title: EZH1 and EZH2 Co-Govern Histone H3-K27 Trimethylation and Are Essential for Hair Follicle Homeostasis and Wound Repair

status: Public on Jun 09 2011

city: New York

last: Ezhkova

address: 1428 Madison Avenue, Atran Building, AB7-10B

department: DRB

institute: MSSM

summary: Polycomb protein group (PcG)-dependent trimethylation on H3-K27(H3K27me3) regulates identity of embryonic stem cells (SCs). How H3K27me3 governs adult SCs and tissue development is unclear. Here, we conditionally target H3-K27-methyltransferases Ezh2 and Ezh1 to address their roles in mouse skin homeostasis. Postnatal phenotypes appear only in doubly-targeted skin, where H3K27me3 is abolished, revealing functional redundancy in EZH1/2 proteins. Surprisingly, while Ezh1/2-null hair follicles (HFs) arrest morphogenesis and degenerate due to defective proliferation and increased apoptosis, epidermis hyperproliferates and survives engraftment. mRNA-microarray studies reveal that despite these striking phenotypic differences, similar genes are upregulated in HF and epidermal Ezh1/2-null progenitors. Featured prominently are a) PcG-controlled non-skin lineage genes, whose expression is still significantly lower than in native tissues, and b) the PcG-regulated Ink4a/Inkb/Arf locus. Interestingly, even though Ink4a/Arf/Ink4b genes are fully activated in HF cells, they only partially so in epidermal-progenitors. Importantly, transduction of Ink4b/Ink4a/Arf shRNAs restores proliferation/survival of Ezh1/2-null HF progenitors in vitro, pointing towards the relevance of this locus to the observed HF phenotypes. Our findings reveal new insights into Polycomb-dependent tissue control and provide a new twist to how different progenitors within one tissue respond to loss of H3K27me3.

overall_design: RNAs from FACS-purified WT and Ezh1/2 2KO ORS, matrix and epidermal cells (Rendl et al., 2005) were provided to the Genomics Core Facility, MSKCC for quality control, quantification, reverse transcription, labeling and hybridization to MOE430A 2.0 microarray chips (Affymetrix). Arrays were scanned per the manufacturer’s specifications for the Affymetrix MOE430v2 chip. Images were background-subtracted. Probesets were identified as differentially expressed when the absolute fold change was ≥2. Probesets selected for visualization were log2 transformed and were analyzed with hierarchical clustering (Pearson correlation, average linkage), and visualized with heatmaps to assist in interpretation.

last: Fuchs


title: Effects of KLF5 overexpression on renal collecting duct epithelial cell line (mIMCD-3)

status: Public on May 17 2011

city: Tokyo

first: Katsuhito

last: Fujiu

address: 7-3-1 Hongo, Bunkyo

department: Cardiovascular Medicine

country: Japan

institute: University of Tokyo

summary: Analysis of expression changes in renal collecting duct epithelial cells by adenoviral mediated Krüppel like transcription factor 5 (KLF5) overexpression.  KLF5 is a key regulator of static and inflammatory stage in renal collecting duct epithelial cells.  We thought these results provide insights into downstream genes of KLF5 in renal collecting duct epithelial cells.

overall_design: Total RNAs were isolated from adenovirally-mediated KLF5 over expressed cultured mIMCD-3 cells or control adenovirus infected mIMCD-3.  We analyzed these two gene expression profiles after 24 hours after infection.

first: Ichiro

last: Manabe

first: Ryozo

last: Nagai


title: Hematopoietic cells and stem cells

status: Public on May 20 2011

first: Hitoshi

last: Ichikawa

address: 5-1-1 Tsukiji, Chuo-ku

institute: National Cancer Center Research Institute

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

overall_design: Refer to individual Series


title: Gene expression profiling in WT and Alox15-/- HSCs

city: Worcester

first: shaoguang

last: Li

state: MA

address: 364 Plantation street

country: USA

institute: Worcester

summary:
To understand the underlying mechanism by which Alox15 gene is required by HSCs, we performed a comparative DNA microarray analysis using total RNA isolated from wild type Lin-Sca-1+c-Kit+, Alox5-/- Lin-Sca-1+c-Kit+. The result was validated by quantitative real-time PCR analysis of wild type Lin-Sca-1+c-Kit+ and Alox15-/- Lin-Sca-1+c-Kit+.
Cancer stem cells are responsible for the initiation and maintenance of some types of cancer, and few effective target genes in these stem cells have been identified. Here we show that the arachidonate 15-lipoxygenase gene (Alox15) is essential for the survival of leukemia stem cells (LSCs) in BCR-ABL-induced chronic myeloid leukemia (CML). In the absence of Alox15, BCR-ABL failed to induce CML in mice. This Alox15 deficiency caused the impairment of LSC function through affecting cell division and apoptosis, leading to eventual deletion of LSCs. Inhibition of Alox15 function by a chemical compound also impaired the function of LSCs, and cured CML mice. In addition, we show that Alox15 is required for the survival of human CD34+ CML stem cells. The defective CML phenotype in the absence of Alox15 is rescued by depleting P-selectin. The underlying mechanisms are also related to pathways involving PTEN, PI3K/AKT, and ICSBP. These results identify Alox15 as a potential target gene for eradicating LSCs in CML, providing a novel strategy for treating CML patients for cure.

overall_design: we compared the gene profile of HSCs between WT mice  and Alox15-/- mice.

first: Shaoguang

first: Yaoyu

last: Chen

first: Yiguo

last: Hu


title: Exon level expression profiling of colorectal cancer tissue samples (test sample series).

status: Public on May 19 2011

city: Oslo

first: Anita

last: Sveen

address: P.O.Box 4953, Nydalen

department: Department of Molecular Oncology

country: Norway

institute: Institute for Cancer Research, Oslo University Hospital

summary: Colorectal cancer is a heterogeneous disease molecularly characterized by inherent genomic instabilities, chromosome instability and microsatellite instability. In the present study we propose transcriptome instability as an analogue to genomic instability on the transcriptome level. Exon microarray data from two independent series of altoghether 160 colorectal cancer tissue samples was used for global alternative splicing detection using the FIRMA algorithm (aroma.affymetrix). The sample-wise amounts of these alternative splicing scores exceeding a defined threshold (deviating exon usage amounts) were summarized to provide the basis for description of transcriptome instability. This characteristic was shown to be associated with splicing factor expression levels and patient survival in both independent sample series.

overall_design: We analyzed genome-wide expression at the exon-level for two independent series of colorectal cancer tissue biopsies using the Affymetrix Human Exon 1.0 ST platform. This series of samples represents the test series.

first: Trude

middle: H

last: Ågesen

first: Torleiv

middle: O

last: Rognum

first: Ragnhild

middle: A

last: Lothe

first: Rolf

middle: I

last: Skotheim


title: BATF knockout B cells

status: Public on May 15 2011

city: St. Louis

first: Kenneth

middle: M

last: Murphy

address: 660 S. Euclid

department: Pathology and Immunology

institute: Wustl/HHMI

summary:
compare wild type and Batf-/- B cells activated for 0 1 or 2 days in vitro.
WT or Batf deficient B cells were activated in vitro with LPS for 1 or 2 days, or left untreated.

overall_design: B cells were purified by MACS and activated, harvested and prepped for affymetrix gene expression profiling.

first: Wataru

last: Ise


title: Liver expression data from lactating QSi5 mice

status: Public on Jun 21 2011

city: Sydney

first: SJ

last: Arun

state: NSW

address: Faculty of Medicine

country: Australia

institute: unsw

summary:
The liver plays a crucial role in energy partitioning and is particularly important for the increased demand from the mammary gland during lactation. The present study identifies genes associated with negative energy balance in lactating mice.
We used microarrays to detail the gene expression underlying negative energy balance and identified distinct classes of up-regulated genes.

overall_design: The pregnant mice was fed a high GI diet during and throughout pregnancy until peak lactation (HGI group; n = 5). The second group was fed a low GI diet over the same period (LGI group; n = 5). The HGI diet included 51.4% (W/W basis) of glucose and a gross energy of 15.6MJ/Kg and the LGI diet contained 51.4% (W/W basis) of high amylase starch (Hi-Maze) and a gross energy of 16.3MJ/Kg. At the end of this period, mice were euthanazed and livers were removed and microarray was performed.

first: S

middle: J

first: Peter

last: Williamson


title: Expression data from PDGF driven mouse tumors

status: Public on May 23 2011

first: Liang

last: Lei

state: NY

address: 1130 St. Nicholas Ave Rm 1001

institute: Columbia University

summary:
Background
Tumor heterogeneity is a major obstacle for finding effective treatment of Glioblastoma (GBM). Based on global expression analysis, GBM can be classified into distinct subtypes: Proneural, Neural, Classical and Mesenchymal. The signatures of these different tumor subtypes may reflect the phenotypes of cells giving rise to them.
However, the experimental evidence connecting any specific subtype of GBM to particular cells of origin is lacking. In addition, it is unclear how different genetic alterations interact with cells of origin in determining tumor heterogeneity. This issue cannot be addressed by studying end-stage human tumors.

Methodology/Principal Findings
To address this issue, we used retroviruses to deliver transforming genetic lesions to glial progenitors in adult mouse brain. We compared the resulting tumors to human GBM. We found that different initiating genetic lesions gave rise to tumors with different growth rates.
However all mouse tumors closely resembled the human Proneural GBM.
Comparative analysis of these mouse tumors allowed us to identify a set of genes whose expression in humans with Proneural GBM correlates with survival.

Conclusions/Significance
This study offers insights into the relationship between adult glial progenitors and Proneural GBM, and allows us to identify molecular alterations that lead to more aggressive tumor growth. In addition, we present a new preclinical model that can be used to test treatments directed at a specific type of GBM in future studies.

overall_design: Gene expression profiling was performed on 20 tumors (12 Ptenf/f and 8 Ptenf/f; p53f/f) and 3 normal brains from mice. End stage tumors were used for expression array analysis. The platform used was Affymetrix GeneChip Mouse Genome 430A 2.0 Array. The microarray labeling, hybridization and quality controls were performed by following Affymetrix protocol.

last: Canoll


title: Genome-wide map of BACH1 binding in HEK 293T cells

status: Public on May 13 2011

city: Berlin

first: Hans-Jörg

last: Warnatz

address: Ihnestrasse 63-73

department: Vertebrate Genomics

country: Germany

institute: Max Planck Institute for Molecular Genetics

type: Genome binding/occupancy profiling by high throughput sequencing

summary: BTB and CNC homology 1 (BACH1) is a heme-binding transcription factor repressing the transcription from a subset of MAF recognition elements (MAREs) at low intracellular heme levels. Upon heme binding, BACH1 is released from the MAREs, resulting in increased expression of antioxidant response genes. To systematically address the gene regulatory networks involving BACH1, we combined chromatin immunoprecipitation-sequencing (ChIP-seq) analysis of BACH1 target genes in HEK 293 cells with knock-down of BACH1 using three independent types of small interfering RNAs followed by transcriptome profiling using microarrays. The 59 BACH1 target genes identified by ChIP-seq were found highly enriched in genes showing expression changes after BACH1 knock-down, demonstrating the impact of BACH1 repression on transcription. In addition to known and new BACH1 targets involved in heme degradation (HMOX1, FTL, FTH1, ME1, SLC48A1) and redox regulation (GCLC, GCLM, SLC7A11), we also discovered BACH1 target genes effecting cell cycle and apoptosis pathways (ITPR2, CALM1, SQSTM1, TFE3, EWSR1, CDK6, BCL2L11, MAFG) as well as subcellular transport processes (CLSTN1, PSAP, MAPT, vault RNA). The newly identified impact of BACH1 on genes involved in neurodegenerative processes and proliferation provides an interesting basis for future dissection of BACH1-mediated gene repression in neurodegeneration and virus-induced cancerogenesis.

