summary:
In chicks, the avian homologue of the early growth response protein-1 (ZENK) has been shown to be increased in a special cell type of the retina, the glucagonergic amacrine cells, under conditions that lead to a reduction in eye growth (myopic defocus, recovery of myopia) and decreased under conditions that enhance ocular growth (hyperopic defocus, form-deprivation). The investigation of Egr-1 knock-out mice showed that homozygous knock-out mice with no functional Egr-1 protein developed relative axial myopia at the age of 42 and 56 days, compared to heterozygous- and wildtype Egr-1 knock-out mice.
To clarify the role of Egr-1 in the retinal regulation of eye growth, and to get an idea about the biochemical pathways underlying this mechanism, we studied the role of Egr-1 in more detail using Affymetrix microarrays.

overall_design: Retinal samples of young homozygous Egr-1 knock-out and wildtype mice at the age of 30 days (hm30 and wt30; no difference in axial eye length yet) and 42 days (hm42 and wt42; already a difference in axial eye length of 59 µm) were taken to compare the mRNA expression changes over time between these two genotypes and within the same genotype between the two age groups.

first: Ruth

last: Schippert

first: Frank

last: Schaeffel

middle: P


title: Genomic targets of the KRAB and scan domain-containing zinc finger protein 263 (ZNF263).

status: Public on Nov 24 2009

city: Davis

first: Seth

middle: Eric

last: Frietze

address: 451 Health Sciences Dr. GBSF 4617A

department: Genome Center

institute: UC Davis

summary: Half of all human transcription factors use C2H2 zinc finger domains to specify site-specific DNA binding and yet very little is known about their role in gene regulation. Based on in vitro studies, a zinc finger code has been developed that predicts a binding motif for a particular zinc finger factor (ZNF). However, very few studies have performed genome-wide analyses of ZNF binding patterns and thus it is not clear if the binding code developed in vitro will be useful for identifying target genes of a particular ZNF. We performed genome-wide ChIP-seq for ZNF263, a C2H2 ZNF that contains 9 finger domains, a KRAB repression domain, and a SCAN domain and identified more than 5000 binding sites in K562 cells. Our results suggest that ZNF263 binds to a 24 nt site which differs from the motif predicted by the zinc finger code in several positions. Interestingly, many of the ZNF263 binding sites are located within the transcribed region of the target gene. Although ZNFs containing a KRAB domain are thought to function mainly as transcriptional repressors, many of the ZNF263 target genes are expressed at high levels. To address the biological role of ZNF263, we identified genes whose expression was altered by treatment of cells with ZNF263-specific siRNAs. Our results suggest that ZNF263 can have both positive and negative effects on transcriptional regulation of its target genes.

overall_design: Gene expression analysis in siRNA treatment against ZNF263 and a siRNA control.

first: Peggy

middle: J

last: Farnham


title: Expression data from fetal and adult  mouse liver mesothelial cells

status: Public on Nov 10 2009

city: Bunkyo-ku

first: Minoru

last: Tanaka

state: Tokyo

address: 1-1-1 Yoyoi

department: IMCB

country: Japan

institute: University of Tokyo

summary: Characterization and Functional Analyses of Hepatic Mesothelial Cells in Mouse Liver Development. We used microarrays to detail the global programme of gene expression in mesothelial cells during mouse liver development.

overall_design: Mouse liver mesothelial cells  were selected by a cell sorter at E12.5 and adult for RNA extraction and hybridization on Affymetrix microarrays. We obtained PCLP1+ cells and Mesothelin+ cells at each developmental stage in order to analyze expression profiles of mesothelial cells.

first: Izumi

last: Onitsuka

first: Atsushi

last: Miyajima


title: Gene expression profiles of forced miR-200 expression in 344SQ lung adenocarcinoma cells with high metastatic potential

city: Houston

first: Chad

last: Creighton

state: TX

address: One Baylor Plaza, Mail Stop: BCM305

department: Biostatistics, Ducan Cancer Center

institute: Baylor College of Medicine

summary: Metastatic disease is a primary cause of cancer-related death, and factors governing tumor cell metastasis have not been fully elucidated. Here we addressed this question by using tumor cell lines derived from mice that develop metastatic lung adenocarcinoma owing to expression of mutant K-ras and p53. A feature of metastasis-prone tumor cells that distinguished them from metastasis-incompetent tumor cells was plasticity in response to changes in their microenvironment. They transited reversibly between epithelial and mesenchymal states, forming highly polarized epithelial spheres in 3-dimensional culture that underwent epithelial-mesenchymal transition (EMT) following treatment with transforming growth factor-beta or injection into syngeneic mice. This plasticity was entirely dependent upon the microRNA-200 family, which decreased during EMT. Forced expression of miR-200 abrogated the capacity of these tumor cells to undergo EMT, invade, and metastasize and conferred transcriptional features of metastasis-incompetent tumor cells. We conclude that microenvironmental cues direct tumor metastasis by regulating miR-200 expression.

overall_design: Cell lines from p53R172H∆g/+ K-rasLA1/+ mice were derived from tumor tissues removed at autopsy from two different mice (#344 and #393). The tissues were minced, placed in culture, and passed serially in RPMI 1640 supplemented with 10% fetal bovine serum (FBS), which yielded mass populations of tumor cells derived from primary lung tumors (344P and 393P), mediastinal lymph nodes (344LN and 393LN), and a subcutaneous site (344SQ). Stable 344SQ cell lines expressing the miR-200b-200a-429 cluster or control vector were generated by transduction with lentivirus vectors. GFP positive transfectant pools were selected by growth in RPMI 1640 with 10% FBS and puromycin.  RNA samples of miR-200b-200a-429 knockup versus control (from triplicate cultures of each) were processed and analyzed on Affymetrix Mouse Expression Array 430A 2.0 chips.

first: Jon

last: Kurie

first: Yiqun

last: Zhang

first: Don

last: Gibbons

first: Wei

last: Lin


title: Synergistic Action of LIF and Glucocorticoids on pituitary corticotrophs cell line (AtT-20)

status: Public on Nov 16 2009

city: MONTREAL

first: David

last: Langlais

state: QC

address: 740 Ave Dr Penfield, rm 4203, McGill Genome Centre

department: Human Genetics

country: Canada

institute: McGill University

summary: While the hypothalamo-pituitary-adrenal axis (HPA) activates a general stress response by increasing glucocorticoid (Gc) synthesis, biological stress resulting from infections triggers the inflammatory response through production of cytokines. The pituitary gland integrates some of these signals by responding to the pro-inflammatory cytokines IL6 and LIF and to a negative Gc feedback loop. The present work used whole-genome approaches to define the LIF/STAT3 regulatory network and to delineate cross-talk between this pathway and Gc action. Genome-wide ChIP-chip identified 3 449 STAT3 binding sites, whereas 2 396 genes regulated by LIF and/or Gc were found by expression profiling. Surprisingly, LIF on its own changed expression of only 85 genes but the joint action of LIF and Gc potentiated the expression of more than a thousand genes. Accordingly, activation of both LIF and Gc pathways also potentiated STAT3 and GR recruitment to many STAT3 targets. Our analyses revealed an unexpected gene cluster that requires both stimuli for delayed activation: 83% of the genes in this cluster are involved in different cell defense mechanisms. Thus, stressors that trigger both general stress and inflammatory responses lead to activation of a stereotypic innate cellular defense response.

overall_design:
1) Pituitary corticotrophs cell line (AtT-20) response to glucocorticoids and LIF:
AtT-20 cells mRNA extracted after treatment with PBS as control, LIF for 18h, Dex+LIF for 3h and Dex+LIF for 18h. Each treatment were made in duplicate. [GSM471246-GSM471253]

2) Pituitary corticotrophs cell line (AtT-20) response to LIF after 3h treatment:
AtT-20 cells mRNA extracted after treatment with PBS as control or LIF for 3h. Each treatment were made in duplicate. [GSM471254-GSM471257]

3) Pituitary corticotrophs cell line (AtT-20) response to Dex after 3h treatment:
AtT-20 cells mRNA extracted after treatment with PBS as control or Dex for 3h. Each treatment were made in duplicate. [GSM471258-GSM471261]

4) Pituitary corticotrophs cell line (AtT-20) response to Dex after 18h treatment:
AtT-20 cells mRNA extracted after treatment with PBS as control or Dex for 18h. Each treatment were made in duplicate. [GSM471262-GSM471269]

first: Jacques

last: Drouin


title: Analysis of murine hematopoieitic stem cells, multipotent progenitors, PreMegE progenitors and mature CD4+ T cells

status: Public on Nov 09 2009

city: Lund

first: Joanne

last: Attema

address: Tornavagen 10

department: Immunology

country: Sweden

institute: Lund University

summary:
An investigation of the global gene expression signatures of murine hematopoietic stem cell differentiation during steady state hematopoiesis.
This data compliments the miniChIP-chip data obtained from the same cell types as described in Weishaupt et al., 2009 (Blood).

overall_design:
An Affymetrix genechip study using total RNA recovered from three separate FACS isolated HSC and MPP samples. The HSC and MPP gene expression data was analyzed alongside the PreMegEs and CD4+ T cells datasets obtained from our previous work (Pronk et al., 2007, Rolf et al. 2008).

HSCs are phenotypically identified in bone marrow as lineage-, cKit+, Sca1+, CD150+, Flk2/Flt3- (LSKCD150+ cells). MPPs are phenotypically identified in bone marrow as lineage-, cKit+, Sca1+, CD150-, Flk2/Flt3+ (LSKCD150- cells). PreMegEs are phenotypically identified in bone marrow as lineage-, cKit+, Sca1-, CD150+, CD105- and CD41- as described in Pronk et al., 2007. Splenic-derived CD4+ T cells are phentypically identified as CD4+, CD8-, B220-, Nk1.1- cells as described in Rolf et al., 2008.

first: Holger

last: Weishaupt


title: New candidate gene identification for controlling mammalian gonadal sex determination

city: Fort Collins

first: Gerrit

last: Bouma

state: CO

address: 3801 W. Rampart Road

department: Biomedical Sciences

institute: Colorado State University

summary: Mammalian gonadal sex determination is dependent on proper expression of sex determining genes in fetal gonadal somatic support cells (i.e., pre-granulosa and pre-Sertoli cells in XX and XY gonads, resp.). We used a unique transgenic mouse strain combined with microarray profiling to identify all the differentially expressed transcripts  in XX and XY isolated somatic support cells during critical stages of gonadal development and differentiation.

overall_design: XX and XY somatic support cells (SSC) were isolated by flow cytometry from embryonic day (E) 11.5 and E12.5 mouse gonads. Total RNA was isolated from  pools of isolated cells; 3 pools per sex and each timepoint.


