title: Ager (Rage) and Myd88 deletion in resected mouse livers

status: Public on Jun 26 2012

first: Ann

middle: Marie

last: Schmidt

state: NY

department: Department of Surgery

institute: Columbia University

summary: The effect of resection of mouse livers on survival serve as a model for the effect of resection of human livers, which are performed for both the purposes of removing sick tissue and for transplanting healthy tissue. When less than 70% of a mouse liver is resected, the mouse usually lives. However, when more than 70% is resected, there is an increased probability that the mouse will die. We have found that deletion of Ager (Advanced Glycation End products receptor) (Rage) increases the chance of mouse survival relavtive to WT. Conversely, the deletion of Myd88 decreases the chances of survival, as does the simultaneous deletion of both Ager and Myd88. To understand these genotype/phenotype relations, we performed gene expression measurements.

overall_design: Gene expression of livers of WT C57BL/6 mice, Ager-null C57BL/6 mice, Myd88-null C57BL/6 mice, and Ager-null/Myd88-null C57BL/6 mice, all 10-12 weeks-old and sacrificed 2 hours after 85% liver resection, were compared. 4-6 replicates each group.

first: Shan

last: Zeng

first: Qing

middle: Y

last: Zhang

first: Srinivasan

last: Vedantham

first: Rosa

last: Rosario

first: Radha

last: Ananthakrishnan

first: Shi

middle: F

last: Yan

first: Richard

last: Friedman

first: Jean

middle: C

last: Emond


title: Effects of the long noncoding RNA Malat1 on gene expression [Mouse430_2]

status: Public on Jun 25 2012

city: Wako

first: Yuen Yan

middle: Joanna

last: Ip

state: Saitama

address: 2-1 Hirosawa

department: Advanced Science Institute

country: Japan

institute: RIKEN

summary:
Malat1 is an abundant long noncoding RNA that localizes to nuclear bodies known as nuclear speckles, which contain a distinct set of pre-mRNA processing factors. Previous in vitro studies have demonstrated that Malat1 interacts with pre-mRNA splicing factors, including the serine- and arginine-rich (SR) family of proteins, and regulates a variety of biological processes, including cancer cell migration, synapse formation, cell cycle progression, and responses to serum stimulation. To address the physiological function of Malat1 in a living organism, we generated Malat1-KO (KO) mice using homologous recombination. Unexpectedly, the Malat1-KO mice were viable and fertile, showing no apparent phenotypes. Nuclear speckle markers were also correctly localized in cells that lacked Malat1. However, the cellular levels of another long noncoding RNA, Neat1, which is an architectural component of nuclear bodies known as paraspeckles, were downregulated in a particular set of tissues and cells lacking Malat1.
To address if the the absence of Malat1 affects the expression of other genes, including other long noncoding RNA, microarrays were used to study the impact of knocking-out Malat1 on global gene expression in mouse embryonic fibroblasts (MEFs).

overall_design: MEFs were prepared from E13.5 mouse embryos from wildtype and Malat1 knock-out mice. RNA harvested from these cells were hybridized to Affymetirx mouse gene expression array.

first: Shinichi

last: Nakagawa

first: Joanna


title: Myc and Miz-1 control melanocyte senescence by regulating intracellular cystathionase levels

status: Public on Jul 03 2012

city: Wuerzburg

first: Susanne

middle: Elma

last: Kneitz

address: Biozentrum, Am Hubland

department: Physiologigcal Chemistry

country: Germany

institute: University of Wuerzburg

summary: The development of malignant melanoma is a highly complex process which is still poorly understood despite extensive research. A majority of human melanomas are found to express a handful of oncogenic proteins, such as mutant RAS and BRAF. However, these oncogenes are also found in nevi, and it is now a well-accepted fact that their expression alone leads to senescence. This renders the understanding of senescence escape mechanisms an important criterion to understand tumor development.   Here, we describe the ability of the transcription factor MYC to drive the evasion of reactive oxygen stress-induced melanocyte senescence, caused by activated receptor tyrosine kinase signaling. Conversely, MIZ1, the growth suppressing interaction partner of MYC, is involved in mediating melanocyte senescence. Both, MYC overexpression and Miz1 knockdown led to a strong reduction of endogenous reactive oxygen species (ROS), DNA damage and senescence. We identified the cystathionase (CTH) gene product as mediator of the ROS-related MYC and MIZ1 effects. Blocking CTH enzymatic activity in MYC-overexpressing and Miz1 knockdown cells increased intracellular stress and senescence. Importantly, pharmacological inhibition of cystathionase in human melanoma cells also reconstituted senescence in many cell lines, and CTH knockdown reduced tumorigenic effects such as proliferation, H2O2 resistance and soft agar growth. Thus, we identified cystathionase as new MYC target gene with an important function in MYC-mediated senescence evasion.

overall_design: total samples analysed are 4

first: Claudia

last: Leikam

first: Anita

last: Hufnagel

last: Walz

first: Martin

last: Eilers

first: Manfred

last: Schartl

first: Svenja

last: Meierjohann


title: Microarray of Rnaseh2b KOF and RnaseH2b wild type fetal liver

city: Dresden

first: Björn

last: Hiller

address: Fiedlerstrasse 42

department: Institute for Immunology

institute: TU Dresden

summary: Fetal liver of E14.5 RNaseh2b KOF and Rnaseh2b wild type embryos was isolated, RNA was extracted and microarray analysis using Affymetrix Mouse 430 2.0 gene chip was performed

overall_design: three Rnaseh2b KOF and three RNaseh2b wild type littermates were compared

first: Axel

last: Roers


title: Effect of TIF1γ gene deletion on hematopoietic stem cells

city: Illkirch

first: Doulaye

last: Dembele

address: 1 rue Laurent Fries

department: Biopuces

country: France

institute: IGBMC

summary:
Analysis of KLS cells purified from bone marrow of mice conditionally inactivated for TIF1γ gene. TIF1γ deletion results in multiple defects in adult hematopoiesis. Results provide insight into the role of TIF1γ in hematopoietic stem cells functions.
We used microarrays to characterize the molecular mechanisms underlying the biological properties of KLS cells lacking TIF1γ

overall_design: KLS (lin-,c-kit+, Sca+) cells were purified by cell sorting

first: Paul-Henri

last: Romeo


title: Diverse epigenetic strategies interact to control epidermal differentiation

status: Public on Jun 24 2012

city: Cambridge

first: Chandra

last: Chilamakuri

address: Robinson Way

country: United Kingdom

institute: Cancer Research UK Cambridge Institute

type: Genome binding/occupancy profiling by high throughput sequencing

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

overall_design: Refer to individual Series


title: Preoperative Diagnosis of Benign Thyroid Nodules with Indeterminate Cytology

city: South San Francisco

first: James

last: Diggans

state: CA

address: 7000 Shoreline Ct

country: USA

institute: Veracyte Inc.

summary:
BACKGROUND: Following fine needle aspiration, 15-30% of thyroid nodules are not clearly benign or malignant. These cytologically indeterminate nodules are often referred for diagnostic surgery, though most prove benign. A novel diagnostic test measuring the expression of 167 genes has shown promise in improving pre-operative risk assessment. We evaluated this test in a prospective, multicenter study.

METHODS: Over 19 months, we performed a prospective study at 49 clinical sites enrolling 3,789 patients and collecting 4,812 samples from thyroid nodules >1cm requiring evaluation. We obtained 577 cytologically indeterminate aspirates with corresponding histopathology of excised lesions on 413. Central blinded histopathologic review served as the reference (“gold”) standard. After applying inclusion criteria, gene expression classifier results were obtained for 265 indeterminate nodules used in this analysis, and performance was calculated.

RESULTS: 85 of 265 indeterminate nodules were malignant. The gene expression classifier correctly identified 78 of 85 as ‘suspicious’ (92% sensitivity, [84%-97%] 95% CI). Specificity was 52%, [44%-59%]. The negative predictive value was 95%, 94%, and 85%, respectively, for aspirates with AUS/FLUS, FN/SFN, or ‘suspicious’ cytology. Analysis of 7 false negative cases revealed 6 with a paucity of thyroid follicular cells, suggesting that insufficient sampling of the nodule had occurred.

CONCLUSIONS: Though individualized clinical care is recommended, these data support consideration of a conservative approach for most patients with indeterminate FNA cytology and benign gene expression classifier results.

overall_design:
265 cytologically indetermine samples, 47 cytologically benign and 55 cytologically malignant samples.

Note: The CDF file for Platform GPL14961 is proprietary.

first: Erik

middle: K

last: Alexander

first: Giulia

last: Kennedy

first: Zubair

middle: W

last: Baloch

first: Edmund

middle: S

last: Cibas

first: Darya

last: Chudova

first: Lyssa

middle: T

last: Kloos

first: Virginia

middle: A

last: LiVolsi

first: Susan

middle: J

last: Mandel

first: Stephen

last: Raab

first: Juan

last: Rosai

first: David

middle: L

last: Steward

first: Sean

last: Walsh

first: Jonathan

middle: I

last: Wilde

first: Martha

last: Zeiger

middle: B

last: Lanman

first: Bryan

middle: R

last: Haugen


title: Genome wide analysis of pancreatic gene expression by Interleukin 1β in human epithelial pancreatic Mia Paca-2 cells.

status: Public on Jun 21 2012

city: Delhi

first: Malabika

last: Datta

address: Mall Road

country: India

institute: Institute of Genomics and Integrative Biology

summary: Analysis of the pancreatic gene expression with IL-1β stimulation. Components of the integrin pathway were significantly altered with IL-1β which play critical role in the execution of apoptosis.The results revealed several important cellular pathways and the biological processes of the genes (Up and Downregulated) altered by IL-1β induction.

overall_design: Total RNA was isolated from cells incubated in the absence (Control) and presence of IL-1β (2ng/ml) for 36 hours. These were then subjected to microarray hybridisation in a WG_6_V3 bead chip, Illumina. Differentially expressed genes were functionally categorised into biological processess and cellular pathways using the PANTHER Classification system. The significantly emerging cellualr pathway was validated by Western Blot analyses.

first: Gaurav

last: Verma


title: Wild Type Tumor Repressor Protein 53 (TRP53) Promotes Ovarian Cancer Cell survival

city: Houston

first: JoAnne

last: Richards

state: TX

address: One Baylor Plaza

department: Molecular and Cellular Biology

institute: Baylor College of Medicine

summary: Loss of Pten in the KrasG12D;Amhr2-Cre mutant mice leads to the transformation of ovarian surface epithelial (OSE) cells and rapid development of low-grade, invasive serous adenocarcinomas. Tumors occur with 100% penetrance and express elevated expression of wild type tumor repressor protein 53 (TRP53).  To test the functions of TRP53 in the Pten;Kras (Trp53+) mice, we disrupted the Trp53 gene yielding Pten;Kras(Trp53-) mice.   By comparing morphology and gene expression profiles in the Trp53+ and Trp53- OSE cells, we document that wild-type TRP53 acts as a major promoter of OSE cell survival and differentiation: cells lacking Trp53 are transformed yet are less adherent, migratory and invasive and exhibit a gene expression profile more like normal OSE cells. These results provide a new paradigm: wild type TRP53 does not preferentially induce apoptotic or senescent related genes in the Pten;Kras(Trp53+) cancer cells but rather increases genes regulating DNA repair, cell cycle progression and proliferation and decreases putative tumor suppressor genes. However, if TRP53 activity is forced higher by exposure to nutlin-3a (an MDM2 antagonist), TRP53 suppresses DNA repair genes and induces the expression of genes that control cell cycle arrest and apoptosis.  Thus, in the Pten;Kras(Trp53+) mutant mouse OSE cells and likely in human TP53+ low grade ovarian cancer cells, wild type TRP53 controls global molecular changes that are dependent on its activation status. These results suggest that activation of TP53 may provide a promising new therapy for managing type I ovarian cancer and other cancers in humans where wild-type TP53 is expressed.

