title: Foxp3 expression is required for the induction of therapeutic tissue tolerance

status: Public on Oct 03 2012

city: Framingham

first: Duncan

last: Howie

address: 49 New York Avenue

institute: Genzyme Corporation/Sir William Dunn School of Pathology Oxford University

summary: CD4+Foxp3+ regulatory T cells (Treg) are essential for immune homeostasis and maintenance of self-tolerance. They are produced in the thymus and also generated de novo in the periphery in a TGFB dependent manner. Foxp3+ Treg are also required to achieve tolerance to transplanted tissues when induced by co-receptor or costimulation blockade. Using TCR transgenic mice to avoid issues of autoimmune pathology we show that Foxp3 expression is necessary and sufficient for tissue tolerance by coreceptor blockade. Moreover, the known need in tolerance induction for TGFB signalling to T cells, can wholly be explained by its role in induction of Foxp3, as such signalling proved dispensable for the suppressive process. We analysed the relative contribution of TGFB and Foxp3 on the transcriptome of TGFB induced Treg. TGFB elicited a large set of downregulated signature genes. The number of genes uniquely modulated due to the influence of Foxp3 alone was surprisingly limited. Retroviral conditional Foxp3 expression proved sufficient to confer transplant-suppressive potency on CD4+ T cells, and was lost once nuclear Foxp3 expression was extinguished. Thus despite the large genetic influence of TGFB exposure on iTreg the crucial Foxp3 influenced signature independent of TGFB is small. These data support a dual role for TGFB and Foxp3 in induced tolerance, where TGFB stimulates Foxp3 expression whose sustained expression is associated with acquisition of tolerance

overall_design: 21 samples were analyzed. 5 replicates of Marilyn.Foxp3hCD2 activated (HY)(Untreated) and TGFB-induced (HYT) cells sorted as CD4+hCD2+ and CD4+hCD2- and 3 replicates of Marilyn.Foxp3-/- activated and TGFβ-experienced (but Foxp3-) cells sorted as CD4+CD2. Pairwise comparisons were generated for the Marilyn Foxp3hCD2 UT versus TGFB induced populations and also for the Marilyn Foxp3-/- UT versus the TGFB experienced cells sorted as CD4+CD2

first: S

last: Madhiwalla

first: M

last: Zhang

first: D


title: Acute and long-term effects of mutant p53 in vivo

status: Public on Dec 31 2012

city: Singapore

first: Kanaga

last: Sabapathy

state: Singapore

address: 11 Hospital Drive

country: Singapore

institute: National Cancer Centre Singapore

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

overall_design: Refer to individual Series

first: Ming

middle: K

last: Lee

first: Wei

middle: W

last: Teoh


title: Gene expression profiling using exon arrays during interference with PPAR gamma signaling in thoracic aorta

city: Iowa City

first: Henry

last: Keen

state: IA

department: Pharmacology

country: USA

institute: University of Iowa

summary: Pharmacological activation of the transcription factor PPAR gamma lowers blood pressure and improves glucose tolerance in humans.  In contrast, naturally occurring mutations (e.g., P467L, V290M) in the ligand binding domain of PPAR gamma in humans leads to severe insulin resistance and early-onset hypertension. Experimental evidence, including whole genome expression profiling, suggests that these mutant versions of PPAR gamma act in a dominant negative manner. Because PPAR gamma is expressed in a variety of cell types and tissues, we generated a transgenic mouse model (SP467L) specifically targeting dominant negative PPAR gamma to the vascular smooth muscle cells in order to determine the action of PPAR gamma in the blood vessel independent of its systemic metabolic actions.   In the data set provided herein, we examined the gene expression profile in thoracic aorta from SP467L mice and their control littermates using the Affymetrix mouse exon 1.0 ST array.

overall_design: We generated transgenic mice specifically targeting expression of mutant dominant negative human PPAR gamma (P467L) to vascular smooth muscle using a smooth muscle-specific promoter (smooth muscle myosin heavy chain or SMMHC).  Thoracic aortas were isolated from 7 male transgenic  mice and 5 non-transgenic littermate controls. Total RNA was prepared using conventional methods and quality was assessed using the Bioanalyzer 2100 (Agilent Technologies). For the microarray hybridizations, each sample corresponded to aorta derived from one mouse. All procedures were conducted at the University of Iowa DNA Core facility using standard Affymetrix protocols. In brief, approximately 50 ng of total RNA was used as input to a two-step amplification procedure (NuGen, http://www.nugeninc.com/) to generate biotin-labeled RNA fragments for hybridization to the Affymetrix mouse exon 1.0 ST array.

middle: L

first: Curt

middle: D

last: Sigmund


title: Acute and long-term effects of mutant p53 in vivo [Thymus]

summary: The specific roles of mutant p53’s dominant-negative (DN) or gain-of-function (GOF) properties in regulating acute response and long-term tumorigenesis is unclear.   Using “knock-in” mouse strains expressing varying R246S mutant levels, we show that DN effect on transactivation is universally observed after acute p53 activation whereas the effect on cellular outcome is cell-type specific.  Reducing mutant p53 levels abrogated the DN effect.   Mutant p53’s DN effect protected against radiation-induced death, but did not accentuate tumorigenesis.  Furthermore, the R246S mutant did not promote tumorigenesis compared to p53-/- mice in various models, even in the absence of MDM2, unlike the R172H mutant.  Together, these data demonstrate that mutant p53’s DN property only affects acute responses, whereas GOF is not universal, being mutation-type specific.

overall_design: Transcriptomes of 10 normal thymi harvested from 4-5 weeks old mice of different p53 and mdm2 genotype were profiled.  Data was analysed by mixed model ANOVA using Partek.


title: Age-related changes in gene expression in retinal microglia

status: Public on Dec 01 2012

city: Rockville

first: Radu

last: Cojocaru

state: MD

address: 5635 Fishers Lane, Suite 510

institute: Elsevier

summary: In order to evaluate the gene expression profile of retinal microglia cells in different age, we purified CD11b-positive microglia from the retinas of wild type C57BL/6 mice at 3, 12, 18, and 24 months age using cell sorting method with flow cytometry.  Age-related genes from isolated retinal microglia were performed using 16 Affymetrix GeneChips of Mouse Exon 1.0ST Arrays. Gene expression level between consecutive age groups (i.e. between 3 and 12 months, 12 and 18 months, and 18 and 24 months) was examined to identify microglia relevant aging genes that demonstrated significant changes. We identified a total 719 genes that showed increasing or decreasing more than 1.5-fold change (p<0.05, one-way ANOVA) for at least one of the three inter age-group comparisons. These identified genes were subjected to a hierarchical cluster analysis to visualize trends in differential expression across individual biological repeats in the 4 age groups.

overall_design: The microglia cells were isolated from wild type C57BL/6 mice with microglia cell specific marker CD11b conjugated with FITC using flowcytometry sorting. The aging time point was designed as 4 groups: 3 moth, 12 month, 18 month and 24 month; each group includes 4 repeats. The total RNA was extracted from isolated retinal microglia cells and reverse transcripted to cDNA after amplification and labeling. The gene expression profile was detected with Affymetrix GeneChip of Mouse Exon 1.0ST Arrays

first: Wenxin

last: Ma

middle: I

first: Norimoto

last: Gotoh

first: Linn

last: Gieser

first: Tiziana

last: Cogliati

first: Anand

last: Swaroop

first: Wai

middle: T

last: Wong


title: Analysis of liver gene expression profile in male mice fed alcoholic (Lieber-Decarli's) diet and calorie-matched control diet for 6 weeks

status: Public on Dec 19 2012

city: Columbus

first: kalpana

last: ghoshal

state: OH

address: 420 W. 12th Avenue

department: Molecular and Cellular Biochemistry

institute: The Ohio State University

summary: Microarray analysis showed dysregulation of genes involved in lipid, xenobiotic and glutathione metabolism as well as those involved in mitochondrial function and cell proliferation in the livers of C57BL6 mice fed alcoholic liquid diet for 6 weeks.

overall_design: We analyzed liver RNA from 4 mice fed alcoholic diet and 4 mice fed control diet  using the Affymetrix Mouse Exon 1.0 ST platform. Array data was processed by Affymetrix Exon Array Computational Tool.

first: Kalpana

last: Ghoshal

first: Huban

last: Kuta

first: Lianbo

last: Yu

first: Sarah

last: Werner

first: Timothy

last: Wise


title: Interference with PPAR gamma signaling in mesenteric artery

status: Public on Sep 24 2012

summary: Pharmacological activation of the transcription factor PPAR gamma lowers blood pressure and improves glucose tolerance in humans.  In contrast, naturally occurring mutations (e.g., P467L, V290M) in the ligand binding domain of PPAR gamma in humans leads to severe insulin resistance and early-onset hypertension. Experimental evidence, including whole genome expression profiling, suggests that these mutant versions of PPAR gamma act in a dominant negative manner. Because PPAR gamma is expressed in a variety of cell types and tissues, we generated a transgenic mouse model (SP467L) specifically targeting dominant negative PPAR gamma to the vascular smooth muscle cells in order to determine the action of PPAR gamma in the blood vessel independent of its systemic metabolic actions.   In the data set provided herein, we examined the gene expression profile in mesenteric vessels from SP467L mice and their control littermates using  the Affymetrix mouse exon 1.0 ST array.

overall_design: We generated transgenic mice specifically targeting expression of mutant dominant negative human PPAR gamma (P467L) to vascular smooth muscle using a smooth muscle-specific promoter (smooth muscle myosin heavy chain or SMMHC).  Mesenteric arteries were isolated from 3 male transgenic mice and 4 non-transgenic littermate controls. Total RNA was prepared using conventional methods and quality was assessed using the Bioanalyzer 2100 (Agilent Technologies). For the microarray hybridizations, each sample corresponded to mesenteric artery derived from one mouse. All procedures were conducted at the University of Iowa DNA Core facility using standard Affymetrix protocols. In brief, approximately 50 ng of total RNA was used as input to a two-step amplification procedure (NuGen, http://www.nugeninc.com/) to generate biotin-labeled RNA fragments for hybridization to the Affymetrix mouse exon 1.0 ST array.


title: Effect of Gadd45a overexpression on mouse skeletal muscle mRNA levels.

status: Public on Sep 15 2012

first: Christopher

last: Adams

address: 540G EMRB, 200 Hawkins Drive

summary:
Gadd45a is a stress-induced protein that causes skeletal muscle atrophy. The goal of these studies was to determine the effects of Gadd45a overexpression on mRNA levels in mouse skeletal muscle.
For additional details see Ebert et al, Stress-Induced Skeletal Muscle Gadd45a Expression Reprograms Myonuclei and Causes Muscle Atrophy. JBC epub. June 12, 2012.

overall_design: Tibialis anterior (TA) muscles from muscle-specfic ATF4 knockout mice (ATF4 mKO) were transfected with either 20 mg empty plasmid (pcDNA3) (left TA) or 20 mg pCMV-FLAG-Gadd45a (right TA) and harvested 7 days later.  mRNA levels in Gadd45a-transfected muscles were normalized to levels in control transfected muscles.

first: Scott

middle: M

last: Ebert


title: Effect of ATF4 overexpression on mRNA levels in differentiated C2C12 myotubes.

