title: Gene expression profiles of breast cancer subtypes are detectable in histologically normal breast epithelium

status: Public on Dec 07 2010

first: Kelly

last: Graham

address: 650 Albany Street

department: Hematology/Oncology

institute: Boston University School of Medicine

summary:
Background: We hypothesize that important genomic differences between breast cancer subtypes occur early in carcinogenesis. Therefore, gene expression might distinguish histologically normal breast epithelium (NlEpi) from breasts containing estrogen receptor positive (ER+) compared with estrogen receptor negative (ER-) cancers.
Methods: We examined gene expression in 46 cases of microdissected NlEpi from previously untreated women undergoing breast cancer surgery. From 30 age-matched cases (15 ER+, 15 ER-) we used Affymetryix U133A arrays. From 16 independent cases (9ER+, 7 ER-), we validated seven selected genes using qPCR. We then compared gene expression between NlEpi and invasive breast cancer using 4 publicly available datasets.
Results: 216 probes (corresponding to 198 unique genes) distinguished the NlEpi from breasts with ER+ (NlEpiER+) compared to ER- cancers (NlEpiER-). These include genes characteristic of ER+ and ER- cancers themselves, (e.g., ESR1, GATA3, and CX3CL1, FABP7, respectively). QPCR validated the microarray results in both a sampling of the 30 original cases (84%) and all of the 16 independent cases (77%). Gene expression in NlEpiER+ and NlEPIERNlEpiER- resembled gene expression in ER+ and ER- cancers, respectively: 36%-53% of the genes or probes examined in each the 4 external datasets overlapped between NlEpi and the corresponding cancer subtype.
Conclusions: Gene expression differs in NlEpi of breasts containing ER+ compared to ER- breast cancers.  These differences echo differences in ER+ and ER- invasive cancers. Thus, breast cancer subtypes may be detectable before histologic abnormalities. NlEpi gene expression may help define subtype-specific risk signatures, identify initial subtype specific genomic differences, and suggest new targets for subtype-specific prevention and therapy.

We determined that 216 probesets significantly differed between histologically normal epithelium from ER+ breast cancer patients and from ER- breast cancer patients, and that gene expression in each type of histologically normal epithelium resembles expression of the corresponding subtype of invasive breast cancer (i.e., ER+ or ER-). These findings suggest that characteristic features of breast cancer subtypes are detectable prior to any histologic abnormality. This suggestion has implications for understanding breast cancer biology and devising new tools for assessing breast cancer risk.

overall_design:
30 total laser capture microdissected histologically normal breast tissue samples were analyzed with Affymetrix HU133A microarrays. All samples were age-matched between histologically normal epithelial samples from ER+ breast cancer patients (n=15) and histologically normal epithelial samples from ER- breast cancer patients (n=15). Sample numbers correspond to individual patient samples.

Of the 4 publicly available datasets mentioned above, the only dataset with a GEO number was GSE3494, corresponding to the Miller dataset.  The supplementary file below lists the 251 Samples used from the GSE3494 study.  We did not reanalyze the data - there was no change made to the Miller dataset; we only used these data for confirmation of our own dataset.

first: Carol

last: Rosenberg


title: Chromosomal Fragile Site FRA16D tumor suppressor gene Wwox contributes to aerobic metabolism and oxidative stress response

city: Brisbane

first: Gareth

last: Price

state: Queensland

address: Carmody Road

country: Australia

institute: Queensland Facility for Advanced Bioinformatics

summary: The WWOX gene spans chromosomal fragile site FRA16D, a region of DNA instability in cancer. While WWOX has some tumor suppressor characteristics, its normal role and functional contribution to cancer are unclear. Drosophila homozygous Wwox mutants are viable with no discernable phenotype. Drosophila Wwox interactors, identified by proteomics and micro-array analyses, mainly have roles in aerobic metabolism. Functional relationships between Wwox and either isocitrate dehydrogenase (IDH) or superoxide dismutase 1 (Sod1) were confirmed by phenotype modification, including Sod1 ‘crinkled-wing’, indicative of oxidative stress response. Endogenous reactive oxygen species levels reflect Wwox levels in Drosophila. WWOX mRNA levels in Drosophila and human cells correlate with IDH and Sod1 levels. Wwox therefore contributes to pathways involving glucose metabolism and oxidative stress response.

overall_design: Drosophila embryos were harvested between 4-8hrs and total RNA isolated to look for gene-expression differences induced by the presence of one of two altered Wwox alleles relative to wild-type. The two alleles were Wwox (a null mutation generated by homologous recombination) and Wwoxf04545 carrying a pBac insertion in exon 2 (O’Keefe et al., 2005, 2007). Embryo pools were isolated in triplicate, providing 3 biological replicates.

first: Alex

last: Colella

first: Louise

last: O’Keefe

first: Sonia

last: Dayan

first: Qingwen

last: Chen

first: Amanda

last: Choo

first: Reuben

last: Jacob

first: Deon

last: Venter

first: Robert

last: Richards


title: Expression data from Arabidopsis thaliana under phosphate starvation stress

status: Public on Dec 09 2010

city: Campus de Cantoblanco

first: Regla

last: Bustos

state: Madrid

address: Darwin 3

country: Spain

institute: CNB-CSIC

summary: We performed a transcriptomic analysis of Pi starvation responses in Arabidopsis thaliana (Columbia-0) wild type plants under phosphate starvation stress and in plants with altered PHR1(-like) activity, comparing mutants of phr1 and phr1-phl1 grown in phosphate-lacking medium. Results show the central role of PHR1 and functionally redundant members of its family in the control of transcriptional responses to Pi starvation.

overall_design: The analysis was performed in wild-type plants grown for seven days in complete (+Pi) and Pi-lacking (-Pi) Johnson solid media and the single phr1 and double phr1-phl1 mutants grown for 7 days in –Pi medium. Three independent biological samples of total RNA from shoot and root were hybridized separately.

first: Gabriel

last: Castrillo

first: Javier

last: Paz-Ares


title: Expression data from type 2 diabetic and non-diabetic isolated human islets

status: Public on Dec 01 2010

city: Pisa

first: Marco

last: Bugliani

address: via Paradisa, 2

department: Dept. Endocrinology and Metabolism

country: Italy

institute: University of Pisa

summary: We performed microarray analysis to evaluate differences in the transcriptome of type 2 diabetic human islets compared to non-diabetic islet samples.

overall_design: Human islets were isolated from the pancreas of organ donors by collagenase digestion followed by density gradient purification, then hand-picked and cultured 2 days in M199 culture medium.


title: Histone acetylation dependent microarray analysis uncovers a role for Tip60 HAT activity in nervous system function and general metabolism

status: Public on Nov 29 2010

city: Philadelphia

first: Felice

last: Elefant

state: PA

address: 3141 Chestnut Street, Stratton Hall 226

department: Biology

country: USA

institute: Drexel University

summary: Tip60 is a key histone acetyltransferase (HAT) enzyme that plays a central role in diverse biological processes critical for general cell function, however the chromatin-mediated cell-type specific developmental pathways that are dependent exclusively upon the HAT activity of Tip60 remain to be explored. Here, we investigate the role of Tip60 HAT activity in transcriptional control during multicellular development, in vivo by examining genome-wide changes in gene expression in a Drosophila model system specifically depleted for endogenous dTip60 HAT function. We show that amino acid residue E431 in the catalytic HAT domain of dTip60 is critical for the acetylation of endogenous histone H4 in our fly model in vivo, and demonstrate that dTip60 HAT activity is essential for multicellular development. Moreover, our results uncover a novel role for Tip60 HAT activity in controlling neuronal specific gene expression profiles essential for nervous system function as well as a central regulatory role for Tip60 HAT function in general metabolism.

overall_design: Drosophila larvae ubiquitously expressing either our dTIP60 HAT specific mutant or an additional copy of wild type dTIP60 were selected along with age-matched wild type controls for RNA extraction. Two samples, each containing a pool of thirty-five staged whole larvae, were collected from each respective genotypic cross, and were used for hybridization on a separate Affymetrix microarray.


title: Integrative responses to IL-17 and TNF-α in human keratinocytes account for key inflammatory pathogenic circuits in psoriasis

status: Public on Nov 24 2010

city: New York

first: Mayte

last: Suarez-Farinas

state: NY

address: 1425 Madison Ave, L2-70C, Box 1077,

institute: Mount SinaiSchool of Medicine

summary: We sought to provide a comprehensive evaluation of the effects of TNF-α and IL-17 on the keratinocyte gene profile in order to identify genes that might be co-regulated by these cytokines. We then sought to determine how genes that were synergistically activated by both cytokines relate to the psoriasis transcriptome. Here, we identified 160 unique genes that were synergistically up-regulated by IL-17 and TNF-α and 188 unique genes where the two cytokines had at least an additive effect. Among highly up-regulated genes were those involved in neutrophil and lymphocyte chemotaxis, inflammation, and epidermal differentiation. Synergistically up-regulated genes included some of the highest expressed genes in lesional psoriatic skin with an impressive correlation between IL-17/TNF-α induced genes and the psoriasis gene signature. In conclusion, keratinocytes may be key drivers of pathogenetic inflammatory circuits in psoriasis through integrating responses to TNF-α and IL-17. This may explain high efficacy of targeting psoriasis with either anti-TNF-α or agents that block Th17 T-cells/IL-17 and has important implications for the development of new therapeutic agents.

overall_design: Comparison of keratinocyte responses to IL-17, TNF-α (1 ng mL-1 and 10 ng mL-1), and the combination of both cytokines in psoriasis.

first: James

middle: G

last: Krueger


title: FoxA1 is a critical determinant of Estrogen Receptor function and endocrine response (part II)

status: Public on Nov 17 2010

city: Cambridge

first: Roslin

last: Russell

address: Robinson Way

country: United Kingdom

institute: Cambridge Research Institute, Cancer Research UK

summary: Estrogen Receptor-a (ER) is the key feature in the majority of breast cancers and ER binding to the genome correlates with the Forkhead protein FOXA1 (HNF3a), but mechanistic insight is lacking. We now show that FOXA1 is the defining factor that governs differential ER-chromatin interactions. We show that almost all ER-chromatin interactions and gene expression changes are dependent on the presence of FOXA1 and that FOXA1 dictates genome-wide chromatin accessibility. Furthermore, we show that CTCF is an upstream negative regulator of FOXA1-chromatin interactions. In ER responsive breast cancer cells, the dependency on FOXA1 for tamoxifen-ER activity is absolute and in tamoxifen resistant cells, ER binding occurs independently of ligand, but in a FOXA1 dependent manner. Importantly, expression of FOXA1 in non-breast cancer cells is sufficient to alter ER binding and response to endocrine treatment. As such, FOXA1 is the primary determinant that regulates estrogen-ER activity and endocrine response in breast cancer cells and is sufficient to program ER functionality in non-breast cancer contexts.

overall_design: FoxA1 silenced breast cancer MCF-7 cell lines or control siRNA in the presence of Estrogen or a vehicle. MCF-7 cells were hormone-depleted for 3 d and treated with 100 nM estrogen for 6 h. There were three biological replicates for each of the four different groups.

first: Antoni

middle: H

last: Rodriguez

first: Jason

middle: S

last: Carroll


title: FoxA1 is a critical determinant of Estrogen Receptor function and endocrine response

