title: The delta subunit of RNA polymerase, RpoE, is a global modulator of Streptococcus mutans environmental adaptation

status: Public on Sep 21 2010

city: Braunschweig

first: Xiaoli

last: Xue

address: Inhoffenstr. 7

department: Cell Biology

institute: Helmholtz Center for Infection Research

summary:
Transcriptional profiling of S. mutans rpoE knockout mutant comparing to the wild type. The mutation of rpoE cause dramatic changes in phenotypes. The goal is to determine the genes affected by rpoE.
The delta subunit of RNA polymerase, RpoE, is wide spread in low G+C Gram-positive bacteria and is thought to play a role in enhancing transcriptional specificity by blocking RNA polymerase binding at weak-promoter sites and stimulating RNA synthesis by accelerating core enzyme recycling. Despite the well-studied biochemical properties of RpoE, a role for this protein in vivo has not been defined in depth. In this study, we show that inactivation of rpoE in the human dental caries pathogen Streptococcus mutans causes impaired growth, and loss of important virulence traits, including biofilm formation, resistance to antibiotics, and tolerance to environmental stresses. Complementation of the mutant with rpoE expressed in trans restored its phenotype to wild type. The luciferase fusion reporter showed that rpoE was highly transcribed throughout growth, and that acid and hydrogen peroxide stresses repressed rpoE expression. Transcriptome profiling of wild type and ΔrpoE cells in the exponential and early stationary phase of growth, under acid and hydrogen peroxide stress and under both stresses combined revealed that genes involved in histidine synthesis, malolactic fermentation, biofilm formation, and antibiotic resistance were down-regulated in the ΔrpoE mutant in all conditions. Moreover, the loss of RpoE resulted in dramatic changes in transport and metabolism of carbohydrates and amino acids. Interestingly, differential expression, mostly up-regulation, of 330 non-coding regions was found. In conclusion, this study demonstrates that RpoE is an important global modulator of gene expression in S. mutans, which is required for optimal growth and environmental adaptation.

overall_design: 5 conditions, mutant vs wild type, biological replicates: 2,  technical replicates: 2

first: Jürgen

last: Tomasch

first: Helena

last: Sztajer

first: Irene

last: Wagner-Döbler


title: Transcriptional analysis of Chlamydia trachomatis Serovar D genes under different in-vitro hormonal conditions

status: Public on Sep 16 2010

city: Brisbane

first: Ashkan

last: Amirshahi

state: QLD

address: 60 Musk ave, Kelvin Grove

department: Infectious diseases

country: Australia

institute: Institute of Health and Biomedical Innovation (IHBI)

summary: In this project we examined in-vitro effect of female sex hormones, estradiol and progesterone at average physiological concentration level on Chlamydia trachomatis gene expression level.

platform_organism:
Chlamydia trachomatis
Chlamydia pneumoniae CWL029

overall_design: Regulation of chlamydial gene expression by the female sex hormones oestradiol and progesterone was examined. A total of 16 chlamydial arrays were analysed with the 4 culture conditions (no hormone, E, P, E+P) x four replicates. Bacterial samples were grown in non-hormone treated culture were used as control

first: Charles

last: Wan

first: Ken

last: Beagley

first: Peter

last: Timms


title: Beyond the Macrophage: System-wide Cellular and Molecular Dysregulation in GBA1 Deficient Mice Recapitulates Human Non-neuronopathic, Type 1 Gaucher Disease

status: Public on Jul 30 2010

city: New Haven

first: Pramod

middle: K

last: Mistry

state: CT

address: 333 Cedar Street

department: Pediatrics

country: USA

institute: Yale University

summary: In non-neuronopathic type 1 Gaucher disease (GD1) mutations in GBA1 gene results in deficiency of glucocerebrosidase and the accumulation of glucocerebroside in lysosomes of mononuclear phagocytes. The metabolic defect leads to a complex phenotype involving the viscera, the bone marrow and the skeleton. However the prevailing macrophage-centric view of the disease does not explain emerging aspects of the disease such as hematological malignancies, autoimmune diathesis, Parkinson’s disease and osteoporosis poorly responsive to macrophage targeted enzyme therapy or anti-resorptive therapies. We developed a conditional KO mouse model of GD1 to delineate cells and pathways in GD1. By targeting the cells of the hematopoetic and mesenchymal cell lineages through an Mx1 promoter, we recapitulated human GD1.    We show that, in addition to significant visceral and hematologic disease, GD1 mice show profound osteopenia due to a bone formation defect.  Cytokine measurements, microarray analysis and cellular immunophenotyping together point to widespread dysfunction of macrophages and other immune cells together with a striking abnormality in thymic T-cell development. Our study provides the first direct evidence for the involvement of cell lineages other than mononuclear phagocytes, most notably osteoblasts and T cells, in the pathophysiology of the clinical spectrum of type 1 GD. These findings have important implications for treatment of GD1.

overall_design: We hypothesize that regulation of gene expression is different in Gaucher disease compared with the normal controls. This difference may even be evident in the different stages of this disease. In order to gain insight to the genes that are potentially involved in the development of Gaucher disease in its different clinical stages, exon-array is chosen for this genome-wide association studies.  Mouse liver and spleen samples from normal control, GD with moderate to severe splenomegaly/hepatomegaly, together nine samples were chosen.  The goal is to find out genes of which the expression may relate to the GD or the severity of GD and thus help identify genetic modifier genes that may contribute to the onset and development of Gaucher disease.


title: Expression data from untreated and rottlerin-treated normal and systemic sclerosis-derived human fibroblasts

status: Public on Aug 22 2010

city: Philadelphia

middle: Joseph

last: Wermuth

state: PA

address: 233 South 10th Street

department: Dermatology and Cutaneous Biology

institute: Thomas Jefferson University

summary:
PKC-δ inhibition with the selective inhibitor, rottlerin, resulted in potent downregulation of type I collagen expression and production in normal human dermal fibroblasts and abrogated the exaggerated type I collagen production and expression in fibroblasts cultured from affected skin from patients with the fibrosing disorder, systemic sclerosis (SSc).  To elucidate the mechanisms involved in the ability of PKC-δ to regulate collagen production in fibroblasts, we examined the effects of PKC-δ inhibition on the transcriptome of normal and SSc-derived human dermal fibroblasts.
We used microarrays to detail the effects of PKC-δ inhibition with rottlerin on the transcriptome of normal and SSc-derived human dermal fibroblasts and to identify gene networks that might be involved in the regulation of extracellular matrix by PKC-δ.

overall_design: Early passage normal and SSc human dermal fibroblasts were incubated with rottlerin (50 µg/mL) for 24 hours, followed by RNA extraction of treated and untreated samples and hybridization on Affymetrix microarrays. Early passage fibroblasts derived from normal and SSc dermal biopsies were utilized in this study to ensure that phenotypes remained as close as possible to original biopsy tissue.  SSc patient sample biopsies were isolated from leading edge of forearm lesion; normal biopsies were obtained from forearm dermis.

middle: J

first: Sankar

last: Addya

first: Sergio

middle: A

last: Jimenez


title: Ultrastructural and transcriptional profiling of neuropathological misregulation of CREB function

status: Public on Apr 20 2010

city: Sant Joan d'Alacant

first: Angel

last: Barco

state: Alicante

address: Av. Santiago Ramón y Cajal

country: Spain

institute: Instituto de Neurociencias (UMH-CSIC)

summary: We compare here the neurodegenerative processes observed in the hippocampus of bitransgenic mice with chronically altered levels of cAMP-response element-binding protein (CREB) function. The combination of genome-wide transcriptional profiling of degenerating hippocampal tissue with microscopy analyses reveals that the sustained inhibition of CREB function in A-CREB mice is associated with dark neuron degeneration, whereas its strong chronic activation in VP16-CREB mice primarily causes excitotoxic cell death and inflammation. Furthermore, the meta-analysis with gene expression profiles available in public databases identifies relevant common markers to other neurodegenerative processes and highlights the importance of the immune response in neurodegeneration. Overall, these analyses define the ultrastructural and transcriptional signatures associated with these two forms of hippocampal neurodegeneration, confirm the importance of fine-tuned regulation of CREBdependent gene expression for CA1 neuron survival and function, and provide novel insight into the function of CREB in the etiology of neurodegenerative processes.

overall_design: For each mouse genome 430 2.0 gene expression array (Affymetrix, Santa Clara, CA, USA), total RNA was extracted from the hippocampi of three to four mice with the same age, sex, and genotype to produce one pooled sample. We analyzed three late A-CREB pooled samples (6-week-old mice) and three late VP16-CREB pooled samples (3-week-off dox) with their corresponding control littermate samples (three pooled samples for each strain). To compare with early changes, we included two pooled A-CREB early samples (3-week-old mice) and two pooled VP16-CREB early samples (1-week-off dox) with their corresponding control littermate samples. In the case of A-CREB mice, we used the dataset GSE14320. We prepared new samples from bitransgenic mice and control littermates 1 week after transgene induction and hybridized them to mouse genome 430 2.0 genechips. The arrays were hybridized, washed, and screened for quality according to the manufacturer’s protocol.

first: Luis

middle: M

last: Valor

first: Dragana

last: Jancic

first: Rafael

last: Luján


title: Orchestration of Floral Initiation by APETALA1

status: Public on Apr 02 2010

city: Wageningen

first: Gerco

last: Angenent

address: Bornsesteeg 65

country: Netherlands

institute: Plant Research International

type: Genome binding/occupancy profiling by high throughput sequencing

summary: The MADS-domain transcription factor APETALA1 (AP1) is a key regulator of Arabidopsis flower development. To understand the molecular mechanisms underlying AP1 function, we identified its target genes during floral initiation using a combination of gene expression profiling and genome-wide binding studies. Many of its targets encode transcriptional regulators, including known floral repressors. The latter genes are down-regulated by AP1, suggesting that it initiates floral development by abrogating the inhibitory effects of these genes. While AP1 acts predominantly as a transcriptional repressor during the earliest stages of flower development, regulatory genes known to be required for floral organ formation were found to be activated by AP1 at more advanced stages, indicating a dynamic mode of action. Our results further imply that AP1 orchestrates floral initiation by integrating growth, patterning and hormonal pathways.