overall_design: Examination of BACH1 binding in HEK 293T cells by chromatin immunoprecipitation-sequencing (CHIP-seq) with input DNA as control.

first: Dominic

last: Schmidt

first: Marie-Laure

last: Yaspo


title: Notch signaling in HSC

status: Public on May 12 2011

city: Paris

first: Camille

last: Lobry

address: 16 rue de la Grange aux Belles

department: IRSL Inserm U944 / CNRS UMR7212

country: France

institute: Inserm


title: Expression data from LSK WT and LSK NcstnKO

summary:
Notch signaling is one of the central regulators of differentiation in a variety of organisms and tissue types. Within the hematopoietic system, Notch is essential for the emergence of definitive HSC during fetal life and controls adult HSC differentiation to the T-cell lineage. Notch activation is controlled by the gamma-secretase complex complex, composed of presenilin, nicastrin (Ncstn), anterior pharynx-1 (Aph1), and presenilin enhancer-2
To determine other role of Notch signaling in HSC we designed a conditional mouse model of Nicastrin deletion. WT and KO HSC were analysed to determined genes controlled by Notch signaling.

overall_design: Bone marrow lineage negative, cKit+, Sca1+ cells were sorted from WT and Ncstn KO littermates for RNA extraction and hybridization on Affymetrix microarrays

first: Apostolos

last: Klinakis

first: Omar

last: Abdel-Wahab

first: Philmo

last: Oh

first: Hiroshi

last: Haeno

first: Silvia

last: Buonamici

first: Inge

last: van DeWalle

first: Severine

last: Cathelin

first: Thomas

last: Trimarchi

first: Elisa

last: Araldi

first: Cynthia

last: Liu

first: Sherif

last: Ibrahim

first: Miroslav

last: Beran

first: Jiri

last: Zavadil

first: Argiris

last: Efstratiadis

first: Tom

last: Taghon

first: Franziska

last: Michor

first: Ross

middle: L

last: Levine

first: Iannis

last: Aifantis


title: Overexpression of Dmrt5 in in vitro differentiated neural progenitor cells regulates gene expression

status: Public on May 18 2011

city: London

first: Xinsheng

state: England

address: Hammersmith Hospital

country: United Kingdom

institute: MRC Clinical Science Centre

summary: To test the regulatory effects of Dmrt5 on gene expression, we designed tetracycline inducible lines of Dmrt5 transgenic mouse ESCs. Overexpression of Dmrt5 was induced upon addition of Doxycycline (Dox). To evaluate the effects of Dmrt5 on gene expression in different stages of in vitro differentiated NPC derived from mouse embryonic stem cells (ESC), we analyzed gene expression profiles at differentiation day 7 and day 9 with or without Dox. The data revealed that overexpression of Dmrt5 in in vitro differentiated neural progenitor cells (NPC) regulates gene expression. Addition of Dox to the medium of the control cell line rtTA did not significantly alter gene expression profile, demonstrating that the observed effects were through induction of Dmrt5, but not simply through Dox.

overall_design: A tetracycline-inducible rtTA-Dmrt5 ES cell line and the parental rtTA cell line were used for the experiment. These ES cells were differentiated using a monolayer differentiation (MD) protocol in N2B27 medium. At MD day 5, cells were treated with Dox or without. RNA was extracted from cells harvested at MD day 7 and day 9. Two replicates for each group were used for the experiment.

first: Nicole

last: Gennet

first: Meng

last: Li


title: Expression data from LSK WT and LSK N1-C+

first: Camille

last: Lobry

summary:
Notch signaling is one of the central regulators of differentiation in a variety of organisms and tissue types. Within the hematopoietic system, Notch is essential for the emergence of definitive HSC during fetal life and controls adult HSC differentiation to the T-cell lineage. Notch activation is controlled by the gamma-secretase complex complex, composed of presenilin, nicastrin (Ncstn), anterior pharynx-1 (Aph1), and presenilin enhancer-2
To determine other role of Notch signaling in HSC we designed a conditional mouse model of Notch activation. WT and N1-IC+ HSC were analysed to determined genes controlled by Notch signaling.

overall_design: Bone marrow lineage negative, cKit+, Sca1+ cells were sorted from WT and N1-IC+ littermates for RNA extraction and hybridization on Affymetrix microarrays

first: Apostolos

last: Klinakis

first: Omar

last: Abdel-Wahab

first: Philmo

last: Oh

first: Hiroshi

last: Haeno

first: Silvia

last: van De Walle


title: Ath29 congenic mice - gene expression in aorta

status: Public on May 11 2011

city: charlottesville

first: qian

last: wang

state: virginia

address: 480 Ray C Hunt Drive

department: radiology

institute: university of virginia

summary:
A congenic mouse line was constructed by introgressing a C3H chromosome 9 region harboring Ath29 into the C57BL/6 apoE-deficient background.  RNA was extracted from aorta using a QIAGEN kit . Total RNA was pooled in an equal amount from 3 mice for each group. Standard Affymetrix procedures were performed using 8ug of total RNA.
Microarrays were used to detect gene expression in the aorta  of Ath29 congenic mice and C57BL/6 apoE-deficient mouse strains fed a chow or western diet.

overall_design: 4 groups of mice were studied: C57BL/6 apoE-/- control mice and Ath29 congenic mice fed a chow or Western diet.  After fed a  Western diet for 2 weeks, aorta was harvested and total RNA prepared.

first: Weibin

last: Shi

first: Qian

last: Wang

first: Ani

last: Manichaikul


title: Murine skin gene expression analysis of skin-specific Scd1-deficient and control mice

status: Public on May 09 2011

city: Madison

first: Matthew

last: Flowers

state: WI

address: 433 Babcock Drive

department: Biochemistry

institute: University of Wisconsin-Madison

summary:
To help elucidate the metabolic changes in the skin that contribute to the obesity resistance and skin pathology in mice lacking Scd1, we performed microarray analysis of skin gene expression in male skin Scd1 knockout (SKO) and Scd1 flox/flox control (Lox) mice fed a standard rodent diet.
We identified an extraordinary number of differentially expressed genes that support the previously documented histological observations of sebocyte atrophy, inflammation and epidermal hyperplasia in SKO mice. Additionally, transcript levels were reduced in skin of SKO mice for genes involved in fatty acid synthesis, elongation and desaturation, which may be attributed to decreased abundance of key transcription factors including SREBP1c, ChREBP and LXRα. Conversely, genes involved in cholesterol synthesis were increased, suggesting an imbalance between skin fatty acid and cholesterol synthesis. Unexpectedly, we observed a robust elevation in skin retinol, retinoic acid and retinoic acid-induced genes in SKO mice. These results highlight the importance of monounsaturated fatty acid synthesis for maintaining retinol homeostasis and point to disturbed retinol metabolism as a novel contributor to the Scd1 deficiency-induced skin pathology.

overall_design: We analyzed dorsal skin gene expression in non-fasted 8-9 week old male skin Scd1 knockout (SKO) mice (n=3) and Scd1flox/flox (Lox) control mice (n=3)on a C57BL/6J background using Affymetrix 430 2.0 microarrays.

middle: T

first: Kevin

last: Scheisser

first: John

last: Dawson

first: Christina

last: Kendziorski

first: James

last: Ntambi


title: The transcriptome of human epicardial, mediastinal and subcutaneous adipose tissues in men with coronary artery disease

city: Quebec

first: Sandra

last: Guauque-Olarte

address: 2725, chemin Sainte-Foy

country: Canada

institute: CRIUCPQ

summary: The biological functions of epicardial adipose tissue (EAT) remain largely elusive. However, the proximity of EAT to the coronary arteries suggests a role in the pathogenesis of coronary artery disease (CAD). Objectives of this study were to identify genes that are up- or down-regulated among three adipose tissues (AT), namely EAT, mediastinal (MAT) and subcutaneous (SAT) and to study their possible relationships with the development of cardiovascular diseases. Samples were collected from patients undergoing coronary artery bypass grafting surgeries. Gene expression was evaluated in all three AT depots of six men using the lllumina® HumanWG-6 v3.0 expression BeadChips. Twenty-two and 73 genes were up-regulated in EAT compared to mediastinal and subcutaneous AT, respectively. Ninety-four genes were down-regulated in EAT compared to subcutaneous adipose depot. However, none were significantly down-regulated in EAT compared to mediastinal fat. More specifically, the expression of the adenosine A1 receptor (ADORA1), involved in myocardial ischemia, was significantly up-regulated in EAT. Levels of the prostaglandin D2 synthase (PTGDS) gene, recently associated with the progression of atherosclerosis, were significantly different in the three pairwise comparisons (epicardial > mediastinal > subcutaneous). The results of ADORA1 and PTGDS were confirmed by qPCR in 25 biological replicates. Overall, the transcriptional profiles of EAT and MAT were similar compared to the subcutaneous compartment. Despite this similarity, two genes involved in cardiovascular diseases, ADORA1 and PTGDS, were up-regulated in EAT. These results provide insights about the biology of EAT and its potential implication in CAD.

overall_design: Samples of epicardial, mediastinal and subscutaneous adipose tissue were collected from the chest of 6 male patients undergoing coronary artery bypass grafting surgeries. The RNA was labeled and hybridized using a standard Illumina protocol (https://icom.illumina.com/Login?ReturnUrl=%2ficom%2fsoftware.ilmn%3fid%3d214&id=214). Three pairwise comparison among the three adipose tissue were made using significance analysis of microarrays.

first: Patrick

last: Mathieu

first: Yohan

last: Bossé


title: Differential expression between floor plate and ventral lateral region in E10.5 mouse embryo midbrain

first: Xinsheng

summary: The data revealed differential expression between floor plate and ventral lateral region in E10.5 mouse embryo midbrain. Several differentially expressed genes in these regions have been reported in the literature, demonstrating reliability of tissue dissection.

overall_design: Midbrain floor plate and non-overlapping adjacent ventral lateral region of mouse E10.5 embryo midbrain was dissected. Each sample was a pool from 6 embryos. Three replicates for each region were used for the experiment.

first: Emily

last: Gale

first: Meng

last: Li


title: Zebularine effect on mouse embryonic stem cells manifested as cardiod-myogenic potential: testable hypothesis generation using microarray data

status: Public on May 05 2011

city: Sevilla

first: Abdelkrim

last: Hmadcha

address: Avda Américo Vespucio 24, Parque Científico y Tecnológico Cartuja

department: Regeneration and Cell Therapy

country: Spain

institute: CABIMER

summary: Lineage commitment during Embryonic Stem Cells (ESCs) differentiation is controlled not only by a gamut of transcription factors but also by epigenetic events, mainly histone deacetylation and promoter DNA methylation. Moreover, the DNA demethylation agent 5′-Aza-2′-deoxycytidine (AzadC) has been widely described in the literature as an effective chemical stimulus used to promote cardiomyogenic differentiation in various stem cell types; however, its toxicity and instability complicate its use. Thus, the purpose of this study was to examine the effects of zebularine, a stable and non-toxic DNA cytosine methylation inhibitor, on ESCs differentiation. Herein are the Affymetrix Expression data obtained from RNA of murine ESCs treated with zebularine.

overall_design: 9 control samples (replicates) and 9 zebularine samples (replicates).

