title: Suppression of T Cell Activation and Collagen Accumulation by an Anti-IFNAR1 mAb, Anifrolumab, in Adult Patients with Systemic Sclerosis

city: Gaithersburg

first: Xiang

address: One MedImmune Way

department: Translational Sciences

institute: MedImmune

summary: Type I IFNs are implicated in the pathophysiology of systemic sclerosis (SSc). Recently, a Phase I open-label trial was conducted with an anti-IFNAR1 receptor antibody (anifrolumab) in adult SSc patients. In this study, we aim to assess the downstream effects of anifrolumab and elucidate the role of type I IFN in SSc. Serum proteins and extracellular matrix (ECM) markers were measured in relation to IFN pathway activation status and SSc disease activity. Our results demonstrated a robust overexpression of multiple serum proteins in SSc patients, particularly those with an elevated baseline type I IFN gene signature. Anifrolumab administration was associated with significant downregulation of T cell–associated proteins and upregulation of type III collagen degradation marker. Whole-blood and skin microarray results also indicated the inhibition of T cell receptor and ECM–related transcripts by anifrolumab. In summary, our study demonstrates suppressive effects of anifrolumab on T cell activation and collagen accumulation through which tissue fibrosis may be reduced in SSc patients. The relationship between these peripheral markers and the clinical response to anifrolumab may be examined in larger double-blind, placebo-controlled trials.

overall_design: PAXGene whole blood tubes were collected from 29 SSc subjects at baseline and day 56 after anifrolumab administration, and skin biopsies were procured from 10 SSc subjects at baseline and day 28 after multiple-doses of anifrolumab administration.

first: Brandon

last: Higgs


title: Hematopoietic cells-derived Jnk1 is crucial for chronic inflammation and carcinogenesis in an experimental model of liver injury

status: Public on Jun 22 2015

city: Wageningen

first: Guido

last: Hooiveld

address: HELIX, Stippeneng 4

department: Div. Human Nutrition & Health

country: Netherlands

institute: Wageningen University

summary: Chronic liver injury triggers complications such as liver fibrosis and hepatocellular carcinoma (HCC), which are associated with alterations in distinct signaling pathways. Of particular interest is the interaction between mechanisms controlled by IKKγ/NEMO, the regulatory IKK subunit, and Jnk activation for directing cell death and survival. In the present study, we aimed to define the relevance of Jnk in hepatocyte-specific NEMO knockout mice (NEMOΔhepa), a genetic model of chronic inflammatory liver injury. We generated global Jnk1-/-/NEMOΔhepa and Jnk2-/-/NEMOΔhepa mice by crossing NEMOΔhepa mice with Jnk1-/- and Jnk2-/- animals, respectively, and examined the progression of chronic liver disease. Moreover, we investigated the expression of Jnk during acute liver injury, evaluated the role of Jnk1 in bone marrow-derived cells, and analyzed the expression of NEMO and pJnk in human diseased-livers. Deletion of Jnk1 significantly aggravated the progression of liver disease, exacerbating apoptosis, compensatory proliferation and carcinogenesis in NEMOΔhepa mice. Jnk2-/-/NEMOΔhepa showed increased RIP-1 and RIP-3 expression and hepatic inflammation. Jnk1 in hematopoietic cells rather than hepatocytes had an impact on the progression of chronic liver disease in NEMOΔhepa livers. These findings are of clinical relevance since NEMO expression was down-regulated in hepatocytes of patients with HCC whereas NEMO and pJnk were expressed in a large amount of infiltrating cells. While Jnk1 is protective in NEMOΔhepa-depleted hepatocytes, Jnk1 in hematopoietic cells rather than hepatocytes is a crucial driver of hepatic injury. These results elucidate the complex function of Jnk in chronic inflammatory liver disease.

overall_design: Livers from global knockout mice for Jnk1 (Jnk1-/-) and Jnk2 (Jnk2-/- ), and double-knockout mice for Jnk1/NEMO (global Jnk1-/-/NEMOΔhepa) and Jnk2/NEMO (global Jnk2-/-/NEMOΔhepa), were subjected to gene expression profiling.