overall_design: We used the  AP1-GR system to conduct chromatin immunoprecipitation experiments with AP1-specific antibodies followed by deep-sequencing (ChIP-Seq) in order to determine AP1 binding sites on a genome-wide scale. Samples were generated from  tissue in which the AP1-GR protein was induced for 2h using a single treatment of 1 uM DEX to the shoot apex. As control, we performed ChIP experiments using the same antibody on uninduced tissue. Experiments were done in two biological replicates.

first: Kerstin

last: Kaufmann

first: Jose

last: Muino


title: Genomic approach in B-cell Chronic Lymphocytic Leukemia: molecularly distinct subgroups of patients with 13q14 deletion

status: Public on Sep 01 2010

city: MILAN

first: Luca

last: Agnelli

address: Venezian 1

department: Department of Advanced Diagnostics

country: Italy

institute: IRCCS Istituto Nazionale dei Tumori

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

summary: B-cell chronic lymphocytic leukemia (B-CLL) is characterized by a highly variable clinical course that reflects its heterogeneous genomic pattern. To better define molecular subtypes of the disease, we performed SNP and gene expression profiling microarray analyses in a panel of early stage (Binet A) patients. A clustering analysis of genomic profiles identified four significant groups mainly driven by del(13)(q14) and trisomy 12. Notably, patients with del(13)(q14) were grouped in two separate clusters based on the presence of a biallelic loss and the extension of the deletion. The shorter monoallelic deleted 13q14 region was found to be 635 kb in length, not encompassing the mir-15a/16-1 locus. Interestingly, the mir-15a and mir-16 expression was found to be significantly down-regulated only in patients with biallelic loss. Furthermore, a multiclass supervised analysis identified a different transcriptional signatures in the two genomic subgroups with del(13)(q14). Finally, an integrative approach identified 93 transcripts, mainly mapped to chromosome 12 and 13q12-q14.3, whose expression was significantly correlated with the DNA copy number. Overall, our data further support the notion that transcription deregulation in B-CLL could be mostly due to a gene dosage effect and underscore the presence of two distinct molecular types of 13q14 deleted patients with potential clinical relevance.

overall_design:
Transcriptional analysis of 60 B-CLL patients, and genotyping analysis of 100 B-CLL patients, in early stage disease (Binet A).

This series of microarray experiments contains the gene expression profiles of purified B-cell chronic lymphocytic leukemia (B-CLL) cells obtained from 60 newly diagnosed patients (Binet stage A). Peripheral blood mononuclear cells from B-CLL patients were isolated by Ficoll-Hypaque density-gradient centrifugation and the proportion of CD5/CD19/CD23 triple positive B cells in the suspension was determined by direct immunofluorescence performed using a FACS-sort flow cytometer with antibodies to: CD19 FITC/PE, CD23 PE and CD5 Cy-Chrome. If B-CLL cells were less than 90%, T cells, NK cells and monocytes were removed by negative selection using CD3, CD56, CD16, and CD14 monoclonal antibody treatment followed by magnetic beads. 3 micrograms of total RNA was processed and, in accordance with the manufacturer's protocols, 15 micrograms of fragmented biotin-labelled cRNA were hybridized on GeneChip Human Genome U133A Arrays (Affymetrix Inc.). The arrays were scanned using the GeneChip Scanner 3000 7G. The images were acquired using Affymetrix GeneChip Operating Software (GCOS version 1.4) and the probe level data converted to expression values using the Bioconductor function for the Robust Multi-Array average (RMA) procedure (Irizarry et al, 2003), in which perfect match intensities are background adjusted and quantile-quantile normalised.

This series of microarray experiments contains the genome-wide profiles of purified B-cell chronic lymphocytic leukemia (B-CLL) cells obtained from 100 newly diagnosed patients (Binet stage A). Peripheral blood mononuclear cells from B-CLL patients were isolated by Ficoll-Hypaque density-gradient centrifugation and the proportion of CD5/CD19/CD23 triple-positive B cells in the suspension was determined by direct immunofluorescence performed using a FACS-sort flow cytometer with antibodies to: CD19 FITC/PE, CD23 PE and CD5 Cy-Chrome. If B-CLL cells were less than 90%, T cells, NK cells and monocytes were removed by negative selection using CD3, CD56, CD16, and CD14 monoclonal antibody treatment followed by magnetic beads. 250 nanograms of genomic DNA was processed and, in accordance with the manufacturer's protocols, 90 micrograms of fragmented biotin-labeled DNA were hybridized on GeneChip Human Mapping 250K NspI Arrays (Affymetrix Inc.). The arrays were scanned using the GeneChip Scanner 3000 7G. The images were acquired using Affymetrix GeneChip Operating Software (GCOS version 1.4). The raw data for individual SNPs were extracted from CEL files and converted into signal intensities using GTYPE 4.1 and Affymetrix Copy Number Analysis Tool (CNAT 4.0.1) softwares using the Hidden Markov Model algorithm with a genomic smoothing window set to 0. After the pre-processing, piecewise constant estimates of the underlying local DNA copy number (CN) variation was calculated using the DNAcopy Bioconductor package, which looks for optimal breakpoints using circular binary segmentation (CBS).

first: Laura

last: Mosca

first: Sonia

last: Fabris

first: Marta

last: Lionetti

first: Fortunato

last: Morabito

first: Giovanna

last: Cutrona

first: Katia

last: Todoerti

first: Serena

last: Matis

first: Francesco

last: Ferrari

first: Massimo

last: Gentile

first: Mauro

last: Spriano

first: Vincenzo

last: Callea

first: Gianluca

last: Festini

first: Stefano

last: Molica

first: Giorgio

last: Lambertenghi Deliliers

first: Silvio

last: Bicciato

first: Manlio

last: Ferrarini

first: Antonino

last: Neri


title: Gene expression patterns in bone following mechanical loading

status: Public on Jun 12 2010

city: Indianapolis

first: Charles

middle: H

last: Turner

state: IN

address: 723 W. Michigan St. SL 220C

department: Biomedical Engineering

institute: Indiana University Purdue University Indiapanolis

summary: The advent of high-throughput measurements of gene expression and bioinformatics analysis methods offers new ways to study gene expression patterns.  The primary goal of this study was to determine the time sequence for gene expression in a bone subjected to mechanical loading, during key periods of the bone formation process, including expression of matrix-related genes, the appearance of active osteoblasts, and bone desensitization.  A standard model for bone loading was employed in which the right forelimb was loaded axially for three minutes per day, while the left forearm served as a non-loaded, contralateral control.  We evaluated loading-induced gene expression over a time course of 4 hours to 32 days after the first loading session.  Six distinct, time-dependent patterns of gene expression were identified over the time course and categorized into three primary clusters:  genes upregulated early in the time course, genes upregulated during matrix formation, and genes downregulated during matrix formation.  Genes were then grouped based on function and/or signaling pathways.  Many gene groups known to be important in loading-induced bone formation were identified within the clusters, including AP-1-related genes in the early response cluster, matrix-related genes in the upregulated gene clusters, and Wnt/β-catenin signaling pathway inhibitors in the downregulated gene clusters.  Several novel gene groups were identified as well, including chemokine-related genes which were upregulated early but downregulated later in the time course, solute carrier genes which were both up- and downregulated, and muscle-related genes which were primarily downregulated.

overall_design: Time Course with 11 time points, each plus & minus mechanical stimulation with 5 replicates per experimental group (except 12d group which has 4 replicates).  Daily mechanical loading was applied to the forearm (24 hours between loading sessions), and ulnae were sampled at indicated time points (4h, 12h, 1d, 2d, 4d, 6d, 8d, 12d, 16d, 24d, or 32d).

first: Sara

last: Mantila Roosa

first: Yunlong

last: Liu


title: Ets-1 over-expression in ovarian cancer cells

status: Public on May 31 2010

city: Hamilton

first: Meghan

last: Verschoor

state: Ontario

address: 699 Concession St

department: Medical Sciences

country: Canada

institute: McMaster University

summary: The transcription factor Ets-1 is over-expressed in a wide variety of cancers, and has been strongly associated with the upregulation of factors involved in metastasis and angiogenesis. In this study, we created an inducible Ets-1 over-expressing ovarian cancer cell line from parental 2008 ovarian cancer cells that do not express detectable levels of Ets-1 protein. This microarray compares the stable over-expressing Ets-1 ovarian cancer cell line (2008-Ets1) to their parental 2008 cells to examine differences in gene expression beyond metastasis and angiogenesis.

overall_design: Two samples were used: 2008 ovarian cancer cells, and 2008-Ets1 ovarian cancer cells which over-express Ets-1. Included in this analysis are three independent replicates for each sample.

middle: L

first: Chris

middle: P

first: Gurmit

last: Singh


title: Orchestration of development by the bifunctional transcription factor, APETALA2

status: Public on Apr 13 2010

city: Tuebingen

first: Felix

last: Ott

address: Spemannstr. 35-39

country: Germany

institute: Max Planck Institute for Developmental Biology

summary: The emerging picture of transcriptional regulation is one of unexpected complexity. It is now clear that single transcription factors control hundreds, if not thousands, of direct targets by binding their genomic loci, but it is not understood how many of these are major players and how many are supporting cast. To address this, we leverage a well-characterized developmental network in Arabidopsis and map genome-wide binding of related proteins in multiple tissues. The transcription factor APETALA2 (AP2) has numerous functions, including roles in floral organ identity, seed development and stem cell maintenance. We focus on the role of AP2 in the floral transition and map direct targets on a genome-wide scale. We show that ap2 mutants flower early in long and short days, and that AP2 binds to many loci, most prominently floral pathway integrators, microRNAs and floral organ identity genes, many of which exhibit AP2-dependent transcription. Opposing, logical effects are evident in AP2 binding to two developmental microRNA genes that control AP2 expression, with AP2 positively regulating miR156 and negatively regulating miR172, forming a complex direct feedback loop, which also included all but one of the AP2-like miR172 target clade members. We also seek conserved targets by comparing the genome-wide direct target repertoire of AP2 with that of SCHLAFMÜTZE (SMZ), another member of the AP2-like miR172 target clade that shares partial redundancy, as evidenced by a hexuple mutant for the entire clade that flowered extremely early. Clear similarities and divergence are exposed in the AP2 and SMZ direct target repertoires. Finally, using an inducible expression system, we demonstrate that AP2 has dual molecular roles. It functions both as a transcriptional activator and repressor, directly inducing the expression of the floral repressor AGAMOUS-LIKE 15 (AGL15), and directly repressing the transcription of floral activators like SUPPRESSOR OF OVEREXPRESSION OF CONSTANS 1 (SOC1).

