title: Culturing Cytotrophoblasts Reverses Gene Dysregulation in Preeclampsia Revealing Possible Causes

status: Public on Aug 17 2012

city: SAN FRANCISCO

first: Susan

last: Fisher

state: CA

address: 513 PARNASSUS AVE

department: Obstretrics, Gynecology and Reproductive Sciences

institute: UCSF

summary: During human pregnancy, a subset of placental cytotrophoblasts (CTBs) differentiates into cells that aggressively invade the uterus and its vasculature, anchoring the progeny and rerouting maternal blood to the placenta. In preeclampsia (PE), CTB invasion is limited, reducing placental perfusion and/or creating intermittent flow. This syndrome, affecting 4-8% of pregnancies, entails maternal vascular alterations (e.g., high blood pressure, proteinuria, and edema) ± fetal growth restriction. The only cure is removal of the faulty placenta, i.e., delivery. Previously we showed that defective CTB differentiation contributes to the placental component of PE, but the causes were unknown. Here, CTBs isolated from PE and control placentas were cultured for 48 h, enabling differentiation/invasion. In various severe forms of PE, transcriptomics revealed common aberrations in CTB gene expression immediately after isolation that resolved in culture. The upregulated genes included SEMA3B. Adding this protein to normal CTBs inhibited invasion and re-created aspects of the phenotype of these cells in PE. Additionally, SEMA3B downregulated VEGF signaling through the PI3K/AKT and GSK3 pathways, effects that were observed in PE CTBs. We propose that, in severe PE, the in vivo environment dysregulates CTB gene expression, the autocrine actions of the upregulated molecules, including SEMA3B, impair differentiation/invasion/signaling and patient-specific factors determine the signs.

overall_design: Villous cytotrophoblasts were isolated from preeclampsia placentas (PRE, n=5) and placentas of preterm labor patients without signs of infection (PTL, n=5), which served as gestation-matched controls. To better understand the CTB phenotype in the context of PE variants, we included patients with the most clinically significant forms of this condition that necessitated preterm delivery: women with severe PE ± intrauterine growth restrictions, PE with superimposed hypertension and HELLP syndrome (hemolysis, elevated liver enzymes; low platelet count). RNA was purified immediately after the cells were isolated (0 h) and after 12, 24 and 48 h in culture. The relative gene expression across the whole genome was profiled using the Affymetrix HG-U133Plus 2.0 GeneChip platform. Array quality was assesed using RMAExpress. One sample of preterm labor collected at 48h was omitted (39 arrays total). We used both LIMMA and maSigPro (R/Bioconductor) to determine differentially expressed genes.

first: Yan

last: Zhou

first: Matthew

middle: J

last: Gormley

first: Nathan

middle: M

last: Hunkapiller

first: Mirhan

last: Kapidzic

first: Yana

last: Stolyarov

first: Victoria

last: Feng

first: Masakazu

last: Nishida

first: Penelope

last: Drake

first: Katherine

last: Bianco

first: Fei

first: Michael

middle: T

last: McMaster


title: DEPTOR cell-autonomously promotes adipogenesis and associates with obesity

status: Public on Aug 15 2012

city: Ljubljana

first: Peter

last: Juvan

address: Zaloska 4

department: Institute of Biochemistry

country: Slovenia

institute: Faculty of Medicine, University of Ljubljana

summary: An understanding of the mechanisms regulating white adipose tissue (WAT) formation is key for developing of new tools to treat obesity and its related diseases. Here, we identify DEPTOR as a positive regulator of adipogenesis whose expression is associated with obesity. In a polygenic mouse model of obesity/leanness, Deptor is part of the Fob3a QTL linked to obesity and we fine that Deptor is the highest priority candidate gene regulating WAT accumulation in this model. Using a doxycycline-inducible mouse model for Deptor overexpression, we confirmed that Deptor promotes WAT expansion in vivo. DEPTOR expression is elevated in WAT of obese humans and strongly correlates with the degree of obesity. We show that DEPTOR is induced during adipogenesis and that its overexpression cell-autonomously promotes, while its suppression blocks, adipogenesis. DEPTOR positively regulates adipogenesis by promoting the activity of the pro-adipogenic factors Akt/PKB and PPAR-gamma. These results establish DEPTOR as a physiological regulator of adipogenesis and provide new insights into the molecular mechanisms controlling WAT formation.

overall_design: 2 groups of F2 mice for opossing genotype at Fob3a QTL (FF versus VV) - parental strains of the F2 cross were the Fat line and congenic V-line; 5 biological replications per group; reference for Fat line: Horvat S. et al. (2000) MAMMALIAN GENOME  11(1): 2-7

first: Mathieu

last: Laplante

first: Simon

last: Horvat

first: Kivanc

last: Birsoy

first: Zala

last: Prevorsek

first: Alejo

last: Efeyan

first: David

last: Sabatini


title: Expression profiling of host genes altered after chemical-induced recurrent Epstein-Barr virus reactivation in nasopharyngeal carcinoma cells

city: Zhounan, Miaoli

first: Chih-Yeu

last: Fang

address: 35, Keyan Rd.

department: National Cancer Research Institute

country: Taiwan

institute: National Health Research Institutes

summary:
Seroepidemiological studies imply a correlation between Epstein-Barr virus (EBV) reactivation and the development of nasopharyngeal carcinoma (NPC). Phorbol esters, butyrates and N-nitroso compounds are known chemical carcinogens in foodstuffs and cigarettes that have been implicated as risk factors contributing to the development of NPC. We have demonstrated previously that low dose N-methyl-N'-nitro-N-nitrosoguanidine (MNNG, 0.1 microg/ml) had a synergistic effect with 12-O-tetradecanoylphorbol-13-acetate (TPA) and sodium butyrate (SB) in enhancing EBV reactivation (Chem Biol Interact 188: 623-634). Since residents of areas with a high risk of NPC are reported to contact with these carcinogens (TPA, SB or nitrosamines) frequently, we sought to determine the consequence of repeated exposure of EBV-harboring nasopharyngeal cells to these carcinogens in a long-term, low dose, repeated manner. An NPC cell line latently infected with EBV, NA, was periodically treated with TPA/SB combined with MNNG for recurrent EBV reactivation. After 10 times of chemically-induced recurrent reactivation of EBV, the expression profile analysis indicates that many carcinogenesis-related genes were altered in recurrent reactivated NA cells when compared to the parental NA cells.
The expression profile was analyzed in the recurrent EBV reactivated NA cells and the parental NA cells.

overall_design: The expression profile of two NA cells, NA-P10/TS-MG and NA-P1/mock, were analyzed in this study. NA-P10/TS-MG cells were subject to 10 times of repeated chemical exposure by incubating these cells periodically with TPA/SB (10 ng/ml and 1.0 mM) in combination with MNNG (0.1 microg/ml). The NA cells at the beginning of this experiment were defined as passage 0 (P0) cells. 24 h after seeding, the cells were subjected to a 24 h period of mock or chemical treatment. After this 24 hr treatment, the cells were recovered by replacing the medium with fresh (treatment-free) medium and incubation for a further 48 h. The resulting cells were defined as passage 1 (P1) cells. Cells from P1 were trypsinized and transferred and the process repeated again to obtain the P2 cells. A total of ten treatments were applied to the cells in this study. “NA-P10/TS-MG” refers to NA cells with 10 times of combined TPA/SB and MNNG (TS-MG) treatments. NA-P1/mock is mock-treated NA cells with one time of passage that was used as reference in this study. Replicates were included for each samples.

first: Jen-Yang

last: Chen


title: Expresion profile of MEF reprogrammed with Yamanaka´s factor together with FoxA2 and Gata4

status: Public on Aug 30 2012

city: Valencia

first: Roque

last: Bort

address: Campanar 21

department: Unidad Hepatologia Experimental

country: Spain

institute: IIS La Fe

summary: In a pilot experiment to reprogramme MEF into endoderm, we infected MEF with the Yamanaka´s factors (O: Oct4, K: Klf4, S: Sox2, M:Myc), FoxA2 (F) and Gata4 (G). Global gene expression of isolated clones was performed.

overall_design: After infection of MEF with the Yamanaka´s factor (OKS/M), FoxA2 and Gata4, the cells were grown until colonies could be isolated and expanded independently. Global gene expression of several clones was performed.


title: Lymphoid Priming in Human Bone Marrow Begins Prior to CD10 Expression with Up-Regulation of L-selectin

city: los angeles

first: Lisa

last: Kohn

state: ca

address: 650 charles e young drive south

country: USA

institute: UCLA

summary: Studies of adult human hematopoiesis have until now relied on the expression of CD10 to define lymphoid commitment. We report a novel lymphoid-primed population in human bone marrow that is generated from hematopoietic stem cells (HSC) prior to the onset of CD10 expression and B cell commitment, and is identified by high levels of the homing molecule L-selectin (CD62L). CD10-CD62Lhi progenitors have full lymphoid (B/T/NK) potential, and show reduced myeloid and absent erythroid potential. Genome-wide gene expression analysis demonstrates that the CD10-CD62Lhi population represents an intermediate stage of differentiation between CD34+CD38- HSC and CD34+lin-CD10+ progenitors marked by down-regulation of TAL1 and MPL, upregulation of E2A, CD3E and IL2RG expression, and absent B cell commitment or RAG1/2 expression. Immature CD34+CD1a- thymocytes are also CD62Lhi and L-selectin ligands are expressed at the cortico-medullary junction, suggesting a possible role for L-selectin in human thymic homing. These studies identify the earliest stage of lymphoid priming in human bone marrow.

overall_design: Freshly harvested human bone marrow was ficoll purified, enriched for CD34+, and then FACS sorted. It was then sorted into 3 samples CD34+CD38-, CD34+ CD10- CD62L++, and CD34+ CD10+, with 3 independent biological replicates

middle: A

first: Qian-Lin

last: Hao

first: Rajkumar

last: Sasidharan

first: Chintan

last: Parekh

first: Shundi

last: Ge

first: Judy

last: Zhu

first: Hanna

last: Mikkola

first: Gay

last: Crooks


title: An integrated genomic and expression analysis of 7q deletion in splenic marginal zone lymphoma (Main Study)

city: Cambridge

first: Alan

last: Watkins

address: Addenbrooke's Hospital

country: United Kingdom

institute: University of Cambridge

type: Genome variation profiling by genome tiling array

summary:
Splenic marginal zone lymphoma (SMZL) is an indolent B-cell lymphoproliferative disorder characterised by 7q32 deletion, but the target genes of this deletion remain unknown.  In order to elucidate the genetic target of this deletion, we performed an integrative analysis of the genetic, epigenetic, transcriptomic and miRNomic data.  High resolution array comparative genomic hybridization of 56 cases of SMZL delineated a minimally deleted region (2.8Mb) at 7q32, but showed no evidence of any cryptic homozygous deletion or recurrent breakpoint in this region.  Integrative transcriptomic analysis confirmed significant under-expression of a number of genes in this region in cases of SMZL with deletion, several of which showed hypermethylation.   In addition, a cluster of 8 miRNA in this region showed under-expression in cases with the deletion, and three (miR-182/96/183) were also significantly under-expressed (P <0.05) in SMZL relative to other lymphomas.   Genomic sequencing of these miRNA and IRF5, a strong candidate gene, did not show any evidence of somatic mutation in SMZL.