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

overall_design: Refer to individual Series


title: Larval host gene expression study in Drosophila post parasitic wasp-infection

status: Public on Nov 23 2010

first: Shubha

last: Govind

address: 160 Convent Avenue

institute: The City College of New York

summary: Upon pathogenic infection, drosophila larval host mounts an immune response. Parasitic wasps inject venom that contain virulence factors during oviposition, which can elicit host immune response, and in some cases, suppress host immune responses altogether. Several microarray experiments have been performed on different classes of parasitic wasps. We wanted to compare how Ganaspis xanthopoda-infected hosts respond compared to other classes of parasitic wasps.

overall_design: Third instar y w larvae from a 2-day egglay were infected with G. xanthopoda for three and six hours, respectively, by introducing waps in petri-dish containing larvae. Controls were handled side-by-side without introducing wasps. Host larvae were immediately dissected, infection confirmed by presence of wasp egg, and frozen in liquid nitrogen and ground in Trizol. RNA was isolated and checked by agarose gel-electrophoresis. Samples were then sent to the Microarray Core Facility at Weill Cornell Medical College.


title: The impact of BRCA2A and SSN2 on plant defense genes

status: Public on Nov 21 2010

city: Durham

first: shui

last: wang

state: NC

address: 124 Science Dr

institute: Duke University

summary:
BRCA2A: We used microarrays to identify differentially expressed genes. We focused on those genes that were dramatically salicylic acid-induced (>2-fold) and BRCA2A-dependent in npr1 sni1 double mutants
SSN2: We used microarrays to identify differentially expressed genes. We focused on those genes that were dramatically salicylic acid-induced (P<0.05) and SSN2-dependent in npr1 sni1 double mutants

overall_design:
BRCA2A: 3-week old npr1 sni1 and npr1 sni1 brca2a mutants were treated with salicylic acid for 16 hours. Replicates are derived from three independent biological experiments.
SSN2: 3-week old npr1 sni1 ssn2 mutants were treated with salicylic acid for 16 hours. Replicates are derived from two (SA treated) or three (water treated) independent biological experiments.

first: Shui

last: Wang


title: Microarray Analysis Reveals Distinct Gene Expression Profiles Among Different Tumor Histology, Stage and Disease Outcomes in Endometrial Adenocarcinoma

city: Buffalo

first: song

last: liu

address: Elm and Carlton Streets

institute: Roswell Park Cancer Institute

summary: The goal of this study was to identify differentially expressed genes (DEG) between early vs. late stage endometrioid adenocarcinoma (EAC) and uterine serous carcinoma (USC), as well as between disease outcomes in each of the two histological subtypes.

overall_design: Gene expression profiles of 20 cancer samples were analyzed (EAC =10, USC =10) using the human genome wide illumina bead microarrays carrying 48,000 genes.

first: Paulette

last: Mhawech-Fauceglia

first: Dan

first: Joshua

last: Kesterson

first: Kimberly

last: Clark

first: Kunle

last: Odunsi

first: Shashikant

last: Lele

first: Sing

last: Liu


title: Molecular characterization of the submergence response of Arabidopsis thaliana ecotype Columbia

status: Public on Nov 12 2010

city: Riverside

first: Seung Cho

last: Lee

state: CA

address: 2150 Batchelor Hall

department: Botany & Plant Sciences

institute: University of California Riverside

summary: This study profiles transcriptomic changes of Arabidopsis thaliana Col-0 in response to submergence. This dataset includes CEL files, RMA signal values and MAS5 P/M/A calls from total mRNA populations of plants at 9 to 10 leaf rosette stage. Biological replicates of root and shoot tissues were harvested after 7 h and 24 h of submergence in darkness along with corresponding non-submerged dark controls. To characterize the dark response, non-submerged light controls plants were harvested at the 0 h time point. Quantitative profiling of cellular mRNAs was accomplished with the Affymetrix ATH1 platform. Changes in the transcriptome in response to submergence and early darkness were evaluated, and the data led to identification of genes co-regulated at the conditional and organ-specific level.

overall_design: 20 samples, 5 conditions (7 h submergence in darkness, 7 h darkness, 24 h submergence in darkness, 24 h darkness, 0 h light control), 2 RNA pools (rosette leaf and root tissues), 2 independent biological replicate experiments

first: Seung

middle: C

first: Angelika

last: Mustroph

first: Rashmi

last: Sasidaharan

first: Divya

last: Vanashisht

last: Voesenek

first: Julia

last: Bailey-Serres


title: FoxA1 is a critical determinant of Estrogen Receptor function and endocrine response (part I)

first: Roslin

last: Russell

overall_design: breast cancer MCF-7 cell lines were treaated in the presence of Estrogen, Estrogen plus Tamoxifen, Tamoxifen or a vehicle. MCF-7 cells were hormone-depleted for 3 d and treated with 100 nM estrogen or 1 microM Tamoxifen for 6 h. There were four biological replicates for each of the four different groups.

first: Antoni

last: Rodriguez

first: Jason

last: Carroll


title: High resolution NO3 response of Arabidopsis Roots

status: Public on Nov 10 2010

city: Montpellier

first: Gabriel

last: Krouk

address: 2 Place Pierre Viala

country: France

institute: CNRS

summary: This work uses a time series in order to decipher gene relationships and consequently to build core regulatory networks involved in Arabidopsis root adaptation to NO3- provision. The experimental approach has been to monitor genome response to NO3- at 3, 6, 9, 12, 15 and 20 min, using ATH1 chips. This high-resolution time course analysis demonstrated that the previously known primary nitrate response is actually preceded by very fast (within 3 min) gene expression modulation, involving genes/functions needed to prepare plants to use/reduce NO3-. State-space modeling (a machine learning approach) has been used to successfully predict gene behavior in unlearnt conditions.

overall_design: 26 Samples: 2 at time 0 with no treatment; 4 at time 3, 2 with KCL and 2 with KNO3 treatment; 4 at time 6, 2 with KCL and 2 with KNO3 treatment; 4 at time 9, 2 with KCL and 2 with KNO3 treatment; 4 at time 12, 2 with KCL and 2 with KNO3 treatment; 4 at time 15, 2 with KCL and 2 with KNO3 treatment;  4 at time 20, 2 with KCL and 2 with KNO3 treatment;


title: Examining the transcriptome of growth arrested keratinocytes

status: Public on Oct 28 2010

city: Woolloongabba

first: Orla

last: Gannon

state: QLD

address: Ipswich Road

institute: Diamantina Institute

summary: Samples of RNA from subconfluent, proliferative keratinocytes, TGF β1 treated keratinocytes and 7 days post confluent keratinocytes were hybridised to an RNA microarray to identify genes differentially expressed upon reversible (TGF B1) and irreversible (Confluence induced) growth arrest.

overall_design: Quadruplicate total RNA isolated from proliferative, subconfluent keratinocytes, 15ng/mL TGF B1 treated keratinocytes and 7 days post confluent keratinocytes were hybridised to an RNA microarray to identify genes differentially expressed upon growth arrest.

middle: M

first: Nicholas

middle: A

last: Saunders


title: Genome-wide analysis of human pulmonary artery endothelial cells after knockdown of either BMPRII or beta-catenin

status: Public on Nov 06 2010

city: Baltimore

first: Molong

last: Li

state: MD

address: 733 N. Broadway

department: School of Medicine

institute: Johns Hopkins University

summary: Expression analysis of genes potentially regulated by BMPRII and beta-catenin. BMPRII has been linked as a genetic factor to the disease pulmonary arterial hypertension.

overall_design: Comparison of total mRNA obtained from human pulmonary artery endothelial cells treated with control, bone morphogentic protein receptor II, or beta-catenin siRNA

first: Tero-Pekka

last: Alastalo

first: Marlene

last: Rabinovitch


title: Comparison of hiPSCs, hESCs and fibroblasts

status: Public on Oct 20 2010

city: SINGAPORE

first: NA-YU

last: CHIA

address: 30 Biopolis Way

department: STEM CELL 6

country: Singapore

institute: Genome Institute of Singapore

summary: In our study, PRDM14 and NFRkB were found to enhance the reprogramming of human fibroblasts to hiPSCs in the presence of OCT4, SOX2, KLF4, with/without c-MYC (OSK/OSKC). To examnie if the obtained hiPSC share similar expression signature with hESC, we conducted the microarray analysis on the hiPSCs,  hESCs and fibroblasts. The result showed that all of the examined hiPSCs resembled hESCs, but differed from fibroblasts MRC5.

overall_design: 4 hiPSC lines, 2 hESC lines and 1 type of fibroblasts were analyzed in total.  Each sample is done in duplicates.

first: Ng

last: Huck-Hui

first: Bo

last: Feng

first: Na-Yu

last: Chia


title: Gene expression analysis of TRIM5 KD in the THP1 cell line

status: Public on Nov 02 2010

city: Lausanne

first: Federico

last: Santoni

address: rue du Bugnon, 7

country: Switzerland

institute: CHUV

summary: We had evidence that TRIM5 regulates signal transduction, specifically NFkB and MAPK pathways. To test the role of endogenous TRIM5 we used the myelomonocytic leukemia cell line THP1. These cells were transduced with a lentiviral vector that delivers a miRNA engineered to knockdown TRIM5. The vector also encoded a puromycin-resistance cassette and transduced cells were selected in poold with puromycin. As a control, cells were transduced with a vector targeting luciferase instead of TRIM5.

overall_design: After selection in puromycin, the TRIM5 KD and Luciferase KD cells were differentiated into macrophages by treatment with PMA. 3 days later, RNA was harvested for analysis.

first: Jeremy

last: Luban


title: Expression profiling in whole blood in ankylosing spondylitis patients and controls

status: Public on Nov 04 2010

first: Gethin

last: Thomas

address: Princess Alexandra Hospital

institute: University of Queensland Diamantina Institute

summary: Introduction: A number of genetic-association studies have identified genes contributing to AS susceptibility but such approaches provide little information as to the gene activity changes occurring during the disease process. Transcriptional profiling generates a “snapshot” of the sampled cells activity and thus can provide insights into the molecular processes driving the disease process. We undertook a whole-genome microarray approach to identify candidate genes associated with AS and validated these gene-expression changes in a larger sample cohort.  Methods: 18 active AS patients, classified according to the New York criteria. and 18 gender-and age-matched controls were profiled using Illumina HT-12 Whole-Genome Expression BeadChips which carry cDNAs for 48000 genes and transcripts. Class comparison analysis identified a number of differentially expressed candidate genes. These candidate genes were then validated in a larger cohort using qPCR-based TaqMan Low Density Arrays (TLDAs).  Results: 239 probes corresponding to 221 genes were identified as being significantly different between patients and controls with a p-value <0.0005 (80% confidence level of false discovery rate). Forty seven genes were then selected for validation studies, using the TLDAs. Thirteen of these genes were validated in the second patient cohort with 12 down-regulated 1.3-2-fold and only 1 upregulated (1.6-fold). Among a number of identified genes with well-documented inflammatory roles we also validated genes that might be of great interest to the understanding of AS progression such as SPOCK2 (osteonectin) and EP300 which modulate cartilage and bone metabolism.  Conclusion: We have validated a gene expression signature for AS from whole blood and identified strong candidate genes that may play roles in both the inflammatory and joint destruction aspects of the disease.

overall_design: RNA was extracted from whole blood using PAXGene tubes. 16 AS patients with active disease and 16 gender- and age-matched controls were analysed.

