title: Gene expression profiling of PBL in response to ionising radiation and modeled microgravity

status: Public on Apr 10 2012

city: Padova

first: Gerolamo

last: Lanfranchi

address: Via U. Bassi, 58/B

department: CRIBI - Biotechnology Center and Biology Department

institute: University of Padova

summary:
BACKGROUND:
Ionizing radiation (IR) can be extremely harmful for human cells since an improper DNA-damage response (DDR) to IR can contribute to carcinogenesis initiation. Perturbations in DDR pathway can originate from alteration in the functionality of the microRNA-mediated gene regulation, being microRNAs (miRNAs) small noncoding RNA that act as post-transcriptional regulators of gene expression. In this study we gained insight into the role of miRNAs in the regulation of DDR to IR under microgravity, a condition of weightlessness experienced by astronauts during space missions, which could have a synergistic action on cells, increasing the risk of radiation exposure.
METHODOLOGY/PRINCIPAL FINDINGS:
We analyzed miRNA expression profile of human peripheral blood lymphocytes (PBL) incubated for 4 and 24 h in normal gravity (1 g) and in modeled microgravity (MMG) during the repair time after irradiation with 0.2 and 2Gy of γ-rays. Our results show that MMG alters miRNA expression signature of irradiated PBL by decreasing the number of radio-responsive miRNAs. Moreover, let-7i*, miR-7, miR-7-1*, miR-27a, miR-144, miR-200a, miR-598, miR-650 are deregulated by the combined action of radiation and MMG. Integrated analyses of miRNA and mRNA expression profiles, carried out on PBL of the same donors, identified significant miRNA-mRNA anti-correlations of DDR pathway. Gene Ontology analysis reports that the biological category of "Response to DNA damage" is enriched when PBL are incubated in 1 g but not in MMG. Moreover, some anti-correlated genes of p53-pathway show a different expression level between 1 g and MMG. Functional validation assays using luciferase reporter constructs confirmed miRNA-mRNA interactions derived from target prediction analyses.
CONCLUSIONS/SIGNIFICANCE:
On the whole, by integrating the transcriptome and microRNome, we provide evidence that modeled microgravity can affects the DNA-damage response to IR in human PBL.

overall_design: Gene expression signature was defined in PBL irradiated with gamma-rays (2.0 Gy) and incubated in modeled microgravity (mmg) and in parallel ground conditions (1g) for 24h. Five independent experiments were performed for each donor to address wich mRNAs were regulated on IR stress. The level of each transcript was represented as Log2.

first: Cristina

last: Girardi

first: Cristiano

last: De Pittà

first: Silvia

last: Casara

first: Gabriele

last: Sales

first: Lucia

last: Celotti

first: Maddalena

last: Mognato


title: Direct conversion of fibroblasts into stably expandable neural stem cells

status: Public on Apr 12 2012

city: Bonn

first: Frank

last: Edenhofer

address: Sigmund-Freud Str. 25

department: Institute of Reconstructive Neurobiology

country: Germany

institute: University of Bonn - Medical Center

summary: Recent advances have suggested that direct induction of neural stem cells could provide an alternative to derivation from somatic tissues or pluripotent cells. Here we show direct derivation of stably expandable NS cells from mouse fibroblasts through a curtailed version of reprogramming to pluripotency. By constitutively inducing Sox2, Klf4, and c-Myc while strictly limiting Oct4 activity to the initial phase of reprogramming, we generated neurosphere-like colonies that could be expanded for more than 50 passages and do not depend on sustained expression of the reprogramming factors. These induced NS (iNS) cells uniformly display morphological and molecular features of NS cells such as the expression of Nestin, Pax6, and Olig2 and have a similar genome-wide transcriptional profile to brain-derived NSCs. iNS cells can differentiate into neurons, astrocytes and oligodendrocytes in vitro and in vivo. Our results demonstrate that functional neural stem cells can be generated from somatic cells by factor-driven induction.

overall_design: mRNA extracted from Murine Embryonic Fibroblasts (MEF), murine Embryonic Stem Cell (ES), murine Neuronal Stem Cell (NS) and three murine induces Neuronal Stem Cell clones 2, 3 and 5 (iNS2, iNS3, iNS5) has been hybridized on Illumina MouseWG6 V2 arrays for genome wide expression analysis. Samples were run at least as triple, MEF, iNS3, iNS5 as quadruple technical replicates. Differential gene expression analysis has been performed on the grouped expression data with the Murine Embryonic Fibroblasts group as the reference.

first: Marc

last: Thier

first: Philipp

last: Woersdoerfer

first: Yenal

middle: B

last: Lakes

first: Raphaela

last: Gorris

first: Stefan

last: Herms

first: Thoralf

last: Opitz

first: Dominic

last: Seiferling

first: Tamara

last: Quandel

first: Per

last: Hoffmann

first: Markus

middle: M

last: Noethen

first: Oliver

last: Bruestle


title: Whole-genome expression analysis of Rnaseh2b(E202X/E202X) embryos

status: Public on Apr 20 2012

city: Edinburgh

first: Rachel

middle: Elizabeth

last: Rigby

address: IGMM, Western General Hospital, Crewe Road

department: MRC Human Genetics Unit

country: United Kingdom

institute: University of Edinburgh

summary: The transcriptome of E9.5 embryos lacking functional RNase H2 (Rnaseh2bE202X/E202X) was compared to age-matched wild type controls to investigate the molecular basis of growth arrest in Rnaseh2-/- mice.

overall_design: Total RNA extracted from three E9.5 embryos of Rnaseh2+/+ and Rnaseh2E202X/E202X were compared

middle: E

first: Kirstie

middle: A

last: Lawson

first: Graeme

last: Grimes

first: Andrew

middle: P

last: Jackson


title: Gene and microRNA expression in pulmonary tuberculosis and sarcoidosis

status: Public on Apr 14 2012

city: Berlin

first: Jeroen

last: Maertzdorf

address: Chariteplatz 1

institute: MPIIB

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

summary: Common gene and microRNA expression patterns in TB and sarcoidosis

overall_design: Gene and microRNA expression analysis of whole blood RNA from tuberculosis and sarcoidosis patients and healthy controls

first: January

last: Weiner

first: Hans

middle: J

last: Mollenkopf

middle: H

last: Kaufmann


title: Expression data from human induced pluripotent stem cell derived NSCs and striatal-like cells

status: Public on Apr 25 2012

city: Irvine

first: Leslie

last: Thompson

state: CA

address: Biological Sciences III

country: USA

institute: University of California, Irvine

summary: Huntington's disease (HD) is an inherited neurodegenerative disorder caused by an expanded stretch of CAG trinucleotide repeats that results in neuronal dysfunction and death. We made induced pluripotent stem cell (iPSC) lines from HD patients and controls. Though no obvious effects of the CAG expansion on reprogramming or subsequent neural stem cell (NSC) production were seen, HD-NSCs showed CAG expansion-associated gene expression patterns and, upon differentiation, changes in electrophysiology, metabolism, cell adhesion, and ultimately an increased risk of cell death for both medium and longer CAG repeat expansions, with some deficits greater in cells from longer repeat HD NSCs. The HD180 lines were more vulnerable than control lines to cellular stressors and BDNF withdrawal using a range of assays across consortium laboratories. This HD iPSC collection represents a unique and well-characterized resource to elucidate disease mechanisms in HD and provides a novel human stem cell platform for screening new candidate therapeutics.

overall_design:
8 NSC samples (5 HD, 3 control), of which 3 were run as replicates (2HD, 1 control), and 5 striatal-like samples (3 HD, 2 control)
Contributor:  The HD iPS consortium


title: Prolonged halting of gene expression in early G1 arrest by inhibition of CDK4/CDK6 reprograms myeloma cells for cytotoxic killing

status: Public on Apr 07 2012

city: New York

first: Xiangao

last: Huang

state: New York

address: 1300 York Avenue

department: Pathology and Laboratory Medicine

institute: Weill Cornell Medical College

summary: By selective and reversible inhibition of CDK4/CDK6, we have developed a strategy to both inhibit proliferation and enhance cytotoxic killing of cancer cells.  Induction of prolonged early-G1 arrest (pG1) by CDK4/CDK6 inhibition halts gene expression in early-G1 and prevents expression of genes programmed for other cell cycle phases.  S-phase synchronization upon removal of the early-G1 block (pG1-S) fails to completely restore scheduled gene expression.  Consequently, coordinate loss of IRF4 and gain of Bim and Noxa expression sensitize myeloma tumor cells to bortezomib-induced apoptosis in pG1 and more profoundly in pG1-S in vitro.  Induction of pG1 and pG1-S by CDK4/CDK6 inhibition augments tumor-specific bortezomib killing in myeloma xenografts.  Inhibition of CDK4/CDK6 in combination therapy thus represents a novel mechanism-based cancer therapy.

overall_design: PD 0332991 (PD) is the only known specific and reversible CDK4/CDK6 inhibitor. Gene expression was measured in myeloma MM1.S cells treated with PD (0.25 uM) in triplicate for 12, 24 or 36 h, or in cells released from G1, induced by 24hPD, for 4 or 18 h.

first: Maurizio

last: Di Liberto

first: Jamie

last: Bretz

first: Selina

last: Chen-Kiang


title: Prostasphere-forming cells of human prostate cancer cell LNCaP: Control vs. Hormone treated

status: Public on Apr 24 2012

city: Frederick

first: Ji

last: Zheng

state: MD

address: 1050 Boyles St.

institute: National Cancer Institute

summary: Transcriptional profiling of LNCaP prostasphere-forming cells,  comparing control untreated sphere-forming cells with hormone treated sphere-forming cells. Both estrogen (estradiol) and androgen (R1881) promote the sphere formation of human prostate cancer cell LNCaP. Goal was to determine the effects of hormones on global gene expression of LNCaP sphere-forming cells.

overall_design: Five samples were analyzed. Control (ethanol 1hr), estradiol 1 hour, estradiol 24 hour, R1881 1 hour, R1881 24 hour.

first: Elaine

last: Hurt


title: Gene expression profiles of uterine leiomyosarcoma (ULMS)

status: Public on Apr 27 2012

city: Houston

first: Chad

last: Creighton

state: TX

address: One Baylor Plaza, Mail Stop: BCM305

department: Biostatistics, Ducan Cancer Center

institute: Baylor College of Medicine

summary: Uterine leiomyosarcoma (ULMS) is a poorly understood gynecologic cancer with few effective treatments. This study explores molecular events involved in ULMS with the goal of identifying strategies.

overall_design: Genome-wide transcriptional profiling were used to compare clinically well-annotated specimens of myometrium, leiomyoma and leiomyosarcoma.

first: Anderson

last: Matthew

first: Shan

last: Weiwei


title: Genome-wide analysis of transcription factor FoxO1-responsive gene expression in the ventromedial hypothalamus

status: Public on Mar 31 2012

city: Dallas

first: Ki Woo

last: Kim

state: Texas

address: 5323 Harry Hines Blvd.

department: Internal Medicine and Pharmacology

institute: UT-Southwestern

summary:
Analysis of gene expression regulated by FoxO1 in the ventromedial hypothalamus (VMH) of wildtype and knockout mice. Results provide important information of gene expression in the VMH.