first: Angelica

last: Horrillo

first: Eloisa

last: Andujar

first: Fátima

last: Núñez


title: Comparative transcriptome analysis of APPsα-DM and APLP2-KO brains

status: Public on May 10 2011

city: Heidelberg

first: Ulrike

last: Müller

address: Im Neuenheimer Feld 364

department: Bioinformatics and Functional Genomics

institute: Institute of Pharmacy and Molecular Biotechnology, University of Heidelberg

summary: Despite its key role in Alzheimer pathogenesis, the physiological function(s) of the amyloid precursor protein (APP) and of its proteolytic fragments are still poorly understood. The secreted APPsα ectodomain has been shown to be involved in neuroprotection and synaptic plasticity. The γ-secretase generated APP intracellular domain, AICD, functions as a transcriptional regulator in heterologous reporter assays although its role for endogenous gene regulation has remained controversial. Previously, we have generated APPsα knockin (KI) mice expressing solely the secreted ectodomain APPsα. Here, we generated double mutants (APPsα-DM) by crossing APPsα-KI mice onto an APLP2-deficient background and show that APPsα rescues the postnatal lethality of the majority of APP/APLP2 double knockout mice. Despite normal CNS morphology and unaltered basal synaptic transmission, young APPsα-DM mice already showed pronounced hippocampal dysfunction, impaired spatial learning and a deficit in LTP. To gain further mechanistic insight into which domains/proteolytic fragments are crucial for hippocampal APP/APLP2 mediated functions, we performed a DNA microarray transcriptome profiling of prefrontal cortex and hippocampus of adult APLP2-KO (APLP2-/-) and APPsα-DM mice (APPα/αAPLP2-/- mice).Interestingly, this analysis failed to reveal major genotype-related transcriptional differences. Expression differences between cortex and hippocampus were, however, readily detectable.

overall_design: Prefrontal cortices and hippocampi of adult mice (38 - 40 weeks) of the following genotypes were analyzed: APLP2-KO (APLP2-/-) (n=3) and APPsα-DM (APPα/αAPLP2-/-) (n=3).

first: Dorothee

last: Aydin

first: Mikhail

last: Filippov

first: Sascha

last: Weyer

first: Norbert

last: Gretz

first: Benedikt

last: Brors

middle: C


title: Ebf1 or Pax5 Haploinsufficiency Synergizes with STAT5 Activation to Initiate Acute Lymphoblastic Leukemia

city: Minneapolis

first: Lynn

last: Heltemes Harris

state: MN

address: 2101 6th St. SE

institute: University of Minnesota

summary: STAT5 is critical for differentiation, proliferation and survival of progenitor B cells suggesting a possible role in Acute Lymphoblastic Leukemia (ALL). Herein, we show increased expression of activated STAT5 in ALL patients, which correlates with treatment outcome.  Mutations in Ebf1 and Pax5, genes critical for B cell development have also been identified in human ALL.  To determine whether mutations in Ebf1 or Pax5 synergize with STAT5 activation to induce ALL we crossed mice expressing a constitutively active form of STAT5 (Stat5b-CA) with mice heterozygous for Ebf1 or Pax5. Haploinsufficiency of either Pax5 or Ebf1 synergized with Stat5b-CA to rapidly induce ALL in 100% of the mice. The leukemic cells displayed reduced expression of both Pax5 and Ebf1 but this had little affect on most EBF1 or PAX5 target genes.  However, a subset of these genes was deregulated and included a large percentage of potential tumor suppressor genes and oncogenes.  Further, most of these genes appear to be jointly regulated by both EBF1 and PAX5.  Our findings suggest a model whereby small perturbations in a self-reinforcing network of transcription factors critical for B cell development, specifically PAX5 and EBF1, cooperate with STAT5 activation to initiate ALL.

overall_design: Gene expression profiling was performed on cells isolated from lymph nodes of Stat5b-CA x Ebf1+/- and Stat5b-CA x Rag2-/- leukemic mice and pre B cells sorted from bone marrow of C57BL/6 mice and Stat5b-CA transgenic mice. 17 Samples.

last: Heltemes-Harris

first: Mark

last: Willette

first: Laura

last: Ramsey

first: Yi

last: Qiu

first: E

middle: S

last: Neeley

first: Nianxiang

last: Zhang

first: Debra

last: Thomas

first: Thearith

last: Koeuth

last: Gillespie

first: Steven

last: Kornblau

first: Michael

last: Farrar


title: Gene expression between high and low altitude Mus musculus domesticus

status: Public on May 06 2011

city: Reno

first: Monica

last: Baze

state: NV

address: Dept. of Biology/ 314

department: Biology

institute: University of Nevada, Reno

summary:
Analysis of gene expression profiles is an attractive method for discovering how animals respond to environmental challenges in nature. Compared to low altitudes, high altitudes are characterized by reduced partial pressures of oxygen (hypoxia) and cooler ambient temperatures
To better understand how mammals cope with high altitudes, we trapped wild house mice (Mus musculus domesticus) from 3 populations in La Paz, Bolivia (3000 - 3600 m) and 3 populations in Lima, Peru (0 – 200 m). Affymetrix GeneChip® Mouse Genome 430 2.0 Arrays were use to measure mRNA abundance in the livers of these mice.

overall_design: Eighteen male house mice were trapped from three different locations (3 mice per location)at high alttiude (La Paz, Bolivia, 3600 m) and from three locations  at low altiditude (Lima, Peru, 100 m). Total mRNA was extracted from the livers and used for hybridization of Affymetrix GeneChip Mouse expression set 420.

first: Chris

last: Seidel

first: Karen

last: Schlauch

first: Jack

middle: P

last: Hayes


title: Microarray gene expression data from Hdh knock-out, wild-type and knock-in embryonic stem cells

status: Public on May 04 2011

city: Boston

first: Jong-Min

last: Lee

address: 185 Cambridge Street

department: Center for Human Genetic Research

institute: Massachusetts General Hospital

summary: Huntington's disease (HD) features a unique disease-initiating mechanism hypothesized to entail an impact of the CAG repeat encoded polyglutamine region on the full-length huntingtin protein, with dominant effects that are continuous with CAG size, in a simple gain of function. To evaluate these predictions, we generated a series of heterozygous Hdh CAG knock-in mouse embryonic stem (ES) cell lines, with 18, 48, 89, 109 CAGs, and found that a continuous analytic strategy efficiently identified, from genome-wide datasets, 73 genes and 172 pathways whose expression varied continuously with CAG length. The CAG-correlated genes were distinct from the set of 754 genes that distinguished huntingtin null ES cells from wild-type controls, and CAG-correlated pathways did not display a one-to-one correspondence with the 238 pathways altered in huntingtin null ES cells. Rather, the genes that varied with CAG size were either members of the same pathways as altered genes in huntingtin null cells or were members of unique pathways related to these pathways. These findings falsified a gain of function/loss of function proposal but were consistent with the simple gain of novel function mechanism hypothesis. The dominant CAG correlated gene expression changes conformed to the genetic features of the HD initiating mechanism and were system-wide and inter-related with pathways perturbed by lack of full-length huntingtin function, urging system-wide approaches for the discovery and validation of potential modulating factors, in the search for effective HD therapeutics.

overall_design: Undifferentiated mouse embryonic stem cells without Hdh or with knock-in alleles with different Hdh CAG repeat sizes were profiled by Affymetrix MG 430 2.0 arrays.

first: Jessie

last: Jacobson

first: Juliana

last: Woda

first: Jillian

last: Gregory

first: Marcy

middle: E

last: Macdonald


city: Stanford

first: Rami

last: Rauch

state: CA

address: 300 Pasteaur Dr

institute: Stanford U

type: Methylation profiling by high throughput sequencing

summary:
Publication title:  Distinct DNA methylation patterns characterize differentiated human embryonic stem cells and developing human fetal liver
To investigate the role of DNA methylation during human development, we developed Methyl-seq, a method that assays DNA methylation at more than 90,000 regions throughout the genome.  Performing Methyl-seq on human embryonic stem cells (hESCs), their derivatives and human tissues allowed us to identify several trends during hESC and in vivo liver differentiation.  First, differentiation results in DNA methylation changes at a minimal number of assayed regions, both in vitro and in vivo (2-11%).  Second, in vitro hESC differentiation is characterized by both de novo methylation and demethylation, whereas in vivo fetal liver development is characterized predominantly by demethylation.  Third, hESC differentiation is uniquely characterized by methylation changes specifically at H3K27me3-occupied regions, bivalent domains and low-density CpG promoters (LCPs) suggesting that these regions are more likely to be involved in transcriptional regulation during hESC differentiation.  Although both H3K27me3-occupied domains and LCPs are also regions of high variability in DNA methylation state during human liver development, these regions become highly unmethylated, which is a distinct trend from that observed in hESCs.  Taken together, our results indicate that hESC differentiation has a unique DNA methylation signature that may not be indicative of in vivo differentiation.
Keywords: Methyl-seq, hESC differentiation

For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODEDataReleasePolicyFinal2008.pdf

overall_design: High-throughput sequencing of ES cell lines, ES-derived cells, and fetal and normal livers (17 samples). Raw data: SRA008154 http://www.ncbi.nlm.nih.gov/sites/entrez?db=sra&cmd=search&term=SRA008154

first: Alayne

last: Brunner

first: David

last: Johnson

first: Si

middle: W

last: Kim

first: Anton

last: Valouev

first: Timothy

last: Reddy

first: Norma

middle: F

last: Neff

first: Elizabeth

last: Anton

first: Catherine

last: Medina

first: Loan

last: Nguyen

first: Eric

last: Chiao

first: Chuba

middle: B

last: Oyolu

first: Gary

last: Schroth

first: Devin

last: Absher

first: Julie

last: Baker

first: Richard

last: Myers


title: Differentially regulated splice variants and systems biology analysis of Kaposi's Sarcoma-associated Herpesvirus-infected lymphatic endothelial cells

city: Taipei

first: Ting-Yu

last: Chang

address: No155, LiNong St

country: Taiwan

institute: National Yang-Ming University

summary:
Alternative RNA splicing greatly increases proteome diversity, and the possibility of studying genome-wide alternative splicing (AS) events becomes available with the advent of high-throughput genomics tools devoted to this issue. Kaposi’s sarcoma associated herpesvirus (KSHV) is the etiological agent of KS, a tumor of lymphatic endothelial cell (LEC) lineage, but little is known about the AS variations induced by KSHV. We analyzed KSHV-controlled AS using high-density microarrays capable of detecting all exons in the human genome. Splicing variants and altered exon-intron usage in infected LEC were found, and these correlated with protein domain modification. The different 3’ UTR used in new transcripts also help isoforms to escape microRNA-mediated surveillance. Exome-level analysis further revealed information that cannot be disclosed using classical gene-level profiling: a significant exon usage difference existed between LEC and CD34+ precursor cells, and KSHV infection resulted in LEC-to-precursor, dedifferentiation-like exon level reprogramming.
Our results demonstrate the application of exon arrays in systems biology research, and suggest the regulatory effects of AS in endothelial cells are far more complex than previously observed. This extra layer of molecular diversity helps to account for various aspects of endothelial biology, KSHV life cycle and disease pathogenesis that until now have been unexplored.

overall_design: 5 samples were analyzed. 3 were KSHV infected lymphatic endothelial cells (LECs), and 2 were non-infected control samples.