middle: P

first: Fernando

last: Pimentel-Santos


title: Translocations Activating IRF4 Identify a Subtype of Germinal-Center-Derived B-cell Lymphoma Affecting Predominantly Children and Young Adults

status: Public on Jun 24 2011

city: Regensburg

first: Christian

middle: W

last: Kohler

state: Bavaria

address: Am BioPark 9

department: Institute of Functional Genomics

country: Germany

institute: University of Regensburg

summary:
Background: Germinal center B-cell (GCB) lymphomas are common in children and adults. The prognosis strongly depends on age. Subgroups of GCB-lymphomas are characterized by chromosomal translocations affecting immunoglobulin (IG) loci leading to oncogene deregulation.
Methods: Novel IG translocation partners were cloned within the network “Molecular Mechanisms in Malignant Lymphomas” (MMML) by long-distance inverse polymerase chain reaction. Mature aggressive B-cell lymphomas from the MMML as well as pediatric and adult lymphoma trials were analyzed by fluorescence in situ hybridization (FISH) and immunhistochemistry. Data from 438 MMML cases characterized by gene expression profiling were mined.
Results: Cloning of unknown IG partners identified a t(6;14)(p25;q32) juxtaposing the IRF4 oncogene with the IGH-locus as novel recurrent aberration in GCB lymphoma. FISH analyses of 427 mature B-cell lymphomas for IRF4 translocations revealed 20 IG/IRF4 positive lymphomas (17 IGH/IRF4, 2 IGL/IRF4, 1 IGΚ/IRF4). IG/IRF4-positive lymphomas were predominantly GCB-type diffuse large B-cell lymphomas (DLBCL) or follicular lymphoma grade 3, shared overexpression of IRF4/MUM1 and BCL6 and lacked PRDM1/BLIMP1 expression and t(14;18)/BCL2 breaks. BCL6 aberrations were common. The gene expression profile of IG/IRF4-positive lymphomas was different from other subtypes of DLBCL and a classifier for IG/IRF4 positivity containing 27 genes allowed prediction of 3 additional MMML IG/IRF4-positive cases subsequently proven by FISH. IG/IRF4-positivity was associated with a favorable outcome likely due to significant enrichment of IG/IRF4-positive lymphomas in childhood and young adulthood.
Conclusions: Our results suggest IRF4 translocations to be primary genetic alterations in a novel molecularly defined subset of GC-derived lymphomas predominantly affecting children.

overall_design: 271 diffuse large B-Cell lymphoma samples were hybridized to HGU133A Affymetrix GeneChips.

first: Itziar

last: Salaverria

first: Claudia

last: Philipp

first: Ilske

last: Oschlies

first: Markus

last: Kreuz

first: Monika

last: Szczepanowski

first: Birgit

last: Burkhardt

first: Heiko

last: Trautmann

first: Stefan

last: Gesk

first: Miroslaw

last: Andrusiewicz

first: Hilmar

last: Berger

first: Miriam

last: Frey

first: Lana

last: Harder

first: Dirk

last: Hasenclever

first: Michael

last: Hummel

last: Loeffler

first: Friederike

last: Hahn

first: Christiane

last: Pott

last: Pfreundschuh

first: Alfred

last: Reiter

first: Julia

last: Richter

first: Maciej

last: Rosolowski

first: Carsten

last: Schwaenen

first: Harald

last: Stein

first: Lorenz

last: Trümper

first: Swen

last: Wessendorf

first: Rainer

last: Spang

first: Ralf

last: Küppers

first: Wolfram

last: Klapper

first: Reiner

last: Siebert


title: Optimizing molecular signatures for prostate cancer recurrence

status: Public on Nov 05 2010

city: Orlando

first: Steve

last: Goodison

address: 6900 Lake Nona Blvd

department: Cancer Research Institute

institute: M. D. Anderson Cancer Center Orlando

summary: The derivation of molecular signatures indicative of disease status and predictive of subsequent behavior could facilitate the optimal choice of treatment for prostate cancer patients. In this study, we conducted a computational analysis of gene expression profile data obtained from 79 cases, 39 of which were classified as having disease recurrence, to investigate whether advanced computational algorithms can derive more accurate prognostic signatures for prostate cancer.  At the 90% sensitivity level, a newly derived prognostic genetic signature achieved 85% specificity. This is the first reported genetic signature to outperform a clinically used postoperative nomogram. Furthermore, a hybrid prognostic signature derived by combination of the nomogram and gene expression data significantly outperformed both genetic and clinical signatures, and achieved a specificity of 95%.  Our study demonstrates the feasibility of utilizing gene expression information for highly accurate prostate cancer prognosis beyond the current clinical systems, and shows that more advanced computational modeling of tissue-derived microarray data is warranted before clinical application of molecular signatures is considered.

overall_design: mRNA profiling was performed using 79 cases of prostate cancer of known disease recurrence status

first: Yijun

last: Sun


title: Transcriptional regulation of ROS controls the transition from proliferation to differentiation in the root

first: HIRONAKA

last: TSUKAGOSHI

address: 4128 FFSC Building

institute: Duke university

summary:
We isolated the meristematic and elongation zones of Col-0, upb1-1 mutant and 35S::UPB1-3YFP/upb1-1 plants by micro-dissection and extracted RNA from each section independently.
To identify genes that might mediate UPB1 function we conducted a series of microarray experiments. The spatial distribution of the UPB1 protein suggested that it might exert a different effect on gene expression in the meristematic and elongation zones. Therefore, we isolated the meristematic and elongation zones by micro-dissection and extracted RNA from each section independently.

overall_design: Total RNA was isolated from approximately 60 meristem- and elongation zones of Col-0, upb1-1 and 35S::UPB1-3YFP #2 6 day old plants. Two biological replicates were performed for each experiment.

first: Hironaka

last: Tsukagoshi

first: Wolfgang

last: Busch


title: 0.6% Methamphetamine feeding experiments

status: Public on Oct 31 2010

city: Urbana

first: Hongmei

last: LI

state: IL

address: 505 S. Goodwin Ave

department: Entomology

institute: University of Illinois at Urbana-Champaign

summary: Methamphetamine can trigger dopamine releasing in human brain, now used as abuse drug. Some studies have shown that specific genes and proteins responded to, methamphetamine, but little is known about the overall “omic” response of organisms to this illicit substance.   Here we demonstrate that Drosophila melanogaster has the potential to give us significant insights into evolutionarily conserved responses to methamphetamine.  We performed metabolome, proteome, and transciptome profiling with Drosophila treated with methamphetamine.  The proteomic profiling revealed responses associated with known physiological problems that occur with methamphetamine usage in mammals.  The metabolomic result showed that the metabolite trehalose was decreased significantly after methamphetamine exposure, suggesting an oxidative stress response to this drug.  Many of the differential transcribed genes, including detoxification enzymes, had the potential transcription factor-binding motif YY1 associated with their upstream regulatory regions.  YY1 is known to be responsive to amphetamines in mammals.

overall_design: For each sample, 20 virgin male flies were used to extract the mRNA. Three replicates were produced for each treatments. Two treatments were produced (control VS 0.6% 24 h meth-fed).

first: Lijie

last: Li

first: Venu

last: Margam

first: Weilin

first: Barry

last: Pittendrigh


title: PRDM14 Knockdown in human embryonic stem cells

first: NA-YU

last: CHIA

summary: To identify the gene changes after PRDM14 knockdown

overall_design: 6 samples were collected in total. Each sample is done in triplicate and samples were collected at 3 days after transfection. Luciferase knockdown serves as negative control and PRDM14 knockdown is the experimental sample.

first: Huck-Hui

last: Ng

first: Na-Yu

last: Chia


title: Regulation of Angiogenesis by EZH2

status: Public on Oct 12 2010

city: Houston

first: Sangbae

last: Kim

state: TX

address: 1 Baylor plaza

department: HGSC

institute: Baylor Colleage of Medicine

summary: While VEGF-targeted therapies are showing promise in clinical studies, new angiogenesis targets are needed to make additional gains. Here, we show that increased Zeste homologue 2 (EZH2) expression in either tumor cells or in tumor vasculature is predictive of poor clinical outcome. The increase in endothelial EZH2 is a direct result of VEGF stimulation and indicates the presence of a paracrine circuit that promotes angiogenesis by methylating and silencing vasohibin 1 (VASH1). EZH2 silencing in the tumor-associated endothelial cells resulted in inhibition of angiogenesis mediated by reactivation of VASH1, and reduced ovarian cancer growth.  Combined, these data provide a new understanding of the regulation of tumor angiogenesis and support the potential for targeting EZH2 as a novel therapeutic approach.

overall_design: Pre-clinical study, DNA microarray (Illumina HumanHT-12)

first: Lingegowda

last: Mangala

first: Hee-Dong

last: Han

first: Chunhua

last: Lu

first: Rouba

last: Ali-Fehmi

first: Christopher

last: Newton

first: Laurent

last: Ozbun

first: Guillermo

last: Armaiz-Pena

first: Wei

last: Hu

first: Rebecca

middle: L

last: Stone

first: Adnan

last: Munkarah

first: Murali

middle: K

last: Ravoori

first: Mian

last: Shahzad

first: Jeong-Won

last: Lee

first: Edna

last: Mora

first: Robert

middle: R

last: Langley

first: Amy

last: Carroll

first: Koji

last: Matsuo

first: Whitney

last: Spannuth

first: Rosemarie

last: Schmandt

first: Nicholas

middle: B

last: Jennings

first: Blake

last: Goodman

last: Jaffe

first: Alpa

last: Nick

first: Eylem

middle: O

last: Guven

first: Ya-Huey

last: Chen

first: Long-Yuan

first: Min-Chuan

last: Hsu

last: Coleman

first: George

last: Calin

first: Emir

last: Denkbas

first: Jae-Yun

last: Lim

first: Ju-Seog

first: Vikas

last: Kundra

first: Michael

middle: J

last: Birrer

first: Mien-Chie

last: Hung

first: Gabriel

last: Lopez-Berestein

first: Anil


title: Pausing of RNA polymerase II disrupts DNA-specified nucleosome organization to enable precise gene regulation: Expression data

status: Public on Oct 18 2010

city: Boston

first: Karen

last: Adelman

state: MA

address: 45 Shattuck St. LHRRB-201a

department: Biological Chemistry and Molecular Pharmacology

institute: Harvard Medical School

summary: Metazoan transcription is controlled through either coordinated recruitment of transcription machinery to the gene promoter, or subsequently, through regulated pausing of RNA polymerase II (Pol II) in early elongation. We report that a key difference between genes that use these distinct regulatory strategies lies in the chromatin architecture specified by their DNA sequences. Pol II pausing is prominent at highly-regulated genes whose sequences inherently disfavor nucleosome formation within the gene, but favor nucleosomal occlusion of the promoter. Pausing of polymerase maintains these genes in an active state by inhibiting the formation of repressive promoter chromatin. In contrast, promoters of housekeeping genes that lack paused Pol II are deprived of nucleosomes regardless of polymerase binding, but show higher nucleosome occupancy downstream. Our results suggest that the “default” chromatin state of a gene instructs its regulation, and that highly-regulated promoters have evolved to encourage competition between nucleosomes and paused Pol II for promoter occupancy.