overall_design: A direct comparison of ovarian surface epithelia cells from three different genotype mice

first: Lisa

last: Mullany

first: Zhilin

last: Liu

first: Erin

last: King

first: Kwong-Kwok

last: Wong


title: Global Differential Gene Expression Analysis of Spontaneous Lung Tumors in B6C3F1 Mice: Comparison to Human Non-Small Cell Lung Cancer

status: Public on Jun 22 2012

city: RTP

first: NIEHS

last: Microarray Core

state: NC

address: 111 T.W. Alexander Drive

department: DIR

institute: NIEHS

summary: Introduction: Lung cancer is the leading cause of cancer-related death in people. There are several chemically induced and genetically modified mouse models used to study lung cancer. We hypothesized that spontaneous murine (B6C3F1) lung tumors can serve as a model to study human non-small cell lung cancer (NSCLC).    Methods: RNA was extracted from untreated 2-year-old B6C3F1 mouse spontaneous lung (SL) tumors and age-matched normal lung tissue from a chronic inhalation NTP study. Global gene expression analysis was performed using Affymetrix Mouse Genome 430 2.0 GeneChip® arrays. After data normalization, for each probe set, pairwise comparisons between groups were made using a bootstrap t-test while controlling the mixed directional false discovery rate (mdFDR) to generate a differential gene expression list. IPA, KEGG, and EASE software tools were used to evaluate the overrepresented cancer genes and pathways.     Results: MAPK and TGF-beta pathways were overrepresented within the dataset. Almost all of the validated genes by quantitative real time RT-PCR had comparable directional fold changes with the microarray data. The candidate oncogenes included Kras, Braf, Raf1, Id2, Hmga1, Cks1b, and Foxf1. The candidate tumor suppressor genes included Rb1, Cdkn2a, Hnf4a, Tcf21, Ptprd, Hpgd, Hopx, Ogn, Id4, Hoxa5, Smad6, Smad7, Zbtb16, Cyr61, Dusp4, and Ifi16. In addition, several genes important in lung development were also differentially expressed, such as Smad6, Hopx, Sox4, Sox9 and Mycn.     Conclusion: In this study, we have demonstrated that several cancer genes and signaling pathways relevant for human NSCLC were similarly altered in spontaneous murine lung tumors.

overall_design: Six spontaneous lung tumors and six normal lungs (as controls) from 2-year-old B6C3F1 mice.

first: Arun

last: Pandiri

first: Mark

last: Hoenerhoff

first: Vincent

last: Ziglioli

first: Stephanie

last: Lahousse

first: Thai-Vu

last: Ton

first: Hue-Hae

last: Hong

first: Shyamal

middle: D

last: Peddada

first: Keith

last: Shockley

first: Pierre

last: Bushel

first: Scott

last: Auerbach

first: Kevin

middle: E

last: Gerrish

first: Robert

last: Sills


title: Diverse epigenetic strategies interact to control epidermal differentiation [Illumina bead array]

first: Chandra

last: Chilamakuri

summary: It is becoming clear that interconnected functional gene networks, rather than single genes in isolation, govern stem cell self-renewal and differentiation. To identify potential epigenetic networks that impact on human epidermal stem cells we performed siRNA based genetic screens for 332 chromatin modifiers. We developed a Bayesian mixture model to predict putative functional interactions between those epigenetic modifiers that regulated differentiation. This allowed us to discover a network of genetic interactions involving EZH2, UHRF1 (both known to regulate epidermal self-renewal), ING5 (a MORF complex component), BPTF and SMARCA5 (NURF complex components). Genome-wide localisation and global mRNA expression analysis revealed that these factors impact two distinct but functionally related gene sets, including integrin extracellular matrix receptors that mediate anchorage of epidermal stem cells to their niche. Using a competitive epidermal reconstitution assay we confirmed that ING5, BPTF, SMARCA5, EZH2 and UHRF1 control differentiation under physiological conditions. Thus, regulation of distinct gene expression programs through the interplay between diverse epigenetic strategies protects epidermal stem cells from differentiation.

overall_design: Primary human keratinocytes (line Lka, passage 2) were cultured in Keratinocyte Serum Free Medium (KSFM) to 70% confluency in 10 cm dishes. Cells were treated with: vehicle (0.2% DMSO), the EGFR inhibitor AG1478 (10 uM), recombinant human BMP2/7 heterodimer (200 ng/ml) or a combination of AG1478+BMP2/7 (10 uM and 200 ng/ml, respectively) for 48 hours. RNA was extracted directly using a Qiagen RNeasy kit

first: Klaas

last: Mulder

first: Fiona

middle: M

last: Watt


title: Saturated fat stimulates obesity and hepatic steatosis and affects gut microbiota composition by an enhanced overflow of dietary fat to the distal intestine

status: Public on Jun 18 2012

city: Wageningen

first: Guido

last: Hooiveld

address: HELIX, Stippeneng 4

department: Div. Human Nutrition & Health

country: Netherlands

institute: Wageningen University

summary:
We studied the effect of dietary fat type, varying in polyunsaturated/saturated fatty acid ratio's (P/S) on development of metabolic syndrome. C57Bl/6J mice were fed purified high-fat diets (45E% fat) containing palm oil (HF-PO; P/S 0.4), olive oil (HF-OO; P/S 1.1) or safflower oil (HF-SO; P/S 7.8) for 8 weeks. A low-fat palm oil diet (LF-PO; 10E% fat) was used as a reference. Additionally, we analyzed diet-induced changes in gut microbiota composition and mucosal gene expression. The HF-PO diet induced a higher body weight gain and liver triglyceride content compared to the HF-OO, HF-SO or LF-PO diet. In the intestine, the HF-PO diet reduced microbial diversity and increased the Firmicutes/Bacteroidetes ratio. Although this fits a typical obesity profile, our data clearly indicate that an overflow of the HF-PO diet to the distal intestine, rather than obesity itself, is the main trigger for these gut microbiota changes. A HF-PO diet-induced elevation of lipid metabolism-related genes in the distal small intestine confirmed the overflow of palm oil to the distal intestine. Some of these lipid metabolism-related genes were previously already associated with the metabolic syndrome. In conclusion, our data indicate that saturated fat (HF-PO) has a more stimulatory effect on weight gain and hepatic lipid accumulation than unsaturated fat (HF-OO and HF-SO). The overflow of fat to the distal intestine on the HF-PO diet induced changes in gut microbiota composition and mucosal gene expression. We speculate that both are directly or indirectly contributive to the saturated fat-induced development of obesity and hepatic steatosis.

Keywords: Diet intervention study

overall_design: Nine-week-old C57Bl/6J mice were fed a low-fat diet (LF-PO) and three different types of high-fat diet, based on palm oil (HF-PO; P/S1.0), olive oil (HF-OO; P/S4.6) and safflower oil (HF-SO; P/S10.1) for 8 weeks. Body weight was recorded weekly and after 7 weeks of diet intervention an oral glucose tolerance test was performed. After 2 weeks of diet intervention, 6 mice per high-fat diet group were anaesthetized with a mixture of isofluorane (1.5%), nitrous oxide (70%) and oxygen (30%) and the small intestines were excised. Adhering fat and pancreatic tissue were carefully removed. The small intestines were divided in three equal parts along the proximal to distal axis (SI 1, SI 2 and SI 3) and microarray analysis was performed on mucosal scrapings.

first: Nicole

last: de Wit

first: Els

last: Oosterink

first: Hanneke

last: Bosch-Vermeulen

first: Shohreh

last: Keshtkar

first: Caroline

last: Duval

first: Johan

last: de Vogel-van den Bosch

first: Michael

last: Muller

first: Roelof

last: van der Meer


title: Polyglutamine expanded huntingtin dramatically alters the genome-wide binding of HSF1 (mRNA)

status: Public on Jun 19 2012

first: Laura

last: Riva

state: MA

address: 77 Massachusetts Avenue

department: Biological Engineering

institute: MIT

summary: In Huntington’s disease (HD), polyglutamine  expansions in the huntingtin (Htt) protein cause subtle changes in cellular functions that, over-time, lead to neurodegeneration and death. Studies have indicated that activation of the heat shock response can reduce many of the effects of mutant Htt in disease models, suggesting that the heat shock response is impaired in the disease. To understand the basis for this impairment, we have used genome-wide chromatin immunoprecipitation followed by massively parallel sequencing (ChIP-Seq) to examine the effects of mutant Htt on the master regulator of the heat shock response, HSF1. We find that, under normal conditions, HSF1 function is highly similar in cells carrying either wild-type or mutant Htt. However, polyQ-expanded Htt severely blunts the HSF1-mediated stress response. Surprisingly, we find that the HSF1 targets most affected upon stress are not directly associated with proteostasis, but with cytoskeletal binding, focal adhesion and GTPase activity.  Our data raise the intriguing hypothesis that the accumulated damage from life-long impairment in these stress responses may contribute significantly to the etiology of Huntington's disease.

overall_design: Affymetrix MG430 2.0 expression levels of wild-type (STHdhQ7/Q7) and mutant (STHdhQ111/Q111) striatal cells under growth condition (33°C) and upon heat shock (42°C for six hours)

first: Martina

last: Koeva

first: Ferah

last: Yildirim

first: Leila

last: Pirhaji

first: Deepika

last: Dinesh

first: Tali

last: Mazor

first: Martin

last: Duennwald

first: Ernest

last: Fraenkel


title: Expression analysis of mouse embryo fibrobalsts lacking Tgif1

city: Charlotesville

first: David

last: Wotton

department: Biochemistry and Molecular Genetics

institute: University of Virginia

summary:
Tgif1 is a transcriptional corepressor that limits TGFβ responsive gene expression. TGFβ signaling has antiproliferative effects in several cell types, generally resulting in a G1 arrest. Mouse embryo fibroblasts (MEFs) are primary cells with limited life-span, that senesce after several passages in culture.
We compared expression profiles of primary MEFs lacking Tgif1 with wild types at passage three, and with wild type MEFs at passage 5, to identify changes in gene expression due to loss of Tgif1 and due to increasing passage number.

overall_design: Primary MEFs were passaged on a 3T3 protocol and were harvested at passage 3 or 5, for RNA isolation and hybridization to Affymetrix microarrays.

first: Brad

last: Zerlanko


title: Early transcriptional changes linked to naturally occurring Huntington's disease mutations in human embryonic stem cells

status: Public on Jun 20 2012

city: CARDIFF

first: Peter

last: Giles

address: Heath Park

institute: Cardiff University

summary: Multiple human embryonic stem (ES) cell lines derived from blastocysts diagnosed as carrying the mutant huntingtin gene by pre-implantation diagnosis were used to explore early developmental changes in gene expression. How mutant huntingtin impacts on signalling pathways in the pre-symptomatic period has remained essentially unexplored in humans due to a previous lack of appropriate models.

overall_design: Total RNA was isolated from 10 human ES cell lines, 6 HD and 4 wild type control, and their neural stem cell (NSC) progeny.