summary:
ATF4 is a bZIP transcription factor that that promotes skeletal muscle atrophy. The goal of these studies was to determine the effects of ATF4 overexpression on mRNA levels in differentiated C2C12 myotubes.
For additional details see Ebert et al, Stress-Induced Skeletal Muscle Gadd45a Expression Reprograms Myonuclei and Causes Muscle Atrophy. JBC epub. June 12,2012

overall_design: C2C12 myotubes were infected with adenovirus co-expressing eGFP and ATF4-FLAG.  Control myotubes were infected with adenovirus co-expressing eGFP and a transcriptionally inactive ATF4 construct (ATF4∆bZIP).


title: Effect of ATF4 gene knockout on skeletal muscle mRNA levels in fasted mice.

summary:
ATF4 is a fasting-induced trascription factor that promotes skeletal muscle atrophy. The goal of these studies was to determine how of loss of ATF4 affects skeletal muscle mRNA expression.
For additional details see Ebert et al, Stress-Induced Skeletal Muscle Gadd45a Expression Reprograms Myonuclei and Causes Muscle Atrophy. JBC epub. June 12, 2012.

overall_design: Muscle-specfic ATF4 knockout (ATF4 mKO) mice and littermate controls were fasted for 24 hours and then tibialis anterior muscles were harvested.  mRNA levels in ATF4 mKO muscles were normalized to levels in littermate control muscles.


title: Argonaute proteins couple chromatin silencing to alternative splicing (exon array)

status: Public on Sep 10 2012

city: Paris

first: Eric

last: Batsche

address: 7-9, Quai Saint Bernard

department: B2A Biological Adaptation and Ageing - UMR8256 CNRS

country: France

institute: IBPS - Institut Biologie Paris Seine

summary:
While Argonaute (AGO) proteins play a major role in transcriptional gene silencing (TGS) in many organisms, their role in the nucleus of somatic mammalian cells remains elusive. Here, we have purified AGO1 and AGO2 chromatin-embedded complexes, and found these proteins associated with previously described partners, but also with chromatin modifiers and, rather unexpectedly, with different splicing factors. Using the CD44 gene as a model for alternative splicing, we show that both AGO1 and AGO2 are required for Protein Kinase C (PKC)-dependent variant exon inclusion. AGO proteins facilitate the spliceosome recruitment and modulate the elongation rate of RNA polymerase II (RNAPII). The recruitment of AGO proteins to CD44 transcribed region is dependent on both the endonuclease Dicer and the chromodomain-containing protein HP1g, and results in locally increased levels of histone H3 lysine 9 (H3K9) methylation on variant exons. Genome wide analysis of splicing in either AGO2 or Dicer null cells showed that the two proteins have similar effects on many splicing events. Finally, sRNAs associated with nuclear AGO2 are mostly in sense orientation relative to protein-coding genes, supporting a role for intragenic antisense non-coding RNAs in the recruitment AGO and splicing factors. Together, our data demonstrate for the first time that the endogenous RNAi pathway is involved in alternative splicing decisions, unravelling a new model in which AGO proteins couple RNAPII elongation and chromatin modification.
Study of AGO2 or Dicer knock-out on gene expression and splicing regulation in MEF cells

overall_design: Transcriptome analysis of AGO2 and Dicer null MEF cells on GeneChip® Mouse Exon 1.0 ST Arrays (Affymetrix). Dicer null MEF cells and wild-type MEF cells were from M. Otsuka. AGO2 null MEF cells were from A. Tarakhovsky. Experiment has been done in experimental triplicates.  9 Total samples were analyzed.

first: M

last: Ameyar-Zazoua

first: C

last: Muchardt

first: A

last: Harel-Bellan

first: E

last: Batsché


title: Effect of denervation on mouse skeletal muscle mRNA levels.

summary:
Muscle denervation causes skeletal muscle atrophy. The goal of these studies was to determine the effects of denervation on skeletal muscle mRNA levels in C57BL/6 mice.
For additional details see Ebert et al, Stress-Induced Skeletal Muscle Gadd45a Expression Reprograms Myonuclei and Causes Muscle Atrophy. JBC epub. June 12, 2012.

overall_design: Left sciatic nerves of C57BL/6 mice were transected. Seven days later bilateral tibialis anterior muscles were harvested.  mRNA levels in denervated muscles were normalized to levels in contralateral innervated muscles.


title: Expression Analysis of Whole Thymus and Thymic Tumors on the Sdl Mouse Model

status: Public on Sep 01 2012

city: Madison

first: Bruce

last: Bagley

state: WI

address: 777 Highland Ave.

department: Pharmacy

institute: University of Wisconsin - Madison

summary:
Here we report the isolation of a murine model for heritable T cell lymphoblastic leukemia/lymphoma (T-ALL) called Spontaneous dominant leukemia (Sdl). Sdl heterozygous mice develop disease with a short latency and high penetrance; while mice homozygous for the mutation die early during embryonic development. Sdl mice harbor increased numbers of spontaneous micronuclei, and Sdl T-ALLs harbor small amplifications and deletions, including activating deletions at the Notch1 locus. Sdl mice harbor a spontaneously acquired mutation in Mcm4 (Mcm4D573H). MCM4 is part of the heterohexameric complex of MCM2-7 that is important for licensing of DNA origins prior to S phase and also serves as the core of the replicative helicase that unwinds DNA at the replication fork.
This exon array was conducted to determine the expression changes that occur in pre-leukemic thymus samples at 21 days of age, as well as thymic tumors in the Sdl model.

overall_design: generated pairwise comparisons of wild-type > pre-leukemic and wild-type > thymic tumor.  Transcripts with a posterior probability of differential expression >95% and a q-value < 0.05 were considered to be significantly differentially expressed.

middle: N

first: Erin

last: Riley

first: Christina

last: Kendziorski

first: Lara

middle: S

last: Collier


title: Sleep in a dish: key electrophysiological, molecular, and metabolic signatures of sleep and wakefulness revealed in primary cortical cultures

status: Public on Aug 31 2012

city: Lausanne

first: Sylvain

last: Pradervand

address: Genopode

department: CIG

country: Switzerland

institute: UNI Lausanne

summary:
Although at the organismal level sleep is defined as a behavioral state, at the level of the cerebral cortex sleep has a distinct local and use-dependent aspect. This observation raises the question whether sleep is a functional property of a complex brain or occurs at the level of neuronal assemblies with populations that were active more during wakefulness needing more intense sleep to recover. Here we show that primary cortical cultures have the capacity to change between  sleep- and wake-like states that share key signatures with their in vivo counterparts. Cortical cultures initially exhibit random firing activity that is gradually replaced by a “sleep-like” synchronized burst-pause firing activity as neurons mature and make connections. When stimulated with excitatory neurotransmitters, transient tonic firing is observed, followed by the reappearance of a “sleep-like” state. Besides electrophysiological similarities also the transcriptional profile of stimulated cortical cultures greatly resembles that of the cortex of sleep deprived animals. We then used our in vitro model to map the metabolic pathways activated by the “wake-like” state and found evidence for increased lysolipid release, strongly suggesting that sleep plays a role in neuronal membrane homeostasis. With our in vitro model the cellular and molecular consequences of sleep loss and the genetic  determinants of disturbed sleep can now be investigated in a dish.
Keywords: stress response

overall_design: For the in vivo transcriptome analyses mice were sleep deprived for 6 hours and brain harvested immediately afterwards. For the in vitro analyses, cortical cultures were stimulated with a neurotransmitter cocktail and cells harvested 3 hours afterwards. Control mice were kept undisturbed in their home cage and control cultures were sham stimulated with water. Also, another set of sleep deprived mice as well as stimulated cultures were allowed to recover before being sampled the next day at the time of day at which sleep deprivation or stimulation started the day before).

first: Valérie

last: Hinard

first: Cyril

last: Mikhail

first: Mehdi

last: Tafti


title: Splicing switch of an epigenetic regulator by RNA helicases promotes tumor-cell invasiveness

status: Public on Sep 11 2012

city: New York

first: Etienne

last: Dardenne

state: NY

address: 1300 York Avenue

department: Pathology

institute: Weill Cornell Medecine

summary: Both epigenetic and splicing regulation contribute to tumor progression, but the potential links between these two levels of gene-expression regulation in pathogenesis are not well understood. Here, we report that the mouse and human RNA helicases ddx17 and ddx5 contribute to tumor-cell invasiveness by regulating alternative splicing of several DNA- and chromatin-binding factors, including the macroH2A1 histone. We show that macroH2A1 splicing isoforms differentially regulate the transcription of a set of genes involved in redox metabolism. In particular, the SOD3 gene that encodes the extracellular superoxide dismutase and plays a part in cell migration is regulated in an inverse manner by macroH2A1 splicing isoforms. These findings reveal a new regulatory pathway in which splicing factors control the expression of histone-variant isoforms that in turn drive a transcription program to switch tumor cells to an invasive phenotype.

overall_design:
We analyzed 4T1 cells depleted or not for ddx5 and ddx17 RNA helicases using the Affymetrix Human Exon 1.0 ST platform. Array data was processed by Affymetrix Exon Array Computational Tool. Four techinical replicates were performed.
We analyzed 4T1 cells depleted for ddx5 and ddx17 RNA helicases and macroH2A1.1 or macroH2A1.2 using the Affymetrix Human Exon 1.0 ST platform. Array data was processed by Affymetrix Exon Array Computational Tool. Three techinical replicates were performed.

first: Sandra

last: Pierredon

first: Keltouma

last: Driouch

first: Lise

last: Gratadou

first: Magali

last: Lacroix-Triki

first: Micaela

middle: P

last: Espinoza

first: Eleonora

last: Zonta

first: Sophie

last: Germann

first: Hussein

last: Mortada

first: Jean-Philippe

last: Villemin

first: Martin

last: Dutertre

first: Rosette

last: Lidereau

first: Stéphan

last: Vagner

first: Didier

last: Auboeuf


title: Expression data from P7 mouse cerebral cortex and hippocampus -CTCF Nex-Cre mediated conditional knockout

status: Public on Jul 26 2012

city: suita

first: teruyoshi

last: hirayama

state: osaka

address: 1-3 yamadaoka

department: graduate school of frontier biosciences

country: Japan

institute: osaka university

summary:
The CCCTC-binding factor (CTCF) is key to chromatin conformational changes that promote cellular diversity, but nothing is known about its role in neurons. Here we produced mice with a conditional knockout (cKO) of CTCF in postmitotic projection neurons, mostly in the dorsal telencephalon.
390 transcripts were expressed at significantly different levels between CTCF-deficient and control cortex and hippocampus.

overall_design: 14 Total samples were analyzed. Statistical analysis was performed by ANOVA, using the core probe sets defined by Affymetrix with the revision of the clustered Pcdhs. A list of genes showing a significant difference by Ctcf deletion was generated using a false discovery rate (FDR) <0.05 with a fold difference of < -1.2 or > 1.2 as a cutoff value.

first: T

last: Hirayama

last: Yagi


title: Expression data from Flt3L-derived bone marrow dendritic cells from WT or Clec9agfp/gfp mice treated or not with dead cells

status: Public on May 01 2012

city: London

first: Santiago

last: Zelenay

address: 44 Lincoln's Inn Fields

country: United Kingdom

institute: Cancer Research UK London Research Institute

summary: DNGR-1 (CLEC9A) is expressed in CD8-like dendritic cells (DCs) and detects a ligand exposed on necrotic cells. We have characterized the transcripts that are induced in cultures of Flt3L-derived bone-marrow-derived WT or DNGR1-deficient DCs upon incubation with dead cells. Microarray analysis of the transcriptome of DNGR-1-deficient and WT DCs cultured with dead cells failed to reveal any DNGR-1-dependence in the transcriptional response to dead cells.