first: Hsei-Wei

last: Wang


title: Heterogeneity in SDF-1 production defines the vasculogenic potential of c-kit+ cardiac progenitor cells

status: Public on May 01 2011

city: Miami

first: Lina

last: Shehadeh

state: FL

address: 1600 NW 10th Ave

department: Medicine

institute: University of Miami Miller School of Medicine

summary: Five Cardiac Progenitor Clones Isolated were from the left ventricle of mouse heart. The 5 cardiac progenitor clones differ in morphology and vasculogenic potential. Total RNA was isolated and hybridized on mouse Affymetrix MOE_430_2 arrays to compare basal gene expression levels and correlate the gene expression with fuctional studies.

overall_design: Five cardiac progenitor clones were analyzed. No fold changes were calculated. Hierachical clustering based on Gene Ontologies was examined based .


title: Expression profiling of the Otx2 CKO retina

city: Suita

first: Takahisa

last: Furukawa

state: Osaka

address: 6-2-4 Furuedai

department: Developmental Biology

institute: Osaka Bioscience Institute

summary: In the vertebrate retina, the Otx2 transcription factor plays a crucial role in the cell fate determination of both rod and cone photoreceptors.  Otx2 conditional knockout (CKO) mice exhibited a total absence of rods and cones in the retina due to their cell fate conversion to amacrine-like cells.  In order to investigate the entire transcriptome regulated by Otx2 in the developing retina, we performed microarray analysis on the Otx2 CKO retina.

overall_design: In order to clarify the molecular role of Otx2 in transcriptional regulation during development, we investigated the expression profile of the Otx2 CKO retina compared with that of the control retina with the genotype Otx2flox/flox;Crx-cre- using microarrays at two time points, P1 and P12.

first: Yoshihiro

last: Omori

first: Shigeru

last: Sato


title: Expression data from LSK WT, GMP WT and GMP NcstnKO

first: Camille

last: Lobry

overall_design: Bone marrow lineage negative, cKit+, Sca1+ and lineage negative, cKit+, Sca1- CD34+ FcgammaRII/III+ cells were sorted from WT and Ncstn KO littermates for RNA extraction and hybridization on Affymetrix microarrays

first: Apostolos

last: Klinakis

first: Omar

last: Abdel-Wahab

first: Philmo

last: Oh

first: Hiroshi

last: Haeno

first: Silvia

last: Buonamici

first: Inge

last: van De Walle

first: Severine

last: Cathelin

first: Thomas

last: Trimarchi

first: Elisa

last: Araldi

first: Cynthia

last: Liu

first: Sherif

last: Ibrahim

first: Miroslav

last: Beran

first: Jiri

last: Zavadil

first: Argiris

last: Efstratiadis

first: Tom

last: Taghon

first: Franziska

last: Michor

first: Ross

last: Levine

first: Iannis

last: Aifantis


title: Differential gene expression in adrenal medulla after cardiac pressure overload

status: Public on May 03 2011

city: Freiburg

first: Ralf

last: Gilsbach

address: Albertstr. 25

institute: Institute of Pharmacology

summary: Transcriptom analysis of microdissect adrenal medulla after 8 weeks of cardiac pressure overload caused by transverse aortic constriction.

overall_design: Comparative transcriptome analysis was determined using the GeneChip Mouse Genome 430 2.0 Array (Affymetrix, Santa Clara, CA, USA). Six microarrays from microdissected adrenal medulla of mice were performed 8 weeks after transverse aortic constriction or sham operation.

first: Johanna

last: Schneider

first: Ivacevic

last: Tomi

first: Lutz

last: Hein


title: Polycomb Group Protein Bmi1 Promotes Hematopoietic Cell Development from ES Cells

status: Public on Apr 29 2011

city: Aachen

first: Martin

last: Zenke

state: NRW

address: Universitatsklinikum Aachen, RWTH

department: Cell Biology

institute: Institute for Biomedical Engineering

summary: Bmi1 is a component of the Polycomb-repressive complexes (PRC) and essential for maintaining the pool of adult stem cells. PRC are key regulators for embryonic development by modifying chromatin architecture and maintaining gene repression. To assess the role of Bmi1 in pluripotent stem cells and upon exit from pluripotency during differentiation, we studied forced Bmi1 expression in mouse embryonic stem cells (ESC). We found that ESC do not express detectable levels of Bmi1 RNA and protein and that forced Bmi1 expression had no obvious influence on ESC self-renewal. However, upon ESC differentiation Bmi1 effectively enhanced development of hematopoietic cells. Global transcriptional profiling identified a large array of genes that were differentially regulated during ESC differentiation by Bmi1. Importantly, we found that Bmi1 induced a prominent up-regulation of Gata2, a zinc finger transcription factor, which is essential for primitive hematopoietic cell generation from mesoderm. In addition, Bmi1 caused sustained growth and a more than 100-fold expansion of ESC-derived hematopoietic stem/progenitor cells within 2-3 weeks of culture. The enhanced proliferative capacity was associated with reduced Ink4a/Arf expression in Bmi1-transduced cells. Taken together, our experiments demonstrate distinct activities of Bmi1 in ESC and ESC-derived hematopoietic progenitor cells. In addition, Bmi1 enhances the propensity of ESC in differentiating towards the hematopoietic lineage. Thus, Bmi1 could be a candidate gene for engineered adult stem cell derivation from ESC.

overall_design:
8 samples in total.

 Bmi1 embryoid body sample_1 (Bmi1_EB_1)
 Bmi1 embryoid body sample_2 (Bmi1_EB_2)
 Empty vector control embryoid body sample_1 (Vector_EB_1)
 Empty vector control embryoid body sample_2 (Vector_EB_2)
 Bmi1 embryonic stem cells sample_1 (Bmi1_ESC_1)
 Bmi1 embryonic stem cells sample_2 (Bmi1_ESC_2)
 Untreated CCE embryonic stem cells (CCE_ESC_Control)
 Empty vector CCE embryonic stem cells (CCE_ESC_Vector)

first: XiaoLei

last: Ding

first: Qiong

last: Lin

first: Roberto

last: Ensenat-Waser

first: Stefan

last: Rose-John


title: Bglu3 congenic mice - gene expression in liver

first: qian

last: wang

summary:
A congenic line was constructed by introgressing a C3H chromosome 1 region harboring Bglu3 into C57BL/6 apoE-/- background. RNA was extracted from liver using a QIAGEN kit . Total RNA was pooled in an equal amount from 3 mice for each group. Standard Affymetrix procedures were performed using 8ug of total RNA.
Microarrays were used to detect gene expression in the liver  of Bglu3 congenic mice and C57BL/6 apoE-deficient mouse strains fed a western diet.

overall_design: 2 groups of mice were studied: C57BL/6 apoE-/- control mice and Bglu3 congenic mice.  After fed a  Western diet for 12 weeks, liver was harvested and total RNA prepared.

first: Weibin

last: Shi

first: Qian

last: Wang

first: Jing

last: Li


title: Identification of microRNA targets in the mammalian inner ear using a comprehensive transcriptome and proteome integrated approach

status: Public on Apr 20 2011

city: Tel Aviv

first: Tal

last: Elkan-Miller

address: P.O.B. 39040, Ramat Aviv

country: Israel

institute: Tel Aviv University

summary: We have employed a novel approach for the identification of functionally important microRNA (miRNA)-target interactions using integrated miRNA, transcriptome and proteome profiles with advanced in silico analysis. By looking at both the transcript and protein levels of expression, a thorough coverage of miRNA regulation was obtained. Microdissected auditory and vestibular sensory epithelia were used as the model system, thus being the first time such a comparison was carried out in a neuroepithelial system. Moreover, this is one of only a few studies employing proteome screening for the identification of miRNA targets. Notably, this approach can be employed for the study of other tissues and organs. We detected the expression of 157 miRNAs in the inner ear sensory epithelia, with 53 miRNAs differentially expressed between the cochlea and vestibule. By searching for enrichment and depletion of miRNA targets in the transcript and protein datasets with a reciprocal or similar expression, respectively, as the regulatory miRNA, we identified functionally important miRNAs. Finally, the interaction between miR-135b and PSIP1-P75, a transcriptional coacitvator previously unknown in the inner ear, was identified and validated experimentally. We suggest that miR-135b may serve as a cellular effector, involved in regulating some of the differences between the cochlear and vestibular hair cells.

overall_design: We investigated the mRNA expression profile of the cochlear and vestibular sensory epithelia from inner ears of postnatal day 2 mice using the Affymetrix GeneChip® 430 2Mouse Genome array. Cochlear and vestibular sensory epithelia were dissected from wild type C3H mice and collected separately. The vestibular epithelia consisted of the saccule, utricle and the lateral and anterior cristae. Both the cochlear and vestibular sensory epithelia were dissected with their underlying mesenchyma. Altogether three pools, three biological replicates, of each tissue type were collected consisting of cochlear or vestibular sensory epithelia dissected from 10 to 12 inner ears.

first: Karen

last: Avraham


title: Gene expression profile of  Age associated B cells, Follicular B cells, and B1 cells

status: Public on Apr 28 2011

city: Denver

first: Anatoly

middle: V

last: Rubtsov

address: 1400 Jackson St

institute: National Jewish Health

summary: We performed gene expression profile of different B cell populations found in old (18 months old) C57BL/6 female mouse (B1 cells were recovered from both young and old C57BL/6 mice). Mice were naïve and healthy (no autoimmunity was detected at the time of the experiment).

overall_design: Different B cell populations were sorted using flow cytometry and RNA was isolated.

first: Kira

last: Rubtsova

first: Philippa

last: Marrack


title: Early B Cell Factor 2 Regulates Hematopoietic Stem Cell Homeostasis in a Cell-Nonautonomous Manner

status: Public on Apr 26 2011

first: Rudolf

last: Grosschedl

address: Stübeweg 51

institute: Max-Planck Institute of Immunobiology

summary: Hematopoiesis requires the interaction of hematopoietic stem cells (HSCs) with various stromal microenvironments. Here, we examine the role of early B cell factor 2 (Ebf2), a transcription factor expressed in a subset of immature osteoblastic cells. Ebf2-/- mice show decreased frequencies of HSCs and lineage-committed progenitors. This defect is cell nonautonomous, as shown by the fact that transplantation of Ebf2-deficient bone marrow into wild-type hosts results in normal hematopoiesis. In coculture experiments, Ebf2 Ebf2-/-osteoblastic cells have reduced potential to support short-term proliferation of HSCs. Expression profiling of sorted Ebf2-/- osteoblastic cells indicated that several genes implicated in the maintenance of HSCs are downregulated relative to Ebf2+/- cells, whereas genes encoding secreted frizzled-related proteins are upregulated. Moreover, HSCs from Ebf2-/- mice and wild-type HSCs cocultured with Ebf2-/- osteoblastic cells show reduced Wnt responses. Thus, Ebf2 acts as a transcriptional determinant of an osteoblastic niche that regulates the maintenance of hematopoietic progenitors, in part by modulating Wnt signaling.

overall_design: Osteoblastic cells from tibia and femur of Ebf2 heterozygous and knockout mice (n=3 each) were loaded with FDG, FACS sorted and total RNA was isolated. cDNA was synthesised using the One-Cycle cDNA Synthesis Kit (Affymetrix), and labeled cRNA was synthesized by transcription in vitro, using the IVT labelling kit (Affymetrix). The labeled RNA was fragmented and hybridized to GeneChip® Mouse genome 430 2.0 arrays (GPL1261), according to the manufacturer’s instructions.