title: Expression data from Gcn2 wild-type and knockout mouse liver perfused with or without methionine

city: Hershey

first: An

last: Dang Do

state: PA

address: 500 University Drive

department: Cellular and Molecular Physiology

institute: Penn State College of Medicine

summary:
In eukaryotes, regulation of mRNA translation enables a fast, localized and finely tuned expression of gene products.  Within the translation process, the first stage of translation initiation is most rigorously modulated by the actions of eukaryotic initiation factors (eIFs) and their associated proteins.  These 11 eIFs catalyze the joining of the tRNA, mRNA and rRNA into a functional translation complex.  Their activity is influenced by a wide variety of extra- and intracellular signals, ranging from global, such as hormone signaling and unfolded proteins, to specific, such as single amino acid imbalance and iron deficiency.  Their action is correspondingly comprehensive, in increasing or decreasing recruitment and translation of most cellular mRNAs, and specialized, in targeting translation of mRNAs with regulatory features such as a 5’ terminal oligopyrimidine tract (TOP), upstream open reading frames (uORFs), or an internal ribosomal entry site (IRES).  In mammals, two major pathways are linked to targeted mRNA translation.  The target of rapamycin (TOR) kinase induces translation of TOP and perhaps other subsets of mRNAs, whereas a family of eIF2 kinases does so with mRNAs containing uORFs or an IRES.  TOR targets translation of mRNAs that code for proteins involved in translation, an action compatible with its widely accepted role in regulating cellular growth.  The four members of the eIF2 kinase family increase translation of mRNAs coding for stress response proteins such as transcription factors and chaperones.  Though all four kinases act on one main substrate, eIF2, published literature demonstrates both common and unique effects by each kinase in response to its specific activating stress.  This suggests that the activated eIF2 kinases regulate the translation of both a global and a specific set of mRNAs.  Up to now, few studies have attempted to test such a hypothesis; none has been done in mammals.
We use array analysis to determine the global mRNA shift into polysomes following a stress response, and to compare the translational response following activation of GCN2 versus PERK, two of the four eIF2alpha kinases.

overall_design: Gcn2 wild-type or knockout mouse liver were perfused with complete amino acids media or media lacking methionine for RNA extraction and hybridization of Affymetrix microarrays.  RNA was extracted from unfractionated liver samples and polysome fraction of samples separated on sucrose density gradient.  To minimize biological variations, we pooled RNA from two perfused liver samples to use in each array analysis.  The conditions were total and polysome fraction of Gcn2+/+, +Met or -Met; total and polysome fraction of Gcn2-/-, +Met or -Met.  Each array analysis was done in duplicate.

middle: N

first: Scot

middle: R

last: Kimball

first: Douglas

last: Cavener

first: Leonard

last: Jefferson


title: Epigenetic chromatin states uniquely define the developmental plasticity of murine hematopoietic stem cells

type: Genome binding/occupancy profiling by genome tiling array

first: Mikael

last: Sigvardsson


title: Foxl2 mediated expression data from KK1 granulosa cells

status: Public on Nov 05 2009

city: Kingsville

first: Ken

last: Escudero

address: 700 University Blvd MSC 158

department: Biological & Health Sciences

institute: Texas A&M-Kingsville

summary: The Foxl2 transcription factor is required for ovarian function during follicular development.  Our approach to begin to understand Foxl2 function is through the identification of Foxl2 regulated genes in the ovary. Transiently transfected KK1 mouse granulosa cells were used to identify genes that are potentially regulated by Foxl2.  KK1 cells were transfected in three groups (mock, activated, and repressed) and twenty-four hours later RNA was isolated and submitted for Affymetrix microarray analysis.

overall_design: To increase the potential of Foxl2 to alter gene expression levels of putative target genes, two fusions were constructed consisting of Foxl2 fused to the activation domain of the Herpes simplex virus VP16 transcription factor (Foxl2-VP16) and Foxl2 fused to the repression domain of the murine MAD transcription factor (Foxl2-MAD).  Levels of gene expression were compared between mock transfected cells and those that were transfected with Foxl2-VP16 and Foxl2-MAD, respectively.

first: Kenneth

middle: W


title: Transcript profiling of WT and Nxf2 KO post-natal day 21 testes

city: Philadelphia

first: Jieyan

last: Pan

address: 3800 Spruce Street

department: Department of Animal Biology

institute: University of Pennsylvania

summary:
In euakryotes, mRNAs must be exported from the nucleus to the cytsoplasm. NXF2 is highly expressed in the mouse male germ cells.  We are interested in its function in spermatogenesis, espically in the nuclear RNA export in the testis. To this end, we made Nxf2 mutant mice by gene targeting. In an attempt to identify the mRNA substrates of NXF2, we perform the microarray experiments on testes.
We used microarrays to check the expression profiles of the Nxf2 WT and KO 21d testes on C57BL/6 background.

overall_design: To examine the expression difference between WT and Nxf2 KO testes, we collected testes from juvenile mice of three ages ( 21d, 26d, 28d). Testis weight was similar between WT and KO mice at post-natal day 21.  Three pairs of WT and KO 21d testes were chosen for microarray analysis.

first: P

last: Wang


title: Expression data from Fus/TLS-null KSL hematopoietic stem/progenitor cells

status: Public on Nov 03 2009

city: Chiba

first: ATSUSHI

last: IWAMA

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

department: Department of Cellular and Molecular Medicine

institute: Graduate School of Medicine, Chiba University

summary: Fus is the gene for a member of the FET family of RNA-binding proteins often involved in chromosomal translocations to generate oncogenic fusion genes in human cancers. Fus participates in multiple cellular functions, including RNA processing and transport, transcriptional regulation, and genome integrity. We uncovered its critical role in the maintenance of hematopoietic stem cells (HSCs). Fus-/- fetal livers developed normally except for a mild reduction in numbers of colony-forming cells compared to the wild type. The proliferation and differentiation of Fus-/- hematopoietic progenitors were normal in vitro. However, the number of colony-forming cells present in long-term cocultures of Fus-/- hematopoietic progenitors and stromal cells was significantly reduced. Fus-/- HSCs had an impaired long-term repopulating capacity and failed to repopulate in tertiary recipient mice. Fus-/- HSCs were highly susceptible to radiation both in vitro and in vivo and showed retardation of radiation-induced DNA damage repair. These findings define Fus as a novel regulator of HSCs and implicate it in stress-resistance and maintenance of the genomic integrity of HSCs.  Therefore, it would be of importance to analyze the gene expression profiles of Fus-knockout hematopoietic stem/progenitor cells to understand its role in HSCs.

overall_design: Purified wild-type and Fus–/– KSL cells from BM of recipient mice repopulated with wild-type and Fus–/– fetal liver cells were subjected to RNA extraction and hybridization on Affymetrix microarrays. Data were obtained from dublicate samples.

first: Atsushi

last: Iwama

first: Takeaki

last: Sugawara

first: Hitoshi

last: Ichikawa


title: Effects of extensive fasting and subsequent feeding on hepatic transcription

status: Public on Nov 23 2009

first: Christopher

last: Vollmers

summary: Temporally restricted feeding has a profound effect on the circadian clock. Fasting and feeding paradigms are known to influence hepatic transcription. This dataset shows the dynamic effects of refeeding mice after a 24hour fasting period.

overall_design:
Mice were entrained for two weeks under ad libitum access to food. Mice were then released into constant darkness and food was withdrawn at CT4 on the first day in constant darkness. On the second day in constant darkness mice were either fed (Refed) or continously fasted (Fast) at CT4.
Liver tissue was collected at the indicated timepoints. Total RNA was extracted and standard Affymetrix protocol were used for amplification, labeling and hybridization

first: Shubroz

last: Gill

first: Luciano

last: DiTacchio

first: Hiep

last: Le

first: Sandyarani

last: Pulivarthy

first: Satchidananda

last: Panda


title: Mouse KIAA1718 knockdown ES cells

status: Public on Nov 04 2009

city: shanghai

first: Huang

last: Chengyang

address: Yue Yang Road 320

country: China

institute: Institute of biochemistry and cell biology

summary: Compare the gene expression profiles of ESCs stably expressing control and KIAA1718 short hairpin RNA, using Affymetrix microarray.

overall_design: Mouse ES cells R1 were transformed with the respective lenti-virus expressing Luc shRNA or KIAA1718 shRNA1. The transformed ES cells were sorted for GFP. Total RNAs were extracted from cells using Trizol reagent (Invitrogen, Carlsbad, CA). For microarray experiments, RNA was processed and hybridized to Mouse Genome 430 2.0 arrays (Affymetrix) according to the manifacture’s instruction.

first: Chengyang

last: Huang

first: Yang

last: Xiang

first: Degui

last: Chen

first: Naihe

last: Jing


title: KIAA1718 is a dual specific histone demethylase involved in early neural development

summary:
Histone methylation is a complex posttranslational modification regulating transcription and chromatin dynamics, and plays important roles in development and disease processes. Recent studies indicate that histone lysine methylation is a reversible modification and several JmjC-domain-containing proteins have been identified as histone lysine demethylases. Here we show that KIAA1718, a JmjC-domain-containing protein, is a histone demethylase. KIAA1718 demethylated dimethylation of H3 lysine 9 and 27 (H3K9me2 and H3K27me2), two important epigenetic marks associated with embryonic development6-10. In mouse embryonic stem cells (ESCs), KIAA1718 expression increased at the early phase of neural differentiation. RNA interference inhibition of KIAA1718 blocked neural differentiation and the effect was rescued by wild-type human gene, but not by a catalytically inactive mutant. In chick embryos, KIAA1718 is exclusively expressed in the epiblast cells of the primitive streak, an organizer contributing to neural induction. Knockdown of KIAA1718 resulted in defects in neural formation, while its overexpression led to neural expansion. The pro-neural effect is mediated through transcriptional activation of FGF4, a growth factor implicated in neural induction. Thus, our study identifies a dual specific histone demethylase as a novel epigenetic factor integrated with growth factor signaling, which has important roles in the early neural development.

This SuperSeries is composed of the SubSeries listed below.

overall_design: Refer to individual Series.


title: Conjugated linoleic acid activates AMPK and reduces adiposity more effectively when used with metformin

status: Public on Nov 01 2009

city: Lincoln

first: Jean-Jack

middle: M.

last: Riethoven

state: NE

address: 1901 Vine Street

department: Beadle Center for Biotechnology

institute: University of Nebraska-Lincoln

summary:
Trans-10, cis-12 conjugated linoleic acid (t10c12 CLA) causes dramatic reductions in white adipose tissue in mice but has had limited effectiveness in humans.  Determination of the signaling pathways involved may lead to better regulation of adiposity. T10c12 CLA was found to activate AMP-activating protein kinase (AMPK), a central regulator of cell metabolism.  Compound C, a potent inhibitor of AMPK, prevents many of the typical responses to treatments with t10c12 CLA including the integrated stress response (ISR), the inflammatory response, the reduction in key lipogenic transcription factors, and delipidation. Treatment of adipocytes or mice with t10c12 CLA in conjunction with AMPK activator metformin results in more delipidation than treatment with the individual chemicals.   Additionally, the combination showed a reduced inflammatory response relative to a t10c12 CLA treatment alone. The combination of t10c12 CLA and metformin, widely used to treat insulin resistance and Type II diabetes, has potential as a treatment for reducing adiposity in humans.