overall_design: Flt3L-BMDC from WT or DNGR-1-deficient (Clec9a gfp/gfp) mice were left untreated or were cultured for 5 hours with UV-treated dead cells at a 1:2 ratio. CD24hi CD11blow B220- CD8α+-like DC were purified by cell sorting and RNA was extracted. There were 3 replicates for each of the four experimental conditions.

first: Caetano

last: Reis e Sousa


title: Expression data from hepatocyte specific Klf6 knockout mice vs. control on high fat diet

status: Public on Mar 23 2012

first: Weijia

last: Zhang

address: 1425 Madison Avenue

department: Department of Medicine

institute: Mount Sinai School of Medicine

summary:
Dysregulated glucose homeostasis and lipid accumulation characterize non-alcoholic fatty liver disease (NAFLD), but underlying mechanisms are obscure. We report here that Krüppel-like factor 6 (KLF6), a ubiquitous transcription factor that promotes adipocyte differentiation, also provokes the metabolic abnormalities of NAFLD.
Mice with either hepatocyte-specific knockdown of KLF6 (DeltaHepKlf6) or global KLF6 heterozygosity (Klf6 +/-) have reduced body fat content and improved glucose and insulin tolerance. Mice with KLF6 depletion, compared to wild type mice, are protected from high fat diet-induced steatosis.

overall_design: Three mice with a hepatocyte-specific knockdown of KLF6 (DeltaHepKlf6) on high fat diet and 3 littermate controls on the same diet were sacrificed after 8 weeks of  diet. Liver tissue was preserved in RNAlater® (Ambion, Austin, TX). RNA was isolated from liver tissue and homogenized in TRIzol® reagent (Invitrogen, Carlsbad, CA). In order to identify potential KLF6 targets that contributed to changes in glucose- and lipid-metabolism, we performed an Affymetrix Exon1 S.T. Genearray® (Affymetrix, Santa Clara, CA).

first: Lars

last: Bechmann

first: Diana

last: Vetter

first: Junichi

last: Ishida

first: Rebekka

middle: A

last: Hannivoort

first: Ursula

middle: E

last: Lee

first: Peri

last: Kocabayoglu

first: M

last: Fiel

last: Muñoz

first: Gillian

last: Patman

first: Fengxia

last: Ge

first: Shoshana

last: Yakar

first: Xiaosong

last: Li

first: Loranne

last: Agius

first: Young-Min

first: Gary

middle: J

last: Schwartz

first: Derek

last: LeRoith

first: Paul

last: Berk

first: Ryozo

last: Nagai

first: Toru

last: Suzuki

first: Helen

last: Reeves

first: Scott

last: Friedman


title: Effects of the long noncoding RNA Malat1 on gene expression [MoEx-1_0-st]

status: Public on Jun 25 2012

city: Wako

first: Yuen Yan

middle: Joanna

last: Ip

state: Saitama

address: 2-1 Hirosawa

department: Advanced Science Institute

institute: RIKEN

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

overall_design: Hippocampi were dissected from two sets of wildtype and Malat1 knock-out mice and RNA from these neurons were hybridized to Affymetix mouse exon array. Individual animals from each pairs of wildtype and knock-out are littermates.

first: Shinichi

last: Nakagawa

first: Joanna

middle: Y


title: Transcriptome analysis of medulloblastoma tumors in mice

status: Public on Mar 20 2012

city: San Francisco

first: William

middle: A.

last: Weiss

state: CA

address: 1450 3rd Street, HD-220

department: Neurology

institute: University of California, San Francisco

summary: The proto-oncogene MYCN is mis-expressed in various types of human brain tumors. To clarify how developmental and regional differences influence transformation, we transduced wild-type or mutationally-stabilized murine N-mycT58A into neural stem cells (NSCs) from perinatal murine cerebellum, brain stem and forebrain. Transplantation of Nmyc WT NSCs was insufficient for tumor formation. N-mycT58A cerebellar and brain stem NSCs generated medulloblastoma/primitive neuroectodermal tumors, whereas forebrain NSCs developed diffuse glioma. Expression analyses distinguished tumors generated from these different regions, with tumors from embryonic versus postnatal cerebellar NSCs demonstrating SHH-dependence and SHH-independence, respectively. These differences were regulated in-part by the transcription factor SOX9, activated in the SHH subclass of human medulloblastoma. Our results demonstrate context-dependent transformation of NSCs in response to a common oncogenic signal.

overall_design: 9 (total) orthotopic tumors generated from E16C, P0C, and P0F NSCs transduced with a mutation-stabilized N-Myc were compared to transduced (but not transplanted) NSCs, NSCs transduced with GFP, and cells derived from the orthotopic tumors.  These were also compared to 5 normal P7 cerebella, and 32 medulloblastoma tumors from the GTML mouse model.  A cell line derived from a tumor from the GTML mouse model is also included in the comparison.

first: Fredrik

last: Swartling

first: Vasil

last: Savov

first: Anders

last: Persson

first: Justin

last: Chen

first: Christopher

last: Hackett

last: Northcott

first: Matthew

middle: R

last: Grimmer

first: Jasmine

last: Lau

first: Louis

last: Chesler

first: Arie

last: Perry

last: Phillips

first: Michael

last: Taylor


title: Clock rescue in the brain restores 12- and 24- hour rhythms in the liver

status: Public on Jun 01 2012

city: Philadelphia

last: Hughes

state: PA

address: 421 Curie Bvd, Brb 835

institute: UPenn

summary: Circadian profiling was performed in mouse livers from three different genotypes/treatments: Wildtype, Clock mutant, and brain-specific Clock rescue. Rescuing Clock specifically in the brain partially rescued robust circadian and harmonic rhythms.

overall_design: Samples were collected every 2 hours for 48 hours from 2-4 mice per time point; samples were pooled and analyzed using Affymetrix Mouse Exon arrays, analyzed at the gene level.

first: Heekyung

last: Hong

first: Jason

last: Chong

first: Joseph

last: Takahashi

first: John

last: Hogenesch


title: Female- and male-specific transcriptomic and epigenetic placental signatures in response to a maternal high fat diet in mice

status: Public on Apr 01 2012

first: Jean-Philippe

last: Jais

address: 149 rue de Sevres

institute: Université Paris Descartes - Hopital Necker-Enfants Malades

summary:
Overnutrition during pregnancy inﬂuences the future health of the offspring, with outcomes differing depending on the child’s sex. The placenta is involved in the programming of obesity, type 2 diabetes and cardiovascular disease. Sex-specific adaptation of the placenta may be central to the differences in fetal growth and survival. The impact of diet and fetal sex on placental gene expression and epigenetic marks was investigated in mice fed a high-fat (HFD) or a control diet (CD), during the first 15 days of gestation
Microarrays analysis revealed that expression was affected by maternal diet and was sexually dimorphic.

overall_design: We analyzed the placentae of 4 mice litters fed with an high-fat diet (HFD) and 4 with a control diet (CD). For each litter, the placenta transcriptome was analysed according to the foetus sex using the Affymetrix Human Exon 1.0 ST platform. Array data was processed by Affymetrix Exon Array Computational Tool. No technical replicates were performed.

first: Anne

last: Gabory

first: Jean-David

last: Gothié

first: Laure

last: Ferry

first: Alexandre

last: Vigé

first: Cécile

last: Fleur

first: Catherine

last: Gallou-Kabani

first: Marie-Sylvie

last: Gross

first: Isabelle

last: Fajardy

last: Vambergue

first: Jean

last: Lesage

first: Brigitte

last: Reusens

first: Didier

last: Vieau

first: Claude

last: Remacle

first: Luc

last: Jouneau

first: Claudine

last: Junien


title: Distinct tumorigenic pathways within hereditary nonpolyposis colorectal cancer

status: Public on Mar 08 2012

city: Lund

first: Mev

last: Dominguez

address: Klinikgatan 28

department: Oncology

country: Sweden

institute: Lund University

summary: Gene expression profiling has discriminated between sporadic microsatellite instable (MSI) and microsatellite stable (MSS) colorectal cancers (CRCs), whereas the expression pattern of familial colorectal cancer type X (FCCTX) and Lynch syndrome (LS) associated CRCs remain largely unknown. The purpose of this study is to use gene expression profiling of formalin-fixed paraffin-embedded (FFPE) tumor specimens from FCCTX, LS and sporadic CRC as a control to detect expression patterns and to identify signaling pathways differing between FCCTX and LS tumors.

overall_design: RNA extracted from 132 FFPE specimens (40 FCCTX, 42 LS, 50 sporadic) were profiled for differential gene expression by the whole genome cDNA-mediated annealing, selection, extension, and ligation (WG-DASL) assay containing 18626 genes.

last: Valentin

first: Christina

last: Therkildsen

first: Srinivas

last: Veerla

first: Mats

last: Jonsson

first: Inge

last: Bernstein

first: AKe

last: Borg

first: Mef

last: Nilbert


title: Whole genome sequencing of murine induced Pluripotent Stem (iPS) cell clones

status: Public on Mar 15 2012

city: St Louis

first: Rekha

last: Meyer

state: MO

address: 4320 Forest Park Av

institute: Washington University School of Medicine

summary: Whole genome sequencing was performed on several murine iPS cell clones (and their parental cells) from each of three independent reprogramming experiments. Hundreds of single nucleotide variants (SNVs) were detected in each clone, with an average of 11 in coding regions. Affymetrix Mouse Exon 1.0ST arrays were used to compare expression patterns in MPSVII iPS lines, and embryo-derived MPSVII ES cells. Unsupervised hierarchal clustering analysis showed that the iPS clones and ES cell lines clustered randomly, suggesting that their global patterns of gene expression are highly similar. Taken together, our data suggest that most of the genetic variation in iPS cell clones is not caused by reprogramming, but is rather a consequence of cloning individual cells, “capturing” random mutations that preexisted in the single cells that were reprogrammed. These mutations can sometimes contribute to reprogramming “fitness”, thus providing a selective advantage for rare cells when they overexpress reprogramming factors.

overall_design: Mouse embryonic fibroblasts (MEFs) derived from a murine disease model (Mucopolysaccaridosis type VII- MPSVII) were used. Affymetrix Mouse Exon 1.0ST arrays were used to compare expression patterns in MPSVII iPS lines, and embryo-derived MPSVII ES cells. Expression patterns in four separate iPS clones were compared to MPSVII ES cells.  Control hybridization was performed with B6 Blu ES cells and MEFs.

first: Margaret

last: Young

first: Timothy

last: Ley


title: Gene expression profile in CD11c+ splenic dendritic cells and CD11c+CD103+ dendritic cells from mesenteric lymph nodes (MLN) of mice with DC-specific targeting of TGFBR2

city: Tucson

first: Pawel

middle: R.

last: Kiela

state: AZ

address: 1501 N. Campbell Ave.

department: Pediatrics

institute: University of Arizona

summary:
Transcriptome analysis of dentritic cells from the spleen (CD11c+) or MLN (CD11c+CD103+) of mice with DC-specific deletion of TGFBR2 gene, or their control littermates.
TRGFR2 gene was deleted in dendritic cells using Cre/lox approach. Mice with this deletion develop spontaneous multi-organ autoimmune inflammation and die by 15 weeks of age.