overall_design: ChIP-Seq of two biological replicates for ATH-AP2 and respective control samples

first: Levi

last: Yant

first: Johannes

last: Mathieu

first: Thanh

middle: T

last: Dinh

first: Christa

last: Lanz

first: Heike

last: Wollmann

first: Xuemei

last: Chen

first: Markus

last: Schmid


title: Effect of methylene blue on the genomic response to reperfusion injury induced by cardiac arrest and cardiopulmonary resuscitation in porcine brain

status: Public on Jun 05 2010

city: Uppsala

first: Cecile

last: Martijn

address: FOA2, Ing70, 3tr

department: Surgical Sciences

country: Sweden

institute: Uppsala University

summary:
Background: Cerebral ischemia/reperfusion injury is a common secondary effect of cardiac arrest which is largely responsible for postresuscitative mortality. Therefore development of therapies which restore and protect the brain function after cardiac arrest  is essential. Methylene blue (MB) has been experimentally proven neuroprotective in a porcine model of global ischemia-reperfusion in experimental cardiac arrest. However, no comprehensive analyses have been conducted at gene expression level.
Methods: Pigs underwent either untreated cardiac arrest (CA) or CA with subsequent cardiopulmonary resuscitation (CPR) accompanied with an infusion of saline or an infusion of saline with MB. Genome-wide transcriptional profiling using the Affymetrix porcine microarray was performed to 1) gain understanding of delayed neuronal death initiation in porcine brain during ischemia and after 30, 60 and 180 min following reperfusion, and 2) identify the mechanisms behind the neuroprotective effect of MB after ischemic injury (at 30, 60 and 180 min).
Results: Our results show that restoration of spontaneous circulation (ROSC) induces major transcriptional changes related to stress response, inflammation, apoptosis and even cytoprotection. In contrast, the untreated ischemic and anoxic insult affected only few genes mainly involved in intra-/extracellular ionic balance. Furthermore, our data show that the neuroprotective role of MB is diverse and fulfilled by regulation of the expression of soluble guanylate cyclase and biological processes accountable for inhibition of apoptosis, modulation of stress response, neurogenesis and neuroprotection.
Conclusions: Our results support that MB could be a valuable intervention and should be investigated as a therapeutic agent against neural damage associated with I/R injury induced by cardiac arrest.

overall_design: One group of pigs underwent cardiac arrest (CA) without subsequent cardiopulmonary resuscitation (CPR) and the brain of the animals was removed after 5, 20 or 30 min post CA for genome-wide expression study. Two groups of pigs underwent first CA for 12 min with a subsequent 8 min-long CPR and received either an infusion of saline or an infusion of saline with MB from one minute after the start of CPR until 50 min after return of spontaneous circulation (ROSC). In both latter groups the brains were removed for microarray analysis at the following time points: 30, 60, 180 min.

first: Lars

last: Wiklund


title: Whole-genome microarray analysis of primary, secondary, tertiary and quaternary memory CD8 T cells

status: Public on Jul 10 2010

city: Nutley

first: Hai-Hui

last: Xue

state: NJ

address: 111 Ideation Way

department: Center for Discovery and Innovation

institute: Hackensack University Medical Center

summary: The transcriptome of naive OT-I T cells was compared to memory CD8 T cells after 1, 2, 3, or 4 infection with ovalbumin expressing Listeria monocytogenes (LM-OVA).

overall_design:
Naive Thy1.1 OT-I T cells were adoptively transferred into Thy1.2 naive hosts prior to infection with LM-OVA. The resulting memory CD8 T cell population was again adoptively transferred into naive hosts and the recipient mice were again infected with LM-OVA. The adoptive transfer was repeated up to four times to generate memory CD8 T cells with up to four consecutive antigen stimulations. Three individual mice were analyzed for each group. For quaternary memory CD8 T cells, spleens from two to three mice were pooled for each sample. Naive OT-I T cells served as control samples.

http://dx.doi.org/10.1016/j.immuni.2010.06.014

first: Thomas

middle: C

last: Wirth

first: Deepa

last: Rai

first: Jaime

last: Sabel

first: Tom

last: Bair

first: John

last: Harty

first: Vladimir

last: Badovinac


title: Hepatic gene expression in transgenic mice with conditional liver-specific expression of the SV40 17kT/LT oncoproteins

status: Public on Apr 01 2010

city: New York

first: Nikolaus

last: Schultz

state: NY

address: 1275 York Ave, Box 460

department: Computational Biology Center

institute: Memorial Sloan-Kettering Cancer Center

summary:
The SV40 large (LT) and small (st) antigens are produced from a single alternatively spliced pre-mRNA, that when co-expressed, transform a variety of cells in vitro and in vivo.  However, 17kT, a relatively uncharacterized third protein that is co-linear with LT for the first 131 amino acids, is also produced from the early viral pre-mRNA by removal of an additional intron from the LT transcript.  Here we report a line of transgenic mice expressing a liver-specific dox-inducible viral transcript that fails to yield any detectable LT protein, yet produces abundant 17kT.  Comparative analysis of livers of transgenic mice expressing either 17kT or LT demonstrates that while 17kT is a potent stimulator of cell proliferation, it is ineffective at inducing liver tumor development, due in part, to the failure of 17kT to effectively induce the expression of growth regulators and reactivate expression of imprinted and developmentally regulated hepatic genes. These studies highlight key functional differences between LT and 17kT in their ability to transform quiescent primary epithelial cells in vivo, and demonstrate how specific functional domains within LT impact cell-specific gene expression to promote oncogenesis.

Keywords: genetic modification, SV40, 17kT, LT, Rb, p53, hepatocellular carcinoma, hepatic hyperplasia, differentiation.

overall_design: Affymetrix mouse genome 430 A and B platform was used, single measurements for wild-type and transgenic animals.

first: Sarah

last: Comerford

first: Robert

middle: E

last: Hammer


title: Transcription profiling of fertilization and early seed development events in a solanaceous species using a 7.7K cDNA microarray from Solanum chacoense ovules

status: Public on May 13 2010

city: Québec

first: Faiza

last: Tebbji

address: 2705 Boulevard Laurier

institute: CHU Québec

summary: To provide a broad analysis of gene expression changes in developing embryos from a solanaceous species, we produced amplicon-derived microarrays with 7741 ESTs isolated from Solanum chacoense ovules bearing embryos from all developmental stages. Our aims were to: 1) identify genes expressed in a tissue-specific and temporal-specific manner; 2) define clusters of genes showing similar patterns of spatial and temporal expression; and 3) identify stage-specific or transition-specific candidate genes for further functional genomic analyses.We analyzed gene expression during S. chacoense embryogenesis in a series of experiments with probes derived from ovules isolated before and after fertilization (from 0 to 22 days after pollination), and from leaves, anthers, and styles. From the 6374 unigenes present in our array, 1024 genes were differentially expressed (≥ ±2 fold change, p value ≤ 0.01) in fertilized ovules and only limited expression overlap was observed between these genes and the genes expressed in the other tissues tested, with more than three quarters of the fertilization-regulated genes specifically or predominantly expressed in ovules. During embryogenesis three major expression profiles corresponding to early, middle and late stages of embryo development were identified. From the early and middle stages, a large number of genes corresponding to cell cycle, DNA processing, signal transduction, and transcriptional regulation were found. Defense and stress response-related genes were found in all stages of embryo development. Protein biosynthesis genes, genes coding for ribosomal proteins and other components of the translation machinery were highly expressed in embryos during the early stage. Genes for protein degradation were overrepresented later in the middle and late stages of embryo development. As expected, storage protein transcripts accumulated predominantly in the late stage of embryo development. Our analysis provides the first study in a solanaceous species of the transcriptional program that takes place during the early phases of plant reproductive development, including all embryogenesis steps during a comprehensive time-course. Our comparative expression profiling strategy between fertilized and unfertilized ovules identified a subset of genes specifically or predominantly expressed in ovules while a closer analysis between each consecutive time points allowed the identification of a subset of stage-specific and transition-specific genes.

overall_design: We produced amplicon-derived microarrays with 7741 ESTs isolated from Solanum chacoense ovules bearing embryos from all developmental stages.  To monitor the expression pattern from genes involved in fertilization and embryogenesis processes, flowers were hand-pollinated and ovules were isolated every two days during a 22 days period after pollination. Four independent biological replicates were produced from each time points. In addition, to isolate genes specifically or predominantly expressed in ovules, four biological replicates of leaf, anther, and style tissue mRNA preparations were individually hybridized against unfertilized ovule mRNAs and compared with the data obtained from unfertilized and fertilized ovules at various time points after pollination. To estimate reproducibility and to produce control data for statistical analysis, a large number of unfertilized ovules were isolated and separated between seven independent control groups. RNA from randomly selected pairs of control was hybridized on six microarrays. 6374 unigenes present in our array in duplicate.

first: André

last: Nantel

first: Daniel

last: Matton


title: Expression data from human adipose tissue using an expanded patient cohort

status: Public on Mar 25 2010

city: Worcester

first: Olga

middle: Theresa

last: Hardy

state: MA

address: 373 Plantation Street, Biotech Two, Suite 100

department: Molecular Medicine

institute: University of Massachusetts

summary:
Obesity is a risk factor for numerous metabolic disorders; however, not all obese individuals are prone to insulin resistance.  The central aim of this study was to identify molecular pathways directly related to insulin resistance independent of BMI in obesity.
We sought to determine the gene expression signature of adipose tissue in a body mass index (BMI)-matched obese cohort of patients that are either insulin sensitive or insulin resistant.

overall_design:
We determined the global gene expression signatures of omental and subcutaneous adipose tissue samples obtained from insulin-sensitive obese and insulin-resistant obese patients undergoing gastric bypass surgery.
The SQ sample for Insulin Resistant Patient 6 has been removed from the study.