This SuperSeries is composed of the SubSeries listed below.

overall_design:
For aCGH, 21 cases were done under accession number GSE35425.
21 fresh frozen splenic samples from patients with SMZL were hybridized against a reference control of pooled PBMC genomic DNA from 10 normal subjects. High-resolution oligonucleotide analysis of copy number variations in splenic marginal zone lymphoma (SMZL) in regions of recurrent alteration. Regions included on the array: 7q (2k resolution) and regions of interest on chromosomes 3q, 6q and 9q at 12k resolution.

For gene expression microarrays, 24 cases were done under accession number GSE35426.
A total of 48 cases of SMZL (including 15 with 7q deletion) were analysed using the Affymetrix HG-U133 Plus 2.0 platform (Affymetrix, Santa Clara, California, USA).  Arrays were performed according to the manufacturer’s instructions.  Briefly, RNA was extracted from snap frozen tissues with >70% tumour cells using the RNEasy extraction kit (Qiagen) and subjected to DNAse treatment (Turbo DNAse kit, Ambion).  RNA integrity was assessed using an Agilent 2100 Bioanalyzer.   cDNA synthesis was carried out with 2ug RNA using the GeneChip® One-Cycle cDNA Synthesis Kit (Affymetrix), followed by in vitro transcription with biotin-labelled nucleotides using GeneChip® IVT Labeling Kit.  Biotinylated cRNA was purified and hybridized to the Affymetrix HG-U133 Plus 2.0 chips in a GeneChip® Hybridisation Oven 640 at 45oC for 14 hours.  The arrays were then washed and stained using the Fluidics station 450 system (Affymetrix).  The arrays were scanned using the Affymetrix GeneArray® Scanner 3000.  Hybridisation and labelling controls were included according to the manufacturer’s instructions, and quality control analysis of microarrays was performed to published standards.

For methylation arrays, 24 cases were done under accession number GSE35424.
Epigenetic methylation analysis was performed using the Infinium Human Methylation 27 array (Illumina, San Diego, California, USA).  The array contained 27,568 CpG islands within the proximal promoter regions of transcription start sites of 14,475 RefSeq genes, including 12,883 well annotated genes (NCBI CCDS database: Build 36).    The methylation array was carried out in 12 SMZL (6 cases with 7q deletion), 6 follicular lymphomas (FL) and 6 mantle cell lymphomas (MCL) as per the manufacturer’s instructions.  Briefly, 2μg genomic DNA extracted from frozen tissues with >70% tumour cells was bisulphite modified using the EZ DNA Methylation Kit (Zymo Research Corporation).  Bisulphite modified DNA was then amplified using the MSM master mix (Illumina) and incubated at 37oC for 22 hours.  Amplified DNA was then fragmented and hybridised to BeadChips in an Illumina Hybridisation Oven at 48oC for 18 hours.  Following hybridisation, single base extension of hybridised DNA using hapten labelled bases was performed.  Staining was then developed using immunochemical stains catalysed by the haptens, and the arrays washed.  The chips were scanned using the BeadArray™ Reader (Illumina) and the BeadScan™ software (Illumina) using the Infinium Methylation Scan setting.  The scanned data was then analysed in GenomeStudio™ (Illumina) using the Methylation analysis module.

**Samples from Series GSE35278 and GSE35348 was also used in this study:

GSE35278: Oligo aCGH on 35 SMZL cases were carried out by the Mayo clinic group using the Agilent Oligo aCGH 244A platform (6.4Kb resolution)

GSE35348: Gene expression profiling was carried out by the Mayo clinic group on 24 SMZL cases using the Affymetrix HG-U133 plus2 gene expression microarrays

first: Rifat

last: Hamoudi

first: Naiyan

last: Zeng

first: Qingguo

last: Yan

first: Yuanxue

last: Huang

first: Hongxiang

last: Liu

first: Jianzhong

last: Zhang

first: Esteban

last: Braggio

first: Rafael

last: Fonseca

first: Laurence

last: de Leval

first: Peter

middle: G

last: Isaacson

first: Andrew

last: Wotherspoon

first: Ellen

middle: D

last: McPhail

first: Ahmet

last: Dogan

first: Ming

middle: Q

last: Du


title: Expression data of normal human extraocular muscle and strabismic human extraocular muscle

status: Public on Aug 14 2012

city: Reno

first: Amy

middle: L.

last: Altick

state: NV

address: No. Virginia St., MS 352

department: Physiology and Cell Biology

institute: University of Nevada, Reno

summary:
Human strabismic extraocular muscles (EOMs) differ from normal EOMs in structural and functional properties, but the gene expression profile of these two types of human EOM has not been examined. Differences in gene expression may inform about causes and effects of the strabismic condition in humans. Our samples are from human strabismic patients undergoing corrective surgery, and from human organ donors with no history of EOM disease.
Microarray analysis showed that 604 genes in these samples have significantly different expression. Expression was predominantly up-regulated in genes involved in extracellular matrix structure and down-regulated in genes related to contractility.

overall_design: We used four normal samples and four strabismic samples. Three normal samples were from independent donors. One normal sample was a different piece of the same EOM from one of the 3 donors. All four strabismic samples were independent samples.

middle: L

first: Cheng-Yuan

last: Feng

first: Karen

last: Schlauch

first: L

last: Johnson

first: Christopher

middle: S

last: von Bartheld


title: Expression data from WT and VAChT KDHOM whole hearts

city: London

first: David

middle: E

last: Carter

state: ON

address: 1151 Richmond Street North

department: London Regional Genomics Centre

country: Canada

institute: Robarts Research Institute

summary:
VAChT KDHOM mice have a 70% decrease in the vesicular acetylcholine transporter (VAChT) and this leads to a systemic decrease in ACh release and cardiac dysfunction.
We used this microarray to determine whether there were transcriptional alterations in the cardiomyocytes of mutant mice as a result of this long-term decrease in cholinergic tone.
We used this microarray to determine whether there were transcriptional alterations in the hearts of mutant mice as a result of this long-term decrease in cholinergic tone.

overall_design:
We isolated ventricular cardiomyocytes from the hearts of 3-month-old WT and VAChT KD mice and used them for RNA extraction and hybridization on Affymetrix microarrays. We sought to obtain homogenous populations for each sample and, as such, pooled together two RNA samples to generate one microarray sample.
We isolated whole hearts from 3-month-old WT and VAChT KD mice and used them for RNA extraction and hybridization on Affymetrix microarrays. We sought to obtain homogenous populations for each sample and, as such, pooled together two RNA samples to generate one microarray sample.

first: Marco

last: Prado

first: Robert

last: Gros


title: miR-196b targets both oncogenic and tumor suppressor genes in MLL-associated leukemia

status: Public on Aug 13 2012

city: chicago

first: chunjiang

last: he

state: il

address: 900 east 57th st

institute: university of chicago

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

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus

overall_design: Refer to individual Series

first: Zejuan

last: Li

first: Jianjun

last: Chen


title: Tuberculosis Patients Blood Gene Expression Through Treatment

status: Public on Aug 10 2012

first: Jackie

last: Cliff

address: Keppel Street

department: Immunology and Infection

institute: London School of Hygiene & Tropical Medicine

summary: Background  Accurate assessment of treatment efficacy would facilitate clinical trials of new anti-tuberculosis drugs. TB patients exhibit altered peripheral immunity which reverts during successful treatment. We hypothesised that these changes could be observed in whole blood transcriptome profiles.  Methods  Ex vivo blood samples from 27 pulmonary TB patients were assayed at diagnosis and during conventional treatment. RNA was processed and hybridised to Affymetrix GeneChips, to determine expression of over 47,000 transcripts.  Findings  There were significant changes in expression of over 4,000 genes during treatment. Rapid, large scale changes were detected, with down-regulated expression of ~1,000 genes within the first week, including inflammatory markers such as the complement components C1q and C2. This was followed by slower changes in expression of different networks of genes, including a later increase in expression of B cell markers, transcription factors and signalling molecules.  Interpretation  The expression of many genes is drastically altered during TB disease, with components of the humoral immune response being markedly affected. The treatment-induced restoration reflects the simultaneous suppression and activation of different immune responses in TB. The rapid initial down-regulation of expression of inflammatory mediators coincides with rapid killing of actively dividing bacilli, whereas slower delayed changes occur as drugs act on dormant bacilli and as lung pathology resolves. Measurement of biosignatures during clinical trials of new drugs could be useful predictors of rapid bactericidal or sterilizing drug activity.

overall_design: Ex vivo blood samples analysed for 27 first episode pulmonary TB patients, at diagnosis and after 1, 2, 4 and 26 weeks of treatment.

first: Jacqueline

first: Ji-Sook

last: Lee

first: Nicholas

last: Constantinou

first: Jang-Eun

last: Cho

first: Taane

last: Clark

first: Katharina

last: Ronacher

first: Elizabeth

last: King

first: Pauline

last: Lukey

first: Ken

last: Duncan

first: Paul

last: Van Helden

first: Gerhard

last: Walzl

first: Hazel

last: Dockrell


title: Tuberculosis Patients Blood Gene Expression Through Treatment (cured and end-of-treatment patients)

overall_design: Ex vivo blood samples analysed during TB treatment. These samples are from 9 successfully cured patients at diagnosis and end-of-treatment at 26 weeks.

middle: C


title: The Stockholm Atherosclerosis Gene Expression (STAGE) study: Global Gene Expression data from coronary and carotid artery disease patients

status: Public on Aug 21 2012

city: Stockholm

first: Johan

middle: Lars Markus

last: Björkegren

state: Stockholm

address: Scheelesv. 2

department: The Department of Medical Biophysics and Biochemistry

country: Sweden

institute: The Vascular Biology Unit

summary:
Tissue samples have been isolated during corornary artery  by-pass grafting (CABG)surgery from the atheroscelrotic arterial wall (AAW, aortic root puncture for proxmal ligation of by-pass vessel), non-atherosclertoci arterial wall (NAAW, distal part of mammary artery used a graft for LAD), liver, skeletal muscle (Recturs m), pericardial mediastinal visceral fat) in CAD patients. Carotid lesions samples from 25 validation patients.
We used microarrays to measure global gene expression in these tissues to cluster groups of functionally associated genes and then, second step clustering of patients within each cluster  to link clusters to patient phenotypes primarily coronary stenosis (CAD) and Intima media thickness (IMT) in carotid stenosis patients. .

overall_design: All samples were taken during surgery. The time of operation was less than 3 hours in most instances. Sammon plots show strong clustering of tissue-specific arrays. Even separating AAW from NAAW and carotid lesions.