Keywords: control/treatment

overall_design: Mouse 3T3-L1 RNA for was isolated from control linoleic acid (LA) and treatment (CLA, CLA+metformin, metformin) samples for analysis on microarrays with three biological reps.

first: Shan

last: Jiang

first: Zhigang

middle: M

first: Yuannan

last: Xia

first: Jess

last: Miner

first: Michael

middle: E

last: Fromm


title: Expression data from NFI-C knock out embryonic fibroblasts

city: Lausanne

first: Milos

last: Pjanic

state: VD

address: EPFL CH B1 426 Station 6

department: Institute of Biotechnology

country: Switzerland

institute: Faculty of Biology and Medicine, University of Lausanne

summary:
The Nuclear Factor I C (NFI-C) transcription factor has been implicated in TGF-β signaling, extracellular matrix deposition and skin appendage pathologies.

We performed a global gene expression analysis in NFI-C-/- and wild-type embryonic primary murine fibroblasts. This indicated that NFI-C acts mostly to repress gene expression in response to TGF-β1. Misregulated genes featured a prominent over-representation of regulators of connective tissue inflammation and repair.

overall_design: mRNAs were isolated from embryonic fibroblasts obtained from 3 wild-type and 3 NFI-C knock-out mice, and their levels were probed using microarrays. Prior to RNA extraction, fibroblast cultures were treated or not with TGF-β1 for 1 hour to examine the immediate response to the growth factor, or treated for 10 hours to assess the delayed response.

first: Genta

last: Plasari

first: Alessandra

last: Calabrese

first: Nicolas

last: Mermod


title: Effect of PGF receptor FP on bleomycin-induced pulmonary fibrosis in mice

status: Public on Oct 30 2009

city: Kyoto

first: Sakata

last: Daiji

state: Kyoto

address: Yoshida-konoe, Sakyo

department: pharmacology

institute: Kyoto University

summary:
We purposed to examine the effect of PGF receptor FP in development of
bleomycin-induced pulmonary fibrosis in mice.  We performed gene
expression analysis in the lung of WT and FP-KO mice on Days 0, 7 and
14. We found out that fibrosis-related genes such as various isoforms
of collagen, which were induced on Day 7 and continued to increase or
remained unchanged on Day 14, were induced to less extent in FP-KO
mice. In contrast, expression of inflammation-related genes peaked on
Day 7 similarly in WT and FP-KO mice. These results suggest that FP
functions in fibrosis-phase, not in peak inflammation phase, and
facilitates fibrogenesis by enhancing expression of fibrosis-related
genes.

overall_design:
RNA was prepared from the lung of WT and FP-KO mice on Day 0, 7 and 14
(n=4-5 for each group at each time point) after bleomycin instillation,
and used for hybridization with Affymetrics mouse 430 2.0 microarrays.
Time-dependent changes in expression of genes in FP-KO mice were
compared with those in WT mice.

first: Toru

last: Oga

first: Daiji

last: Sakata

first: Kimiko

last: Nonomura

first: Toshiyuki

last: Matsuoka

first: Shuh

last: Narumiya


title: Translational response following activation of GCN2 versus PERK

first: An

last: Dang Do

summary:
In eukaryotes, regulation of mRNA translation enables a fast, localized and finely tuned expression of gene products.  Within the translation process, the first stage of translation initiation is most rigorously modulated by the actions of eukaryotic initiation factors (eIFs) and their associated proteins.  These 11 eIFs catalyze the joining of the tRNA, mRNA and rRNA into a functional translation complex.  Their activity is influenced by a wide variety of extra- and intracellular signals, ranging from global, such as hormone signaling and unfolded proteins, to specific, such as single amino acid imbalance and iron deficiency.  Their action is correspondingly comprehensive, in increasing or decreasing recruitment and translation of most cellular mRNAs, and specialized, in targeting translation of mRNAs with regulatory features such as a 5’ terminal oligopyrimidine tract (TOP), upstream open reading frames (uORFs), or an internal ribosomal entry site (IRES).  In mammals, two major pathways are linked to targeted mRNA translation.  The target of rapamycin (TOR) kinase induces translation of TOP and perhaps other subsets of mRNAs, whereas a family of eIF2 kinases does so with mRNAs containing uORFs or an IRES.  TOR targets translation of mRNAs that code for proteins involved in translation, an action compatible with its widely accepted role in regulating cellular growth.  The four members of the eIF2 kinase family increase translation of mRNAs coding for stress response proteins such as transcription factors and chaperones.  Though all four kinases act on one main substrate, eIF2, published literature demonstrates both common and unique effects by each kinase in response to its specific activating stress.  This suggests that the activated eIF2 kinases regulate the translation of both a global and a specific set of mRNAs.  Up to now, few studies have attempted to test such a hypothesis; none has been done in mammals.

We use array analysis to determine the global mRNA shift into polysomes following a stress response, and to compare the translational response following activation of GCN2 versus PERK, two of the four eIF2alpha kinases.

This SuperSeries is composed of the SubSeries listed below.

overall_design: Refer to individual Series

first: Scot

last: Kimball

first: Douglas

last: Cavener

first: Leonard

last: Jefferson


title: Hedgehog is an anti-inflammatory epithelial signal for the intestinal lamina propria

status: Public on Oct 31 2009

city: Ann Arbor

first: William

last: Zacharias

state: MI

address: 109 Zina Pitcher Place

department: Department of Cell and Developmental Biology

institute: University of Michigan Medical School

summary: Epithelial Hedgehog (Hh) ligands regulate several aspects of fetal intestinal organogenesis and emerging data implicate the Hh pathway in inflammatory signaling in adult colon.  We investigated the effects of chronic Hh inhibition in vivo and profiled molecular pathways acutely modulated by Hh signaling in the intestinal mesenchyme.

overall_design: E18.5 intestinal mesenchyme was isolated and cultured.  Mesenchyme was treated with Sonic (Shh) or Indian (Ihh) hedgehog ligand or Vehicle (control) acutely to identify targets regulated by Hh signaling in intestinal mesenchyme.

first: Xing

last: Li

first: Blair

middle: B

last: Madison

first: Katherine

last: Kretovich

first: John

middle: Y

last: Kao

first: Juanita

middle: L

last: Merchant

first: Deborah

last: Gumucio


title: Altered Hepatic Gene Expression Profiles Associated with Myocardial Ischemia

city: Kanazawa

first: Hiroshi

last: Ootsuji

state: Ishikawa

address: 13-1 Takara-machi

department: Department of Disease Control and Homeostasis

institute: Kanazawa University Graduate School of Medical Science

summary:
Background–Acute coronary syndrome (ACS) is sometimes accompanied by accelerated coagulability, lipid metabolism, and inflammatory responses, which are not attributable to the cardiac events alone. We hypothesized that the liver plays a pivotal role in the pathophysiology of ACS. We simultaneously analyzed the gene expression profiles of the liver and heart during acute myocardial ischemia in mice.
Methods and Results–Mice were divided into three treatment groups: sham-operation, ischemia-reperfusion (I/R), and myocardial infarction. Mice with liver I/R were included as additional controls. Marked changes in hepatic gene expression were observed after 24 hours, despite the lack of histological changes in the liver. Genes related to tissue remodeling, adhesion molecules, and morphogenesis were significantly upregulated in the livers of mice with myocardial I/R or infarction, but not in those with liver I/R. Myocardial ischemia, but not changes in the hemodynamic state, was postulated to significantly alter hepatic gene expression. Moreover, detailed analysis of the signaling pathway suggested the presence of humoral factors that intervened between the heart and liver. To address these points, we utilized isolated primary hepatocytes and showed that osteopontin released from the heart actually altered the signaling pathways of primary hepatocytes to those observed in the livers of mice under myocardial ischemia. Moreover, osteopontin stimulated primary hepatocytes to secrete vascular endothelial growth factor-A, which is important for tissue remodeling.
Conclusions– Hepatic gene expression is potentially regulated by cardiac humoral factors under myocardial ischemia. These results provide new insights into the pathophysiology of ACS.

overall_design: C57BL/6J mice (n=46, BW 24.1±1.42 g, 8–10 weeks of age; Charles River Laboratories) were divided into the following treatment groups: sham-operated (n=11), I/R (n=10), myocardial infarction (n=10), liver I/R (n=10), and sham-operated plus hydralazine (n=5). In this study, we examined the response of hepatic gene expression to myocardial ischemia. Given the systemic inflammation that characterizes acute coronary syndromes, we postulated that regulation of hepatic genes occurs via inflammatory mediators and not via alterations in hemodynamics or hepatic perfusion. We therefore used whole genome transcriptional profiling to identify hepatic genes selectively regulated in the setting of myocardial ischemia. Moreover, detailed analysis of the signaling pathway suggested the presence of humoral factors that intervened between the heart and liver under myocardial ischemia. As a candidate humoral factors, osteopontin was further investigated. To evaluate whether the cardiac secreted protein affects hepatic gene expressions, we investigated primary hepatocytes treated with osteopontin by using microarray analysis. Affymetrix GeneChip Mouse Genome 430 2.0 Array was used to measure gene expression levels in primary hepatocytes at 8 hours after osteopontin stimulation (mock: n=3 and osteopontin: n=3).

first: Masao

last: Honda

first: Masayuki

last: Takamura

first: Soichiro

last: Usui

first: Hikari

last: Okada

first: Katsuhisa

last: Horimoto

first: Shuichi

last: Kaneko


title: Transcriptional profile of isoproterenol-induced cardiomyopathy and comparison to exercise-induced cardiac hypertrophy

city: Pittsburgh

first: Cristi

middle: Lara

last: Galindo

state: Pennsylvania

address: 200 Lothrop Avenue

institute: University of Pittsburgh

summary: We performed microarray analyses on RNA from mice with isoproterenol-induced cardiac hypertrophy and mice with exercise-induced physiological hypertrophy and identified 865 and 2,534 genes that were significantly altered in pathological and physiological cardiac hypertrophy models, respectively.

overall_design: Three different sets of mouse hearts were compared: Sedentary mice, mice that were exercised (swimming) for 3 months, and mice that were given isoproterenol via a surgically implanted pump. Each experiment was performed in triplicate - one heart per array. This resulted in a total of 9 arrays.

first: Harold

last: Garner

first: Michael

middle: A

last: Skinner


title: Dual role for the methyltransferase G9a in the maintenance of ß-globin gene expression

city: Ottawa

first: Theodore

last: Perkins

state: ON

address: 501 Smyth Rd.

department: Cellular and Molecular Medicine

institute: Ottawa Hospital Research Institute

summary: MEL clone 745 cells that are blocked at the pro-erythroblast stage serve as a model for terminal erythroid differentiation when treated  with DMSO. A stable MEL cell line expressing (Dox)-dependent shRNA sequence targeting different regions of G9a mRNA was established and screened as previously described in (Demers, 2007 PMID17707229). Knock down was induced by adding 5 micrograms/ml final of Dox in the culture medium. For a total of six samples, 10 micro grams of RNA was extracted from each three biological replicates of mouse erythroleukemia (MEL) cells and their corresponding G9a knock downs. The RNA was extracted and purified using the RNeasy Mini Kit (Qiagen) including the on-column DNAse I digestion step.