first: Francisco

middle: J

last: Cubero

first: Gang

last: Zhao

first: Yulia

middle: A

last: Nevzorova

first: Maximilian

last: Hatting

first: Malika

last: Al Masaoudi

first: Julien

last: Verdier

first: Jin

last: Peng

first: Frederik

middle: M

last: Schaefer

first: Nadine

last: Hermanns

first: Mark

middle: V

last: Boekschoten

first: Christoph

last: Grouls

first: Nikolaus

last: Gassler

first: Fabian

last: Kiessling

first: Michael

last: Muller

first: Roger

last: Davis

first: Christian

last: Liedtke

last: Trautwein


title: Genome-wide analysis of gene methylation by effect of proton beam on breast cell line MCF-7

status: Public on Jun 19 2015

city: Gyungkido

first: Byungtak

last: Kim

address: Siksadong

country: South Korea

institute: Dongguk University

type: Methylation profiling by genome tiling array

summary: Genome wide DNA methylation profiling of estrogene receptor postive breast cancer cell line MCF-7, treating proton beam. The Illumina Infinium Human Methylation 450k Bead chip was used to obtain DNA methylation profiles across approximately 450,000 CpGs. This profiling indicates that proton beam induces epigenetic and cellular changes.

overall_design: Genomic DNA obtained from  MCF-7 effected by proton beam

first: Sun


title: Comprehensive genomic analysis of relapse neuroblastoma [methylation]

city: Essen

first: Alexander

last: Schramm

address: Hufelandstr. 55

department: Childrens Hospital

country: Germany

institute: University Hospital Essen

summary:
Relapse neuroblastoma were characterized by sequencing, gene expression, arrayCGH and genome-wide methylation.
This data set contains genome-wide methylation data.

overall_design: Array from tumours at relapse were compared to pretreatment tumours and corresponding normal samples.

first: Peter

last: Schmezer


title: Methyome profiling in serrated carcinoma

status: Public on Jun 21 2015

city: Valencia

first: Patricia

last: Sebastian-Leon

state: Valencia

address: Av Autopista del Saler, 16

department: Bioinformatics and Genomics

country: Spain

institute: CIPF

summary: Serrated adenocarcinoma (SAC) is a recently recognized colorectal cancer (CRC) subtype accounting for 7.5 - 8.7% of CRCs. It has been shown that SAC has a worse prognosis and has different molecular and immunohistochemical features compared to conventional carcinoma (CC) but, to date, there is no study analysing its methylome profile. We have investigated the methylation status of 450,000 CpG sites using the Infinium Human Methylation 450 BeadChip array in 103 colorectal specimens from Spanish and Finnish patients. The comparison between the epigenetic signature of 36 SACs and 34 matched CCs was established with the aim of identifying the functions which characterize SAC biology and also the most differentially methylated genes for subsequent validatation by pyrosequencing, methylation-specific PCR, qPCR and immunohistochemistry, including additional cases. Microarray data showed a higher representation of morphogenesis-, neurogenesis-, cytoskeleton- and vesicle-transport-related functions and also significant differential methylation of 15 genes, including the iodothyronine deiodinase DIO3 and the forkhead family transcription factor FOXD2 genes which were validated at the CpG, mRNA and protein level. A quantification study of the methylation status of CpG sequences in FOXD2 demonstrated a novel region controlling gene expression. Moreover, differences in these markers were also evident when comparing SAC with CRC showing molecular and histological features of high level microsatellite instability. This methylome study demonstrates that SAC has a distinct epigenetic regulation pattern resulting in different biological functions and that DIO3 and FOXD2 might be molecular targets for a specific histology-oriented treatment of CRC.

overall_design: HumanMethylation450K BeadChip (Illumina, Inc, San Diego, CA), using Infinium HD Methylation assay for genome-wide DNA methylation screening, was employed. In brief, genomic DNA (1000 ng) from each sample was bisulfite converted with the EZ DNA Methylation Kit  (Zymo Research, Orange, CA) according to the manufacturer´s recommendations. Bisulfite-treated DNA was isothermally amplified at 37°C (20-24h) and the DNA product was fragmented by an endpoint enzymatic process, then precipitated, resuspended, applied to an Infinium Human Methylation450K BeadChip (Illumina, San Diego, CA, USA) and hybridized at 48°C (16-24h). The fluorescently-stained chip was imaged by the Illumina i-SCAN and Illumina's Genome Studio program (Methylation Module) was used to analyze BeadArray data to assign site-specific DNA methylation β-values to each CpG site.