first: Sara

last: Hägg

first: Josefin

last: Skogsberg

first: Jesper

last: Lundström

first: Peri

last: Noori

first: Roland

last: Nilsson

first: Hua

last: Zhong

first: Shohreh

last: Maleki

first: Ming-Mei

last: Shang

first: Björn

last: Brinne

first: Maria

last: Bradshaw

first: Vladimir

middle: B

last: Bajic

first: Ann

last: Samnegård

first: Angela

last: Silveira

first: Lee

last: Kaplan

first: Bruna

last: Gigante

first: Karin

last: Leander

first: Ulf

last: de Faire

first: Stefan

last: Rosfors

last: Lockowandt

first: Jan

last: Liska

first: Peter

last: Konrad

first: Rabbe

last: Takolander

first: Anders

last: Franco-Cereceda

first: Eric

last: Schadt

first: Torbjörn

last: Ivert

last: Hamsten

last: Tegnér


first: chunjiang

last: he

summary: To identify such targets of leukemia-related miRNAs such as miR-196b, we conducted Affymetrix gene arrays of leukemic BM samples from 24 mice including 9 primary (including 3 each of negative control, MLL-AF9, and miR-196b+MLL-AF9) and 15 secondary (including 3 negative control, 6 MLL-AF9, and 6 miR-196b+MLL-AF9) recipient mice

overall_design: A total of 24 mouse bone marrow samples including 9 primary (including 3 each of negative control, MLL-AF9, and miR-196b+MLL-AF9) and 15 secondary (including 3 negative control, 6 MLL-AF9, and 6 miR-196b+MLL-AF9) obtained from the in vivo mouse bone marrow reconstitution assays were analyzed by use of Affymetrix GeneChip Mouse Gene 1.0 ST Array (Affymetirx, Santa Clara, CA)

first: Zejuan

last: Li

first: Hao

last: Huang

first: Ping

last: Chen

first: Miao

last: He

first: Yuanyuan

first: Jianjun


title: Expression data comparing Pten-, p53-, and combined deficient mouse mammary tumors

status: Public on Aug 09 2012

city: Toronto

first: Jeff

last: Liu

state: Ontario

address: 101 College Street, RM 4-601

department: Princess Margaret Cancer Center

institute: University Health Network

summary:
To model the effect of Pten loss on breast cancer, we deleted Pten using a floxed allele and the deleter lines MMTV-Cre(NLST), which targets stem/bi-potent progenitor cells, and WAP-Cre, which targets CD24-positive, pregnancy-identified stem cells/alveolar progenitors. Mammary tumors were detected in WAP-Cre:Ptenf/f females with a latency of 15.2 months. By 18 months, nearly all mice had succumbed to cancer. MMTV-Cre:Ptenf/f mice developed mammary tumors after a longer latency of 26.4 months and reduced penetrance (70%) compared to WAP-Cre:Ptenf/f mice. Tumors from both models were heterogeneous, consisting primarily of differentiated adenocarcinoma (adenomyoepithelioma; ~70%) and adenosquamous carcinoma (20-25%). In addition, a small fraction of tumors was classified as acinar and poorly differentiated adenocarcinoma (4-7%) and adenosarcoma (3-4%). To test the consequences of combined Pten and p53 gene mutation on breast cancer, we deleted both genes via MMTV-Cre or WAP-Cre. Kaplan-Meier tumor free survival curves revealed that WAP-Cre:Ptenf/f:p53f/f and MMTV-Cre:Ptenf/f:p53f/f females developed tumors with reduced latency of 11.3 and 9.8 months, compared with 15.2, 26.4, and 16.9 months for single-mutant WAP-Cre:Ptenf/f, MMTV-Cre:Ptenf/f or MMTV-Cre:p53f/f mice, respectively. In contrast to the heterogeneity of Pten  tumors and small percentage of adenosarcomas in these mice, ~70% of Pten:p53 lesions were histologically classified as adeno-sacrcomatoid-like or mesenchymal-like breast cancer, with the rest exhibiting mixed mesenchymal plus adenocarcinomas and differentiated adenocarcinomas. The adeno-sacrcomatoid-like tumors expressed the mesenchymal markers vimentin, K5, SMA, N-cadherin and desmin but not ER, as well as islands of luminal-like K18 expressing cells surrounded by a layer of K14-positive cells.
We used microarrays to detect differentially expressed genes in the Pten:p53 double-knock-out vs Pten or p53 single deletions

overall_design: Total RNA was extracted from tumors developed by double Trizol method and hybridized on Affymetrix microarrays.

first: Sharon

last: Wang

first: Robert

last: Jones

first: Eldad

last: Zacksenhaus


title: Gene expression by Treg subsets

status: Public on Aug 07 2012

city: Miami

first: Thomas

middle: R

last: Malek

state: FL

address: 1600 NW 10th Avenue

department: Microbiology/Immunology

institute: University of Miami

summary:
Thymic-derived natural T regulatory cells (nTregs) are characterized by functional and phenotypic heterogeneity. Recently, a small fraction of peripheral Tregs have been shown to express Klrg1, but it remains unclear the extent Klrg1 defines a unique Treg subset. Here we show that Klrg1+ Tregs represent a terminally differentiated Treg subset derived from Klrg1- Tregs. This subset is a recent antigen-responsive and a highly activated short-lived Treg population that expresses enhanced levels of Treg suppressive molecules and that preferentially resides within mucosal tissues. The development of Klrg1+ Tregs also requires extensive IL-2R signaling. This activity represents a distinct function for IL-2, independent from its contribution to Treg homeostasis and competitive fitness. These and other properties are analogous to terminally differentiated short-lived CD8+ T effector cells. Our findings suggest that an important pathway driving antigen-activated conventional T lymphocytes also operates for Tregs.
Gene expression analysis was performed of this and other Treg subsets based on expression of CD62L, CD69, and Klrg1 to define the molecular properties of Klrg1+ Tregs and its relationship to other Treg subsets found in the peripheral immune tissues.

overall_design: Mice were euthanized, spleen cell preparations were made, and each Treg subset was isolated by FACS cell sorting. RNA was immediately prepared for processing.


title: Expression data from SP and non-SP sorted anti-EpCAM treated A549 cells

status: Public on Aug 08 2012

city: Hannover

last: Krüwel

address: Nikolai-Fuchs-Str. 1

country: Germany

institute: Fraunhofer Institute for Toxicology and Experimental Medicine

summary:
Targeted therapies against cancer stem cells which are enriched in side populations (SP) involves interruption of Wnt-signalling. Furthermore, EpCAM is a SP marker and modulator of Wnt-signalling. Therefore, the effects of an anti-EpCAM treatment on SP-cells and WNT/β-catenin signalling was studied.
SP of the human lung adenocarcinoma cell line A549 was obtained by fluorescence activated cell sorting and whole genome scans helped to define their molecular phenotype after anti-EpCAM antibody treatment.

overall_design: Anti-EpCAM treated and untreated A549 cells were subjected to Hoechst 33342 dye exclusion assay and sorted to SP and non-SP fractions by FACS. Three biological replicates.

first: Astrid

last: Rohrbeck


title: Experimental identification of miR-378-3p targets by overexpression and silencing in murine NIH-3T3 fibroblasts

city: Manchester

first: Dominik

middle: Andreas

last: Rückerl

address: Oxford Road

department: Faculty of Biology, Medicine and Health

institute: The University of Manchester

summary: MicroRNAs (miRNAs) are short noncoding RNA molecules regulating the expression of mRNAs. Target identification of miRNAs is computationally difficult due to the relatively low homology between miRNAs and their targets. We provide data here utilizing an experimental approach to identify targets of mmu-miR-378-3p, where mmu-miR-378-3p was overexpressed and silenced in NIH-3T3 murine fibroblasts and compared to control RNA transfected cells (RISC-free siRNA). Expression of mRNAs was profiled and differentially expressed genes following either treatment as compared to control transfected cells were identified. In this way we identified 491 significantly differentially expressed genes with more than 1.4 fold change in either comparison. One of the putative targets Akt-1 was subsequently confirmed by luciferase reporter assay.

overall_design: All conditions were assayed in triplicates. A commercially available mimic or inhibitor of mmu-miR-378-3p or control RNA (RISC-free siRNA) were transfected into NIH-3T3 fibroblasts using a chemical transfection system (DharmaFECT 1). 48h post transfection total RNA was isolated and mRNA-expression profiled.

first: Amy

middle: H

last: Buck

first: Nouf

middle: N

last: Laqtom

last: Ruckerl


title: Network Biology of Tumor Stem-like Cells Identified a Regulatory Role of CBX5 in Lung Cancer

city: Boston

first: YAU-HUA

last: YU

state: Massachusetts

address: 1 Kneeland Street

institute: Tufts Univ. School of Dental Medicine

summary:
Mounting evidence points to a link between a cancer possessing stem-like properties and a worse prognosis. To understand the biology, a common approach is to integrate network biology with signal processing mechanics. That said, even with the right tools, predicting the risk for a highly susceptible target using only a handful of gene signatures remains very difficult. By compiling the expression profiles of a panel of tumor stem-like cells (TSLCs) originating in different tissues, comparing these to their parental tumor cells (PTCs) and the human embryonic stem cells (hESCs), and integrating network analysis with signaling mechanics, we propose that network topologically-weighted signaling processing measurements under tissue-specific conditions can provide scalable and predicable target identification.
All function codes related to this project could be accessed at the supplementary website.

overall_design: We hypothesized that the transcriptional stochastic element of lung tumors modeled by the lung-TSLC networks could be utilized to estimate the prognostic survival times. A scalable, network-based signal-processing model was devised to analyze the transcriptional signal for a single gene or for a set of genes relating to other gene players in the networks. We tested our hypothesis in the following three steps: (1) construct the consensus TSLC networks and the lung-TSLC networks by analyzing the transcriptomes of three panels of cells: the parental tumor cells (PTCs), the cultivated TSLCs, and the human embryonic stem cels (hESCs); (2) develop network topologically-weighted signal processing measurements and apply such measurements to find the survival correlation and to identify potential targets for biological validation; and (3) verify a potential regulatory target - Cbx5 - in another clinical cohort of LACs as well as in knock-down experiments in lung TSLCs functional assays and in animal models.

first: Yau-Hua

last: Yu

first: Shih-Hwa

last: Chiou

first: Jeng-Fan

last: Lo


title: Gene Expression Profile of Endotoxin-stimulated Leukocytes of the Newly Born: Control of Cytokine Gene Expression by Interleukin-10.

status: Public on Aug 03 2012

city: Manhasset

first: Dennis

last: Davidson

state: New York

address: 350 Community Dr

department: Pediatrics

institute: The Feinstein Institute for Medical Research

summary:
Introduction: Increasing evidence now supports the association between the fetal inflammatory response syndrome (FIRS) with the pathogenesis of preterm labor, intraventricular hemorrhage and bronchopulmonary dysplasia. These disorders are among the most important causes of mortality and morbidity in the perinatal period. During the fetal inflammatory response syndrome (FIRS) polymorphonuclear leukocytes (PMNs) and monocytes (MONOs) are sequentially recruited into the placenta; the same process occurs in the lung of the newborn during the development of bronchopulmonary dysplasia (BPD). The aim of the study was to reveal cell-specific differences in gene expression and cytokine release in response to endotoxin that would elucidate inflammatory control mechanisms in the newly born.
Results: Compared to PMNs, MONOs had a greater diversity and more robust expression of pro-inflammatory (PI) gene expression at 4h. Only MONOs had genes changing expression in the JAK/STAT pathway including interleukin-10.

overall_design: Isolation of cord blood polymorphonuclear leukocytes and monocytes separately from 5 subjects. Endotoxin stimulation in cell culture for 4 hours. Comparison of gene expression between PBS versus endotoxin (LPS).