first: Matthias

last: Kieslinger

first: Silvia

last: Hiechinger

first: Gergana

last: Dobreva

first: Giacomo

last: Consalez


title: Expression data from stomach of germ-free and gnotobiotic mice

city: Odawara

first: Yukio

last: Asami

state: Kanagawa

address: 540 Naruda

department: Functional Evaluation

institute: Meiji Corporation, Food Science Institute

summary: The aim of this study was to examine the role of indigenous lactobacilli in the physiological development of the stomach in mice using microarray analysis. In lactobacilli-associated gnotobiotic mice, an increased expression of the genes related to the muscle system development, such as nebulin and troponin, was observed. On the other hand, the expression of the gastrin gene dramatically decreased. A microarray analysis of the stomachs infected with H. pylori also showed both the up-regulation of muscle cell genes and the down-regulation of gastrin genes.

overall_design: Male germfree BALB/c mice were orally inoculated with 109 CFU lactobacilli and their stomachs were excised after 10 days for analyses. In the other experiment, 8-week-old mice were orally inoculated using a stomach tube on three consecutive days with 109 CFU of H. pylori. The stomachs of the germfree mice were used as controls. For the DNA microarray analysis, RNA was prepared from the stomach and then applied to a genome array.

first: Yasuhiro

last: Koga

first: Hidenori

last: Takahashi


title: Expression data from Smad4-siRNA bEnd3 cells

status: Public on Apr 17 2011

city: Beijing

first: Xiao

last: Yang

address: 20 Dongdajie

country: China

institute: Beijing Institute of Biotechnology

summary: TGF-beta/Smads signaling plays important roles in vascular integrity. To identify potential Smad4 target genes in brain endothelial cells that control cerebrovascular integrity, the microarray assay was performed to compare the gene expression profiles of bEnd3 transfected with Smad4-siRNA and control-siRNA.

overall_design: bEnd3 cells were infected by Smad4-siRNA or control-siRNA retrovirus particles produced by PLAT-E packaging cells and selected by puromycin. The specific and control RNAi cells were used for RNA extraction and hybridization on Affymetrix microarrays. Two independent infections were performed and samples were pooled in order to obtain representative populations.

first: Fangfei


title: Genome-wide Regulation of 5hmC, 5mC and Gene Expression by Tet1 Hydroxylase in Mouse Embryonic Stem Cells (expression data)

status: Public on Apr 21 2011

city: Shanghai

first: Feizhen

last: Wu

state: Shanghai

address: Zhangheng Road 825, Pudong

department: Intelligent Medicine Institute

institute: Fudan Univ, Shanghai, China

summary: DNA methylation of C5-cytosine (5mC) in the mammalian genome is a key epigenetic event that is critical for various cellular processes. However, how the genome-wide 5mC pattern is dynamically regulated remains a fundamental question in epigenetic biology. The TET family of 5mC hydroxylases, which convert 5mC to 5-hydroxymethylcytosine (5hmC), have provided a new potential mechanism for the dynamic regulation of DNA methylation. The extent to which individual Tet family members contribute to the genome-wide 5mC and 5hmC patterns and associated gene network remains largely unknown. Here we report genome-wide mapping of Tet1 and 5hmC in mESCs and reveal a mechanism of action by which Tet1 controls 5hmC and 5mC levels in mESCs. In combination with microarray and mRNA-seq expression profiling, we identify a comprehensive yet intricate gene network influenced by Tet1. We propose a model whereby Tet1 controls DNA methylation both by binding to CpG-rich regions to prevent unwanted DNA methyltransferase activity, and by converting the existing 5mC to 5hmC through its enzymatic activity. This Tet1-mediated antagonism of CpG methylation imparts differential maintenance of DNA methylation status at Tet1 target loci, thereby providing a new regulatory mechanism for establishing the epigenetic landscape of mESCs, which ultimately contributes to mESC differentiation and the onset of embryonic development.

overall_design: Tet1 protein was depleted in J1 or E14 mouse ES cells by siRNA or shRNA treatment. Total RNA was purified and used to determine the global gene transcription profiles by microarray assays. The Tet1-regulated genes were identified by comparing the  gene expression profiles of control and Tet1-depleted ES cells.

first: Yufei

last: Xu

first: Yujiang

last: Shi


title: Renal gene expression in uninephrectomized diabetic OVE26 mice

status: Public on Apr 15 2011

city: Louisville

first: Shirong

last: Zheng

state: KY

address: 570 S Preston St.

department: Pediatrics

institute: University of Louisville

summary: OVE26 (OVE) mice provide a useful model of advanced diabetic nephropathy (DN) with respect to albuminuria and pathologies. We showed that albuminuria, reduced GFR and interstitial fibrosis, which normally take 8-9 months to develop, are more advanced in uninephrectomized OVE mice within 10 weeks of surgery, at 4.5 months of age.  The accelerated progression of renal damage, especially renal fibrosis in OVE-uni mice, was also identified at the gene expression level. The hepatic fibrosis/hepatic stellate cell activation pathway was by far the most significant Ingenuity canonical pathway identified by gene array in OVE-uni mice.  Many inflammatory- and immune-related pathways were found among the top pathways up-regulated in OVE-uni kidneys, including acute-phase response signaling, leukocyte extravasation, IL6, IL10, IL12 signaling, TREM1 signaling, dendritic cell maturation and the complement system. These pathways were also dramatically up-regulated in 8-month-old OVE mice (GSE20636).  Nephrectomized OVE mice are a much faster alternative model for studying advanced renal disease in diabetes.

overall_design:
Study of renal gene expression in diabetic OVE26 mice. Uninephrectomy was used as an accelerating factor.

Pooled RNA samples from 4 individual mice in each treatment group (OVE-uni, OVE-sham, FVB-uni, FVB-sham) were used for probe hybridization.

Treatment groups:
OVE-uni: uninephrectomy treatment in diabetic mice
OVE-sham: sham surgery treatment in diabetic mice
FVB-uni: uninephrectomy treatment in nondiabetic mice
FVB-sham: sham surgery treatment in nondiabetic mice

first: Paul

middle: N

last: Epstein


title: Transcriptome expressed in the mouse suprachiasmatic nucleus

status: Public on Apr 22 2011

city: Kyoto

first: Hitoshi

last: Okamura

department: Department of Systems Biology

institute: Kyoto University, Graduate School of Pharmaceutical Sciences

summary: This array set was used to identify the genes that are highly expressed in the mouse suprachiasmatic nucleus (SCN). Because pharmacological inhibition of Gai/o activity with pertussis toxin hampers intercellular synchronization and causes dampened rhythms of the entire SCN, we hypothesized that member(s) of the Regulator of G protein Signaling (RGS) family might contribute to synchronized cellular oscillations in the SCN. To test this hypothesis, we surveyed all known mouse Rgs genes for their expression by using GeneChip and selected the genes that are highly expressed in the SCN for further analysis.

overall_design: 12h light:12h dark cycle entrained animals were released into constant darkess. SCN punches were taken from 10 animals at CT2 and 10 animals at CT14, pooled together, and subjected to DNA microarray analysis. CT2 and CT14 correspond, respectively, to 2 and 14 hours after presumptive onset of daytime under constant darkness.

first: Masao

last: Doi

first: Gozoh

last: Tsujimoto

first: Soken

last: Tsuchiya


title: Expression data from transgenic mice overexpressing RXR-gamma in the skeletal muscle (RXR-gamma mice)

status: Public on Apr 08 2011

city: Tokyo

first: Takako

last: Takai

address: 1-5-45 Yushima, Bunkyo-Ku

department: Bioinformatics

institute: Tokyo Medical and Dental University

summary: Retinoid X receptor (RXR)-gamma is a nuclear receptor-type transcription factor expressed mostly in the skeletal muscle, and regulated by nutritional conditions. Previously, we established transgenic mice overexpressing RXR-gamma in the skeletal muscle (RXR-gamma mice), which showed lower blood glucose than the control mice. We used microarrays to investigate their glucose metabolism gene expression change.

overall_design: RNA was isolated from the skeletal muscle of sex- and age-matched RXR-gamma mice and non-transgenic control mice (females at 4 months of age, five samples from each group were combined). Each of the combined samples of the two groups was hybridized to the Affymetrix MG430 microarray.

first: Yasutomi

last: Kamei

first: Hiroyuki

last: Aburatani


city: Bethesda

first: Jennifer

last: Barb

state: MD

address: 12 South Drive Bldg 12A Room 2001

department: DCB

institute: NIH

summary:
Caloric Restriction in Leptin Deficiency Worsens Myocardial Steatosis: Failure to Upregulate PPAR gamma and Thermogenic Glyecrolipid/Fatty Acid Cycling

Growing evidence supports an anti-lipotoxic role for leptin in preventing inappropriate peripheral tissue lipid deposition.  Obese, leptin deficient ob/ob mice develop left ventricular (LV) hypertrophy and myocardial steatosis with increased apoptosis and decreased longevity.  Here we investigated the cardiac effects of caloric restriction in leptin deficiency. Echocardiography was performed on C57Bl/6 wild-type mice (WT) and 7-month-old ob/ob mice fed ad lib, leptin-repleted (LR-ob/ob), or calorie-restricted (CR-ob/ob) for four weeks.  Ventricular tissue was examined by electron microscopy (EM), mitochondrial coupling assay, and microarray expression profiling. LR and CR-ob/ob mice showed decreased body weight, heart weight, and LV wall thickness compared to ad lib ob/ob mice.  LV fractional shortening was decreased in ad lib ob/ob mice, but restored to WT levels in LR and CR groups.  However, EM revealed severe cardiac steatosis in the CR-ob/ob group compared to only moderate steatosis in ad lib ob/ob . Despite marked cardiac steatosis, CR (like LR) restored mitochondrial coupling to WT levels.  CR up-regulated genes associated with oxidative stress and cell death, changes suggestive of cardiac lipotoxicity. LR, but not CR was shown to induce core genes involved in glycerolipid/free fatty acid cycling, a highly thermogenic pathway that can reduce intracellular lipid stores. LR, but not CR up-regulated and restored PGC1-alpha and PPAR-alpha to wild type levels; CR paradoxically further suppressed cardiac PPAR-alpha. Thus, leptin is essential in protecting the heart from lipotoxicity, and the inability to up-regulate the thermogenic glycerolipid/free fatty acid cycling pathway may impair the response of leptin deficient animals to the lipotoxic stress of calorie restriction.

overall_design: 6 month aged ob/ob mice were either leptin repleted with osmotic mini-pumps, calorie restricted to match the caloric intake of the leptin repleted mice, or fed ad lib for one month.  6-8 month C57Bl/6J mice were aged to serve as controls.

first: J

last: Rame

first: Lili

last: Barouch

first: Michael

last: Solomon

first: Robert

last: Danner


title: Expression data from metadherin (MTDH) knockdown in the Ishikawa H endometrial cancer cell line

city: Iowa City

first: xiangbing

last: meng

state: IA

address: 375 Newton Road

institute: University of Iowa

summary: Understanding the molecular underpinnings of chemoresistance is vital to design therapies to restore chemosensitivity. In particular, metadherin (MTDH) has been demonstrated to have a critical role in chemoresistance. Over-expression of MTDH has recently been implicated in poor clinical outcome in breast cancer, neroblastoma, hepatocellular carcinoma and prostate cancer. In this present study, we focused on the therapeutic benefit of MTDH depletion to restore sensitivity to cell death mediated by a combinatorial therapy of tumor necrosis factor-alpha-related apoptosis-inducing ligand (TRAIL), which promotes death of cancerous cells of the human reproductive tract, and histone deacetylase (HDAC) inhibitors, which have been shown to increase sensitivity of cancer cells to TRAIL-induced apoptosis. Our data indicate that depletion of MTDH in endometrial cancer cells results in sensitization of cells that were previously resistant to cell death mediated by combinatorial treatment with TRAIL and HDAC inhibitor LBH589. MTDH was found to be involved in G2/M checkpoint regulation in response to LBH589 alone or LBH589 in combination with TRAIL, suggesting that MTDH functions at the cell cycle checkpoint to accomplish resistance.Using microarray technology, we identified 57 downstream target genes of MTDH, including Calbindin 1 and Galectin 1, which may contribute to MTDH-mediated resistance to combinatorial TRAIL and HDAC inhibitor targeted therapy. Inhibition of PDK1,AKT phosphorylation and increase Bim expression and XIAP degradation may result in sensitivity to cell death induction in MTDH depleted Hec50co cells by TRAIL and LBH 589 combination treatment. These findings indicate that depletion of MTDH is a potentially novel avenue for effective cancer therapy.