overall_design: Splenic CD11c+ Dc were isolated by magetic cell sorting. MLN CD11c+CD103+ DC were flow sorted. RNA was isolated using RNAqueous-Micro kit (Ambion) and analyzed using Affymetrix Mouse Exon 1.0 ST Array

first: Rajalakshmy

last: Ramlingam

first: Claire

middle: B

last: Larmonier

first: Robert

last: Thurston

first: Monica

last: Midura-Kiela

first: Song-Guo

last: Zheng

first: Fayez

middle: K

last: Ghishan


title: Expression data from the Cancer Cell Line Encyclopedia (CCLE)

city: Cambridge

first: Nicolas

last: Stransky

state: MA

address: 7 Cambridge center

department: Cancer Program

institute: Broad Institute

summary:
The Cancer Cell Line Encyclopedia (CCLE) project is a collaboration between the Broad Institute, the Novartis Institutes for Biomedical Research and the Genomics Novartis Foundation to conduct a detailed genetic and pharmacologic characterization of a large panel of human cancer models
It consists of a compilation of gene expression, chromosomal copy number, and massively parallel sequencing data from nearly 1,000 human cancer cell lines. All raw and processed data are available through an integrated portal on www.broadinstitute.org/ccle

overall_design: The final cell line collection spans 36 cancer types. Representation of cell lines for each cancer type was mainly driven by cancer mortality in the United States, as a surrogate of unmet medical need, as well as availability.


title: Comparison of gene expression profiles in NOD and Idd9 CD4+ T cells

status: Public on Feb 01 2012

city: La Jolla

first: Steven

last: Head

address: 10550 N Torrey Pines Rd

institute: The Scripps Research Institute

summary: Nonobese diabetic (NOD) mice congenic for B10 derived genes in the Idd9 region of chromosome 4 are highly protected from the development of diabetes. In order to identify possible candidate genes within the Idd9 susceptibility region and possible downstream mediators of protection, we compared gene expression between NOD and Idd9 CD4+ T-cells. CD4+ T-cells with an activated phenotype (CD44-high/CD62L-low) were sorted from the pancreatic lymph nodes of female 8-week old mice.

overall_design:
Mice were bred at Taconic farms and were line 905 (NOD.B10-Idd9 congenic) and line 6359 (NOD-like control strain with a B10 congenic region on chromosome 1 which does not modify diabetes incidence).
Three replicate samples were prepared, each from four pooled pancreatic lymph nodes. CD4+CD44-highCD62L-low T-cells were sorted from each sample.

first: Emma

last: Hamilton-Williams

first: Daniel

last: Rainbow

first: Jocelyn

last: Cheung

first: Linda

last: Wicker

last: Sherman


title: Expression data of Sorted CD11b+Gr1+ cells from mice with or without LLC tumor challenging

status: Public on Jan 01 2012

first: Dingcheng

last: Gao

address: 1300 York Ave

department: CT Surgery

institute: Weill Cornell Medical College

summary:
We sought to identify genes that are differentially regulated in CD11b+Gr1+ cells after tumor challenging. Mice were challenged with LLC-RFP cells (5×10^6 cells, subcutaneous injection) for 9 days. Single cell suspensions were prepared from lungs of both tumor challenged and control wild type mice and stained with antibodies against CD11b and Gr1. Approximately 1×10^5 CD11b+GR1+ myeloid progenitor cells were sorted by FACS (Aria II, BD Bioscience). Total RNA was extracted from the sorted cells for microarray analysis.
In this dataset, we include the expression data of CD11b+Gr1+ cells obtained from both control wild type and tumor challenged mice. These data were used to obtain 22 genes that are upregulated in response to tumor challenging.

overall_design: We analyzed 3 samples from control mice and 2 samples tumor challenged mice. The mean values of the groups were used in the analysis. Genes that were upregulated >2 fold were sorted out and generate the table in the Matrix datasheet.

first: Seongho

last: Ryu


title: Analysis of genes regulated by the transcription factor LUMAN identifies ApoA4 as a target gene in dendritic cells

status: Public on Dec 31 2011

city: Nijmegen

first: Anna

last: Sanecka

address: Geert Grooteplein 26/28

department: Tumor Immunology Lab

country: Netherlands

institute: UMC St Radboud Nijmegen, NCMLS

summary: Differential gene expression upon overexpression of the active form of the transcription factor LUMAN in mouse dendritic cell line D2SC/1

overall_design: retroviral overexpression of the active form of LUMAN, as a control GFP overexpression was used, two time points = 6h and 18h from the infection start point, time point zero=untreated D2SC/1 cells

first: Marleen

last: Ansems

first: Maaike

last: van Hout-Kuijer

last: Looman

first: Christian

last: Gilissen

first: Joris

last: Veltman

first: Bastiaan

last: Jansen

first: Dagmar

last: Eleveld-Trancikova

first: Gosse

last: Adema


title: Expression data from day 3 Flk-1 mesoderm between ER71 overexpressed and ER71 knockout mouse embryonic stem cell

status: Public on Feb 20 2012

city: St. Louis

first: Fang

last: Liu

address: 660S Euclid Ave.

department: Pathology & Immunology

institute: Washington University in St. Louis

summary:
Ets transcription factor ER71 is critical for Flk-1 mesoderm specification to different cell lineages.
In this dataset, we determine to investigate the mechanisms by which ER71 regulates hematopoietic and endothelial cell versus cardiac cell lineage development.

overall_design: Expression of all four Flk-1+ mesoderm populations (i.e. Er71 overexpressed versus control, Er71 deficient versus control Flk-1+ mesoderm) was compared. Specifically, we sorted Flk-1+ mesoderm  from day 3 differentiated embryonic stem(ES) cells, including induced Er71 and control ES cells, as well as  Er71+/+ as well as Er71-/- ES cells .

first: Li-Wei

last: Chang

first: Kyunghee

last: Choi


title: Pten signaling in fibroblasts effects gene expression in endothelial and epithelial cells

status: Public on Dec 18 2011

city: Columbus

first: Julie

last: Wallace

address: 460 W. 12th Ave 840 BRT

institute: OSUCCC

summary: These experiments aim determine the effects of Pten signaling in fibroblasts on gene expression in other cell compartments in the mammary gland.

overall_design: To achieve this, we used a genetic model in which the tumor suppressor gene Pten was specifically inactivated in stromal fibroblats.  We then isolated fibroblasts, epithelial cells and endothelial cells from the mammary glands of mice with either wild type or Pten null fibroblasts.  Comparisons were made between wild type and Pten counterparts, not between the various cell types.

first: Michael

middle: C

last: Ostrowski


title: Developmental time-course of adult cell-type-specific retina genes of amacrine cells

status: Public on Nov 30 2011

city: Basel

first: Sandra

last: Siegert

address: Maulbeerstrasse 66

institute: Friedrich Miescher Institute

summary:
Brain circuits are assembled from a large variety of morphologically and functionally diverse cell types. It is not known how the intermingled cell types of individual brain regions differ in their expressed genomes. Here we describe an atlas of cell type transcriptomes of the adult retina. We found that each adult cell type expresses a specific set of genes, including a unique set of transcription factors, forming a “barcode” for cell identity. Cell type transcriptomes carry enough information to categorize cells into corresponding morphological classes and types. Surprisingly, several barcode genes are eye disease-associated genes that we demonstrate to be specifically expressed not only in photoreceptors but also in particular retinal circuit elements such as inhibitory neurons as well as in retinal microglia. Our data suggest that distinct cell types of individual brain regions are characterized by marked differences in their expressed genomes.
To obtain insight into the developmental time course of adult cell type-specific gene expression, we followed gene expression in one amacrine cell group, Arc cells, for 20 postnatal days (P) starting at P1. Qualitative analysis of the expression time-course of cell type-specific genes revealed four patterns: increasing, decreasing or constant expression from P1 to P20, or a biphasic time-course (constant and increasing) with a switch at P9-P10. At this latter time point, bipolar cells begin to form synapses with amacrine and ganglion cells and the retina becomes light responsive. Pairwise correlations across the transcriptomes measured on each day exposed two major clusters, from P1 to P9 and from P10 to P20, which also suggested a transcriptional switch during the transition from P9 to P10. Thus, most adult cell type-specific genes are also expressed during development but at levels different to those in the adult.

overall_design: We performed gene expression analysis of one amacrine cell group, Arc, from P0 to P20 and for Starburst amacrine cells for the time point P3 and P18. All experiments were performed in biological triplicates. 1 retina was used for each time point and each sample of the biological triplicate.

first: Botond

last: Roska

first: Erik

last: Cabuy

first: Dimos

last: Gaidatzis


title: Differential gene expression caused by Dicer knockout in small intestine

status: Public on Jan 07 2012

city: Baltimore

first: Tai-Chung

last: Huang

address: 733 N Broadway BRB R560

department: Institute of Genetic Medicine

institute: Johns Hopkins University School of Medicine

summary: Dicer knockout cause lipid metabolism dysregulation in small intestine. Analyses of transcriptomics and proteomics reveal key enzymes affected by Dicer knockout.

overall_design: Conditional knockout of Dicer in adult mice

first: Huang

last: Tai-Chung

first: Yang

last: Yi

first: Pandey

last: Akhilesh


title: Differential expression caused by Dicer knockout in small intestine

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

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

platform_organism:
Mus musculus
synthetic construct

overall_design: Refer to individual Series


title: Expression data from normal murine mammary epithelial cell line NMuMG stimulated with TGF-beta

status: Public on Nov 01 2011

city: Tokyo

first: Daizo

last: Koinuma

address: Hongo 7-3-1, Bunkyo-ku

institute: University of Tokyo

summary:
TGF-beta is one of the most important cytokines that induce epithelial to mesenchymal transition (EMT).
In this dataset, we examined TGF-beta induced changes in gene and exon level expression.

overall_design: Core probesets of two samples were analyzed. NMuMG cells were stimulated with TGF-beta for 24 h or left untreated.

first: Kana

last: Horiguchi

first: Kohei

last: Miyazono


title: Gene Array Analyzer (GAA): Alternative usage of gene arrays to study alternative splicing events (MoEx array)

status: Public on Nov 28 2011

city: Bad Nauheim

first: Pascal

last: Gellert

address: Ludwigstr. 43

department: Cardiac Development and Remodelling

country: Germany

institute: Max Planck Institut for Heart and Lung Research

summary: The latest version of microarrays released by Affymetrix, the GeneChip Gene 1.0 ST Arrays (gene arrays), are designed in a similar fashion as exon arrays, which enables to identify differentially expressed exons, rather than only the expression level of whole transcripts. Here, we propose an extension, Gene Array Analyzer (GAA), to our previously published Exon Array Analyzer (EAA). GAA enables to analyse gene arrays on exon level and therefore supports to identify alternative splicing with gene arrays. To show the applicability of GAA, we used gene arrays to profile alternative splice events during the development of the heart. Further re-analysis of published gene arrays could show, that some of these splice events reoccur under pathological conditions. The web interface of GAA is user friendly, functional without set up and freely available at http://GAA.mpi-bn.mpg.de.

overall_design: Alternative splicing and gene expression analysis during development of the heart and cardiomyoyte differentiation.