first: Veronika

last: Miskolci


title: Amniotic fluid-derived cells: genome-wide expression in early and late cultures

city: NEW BRUNSWICK

first: Ashwin

last: Jadhav

address: 125 PATERSON STREET

department: OBGYN

institute: UMDNJ-RWJMS

summary: Amniotic fluid stem cells (AFSCs) are of interest in regenerative medicine as a non-controversial and potentially 'abundant' source of stem cells. Progress has been made in understanding amniotic fluid stem cell biology, and amniotic fluid-derived cells have been induced to form neurons, osteoblasts, muscle cells, and others. Our study evaluates change in the genome-wide expression profile of amniotic fluid stem cells during in-vitro culture, using Affymetrix U133 Plus 2.0 microarray chips. We found that only 3.08% of gene probes were differentially expressed from early to late passage of AFSC culture. The differentially expressed genes were related to biological processes or cellular function - including transcription factors, protein kinases, and cytokines/growth factors. Other gene-sets of interest were oncogenes and tumor suppressor genes, which were a very small number of genes. We further analyzed the gene sets of interest using NIH DAVID and GSEA bioinformatics databases for gene annotations analysis. Applying false discovery rate correction, there was no significant difference in the genome-wide expression profiling between early and late passage. AFSCs maintain their genome-wide expression profile during in-vitro culture.

overall_design: Amniotic fluid-derived c-kit-positive cells were maintained in stem cell culture and genome-wide expression changes were studied and compared between early passage and late passage in culture.

first: Jiri

last: Zavadil

first: Mary

last: Perle

first: Ross

last: Basch

first: Bruce

middle: K

last: Young


title: Expression data from patients with large granular lymphocyte leukemia

first: Bartlomiej

middle: Przemyslaw

last: Przychodzen

address: Coldharbour Lane

department: Department of Haematology

institute: King's College

summary: Our results suggest that STAT3 can be activated independent of key oncogenic driver mutations in its SH2 domain in a subset of patients with large granular lymphocyte disorders. We examined the gene expression pattern in T-LGL leukemias compared to controls, and the impact of the presence of STAT3 mutations on the transcriptional regulation of a specific set of genes previously described.

overall_design: Mononuclear cells were separated from peripheral blood by density gradient sedimentation (Mediatech, Herndon, VA, USA). LGL cells were separated by flow cytometric sorting using anti-VB and CD8 mAb as described previously. Healthy, donor-derived CD8+CD57+ cells were isolated by flow cytometric sorting using CD3, CD8, and CD57 mAb. Total RNA was extracted from cells using Trizol (Invitrogen, Carlsbad, CA, USA) Phase-Lock gel tubes (Eppendorf, Hamburg, Germany), cleaned RNAeasy columns (Qiagen, Valencia CA, USA), and dissolved diethylpyrocarbonate water. Total cRNA was prepared using the in vitro-transcribed (Affymetrix, Santa Clara, CA, USA) and hybridized to U133 arrays, according to the manufacturer's instructions (Affymetrix). All microarrays were examined for surface defects, grid placement, background intensity, housekeeping gene expression, and a 3:5  ratio of probe from genes of varying length. Expression analysis was conducted using standard  Affymetrix analysis software algorithms (Microarray Suite 5.0). Comparative analysis between expression profiles was carried out on GeneSpring' software, Version 7.1 (Agilent, Clara, CA, USA). Scanned images of Affymetrix chips were converted spreadsheet numbers using Affymetrix proprietary GeneChip Operating software (GCOS).

first: A

last: Jerez

first: M

last: Wlodarski


title: Expression data of cystic fibrosis and non-cystic fibrosis airway cell lines under oxidative stress

city: Montréal

first: greg

last: VOISIN

state: QC

address: 3840 Saint-Urbain

department: Département de Médecine, Centre de Recherche

institute: Centre Hospitalier de l'Université de Montréal Hôtel Dieu

summary:
CF's physiopathology is poorly explained by the mutation alone. The oxydative stress could be a major factor of this illness . Study its impact on transcriptome's CF cell line could be ameliorate our understanding of the evolution of cystic fibrosis.
we used microarray technology to evaluate  under oxydative stress,  the transcriptional state  of an epithelial lung cell issued from a human with cystic fibrosis and to identify a set of modulated genes associated to survival cell processes.

overall_design: the two cell lines are cultivated to Air-liquid Interface for RNA extraction and hybridization on Affymetrix microarrays. Each condition is triplicated. For the oxidative stress conditions, the two cell lines are treated on apical site by 15 µl of DMNQ (2,3-dimethoxy-1,4-naphtoquinone) ,concentrated at 15 µM, during 24 hours before RNA extraction.

first: G

last: Voisin

first: Y

last: Berthiaume


title: The interferon induced transmembrane protein 1 (Ifitm1): detailed analysis on its assumed functions

status: Public on Aug 06 2012

city: Neuherberg

first: Johannes

last: Beckers

address: Ingolstaedter Landstr. 1

department: Institute of Experimental Genetics

institute: Helmholtz Zentrum Muenchen

summary:
Several functions have been suggested for the interferon induced transmembrane protein 1 (Iftitm1) gene in mammals. Originally it was identified as a member of a gene family that is highly inducible by type I and type II inteferons. Based on its expression during primordial germ CELl (PGC) specification it was suggested to be required for normal PGC migration. Ifitm1 targeted knockdown experiments in mouse embryos provided evidence that the gene might be necessary for normal somitogenesis. Finally, the complete deletion of the Ifitm gene cluster on mouse chromosome 7 revealed that the five deleted Ifitm1 genes are not essential for PCG migration and fertility. Here, we generated a novel targeted knockin allele of the Ifitm1 gene by replacing its coding region with a lacZ reporter gene to systematically reassess the suggested functions of this gene.
We find that during embryogenesis somites and in the adult the vertebral column appear normal in homozygous Ifitm1 knockout mice, strongly suggesting that Ifitm1 is not essential for normal segmentation of the paraxial mesoderm. In addition, homozygous Ifitm1 mutant mice are fertile, reproduce normally and have normal sperm quality. Furthermore, we show that the Ifitm1 loss-of-function allele does not cause immunological mutant phenotypes in unchallenged as well as in Listeria challenged homozygous mutant animals. To further focus on unique functional requirements of Ifitm1, we took advantage of the lacZ reporter gene in the Ifitm1 locus to analyze for the first time in detail and with high sensitivity its complex expression pattern in mouse embryos from E8.5 to E14.5 and in adult organs. The detailed description of the Ifitm1 expression domains will support the identification of organs that might be affected by the loss of Ifitm1 function.

overall_design: We performed gene expression microarray analysis of ten lung tissues from male adult Ifitm1-deficient and control mice

first: Ingeborg

last: Teppner

first: Martin

last: Irmler


title: Expression data from SP and non-SP sorted anti-EpCAM treated A2C12 and A549 cells compared to non-transgenic lung tissue

first: Thomas

last: Krüwel


title: Identification of gene targets of Meis1

city: St. Louis

first: Mi

last: Cai

state: MO

address: 660 S. Euclid Ave.

department: Immunology and Pathology

institute: Washington University School of Medicine

summary: The homeodomain protein Meis1 is essential for definitive hematopoiesis and vascular patterning in the mouse embryo. Our present study suggested it exerts two distinguishable effects in differentiating ES cells.  First, it increases the numbers of hematopoietic progenitors and extends their persistence in culture. Second, Meis1 skews hematopoietic differentiation by suppressing erythroid while enhancing megakaryocytic progenitor differentiation. To identify the underlying transcriptional bases of these actions, we carried out microarray analysis to compare the various populations of cells developing in ES differentiation cultures in the presence and absence of Meis1 induction.

overall_design: ES cells with dox-inducible Meis1 (A2lox.Meis1) were differentiated as embryoid bodies (EBs) for 6 days before plating on OP9-GFP cell monolayers and cytokines, and treated with (+) or without (-) doxycycline (dox). Cells were purified by cell sorting on day 7 or 8 into various populations based on levels of CD41 expression: GFP-CD41-, GFP-CD41+ (day 7) and GFP-CD41-,GFP-CD41int, and GFP-CD41hi (day 8). Gene expression of these purified populations was determined by microarray analysis.

first: Theresa

last: Murphy

first: Kenneth

middle: M


title: Expression data from human Kidney cell line induced by PCB77

city: Washington DC

first: Sisir

middle: K.

last: Dutta

state: DC

address: 415 College Street, NW

department: Biology

institute: Howard University

summary:
Exposure to Polychlorobiphenyls (PCBs) is known to cause serious health effects in human but the gene expression profiles leading to development of differnet diseases is not fully understood. The knowledge of global gene expression will help us to devlop early diagnostic biomarkers for PCB induced health effects.
We used microarrays to detail the global gene expression profile underlying the effects of PCB77 on human Kidney cells leading to identification of distinct classes of up-regulated and down-regulated genes and cellular processes.

Keywords: time course

overall_design: The HK2 cells are grown in Keratinocyte-Serum Free Medium supplemented 5ng/ml recombinant epidermal growth factor and 0.05mg/ml bovinepituitary extract and 1X Pennicilllin-Streptromycin and were treated with 40 micro molar of PCB77 with different exposure time. Trizol extraction of total RNA was performed according to the manufacturer's instructions. Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 6 microgram of total RNA (Expression Analysis Technical Manual, 2001, Affymetrix). Following fragmentation, 10 microgram of cRNA were hybridized for 16 hr at 45C on GeneChip Human Genome Array (HGU133 plus 2.0). GeneChips were washed and stained in the Affymetrix Fluidics Station 450 and scanned using the Affymetrix GeneArray Scanner 3000. The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings and global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 150.

first: Somiranjan

last: Ghosh

first: Supriyo

last: De

first: Y-Q

last: Chen

first: Linda

last: Moses

first: Eric

middle: P

last: Hoffman


title: Genome-wide methylation profile of head and neck squamous cell carcioma (HNSCC)

city: New York

first: Athanasios

last: Zavras

state: NY

address: 630 West 168th St.

institute: Columbia University

type: Methylation profiling by genome tiling array

summary: Genome wide DNA methylation profiling of normal and HNSCC blood samples. The Illumina Infinium 450k Human DNA methylation Beadchip was used to obtain DNA methylation profiles across approximately 450,000 CpGs in serum samples. Samples included 12 cancer-free healthy controls, and 12 HNSCC cases.

overall_design: Bisulphite-converted DNA from the 24 samples were hybridised to the Illumina Infinium 450k Human Methylation Beadchip.

first: Zavras

last: Athanasios

first: Angela

last: Yoon

first: Shuang

last: Wang


title: Altered miRNA and gene expression in acute myeloid leukemia with complex karyotype identify networks of prognostic relevance

city: Berlin

first: Lars

last: Bullinger

address: Augustenburger Platz 1

department: Hematology, Oncology and Tumorimmunology

institute: Charité

summary:
Recently, the p53-miR-34a network was identified to play an important role in tumorigenesis. As in acute myeloid leukemia with complex karyotype (CK-AML) TP53 alterations are the most common known molecular lesion, we further analyzed the p53-miR-34a axis in CK-AML with known TP53 status. Clinically, low miR-34a expression and TP53 alterations predicted for chemotherapy resistance and inferior outcome. Notably, in TP53unaltered CK-AML high miR-34a expression predicted for inferior overall survival (OS), whereas in TP53biallelic altered CK-AML high miR-34a expression pointed to better OS.
To further investigate miR-34a-associated gene expression patterns, we analyzed distinct subgroups defined by TP53 alteration and miR-34a expression status. Exemplary samples from TP53unaltered (n=6) and TP53biallelic altered (n=6) CK-AML characterized by either high (CK+/miR-34ahigh expression, above median miR-34a expression of the entire cohort), or low (CK+/miR-34alow expression, below median miR-34a expression of the entire cohort) miR-34a expression (n=3 in each group), were analyzed. This molecular profiling linked impaired p53 to decreased miR-34a expression but also identified p53-independent miR-34a induction mechanisms, as shown in TP53biallelic altered cell lines treated with 15-deoxy-∆12,14-prostaglandin (PGJ2). An improved understanding of this mechanism might provide novel therapeutic options to restore miR-34a function and thereby induce cell cycle arrest and apoptosis in TP53altered CK-AML.