overall_design: Drosophila melanogaster S2 cells (Drosophila Genomics Resource Center) were untreated, or treated with dsRNA for 96 hours, as described in Armknecht, S. et al. (2005) Methods in Enzymology, 392: pp. 55-73. Total RNA was then extracted using the RNeasy RNA extraction kit, with on column DNAse digestion (Qiagen), according to manufacturer’s protocol. Gene expression analysis was conducted using Drosophila Genome 2.0 Genechip® arrays (Affymetrix, Santa Clara, CA). Starting with 1ug of total RNA, biotin-labeled cRNA was produced using the Affymetrix 3’ Amplification One-Cycle Target labeling kit according to manufacturer’s protocol. For each array, 10ug of amplified cRNAs were fragmented and hybridized to the array for 16 hours in a rotating hybridization oven using the Affymetrix Eukaryotic Target Hybridization Controls and protocol. Slides were stained and washed as indicated in the Antibody Amplification Stain for Eukaryotic Targets protocol using the Affymetrix Fluidics Station FS450. Arrays were then scanned with an Affymetrix Scanner 3000 and data was obtained using either Genechip® Operating Software (Version 1.2.0.037) or Affymetrix GeneChip Command Console (V. 1.1) and imported into the Rosetta Resolver system (Version 6.0) as outlined in the scan and data processing protocols.

first: Daniel

last: Gilchrist

first: Gilberto

last: Dos Santos

first: David

last: Fargo

first: Bin

last: Xie

first: Yuan

last: Gao

first: Leping

last: Li


title: Depleting cytosolic cysteine compromises the antioxidant capacity of the cytosol in Arabidopsis thaliana

status: Public on Oct 01 2010

city: Sevilla

first: Cecilia

last: Gotor

address: Avda. Américo Vespucio, 49

institute: Instituto de Bioquímica Vegetal y Fotosíntesis

summary: Plant cells contain different O-acetylserine(thiol)lyase (OASTL) enzymes involved in Cys biosynthesis and located in different subcellular compartments. These enzymes are made up of a complex variety of isoforms resulting in different subcellular Cys pools. To unravel the contribution of cytosolic Cys to plant metabolism, we characterized the knockout oas-a1.1 and osa-a1.2 mutants, deficient in the most abundant cytosolic OASTL isoform in Arabidposis thaliana. Total intracellular Cys and glutathione concentrations were reduced, and the glutathione redox state was shifted in favour of its oxidized form. Interestingly, the capability of the mutants to chelate heavy metals did not differ from that of the wild type, but the mutants have an enhanced sensitivity to Cd. With the aim of establishing the metabolic network most influenced by the cytosolic Cys pool, we used the ATH1 GeneChip for evaluation of differentially expressed genes in the oas-a1.1 mutant grown under non-stress conditions. The transcriptomic footprints of mutant plants had predicted functions associated with various physiological responses that are dependent on reactive oxygen species and suggested that the mutant was oxidatively stressed. To further elucidate the specific function(s) of the OAS-A1 isoform in the adaptation response to cadmium we extended the trasncriptome experiment to the wild type and oas-a1.1 mutant plants exposed to Cd. The comparison of transcriptomic profiles showed a higher proportion of genes with altered expression in the mutant than in the wild type, highlighting up-regulated genes identified as of the general oxidative stress response rather than metal-responsive genes.

overall_design: Wild type and oas-a1.1 mutant plants were grown hydroponically and, after a two-week acclimation period, the roots and shoots were harvested separately. Total RNA was then prepared and analyzed using the Affymetrix-Arabidopsis ATH1GeneChip array. Three biological replicates were performed for each sample. We made two different comparisons to classify the differently expressed genes in the mutant plant: oas-a1.1 roots versus wild-type roots and oas-a1.1 shoots versus wild-type shoots. Hydroponically-grown wild type and oas-a1.1 mutant plants were further treated with 50µM CdCl2 and 18h-treated-roots and 24h-treated-shoots were harvested. Total RNA was then prepared and analyzed using the Affymetrix-Arabidopsis ATH1GeneChip array. Three biological replicates were performed for each sample. Different comparisons were performed as follows: 18h Cd-treated wild type roots versus untreated wild type roots; 24h Cd-treated wild type shoots versus untreated wild type shoots; 18h Cd-treated oas-a1.1 roots versus untreated oas-a1.1 roots; 24h Cd-treated oas-a1.1 shoots versus untreated oas-a1.1 shoots; 18h Cd-treated oas-a1.1 roots versus 18h Cd-treated wild type roots; 24h Cd-treated oas-a1.1 shoots versus 24h Cd-treated wild type shoots

first: Carmen

last: López-Martín

first: Luis

last: Romero


title: Imatinib Treatment of GIST882

status: Public on Oct 13 2010

first: Yu

last: Chen

address: 1275 York Ave, Box 20

department: Human Oncology and Pathogenesis Program

institute: Memorial Sloan Kettering Cancer Center

summary: Gastrointestinal Stromal Tumor frequently harbor mutations in the KIT receptor tyrosine kinase and depend on its activity for growth. This underlies the efficacy of imatinib, a inhibitor of KIT activity, in GIST management. GIST882 is a patient derived GIST cell line that harbor a K640E exon 13 KIT mutation and is sensitive to imatinib treatment. To analyze the downstream effect of KIT inhibition, GIST882 cells were treated for 8 hours with  1μM Imatinib.

overall_design: GIST882 cells were treated in triplicate with 0.1% DMSO or 1μM Imatinib for 8 hours. RNA was isolated and analyzed by Illumina Human HT-12 beadarray.

first: Ping

last: Chi

first: C

middle: D

last: Allis

first: Charles

last: Sawyers


title: Native functions of the androgen receptor are essential to pathogenesis in a Drosophila model of spinobulbar muscular atrophy

status: Public on Sep 23 2010

city: Memphis

first: Geoffrey

last: Neale

state: TN

address: 262 Danny Thomas Place

department: Hartwell Center

institute: St Jude Childrens Research Hospital

summary: Spinobulbar muscular atrophy (SBMA) is a neurodegenerative disease caused by expansion of a polyglutamine tract in the androgen receptor (AR). This mutation confers toxic function to AR through unknown mechanisms. Mutant AR toxicity requires binding of its hormone ligand, suggesting that pathogenesis involves ligand-induced changes in AR. However, whether toxicity is mediated by native AR function or a novel AR function is unknown. We systematically investigated events downstream of ligand-dependent AR activation in a Drosophila model of SBMA. We show that nuclear translocation of AR is necessary but not sufficient for toxicity and that DNA binding by AR is necessary for toxicity. Mutagenesis studies demonstrated that a functional AF-2 domain is essential for toxicity, a finding corroborated by a genetic screen that identified AF-2 interactors as dominant modifiers of degeneration. These findings indicate that SBMA pathogenesis is mediated by misappropriation of native protein function, a mechanism that may apply broadly to polyglutamine diseases.

overall_design: We used Affymetrix arrays to generate a molecular phenotype of degeneration in profile flies expressing wild-type or polyglutamine-expanded AR. We also expressed in the fly eye polyglutamine-expanded AR with point mutations affecting the DNA binding domain and the AF-2 domain. In some experiments, GMR-GAL4; UAR-AR flies were crossed to flies carrying a chromosomal duplication of the limpet gene. Transgene expression was induced in the eye using GMR-GAL4. Flies were crossed at 29 deg C on food containing either 1mM DHT or 1% ethanol (vehicle).

first: Natalia

last: Nedelsky

first: Maria

last: Pennuto

first: Rebecca

last: Smith

first: Isabella

last: Palazzolo

first: Jennifer

last: Moore

first: Zhiping

last: Nie

first: J

last: Taylor


title: Therapeutic globin expression in thalassemia patient induced pluripotent stem cells from genomic safe harbors

status: Public on Oct 26 2010

city: Seattle

first: Manu

last: Setty

state: WA

address: 1100 Fairview Ave N

department: Basic Sciences Division

institute: Fred Hutchinson Cancer Center

summary: The advent of human induced pluripotent stem (iPS) cells enables for the first time the derivation of unlimited numbers of patient-specific stem cells and holds great promise for regenerative medicine. However, realizing the full potential of iPS cells requires robust, precise and safe strategies for their genetic modification. Safe human iPS cell engineering is especially needed for therapeutic applications, as stem cell-based therapies that rely on randomly integrated transgenes pose oncogenic risks. Here we describe a strategy to genetically modify iPS cells from patients with beta-thalassemia in a potentially clinically relevant manner. Our approach is based on the identification and selection of “safe harbor” sites for transgene expression in the human genome. We show that thalassemia patient iPS cell clones harboring a  transgene can be isolated and screened according to chromosomal position. We next demonstrate that iPS cell clones that meet our “safe harbor” criteria resist silencing and allow for therapeutic levels of beta-globin expression upon erythroid differentiation without perturbation of neighboring gene expression. Combined bioinformatics and  functional analyses thus provide a robust and dependable approach for achieving desirable levels of transgene expression from selected chromosomal loci. This approach may be broadly applicable to introducing therapeutic or suicide genes into patient specific iPS cells for use in cell therapy.

overall_design: iPS cell clones were derived from beta-thalassemia patients. A single copy of beta-globin transgene cis-linked to locus control region (LCR) elements and an excisable Neo-eGFP transcription unit were inserted into these cell clones. beta-globin expression was induced by erythroid differentiation.

first: Eirini

last: Papapetrou

first: Gabsang

last: Lee

first: Nirav

last: Malani

first: Isabelle

last: Riviere

first: Laxmi

last: Tirunagari

first: Kyuichi

last: Kadota

first: Shoshannah

last: Roth

first: Patricia

last: Giardina

first: Agnes

last: Viale

first: Christina

last: Leslie

first: Frederic

last: Bushman

first: Lorenz

last: Studer

first: Michel

last: Sadelain


title: Expression data from Arabidopsis suspension cells overexpressing VND6 and SND1

city: tokyo

first: Kyoko

last: Ohashi-Ito

address: 7-3-1 hongo bunkyo-ku

department: biological sciences

country: Japan

institute: the university of tokyo

summary: Xylem consists of three types of cells: vessel cells, also referred to as tracheary elements (TEs), parenchyma cells, and fiber cells. TE differentiation includes two essential processes, programmed cell death (PCD) and secondary cell wall formation. These two processes are tightly coupled. However, little is known about the molecular mechanism of their gene regulation. Here, we show that VASCULAR-RELATED NAC-DOMAIN 6 (VND6), a master regulator of TEs, regulates these processes in a coordinated manner. We first identified specific genes downstream of VND6 by comparing them with those of SECONDARY WALL-ASSOCIATES NAC DOMAIN PROTEIN1 (SND1), a master regulator of xylem fiber cells, with transformed suspension culture cells in microarray experiments.

overall_design: We used three types of Arabidopsis cultured cells: wild type cells, estrogen-inducible VND6 transformed cells, estrogen-inducible SND1 cells. To examine the initial molecular events induced by VND6 and SND1, we sampled three types of cells at 0h and 12h after the addition of estrogen with triplicates.