first: Mizue

last: Teranishi

first: Katharina

last: Jenniches

first: Piera

last: De Gaspari

first: David

last: John

first: Karsten

last: grosse Kreymborg

first: Thomas

last: Braun

first: Shizuka

last: Uchida


title: Distal airway stem cells yield alveoli in vitro and during lung regeneration following H1N1 influenza infection (LCM_Four populations of cells)

city: Singapore

first: Frank

middle: Daniel

last: McKeon

address: 60 Biopolis street

department: Stem cell and Developmental Biology 7

institute: Genome Institute of Singapore

summary: The extent of lung regeneration following catastrophic damage and the potential role of adult stem cells in such a process remains obscure.  Sublethal infection of mice with an H1N1 influenza virus related to that of the 1918 pandemic triggers massive airway damage followed by apparent regeneration.  We show here that p63-expressing stem cells in the bronchiolar epithelium undergo rapid proliferation after infection and radiate to interbronchiolar regions of alveolar ablation.  Once there, these cells assemble into discrete, Krt5+ pods and initiate expression of markers typical of alveoli.  Gene expression profiles of these pods suggest that they are intermediates in the reconstitution of the alveolar-capillary network eradicated by viral infection.  The dynamics of this p63-expressing stem cell in lung regeneration mirrors our parallel findings that defined pedigrees of human distal airway stem cells assemble alveoli-like structures in vitro and suggests new therapeutic avenues to acute and chronic airway disease.

overall_design: H1N1 infected mice were sacrificed at 25 dpi and the lungs were snap frozen and embedded in OCT. Sections were cut and stained for several markers and consecutive sections were used for Laser Capture Microdissection.The PALM® Robot Microbeam laser microdissection system (P.A.L.M. GmbH, Bernried, Germany) in combination with a Zeiss microscope was used to dissect out desired cells.Four population of cells were collected namely alveoli, Krt5+,Spc+ and K5&SPC-. Isolated cells were collected in adhesive caps (Carl Zeiss, Inc.) and RNA was extracted using the Pico Pure RNA extraction kit (Arcturus).

first: Pooja

last: Kumar

first: Yuanyu

last: Hu

first: Yusuke

last: Yamamoto

first: Neo

last: Hoe

first: Tay

last: Wei

first: Dakai

last: Mu

first: Yan

last: Sun

first: Lim

last: Joo

first: Rania

last: Daghers

first: Elisabeth

last: Zielonka

first: De

last: Wang

first: Vincent

last: Chow

first: Christopher

last: Crum

first: Wa

last: Xian


title: Interleukin 1b triggers catabolism via a central nervous system-mediated pathway in mice and rat

status: Public on Nov 03 2011

city: Edmonton

first: Kathryn

last: Graham

state: Alberta

address: 11560 University Ave

country: Canada

institute: University of Alberta

summary:
Hypothalamic interleukin-1 beta (IL-1β) production is induced in multiple inflammatory diseases associated with muscle catabolism.
To determine whether IL-1β signaling in the CNS plays a role in the muscle wasting of inflammatory disease, we examined the ability of intracerebroventricular (ICV) IL-1β injection at pathophysiologically relevant concentrations, to generate catabolic changes in skeletal muscle.
Changes in gene expression associated with these catabolic changes were monitored using gene expression exon arrays.

overall_design: 28 samples were analyzed. The following comparisons were made: 6 groups were defined on the basis of treatment and time. Differences between groups were assesed by one way-ANOVA. P values were corrected for multiple comparisons using the Benjamini Hochberg correction at a false discovery rate of 1%. Probes were considered that showed a 1.75 fold or greater up or down regulation at any of the three timepoints.

first: Theodore

last: Braun

first: Xin

middle: X

last: Zhu

first: Marek

last: Szumoski

first: Gregory

middle: D

last: Scott

first: Aaron

last: Grossberg

first: Sheehan

last: Kahn

first: Sambasivarao

last: Damaraju

first: William

middle: F

last: Colmers

first: Vicki

last: Baracos

first: Daniel

middle: L

last: Marks


title: array-CGH profiling of human neuroblastoma samples obtained from infants included in the INES99.1, INES99.2 and INES99.3 trials

status: Public on Dec 07 2011

city: PARIS

first: Gudrun

last: Schleiermacher

address: 26 rue d'Ulm

department: Department of Pediatric Oncology

institute: Institut Curie

type: Genome variation profiling by genome tiling array

summary: In neuroblastoma (NB), the presence of segmental chromosome alterations (SCA) is associated with a higher risk of relapse, even when occurring together with numerical chromosome alterations (NCA). Furthermore, recent evidence shows that SCAs play a role in tumor progression. In order to analyze the role of SCAs in infants with NB, we have performed an extensive retrospective array-CGH analysis of tumours from infants enrolled in the European INES 99.1, 99.2 and 99.3 trials. Tumour samples from 221/300 enrolled patients could be analyzed. SCAs were observed in 11%, 20% and 59% of infants enrolled in trial 99.1 (localised unresectable NB), 99.2 (INSS stage 4s) and 99.3 (INSS stage 4), respectively (p<0.001), and were associated with the presence of bone metastasis (p<0.003). Progression-free survival was poorer in patients whose tumours harbored at least one SCA, in the whole population as well as in trials 99.1 and 99.2. In multivariate analysis, taking into account single genetic alterations, the protocol arm and genomic profile, the SCA genomic profile was the strongest predictor of poor outcome. Although overall survival was excellent, patients with stage 4s disease and a SCA genomic profile had a higher risk of relapse also in the absence of clinical symptoms at diagnosis and required a higher treatment burden for salvage. In conclusion, in infants with NB, a SCA genomic profile is useful to identify patients who will require upfront treatment even in the absence of other clinical indication for therapy, whereas an NCA genomic profile can identify a patient subpopulation in whom treatment reduction can be considered safe.

overall_design: Each of the 218 tumoral genomic DNAs was hybridized against non-tumoral DNA reference on BAC/PAC array or commercial supports in order to determine an overall genomic profile. The reference DNA was obtained from the blood of a single normal individual.

first: Jean

last: Michon

first: Agnès

last: Ribeiro

first: Gaelle

last: Pierron

first: Véronique

last: Mosseri

first: Hervé

last: Rubie

first: Caroline

last: Munzer

last: Bénard

first: Nathalie

last: Auger

first: Valérie

last: Combaret

first: Isabelle

last: Janoueix-Lerosey

first: Andrew

last: Pearson

first: Deborah

last: Tweddle

first: Nick

last: Bown

first: Mary

last: Gerrard

first: Kate

last: Wheeler

first: Rosa

last: Noguera

first: Eva

last: Villamon

first: Adela

last: Cañete

first: Victoria

last: Castel

first: Barbara

last: Marques

first: Ana

last: de Lacerda

first: Gian

middle: P

last: Tonini

first: Katia

last: Mazzocco

first: Raffaella

last: Defferrari

first: Bruno

last: de Bernardi

first: Andrea

last: di Cataldo

first: Nadine

last: van Roy

first: Bénédicte

last: Brichard

first: Ruth

last: Ladenstein

first: Inge

last: Ambros

first: Peter

first: Klaus

last: Beiske

first: Olivier

last: Delattre

first: Jérôme

last: Couturier


title: Identification of the altered transcripts in the NMF291–/– cerebellum by exon array.

status: Public on Oct 20 2011

city: Paris

first: Pierre

last: de la Grange

address: 29, rue du Faubourg Saint-Jacques

department: Paris Biotech Santé

institute: GenoSplice technology

summary: The U2 snRNA is a basal component of the major spliceosome, which is responsible for >90% human pre-mRNA splicing. A 5-nucleotide deletion in one of the mouse U2 snRNA genes (Rnu2-8) causes cerebellar granule cell degeneration in the NMF291 mouse mutant strain. To identify the altered transcripts in the NMF291–/– cerebellum, we interograted Affy. mouse 1.0 ST Exon arrays with total RNAs from three postnatal-30-day (P30) wild type and three NMF291–/– cerebella.

overall_design: Affy. mouse 1.0 ST Exon arrays were hybridized with total RNAs derived from three P30 female wild type and NMF291–/– mice (biological replicates).

first: Yichang

last: Jia

first: Susan

last: Ackerman


title: 5-hydroxymethylcytosine-mediated epigenetic dynamics during neurodevelopment and aging [mRNA profiling]

status: Public on Oct 30 2011

city: Atlanta

first: Keith

last: Szulwach

state: GA

address: 615 Michael Street, Whitehead Suite 301

department: Human Genetics

institute: Emory University

summary: DNA methylation dynamics influence brain function and are altered in neurological disorders. 5-hydroxymethylcytosine (5-hmC), a DNA base derived from 5-methylcytosine (5mC) accounts for ~40% of modified cytosine in brain, and has been implicated in DNA methylation-related plasticity. Here we map 5-hmC genome-wide across three ages in mouse hippocampus and cerebellum, allowing assessment of its stability and dynamic regulation during postnatal neurodevelopment through adulthood. We find developmentally programmed acquisition of 5-hmC in neuronal cells. Epigenomic localization of 5-hmC-regulated regions reveals stable and dynamically modified loci during neurodevelopment and aging. By profiling 5-hmC in human cerebellum we establish conserved genomic features of 5-hmC. Finally, we implicate 5-hmC in neurodevelopmental disease by finding that its levels are inversely correlated with methyl-CpG-binding protein 2 (Mecp2) dosage, a protein encoded by a gene in which mutations cause Rett Syndrome. These data point toward critical roles for 5-hmC-mediated epigenetic modification in neurodevelopment and diseases.

overall_design: Gene expression data derived from P7 and 6wk mouse cerebellum used for determining expression outcomes associated with dynamic alterations in 5-hydroxymethylcytosine

first: Peng

last: Jin


title: Distal airway stem cells yield alveoli in vitro and during lung regeneration following H1N1 influenza infection (colony)

first: Frank

last: McKeon

overall_design: 3 colonies fron control and H1N1 influenza treated lungs (12 dpi) ,each were picked for whole genome microarray analysis

first: Pooja

middle: A

last: Kumar

first: Yuanyu

last: Hu

first: Yusuke

last: Yamamoto

first: Neo

last: Hoe

first: Tay

middle: S

last: Wei

first: Dakai

last: Mu

first: Yan

last: Sun

first: Lim

last: Joo

first: Rania

last: Daghers

first: Elisabeth

last: Zielonka

first: De

last: Wang

first: Vincent

middle: T

last: Chow

first: Christopher

last: Crum

first: Wa

last: Xian


title: Transcriptional signatures of regulatory and toxic responses to benzo-[a]-pyrene exposure

city: Dresden

first: Jacob

last: Michaelson

address: Tatzberg 47/49

institute: BIOTEC, TU Dresden

summary: Small molecule ligands often have multiple effects on the transcriptional program of a cell: they trigger a receptor specific response and additional, indirect responses ("side effects"). Distinguishing those responses is important for understanding secondary effects of drugs and for elucidating molecular mechanisms of toxic chemicals. We addressed this problem by exposing cells to the environmental contaminant benzo-a-pyrene (B[a]P). B[a]P exposure activates the aryl hydrocarbon receptor (Ahr) and causes toxic stress resulting in transcriptional changes that are not regulated through Ahr. We sought to distinguish these two types of responses based on a time course of expression changes measured after B[a]P exposure. Using Random Forest machine learning we classified 81 direct Ahr targets and 1,308 genes regulated as secondary exposure effects. Subsequent weighted clustering gave further insight into the connection between expression pattern, mode of regulation, and biological function. Finally, the accuracy of the predictions was supported through extensive experimental validation. This study presents a strategy for distinguishing receptor dependent and secondary responses based on expression time courses.