overall_design: Mouse erythroleukemia cells: wild type vs G9 knock down. For each microarray hybridization, data analysis was performed using MAS and GCRMA.

first: Marjorie

last: Brand

first: Carolina

last: Perez-Iratxeta


title: Gene expression profile from mouse natural helper cell

status: Public on Oct 28 2009

city: Sinjuku-ku Shinanomachi

first: kazuyo

last: moro

department: Microbiology and Immunology

institute: Keio University school of medicine

summary: Innate immune responses are important in combating various microbes during the early phases of infection. Natural killer (NK) cells are innate lymphocytes that, unlike T and B lymphocytes, do not express antigen receptors but rapidly exhibit cytotoxic activities against virus infected cells and produce various cytokines1,2. We report here a new type of innate lymphocyte present in a novel lymphoid structure associated with adipose tissues in the peritoneal cavity. These cells do not express lineage (Lin) markers but express c-Kit, Sca-1, IL-7R and IL-33R. Similar lymphoid clusters were found in both human and mouse mesentery and we term this tissue “FALC” for fat-associated lymphoid cluster. FALC Lin-c-Kit+Sca-1+ cells are distinct from lymphoid progenitors3 and lymphoid tissue inducer (LTi) cells4. These cells proliferate in response to IL-2 and produce large amounts of Th2 cytokines such as IL-5, IL-6 and IL-13. IL-5 and IL-6 regulate B cell antibody production and self-renewal of B1 cells5-7. Indeed, FALC Lin-c-Kit+Sca-1+ cells support the self-renewal of B1 cells and enhance IgA production. IL-5 and IL-13 mediate allergic inflammation and protection against helminth infection8,9. Upon helminth infection and in response to IL-33, FALC Lin-c-Kit+Sca-1+ cells produce large amounts of IL-13, which leads to goblet cell hyperplasia, a critical step for helminth expulsion. In mice devoid of FALC Lin-c-Kit+Sca-1+ cells such goblet cell hyperplasia was not induced. Thus, FALC Lin-c-Kit+Sca-1+ cells are Th2-type innate lymphocytes and we propose that these cells be called “natural helper cells”.

overall_design: Natural helper cells (Lin- c-kit+ Sca-1+) were isolated from mesentery of C57BL/6 for RNA extraction and hybridization on Affymetrix microarrays. For the control of this experiment, we use double negative cells (DN2) from thymus of C57BL/6 or lymphoid tissue inducer cells (LTi). Thymic DN2 cells were prepared from adult thymocytes. Thymocytes were stained with magnetic beads conjugated with anti-CD4 and anti-CD8α mAbs and CD4-CD8- double negative (DN) cells were negatively sorted by AutoMACS. DN cells were further stained with anti-CD25 and anti-CD44 mAbs and CD25+CD44+ cells were sorted as DN2 cells on a FACSAria.Thy-1+CD4- LTi cells were prepared from fetal liver cells as described previously. c-Kit+α4β7+IL-7Rα+ fetal liver cells from day 13 embryos were cultured on TSt4 cells for 17 days.

first: Kazuyo

last: Moro


title: Response of gastric epithelial progenitors to H. pylori isolates from Swedish patients with chronic atrophic gastritis 1

status: Public on Oct 27 2009

city: Saint Louis

first: Jeremiah

last: Faith

state: MO

address: Campus Box 8510

institute: Washington University in St. Louis

summary: Helicobacter pylori infection is associated with development of gastric adenocarcinoma in a subset of infected humans, especially those that develop an antecedent condition, chronic atrophic gastritis (ChAG) characterized by loss of acid-producing parietal cells. Studies in a gnotobiotic transgenic mouse model of ChAG, with an engineered ablation of parietal cells and an associated expansion of gastric epithelial progenitors (GEPs), have shown that a subset of GEPs is able to harbor intracellular collections of H. pylori.  To better understand H. pylori’s adaptation to ChAG, we sequenced the genomes of 24 isolates, obtained from 6 individuals, each sampled over a 4-year interval, as they maintained normal gastric histology, or progressed from normal histology to ChAG, or experienced worsening ChAG, or proceeded from ChAG to cancer. Analyses of gene content and single nucleotide polymorphisms (SNPs) demonstrated that H. pylori populations within study participants were largely clonal, and remarkably stable over the 4-year interval, regardless of disease state. Because they exhibited such broad inter-host variation (38.6±4.7 SNPs/1000bp of genome), and did not cluster according to host pathology, we sought to identify common functional properties by performing GeneChip studies of the responses of a cultured mouse gastric stem cell-like line (mGEPs) to infection with sequenced strains. The results yielded a shared 695-member set of genes differentially expressed after infection with ChAG-associated, but not normal or heat killed strains: 434 of these genes were also represented in dataset of responses to the cancer-associated strain.  Ingenuity Pathway Analysis revealed that ChAG- and ChAG/cancer- associated responses were  significantly enriched in genes associated with tumorigenesis in general, and gastric carcinogenesis in specific cases. Whole genome transcriptional profiling of a sequenced ChAG strain during mGEP infection disclosed a set of responses that included upregulation of hopZ, an adhesin belonging to a family of outer membrane proteins. Expression profiles of wild-type and hopZΔ strains revealed a number of pH-regulated genes affected by loss of HopZ, including HopP which binds sialylated glycans produced by GEPs in vivo. Genetic inactivation of hopZ produces a fitness defect in gnotobiotic transgenic mice but not their wild-type littermates. This study illustrates an approach for identifying GEP responses specific to ChAG, and bacterial genes important for survival in a gastric ecosystem that lacks parietal cells.

overall_design: mGEPs and npGECs were seeded and grown to 70% confluency in RPMI1640 medium supplemented with 10% FBS before being infected with H. pylori strains that had been grown to log phase. After 24h, media and non-attached bacteria were washed off and the cells harvested by trypsinization. RNA was prepared from triplicate cultures of mGEP or npGECs cells.

first: M

last: Giannakis

first: J

middle: I

last: Gordon


title: Functional differences among human postnatal stem cells of different origin are reflected by their transcriptome

status: Public on Oct 22 2009

city: Nijmegen

first: Bastiaan

last: Jansen

address: PO Box 9101

department: Tumor Immunology

country: Netherlands

institute: Nijmegen Centre for Molecular Life Sciences, Radboud University Nijmegen Medical Center Nijmegen

summary:
GENES ASSOCIATED WITH THE CELL CYCLE, LINEAGE COMMITMENT AND IMMUNOMODULATORY POTENTIAL DISCRIMINATE HUMAN POSTNATAL STEM CELLS OF DIFFERENT ORIGIN.
Stem cells hold great promise for future clinical use. Their intrinsic biological properties are, however, not fully understood and many of their therapeutic benefits still unclear. Better understanding of their genetic and biological properties is essential for the development of clinically relevant stem cell applications. The neonatal unrestricted somatic stem cell (USSC) from cord blood has the capacity to differentiate into cells from all three germ layers. Here we investigate the gene expression profile of USSC using the Affymetrix Exon Array platform and compare it with those of bone-marrow derived mesenchymal adult stem cells (BM-MSC) and adipose tissue-derived adult stem cells (AdAS). Extensive data analysis revealed limited variation in the expression profile of the different cell lines from the same origin, while stem cells from different origins showed distinct profiles, with the BM-MSC and AdAS being more closely related to each other than to USSC. Interestingly, USSC expressed genes involved in the cell cycle at much higher levels, indicative of their relatively higher cycling rate (~ 24 hrs as opposed to more than 2 days for BM-MSC and AdAS). They also show higher expression of genes involved in neurogenesis, consistent with their reported neuronal differentiation capacity. The BM-MSC signature indicates that they are primed towards developmental processes of tissues and organs derived from the mesoderm and endoderm. Remarkably, AdAS appear to be highly enriched in immune-related genes. Together, the data suggest that the different mesenchymal stem cell types have distinct gene expression profiles,that reflect their origin and differentiation potential.

Keywords: Adult stem cells, developmental biology, gene expression, genomics, human cord blood, mesenchymal stem cells, cell type comparison

overall_design: Cells from 3 different donors per stem cell type were cultured under proliferative, non-differentiating conditions. Total RNA was isolated and used and hybridized exon array hybridizations in order to generate stem cell type-specific gene expression profiles.

first: Christian

last: Gilissen

first: Helene

last: Roelofs

first: Aneta

last: Schaap-Oziemlak

first: Joris

last: Veltman

first: Reinier

last: Raymakers

first: Joop

middle: H

first: Gesine

last: Kögler

first: Carl

middle: G

last: Figdor

first: Ruurd

last: Torensma

first: Gosse

last: Adema


title: Induction of intestinal Th17 cells by segmented filamentous bacteria

city: New York

first: Dan

last: Littman

state: NY

address: 540 1st ave

institute: NYU Medical Center

summary: The gastrointestinal tract of mammals is inhabited by hundreds of distinct species of commensal microorganisms that exist in a mutualistic relationship with the host. The process by which the commensal microbiota influence the host immune system is poorly understood. We show here that colonization of the small intestine of mice with a single commensal microbe, segmented filamentous bacterium (SFB), is sufficient to induce the appearance of CD4+ T helper cells that produce IL-17 and IL-22 (Th17 cells) in the lamina propria. SFB adhere tightly to the surface of epithelial cells in the terminal ileum of mice with Th17 cells but are absent from mice that have few Th17 cells. Colonization with SFB was correlated with increased expression of genes associated with inflammation, anti-microbial defenses, and tissue repair, and resulted in enhanced resistance to the intestinal pathogen Citrobacter rodentium. Control of Th17 cell differentiation by SFB may thus establish a balance between optimal host defense preparedness and potentially damaging T cell responses.  Manipulation of this commensal-regulated pathway may provide new opportunities for enhancing mucosal immunity and treating autoimmune disease.

overall_design: We compared the gene expression profiles in the terminal ileum of Swiss-Webster GF mice before and after colonization with SFB, which induced robust Th17 cell differentiation. To sieve out host effects, the role of other microbiota, as well as other factors, we also evaluated the transcriptional program induced in Jackson C57BL/6 mice after co-housing with Taconic B6 animals, which also induces Th17 cell differentiation. 0.5 cm of the most distal part of the small intestine was dissected. Total RNA was extracted with TRIzol. RNA was labeled and hybridized to GeneChip Mouse Genome 430 2.0 arrays following the Affymetrix protocols. Data were analyzed in GeneSpring GX10.