first: Sayaka

last: Isu


title: Examination of impact of pathogenic mutations in LRRK2 upon gene expression in patient fibroblasts and HEK cells

status: Public on Dec 03 2010

city: Bethesda

first: Marcel

last: van der Brug

address: 9000 Rockville Pike

department: NIA

institute: NIH

summary: Analysis of global gene expression changes due to the induction of wt or mutant Lrrk2 expression

overall_design:
For GSM628620-GSM628655: RNA from HEK cells, stably transfected with an inducable lrrk2 expression vector
For GSM628657-GSM628676: RNA from patient derived fibroblast cells

first: Patrick

last: Lewis


title: Comparative global transcriptomic profiling of human ES and iPSs cells and their derived microdissected cardiac clusters

status: Public on Sep 15 2010

city: Bonn

first: Joachim

last: Schultze

state: NRW

address: Carl-Troll-Strasse 31

department: Genomics and Immunoregulation

institute: LIMES (Life and Medical Sciences Center Genomics and Immunoregulation)

summary: Recent establishment of induced pluripotent stem (iPS) cells opened new avenues for generating human patient-specific stem cell derivatives that can be used for in vitro modeling of human disease, drug development and cell replacement therapy. In this study we analyzed the molecular and functional properties of cardiomyocytes (CM) differentiated from human iPS cells. Clusters of synchronously beating cells were first observed at day 11 of iPS cell differentiation. Beating clusters that were microdissected at day 18 of differentiation expressed high levels of cardiospecific transcripts NKx2.5, alpha-MHC, MLC2v, alpha-actinin and troponin T. Immunocytochemical stainings  for alpha-actinin and troponin T revealed cross-striations typical of CM. Functional assessment of iPS cell-derived CM showed that these cells possess intact calcium transients and respond to beta-adrenergic and muscarinic stimulation. Molecular, structural and electrophysiological properties of iPS cell-derived CMs were highly comparable to their human ES cell-derived counterparts at the same differentiation stage. Comparison of global gene expression profiles of human ES and iPS cells and the corresponding microdissected beating areas further confirmed their similarity. We conclude that human iPS cells can differentiate into functional CM, which are indistinguishable from human ES cell-derived CMs and may fulfill the basic requirement for their use in disease modeling, drug screening and future therapeutic applications.

overall_design: Six different experimental groups were included into analysis: undifferentiated human ES cells (1) and undifferentiated human iPS cells (2), human ES cell-derived cardiomyocytes (3) and human iPS cell-derived cardiomyocytes (4) enriched by microdissection of spontaneously contracting embryoid body outgrowths, and human fetal (5) and adult (6) heart tissue. Total RNA samples were prepared from three independent biological replicates in groups 1-4. In groups 5 and 6, single RNA probes were analyzed as three technical replicates.

first: Tomo

last: Saric

first: Manoj

last: Gupta

first: Damir

last: Illich

first: Andrea

last: Gaarz

first: Jürgen

last: Hescheler


title: Effect of hit compounds on ethylene mutant eto1-4

city: Taipei

first: Kevin Long-Chi

last: WANG

address: 128 Section 2, Academia Road

department: Institute of Plant and Microbial Biology

country: Taiwan

institute: Academia Sinica

summary: Analysis of ethylene mutant (eto1-4) genome expression profile altered by ethylene antagonists. Results uncovered a significant number of genes that were co-regulated by the ethylene antagonists which may contribution on phenotype difference between WT and eto1-4.

overall_design: WT (Col-0) or ethylene mutant (eto1-4) were etiolated growth 3-day on 0.5x MS medium as control. Ethylene mutant (eto1-4) etiolated growth 3-day on 0.5x MS medium containing 10 μM different ethylene antagoinsts were used as experimental set. Whole seedling was used for total RNA extraction and cDNA synthesis. cDNA labeling, array hybridization, and scanning followed by standard Affymetrix expression array protocol. Two independent sets of microarray analyses were performed in this assay.

first: Li-Chung

last: Lin

first: Long-Chi

last: Wang


title: Oscillating gene expression determines competence for periodic branching in the Arabidopsis root

status: Public on Sep 12 2010

city: Durham

first: Miguel

middle: Angel

last: Moreno-Risueno

address: 124 Science Dr

institute: Duke University

summary:
The Oscillation Zone (OZ) of unsynchronized roots was disected and divided into an upper (OZ2) and lower (OZ1) half .
Samples were ordered according to DR5:GUS expression as analyzed by real time PCR to find periodic expression patterns

overall_design: Seedlings were grown for 5 days. 39 individual roots were dissected for RNA extraction. These microarray samples profile a specific region of the root tip designated as the Oscillation zone. Arrangement of the samples in the following order: OZ1-1, OZ1-4, OZ1-23, OZ1-14, OZ1-17, OZ1-2, OZ1-6, OZ1-13, OZ1-15, OZ1-16, OZ1-10, OZ1-32, OZ1-3, OZ1-31, OZ1-22, OZ1-35, OZ1-19, OZ1-9, OZ1-33, OZ1-20, OZ2-4, OZ2-23, OZ2-14, OZ2-6, OZ2-13, OZ2-15, OZ2-10, OZ2-32, OZ2-22, OZ2-35, OZ2-19, OZ2-9, OZ2-20, OZ2-36, OZ2-39, OZ2-21, OZ2-40, OZ2-38, OZ2-1, was used to identify periodic expression patterns.

first: Philip

middle: N

last: Benfey


title: Gene expression profiles of trophoblast cell lines

city: Vienna

first: Stefanie

last: Tauber

address: Dr. Bohr-Gasse 9

department: CIBIV

country: Austria

institute: MFPL

summary: Invasive extravillous trophoblasts (EVTs) of the human placenta are critically involved in successful pregnancy outcome since they remodel the uterine spiral arteries to increase blood flow and oxygen delivery to the placenta and the developing fetus. To gain more insights into their biological role different primary cell culture models are commonly utilised. However, access to early placental tissue may be limited and primary trophoblasts rapidly cease proliferation in vitro impairing genetic manipulation. Hence, trophoblastic cell lines have been widely used as surrogates to study EVT function. Although the cell lines share some molecular marker expression with their primary counterpart, it is unknown to what extent they recapture the invasive phenotype of EVT. Therefore, we here report the first thorough GeneChip analyses of SGHPL-5, HTR-8/SVneo, BeWo, JEG-3 and the novel ACH-3P trophoblast cells in comparison to previously analysed primary villous cytrophoblasts and extravillous trophoblasts.

overall_design: To identify EVT-specific gene expression signatures in trophoblast cell lines, we calcuted differentially expressed genes between pre-defined groups based on the distinct origins of the five trophoblast cell lines under investigation. Comparison 1 comprised EVT, HTR-8/Svneo and SGHPL-5 vs choriocarcinoma cells (ACH-3P, BeWo, JEG-3). Comparison 2 comprised EVT, ACH-3P, BeWo, JEG-3 vs extravillous trophoblast cell lines (HTR-8/SVneo, SGHPL-5).

first: Martin

last: Bilban

last: Knöfler


title: Expression data of  Arabidopsis thaliana wild-type plants and quadruple nas T-DNA insertion mutants grown under different Fe supply conditions

status: Public on Sep 25 2010

city: Saarbrücken

first: Mara

last: Schuler

address: Campus SB, Geb.A2 4

institute: Saarland University

summary: Essential metals such as iron are required for healthy plant growth. Fe is an important cofactor and catalytic element in many biological processes. Fe and other metals can also be toxic when present in excess. Therefore plants have mechanisms of metal homeostasis which involve coordination of metal ion transporters for uptake, translocation and compartmentalisation. The NAS genes are supposed to play an important role in Fe homeostasis. They are coding for enzymes called nicotianaminesynthase (NAS), which synthesize nicotianamine (NA) by a one-step condensation reaction of three molecules S-adenosyl-methionine. NA acts as a chelator for Fe, Cu, Ni and Zn and might be involved in the transport and allocation of Fe throughout the plant. We generated quadruple T-DNA insertion mutant nas plants to investigate NA function as described in Klatte et al., 2009, Plant Physiol. The nas4x-1 plants show an interveinal leaf chlorosis when turning from vegetative to reproductive stage, which intensifies when growing under Fe deficiency conditions. nas4x-1 plants have strongly reduced NA contents and show an elevated Fe deficiency response in roots. By performing microarray experiments we want to reveal global changes on transcriptional level in roots and leaves of nas4x-1 mutant compared to wild type plants grown under Fe supply and Fe deficiency conditions, respectively. The loss of NAS genes has a strong impact on the regulation of other metal homeostasis genes and allows to draw conclusions about nicotianamine function in metal homeostasis of A.thaliana.

overall_design: For this study, four-week old nas4x-1 mutant and wild type plants were exposed for 7 days to plant medium with and without Fe supply. These conditions have been established previously and have resulted in a reproducibly strong interveinal leaf chlorosis of nas4x-1 plants compared to wild type, especially upon Fe deficiency conditions. The experiment was repeated three times in consecutive weeks to obtain three independent biological repetitions. Rosette leaves and roots of five week-old plants were harvested, RNA was isolated and microarray hybridization was performed. 24 Total samples were analyzed. We generated the following pairwise comparisons: WT + Fe vs. – Fe, nas4x-1 + Fe vs. – Fe, + Fe WT vs. + Fe nas4x-1, - Fe WT vs. - Fe nas4x-1, roots and leaves

first: Andreas

last: Keller

first: Katrin

last: Philippar

first: Petra

last: Bauer


title: Expression data from 2-week-old Arabidopsis untreated seedlings grown under a short day condition

status: Public on Sep 21 2010

city: Riverside

first: Tokuji

last: Tsuchiya

address: 3220 Batchelor Hall, University of California at Riverside

department: Botany and Plant Sciences

institute: University of California at Riverside

summary:
The Arabidopsis thaliana defense regulator EDM2 was previously shown to be specifically required for disease resistance to the pathogenic oomycete Hyaloperonospora parasitica aradidopsis mediated by the R protein RPP7. We found EDM2 to have a promoting effect on several distinct developmental processes, such as leaf pavement cell development, vegetative phase change or the floral transition. We further identified the atypical protein kinase WNK8 to physically interact with EDM2 in nuclei.
Microarray data support regulatory interactions between WNK8 and EDM2 as well as their functional association with the autonomous floral promotion pathway.

overall_design: To assess interactions between EDM2 and WNK8 at the transcriptome level, we profiled transcript patterns of Col-0, edm2-2, wnk8-1, wnk8-2, wnk8-3 and an edm2-2 complementation line pXVE:HA-EDM2-a seedlings using Affymetrix ATH1 whole genome arrays. Plant materials were grown under short day conditions for 2 weeks. Total RNA was isolated from untreated seedlings and hybridized to the GeneChip following the manufacturer's instructions. Each genotype has three independent biological replicates.

first: Thomas

last: Eulgem


title: Effect of polymorphic Y chromosomes on XXY females

status: Public on Oct 02 2010

city: Cambridge

first: Bernardo

last: Lemos

address: 16 Divinity Avenue, Room 2105

institute: Harvard University

summary: see publication, arrays from 4 XXY genotypes containing polymorphic Y chromosomes

overall_design: Dye swaps, loop design.