overall_design: All samples were obtained from untreated patients at the time of diagnosis. Cells used for microarray analysis were collected from the purified fraction of mononuclear cells after Ficoll density centrifugation. Routine diagnostic algorithms, including the characterization of molecular markers are performed.


title: Dual actions of Meis1 inhibit erythroid progenitor development and sustain general hematopoietic cell proliferation

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

overall_design: Refer to individual Series


title: Microarray analysis of U87 glioma cells after transient knockdown of FOXM1

status: Public on Aug 11 2012

city: guangzhou

first: nu

last: zhang

address: no.58 Zhongshan 2 road

department: neurosurgery

country: China

institute: 1st affiliated hospital of Sun Yat-sen university

summary: FOXM1 plays a key role in M phase in normal cells and is overexpressed in human glioma. We found that FOXM1 deprivation could sensitize the glioma cells to TMZ chemotherapy. To find out the mechanistic regulation of FOXM1 in chemo-resistant genes, we used microarrays to select the potential genes regulated by FOXM1 which dominates in glioma chemo-resistance.

overall_design: U87 glioma cells were transiently transfected with none-target siRNA or FOXM1 siRNA. Total RNA were extracted after 48 hours and subjected to the microarray.

first: Nu

last: Zhang


title: Bmal1 controls circadian cell proliferation and susceptibility to UVB-induced DNA damage in the epidermis [Bmal1 KO]

status: Public on Aug 02 2012

city: Irvine

first: mikhail

middle: viktorovich

last: geyfman

address: 839 Medical Sciences Court 250 Sprague Hall

department: Medicine

institute: university of California Irvine

summary: While several physiological skin parameters vary in a circadian manner, the identity of genes participating in chronobiology of skin remains unknown, leading us to define the circadian transcriptome of mouse skin at two different stages of the hair cycle, telogen and anagen.  The circadian transcriptomes of telogen and anagen skin are largely distinct, with the former dominated by genes involved in cell proliferation and metabolism. The expression of many metabolic genes is antiphasic to cell cycle related genes, the former peaking during the day and the latter peaking at the night.  Consistently, accumulation of reactive oxygen species, a byproduct of oxidative phosphorylation, and S-phase are antiphasic to each other in telogen skin.  Furthermore, the circadian variation in S-phase is controlled by BMAL1 intrinsic to keratinocytes as keratinocyte-specific deletion of Bmal1 obliterates time of day dependent synchronicity of cell division in the epidermis leading to a constitutively elevated cell proliferation.  Consistent with higher cellular susceptibility to UV-induced DNA damage during S phase, we found that mice are most sensitive to UVB-induced DNA damage in the epidermis at night. As maximum numbers of keratinocytes go through S phase in the late afternoon in the human epidermis, we speculate that in humans the circadian clock imposes regulation of epidermal cell proliferation such that skin is at a particularly vulnerable stage during times of maximum UV exposure, thus contributing to the high incidence of human skin cancers.

overall_design: Whole skin was collected at ZT22.  Where ZT number indicates the number of hours elapsed from when lights are switched on.  ZT0 = lights on (6am). ZT12=lights off (6pm).  Het mice designate a presence of one Bmal1 mutant allele and one wt allele.  KO mice designate mice germline deleted for both copies of Bmal1 allele.  Total RNA was purified from the skin of each biological littermate replicate.

first: Mikhail

last: Geyfman

first: Vivek

last: Kuman

first: Qiang

last: Liu

first: Rolando

last: Ruiz

first: William

last: Gordon

first: Francisco

last: Espitia

last: Cam

first: Sarah

last: Millar

first: Padhraic

last: Smyth

first: Alexander

last: Ihler

first: Joseph

last: Tahahahsi

first: Bogi

last: Andersen


title: Expression data from human Kidney cell line induced by PCB153

first: Sisir

last: Dutta

summary:
Exposure to Polychlorobiphenyls (PCBs) is known to cause serious health effects in human but the gene expression profiles leading to development of differnet diseases is not fully understood. The knowledge of global gene expression will help us to devlop early diagnostic biomarkers for PCB induced health effects.
We used microarrays to detail the global gene expression profile underlying the effects of PCB153 on human Kidney cells leading to identification of distinct classes of up-regulated and down-regulated genes and cellular processes.

Keywords: time course

overall_design: The HK2 cells are grown in Keratinocyte-Serum Free Medium supplemented 5ng/ml recombinant epidermal growth factor and 0.05mg/ml bovinepituitary extract and 1X Pennicilllin-Streptromycin and were treated with PCB153 for different times. Trizol extraction of total RNA was performed according to the manufacturer's instructions. Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 6 microgram of total RNA (Expression Analysis Technical Manual, 2001, Affymetrix). Following fragmentation, 10 microgram of cRNA were hybridized for 16 hr at 45C on GeneChip Human Genome Array (HGU133 plus 2.0). GeneChips were washed and stained in the Affymetrix Fluidics Station 450 and scanned using the Affymetrix GeneArray Scanner 3000. The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings and global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 150.

first: Somiranjan

last: Ghosh

first: Supriyo

last: De

first: Y-Q

last: chen

first: Linda

last: Mosses

first: Eric

last: Hoffman


title: Identifying novel anti-angiogenic targets in human breast cancer

city: London

first: Dylan

middle: Trefor

last: Jones

state: UK

address: Charterhouse square

department: Tumour Biology

institute: Barts Cancer Institute

summary: We analysed gene expression in normal breast blood vessels and breast invasive ductal carinoma blood vessels.

overall_design: Normal breast sections and IDC breast sections were immunostained for endothelial-specific CD31. Vessels were dissected and captured with laser capture microscopy, and RNA was extracted and analysed on an Affymetrx array chip.  In total, gene expression in blood vessels from 3 normal breast and 3 IDC breast was analysed.

middle: T

first: Tanguy

last: Lechertier

first: Richard

last: Mitter

first: John

last: Herbert

first: Roy

last: Bicknell

first: J

first: Francesca

last: Buffa

first: Adrian

last: Harris

first: Kairbaan

last: Hodivala-Dilke


title: Bmal1 controls circadian cell proliferation and susceptibility to UVB-induced DNA damage in the epidermis

first: mikhail

last: geyfman

first: Mikhail

last: Geyfman

first: Vivek

last: Kuman

first: Qiang

last: Liu

first: Rolando

last: Ruiz

first: William

last: Gordon

first: Francisco

last: Espitia

last: Cam

first: Sarah

last: Millar

first: Padhraic

last: Smyth

first: Alexander

last: Ihler

first: Joseph


title: Bmal1 controls circadian cell proliferation and susceptibility to UVB-induced DNA damage in the epidermis [Anagen]

overall_design: Whole skin was collected at 4 hour intervals for 48 hours.  ZT number indicates the number of hours elapsed from when lights are switched on.  ZT0 = lights on (6am). ZT12=lights off (6pm). Total RNA was purified from the skin of each mouse and equal amount of RNA from the 3 replicates for each time point were pooled. Anagen samples were collected from skin of P30 male mice.

first: Eric

last: Tahahahsi

first: Bogi

last: Andersen


title: Expression Data from Human Kidney Cell Line (HK2)

first: Sisir

last: Dutta


title: Bmal1 controls circadian cell proliferation and susceptibility to UVB-induced DNA damage in the epidermis [telogen].

overall_design: Whole skin was collected at 4 hour intervals for 48 hours. Where ZT number indicates the number of hours elapsed from when lights are switched on.  ZT0 = lights on (6am). ZT12=lights off (6pm).  Total RNA was purified from the skin of each mouse and equal amount of RNA from the 3 replicates for each time point were pooled. Telogen samples were collected from skin of P46 male mice.


title: SIN3A-regulated LIF-responsive genes in MCF7 cells

city: Leuven

first: Rekin's

last: Janky

address: Herestraat 49 Box 816

department: Nucleomics Core

country: Belgium

institute: VIB

summary: Tyrosine phosphorylation is a hallmark for activation of Signal Transducer and Activator of Transcription (STAT) proteins, but their transcriptional activity also depends on other secondary modifications. Type I interferons (IFNs) can activate both the ISGF3 (STAT1:STAT2:IRF9) complex and STAT3, but with cell-specific, selective triggering of only the ISGF3 transcriptional program. Following a genome-wide RNAi screen, we identified the Sin3a complex as an important mediator of this STAT3 transcriptional repression. Sin3a directly interacts with the DNA-binding domain of STAT3 and alters its acetylation status. SIN3A silencing enhances recruitment of STAT3 and enhanceosome components to the SOCS3 promoter, resulting in histone hyperacetylation and enhanced transcription. Conversely, Sin3a is required for ISGF3-dependent gene transcription and for an efficient IFN-mediated antiviral protection against Influenza A and hepatitis C viruses. The Sin3a complex therefore acts as a context-dependent STAT1/3 transcriptional switch.

overall_design: MCF7 cells were transfected with 50nM Renilla luciferase (control) or SIN3A-specific siRNA. 72h later, cells were cultured for 4h in absence of FCS and left non-stimulated or stimulated with LIF (10ng/ml, 1h). Total RNA was extracted. For each of the 4 conditions, 3 biological replicates were included. Nevertheless, one sample (SIN3A_siRNA_LIF1h_rep3) was discarded. In total 11 samples were analyzed.

first: Laura

last: Icardi

first: Raffaele

last: Mori

first: Viola

last: Gesellchen

first: Sven

last: Eyckerman

first: Lode

last: De Cauwer

first: Judith

last: Verhelst

first: Koen

last: Vercauteren

first: Xavier

last: Saelens

first: Philip

last: Meuleman

first: Geert

last: Leroux-Roels

first: Karolien

last: De Bosscher

first: Michael

last: Boutros

first: Jan

last: Tavernier


title: The role of Foxp1/4 in lung development

city: Philadelphia

first: Shanru

last: Li

state: PA

address: 3400 Civic Center Blvd, Bldg 421

institute: University of Pennsylvania

summary:
Foxp1/4 transcription factors are conserved transcriptional repressors expressed in overlapping patterns during lung development as well as in the adult lung. However, the role of Foxp1/4 in development and homeostasis of the pseudostratified epithelium of the proximal airways and trachea is unknown.
We propose to determine the roles for Foxp1/4 in lung development by deleting these genes in lung epithelial specific knockout mice.

overall_design: To explore the genome wide consequences of Foxp1/4 deficiency on secretory epithelial differentiation in the lung, we performed microarray analysis of Shh- cre control and Foxp1/4ShhcreDKO mutants lungs at E14.5, 3 embryos, respectively.