first: Ivaylo

last: Ivanov

first: Koji

last: Atarashi

first: Nicolas

last: Manel

first: Eoin

last: Brodie

first: Tatsuichiro

last: Shima

first: Ulas

last: Karaoz

first: Dongguang

last: Wei

first: Katherine

middle: C

last: Goldfarb

first: Clark

last: Santee

first: Susan

middle: V

last: Lynch

first: Takeshi

last: Tanoue

first: Akemi

last: Imaoka

first: Kikuji

last: Itoh

first: Kiyoshi

last: Takeda

first: Yoshinori

last: Umesaki

first: Kenya

last: Honda


title: WNT4 is required for ovarian follicle development and female fertility

status: Public on Oct 23 2009

city: Saint-Hyacinthe

first: Derek

last: Boerboom

address: 3200 Sicotte

department: Département de biomédecine Vétérinaire

institute: Université de Montréal, Faculty of veterinary medicine

summary: To study the physiological role of WNT4 in the postnatal ovary, a mouse strain bearing a floxed Wnt4 allele was created and mated to the Amhr2tm3(cre)Bhr strain to target deletion of Wnt4 to granulosa cells. Wnt4flox/-;Amhr2tm3(cre)Bhr/+ mice had significantly reduced ovary weights and produced smaller litters (P<0.05). Serial follicle counting demonstrated that, while Wnt4flox/-;Amhr2tm3(cre)Bhr/+ mice were born with a normal ovarian reserve and maintained normal numbers of small follicles until puberty, they had only 25.2% of the normal number of healthy antral follicles. Some Wnt4flox/-;Amhr2tm3(cre)Bhr/+ mice had no antral follicles or corpora lutea and underwent premature follicle depletion. RTPCR analyses of Wnt4flox/-;Amhr2tm3(cre)Bhr/+ granulosa cells and cultured granulosa cells that overexpress WNT4 demonstrated that WNT4 regulates the expression of Star, Cyp11a1 and Cyp19, steroidogenic genes previously identified as downstream targets of the WNT signaling effector CTNNB1. WNT4- and CTNNB1-overexpressing cultured granulosa cells were analyzed by microarray for alterations in gene expression, which showed that WNT4 also regulates a series of genes involved in late follicle development and the cellular stress response via the WNT/CTNNB1 signaling pathway. Together, these data indicate that WNT4 is required for normal antral follicle development, and may act by regulating granulosa cell functions including steroidogenesis.

overall_design: Granulosa cells were obtained from 20-26 day-old mice of various genotypes 48h after eCG treatment, using the needle puncture method as previously described. Cells were then infected with adenoviruses to express eGFP or Cre, or overexpress WNT4 in serum-free medium, and subsequently harvested for RNA extraction as described below. Preliminary experiments demonstrated that an infection efficiency of >80% could be obtained at an MOI of ~50 (as determined by analysis of fluorescent signal in Ad-eGFP-infected cells) and that the Ad-Cre and Ad-WNT4 viruses produced efficient recombination of the floxed Ctnnb1 alleles and robust WNT4 overexpression, respectively. Microarray analyses were done using triplicate RNA samples from each adenoviral treatment described above, and using mouse expression set 430 microarrays (Affymetrix, Santa Clara, CA).

first: Alexandre

last: Boyer

first: Evelyne

last: Lapointe

first: Xiaofeng

last: Zheng

first: Robert

last: Cowan

first: Huaiguang

last: Li

last: Quirk

first: Francesco

middle: J

last: DeMayo

first: JoAnne

middle: S

last: Richards


title: Circadian gene profiling in the distal nephron and collecting ducts

first: Sylvain

last: Pradervand

address: Genopode

department: CIG

institute: UNI Lausanne

summary:
Renal excretion of water and major electrolytes exhibits a significant circadian rhythm. This functional periodicity is believed to result, at least in part, from circadian changes in secretion/reabsorption capacities of the distal nephron and collecting ducts. Here, we studied the molecular mechanisms underlying circadian rhythms in the distal nephron segments, i.e. distal convoluted tubule (DCT) and connecting tubule (CNT) and, the cortical collecting duct (CCD). Temporal expression analysis performed on microdissected mouse DCT/CNT or CCD revealed a marked circadian rhythmicity in the expression of a large number of genes crucially involved in various homeostatic functions of the kidney. This analysis also revealed that both DCT/CNT and CCD possess an intrinsic circadian timing system characterized by robust oscillations in the expression of circadian core clock genes (clock, bma11, npas2, per, cry, nr1d1) and clock-controlled Par bZip transcriptional factors dbp, hlf and tef. The clock knockout mice or mice devoid of dbp/hlf/tef (triple knockout) exhibit significant changes in renal expression of several key regulators of water or sodium balance (vasopressin V2 receptor, aquaporin-2, aquaporin-4, alphaENaC). Functionally, the loss of clock leads to a complex phenotype characterized by partial diabetes insipidus, dysregulation of sodium excretion rhythms and a significant decrease in blood pressure. Collectively, this study uncovers a major role of molecular clock in renal function.

Keywords: time course

overall_design: We examined the temporal profiles of gene expression in mouse distal nephron segments and collecting ducts. The RNA was extracted from microdissected distal convoluted tubules and connecting tubules (DCT/CNT samples) or, cortical collecting ducts (CCD samples). Animals were sacrificed for microdissection every 4 hours, i.e. at ZT0, ZT4, ZT8, ZT12, ZT16 and ZT20 (ZT – Zeitgeber (circadian) time, indicates time of light-on as ZT0 and time of light-off as ZT12). The microarray hybridization was performed in duplicates on two pools of RNA composed of equivalent amounts of RNA prepared from five animals at each ZT time-point.

first: Anne

last: Mercier Zuber

first: Gabriel

last: Centeno

first: Svetlana

last: Nikolaeva

first: Lionel

last: Maquelin

first: Léonard

last: Cardinaux

first: Olivier

last: Bonny

first: Dmitri

last: Firsov


title: Development of mammary luminal progenitor cells is controlled by the transcription factor STAT5A

status: Public on Oct 21 2009

city: Bethesda

first: WeiPing

last: Chen

state: MD

address: Bldg 8, Room 1A11, NIDDK/NIH

department: GCL

institute: NIDDK/NIH

summary: Mammary alveologenesis is abrogated in the absence of the transcription factors STAT5A/5B that mediate cytokine signaling.  To reveal the underlying causes for this developmental block we studied mammary stem and progenitor cells.  While loss of STAT5A/5B did not affect the stem cell population and their ability to form mammary ducts, luminal progenitors were greatly reduced and unable to form alveoli during pregnancy.  Temporally-controlled expression of transgenic STAT5A in mammary epithelium lacking STAT5A/5B restored the luminal progenitor population and rescued alveologenesis in a reversible fashion in vivo.  Taken together, STAT5A is necessary and sufficient for the establishment of luminal progenitor cells.

overall_design: The mammary tissues from two mice of each genotype were collected 6 days (sample 9 and 11 were WT)

first: Daisuke

last: Yamaji

first: Gertraud

last: Robinson

first: Risu

first: Yonatan

last: Feuermann

first: Susanne

last: Pechhold

first: Weiping

first: Lothar

last: Hennighausen


title: Expression data from mouse induced chondrogenic cells

status: Public on Oct 20 2009

city: Osaka, Suita City

first: Kunihiko

last: Hiramatsu

address: 2-2, Yamadaoka

department: Bone and Cartilage Biology

institute: Osaka University

summary:
We induced chondrogenic cells from adult mouse dermal fibroblast culture by transduction of c-Myc, Klf4, and SOX9 using retroviral vectors. We selected chondrogenic cells for promoter / enhancer activities of the Col11a2 gene, and established cell lines.
We analyzed global gene expression profile of four induced chondrogenic cell lines (MK-4, MK-5, MK-7, and MK-10) using microarrays.

overall_design: Induced chondrogenic cells (passage 6) were cultured in 60 mm dishes. After reaching confluence, total RNAs were extracted.

first: Noriyuki

last: Tsumaki


title: Expression Data from Pten Null Fibroblasts

city: Columbus

first: Julie

last: Wallace

state: OH

address: 460 W. 12th Ave 840 BRT

institute: OSUCCC

summary:
The tumor stroma is believed to contribute to some of the most malignant characteristics of epithelial tumors.  However, signaling between stromal and tumor cells is complex and remains poorly understood.  Here we show that genetic inactivation of Pten in stromal fibroblasts of mouse mammary glands accelerated the initiation, progression and malignant transformation of mammary epithelial tumors.
Global gene expression profiling in mammary stromal cells identified a Pten-specific signature associated with massive extra-cellular matrix (ECM) remodeling, innate immune cell infiltraion and increased angiogenesis.  Execution of this transcriptional program was mediated, in part, by the induction, phosphorylation and recruitment of Ets2 to target promoters.  Remarkably, Ets2 inactivation in Pten stroma-deleted tumors was sufficient to decrease tumor growth and progression.  These findings identify the Pten-Ets2 axis as a critical stroma-specific signaling pathway that suppresses mammary epithelial tumors.

overall_design: Wild type and Pten null primary mammary fibroblasts isolated from 8 week old female mice were cultured, RNA was extracted and Affymetrix gene expression arrays were performed.

first: Carmen

middle: Z

last: Stone

first: Karl

last: Kornacker

first: Gustavo

last: Leone

first: Michael

last: Ostrowski


title: Expression data from mutant SOD1(G93A) transgenic mice

status: Public on Oct 17 2009

city: Washington

first: Bruce

last: Lerman

state: DC

address: 111 Michigan Ave NW

department: Research Center for Genetic  Medicine

institute: Children's National Medical Center

summary:
Expression profiling of spinal cord from SOD1(G93A) mice and age matched controls at ages 28, 42, 56, 70,98,112, and 126 days of age.
We used microarrays to determine differential gene expression throughout disease progression in the spinal cord of mutant SOD1(G93A) model of ALS.

overall_design: Samples were collected from male B6SJL SOD1(G93A) and age matched controls. 3 samples were collected representing each genotype and age group for RNA extraction and hybridization on Affymetrix microarrays.

first: Eric

last: Hoffman


title: Expression profiling of P14 and P28 mouse retina from 4 genotypes: +/+, Rorb-/- , +/+;CrxpNrl and Rorb-/-;CrxpNrl

status: Public on Oct 19 2009

first: Douglas

last: Forrest

address: 10 Center Drive

department: Clinical Endocrinology Branch

institute: National Institute of Diabetes and Digestive and Kidney Diseases (NIDDK)

summary:
Rorb is essential for rod photoreceptor development in the mouse retina. Using Affymetrix mouse GeneChips, we have generated expression profiles of the +/+, Rorb-/- , +/+;CrxpNrl and Rorb-/-;CrxpNrl retina at P14 and P28.