first: Juerg

last: Straubhaar


title: microRNA expression profiling of human myeloid precursors

status: Public on Mar 31 2010

city: Modena

first: Elena

last: Tenedini

state: MO

address: Via Campi, 287

department: Biomedical Sciences

institute: University of Modena and Reggio Emilia

summary: Hemopoiesis entails a series of hierarchically organized events that proceed throughout cell specification and terminates with cell differentiation. Commitment needs the transcription factors effort that, in concert with microRNAs, drives cell fate specification, answering to promiscuous patterns of gene expression by turning on lineage-specific genes and repressing alternate lineage transcripts. Therefore microRNAs and mRNAs cooperate to direct cell fate decisions. We obtained microRNAs profiles from human CD34+ hemopoietic progenitor cells and in-vitro differentiated erythroblasts, megakaryoblasts, monoblasts and myeloblasts precursors and we analyzed them together with the gene expression profiles of the same populations. We found that for most part of microRNAs specifically up-regulated in one single cell progeny an inverse correlation between microRNAs and down-regulated putative targets expression levels occurs. We chose hsa-mir-299-5p as a model to get further insights into the possible biological relevance of this microRNAs-mRNAs expression integrated analytical approach and we asked if the forced expression of a single lineage-specific microRNA is able to control the cell fate of CD34+ progenitors grown in multilineage culture conditions. Gain and loss of-function experiments established that mir-299-5p regulates hemopoietic progenitors fate modulating reciprocally megakaryocytic-granulocytic versus erythroid-monocytic differentiation and has at least two genuine targets, the transcription factors CTCF and SOX4.

overall_design: Total cellular RNA was extracted from five CD34 HPCs, MYELO, MONO, MKC and ERY populations Five RNAs for each cellular context were then pooled and miroRNA expression profiles were analyzed by means of RealTime-PCR TaqMan MicroRNA Assays Human Panel Early Access Kit (Life Technologies-Applied Biosystems)

first: Enrica

last: Roncaglia

first: Francesco

last: Ferrari


title: microRNA profiling in vitro activated primary hepatic stellate cells

status: Public on Dec 15 2009

city: Singapore

first: jinmiao

last: chen

address: Biopolis

country: Singapore

institute: Singapore Immunology Network

summary:
pHSCs were isolated from Wistar rats and cultivated in cell culture flasks.
The miRNA was isolated at day 0 and 10 and hybridized onto the Ncode Multi-species miRNA microarray V2 from Invitrogen

platform_organism:
Caenorhabditis elegans
Drosophila melanogaster
Danio rerio
Homo sapiens
Mus musculus
Rattus norvegicus

overall_design: 3 samples from different rats were analyzed on miRNA microarray performing dye swap

first: Gunter

last: Maubach

first: Michelle

last: Lim


title: Detection of Treatment-Induced Changes in Signaling Pathways in GI Stromal Tumors using Transcriptomic Data

status: Public on Nov 17 2009

city: Baltimore

first: Michael

middle: F

last: Ochs

state: MD

address: 550 North Broadway, Ste 1103

department: Oncology Biostatistics

institute: Johns Hopkins University

summary: Time series data from the GIST-T1 imatinib responsive cell line treated with imatinib mesylate for 0 - 48 hours.  The goal of this study was the development of methods to deduce global changes in cell signaling during treatment with targeted therapeutics.

overall_design: 26 samples, triplicate measurements at 0, 2, 4, 6, 9, 12, 18, and 48 hrs of 10 microM IM treatment of GIST-T1 cells, duplicate measurements at 24 hr

first: Lori

last: Rink

first: Andrew

last: Godwin


title: Expression data for rno-miR-146a overexpressing cell line HSC-2

status: Public on Dec 08 2009

summary:
HSC-2 (hepatic stellate cells line from rat) were stably transfected with rno-miR-146a. Three different clones were selected (S1, S4, S5).
We used Affymetrix rat genome RAT230 2.0 chip to monitor global transcriptome changes.

overall_design: Two passages of each sample were used. Control - HSC-2 and GFPscr.


title: miR-335 orchestrates cell proliferation, migration and differentiation in human mesenchymal stem cells

status: Public on Mar 01 2010

city: Madrid

first: Manuel

middle: Angel

last: Gonzalez

address: Melchor Fernandez Almagro, 3

institute: CNIC

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

summary: Human mesenchymal stem cells (hMSC) have an extensive potential for clinical applications in cell therapy. However, very little is known of the specific molecular regulatory mechanisms that control the therapeutical properties of these cells. We aimed to identify microRNAs (miRNAs) that could be involved in controlling the transition between the self-renewing (undifferentiated) and the reparative (differentiated) phenotypes of hMSCs. MicroRNA microarrays were used to identify miRNAs that are upregulated in undifferentiated hMSCs. For that, we compared the miRNA expression profiles of undifferentiated bone marrow-derived hMSCs with the same primary cell lines after 9 days of in vitro adipogenic or osteogenic induction. We also compared the miRNA expression profiles of undifferentiated hMSCs with skin fibroblasts (a mesenchymal cell lineage with a more restricted differentiation potential). These experiments allowed us to identify miR-335 as the only miRNA downregulated upon MSC differentiation as well as in MSCs in comparison with skin fibroblasts. Gene expression microarrays were used to identify genes that are downregulated in hMSCs overexpressing miR-335. We compared the miRNA expression profiles of hMSCs transduced with a lentiviral vector encoding miR-335 with MSCs transduced with a control lentiviral vector. Our results suggest miR-335 downregulation could be a critical trigger for the initiation of MSCs activities involved in tissue repair and remodelling, including cell proliferation, migration and differentiation.

overall_design: We compared the miRNA expression profiles of undifferentiated bone marrow-derived hMSCs with the same primary cell lines after 9 days of adipogenic or osteogenic induction, as well as with skin fibroblasts. A total of four independent samples were used for each condition. For the adipogenic/osteogenic vs. undifferentiated MSC comparison, the RNA samples were pooled (two independent samples/pool) before labeling. We also compared the miRNA expression profiles of hMSCs transduced with the lentiviral vector pLV-EmGFP-MIRN335 with MSCs transduced with the control vector pLV-EmGFP-Mock. For the gene expression microarrays, a total of three independent samples were used for each condition.

first: María

last: Tomé

first: Pedro

last: López-Romero

first: Benjamín

last: Fernández-Gutiérrez

first: Ana

last: Dopazo

first: Antonio

last: Bernad

last: González


title: A survey of gene expression in adult chicken tissues using a chicken 20K oligonucleotide microarray

status: Public on Mar 08 2010

first: Haisheng

last: Nie

address: Marijkeweg 40

institute: Wageningen University

summary: Transcriptional profiling of eight normal adult chicken tissues in 10-week old brown (lohmann brown) hens, the eight tissues include brain, bursa of Fabricius, jejunum, kidney, liver, lung, spleen, thymus. Keywords: normal chicken tissues, transcriptional profiling.

overall_design: eight different normal chicken adult tissue types, five biological replicates per tissue, each individual sample was hybridized with a common reference pool (pool of RNA samples from all individual samples). All individual samples were labeled with Cy3, common reference was labeled with Cy5.

first: Richard

last: Crooijmans

first: Martien

last: Groenen


title: MicroRNA function is globally suppressed in mouse oocytes and early embryos

status: Public on Feb 05 2010

city: San Francisco

first: Robert

last: Blelloch

state: CA

address: 513 Parnassus Avenue, Campus Box #0525

institute: University of California, San Francisco

summary:
Dicer, which is required for the processing of both microRNAs (miRNAs) and small interfering RNAs (siRNAs), is essential for oocyte maturation. Oocytes express both miRNAs and endogenous siRNAs (endo-siRNAs). To determine whether the abnormalities in Dicer knockout oocytes during meiotic maturation are secondary to the loss of endo-siRNAs and/or miRNAs, we deleted Dgcr8, which encodes a RNA binding protein specifically required for miRNA processing.  In striking contrast to Dicer, Dgcr8 deficient oocytes matured normally and, when fertilized with wild-type sperm, produced healthy appearing offspring, even though miRNA levels were reduced to similar levels as Dicer deficient oocytes.  Furthermore, the deletion of both maternal and zygotic Dgcr8 alleles did not impair preimplantation development including the determination of the inner cell mass (ICM) and trophectoderm.  Most surprisingly, the mRNA profiles of wild-type and Dgcr8 null oocytes were essentially identical while Dicer null oocytes showed hundreds of misregulated transcripts. These findings show that miRNA function is globally suppressed during oocyte maturation and preimplantation development and that endo-siRNAs, rather than miRNAs, underlie the Dicer knockout phenotype in oocytes.
We used microarrays to understand at the global level how loss of miRNAs and/or siRNAs is impacting mRNA levels in mouse oocytes.

overall_design: 9 samples were analyzed, 3 biological replicates each of wild-type, Dgcr8 knockout, and Dicer knockout oocytes

first: N

last: Suh

first: R


title: MicroRNA studies in in vitro and in vivo activated rat hepatic stellate cells: Emphasis on miR-146a

first: jinmiao

last: chen

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

overall_design: Refer to individual Series


title: Effect of radiation and cigarette smoke on breast cells

status: Public on Jun 21 2010

first: Venu

last: Raman

address: 733 North Broadway

department: Rad MR Research

institute: The Johns Hopkins University School of Medicine

summary: Exposure to genotoxic stresses such as cosmic radiation and second-hand tobacco smoke may increase the risk of breast cancer formation. Towards an understanding of how exposure to these genotoxic agents affect breast cancer biogenesis, we have shown that treating non-tumorigenic immortalized breast MCF 10A cells with low doses (0.1 Gray) of radiation as well as cigarette smoke condensate can generate a neoplastic breast cancer phenotype. The transformed phenotype promoted increased mammosphere numbers, altered cell cycle phases, and increased invasion and motility. In addition, exclusion of Hoechst 33342 dye, a surrogate marker for increased ABC transporters, was observed, which indicates a possible increase in drug resistance. Furthermore, differential gene expression profiles were generated from the individual and combination treatment. Overall, the results indicate that when normal breast cells are exposed to low dose radiation in combination with cigarette smoke condensate a phenotype is generated that exhibits traits indicative of neoplastic transformation. Taken together, these results provide a new insight into a possible etiology for breast cancer formation in individuals exposed to cosmic radiation and second-hand smoke.

