title: Specified Bacterial Species in Gingival Crevicular Fluid Predict Diversity of  Unattached Subgingival Microbiota

status: Public on May 21 2010

first: Bruce

last: Paster

address: 140 Fenway

institute: The Forsyth Institute

summary: Analysis of gingival crevicular fluid (GCF) samples may give information of the identity of unattached (planktonic) subgingival bacteria, the 35 forefront candidates for systemic dispersal via ulcerated periodontal pocket  epithelium. Our study represents the first one targeting the identity of bacteria in gingival crevicular fluid. Methodology/Principal findings: We determined bacterial species diversity in GCF samples of a group of periodontitis patients and delineated contributing bacterial and host-associated factors. Subgingival paper point (PP) samples from the same sites were taken for comparison. After DNA extraction, 16S rRNA genes were PCR amplified and DNA-DNA hybridization was performed using a microarray for over 300 bacterial species or groups. Altogether 133 species from 41 genera and 8 phyla 45 were detected with 9 to 62 and 18 to 64 species in GCF and PP samples, respectively, 46 per patient. Projection to latent structures by means of partial least squares (PLS) was applied to the multivariate data analysis. PLS regression analysis showed that species of genera including Campylobacter, Selenomonas, Porphyromonas, Catonella, Tannerella, Dialister, Peptostreptococcus, Streptococcus and Eubacterium had significant positive correlations and the number of teeth with low-grade attachment loss a significant negative correlation to species diversity in GCF samples.  OPLS/O2PLS discriminant analysis revealed significant positive correlations to GCF  sample group membership for species of genera Campylobacter, Leptotrichia, Prevotella, Dialister, Tannerella, Haemophilus, Fusobacterium, Eubacterium, and Actinomyces. Conclusions/Significance: Among a variety of detected species those traditionally classified as Gram-negative anaerobes growing in mature subgingival biofilms were the main predictors for species diversity in GCF samples as well as responsible for distinguishing GCF samples from PP samples. GCF bacteria may provide new prospects for studying dynamic properties of subgingival biofilms.

overall_design: The microbial profiles of GCF and subgingival plaque were analyzed from 17 subjects with periodontal disease.

first: Sirkka

last: Asikainin


title: Time-dependent expressed markers and their characterization for premature senescence induced by ionizing radiation in MCF7

status: Public on May 31 2010

city: Seoul

first: Cheol-Koo

last: Lee

address: Korea University, Biotechnology #318 West building, Anam-dong, Seongbuk-gu

department: Biotechnology

country: South Korea

institute: Korea University

summary: Recently, senescence has been suggested as a defense mechanism to block sporadic induction of cancer cells. Radiation treatment induces proliferating cancer cells to turn into non-proliferating senescent cells in vitro. To characterize transcriptional reprogramming after radiation treatment, we measured the gene expression profiles of MCF7 at different time points after treatment. In these experiments, we found that IR induced premature senescence in MCF7 cells, and IR treatment resulted in significant changes in the expression of 305 marker genes (less than 1% FDR), which were strongly correlated (|r|>0.9) with IR treatment in a time-dependent manner. Functional analysis of these markers indicated that the dynamics of cytoskeletal structure and lysosomal activity gradually increased. The expression of marker genes for modulator proteins, that were responsible for the dynamics of actin stress fibers and focal adhesion, displayed a particularly strong positive correlation with senescence-associated (SA) morphological changes through time. We also observed a strong induction of genes related to lysosomal metabolic activity, which was accompanied by an increase in the number of SA-beta-Gal positive cells. However, the expression of genes for the cell cycle progression, the post-transcription and the translation activities gradually decreased after radiation treatment. Especially, we observed clear cell cycle arrest specifically at the S and G2/M phases with consistent down-regulation of genes for microtubule assembly/disassembly or spindle biogenesis.

overall_design: Gene expression profiles were obtained from human MCF7 cells after ionizing radiation (6 Gy) at day 0 (no ionizing radiation), day 1 (after ionizing radiation), day 2, day 3, and day 4.


title: Fenofibrate increases VLDL-triglyceride production despite reducing plasma triglyceride levels in APOE*3-Leiden.CETP mice

status: Public on May 27 2010

city: Zeist

first: Marijana

last: Radonjic

address: Utrechtseweg 48

country: Netherlands

institute: TNO

summary: The PPARα activator fenofibrate efficiently decreases plasma triglycerides (TG), which is generally attributed to enhanced VLDL-TG clearance and decreased VLDL-TG production. However, since data on the effect of fenofibrate on VLDL production are controversial, we aimed to investigate in (more) detail the mechanism underlying the TG-lowering effect by studying VLDL-TG production and clearance using APOE*3-Leiden.CETP mice, a unique mouse model for human-like lipoprotein metabolism. Male mice were fed a Western-type diet for 4 weeks, followed by the same diet without or with fenofibrate (30 mg/kg bodyweight/day) for 4 weeks. Fenofibrate strongly lowered plasma cholesterol (-38%; P<0.001) and TG (-60%; P<0.001) caused by reduction of VLDL. Fenofibrate markedly accelerated VLDL-TG clearance, as judged from a reduced plasma half-life of intravenously injected glycerol tri[3H]oleate-labeled VLDL-like emulsion particles (-68%; P<0.01). This was associated with an increased post-heparin LPL activity (+110%; P<0.0001) and an increased uptake of VLDL-derived fatty acids by skeletal muscle, white adipose tissue and liver. Concomitantly, fenofibrate markedly increased the VLDL-TG production rate (+73%; P<0.0001) but not the VLDL-apoB production rate. Kinetic studies using [3H]palmitic acid showed that fenofibrate increased VLDL-TG production by equally increasing incorporation of re-esterified plasma FA and liver TG into VLDL, which was supported by hepatic gene expression profiling data. We conclude that fenofibrate decreases plasma TG by enhancing LPL-mediated VLDL-TG clearance, which results in a compensatory increase in VLDL-TG production by the liver.

overall_design: Male mice were fed a Western-type diet for 4 weeks, followed by the same diet without or with fenofibrate (30 mg/kg bodyweight/day) for 4 weeks. After 4 hours fasting, livers were isolated and individual gene arrays were performed.

first: Silvia

last: Bijland

first: Elsbet

middle: J

last: Pieterman

first: Annemarie

middle: C

last: Maas

first: José

middle: W

last: van der Hoorn

first: Marjan

last: van Erk

first: Jan

middle: B

last: van Klinken

first: Louis

middle: M

last: Havekes

first: Ko

last: Willems van Dijk

first: Hans

last: Princen

first: Patrick

last: Rensen


title: Genome-wide identification of SCL/Tal1’s functional targets; insights into its mechanisms of action in primary erythroid cells

status: Public on May 18 2010

city: Oxford

first: Catherine

last: Porcher

address: John Radcliffe Hospital

department: Weatherall Institute of Molecular Medicine

country: United Kingdom

institute: Oxford University

summary: Coordination of cellular processes through the establishment of tissue-specific gene expression programmes is essential for lineage maturation. The basic helix-loop-helix haemopoietic transcriptional regulator SCL/Tal1 is required for terminal differentiation of red blood cells. To gain insight into SCL function and mechanisms of action in erythropoiesis, we performed ChIP-sequencing and gene expression analyses from primary fetal liver erythroid cells. We show that SCL coordinates expression of genes in most known red cell-specific processes. The majority of SCL’s genomic targets require direct DNA-binding activity. However, one fifth of SCL’s target sequences, mainly amongst those showing high affinity for SCL, can recruit the factor independently of its DNA binding activity. An unbiased DNA motif search of sequences bound by SCL identified CAGNTG as SCL-preferred E-box motif in erythroid cells. Novel motifs were also characterised that may help distinguish activated from repressed genes and suggest a new mechanism by which SCL may be recruited to DNA. Finally, analysis of recruitment of GATA1, a protein partner of SCL, to sequences occupied by SCL suggests that SCL’s binding is necessary prior or simultaneous to that of GATA1. This work provides the framework to study regulatory networks leading to erythroid terminal maturation and to model mechanisms of action of tissue-specific transcription factors.

overall_design: Total RNA extracted from wild-type (WT) day E12.5 fetal liver Ter119- erythroid progenitor cells was compared to total RNA extracted from E12.5 fetal liver Ter119- cells expressing a DNA-binding mutant form of SCL (SclRER/RER).

first: Mira

last: Kassouf

first: Shamit

last: Soneji


title: Genomic Phenotype Of Non-Cultured IPF Fibroblasts

status: Public on May 19 2010

city: Manassas

first: Margaret

middle: Claire

last: Emblom-Callahan

state: VA

address: 10900 University Blvd.

department: Molecular and Microbiology

country: USA

institute: George Mason University

summary: The activated fibroblast is the central effector cell for the progressive fibrotic process that characterizes idiopathic pulmonary fibrosis (IPF). An understanding of the genomic phenotype of this cell in isolation is essential to the understanding of disease pathogenesis and is integral to strategizing therapeutic trials. Employing a unique technique that minimizes cellular phenotypic alterations, we characterized the genomic phenotype of non-cultured pulmonary fibroblasts from the lungs of patients with advanced IPF.  This approach revealed several novel genes and pathways previously unreported in IPF fibroblasts. Specifically, we demonstrate altered expression in proteasomal constituents, ubiquitination mediators, the Wnt pathway and several cell cycle regulators suggestive of loss of normal cell cycle controls.   The pro-inflammatory cytokine CXCL12 was also up-regulated which may provide a mechanism for fibrocytes’ recruitment, while up-regulated oncogenic KIT may promote fibroblast over proliferation. Paradoxically, pro-apoptotic inducers such as death inducing ligand TRAIL (TNFSF10) and pro-apoptotic Bax were also up-regulated.  This comprehensive description of altered gene expression within IPF fibroblasts sheds further light on the complex interactions that characterize IPF. Further studies including therapeutic interventions directed at these pathways hold promise for the treatment of this devastating disease.

overall_design: 58 samples of total RNA isolated from 12 lungs of patients with end-stage idiopathic pulmonary fibrosis and 6 donors of normal lungs (controls) who were designated brain dead, non-diseased donors whose lungs failed criteria for transplantation and who were organ donors for research.  RNA extraction followed the Qiagen RNeasy Kit using QIshredder columns for shredding of DNA contiminants. Experimental/control samples were amplified amino-allylated RNA labeled with Cy5 and Stratagene Reference RNA was amplified and amino-allylated and labeled with Cy3. Amplification was one round using Ambion MessageAmp II kit with amino-allylated UTP according to the protocol of the Duke University Institute for Genome Sciences and Policy.  Amplification and amino-allylation of the Stratagene Reference RNA and Hybridization of Reference with patient samples and controls was done by the Duke Institute for Genomic Sciences and Policy.

first: Mantej

middle: K

last: Chhina

first: Oksana

middle: A

last: Shlobin

first: Shahzad

last: Ahmad

first: Erika

middle: S

last: Reese

first: Eswar

middle: P

last: Iyer

first: Daniel

middle: N

last: Cox

first: Renee

last: Brenner

first: Nelson

last: Burton

first: Geraldine

last: Grant

first: Steven

middle: D

last: Nathan


title: Dynamic transcriptomic profiles of zebrafish gills in response to zinc supplementation.