first: Pablo

last: Conesa-Zamora

first: José

last: García-Solano

first: María

last: del Carmen Turpin

last: Sebastián-León

first: Daniel

last: Torres-Moreno

first: Eduardo

last: Estrada

first: Anne

last: Tuomisto

first: Jamie

last: Wilce

first: Markus

last: Mäkinen

first: Miguel

last: Pérez-Guillermo

first: Ana

last: Conesa


title: Comprehensive genomic analysis of relapse neuroblastoma

type: Genome variation profiling by genome tiling array

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

overall_design: Refer to individual Series


title: mRNA expression data from BCR-ABL, MYC and CD22DE12 transgenic mouse models

status: Public on Jun 25 2015

city: St. Peter

first: Sanjive

last: Qazi

state: MN

address: 800 west College Av

department: Biology

country: USA

institute: Gustavus Adolphus College

summary: Leukemic splenocytes from these commercial transgenic mice that developed fatal leukemia with massive splenomegaly were isolated at the time of the necropsy and subjected to gene expression profiling and phosphoprotein profiling in side by side comparison with CD22DE12-Tg BPL or CD22DE12_BCR-ABL double transgenic cells.

overall_design: Mouse leukemia cells were isolated from markedly enlarged spleens of CD22DE12-Tg (N=2), BCR-ABL-Tg (N=2), Eµ-MYC Tg mice (N=2) and Splenocytes from wildtype healthy C57BL/6 mice served as controls (N=4).

first: Fatih

last: Uckun


title: Stromal transcriptional profiles reveal hierarchies of anatomical site, serum response and disease and identify disease specific pathways

city: Liverpool

first: Philipp

last: Antczak

state: Merseyside

address: Crown Street

country: United Kingdom

institute: University of Liverpool

summary: Synovial fibroblasts in persistent inflammatory arthritis have been suggested to have parallels with cancer growth and wound healing, both of which involve a stereotypical serum response program. We tested the hypothesis that a serum response program can be used to classify diseased tissues, and investigated the serum response program in fibroblasts from multiple anatomical sites and two diseases. To test our hypothesis we utilized a bioinformatics approach to explore a publicly available microarray dataset including RA, OA and normal synovial tissue, then extended those findings in a new microarray dataset representing matched synovial, bone marrow and skin fibroblasts cultured from RA and OA patients undergoing arthroplasty. The classical fibroblast serum response program discretely classified RA, OA and normal synovial tissues. Analysis of low and high serum treated fibroblast microarray data revealed a hierarchy of control, with anatomical site the most powerful classifier followed by response to serum and then disease. In contrast to skin and bone marrow fibroblasts, exposure of synovial fibroblasts to serum led to convergence of RA and OA expression profiles. Pathway analysis revealed three inter-linked gene networks characterising OA synovial fibroblasts: Cell remodelling through insulin-like growth factors, differentiation and angiogenesis through β3 integrin, and regulation of apoptosis through CD44. We have demonstrated that Fibroblast serum response signatures define disease at the tissue level, and that an OA specific, serum dependent repression of genes involved in cell adhesion, extracellular matrix remodelling and apoptosis is a critical discriminator between cultured OA and RA synovial fibroblasts.

overall_design: Fibroblasts were isolated from synovium, bone marrow and skin tissue samples taken at the time of knee or hip replacement surgery from 12 rheumatoid arthritis patients meeting the 1987 ACR criteria and 6 osteoarthritis patients diagnosed on the basis of characteristic x-ray findings and the absence of features suggestive of inflammatory arthritis. Only one hip sample was present in either disease group. Fibroblasts were maintained in fibroblast medium (consisting of 81.3% RPMI 1640, 10% FCS, 0.81x MEM non-essential amino acids, 0.81mM sodium orthopyruvate, 1.62mM glutamine, 810U/ml penicillin and 81μg/ml streptomycin) at 37°C in a humidified 5% CO2 atmosphere.