first: Maxime

last: Feyeux

first: Amanda

last: Redfern

first: Nicholas

last: Allen

first: Anselme

last: Perrier


title: Transcriptional profiling of ex vivo isolated mouse blood vascular and lymphatic endothelial cells

status: Public on Jun 16 2012

city: Zurich

first: Giorgia

last: Jurisic

address: Wolfgang-Pauli Strasse 10

department: Institute of Pharmaceutical Sciences

country: Switzerland

institute: ETH Zurich

summary: The lymphatic vascular system plays important roles in the maintenance of interstitial fluid pressure, the afferent immune response and the absorption of dietary lipids. However, the molecular mechanisms that control lymphatic vessel network maturation and function remain largely unknown. To identify novel players in lymphatic vessel function, we isolated pure populations of lymphatic and blood vascular endothelial cells from mouse intestine using fluorescence-activated high-speed cell sorting and performed transcriptional profiling. We found that the axonal guidance molecules semaphorin 3A (Sema3A) and Sema3D were specifically expressed by lymphatic vessels. Quantitative PCR of ex vivo isolated cells and immunohistochemical analysis confirmed these results. Importantly, we found that the semaphorin receptor neuropilin-1 (Nrp-1) is expressed on the valves of collecting lymphatic vessels.  Treatment of mice in utero (E12.5-E16.5) with an antibody that blocks Sema3A binding to Nrp-1, but not with an antibody that blocks VEGFA binding to Nrp-1, resulted in abnormal development of collecting lymphatic vessels and valves, and aberrant smooth muscle cell coverage. Conversely, Sema3A-deficient mice displayed branching defects of collecting lymphatic vessels as well as impaired valve development. Together, these results reveal an unanticipated role of Sema3A/Nrp-1 signaling in the maturation of the lymphatic vascular network.

overall_design: Colon single-cell suspensions were prepared by a fast protocol that minimizes the RNA degradation. Fluorescence-activated cell sorting (FACS) was used to sort blood vascular endothelial cells (BEC) and lymphatic endothelial cells (LEC). 4 animal-matched pairs of LEC and BEC were chosen based on the quality of extracted and amplified material to provide homogenous groups of biological replicates. This gave 8 samples to analyze. Samples present LEC and BEC isolated from 4 healthy normal mice. The 4 mice used present the 4 biological replicates.

first: Michael

last: Detmar


title: Genome-wide analysis of three clonal neural stem cell lines derived from human foetal spinal cord tissue.

city: London

first: Graham

last: Cocks

address: The James Black Centre, 125 Coldharbour Lane

department: Neuroscience

institute: King's College London

summary: Stem cells have received substantial interest both for their potential as in vitro tools to study development and as potential therapeutic agents in a range of degenerative diseases of the nervous system. We have generated clonal neural stem cell lines from human foetal spinal cord conditionally immortalised with 4-hydroxy tamoxifen inducible cMyc (cMycERTAM), and performed a detailed assessment of their identity in terms of their expression of homeodomain transcription factors and their capacity to generate particular neuronal subtypes of the spinal cord. These lines retain a ventral spinal cord progenitor phenotype and give rise to electrically active neuronal subtypes characteristic of specific ventral progenitor subdomains. Upon grafting into lesioned rat spinal cord these cells differentiate into ChAT+ve motorneurons and show robust survival after 4 months.

overall_design: Total RNA was obtained from three proliferative undifferentiated neural stem cell lines at 75% confluence in culture. Two replicates of each clonal line were generated for microarray analysis.

first: Aaron

last: Jeffries

first: Jack

last: Price


title: Dicer1 deletion in myeloid-committed progenitors causes neutrophil dysplasia and blocks macrophage/dendritic cell development in mice

city: Rotterdam

first: Stefan

last: Erkeland

address: Dr. Molewaterplein 50

department: Hematology

institute: ErasmusMC

summary: MiRNAs have the potential to regulate cellular differentiation programs. However, miRNA-deficiency in primary hematopoietic stem cells (HSCs) results in HSC depletion in mice, leaving the question of whether miRNAs play a role in early-lineage decisions unanswered. To address this issue, we deleted Dicer1, which encodes an essential RNaseIII enzyme for miRNA biogenesis, in murine CCAAT/enhancer-binding protein alpha (C/EBPA)-positive myeloid-committed progenitors in vivo. In contrast to the results in HSCs, we found that miRNA depletion affected neither the number of myeloid progenitors nor the percentage of C/EBPA-positive progenitor cells. Analysis of gene-expression profiles from wild type and Dicer1-deficient granulocyte-macrophage progenitors (GMPs) revealed that 20 miRNA families were active in GMPs. Of the derepressed miRNA targets in Dicer1-null GMPs, 27% are normally exclusively expressed in HSCs or are specific for multi-potent progenitors and erythropoiesis, indicating an altered gene-expression landscape. Dicer1-deficient GMPs were defective in myeloid development in vitro and exhibited an increased replating capacity, indicating a regained self-renewal potential of these cells. In mice, Dicer1 deletion blocked monocytic differentiation, depleted macrophages and caused myeloid dysplasia with morphological features of Pelger-Huët anomaly. These results provide evidence for a miRNA-controlled switch for a cellular program of self-renewal and expansion towards myeloid differentiation in GMPs.

overall_design: To generate Cebpa-Cre;R26-LSL-Eyfp;Dicer1wt/fl/Dicer1fl/fl mice,  we crossed mice that contain floxed Dicer1 alleles (Dicer1fl) with Cebpa-Cre;R26-LSL-Eyfp reporter mice 2. Fetal livers were obtained on embryonic day (E) 13.5. Routine genotyping of Dicer1; Cebpa-Cre;R26-LSL-Eyfp mice was performed by PCR assays of DNA from tail or toe biopsies. For transplantation, 6 to 8-week-old recipient mice (C57Bl/6, Jackson Laboratories) were irradiated (8.5 Gy) and tail-vein injected with fetal liver single-cell suspensions. Typically, cells from each fetal liver were transplanted into two recipient mice. Hematopoietic tissues were analyzed 6-10 weeks post transplantation. EYFP positive GMPs from the bone marrow of Dicer wt control (n=3), Dicer -/wt (n=3 and Dicer fl/fl (n=3) were sorted and analyzed for gene expression profiles.

first: Mir

middle: F

last: Alemdehy

first: Nicole

middle: G

last: van Boxtel

first: Hans

last: de Looper

first: Iris

last: van den Berge

first: Mathijs

last: Sanders

first: Tom

last: Cupedo

first: Ivo

middle: P

last: Touw


title: MicroRNA profiling in TGFβ signaling and development of fibrosis.

status: Public on Jun 15 2012

city: StLouis

first: Nobish

last: Varghese

state: MO

address: 4444 Forest Park Ave.

institute: Washington University in St.Louis

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

summary: End stage liver disease due to Hepatitis C Virus (HCV) infection is a major health concern worldwide. Liver fibrosis following chronic HCV infection plays a pivotal role in loss of liver function and end stage liver disease. However the dynamics and molecular events that lead to fibrosis in HCV infection are poorly defined. Therefore, we determined the influence of HCV infection in altering the miRNA expression levels which can modulate immune responses to HCV leading to fibrosis. Analysis of the miRNA expression profiles of HCV infected liver biopsies revealed that 45 miRNAs were differentially expressed in the HCV infected liver when compared to normal livers.  In silico target prediction of these differentially expressed miRNAs indicated that their targets include chemokine/cytokine signaling, cell cycle genes and extracellular matrix protein gene expression. Gene expression profiling using whole genome microarray demonstrated that 1320 genes were differentially expressed in chronic HCV liver when compared to normal. These genes could be functionally grouped into those involved in cell cycle regulation, cytokines and chemokines expression, cell adhesion, intracellular signaling and enzymes. Further pathway analysis using GeneGo software identified cell adhesion, cytoskeleton remodeling, cytokine signaling and metabolic pathways as the major pathways activated in chronic HCV. Combinatorial target prediction analysis of miRNA expression along with gene expression analysis indicated that differentially expressed microRNAs in HCV significantly impact transforming growth factor beta (TGF-β) signaling pathway, cell adhesion (integrin expression), chemokine signaling, Notch signaling and cell-cycle( Cyclin D,K) regulation. Overall these results demonstrate that chronic HCV infection induces specific miRNA signatures that will modulate genes involved in the cytoskeletal remodeling and cytokine signaling that can promote the development of fibrosis following HCV infection.

overall_design: Liver biopsies from chronic HCV patients and control liver biopsies from normal subjects (donor liver prior to transplantation) were used to analyze the miRNA and gene expression profile. Patients with HBV and/or HIV were excluded from the study.

first: Sabrinathan

last: Ramachandran


title: c-JUN REPROGRAMS SCHWANN CELLS OF INJURED NERVES TO GENERATE A REPAIR CELL ESSENTIAL FOR REGENERATION

status: Public on Jun 14 2012

first: Kristjan

middle: R.

last: Jessen

address: Gower Street

institute: University College London

summary: The striking PNS regenerative response to injury rests on the plasticity of adult Schwann cells and their ability to transit between differentiation states, a highly unusual feature in mammals. Using mice with  inactivation of Schwann cell c-Jun, we show that the injury response involves c-Jun dependent natural reprograming of differentiated cells to generate a distinct Schwann cell state specialized to promote regeneration. Transected distal stumps of c-Jun mutants show 172 disregulated genes, resulting in abnormal expression of growth factors, adhesion molecules and cytoskeletal changes that lead to neuronal death, inhibition of axon growth and striking failures of functional repair after injury.  These observations provide a molecular basis for understanding Schwann cell plasticity and nerve regeneration. They offer conclusive support for the notion that Schwann cells control repair in the PNS, using dedicated transcriptional controls to generate a distinct repair cell, a transition that shows similarities to transdifferentiation seen in other systems.

overall_design: Total RNA was purified from a 10mm segment of the distal stump and uninjured contralateral nerve from c-Jun mutants and control mice 7 days after nerve cut. For each condition (injured/uninjured) and genotype (control/ knock-out) 2 independent samples (replicates) were generated from pooled nerves of 4/6 mice resulting in a total of 8 samples: CTRL.cut.R1, CTRL.cut.R2, CTRL.uncut.R1, CTRL.uncut.R2, KO.cut.R1, KO.cut.R2, KO.uncut.R1,KO.uncut.R2.

first: Peter

last: Arthur-Farraj

first: Morwena

last: Latouche

first: Daniel

last: Wilton

first: Susanne

last: Quintes

first: Elodie

last: Chabrol

first: Ambily

last: Banerjee

first: Ashwin

last: Woodhoo

first: Billy

last: Jenkins

first: Mary

last: Rahman

first: Mark

last: Turmaine

first: Grzegorz

last: KWicher

first: Linda

last: Greensmith

first: Axel

last: Behrens

first: Gennadij

last: Raivich

first: Rhona

last: Mirsky

first: Kristján


title: Lyl-1 knockout vs wildtype Lymphoid Primed Multipotent Progenitors (LMPPs)

first: Margaret

last: Goodell

address: One Baylor Plaza, N1030

department: Center for Cell and Gene Therapy

summary:
We compared gene expression differences in Lyl-1 knockout vs wildtype LMPPs
KO allele described in Pub Med ID: 21387538

overall_design: LMPPS were purified as Lineage-negative, Sca-1+ c-Kit+ (LSK) and Flt3-high from both Lyl1-null and WT mice on C57Bl/6 background

first: Fabian

last: Zohren


title: Temporal changes of gene expression in mouse heart, kidney and lung during juvenile growth

city: Bethesda

first: Julian

middle: CK

last: Lui

state: MD

address: 10 Center Drive

institute: NICHD, NIH

summary: Temporal changes of gene expression from 1-wk- to 4-wk and 8-wk-old mouse in heart, kidney and lung. Mammalian somatic growth is rapid in early postnatal life but then slows and eventually ceases in multiple tissues. We hypothesized that there exists a postnatal gene expression program that is common to multiple tissues and is responsible for this coordinate growth deceleration. Consistent with this hypothesis, microarray analysis identified >1600 genes that were regulated with age coordinately in kidney, lung, and heart of juvenile mice, including many genes that regulate proliferation. As examples, we focused on three growth-promoting genes, Igf2, Mest, and Peg3, that were markedly downregulated with age. We conclude that there exists an extensive genetic program occurring during postnatal life. Many of the involved genes are regulated coordinately in multiple organs, including many genes that regulate cell proliferation. At least some of these are themselves apparently regulated by growth, suggesting that, in the embryo, a gene expression pattern is established that allows for rapid somatic growth of multiple tissues but then, during postnatal life, this growth leads to negative-feedback changes in gene expression that in turn slow and eventually halt somatic growth, thus imposing a fundamental limit on adult body size.