The transcription factor FoxO1 contributes to leptin and insulin action, including cells in the brain. However, the neurons mediating these effects and the identity of the molecular targets through which FoxO1 exerts metabolic actions remains to be defined.

overall_design: For the gene expression profiling, total RNA was obtained from the VMH of WT and VMH-specific FoxO1 KO mice using Qiagen RNeasy Lipid Tissue Mini Kit (Qiagen Sciences, Maryland) and Phase Lock Gel (5 Prime Inc., Gaithersburg, MD). To make sure reproducibility and biological significance, triple hybridizations were performed for each genotype with the RNA from three independent VMH samples, each sample contains RNA from three animals (biological replicates). Genomics and Microarray Core Facility at UT-Southwestern (http://microarray.swmed.edu/) checked RNA quality with Bioanalyzer Chip and processed the samples for hybridization with Illumina Mouse-6 V2 BeadChip (Illumina Inc., San Diego, CA).  We used Partek Genomics Suite 6.5  (Partek Inc., St Louis, MO) and Ingenuity Pathway Analysis (Ingenuity Systems, Inc., Redwood City, CA) for data analysis.

first: Ki

middle: W

first: Joel

middle: K

last: Elmquist


title: Gene Expression profiles in Retinoblastoma

city: Bangalore

first: Genotypic

last: technology

state: Karnataka

address: 259, Apoorva 4th cross,80 feet Road,RMV 2ND STAGE

country: India

institute: Genotypic Technology

summary: Gene expression profiles in retinoblastoma by whole Human Genome DNA microarrays in comparison to  the normal retina gave an insight into several genes and pathways that were regulated in the tumor. The upregulated and the downregulated genes were further validated by quantitative real time PCR and tissue microarray (TMA) on retinoblastoma tumors. Theoverall  goal is to determine the global gene expression profile in retinoblastoma tumors which is first of its kind on a whole genome microarray.

overall_design: Two coloured microarray:retinoblastoma tumor (4 samples) vs. normal retina (4 samples).

first: Rekha

middle: V

last: Kumar

first: P

last: Bhuvaneswari


title: Global gene expression in adult cardiac fibroblasts transduced with cardiac transcription factor

status: Public on Apr 06 2012

first: Kunhua

last: Song

address: 5323 Harry Hines Boulevard

institute: UT Southwestern Medical Center

summary: Four transcription factors, GATA4, Hand2, MEF2C, Tbx5 (GHMT) activated cardiac gene expression in cardiac fibroblasts, suggesting that these factors are able to reprogram fibroblasts toward a cardaic cell fate.

overall_design: Total RNA isolated from adult cardiac fibroblasts transduced with empty retroviral vector or GHMT-retroviruses for 2, and 4 weeks.

first: Eric

middle: N

last: Olson


title: Combinatorial effects of microRNA to suppress the myc oncogenic pathway (mRNA data)

status: Public on Apr 09 2012

city: Madrid

first: Lorena

last: Di Lisio

address: C/ Melchor Fernández Almagro, 3

country: Spain

institute: CNIO

summary: microRNA importance in the myc pathway in Burkitt lymphoma.

overall_design: Gene expression data of Burkitt lymphoma samples and non-tumoral controls. 6 Burkitt lymphomas were compared with 16 non-tumoral controls. Universal Human Reference RNA was used as the reference sample. Significantly deregulated miRNAs were computed using the Significant Analysis of Microarray (SAM) analysis from the TM4 pathway and the limma package.

first: María

last: Bueno

first: Gonzalo

last: Gómez-López

first: Nerea

last: Martínez

first: Miguel

last: Piris

first: Marcos

last: Malumbres


title: IDR-1018 treatment of mice infected with Plasmodium berghei, spleen and brain expression data

city: Parkville

first: Gordon

last: Smyth

state: Vic

address: 1G Royal Pde

department: Bioinformatics

country: Australia

institute: Walter and Eliza Hall Institute of Medical Research

summary: Severe malaria encompasses a range of syndromes manifesting systemically or in diverse organs. These are believed to represent the end-stage processes of local parasite sequestration and inflammatory cascades. Classical anti-malarial drugs target parasites only. In treatment of severe disease, adjunctive therapies capable of controlling the inflammatory processes could be beneficial. Innate defense regulator (IDR) peptides display multiple immune modulatory activities. In this study, we assessed peptide IDR-1018, which shows promise as an anti-inflammatory drug, as a lead candidate for adjunctive host-directed therapy of established disease in the P. berghei ANKA model of experimental cerebral malaria (ECM). Intravenously administered IDR-1018 partially protected mice from ECM both prophylactically and in adjunctive treatment with classical anti-malarial drugs. We used transcriptional data from spleens and brains taken early in infection (day 3) of prophylactically treated mice to investigate the protective mechanisms.

overall_design: The microarrays compared spleens and brains from nine IDR-1018 i.v. treated, infected mice (IDR-1018-treated infected) with three saline i.v. treated infected mice (saline-treated infected) and three uninfected untreated control mice (controls). RNA samples were hybridized in randomized order to five Illumina WG-6 v2 BeadChips . No technical replicates were performed.

first: Ariel

last: Achtman

first: Sandra

last: Pilat

first: Charity

last: Law

first: Louis

last: Schofield


title: Inhibition of Bcl6-SMRT/NCoR interactions by an inhibitory peptide affects inflammatory pathways

status: Public on Mar 30 2012

city: La Jolla

first: Ruth

middle: T

last: Yu

address: 10010 N Torrey Pines Rd

department: Gene Expression Lab

institute: Salk Institute

summary: Using microarrays, we compared the changes in levels of gene expression between wild type mouse bone marrow derived macrophages upon treatment with the Bcl6 peptide inhibitor, RI-BPI, that specifically blocks interaction between BCL6 and the co-repressors NCoR or SMRT.

overall_design: Total RNA was obtained from cultered wild type primary bone marrow-derived macrophages that were treated with either 5 μM control or RI-BPI peptide in MSF media for 12 hours.

first: Grant

middle: D

last: Barish

first: Ronald

last: Evans


title: Combinatorial effects of microRNA to suppress the myc oncogenic pathway

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

summary:
Many mammalian transcripts contain target sites for multiple miRNAs, although it is not clear to what extent miRNAs may coordinately regulate single genes. We have mapped the interactions between down-regulated miRNAs and overexpressed target protein-coding genes in murine and human lymphomas. Myc, one of the hallmark oncogenes in these lymphomas, stands out as the up-regulated gene with the highest number of genetic interactions with down-regulated miRNAs in mouse lymphomas. The regulation of Myc by several of these miRNAs is confirmed by cellular and reporter assays. The same approach identifies MYC and multiple Myc targets as a preferential target of down-regulated miRNAs in human Burkitt lymphoma, a pathology characterized by translocated MYC oncogenes. These results indicate that several miRNAs must be coordinately down-regulated to enhance critical oncogenes, such as Myc. Some of these Myc-targeting miRNAs are repressed by Myc, suggesting that these tumors are a consequence of the unbalanced activity of Myc versus miRNAs.

This SuperSeries is composed of the SubSeries listed below.

overall_design: Refer to individual Series.


title: Human breast cancer cell lines: vehicle vs. BMP4 incubation

status: Public on Mar 22 2012

city: Tampere

first: Alejandra

last: Rodriguez-Martinez

address: Biokatu 6

department: Institute of Biomedical Technology

country: Finland

institute: University of Tampere

summary: Bone morphogenetic proteins (BMPs) are members of the TGF-β superfamily of growth factors. They are known for their roles in regulation of osteogenesis and developmental processes and, in recent years, evidence has accumulated of their crucial functions in tumor biology. BMP4, in particular, has been implicated in breast cancer. However, little is known about BMP target genes in the context of tumor. We therefore explored the effects of BMP4 treatment on global gene transcription in five breast cancer cell lines during a 6-point time series. Data analysis included hierarchical clustering of differentially expressed genes, gene ontology enrichment analyses and model based clustering of temporal data. BMP4 had a strong effect on gene expression. The cellular functions most strongly affected were regulation of transcription and development. The observed transcriptional response, as well as its functional outcome, followed a temporal sequence, with regulation of gene expression and signal transduction leading to changes in metabolism and cell proliferation. Hierarchical clustering revealed distinct differences in the response of individual cell lines to BMP4, but also highlighted a synexpression group of genes. Finally, this study provides a list of potential novel BMP target genes relevant in breast cancer.

overall_design: Two-condition experiment, vehicle-treated vs. BMP4-treated. Five cell lines were tested at six time points each, what makes a total of 30 samples. RNA samples from three biological replicates were pooled before hybridization.

first: Emma-Leena

last: Alarmo

first: Lilli

last: Saarinen

first: Johanna

last: Ketolainen

first: Kari

last: Nousiainen

first: Sampsa

last: Hautaniemi

first: Anne

last: Kallioniemi


title: Human breast cancer cell lines: vehicle vs. BMP7 incubation

summary: Bone morphogenetic proteins (BMPs) are members of the TGF-β superfamily of growth factors. They are known for their roles in regulation of osteogenesis and developmental processes and, in recent years, evidence has accumulated of their crucial functions in tumor biology. BMP7, in particular, has been implicated in breast cancer. However, little is known about BMP target genes in the context of tumor. We therefore explored the effects of BMP7 treatment on global gene transcription in five breast cancer cell lines during a 6-point time series. Data analysis included hierarchical clustering of differentially expressed genes, gene ontology enrichment analyses and model based clustering of temporal data. BMP7 had a strong effect on gene expression. The cellular functions most strongly affected were regulation of transcription and development. The observed transcriptional response followed a temporal sequence. Hierarchical clustering revealed distinct differences in the response of individual cell lines to BMP7, but also highlighted a synexpression group of genes. Finally, this study provides a list of potential novel BMP target genes relevant in breast cancer.

overall_design: Two-condition experiment, vehicle-treated vs. BMP7-treated. Five cell lines were tested at six time points each, what makes a total of 30 samples. RNA samples from three biological replicates were pooled before hybridization.


title: Human breast cancer cell lines

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

overall_design: Refer to individual Series


title: TCF7 is a key regulator of the switch of self-renewal and differentiation in a multipotential hematopoietic cell line

city: New Haven

first: Vince

last: Schulz

state: CT

address: 333 Cedar St. LMP 4085

department: Department of Pediatrics

institute: Yale University

summary: A critical problem in biology is understanding how cells choose between self-renewal and differentiation. To generate a comprehensive view of the mechanisms controlling early hematopoietic precursor self-renewal and differentiation, we used systems-based approaches and murine EML multipotential hematopoietic precursor cells as a primary model.  EML cells give rise to a mixture of self-renewing Lin-SCA+CD34+ cells and partially differentiated non-renewing Lin-SCA-CD34- cells in a cell autonomous fashion. We identified and validated the HMG box protein TCF7 as a key regulator in this self-renewal/differentiation switch, and it operates in the absence of canonical Wnt signaling. We found that TCF7 is the most downregulated transcription factor when CD34+ cells switch into CD34- cells using RNA-Seq. We subsequently identified the target genes bound by TCF7 using ChIP-Seq. We show that TCF7 binds to Runx1 (Aml1) promoter region, and RUNX1 and TCF7 co-regulate. Gene Set Enrichment Analysis suggests that TCF7 primarily acts as a positive regulator of genes preferentially expressed in CD34+ cells. Consistent with this possibility, knocking-down TCF7 represses many up-regulated genes in Lin-CD34+ cells. Finally a network of up-regulated transcription factors of CD34+ cells which defines the self-renewing state was constructed. These studies in EML cells demonstrate fundamental cell-intrinsic properties of the switch between self-renewal and differentiation, and yield valuable insights for manipulating HSCs and other differentiating systems.

overall_design: The gene expression changes when TCF7 is knocked-down by shRNA in Lin-SCA+CD34+ cells were identified by microarray analysis of one control and two experimental samples.