overall_design: The microarray was performed on three biological triplicates as well as three experimental triplicates of stable knockdown and control cells.  MTDH was knocked down using a shRNA.

first: Xiangbing

last: Meng

first: Pavla

last: Brachova

first: Kimberly

last: Leslie


title: Prognostic Gene Expression Signature of Carcinoma Associated Fibroblasts in Non-Small Cell Lung Cancer [expression profiling_CAFs]

city: Toronto

first: Ming-Sound

last: Tsao

institute: Ontario Cancer Institute/ Princess Margaret Hospital

summary: The tumor microenvironment strongly influences cancer development, progression and metastasis. The role of carcinoma-associated fibroblasts (CAFs) in these processes and their clinical impact has not been studied systematically in non-small cell lung carcinoma (NSCLC). We established primary cultures of CAFs and matched normal fibroblasts (NFs) from 15 resected NSCLC. We demonstrate that CAFs have greater ability than NFs to enhance the tumorigenicity of lung cancer cell lines. Microarray gene expression analysis of the 15 matched CAF and NF cell lines identified 46 differentially expressed genes, encoding for proteins that are significantly enriched for extracellular proteins regulated by the TGF-beta signaling pathway. We have identified a subset of 11 genes that formed a prognostic gene expression signature, which was validated in multiple independent NSCLC microarray datasets. Functional annotation using protein-protein interaction analyses of these and published cancer stroma-associated gene expression changes revealed prominent involvement of the focal adhesion and MAPK signalling pathways. Fourteen (30%) of the 46 genes also were differentially expressed in laser-capture micro-dissected corresponding primary tumor stroma compared to the matched normal lung. Six of these 14 genes could be induced by TGF-beta1 in NF. The results establish the prognostic impact of CAF-associated gene expression changes in NSCLC patients.

overall_design: 30 samples: 15 primary NSCLC fibroblast cell lines, 15 normal lung fibroblast cell lines

first: Roya

last: Navab

first: Dan

last: Strumpf


title: Expression data from mouse small intestinal γδ intraepithelial lymphocytes

status: Public on Apr 06 2011

city: Dallas

first: Lora

last: Hooper

state: TX

address: 5323 Harry Hines Blvd.

department: Immunology

institute: The University of Texas Southwestern Medical Center at Dallas

summary:
The mammalian gastrointestinal tract harbors thousands of bacterial species that include symbionts as well as potential pathogens. The immune responses that limit access of these bacteria to underlying tissue remain poorly defined.
In this study, we used microarrays to uncover the transcriptional responses that occur in small intestinal γδ intraepithelial lymphocytes following bacterial challenge.

overall_design: γδ intraepithelial lymphocytes (γδ IEL) were isolated by flow cytometry from the small intestines of germ-free mice, or from age- and sex-matched conventionally-raised counterparts. We extracted RNAs from these purified γδ IEL for analysis on Affymetrix DNA microarrays. The mice were all >8 weeks in age, and each sample represents a pool of RNAs from 5-8 mice.

first: Anisa

last: Ismail


title: Upregulated stromal EGFR and vascular remodeling in human NSCLC murine models (xenografts) of VEGF inhibitor resistance

city: Houston

first: Tina

last: Cascone

address: 1515 Holcombe Blvd.

department: Cancer Medicine

institute: UT MD Anderson Cancer Center

summary: The mechanisms by which tumors develop resistance to angiogenesis inhibitors, and the relative contributions of tumor cells and stroma to resistance, are not completely understood. We developed three human lung adenocarcinoma murine models of resistance to the VEGF inhibitor bevacizumab and, using species-specific profiling, separately investigated tumor cell and stromal molecules associated with resistance. Gene expression changes associated with acquired resistance occurred predominantly in stromal (mouse) and not tumor (human) cells. Components of the EGFR and FGFR2 pathways were significantly upregulated in stroma, but not in tumor cells. Increased activated EGFR was detected on pericytes of xenografts that acquired resistance and on endothelium of tumors with relative primary resistance. Acquired resistance was associated with a pattern of pericyte-covered, normalized revascularization, whereas tortuous, uncovered vessels were observed in relative primary resistance. Dual targeting of VEGF and EGFR pathways with bevacizumab and erlotinib, or the VEGFR/EGFR inhibitor vandetanib, reduced pericyte coverage and increased progression-free survival. These findings demonstrate that alterations in tumor stromal pathways, including EGFR and FGFR2, are associated with, and may contribute to VEGF inhibitor resistance and that targeting these pathways may improve therapeutic efficacy. Understanding stromal signaling may be critical for developing biomarkers for angiogenesis inhibitors and improving combination regimens.

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus

overall_design: To identify changes in stromal and tumor gene expression associated with acquired resistance to anti-VEGF therapy, we performed RNA microarray analyses comparing H1975 control (vehicle-treated) and BV-resistant (bevacizumab-treated until progression) xenografts (n=3 biologic replicates per group of treatment) using Illumina mouse (WG-6 v2) and human (WG-6 v3)-specific expression arrays. Probes in these arrays have been designed to minimize cross-species reactivity and consistent with this essentially no cross reactivity was observed in experiments mixing human and mouse cell lines.Total RNA was extracted from snap-frozen tissues using the mirVanaTM miRNA Isolation Kit (Ambion, Austin, TX) according to manufacturer’s protocol. Biotin labeled cRNA samples for hybridization were prepared by using Illumina Total Prep RNA Amplification Kit (Ambion Inc., Austin, TX). One microgram of total RNA was used for the synthesis of cDNA and followed by an amplification and biotin labeling. Each of 1.5 μg of biotinylated cRNAs was hybridized to both mouseWG-6 v2 and human WG-6v3 Expression BeadChips (Illumina®, San Diego, CA) at the same time, for analysis of murine and human transcriptomes. Signals were developed by Amersham fluorolink streptavidin-Cy3 (GE Health care Bio-Sciences, Little Chalfont, UK). Gene expression data were collected by using Illumina bead Array Reader confocal scanner (BeadStation 500GXDW; Illumina Inc.). Data were analyzed using the BRB-ArrayTools Version 3.7.0 Beta platform developed by Dr. Richard Simon and the BRB-Array Tools development team. A log base 2 transformation was applied to the data set prior to data normalization. A median array was selected as the reference array for normalization and statistical significance was set using a p<0.01. Genes differentially expressed between groups were determined applying univariate t-test with estimation of the false discovery rate (FDR). Genes were determined using selection criteria of a p<0.005 and a fold-change ≥1.5.

first: Matthew

middle: H

last: Herynk

first: Li

last: Xu

first: Zhiqiang

last: Du

first: Humam

last: Kadara

first: Monique

last: Nilsson

first: Carol

last: Oborn

first: Yun-Yong

last: Park

first: Baruch

last: Erez

first: Jörg

last: Jacoby

first: Ju-Seog

last: Lee

first: Heather

middle: Y

last: Lin

first: Fortunato

last: Ciardiello

first: Roy

last: Herbst

middle: R

last: Langley

first: John

last: Heymach


title: Evaluating Gene Expression in C57BL/6J and DBA/2J Mouse Striatum Using RNA-Seq and Microarray

status: Public on Apr 12 2011

city: Portland

first: Nicole

last: Walter

state: OR

address: 3181 SW Sam Jackson Park Road

department: Behavioral Neuroscience

institute: Oregon Health & Science University

summary: C57BL/6J (B6) and DBA/2J (D2) are two of the most commonly used inbred mouse strains in neuroscience research. However, the only currently available mouse genome is based entirely on the B6 strain sequence. Subsequently, oligonucleotide microarray probes are based solely on this B6 reference sequence, making their application for gene expression profiling comparisons across mouse strains dubious due to their allelic sequence differences, including single nucleotide polymorphisms (SNPs). The emergence of next-generation sequencing (NGS) and the RNA-Seq application provides a clear alternative to oligonucleotide arrays for detecting differential gene expression without the problems inherent to hybridization-based technologies. Using RNA-Seq, an average of 22 million short sequencing reads were generated per sample for 21 samples (10 B6 and 11 D2), and these reads were aligned to the mouse reference genome, allowing 16,183 Ensembl genes to be queried in striatum for both strains. To determine differential expression, 'digital mRNA counting' is applied based on reads that map to exons. The current study compares RNA-Seq (Illumina GA IIx) with two microarray platforms (Illumina MouseRef-8 v2.0 and Affymetrix MOE 430 2.0) to detect differential striatal gene expression between the B6 and D2 inbred mouse strains. We show that by using stringent data processing requirements differential expression as determined by RNA-Seq is concordant with both the Affymetrix and Illumina platforms in more instances than it is concordant with only a single platform, and that instances of discordance with respect to direction of fold change were rare. Finally, we show that additional information is gained from RNA-Seq compared to hybridization-based techniques as RNA-Seq detects more genes than either microarray platform. The majority of genes differentially expressed in RNA-Seq were only detected as present in RNA-Seq, which is important for studies with smaller effect sizes where the sensitivity of hybridization-based techniques could bias interpretation.

overall_design:
There are 5 male and 5 female C57BL/6J animals and 5 male and 5 female DBA/2J. These are adult, naïve animals. One array is run for each animal for a total of 20 Mouse MOE430 2.0 arrays. The purpose is to determine baseline (naïve) gene expression differences in striatum for these two inbred strains.

There are 12 male C57BL/6J animals and 12 male DBA/2J. These are adult, naïve animals. One array is run for each animal for a total of 24 Mouse Ref8 v2 arrays. The purpose is to determine baseline (naïve) gene expression differences in striatum for these two inbred strains.