overall_design: To compare gene expression between fast-growing animals and more slowly growing animals, we extracted total mRNA from kidney and lung in 1-wk, 4-wk, and 8-wk-old mice (5 animals each).

first: J

middle: C

first: O

last: Nilsson

last: Baron


title: DNA methylation dynamics during in vivo differentiation of blood and skin stem cells

status: Public on Jul 15 2012

city: Vienna

first: Christoph

last: Bock

address: Lazarettgasse 14

country: Austria

institute: CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences

type:
Expression profiling by array
Third-party reanalysis

summary: DNA methylation is a mechanism of epigenetic regulation that is common to all vertebrates. Functional studies support its relevance for tissue homeostasis, but the global dynamics of DNA methylation during in vivo differentiation have not been worked out in detail. Here we report high-resolution DNA methylation maps of adult stem cell differentiation in mouse, focusing on 19 purified cell populations of the blood and skin lineages. Except for global demethylation in erythrocytes, observed DNA methylation changes were locus-specific and relatively modest in size. They frequently overlapped with lineage-associated transcription factors and their binding sites, suggesting that DNA methylation may protect cells from aberrant transcription factor activation. DNA methylation and gene expression provided highly complementary information, and combining the two enabled us to infer the blood lineage hierarchy directly from genomic data. In summary, our dataset and analysis demonstrate that in vivo differentiation of adult stem cells is associated with small but informative changes in the distribution of DNA methylation across the mouse genome.

overall_design:
We used microarray data to compare the gene expression profiles between various purified cell populations of the blood and skin lineages. Microarray data were obtained for 13 blood cell types (HSC, MPP1, MPP2, CLP, CMP, MEP, GMP, CD4, CD8, B-cell, Eryth, Granu, Mono) and 6 skin cell types (TBSC, ABSC, MTAC, CLDC, EPro, EDif). A subset of these microarray profiles have already been uploaded to GEO as part of previous research and were reused for the current study (GSE20244: MPP1, MPP2, CLP, CMP, GMP; GSE6506: CD4, CD8, B-cell, Eryth, Granu, Mono; GSE31028: TBSC, ABSC, MTAC). All microarray profiles that had not been made public previously are included here (HSC, MEP, CLDC, EPro, EDif). Furthermore, all data are available for download from the paper's supplementary website (http://invivomethylation.computational-epigenetics.org/).

This submission includes the gene expression component of the study.

The complete dataset representing the GSE38557 Samples, and the GSE20244, GSE6506, and GSE31028 Samples listed above, is linked below as a supplementary file.

first: Isabel

last: Beerman

first: Wen

middle: H

last: Lien

first: Derrick

last: Rossi

first: Alexander

last: Meissner


title: Gene expression in mouse germinal center light zone and dark zone B cells

first: Gabriel

last: Victora

address: 9 Cambridge Center

institute: Whitehead Institute

summary:
Microarrays of gene expression in mouse germinal center light zone and dark zone B cells sorted according to the expression of cell surface molecules CD83 and CXCR4
We used microarray data to identify genes differentially expressed by B cells in the light and dark zones of germinal centers from mouse skin-draining lymph nodes 12 days after subcutaneous immunization with NP-OVA in alum.

overall_design: Germinal center B cells (B220+CD38-CD95+) were sorted from immunized mouse lymph nodes into light zone (CXCR4hi/CD83lo) and dark zone (CXCR4lo/CD83hi) populations, from which RNA was extracted

first: David

last: Dominiguez-Sola

first: Riccardo

last: Dalla-Favera

first: Michel

last: Nussenzweig


status: Public on Jun 12 2012

city: Biella

first: giovanna

last: chiorino

address: via malta 3

department: Cancer Genomics

country: Italy

institute: Fondo Edo Tempia

summary:
It is currently unclear whether tissue changes surrounding multifocal epithelial tumors are a cause or consequence of cancer. Here, we provide evidence that loss of mesenchymal Notch/CSL signaling causes tissue alterations, including stromal atrophy and inflammation, which precede and are potent triggers for epithelial tumors. Mice carrying a mesenchymal-specific deletion of CSL/RBP-JK, a key Notch effector, exhibit spontaneous multifocal keratinocyte tumors that develop after dermal atrophy and inflammation. CSL-deficient dermal fibroblasts promote increased tumor cell proliferation through up-regulation of c-Jun and c-Fos expression and consequently higher levels of diffusible growth factors, inflammatory cytokines, and matrix remodeling enzymes. In human skin samples, stromal fields adjacent to cutaneous squamous cell carcinomas and multifocal premalignant actinic keratosis lesions exhibit decreased Notch/CSL signaling and associated molecular changes. Importantly, these changes in gene expression are also induced by UVA, a known environmental cause of cutaneous field cancerization and skin cancer.
We used microarrays to detail the global changes in gene expression in dermal fibroblasts with in vivo and in vitro deletion of the RBP-Jk gene, compared to corresponding controls

overall_design: Global changes in gene expression in dermal fibroblasts with in vivo and in vitro deletion of the RBP-Jk gene were assessed, in parallel with the corresponding controls

first: Bing

last: Hu

first: Einar

last: Castillo

first: Louise

last: Harewood

first: Paola

last: Ostano

first: Alexandre

last: Reymond

first: Reinhard

last: Dummer

first: Wassim

last: Raffoul

first: Wolfram

last: Hoetzenecker

first: Günther

last: Hofbauer

first: G

last: Dotto


title: Expression data from E12.5 NSP cells, CTL v REST shRNA

status: Public on Jun 07 2012

city: Stony Brook

first: Matthew

last: Covey

state: New York

address: 350 CMM Building

department: Biochemistry

institute: Stony Brook University

summary:
REST is a master regulator of genes that are involved in the acqusition of neuronal fate. The role of REST is not well understood so we attempted to investigate the role of REST in the development of neural cells by analysing the genes that are upregulated when REST is knocked down via shRNA
We used microarrays to assess the genes which were up and down regulated after REST is knocked down

overall_design: E12.5 NSP cells were infected with either control or REST shRNA expressing lentiviruses and collected after 6 days for RNA extraction

first: Nurit

last: Ballas

first: Jeff

last: Streb

first: Roman

last: Spektor

first: Qi

last: Wang


title: Expression data from primary bone marrow-derived wild-type C57BL/6 and bcl6 knockout macrophages

status: Public on Jun 08 2012

city: La Jolla

first: Ruth

middle: T

last: Yu

address: 10010 N Torrey Pines Rd

department: Gene Expression Lab

institute: Salk Institute

summary:
We used microarrays to compare gene expression changes in macrophages caused by deletion of bcl6.

Keywords: BCL6 deletion compared to wild-type

overall_design: Primary bone marrow-derived macrophages were isolated from C57BL/6 mice transplanted and reconstituted with wild type or bcl6 knockout bone marrow.

first: Grant

last: Barish

first: Ronald

last: Evans


title: Expression data of 4T1 mammary cancer cells cultured in MSC-conditioned medium or co-cultured with MSCs

city: Taipei

first: Oscar

middle: K.

last: Lee

address: No. 155, Li-Long St.

country: Taiwan

institute: National Yang Ming University

summary:
4T1 mammary cancer cells exihibit higher proliferation and metastatic ability when cultured in conditioned medium from mesenchymal stem cells . Also, co-implantation with MSCs, 4T1 tumors show higher tumor growth and metastasis.
We used microarrays to detail the global programme of gene expression underlying the alteration of cell behaviour

overall_design: RNA was extrated from 4T1 cells cultured in MSC-CM or regular medium as well as 4T1 cells isolated from co-cultured with MSCs. Gene expression of these cell groups was acquired from Affymetrix microarray analysis using mouse 430 2.0 array chip.

middle: K

first: Chien-Chih

last: Ke


title: Histone H2A mono-ubiquitination is a crucial step to mediate PRC1 dependent repression of developmental genes to maintain ES cell identity.

city: Yokohama

first: Takaho

middle: A.

last: Endo

state: Kanagawa

address: 1-7-22 Suehiro, Tsurumi

department: IMS

institute: RIKEN

type: Genome binding/occupancy profiling by array

summary:
Two distinct Polycomb complexes, PRC1 and PRC2, collaborate to maintain epigenetic repression of key developmental loci in embryonic stem cells (ESCs). PRC1 and PRC2 have histone modifying activities, catalyzing mono-ubiquitination of histone H2A (H2AK119u1) and trimethylation of H3 lysine 27 (H3K27me3) respectively. Compared to H3K27me3, localization and role of H2AK119ub1 is not fully understood in ESCs. Here we present genome-wide H2AK119u1 maps in ESCs and identify a group of genes at which H2AK119u1 is deposited in a Ring1-dependent manner. These genes are a distinctive subset of genes with H3K27me3 enrichment and are the central targets of Polycomb silencing that are required to maintain ESC identity. We further show that the H2A ubiquitination activity of PRC1 is dispensable for its target binding and its activity to compact chromatin at Hox loci, but is indispensable for efficient repression of target genes and thereby ESC maintenance. These data demonstrate that multiple effector mechanisms including H2A ubiquitination and chromatin compaction combine to mediate PRC1-dependent repression of genes that are crucial for the maintenance of ESC identity. Utilization of these diverse effector mechanisms might provide a means to maintain a repressive state that is robust yet highly responsive to developmental cues during ES cell self-renewal and differentiation.