In this dataset, we include the expression data obtained from retina of wt and mutants. These data are used to obtain 1189 genes that are differentially expressed in Rorb-/- vs wt.

overall_design: 31 total samples were analyzed

first: Li

last: Jia

first: Edwin

last: Oh

first: Matthew

last: Brooks

first: Anand

last: Swaroop


title: Androgen-Induced Rhox Homeobox Genes Modulate the Expression of AR-Regulated Genes

status: Public on Oct 29 2009

city: San Diego

first: miles

last: wilkinson

state: CA

address: 4168 Front Street

department: reproduction

institute: ucsd

summary: Rhox5, the founding member of the reproductive homeobox on the X chromosome (Rhox) gene cluster, encodes a homeodomain-containing transcription factor that is selectively expressed in Sertoli cells, where it promotes the survival of male germ cells.  To identify Rhox5-regulated genes, we generated 15P-1 Sertoli cell clones expressing physiological levels of Rhox5 from a stably transfected expression vector.  Microarray analysis identified many genes altered in expression in response to Rhox5, including those encoding proteins controlling cell cycle regulation, apoptosis, metabolism, and cell-cell interactions.  Fifteen of these Rhox5-regulated genes were chosen for further analysis.  Analysis of Rhox5-null male mice indicated that at least 9 of these are Rhox5-regulated in the testes in vivo.  Many of them have distinct postnatal expression patterns and are regulated by Rhox5 at different postnatal time points.  Most of them are expressed in Sertoli cells, indicating that they are candidates to be directly regulated by Rhox5.  Transfection analysis with expression vectors encoding different mouse and human Rhox family members revealed that the regulatory response of a subset of these Rhox5-regulated genes is both conserved and redundant.  Given that Rhox5 depends on AR for expression in Sertoli cells, we examined whether some Rhox5-regulated genes are also regulated by androgen receptor (AR).  We provide several lines of evidence that this is the case, leading us to propose that RHOX5 serves as a key intermediate transcription factor that directs some of the actions of AR in the testes.

overall_design: Four 15P-1 Sertoli cell clones stably transfected with mouse Rhox5-expression vector were used for microarray analysis. Among them, two clones (6 and 24) expressed highest level of Rhox5 mRNA, and other two clones (14 and 16) expressed the lowest level of Rhox5 mRNA.

first: Zhiying

last: Hu

first: Miles

middle: F

last: Wilkinson


title: Punctual ablation of Foxp3+ T cells unleashes an autoimmune lesion

status: Public on Oct 15 2009

city: Boston

first: CBDM

last: Lab

state: MA

address: 77 Avenue Louis Pasteur

department: Microbiology and Immunobiology

institute: Harvard Medical School

summary:
How do Treg cells control an autoimmune lesion? We depleted Foxp3+ Treg cells in autoimmune prone TCR transgenic BDC2.5 mice on the NOD background
Kinetic of gene-expression changes in CD4 T cells isolated for pancreas and pancreas draining lymph node (PLN) of Foxp3-DTR.BDC2.5/NOD mice after Treg cell ablation

Keywords: T cell activation/ differentiation after Treg depletion timecourse

overall_design: CD4 T cells were isolated from pancreas and PLN at 0, 15 and 24 hours after diphtheria toxin application into 4-6 week old female Foxp3-DTR.BDC2.5/NOD transgenic mice

first: Markus

last: Feuerer

first: Christophe

last: Benoist

first: Diane

last: Mathis


title: Naïve B cells vs germina center B cells

city: Yokohama

first: Keiichiro

last: Suzuki

state: Kanagawa

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

department: Research Center for Allergy and Immunology

institute: RIKEN

summary:
Activation-induced cytidine deaminase (AID) is essential for the generation of antibody memory but also targets oncogenes among others. We investigated the transcriptional regulation of the AID gene, Aicda, in the class switch–inducible CH12F3-2 cells, and found that the Aicda regulation involves derepression by several layers of positive regulatory elements in addition to the 5’ promoter region. The 5’ upstream region contains functional motifs for the response to signaling by cytokines, CD40-ligand, or stimuli that activate NF-κB. The first intron contains functional binding elements for the ubiquitous silencers c-Myb and E2f and for B cell–specific activator Pax5 and E-box-binding proteins.
To confirm involvement of these transcription factors in Acida regulation, we examined their expression profile of these factors in naïve and germinal center  B cells.

overall_design: Naïve B cells were defined as B220+PNA-Fas- and germinal center B cells were defined as B220+PNA+Fas+ cells. These cells were purified from immunized mouse lymph nodes or mouse Peyer's patches by using FACS Aria. Samples are as follows: pLN GC, pLN naïve, PP GC, PP naïve, (each 1 sample, prepared from pooled 3-5 mice)

first: Thinh

last: Tran

first: Mikiyo

last: Nakata

first: Nasim

last: Begum

first: Reiko

last: Shinkura

first: Sidonia

last: Fagarasan

first: Tasuku

last: Honjo

first: Hitoshi

last: Nagaoka


title: Hypoxic gene regulation on mice Quadriceps muscle

status: Public on Oct 10 2009

city: Philadelphia

first: Murat

middle: T

last: Budak

institute: University of Pennsylvania

summary:
To address whether hypoxia contributes to muscle patho-physiology, normal, adult C57 mice were exposed to chronic, normobaric and hypobaric hypoxic environments for 2 weeks in order to simulate levels of hypoxaemia reported in DMD patients with advanced respiratory insufficiency. Control mice were maintained under normoxic conditions. Control and experimental mice were studied.
Keywords: Hypoxia effect, Comparison type

overall_design:
Adult male C57Bl/10 mice were used in experiments. At the beginning of the experiment mice were divided into two groups, control (room condition) and hypoxic (hypoxic condition), over a period of 2 weeks. The hypoxic group was gradually exposed to lower levels of hypoxia in an especially designed and hermetically closed hypoxic chamber. A Pegas 4000 MF(Columbus Instruments) gas blending system was used. The oxygen level was gradually decreased from 21% to 8% over one week and animals were kept at 8% oxygen for another 7 days. Animal’s weights were monitored daily. Food and water were changed daily for the time of the experiment. After two weeks animals were euthanized using CO2, Extensor digitorum longus (EDL) and Soleus muscles were dissected for physiological studies. Prior to physiological analysis each group was divided into two smaller groups (subgroups). In the first subgroup the primary focus on physiological muscle analysis was on (EDL) while in the other subgroup it was on Soleus. This division allowed us that both muscles, EDL and Soleus were analyzed at the same time after euthanization.
RNA isolation
Total RNA was isolated from each QF muscle by Tri-Reagent (Ambion, Austin, TX) as described by manufacturer. Isolated total RNA were cleaned up by RNeasy mini kit (Qiagen, Valencia, CA) as described by manufacturer. The purity and concentration of total RNA were determined by measurement of absorbance at 260 and 280nm using a Nanodrop ND-1000 spectrophotometer (NanoDrop Technologies, Wilmington, DE). To satisfy our purity criteria, we discarded all RNA samples that did not have a 260/280 ratio between 1.8 and 2.1. To satisfy our criteria for integrity, we required that all RNA used in our experiments have single peaks for the 18S and 28S bands as determined by the Agilent 2100 Bioanalyzer (Agilent Technologies Inc., Palo Alto, CA).
Linear amplification and cRNA labeling
Three microliter total RNA was used for each sample to obtain linearly amplified labeled cRNA by using GeneChip® One-Cycle Target Labeling kit (Affymetrix, Santa Clara, CA) as manufacturer described. Briefly; total RNA was used to generate double-stranded cDNA with the T7-oligo (dT) primer. This double-stranded cDNA was used in vitro transcription and biotin labeling steps. Labeled cRNA yield and purity were determined by measuring the absorbance at 260 and 280nm. All the cRNA 260/280 ratios were between 1.9 and 2.1. Quality control (QC) of the labeled cRNA products was assessed by performing 1µg labeled cRNA on 2% agarose gel to see similar RNA smear type.
Fragmentation and microarray hybridization
Fifteen micrograms labeled cRNA of hypoxic or normoxic QF muscle was fragmented, and 10μg was hybridized to Affymetrix® Mouse 430 ver 2.0 GeneChip arrays for 18–24h (Affymetrix Inc.). Each microarray was washed and stained with streptavidin–phycoerythrin and scanned at a 6-μm resolution with Agilent model G2500A GeneArray scanner A visual quality control measurement was performed to ensure proper hybridization after each chip was scanned.

first: Gabriel

last: Willmann

first: Sasha

last: Bogdanovich

first: Santosh

last: Baby

first: Martin

last: Wiesen

first: Qinghao

last: Fu

first: Henry

middle: W

last: Querfurth

first: Matias

last: Mosqueira

first: Rodrigo

last: Iturriaga

first: Sukhamay

last: Lahiri

first: Tejvir

last: Khurana


title: Lactobacillus acidophilus induces virus immune defense genes in murine dendritic cells by a TLR-2 dependent mechanism

status: Public on Oct 08 2009

city: Kongens Lyngby

first: Simon

last: Rasmussen

address: Kemitorvet, Building 208

department: Department of Systems Biology

country: Denmark

institute: Technical University of Denmark

summary: Lactobacilli are probiotics that, among other health promoting effects, have been ascribed immunostimulating and virus preventive properties. Certain lactobacilli species have been shown to possess strong IL-12 inducing properties. As IL-12 production depends on the up-regulation of type I interferons, we hypothesized that the strong IL-12 inducing capacity of  L. acidophilus NCFM in murine bone marrow derived DC is caused by an up-regulation of IFN-β, which subsequently stimulates the induction of IL-12 and the dsRNA binding toll like receptor (TLR)-3. The expression of the genes encoding IFN-β, IL-12, IL-10 and TLR-3 in DC upon stimulation with L. acidophilus NCFM was measured. L. acidophilus NCFM induced a much stronger expression of ifn-β, il-12 and il-10 compared to the synthetic dsRNA ligand Poly I:C, whereas the levels of expressed tlr-3 were similar. By the use of whole genome microarray gene expression, we investigated whether other genes related to the viral defence were up-regulated in DC upon stimulation with L. acidophilus NCFM and found that various virus defence related genes, both early and late, were among the strongest up-regulated genes. The IFN-β stimulating capability was also detected in another L. acidophilus strain, but was not a property of other probiotic bacteria tested (B. bifidum and E. coli nissle).The IFN-β inducing capacity was markedly reduced in TLR-2 -/- DCs, dependent on endocytosis and the major cause of the induction of il-12 and tlr-3 in L. acidophilus NCFM stimulated cells. Collectively, our results reveal that certain lactobacilli trigger the expression of viral defence genes in DC in a TLR-2 manner through induction of IFN- β.

overall_design: In the experiment Lactobacillus NCFM were added to murine dendritic cells and stimulated for 4, 10 or 18 hours. These were compared to control experiment at the same timepoints. Experiments were run in triplicates except for control 10h and control 18h which were only in duplicate, giving a total of 16 arrays.

first: Gudrun

middle: M

last: Weiss

first: Louise

last: Zeuthen

first: Birgit

middle: N

last: Nielsen

first: Lene

last: Jepsersen

first: Hanne

last: Frøkiær


title: RNA expression data of embryonic E16.5 mouse temporomandibular joint (TMJ)

first: Daniel

middle: Joseph

last: OConnell

address: 77 Louis Pasteur

department: Genetics

summary: We conducted a genetic analysis of the developing temporo-mandibular joint (TMJ), a highly specialized synovial joint that permits movement and function of the mammalian jaw.  First, we used laser capture microdissection to perform a genome-wide expression analysis of each of its developing components. The expression patterns of genes identified in this screen were examined in the TMJ and compared to other synovial joints including the shoulder joint and the hip joint. Striking differences were noted, indicating that the TMJ forms via a distinct molecular program. Several components of the Hedgehog (Hh) signaling pathway are among the genes identified in the screen, including Gli2, which is expressed specifically in the condyle and in the disk of the developing TMJ. We found that mice deficient in Gli2 display aberrant TMJ development such that the condyle loses its growth plate-like cellular organization and no disk is formed. In addition, we utilized a conditional strategy to remove activity of the Hh co-receptor encoded by Smo from chondrocyte progenitors. This cell autonomous loss of Hh signaling allows for disk formation, but the resulting structure fails to separate from the condyle.  Thus, these experiments establish that Hh signaling acts at two distinct steps in disk morphogenesis, condyle initiation and disk-condyle separation, and provide a molecular framework for future studies of the TMJ.