first: Jia

middle: Q

last: Wu

first: Montrell

last: Seay

first: Vincent

first: David

last: Tuck

first: Jin

last: Lian

first: Manoj

last: Hariharan

first: Minyi

last: Shi

first: Zhijia

last: Ye

first: Jiang

last: Du

first: Mark

last: Gerstein

first: Michael

last: Snyder

first: Sherman

last: Weissman


title: Effects of choline intake and pregnancy on peripheral blood leukocyte gene expression

status: Public on Mar 16 2012

city: Ithaca

first: Xinyin

last: Jiang

state: NY

address: 241 Kinzelberg Hall, Cornell University

department: Nutritional Sciences

institute: Cornell University

summary: To explore the influence of choline intake and pregnancy status on gene expression, we employed whole genome microarray expression profiling to identify genes that were differentially expressed between two choline intake groups and between pregnant and non-pregnant women. Healthy third trimester (gestational week 26-29) pregnant women and non-pregnant women were randomized to a 12-week choline controlled feeding study. The participants  consumed  either 480 (n=6 pregnant and n=5 non-pregnant) or 930 (n=6 pregnant and n=5 non-pregnant) mg choline/d. Fasting peripheral blood leukocyte samples were collected at week 0 and week 12 to extract RNA and perform the arrays.

overall_design: Healthy third trimester (gestational week 26-29) pregnant women and non-pregnant women were randomized to a 12-week choline controlled feeding study. The participants  consumed  either 480 (n=6 pregnant and n=5 non-pregnant) or 930 (n=6 pregnant and n=5 non-pregnant) mg choline/d for 12 weeks. Fasting (10-h) peripheral blood leukocyte gene expression were measured at week 0 and week 12.

first: Marie

last: Caudill

first: Haim

middle: Y

last: Bar

first: Jian

last: Yan

first: Allyson

last: West

first: Cydne

last: Perry


title: Transcriptomic profiling of peripheral blood mononuclear cells from patients with Parkinson’s disease and control subjects.

status: Public on Mar 20 2012

city: lille

first: frédéric

last: leprêtre

address: Boulevard du Pr Leclercq

department: CHU of Lille, CBP

country: France

institute: Lille University

summary: To get insight into systemic molecular events associated with Parkinson’s disease (PD), an age-related neurodegenerative disorder, we compared gene expression patterns of peripheral blood mononuclear cells (PBMC) derived from elderly healthy controls and from PD patients.

overall_design: Transcriptomic profiling of patients with Parkinson’s disease and control subjects. RNA were extracted  from peripheral mononuclear blood cells and were hybridized on 4x44k Agilent expression microarrays.

first: Marie-Christine

last: Chartier-Harlin


title: microRNA and Gene expression profiles in colorectal cancer stromal tissue

status: Public on Mar 14 2012

city: Beppu

first: Koshi

last: Mimori

state: Oita

address: 4546 Tsurumihara

department: Department of Surgery

country: Japan

institute: Kyushu university

summary: Using Laser Microdissection System (Leica Microsystems), RNA samples specific for stroma or epithelium were separately collected from thirteen colorectal cancer tissues and four normal tissues. Both microRNA microarray and gene expression microarray were performed in these samples.

overall_design: Tissue samples from thirteen colorectal cancer tissues and  four normal tissues were microdissected using Laser Microdissection System (Leica Microsystems), and RNA samples specific for stroma or epithelium were separately collected.MicroRNA and Gene expression profiles obtained from cancer stromal tissues were compared with that of normal colon stromal tissues. we used the commercially available Human Whole Genome Oligo DNA Microarray Kit (Agilent Technologies) for gene expresson analysis and microRNA array for microRNA analysis.

first: Masaki

last: Mori

first: Naohiro

last: Nishida


title: Gene Expression Analysis of Blood Reveals S100A11 and AQP9 as Potential Biomarkers of Infective Endocarditis

status: Public on Mar 12 2012

city: marseille

first: adil

last: ef

address: 27 bd jean Moulin

institute: URMITE

summary:
Background—Diagnosis and pronostic assessment are challenging in infective endocarditis (IE). To investigate the host response during IE and identify potential biomarkers, we determined the circulating gene expression profile through a whole genome microarray analysis.
Methods and Results—A transcriptomic case-control study was performed on blood samples from patients with native valve IE (n=39), excluded IE after an initial suspicion (n=10) at patient’s admission, and age-matched healthy controls (n=10). The whole genome microarray analysis showed that patients with IE exhibited a specific transcriptional program with a predominance of gene categories associated with cell activation, innate immune and inflammatory responses. These categories were organized in a dense network from which arose numerous subnetworks including major histocompatibily complex and natural killer cell network, type 1 interferon pathway and intracellular traffic. Quantitative real-time RT-PCR performed on a selection of highly modulated genes showed that the expression of the gene encoding S100 calcium binding protein A11 (S100A11) was significantly increased in patients with IE in comparison with controls (P<0.001) and patients with excluded IE (P<0.05). Interestingly, the upregulated expression of S100A11 gene was more pronounced in staphylococcal IE than in streptococcal IE (P<0.01). These results were confirmed by serum concentrations of the S100A11 protein. Finally, we showed that, in patients with IE, the upregulation of aquaporin-9 gene (AQP9) was significantly related to the occurrence of acute heart failure (P=0.02).
Conclusions— Using transcriptional signatures of blood samples, we identified S100A11 as a potential diagnostic marker of IE. In addition, the determination of AQP9 may improve the prognostic assessment of IE.

overall_design: The transcriptomic case-control study was performed in 39 consecutive patients with  native valve IE (IE group) diagnosed by a multidisciplinary team who applied the modified Duke criteria,12 10 patients admitted for a suspicion of IE but with a final excluded IE diagnosis. Ten IE patients and five controls were arbitrary selected and investigated with microarrays.

first: Franck

last: Thuny

first: Amira

last: Amara

first: Adil

last: Filali

first: Christian

last: Capo

first: Gilbert

last: Habib

first: Didier

last: Raoult

first: Jean-Louis

last: Mege


title: Id proteins synchronize stemness and anchorage to the niche of neural stem cells

status: Public on Mar 15 2012

city: Napoli

first: Mario

last: Lauria

address: via P. Castellino 111

country: Italy

institute: TIGEM

summary: Stem cell functions require activation of stem cell-intrinsic transcriptional programs as well as intimate extracellular interactions with a niche microenvironment. How the core pluripotency transcriptional machinery controls residency of stem cells in the niche microenvironment is unknown. Here we show that the helix loop helix transcriptional regulators Id (Inhibitors of DNA binding) are the master regulators that coordinate stem cell activities with anchorage of neural stem cells (NSCs) to the embryonic and postnatal niche. Conditional inactivation of Id genes (Id1, Id2 and Id3) in the mouse NSC compartment triggered detachment of embryonic and post-natal NSCs from the ventricular and vascular niche respectively, followed by premature differentiation. Through an unbiased interrogation of the gene modules directly targeted by deletion of Id genes in NSCs, we discovered that Id proteins repress the bHLH-mediated activation of Rap1GAP, thus serving to maintain the GTPase activity of RAP1, a key mediator of cell adhesion.  Preventing the elevation of Rap1GAP efficiently countered the consequences of Id loss on NSC-niche interaction and stem cell identity. Thus, by preserving anchorage to the extracellular environment of NSCs, Id activity synchronizes NSC functions to residency in the specialized niche.

overall_design: We generated Id-cTKO mice carrying a Cre-recombinase-oestrogen-receptor-T2 (Cre-ER) allele targeted to the ubiquitously expressed ROSA26 locus (Id-cTKO-Rosa-Cre-ER). In this system, 4-hydroxytamoxifen (4-OHT) releases the Cre recombinase inhibition and allows recombination of genomic loxP sites. Indeed, efficient deletion of Id1 and Id2 with complete loss of Id protein expression was detectable after treatment of NSCs with 4-OHT for 72 h. Total RNA was extracted from triplicate samples of Id-cTKO-Rosa-Cre-ER NSCs treated for different times (6 h, 12 h, 18 h, 24 h, 48 h, 96 h, 144 h) with 4-OHT or control vehicle and used for analysis on Illumina MouseWG-6 expression BeadChip. The raw array data was normalized using the Bioconductor package Lumi using quantile normalization.

first: Francesco

last: Niola

first: Xudong

last: Zhao

first: Devendra

last: Singh

first: Angelica

last: Castano

first: Ryan

last: Sullivan

first: Hyung-song

last: Nam

first: Yuan

last: Zhuang

first: Robert

last: Benezra

first: Diego

last: Di Bernardo

first: Antonio

last: Iavarone

first: Anna

last: Lasorella


title: MicroRNAs Associated with Metastatic Prostate Cancer

status: Public on Mar 11 2012

city: Vancouver

first: Yuzhuo

last: Wang

state: BC

address: 675 West 10th Avenue

department: Experimetnal Therapeutics

country: Canada

institute: BC Cancer Research Centre

summary: To identify genes with the potential target of differentially expressed miRNA in metastatic prostate cancer, we have employed whole genome microarray expression profiling. Transplantable metastatic versus a non-metastatic prostate cancer xenograft line, both derived from one patient’s primary cancer, were developed via sub-renal capsule grafting of cancer tissue into NOD/SCID mice. The same RNA samples from both lines were also used for miRNA sequencing. Overlapped genes of predicted targets of differentially expressed miRNAs and differentially expressed in microarray platform showed potential markers of combination of miRNA and gene in metastatic prostate cancer.

overall_design:
Gene expression in metastatic/non-metastatic prostate cancer was measured. Same total RNA samples were used for small RNA library construction for miRNA sequencing.

This submission represents the gene expression component of the study.

first: Akira

last: Watahiki

first: Yuwei


title: Biological Aging and Circadian Mechanisms in Murine Brown Adipose Tissue, Inguinal White Adipose Tissue, and Liver (Nov 2009 dataset)

city: Baton Rouge

first: Jeffrey

last: Gimble

state: LA

address: 6400 Perkins Rd

institute: Pennington Biomedical Research Center

summary:
The circadian profile of the transcriptomes in murine tissues was compared between groups of young and old male mice. The oscillatory phase and absolute expression levels were
evaluated as a function of biological age. Distinct differences in multiple pathways were apparent based on biological and circadian time in a tissue specific manner.

overall_design: A total of 18 young (5 month) and old (24 month) C57BL/6 mice were acclimated to a set 12 hr light dark cycle and fed ad lib on standard lab chow for 2 weeks in the PBRC Comparative Biology Core Facility. Five days prior to the study, the mice were converted to constant darkness (red light) regimen. On the day of the study, mice were euthanized by CO2 asphyxiation after ad lib feeding overnight in groups of 3 animals per young or old cohort at 4 hr intervals beginning at 7 AM and ending at 3 AM on a single day (July, 2009). The body weight of each animal was recorded prior to dissection of the following tissues: brown adipose tissue (BAT), inguinal white adipose tissue (iWAT), and liver. Individual tissues were weighed prior to freezing in liquid nitrogen. Samples were stored at -80oC until use.Total RNA was isolated from the BAT, eWAT, and liver tissues using TriReagent (MRC, Cincinnati OH) in accordance with the manufacturer’s recommendations. The Illumina TotalPrep RNA Amplification Kit (Applied Biosystems Inc., Foster City, CA, Catalog #AMIL1791) was used to create labeled cRNA from 750ng of input total RNA according to the manufacturer’s protocol. The labeled cRNA samples were then assessed for quality and quantity using a NanoDrop and an Agilent Bioanalyzer. The MouseWG-6 v2 Beadchip (Illumina Sentrix Beadchip Array #11278593) contains 45,200 transcripts and allows 6 samples to be interrogated in parallel. 1.5ug of each labeled cRNA was hybridized to each array according to the manufacturer's protocol. Experimental group samples were distributed randomly across all beadchips. After an 18 hour hybridization at 58°C, the beadchips were processed according to manufacturer’s protocol and scanned using an Illumina BeadArray Reader (Illumina, Inc., San Diego, CA).