This SuperSeries is composed of the SubSeries listed below.

overall_design:
Total RNAs were extracted from the respective ES cells, and were subjected to microarray analysis using Affymetrix GeneChip Mouse Genome 430A 2.0 arrays.
ChIP on chip analysis was carried out using the Mouse Promoter ChIP-on-chip Microarray Set (G4490A, Agilent, Palo Alto, Calif., USA). MEFs were subjected to ChIP assay using various antibodies. Purified immunoprecipitated and input DNA was subjected to T7 RNA polymerase-based amplification. Labeling, hybridization and washing were carried out according to the Agilent mammalian ChIP-on-chip protocol (ver.9.0). Scanned images were quantified with Agilent Feature Extraction software under standard conditions.

first: Mitsuhiro

last: Endoh

middle: A

first: Haruhiko

last: Koseki


title: Expression data from Ring1A(-/-);Ring1B(fl/fl);R26::CreERT2 ES cells expressing either of mock, WT or mutant Ring1B construct before or after OHT treatment

status: Public on Jun 11 2012

summary: We used microarrays to investigate the restoration of repression of PRC1 target gene expression in Ring1A/B-dKO ES cells stably expressing either of mock, WT or mutant Ring1B construct.

overall_design: Total RNAs were extracted from the respective ES cells, and were subjected to microarray analysis using Affymetrix GeneChip Mouse Genome 430A 2.0 arrays


title: Expression profile of miR-17-92a-MSCV-IRES-Thy1.1 transduced P14 CD8+ T cells

status: Public on Jun 05 2012

city: ATLANTA

first: Tuoqi

last: Wu

state: GA

address: 1510 Clifton Rd, Room G211

institute: Emory University

summary:
During acute viral infections, effector CD8+ T cells differentiate into memory precursors or short-lived terminal effectors. miR-17-92a over-expression skews CD8+ effector cells to the terminal differentiation.
We used microarray to identify the genes that are differentially expressed caused by miR-17-92a over-expression.

overall_design: CD8+ T cells from P14 TCR transgenic mice were infected with miR-17-92a-MSCV-IRES-Thy1.1 vector and transfer to C57BL6 recipients. Chimeras were infected with LCMV Armstrong. Thy1.1+ miR-17-92a-MSCV-IRES-Thy1.1 transduced P14 cells and Thy1.1- non-transduced P14 cells were sorted by FACS. RNA was extracted from samples, labeled, and hybridized to Affymetrix microarrays.

first: Rafi

last: Ahmed


title: Transcriptome kinetics of circulating neutrophils during human experimental endotoxemia

city: Nijmegen

first: Stan

middle: de

last: Kleijn

address: Kapittelweg 29

department: Laboratory of pediatric infectious diseases

institute: Radboud University Nijmegen Medical Centre

summary: Polymorphonuclear cells (neutrophils) play an important role in the systemic inflammatory response syndrome and the development of sepsis. These cells are essential for the defense against microorganisms, but may also cause tissue damage. Therefore, neutrophil numbers and activity are considered to be tightly regulated. Previous studies have investigated gene transcription during experimental endotoxemia in whole blood and peripheral blood mononuclear cells. However, the gene transcription response of the circulating pool of neutrophils to systemic inflammatory stimulation in vivo is currently unclear. We examined neutrophil gene transcription kinetics in healthy human subjects (n=4) administered a single dose of endotoxin (LPS, 2 ng/kg iv). In addition, freshly isolated neutrophils were stimulated ex vivo with LPS, TNFα, G-CSF and GM-CSF to identify stimulus-specific gene transcription responses. Whole transcriptome microarray analysis of circulating neutrophils at 2, 4 and 6 hours after LPS infusion revealed activation of inflammatory networks which are involved in signaling of TNFα and IL-1α and IL-1β. The transcriptome profile of inflammatory activated neutrophils in vivo reflects extended survival and regulation of inflammatory responses. We show that these changes in neutrophil transcriptome are most likely due to a combination of early activation of circulating neutrophils by TNFα and G-CSF and a mobilization of young neutrophils from the bone marrow.

overall_design: After LPS infusion blood was taken at t=0, t=2, t=4 and t=6 hours. Neutrophils were isolated and gene expression of these cells was assessed. T=2, t=4 and t=6 were related to t=0 as control condition

middle: d

last: Ferwerda


title: Expression data from mouse lungs, exposed in-utero to second-hand smoke (SHS) and challenged with ovalbumin (OVA) as adults.

status: Public on Jun 02 2012

city: New York

first: Rui

last: Xiao

address: 630 West 168th Street

department: Anesthesiology

institute: Columbia University

summary:
SHS exposure during pregnancy has adverse effects on offspring.
We used microarrays to characterize the gene expression changes caused by in-utero SHS exposure and adult (19-23 weeks) OVA challenge in 23-week mouse lungs.

overall_design: Left lungs from Balb/c male and female mice were collected at 23 weeks of age for RNA extraction and hybridization on Affymetrix mouse 430 2.0 microarrays. Based on the gender differences and in-utero exposure status, there are 4 groups of mice, females and males, exposed in-utero to filtered-air or SHS. All were exposure to OVA (19-23 weeks). We extracted RNA from 4 animals from each group for microarray analysis (total N = 16 samples).

first: Arthur

last: Penn

first: Zakia

last: Perveen

first: Paula

last: Polk


title: Comparison of gene expression in NOD versus NOD.NOR-Chr4 (NR4) splenic B cells.

city: Darlinghurst

first: Pablo

middle: Alejandro

last: Silveira

state: NSW

address: 384 Victoria St

department: Immunology Program

country: Australia

institute: Garvan Institute

summary: Type 1 Diabetes (T1D) in humans and the non-obese diabetic (NOD) mouse model results from autoreactive T cell destruction of pancreatic beta cells. A pathogenic role for B lymphocytes (B cells) in T1D first became evident when NOD mice made deficient in this population through introduction of an inactivated Igµ heavy chain gene (NOD.Igµnull) or chronic treatment with anti-IgM antibodies were strongly protected from disease. We produced an NOD background strain developing a greatly decreased T1D incidence due to a NOR-derived 44.31Mb congenic region from rs3674285 to D4Mit127 on distal Chr. 4 (termed NOD.NOR-Chr4 (NR4)) containing disease resistance alleles decreasing the pathogenic activity of autoreactive B cells. Microarrays were conducted on B cells purified from spleens of NOD and NR4 mice to highlight differentially expressed genes within the distal Chr. 4 locus. B cells were either cultured in media alone (unstimulated) or with BCR cross-linking anti-IgM-F(ab’)2 fragments (stimulated) for 2h before RNA was extracted for transcript analysis.

overall_design: B cells from three independent lots of pooled spleens (n=7-8) from NOD or NR4 female mice, respectively, were purified using a magnetic-activated cell sorting (MACS) negative depletion strategy. Purified B cells from each lot were resuspended at 1x10<7> cells/ml for 2h in complete RPMI media alone or with 10µg/ml AffiniPure goat anti-mouse IgM F(ab’)2 fragments. RNA was then purified from B cells and subjected to one-cycle linear amplification and biotin labeling. Two BCR-stimulated and three unstimulated NOD B cell samples plus three BCR-stimulated and three unstimulated NR4 B cell samples were hybridized to Mouse Genome 430 2.0 Arrays.

first: David

middle: V

last: Serreze


title: Temporal expression of miR-17-92a regulates effector and memory CD8+ T cell differentiation

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

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

overall_design: Refer to individual Series


title: Genome-wide characterization of menin-dependent H3K4me3 reveals a specific role for menin in the regulation of genes implicated in MEN1-like tumors (mRNA)

status: Public on Jun 01 2012

city: RTP

first: Raja

last: Jothi

address: 111 TW Alexander Drive; A314

department: National Institute of Environmental Health Sciences

institute: National Institutes of Health

summary: Inactivating mutations in the MEN1 gene predisposing to the multiple endocrine neoplasia type 1 (MEN1) syndrome can also cause sporadic pancreatic endocrine tumors. MEN1 encodes menin, a subunit of MLL1/MLL2-containing histone methyltransferase complexes that trimethylate histone H3 at lysine 4 (H3K4me3). The importance of menin-dependent H3K4me3 in normal and transformed pancreatic endocrine cells is unclear. To study the role of menin-dependent H3K4me3, we performed in vitro differentiation of wild-type as well as menin-null mouse embryonic stem cells (mESCs) into pancreatic islet-like endocrine cells (PILECs). Gene expression analysis and genome-wide H3K4me3 ChIP-Seq profiling in wild-type and menin-null mESCs and PILECs revealed menin-dependent H3K4me3 at the imprinted Dlk1-Meg3 locus in mESCs, and all four Hox loci in differentiated PILECs. Specific and significant loss of H3K4me3 and gene expression was observed for genes within the imprinted Dlk1-Meg3 locus in menin-null mESCs and the Hox loci in menin-null PILECs. Given that the reduced expression of genes within the DLK1-MEG3 locus and the HOX loci is associated with MEN1-like sporadic tumors, our data suggests a possible role for menin-dependent H3K4me3 at these genes in the initiation and progression of sporadic pancreatic endocrine tumors. Furthermore, our investigation also demonstrates that menin-null mESCs can be differentiated in vitro into islet-like endocrine cells, underscoring the utility of menin-null mESC-derived specialized cell types for genome-wide high-throughput studies.

overall_design: Genome-wide mapping of H3K4me3 and microarray gene expression profiling in TC-1 wild-type (WT) mESCs, menin-null (Men1-ko) mESCs (3.2N), pancreatic islet-like endocrine cells (PILECs) derived from WT mESCs, and PILECs derived from Men1-ko mESCs.

first: Sunita

last: Agarwal


title: Effect of fluoxetine treatment on translational profiles of S100a10 cortical pyramidal cells in p11 KOs

first: Eric

last: Schmidt

address: 1230 York Avenue

institute: The Rockefeller University

summary:
Molecular phenotyping of cell types and neural circuits underlying pathological neuropsychiatric conditions and their responses to therapy provides one avenue for the development of more specific and effective treatments. In this study, we identify a cell population in the cerebral cortex that shows robust and specific molecular adaptations following long-term SSRI treatment.

We employed the bacTRAP strategy, which uses BAC transgenic mice expressing EGFP-tagged ribosomal protein L10a in specific cell populations, to affinity purify polysome-bound mRNAs from S100a10-expressing corticostriatal projection neurons. We show that the S100a10 cells are a unique population of cortical cells that are strongly and specifically responsive to chronic SSRI administration and that this response requires p11 (the protein product of S100a10).

Our data demonstrate that the beneficial actions of antidepressant therapy can be mediated by a single cell type that is positioned to normalize activity between cortical and subcortical sites, and suggest that development of drugs that specifically target the activity of these cells may result in improved therapies to treat depression.

overall_design: S100a10 bacTRAP mice crossed to constitutive p11 KO mice (S100a10 bacTRAP/p11 KO) were administered either fluoxetine (FLX) or vehicle (VEH) in their drinking water for 15-18 days. Three independent TRAP replicates from the cortex of each group were then collected. Total RNA from the immunoprecipitates was amplified and hybridized. Data were normalized with the GCRMA algorithm and replicates were averaged across conditions. We recommend filtering data to remove probe sets with normalized expression values less than 50 in at least one condition. Because the S100a10 BAC labels some non-neuronal cells, we recommend only probe sets listed in Table S1 of the accompanying paper be included in the analysis.

first: Jennifer

middle: L

last: Warner-Schmidt

first: Benjamin

last: Otopolik

first: Sarah

middle: B

last: Pickett

first: Paul

last: Greengard

first: Nathaniel

last: Heintz


title: Comparative analysis of S100a10 and Glt25d2 cortical pyramidal cells

middle: F

overall_design: Three independent TRAP replicates from cortex of S100a10 or Glt25d2 bacTRAP mice were collected. Total RNA from the immunoprecipitates was amplified and hybridized. Data were normalized with the GCRMA algorithm and replicates were averaged across conditions. We recommend filtering data to remove probe sets with normalized expression values less than 50 in at least one condition. Because the S100a10 BAC labels some non-neuronal cells, we recommend only probe sets listed in Table S1 of the accompanying paper be included in the analysis.

middle: G


title: Screening of genes involved in chromosome segregation in meiosis I

status: Public on Jun 04 2012

city: Toyoake

first: Makiko

last: Tsutsumi

state: Aichi

address: 1-98 Dengakugakubo, Kutsukake-cho

department: ICMS

institute: Fujita Health University

summary: Prophase I of meiosis involves dynamic chromosome segregation processes including synapsis, meiotic recombination, and cohesion. Genetic defects in genes participating in these processes consistently cause reproduction failure in mice. To identify candidate genes responsible for infertility or recurrent pregnancy loss in humans, we performed expression profiling of male and female gonads of mice undergoing meiotic prophase I.

overall_design: Both male and female gonads at 15.5 days postcoitum, neonatal day 1 and 10 weeks postpartum were dissected from mice for RNA extraction and subjected to hybridization on Affymetrix microarrays.