overall_design: Mouse embryos fresh frozen and TMJ tissue captured by LCM. 3 samples in biological triplicate.

first: Patricia

last: Purcell

first: Clifford

last: Tabin


title: Global changes in processing of 3'-UTR characterize clinically distinct tumor types

city: Bar Harbor

first: priyam

last: singh

state: ME

address: 600 Main St

institute: The Jackson Laboratory

summary: We used a novel probe-level microarray analysis, revealing connections between mRNA processing and lymphoid neoplasia, in a mouse leukemia model. Characteristic differences in mRNA processing, primarily in the 3’-untranslated region, distinguished histologically similar tumor subtypes with different survival characteristics. Gene sets with specific processing in each tumor subtype defined signatures useful for tumor subclassification, as demonstrated by internal cross-validation with up to 80% discrimination accuracy. A combination of mRNA expression and sequence analysis suggested that differences in isoform abundance likely arose from both alternative polyadenylation and differential degradation.

overall_design: 5 types of samples were analyzed with multiple biological replicates. Progenitor B-cells, mature B-cells were the control. LPC, APC, APN were the tumor cells. LPC (Lig4/P53 deficient cells developed pro-B lymphoma with c-myc amplification), APC (Artemis/P53 deficient cells developed pro-B lymphoma with c-myc amplification), APN (Artemis/P53 deficient cells developed pro-B lymphoma with N-myc amplification)

first: Priyam

last: Singh

first: Travis

last: Alley

first: Sarah

last: Wright

first: Sonya

last: Kamdar

first: William

last: Schott

first: Robert

last: Wilpan

first: Kevin

last: Mills

first: Joel

last: Graber


title: Response of gastric epithelial progenitors to H. pylori isolates from Swedish patients with chronic atrophic gastritis

first: Jeremiah

last: Faith

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

sample_organism:
Helicobacter pylori
Mus musculus

platform_organism:
Helicobacter pylori
Mus musculus

overall_design: Refer to individual Series


title: Immortalized colonic epithelial progenitor cells express stem cell markers and differentiate in vitro

status: Public on Oct 07 2009

city: Dallas

first: Andres

last: Roig

state: TX

address: 5323 Harry Hines Blvd

department: Cell Biology

institute: UT Southwestern

summary:
Immortalized colonic epithelial progenitor cells derived from normal human colon biopsies express stem cell markers and differentiate in vitro
The sustained growth of normal non-transformed human colonic epithelial cells has historically been exceptionally challenging.  We here report the successful long-term propagation of colon biopsy derived cells expressing both epithelial and mesenchymal features, intestinal stem cell markers, and demonstrating multilineage epithelial differentiation capability.  Cells isolated from the biopsies of two patients undergoing routine screening colonoscopy have been successfully passaged in vitro, subsequently immortalized with non-oncogenic proteins (cyclin dependent kinase 4 [CDK4] and the catalytic component of human telomerase [hTERT]), and maintained for well over a year in continuous cell culture. Immunofluorescence experiments reveal the immortalized populations of cells significantly express the progenitor epithelial cell marker mucin-1 and the colon epithelial specific marker A33. In addition, staining shows subsets of cells express chromogranin A, mucin-2, and dipeptyl peptidase 4, corresponding to neuroendocrine, mucus secreting, and absorptive colonic cell lineages, respectively. The cells also possess some mesenchymal features, including vimentin and α- smooth muscle actin expression when proliferating actively.  Finally, immortalized cells express various stem cell markers including LGR5, BMI1, CD29, and CD44.  When cells are seeded at low density in Matrigel® in the absence of a mesenchymal feeder layer individual cells are able to divide and form self-organizing, cyst-like structures with a subset of cells exhibiting either mucin-2 or polarized villin staining. These findings demonstrate that the immortalized human colonic cells are capable of self renewal and multilineage differentiation.  These cells should serve as valuable cellular reagents for studying normal colon stem cell biology, differentiation, and disease development.

overall_design: Microarrays were performed on colonic epithelial cells from the two patients. These include:1. Log-growth phase early passage non-immortalized cells (controls). 2. Log-growth phase immortalized cells. 3. Immortalized cells in reduced serum (0.1% ) and reduced epithelial growth factor (EGF) (slow-growing cells). Immortalized cells in reduced serum (0.1% ), reduced EGF, and treated with GSK-3 beta inhibitor 6-bromoindirubin-3-oxime (BIO), (growth-arrested cells). duplicates were submitted for all four samples from each patient.

first: Ugur

last: Eskiocak

first: Suzie

middle: K

last: Hight

first: Sang

middle: B

last: Kim

first: Oliver

last: Delgado

first: Rhonda

last: Souza

first: Stuart

last: Spechler

first: Woodring

middle: E

first: Jerry

last: Shay


title: Expression data from AFB1-treated GNMT knockout mice

status: Public on Oct 02 2009

city: Taipei

first: Yi-Ming

middle: Arthur

last: Chen

state: Taiwan

address: 155, Li-Noun St., Sec. 2

department: AIDS Prevention and Research Center

country: Taiwan

institute: National Yang-Ming University

summary:
We report that liver nodules from 5/8 (62.5%) male and 4/5 (80%) female Gnmt-/- mice were diagnosed as having HCC.
Microarray analysis showed that genes involved in the following pathways were deregulated in different stages of tumorigenesis: Methylation, metabolism, signal transduction, cell proliferation, and cell adhesion.
This study reveals that GNMT plays an important role in the prevention of hepatotumorigenesis through regulating detoxification pathways. We postulate that GNMT is a stress-responsive protein and its expression may account for the gender difference of the susceptibility to liver cancer.

overall_design: Liver tissues from aflatoxin B1 (AFB1)-treated wild-type or Gnmt knockout mice at 11weeks old were used for RNA extraction and hybridization on Affymetrix microarrays. Total RNA were mixed in equal proportion from 3 mice.

first: Yi

first: S

middle: P

last: Liu

first: Y

last: Li

first: C

last: Lee

last: Yen

last: Liao


title: Expression profiling of NB4 cells after treatment with ATRA

status: Public on Oct 06 2009

first: Joop

middle: H.

last: Jansen

address: Geert Grooteplein Zuid 8

department: Laboratory for Hematology

institute: Radboud University Nijmegen Medical Centre

summary: In acute promyelocytic leukemia (APL), differentiation therapy with all-trans retinoic acid (ATRA)

overall_design: 4 samples at various times. No replicats

middle: H

first: Bert

middle: A

last: van der Reijden


title: Murine CD4+ T cells from DEREG mice expressing GFP under the control of the FoxP3 promotor

status: Public on Oct 03 2009

city: Braunschweig

first: Robert

last: Geffers

address: Inhoffenstr. 7

department: Dep. Molecular Bacteriology

institute: HCI - Helmholtz Centre for Infection Research

summary:
Naturally occurring CD25+CD4+ regulatory T cells (T reg cells) are currently intensively characterized because of their major importance in modulating host responses to tumors and infections, in preventing transplant rejection, and in inhibiting the development of autoimmunity and allergy. Originally, CD4+ T reg cells were identified exclusively by the constitutive expression of CD25, and many in vivo experiments have been performed using depleting antibodies directed against CD25. However, both the existence of CD25– T reg cells, especially within peripheral tissues, as well as the expression of CD25 on activated conventional T cells, which precludes discrimination between T reg cells and activated conventional T cells, limits the interpretation of data obtained by the use of anti-CD25 depleting antibodies. The most specific T reg cell marker currently known is the forkhead box transcription factor Foxp3, which has been shown to be expressed specifically in mouse CD4+ T reg cells and acts as a master switch in the regulation of their development and function. To address the question of the in vivo role of T reg cells in immunopathology, we have generated bacterial artificial chromosome (BAC)–transgenic mice termed depletion of regulatory T cell (DEREG) mice, which express a diphtheria toxin receptor (DTR) enhanced GFP (eGFP) fusion protein under the control of the foxp3 locus, allowing both detection and inducible depletion of Foxp3+ T reg cells. The gene expression profile of both CD4+eGFP+FoxP3+ and CD4+eGFPnegFoxP3neg cells isolated from DEREG mice was here analyzed by micro array.

Keywords: DEREG, FoxP3, FoxP3-EGFP, mouse, regulatory T cell, CD4

overall_design: CD4+GFP+FoxP3+ and CD4+GFPnegFoxP3neg cells were isolated from DEREG mice by negative selection of CD4+ T cells (Invitrogen Kit) and subsequent FACS sorting for GFP+ and GFPneg cells. Purity was greater than 99 %. cRNA was prepared according to the Affymetrix Labeling Protocol, fragmented and hybridized to Affymetrix GeneChip Mouse Genome 430.

first: R

first: K

last: Lahl

first: T

last: Sparwasser

first: D

last: Antz


title: Pathogenicity of a disease-associated human IL-4 receptor allele in experimental asthma

status: Public on Oct 01 2009

city: los angeles

first: Brian

last: O'Connor

address: 2018 Griffith Park Blvd

institute: UCLA

summary:
Polymorphisms in the interleukin-4 receptor α chain (IL-4Rα) have been linked to asthma incidence and severity, but a causal relationship has remained uncertain. In particular, a glutamine to arginine substitution at position 576 (Q576R) of IL-4Rα has been associated with severe asthma, especially in African Americans. We show that mice carrying the Q576R polymorphism exhibited intense allergen-induced airway inflammation and remodeling. The Q576R polymorphism did not affect proximal signal transducer and activator of transcription (STAT) 6 activation, but synergized with STAT6 in a gene target– and tissue-specific manner to mediate heightened expression of a subset of IL-4– and IL-13–responsive genes involved in allergic inflammation. Our findings indicate that the Q576R polymorphism directly promotes asthma in carrier populations by selectively augmenting IL-4Rα–dependent signaling.