status: Public on May 20 2010

city: Cardiff

first: Peter

last: Kille

address: Park Place

department: Cardiff School of Biosciences

institute: Cardiff University

summary: Dietary zinc is routinely supplemented to promote growth, boost the immune system, protect against diabetes or aid recovery from diarrhoea. We exploited the zebrafish (Danio rerio) gill as a unique vertebrate ion transporting epithelium model to study the time-dependent regulatory networks of gene-expression leading to homeostatic control during zinc supplementation. This organ forms a conduit for zinc uptake whilst exhibiting conservation of zinc trafficking components. Fish were maintained with zinc supplemented water (4.0 uM) and diet (2023 mg zinc kg-1) or in un-amended water and diet, containing Zn2+ at 0.25 µM and 233 mg zinc kg-1 respectively. Gill tissues were harvested at five time points (8 hours to 14 days) and transcriptome changes analysed in quintuplicate using a 16K microarray.

overall_design: Global transcript levels were measured in zebrafish gills using a oligonucleotide array either zinc-adequate or zinc-supplemented diet. Gill samples were collected at five time points and transcriptome changes analysed in quintuplicate using a 16K oligonucleotide array

first: Dongling

last: Zheng

first: Graham

last: Feeney

first: Phil

last: Cunningham

first: Richard

last: Handy

first: Christer

last: Hogstrand


title: ADAM-28: A potential oncogene involved in asbestos-related lung adenocarcinomas

status: Public on May 28 2010

city: Brisbane

first: Jill

middle: Everland

last: Larsen

state: Queensland

address: Rode Road, Chermside

department: Thoracic Medicine

country: Australia

institute: The Prince Charles Hospital

summary: To identify gene expression biomarkers associated with asbestos-related lung adenocarcinoma, we analyzed primary tumour gene expression for a total of 36 primary lung adenocarcinomas on 22,323 element microarrays, comparing 12 patients with lung asbestos body counts above levels associated with urban dwelling (ARLC-AC: asbestos-related lung cancer-adenocarcinoma) with 24 patients with no asbestos bodies (NARLC-AC: non-asbestos related lung cancer-adenocarcinoma).

overall_design: To identify gene expression biomarkers associated with asbestos-related lung tumorigenicity, we performed gene expression array analysis on tumours of 36 patients with primary lung adenocarcinoma, comparing twelve patients with lung asbestos body counts above levels associated with urban dwelling (ARLC-AC: asbestos-related lung cancer-adenocarcinoma) with twenty-four patients with no asbestos bodies (NARLC-AC: non-asbestos related lung cancer-adenocarcinoma). Synthesis of the labelled first strand cDNA was conducted using Amersham CyScribe Post-Labelling kit with starting material of 20 ug of total RNA. The amino-allyl labeled dNTP mix was added to the reaction to generate amino-allyl labelled second strand cDNA. Following the hydrolysis reaction, single-stranded cDNA probes were purified using Amersham GFX columns. Dye coupling reactions were performed by mixing the cDNA samples with Amersham Cy3 (reference) or Cy5 (tumour) and incubating in the dark. The reactions were purified with Amersham GFX columns to remove the unincorporated/quenched dyes. After the purification samples were combined for hybridization, the labeled cDNAs were co-hybridized to 22K oligo microarrays. Slides were scanned on GMS418 confocal scanner (Agilent). Genes differentially expressed between ARLC-AC and NARLC-AC were identified on fold change and P-value, and then prioritised using gene ontology.

first: Casey

last: Wright

middle: E

first: Nicholas

last: Hayward

first: Maria

last: Martins

first: Maxine

last: Tan

first: Morgan

middle: R

last: Davidson

first: Santiyagu

last: Savarimuthu

first: Rebecca

last: McLachlan

first: Linda

middle: H

last: Passmore

last: Windsor

first: Belinda

last: Clarke

first: Edwina

last: Duhig

first: Ian

last: Yang

first: Rayleen

middle: V

last: Bowman

first: Kwun

last: Fong


title: Increased leaf size: different means to an end (experiment 3)

city: Gent

first: Nathalie

last: Gonzalez

address: Technologiepark 927

department: Plant System Biology

country: Belgium

institute: VIB

summary: The final size of plant organs such as leaves is tightly controlled by environmental and genetic factors that must spatially and temporally coordinate cell expansion and cell cycle activity. However this regulation of organ growth is still poorly understood. The aim of this study is to gain more insight in the genetic control of leaf size in Arabidopsis by performing a comparative analysis of transgenic lines that produce larger leaves under standardized environmental conditions. To this end, we selected five genes, belonging to different functional classes, that all positively affect leaf size when over-expressed: AVP1, GRF5, JAW, BRI1 and GA20OX1. We show that the increase in leaf area in these lines depends on leaf position and growth conditions and that all five lines affect leaf size differently. However, in all cases an increase in cell number is, entirely or predominantly, responsible for the leaf size enlargement. By means of analyses of hormone levels, transcriptome and metabolome we provide deeper insight in the molecular basis of the growth phenotype for the individual lines. A comparative analysis between them indicates that enhanced organ growth is governed by different, seemingly independent pathways. The analysis of transgenic lines simultaneously over-expressing two growth-enhancing genes further supports the concept that multiple pathways independently converge on organ size control in Arabidopsis.

overall_design: Total RNAs were extracted using RNeasy plant mini kit (Qiagen) from vegetative part of seedlings at stage 1.03 grown in vitro. RNAs from three biological repeats of wild type (wt, control) and the GRF5 overexpressing line were submitted to ATH1 array hybridization.

first: Stefanie

last: De Bodt

first: Ronan

last: Sulpice

first: Yusuke

last: Jikumaru

first: Eunyoung

last: Chae

first: Twiggy

last: Van Daele

first: Liesbeth

last: De Milde

first: Detlef

last: Weigel

first: Yuji

last: Kamiya

first: Mark

last: Stitt

first: Gerrit

middle: T

last: Beemster

first: Dirk

last: Inzé


title: Increased leaf size: different means to an end

summary:
The final size of plant organs such as leaves is tightly controlled by environmental and genetic factors that must spatially and temporally coordinate cell expansion and cell cycle activity. However this regulation of organ growth is still poorly understood. The aim of this study is to gain more insight in the genetic control of leaf size in Arabidopsis by performing a comparative analysis of transgenic lines that produce larger leaves under standardized environmental conditions. To this end, we selected five genes, belonging to different functional classes, that all positively affect leaf size when over-expressed: AVP1, GRF5, JAW, BRI1 and GA20OX1. We show that the increase in leaf area in these lines depends on leaf position and growth conditions and that all five lines affect leaf size differently. However, in all cases an increase in cell number is, entirely or predominantly, responsible for the leaf size enlargement. By means of analyses of hormone levels, transcriptome and metabolome we provide deeper insight in the molecular basis of the growth phenotype for the individual lines. A comparative analysis between them indicates that enhanced organ growth is governed by different, seemingly independent pathways. The analysis of transgenic lines simultaneously over-expressing two growth-enhancing genes further supports the concept that multiple pathways independently converge on organ size control in Arabidopsis.

This SuperSeries is composed of the SubSeries listed below.

overall_design: Refer to individual Series


title: Dynamic transcriptomic profiles of zebrafish gills in response to zinc

first: Peter

last: Kille

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


title: Increased leaf size: different means to an end (experiment 1)


title: Increased leaf size: different means to an end (experiment 2)


title: ChIP for H3K27me3 in Murine ES Cells: wild type and Ring1B-/- cells

status: Public on May 14 2010

city: Edinburgh

first: Graeme

middle: Richard

last: Grimes

address: Western General Hospital, Crewe Road

department: Human Genetics Unit

institute: University of Edinburgh, The Institute of Genetics and Cancer

type: Genome binding/occupancy profiling by genome tiling array

summary:
Native ChIP on chip for H3K27me3 in murine ES cells comparing WT and Ring1B-/- cells.
Paper Abstract: How polycomb group proteins repress gene expression in vivo is not known. Whilst histone modifying activities of the polycomb repressive complexes have been studied extensively, in vitro data has suggested a direct activity of the PRC1 complex in compacting chromatin. Here, we investigate higher-order chromatin compaction of polycomb targets in vivo. We show that polycomb repressive complexes are required to maintain a compact chromatin state at Hox loci in embryonic stem (ES) cells. There is specific decompaction in the absence of PRC2 or PRC1. This is due to PRC1, since decompaction occurs in Ring1B null cells that still have PRC2-mediated H3K27 methylation. Moreover, we show that the ability of Ring1B to restore a compact chromatin state, and to repress Hox gene expression in ES cells, is not dependent on its histone ubiquitination activity. We suggest that Ring1B-mediated chromatin compaction acts to directly limit transcription in vivo.

overall_design: Biological replicates: 3 independently grown, harvested,preplated, micrococcal nuclease digested and ChIP for H3K27me3. 5 Technical replicates.

first: Ragnhild

last: Eskeland

first: Wendy

last: Bickmore


title: Murine Embryonic Stems Cells: H3K27me3 in Undifferentiated (UD) and Day 3 (D3) differentiated ES cells

summary:
ChIP on chip for H3K27me3 in murine ES cells comparing Undifferentiated and Day 3 differentiated.
Paper Abstract: How polycomb group proteins repress gene expression in vivo is not known. Whilst histone modifying activities of the polycomb repressive complexes have been studied extensively, in vitro data has suggested a direct activity of the PRC1 complex in compacting chromatin. Here, we investigate higher-order chromatin compaction of polycomb targets in vivo. We show that polycomb repressive complexes are required to maintain a compact chromatin state at Hox loci in embryonic stem (ES) cells. There is specific decompaction in the absence of PRC2 or PRC1. This is due to PRC1, since decompaction occurs in Ring1B null cells that still have PRC2-mediated H3K27 methylation. Moreover, we show that the ability of Ring1B to restore a compact chromatin state, and to repress Hox gene expression in ES cells, is not dependent on its histone ubiquitination activity. We suggest that Ring1B-mediated chromatin compaction acts to directly limit transcription in vivo.

overall_design: Biological replicates: 3 independently grown, harvested, micrococcal nuclease digested and ChIP for H3K27me3. 6 Technical replicates.


title: miRNA expression profile of human subcutaneous adipose

status: Public on May 13 2010

city: Girona

first: Francisco

middle: Jose

last: Ortega

state: Catalunya

address: Av. de Franca, s/n

department: Unitat de Diabetes, Endocrinologia i Nutricio (UDEN)

country: Spain

institute: Institut d'Investigació Biomedica de Girona (IdIBGi)

summary:
Objective: Potential regulators of adipogenesis include microRNAs (miRNAs), small non-coding RNAs that have been recently shown related to adiposity and differentially expressed in fat depots. However, to date no study is available regarding the relationship of miRNAs expression profile, biological pathway and cellular phenotype during human adipogenesis. Thereby, the aim of this study was to investigate whether miRNA expression profile in human adipocytes is related to adipogenesis and to test whether miRNA profile in human subcutaneous adipose tissue is associated to human obesity and co-morbidities.

Keywords: miRNA expression

overall_design: subcutaneous fat samples from non-obese (n=6) and obese with (n=9) and without (n=13) Type 2 Diabetes Mellitus (DM-2) women.

middle: J

first: José

last: Fernández-Real


title: Microarray analysis of colonic mucosa gene expression in wild type and foxo4 knock out mice

status: Public on May 12 2010

city: Dallas

first: wen

last: zhou

state: TX

address: 6000 Harry Hines Blvd NB11.110

department: Internal Medicine ,Cardiology

institute: UT Southwestern Medical Center at Dallas

summary:
Analysis of mechano-regulation of tenocyte metabolism at gene expression level. The hypothesis tested in the present study was that cyclic tensile strain influence the balance of anabolism/catabolism of tenocytes.