first: Hiroe

last: Kowa-Sugiyama

first: Hasbaira

last: Bolor

first: Hiroshi

last: Kogo

first: Hidehito

last: Inagaki

first: Tamae

last: Ohye

first: Kouji

last: Yamada

first: Mariko

last: Taniguchi

first: Tatsushi

last: Toda

first: Hiroki

last: Kurahashi


title: Effect of fluoxetine treatment on translational profiles of Glt25d2 cortical pyramidal cells

overall_design: Glt25d2 bacTRAP mice were administered either fluoxetine (FLX) or vehicle (VEH) in their drinking water for 15-18 days. Three independent TRAP replicates from cortex of each group were then collected. Total RNA from the immunoprecipitates was amplified and hybridized. Data were normalized with the GCRMA algorithm and replicates were averaged across conditions. We recommend filtering data to remove probe sets with normalized expression values less than 50 in at least one condition. Because the S100a10 BAC labels some non-neuronal cells, we recommend only probe sets listed in Table S1 of the accompanying paper be included in the analysis.


title: MicroRNA profiling of primary high-grade soft tissue sarcomas

city: Heidelberg

first: Thomas

last: Wolf

address: Im Neuenheimer Feld 580

institute: DKFZ

summary: This screening revealed unique miRNA expression patterns for synovial sarcomas , myxoid liposarcomas, and leiomyosarcomas, and defined unique sets of miRNAs discriminating the different liposarcoma subtypes from non-neoplastic adipose tissue.

overall_design: We performed a comprehensive miRNA expression analysis in a series of 76 untreated, primary high-grade soft tissue sarcomas representing eight subtypes, and in 15 sarcoma cell lines using microarray technology. Additionally, two normal fat samples were analysed.

first: Marcus

last: Renner

first: Esteban

last: Czwan

first: Wolfgang

last: Hartmann

first: Roland

last: Penzel

first: Benedikt

last: Brors

last: Eils

first: Reinhard

last: Büttner

first: Peter

last: Lichter

last: Schirmacher

first: Gunhild

last: Mechtersheimer


title: Identification of the cortical neurons that mediate antidepressant responses

first: Eric

last: Schmidt


title: JAK2 Naive and Persitent Murine BaF3 cells infected with MPLW515L

status: Public on May 31 2012

first: Ross

last: Levine

department: Human Oncology & Pathogenesis Program

institute: Memorial Sloan-Kettering Cancer Center

summary: Transcriptional profiling of Murine BaF3 cells infected with MPLW515L grown under either normal conditions (Naive) or in 0.8 uM INCB18424 for 4-6 weeks (Persistent). Naive and Persistent cells were then treated with either DMSO (Control) or 0.8 uM INCB18424 for 4 hours. Goal was to determine transcriptional changes conditioned upon sensitivity/resistance of BaF3 MPLW515L mutants to JAK1/2 specific inhibitor.

overall_design: 3 condition experiment consiting of: 1) Naive cells treated with DMSO (Control) , 2) Naïve cells treated with 0.8 uM INCB18424 for 4 hours (Acute) and 3) Persistent cells treated with 0.8 uM INCB18424 for 4 hours (Persistent). Biological replicates: 3 DMSO control replicates, 3 Acute replicates, 3 Persistent replicates.

first: R

first: P

last: Koppikar


title: Reduction in nuclear speckles and transcriptome de-regulation in fibroblast of intellectually disabled patients with mutations at the FRAXE site

city: North Adelaide

first: Jozef

last: Gecz

state: South Australia

address: 72 King William Rd

department: Genetics Medicine

institute: SA Pathology

summary:
Loss of function of FMR2 due to either hypermethylation of the CpG island as a consequence of the expansion of the CCG repeat near its transcription start site, or internal deletion of FMR2 is considered to be the major cause of FRAXE fragile site associated intellectual disability. FMR2 was shown to be a potent transcription activator as well as an RNA binding protein capable of regulating alternative splicing.
Using whole transcriptome approach, we aimed to identify genes regulated by FMR2 and to study their contribution to the underlying causes of intellectual disability in the patients.

overall_design: We subjected total RNA extracted from fibroblasts of FRAXE patients (n=8), and unrelated controls (n=4) to Affymetrix Human Exon 1.0 ST array

first: Mireille

last: Melko

first: Lam

middle: S

last: Nguyen

first: Marie

last: Shaw


title: Comprehensive Analysis of Genes Expressed by Rare Microchimeric Fetal Cells in Maternal Mouse Lung

city: Boston

first: Stephanie

last: Pritchard

address: 800 Washington St, Box 396

department: Genetics

institute: Tufts University

summary:
During pregnancy, cells from each fetus travel into the maternal circulation and organs, resulting in the development of microchimerism. Identification of the cell types in this microchimeric population would permit better understanding of possible mechanisms by which they affect maternal health. However, comprehensive analysis of fetal cells has been hampered by their rarity. In this study, we sought to overcome this obstacle by combining flow cytometry with multidimensional gene expression microarray analysis of fetal cells isolated from the murine maternal lung during late pregnancy. Fetal cells were collected from the lungs of pregnant female mice. cDNA was amplified and hybridized to gene expression microarrays. The resulting fetal cell core transcriptome was interrogated using multiple methods including Ingenuity Pathway Analysis, the BioGPS gene expression database, principal component analysis, the Eurexpress gene expression atlas and primary literature.  Here we report that small numbers of fetal cells can be flow sorted from the maternal lung, facilitating discovery-driven gene expression analysis.  We additionally show that gene expression data can provide functional information about the fetal cells. Our results suggest that fetal cells in the murine maternal lung are a mixed population, consisting of trophoblasts, mesenchymal stem cells and cells of the immune system. The detection of trophoblasts and immune cells in the maternal lung may facilitate future mechanistic studies related to the development of immune tolerance and pregnancy-related complications, such as preeclampsia. Furthermore, the presence and persistence of mesenchymal stem cells in maternal organs may have implications for long-term postpartum maternal health.
Comprehensive gene expression microarray analysis of fetal cells isolated from the pregnant murine maternal lung.

overall_design: Seven individual replicates were performed.

first: Heather

last: Wick

first: Donna

last: Slonim

first: Kirby

last: Johnson

first: Diana

middle: W

last: Bianchi


title: Brain transcriptomic profiling in idiopathic and LRRK2-associated Parkinson's disease

city: Barcelona

first: Teresa

last: Botta

address: Casanova 143

department: Serveis Científicotècnics

country: Spain

institute: IDIBAPS-Universitat de Barcelona-Hospital Clínic

summary: LRRK2 mutations are the most common genetic cause of Parkinson’s disease (PD). We performed a whole-genome RNA profiling of locus coeruleus post-mortem tissue from idiopathic PD (IPD) and LRRK2-associated PD patients. The differentially expressed genes found in IPD and LRRK2-associated PD were involved in the gene ontology terms of synaptic transmission and neuron projection. In addition, in the IPD group we found associated genes belonging to the immune system. Pathway analysis of the differentially expressed genes in IPD was related with neuroactive-ligand receptor interaction and with immune system pathways. Specifically, the analysis highlighted differential expression of genes located in the chromosome 6p21.3 belonging to the class II HLA. Our findings support the hypothesis of a potential role of neuroinflammation and the involvement of the HLA genetic area in IPD pathogenesis. Future studies are necessary to shed light on the relation of immune system related pathways in the etiopathogenesis of PD.

overall_design: Number of samples analyzed: 10 brain tissue (locus coeruleus). Control (C) samples, no pathological changes: C1, C2, C4, C5. Samples from idiopathic Parkinson's disease (IPD) patients: IPD1, IPD3, IPD4, IPD5. Samples from Parkinson's disease patients who are carriers of the G2019S LRRK2 mutation (MPD): MPD1, MPD2. No replicates.

last: Botta-Orfila

first: Alex

last: Sánchez-Pla

first: Manel

last: Fernández

first: Francesc

last: Carmona

first: Mario

last: Ezquerra

first: Eduard

last: Tolosa


title: Expression data from Ezh2-null leukemic cells

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: The polycomb group (PcG) proteins function in gene silencing through histone modifications. They form chromatin-associated multiprotein complexes, termed polycomb repressive complex (PRC) 1 and PRC2. These two complexes work in a coordinated manner in the maintenance of cellular memories through transcriptional repression of target genes. EZH2 is a catalytic component of PRC2 and trimethylates histone H3 at lysine 27 to transcriptionally repress the target genes. PcG proteins have been characterized as general regulators of stem cells, but recent works also unveiled their critical roles in cancer.

overall_design: Purified leukemic cells from BM of recipient mice transplanted with wild-type  and  Ezh2-/- leukemic cells transformed with MLL-AF9 leukemic fusion gene were subjected to RNA extraction and hybridization on Affymetrix microarrays.

first: Atsushi

last: Iwama

first: Misato

last: Tanaka


title: Gene expression profile of E1A infected C2C12 myotubes

city: San Giovanni Rotondo (FG)

first: Fabrizio

state: Outside U.S. & Canada

address: Viale Padre Pio 7

institute: Fondazione IRCCS Casa Sollievo della Sofferenza

summary:
Proliferating C2C12 myoblasts were induced to differentiate into myotubes and then infected with adenovirus expressing E1A (Ad-E1A), which induces cell cycle re-entry and dedifferentiation.
We analyzed the transcriptional profile of E1A infected C2C12-myotubes through the Affymetrix Mouse Genome 430 2.0 Array, searching for genes that were significantly regulated between two independent biological replicates at two different time points (24h and 36h after infection with Ad-E1A). In addition, we took advantage of the E1A mutant known as YH47/dl928 (hereafter referred as YH47), which bears two mutations in the pocket-binding region of E1A (Y48H, C124G) able to disrupt the interaction with Rb and its cognate proteins and to impair cell-cycle re-entry phenotype. YH47 mutant was used to identify the Rb independent transcriptional reprogramming of C2C12.

overall_design: C2C12 cells were differentiated in vitro to myotubes as previously described. Myotubes were, then, infected with an adenovirus carrying the 12S form of E1A (dl520), with the YH47 E1A mutant (dl928) or with a control adenovirus (CTR) expressing a deletion of essentially the entire E1A gene (dl312). Two different time points after infection were considered (24 hours and 36 hours) to evaluate changes in C2C12 cells expression profile. Technical (A or B) and biological replicates (EXP1 or EXP2) were done for each condition.

first: Francesco

last: Nicassio

first: Pier

middle: P

last: Di Fiore


title: Role of Adenosine 2A Receptors (A2AR) on regulatory T cells (Tregs)

city: Charlottesville

first: Gilbert

middle: R

last: Kinsey

state: Virginia

institute: University of Virginia

summary: The adenosine 2A receptor (A2AR) is expressed on regulatory T cells (Tregs), but the functional significance is currently unknown.  We compared the gene expression between wild-type (WT) and A2AR knockout (KO) Tregs and between WT Tregs treated with vehicle or a selective A2AR agonist.

overall_design: FACS-sorted GFP positive Tregs from WT or A2AR KO FoxP3GFP mouse spleen and lymph nodes were incubated 18 hr with vehicle (DMSO), a separate set of WT Tregs were incubated with the selective A2AR agonist ATL1222 10 nM (Dogwood Pharmaceuticals, Inc.) for 18 hr prior to RNA isolation.