overall_design: 36 samples were analyzed in total. Time-course data for four different time points, two different benzo(a)pyrene concentrations, including a vehicle control for each time points. Three biological replicates were generated for each treatment and time point.

middle: J

first: Saskia

last: Trump

first: Susanne

last: Rudzok

first: Carolin

last: Gräbsch

first: Danielle

last: Madureira

first: Franziska

last: Dautel

first: Juliane

last: Mai

first: Sabine

last: Attinger

first: Kristin

last: Schirmer

first: Martin

last: von Bergen

first: Irina

last: Lehmann

first: Andreas

last: Beyer


status: Public on Aug 01 2011

city: Dallas

first: Yujin

last: Hoshida

state: TX

address: 5323 Harry Hines Blvd

institute: University of Texas Southwestern Medical Center

summary:
Gene-expression profiles of liver and hepatocellular carcinoma induced by diethylnitrosamine (DEN) in KLF6 +/- and wild type KLF6 mice.
Inactivation of the KLF6 tumor suppressor is common in HCC due to hepatitis C virus (HCV), consistent with its anti-proliferative activity in HCC-derived cell lines and in hepatocytes of transgenic mice. We have evaluated the impact of KLF6 depletion on human HCC and experimental hepatocarcinogenesis. In patients with surgically resected HCC, those with significantly reduced tumor expression of KLF6 had a significantly decreased survival. We modeled this event in KLF6 +/- mice, which displayed significantly more tumorigenicity than KLF6 +/+ animals in response to the hepatic carcinogen DEN, associated with recapitulation of gene signatures in both surrounding tissue and tumors that are  associated with aggressive human HCCs.  In DNA  microarrays, mdm2 mRNA expression was increased in tumors from KLF6 +/- compared to KLF6 +/+ mice, which was validated by realtime qPCR and Western blot in both human HCC and DEN-induced murine tumors. Moreover, chromosomal immunoprecipitation and co-transfection assays established the P2 intronic promoter of mdm2 as a bona fide transcriptional target repressed by KLF6. Whereas KLF6 over-expression in HCC cell lines led to reduced MDM2 levels and increased p53 protein and transcriptional activity, reduction in KLF6 by siRNA led to increased MDM2 and reduced p53. Our findings indicate that KLF6 deficiency contributes significantly to the carcinogenic milieu in human and murine HCC, and uncover a novel tumor suppressor activity of KLF6 in HCC, by linking its transcriptional repression of MDM2 to stabilization of p53.

Keywords: Liver, Hepatocellular carcinoma, Expression array, Exon array, Affymetrix

overall_design: KLF6 +/- mice were previously generated by homologous recombination in which exon 2 was targeted using an 11-kb targeting construct, and replaced with neomycin/lacZ cassette. After selection with neomycin, the ES clones were injected into C57BL/6 mouse blastocysts and implanted into pseudo pregnant females; two lines of KLF6 +/- mice were generated from the resulting chimeric animals (Blood 107;1357, Oncogene 26;4428).  Whereas KLF6 -/- mice are embryonic lethal, KLF6 +/- animals had no demonstrable abnormalities in the absence of any stressor. Male KLF6 +/- mice were bred with wild type C57BL/6 to generate mixed litters of KLF6 +/- and KLF6 +/+ animals. Progeny were genotyped using PCR-amplified tail DNA, using primers as previously described (Oncogene 26;4428). Amplified fragments were separated on a 2.5% agarose gel, revealing bands of ~200 bp (wild type KLF6) and ~100 bp (Neo), as expected.  At 2 weeks of age, KLF6 +/+ and KLF6 +/- mice were injected intraperitoneally with either a single dose of diethyl nitrosamine (DEN), 5 µg/g body weight in 100 µl of saline, or vehicle alone. Vehicle and DEN-treated mice were maintained on standard chow, and then sacrificed 3, 6 or 9 months later.  At the time of sacrifice the animals were weighed, and blood and liver samples were harvested for analysis and tumor quantification.

first: Mirko

last: Tarocchi

first: Rebekka

last: Hannivoort

first: Ursula

middle: E

last: Lee

first: Johnny

last: Loke

first: Goutham

last: Narla

first: Augusto

last: Villanueva

first: Josep

middle: M

last: Llovet

first: Moshe

last: Oren

first: Scott

last: Friedman


title: Gene and exon expression change in cardiac hypertrophy with pressure overload

status: Public on May 01 2011

city: Seoul

first: Jiyeon

last: Park

address: 222, Banpo-daero

department: Catholic Center for Precision Medicine Research

country: South Korea

institute: The Catholic University of Korea

summary: Pathological cardiac hypertrophy was induced by pressure overload on the heart. We performed genome-wide exon array experiments with left ventricles of mice with 1 week and 4 week of transverse aortic constriction (TAC). The exon level analysis revealed widespread regulation of alternative splicing and alternative polyadenylation during hypertrophy.

overall_design: Exon and gene expression changes were examined in 1 week and 4 week TAC-operated hearts compared to sham-operated hearts. We used C57/BL6 wildtype mice, and their left ventricles were subject to surgery (each n=2).

first: Ji-Yeon

first: Wencheng

last: Li

first: Dinghai

last: Zheng

first: Yun

last: Zhao

first: Takahisa

last: Matsuda

first: Stephen

last: Vatner

first: Junichi

last: Sadoshima

first: Bin

last: Tian


title: Determination of the relative abundance of mRNAs in a polyribosome-associated pool

status: Public on Jul 21 2011

city: New York

first: Chaolin

last: Zhang

address: 1230 York Ave

department: Molecular Neuro-Oncology

institute: Rockefeller University

summary: Polyribosomal fractions derived from P25 mice were the starting material for IPs of the FMRP protein and associated mRNA.  Therefore we wanted to determine the relative abundance of all mRNAs in the starting pool for the IP as a denominator with which to compare the IPed material.

overall_design: [mRNA profiling]: We prepared polyribosomes on sucrose gradients in duplicate from 2 FVB WT mice, age P25, and purified RNA from polyribosomal fractions of each of the two gradients.

first: Robert

last: Darnell

first: Jennifer

first: John

last: Fak


title: Effect of ursolic acid on mouse skeletal muscle mRNA levels

status: Public on Jun 08 2011

city: Iowa City

first: Christopher

last: Adams

address: 540G EMRB, 200 Hawkins Drive

institute: University of Iowa

summary: The goal of these studies was to determine the effects of ursolic acid on skeletal muscle mRNA levels in wild-type mice

overall_design: C57BL/6 mice were allowed ad libitum access to standard chow or standard chow containing 0.27% ursolic acid for 5 weeks before gastrocnemius muscle RNA was harvested.  Each sample represents pooled gastrocnemius RNA from 2 mice.  mRNA levels in mice treated with ursolic acid were normalized to levels in untreated mice, which were set at 1.


title: SNP and Expression data from the Cancer Cell Line Encyclopedia (CCLE)

status: Public on Mar 20 2012

city: Cambridge

first: Nicolas

last: Stransky

address: 7 Cambridge center

institute: Broad Institute

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


title: Strain-dependent Dissociation of Airway Hyper-responsiveness from Inflammation in a House Dust Mite Model of Asthma

status: Public on Nov 30 2010

city: Bethesda

last: Pan

address: Rm 5228, Bldg 50, South Dr.

department: NHGRI

institute: NIH

summary:
Gene expression analysis of Der p 1-treated mouse lungs.

We developed a new mouse model of allergic airway disease employing the house dust mite allergen Der p 1.  This model produces qualitatively and quantitatively different effects in two commonly used inbred strains of mice, C57BL/6J and BALB/cJ, demonstrating that genetic background is an important determinant of response to Der p 1.  To identify the genes and pathways associated with inflammation and pathophysiology, we used microarrays and found genes that were shared by both strains or were distinct.  Among the latter, we identified three G-protein coupled receptors and a number of other genes and pathways whose expression patterns clearly distinguish the divergent physiologic responses of the two strains.  We conclude that genetic background is a strong determinant of the type and intensity of response to Der p 1, including the degree of airway hyper-responsiveness and/or inflammation.

overall_design: We analyzed whole lung RNAs from control (n=10-12) and Der p 1 treated (n=12-14) mice of two strains (BALB/cJ and C57BL/6J) using the Affymetrix Mouse Exon 1.0 ST platform. Array data was processed using Partek Genomics Suite software. Three techinical replicates were performed on a subset of samples.

first: Samir

middle: N

last: Kelada

first: Mark

last: Wilson

first: Kari

last: Kubalanza

first: Urraca

last: Tavarez

first: Danielle

last: Carpenter

first: Bhavesh

last: Borate

first: Greg

last: Whitehead

first: Shuichiro

last: Maruoka

first: David

last: Brass

first: Thomas

last: Wynn

last: Evans

last: Schwartz

first: Francis

last: Collins


title: MLL Fusion Proteins Preferentially Regulate a Small Set of Wild Type MLL Target Genes in the Leukemic Genome

status: Public on Apr 28 2011

city: Beijing

first: Jun

last: Wu

address: No.7 Beitucheng West Road

country: China

institute: Beijing Institue of Genomics, Chinese Academy of Science

type: Genome binding/occupancy profiling by genome tiling array

summary: MLL encodes a histone methyltransferase that is critical in maintaining gene expression during embryonic development and hematopoiesis. 11q23 translocations encode chimeric MLL fusions that act as potent drivers of acute leukemia. However, it remains unclear what portion of the leukemic genome is under the direct control of the MLL fusion protein. By comparing patient-derived leukemic cell lines, we find that MLL fusion-bound genes are a small subset of that recognized by wild-type MLL. In an inducible MLL-ENL cellular model, binding of the MLL fusion protein and changes in H3K79 methylation are limited to a specific portion of the genome, whereas wild-type MLL distributes to a much larger set of gene loci. Surprisingly, among 223 MLL fusion-bound genes, only 12 demonstrate a significant increase in mRNA expression upon induction of the fusion protein. In addition to Hoxa9 and Meis1, this includes Eya1 and Six1 which comprise a heterodimeric transcription factor important in several developmental pathways. We show that Eya1 has the capacity to immortalize hematopoietic progenitor cells in vitro and collaborates with Six1 in hematopoietic transformation assays. Altogether, our data suggest that MLL fusions contribute to the development of acute leukemia through direct activation of a small set of target genes.