Keywords: Cell population analysis

overall_design: To determine potential mechanisms underlying the trophic effects of the R576 allele on airway inflammation and remodeling, we first compared the gene expression profile in the lungs of doxycycline-treated B6.129Il4raR576/R576/IL-13tg mice versus B6.129Il4raR576/R576 littermates that lacked the IL-13tg (n = 11 and 5, respectively). We similarly compared the gene expression profile in the lungs of doxycycline-treated B6.Il4raQ576/Q576/IL-13tg mice versus tg-negative littermates (n = 8 and 5, respectively). Lastly, we directly compared the gene expression profiles in the doxycycline-treated B6.129Il4raR576/R576/IL-13tg versus B6.Il4raQ576/Q576/IL-13tg mice.

middle: D

first: Talal

last: Chatila


title: Analysis of gene expression in FACS-purified cortical projection neurons using Affymetrix 430 2.0 microarrays

first: Bradley

last: Molyneaux

department: MGH-HMS Center For Nervous System Repair

summary: 3 subtypes of cortical projection neurons were purified by fluorescence-activated cell sorting (FACS) at 4 different stages of development from mouse cortex. A detailed description of the data set is described in Arlotta, P et al (2005) and Molyneaux, BJ et al (2009). The hybridization cocktails used here were originally applied to the Affymetrix mouse 430A arrays and submitted as GEO accession number GSE2039. The same hybridization cocktails were then applied to the Affymetrix mouse 430 2.0 arrays, and those data are contained in this series.

overall_design: Three subtypes of cortical neurons were purified by FACS at multiple stages of mouse brain development. The neuron subtypes are: corticospinal motor neurons (CSMN), callosal projection neurons (CPN), and corticotectal projection neurons (CTPN). The stages of development included embryonic day 18 (E18), postnatal day 3 (P3), postnatal day 6 (P6), and postnatal day 14 (P14). CSMN and CPN were analyzed at all four stages, while CTPN were only analyzed at P14. The replicates included in the data set are all true biological replicates with independent sample collection for each.

middle: J

first: Paola

last: Arotta

first: Jeffrey

last: Macklis


title: DNA hypomethylation leads to derepression of myeloerythroid genes in hematopoietic stem cells (HSC)

city: Berlin

first: Frank

last: Rosenbauer

state: Berlin

address: Robert-Rössle-Str. 10

institute: Max Delbrück Center for Molecular Medicine (MDC)

summary: Analysis of hematopoietic stem cells (HSC, LSK Flt3-) and myeloid progenitors (MP, LK CD34+) sorted from wildtype and Dnmt1 hypomorph mice

overall_design: We FACS sorted HSCs and MPs from bone marrow of 8-12 week old wildtype or Dnmt1 hypomorph (Dnmt1-/chip) mice.

first: Ann-Marie

last: Bröske

first: Lena

last: Vockentanz

first: Matthew

middle: R

last: Huska

first: Miguel

last: Andrade-Navarro


title: Gene expression in FACS-purified cortical projection neurons


title: Gene Expression Profiling of Glomeruli from a mouse model of Denys-Drash Syndrome

city: Paris

first: julien

last: Ratelade

address: 149 rue de Sèvres

country: France

institute: INSERM U574

summary:
The Wilms tumor-suppressor gene WT1, a key player in renal development, also has a crucial role in maintenance of the glomerulus in the mature kidney. However, molecular pathways orchestrated by WT1 in podocytes, where it is highly expressed, remain unknown. Their defects are thought to modify the cross-talk between podocytes and other glomerular cells and ultimately lead to glomerular sclerosis, as observed in diffuse mesangial sclerosis (DMS) a nephropathy associated with WT1 mutations.
To identify podocyte WT1 targets, we generated a novel DMS mouse line, performed gene expression profiling in isolated glomeruli, and identified excellent candidates that may modify podocyte differentiation and growth factor signalling in glomeruli. Scel, encoding sciellin, a protein of the cornified envelope in the skin, and sulf1, encoding a 6-O endosulfatase, are shown to be expressed in wild type podocytes and to be strongly down-regulated in mutants. Co-expression of Wt1, Scel and Sulf1 was also found in a mesonephric cell line, and siRNA-mediated knockdown of WT1 decreased Scel and Sulf1 mRNAs and proteins. By ChIP we show that Scel and Sulf1 are direct WT1 targets. Cyp26a1, encoding an enzyme involved in the degradation of retinoic acid, is shown to be up-regulated in mutant podocytes. Cyp26a1 may play a role in the development of glomerular lesions but does not seem to be regulated by WT1. These results provide novel clues in our understanding of normal glomerular function and early events involved in glomerulosclerosis.

overall_design: Isolation of glomeruli from mutant (FVB-N4 Wt1+/R394W) and wild-type (FVB-N4 Wt1+/+) was performed after cardiac Dynabead perfusion. GeneChip analysis of glomeruli from 5 Wt1+/R394W mice and 5 Wt1+/+ littermates (N4-FVB) were performed independently. Animals were unweaned 27-day-old males. The Wt1+/R394W mice used were showing little albuminuria (<3 ug/ul on Coomassie blue stained SDS-PAGE gel) and no evidence of mesangial lesions by light microscopy.

first: Julien

first: Christelle

last: Arrondel

first: Ghislaine

last: Hamard

first: Serge

last: Garbay

first: Scott

last: Harvey

first: Nathalie

last: Biebuyck

first: Herbert

last: Schulz

first: Nick

last: Hastie

first: Marco

last: Pontoglio

first: Marie-Claire

last: Gubler

first: Corinne

last: Antignac

first: Laurence

last: Heidet


title: Transcriptional regulation by Norrin-Frizzled4 signaling

city: Baltimore

first: Xin

last: Ye

address: 725 N Wolfe Street, PCTB 805

institute: Johns Hopkins School of Medicine


title: Effect of age on the arthritis susceptibility of BALB/c mice

status: Public on Oct 09 2009

city: Chicago

first: Tibor

last: Glant

state: IL

address: 1735 West Harrison

department: Orthopedic Surgery

institute: Rush University Medical Center

summary:
Rheumatoid arthritis (RA) usually begins in females in their 4th-5th decade, suggesting that the aging of the immune system (immunosenescence) has a major impact on this disease.
In the present microarray study, we set out to identify age- and arthritis-related gene expression pattern changes in proteoglycan (aggrecan)-induced arthritis (PGIA) model.

Keywords: disease state analysis

overall_design: We compared the gene expression profile of spleens from PG-immunized but non-arthritic old (older than 4 months) and young (1 month old) mice, and then made a comparison between non-arthritic and age-matched arthritic mice.

first: Ferenc

last: Boldizsar

first: Oktavia

last: Tarjanyi

first: Peter

last: Larsen

first: Anna

last: Laszlo


title: Long-term effect on the transcriptome of a decrement in Norrin/Frizzled4/Lrp signaling in retinal endothelial cells

summary: To characterize the long-term effect on the transcriptome of a decrement in Norrin/Fz4/Lrp signaling, microarray hybridization was performed with RNA from acutely dissociated and anti-PECAM immunoaffinity-purified adult WT, Fz4-/-, Lrp5-/-, and Norrin- retinal vascular cells.

overall_design: Retinal endothelial cells from 5-10 adult mice were pooled for each sample, the cell immuno-purification procedure follows that described by Matsubara et al. (2000) and Su et al. (2003). 3 replicates of each mutant and 6 replicates of control wild type animals were analyzed.

first: Yanshu

last: Wang

first: Jeremy

last: Nathans


title: Transcriptional regulation by Norrin-Frizzled4 signaling in the embryonic yolk sac

summary: Transcriptional profiles of the embryonic yolk sac from embryos with ectopic Norrin expression were compared to their wild type littermate controls. The goal is to identify the transcriptional response to Norrin-Frizzled 4 signaling during embryonic angiogenesis.

overall_design: Ectopic Norrin expression was achieved using a conditional over-expression strategy. Yolk sacs from 3-5 embryos were pooled for each sample and 3 replicates of both control and experimental groups were analyzed.


title: Transcriptional response to Frizzled4 signaling in cultured retinal endothelial cells

summary: Transcriptional profiles of Fz4-/- retinal endothelial cells were compared to that of wild type endothelial cells under various culture conditions. The goal was to identify the transcriptional response to Frizzled 4 signaling in cultured retinal endothelial cells. To analyze the Norrin response of WT and Fz4-/- retinal endothelial cells in culture, we co-cultured these cells either with HEK293 cell line that stably expresses Norrin or with control 293 cells.

overall_design: To isolate the requisite retinal endothelial cell lines, we crossed Fz4-/- and control animals into the "Immorto-mouse" line in which a gamma interferon responsive H2Kb promoter directs the expression of a temperature sensitive SV40 large T-antigen (Jat et al., 1991). When cultured at 33°C in the presence of gamma interferon, this conditional oncogene system extends the proliferative capacity of a variety of cell types, which can be subsequently analyzed under phenotypically reverting conditions (37°C without gamma interferon). The cell immuno-purification procedure follows that described by Matsubara et al. (2000) and Su et al. (2003). The purified cells were then cultured and passaged at 33°C on dishes coated with 1% gelatin. For RNA preparation, cells were cultured at 37°C in the absence of interferon gamma. For the Matrigel experiments, endothelial cells previously starved for 24 hrs in DMEM with 1% FBS were trypsinized and plated on the Matrigel layer. The cells were incubated in DMEM with 1% FBS for 6 hours at 37°C before harvesting for RNA extraction. For the 293 cell co-culture experiments, endothelial cells were co-cultured with a human embryonic kidney (HEK) 293 cell line that stably expresses Norrin, or with control 293 cells.


title: Long-term effect on the transcriptome of loss of Frizzled4 signaling in cerebellar endothelial cells

summary: Transcriptional profiles of the cerebellar endothelial cells from P16 Fz4-/- animals were compared to their wild type littermate controls. The goal is to characterize the long-term effect on the transcriptome of loss of Fz4 signaling in cerebellar endothelial cells.

overall_design: Endothelial cells were immuno-purification from P16 cerebellum using anti-PECAM antibody coated dynabeads. The cell immuno-purification procedure follows that described by Matsubara et al. (2000) and Su et al. (2003). 3 replicates of both wild type and Fz4-/- cerebellar endothelial cells were analyzed.


title: Estimating accuracy of absolute gene expression measurement by RNA-Seq and microarrays with proteomics

city: Shanghai

first: Xing

last: Fu

address: 3888 Chenhua Road

institute: Shanghai Center for Plant Stress Biology, Chinese Academy of Sciences

summary:
Microarrays revolutionized biological research by enabling gene expression comparisons on a transcriptome-wide scale. Microarrays, however, do not estimate absolute expression level accurately. At present, high throughput sequencing is emerging as an alternative methodology for transcriptome studies. Although free of many limitations imposed by microarray design, its potential to estimate absolute transcript levels is unknown.
In this study, we evaluate relative accuracy of microarrays and transcriptome sequencing (RNA-Seq) using third methodology: proteomics. We find that RNA-Seq provides a better estimate of absolute expression levels.

overall_design:
We first determined whether we could reproduce the agreement between mRNA expression estimates measured by microarrays and by RNA-Seq reported in other studies. For this purpose, we collected mRNA expression data in two independent cerebellar samples, each containing pooled mRNA from 5 adult human individuals, using both methodologies.
Next, to test whether biological variation among samples would substantially reduce correlation strength, we compared expression levels determined by RNA-Seq in two pooled samples to the microarray data obtained from different individuals. For this purpose we used expression measurements obtained using Affymetrix Exon Arrays in 5 individual adult human cerebellar samples, none of which were included in the two pooled samples.
Further, since technical and stochastic variation are extremely unlikely to result in better correlation between mRNA and protein expression measurements, we argue that the technology resulting in better correlation must provide more accurate measurements.

first: Song

last: Guo

first: Zheng

last: Yan

first: Philipp

last: Khaitovich