Forkhead box O (FoxO) proteins are a family of transcription factors implicated in many biological processes including immune regulation.  In this study, we found that mice null for Foxo4, a member of the FoxO family, are more susceptible to 2,4,6-trinitrobenzene sulfonic acid (TNBS)-induced colitis than wild type controls. To understand the mechanism of elevated colitis susceptibility and the nature of the TNBS-induced colitis in Foxo4-null mice, we performed microarray analysis with mucosal cDNA samples from large intestines of untreated, ethanol and TNBS-treated wild type and Foxo4 KO mice. Unexpectedly, we found that cytokine CCL5, CXCL9, TNFalpha, and IFNgamma were already significantly upregulated in untreated Foxo4-null mice compared to WT controls despite lack of visible colonic phenotypes. Consistent with the exacerbated inflammatory phenotype in TNBS-treated Foxo4 KO mice, expressions of these inflammatory cytokines are further upregulated after TNBS-treatment. In addition, we observed many more inflammatory cytokines that were upregulated in TNBS-treated Foxo4 KO mice, including chemokines (CCL3, 4, 7, 8, 11, 12, 21b and CXCL1, 12, 14), chemokine receptors (CCR7, CCRl2, 8,CXC3CR1), cytokines (IL-1, IL-6, IL-11, IFI205), and cytokine receptors (TNFrsf).
Interestingly, many of the anti-bacterial peptides were also up-regulated in TNBS treated Foxo4 KO mice including defensin related cryptdin (Defcr3,5,6, 9,13) and Defcr related sequence (Defcr-cr1,2,10,12). Up-regulation of basal level of IFNgamma, TNFalpha, CCL5, and CXCL9 expression in Foxo4 KO mice is specific to colonic tissues, as no significant difference of these gene transcript levels between wild type and Foxo4 KO mice was observed in other tissues including thymus.
IFNgamma, TNFalpha, and IL-1beta, which are upregulated in TNBS-treated Foxo4 KO mice, are Th1 type cytokines. This is consistent with the Th1 inflammatory phenotype observed in TNBS-treated Foxo4-KO mice. We also tested whether the expression of Th2 cytokines (IL-4, IL-5, and IL-13) is altered in TNBS-treated WT and Foxo4-null mice in comparison to ethanol-treated mice and observed no significant differences suggesting that the TNBS-induced colitis in Foxo4-null FVB mice is predominantly Th1 in nature.

overall_design: Colonic mucosal tissues from five mice per treatment group (untreated, two days after ethanol or TNBS-treatment) were pooled. Total RNA obtained from colon mucosa isolated tendon fascicles subjected to 1 or 24 hours in vitro cyclic tensile strain compared to unstrained control fascicles.

first: Wen

last: Zhou

first: Zhi-Ping

last: Liu


title: Gene signatures in wound tissue as evidenced by molecular profiling in the chicken embryo model

status: Public on May 06 2010

city: Birmingham

first: Philipp

last: Antczak

state: West-Midlands

address: Edgbaston Park Road

department: Bioscience

institute: University of Birmingham

summary: Modern functional genomic approaches may help to better understand the molecular events involved in tissue morphogenesis and to identify molecular signatures and pathways. We have recently applied transcriptomic profiling to evidence molecular signatures in the development of the normal chicken chorioallantoic membrane and in tumor engrafted on the CAM. We have now extended our studies by performing a transcriptome analysis in the “wound model” of the chicken CAM which is another relevant model of tissue morphogenesis. To induce granulation tissue formation, we performed wounding of the chicken CAM and compared gene expression to normal CAM at the same stage of development. Matched control samples from the same individual were used. We observed a total of 282 genes up-regulated and 44 genes downregulated assuming a false-discovery rate at 5 % and a fold change > 2. Furthermore, bioinformatics analysis lead to the identification of several categories that are associated to organismal injury, tissue morphology, cellular movement, inflammatory disease, development and immune system. Endothelial cell data filtering leads to the identification of several new genes with an endothelial cell signature. In summary, the chick chorioallantoic wound model allows the identification of gene signatures involved in granulation tissue formation and neoangiogenesis. This may constitute a fertile ground for further studies.

overall_design: CAM tissue from brown leghorn eggs was excised from three Control and Wound groups.

first: Fabienne

last: Soulet

first: Witold

middle: W

last: Kilarski

first: John

last: Herbert

first: Roy

last: Bicknell

first: Francesco

last: Falciani

first: Andreas

last: Bikfalvi


title: Tissue Type-Specific Expression of the dsRNA-Binding Protein 76 and Genome-wide Elucidation of its Target mRNAs

status: Public on May 04 2010

city: Durham

first: Neelanjan

last: Mukherjee

state: NC

address: 101 Science Drive

department: Institute for Genome Sciences & Policy

institute: Duke University

summary:
RNA-binding proteins accompany all steps in the life of mRNAs and provide dynamic gene regulation functions for rapid adjustment to changing extra- or intracellular conditions. The association of RNA-binding proteins with their targets is regulated through changing sub-cellular distribution, post-translational modification or association with other proteins. Tissue type-specific isoform distribution and target mRNA binding patterns are major determinants of post-transcriptional gene regulation by RNA-binding proteins.We demonstrate that the dsRNA binding protein 76 (DRBP76), synonymous with nuclear factor 90, displays inherently distinct tissue type-specific sub-cellular distribution in the normal human central nervous system and in malignant brain tumors of glial origin. Altered sub-cellular localization and isoform distribution in malignant glioma indicate that tumor-specific changes in DRBP76-related gene products and their regulatory functions may contribute to the formation and/or maintenance of these tumors. To identify endogenous mRNA targets of DRBP76, we performed RNA-immunoprecipitation and genome-wide microarray analyses in HEK293 cells, and identified specific classes of transcripts encoding critical functions in cellular metabolism. Our data suggest that DRBP76 expression, isoform distribution and sub-cellular localization are profoundly disturbed upon malignant transformation in the CNS. Thus, DRBP76’s roles in co- or post-transcriptional gene regulation may contribute to the neoplastic phenotype.

Keyword: RIP-chip

overall_design: 5 biological replicates of DRBP76 Immunoprecipitation samples, Mock Immunoprecipiation samples, Total mRNA samples were collected and analyzed using oligo microarrays. For each microarray, biological samples were labelled with Cy3 and human reference RNA was labelled with Cy5.

first: Valentina

last: Neplioueva

first: Elena

middle: Y

last: Dobrikova

first: Jack

last: Keene

first: Matthias

last: Gromeier


title: Gene expression analysis in gut biopsies of Crohn's Disease patients and patients with Spondylarthropathy

status: Public on May 01 2010

city: Leuven

first: Rekin's

last: Janky

address: Herestraat 49 Box 816

department: Nucleomics Core

summary:
A focussed microarray chip was constructed specifically for studying basal colonic gene expression in patients with Spondyloarthropathy (SpA) and Crohn's disease (CD) (ref: PMID 16476712). These focus microarrays were used 1) to study common changes in gene expression between SpA and CD, providing early markers in the follow-up study of patients with SpA and particularly these patients that evolve into clinically overt CD; and 2) to identify new candidate genes for CD by integrating gene expression data with genetic information.

Keywords: Crohn's Disease, Spondylarthropathy, biopsies

overall_design: This experiment was done in a dye-swap design in which all samples of interest were compared to a pooled sample.

first: Debby

last: Laukens

first: Paul

last: Van Hummelen

first: Pieter

last: Rottiers

first: Erik

last: Remaut

first: Martine

last: De Vos

first: Filip

last: De Keyser

first: Harald

last: Peeters

first: Dirk

last: Elewaut


title: Mouse Lung Response to Stainless Steel and Mild Steel Welding Fume

status: Public on Apr 30 2010

city: Morgantown

first: Patti

middle: Christine

last: Zeidler-Erdely

state: WV

address: 1095 Willowdale Road

department: HELD

institute: CDC/NIOSH

summary: A/J mice are genetically predisposed to spontaneous and/or chemically-induced lung tumors while C57BL/6J (B6) mice are resistant.  This genetic disparity provides a unique scenario to identify molecular mechanisms associated with the lung response to welding fume at the transcriptome level.

overall_design: Four mice per group were exposed four times by pharyngeal aspiration to 5mg/kg mild steel (MS) fume, stainless steel (SS) fume, or saline vehicle and were necropsied 28 days and 16 weeks after the last exposure.  Whole lung microarray using Illumina Mouse Ref-8 version 1.1 expression beadchips was done.

middle: C


title: Mouse Immune system

status: Public on May 03 2010

city: Cincinnati

first: Bruce

last: Aronow

state: OH

institute: Cincinnati Children's Hospital Medical Center

summary:
Groups of samples used in Microarray and comparative genomics-based identification of genes and gene regulatory regions of the mouse immune system
profiles.
Keywords: other

first: Mitchell

last: Cohen

first: Michael

last: Bates

first: Dan

last: Wiginton

first: Chris

last: Erwin

first: Kathleen

last: Anderson

first: Sandra

last: Degen

first: Susan

last: Waltz

first: Belinda

last: Peach

first: Thomas

last: Doetschman

first: Jonathan

last: Katz

first: Steve

last: Potter

first: Jorge

middle: A

last: Bezerra

last: Mucenski

first: James

last: Lessard

first: MaryBeth

last: Genter

first: Amy

last: Moseley

first: Jianhua

last: Zhang

last: Lehman

first: Ming

last: Xu

first: John

last: Maggio

first: Linda

last: Parysek

first: R

last: Hirsch

last: Dedman


title: Transcriptional profiling during fetal skeletal muscle development of Piau and Yorkshire-Landrace crossbred pigs

status: Public on Apr 22 2010

city: East Lansing

first: Catherine

middle: W.

last: Ernst

state: MI

address: 3330 Anthony Hall

department: Animal Science

institute: Michigan State University

summary: The aim of this study was to identify differentially expressed genes and pathways in longissimus dorsi (LD) of pigs at 40 and 70 d of gestation (stages encompassing the transition from primary to secondary fiber formation) in U.S. commercial crossbred pigs (Yorkshire x Landrace) and Brazilian native Piau pigs. We confirmed the expression patterns for a subset of genes by qRT-PCR. Pathway analysis revealed functionally related genes, and indicated commonalities and differences between the breed types and developmental ages evaluated. Results from qRT-PCR analysis confirmed the expression patterns observed on the array for most of the genes tested (85%). This study reveals transcriptional profiles in LD at 40 and 70 d gestation for commercial and Piau pigs, which helps elucidate phenotypic differences between these breed types.

overall_design: This study utilized the Swine Protein-Annotated Oligonucleotide Microarray which contains 20,400 70-mer oligonucleotides (http://www.pigoligoarray.org). Total RNA was isolated from fetuses obtained from gilts at each gestational age (n=3 crossbred gilts; n=4 Piau gilts) and RNA from 3 fetuses per litter was pooled. Samples were evaluated with a connected loop design using 13 slides such that six breed comparisons and seven age comparisons were performed. Fluorescence intensity data was LOESS normalized and analyzed with a mixed model.