first: Yi

last: Wang

first: Yuzheng

last: Zhang

first: Min

last: Lu

first: Francesco

last: DeMayo

first: Joseph

last: Dekker

last: Tucker

first: Edward

last: Morrisey


title: Glioma-propagating cells as an in vitro screening platform: PLK1 as a case study

city: Singapore

first: Edwin

last: Sandanaraj

address: 11 Jalan Tan Tock Seng

department: Research

country: Singapore

institute: NNI

summary: Gliomas are the most devastating of primary adult malignant brain tumors. These tumors are highly infiltrative and can arise from cells with extensive self-renewal capability and chemoresistance, frequently termed glioma-propagating cells (GPCs). GPCs are thus the plausible culprits of tumor recurrence. Treatment strategies that eradicate GPCs will greatly improve disease outcome. Such findings support the use of GPCs as in vitro cellular systems for small molecule screening. However, the nuances in utilizing GPCs as a cellular screening platform are not trivial. These slow-growing cells are typically cultured as suspension, spheroid structures in serum-free condition supplemented with growth factors. Consequently, replenishment of growth factors throughout the screening period must occur to maintain cells in their undifferentiated state, as the more lineage-committed, differentiated cells are less tumorigenic. We will present a case study of a small molecule screen conducted with GPCs and explain how unique sphere activity assays were implemented to distinguish drug efficacies against the long-term, self-renewing fraction, as opposed to transient-amplifying progenitors, latter of which are detected in conventional viability assays. We identified Pololike kinase 1 as a regulator of GPC survival. Finally, we leveraged on public glioma databases to illustrate GPC contribution to disease progression and patient survival outcome.

overall_design: Total RNA from primary neurosphere culture of brain tumor specimens were hybridized in baseline condition.  Specimens were obtained from 11 patients and replicate arrays were performed for all 11 neurosphere cultures.

first: Charlene

last: Foong

first: Robert

last: Campbell

first: Beng

last: Ang

first: Yuk

last: Chong

first: Carol

last: Tang


title: Differential DNA Methylation in Purified Human Blood Cells

city: Huddinge

first: Lovisa

last: Reinius

address: Novum, Halsovagen 7-9

department: Department of Biosciences and Nutrition

institute: Karolinska Institutet

summary: Methylation of cytosines at CpG sites is a common epigenetic DNA modification that can be measured by a large number of methods, now even in a genome-wide manner for hundreds of thousands of sites. The application of DNA methylation analysis is becoming widely popular in complex disorders, for example, to understand part of the “missing inheritance”. The DNA samples most readily available for methylation studies are derived from whole blood. However, blood consists of many functionally and developmentally distinct cell populations in varying proportions. We studied whether such variation might affect the interpretation of methylation studies based on whole blood DNA. We found in healthy male blood donors there is important variation in the methylation profiles of whole blood, mononuclear cells, granulocytes, and cells from seven selected purified lineages. CpG methylation between mononuclear cells and granulocytes differed for 22% of the 8252 probes covering the selected 343 genes implicated in immune-related disorders by genome-wide association studies, and at least one probe was differentially methylated for 85% of the genes, indicating that whole blood methylation results might be unintelligible. For individual genes, even if the overall methylation patterns might appear similar, a few CpG sites in the regulatory regions may have opposite methylation patterns (i.e., hypo/hyper) in the main blood cell types. We conclude that interpretation of whole blood methylation profiles should be performed with great caution and for any differences implicated in a disorder, the differences resulting from varying proportions of white blood cell types should be considered.

overall_design: Six healthy male blood donors, age 38 ± 13.6 years, were included in the study. From each individual, global DNA methylation levels were analyzed in whole blood, peripheral blood mononuclear cells (PBMC) and granulocytes as well as for seven isolated cell populations (CD4+ T cells, CD8+ T cells, CD56+ NK cells, CD19+ B cells, CD14+ monocytes, neutrophils, and eosinophils), n=60 samples analyzed in total.

first: Nathalie

last: Acevedo

first: Maaike

last: Joerink

first: Göran

last: Pershagen

first: Sven-Erik

last: Dahlén

first: Dario

last: Greco

first: Cilla

last: Söderhäll

first: Annika

last: Scheynius

first: Juha

last: Kere


title: Identification of gene targets of Meis2

first: Mi

last: Cai

summary: The homeodomain protein Meis1 is essential for definitive hematopoiesis and vascular patterning in the mouse embryo. Meis2, another member of the same family, shares 82% protein identities with Meis1. Our present study suggested Meis2 exerts two distinguishable effects in differentiating ES cells.  First, it increases the numbers of hematopoietic progenitors and extends their persistence in culture. Second, Meis2 skews hematopoietic differentiation by suppressing erythroid while enhancing megakaryocytic progenitor differentiation. To identify the underlying transcriptional bases of these actions, we carried out microarray analysis to compare the various populations of cells developing in ES differentiation cultures in the presence and absence of Meis2 induction.

overall_design: ES cells with dox-inducible Meis2 (A2lox.Meis2) were differentiated as embryoid bodies (EBs) for 6 days before plating on OP9-GFP cell monolayers and cytokines, and treated with (+) or without (-) doxycycline (dox). Cells were purified by cell sorting on day 7 or 8 into various populations based on levels of CD41 expression: GFP-CD41-, GFP-CD41+ (day 7) and GFP-CD41-,GFP-CD41int, and GFP-CD41hi (day 8). Gene expression of these purified populations was determined by microarray analysis.

first: Theresa

middle: L

last: Murphy

first: Kenneth


title: Expression data of Sox9+ and Ngn3+ mouse pancreas cells at different stages of development

city: La Jolla

first: Brandon

last: Taylor

address: Sanford Consortium for Regenerative Medicine, 2880 Torrey Pines Scenic Dr., Room 3101

department: Pediatrics and Cellular & Molecular Medicine

institute: University of California, San Diego

summary:
Genes specific to Sox9+ pancreatic progenitors were identified by comparing the gene expression in embryonic and adult Sox9+ cells.
We used microarray analysis to detail the global changes in gene expression as Sox9 positive embryonic pancreatic progenitors differentiatiate into adult ductal cells or the endocrine lineage.

overall_design: GFP positive cells from Sox9-EGFP mouse pancreas were isolated by FACS at different stages of development (e10.5, e15.5, and p23) for RNA extraction and hybridization to Affymetrix microarrays. To obtain populations highly enriched in Sox9 expression, we collected only GFP Hi populations for analysis.  To identify gene expression changes specific to the differentiation of progenitors to ductal cells or endocrine cells, we also isolated and analyzed the gene expression profile of GFP negative cells isolated at p23, as well as GFP positive cells isolated from Ngn3-EGFP mouse pancreas at e15.5. These two populations allow the identification of genes whose expression is associated with the newly differentiated endocrine progeny in the embryo (Ngn3-GFP positive) and adult acinar and endocrine cells at p23.

first: Maike

last: Sander

first: Janel

last: Kopp

first: Kristine

last: Freude


title: Identification of novel tissue-specific transcription arising from E-cadherin/CDH1 intron2: a novel protein isoform increases gastric cancer cell invasion and angiogenesis.

city: Trieste

first: Danilo

last: Licastro

department: Genomica Funzionale

country: Italy

institute: CBM

summary:
E-cadherin, a protein encoded by the CDH1 gene is the dominant epithelial cell adhesion molecule playing a crucial role in epithelial tissue polarity and structural integrity. The progression of 90% or more carcinomas is believed to be mediated by disruption of normal E-cadherin expression, subcellular localization or function. Despite the strong correlation between E-cadherin loss and malignancy the mechanism through how this occurs is not known in most sporadic and hereditary epithelial carcinomas. Previous works have shown the importance of CDH1 intron 2 sequences for proper gene and protein expression supporting the possibility of these being cis-modulators of E-cadherin expression/function. but when co-expressed it led to reduced cell-cell adhesiveness, increased invasion and angiogenesis. By expression array analysis, IFITM1 and IFI27 levels were found to be increased upon CDH1a overexpression. Importantly, CDH1a was found to be de novo expressed in gastric cancer cell lines when compared to normal stomach.
Results: In this sense we have searched for additional CDH1 transcripts arising from intron 2. From the four found, one (CDH1a) was demonstrated to be tissue specific and to be translated in vivo. When overexpressed in an E-cadherin negative context CDH1a replaced the canonic protein functions
Conclusions: We have demonstrated, for the first time, transcripts arising from CDH1 intron 2. One of these, CDH1a, was found to modulate E-cadherin function representing a novel mechanism underlying invasion and angiogenesis in epithelial cancers and opening the way for novel therapeutic approaches.

overall_design: Total RNA obtained from human gastric tubular adenocarcinoma Mkn28 cell line. Three independent replicas of each conditions(i.e  pLenti transduced cell lines overexpressing CDH1a , pLenti with empty vector and pLenti transduced cell lines overexpressing wild type CDH1) has been employed.

first: Hugo

last: Pinheiro

middle: D


title: PGE2-induced OSM expression

city: Columbus

first: Sashwati

last: Roy

state: OH

department: Surgery

institute: Ohio State University

summary: The objective of the study was to compare the wound macs with corresponding macs derived from peripheral blood monocytes (MDMs). Wound site macrophage (wound macs were isolated from human subjects with chronic wounds. Matching blood monocyte derived macrophages (MDM) were obtained from same subjects. Transcriptome profiling (GeneChip, Affymetrix) was performed.The expression values of genes were normalized using global scaling approach.

overall_design:
Blood monocyte derived macrophages or human wound macrophages were isolated and transcriptome analysis was performed using affymetrix gene chip analysis.

Group -1 MDMs (n=3)
Mac-1
Mac-2
Mac-3
Group -2 Wound macs (n=3)
Wmac-1
Wmac-2
Wmac-3

first: Kasturi

last: Ganesh

first: Chandan

last: Sen

first: Amitava

last: Das


title: Blood gene expression signatures distinguish autism spectrum disorders from controls

status: Public on Aug 01 2012

city: Boston

first: Sek Won

last: Kong

state: MA

address: 300 Longwood Avenue

department: Informatics Program

institute: Boston Children's Hospital

summary: Autism Spectrum Disorder (ASD) is a common pediatric cognitive disorder with high heritability. Yet no single genetic variant has accounted for more than a small fraction of cases. We sought to determine whether we could classify patients as having ASD vs. controls solely based on a multi-gene expression profiling of their peripheral blood cells.

overall_design: To test whether peripheral blood gene expression profiles could be used as a molecular diagnostic tool for distinguishing ASD from controls, we performed peripheral blood gene expression profiling on 170 patients with ASD and 115 controls collected from Boston area hospitals.  We developed a 55-gene prediction model with a sample cohort of 66 male patients with ASD and 33 age-matched male controls using cross-validation strategy.  Subsequently, 104 ASD and 82 controls were recruited and used as first and second validation sets, respectively.

first: SekWon

first: Christin

last: Collins

first: Ingrid

middle: A

last: Holm

first: Louis

last: Kunkel

first: Isaac

middle: S

last: Kohane


title: Expression of Data from EHMT1 siRNA transfected HeLa cell treated with TNF

status: Public on Jul 31 2012

city: pasadena

first: chee-kwee

last: ea

state: CA

address: 1200 E california blvd

department: biology

institute: california institute of technology

summary:
We used microarrays to detail the global programme of gene expression to identify TNF-induced genes that are negatively regulated by EHMT1
Transcriptional homeostasis relies on the balance between positive and negative regulation of gene transcription. Methylation of histone H3 lysine 9 (H3K9) is commonly correlated with gene repression. Here, we report that a euchromatic H3K9 methyltransferase, EHTM1, functions as a negative regulator in both the NF-κB- and type I interferon-mediated gene induction pathways. EHMT1 catalyzes H3K9 methylation at promoters of NF-κB target genes. Moreover, EHMT1 interacts with p50 and, surprisingly, p50 appears to repress the expression of type I interferon genes and genes activated by type I interferons by recruiting EHMT1 to catalyze H3K9 methylation at their promoter regions. Silencing the expression of EHMT1 by RNA interference enhances expression of a subset NF-κB regulated genes, augments interferon production and augments antiviral immunity.