first: Alan

middle: T

last: Branco


title: RAS signaling in colon carcinoma: Target gene deregulation and growth control through Y-box-binding protein 1

status: Public on Oct 09 2010

city: Berlin

first: Karsten

last: Jürchott

address: Luisenstraße

department: Rahel Hirsch Center

institute: BIH at Charité

summary:
The perturbation of the genetic program due to mutational activation of KRAS- or BRAF-mediated signal transduction is a prerequisite for the expression of neoplastic phenotypes; however, the mechanisms of cancer cell-specific transcriptional deregulation are poorly understood. We have analyzed the human colorectal cancer cell lines HCT116, HT29 and SW480 using an integrated approach combining transcriptional profiling, small molecule inhibitors targeting signaling pathway effectors, and computational prediction of regulatory elements in promoters of co-expressed genes with chromatin-based and cellular assays. We identified groups of coexpressed genes involved in similar biological processes, demonstrating a link between biological function and transcriptional organization.
Among them we found groups of proliferation associated genes which responded to MEK/MAPK inhibition in all three cell lines. We predicted by computational analysis of the promoter regions of these genes, that NFY binding sites might be important regulatory elements for the MEK/MAPK-dependent transcriptional control. We validated this prediction in reporter gene assays by using a fragment of the CCNB1 promoter as a model. We discovered YBX1 to be associated with the endogenous CCNB1 promoter and the promoters of 62 additional genes within the proliferation associated gene groups by a ChIP-on-chip assay. Silencing of YBX1 expression by siRNA prevents CCNB1 expression and partially inhibits proliferation of HCT116 cells. In view of multiple known YBX1 functions in stress response, chromatin remodeling, transcriptional and translational regulation, our results indicate that this factor may also contribute to RAS-induced pleiotropic effects in cancer.

overall_design: The cells were treated with certain inhibitors for 48 hours. We used one sample per cell line treated with DMSO as a control, and one sample for each of the treatments.

first: Reinhold

last: Schäfer


title: Effect of T350 phosphorylation on gene repression activity of EZH2 in BJ cells

status: Public on Nov 10 2010

city: Minneapolis

first: Shuai

last: Chen

state: MN

address: MMC 806, 420 Delaware Street S.E.

department: Cancer Center

institute: University of Minnesota

summary: The Polycomb group (PcG) protein enhancer of zeste homolog 2 (EZH2) plays an essential role in histone methylation-mediated epigenetic gene silencing. We demonstrate that under physiological conditions, cyclin-dependent kinase 1 (CDK1) and 2 (CDK2) bind to and phosphorylate EZH2 at threonine 350 (T350) in an evolutionally conserved motif. T350 phosphorylation is required for EZH2 function in silencing of genes that promote differentiation and inhibit proliferation and migration. Blockage of T350 phosphorylation by generating a T350A mutation largely diminishes the global effect of EZH2 on gene silencing.

overall_design: Four experiments have been designed. BJ cells were transfected with si-Control, si-EZH2, si-EZH2 plus RNAi resistant lentivirus expressed EZH2, or si-EZH2 plus RNAi resistant lentivirus expressed T350A mutant for 60 hours. Each experiment was triplicated.

first: Haojie

last: Huang


title: Control of endothelial sprouting by a Tel-CtBP complex

status: Public on Sep 09 2010

city: Utrecht

first: Guy

last: Roukens

address: Uppsalalaan 8

country: Netherlands

institute: Hubrecht Institute

summary: Branching from conduits is a defining feature of the gas delivery systems of invertebrates (tracheae built from epithelial cells) and vertebrates (vasculature lined by endothelial cells). Here, we show that the vertebrate transcriptional repressor Tel plays an evolutionarily conserved role in angiogenesis: it is indispensable for sprouting of primary human endothelial cells and for the normal development of the Danio rerio embryo blood circulatory system. Tel controls endothelial sprouting via binding to the generic co-repressor C-terminal binding protein (CtBP). In endothelial cells, the Tel:CtBP complex temporally restricts a VEGF-mediated pulse of dll4 expression and consequently integrates VEGFR intracellular signaling and intercellular Notch-Dll4 signaling. It further refines branching by regulating expression of other factors that constrain angiogenesis such as sprouty family members and ve-cadherin. Thus, the Tel:CtBP complex moderates the balance between positive and antagonistic angiogenesis cues and thereby conditions endothelial cells for angiogenesis. Since the activity of CtBP is attuned to intracellular NADH levels, our results raise the possibility that Tel-mediated sprouting could be sensitized to the metabolic status of the tissue. Tel control of branching appears to be evolutionarily conserved since Yan, the invertebrate orthologue of Tel, is similarly required for branching morphogenesis of the invertebrate tracheae. Collectively, our work suggests that Tel is a central regulator of angiogenesis and highlights Tel and its associated networks as potential targets for the development of therapeutic strategies to inhibit pathological angiogenesis.

overall_design:
2 independent screens were performed testing effects of knockdown of Tel or CtBP (screen 1) or effects of VEGF-A (screen 2) on Human Umbilical Vein Endothelial Cells (HUVECs).
For screen 1 we tested 3 different conditions. We established stable HUVEC cell lines which were either infected with control lentivirus (Mock), or lentivirus expressing short hairpin RNA constructs for the specific knockdown of Tel(Teli) or CtBP2 (CtBP2i). Expression in the Teli and CtBP2i cell lines was compared to expression in the Mock cell line for screen 1.
For screen 2 we tested 2 conditions. We exposed HUVECs to VEGF (50ng/mL) for 30 minutes (samplename: VEGF30) and compared the transcriptome of these cells to untreated HUVECs (VEGF0).
For each condition 2 independent repeats were analyzed and expression of genes was averaged for each repeat. HUVECs were grown under standard conditions (37degrees Celsius, 5% CO2) in EGM2 medium (Lonza).

first: M

middle: G

first: David

last: Baker


title: ETV1 knockdown in GIST cell lines

city: New York

first: Yu

summary: ETV1 is highly expressed in GIST cells and required for their survival and growth. To identify genes and pathways regulated by ETV1 in GIST, we performed expression profiles of GIST cells after ETV1 knockdown.

overall_design: Two GIST cell lines (GIST48 and GIST882) were infected in duplicate with three shRNA viruses (Scrambled, ETV1sh1-B11TRCN0000013923, ETV1sh2-TRCN0000013925). Four days after infection, RNA was harvested for expression profiling.

first: Ping

last: Chi

first: C

last: Allis

first: Charles

last: Sawyers


title: PITX1 suppresses TERT transcription

status: Public on Sep 10 2010

city: yonago

first: hiroyuki

last: kugoh

state: tottori

department: Biomedical Science

institute: Tottori University

summary: Using microcell-mediated chromosome transfer (MMCT) into the mouse melanoma cell line, B16F10, we have previously found that human chromosome 5 carries a gene, or genes, that can negatively regulate TERT expression. To identify the gene responsible for the regulation of TERT transcription, we performed cDNA microarray analysis using parental B16F10 cells, telomerase negative B16F10 microcell hybrids with a human chromosome 5 (B16F10MH5), and its revertant clones (MH5R) with reactivated telomerase. Here we report the identification of PITX1, whose restoration  leads to the downregulation of mouse tert (mtert) transcription, as a TERT suppressor gene. Additionally, both human TERT (hTERT) and mouse TERT (mtert) promoter activity can be suppressed by PITX1. We showed that three and one binding sites, respectively, within the hTERT and mtert promoters that express a unique conserved region are responsible for the transcriptional activation of TERT. Furthermore, we showed that PITX1 binds to the TERT promoter both in vitro and in vivo. Thus, PITX1 suppresses TERT transcription through direct binding to the TERT promoter, which ultimately regulates telomerase activity.

overall_design: We transferred intact human chromosome 5 into mouse melanoma B16F10 cells by microcell fusion. The microcell hybrids (MH5) exhibited suppression of telomerase, we also obtained revertant clones (MH5R) in which telomerase is reactivated. To identify the differentially expressed genes on human chromosome 5, we performed expression microarray analysis using these two clones and parental B16F10 cells.

first: Hiroyuki

last: Kugoh

first: Dong-Lai

last: Qi

first: Takahito

last: Ohhira

first: Chikako

last: Fujisaki

first: Toshiaki

last: Inoue

first: Mitsuhiko

last: Osaki

first: Tsutomu

last: Ohta

first: Mitsuo

last: Oshimura


title: Lymphoblastoid gene expression analysis

status: Public on Aug 27 2010

city: Edinburgh

first: Nick

last: Gilbert

address: Crewe Rd South

department: Institute of Genetics and Molecular Medicine

institute: The University of Edinburgh

summary: Analysis of gene expression profile of SATO3 (female lymphoblastoid) cells

overall_design: Three independent biological samples were analysed


title: Adult grade II astrocytomas are genetically distinct from their pediatric counterparts, and display a more stem cell-like expression pattern linked with more aggressive behaviour

status: Public on Aug 31 2010

middle: T W

last: Jones

address: Box 231, Level 3 Lab Block, Addenbrooke's Hospital

department: Pathology

institute: University of Cambridge

type: Genome variation profiling by genome tiling array

summary:
We have used microarray comparative genomic hybridization (aCGH) at 1Mb resolution to study copy number changes in a series of WHO Grade II Astrocytomas (n=21).
We have used Illumina arrays to study genome-wide expression patterns in a series of WHO Grade II Astrocytomas (n=10).

Keywords: Array Comparative Genomic Hybridization (aCGH), Expression microarray

overall_design:
[aCGH]: Single hybridization per case. 21 astrocytomas WHO grade II were analyzed. Target (tumor) labelled with Cy5 and reference with Cy3. Mixture of 20 normal male or female genomic DNA was used in sex-mismatched hybridization.

[mRNA]: Single hybridization per case. 10 astrocytomas WHO grade II were analyzed (5 adult, 5 pediatric)

first: Lu

last: Liu

first: Danita

last: Pearson

first: Shani

last: Mulholland

first: Magnus

last: Backlund

first: Koichi

last: Ichimura

first: V

last: Collins


title: Analysis of active and inactive X chromosome architecture reveals the independent organization of 30-nm and large scale chromatin structures

type: Genome binding/occupancy profiling by SNP array

summary:
Using a genetic model, we present a high resolution chromatin fibre analysis of transcriptionally active (Xa) and inactive (Xi) X chromosomes packaged into euchromatin and facultative heterochromatin. Our results show that gene promoters have an open chromatin structure that is enhanced upon transcriptional activation but the Xa and the Xi have similar overall 30-nm chromatin fibre structures. Therefore, the formation of facultative heterochromatin is dependent on factors that act at a level above the 30-nm fibre and transcription does not alter bulk chromatin fibre structures.

However, large scale chromatin structures on Xa are decondensed compared to the Xi and transcription inhibition is sufficient to promote large scale chromatin compaction. We show a link between transcription and large scale chromatin packaging independent of the bulk 30-nm chromatin fibre and propose that transcription, not the global compaction of 30-nm chromatin fibres, determines the cytological appearance of large scale chromatin structures.

This SuperSeries is composed of the SubSeries listed below.

sample_organism:
Homo sapiens
Mus musculus

overall_design: Refer to individual Series


title: Prognostic and Predictive Gene Signature for Adjuvant Chemotherapy in Resected Non-Small-Cell Lung Cancer

city: Toronto

first: Ming

last: Tsao

state: Ontario

address: 610 University Avenue

department: Ontario Cancer Institute

country: Canada

institute: University of Toronto

summary:
Purpose: The JBR.10 trial demonstrated benefit from adjuvant cisplatin/vinorelbine (ACT) in early-stage non-small-cell lung cancer (NSCLC). We hypothesized that expression profiling may identify stage-independent subgroups who might benefit from ACT.