first: Bruna

middle: P

last: Sollero

first: Simone

middle: F

last: Guimaraes

first: Valencia

last: Rilington

first: Robert

last: Tempelman

first: Nancy

last: Raney

first: Juan

last: Steibel

first: Jose

first: Marcos

middle: S

last: Lopes

first: Paulo


title: TRRAP-mediated regulation of Wee1

status: Public on Apr 11 2010

city: Singapore

first: Majid

last: Eshaghi

state: Singapore

address: Biopolis

department: Bilogical Investigation

country: Singapore

institute: Genome Institute of Singapore

summary: The G2 DNA damage checkpoint inhibits Cdc2 and mitotic entry through the dual regulation of Wee1 and Cdc25 by the Chk1 effector kinase. Up-regulation of Chk1 by mutation or overexpression bypasses the requirement for up-stream regulators or DNA damage to promote a G2 cell cycle arrest. We screened in fission yeast for mutations that rendered cells resistant to overexpressed Chk1. We identified a mutation in tra1, which encodes one of two homologs of TRRAP, an ATM/R-related pseudokinase that scaffolds several histone acetyltransferase (HAT) complexes. Inhibition of histone deacetylases reverts the resistance to overexpressed Chk1, suggesting this phenotype is due to a HAT activity, though expression of checkpoint and cell cycle genes is not greatly affected. Cells with mutant or deleted tra1 activate Chk1 normally and are checkpoint proficient. However, these cells are semi-wee even when overexpressing Chk1, and accumulate inactive Wee1 protein. The Cdr (changed division response) kinases Cdr1 and Cdr2 are negative regulators of Wee1, and while best characterized in the cellular response to limited nutrition, we show that they are required for the Tra1-dependent alterations to Wee1 function. This identifies Tra1 as another component controlling the timing of entry into mitosis via Cdc2 activation.

overall_design: Two and three independent microaaray experiments were done for wild type and the mutant (tra1-1) respectively.

first: JianhuaL

last: Liu


title: The relationship between the gene expression profile in the synovium of RA patients at baseline and the clinical response to infliximab treatment

status: Public on Apr 28 2010

city: Stockholm

first: Johan

last: Lindberg

address: Roslagstullsbacken 21, Floor 3

country: Sweden

institute: Royal Institute of Technology

summary:
Background: Although the use of TNF inhibitors has fundamentally changed the way rheumatoid arthritis (RA) is treated, not all patients respond well. It is desirable to facilitate the identification of responding and non-responding patients prior to treatment, not only to avoid unnecessary treatment but also for financial reasons. In this work we have investigated the transcriptional profile of synovial tissue sampled from RA patients before anti-TNF treatment with the aim to identify biomarkers predictive of response.
Methodology/Principal Findings: Synovial tissue samples were obtained by arthroscopy from 62 RA patients before the initiation of infliximab treatment. RNA was extracted and gene expression profiling was performed using an in-house spotted long oligonucleotide array covering 17972 unique genes. Tissue sections were also analyzed by immunohistochemistry to evaluate cell infiltrates. Response to infliximab treatment was assessed according to the EULAR response criteria. The presence of lymphocyte aggregates dominated the expression profiles and a significant overrepresentation of lymphocyte aggregates in good responding patients confounded the analyses. A statistical model was set up to control for the effect of aggregates, but no differences could be identified between responders and non-responders. Subsequently, the patients were split into lymphocyte aggregate positive- and negative patients. No statistically significant differences could be identified except for 38 transcripts associated with differences between good- and non-responders in aggregate positive patients. A profile was identified in these genes that indicated a higher level of metabolism in good responding patients, which indirectly can be connected to increased inflammation.
Conclusions/Significance: It is pivotal to account for the presence of lymphoid aggregates when studying gene expression patterns in rheumatoid synovial tissue. In spite of our original hypothesis, the data do not support the notion that microarray analysis of synovial biopsy specimens can be used in the context of personalized medicine to identify non-responders to anti-TNF therapy before the initiation of treatment.

overall_design: All patients were hybridized in a dual channel reference design where the reference was always labeled with cy3 and the samples with cy5. In total, RNA was extracted from synovial biopsies of 62 patients. 18 patients were good responding, 30 moderate responding and 14 non-responding. Universal Human Reference RNA from Stratagene was used as reference. All samples were amplified with the RiboAmp II kit before labeling and hybridization.

first: Carla

last: Wijbrandts

first: Lisa

middle: G

last: vanBaarsen

first: Gustavo

last: Nader

first: Lars

last: Klareskog

first: Anca

last: Catrina

first: Rogier

last: Thurlings

first: Margriet

last: Vervoordeldonk

first: Joakim

last: Lundeberg

first: Paul

last: Tak


title: Genome wide screening of human growth plates during early and progressed stage puberty in one patient

city: leiden

first: joyce

middle: AM

last: emons

institute: lumc

summary: In progressed puberty, estrogen is responsible for the deceleration of growth by stimulating growth plate maturation. The mechanism of action is largely unknown. We obtained pubertal growth plate specimens of the same girl at Tanner stage B2 and Tanner stage B3, which allowed us to address this issue in more detail. Histological analysis showed that progression of puberty coincided with characteristic morphological changes associated with growth plate maturation, such as decreases in total growth plate height (p=0.002), height of the individual zones (p<0.001) and a increase in intercolumnar space (p<0.001). Microarray analysis of the specimens identified 394 genes (72% upregulated, 28% downregulated) changing with progression of puberty. Overall changes in gene expression were small (average 1.1 fold change). The 394 genes mapped to 13 significantly changing pathways (p<0.05) in majority belonging to extracellular matrix, cell cycle and cell death, which are all related to growth plate maturation. We next scanned the upstream promoter regions of the 394 genes for the presence of evolutionary conserved binding sites for transcription factors implemented in growth plate maturation such as Estrogen Receptor, Androgen Receptor, Elk1, Stat5b, CREBP and Runx2. Runx2 and Elk1, but not estrogen receptor binding sites were enriched and were present in 87 and 43 out of the 394 genes, respectively.In conclusion, our data suggest a role for Runx2 and Elk1 in growth plate maturation and provides suggestive evidence that the effect of estrogen on growth plate maturation is not mediated by activating genomic estrogen signalling in growth plate chondrocytes.

overall_design: 2 replicate samples for each developmental stage for a total of 6 samples

first: Joyce

last: Emons

first: Bas

last: Dutilh

first: Eva

last: Decker

first: Heide

last: Pfirzer

first: Carsten

last: Sticht

first: Norbert

last: Gretz

first: Gudrun

last: Rappold

last: Wit

first: M.

last: Karperien


title: A role for the atopy-associated gene PHF11 in T-cell activation and viability.

status: Public on May 07 2010

city: Westmead

first: Graham

last: Jones

state: NSW

address: Darcy Road

department: Immunology

institute: Westmead Millennium Institute

summary: Analysis of changes in gene expression in normally proliferating Jurkat T-cells that over-express a myc-tagged recombinant PHF11 relative to Jurkat T-cells transfected with an empty vector only.

overall_design: Total RNA was obtained from paired samples.


title: Adipocyte differentiation

first: Francisco

last: Ortega

overall_design: Three biological replicates of fat cells from both lean (BMI<25.0Kg/m2) and obese (BMI>30.0Kg/m2) subjects during differentiation (days 0, 7 and 14) were performed.

first: José

middle: M

last: Fernández-Real


title: Global methylation profiling of lymphoblastoid cell lines reveals epigenetic contributions to autism spectrum disorders

status: Public on Apr 27 2010

city: Washington

first: Valerie

middle: Wailin

last: Hu

state: DC

department: Biochemistry and Molecular Medicine

institute: The George Washington University School of Medicine and Health Sciences

summary: Autism is currently considered a multigene disorder with epigenetic influences.  To investigate the contribution of DNA methylation to autism spectrum disorders, we have recently completed large-scale methylation profiling by CpG island microarray analysis of lymphoblastoid cell lines (LCL) derived from monozygotic twins discordant for diagnosis of autism and their nonautistic siblings.  Methylation profiling revealed many candidate genes differentially methylated between discordant MZ twins as well as between both twins and nonautistic siblings. Bioinformatics analysis of the differentially methylated genes demonstrated enrichment for high level functions including gene transcription, nervous system development, cell death/survival, and other biological processes implicated in autism.  The methylation status of two of these candidate genes, BCL-2 and retinoic acid receptor (RAR)-related orphan receptor alpha (RORA), was further confirmed by bisulfite sequencing and methylation-specific PCR, respectively.  Immunohistochemical analyses of tissue arrays containing slices of the cerebellum and frontal cortex of autistic and age- and sex-matched control subjects revealed decreased expression of RORA and BCL-2 proteins in the autistic brain.  Our data thus confirm the role of epigenetic regulation of gene expression via differential DNA methylation in idiopathic autism, and furthermore link molecular changes in a peripheral cell model with brain pathobiology in autism.

overall_design: Global methylation profiling was performed on lymphoblastoid cell lines (LCLs) derived from three pairs of male monozygotic twins discordant for diagnosis of autism as determined by the Autism Diagnostic Interview-Revised (ADI-R).   As controls, cell lines derived from non-autistic siblings of two pairs of twins were also included in the analyses, in addition to cell lines derived from a set of monozygotic twins unaffected by autism.  For all paired analyses, a direct comparison was performed in which the methylation-enriched fractions from two individuals were pooled and hybridized onto the same microarray.  In addition, indirect comparisons were performed by co-hybridizing the methylation-enriched (MIRA) fraction with the respective unenriched DNA fraction obtained from the same individual.  For each paired analysis (between autistic MZ twins and/or between autistic co-twin and unaffected sibling), a total number of 4 replicates were performed, including direct and indirect comparisons.

first: AnhThu

middle: N

last: Nguyen

first: Tibor

last: Rauch

first: Gerd

last: Pfeifer


title: Responses of Arabidopsis leaves to prolonged osmotic stress are mediated by their developmental stage

first: aleksandra

last: skirycz

institute: Ghent University

summary: Drought is an important environmental factor affecting plant growth and biomass production. Despite this importance, little is known on the molecular mechanisms regulating plant growth under water limiting conditions. The main goal of this work was to investigate, using a combination of growth and molecular profiling techniques, how Arabidopsis thaliana leaves adapt their growth to prolonged mild osmotic stress.  Fully proliferating, expanding and mature leaves were harvested from plants grown on plates without (control) or with 25mM mannitol (osmotic stress) and compared to seedlings at stage 1.03.

overall_design: Total RNAs were extracted using Trizol  method from vegetative part of seedlings at stage 1.03 and leaves that are fully proliferating, expanding or mature. All plants were grown in vitro on medium without (0mM) or with mannitol (25mM) in three independent biological experiments. Each sample was pooled from multiple plants and multiple plates in one experiment. RNA samples were submitted to ATH1 array hybridization.