***This submission represents the microarray component of the study

middle: A

first: Daniel

last: Bottomly

first: Jessica

last: Hunter

first: Priscila

last: Darakjian

first: Sunita

last: Kawane

first: Kari

last: Buck

first: Robert

last: Searles

first: Michael

last: Mooney

first: Shannon

middle: K

last: McWeeney

last: Hitzemann


title: KMT1E Mediated H3K9 Methylation Is Required for the Maintenance of Embryonic Stem Cells by Repressing Trophectoderm Differentiation

city: Cambridge

first: Felix

last: Lohmann

state: MA

address: 250 Mass Ave

institute: Novartis Institutes for BioMedical Research

summary: Dynamic regulation of histone methylation by methyltransferases and demethylases plays a central role in regulating the fate of embryonic stem (ES) cells. The histone H3K9 methyltransferase KMT1E, formerly known as ESET or Setdb1, is essential to embryonic development as the ablation of the Setdb1 gene results in peri-implantation lethality and prevents the propagation of ES cells. However, Setdb1- null blastocysts do not display global changes in H3K9 methylation or DNA methylation, arguing against a genome- wide defect. Here we show that conditional deletion of the Setdb1 gene in ES cells results in the upregulation of lineage differentiation markers, especially trophectoderm-specific factors, similar to effects observed upon loss of Oct3/4 expression in ES cells. We demonstrate that KMT1E deficiency in ES cells leads to a decrease in histone H3K9 methylation at and derepression of trophoblast-associated genes such as Cdx2. Furthermore, we find genes that are derepressed upon Setdb1 deletion to overlap with known targets of polycomb mediated repression, suggesting that KMT1E mediated H3K9 methylation acts in concert with polycomb controlled H3K27 methylation. Our studies thus demonstrate an essential role for KMT1E in the control of developmentally regulated gene expression programs in ES cells.

overall_design: Analysis of KMT1E-deficiency in mouse embryonic stem cells using a Setdb1 conditional allele and tamoxifen-inducible Cre/loxP recombination

first: Joseph

last: Loureiro

first: Shilpa

last: Kadam


title: Transcriptional profiling of immortalized LECs (imLECs)

status: Public on Apr 01 2011

city: Zurich

first: benjamin

last: vigl

address: W.-Pauli-Str. 10, HCI, G490

department: Institute of Pharmaceutical Sciences

country: Switzerland

institute: ETH Zurich

summary: In contrast to the migration of leukocytes from blood vessels into tissues, and the involvement of adhesion molecules and chemokines in this process, the migration of leukocytes from the tissue into lymphatic vessels is much less well understood. This can, in part be explained by the fact that murine lymphatic endothelial cells (LECs) have proven particularly hard to isolate and propagate in culture. Hence, it has been difficult to establish suitable models to study this process in vitro. Combining magnetic bead-based purification and fluorescence-activated cell sorting (FACS), we have isolated LECs (immorto-LECs) from the skin of mice which express a temperature-sensitive SV40 large T antigen (H-2Kb-tsA58 mice; ImmortoMice) in all cell types under the control of the MHC-class-I-promotor, H-2Kb.  The isolated cells are viable for more than 30 passages when cultured at 33 ºC, the temperature at which the large T antigen is stably expressed. Furthermore, immorto-LECs tolerate several days of culture at 37 ºC, but become senescent if continuously cultured at this temperature. All cells stably express endothelial and lymphatic markers like CD31, podoplanin, Prox-1 and VEGFR-3 up to passage 30. When cultured in presence of tumor necrosis factor-alpha (TNF-a), immorto-LECs upregulate adhesion molecules, such as ICAM-1, VCAM-1 and E-selectin, similarly to what has been reported to occur under inflammatory conditions in vivo. Overall, our findings establish immorto-LECs as a useful and handy tool for the in vitro investigation of immune cell transmigration across lymphatic endothelium.

overall_design: imLEC were cultured at 33 ºC until they reached approx. 70% confluence. Cells were then transferred to 37 ºC and cultured for 3 days in order to induce T antigen degradation. RNA was isolated from 3 different cultures of passages 13, 14 and 18

first: B

last: Vigl

first: M

last: Iolyeva

first: C

last: Halin


title: [E-MTAB-368] Transcription profiling by array of mouse embryos at 8 different stages

status: Public on Apr 05 2011

city: Kobe

first: Naoki

last: Irie

state: Hyogo

address: 2-2-3 Minatojima-minami Chuo-ku

institute: RIKEN Center for Developmental Biology

summary:
Transcription profiling of mouse development
The experiment were perfomed as a part of our Vertebrate Evo-Devo project. The aim of the project is to compare transcription profiles of normal (unmanipulated, wild-type, whole embryo) vertebrate embryos.

overall_design: Total RNA was collected from wild type C57BL/6 mice, whole embryos at 8 different stages (Stages:E7.5, E8.5, E9.5, E10.5, E12.5, E14.5, E16.5, E18.5), and hybridized to Affymetrix Mouse Genome 430 2.0 Array. All the stages contains data from 2 to 3 biological replications. Each staged-samples consists of pooled total RNA from several whole embryos.


title: Prognostic Gene Expression Signature of Carcinoma Associated Fibroblasts in Non-Small Cell Lung Cancer

first: Ming-Sound

last: Tsao

type:
Expression profiling by array
Methylation profiling by array
Genome variation profiling by SNP array
SNP genotyping by SNP array

summary:
The tumor microenvironment strongly influences cancer development, progression and metastasis. The role of carcinoma-associated fibroblasts (CAFs) in these processes and their clinical impact has not been studied systematically in non-small cell lung carcinoma (NSCLC). We established primary cultures of CAFs and matched normal fibroblasts (NFs) from 15 resected NSCLC. We demonstrate that CAFs have greater ability than NFs to enhance the tumorigenicity of lung cancer cell lines. Microarray gene expression analysis of the 15 matched CAF and NF cell lines identified 46 differentially expressed genes, encoding for proteins that are significantly enriched for extracellular proteins regulated by the TGF-beta signaling pathway. We have identified a subset of 11 genes that formed a prognostic gene expression signature, which was validated in multiple independent NSCLC microarray datasets. Functional annotation using protein-protein interaction analyses of these and published cancer stroma-associated gene expression changes revealed prominent involvement of the focal adhesion and MAPK signalling pathways. Fourteen (30%) of the 46 genes also were differentially expressed in laser-capture micro-dissected corresponding primary tumor stroma compared to the matched normal lung. Six of these 14 genes could be induced by TGF-beta1 in NF. The results establish the prognostic impact of CAF-associated gene expression changes in NSCLC patients.

This SuperSeries is composed of the SubSeries listed below.

overall_design: Refer to individual Series.

first: Roya

last: Navab

first: Dan

last: Strumpf


title: Comparative transcriptome analysis reveals vertebrate phylotypic period during organogenesis

summary:
One of the central issues in evolutionary developmental biology is how we can formulate the relationships between evolutionary and developmental processes. Two major models have been proposed: the 'funnel-like' model, in which the earliest embryo shows the most conserved morphological pattern, followed by diversifying later stages, and the 'hourglass' model, in which constraints are imposed to conserve organogenesis stages, which is called the phylotypic period. Here we perform a quantitative comparative transcriptome analysis of several model vertebrate embryos and show that the pharyngula stage is most conserved, whereas earlier and later stages are rather divergent. These results allow us to predict approximate developmental timetables between different species, and indicate that pharyngula embryos have the most conserved gene expression profiles, which may be the source of the basic body plan of vertebrates.

This SuperSeries is composed of the SubSeries listed below.

sample_organism:
Xenopus laevis
Gallus gallus
Mus musculus


title: A novel approach to investigate tissue-specific trinucleotide repeat instability - A validation set of prediction model

city: Boston

first: Jong-Min

last: Lee

address: 185 Cambridge Street

department: Center for Human Genetic Reseaarch

institute: Massachusetts General Hospital

summary:
In Huntington’s disease (HD), an expanded CAG repeat produces characteristic striatal neurodegeneration. Interestingly, the HD CAG repeat, whose length determines age at onset, undergoes tissue-specific somatic instability, predominant in the striatum, suggesting that tissue-specific CAG length changes could modify the disease process. Therefore, understanding the mechanisms underlying the tissue specificity of somatic instability may provide novel routes to therapies. However progress in this area has been hampered by the lack of sensitive high-throughput instability quantification methods and global approaches to identify the underlying factors.
Here we describe a novel approach to gain insight into the factors responsible for the tissue specificity of somatic instability. Using accurate genetic knock-in mouse models of HD, we developed a reliable, high-throughput method to quantify tissue HD CAG instability and integrated this with genome-wide bioinformatic approaches. Using tissue instability quantified in 16 tissues as a phenotype and tissue microarray gene expression as a predictor, we built a mathematical model and identified a gene expression signature that accurately predicted tissue instability. Using the predictive ability of this signature we found that somatic instability was not a consequence of pathogenesis. In support of this, genetic crosses with models of accelerated neuropathology failed to induce somatic instability. In addition, we searched for genes and pathways that correlated with tissue instability. We found that expression levels of DNA repair genes did not explain the tissue specificity of somatic instability. Instead, our data implicate other pathways, particularly cell cycle, metabolism and neurotransmitter pathways, acting in combination to generate tissue-specific patterns of instability.
Our study clearly demonstrates that multiple tissue factors reflect the level of somatic instability in different tissues. In addition, our quantitative, genome-wide approach is readily applicable to high-throughput assays and opens the door to widespread applications with the potential to accelerate the discovery of drugs that alter tissue instability.

overall_design: Mouse striatum and cerebellum, 5 months old, Affymetrix MG430 2.0 arrays, gcRMA.


title: Expression data from mouse dendritic cells

city: Ann Arbor

first: yaping

last: sun

state: Michigan

address: 1500 E Medical Center Dr.

department: internal medicine

institute: university of michigan

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

summary:
Dendritic cells (DCs) are pivotal for both recognition of antigens and control of an array of immune responses by recognizing microbes through distinct pattern recognition receptors (PRRs). The first microbial component to be  studied in detail and known to cause septic shock is endotoxin (LPS). DCs recognize LPS via Toll-like receptor TLR-47. LPS causes many changes in the DCs, but the elicitation of cytokine production is perhaps the one with clear biologic relevance.
We used microarrays to detail the global programme of gene expression underlying regulation of TLR 4 signaling and identified the upregulated and downregulated genes in response to LPS treatment in mouse dendritic cells.

We use microarray to determine the conserved hematopoietic miRNAs to study their potential  contribution  to regulating many different immunological cellular processes and contexts.

overall_design:
To obtain  overall gene expression profile, we extracted bone marrow cells from at least 3 mice for each experiment.  Purified ( 97~98% purity) mouse dendritic cells, treated with LPS or control diluent, were used for RNA extraction and hybridization on Affymetrix microarrays.

To obtain  overall miRNA expression profile, we extracted bone marrow cells from at least 3 mice (C57BL/6)   for each experiment.  Purified ( 97~98% purity for CD11C+ ) mouse dendritic cells were used for RNA extraction and hybridization on Exiqon miRCURY LNATM microRNA array.

first: Yaping

last: Sun

first: Pavan

last: Reddy


title: Crosstalk between gene body DNA methylation, H3K9me3 and H3K36me3 chromatin marks and transcription [HuEx-1_0-st, transcript]

status: Public on Mar 31 2011

city: Duarte

first: Xiwei

last: Wu

address: 1500 E. Duarte Rd.