first: Andrey

last: Ptitsyn

first: Elizabeth

last: Floyd

first: Xiying

last: Wu

first: Susan

last: Newman

first: Bruce

last: Bunnell


title: Biological Aging and Circadian Mechanisms in Murine Brown Adipose Tissue, Inguinal White Adipose Tissue, and Liver (Jan 2010 dataset)

summary: The circadian profile of the transcriptomes in murine tissues was compared between groups of young and old male mice. The oscillatory phase and absolute expression levels were evaluated as a function of biological age. Distinct differences in multiple pathways were apparent based on biological and circadian time in a tissue specific manner.


title: Biological Aging and Circadian Mechanisms in Murine Brown Adipose Tissue, Inguinal White Adipose Tissue, and Liver


title: Identification of target genes of miR-193b

city: Tokyo

first: Toru

last: Furukawa

address: 8-1 Kawadacho, Shinjuku-ku

department: Institute for Integrated Medical Sciences

institute: Tokyo Women's Medical University

summary: Searching of target genes of miR-193b by transcriptome assay using 44K Whole Human Genome Microarray system (Agilent Technologies, Palo Alto, CA) resulted in finding of several candidate genes.

overall_design: To search of targets genes of miR-193b, we performed transcriptome analysis to compare expression profiles between human pancreatic cancer cells, MIA PaCa-2, transfected with precursor of miR-193b and those transfected with a negative control precursor.

first: Yushi

last: Ikeda

first: Etsuko

last: Tanji

first: Naohiko

last: Makino

first: Sumio

last: Kawata


title: The response of human primary airway epithelial cells to Influenza or RSV infection [hAECs_Agilent].

city: COLUMBUS

first: IOANNIS

last: IOANNIDIS

state: OH

address: 700 CHILDRENS DRIVE

department: VACCINES AND IMMUNITY

institute: NATIONWIDE CHILDRENS HOSPITAL

summary: To investigate how human airway epithelial cells respond to Influenza or RSV infection, we harvested airway epithelial cells from the mainstream bronchi of human donors and cultured them as previously described (Pickles et al,1998) in a polarized system  that resembles the in vivo mucociliary pseudostratified epithelium. Quadruplicate hAEC cultures were infected with 2X105 PFUs Influenza A (Udorn) or with 1x106 PFUs RSV for 2h or mock inoculated and harvested 24h after Influenza infection and 48h after RSV infection.

overall_design: Quadruplicate polarized airway epithelial cell cultures were mock treated or infected with 2x10^5 PFUs of Influenza A (Udorn) for 2h  or  infected with 1x10^6 PFUs RSV and harvested 24 h post infection for Influenza or 48h post infection for RSV. Total RNA was harvested and gene expression was studied using Genespring GX v7.3.1.

first: Ioannis

last: Ioannidis

first: Beth

last: McNally

first: Meredith

last: Willette

first: Emilio

last: Flano


title: Genome-wide expression analysis of wide-type and PirBTM MLL-AF9 LSCs

status: Public on Mar 08 2012

first: Chaozheng

last: Zhang

institute: UT southwestern medical center

summary: How the stemness of adult stem cells and cancer stem cells is regulated by environmental cues through surface receptors is poorly understood. In this gene expression analysis, we found that, in the mouse MLL-AF9 acute myeloid leukemia (AML) model, a deficiency in intracellular signaling of inhibitory receptor PIR-B resulted in increased differentiation and decreased stemness of leukemia stem cells, revealing that PIR-B supports leukemia development. Our study indicates unexpected functional significance of a classical immune inhibitory receptor in the maintenance of stemness of cancer stem cells.

overall_design: Total RNA obtained from wild-type MLL-AF9 LSCs compared to PirBTM MLL-AF9 LSCs

first: Junke

last: Zheng

first: Masato

last: Umikawa

first: Changhao

last: Cui

first: Xiaoli

last: Chen

first: HoangDinh

last: Hyunh

first: Robert

last: Silvany

first: Chengcheng


title: Immune-activation as a therapeutic direction for patients with high-risk ovarian cancer based on gene expression signature (2)

status: Public on Mar 01 2012

city: Niigata

first: Kosuke

last: Yoshihara

address: 1-757 Asahimachi-dori

department: Obstetrics and Gynecology

institute: Niigata University

summary: Advanced-stage ovarian cancer is one of the most lethal gynecologic malignancies. To improve prognosis of patients with ovarian cancers, a predictive biomarkers leading to personalized treatments are required. In this large-scale cross-platform study of six microarray datasets consisting of 1054 ovarian cancer patients, we developed a novel risk classification system based on a 126-gene expression signature for predicting overall survival by applying elastic net7 and 10-fold cross validation to a Japanese dataset A (n = 260). We further validated its predictive ability with the five other datasets using multivariate analysis. Also, through gene ontology and pathway analyses of 1109 high-risk ovarian cancer specific transcripts, we identified a significant reduction of expression of immune-response related genes, especially on the antigen presentation pathway. Furthermore, an immunohistochemical analysis demonstrated that the number of CD8 T lymphocytes infiltrating into tumor tissue was significantly decreased in high-risk ovarian cancers. These predictive biomarkers based on the 126-gene expression signature will identify high-risk ovarian cancer patients who need novel immune-activating therapeutic approaches, leading to improved outcomes for such patients.

overall_design: 40 patients who were diagnosed as advanced-stage high-grade serous ovarian cancer were recruited in this study.

first: Group

last: The Japanese Serous Ovarian Cancer Study


title: CDK8 knockdown in HT-29 human colon cancer cells

status: Public on Mar 05 2012

city: South San Francisco

first: Adam

middle: S

last: Adler

address: 1 DNA Way

institute: Genentech

summary: Transcriptional profiling of HT-29 human colon cancer cells transfected with non-targeting control (NTC) siRNA and two different siRNA sequences against CDK8 (siCDK8-1 and siCDK8-2).

overall_design: Three condition experiment comparing siNTC versus siCDK8-1 and siCDK8-2 after 3 days (3 biological replicates each); in total 9 samples profiled.

first: Zora

last: Modrusan


title: Influence of cell permeable Tre-recombinase (CPTR) treatment on T-cell gene expression

status: Public on Feb 22 2012

city: Hamburg

first: Nicole

last: Walz

address: Martinistr. 52

institute: Heinrich-Pette-Institut

summary: CEM-ss cells were treated with or without a recombinantly expressed recombinase and gene expression profiles were compared.

overall_design: Two-condition experiment,  Untreated CEM-ss vs. CPTR treated CEM-ss cells

first: Lakshmikanth

last: Mariyanna

first: Poornima

last: Priyadarshini

first: Helga

last: Hofmann-Sieber

first: Marcel

last: Krepstakies

last: Grundhoff

first: Frank

last: Buchholz

first: Eberhard

last: Hildt

first: Joachim

last: Hauber


title: The role of FOG-1 in GATA-1 transcriptional regulation of megakaryocyte differentiation

city: Cincinnati

first: Timothy

middle: Michael

last: Chlon

address: 3333 Burnet Ave

department: Oncology

institute: Cincinnati Children's

summary: We explored the role of FOG-1 in GATA-1 transcriptional regulation of megakaryocyte differentiation through expression of wild-type GATA-1 and the FOG-binding mutant of GATA-1 (GATA-1^V205G) in G1ME cells.

overall_design: G1ME cells were derived from Gata1-null mouse ES cells and have both megakaryocyte and erythrocyte differentiation potential upon reconstitution of GATA-1 expression (Stachura 2006).  HA-tagged wild-type or mutant GATA-1 were expressed in G1ME cells grown in TPO via retroviral transductions.  The cells were sorted for GFP positivity 68 hours post-transduction and then were allowed to recover in normal growth medium for 4h.  Total RNA was then isolated using RNeasy kit from Qiagen 72 hours post-transduction.

first: John

last: Crispino


title: Gene expression in liver and lung of a high-fat diet fed, metastasizing mammary tumor-bearing and obesity-resistant mice

city: Chuncheon

first: Eun Ji

last: Kim

address: 1 Hallymdaehak-gil

country: South Korea

institute: Hallym University

summary: We explored early changes in gene expression in the livers and lungs of the HFD-fed, metastasizing mammary tumor-bearing and obesity-resistant mice mice. These alterations may have led to favorable conditions for both the formation of pro-inflammatory and pro-mitotic microenvironments in the target organs that promote immune cell infiltration and differentiation, as well as infiltration and proliferation of metastatic tumor cells.

overall_design: Total RNA was isolated from hepatic and pulmonary tissues of high fat diet fed-4T1 cell-injected mice or high fat diet fed-sham mice. Gene expressions were compared to control diet fed-same conditional mice.

first: Eun

first: Hea

last: Oh


title: CDK8 knockdown in HT-29 cells and CDK8 & MED12 knockdown in R1 cells

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

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus

overall_design: Refer to individual Series


title: Genome-wide gene expression profiling analysis of bone metastases of human non-small cell lung cancer (NSCLC) in mice

status: Public on Feb 21 2012

city: Tokushima

first: Le

middle: Tan

last: Dat

state: Tokushima

address: 3-18-15, Kuramoto-cho

department: Genome center

institute: Tokushima university

summary: Using a multiorgan metastasis model of human NSCLC cells (ACC-LC319/bone2) in NK cell-depleted SCID mice, we attempted to identify genes involved in the organ-selective nature of lung cancer-metastasis process, especially bone metastasis. Genome-wide gene expression profile of 15 metastatic lesions from three organs (bone, lung and liver) in this mouse model revealed lot of genes that seemed to reflect the organ specificity of metastatic cells. Among bone-specifically-expressed genes, dozen of genes involved in cell adhesion, cytoskeleton/cell motility, extracellular matrix remodeling, and cell-cell signaling. The upregulation of 11 genes, some of them were either previously reported to be involved in metastatic characteristics, were confirmed by quantitative RT-PCR.

overall_design: The high ability for bone metastasis human lung adenocarcinoma cell line ACC-LC319/bone2 was established in our laboratory from the parental cell line ACC-LC319 (a kind gift from Dr T. Takahashi, Nagoya University, Nagoya, Japan). ACC-LC319 cells with low capacity of bone metastatic ability were selected in vivo for two cycles in bone metastasis mouse models. After two cycles of selection, the derivative cell line designated as ACC-LC319/bone2 showed increased bone metastatic ability compared to parental cell line (Otsuka S., Oncol Res 2009). In this multiorgan metastasis model, SCID mice were depleted NK cells, and two days later, these mice were intravenously injected 1x10^6 cells. The mice were followed up for clinical symptoms and signs of metastases, and were sacrificed on day 34 after tumor inoculation. Metastastic tissues in lung, liver and bone were collected and snap frozen in liquid nitrogen then keep at -80C until cryosection. Laser microbeam microdissection was used to capture pure population of cancer cells in each organ as well as mouse normal tissues in corresponding organ (i.e. the surrounding normal tissues with no microscopic metastasis). Totally, there were 19 samples, including one sample for metastases in each organ (bone, lung and liver) in five mice (i.e., 15 samples); one for each normal mouse tissue (i.e.,three samples); and one for the in vitro cell line (ACC-LC319/bone 2). DNA microarray were performed using Agilent platform, and the gene expression profile of metastases in bone were compared with the gene expression profile of metastases in other two organs (lung, liver). Those genes whose expression in mouse normal tissues was above the cut off value were excluded. The expression of genes in the in vitro cells was used as the universal normalization for the in vivo genes expression.

first: Taisuke

last: Matsuo

first: Tetsuro

last: Yoshimaru

first: Takuya

last: Kuramoto

first: Masaki

last: Hanibuchi

first: Hisatsugu

last: Goto

first: Soji

last: Kakiuchi

first: Yasuhiko

last: Nishioka

first: Saburo

last: Sone

first: Toyomasa

last: Katagiri


title: Med13 overexpression

status: Public on Feb 18 2012

city: Dallas

first: Chad

last: Grueter

address: 6000 Harry Hines Blvd

institute: UT Southwestern Medical Center

overall_design:
Med13 cardiac transgenic mice were back-crossed 4 or more generations to C57Bl6 mice.