Patients and Methods: Gene expression profiling was conducted on mRNA from 133 frozen JBR.10 tumor samples (62 observation [OBS], 71 ACT). The minimum gene set that was selected for the greatest separation of good and poor prognosis patient subgroups in OBS patients was identified. The prognostic value of this gene signature was tested in four independent published microarray data sets and by quantitative reverse-transcriptase polymerase chain reaction (RT-qPCR).

Results: A 15-gene signature separated OBS patients into high-risk and low-risk subgroups with significantly different survival (hazard ratio [HR], 15.02; 95% CI, 5.12 to 44.04; P .001; stage I HR, 13.31; P .001; stage II HR, 13.47; P .001). The prognostic effect was verified in the same 62 OBS patients where gene expression was assessed by qPCR. Furthermore, it was validated consistently in four separate microarray data sets (total 356 stage IB to II patients without adjuvant treatment) and additional JBR.10 OBS patients by qPCR (n 19). The signature was also predictive of improved survival after ACT in JBR.10 high-risk patients (HR, 0.33; 95% CI, 0.17 to 0.63; P .0005), but not in low-risk patients (HR, 3.67; 95% CI, 1.22 to 11.06; P = .0133; interaction P .001). Significant interaction between risk groups and ACT was verified by qPCR.

Conclusion: This 15-gene expression signature is an independent prognostic marker in early-stage, completely resected NSCLC, and to our knowledge, is the first signature that has demonstrated the potential to select patients with stage IB to II NSCLC most likely to benefit from adjuvant chemotherapy with cisplatin/vinorelbine.

overall_design: A total of 133 non-small cell lung cancer samples was profiled for gene expression by using Affymetrix U133A platform. Raw cel data were preprocessed by RMA v0.5. The assocaition of individual gene with patients' prognosis was evoluated by Cox proportional hazards model and genes with p value of less than 0.005 were preselected and then a 15-gene signature was selected using MARSA algorithm. The prognostic value of the 15-gene signature was subsequently validated in silico in 4 independent data sets. Its predictiveness for adjuvant chemotherapy was validated in cases not being included in the training set by qPCR.

middle: S

first: Chang

middle: Q

last: Zhu

first: Keyue

last: Ding

first: Dan

last: Strumpt


title: Parent-of-origin effects in seeds of Arabidopsis thaliana: Affymetrix

status: Public on Aug 26 2010

city: London

first: Reiner

last: Schulz

address: 8th floor Guy's Tower

department: Medical & Molecular Genetics

institute: King's College London

summary: Crossing plants of the same species but different ploidies can have dramatic effects on seed growth, but little is known about the alterations to transcriptional programmes responsible for this. Parental genomic imbalance particularly affects proliferation of the endosperm, with an increased ratio of paternally to maternally contributed genomes (‘paternal excess’) associated with overproliferation, while maternal excess inhibits endosperm growth. One interpretation is that interploidy crosses disrupt the balance in the seed of active copies of parentally imprinted genes. This is supported by the observation that mutations in imprinted FIS-class genes of Arabidopsis thaliana share many features of the paternal excess phenotype. Here we investigated gene expression underlying parent-of-origin effects in Arabidopsis through transcriptional profiling of siliques generated by interploidy crosses and FIS-class mutants.

overall_design: Two biological replicate samples each of 2xX2x, 2xX4x, 2xX6x, 6xX2x, 4xX2x and fis1X2x and a single sample of msi1. Each sample was hybridised to a separate array.

first: Sushma

last: Tiwari


title: Whole blood transcriptional profiles of patients with active tuberculosis (TB) and other inflammatory and infectious diseases

status: Public on Aug 11 2010

city: Dallas

first: Damien

last: Chaussabel

address: 3434 Live Oak

institute: Baylor Institute for Immunology Research

summary: Tuberculosis (TB), caused by infection with Mycobacterium tuberculosis (M. tuberculosis), is a major cause of morbidity and mortality worldwide and efforts to control TB are hampered by difficulties with diagnosis, prevention and treatment. Most people infected with M. tuberculosis remain asymptomatic, termed latent TB, with a 10% lifetime risk of developing active TB disease, but current tests cannot identify which individuals will develop disease. The immune response to M. tuberculosis is complex and incompletely characterized, hindering development of new diagnostics, therapies and vaccines. The goals of this study include: 1. Identify a transcript signature for active TB in intermediate and high burden settings, correlating with radiological extent of disease and reverting to that of healthy controls following treatment; 2. Identify a specific transcript signature that discriminated active TB from other inflammatory and infectious diseases; 3. Classify TB signature using modular and pathway analysis tools.

overall_design: Three milliliters of whole blood was collected in Tempus tubes from 12 pediatric streptococcus, 40 pediatric staphylococcus, 31 still’s disease, 82 pediatric systemic lupus erythematosus (SLE) and 28 adult SLE patients. RNA was extracted and globin reduced. Labeled cRNA was hybridized to Illumina Human HT-12 Beadchips. Healthy controls were included to match patients’ demographic data. Genespring software was used to analyze active TB transcript signatures, comparing with healthy controls and other inflammatory and infectious diseases.


title: Blood Transcriptional Profiles of Active and Latent TB (UK Test Set)

summary: This dataset aims to validate and confirm the signature identified in the training set.  The aim of the experiment was to define transcriptional signatures in whole blood of TB patients (before drug treatment) and healthy controls to distinguish the signature of Latent and Active TB patients from each other and from healthy controls. This will help in diagnosis of active tuberculosis which normally relies on culture of the bacilli, which can take up to 6 wks, and sometimes the bacilli cannot be obtained from sputum thus requiring invasive techniques obtaining bronchoalveolar lavage (BAL). In some cases the bacill cannot be grown from sputum or BAL.   Secondly the aim was to determine whether Latent patients have a homogeneous or heterogeneous signature, one may expect the latter since it is not possible to determine by the present tests (Tuberculin skin test - TST - or MTb antigen responsiveness of blood cells to produce IFN-gamma - IGRA assay) whether the mycobacteria has been cleared, is still present but is controlled, or if patients are recently infected or reactivated and will develop active TB.

overall_design: Experimental design : Whole blood collected in tempus tubes from patients with different spectra of TB disease and healthy controls.  All patients were sampled prior to the initiation of any antimycobacterial therapy.  Active Pulmonary TB: PTB - All patients confirmed by isolation of Mycobacterium Tuberculosis on culture of sputum or bronchoalvelolar lavage fluid.  Latent TB: LTB - All patients were screened at a tuberculosis clinic, being either new entrants to the UK from endemic countries or being household contacts of infectious cases. All were positive by tuberculin skin test (>14mm if BCG vaccinated, >5mm if not vaccinated) and were also positive by Interferon-Gamma Release assay(IGRA); specifically Quantiferon Gold In-Tube Assay (Cellestis, Australia). Latent patients had no clinical, radiological or microbiological evidence of active infection and were asymptomatic.  Healthy controls - these were volunteers without exposure to TBwho were negative by both tuberculin skin test (<15mm if BCG vaccinated, <6mm if unvaccinated); who were also negative by IGRA (as described above).  This dataset:  PTB, n= 21.  LTB, n = 21.  BCG+, n = 12.  Experimental variables : Patient group: Active PTB; Latent TB, Healthy controls (BCG vaccinated only).  ethnicity - a wide range of ethnic groups is represented.   The active PTB group incorporates a range of smear positive and smear negative disease and  a spectrum of disease extent/severity.


title: Transcriptional profiles underlying parent-of-origin effects in seeds of Arabidopsis thaliana

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


title: Endocrine Sensitivity Index Validation Dataset

status: Public on Aug 13 2010

city: Woburn

first: Christos

last: Hatzis

address: 400 West Cummings Park, Suite 5350

institute: Nuvera Biosciences

summary:
Validation dataset of 298 ER-positive patients treated with tamoxifen for 5 years.

All patients in this dataset have ER+ breast cancer and were uniformly treated with tamoxifen for 5 years. The objective of the study was to correlate levels of genomic markers to outcomes (relapse free survival) in this cohort of uniformly treated patients.

overall_design: Tissue samples were processed and profiled by two different labs (MD Anderson Cancer Center and Jules Bordet Institute).

first: W

middle: F

last: Symmans

last: Sotiriou

first: Fabrice

last: Andre

first: Peter

last: Regitnig

first: Guenter

last: Daxenbichler


title: Blood Transcriptional Profiles of Active TB (UK Test Set Separated)

summary: This dataset aims to dissect the whole blood transcriptional signature by determining if elements of the whole blood signature are still present in purified cell subpopulations. We aimed to characterise the transcriptional response during TB and identify if cell subsets drove changes in whole blood cellular composition.  The aim of the experiment was to define transcriptional signatures in neutrophils, monocytes, CD4+ and CD8+ cells from blood of active TB patients and healthy controls to distinguish the signature of  active TB patients from each other and from healthy controls. This will help in the diagnosis of active tuberculosis, which normally relies on culture of the bacilli, which can take up to 6 weeks, sometimes the bacilli cannot be obtained from sputum thus requiring invasive techniques obtaining bronchoalveolar lavage (BAL). In some cases the bacill cannot be grown from sputum or BAL.

overall_design: Experimental design : Whole blood collected in EDTA tubes from patients with active TB disease and healthy controls. Blood was then processed or separated sequentially into neutrophil, monocyte, CD4+ or CD8+ populations and then processed.  All patients were sampled prior to the initiation of any antimycobacterial therapy.  Active pulmonary TB: PTB - all patients confirmed by isolation of Mycobacterium tuberculosis on culture of sputum or bronchoalvelolar lavage fluid.  Healthy controls - these were volunteers without exposure to TB who were negative by both tuberculin skin test (<15mm if BCG vaccinated, <6mm if unvaccinated); who were also negative by IGRA (as described above).  This dataset:  PTB, n = 7 patients (whole blood, neutrophils, monocytes, CD4+ or CD8+).  BCG+, n = 4 patients (whole blood, neutrophils, monocytes, CD4+ or CD8+).  Experimental variables : Patient group: Active PTB; Healthy controls (BCG vaccinated only) and Cell populations: Neutrophils, Monocytes, CD4+, CD8+.  Ethnicity - a range of ethnic groups is represented.


title: Blood Transcriptional Profiles in Active and Latent Tuberculosis UK (Training Set)

summary: The aim of the project was to define transcriptional signatures in whole blood of TB patients (before drug treatment) and healthy controls to distinguish the signature of Latent and Active TB patients from each other and from healthy controls. This will help in diagnosis of active tuberculosis which normally relies on culture of the bacilli, which can take up to 6 wks, and sometimes the bacilli cannot be obtained from sputum thus requiring invasive techniques obtaining bronchoalveolar lavage (BAL). In some cases the bacill cannot be grown from sputum or BAL.   Secondly the aim was to determine whether Latent patients have a homogeneous or heterogeneous signature, one may expect the latter since it is not possible to determine by the present tests (Tuberculin skin test - TST - or MTb antigen responsiveness of blood cells to produce IFN-gamma - IGRA assay) whether the mycobacteria has been cleared, is still present but is controlled, or if patients are recently infected or reactivated and will develop active TB. The latter situation may be determined if Latent patients have a blood transcriptional signature similar to that in Active patients. The transcriptional signature in Active TB patients may also provide information as to the factors leading to immunopathogenesis, thus possibly identifying therapeutic targets. The transcriptional profile in Latent TB may give information as to the protective factors controlling the infection, thus important for monitoring vaccine development.   A further aim was to examine the transcriptional blood profile of active TB patients at the time of recruitment (before drug treatment) and then subsequently at specific time points after drug treatment to determine whether the signature is extingsuihed with treatment and when. London is a site of intermediate burden of TB - the study was initiated in London, across a broad range of ethnicities to obtain a robust signature that could be used in different developing countries where there is a high burden TB disease.