overall_design: To study the effects of low dose ionizing radiation and tobacco smoke on breast cells, MCF 10A cells were treated either with radiation (Rad - 0.1 Gray) or cigarette smoke condensate (Csc - 10 microgram/ml of medium) or a combination of Rad + Csc). Following treatments, the cells were incubated for 72 hr, RNA extracted and analyzed for differential gene expression pattern.

first: Mahendran

last: Botlagunta

first: Paul

last: Winnard Jr


title: Syndromic features and mild cognitive impairment in mice with genetic reduction on p300 activity

status: Public on Oct 03 2009

first: Angel

last: Barco

address: Av. Santiago Ramón y Cajal

institute: Instituto de Neurociencias (UMH-CSIC)

summary:
Rubinstein-Taybi syndrome (RSTS) is a complex autosomal-dominant disease characterized by mental and growth retardation and skeletal abnormalities. A majority of the individuals diagnosed with RSTS carry heterozygous mutation in the gene CREBBP, but a small percentage of cases are caused by mutations in EP300. To investigate the contribution of p300 to RSTS pathoetiology, we carried out a comprehensive and multidisciplinary characterization of p300+/- mice. These mice exhibited facial abnormalities and impaired growth, two traits associated to RSTS in humans. We also observed abnormal gait, reduced swimming speed, enhanced anxiety in the elevated plus maze, and mild cognitive impairment during the transfer task in the water maze. These analyses demonstratethat p300+/- mice exhibit phenotypes that are reminiscent of neurological traits observed in RSTS patients, but their comparison with previous studies on CBP deficient strains also indicate that, in agreement with the most recent findings in human patients, the activity of p300 in cognition is likely less relevant or more susceptible to compensation than the activity of CBP.
To identify those genes whose expression was altered in the hippocampus of p300 deficient mutants, we performed a gene profiling analysis of hippocampal tissue using high-density oligonucleotide microarrays.

overall_design: We obtained triplicate samples containing total RNA from the hippocampi of four 3-month old females of either genotype (in total 12 p300+/- mice and 12 wild type littermates were used in the experiment).

first: Jose

last: Viosca

last: Lopez Atalaya

first: Roman

last: Olivares

last: Eckner


title: Expression data from human amniotic fluid-derived stem cells (AFSC) treated with ethanol

status: Public on Sep 30 2009

city: Winston-Salem

first: Jennifer

last: Hipp

state: NC

address: Medical Center Blvd

department: Institute for Regenerative Medicine

institute: Wake Forest School of Medicine

summary:
The effects of ethanol may vary from induction of apoptosis to the inhibition of proliferation, differentiation, migration or other function.  The complex and diverse response of fetal cells to ethanol has prompted us to use a bioinformatics approach to study the effect of ethanol on fetal stem cells derived from the amniotic fluid-derived (AFSC).

To characterize the global response of human AFSC to ethanol, gene expression profiles of AFSC treated with or without 100mM ethanol for 48 hours were analyzed.

Keywords: stem cells, amniotic fluid-derived stem cells, ethanol, alcohol

overall_design: Two microarrays were performed (AFSC sealed with parafilm for 48 hours treated with or without 100 mM of ethanol).  Total RNA was isolated using RNA Bee according to manufacturer's instructions.  Fragmented antisense cRNA was used for hybridizing with human U133 A arrays (Affymetrix, Inc. Santa Clara, CA, USA) at the Core Genomic Facility of Wake Forest University School of Medicine.  Raw CEL files were provided by the Microarray Core Facility of the Wake Forest University School of Medicine and were then analyzed with a software package AffylmGUI (Affymetrix LIMMA, Linear Models for Microarray Data, Graphical User Interfaces).  AffylmGUI reads the raw Affymetrix CEL files directly, summarizes the gene expression values using RMA, and then uses LIMMA to identify statistically significant differences in gene expression.  LIMMA fits a linear model for every gene (like ANOVA or multiple regression analysis), and adjusts P values for multiple testings.  Differentially expressed genes were identified with a fold change  > 1.8.


title: Expression data of multiple sclerosis patients receiving intramuscular Interferon-beta-1a therapy [U133 A and B]

status: Public on Dec 03 2009

city: Rostock

first: Michael

last: Hecker

address: Gehlsheimer Str. 20

department: Department of Neurology

institute: University of Rostock

summary:
The purpose of this study was to characterize the transcriptional effects induced by intramuscular IFN-beta-1a treatment (Avonex, 30 µg once weekly) in patients with relapsing-remitting form of multiple sclerosis (MS). By using Affymetrix DNA microarrays, we obtained genome-wide expression profiles of peripheral blood mononuclear cells from 24 MS patients within the first four weeks of IFN-beta administration.

Keywords: Multiple sclerosis, Interferon, Pharmacogenomics, Affymetrix

overall_design: EDTA blood samples were taken from all patients immediately before first, second and fifth IFN-beta injection. Total RNA of Ficoll-isolated peripheral blood mononuclear cells from each sample was extracted, labeled and hybridized to Affymetrix Human Genome U133 A and B arrays to quantify the mRNA levels.

first: Dirk

last: Koczan

last: Goertsches

first: Uwe

last: Zettl


title: Responsiveness of a frog cell line to the AHR ligands FICZ and TCDD

status: Public on Jun 24 2009

city: Gambier

first: Wade

last: Powell

state: OH

address: 302A College Park St.

department: Biology Dept.

institute: Kenyon College

summary: The aryl hydrocarbon receptor (AHR) mediates the toxic effects of environmental contaminants, such as 2,3,7,8-tetrachlorodibenzo-p-dioxin (TCDD). Frogs are very insensitive to the toxic effects of TCDD.

overall_design:
XLK-WG cells (ATCC) were grown to ~90% confluence in RPMI-1640 media supplemented with 20% FBS at 29 degrees and 5% CO2.  Cells were subsequently exposed to 100 nM TCDD, FICZ, or DMSO vehicle (0.25%) for 3 hr prior to extraction of total RNA.
Study included three complete biological replicates of each treatment.

first: Leo

middle: B

last: Laub

first: Brian

middle: D

last: Jones

first: Sandra

middle: S

last: Boundarant


title: Selective boosting of transcriptional and behavioral responses to drugs of abuse by histone deacetylase inhibition

status: Public on Aug 22 2009

city: Sant Joan d'Alacant

summary: Histone acetylation and other modifications of the chromatin are important regulators of gene expression and, consequently, may contribute to drug-induced behaviors and neuroplasticity. Previous studies have shown that a reduction on histone deacetylase (HDAC) activity results on the enhancement of some psychostimulant-induced behaviors. In the present study, we extend those seminal findings by showing that the administration of the HDAC inhibitor sodium butyrate enhances morphine-induced locomotor sensitization and conditioned place preference. In contrast, this compound has no effects on the development of morphine tolerance and dependence. Similar effects were observed for cocaine and ethanol-induced behaviors. These behavioral changes were accompanied by a selective boosting of a component of the transcriptional program activated by chronic morphine administration that included circadian clock genes and other genes relevant in addictive behavior. Our results support an specific role for histone acetylation and the epigenetic modulation of transcription at a reduced number of biologically relevant loci on non-homeostatic, long lasting, drug-induced behavioral plasticity. To further investigate the molecular bases of sodium butyrate action on long-lasting behavioral responses to morphine, we screened for potential substrates of their interaction by performing a genome-wide comparison of the striatal transcriptome after chronic administration of morphine in the absence or presence of sodium butyrate.

overall_design: Striatal tissue was dissected from two months-old Swiss-Albino male mice subjected to behavioral sensitization. Behavioural sensitization: Locomotor sensitization induced by morphine was evaluated using a protocol divided into two phases: induction and challenge. The induction phase involved six trials on alternate days, one trial per day. On each one of these trials, mice received and injection of saline or sodium butyrate (300 mg/kg) immediatedly followed by a second injection of morphine (20 mg/kg). The challenge phases consisted of a single trial conducted 7 days after the last test of the induction phase. In this case, all animals received a single injection of morphine (20 mg/kg). Striatal RNA was extracted 1h after the morphine challenge in groups of four animals that received either saline (N=6) or morphine (N=3), or the sodium butyrate-morphine (N=3) co-treatment during the sensitization induction phase.

first: Carles

last: Sanchis


title: BMP4 effect on gene expression program in human primary epidermal keratinocytes and dermal fibroblasts

status: Public on Jun 15 2009

city: Bradford

last: Fessing

state: West Yorkshire

address: Richmond Road

department: Medical Biosciences

country: United Kingdom

institute: University of Bradford

summary:
BMP signalling is a potent regulator of skin morphogenesis, homeostasis and remodelling. However, molecular mechanisms underlying its involvement in regulating gene expression programs in keratinocytes and fibroblasts remain largely unknown.
We analyzed the effect of BMP4 tratment on gene expression programs in human primary epidermal keratinocyte and dermal fibroblasts cultures. We identified specific changes in gene expression programs for each cell type.

overall_design: The primary human epidermal keratinocytes and dermal fibroblasts were treated with recombinant BMP4 or solvent control for 8 hours to reveal early and intermediate response genes. The RNA was isolated and used for micro-array analysis.  Changes in gene expression programs were analyzed for each cell type and were compared between cell types.

middle: Y

first: Vladimir

last: Botchkarev


title: Expression data from Mayo Clinic Pancreatic Tumor and Normal samples

status: Public on Jun 10 2009

city: Rochester

first: Liewei

last: Wang

state: MN

address: 200 First street SW

department: Molecular Pharmacology and Experimental Therapeutics

institute: Mayo Clinic

summary: We used microarrays to identify the expression differences of FKBP5 gene between the pancreatic tumor and normal samples.On average normal samples had more FKBP5 expression compared to tumor samples

overall_design: This experiment consists of 36 tumor samples and 16 normal samples; a total of 52 samples.  16 samples consist of both tumor and normal expression data, whereas 20 samples consist of only tumor data.