first: Andrew

last: Filer

first: Greg

middle: N

last: Parsonage

first: Holly

last: Legault

first: Margot

last: O'Toole

first: Mark

last: Pearson

last: Thomas

first: Dagmar

last: Scheel-Toellner

first: Karim

last: Raza

first: Christopher

middle: D

last: Buckley

first: Francesco

last: Falciani


title: Phosphoproteome and gene expression analysis in leukemic transgenic mouse models

type:
Expression profiling by array
Protein profiling by protein array

platform_organism:
Homo sapiens
Mus musculus
Rattus norvegicus


title: Gene expression profiles of human immature dendritic cells co-cultivated with Aspergillus fumigatus, Candida albicans and LPS for 6h

status: Public on Jun 23 2015

city: Würzburg

first: Kristin

last: Czakai

address: Josef-Schneider-Straße 2

department: Department of Internal Medicine II

institute: University Hospital of Würzburg

summary: In a whole-transcriptome study, cellular responses of DCs confronted with the fungi A. fumigatus, C. albicans or the bacterial cell wall component LPS were investigated. Therefore DCs of four independent donors were analyzed after 6  hours co-culture with A. fumigatus, C. albicans and LPS by Affymetrix whole genome expression arrays. In general, transcriptomic analysis revealed a clustering of the A. fumigatus and C. albicans stimulated DCs. However, LPS and fungi-dependent gene expression showed more common similarities compared to the untreated control.  Stimulation with LPS induced a differential regulation of 2793 genes after 6h, while confrontation with A. fumigatus and C. albicans resulted in 743 and 974 differentially regulated genes, respectively. Kruppel-like factor 4 (KLF4) was identified as the only transcription factor that was down-regulated in DCs by both fungi but induced by stimulation with LPS.

overall_design: Human DCs were generated from 4 independent, healthy blood donors. moDCs were either left untreated or co-cultivated  with Aspergillus fumigatus 46645 germ tubes or Candida albicans SC5314 (MOI1) and or LPS (1µg/ml) for 6h.

first: Ines

last: Leonhard


title: Expression data from human PBMC induced by mixed Congeners of PCBs at Human equivalence

city: Washington DC

first: Sisir

middle: K.

last: Dutta

state: DC

address: 415 College Street, NW

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 and disorders are not fully understood. The knowledge of global gene expression will help us to devlop early disease or disorder biomarkers for PCB induced health effects.
We used microarrays to detail the global gene expression profile underlying the effects of mixed PCB exposure at Slovak Human equivalance Level on human PBMC leading to identification of distinct classes of up-regulated and down-regulated genes and cellular processes.

overall_design: PBMC cells are grown for 48 hours in RPMI 1640 supplemented with 10% FBS and 1X Pennicilllin-Streptromycin with 1.25 mircogram/ml PHA-M and 0.15% (v/v)pokeweed mitogen and 50 microgram Beta-mercaptoethanol.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: Partha

last: Mitra

middle: K

first: Tomas

last: Trnovec

first: Lubica

last: Pulkovicova

first: Eric

middle: P

last: Hoffman

first: Irva

last: Hertz-Picciotto

first: Dean

last: Sonneborn

first: Svetlana

last: Ghimbovschi


title: Genomic profile of fatigued men receiving localized radiation therapy

status: Public on Jun 17 2015

city: Bethesda

first: Leorey

last: Saligan

state: MD

address: 3 Center Drive, Building 3, Room 5E14

department: National Institute of Nursing Research

institute: National Institutes of Health

summary:
Microarray gene expression of peripheral blood of the prostate cancer patients receiving localized external beam radiation therapy (EBRT)
Assay processed at EBRT time points, baseline, midpoint (days 19-21) and endpoint (days 38-42)

overall_design:
Explore the effect of fatigue on gene expression at the three EBRT time points
Citation: Biol. Res. Nurs. (2015 Accepted)

first: Chao-Pin

last: Hsiao

first: Swarnalatha

middle: Y

last: Reddy

first: Mei-Kuang

last: Chen


title: Methylation microarray studies highlight PDGFA expression as a factor in biliary atresia

status: Public on Jun 18 2015

city: Philadelphia

first: Randolph

last: Matthews

address: 3615 Civic Center Blvd

institute: Children's Hospital of Philadelphia

summary: Biliary atresia (BA) is a progressive fibro-inflammatory disorder that is the leading indication for liver transplantation in children.  Although there is evidence implicating genetic, infectious, environmental, and inflammatory causes, the etiology of BA remains unknown.  We have recently reported that cholangiocytes from BA patients showed decreased DNA methylation relative to disease- and non-disease controls, supporting a potential role for DNA hypomethylation in BA etiopathogenesis.