first: Aleksandra

last: Skirycz

first: Dirk

last: Inzé


title: p53-mediated hematopoietic stem and progenitor cell competition

status: Public on Apr 01 2010

city: New Haven

first: Tanya

last: Bondar

state: CT

address: 300 Cedar str TAC S660

institute: Yale University

summary: Cell competition was originally described in Drosophila as a process for selection of the fittest cells. Using genetic mosaic mouse models and bone marrow chimeras, we have characterized a form of cell competition that selects for the least damaged cells. This competition is controlled by p53 but is distinct from the classical p53-mediated DNA damage response: it persists for months, is specific to the hematopoietic stem and progenitor cells, and depends on the relative rather than absolute level of p53 in competing cells. The competition appears to be mediated by a non-cell autonomous induction of growth arrest and senescence-related gene expression in outcompeted cells with higher p53 activity. p53-mediated cell competition of this type could potentially contribute to the clonal expansion of incipient cancer cells. This microarray experiment is aimed at identification of candidate genes that mediate this competition. It compares mRNA expression patterns of  HSCs with different levels of p53 activity in either competitive or non-competitive conditions (isolated from either wild type, mutant p53, or mosaic wt/mutant p53 mice (R26-mp53mice) after irradiation).

overall_design: Wild type (WT), fully recombined R26-mp53, or R26-mp53 mosaic mice were euthanized 3 weeks after exposure to 2.5 Gy. In mosaic mice, cells expressing mutant p53 co-expressed GFP, and WT cells were GFP-negative. HSCs (lineage- c-kit+ Sca-1+ CD48- CD150+ cells) from these mice were FACS sorted from bone marrow into Trizol, and mRNA was amplified followed by hybridization to Illumia chips.

first: Ruslan

last: Medzhitov


title: ER stress impairs the insulin signaling pathway through mitochondrial damage in SH-SY5Y human neuroblastoma cells (part 2)

status: Public on Oct 07 2010

city: seoul

first: hyun-jung

last: koo

address: hoegi-dong,dongdaemun-gu

institute: Kyung Hee University

summary: To investigate atrazine induced transcriptomes in SH-SY5Y cells

overall_design: Total RNA obtained from SH-SY5Y cells were treated with control vehicle (DMSO) or atrazine (ATZ).

first: Hyun-Jung

last: Koo

first: Youngmi

middle: K

last: Pak


title: Expression in arp6 and swr1 deletion mutants

city: Sendai

first: Masahiko

last: Harata

address: Tsutsumidori-Amamiyamachi 1-1

department: Graduate School of Agricultural Science

country: Japan

institute: Tohoku University

summary: Actin-related proteins are ubiquitous components of chromatin remodelers, and are conserved from yeast to man. We have examined the role of the budding yeast actin-related protein Arp6 in gene expression, both as a component of the SWR1 complex (SWR-C) and in its absence. We mapped Arp6-binding sites genome-wide using chromatin immunoprecipitation in mutant and wild-type cells. We find that the majority of Arp6-binding sites in euchromatin coincide with binding sites of Swr1, the catalytic subunit of SWR-C, and with the histone H2A variant Htz1. However, the remaining Arp6 binding in telomeres, centromeres, and the promoters of ribosomal protein (RP) genes are independent of Swr1 and Htz1 deposition. We show that Arp6 can position chromatin at nuclear pores, and is required for the pore association of the RP genes to which it binds. This anchoring is also independent of Swr1. Loss of Arp6, but not Htz1, leads to an up-regulation of RP genes and loss of relocalization. This is in contrast to the Htz1-mediated pore-association of GAL1, for which loss of Arp6 impairs activation. Given that Arp6 is required for SWR-C dependent deposition of Htz1, we conclude that Arp6 contributes to both H2AZ-dependent and H2AZ-independent association with nuclear pores and subsequent effects on gene expression. These data illustrate how nuclear actin-related proteins contribute to the long-range organization of chromatin domains in the interphase nucleus.

overall_design: Four replicates for the arp6 deletion mutant and three replicates for the swr1 deletion mutant compared to wild-type.

first: Takahito

last: Yoshoda

first: Hitoshi

last: Iwahasghi


title: human Nalm6 Cells: WT vs. OGFOD1 KO

status: Public on Apr 29 2010

city: Okinawa

first: Masayuki

last: Matsushita

address: 207 Uehara, Nishihara

department: Molecular and Cellular Physiology

institute: University of Ryukyus School of Medicine

summary: The 2-OG-Fe(II) dioxygenase family are critical for cellular adaptation to changes in oxygen concentration. We found that cells with OGFOD1 gene silencing in this family showed resistance to cell death under ischemia, and cDNA microarray analysis of OGFOD1 knockout human cells revealed downregulation of ATPAF1. Although reintroduction of the OGFOD1 wild-type gene to OGFOD1 KO cells restored ATPAF1 mRNA levels, the catalytically inactive OGFOD1 mutant did not.

overall_design: wild-type vs. OGFOD1 knock-out cells

first: Ken

last: Saito


title: expression profile of prostate basal epithelial cells relative to luminal epithelial cells

status: Public on Apr 14 2010

city: Wynnewood

first: Janet

last: Sawicki

address: 100 Lancaster Ave.

institute: lankenau Institute for Medical research

summary: We present the results of a microarray analysis in which we compare gene expression in CFP+ basal and CFP- luminal epithelia cell populations derived from whole prostates of CK5/CFP adult mice. Several genes that have previously been identified as potential stem cell markers in stem cells from various organs are over-expressed in CFP+ cells relative to CFP- cells.

overall_design: We isolated prostate epithelial cells from CK5/CFP transgenic mouse. We sorted out CFP+ basal cells and CFP- luminal cells and got gene expression list that is up-regulated in basal epithelial populations.

first: Weidan

last: peng


title: Identification and validation of the pathways and functions regulated by the ROR alpha1 in skeletal muscle

city: St Lucia

first: Michael

middle: Andrew

last: Pearen

address: The University of Queensland

institute: Institute for Molecular Bioscience

summary:
Identification and validation of the pathways and functions regulated by the orphan nuclear receptor, ROR alpha1, in skeletal muscle

The retinoic acid receptor-related orphan receptor (ROR) alpha has been demonstrated to regulate lipid metabolism. We were interested in the physiologically relevant roles, and pathways regulated by RORalpha1 action in skeletal muscle. This major mass organ accounts for ~40% of the total body mass, and significant levels of lipid catabolism, glucose disposal and energy expenditure. We utilized the strategy of targeted muscle specific expression of a truncated (dominant negative) RORalpha∆DE in transgenic mice, to investigate RORalpha1 signalling (and function) in this peripheral tissue. Expression profiling and pathway analysis indicated that RORalpha regulated genes involved in: (i) lipid and carbohydrate metabolism, cardiovascular and metabolic disease; and (ii) the LXR nuclear receptor signaling pathway and, (iii) the Akt and AMPK signaling cascades. This analysis was extensively validated by rigorous qPCR analysis using TaqMan Low Density Arrays, coupled to rigorous statistical analysis (with Empirical Bayes, and Benjamini-Hochberg). Moreover, westerns and metabolic profiling were utilized to validate the genes, proteins and pathways (lipogenic, Akt, AMPK and fatty acid oxidation) involved in the regulation of metabolism by RORalph1. The identified genes and pathways were in concordance with the demonstration of hyperglycemia, glucose intolerance, attenuated insulin stimulated phosphorylation of Akt, and impaired glucose uptake in the transgenic heterozygous Tg-RORalpha∆DE animals. In conclusion, we propose that RORalpha1 is involved in regulating the Akt2-AMPK signalling pathways in the context of lipid homeostasis in skeletal muscle.

overall_design: Total RNA was compared from quadriceps femoris of both transgenic and wild type mice. Transgenic mice contained a truncated version of human RORalpha1 (RORalpha1delDE) where the entire E region and part of the hinge/D region have been removed. This transgene is driven by a skeletal muscle specific human skeletal alpha-actin (HSA) promoter.

first: Surya

last: Raichur

first: Rebecca

middle: L

last: Fitzsimmons

first: Stephen

last: Myers

first: Patrick

last: Lau

first: Natalie

last: Eriksson

first: Shu-Ching

last: Wang

first: George

middle: E

last: Muscat


title: Global gene expression profile of colon from wild-type and AE2-knockout mice.

first: Gary

last: Shull

address: 231 Albert Sabin Way ML0524

institute: University of Cincinnati

summary: The objective of this study was to identify changes in gene expression levels between wild-type and AE2-knockout colon.

overall_design: 7 wild-type and 7 AE2-null colon RNA samples were compared to identify genes that are differentially expressed in the colon of AE2 knockout mice. Total RNA was collected from both male and female wild-type and AE2-null colons (including both proximal and distal colon) when the mice were 18 days old.  All pairs were gender- and aged-matched, and all mice were on a mixed 129 Black Swiss background. To facilitate statistical analysis and reduce any affects of Cy3 and Cy5 labeling, comparisons of two wild-type and two AE2-null samples were repeated using a dye flip.

first: Emily

last: Bradford

first: Lara

middle: R

last: Gawenis


title: Genetic and immunohistochemical analysis in a case of pleuropulmonary blastoma with renal tumor and small bowel polyps

status: Public on Apr 02 2010

city: Amsterdam

first: Daoud

last: Sie

address: De Boelelaan 1117

department: Pathology

institute: Vrije Universiteit Medical Center

summary: The genetic cause for PPB in association with renal tumor and small bowel polyps remains to be identified. Activation of components of the mTOR signalling pathway in the disease lesions suggests that this signal transduction route may be involved in disease pathogenesis and that rapamycin, an inhibitor of mTOR, might be effective in the treatment of PPB and associated lesions.

overall_design: A combination of molecular cytogenetics and gene-specific mutation screens were performed to search for an underlying genetic cause for PPB in association with small bowel polyps. Immunohistochemical analysis to measure mTOR activation was performed on tissue from renal and lung tumor and small bowel polyps from the index case

last: van Roij

first: M.

last: Nellist

last: Wijnaendts

last: Groothoff

first: A.

last: Bokenkamp

last: Kaspers

last: Heij

last: Nieuwint

last: Sistermans

first: B.

last: Ylstra

last: van Hagen


title: Macrophage-specific gene functions in Spi1-directed innate immunity

city: Leiden

first: Anna

middle: Magdalena

last: Zakrzewska

address: Wassenaarseweg 64

department: IBL

institute: University of Leiden

summary: The Spi1/ Pu.1 transcription factor plays a crucial role in myeloid cell development across many species. Several Spi1 target genes have been identified so far, yet the Spi1-dependent gene group remains largely unknown. To identify novel genes downstream of Spi1 we employed a microarray strategy using zebrafish embryos. We established the gene group down-regulated upon spi1 knockdown while simultaneously enriched in FACS-sorted embryonic myeloid cells of a spi1:GFP transgenic line, thus representing putative myeloid-specific Spi1 target genes. This gene group contained all previously identified Spi1-dependent zebrafish genes, confirming the validity of the approach, as well as novel immune-related genes. Colocalization studies with neutrophil and macrophage markers revealed that genes cxcr3.2, mpeg1, ptpn6 and mfap4 were expressed specifically in early embryonic macrophages. The analysis of adult zebrafish hematopoietic tissue showed that genes mfap4 and mpeg1 remained macrophage specific within the myeloid fraction throughout zebrafish life. We also demonstrated that gene cxcr3.2, coding for chemokine receptor 3.2, functions in macrophage migration to the site of bacterial infection. These results establish a myeloid-specific gene group dependent on Spi1 in zebrafish and identify novel early macrophage-specific marker genes, which will facilitate further studies of macrophage development and innate immune function.

overall_design:
Zebrafish strains
Zebrafish (Danio rerio) were handled in compliance with the local animal welfare regulations and maintained according to standard protocols (http://ZFIN.org). The spi1-gfp transgenic line used in this study (Pu1-lynEGFP, a gift from Franscesca Peri, EMBL, Heidelberg) contains 4 kb of spi1/pu.1 promoter sequence driving expression of membrane-targeted EGFP.