first: Huadong

last: Pei

first: Liang

last: Li

first: Brooke

last: Fridley

first: Greg

last: Jenkins

first: Krishna

middle: R

last: Kalari

first: Wilma

last: Lingle

first: Petersen

last: Gloria

first: Zhenkun

last: Lou


title: Functional genomics of mountain pine beetle (Dendroctonus ponderosae) midguts and fatbodies

status: Public on Aug 29 2009

city: Reno

first: Claus

last: Tittiger

state: NV

address: Mail Stop 330

department: Biochemistry and Molecular Biology

institute: University of Nevada, Reno

summary: Survey of relative gene expression profiles in larvae, pupae, and midguts and fatbodies of teneral, unfed, and fed adult mountain pine beetles from western Nevada, USA.

overall_design: Array prepared on 4-tile chips (4-plex custom arrays), each feature represented by six different oligonucleotides, three replicate blocks/tile, hybridized with total RNA from 11 samples, each replicated four times. Vector (pDONR222) and two plant sequences included as negative controls.

first: Tidiane

last: Aw

first: Karen

last: Schlauch

first: Christopher

middle: I

last: Keeling

first: Sharon

last: Young

first: Jeremy

last: Bearfield

first: Gary

middle: J

last: Blomquist


title: Adapted Boolean Network Models for Extracellular Matrix Formation

status: Public on Jul 20 2009

city: Hannover

first: René

last: Huber

state: Lower Saxony

address: Carl-Neuberg-Str. 1

department: Institute for Clinical Chemistry

institute: Hannover Medical School

summary:
Background
Rheumatoid arthritis (RA) is a chronic inflammatory disease, characterized by joint destruction and perpetuated by the synovial membrane (SM). In the inflamed SM, activated synovial fibroblasts (SFB) form the major cell type promoting development and progression of the disease by an abnormal expression/secretion of pro-inflammatory cytokines, tissue-degrading enzymes resulting in a predominant degradation of the extra-cellular matrix (ECM), and collagens causing joint fibrosis. We developed a new procedure, based on human knowledge and formal concept analysis (FCA), to simulate and analyze the temporal behaviour of regulatory and signaling networks. It was applied to a regulatory network (containing 18 genes from 5 functional groups) representing ECM formation and destruction in TGFβ - and TNFα -stimulated SFB.
Results
For the modelling of SFB-controlled ECM turnover in rheumatic diseases, Boolean network architecture was used as well as extensive literature information and revision by experimental gene expression data from stimulated SFB. In course of revision, the additional experimental information resulted in different biologically reasonable changes, yielding two Boolean networks that describe TGFβ and TNFα effects, respectively. The final simulations were further analyzed by the attribute exploration algorithm of FCA, integrating again the observed time series in a more fine-grained and automated manner. The generated temporal rules clearly reveal subtle regulatory relationships between different genes, co-expression patterns and converse gene expression regulation in rheumatic diseases.
Conclusion
The developed Boolean network based method for the dynamical analysis of regulatory and signaling networks represents a reliable systems biological solution for the improved understanding of complex regulatory pathways and the interactions among different genes in disease. The resulting knowledge base can be used for further analysis of the ECM system in human fibroblasts and may be queried to predict the functional consequences of observed (e.g. in diseases as RA) or hypothetical (e.g. for therapeutic purposes) gene expression disturbances.

overall_design:
Patients and tissue samples:
Synovial membrane samples were obtained within 10 min following tissue excision upon joint replacement/synovectomy from RA and OA patients (n = 3 each). After removal, tissue samples were frozen and stored at -70°C. Informed patient consent was acquired and the study was approved by the ethics committees of the respective universities. RA patients were classified according to the American College of Rheumatology (ACR) criteria, OA patients according to the respective criteria for osteoarthritis. The preparation of primary semi-transformed synovial fibroblasts from RA and OA patients was performed as previously described (Zimmermann et al., Arthritis Res. 2001;3(1):72-6). Briefly, the tissue samples were minced and digested with trypsin/collagenase P. The resulting single cell suspension was cultured for seven days. Non-adherent cells were removed by medium exchange. SFB were then negatively purified using Dynabeads® M 450 CD14 and subsequently cultured over 4 passages in DMEM containing 100 μg/ml gentamycin, 100 μg/ml penicillin/streptomycin, 20 mM HEPES, and 10% FCS.
Cell stimulation and isolation of total RNA :
At the end of the fourth passage, the SFB were stimulated by 10 ng/ml TGFβ or TNFα in serum-free DMEM for 0, 1, 2, 4, and 12 h. At the end of each time point, medium was removed and the cells were digested with trypsin/versene (0.25%). Following centrifugation and washing with PBS, the cells were lysed with RLT buffer (Qiagen) and frozen at  70°C. Total RNA was isolated using the RNeasy Kit (Qiagen) according to the supplier's recommendation.
Microarray data analysis:
RNA probes were labelled according to the supplier's instructions (Affymetrix®, Santa Clara, CA, USA). Analysis of gene expression was performed using U133 Plus 2.0 RNA microarrays. Hybridization and washing was performed according to the supplier's instructions. Microarrays were analyzed by laser scanning (Hewlett-Packard Gene Scanner). Background-corrected signal intensities were determined using the MAS 5.0 software (Affymetrix®) and normalized among arrays to facilitate comparisons between different patients. For this purpose, arrays were grouped according to patient class the respective stimulus (TGFβ and TNFα, n=6 each). The arrays in each group were normalized using quantile normalization.

See publication for further details.

first: Johannes

last: Wollbold

first: Ulrike

last: Gausmann

first: Dirk

last: Pohlers

last: Koczan

first: Hans-Juergen

last: Thiessen

first: Reinhard

last: Guthke

first: Raimund

middle: W

last: Kinne


title: Target genes of the MADS transcription factor SEPALLATA3, ChIP-chip

status: Public on Apr 21 2009

city: Wageningen

first: Gerco

last: Angenent

address: Bornsesteeg 65

institute: Plant Research International

type: Genome binding/occupancy profiling by array

summary:
The molecular mechanisms by which floral homeotic genes act as major developmental switches to specify the identity of floral organs, are still largely unknown. Floral homeotic genes encode transcription factors of the MADS-box family, which are supposed to assemble in a combinatorial fashion into organ-specific multimeric protein complexes. Major mediators of protein interactions are MADS-domain proteins of the SEPALLATA subfamily, which play a crucial role in the development of all types of floral organs. In order to characterize the roles of the SEPALLATA3 transcription factor complexes at the molecular level, we analyzed genome-wide the direct targets of SEPALLATA3. We used chromatin immunoprecipitation followed by ultrahigh-throughput sequencing or hybridization to whole-genome tiling arrays to obtain genome-wide DNA-binding patterns of SEPALLATA3. The results demonstrate that SEPALLATA3 binds to thousands of sites in the genome. Most potential target sites that were strongly bound in wild-type inflorescences, are also bound in the floral homeotic agamous mutant, which displays only the perianth organs, sepals and petals. Characterization of the target genes shows that SEPALLATA3 integrates and modulates different growth-related and hormonal pathways in a combinatorial fashion with other MADS-box proteins and possibly with non-MADS transcription factors. In particular, the results suggest multiple links between SEPALLATA3 and auxin signaling pathways. Our gene expression analyses link the genomic binding site data with the phenotype of plants expressing a dominant repressor version of SEPALLATA3, suggesting that it modulates auxin response to facilitate floral organ outgrowth and morphogenesis. Furthermore, the binding of the SEPALLATA3 protein to cis-regulatory elements of other MADS-box genes and expression analyses reveal that this protein is a key component in the regulatory transcriptional network underlying the formation of floral organs.

Keywords: ChIP-chip

overall_design: ChIP experiments were performed on Arabidopsis wildtype inflorescences using an antibody raised against a C-terminal peptide of SEP3. For the control experiment, we used unamplified, sheared chromatin from the same biological sample like the ChIP-DNA (“input DNA”).

first: Kerstin

last: Kaufmann

first: Jose

middle: M

last: Muino

first: Ruy

last: Jauregui

first: Chiara

last: Airoldi

first: Cezary

last: Smaczniak

first: Pawel

last: Krajewski


title: Characterization of expression changes in armi,rhino,aub,ago3 mutants by tiling array

status: Public on May 03 2009

city: Boston

first: Hualin

last: Xi

address: 44 Cummington Street

institute: Boston University

type: Expression profiling by genome tiling array

summary:
We characterized changes of transposon and mRNA expressions in armi, rhino ,aub, ago3 mutants with respect to wild type using Affy tiling array. In most of these mutants, mRNA expressions were mostly unchanged but increased expressions was observed for many transposons indicating the role of these proteins in silencing transposons in Drosophila ovaries

Keywords: Tiling array transcriptome profiling

overall_design: 3 replicates of each mutants and wild type, total RNA samples hybridized to tiling array.

first: Carla

last: Klattenhoff

first: Nadine

last: Schultz

first: Birgit

last: Koppetsch

first: William

last: Theurkauf


title: Target genes of the MADS transcription factor SEPALLATA3, ChIP-seq

summary: The molecular mechanisms by which floral homeotic genes act as major developmental switches to specify the identity of floral organs, are still largely unknown. Floral homeotic genes encode transcription factors of the MADS-box family, which are supposed to assemble in a combinatorial fashion into organ-specific multimeric protein complexes. Major mediators of protein interactions are MADS-domain proteins of the SEPALLATA subfamily, which play a crucial role in the development of all types of floral organs. In order to characterize the roles of the SEPALLATA3 transcription factor complexes at the molecular level, we analyzed genome-wide the direct targets of SEPALLATA3. We used chromatin immunoprecipitation followed by ultrahigh-throughput sequencing or hybridization to whole-genome tiling arrays to obtain genome-wide DNA-binding patterns of SEPALLATA3. The results demonstrate that SEPALLATA3 binds to thousands of sites in the genome. Most potential target sites that were strongly bound in wild-type inflorescences, are also bound in the floral homeotic agamous mutant, which displays only the perianth organs, sepals and petals. Characterization of the target genes shows that SEPALLATA3 integrates and modulates different growth-related and hormonal pathways in a combinatorial fashion with other MADS-box proteins and possibly with non-MADS transcription factors. In particular, the results suggest multiple links between SEPALLATA3 and auxin signaling pathways. Our gene expression analyses link the genomic binding site data with the phenotype of plants expressing a dominant repressor version of SEPALLATA3, suggesting that it modulates auxin response to facilitate floral organ outgrowth and morphogenesis. Furthermore, the binding of the SEPALLATA3 protein to cis-regulatory elements of other MADS-box genes and expression analyses reveal that this protein is a key component in the regulatory transcriptional network underlying the formation of floral organs.