Refer to individual Series


title: Cardiac over-expression of Med13, non-cardiac tissue analysis

summary: Med13 cardiac over-expression regulates obesity.  Liver, WAT and BAT from alphaMHC-Med13 TG mice was analyzed

overall_design: Liver, WAT and BAT from Med13 alphaMHC transgenic mice and wild type littermates

first: Eric

last: Olson


title: Genome-wide analysis of 1 month old (P30) Tdrd7 null mouse lens

city: Boston

first: Anton

last: Aboukhalil

state: MA

address: 77 Avenue Louis Pasteur, 464

institute: Massachusetts Institute of Technology

summary:
Analysis of Tdrd7 deficiency in mouse lens epithelial-derived cell line at gene expression level. The hypothesis tested was that Tdrd7 is involved in post-transcriptional control of gene expression in the lens. Results provide evidence for differential regulation of genes involved in lens homeostasis and cataract formation in the absence of Tdrd7.
In eukaryotic cells, cytoplasmic RNA granules (RGs) function in the post-transcriptional control of gene expression.  However, the involvement of RGs and their component proteins in vertebrate organogenesis is unknown.  We report two independent cases of pediatric cataract with loss-of-function mutations in TDRD7, which encodes a Tudor domain RNA binding protein.  TDRD7 deficiency in chick lens produces cataracts, and Tdrd7 null mouse mutants develop cataracts, as well as features of glaucoma and male sterility due to azoospermia.  In lens fiber cells, TDRD7 is necessary for the RG-mediated post-transcriptional control of critical lens mRNAs, while in the testis it functions as a component of a specialized RG, the chromatoid body.  These findings define a new role for RGs in vertebrate organogenesis, and a novel mechanism for cataractogenesis.

overall_design: Total RNA obtained from P30 Lens from Tdrd7 null mice compared to that of Tdrd7 heterozygous mice.

first: Salil

last: Lachke

first: Richard

middle: L

last: Maas


title: Cardiac over-expression of Med13

summary: Med13 cardiac over-expression regulates cardiac gene expression and metabolism

overall_design: Hearts from Med13 alphaMHC transgenic mice and wild type littermates


title: A panel of hepatocellular carcinoma cell lines recapitulates the molecular subtypes of the human disease: A model for targeted drug development

status: Public on Feb 15 2012

city: LA

last: Finn

address: 10833 Le Conte, 11-934 Factor Building

department: Medicine-Hem/Onc

institute: UCLA

summary: RNA expression patterns of liver cell lines were compared to those of liver tumors to determine the suitability of cell lines as a model for drug development studies.  The cell lines appear to recapitulate liver tumors.

overall_design: Gene expression of 20 individual liver cell lines relative to a liver cell line reference mix containing equal amounts of 19 liver cell lines.  The expression data was correllated with expression in liver tumors.

first: Alex

last: Aleshin

first: Charles

last: Ginther

first: Judy

last: Dering

first: Dennis

last: Slamon


title: Gene expression analysis of ovarian tumors from mice with knockout of DICER and PTEN

status: Public on Feb 16 2012

city: Houston

last: Creighton

address: One Baylor Plaza, Mail Stop: BCM305

institute: Baylor College of Medicine

summary: The cell of origin of serious ovarian cancer is unknown. To create a mouse model for this lethal cancer and identify early cancer biomarkers, we conditionally deleted both Dicer (essential for microRNA biosynthesis) and Pten (a negative regulator of the PI3K pathway) in the female reproductive tract. Beginning at ~3-5 months, these Dicer/Pten mutant mice develop high-grade serious carcinomas that initiate in the stroma of the fallopian tube through a mesenchymal-to-epithelial transition (MET), subsequently envelop the ovary, and then metastasize throughout the peritoneum, resulting in ascites and 100% lethality by 13 months. The fallopian tube cancers demonstrate upregulation of genes encoding known and novel secreted proteins that are potential biomarkers. This study uncovers a new paradigm for the initiation of high-grade serous ovarian cancer.

overall_design: RNA was isolated from the fallopian tube cancers of independent DKO mice and normal fallopian tubes of control mice  and subjected to mRNA expression analysis using an Illumina platform (MouseWG-6 v2 Expression BeadChip).

first: Marty

last: Matzuk

first: Jaeyeon

last: Kim

first: Shannon

last: Hawkins


title: Analysis of striatal transcriptome in transgenic mice overexpressing human wild-type alpha-synuclein

status: Public on Feb 11 2012

city: Los Angeles

first: Yofre

last: Cabeza-Arvelaiz

state: California

address: 650 Charles E. Young Drive South

department: Pathology and Environmental Health Sciences

institute: University of California, Los Angeles

summary:
Alpha synuclein (SNCA) has been linked to neurodegenerative diseases (synucleinopathies) that include Parkinson’s disease (PD). Although the primary neurodegeneration in PD involves nigrostriatal dopaminergic neurons, more extensive yet regionally selective neurodegeneration is observed in other synucleinopathies.  Furthermore, SNCA is ubiquitously expressed in neurons and numerous neuronal systems are dysfunctional in PD. Therefore it is of interest to understand how overexpression of SNCA affects neuronal function in regions not directly targeted for neurodegeneration in PD. To gain a better understanding of the consequences of excessive SNCA expression on basal ganglia function, we performed transcriptome analysis of striatal tissue from male Thy1-aSyn-mice and wt littermates. The present study investigated the consequences of SNCA overexpression on cellular processes and functions in the striatum of mice overexpressing wild-type, human SNCA under the Thy1 promoter (Thy1-aSyn mice) by transcriptome analysis.  The analysis revealed alterations in multiple biological processes in the striatum of Thy1-aSyn mice, including synaptic plasticity, signaling, transcription, apoptosis, and neurogenesis.
The present study investigated the consequences of SNCA overexpression on cellular processes and functions in the striatum of mice overexpressing wild-type, human SNCA under the Thy1 promoter (Thy1-aSyn mice) by transcriptome analysis.  The analysis revealed alterations in multiple biological processes in the striatum of Thy1-aSyn mice, including synaptic plasticity, signaling, transcription, apoptosis, and neurogenesis.

overall_design: Animal care was conducted in accordance with the U. S. Public Health Service Guide for the Care and Use of Laboratory Animals and procedures were approved by the University of California, Los Angeles (UCLA), I.A.C.U. Committee.  Transgenic (tg) mice overexpressing human wt SNCA under the Thy-1 promoter (Thy1-aSyn) created previously in a mixed C57BL/6-DBA background were kept in this background by breeding mutant females with wt males.  Only male mice were used in the study. The genotype of all tg and wt mice was verified by PCR analysis of tail DNA. Animals were maintained on a 12 hr light/dark cycle with free access to water and food. Six-month old male Thy1-aSyn and wt littermates were sacrificed by decapitation.  For microarray analysis, whole striata from each hemisphere were immediately dissected and pooled for each brain. Tissue was permeated in RNAlater (Qiagen, Valencia, CA), frozen in liquid nitrogen, and stored at - 80º C until used for RNA preparation. For PCR verification of transcriptional changes and for protein extracts preparation, brains from 5 male Thy1-aSyn and 5 wt littermates were obtained as above but then the brains were placed in a metal brain mold with grooves to ensure reproducible cutting of thick brain slices. A first coronal cut was made with a razor blade to remove the frontal part of the brain (at bregma + 1mm, at the anterior level of striatum). The following 1mm coronal slice (including the striatum but no globus pallidus) was used to dissect out striatal tissue.  A horizontal cut was made through the anterior commissures to exclude the nucleus accumbens. One cube of striatum was dissected out from each hemisphere, taking care not to include any corpus callosum, choroid plexus, or subventricular zone.  Samples were stored at -80º C until further processing.  Total RNA was extracted from striata of Thy1-aSyn and wt littermates (all males) with Trizol (Invitrogen, Carlsbad, CA), followed by a clean-up step with RNeasy columns (Qiagen) and RNA integrity check using a Bioanalyzer  (Agilent Tech., Foster city, CA). RNA samples were pooled, one pool representing the six control wt mice and the other representing the six SNCA overexpressing animals.  After synthesis, using Superscript (Invitrogen) and labeling using the ENZO labeling kit (Affymetrix Inc., Santa Clara, CA), cRNA probes were hybridized to mouse MOE-430A GeneChip arrays (Affymetrix) following the manufacturer’s protocol at the UCLA microarray core facility.  Significant differential gene expression between pooled tg and wt samples was ascertained by estimation of signal log2 ratios (or fold changes in expression values), after quality control checks, data normalization and estimating expression values using the Affymetrix Microarray Suite 5.0 Software (MAS 5.0).  After pairwise comparisons and filtering of this gene list using the following criteria: change p-value <0.005 for induce genes, change p-value > 0.995 for decreased genes, signal log2 ratio > 0.6 (> 1.52 fold change), excluding probes called absent in both groups, a list of differentially expressed genes was generated. We used various statistical softwares and databases to ascertain pathways affected by overexpression of SNCA that are associated with overrepresented genes in this gene list, including, the functional annotation tools accessible through DAVID (Database for Annotation, Visualization and Integrated Discovery, http://david.abcc.ncifcrf.gov )


title: Cross-Species Comparisons of Transcriptomic Alterations in Human and Rat Primary Hepatocytes Exposed to 2,3,7,8-Tetrachlorodibenzo-p-dioxin: human samples

status: Public on Feb 03 2012

city: Midland

first: Craig

last: Rowlands

state: MI

address: 1803 Bldg Washington Street

department: Toxicology & Environmental Research & Consulting

institute: The Dow Chemical Company

summary: A toxicogenomics approach was used to qualitatively and quantitatively compare the gene expression changes in human and rat primary hepatocytes exposed to 2,3,7,8-tetrachlorodibenzo-p-dioxin (TCDD). Hepatocytes from five individual rats and five individual humans were exposed for 24 hours to 11 concentrations of TCDD ranging from 0.00001 nM to 100 nM and a vehicle control.  Gene expression changes were analyzed using whole genome microarrays.

overall_design: 60 microarrays representing primary hepatocytes from 5 human subjects, each exposed to 11 doses of TCDD and vehicle controls. Arrays were completed with a one-color design.