Morpholino knock-down experiments
Morpholino oligonucleotides (Gene Tools) were diluted to required concentration in 1x Danieu’s buffer  (58 mM NaCl, 0.7 mM KCl, 0.4 mM MgSO4, 0.6 mM Ca(NO3)2, 5.0 mM HEPES; pH 7.6) containing 1% Phenol red (Sigma) and approximately 1 nl was injected into the 1-2 cell stage embryo using a Femtojet injector (Eppendorf).

Embryo dissociation and FACS (Fluorescent activated cell sorting)
Dissociation of embryos was performed according to Covassin et al. 30. In short, ~300 embryos of spi1:GFP line at 28 hpf were dechorionated by pronase treatment, rinsed in calcium free Ringer solution, followed by digestion with 0.25% trypsin. The obtained cell suspension was centrifuged, rinsed with PBS and resuspended in Leibovitz medium L15 without phenol red, 1% fetal calf serum, 0.8mM CaCl2, penicillin 50 U/ml and streptomycin 0.05 mg/ml. The single cell suspension was subject to FACS at room temperature using a FACSAria (Becton Dickinson) with the BD FACSDiva software version 5.0.3 and a Coherent Sapphire solid state laser 488 nm with 13 mW power. The GFP+ and GFP- cell fractions were collected separately into L15 medium supplemented with 0.8 mM CaCl2, 10% fetal calf serum and penicillin 50 U/ml and streptomycin 0.05 mg/ml.
The standard yield from circa 300 embryos was approximately 2 x 105 GFP+ cells.

Microarray experiment design and analysis
Embryos injected either with 1 mM Pu1 morpholino19 or 1 mM Standard Control morpholino were harvested at 28 hours post fertilization (hpf). As a control, embryos injected with an equal volume of 1% Phenol red in Danieu’s buffer (1xPR/D) were used. Pools of 20-30 embryos were collected. RNA samples from spi1 morphants and standard control morphants were labelled with Cy5 and hybridized against a Cy3-labelled common reference (a mixture of all samples injected with 1xPR/D). This experiment was performed in triplicate. FACS sorted spi1-GFP zebrafish embryos at 28hpf were analyzed as follows: the RNA of GFP-positive fraction was labelled with Cy5 and hybridized against a Cy3-labelled RNA of corresponding GFP-negative fraction of cells from the same pool of embryos. This experiment was performed in duplicate. RNA isolation, synthesis of amino allyl labeled aRNA, coupling of Cy3 and Cy5 dyes, and hybridization conditions were as described31. Microarray analysis was performed using custom-designed 44k Agilent chips (platform accession number in GEO: GPL7735) described elsewhere 31. Microarray data were processed and analyzed as described 31. Significance cut-offs for differentially expressed probe sequences were set at 1.2 fold change at P <10-2.

first: Chao

last: Cui

first: Oliver

last: Stockhammer

first: Erica

last: Benard

first: Valerie

last: Wittamer

first: David

last: Traver

first: Herman

last: Spaink

first: Annemarie

middle: H

last: Meijer


title: Detection of aberrant DNA methylation in colorectal carcinoma samples compared to normal human colon

status: Public on Mar 31 2010

city: Regensburg

first: Michael

last: Rehli

address: F.-J.-Strauss-Allee 11

department: Internal Med III

country: Germany

institute: University Hospital Regensburg

type: Methylation profiling by genome tiling array

type: Genome variation profiling by genome tiling array

summary:
To globally define methylation-’prone’ and -’protected’ CpG islands in colorectal carcinoma we analyzed the methylation status of 23,000 CpG islands of the human genome in ten coleorectal carcinoma samples as well as normal colon using our previously described methyl-CpG immunoprecipitation (MCIp) technique (Gebhard et al. 2006; Schilling and Rehli 2007). This method enriches for highly CpG methylated DNA that can be directly applied to fluorescent labeling and oligonucleotide microarray hybridization without an additional amplification step.

Keywords: MCIp-on-Chip; comparative genomic hybridization

overall_design: CpG-methylated genomic DNA was enriched using methyl-CpG immunoprecipitation (MCIp). On each microarray, the enriched material from colorectal carcinoma samples was compared to the enriched material from normal colon to identify aberrantly methylated regions.

first: Claudia

last: Gebhard


title: Profiling the gene expression for aLTA and pLTA effect in THP1

city: Beijing

first: Jianqing

last: Zhao

address: 18 Life Science Parkway

country: China

institute: Capitalbio. Crop

summary: Staphylococcus aureus lipoteichoic acid (aLTA) and Lactobacillus plantarum LTA (pLTA) engage the same Toll-like receptor 2 (TLR2) signaling pathway, but exert different effects on the innate immune/inflammatory responses. aLTA is the leading cause of gram-positive bacterial sepsis induced by S. aureus, whereas pLTA is considered as a promising therapeutic agent for pathogen-induced septic shock. The mechanisms underlying the different functions of aLTA and pLTA remain unclear. We used human oligo microarrays to investigate the transcriptomes of human THP-1 monocytes upon exposure to aLTA and pLTA. Differential gene expression profiles were observed between the aLTA- and pLTA-treated cells. The expression levels of 1301 genes in aLTA-treated cells were changed more than 2 fold. These genes are critically involved in immune/inflammatory responses, cell adhesion, cell signal transduction, transcription factors, anion transport, proteolysis and oxidative processes. Especially, a variety of genes that encode cytokines/chemokines and other related molecules such as those belonging to the IRAK, TRAF, NF-κB, and STAT families were remarkably up-regulated by aLTA stimulation. In contrast, the expression levels of only 93 genes were altered by more than 1.5 fold in pLTA-treated cells, and these genes are almost not correlative with immune/inflammatory responses and other related processes compared with those of aLTA-treated cells. The different functions of aLTA and pLTA were further compared with the differential expressions of a selected group of genes, i.e., IRAKs, TRAFs and some cytokines/chemokines through RT-PCR and ELISA assays. The gene expression of IRAK2 could be markedly induced by aLTA, but significantly inhibited by pLTA treatment. These results suggest that the different functions of aLTA and pLTA on innate immunity and inflammation might be due to their different effects on the expression of some genes related with the innate immune/inflammatory responses, such as IRAK2 etc.

overall_design: We analyzed gene expression change by aLTA and pLTA in THP1 cell to find the active pathway and related biology function.

first: Rizhong

last: Zeng


title: Identifying genetic loci and spleen gene coexpression networks driving immunophenotypes in the BXD panel

city: Knoxville

first: Rachel

last: Lynch

state: TN

address: 2640 Morgan Circle Drive, 51f McCord Hall

department: Life Sciences

institute: University of Tennessee

summary: The immune system plays a pivotal role in susceptibility to and progression of a variety of diseases. Due to its strong genetic basis, heritable differences in immune function may contribute to differential disease susceptibility between individuals. Genetic reference populations, such as the BXD (C57BL/6J X DBA/2J) panel of recombinant inbred (RI) mouse strains, provide a unique model through which to integrate baseline phenotypes in healthy individuals with heritable risk for disease because of the ability to combine data collected from these populations across multiple studies and time.  We performed basic immunophenotyping (e.g. percentage of circulating B and T lymphocytes and CD4+ and CD8+ T cell subpopulations) in peripheral blood of healthy mice from 41 BXD RI strains to define the phenotypic variation in this model system and to characterize the genetic architecture that unlerlies these traits. Significant QTL models that explained the majority (50-77%) of phenotypic variance were derived for each trait and for the T:B cell and CD4+:CD8+ ratios. Combining QTL mapping with spleen gene expression data uncovered two quantitative trait transcripts (QTTs), Ptprk and Acp1, that which are candidates for heritable differences in the relative abundance of helper and cytotoxic T cells. These data will be valuable in extracting genetic correlates of the immune system in the BXD panel. In addition, they will be a useful resource in prospective, phenotype-driven model selection to test hypotheses about differential disease or environmental susceptibility between individuals with baseline differences in the composition of the immune system.

overall_design: Spleen gene expression was analyzed from 38 BXD strains. Adult mice (8-12 weeks) were euthanized by cervical dislocation and spleens were harvested and stabilized in RNAlater.  Total RNA was extracted and gene expression profiling was performed on the Illumina Sentrix mouse-6 gene expression arrays v1.1. Each BXD sample profiled consisted of a pool of equal amounts of RNA from two individuals of the same sex and strain (approximately 15ug per strain). In addition, flow cytometry was used for the immunophenotyping of male and female mice (average of four mice/sex/strain) from 41 BXD strains (spleen expression profiling was performed on 34 of these strains) and the parental strains. Lymphoctes were identified as CD3+, CD79+, CD4+, or CD8+ to identify T cells, B cells, T helper cells, and cytotoxic T cells, respectively. These data are presented as percentage of lymphoctes with those cell surface markers (e.g. CD3%, CD79%, CD4%, CD8%). Lymphocyte subpopulations are also represented as natural log-transformed ratios (e.g. LN T:B, LN CD4:CD8). In addition, the median expression of MHCII on B cells is reported (LN MHC Med).  The immunophenotype data is available in the supplementary file.

first: Brynn

last: Voy


title: Bioinformatic profiling of the transcriptional response of adult rat cardiomyocytes to distinct fatty acids

status: Public on Mar 24 2010

city: Birmingham

first: Molly

middle: Bray

last: Bray

state: AL

address: 720 20th Street S

department: Genetics

institute: Univ of Alabama at Birmingham

summary: Diabetes mellitus, obesity, and dyslipidemia increase risk for cardiovascular disease, and expose the heart to high plasma fatty acid (FA) levels. Recent studies suggest that distinct FA species are cardiotoxic (e.g., palmitate), while others are cardioprotective (e.g., oleate), although the molecular mechanisms mediating these observations are unclear. The purpose of the present study was to investigate the differential effects of distinct FA species (varying carbon length and degree of saturation) on adult rat cardiomyocyte (ARC) gene expression. ARCs were initialy challenged with 0.4 mM octanoate (8:0), palmitate (16:0), stearate (18:0), oleate (18:1), or linoleate (18:2) for 24 h. Microarray analysis revealed differential regulation of gene expression by the distinct FAs; the order regarding the number of genes whose expression was influenced by a specific FA was octanoate (1,188) . stearate (740) . palmitate (590) . oleate (83) . linoleate (65). In general, cardioprotective FAs (e.g., oleate) increased expression of genes promoting FA oxidation to a greater extent than cardiotoxic FAs (e.g., palmitate), whereas the latter induced markers of endoplasmic reticulum and oxidative stress. Subsequent RT-PCR analysis revealed distinct time- and concentration-dependent effects of these FA species, in a gene-specific manner. For example, stearate- and palmitate-mediated ucp3 induction tended to be transient (i.e., initial high induction, followed by subsequent repression), whereas oleate-mediated induction was sustained. These findings may provide insight into why diets high in unsaturated FAs (e.g., oleate) are cardioprotective, whereas diets rich in saturated FAs (e.g., palmitate) are not.