overall_design: HeLa cells were double-transfected with control or EHMT1 specific siRNAs. The cells were then treated with or without TNFa for 2 hours followed by RNA extraction and hybridization on Affymetrix microarrays.

first: Chee-Kwee

last: Ea

first: Shengli

last: Hao

first: Kok-Siong

last: Yeo

first: David

last: Baltimore


title: Comparative expression profiling identifies differential roles  for Myogenin and p38α MAPK signaling in myogenesis

city: Ottawa

first: Theodore

last: Perkins

address: 501 Smyth Rd.

department: Cellular and Molecular Medicine

institute: Ottawa Hospital Research Institute

summary: Mitogen activated protein kinase (MAPK) signaling regulates differentiation of many cell types. During myogenesis in particular, p38a MAPK (MAPK14) phosphorylates multiple transcriptional regulators to modulate muscle-specific gene expression. Among the p38a MAPK modulated genes is the muscle-specific transcriptional regulator Myogenin (Myog) that is also essential to complete the muscle differentiation program, and while it is known that both p38a MAPK and Myog are critically required for myogenesis, the individual contribution of each of these proteins is poorly defined. Here we show that Myog expression (in the absence of p38a MAPK signaling) is sufficient to establish expression of many late markers of muscle differentiation and to mediate cell migration. However, Myog expression alone did not led to the formation of multinucleated muscle cells, highlighting a critical role for p38a MAPK in myoblast fusion. Using comparative microarray analysis we identified p38a MAPK-dependent genes that are not regulated by Myog

overall_design: We generated a stable C2C12-derived cell line (C2i-Myog) that expresses a Doxycycline (Dox)-inducible cDNA encoding Flag-tagged Myog. In this system, the chemical induction of exogenous Myog (Dox) combined with the pharmacological inhibition of p38a/b MAPK signaling by SB203580 (SB) would allow us to assess the functional contribution of these two pathways during myogenesis

first: F

middle: J

last: Dilworth

first: Carol

last: Perez-Iratxeta

first: Qi

middle: C

last: Liu


title: The National NeuroAIDS Tissue Consortium Brain Gene Array: Two types of HIV-associated neurocognitive impairment

city: Omaha

first: Jessica

last: Winkler

address: 985800 Nebraska Medical Center- DRC I

department: Pharmacology and Experimental Neuroscience

institute: University of Nebraska Medical Center

summary: Finding the differences in gene expression in three regions of the brain, basal ganglia, white matter, and frontal cortex, in normal, HIV infected, HIV infected with neurocognitive impairment, and HIV infected with both neurocognitive impairment and encephalitis patients.

overall_design: Twenty-four human subjects in four groups were examined A) Uninfected controls; B) HIV-1 infected subjects with no substantial neurocognitive impairment (NCI); C) Infected with substantial NCI without HIV encephalitis (HIVE); D) Infected with substantial NCI and HIVE. RNA from neocortex, white matter, and neostriatum was processed with the Affymetrix® array platform.

first: Benjamin

middle: B

last: Gelman


title: KDM4B- and KDM6B-regulated genes in human mesenchymal stem cell osteogenic differentiation

city: Los Angeles

first: Bo

last: Yu

address: CHS 33-030, 10833 Le Conte Ave,

institute: UCLA School of Dentistry

summary: To investigate how histone demethylases KDM4B and KDM6B may be involved in osteogenic commitment of mesenchymal stem cells (MSCs), we performed gene expression profiling and comparison on control, KDM4B- and KDM6B-knockdown MSCs at different stages of osteogenic differentiation.

overall_design: Human MSCs infected with scramble shRNAs, shRNAs against KDM4B or KDM6B are treated with BMP4/7 for 0, 4 and 24hrs. Total RNA were extracted from these 9 samples.

first: Cun-Yu

last: Wang


title: Global transcriptional response of E. coli to the presence and absence of bile salts

city: Bozeman

first: Kate

last: McInnerney

state: MT

address: 109 Lewis Hall

department: Microbiology

institute: Montana State University

summary:
Unlike many other types of diarrheagenic bacteria that act primarily in the small intestine, O157:H7 expresses virulence primarily in the large intestine. In this study, microarray analysis is employed to examine the transcriptional response of O157:H7 to bile treatment, to gain insight into how bile affects virulence and whether bile might be temporally defending the small intestine against virulence by these bacteria.

Keywords: Expression profiling of two different growth conditions

overall_design: Two groups of three replicates were used:  E.coli O157:H7 grown in Luria broth with or without 0.8% bile salts

first: Steve

last: Hamner

first: Kerry

last: Williamson

first: Michael

last: Franklin

first: Timothy

last: Ford


title: INTEGRATIVE ONCOGENOMIC AND HIGH-THROUGHPUT SEQUENCING ANALYSES OF THE COMMONLY DELETED REGION IN CHROMOSOME 7q32 IN SPLENIC MARGINAL ZONE LYMPHOMA

city: Pamplona

first: Vicente

middle: Jose

last: Fresquet

state: Navarra

address: Av Pio XII 55

department: Division of Oncology

institute: Center for Applied Medical Research (Cima)

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

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

overall_design: Refer to individual Series


title: Time-course effect of estradiol and ERa17p on Early Gene expression in MDA-MB-231 cells

city: Heraklion

first: George

last: Notas

address: PO BOX 2208

country: Greece

institute: University of Crete

summary: ERα17p is a synthetic peptide corresponding to the sequence P295LMIKRSKKNSLALSLT311 of the estrogen receptor alpha (ERα) and initially synthesized to mimic its calmodulin binding site. ERα17p was subsequently found to elicit estrogenic responses in E2-deprived ERα-positive breast cancer cells, increasing proliferation and E2-dependent gene transcription.  Surprisingly, in E2-supplemented media, ERα17p induced apoptosis and modified the actin network, influencing thereby cell motility. Here, we report that ERα17p induces a massive early (3h) transcriptional activity in breast cancer cell line MDA-MB-231.

overall_design: Cells after a 4h incubation with medium containing 10% charcoal stripped FBS were incubated with or without E2 (10-6M) or ERa17p in RPMI 1640 supplemented with 10% charcoal stripped FBS, for 3 hours. Total RNA was isolated using Nucleospin II columns (Macheray-Nagel, Dttren, Germany), according to the manufacturer’s instructions. RNA was labeled and hybridized according to the Affymetrix protocol (Affymetrix Gene-Chip Expression Analysis Technical Manual), using the HGU133A plus 2 chip, analyzing a total of 54675 transcripts. Signals were detected by an Affymetrix microarray chip reader.

first: Marilena

last: Kampa

first: Elias

last: Castanas


title: Time-course effect of estradiol and ERa17p on Early Gene expression in SKBR3 cells

summary: ERα17p is a synthetic peptide corresponding to the sequence P295LMIKRSKKNSLALSLT311 of the estrogen receptor alpha (ERα) and initially synthesized to mimic its calmodulin binding site. ERα17p was subsequently found to elicit estrogenic responses in E2-deprived ERα-positive breast cancer cells, increasing proliferation and E2-dependent gene transcription.  Surprisingly, in E2-supplemented media, ERα17p induced apoptosis and modified the actin network, influencing thereby cell motility. Here, we report that ERα17p induces a massive early (3h) transcriptional activity in breast cancer cell lines SKBR3). Remarkably, about 75% of the significantly modified transcripts were also modified by E2, confirming the pro-estrogenic profile of ERα17p. The different ER spectra of the used cell lines allowed us to extract a specific ERα17p signature related to ERα and its variant ERα36. With respect to ERα, the peptide activates nuclear (cell cycle, cell proliferation, nucleic acid and protein synthesis) and extranuclear signaling pathways. In contrast, through ERα36 it exerts inhibitory events on inflammation and cell cycle and inhibition of EGFR signaling. This is the first work reporting ERα36 specific transcriptional effects. The fact that a number ERα17p-induced transcripts is different from those activated by E2 revealed that the apoptosis and actin modifying effects of ERα17p are independent from the ER-related actions of the peptide.


title: Expression data from untreated CLL patients

status: Public on Jul 26 2012

first: andrew

last: greaves

state: ca

address: 3855 Health Sciences Dr

department: Cancer Center

institute: UCSD

summary:
The clinical course of patients with chronic lymphocytic leukemia (CLL) is heterogeneous.  Several prognostic factors have been identified that can stratify patients into groups that differ in their relative tendency for disease progression and/or survival.  Here, we pursued a subnetwork-based analysis of gene expression profiles to discriminate between groups of patients with disparate risks for CLL progression.
From an initial cohort of 130 patients, we identified 38 prognostic subnetworks that could predict the relative risk for disease progression requiring therapy from the time of sample collection, more accurately than established markers.  The prognostic power of these subnetworks then was validated on two other cohorts of patients.  We noted reduced divergence in gene expression between leukemia cells of CLL patients classified at diagnosis with aggressive versus indolent disease over time.  The predictive subnetworks vary in levels of expression over time but exhibit increased similarity at later timepoints prior to therapy, suggesting that degenerate pathways apparently converge into common pathways that are associated with disease progression.  As such, these results have implications for understanding cancer evolution and for the development of novel treatment strategies for patients with CLL.

overall_design:
Leukemia cells were isolated from blood samples of CLL patients enrolled in the MILE study who had not received prior therapy for CLL, as per the MILE protocol22.  Expression data were gathered from samples found to have a CLL cell population with greater than 90% CD5+CD19+, as accessed via flow cytometry.  Total RNA was isolated and hybridized to Affymetrix HG-U133+2 GeneChips.
This study is about the time to treatment, ie., prognosis instead of diagnosis.

first: Han-Yu

last: Chuang

first: Laura

last: Rassenti

first: Thomas

last: Kipps


title: Time-course effect of estradiol and ERa17p on Early Gene expression in human breast cancer cell lines


title: Expression data of cartiliage from CBA and STR/ORT mice

first: Andrew

last: Pitsilides

address: Royal College Street

department: Comparative Biomedical Sciences

institute: The Royal Veterinary College

summary: Affymetrix Mouse Gene 1.0 ST Array profiles were generated from acticular cartilage derived from CBA and Str/ort mice at three ages (8W, 18W, 40W), corresponding to stages prior to, at and late after natural osteoarthritis (OA) onset in OA-prone Str/ort mice.

overall_design: Two strains of mice, three ages, and three to four biological replicates.

first: B

last: Poulet

first: V

last: Ulici


title: Transcriptional Programs Controlling Perinatal Lung Maturation

city: Cincinnati

first: Yan

last: Xu

address: 3333 Burnet Ave

institute: Cincinnati Children's Hospital Medical Center

summary: In this study, time dependent genome wide lung mRNA profiling changes were assessed using C57BL/6J and A/J mice. Through comprehensive bioinformatics and functional genomics analyses, we identified both temporal and strain dependent gene expression patterns, systemically mapped key regulators, bioprocesses, and transcriptional networks controlling lung maturation, providing the basis for new therapeutic strategies to enhance lung function in preterm infants.