first: Alan

last: Dombkowski


title: Cross-Species Comparisons of Transcriptomic Alterations in Human and Rat Primary Hepatocytes Exposed to 2,3,7,8-Tetrachlorodibenzo-p-dioxin

sample_organism:
Homo sapiens
Rattus norvegicus

platform_organism:
Homo sapiens
Rattus norvegicus


title: Influence of cell cycle on responses of MCF-7 cells to benzo[a]pyrene

status: Public on Feb 02 2012

city: Sutton

first: Ian

last: Giddings

state: Surrey

address: 15 Cotswold Road

department: Section of Molecular Carcinogenesis

institute: Institute of Cancer Research

summary:
BACKGROUND:
Benzo[a]pyrene (BaP) is a widespread environmental genotoxic carcinogen that damages DNA by forming adducts. This damage along with activation of the aryl hydrocarbon receptor (AHR) induces complex transcriptional responses in cells. To investigate whether human cells are more susceptible to BaP in a particular phase of the cell cycle, synchronised breast carcinoma MCF-7 cells were exposed to BaP. Cell cycle progression was analysed by flow cytometry, DNA adduct formation was assessed by 32P-postlabeling analysis, microarrays of 44K human genome-wide oligos and RT-PCR were used to detect gene expression (mRNA) changes and Western blotting was performed to determine the expression of some proteins, including cytochrome P450 (CYP) 1A1 and CYP1B1, which are involved in BaP metabolism.
RESULTS:
Following BaP exposure, cells evaded G1 arrest and accumulated in S-phase. Higher levels of DNA damage occurred in S- and G2/M- compared with G0/G1-enriched cultures. Genes that were found to have altered expression included those involved in xenobiotic metabolism, apoptosis, cell cycle regulation and DNA repair. Gene ontology and pathway analysis showed the involvement of various signalling pathways in response to BaP exposure, such as the Catenin/Wnt pathway in G1, the ERK pathway in G1 and S, the Nrf2 pathway in S and G2/M and the Akt pathway in G2/M. An important finding was that higher levels of DNA damage in S- and G2/M-enriched cultures correlated with higher levels of CYP1A1 and CYP1B1 mRNA and proteins. Moreover, exposure of synchronised MCF-7 cells to BaP-7,8-diol-9,10-epoxide (BPDE), the ultimate carcinogenic metabolite of BaP, did not result in significant changes in DNA adduct levels at different phases of the cell cycle.
CONCLUSIONS:
This study characterised the complex gene response to BaP in MCF-7 cells and revealed a strong correlation between the varying efficiency of BaP metabolism and DNA damage in different phases of the cell cycle. Our results suggest that growth kinetics within a target-cell population may be important determinants of susceptibility and response to a genotoxic agent.

overall_design: Two-color Agilent array. A reference design was chosen that all samples were hybridised to universal human reference RNA (UHRR from stratagene). 8-condition experiment (4 conditions: G0/G1, S, G2/M and unsynchronised (N); 2 treatments: BaP and DMSO; 1 time point: 12 hours). Three biological replicates for each condition. One replicate per array.

first: Hamza

last: Hamouchene

first: Volker

middle: M

last: Arlt

first: David

last: Phillips


title: Rearrangement of actin stress fiber in HUVECs under cyclic stretch

status: Public on Feb 10 2012

city: Tsukuba

first: Masaya

last: Seki

state: Ibaraki

address: Sengen 2-1-1

department: JEM Utilization Center

institute: Japan Aerospace Exploration agency

summary: Time-course of gene profiles indicate that gene expression changing in cyclic stretch are related to cell adhesion and MAPK signaling.

overall_design:
Gene expression changing by uniaxiali stretch was studied in a time course assay within 1.5 hour.
Six time points (0, 10, 20, 30, 60, 90 min) were triplicated

first: Mari

last: Imamizo-sato

first: Noriaki

last: Ishioka

first: Akira

last: Higashibata


title: Gene expression of Epstein-Barr Virus (EBV) positive nodal peripheral T cell lymphoma, unspecified (PTCL-U)

status: Public on Feb 01 2012

city: Seoul

first: Sang Yun

last: Ha

state: Seoul

address: Ilwondong Kangnamgu

department: Pathology

institute: Samsung Medical center

summary: EBV positive PTCL-U is a very rare but aggressive disease entity. To investigate gene expression profile, we performed gene expression analysis using two different types of microarray kits (Agilent chip 4x44K and 8x60K)

overall_design: We compared gene expression between in 3 EBV positive PTCL-Us and in 6 normal reactive lymph nodes.

first: Young-Hyeh

last: Ko

first: Sang

first: Jiyeon

last: Sung

first: Hyungjung

last: Ju

first: Kennosuke

last: Karube

first: Soek

first: Won

first: Masao

last: Seto


title: Caveolin-1 knockout liver and gonadal adipose tissue

status: Public on Jan 31 2012

first: Thomas

middle: Nathan

last: Person

address: 5323 Harry Hines Blvd

department: Clinical Sciences

institute: UT Southwestern

summary:
mRNA expression was compared in between wild type and caveolin-1 knockout livers
mRNA expression was compared in between wild type and caveolin-1 knockout gonadal adipose tissue

overall_design:
RNA was isolated from livers from male mice in at the light phase
RNA was isolated from gonadal adipose tissues from male mice in at the light phase

first: Ingrid

last: Asterholm

first: Philipp

middle: E

last: Scerer


title: A Common Peripheral Blood Gene-Set for Diagnosis and Prediction of Operational Tolerance in Pediatric and Adult Liver Transplantation

city: Stanford

first: Li

last: Li

state: CA

address: 300 pastuer dr.,

department: Pediatric

institute: Stanford University

summary: The ability to identify a robust means for both pediatric and adult liver transplant recipients for minimization and weaning of immunosuppression is greatly needed.   We analyzed 298 samples from pediatric (n=83) and published adult (n=57) liver transplant recipients, and the public available cell or tissue specific samples (n=158). Biomarkers were first identified from the integration of the cross-platform analysis of Stanford pediatric and adult studies and validated in independent samples from UCLA on microarray. Furthermore, Q-PCR was performed for targets validation and delivers a robust diagnostic assay of predicting potential liver tolerance after liver transplantation.   Thirteen unique genes were identified (FDR<5%) using nearest shrunken centroid classification methods as a minimum gene set to cross-validate and predict Stanford pediatric tolerance samples with 1misclassification, 5 misclassification for adult samples, and 100% sensitivity and 83% specificity for an independent UCLA pediatric samples in microarray platform. These subset of tolerant specific genes are highly expressed CD56+ natural killer cells (p=0.03). Furthermore, the subset can be narrowed down to 3 key genes with combined ROC=0.988 for the liver tolerance prediction from Q-PCR verification and 64% MIS and STA were predicted as tolerance with the >90% prediction probability.   Specific peripheral transcriptional programs can be identified in operational tolerance in pediatric recipients of liver allografts, distinct from those previously identified in adult operationally tolerant liver recipients, and may provide a means to non-invasively monitor patients in a serial manner for immunosuppression minimization. These genes are highly expressed in specific peripheral blood lymphocyte subsets, and their coordinated may support the maintenance of operational tolerance in children, following liver transplantation.

overall_design: Two centers data was included, which are 41 samples from Stanford as the training set and 44 samples from UCLA as the test set. 26 samples from Stanford and 15 samples from UCLA were used in microarray Agilent whole human genome microarray

first: Laura

last: Wozniak

first: Silke

last: Rodder

first: Sue

last: Heish

first: Anita

last: Talisetti

first: Qian

last: Wang

first: Carlos

last: Esquivel

first: Ken

last: Cox

first: Rong

last: Chen

last: McDiarmid

first: Minnie

last: Sarwal


title: Genome-wide analysis of Tdrd7 knockdown in lens epithelial-derived cell line 21EM15

first: Anton

last: Aboukhalil

overall_design: Total RNA obtained from Tdrd7 knockdown cells compared to lentiviral GFP control in 21EM15 lens epithelial-derived cell line

first: Salil

middle: A

last: Lachke

first: Richard

last: Maas


title: Gene expression profiling of mouse mammary tumorspheres, mammospheres, and mammospheres induced to differentiate

status: Public on Jan 30 2012

city: Hamilton

first: Robin

last: Hallett

state: Ontario

address: 1200 Main St W

department: Biochemistry and Biomedical Sciences

institute: McMaster University

summary:
Tumorpsheres and mammospheres were used to propagate mouse breast tumor-initiating cells and their normal stem/progenitor counterparts, respectively.  Mammospheres induced to differentiate were used to model the more differentiated cells of the mouse mammary gland.
We used microarrays to find differentrially expressed genes between tumorspheres, mammospheres, and mammospheres induced to differentiate

overall_design: Primary cells were isolate from either mouse mammary glands (FVB/N) or mouse mammary tumors and placed in stem cell media (MMTV-Neu [N2O2].  Spheres were passaged every 7 days for 3-5 passages and harvested for RNA isolation

first: John

last: Hassell


title: Analysis of the gene expression within the cochlea of aging C57BL6j mice.

status: Public on Jan 21 2012

city: Nedlands

first: Robert

middle: Jeffery

last: Marano

state: Western Australia

address: Sir Charles Gairdner Hospital, Hospital Avenue

department: School of Surgery

institute: Ear Science Institute Australia and the Ear Sciences Centre

summary: Gene expression within the cochlea of C57BL6j mice was examined. The hypothesis was that there was a genetic component to Age Related Hearing Loss and microarray would be useful in detecting candidate genes.

overall_design: Mice were aged in the laboratory to 4, 15 and 45 weeks of age. The cochlea were removed and pooled into groups of 5 for each age group. Total RNA was extracted and used in the micoroarray analysis. Differential expression was analysed between the different age groups i.e 4 - 15, 4 - 45 and 15 - 45 weeks.

middle: J


title: Post-epidemic eosinophilia myalgia syndrome associated with L-Tryptophan

status: Public on Jan 28 2012

city: Lebanon

first: Tammara

last: Wood

state: NH

address: WTRB 674

department: Biomedical Data Science

institute: Dartmouth Medical School

summary: Eosinophilia–myalgia syndrome (EMS) is characterized by subacute onset of myalgias and peripheral eosinophilia, followed by chronic neuropathy and skin induration. The EMS epidemic in 1989 was linked to L-tryptophan consumption originating from a single source. Following the Food and Drug Administration (FDA) ban on the sale of L-tryptophan, the incidence of EMS declined rapidly. Moreover, no new cases have been published since the FDA ban was lifted in 2005. We report the clinical, histopathological and immunogenetic features of a new case of L-tryptophan-associated EMS along with evidence of activated transforming growth factor-ß and interleukin-4 signaling in the lesional skin.

overall_design: 6 samples were analyzed to include EMS patient and two replicates along with three normal controls

first: Jeffrey

last: Allen

first: Alicia

last: Peterson

last: Sufit

first: Monique

last: Hinchcliff

first: J

last: Maloney

first: Frederick

middle: W

last: Miller

first: Michael

last: Whitfield

last: Varga


title: Global analysis of RNA secondary structure conservation between two metazoans

status: Public on Jan 26 2012

first: Fan

last: Li

address: 675 Charles E Young Drive South

department: Pediatrics

institute: University of California Los Angeles

type: Expression profiling by high throughput sequencing

summary: The secondary structure of RNA is necessary for its maturation, regulation, and processing. However, the global influence of RNA folding in eukaryotes is still unclear. Here, we identify evolutionarily conserved features of RNA secondary structure in metazoans by applying our high-throughput, sequencing-based, structure-mapping approach to Drosophila melanogaster and Caenorhabditis elegans. This analysis reveals key structural patterns across protein-coding transcripts that indicate RNA folding is influential to protein translation and microRNA-mediated targeting and/or regulation of mRNAs in animals. Additionally, we uncover a novel population of highly base-paired RNAs, many of which are likely functional, long, non-coding RNAs. Finally, we identify and characterize ~180 structural motifs of mRNAs that are under positive or negative selection in these metazoans, thereby revealing a large set of RNA structures that are likely functional. Overall, our findings highlight the significance of secondary structure within RNA molecules, and provide the first comprehensive evidence of widespread RNA secondary structure conservation in animals.