overall_design:
Comparison of gene expression in adult cardiomyocytes from male Wistar rats following a fatty acid challenge.
Isolated adult rat cardiomyocytes were cultured overnight in serum-free DMEM-containing laminin-ciated plates and challenged with 0.4 mM octanoate, palmitate, stearate, oleate, or linoleate for 24 h, after which RNA was isolated and utilized for gene expression analysis. All FAs were conjugated to defatted BSA, which was present in the culture medium at a final concentration of 1%. Control cells were cultured in the presence of 1% BSA alone.

first: Joseph

middle: B

last: Lockridge

first: Mary

last: Sailors

middle: J

last: Durgan

first: Oluwaseun

last: Egbejimi

first: William

last: Jeong

middle: C

last: Stanley

first: Martin

last: Young


title: Arabidopsis thaliana ecotype Col-0 versus T-DNA mutant sir1-1

status: Public on Mar 12 2010

city: Heidelberg

first: Markus

last: Wirtz

address: Im Neuenheimer Feld 360

department: Molecular Biology of Plants

institute: University of Heidelberg

summary: Arabidopsis thaliana Col-0 plants were compared to sir1-1 T-DNA insertion mutants to investigate transcript levels of sulfur metabolism related genes under standard conditions.

overall_design: For wildtype Col-0 and sir1-1, leaf tissue was harvested from 3 independent plants that were 7 weeks old; total RNA was extracted, reverse transcribed and labeled with Cy3 or Cy5, hybridised on custom made array.

first: Sayyar

last: Khan

first: Florian

last: Haas

first: Rüdiger

last: Hell


title: Detection of aberrant DNA methylation in acute leukemia samples compared to normal human monocytes

last: Rehli

summary:
To globally define methylation-’prone’ and -’protected’ CpG islands in leukemia, we analyzed the methylation status of 23,000 CpG islands of the human genome in eight acute leukemia samples as well as normal blood monocytes using our previously described methyl-CpG immunoprecipitation (MCIp) technique (Gebhard et al. 2006; Schilling and Rehli 2007). This method enriches for highly CpG methylated DNA that can be directly applied to fluorescent labeling and oligonucleotide microarray hybridization without an additional amplification step.

Keywords: MCIp-on-Chip; comparative genomic hybridization

overall_design: CpG-methylated genomic DNA was enriched using methyl-CpG immunoprecipitation (MCIp). On each microarray, the enriched material from leukemia samples was compared to the enriched material from normal blood monocytes to identify aberrantly methylated regions. Three biological replicates were analysed for each cell line.

last: Gebhard


title: calorie-restricted diet effects on obese human liver

status: Public on Mar 25 2010

city: Nantes

first: Mahatsangy

last: Raharijaona

address: Faculte de Medecine - Inserm U915 1 rue gaston Veil

country: France

institute: INSERM

summary: Analysis of obese

overall_design: Analysis of gene expression profiles in liver on obese 11 men/women on 10 days servere calorie-restricted diet and  8 men/women on ad libitum diet.


title: Breast cancer MCF-7 cells and MDA-MB-231 cells: LNA-antimiR-21 transfected cells vs. LNA-control transfected cells

status: Public on Mar 05 2010

city: Guangzhou

first: Li

middle: Xu

last: Yan

state: Guangdong

address: 651# Dong Feng Road East

department: Department of Pathology

institute: Sun Yat-Sen University Cancer Center

summary: Transcriptional profiling of breast cancer cells comparing LNA-control transfected cells with cells transfected with LNA-antimiR-21.We searched for miR-21 targets by systematic screening of mRNA profiling of LNA-antimiR-21 transfected MCF-7 cells and MDA-MB-231 cells.

overall_design: Two-condition experiment, LNA-antimiR-21 Transfected vs. LNA-control Transfected MCF-7 cells. One replicate per array.

first: Li-Xu

first: Yan

last: Zhang

first: Qi-Nian

last: Wu


title: Dynamic gene expression of Recombinant Inbred Lines (RILs) in C. elegans

status: Public on Apr 06 2010

city: London

first: Ana

last: Viñuela

state: London

address: St.Thomas' Hospital Campus Westminster Bridge Road

department: Twin Research & Genetic Epidemiology

institute: King's College London

summary: We mapped quantitative trait loci for genome-wide gene expression (eQTL) in juvenile, reproductive and senescent C. elegans recombinant inbred lines, to determine heritable transcript dynamics

overall_design: in total 54 dual color microarrays were done on three age groups.

first: Jan

last: Kammenga

first: L

last: Snoek


title: Effects of exercise on miRNA expression level in human neutrophils

city: Irvine

first: Shlomit

last: Radom-Aizik

state: CA

address: 101 Academy

department: Pediatrics

institute: University of California, Irvine

summary: Exercise leads to a rapid change in the profile of gene expression in circulating neutrophils. We hypothesized that miRNA expression in circulating neutrophils would also be affected by brief exercise.

overall_design: Eleven healthy men (19-30 yr old) performed 10 2-min bouts of cycle ergometer exercise interspersed with 1-min rest at a constant work equivalent to about 76% of VO2max. A baseline blood sample was taken before the and immediately after the exercise. Neutrophils were isolated using OptiPrep Density Gradient Medium (SIGMA). Total RNA was extracted using TRIzol®. For this study we used Agilent Human miRNA microarrays V2 (total of 22 chips).

first: Frank

last: Zaldivar

first: Dan

last: Cooper


title: Y79 retinoblastoma cells: control vs. curcumin treated

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: miRNA profiling of curcumin treated Y79 cells with untreated Y79 cells (control). Aim of the study to see whether any oncogenes or tumor suppressor genes are regulated on curcumin treatment in Y79 cells.

overall_design: Agilent one-color experiment,Organism: Human ,Agilent-019118 Human miRNA Microarray 2.0 G4470B , Labeling kit: Agilent miRNA labeling reagent and Hybridization Kit Cat # 5190-0408

first: T

last: Seethalakshmi

first: S

last: Krishnakumar


title: in vivo derived apc-mp

status: Public on Feb 28 2010

city: Liverpool

first: Margarita

last: Perez-Casal

state: Merseyside

address: Daulby Street

department: Haematology

institute: Royal Liverpool University Hospital

summary:
Background-The endothelial protein C receptor (EPCR) plays an important role within the protein C (PC) pathway in regulating coagulation and inflammation. Recently, we described a novel mechanism of EPCR release from the surface of primary physiological cells.  Induced by exogenous activated protein C (APC), EPCR is released in microparticulate form.  Its bound APC retains proteolytic anticoagulant activity and we now hypothesise that this microparticulate EPCR-APC complex can also cleave endothelial protease activated receptor 1 (PAR1) to modulate inflammation and cytoprotection.
Methods & Results-The gene profiling effect on human endothelial cells by 40nM APC, in free or microparticulate form, was assessed.  Transcript profile results showed upregulation of anti-apoptotic and inflammatory genes by APC in either form, which were confirmed by RT-PCR.  These translated into increased GM-CSF and interleukin 8 secretion and cytoprotection against staurosporine-induced apoptosis.  PC or PAR1 antagonism reversed these results to demonstrate that induced effects by microparticles were APC specific and PAR1-dependent.  Further analysis of human plasma from septic patients, by confocal microscopy and ELISA, showed evidence of circulating microparticle-associated EPCR during recombinant APC treatment. Functional coagulation and cellular studies demonstrate that these express APC-specific effects on anticoagulation with PAR1-mediated gene induction and anti-apoptotic function.
Conclusions-APC induction of microparticle-associated EPCR release can occur in vivo.  These microparticles could potentially disseminate the function of the EPCR-APC complex to PAR1 on different cells and vascular sites.
Keywords: pre versus rhAPC-treatment mp in vivo

overall_design: MP were isolated from sepsis patients pre and during-rhAPC treatment. MP were counted by FACS using CD13 positivity and same number of mp was used in pre and during treatment comparisons. HUVEC were incubated with the in vivo mps according to mp number or apc content, and controls for both were done using non-treated patients or free-apc. The role of apc and par1 was analysed by including apc blocking antibody or par1 antaginist peptide respectively.

first: Colin

last: Downey

first: Kenji

last: Fufudome

first: Cheng-Hock

last: Toh


title: Detection of aberrant DNA methylation in AML cell lines compared to normal human monocytes

first: Michael

last: Rehli

summary:
To globally define methylation-’prone’ and -’protected’ CpG islands in leukemia, we analyzed the methylation status of 23,000 CpG islands of the human genome in two acute leukemia cell lines as well as normal blood monocytes using our previously described methyl-CpG immunoprecipitation (MCIp) technique (Gebhard et al. 2006; Schilling and Rehli 2007). This method enriches for highly CpG methylated DNA that can be directly applied to fluorescent labeling and oligonucleotide microarray hybridization without an additional amplification step.

Keywords: MCIp-on-Chip; comparative genomic hybridization

overall_design: CpG-methylated genomic DNA was enriched using methyl-CpG immunoprecipitation (MCIp). On each microarray, the enriched material from leukemia cell lines was compared to the enriched material from normal blood monocytes to identify aberrantly methylated regions. Three biological replicates were analysed for each cell line.

first: Claudia

last: Gebhard


title: Expression data from human Wegener’s granulomatosis patients and normal controls in PBMCs and in PMNs

city: Baltimore

first: Alan

middle: E.

last: Berger

state: MD

address: 5501 Hopkins Bayview Circle Room 3B.74C

department: School of Medicine

institute: Johns Hopkins University

summary: Wegener’s granulomatosis (WG) is a systemic inflammatory disease that can lead to substantial morbidity.  This study seeks to further understanding of the biology underlying WG, and to discover markers of disease activity useful in prognosis and treatment guidance.

overall_design: Gene expression profiling was performed on total RNA from PBMC and from granulocyte (PMN) fractions from 41 WG patients and 23 healthy controls, using Illumina HumanRef-8 v2 Expression BeadChips. For each of the 64 subjects, there is expression data for the PBMC and for the PMN fractions, so, for example, the RNA for SAMPLE 1 PBMC and for SAMPLE 1 PMN comes from the same individual.  Note there is no PMN expression data for SAMPLE 35 since that PMN RNA sample failed quality control. Details of the design, and the gene signatures found are given in the paper (PMID 20155833) associated with this GEO Series.

first: Chris

last: Cheadle

first: Felipe

last: Andrade

first: Regina

last: James

first: Kristen

last: Johnson

first: Tonya

last: Watkins

first: Jin

last: Park

first: Yu-Chi

last: Chen

first: Eva

last: Ehrlich

first: Marissa

last: Mullins

first: Frances

last: Chrest

first: Kathleen

last: Barnes

first: Stuart

last: Levine


title: Detection of transcription factor NRF1, YY1 and SP1 bound regions in human peripheral blood monocytes

summary:
To study the correlation between sequence motif appearance, transcription factor binding and aberrant hypermethylation in the cell lines, we performed ChIP-on-chip analyses (on CpG island microarrays) for the transcription factors Sp1, NRF1 and YY1 in normal peripheral blood monocytes.