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus

overall_design: We explored an inducible MLL-ENL cellular model, which was obtained from Dr. Robert Slany (University Erlangen, Germany). We wished to examine the differential expressed genes that are bound by MLL wild type (No 4-OHT) and fusion (4-OHT) proteins, combinding the ChIP-chip data to explore the potential MLL fusion-regulated genes.

first: Qian-fei

last: Wang

first: George

first: Shuangli

last: Mi

first: Fuhong

last: He

first: Jingfang

last: Dong

first: Roger

last: Luo

first: Ryan

last: Mattison

first: Joseph

last: Kaberlein

first: Qianben

first: Shyam

last: Prabhakar

first: Hongkai

last: Ji

first: Michael

last: Thirman


title: Suppression of Lung Adenocarcinoma Progression by Nkx2-1

status: Public on Jan 27 2011

first: Charles

middle: Arthur

last: Whittaker

institute: Koch Institute

summary: Despite the high prevalence and poor outcome of patients with metastatic lung cancer, the mechanisms of tumour progression and metastasis remain largely uncharacterized. We modelled human lung adenocarcinoma, which frequently harbours activating point mutations in KRAS1 and inactivation of the p53-pathway2, using conditional alleles in mice3-5. Lentiviral-mediated somatic activation of oncogenic Kras and deletion of p53 in the lung epithelial cells of KrasLSL-G12D/+;p53flox/flox  mice initiates lung adenocarcinoma development4.  Although tumours are initiated synchronously by defined genetic alterations, only a subset become malignant, suggesting that disease progression requires additional alterations. Identification of the lentiviral integration sites allowed us to distinguish metastatic from non-metastatic tumours and determine the gene expression alterations that distinguish these tumour types. Cross-species analysis identified the NK-2 related homeobox transcription factor Nkx2-1 (Ttf-1/Titf1) as a candidate suppressor of malignant progression. In this mouse model, Nkx2-1-negativity is pathognomonic of high-grade poorly differentiated tumours. Gain- and loss-of-function experiments in cells derived from metastatic and non-metastatic tumours demonstrated that Nkx2-1 controls tumour differentiation and limits metastatic potential in vivo. Interrogation of Nkx2-1 regulated genes, analysis of tumours at defined developmental stages, and functional complementation experiments indicate that Nkx2-1 constrains tumours in part by repressing the embryonically-restricted chromatin regulator Hmga2. While focal amplification of NKX2-1 in a fraction of human lung adenocarcinomas has focused attention on its oncogenic function6-9, our data specifically link Nkx2-1 downregulation to loss of differentiation, enhanced tumour seeding ability, and increased metastatic proclivity. Thus, the oncogenic and suppressive functions of Nkx2-1 in the same tumour type substantiate its role as a dual function lineage factor.

overall_design: 23 cell lines derived from primary tumor or metastasis. 6 samples analyzed to determine the effect of Nkx2-1 knockdown on gene expression

first: Monte

last: Winslow

first: Talya

last: Dayton

first: Roel

middle: G

last: Verhaak

first: Caroline

last: Kim-Kiselak

first: Eric

last: Snyder

last: Feldser

first: Diana

last: Hubbard

first: Michel

last: DuPage

first: Sebastian

last: Hoersch

first: Stephanie

last: Yoon

first: Denise

last: Crowley

first: Roderick

last: Bronson

first: Derek

middle: Y

last: Chiang

first: Matthew

last: Meyerson

first: Tyler

last: Jacks


title: Sall3 controls cone photoreceptor and horizontal cell differentiation

status: Public on Sep 10 2011

first: Seth

last: Blackshaw

address: 733 N. Broadway, Suite 351

department: Neuroscience

institute: The Johns Hopkins University

summary: Transcription factors have been implicated in the specification and differentiation of all cells in the mammalian retina with several transcription factors controlling the development of multiple neuronal subclasses.  Horizontal cells and cone photoreceptors share a particularly intimate functional relationship but have been previously thought to develop through separate and distinct intrinsic molecular processes.  We demonstrate that the zinc finger transcription factor Sall3 regulates development of both S-cone photoreceptors and horizontal cells.  Our data shows that loss of function of Sall3 down-regulates the horizontal cell specific transcription factor Lhx1 and subsequently causes ectopic formation of horizontal-like wide-field amacrine cells partially phenocopying Lhx1-/- mice.  Additionally, horizontal cells which laminate appropriately in Sall3 knockout mice show abnormal horizontal cell gene expression and failures in dendritic arborization.  Over-expression of Sall3 also partially re-specifies cells to a horizontal-like wide-field amacrine fate.  Intriguingly, Sall3 loss of function experiments also generated a massive reduction in the number of S-cone photoreceptors with remaining S-cones showing deficiencies in S-cone gene expression and morphology.  Conversely, over-expression of Sall3 resulted in the ectopic expression of the S-cone specific genes S-opsin (Sop) and cone arrestin (Arr3) in electroporated cells.  Our studies reveal that Sall3 regulates aspects of horizontal cell development in two ways: first, by maintaining Lhx1 expression, and second, by directly regulating expression of horizontal cell specific genes.  We also show that Sall3 is an essential regulator of S-cone development in the mammalian retina and a potent activator of Sop and Arr3.

overall_design: Sall3 wild-type and knockout retinas used for explant cultures were extracted by microdissection at P0 in sterile PBS. Four cuts were made using micro-dissection scissors and the retinas were transferred to Nucleopore Track-Etch membrane filters (Whatman) and the tissue flattened out evenly. Filters were then floated on DMEM/F12, 10% FBS, 1X penicillin/streptomycin in 12 well plates and incubated at 37oC, 5% CO2 for 7 days.  Three retinas (Sall3 knockout or wild-type) were pooled and RNA extracted using the Qiagen RNeasy kit.  This was performed in triplicate for both wild-type and Sall3 knockouts retinas.  A total of three replicates of Sall3 knockout and Sall3 wild-type RNA were analysed (six total samples).

first: Jimmy

last: de Melo

first: Guang-Hua

last: Peng

first: Shiming

last: Chen


title: Alternative splicing is frequent during early embryonic development in mouse

status: Public on Jun 29 2010

city: Montreal

first: Timothee

last: Revil

state: Quebec

address: 4060 Ste-Catherine W PT420

institute: McGill University

summary:
Background
Alternative splicing is known to increase the complexity of mammalian transcriptomes since nearly all mammalian genes express multiple pre-mRNA isoforms. However, our knowledge of the extent and function of alternative splicing in early embryonic development is based mainly on a few isolated examples. High throughput technologies now allow us to study genome-wide alternative splicing during mouse development.

Results
A genome-wide analysis of alternative isoform expression in embryonic day 8.5, 9.5 and 11.5 mouse embryos and placenta was carried out using a splicing-sensitive exon microarray. We show that alternative splicing and isoform expression is frequent across developmental stages and tissues, and is comparable in frequency to the variation in whole-transcript expression. The genes that are alternatively spliced across our samples are disproportionately involved in important developmental processes. Finally, we find that a number of RNA binding proteins, including putative splicing factors, are differentially expressed and spliced across our samples suggesting that such proteins may be involved in regulating tissue and temporal variation in isoform expression. Using an example of a well characterized splicing factor, Fox2, we demonstrate that changes in Fox2 expression levels can be used to predict changes in inclusion levels of alternative exons that are flanked by Fox2 binding sites.

Conclusions
We propose that alternative splicing is an important developmental regulatory mechanism. We further propose that gene expression should routinely be monitored at both the whole transcript and the isoform level in developmental studies.

overall_design: 25 samples were analyzed. Developmental stages e8.5, e9.5 and e11.5 (embryos from all 3, placenta for only e9.5 and e11.5). 5 biological replicates for each.

first: Timothée

first: Daniel

last: Gaffney

first: Christel

last: Dias

first: Jacek

last: Majewski

first: Loydie

last: Jerome-Majewska


title: Expression data from ERK1/2 null endothelial cells

status: Public on Jul 01 2010

city: Columbus

first: Ruchika

last: Srinivasan

address: Rm 840 W12th avenue

institute: The Ohio State University

summary: Angiogenesis is a complex process orchestrated by both growth factors and cell adhesion to the extracellular matrix and is initiated by focal degradation of the vascular basement membrane with subsequent migration and proliferation of endothelial cells (EC).  The Ras/Raf/MEK/ERK pathway is critical for EC function during angiogensis.   Although in vitro studies implicate ERK1 and ERK2 in EC survival, their precise role in EC function in vivo remains poorly defined.  Cre/loxP technology was used to inactivate Erk1 and Erk2 in EC during murine development, resulting in embryonic lethality due to a drastic reduction in angiogenesis.  The angiogenic defect was linked to diminished EC proliferation and migration, but not to increased cell apoptosis.  Expression of key cell cycle regulators was diminished in the double knockout cells.  In addition, both Paxillin and Focal Adhesion Kinase were expressed at lower levels and failed to correctly localize to the cell membrane in EC lacking Erk1 and Erk2, leading to defects in the organization of the cytoskeleton and in cell motility.  The results demonstrate that ERK1 and ERK2 coordinate cell proliferation and migration during angiogenesis.

overall_design: Lentivirus infected cells to generate ERK1/2 WT and ERK1/2 DKO endothelial cells were cultured, RNA was extracted and Affymetrix gene expression arrays were performed.

first: Michael

middle: C

last: Ostrowski


title: Progressive lengthening of 3' untranslated regions of mRNAs by alternative polyadenylation during C2C12 differentiation

status: Public on Aug 31 2010

city: Chicago

first: Zhe

last: Ji

state: ILLINOIS

address: 303 E Superior St, Lurie 6-107

institute: Northwestern University

summary: The 3' untranslated regions (3' UTRs) of mRNAs contain cis-acting elements for posttranscriptional regulation of gene expression. Here, we report that mouse genes tend to express mRNAs with longer 3' UTRs as embryonic development progresses. This global regulation is controlled by alternative polyadenylation and coordinates with initiation of organogenesis and aspects of embryonic development, including morphogenesis, differentiation, and proliferation. Using myogenesis of C2C12 myoblast cells as a model, we recapitulated this process in vitro and found that 3' UTR lengthening is likely caused by weakening of mRNA polyadenylation activity. Because alternative 3' UTR sequences are typically longer and have higher AU content than constitutive ones, our results suggest that lengthening of 3' UTR can significantly augment posttranscriptional control of gene expression during embryonic development, such as microRNA-mediated regulation.

overall_design: Two biological replicates of C2C12 growth and differentiation conditions, repesctively

first: Bin

last: Tian


title: Exon-level transcriptome profiling in murine breast cancer reveals splicing changes specific to tumors with different metastatic abilities

status: Public on May 29 2010

city: Montréal

first: Amandine

last: Bemmo

state: Québec

address: 740, Dr Penfield Avenue

summary:
BACKGROUND: Breast cancer is the second most frequent type of cancer affecting women. We are increasingly aware that changes in mRNA splicing are associated with various characteristics of cancer. The most deadly aspect of cancer is metastasis, the process by which cancer spreads from the primary tumor to distant organs. However, little is known specifically about the involvement of alternative splicing in the formation of macroscopic metastases. Our study investigates transcript isoform changes that characterize tumors of different abilities to form growing metastases.

METHODS AND FINDINGS: To identify alternative splicing events (ASEs) that are associated with the fully metastatic phenotype in breast cancer, we used Affymetrix Exon Microarrays to profile mRNA isoform variations genome-wide in weakly metastatic (168FARN and 4T07) and highly metastatic (4T1) mammary carcinomas. Statistical analysis identified significant expression changes in 7606 out of 155,994 (4%) exons and in 1725 out of 189,460 (1%) intronic regions, which affect 2623 out of 16,654 (16%) genes. These changes correspond to putative alternative isoforms-several of which are novel-that are differentially expressed between tumors of varying metastatic phenotypes. Gene pathway analysis showed that 1224 of genes expressing alternative isoforms were involved in cell growth, cell interactions, cell proliferation, cell migration and cell death and have been previously linked to cancers and genetic disorders. We chose ten predicted splice variants for RT-PCR validation, eight of which were successfully confirmed (MED24, MFI2, SRRT, CD44, CLK1 and HNRNPH1). These include three novel intron retentions in CD44, a gene in which isoform variations have been previously associated with the metastasis of several cancers.