sample_organism:
Caenorhabditis elegans
Drosophila melanogaster

overall_design: Double-stranded (dsRNA) specific RNA sequencing (dsRNA-seq) and single-stranded (ssRNA) specific RNA sequencing (ssRNA-seq) in Drosophila DL1 cells and C. elegans mixed stage N2 worms. Each of the four samples (dsRNA/Dmel, ssRNA/Dmel, dsRNA/Cel, and ssRNA/Cel) was sequenced separately on both Illumina GA-IIx and Hiseq2000, giving a total of eight datasets. Two corresponding smRNA libraries (smRNA-seq) of the same DL1 cells and mixed stage N2 worms are also presented.

first: Qi

last: Zheng

first: Paul

last: Ryvkin

first: Isabelle

middle: C

last: Dragomir

first: Yaanik

last: Desai

first: Subhadra

last: Aiyer

first: Otto

last: Valladares

first: Jamie

last: Yang

first: Shelly

last: Bambina

first: Leah

middle: R

last: Sabin

middle: I

last: Murray

first: Todd

last: Lamitina

first: Arjun

last: Raj

first: Sara

last: Cherry

first: Li-San

last: Wang

first: Brian

last: Gregory


title: Molecular responses of human lung epithelial cells to the toxicity of copper oxide nanoparticles inferred from whole genome expression analysis.

status: Public on Jan 05 2012

first: Taro

last: Takemura

address: 1-2-1 Sengen

department: Nanotechnology Innovation Station

institute: National Institute for Materials Science

summary: This study proposes a molecular mechanism for lung epithelial A549 cell response to copper oxide nanoparticles (CuO-NPs) related to Cu ions released from CuO-NPs. Cells that survived exposure to CuO-NPs arrested the cell cycle as a result of the downregulation of proliferating cell nuclear antigen (PCNA), cell division control 2 (CDC2), cyclin B1 (CCNB1), target protein for Xklp2 (TPX2), and aurora kinase A (AURKA) and B (AURKB). Furthermore, cell death was avoided through the induced expression of nuclear receptors NR4A1 and NR4A3 and growth arrest and DNA damage-inducible 45 β and γ (GADD45B and GADD45G, respectively). The downregulation of CDC2, CCNB1, TPX2, AURKA, and AURKB, the expressions of which are involved in cell cycle arrest, was attributed to Cu ions released from CuO-NPs into medium. NR4A1 and NR4A3 expression was also induced by Cu ions released into the medium. The expression of GADD45B and GADD45G activated the p38 pathway that was involved in escape from cell death. The upregulation of GADD45B and GADD45G was not observed with Cu ions released into medium but was observed in cells exposed to CuO-NPs. However, because the expression of the genes was also induced by Cu ion concentrations higher than that released from CuO-NPs into the medium, the expression appeared to be triggered by Cu ions released from CuO-NPs taken up into cells. We infer that, for cells exposed to CuO-NPs, those able to make such a molecular response survived and those unable to do so eventually died.

overall_design: Two-condition experiment, CuO-NPs exposured vs. non-treated cells. Hybridization: 2 replicates. Scanning: 3 replicates (Gain changed).

first: Nobutaka

last: Hanagata

first: Fei

last: Zhuang

first: Sarah

last: Connolly

first: Jie

first: Nobuhiro

last: Ogawa

first: Mingsheng

last: Xu


title: Rosiglitazone-induced molecular changes in adipose progenitors

status: Public on Jan 18 2012

first: Wei

last: Tang

state: TX

address: 6000 Harry Hines Blvd.

department: Developmental Biology

institute: UT Southwestern Medical Center at Dallas

summary:
White adipose tissue regulates metabolism; the importance of this control is highlighted by the ongoing pandemic of obesity and associated complications such as diabetes, atherosclerosis, and cancer. White adipose tissue maintenance is a dynamic process, very little is known about how pharmacologic stimuli affect such plasticity. Combining in vivo lineage marking and BrdU labeling strategies, we found that rosiglitazone, a member of the thiazolidinedione class of glucose-lowering medicines, markedly increases the evolution of adipose progenitors into adipocytes. Notably, chronic rosiglitazone administration disrupts the adipogenic and self-renewal capacities of the stem cell compartment and alters its molecular characteristics. These data unravel unknown aspects of adipose dynamics and provide a basis to manipulate the adipose lineage for therapeutic ends.
The goal of this gene expression array was to identify changes in molecular expression in adipose progenitors isolated from mice that underwent two-month rosiglitazone treatment.

overall_design: Adipose SV GFP+ cells (adipose progenitors) were FACS-isolated from adult AdipoTrak mice that had been treated with or without rosiglitazone (0.0075%) for 2 months. RNAs isolated from these cells were used for microarray. Each cohort contains 3-4 mice, each experimental group (-TZD and +TZD) contains 3 cohorts.

first: Daniel

last: Zeve

first: Jin

last: Seo

first: A-Young

last: Jo

first: Jonathan

last: Graff


title: Potentiation of glucocorticoid signaling by chloroquine via inhibition of lysosomes

city: Grand Rapids

first: Karl

last: Dykema

address: 333 Bostwick Ave. NE

institute: Van Andel Institute

summary: Anti-malaria drug chloroquine has been used as an anti-inflammatory agent for treating systemic lupus erythematosus and rheumatoid arthritis, without clear mechanism of action.  Here we report that chloroquine potently inhibits the expression of proinflammatory cytokines through transrepression of glucocorticoid receptor (GR). Instead of direct binding to GR, chloroquine synergistically activates glucocorticoid signaling via inhibition of lysosomal functions.  In mouse collagen induced arthritis model, chloroquine synergizes the therapeutic effects of glucocorticoid.  Lysosomal inhibition by bafilomycin A1, an inhibitor of V-type ATPase, or by knockdown of transcription factor EB (TFEB), a master activator of lysosomal biogenesis, mimics the effects of chloroquine.  These results reveal an unexpected regulation of glucocorticoid signaling by lysosomes and provide a mechanistic basis for treating inflammation and autoimmune diseases by combination of glucocorticoids and lysosomal inhibitors.

overall_design: Macrophage THP-1 cells treated with LPS, chloroquine and dexamethasone.


title: Differentially expressed genes in recurrence of squamous cell carcinoma tumors of the oral cavity in a mouse model

city: Heidelberg

first: Gustavo

last: Acuna

address: INF 280

institute: DKFZ

summary: We applied global gene expression with samples derived from a recently established mouse model for oral cancer recurrences and identified a list of genes with differential expression between primary and recurrent tumors.

overall_design: 5 independent primary tumors and respectivce recurrences were analyzed. Two replicates of the original cell line used for the generation of all tumors was also added to the study.

first: Jochen

last: Hess


title: A Wnt-Bmp feedback circuit controls inter-tissue signaling dynamics in tooth organogenesis

status: Public on Jan 13 2012

first: Joshua

middle: WK

last: Ho

address: 41 Avenue Louis Pasteur

department: Department of Medicine

institute: Brigham and Women's Hospital

summary: Gene expression profiling of the epithelial and mesenchymal compartments of the developing mouse tooth using Laser Capture Microdissected (LCM) or enzymatic treatment with Dispase to isolate the dental epithelial and mesenchymal tissue, over a developmental period from E10.0-E14.5. The data is also accessible from http://compbio.med.harvard.edu/ToothCODE/

overall_design: The aim of the study is to investigate the the mode of epithelial-mesenchymal (E-M) interaction through analyzing global gene expression patterns.   We collected wildtype spatiotemporal gene expression data and perturbation data from transcription factor knockouts and signaling molecule treatments to identify differentially regulated genes and reconstruct a gene regulatory network controlling E-M interaction in early tooth development.

last: O'Connell

first: Tada

last: Mammoto

first: Donald

last: Ingber

first: Peter

last: Park

first: Richard

last: Maas


title: mRNA profiles of four developmentally related hematopoietic cell types (LSK, L-S-K+, Gr1+ and Ter119+) isolated from the BM of B6 and D2 mice

status: Public on Jan 25 2012

city: Groningen

first: Leonid

last: Bystrykh

state: Groningen

address: A. Deusinglaan 1

department: European Research Institute for the Biology of Ageing - ERIBA

country: Netherlands

institute: University Medical Center Groningen

summary: The combination of valproic acid and lithium delays hematopoietic stem\progenitor differentiation

overall_design: Microarray-based microRNA profiling study was peformed of four developmentally related hematopoietic cell types isolated from the BM of B6 and D2 mice. Total RNA isolated from purified LSK multilineage cells, committed LS−K+ cells, erythroid TER-119+ cells and myeloid Gr-1+ cells was hybridized to Single Color Illumina mouse WG-6_V2 mRNA arrays. Triplicates were generated for each of the 8 conditions (4 cell types, 2 mouse strains).

first: Marta

last: Walasek

middle: V

first: Vinvent

last: van den Boom

first: Sandra

last: Olthof

first: Albertina

last: Ausema

first: Martha

last: Ritsema

first: Gerwin

last: Huls

first: Gerald

last: de Haan

first: Ronald

last: van Os


title: RIP-chip of HuR in MCF7 cells exposed to doxorubicin

status: Public on Dec 31 2011

city: Povo

first: Toma

last: Tebaldi

state: Trento

address: via Sommarive n. 9

department: Centre for Integrative Biology

institute: University of Trento

summary:
The purpose of the study was to identify mRNA bound to HuR in the presence of doxorubicin in MCF7 cells. We collected cytoplasmic RNA from untreated and treated cells and detected differentially expressed genes (DEGs). We also coimmunoprecipitated HuR and IgG (as control) from doxorubicin treated cells. Comparison between HuR RIP and IgG RIP signals was used to discriminate specific mRNA bound to HuR. HuR coimmmunoprecipitated material was hybridized together with cytoplasmic mRNA of doxorubicin treated cells, enabling the fold enrichment calculation and the selection of mRNAs bound to HuR.
Keywords: RIP-Chip, HuR, doxorubicin, MCF7, HuR consensus binding, post-transcriptional regulation.

overall_design: We subjected MCF7 cells to starvation for 24h and then we added doxorubicin at final concentration of 10 uM, profiling before and after 4 hours of treatment in biological quadruplicate (only on cytoplasmic mRNAs, as HuR was found in the cytoplasm). Differentially expressed genes, altered during the treatment, were identified. Data derived from HuR RIP-Chip and IgG RIP-Chip (in biological quadruplicate) allowed the identification of specific mRNAs bound to HuR. The comparison between HuR RIP-Chip and cytoplasmic extracts from doxorubicin treated cells (in biological triplicate) identified those genes that were more strictly bound to HuR independently from their expression levels.