overall_design: Experimental design : Whole blood collected in tempus tubes from patients with different spectra of TB disease and healthy controls.  All patients were sampled prior to the initiation of any antimycobacterial therapy.  Active Pulmonary TB: PTB - All patients confirmed by isolation of Mycobacterium Tuberculosis on culture of sputum or bronchoalvelolar lavage fluid.  Latent TB: LTB - All patients were screened at a tuberculosis clinic, being either new entrants to the UK from endemic countries or being household contacts of infectious cases. All were positive by tuberculin skin test (>14mm if BCG vaccinated, >5mm if not vaccinated) and were also positive by Interferon-Gamma Release assay(IGRA); specifically Quantiferon Gold In-Tube Assay (Cellestis, Australia). Latent patients had no clinical, radiological or microbiological evidence of active infection and were asymptomatic.  Healthy controls - these were volunteers without exposure to TB who were negative by both tuberculin skin test (<15mm if BCG vaccinated, <6mm if unvaccinated); who were also negative by IGRA (as described above).  In this dataset:  PTB n= 13; LTB n = 17; BCG+ n = 6, BCG-, n =6.  Experimental variables : Patient group: Active PTB; Latent TB, Healthy controls (BCG vaccinated and unvaccinated).  ethnicity - a wide range of ethnic groups is represented. However all controls in this dataset are broadly Caucasian/White.  The active PTB group incorporates a range of smear positive and smear negative disease and  a spectrum of disease extent/severity.


title: Blood Transcriptional Profiles in Human Active and Latent Tuberculosis

summary:
This series regroups different datasets (training set, test set, validation set, longitudinal set, separated cell set) to identify and characterise a specific transcriptional signature for patients with active TB, distinct from patients with latent TB and healthy controls. The training set dataset was used to identify a whole blood transcriptional signature for active TB patients in London, across a range of ethnicity. This signature was then validated in an independent cohort of patients, also recruited in London (the test set), and then further confirmed in an additional independent cohort recruited in Cape Town, South Africa (validation set), in order to confirm that the defined signature was present in both high (Cape Town, South Africa) and medium incidence regions (London, UK). The longitudinal dataset was then used to explore how successful TB treatment modifies this transcriptional signature. The separated cell set compares the transcriptional profiles in purified cell subsets (neutrophils, monocytes and T cells) to assess which cell types are contributing to the whole blood signature, and in what way. These studies may ultimately help to improve the diagnosis of active tuberculosis which normally relies on culture of the bacilli, which can take up to 6 weeks, and sometimes the bacilli cannot be obtained from sputum thus requiring invasive techniques such as bronchoalveolar lavage (BAL). In some cases (30%) the bacill cannot be grown from sputum or BAL. Any diagnostic tool would need to be valid across a range of ethnicities, and be valid in both high and low incidence countries. A further aim was to determine whether latent TB patients have a distinct homogeneous or heterogeneous signature, since it is not currently possible to determine using present tests (Tuberculin skin test - TST - or MTb antigen responsiveness of blood cells to produce IFN-gamma - IGRA assay) whether the mycobacteria have been cleared, are still present but are controlled by an active immune response, or to predict which patients will develop active TB. Defining heterogeneity in the latent TB patients would be an important step in developing diagnostics which could detect those most at risk of developing active TB, and thus enable targeted preventive therapy. The latter situation may be determined if Latent patients have a blood transcriptional signature similar to that in Active patients. The transcriptional signature in whole blood and cell subsets from Active TB patients may also provide information as to the factors leading to immunopathogenesis, thus possibly identifying therapeutic targets. The transcriptional profile in latent TB may give information regarding protective factors controlling the infection, important for vaccine development. Finally, definition of a transcriptional signature which responds to therapy could facilitate the development of surrogate biomarkers for drug or vaccine studies.
Since any active TB signature may reflect common inflammatory responses evoked during many diseases,  we also performed analysis of significance, comparing transcriptional profiles from patients with TB to those from patients with other bacterial and inflammatory diseases to identify a TB specific signature. The resulting signature was then tested against patients normalized to their own controls from 7 independent datasets: TB (Training and Validation Sets), Staphylococcus infection, Group A Streptococcus infection, Still's disease, and adult and pediatric SLE.

This SuperSeries is composed of the SubSeries listed below.

overall_design: Active Pulmonary TB: PTB - All patients were confirmed by isolation of Mycobacterium Tuberculosis on culture of sputum or bronchoalvelolar lavage fluid.  Latent TB: LTB - All patients were screened at a tuberculosis clinic, being either new entrants to the UK from endemic countries or being household contacts of infectious cases, or in the case of the validation set recruited in South Africa, were residents of a high incidence country. All UK patients were positive by tuberculin skin test (>14mm if BCG vaccinated, >5mm if not vaccinated) and were also positive by Interferon-Gamma Release assay(IGRA); specifically Quantiferon Gold In-Tube Assay (Cellestis, Australia). The South African latent TB patients were all positive by Interferon-Gamma Release assay (IGRA); specifically Quantiferon Gold In-Tube Assay. Latent patients had no clinical, radiological or microbiological evidence of active infection and were asymptomatic.  Healthy controls - these were volunteers without exposure to TB who were negative by both tuberculin skin test (<15mm if BCG vaccinated, <6mm if unvaccinated); and IGRA (as described above).   Experimental variables : Patient group: Active PTB; Latent TB, Healthy controls (BCG vaccinated and unvaccinated).  Ethnicity - a wide range of ethnic groups is represented.  The active PTB group incorporates a range of smear positive and smear negative disease and  a spectrum of disease extent/severity.  Experimental methods:  Whole blood was collected into Tempus tubes (Applied Biosystems, Foster City, CA, USA) and stored between -20degrees Celsius and -80 degrees Celsius before RNA extraction. For the training set cohort, and the active TB patients baseline samples in the longitudinal cohort, total RNA was isolated from whole blood using the PerfectPure RNA Blood kit (5 PRIME Inc, Gaithersburg, MD, USA). For the separated cell samples, total RNA was isolated using the Qiagen RNeasy Mini Kit. For all other cohorts Total RNA was isolated from whole blood using the MagMAX 96 well RNA isolation kit (Applied Biosystems, Foster City, CA, USA).  Isolated total RNA was then globin reduced using the GLOBINclear 96-well format kit (Ambion, Austin, TX, USA) according to the manufacturer's instructions.  Total and globin-reduced RNA integrity was assessed using an Agilent 2100 Bioanalyzer (Agilent, Palo Alto, CA).  Biotinylated, amplified RNA targets (cRNA) were then prepared from the globin-reduced RNA using the Illumina CustomPrep RNA amplification kit (Ambion, Austin, TX, USA). Labeled cRNA was hybridized overnight to Sentrix HT12 V3 BeadChip arrays (>48,000 probes, Illumina Inc, San Diego, CA, USA), washed, blocked, stained and scanned on an Illumina BeadStation 500 following the manufacturer's protocols.  Illumina's BeadStudio version 2 software was used to generate signal intensity values from the scans, substract background, and scale each microarray to the median average intensity for all samples (per-chip normalisation). This normalised data was used for all subsequent data analysis.


title: Blood Transcriptional Profiles of TB in South Africa

summary: The aim of this study was to compare the transcriptional response to TB in regions of different incidence / prevalence.

overall_design: Experimental Design:  Whole blood collected in tempus tubes from patients with different spectra of TB disease.  All patients were sampled prior to the initiation of any antimycobacterial therapy.  Active Pulmonary TB: PTB - All patients confirmed by isolation of Mycobacterium Tuberculosis on culture of sputum.  Latent TB: LTB - All patients were screened at a tuberculosis clinic. All were positive by Interferon-Gamma Release assay(IGRA); specifically Quantiferon Gold In-Tube Assay (Cellestis, Australia). Latent patients had no clinical, or microbiological evidence of active infection and were asymptomatic.  Experimental Variables:  Patient group: Active PTB; Latent TB.  There are no healthy controls in this dataset as it was being used for validation only.  Controls:  Latent TB individuals are used as a control for PTB in this dataset since there are few to no unexposed adult controls in Cape Town.


title: Transcriptional profiles in Blood of patients with Tuberculosis - Longitudinal Study

summary: The aim of the longitudinal analysis was to examine the transcriptional blood profile of active TB patients at the time of recruitment (before drug treatment) and then subsequently at specific time points after drug treatment to determine whether the signature is extinguished with treatment and when.

overall_design: Whole blood collected in tempus tubes from patients with different spectra of TB disease and healthy controls.  All patients were sampled prior to the initiation of any antimycobacterial therapy.  Active Pulmonary TB: PTB - All patients confirmed by isolation of Mycobacterium Tuberculosis on culture of sputum or bronchoalvelolar lavage fluid.  Healthy controls - these were volunteers without exposure to TB who were negative by both tuberculin skin test (<15mm if BCG vaccinated, <6mm if unvaccinated); who were also negative by Interferon-Gamma Release assay(IGRA); specifically Quantiferon Gold In-Tube Assay (Cellestis, Australia).  Here the aim of the experiment is to assess the longitudinal effect of antimycobacterial treatment on the active TB signature, during and after treatment.  Blood was taken from the active TB patients at baseline, pre-treatment, 2 months after treatment inititation, and 12 months after treatment initiation, which would be after treatment was completed. These samples were then amplified at the same time with samples from healthy controls and hybridised to the same chips to permit an assessment of whether the post treatment samples had similar transcriptional profiles to healthy controls or were distinct.  In this dataset:  PTB baseline, n = 7; PTB 2 months, n = 7; PTB 12 months, n = 7.  BCG+ control baseline, n =12.  Experimental variables:  Patient group: Active PTB; Healthy controls (all BCG vaccinated).  ethnicity - a wide range of ethnic groups is represented.  The active PTB group incorporates a range of smear positive and smear negative disease and  a spectrum of disease extent/severity.  Timepoint: 0 months = baseline pre-treatment;2 months = 2 months after initiation of treatment; 12 months = 12 months after initiation of treatment.


title: Chromatin marks and matched expression in the aging Drosophila genome

status: Public on Aug 01 2010

city: Providence

first: Sara

last: Hillenmeyer

state: RI

address: 60 Olive St

department: MCB

institute: Brown University

type: Genome binding/occupancy profiling by genome tiling array

summary:
It consists of Chip-chip data for H3K4, PolII (4h8), H3K36, H3K9me3 and HP1 from 10 and 40 day old female Drosophila melanogaster (Canton S), as well as expression array data taken from the same time points.

This SuperSeries is composed of the SubSeries listed below.


title: mRNA expression in female Drosophila melanogaster heads at 10 days and 40 days

summary: Expression data for aging female drosophila melanogaster

overall_design: Female drosophila heads were collected RNA extraction and hybridization on Affymetrix microarrays.

first: J

last: Wood

first: N

last: Neretti

first: S

last: Helfand