CONCLUSION: Our findings reveal that various genes are differently spliced and/or expressed in association with the metastatic phenotype of tumor cells. Identification of metastasis-specific isoforms may contribute to the development of improved breast cancer stage identification and targeted therapies.

overall_design: We used RNA tumor tissues derived from three murine mammary carcinoma cell lines (168FARN, 4T07 and 4T1); four biological replicates of 168FARN, four biological replicates of 4T07, and four biological replicates of 4T1 were hybridized independently at McGill university site.

first: Cristel

first: April

last: Rose

first: Caterina

last: Russo

first: Peter

last: Siegel


title: Gene expression profiles of murine granule neuron precursors and medulloblastoma

status: Public on Jun 03 2010

city: Stanford

first: Eunice

last: Lee

address: 318 Campus Drive

department: Developmental Biology

institute: Stanford University

summary:
Sonic hedgehog (Shh) signals via Gli transcription factors to stimulate proliferation of granule neuron precursor cells (GNPs) in the cerebellum. Deregulation of Shh target genes often results in unrestrained GNP proliferation and eventually medulloblastoma (MB), the most common pediatric brain malignancy.  Gene expression profiling was coupled with transcription factor binding location analysis to determine the Gli1-controlled transcriptional regulatory networks in GNPs and medulloblastoma cells.  We detected significant overlap, as well as differences, in the Gli1-controlled transcriptional regulatory networks in GNPs and MBs.
We determined the presence of gene expression in each dataset.  There were 9260 genes expressed in Gli1-FLAG GNPs and 9185 genes expressed in Gli1-FLAG;Ptc+/- tumors; 8691 of which are in common.  The large overlap is consistent with the cellular origin of these tumors.  When the genes detectably expressed were intersected with our binding data, there were only 132 putative Gli1 target genes shared by both cell populations.  Due to the heightened activation of the Hh pathway in tumors relative to GNPs, we further deduced direct Gli1 target genes exclusive to tumors by determining significantly induced genes in tumors versus in Ptc+/- GNPs.  We identified at least 116 tumor-specific Gli1 target genes.  These data suggest that tumor formation is accompanied by a tremendous change in the battery of Gli target genes.

overall_design: Presence of gene expression was determined for all samples: Gli1-FLAG-expressing GNPs, Ptc+/- GNPs, and Gli1-FLAG;Ptc+/-medulloblastomas.  These datasets were intersected with chIP-chip data to determine potential direct Gli1 target genes.  Differential gene expression was determined by comparing expression profiles from medulloblastoma tumors to those from Ptc+/- GNPs.

first: Matthew

last: Scott

first: Zhengqing

last: Ouyang

first: Wing

middle: H

last: Wong


title: Expression data throughout reprogramming of MEF to iPS using a Dox-inducible promoter

city: Toronto

first: Payman

last: Samavarchi-Tehrani

state: Ontario

address: 600 University Ave

institute: Samuel Lunenfeld Research Institute

summary:
6C secondary MEFs were treated with Dox in mES media to turn on the Oct4, Klf4, cMyc, Sox2. Total RNA was extracted at day 0 (no Dox), day2, 5, 8, 11, 16 and 21 (with Dox) and day 30 (Dox-independent secondary iPS).
RNA from Parental MEFs and Primary-iPS cells were also extracted for reference. 1B secondary MEFs were Dox treated for 5-days followed by RNA extraction. Subsequently, a culture removed of Dox treatment for an additional 5days was also analyzed.

overall_design: Samples from 6C-clones were smoothed using a polynomial fitting. Subsequently, phase analysis was carried out based on point of change greater than 2-fold.

first: Azadeh

last: Golipour

first: Laurent

last: David

first: Knut

last: Woltjen

first: Andras

last: Nagy

first: Jeffrey

last: Wrana


title: Gli1 regulatory networks in granule neuron precursor and medulloblastoma cells

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

overall_design: Refer to individual Series


title: Determining the mechanism of ATF4-mediated myofiber atrophy

status: Public on Jan 30 2010

first: Christopher

last: Adams

state: IA


title: Effect of fasting on mouse skeletal muscle mRNA levels

summary: Fasting increases the level of skeletal muscle ATF4 mRNA, which promotes skeletal myofiber atrophy.   To begin to determine the mechanism of ATF4-mediated myofiber atrophy, we compared the effects of fasting and ATF4 overexpression on global skeletal muscle mRNA expression in C57BL/6 mice.

overall_design: These data are from experiments to determine the effect of fasting.  Mice were allowed ad libitum access to food or fasted for 24 h before TA muscle RNA was harvested.  RNA from 3 mice per group was pooled, and then subjected to exon expression array analysis.  mRNA levels under fasting conditions were normalized to levels under nonfasting conditions, which were set at 1.  These experiments were performed 4 times to generate the final data.

first: Ebert

first: Adams

last: Christopher


title: Timecourse of interferon-beta stimulation of mouse bone marrow derived macrophages

status: Public on Feb 19 2010

city: Roslin

first: Sobia

last: Raza

state: Midlothian

address: Roslin Biocentre

department: Roslin Institute

institute: University of Edinburgh

summary:
Transcriptomic analysis of the temporal changes induced in mouse bone marrow derived macrophages (BMDMs) by the cytokine Interferon-beta over a timecourse of 0 to 24 hours of treatment.
We set out to study the transcriptional events in mouse macrophages over time following stimulation with Interferon-beta. Mouse bone marrow derived macrophages were stimulated for 1, 2, 4, 8 and 24 hours with 10U/mL mouse interferon-beta or left untreated.

overall_design: Mouse BMDMs were stimulated with 10 U/ml recombinant mouse interferon-beta (Ifn-β) and harvested 1, 2, 4, 8 and 24 h following treatment or collected pre-treatment (0 h). RNA from two biological replicates per time-point were processed using the Affymetrix  WT cDNA Synthesis and WT Terminal Labeling Kit and the Mouse Exon 1.0 ST Array platform. Array data was processed using the Affymetrix Expression Console Software and analysed used the Bioconductor package with R and the network-based visualisation tool BioLayout Express3D.

first: Tom

last: Freeman


title: Activation of ER-alpha network in MMTV-Wnt/ILK mammary tumors

status: Public on Jun 16 2010

city: Vancouver

first: Steven

last: McKinney

state: BC

address: 675 West 10th Ave

department: Molecular Oncology

institute: British Columbia Cancer Agency

summary:
A transgenic mouse model, MMTV-Wnt/ILK, with mammary specific expression of both Wnt-1 and ILK, was generated by crossing the two mouse lines MMTV-Wnt-1 and MMTV-ILK.
Affymetrix Mouse Exon chips were hybridized with material from four independent mammary tumors from each MMTV-Wnt-1 and MMTV-Wnt/ILK transgenic model, in order to identify possible signaling differences involved during increased tumor incidence.

overall_design: One-way ANOVA:  MMTV-Wnt vs. MMTV-Wnt/ILK

first: Arusha

last: Oloumi

first: Howard

last: Tearle

first: Mykola

last: Maydan

first: William

last: Muller

first: Samuel

last: Aparicio

first: Shoukat

last: Dedhar


title: Angiotensin II induced aneurysms in male ApoE mice

status: Public on Aug 26 2009

city: Townsville

first: Catherine

last: Rush

state: Queensland

address: Douglas Campus

department: Medicine

country: Australia

institute: James Cook University

summary:
In this study we used microarrays to examine relative genes expression within the aorta of ApoE-/- infused with angiotensin II in relation to aneurysm formation. Infusion of angiotensin II induces aortic dilatation particularly of the suprarenal aorta in ApoE-/- mice. Based on studies carried out in our and other laboratories the response to angiotensin II is variable, with some mice developing large aneurysms but other animals appearing resistant to aneurysm formation with aortic diameters similar to that of saline controls.     We compared RNA expression from whole aortas of 17 week old male ApoE-/- mice exposed to angiotensin II (1.44 µg/kg/min) for 4 weeks where there was clear evidence of aortic aneurysm formation (n=5) with that of mice failing to develop aneurysms (n=7) and those exposed to saline infusion (n=6). AAA was defined as diameter of suprarenal aorta greated than 1.5mm measured on photographs of aortas at necroscopy.

Keywords: Disease state analysis

overall_design: 18 samples analysed, AAA (n=5), no AAA (n=7), saline (n=6). AAA - abdominal aortic aneurysm

first: Jonathan

last: Golledge

first: Moses

last: Nyara


title: Genomic profiling of ductal breast carcinoma to identify high risk small node negative breast cancer patients

status: Public on Nov 25 2009

city: PARIS

first: Gaelle

last: PIERRON

address: 26, rue d'ULM

institute: INSTITUT CURIE

summary: Abstract:   Purpose: To identify a DNA signature to predict metastasis of small node-negative breast carcinoma  Experimental Design: The authors used Comparative Genomic Hybridization (CGH) array to analyze 168 pT1T2pN0 invasive ductal carcinoma patients with either good (no event 5 years after diagnosis: 111 patients) or poor (57 patients with early onset metastasis) outcome. A CGH classifier, identifying low and high-risk groups of metastatic recurrence, was established in a training set of 78 patients. This classifier was based on both genomic regions with statistically different alterations between the two groups of clinical outcome and the number of alterations. It was then tested on a validation set of 90 patients and compared to clinicopathological parameters.  Results: The genomic status of regions located on chromosomes 2p22.2, 3p23 and 8q21-24 and the number of segmental alterations were defined in the training set to classify tumors into low or high-risk groups. In the validation set, this CGH classifier produced a highly significant odds ratio of 10.39 (95%CI: 3.75-28.78, p=6.63×10-6, Wald test) in univariate analysis with a sensitivity of 66%, a specificity of 84% and an accuracy rate of 78%. The 5-year metastasis-free survival analysis showed a highly significant difference between the two predicted groups (Hazard Ratio=5.7, p=1.82×10-7, log-rank test). Together with estrogen receptor and grade, this CGH classifier provided significant prognostic information in multivariate analysis.   Conclusions: In addition to classical parameters, this DNA signature may constitute an accurate tool to identify patients with T1T2N0 luminal tumors, who may benefit from adjuvant treatments.

overall_design: Each of the 168 tumoral genomic DNA was hybridized against the same non tumoral DNA reference following identical protocol

first: Eleonore

last: Gravier

last: Pierron

first: Anne

last: Vincent-Salomon

first: Nadege

last: Gruel

first: Virginie

last: Raynal

first: Alexia

last: Savignoni

first: Yann

last: De Rycke

first: Jean-Yves

last: Pierga

first: Carlo

last: Lucchesi

first: Fabien

last: Reyal

first: Alain

last: Fourquet

first: Sergio

last: Roman-Roman

first: François

last: Radvanyi

first: Xavier

last: Sastre-Garau

first: Bernard

last: Asselain

first: Olivier

last: Delattre


title: Effect of ATF4 overexpression on mouse skeletal muscle mRNA levels

first: Christopher

last: Adams

overall_design: These data are from experiments to determine the effect of ATF4 overexpression.  On day 0, the tibialis anterior (TA) muscles of male C57BL/6 mice were transfected via electroporation as follows: the left TA muscle was transfected with 25 μg empty pcDNA3 vector, and the right TA muscle was transfected with 25 μg pCMV-ATF4-FLAG.  On day 11, TA muscle RNA was harvested, and then subjected to exon expression array analysis.  mRNA levels in the presence of ATF4 (right TA) were normalized to levels in the absence of ATF4 (left TA), which were set at 1. These experiments were performed 4 times to generate the final data.

first: Ebert

last: Scott

first: Adams

last: Christopher