department: Computational and Quantitative Medicine

institute: City of Hope National Medical Center

summary:
This is one of expressional parts of the study. These data were correlated to epigenetic marks and CG density of genes in analyzed cells. The whole study has a following summary: To elucidate possible roles of DNA methylation and chromatin marks in transcription, we performed epigenetic profiling of chromosome 19 in human bronchial epithelial cells (HBEC) and in the colorectal cancer cell line HCT116 as well as its counterpart with double knockout of DNMT1 and DNMT3B (HCT116-DKO). We found that H3K9me3 forms intragenic chromatin blocks along genes with low CpG density in the gene body. Analysis of H3K36me3 profiles indicated that this mark associates either with active genes with low CpG density and H3K9me3 in the gene body or with active genes with high CpG density and DNA hypermethylation in the gene body. In HCT116 cells with double knockout of DNMT1 and DNMT3B, transcription of genes with low CpG density in the gene body was highly elevated and associated with promoter DNA demethylation and rearrangement of H3K9me3 and H3K36me3 occupation. Our finding suggests that similar to DNA methylation, H3K9me3 may play a role in intragenic gene regulation. Further, we observed that a combination of low CpG density in gene bodies together with H3K9me3 and H3K36me3 marking is a specific epigenetic feature of zinc finger (ZNF) genes, which comprise 90% of all genes carrying both histone marks on chromosome 19. For high CpG density genes, transcription and H3K36me3 occupancy were not changed in condition of partial or intensive loss of DNA methylation in gene bodies in the HCT116-DKO cell line. siRNA experiments with SETD2 knockdown in both HBEC and HCT116-DKO cell lines failed to reduce DNA methylation in gene bodies under conditions of H3K36me3 depletion. Our study suggests that the H3K36me3 and DNA methylation marks in gene bodies are established independently from each other and points to similar functional roles of intragenic DNA methylation and intragenic H3K9me3 for CpG-rich and CpG-poor genes, respectively.
Expressional changes associated with SETD2 siRNA transfection in HBEC

overall_design: Compare siRNA vs. control

first: Maria

last: Hahn

first: Arthur

middle: X

last: Li

first: Torsten

first: Gerd

last: Pfeifer


title: The response to ionizing radiation at the exon level

status: Public on May 02 2011

city: East Melbourne

first: Jason

address: St Andrews Pl

institute: Peter MacCallum Cancer Centre

summary: Humans are exposed to ionizing radiation (IR) from background radiation, medical treatments, occupational and accidental exposures. IR causes profound changes in transcription. Transcription is a primary process where protein amount and function can be regulated. One aspect of the transcriptional IR response that little is known about on a whole genome basis is alternative transcription. These investigations focus on the response to IR at the exon level in human cells but also at the whole gene level. Whole genome exon arrays were utilized to comprehensively characterize radiation-induced transcriptional expression products in two human cell types, namely EBV-transformed lymphoblast and primary fibroblast cell lines.

overall_design: 12 human primary fibroblast cell lines and 12 primary lymphoblast cell line samples were used for two doses (0 and 10 Gy) and two time points (0 and 4hr). Additional doses ( 1 Gy, 2 Gy, 5 Gy, and 20 Gy) and time points ( 1hr, 2hr, 8hr, 24hr and 48hr) were assessed in four lymphoblast cell lines and four primary fibroblasts.

first: Carl

last: Sprung

first: Daniel

last: Hovan

first: Michael

middle: J

last: McKay

first: Helen

last: Forrester


title: GBM_SC_retinoic acid_gene_expression

city: Baltimore

first: Shuli

last: Xia

institute: Kennedy-Krieger Institute

summary: This study compared the gene expression change of glioblastoma stem-like cells before and after retinoic acid treatment

overall_design: Glioblastoma neurospheres 10627 and 20913 were treated with retinoic acid for 8h and 48h and compared with control


title: A novel approach to investigate tissue-specific trinucleotide repeat instability

overall_design: Mouse striatum and cerebellum, 10 weeks old, Affymetrix MG430 2.0 arrays, gcRMA.

first: Marcy

last: MacDonald


title: A375 melanoma cells treated with leflunomide 25uM

status: Public on Mar 30 2011

city: New York

first: Richard

middle: Mark

last: White

state: NY

address: 1275 York Avenue MB 424

department: Cancer Biology & Genetics

institute: Memorial Sloan Kettering Cancer Center

summary: Human A375 melanoma cells were treated with leflunomide 25uM for 3 days, then RNA harvested

overall_design: 6 arrays

middle: M


title: Dual functions of Tet1 in transcriptional regulation in mouse embryonic stem cells (mRNA)

first: Hao

state: Massachusetts

address: 149G Warren Alpert Building, 200 Longwood Avenue

department: Genetics

institute: Harvard Medical School/HHMI

summary: Epigenetic modification of the mammalian genome by DNA methylation (5-methylcytosine) has a profound impact on chromatin structure, gene expression and maintenance of cellular identity. Recent demonstration that members of the Ten-eleven translocation (Tet) family proteins can convert 5-methylcytosine (5mC) to 5-hydroxymethylcytosine (5hmC) raised the possibility that Tet proteins are capable of establishing a distinct epigenetic state. We have recently demonstrated that Tet1 is specifically expressed in murine embryonic stem (ES) cells and is required for ES cell self-renewal and maintenance. Using chromatin immunoprecipitation coupled with high-throughput DNA sequencing (ChIP-seq), here we show that Tet1 is preferentially bound to CpG-rich sequences at promoters of both transcriptionally active and Polycomb-repressed genes. Despite a general increase in levels of DNA methylation at Tet1 binding-sites, Tet1 depletion does not lead to down-regulation of all the Tet1 targets. Interestingly, while Tet1-mediated promoter hypomethylation is required for maintaining the expression of a group of transcriptionally active genes, it is also required for repression of Polycomb-targeted developmental regulators. Tet1 contributes to silencing of this group of genes by facilitating recruitment of PRC2 to CpG-rich gene promoters. Thus, our study not only establishes a role for Tet1 in modulating DNA methylation levels at CpG-rich promoters, but also reveals a dual function of Tet1 in promoting transcription of pluripotency factors as well as participating in the repression of Polycomb-targeted developmental regulators.

overall_design: Mouse ES cells infected with control knockdown (KD) or Tet1 KD  lentiviruses  were FACS-sorted for RNA extraction and hybridization on Affymetrix microarrays.  We also investigated the effect of Nanog overexpression (OE) in Tet1 KD mouse ES cells on dys-regulated Tet1 targets. We have collected four biologically independent replicates for each treatment.

first: Ana

last: D'Alessio

first: Shinsuke

last: Ito

first: Kai

first: Zhibin

last: Wang

first: Keji

last: Zhao

first: Yi

first: Kairong

last: Cui

last: Zhang


title: Whole blood gene expression in female Balb/c mice following 2-week Pb exposure and subsequent 2-week recovery period

city: Durham

first: Heather

middle: G.

last: LaBreche

state: NC

address: 101 Science Drive

department: Institute for Genome Sciences and Policy

institute: Duke University

summary:
Background: Current evidence indicates that even low-level lead (Pb) exposure can have detrimental effects, especially in children. We tested the hypothesis that Pb exposure alters gene expression patterns in peripheral blood cells and that these changes reflect dose-specific alterations in the activity of particular pathways.
Methodology/Principal Finding: Using Affymetrix Mouse Genome 430 2.0 arrays, we examined gene expression changes in the peripheral blood of female Balb/c mice following exposure to per os lead acetate trihydrate or plain drinking water for two weeks and after a two-week recovery period. Data sets were RMA-normalized and dose-specific signatures were generated using established methods of supervised classification and binary regression. Pathway activity was analyzed using the ScoreSignatures module from GenePattern.
Conclusions/Significance: The low-level Pb signature was 93% sensitive and 100% specific in classifying samples a leave-one-out crossvalidation. The high-level Pb signature demonstrated 100% sensitivity and specificity in the leave-one-out crossvalidation. These two signatures exhibited dose-specificity in their ability to predict Pb exposure and had little overlap in terms of constituent genes. The signatures also seemed to reflect current levels of Pb exposure rather than past exposure. Finally, the two doses showed differential activation of cellular pathways. Low-level Pb exposure increased activity of the interferon-gamma pathway, whereas high-level Pb exposure increased activity of the E2F1 pathway.

overall_design: We isolate total RNA from 72 mouse whole blood samples. These included samples following a 2-week exposure to lead acetate trihydrate (untreated controls = 7; Low Pb 5ug/mL drinking water = 15; High Pb 50ug/mL drinking water = 15) and additional samples following a 2-week recovery period with plain drinking water (untreated controls = 7; Low Pb group = 15; High Pb group = 13).

middle: G


title: Stabilization of ß-catenin during murine Kidney Development

status: Public on Mar 28 2011

first: Brian

middle: Joseph

last: Cox

state: Ontario

address: 1 King's College Circle, Rm 3360

department: Physiology

institute: University of Toronto

summary: We define a pathogenic role for a ß-catenin-activated genetic pathway in murine renal dysplasia. Cre-mediated stabilization of ß-catenin in the ureteric cell lineage prior to the onset of kidney development increased ß-catenin levels and caused renal aplasia or severe hypodysplasia. A genome-wide analysis of mRNA expression in dysplastic tissue identified down-regulation of genes required for ureteric branching and up regulation of Tgfß2 and Dkk1.

overall_design: Hoxb7-Cre:EGFP mice ( Zhao, et al. (2004) Dev Biol 276:403-415) were crossed with mice containing loxP sites flanking exon 3 of the ß-catenin allele (ß-catdelta3/delta3) (Harada,et al. (2002) Cancer Res 62:1971-1977) to generate ß-catenin gain-of-function mutant mice specific to the uteric bud, termed ß-catGOF-UB .Eighteen ß-catGOF-UB mutant kidneys and 9 WT kidneys were micro-dissected at E12.5. Mutant kidneys were divided into three random pools (n=3) consisting of 6 kidneys each and mRNA expression assessed by microarray.

first: Darren

last: Bridgewater

first: Norman

last: Rosenblum


title: Expression data from E13.5 Fz4-/- and Fz4+/+ kidneys

status: Public on Mar 23 2011

first: Xin

last: Ye

address: 725 N Wolfe Street, PCTB 805

institute: Johns Hopkins School of Medicine

summary:
Fz4 and Fz8 cooperate in regulating the branching morhpogenesis of the developing kidney during mouse embryonic development, hence determines the eventual kidney size.
We used microarrays to study the global gene expression profiles regulated by Fz4 and Fz8 signaling during early kidney development, and to understand the collaboration between the signaling events mediated by Fz4 and Fz8

overall_design: Kidney rudiments were dissected from E13.5 mouse embryos for RNA extraction and hybridization on Affymetrix MOE430.2 arrays. Three biological replicates of each genotype were analyzed.

first: Jeremy

last: Nathans


title: Expression data from E13.5 Fz4-/-Fz8-/- and Fz4+/+Fz8-/- kidneys


title: Phosphorylation of p53 Serine 46 contributes to target gene selectivity of p53 (Exon)

status: Public on Mar 24 2011

city: Nijmegen

first: Marion

last: Lohrum

department: Molecular Biology

country: Netherlands

institute: NCMLS

summary: The tumor suppressor p53 plays a crucial role in cellular growth control inducing a plethora of cellular response pathways. The molecular mechanisms that discriminate between the distinct p53-responses towards different stress treatments have remained largely elusive. Here, we have analyzed the p53-regulated pathways induced by two chemotherapeutical treatments, Actinomycin D inducing growth arrest and Etoposide resulting in apoptosis. We found that the genome-wide p53-binding patterns are almost identical upon both treatments notwithstanding transcriptional differences that we observed in genome-wide transcriptome analysis. To assess the role of post-translational modifications in target gene choice and activation we investigated the extent of phosphorylation of Serine 46 of p53 bound to DNA (p53-pS46), a modification that has been linked to apoptosis-pathways, and the extent of phosphorylation of Serine 15 (p53-pS15), a general p53-activation mark. Interestingly, the overall extent of S46 phosphorylation of p53 bound to DNA is considerably higher in cells directed towards apoptosis while the degree of phosphorylation at S15 of DNA bound p53 remains highly similar upon both treatments. Moreover, our data suggest that, following different chemotherapeutical treatments, the extent of chromatin-associated p53 phosphorylated at S46 but not at pS15 is higher on certain apoptosis related target genes, including the BAX and PUMA genes. These data provide evidence that cell fate decisions are not made primarily on the level of general p53 DNA-binding, but possibly through post-translational modifications of chromatin bound p53.

overall_design: Microarray analysis (Affymetrix Human Exon array) of the p53 response in U2OS cells treated with either Etoposide or Actinomycin D

first: Leonie

last: Smeenk

first: Simon

last: van Heeringen

first: Max

last: Koeppel

first: Eva

last: Janssen-Megens

first: Hendrik

last: Stunnenberg