overall_design: In the current study, we examined the methylation status of specific genes in human BA livers using methylation microarray technology.   We found global DNA hypomethylation in BA samples as compared to disease- and non-disease controls at specific genetic loci.  Hedgehog pathway members, SHH and GLI2, known to be upregulated in BA, were both hypomethylated, validating this approach as an investigative tool.  Another region near the PDGFA locus was the most significantly hypomethylated in BA, suggesting potential aberrant expression.  Validation assays confirmed increased transcriptional and protein expression of PDGFA in BA livers.  We also show that PDGF-A protein is specifically localized to cholangiocytes in human liver samples.  Injection of PDGF-AA protein dimer into zebrafish larvae caused biliary developmental and functional defects.  In addition, activation of the Hedgehog pathway caused increased expression of PDGF-A in zebrafish larvae, providing a previously unrecognized link between PDGF and the Hedgehog pathway.  DNA hypomethylation appears to be a specific factor in mediating overexpression of genes associated with BA.   Our findings validate the role of Hedgehog pathway signaling and implicate PDGF as a new candidate for a role in BA pathogenesis.


title: Comparison of the DNA methylation profiles of CD19+ B lymphocytes of a pair of monozygotic twins discordant for common variable immunodeficiency

city: Badalona, Barcelona

first: Esteban

last: Ballestar

state: N/A = Not Applicable

address: Ctra de Can Ruti, Camí de les Escoles s/n

institute: Josep Carreras Research Institute (IJC)

summary: The methylation profiles of bisulfite-modified DNA of CD19+ cells from MZ twins discordant for CVID were compared using the Infinium HumanMethylation450 BeadChips (Illumina, Inc., San Diego, CA,). This platform allows the interrogation of >485,000 methylation sites per sample at single-nucleotide resolution, and comprises an average of 17 CpG sites per gene in the 99% of RefSeq genes. 96% of CpG islands are covered, with additional coverage in CpG island shores and the regions flanking them. The samples were hybridized in the array following the manufacturer’s instructions.

overall_design: Total DNA isolated by standard procedures from CD19+ cells (total B lymphocytes) corresponding to two monozygotic twins discordant for common variable immunodeficiency.

first: Virginia

middle: C

last: Rodríguez-Cortez

first: Lucia

last: del Pino-Molina

first: Laura

last: Ciudad

first: David

last: Gómez-Cabrero

first: Carlos

last: Company

first: Jesper

last: Tegnér

last: Rodríguez-Gallego

first: Eduardo

last: López-Granados


title: Expression Data from DMSO or SRPIN803 treated ARPE-19 cells

city: Kyoto

first: Masatsugu

last: Denawa

address: Yoshida-Konoe-cho, Sakyo-ku

country: Japan

institute: Kyoto University

summary: We used microarrays to evaluate the effect of SRPIN803 on gene expression in ARPE-19 cells.

overall_design: ARPE-19 cells were treated with SRPIN803 (10 µM) or the negative control (0.1% DMSO) for 4 hours for Total RNA isolation and hybridization on Microarray.

first: Satoshi

last: Morooka

first: Kensuke

last: Ninomiya


title: Placental Transcriptomes in the Common Aneuploidies Reveal Critical Regions on the Trisomic Chromosomes and Genome-Wide Effects