overall_design: ChIP experiments were performed on Arabidopsis wildtype and agamous mutant inflorescences using an antibody raised against a C-terminal peptide of SEP3. As control, ChIP experiments were performed on the sep3 mutant.


title: The genomic effects of dieldrin in the hypothalamus of largemouth bass

status: Public on Jun 06 2009

city: Gainesville

first: Christopher

middle: Joseph

last: Martyniuk

state: FL

address: CEHT Mowry Road

department: Physiological Sciences

institute: UF

summary: This study examines the genomic effects of dieldrin in the hypothalamus of largemouth bass. Dieldrin is an insectide and organic pollutant.

overall_design: Largemouth bass fed diedrin for two months once a day ad libitium; 4 biological replicates for each group

first: Kevin

last: Kroll

first: Daniel

last: Spade

first: Nick

last: Doperalski

first: David

last: Barber

first: Nancy

last: Denslow


title: Transcriptomic response of young adult N2, xpa1, and glp1 nematodes 3h after exposure to 50 J/m2 UVC radiation at 25°C

status: Public on Oct 19 2009

city: RTP

first: NIEHS

last: Microarray Core

address: 111 T.W. Alexander Drive

department: DIR

institute: NIEHS

summary: We compared the transcriptomic response to UVC radiation in widltype (N2), DNA repair-deficient (xpa-1), and germ cell-deficient (glp-1) young adult nematodes. We were interested in the wildtype response to this stressor, and postulated that the early (3h post-exposure) difference might be different in nucleotide excision repair-deficient (xpa-1) nematodes. We also hypothesized that the response would be different in young adults composed entirely of somatic cells (glp-1 strain at this temperature), compared to germ cell-bearing and gravid young adults (N2 and xpa-1). Finally, we compared constitutive differences in gene expression between the strains.

overall_design: Young adult (24 h post-vulval crescent L4 stage) N2, xpa-1, and glp-1 nematodes were reared at 25°C and exposed to 50 J/m2 UVC radiation on K-agar plates without food as described (Meyer et al., 2007 Genome Biology 8(5):R70), placed on OP50-seeded plates for 2 h 45 minutes, washed off plates and rinsed with K-medium 3 times (~5 minutes each) by allowing settling, resuspending, settling again, etc. Nematodes were frozen and RNA extracted. The experiment was performed twice, once in 2007 and once in 2008, with 2 replicates each time, for a total “n” of 4 per strain per treatment (control vs UVC-exposed).

first: Joel

middle: N

last: Meyer

first: Danica

last: Andrews

first: D

last: Lehmann

first: Ben

last: Van Houten


title: Target genes of the MADS transcription factor SEPALLATA3

first: Gerco

last: Angenent


title: Arabidopsis transcriptome microarray from virus infected leafs. Functional Genomic study in virus-infected plants.

status: Public on Apr 10 2009

city: evry

first: Soubigou-Taconnat

last: Ludivine

address: 2 rue gaston crémieux

department: URGV

country: France

institute: INRA

summary:
au07-02_trv - arabidopsis transcriptome microarray from virus infected leafs. - mRNA expression profile in virus-infected Arabidopsis. - mRNA and microRNA expression profile in virus-infected leafs of Arabidopsis.

Keywords: normal vs disease comparison

overall_design: 3 dye-swap - CATMA arrays

first: Jean-Pierre

middle: P

last: Renou

first: Agnes

last: Yu

first: Cesar

last: Llave

first: Marie-Laure

middle: L

last: Martin-Magniette


title: Tobacco Smoke Induces Polycomb-mediated Repression of Dickkopf-1 in Lung Cancer Cells

city: Bethesda

first: maocheng

last: yang

address: 10 Center Drive

department: NCI

institute: National Institutes of Health

summary:
Polycomb-mediated repression of Dkk-1 activates Wnt signaling and enhances tumorigenic potential of lung cancer cells following tobacco smoke exposure

Keywords: tobacco Smoke, lung cancer, epigenetics

overall_design: microarray techniques were used to examine proliferation and gene expression in A549 and Calu-6 lung cancer cells cultured in normal media with or without tobacco smoke condensate (TSC)

first: Mustafa

last: Hussain

first: Mahadev

last: Rao

first: Ashley

middle: E

last: Humphries

first: Julie

middle: A

last: Hong

first: Fang

last: Liu

first: Maocheng

last: Yang

first: Diana

last: Caragacianu

last: Schrump


title: Genome-wide GL3 and GL1 binding sites in Arabidopsis thaliana

status: Public on Mar 02 2009

city: Columbus

first: Kengo

last: Morohashi

address: 1060 Carmack Rd

department: Molecular Genetics

institute: The Ohio State University

type: Genome binding/occupancy profiling by genome tiling array

summary:
GLABRA3 (GL3) and GLABRA1 (GL1) function as selector genes that control the differentiation of a group of protodermal cells into trichomes in Arabidopsis thaliana. We performed genome-wide location (ChIP-chip) analyses by using transgenic Arabidopsis  plants carrying GL3-YFP or GL1-YFP-MYC1 mini genes. These analyses identified statistically significant enriched DNA associated with GL1 and GL3. A total ~540 and ~700 genes were identified as located proximal and downstream to the GL1 and GL3 binding regions, respectively.

Keywords: ChIP-chip

overall_design: Three-week old transgenic Arabidopsis green tissues carryng GL3-YFP or GL1-YFP-MYC mini genes ChIPed with anti-GFP antibody vs Input in GL3-YFP or GL1-YFP-MYC green tissues.

first: Erich

last: Grotewold


title: The Biological Residue of Low Early-Life Social Class

status: Public on Mar 11 2009

city: Vancouver

first: Gregory

last: Miller

state: BC

address: 2136 W Mall

department: Psychology

institute: UBC

summary:
Research shows that children who are reared in households with low socioeconomic status are more vulnerable to heart disease, respiratory infection, and some cancers when they reach adulthood. This study conducted transcriptional profiling of PBMC in healthy adults who were low vs. high in early-life SES to explore the long-lasting genomic effects of early experience.

Keywords: life stress, gene expression, inflammation, socioeconomic status

overall_design: Samples from 30 adults with low early-life SES and 30 adults with high early-life SES

first: Michael

last: Kobor


title: Gene expression in the embryonic serosa of Anopheles gambiae

status: Public on Feb 26 2009

city: Berkeley

first: Yury

last: Goltsev

address: 585 LSA, UC Berkeley

department: MCB

institute: UC Berkeley

summary: Whole-genome transcriptome assays were performed with isolated serosa from A. gambiae embryos. These assays identified a large number of genes implicated in the production of the larval cuticle. In D. melanogaster, these genes are activated just once during embryogenesis, during late stages where they are used for the production of the larval cuticle. Evidence is presented that the serosal cells secrete a dedicated serosal cuticle, which protects A. gambiae embryos from desiccation.

platform_organism:
Plasmodium falciparum
Anopheles gambiae

overall_design: 10.5h mosquito embryos were collected and fixed as described previously (Goltsev et al., 2004) . Following embryo dissection procedure, the empty eggshells remaining on double-sticky tape (Scotch3M) were washed off the tape by Xylenes and equilibrated in ethanol. Total RNA was prepared from fixed eggs, dissected embryos or purified shells using RecoverALL kit (Ambion). Biotin-labeled probes were synthesized using two-step amplification kit (Affymetrix) and hybridized to Plasmodium-Anopheles expression arrays (Affymetrix). Three biological replicates were obtained for every each of the purified shells (serosa) or extracted embryo groups at 10.5h. Log base 2 expression values all probesets on the array were computed using RMAExpress (Bolstad et al., 2003).  Log2Fold values for each probeset were computed by subtracting the average expression value in the whole embryo group from the average expression value in the serosa group.

first: Gustavo

last: Rezende

first: Denise

last: Valle

last: Levine


title: Developmental time course of gene expression in Anopheles gambiae embryo

summary:
In order to examine the gene expression in the course of mosquito embryogenesis, microarray assays were performed on staged A. gambiae embryos, from fertilization to 52 hours of development (which is close to hatching at ~50 hours post-fertilization). RNA was extracted from staged embryos roughly every three hours after fertilization, and then hybridized to the A. gambiae transcriptome microarray.

Keywords: time-course

overall_design: Total RNA from unfixed staged eggs at sequential (2h, 4h, 6h, 7h, 8h, 10h, 13h, 16h, 19h,  22h, 25h, 28.5h, 31h, 34h, 37h, 40h, 43h, 46h, 49h, 52h) time points was purified initially by Trizol (Invitrogen) and then further by RNAeasy (Qiagen) kit. Biotin-labeled probes were synthesized using regular labeling kit (Affymetrix) and hybridized to Plasmodium-Anopheles expression arrays (Affymetrix). All time points were sampled with three independent biological replicates, except for time points 49h and 52h, which were sampled once. RMA-express software was used for processing of raw expression data and estimation of log base 2 expression values.


title: Mouse Reissner's Membrane Gene Expression studies

status: Public on Mar 21 2009

city: Manhattan

first: Daniel

last: Marcus

state: KS

address: 228 Coles Hall

department: Anatomy & Physiology

institute: Kansas State University

summary:
The goal was to screen for the expressed genes in Reissner's membrane (RM) that are related to ion transport and its regulation.  The objectives were 1) to determine whether short-term incubation altered the transcriptome and 2 ) to discover which genes changed expression levels in response to glucocorticoids.
Keywords: drug response

overall_design: RM was dissected free-hand from mouse cochleae and either immediately subjected to RNA extraction or incubated for 24 as explants.  Two series of samples were incubated in the presence or absence of dexamethasone (100 nM) and samples of RM were pooled to obtain sufficient material for gene array analysis.  The pooled samples were used to hybridize 3 gene array chips for each biological sample.