first: Mark

middle: D

last: Okusa


title: Hepatic gene expression in streptozotocin-induced diabetic mice fed a phloridzin diet

status: Public on May 30 2012

city: Tsukuba

first: Masuko

last: Kobori

state: Ibaraki

address: 2-1-13 Kannondai

institute: Food Research Institute, National Agriculture and Food Research Organization

summary:
Phloridzin is a dihydrochalcone typically contained in apples. A diet containing 0.5 % phloridzin significantly improves hyperglycemia but not hypoinsulinemia and tissue lipid peroxidation in streptozotocin (STZ)-induced diabetic mice after 14 days. The phloridzin diet has no effect on the alteration of hepatic gene expression in STZ-induced diabetic mice.
A quantitative RT-PCR analysis showed a reversal of the STZ induction of the sodium/glucose cotransporter gene Sglt1 and the drug-metabolizing enzyme genes Cyp2b10 and Ephx1 in the small intestine of mice fed a 0.5% phloridzin diet. These mice also showed a reversal of the STZ-mediated renal induction of the glucose-regulated facilitated glucose transporter gene Glut2. Dietary phloridzin improved the abnormal elevations in blood glucose level and the overexpression of Sglt1, Cyp2b10 and Ephx1 in the small intestine of STZ-induced diabetic mice.

overall_design: Six-week-old male mice were divided into 4 groups of 6 mice each, housed in groups of 3 per cage. After 1 week mice were intraperitoneally injected with STZ.  Mice (n=6) in the untreated control group did not receive any treatment. After 1 week, 18 mice showing non-fasting blood glucose levels of 330-590 mg/dL were divided into 3 groups: one group was fed with AIN93G only (control group), the others with an AIN93G diet containing 0.1% or 0.5% phloridzin (Funakoshi, Tokyo, Japan) for 2 weeks.


title: Gene expression data from two murine tracheal cell populations

city: Los Angeles

first: Brigitte

last: Gomperts

address: 10833 Le Conte Ave., A2-410 MDCC

department: Pediatrics

institute: UCLA

summary: The airway epithelium is in contact with the environment and therefore constantly at risk for injury. Basal cells have been found to repair the surface epithelium, but the contribution of other stem cell populations to airway epithelial repair have not been identified. We demonstrated that airway submucosal gland duct cells, in addition to basal cells, survived severe hypoxic-ischemic injury. We developed a method to isolate duct cells from the airway. In vitro and in vivo models were used to compare the self-renewal and differentiation potential of duct cells and basal cells. We found that only duct cells were capable of regenerating submucosal gland tubules and ducts, as well as the surface epithelium overlying the submucosal glands. This is of importance to the field of lung regeneration as determining the repairing cell populations could lead to the identification of novel therapeutic targets and cell-based therapies for patients with airway diseases.

overall_design: Murine proximal airway duct and basal cells were isolated from 8-12 week old male and female mice and FACS sorted.  Each sample contains cells that were sorted from a different pool of 10-15 C57Bl/6 mice.  RNA was extracted, labeled, and hybridized to Affymetrix Mouse Genome 430 2.0 Array (GPL1261)

first: Ahmed

middle: E

last: Hegab

first: Kelvin

middle: X

last: Zhang

first: Aik

middle: T

last: Ooi

first: Matteo

last: Pellegrini

first: Derek

last: Nickerson

middle: N


title: Effect of fluoxetine treatment on translational profiles of S100a10 cortical pyramidal cells

first: Eric

last: Schmidt

state: NY

overall_design: S100a10 bacTRAP mice were administered either fluoxetine (FLX) or vehicle (VEH) in their drinking water for 15-18 days. Three independent TRAP replicates from the cortex of each group were then collected. Total RNA from the immunoprecipitates was amplified and hybridized. Data were normalized with the GCRMA algorithm and replicates were averaged across conditions. We recommend filtering data to remove probe sets with normalized expression values less than 50 in at least one condition. Because the S100a10 BAC labels some non-neuronal cells, we recommend only probe sets listed in Table S1 of the accompanying paper be included in the analysis.

first: Jennifer

last: Warner-Schmidt

first: Benjamin

last: Otopolik

first: Sarah

last: Pickett

first: Paul

last: Greengard

first: Nathaniel

last: Heintz


title: Tumor-stroma interaction between RCC cell lines and lung stroma in mouse xenografts

first: Venkata

middle: J

last: Thodima

department: Cell Biology

summary: The leading cause of death in human patients with metastatic renal cell carcinoma (RCC) and malignant cancer in general is the dissemination of the primary tumor to secondary sites. The mechanisms by which RCC colonize the lung microenvironment during metastasis remain largely unknown. To investigate the mechanisms of lung colonization by tumor cells, we grafted human RCC cells with different lung metastatic activities in mice. Gene expression profiling of the mouse lung stromal compartment revealed a gene signature enriched for neutrophil-specific functions, induced preferentially by poorly metastatic cells. Analysis of the gene expression patterns in tumor cells and clinical specimens showed an inverse correlation between metastatic activity and the levels of a number of chemokines, including CXL5 ad IL8. Enforced depletion of CXCL5 and IL8 in tumor cells allowed us to establish a functional link between lung neutrophil infiltration, the secretion of chemokines by cancer cells and metastatic activity. Finally, we showed that human neutrophils displayed a higher cytotoxic activity toward poorly metastatic cells relative to highly metastatic cells. Together, these results support a model in which neutrophils recruited to the lung by tumor-secreted chemokines build an antimetastatic barrier and loss of those neutrophil chemokines in tumor cells is a critical rate-limiting step during lung metastatic seeding.

overall_design: Total 12 samples are analysed from two cell lines (SN12C and LM2) and Normal tissue. There are four biological replicates for each cell line and four biological replicates from normal lung tissue (as reference).

first: Miguel

middle: A

last: Lopez-lago


title: Gene expression data from Ldlr-/-, Apob100/100, Mttp flox/flox Mx1-Cre mice at different stages of atherosclerosis development

city: Stockholm

first: Johan

middle: Lars Markus

last: Björkegren

state: Stockholm

address: Scheelesv. 2

department: The Department of Medical Biophysics and Biochemistry

country: Sweden

institute: The Vascular Biology Unit

summary: Gene expression profiles from the aortic arch of Ldlr-/-Apob100/100 Mttpflox/flox Mx1-Cre mice at different stages of atherosclerosis development

overall_design: Total RNAs from the aortic arch were collected at different time points during atherosclerosis development (10, 20, 30, 40, 50, and 60 weeks of age), 4-7 mice per time point.

first: Josefin

last: Skogsberg

first: Jesper

last: Lundstrom

first: Alexander

last: Kovacs

first: Roland

last: Nilsson

first: Peri

last: Noori

first: Shohreh

last: Maleki

first: Marina

last: Kohler

first: Anders

last: Hamsten

last: Tegner

last: Bjorkegren


title: Comparative analysis of S100a10-expressing cortical pyramidal cells and whole cortex

status: Public on May 25 2012

first: Eric

last: Schmidt

overall_design: Three independent TRAP replicates were collected. Total RNA from the immunoprecipitates or flow-through (unbound) whole cortex lysates were amplified and hybridized. Data were normalized with the GCRMA algorithm and replicates were averaged across conditions. We recommend filtering data to remove probe sets with normalized expression values less than 50 in at least one condition. Because the S100a10 BAC labels some non-neuronal cells, we recommend only probe sets listed in Table S1 of the accompanying paper be included in the analysis.

last: Warner-Schmidt

last: Otopolik


title: Expression data from normal brain/glioma associated macrophages

status: Public on May 28 2012

first: Yujie

last: Huang

address: 510E 70st Street

department: Neurological Surgery

institute: Weill Cornell Medicine

summary:
Tumor associated macrophages are contributing to local invasion, angiogensis, and metastasis during the progression of many kinds of tumor including glioma
We used microrray to study the difference of expression of glioma associated macrophages and normal brain tissue associated macrophages

overall_design: The macrophgages were isolated based on the markers of GFP and F4/80+ from Gl261 glioma and normal brain, RNA were extracted for microarray analysis


title: Blood gene expression profile from mouse C57Bl/10 exposed to chronic hypoxia

status: Public on May 26 2012

first: Matias

last: Mosqueira

state: Baden-Wuttenberg

address: Im Neuenheimer Feld, 326 R414

department: Institute of Physiology and Pathop

institute: Heidelberg University Hospital

summary: In order to study the gene expression profile in C57Bl/10 mouse blood, we exposed three different groups of animals. First was exposed to PO2 21% or normoxia. The second was exposed to chronic hypoxia (from PO2 21% to PO2 8%) and the third was also exposed to the same chronic hypoxia (CH) protocol but followed by two weeks under normoxia, and called as recovery group. The blood was extracted from inferior vena cava, the RNA was extracted, amplified and hybridized to Affimetrix MOE 430 V2.o chip. The results were analyzed using Partek Genome suite software. Using two fold cuttoff and 0% FDR parameters, we observed genes 512 diferentially expressed, of which one gene was up-regulated in both hypoxic and recovery condition, 202 were up-regulated during CH and then down-regulated after the recovery, 18 genes were down-regulated afteh CH and the up-regulated after recovery, ans finally 9 genes were down-regulated in both CH and recovery conditions.

overall_design: Each group of  C57Bl/10 mouse had 4 individuals and they were divided into three different groups of animals. First was exposed to PO2 21% or normoxia for 14 days. The second was exposed to chronic hypoxia (from PO2 21% to PO2 8%) and the third was also exposed to the same chronic hypoxia (CH) protocol but followed by two weeks under normoxia, and called as recovery group. After the exposure period, the animals were anaesthetized with a mix of Ketamine (100 mg/mL) and xylasine (20 mg/mL) in a proportion of 1:1. A incison was made on abdominal area and from kidneis and liver area of inferior vena cava venus blood was collected  The blood was extracted from inferior vena cava. Then, the RNA was extracted, amplified and hybridized to Affimetrix MOE 430 V2.o chip. The results were analyzed using Partek Genome suite software. Using two fold cuttoff and 0% FDR parameters, we observed genes 512 diferentially expressed, of which one gene was up-regulated in both hypoxic and recovery condition, 202 were up-regulated during CH and then down-regulated after the recovery, 18 genes were down-regulated afteh CH and the up-regulated after recovery, ans finally 9 genes were down-regulated in both CH and recovery conditions.

first: Gabriel

last: Willmann

first: Tejvir

last: Khurana

first: Ulrike

last: Zeiger


title: Hepatic gene expression in BALB/c mice fed a quercetin diet

first: Masuko

last: Kobori

summary:
We showed that diets containing 0.1% or 0.5% quercetin lowered the STZ-induced increase in blood glucose levels and improved plasma insulin levels.  A cluster analysis of the hepatic gene expressions showed that 0.5% quercetin diet suppressed STZ-induced alteration of gene expression.  Gene set enrichment analysis (GSEA) and quantitative RT-PCR analysis showed that the quercetin diets had their greatest suppressive effect on the STZ-induced elevation of expression of cyclin dependent kinase inhibitor p21(WAF1/Cip1) (Cdkn1a).
In this experiment, we determined the effect of quercetin on healthy control BALB/c mice that were fed the AIN93G diet containing 0, 0.1, 0.5 or 1% quercetin for 2 weeks. GSEA and one-way ANOVA did not detect any significant changes in hepatic gene expression in normal mice as a result of a quercetin diet.  Using a linear modeling approach and the empirical Bayes statistics, we found that Ubc were significantly reduced by both the 0.5% and 1% quercetin.

overall_design: Six-week-old male mice were divided into 4 groups of 6 mice each, housed in groups of 3 per cage, and fed a standard purified AIN-93G diet containing 0% (Control), 0.1% (0.1), 0.5% (0.5), or 1% quercertin  (1.0) for 2 weeks.