overall_design: In this study, we designed a genome-wide mRNA expression time-course study from E15.5 to Postnatal Day 0 (PND0) using lung RNAs from C57BL/6J and A/J mice that differ significantly in gestational length.

first: Yanhua

last: Wang

first: Valerie

last: Besnard

first: Machiko

last: Ikegami

first: Susan

middle: E

last: Wert

last: Murray

first: Leah

middle: R

last: Donahue

first: Jeffrey

last: Whitsett


title: Suppression of major attributes of tumor-initiating cells through epithelial-mesenchymal transition

status: Public on Jul 24 2012

city: Barcelona

first: Juanjo

last: Lozano

address: C/ Rosselló 153

department: Plataforma de Bioinformatica

institute: CIBEREHD

summary: Malignant progression in cancer has been associated with the emergence of populations of tumor-initiating cells (TIC) endowed with capabilities for unlimited self-renewal, survival under stress and establishment of distant metastases. Additionally, the acquisition of invasive properties driven by the genetic program known as epithelialmesenchymal transition (EMT) may be an essential step in the evolution of neoplastic cells into fully metastatic populations. A widely accepted paradigm is that EMT potentiates tumor cell self-renewal and metastatic behaviour. Here we describe a cellular model in which a clonal population enriched in TIC expresses a genetic program distinct from a second population with traits of stable EMT, and in which both populations cooperate for enhanced local invasiveness and metastasis. Induction of the TIC-enriched population to undergo EMT by several stimuli or by constitutive overexpression of the transcription factor SNAI1 engaged a mesenchymal program while suppressing the CSC program. This suggests that TIC and EMT, contrary to current paradigms, correspond to alternative states. Furthermore, diffusible factors secreted by the population with EMT traits also induced mesenchymal reprogramming of the population enriched in CSCs. Local invasiveness in vitro and lung colonization in vivo of the TIC-enriched population was enhanced by co-injection with the EMT-trait population, and expanded the range of organs to which it metastasized. Thus, in our model, relatively stable TIC and EMT phenotypes reflect alternative genetic programs expressed by distinct clonal populations. We also suggest that dynamic cooperation between tumor subpopulations displaying either TIC or EMT traits may be a general mechanism driving local invasiveness and metastasis.

overall_design: The complete database comprised the expression measurements of 54 675 genes for PC-3/Mc (n=3) and PC-3/S (n=3)

first: A

last: Celià-Terrassa

first: O

last: Meca-Cortés

first: F

last: Mateo

last: de Paz

first: N

last: Rubio

last: Arnal-Estapé

last: Ell

first: R

last: Bermudo

last: Díaz

first: M

last: Guerra-Rebollo

first: J

first: C

last: Estarás

last: Ulloa

first: D

last: Álvarez-Simón

last: Milà

last: Vilella

last: Paciucci

last: Martínez-Balbás

middle: G

last: de Herreros

last: Gomis

first: Y

last: Kang

last: Blanco

first: P

last: Fernández

first: T

last: Thomson


title: mRNA expression data from lymph node tumors from IL10R2-/- patients

status: Public on Jul 23 2012

city: Marseille

first: Emilie

last: Mamessier

address: case 906

country: France

institute: CIML

summary: Gene expression profiles were used to identify coordinately regulated gene sets and pathways actuvated in tumors occuring in IL10R2-/- patients.

overall_design: Frozen tumor biopsies and paired peripheral blood from 2 children with IBD and 2 age-matched tonsil were obtained. Cases were ascertained at the Necker hospital. Sufficient RNA for hybridization to Affymetrix U133 plus 2 arrays was obtained on all cases.

first: B

last: Nevens

first: E


title: Expression data from mouse peritoneal macrophages

city: hangzhou

first: weilin

last: chen

state: zhejiang

address: yuhangtang road 866

institute: zhejiang university

summary:
Biologic functions involved in innate immune response of macrophages rely on the precise regulation of kinds of immune molecular. In the virus infection procession, the macrophages are activated following a tightly controlled genetic programme where specific sets of genes are up-regulated or down-regulated.
We used microarrays to detail the global programme of gene expression underlying VSV infection and identified distinct classes of up-regulated and down-regulated genes during this process.

overall_design: Mouse peritoneal macrophages were selected with/without  VSV infection for 8 hours for RNA extraction and hybridization on Affymetrix microarrays. We sought to obtain expression profiles. We selected macrophages according to VSV infection at two time-points: uninfected macrophage(control) and VSV infected for 8 hour macrophages(VSV).

first: Weilin

last: Chen


title: EMT inducers catalyze malignant transformation of mammary epithelial cells and drive tumorigenesis towards claudin-low tumors [human]

city: Lyon

first: stéphane

last: ansieau

address: 28 rue Laennec

department: Centre Léon Bérard

institute: Inserm U590

summary: The newly identified claudin-low subtype of cancer is believed to represent the most primitive breast malignancies, having arisen from transformation of an early epithelial precursor with inherent stemness properties and metaplastic features. Challenging this hypothesis, we show both in vitro and in vivo that transcription factors inducing epithelial-mesenchymal transition can drive the development of claudin-low tumors from differentiated mammary epithelial cells, by playing a dual role in cell transformation and dedifferentiation.

overall_design: Human mammary epithelial cells (HMEC) were sequentially immortalized by hTert (HMEC-hTert), transduced with Twist1 or Zeb2 or Zeb1 and then with H-RasG12V.  The gene expression profiles of the resulting HMEC-hTert-Twist1+Ras, HMEC-hTert-Zeb1+Ras and HMEC-hTert-Zeb2+Ras cell lines were defined. HMEC-hTert-Twist1+Ras and HMEC-hTert-Zeb2+Ras cell lines were additionally cultured in presence of TGFÃ? and their gene expression profiles were determined. The parental HMEC-hTert, the luminal MCF7 and  the basal B MDMB157cell lines were used as controls.

first: Anne-Pierre

last: Morel

first: Stéphane

last: Ansieau

first: Alain

last: Puisieux

first: Anne

last: Wierinckx

first: Joël

last: Lachuer

first: Nicolas

last: Nazaret

first: Séverine

last: Croze

first: Christelle

last: Lamblot


title: EMT inducers catalyze malignant transformation of mammary epithelial cells and drive tumorigenesis towards claudin-low tumors


title: INTEGRATIVE ONCOGENOMIC AND HIGH-THROUGHPUT SEQUENCING ANALYSES OF THE COMMONLY DELETED REGION IN CHROMOSOME 7q32 IN SPLENIC MARGINAL ZONE LYMPHOMA (expression)

first: Vicente

last: Fresquet

summary: Using high-resolution genomic microarray analysis, a distinct genomic profile was defined in 114 samples from patients with splenic marginal zone lymphoma (SMZL). Notably, deletion or uniparental disomy of chromosome 7q were detected in 39% of SMZLs but in only 9 of 170 (5%) mature B-cell lymphomas (p<10-6). The presence of unmutated IgVH genes, genomic complexity, 17p13-P53 deletion and 8q gain including MYC gene, but not 7q deletion, were correlated with shorter overall survival. Extensive mapping analyses narrowed down the commonly deleted region to 2.7 Mb. in 7q32.1-q32.2 from SND1 to COPG2 genes. High-throughput sequencing analysis of the 7q32 deleted segment in SMZL cells did not identify bi-allelic deletions, insertions or clear pathogenic mutations, but detected six single nucleotide changes in IRF5 (n=2), TMEM209 (n=2), CALU (n=1) and ZC3HC1 (n=1). Comparative expression analysis found that IRF5, TMEM209 and CALU genes had down-regulated expression in lymphomas with 7q32 deletion vs. non-deleted tumors. Ectopic expression of IRF5 in marginal-zone lymphoma cells decreased cell proliferation and induced apoptosis. These results indicate that small deletions, insertions and/or point mutations inactivating genes within 7q32 are not common events in SMZL. Further studies are required to evaluate the putative role of IRF5 in SMZL pathogenesis.

overall_design: 9 samples.  6 patient samples with 7q32 deletion and 3 patient samples without 7q32 deletion. Splenic Marginal Zone Lymphoma patient samples with 7q32 deletion  vs. Splenic Marginal Zone Lymphoma patient samples without 7q32 deletion

first: Eloy

middle: F

last: Robles

first: Anton

last: Parker

first: Javier

last: Martinez-Useros

first: Maria

last: Mena

first: Raquel

last: Malumbres

first: Lorena

last: Fontan

first: Jose

middle: I

last: Martinez-Ferrandis

first: Xabier

last: Aguirre

first: Susana

last: Catarino

first: David

last: Arteta

first: Lourdes

last: Osaba

first: Manuela

last: Mollejo

first: Jesus

middle: M

last: Hernandez-Rivas

last: Calasanz

first: Masanori

last: Daibata

first: A

last: Karpas

first: Martin

last: Dyer

first: Felipe

last: Prosper

first: Esperanza

last: Vizcarra

first: Miguel

last: Piris

last: Oscier

last: Martinez-Climent


title: Expression data from human melanoma specific T cell clones

status: Public on Jul 20 2012

city: Bethesda

first: Udai

last: Kammula

state: MD

address: 9000 Rockville Pike

institute: NIH

summary:
Adoptive immunotherapy using ex vivo expanded tumor reactive lymphocytes can mediate durable cancer regression in selected melanoma patients. Analyses of these trials have associated the in vivo engraftment ability of the transferred cells with their anti-tumor efficacy. Thus, there is significant clinical interest in the prospective isolation of tumor specific T cells that can reliably persist after transfer. Animal studies have suggested that central memory CD8+ T cells (TCM) have divergent capabilities including effector differentiation to target antigen and stem cell-like self renewal that enable long term survival after adoptive transfer. In this study, we sought to isolate human melanoma specific TCM to define their in vivo fate and function after autologous therapeutic transfer to metastatic patients. To facilitate the high throughput identification of these rare cells from patients, we report that TCM have a defined stoichiometric production of IL-2 and IFN-g mRNA after antigen stimulation. Melanoma specific T cells screened for high relative IL-2 production possessed a TCM phenotype and superior in vitro proliferative capacity compared to cells with low IL-2 production. To investigate in vivo effector function and self renewal capability, melanoma specific TCM underwent in vitro expansion and differentiation into lytic effector clones and then were adoptively transferred back into their hosts. These clones targeted skin melanocytes in all five patients and persisted long term and reacquired parental TCM attributes in four patients after transfer. These findings demonstrate the favorable engraftment fitness for human TCM-derived clones, but further efforts to improve their anti-tumor efficacy are still necessary.
We used microarrays to compare the resting gene expression profile of melanoma specific CD8+ T cell clones that were derived from either High IL-2:IFN index precursors or Low IL-2:IFN index precursors.

overall_design: Three melanoma specific effector clones were derived from parental cells that possessed a high IL-2:IFN index from three independent patients with metastatic melanoma. Two melanoma specific effector clones were derived from parental cells that possessed a low IL-2:IFN index from two independent patients with metastatic melanoma. We used microarrays to compare the resting gene expression profile of the CD8+ T cell clones that were derived from either high IL-2:IFN index precursors or low IL-2:IFN index precursors.