middle: C

first: Nithya

last: Raveendran

first: Tao

last: Wu


title: Basal and kainate-induced gene expression in A-CREB mouse hippocampi

status: Public on Jan 12 2009

first: Angel

last: Barco

state: Alicante

address: Av. Santiago Ramón y Cajal

institute: Instituto de Neurociencias (UMH-CSIC)

summary: The cAMP responsive element binding protein (CREB) pathway has been involved in two major cascades of gene expression regulating neuronal function. The first one presents CREB as a critical component of the molecular switch that control longlasting forms of neuronal plasticity and learning. The second one relates CREB to neuronal survival and protection. To investigate the role of CREB-dependent gene expression in neuronal plasticity and survival in vivo, we generated bitransgenic mice expressing A-CREB, an artificial peptide with strong and broad inhibitory effect on the CREB family, in forebrain neurons in a regulatable manner. The expression of ACREB in hippocampal neurons impaired L-LTP, reduced intrinsic excitability and the susceptibility to induced seizures, and altered both basal and activity-driven gene expression. In the long-term, the chronic inhibition of CREB function caused severe loss of neurons in the CA1 subfield as well as in other brain regions. Our experiments confirmed previous findings in CREB deficient mutants and revealed new aspects of CREB-dependent gene expression in the hippocampus supporting a dual role for CREB-dependent gene expression regulating intrinsic and synaptic plasticity and promoting neuronal survival. manufacturer's protocol.

overall_design: Each sample contained total RNA from the hippocampi of a group of 3-4 three weeks old mice. We obtained duplicate samples for each experimental condition (in total 14 WT and 20 A-CREB mice where used in this experiment). Mouse Genome 430 2.0 genechips were hybridized, stained, washed and screened for quality according to the manufacturer's protocol.

first: Dragana

last: Jancic

first: Mikel

last: Lopez de Armentia

first: Luis

last: Valor

first: Roman

last: Olivares


title: High-Resolution DNA Binding Specificity Analysis of Yeast Transcription Factors

status: Public on Jan 15 2009

city: Worcester

first: Cong

last: Zhu

address: 364 Plantation Street

department: Program in Gene Function and Expression

institute: UMass Medical School

summary: We used microarrays to detail the global program of gene expression underlying rRNA processing gene regulation during heat shock.  PBF1 is YBL054W (TOD6) and PBF2 is YER088C (DOT6).

platform_organism:
Schizosaccharomyces pombe
Saccharomyces cerevisiae

overall_design: S. cerevisiae cells were grown @ 25 ºC to O.D. 600 of 0.3~04, in triplicate. Half of the cells were collected at T0 and half of the cells were subjected to 25 ºC-->37 ºC heat shock and cells were collected after 20 min, as samples T20. Total RNAs were collected and used to perform expression microarray analysis on Affymetrix Yeast Array 2.0 platform. The changes of gene expression upon heat shock were analyzed for four strains, wild type BY4741, single deletion mutants delta-pbf1, delta-pbf2 and double mutant delta-pbf1 delta-pbf2.

first: Kelsey

last: Byers

first: Rachel

last: McCord

first: Zhenwei

last: Shi

first: Mickael

middle: F

last: Berger

last: Newburger

first: Katrina

last: Saulrieta

first: Zachary

last: Smith

first: Mita

last: Shah

first: Mathangi

last: Radhakrishnan

first: Anthony

last: Philippakis

first: Yanhui

last: Hu

first: Federico

last: De Masi

first: Marcin

last: Pacek

first: Andreas

last: Rolfs

first: TVS

last: Murthy

first: Joshua

last: Labaer

first: Martha

last: Bulyk


title: Expression studies of HMEC exposed to lactic acidosis and hypoxia

status: Public on Dec 18 2008

city: Durham

first: Julia

middle: Ling-Yu

address: CIEMAS Rm.2141, 101 Science Dr.

institute: Duke university

summary:
Human Mammalian Epithelial Cells (HMEC) were exposed to different environmental stresses, including hypoxia, lactic acidosis, the combination of hypoxia and lactic acidosis, lactosis , as well as acidosis.
We used microarrays to examine the genomic programs of cells incubated under different microenvironments.
Keywords: different environmental stresses

overall_design: HMEC cells were exposed to different environmental stresses and RNAs were extracted and put on Affymetrix microarrays. We gathered RNAs from cells grown in regular media (control), lactic acidosis, hypoxia, the combinatino of lactic acidosis and hypoxia, lactosis, as well as acidosis.

last: Chen

first: Jen-Tsan

last: Chi


title: Gene expression in human myeloid cells

status: Public on Dec 10 2008

city: Modena

first: Francesco

last: Ferrari

address: Via G. Campi 287

department: Department of Biomedical Sciences

institute: University of Modena and Reggio Emilia

summary:
Human myelopoiesis is an exciting biological model for cellular differentiation since it represents a plastic process where pluripotent stem cells gradually limit their differentiation potential, generating different precursor cells which finally evolve into distinct terminally differentiated cells. This study aimed at investigating the genomic expression during myeloid differentiation through a computational approach that integrates gene expression profiles with functional information and genome organization. The genomic distribution of myelopoiesis genes was investigated integrating transcriptional and functional characteristics of genes. The analysis of genomic expression during human myelopoiesis using an integrative computational approach allowed discovering important relationships between genomic position, biological function and expression patterns and highlighting chromatin domains, including genes with coordinated expression and lineage-specific functions.

Keywords: cell differentiation

overall_design: Gene expression data from 20 experiments for 8 different cell types of the human myelopoietic lineage were used to generate an integrated myelopoiesis dataset.

first: Sergio


title: Human Skin: Before and 8 weeks after Isotretinoin Treatment

status: Public on Nov 30 2008

city: Hershey

first: Diane

last: Thiboutot

state: PA

address: 500 University Drive

department: Department of Dermatology; Jake Gittlen Res. Fnd.

institute: The Pennsylvannia State University College of Medicine

summary:
The pathogenesis of acne has been linked to multiple factors such as increased sebum production, inflammation, follicular hyperkeratinization, and the action of Propionibacterium acnes within the follicle. 13-cis Retinoic Acid (13-cis RA, isotretinoin) is the most potent agent in acne treatment.  Surprisingly, its mechanism of action in acne is still unknown.  Gene expression profiling of skin from 8 patients treated with isotretinoin was performed to gain insights into its mechanism of action. Skin biopsies were obtained from the patients at baseline and at 8 weeks isotretinoin treatment. Gene array expression profiling was conducted using Affymetrix HG-U133A 2.0 arrays in order to examine changes in gene expression as a result of treatment. After treatment, 784 genes were significantly changed: 197 up-regulated and 587 down-regulated. The majority of genes that were up-regulated at 8 weeks encode structural proteins of the extracellular matrix such as collagens, fibulin and fibronectin. The preponderance of genes that were down-regulated at 8 weeks are involved in the metabolism of steroids, cholesterol and fatty acids.

Keywords: drug treatment effects

overall_design: Total 16 chips:  8 baseline/before isotretinoin and 8 after 8 weeks isotretinoin treatment.


title: Circulating Mononuclear Cell Transcriptomes in Patients with Atherosclerotic Coronary Artery Disease

status: Public on Dec 01 2008

city: Amsterdam

first: Stephan

middle: Henrik

last: Schirmer

address: Meibergdreef 9

department: Cardiology

institute: Academic Medical Center

summary:
Monocytes and T-cells play an important role in the development of atherosclerotic coronary artery disease (CAD). Differences in transcriptional activity of these cells might reflect the individual's atherosclerotic burden. Transcriptome analysis of circulating mononuclear cells from carefully matched atherosclerotic and control patients will potentially provide insights into the pathophysiology of atherosclerosis and supply biomarkers for diagnostic purposes.   From patients undergoing coronary angiography because of anginal symptoms, we carefully matched 18 patients with severe triple-vessel CAD to 13 control patients without signs of CAD on angiography. All patients were on statin and aspirin treatment. RNA from circulating CD4+ T-cells, CD14+ monocytes, lipopolysaccharide-stimulated monocytes, macrophages and CD34+ progenitor cells was subjected to genome-wide expression analysis. Only CD14+ monocytes demonstrated that a small number of genes involved in activation was overexpressed in control patients, which was verified by real-time polymerase-chain reaction.   In this pilot study, cautious matching of patients with severe atherosclerotic CAD with control patients without angiographic signs of coronary atherosclerosis did not reveal differences in transcriptional activity in four out of five different mononuclear cell types. In resting monocytes from patients without overt CAD some inflammatory genes were overexpressed as compared to patients with severe CAD. Large inter-individual variability prevented the use of single differentially expressed genes as biomarkers.
Keywords: disease-state analysis

overall_design: In total 153 arrays were analyzed with 6 technical replicates (147 biological samples). CD34+ stem cells, CD4+ T-cells, resting CD14+ monocytes, stimulated monocytes and macrophages were analyzed, all from patient with severe coronary atherosclerosis or controls that had no coronary atherosclerosis as determined angiographically, and which were carefully matched for age and gender.

middle: H

first: Joost

middle: O

last: Fledderus

first: Anton

last: Horrevoets

first: N

middle: V

last: Royen


title: Identification of targets specifically regulated by TAp73

status: Public on Nov 08 2008

city: Sapporo

first: Yasushi

last: Sasaki

address: S-1, W-17, Chuo-ku

department: Cancer Research Institute

country: Japan

institute: Sapporo Medical University

summary: The p53 family consists of three members, p53, p73, and p63. These proteins share a high degree of amino-acid sequence similarity and major functional domains. The p53 gene, the first member of the family to be identified, is the most frequent target gene for genetic alterations in human cancers. In contrast, p73 and p63 are mainly involved in normal development and differentiation. These differences among the p53 family are likely to depend on activation or repression of different sets of target genes. In this study, to identify targets specifically regulated by p73, we performed microarray analysis and compared expression patterns in a human steosarcoma cell line Saos-2 infected separately with p53 and TAp73beta expressing adenovirus.

overall_design: Saos2 osteosarcoma cells were infected with p53, TAp73beta expressing or control adenovirus for 24 h and then harvested.

first: Takashi

last: Tokino