first: Elisa

last: Latorre

first: Antonino

last: Spartà

first: Gabriella

last: Viero

first: Alessandro

last: Quattrone

last: Provenzani


title: Cytosolic flagellin receptor NLRC4 protects mice against mucosal and systemic challenges

status: Public on Jan 01 2012

city: Atlanta

first: Gregory

last: Doho

state: GA

address: 1365B Clifton Rd NE

institute: Emory University

summary: Bacterial flagellin is a dominant innate immune activator of the intestine.  Therefore, we examined the role of the intracellular flagellin receptor, NLRC4, in protecting the gut and/or driving inflammation. In accord with NLRC4 acting via transcription-independent pathways, loss of NLRC4 did not reduce the rapid robust changes in intestinal gene expression induced by flagellin administration. Loss of NLRC4 did not alter basal intestinal homeostasis nor predispose mice to development of colitis upon administration of an anti-IL-10R monoclonal antibody.  However, in response to epithelial injury induced by dextran sulfate sodium (DSS), loss of NLRC4 resulted in more severe disease indicating a role for NLRC4 in protecting the gut.  Moreover, loss of NLRC4 resulted in increased mortality in response to flagellate, but not aflagellate Salmonella infection.  Thus, despite not being involved in rapid intestinal gene remodeling upon detection of flagellin, NLRC4-mediated inflammasome activation protects mice from mucosal and systemic challenges

overall_design: Flagellin (FliC) from WT Salmonella enterica serovar Typhimurium (SL3201, fljB–) was purified through sequential cation and anion-exchange chromatography and purity was verified as previously described 4.  WT, T5KO, N4KO and T5/N4-DKO mice (n=6) were given either 0.2 mL PBS or flagellin (10μg/mouse in 0.2 mL PBS) intraperitoneally. After 1h, mice were euthanized and colon was taken and stored in RNAlater (Invitrogen) for 1 day. Total mRNA was isolated from colonic tissues using TRIzol (Invitrogen) and purified using the RNeasy® Plus Mini kit (Qiagen) according to the manufacturer’s instructions

first: Frederic

last: Carvalho

first: Ilke

last: Nalbantoglu

first: Jesse

middle: D

last: Aitken

first: Yueju

last: Su

first: Matam

last: Vijay-Kumar

middle: H

first: Andrew

middle: T

last: Gewirtz


title: Effects of Mysm1 deficiency on gene expression across a range of mouse tissues and cell types (tissue data)

city: Montreal

first: Anastasia

last: Nijnik

state: Quebec

address: 3649 Promenade Sir William Osler

department: Physiology

institute: McGill University

summary: Stem cell differentiation and lineage specification depend on coordinated programs of gene expression, but our knowledge of the chromatin modifying factors regulating these events remains incomplete. Ubiquitination of histone H2A (H2A-K119u) is a common chromatin modification associated with gene silencing, and controlled by the ubiquitin-ligase polycomb repressor complex 1 (PRC1) and H2A-deubiquitinating enzymes (H2A-DUBs). The roles of H2A-DUBs in mammalian development, stem cells, and haematopoiesis have not been addressed. Here we characterized an H2A-DUB targeted mouse line Mysm1-tm1a/tm1a and demonstrated defects in bone marrow haematopoiesis, resulting in lymphopenia, anemia, and thrombocytosis. Development of lymphocytes was impaired from the earliest stages of their differentiation; and there was also a depletion of erythroid cells and a defect in erythroid progenitor function. These phenotypes were due to a cell-intrinsic requirement for Mysm1 in the bone marrow. Importantly, Mysm1-tm1a/tm1a haematopoietic stem cells were functionally impaired, and this was associated with elevated levels of reactive oxygen species, γH2AX DNA damage marker, and p53 protein in the haematopoietic progenitors. Overall these data establish a role for Mysm1 in the maintenance of bone marrow stem cell function, in the control of oxidative stress and genetic stability in haematopoietic progenitors, and in the development of lymphoid and erythroid lineages.

overall_design: Total RNA from different mouse tissues (liver, bone marrow, brain) and cell types (embryonic fibroblasts - MEFs, and embryonic stem cells - ESCs) from wild type, Mysm1+/tm1a (heterozygous), and Mysm1tma1/tm1a (homozygous) mice was analyzed. Tissue and MEFs comparisons are between 3-4 animals per group; ESC comparisons are between three independently passaged samples of wild type, Mysm1+/tm1a, and Mysm1tma1/tm1aES-cells, all on C57BL/6 background. Full allele name: Mysm1tm1a(KOMP)WTSI . This Series includes the data from the tissues.

first: Simon

last: Clare

first: Claire

last: Raisen

first: Peter

last: Ellis

first: Robert

last: Andrews

first: Chris

last: McGee


title: Gene expression profiling of Hodgkin Lymphoma cell line following REL-B depletion

status: Public on Jan 20 2012

city: Bethesda

first: Brian

middle: Andrew

last: Lewis

state: MD

address: 9000 Rockville Pike

department: metabolism Branch

institute: National Cancer Institute-NIH

summary: The expression array data will be merged with Rel-B ChIP-Seq data in HL cell lines. This will show REL-B direct and indirect controlled downstream target genes

overall_design: HL cells were infected with a retrovirus that delivers a specific shRNA sequence to knock down the expression of REL-B

first: Stella

last: Ranuncolo

first: Wenming

last: Xiao

first: George

last: Wright

first: Mones

last: Abu-Asab

first: Stefania

last: Pittaluga

first: Elaine

middle: S

last: Jaffe


title: Effects of Mysm1 deficiency on gene expression across a range of mouse tissues and cell types (cell data)

overall_design: Total RNA from different mouse tissues (liver, bone marrow, brain) and cell types (embryonic fibroblasts - MEFs, and embryonic stem cells - ESCs) from wild type, Mysm1+/tm1a (heterozygous), and Mysm1tma1/tm1a (homozygous) mice was analyzed. Tissue and MEFs comparisons are between 3-4 animals per group; ESC comparisons are between three independently passaged samples of wild type, Mysm1+/tm1a, and Mysm1tma1/tm1aES-cells, all on C57BL/6 background. Full allele name: Mysm1tm1a(KOMP)WTSI . This Series includes the data from the cells.


title: Expression data from 30 medulloblastomas

first: Woong Yang

last: Park

address: 28 Yongondong, Chongnogu

department: Biochemistry and Molecular Biology

institute: Seoul National University

summary: Pediatric medulloblastoma is considered a highly heterogeneous disease, and a new strategy of risk stratification to optimize therapeutic outcomes is required. We aimed to investigate a new risk-stratification approach based on expression profiles of medulloblastoma cohorts. We analyzed gene expression profiles of 30 primary medulloblastomas and detected strong evidence that poor survival outcome was significantly associated with mRNA expression profiles of 17p loss. However, it was not supported in independent cohorts from previously published data (n=100). We speculated that this controversy might come from complex conditions of two important prognostic determinants, loss of tumor suppressors (chromosome 17p) and high expression of oncogenes, c-myc (MYC) or N-myc (MYCN). Simultaneous consideration of these two factors led to a new subgrouping of patients, exhibiting obviously different survival expectancies between the subgroups. Patients with up-regulated WNT signalings were always pre-defined as an independent subgroup, which ultimately removed confounding effect arising from contradictory outcome, favorable prognosis of WNT medulloblastomas despite their high MYC/MYCN expression level. We also found that age is a significant prognostic marker after adjusting for 17p and MYC/MYCN status. Diminished survival in age <3 years was more substantial in groups with high expression of MYC/MYCN or 17p loss, indicating survival outcome might be coordinately affected by these three factors. We suggest a more tailored and easily applicable subgrouping system based on expression profiles of chromosome 17p and MYC/MYCN, while separating WNT medulloblastoma as an independent subgroup, which could provide the basis for a novel risk-stratification strategy in pediatric medulloblastoma.

overall_design: We analyzed gene expression profiles of 30 primary medulloblastomas with the aim of providing a new risk-stratification approach based on expression profiles of medulloblastoma cohorts.

first: Woong-Yang

first: Seung-Ki

last: Kim


title: Expression profile of human ESC, ESC-drived definitive endoderm and endodermal progenitor cells

city: Philadelphia

first: Paul

last: Gadue

state: PA

address: 3501 Civic center Blvd, CTRB 5012

institute: Children's Hospital of Philadelphia

summary:
Endodermal progenitor cells (EP cells) are derived from human embryonic stem cell(ESC)-derived definitive endoderm (DE) cells. EP cells are cultured in high BMP media and DE cells are in high Activin media. Both cells can be further differentiated to liver, pancreas, etc.
We used microarray to detail the global gene expression profile of DE cells and EP cells to delineate the difference of DE cells and EP cells.

overall_design: ESCs were sorted by SSEA3 and SSEA4. DE cells and EP cells were sorted by CXCR4 and CD117. Sorted cells were lysed in RLT buffer. RNA was extracted and hybridized to Affimetrix microarrays. Each group had 3 biological replicates.

first: Lei

last: Ying

first: Xin

last: Chen


title: Hypoxia suppresses neuronal functions in primary neuron, speeds cell cycle progression and affection the differentiation potential of neural stem cells

city: La Jolla

first: Dan

last: Zhou

address: CMG 103, 9500 Gilman Drive, MC0735

institute: University of California, San Diego, School of Medicine

summary: Multiple diseases are associated with a pathological hypoxia in the brain, resulting in various neurological sequalae. Understanding the response to hypoxia of neurons and neural stem cells (NSCs) will help devise better therapeutic strategies. We have exposed primary neurons (PN) and neural stem cells to 1% O2. Both cell types survived well, and neurons showed no obvious morphological changes. The NSCs, however, became fusiform, and displayed a population of cells with accelerated transition in cell cycle. Gene expression profile through microarray analysis revealed major differences in response to hypoxia between NSC and PN. Not only the number of genes significantly changes was ~five-fold higher in NSC, but the types of genes involved and the direction of change was quite different. In particular, NSCs up-regulated multiple growth factors and down-regulated most other cytokines and metalloproteases , while PN down-regulated most neuronal-specific genes, up-regulated growth factors, with no major effect on cytokines. We conclude that hypoxia 1- accelerates cell cycle transition of NSC in a post-transcriptional fashion ; 2-affects cytokines in NSC but not in neurons; 3-result in up-regulation of multiple growth factors in NSC and PN; and 4-suppresses neuronal specific functions.

overall_design:
1) Primary neurons (PN) and neural stem cells were exposed to 1% O2.
2) Gene expression profile through microarray analysis was used to determine the differences in response to hypoxia between NSC and PN.

first: Hady

last: Felfly

first: Jin

last: Xue

first: Gabriel

middle: G

last: Haddad


title: Interaction between endothelium and chronic lymphocytic leukemia B-cells rescues from apoptosis and modulates gene expression profile of leukemic cells

city: Modena

first: Rossana

last: Maffei

state: Modena

address: Via del Pozzo 71

department: Dept of Hematology and Oncology

institute: University of Modena and Reggio Emilia

summary: Chronic lymphocytic leukemic B cells (CLL) reside in close contact with activated endothelial cells (EC) in infiltrated tissues. Here, we investigated the interactions between EC and CLL cells, highlighting molecular networks involved in this cellular crosstalk. We co-cultured purified CLL cells on HUVEC monolayer (HC) or in medium alone. We found that EC protected CLL from spontaneous apoptosis. A 2.2-fold increase in relative viability in  IGHV mutated CLL and a 6.1-fold increase in IGHV unmutated CLL was detected in co-culture. Moreover, the endothelial cell layer decreased the in vitro sensitivity of CLL cells to Fludarabine-induced apoptosis. Physical contact with EC is essential for protection to apoptosis. The insertion of a microporous membrane or blocking adhesion with anti-CD106 and anti-CD18 antibodies determined the complete abrogation of apoptosis protection. On the other hand, a reduction of  apoptosis was measured in CLL cells cultured with conditioned medium collected from HC, implying that survival is partially mediated by soluble factors. Overall 1944 genes were modulated in CLL by co-culture. The EC contact seem to determine on CLL a kind of microenvironmental-driven angiogenic switch, improve the secretion of cytokines regulating tissue elements such as stromal cells and macrophages and also increase anti-apoptotic molecules. Our study support the line of evidence indicating endothelial cells as a major player in the CLL-infiltrated microenvironments are able to create a vicious cycle of cooperation that strongly sustains leukemic cell survival, protects CLL from drug-induced apoptosis and widely modifies CLL phenotype.

overall_design: Large-scale gene expression profiling (GEP) was performed on total RNA extracted from purified CD19+ cells isolated from 9 individual CLL patients which were separated in 3 experimental subsets: (i) freshly isolated cells (CLL baseline), (ii) CLL cells cultured in medium alone for 48 hours (CLL only) and (iii) CLL cells co-cultured 48h on HUVEC layer (CLL HC).

first: Roberto

last: Marasca