title: Genome wide analysis of macrophage gene expression after L. monocytogenes infection

status: Public on May 29 2012

city: Bonn

first: Andrea

last: Nino Castro

state: NRW

address: Carl Troll str. 31

institute: Life and Medical Sciences institute

summary: Analysis of macrophage transcriptome after L. monocytogenes infection

overall_design: Total RNA isolated from Listeria monocytogenes  infected macrophages 24 hours post-infection was compared to control non infected macrophages

first: Joachim

last: Schultze

first: Percy

last: Knolle

last: Castro

first: Zeinab

last: Abdullah


title: Hepatic gene expression in streptozotocin-induced diabetic mice fed a quercetin diet

status: Public on May 23 2012

summary:
Quercetin is a food component that may ameliorate the diabetic symptoms.  We examined hepatic gene expression of BALB/c mice with streptozotocin (STZ)-induced diabetes to elucidate the mechanism of the protective effect of dietary quercetin on diabetes-associated liver injury.
We fed STZ-induced diabetic mice with diets containing 0.1% or 0.5% quercetin for 2 weeks and compared the patterns of hepatic gene expression in these groups of mice using a DNA microarray. Diets containing 0.1% or 0.5% quercetin lowered the STZ-induced increase in blood glucose levels and improved plasma insulin levels. A cluster analysis of the hepatic gene expressions showed that 0.5% quercetin diet suppressed STZ-induced alteration of gene expression.  Gene set enrichment analysis (GSEA) and quantitative RT-PCR analysis showed that the quercetin diets had their greatest suppressive effect on the STZ-induced elevation of expression of cyclin dependent kinase inhibitor p21(WAF1/Cip1) (Cdkn1a).

overall_design: Six-week-old male mice were divided into 4 groups of 6 mice each, housed in groups of 3 per cage. After 1 week mice were intraperitoneally injected with STZ.  Mice (n=6) in the untreated control group did not receive any treatment. After 1 week, 18 mice showing non-fasting blood glucose levels of 230-400 mg/dL were divided into 3 groups: one group was fed with AIN93G only (control group), the others with an AIN93G diet containing 0.1% or 0.5% quercetin (Funakoshi, Tokyo, Japan) for 2 weeks.


title: The transcriptional program controlled by Runx1 during early hematopoietic development (expression data)

city: Cambridge

first: Anagha

middle: M

last: Joshi

address: Wellcome trust/MRC building, Hills road

department: Dept. of haematology, CIMR

institute: University of cambridge

summary: Transcription factors have long been recognised as powerful regulators of mammalian development, yet it is largely unknown how individual key regulators operate within wider regulatory networks.  Here we have used a combination of global gene expression and chromatin-immunoprecipitation approaches across four ES-cell-derived populations of increasing haematopoietic potential to define the transcriptional programme controlled by Runx1, an essential regulator of blood cell specification.  Integrated analysis of these complementary genome-wide datasets allowed us to construct a global regulatory network model, which suggested that core regulatory circuits are activated sequentially during blood specification, but will ultimately collaborate to control many haematopoietically expressed genes.  Using the CD41/integrin alpha 2b gene as a model, cellular and in vivo studies showed that CD41 is controlled by both early and late circuits in fully specified blood cells, but initiation of CD41 expression critically depends on a later subcircuit driven by Runx1.  Taken together, this study represents the first global analysis of the transcriptional programme controlled by any key haematopoietic regulator during the process of early blood cell specification. Moreover, the concept of interplay between sequentially deployed core regulatory circuits is likely to represent a design principle widely applicable to the transcriptional control of mammalian development.

overall_design: 4 samples (Runx1-/VE-cadherin+/Flk1+, Runx1+/VE-cadherin+/CD41+, Runx1+/VE-cadherin+/CD41- and Runx1+/VE-cadherin-/CD41+). 1 x 10^5 undifferentiated ES cells were cultured on confluent OP9 cell layers in 10-cm dishes to induce differentiation. After 6 days of ES cell differentiation, cultured cells were harvested for FACS analysis and sorting.

first: Yosuke

last: Tanaka

first: Nicola

middle: K

last: Wilson

first: Sarah

last: Kinston

first: Shinichi

last: Nishikawa

first: Berthold

last: Göttgens


title: Expression data from murine Fancc-deficient hematopoietic stem and progenitor cells

city: Portland

first: Grover

middle: C

last: Bagby

state: OR

address: 3181 SW Sam Jackson Park Rd.

department: Dept. of Medicine

institute: Oregon Health & Science University

summary: We used gene expression microarrays to identify genes whose expression was influenced differently by TNFa in Fancc-deficient mice compared to wild type (WT) mice. To identify genes whose expression was directly or indirectly influenced by Fancc, we looked in particular for genes either suppressed or induced by TNF in WT cells that were not affected by TNF in Fancc-deficient cells.

overall_design: Enriched populations of KSL cells (marrow mononuclear cells sorted for the c-Kit+/Sca-1+/Lineage (Lin)- fraction from WT and Fancc-deficient mice were exposed for 24 hours in vitro to either hematopoietic growth factors alone (IL-6, IL-11, Flt3L, and SCF) or to those factors plus TNFa (10 ng/ml) after which RNA was prepared and hybridized to Affymetrix microarrays (MOE430 2.0).

first: Jane

last: Yates

first: Kim

middle: H

last: Dao


title: Expression data from gastric tissues: Cancer Samples vs. Matched Adjacent Noncancerous Samples

city: Shanghai

first: Cheng

last: Lei

address: 151 Li Bing Road

country: China

institute: National Engineering Center for Biochip at Shanghai

summary: To elucidate gene expression associated with copy number changes, we performed a genome-wide copy number and expression microarray analysis of 25 pairs of gastric tissues.

overall_design: 25 pairs of gastric tissues: gastric cancer tissues vs. matched adjacent noncancerous tissues.

first: Lei

last: Cheng

first: Sheng

last: Yang

first: Yanqing

first: Wen

last: Zhang

first: Huasheng

last: Xiao

first: Junsong

last: Han

first: Qinghua


title: Cancer Samples vs. Matched Adjacent Noncancerous Samples

type: Genome variation profiling by genome tiling array

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

overall_design: Refer to individual Series


title: Host Response Signature to Staphylococcus aureus alpha-Hemolysin

status: Public on May 21 2012

city: Reno

first: Tong

last: Zhou

state: NV

address: 1664 N Virginia St

institute: University of Nevada School of Medicine

summary: Staphylococcus aureus pneumonia causes significant morbidity and mortality. Alpha-hemolysin (Hla), a pore-forming cytotoxin of S. aureus, has been identified through animal models of pneumonia as a critical virulence factor that induces lung injury. In spite of considerable molecular knowledge of how this cytotoxin injures the host, the precise host response to Hla in the context of infection remains poorly understood. We employed whole-genome expression profiling of infected lung to define the host response to wild-type S. aureus compared with an Hla-deficient isogenic mutant in experimental pneumonia. These data provide a complete expression profile at four and at twenty-four hours post-infection, revealing a unique response to the toxin-expressing strain. Gene ontogeny analysis revealed significant differences in the extracellular matrix and cardiomyopathy pathways, both of which govern cellular interactions in the tissue microenvironment. Evaluation of individual transcript responses to Hla-secreting bacteria was notable for upregulation of host cytokine and chemokine genes, including the p19 subunit of interleukin-23. Consistent with this observation, the cellular immune response to infection was characterized by a prominent TH17 response to wild-type staphylococci. These findings define specific host mRNA responses to Hla-producing S. aureus, coupling the pulmonary TH17 response to the presence of this cytotoxin. Expression profiling to define the host response to a single virulence factor proved to be a valuable tool in identifying pathways for further investigation in S. aureus pneumonia. This approach may be broadly applicable to the study of bacterial toxins, defining host pathways that can be targeted to mitigate toxin-induced disease.

overall_design: Animals were treated with PBS, S. aureus wild-type, or S. aureus Hla-deficient isogenic mutant.

first: Karen

last: Frank

first: Liliana

last: Moreno-Vinasco

first: Brian

last: Hollett

first: Joe

middle: G

last: Garcia

first: Juliane

last: Bubeck-Wardenburg


title: Microarray analysis of WT bone marrow myeloid progenitors, BM cultured with GM-CSF and M-CSF, and monocytes treated with GM-CSF

city: Saint Louis

first: Ansuman

last: Satpathy

state: MO

address: 660 S. Euclid Ave.

department: Pathology and Immunology

institute: Washington University in St. Louis

summary: Analysis of genes induced in DC precursors and in BM cells and monocytes treated with GM-CSF

overall_design: For progenitor arrays, bone marrow progenitors (CMP, GMP, CDP, and pre-cDC) were harvested from WT C57Bl/6 mice.  For culture arrays, BM was cultured in the presence of GM-CSF or M-CSF and adherent and non-adherent cells sorted.  For monocyte cultures, sorted BM monocytes were treated with GM-CSF for 0, 24 or 48 hours.

first: Kenneth

last: Murphy


title: Gene expression in IRF3-/- peritoneal macrophage infected with VSV

status: Public on May 20 2012

city: Meguro-ku, Tokyo

first: hideo

last: negishi

address: Komaba 4-6-1

department: Molecular Immunology

institute: University of Tokyo

summary:
IRF3 is one of the most critical transcription factor in down stream of pattern recognition receptors (such as toll-like receptor and RIG-I-like receptor) signalling pathway. IRF3 is known to induce the expression of type I IFN gene upon virus infection.
To furter examine the role of IRF3 in virus-induced gene expression, we preformed microarray analysis in IRF3-/- peritoneal macrophages infected with VSV, and found that IRF3 suppresses the expression of Il12b gene.

overall_design: Peritoneal macrophages from WT of IRF3-/- B6 mice were infected with VSV(1 M.O.I. ) for 6 hous, and then subjected to microarray analysis.

first: Hideo

last: Negishi

first: Tadatsugu

last: Taniguchi


title: Integrin alpha-6 (CD49f) defines a novel and distinct subset of CD4+ regulatory T cells with potent suppression activity.

status: Public on May 10 2012

city: Augusta

first: Jin-Xiong

last: She

department: Center for Biotechnology and Genomic Medicine

institute: Medical College of Georgia

summary:
A common method used both in vitro and in vivo, to identify Tregs in CD4+ T cells is through the characterization of surface marker CD25. Although CD25 expression is well correlated with regulatory activity in vitro, CD4+CD25+ T cells are not the only regulatory CD4+ T cells in vivo. Studies suggest that in many situations, CD4+CD25– T cells are as effective as CD4+CD25+ T cells in controlling T cell mediated disease. Therefore, CD25 is not a uniquely specific cell surface marker for the identification of Tregs. CD49f is an α6-integrin subunit which dimerizes with either the β 1 or β 4 subunit to form receptors for various laminin isoforms. We found that CD4+ T cells from NOD mice express CD49f, and old non-diabetic NOD mice had an increase of CD4+CD49f+ T cells in the spleen and peripheral lymph node when compared to both young and diabetic mice.
This study was conducted to further characterize CD4+CD49f+ Treg cell subpopulation in NOD mice. It was found that CD4+CD49f+T cells possess suppressive ability and only one third of CD4+CD49f+ T cells expressing CD25. Based on the expression of CD49f and CD25, CD4+ T cells was divided into four populations , CD25+CD49f+ ,CD25+CD49f- ,CD25-CD49f+ but CD25-CD49f- are of suppressive ability, and we further found that Foxp3 expression was highly correlated with the suppressive ability of these three Treg populations. In conclusion our data indicate that CD49f marks a CD4+ CD25+ Treg subset with more potent suppression activity and identifies a CD25-CD4+ T cell population with suppression function in a Foxp3+ expression dependent manner.

overall_design: We divided CD4+ T cells into four populations: CD25+CD49f+, CD25+CD49f-, CD25-CD49f+, CD25-CD49f-; Microarray technology was used to determine gene expression differences among these four groups.

first: Xueqin

last: Chen

first: Ashok

last: Sharma

first: Amber

last: Cyran

first: Bo

first: Xing

last: Zhong