Keywords: ChIP-on-Chip; comparative genomic hybridization

overall_design: Transcription factor bound genomic DNA was enriched using ChIP. On each microarray, the enriched material was compared to the genomic input to identify transcription factor bound regions. Two biological replicates were analysed for each factor.

first: Christian

last: Schmidl


title: HLA-B35 upregulates ET-1 and downregulates eNOS via ER stresss response in endothelial cells

status: Public on Mar 01 2010

city: Houston

first: Filemon

last: Tan

state: TX

address: 6431 Fannin

department: Internal Medicine-Rheumatology

institute: UT Houston Medical School

summary: The presence of the HLA-B35 allele has emerged as an important risk factor for the development of isolated pulmonary hypertension (iPHT) in patients with Scleroderma (SSc), however the mechanisms underlying this association have not been fully elucidated. The goal of our study was to determine the molecular mechanisms that mediate the biological effects of HLA-B35 in endothelial cells (ECs). Our data demonstrate that HLA-B35 expression at the physiological levels using via adenoviral vector resulted in a significantly increased endothelin-1 (ET-1) and a significantly decreased endothelial nitric oxide synthase (eNOS) mRNA and protein levels. Furthermore, HLA-B35 greatly upregulated expression of cytoplasmic chaperones, including heat shock proteins (HSPs) HSP70 (HSPA1A and HSPA1B) and HSP40 (DNAJB1 and DNAJB9), suggesting that HLA-B35 induced the ER stress and unfolded protein response (UPR) in ECs. Examination of selected mediators of the UPR response, including BiP (GRP78), CHOP (GADD153), ERO1 (endoplasmic reticulum oxidase) and PDI (protein disulfide isomerase) has revealed a consistent increase of BiP expression levels. Accordingly, Thapsigargin (TG), a known ER stress inducer, stimulated ET-1 mRNA and protein levels in ECs. This study suggests that HLA-B35 could contribute to endothelial cell dysfunction via ER stress mediated induction of ET-1 in patients with PHT.

overall_design: Three samples: endothelial cells transduced with Adenovirus GFP; cells without gene insert, cell with HLA-B35, and cells with HLA-B8.

first: F


title: K562 leukaemia cell line treated with thalidomide analog

status: Public on Feb 23 2010

city: Szeged

first: Agnes

last: Zvara

address: Temesvari krt 62

country: Hungary

institute: Biological Research Center

summary: We synthesized novel fluorescent thalidomide analogs (2,6-dialkylphenyl-4/5-amino-substituted-5,6,7-trifluorophthalimides) that localize specifically to lipid droplets. By using affinity chromatography interacting proteins were identified: Rab7, Rab10, Rab11, Sec22b, sorting nexin 2, calnexin, protein disulfide isomerase, GRP78, GRP94 among others that are involved in vesicular transport and ER stress response. Amino-trifluoro-phthalimides exerted potent anticancer activities in vitro on different cell lines including melanoma, leukemia, hepatocellular carcinoma, glioblastoma. They are non-toxic to adult animals up-to 1 g/kg but are highly teratogenic to zebrafish embryos at micromolar concentrations resulting defects in developing muscle. The analogs resulted in calcium release from the endoplasmic reticulum (ER), induction of reactive oxygen species (ROS), ER stress and finally apoptosis. Gene expression analysis confirmed the induction of ER stress-mediated apoptosis pathway components, such as growth arrest- and DNA damage-inducible gene 153 (GADD153), ATF3, Luman/CREB3 recruitment factor (LRF) and the ER-associated degradation-related gene HERPUD1. Tumor suppressors, P53, LATS2 and ING3 were also up-regulated in various cell lines after drug treatment. Exogenous docosahexaenoic acid or eicosapentaenoic acid induced calcium release and ROS and synergized with the analogs in vitro, while oleic acid had no such an effect. Different antioxidants partially, intracellular calcium chelator almost completely diminished ROS production. Amino-phthalimides down-regulated the expression of CCL2, which is implicated in tumor metastasis and angiogenesis. Because of the anticancer, anti-angiogenic action and the wide range of applicability of the immunomodulatory drugs, lipid droplet-binding members of this family could represent a new class of agents by affecting ER-membrane integrity and perturbations of ER homeostasis.

overall_design: 4 replica, 2 dye-swap

first: Laszlo

middle: G

last: Puskas

first: Liliana

middle: Z

last: Feher

first: Csaba

last: Vizler

first: Ferhan

last: Ayaydin

first: Erzsebet

last: Raso

first: Eszter

last: Molnar

first: Istvan

last: Magyary

first: Ivan

last: Kanizsai

first: Gabriella

last: Fabian

first: Klaudia

last: Farkas

first: Peter

last: Hegyi

first: Ferenc

last: Baska

first: Bela

last: Ozsvari

first: Klara

last: Kitajka


title: apc derived mp in vitro

first: Margarita

last: Perez-Casal

summary:
Background-The endothelial protein C receptor (EPCR) plays an important role within the protein C (PC) pathway in regulating coagulation and inflammation. Recently, we described a novel mechanism of EPCR release from the surface of primary physiological cells.  Induced by exogenous activated protein C (APC), EPCR is released in microparticulate form.  Its bound APC retains proteolytic anticoagulant activity and we now hypothesise that this microparticulate EPCR-APC complex can also cleave endothelial protease activated receptor 1 (PAR1) to modulate inflammation and cytoprotection.
Methods & Results-The gene profiling effect on human endothelial cells by 40nM APC, in free or microparticulate form, was assessed.  Transcript profile results showed upregulation of anti-apoptotic and inflammatory genes by APC in either form, which were confirmed by RT-PCR.  These translated into increased GM-CSF and interleukin 8 secretion and cytoprotection against staurosporine-induced apoptosis.  PC or PAR1 antagonism reversed these results to demonstrate that induced effects by microparticles were APC specific and PAR1-dependent.  Further analysis of human plasma from septic patients, by confocal microscopy and ELISA, showed evidence of circulating microparticle-associated EPCR during recombinant APC treatment. Functional coagulation and cellular studies demonstrate that these express APC-specific effects on anticoagulation with PAR1-mediated gene induction and anti-apoptotic function.
Conclusions-APC induction of microparticle-associated EPCR release can occur in vivo.  These microparticles could potentially disseminate the function of the EPCR-APC complex to PAR1 on different cells and vascular sites.
Keywords: free apc versus mp-apc

overall_design: MP were isolated from huvec after estimulation with apc; the apc content of the mp was estimated by chromogenic substrate and a standard curve. 40nM apc on mp was used for estimulation of huvec for 4 hours for study of gene expression. APC relevance was studied by blocking experiments with antibody and par1 involvement was studied by including a par1 antagonist. All experiments were done in triplicate. A basline control was obtained by looking at the profile of non-estimulated cells under the same conditions.

first: Colin

last: Downey

first: Kenji

last: Fukudome

first: Cheng-Hock

last: Toh


title: Salvelinus Microarray experiment: selected line vs control line

status: Public on Feb 24 2010

city: Québec

first: Christopher

last: Sauvage

state: QC

address: 1030 Avenue de la médecine - Pavillon Marchand

department: Biology

country: Canada

institute: University Laval

summary: Domestication has been practiced for centuries yet directed towards relatively few terrestrial crops and animals. While phenotypic and quantitative genetic changes associated with domestication have been amply documented, little is known about the molecular changes underlying the phenotypic evolution during the process. Here, we have investigated the brook charr (Salvelinus fontinalis) responses to artificial selection by means of transcriptional analysis of ~ 32 000 cDNA features performed in both a selected and control populations reared under identical environmental conditions during four generations. Our results indicate that selective breeding led to significant changes in the transcription of genes at the juvenile stage, where we observed 4.16% (156/3750) of differentially expressed genes between the two lines. No significant genes were revealed at the earlier life stage. Moreover, when comparing our results to those of previous studies on Atlantic salmon that compared lines that were selected for 5-7 generations for similar traits (e.g. growth), genes with similar biological functions were found to be under selection in both studies. These observations indicate that (1) four generations of selection caused substantial changes in regulation of gene transcription between selected and control populations and (2) selective breeding for improving the same phenotypic traits (e.g. rapid growth) in brook charr and Atlantic salmon tended to select for the same changes in transcription profiles as the expression of a small and similar set of genes were affected by selection.

overall_design: Two conditions environment: direct comparison of control vs domesticated fish for 20 families. No individual replicates but two individuals of  the same family were hybridized on different slides

first: N

last: Derôme

first: Eric

last: Normandeau

first: Jerome

last: St-Cyr

first: Céline

last: Audet

first: Louis

last: Bernatchez


title: Gene expression analysis of genes differentially expressed between CD93-ko mice and wild-type mice in post ischemic mice brain tissue

status: Public on Mar 23 2010

city: Berlin

first: Denise

last: Harhausen

address: Chariteplatz 1

department: Experimental Neurology

institute: Charite University Berlin

summary: To further decipher CD93-dependent pathways, we compared global expression profiles of ischemic (ipsilateral)  hemispheres of CD93-deficient mice (CD93-ko) with expression profiles of wild-type mice.

overall_design: Total RNA obtained from CD93-ko and WT mice at different time points after cerebral ischemia and from untreated brain tissue

first: George

last: Trendelenburg

first: Wilfried

last: Nietfeld


title: Prostate Cancer Gleason Score

first: Nicole

last: Chui Pressinotti

address: Im Neuenheimer Feld 580

institute: DKFZ

summary:
Screening of differentially expressed genes between benign and prostate tumors with respect to different prostate cancer gleason score 6 and 8

Keywords: disease subtype analysis

overall_design: Comparison of microarray data from benign prostate tissues (n=13), prostate tumors Gleason 6 (n=25) and prostate tumors Gleason 8 (n=27).

last: Pressinotti

first: Van-Duc

last: Luu

first: Ruprecht

last: Kuner

first: Holger

last: Sueltmann

first: Markus

last: Ruschhaupt

first: Helmut

last: Klocker

first: Annemarie

last: Poustka


title: SOP/pI vs. Epithelial cells

status: Public on Feb 19 2010

city: Paris

first: Michel

last: Gho

address: 9 quai Saint Bernard

institute: CNRS

summary: RNA profiling of Drosophila sensory organs precursor cells (SOP/pI) compared with neighbouring epithelial cells.

overall_design: Two-condition experiment, SOP/pI vs. epithelial cells from animals at similar developmental age.

first: Eulalie

last: Buffin


title: Expression profiles of (40,XX) and (39,XO) females

city: Porto

first: Alexandra

middle: M.

last: Lopes

address: R. Dr. Roberto Frias s/n

country: Portugal

institute: IPATIMUP

summary:
Gobal expression analysis in four somatic tissues (brain, liver, kidney and muscle) of adult 40,XX and 39,XO mice with the aim of identifying which genes are expressed from both X chromosomes as well as those genes deregulated in X chromosome monosomy.

Keywords: Expression profiling by array

overall_design: For each tissue, the RNA samples of seven 40,XX, eight 39,XpO and eight 39,XmO mice were pooled by genotype into 9 groups, representing 3 biological replicates per genotype, as follows: 39,XpO-1 and 39,XpO-2 (3 pooled individuals each), 39,XpO-3 (2 pooled individuals); 39,XmO-1 and 39,XmO-2 (3 pooled individuals each), 39,XmO-3 (2 pooled individuals); 40,XX-1 and 40,XX-2 (3 pooled individuals each) 40,XX-3 (2 pooled individuals)

middle: M

first: Paul

middle: S

last: Burgoyne

first: Andrew

last: Ojarikre

first: Julien

last: Bauer

first: Carole

last: Sargent

first: Nabeel

middle: A

last: Affara