city: SAN FRANCISCO

first: Susan

last: Fisher

state: CA

address: 513 PARNASSUS AVE

department: Obstretrics, Gynecology and Reproductive Sciences

institute: UCSF

summary: We profiled gene expression at the maternal-fetal interface during the second trimester of pregnancy (13-22 wks) in trisomy 13 (T13; Patau syndrome, n = 4), trisomy 18 (T18; Edwards syndrome, n = 4), trisomy 21 (T21; Down syndrome, n = 8), and in euploid pregnancies (n = 4). FISH confirmed the ploidy of the samples. Global transcriptional profiling identified differentially expressed transcripts (≥ 2-fold) in T21 (n = 160), T18 (n = 80), and T13 (n = 125). The majority were upregulated. Unexpectedly, most of the misexpressed genes were not located on the relevant trisomic chromosome, suggesting genome-wide dysregulation. A much smaller proportion of the differentially expressed transcripts were encoded on the aneuploid chromosome, also implicating gene dosage (1-5). In T21, <10% of the genes were transcribed from that chromosome, all but one from the Down syndrome critical region (21q21-22), which is postulated to play an important role in the clinical phenotype. For T13 and T18, a higher proportion of the overexpressed genes were located on the trisomic chromosome. In T13, 15% of the upregulated genes were on the affected chromosome; 15 resided on the long arm, 13q11-14. In T18, the percentage increased to 24, 15 of which were also located on the long arm (18q11-22). Our data suggested that the placental (and possibly fetal) phenotypes that are associated with T13, T18 and T21 are driven by the combined effects of genome-wide phenomena and increased gene dosage from critical regions of the triploid chromosome.

first: Katherine

last: Bianco

first: Matthew

last: Gormley

first: Jason

last: Farrell

first: Yan

last: Zhou

first: Oliver

last: Oliverio

first: Hannah

last: Tilden

first: Michael

last: McMaster

last: FIsher


title: Hepatic gene expression in various different lots of chimeric mice with highly humanized liver

city: Tokai-mura

first: Shin-Ichiro

last: Nagatsuka

state: Ibaraki

address: 2117 Muramatsu

department: ADME/Tox Research Institute

institute: Sekisui Medical Co.

summary:
In addition to immunodeficiency, host mice for chimeric mice with highly humanized liver should have hepatic malfunction in order to allow higher replacement rate of human hepatocytes in the liver. Urokinase-type plasminogen activator (uPA) whole gene transfer is often employed to achieve hepatic malfunction in the host mice.
We have established uPA cDNA transfer that is far stable, as compared with traditional whole uPA gene transfer. Hepatic gene expression was quite similar between whole uPA gene transfer and uPA cDNA transfer after transplantation of the same lot of human hepatocyte (BD195),, as compared with the variation of gene expression after transplantation of different lots of human hepatocytes to host mice with whole uPA gene transfer.

sample_organism:
Homo sapiens
Mus musculus

overall_design: In SCID host mice with whole uPA gene transfer, 4 different lots of human hepatocytes were transplanted. One lot of human hepatocyte (BD195) was additionally transplanted to homozygous uPA cDNA transfer- and heterozygous uPA cDNA transfer-derived host mice.

first: Shin

middle: I

first: Chise

last: Tateno


title: Bcl11a (Ctip1) controls migration of cortical projection neurons through regulation of Sema3c

city: Ulm

first: Karlheinz

last: Holzmann

address: Helmholtzstreet 8/1

department: Medical Faculty

institute: Ulm University

summary: During neocortical development, neurons undergo polarization, oriented migration, and layer type-specific differentiation. The transcriptional programs underlying these processes are not completely understood. Here we show that the transcription factor Bcl11a regulates polarity and migration of upper layer neurons. Bcl11a-deficient late-born neurons fail to correctly switch from multipolar to bipolar morphology resulting in impaired radial migration. We show that the expression of Sema3c is increased in migrating Bcl11a-deficient neurons and that Bcl11a is a direct negative regulator of Sema3c transcription. In vivo gain-of-function and rescue experiments demonstrate that Sema3c is a major downstream effector of Bcl11a required for the cell polarity switch and for the migration of upper layer neurons. Our data uncover a novel Bcl11a/Sema3c-dependent regulatory pathway used by migrating cortical neurons.

overall_design: Neocortex tissue from three control (Bcl11a+/+) and three Bcl11a mutants (Bcl11aΔflox/Δflox) embryos was collected at E14.5. Total RNA was isolated from each sample separately using the RNeasy kit (Qiagen). The isolated ENA was inspected for integrity and purity using an Agilent Bioanalyzer and a NanoDrop spectrophotometer, respectively. Microarray analyses were performed using 200 ng total RNA as starting material and 5.5 µg ssDNA per hybridization in a GeneChip Fluidics Station 450 (Affymetrix). The total RNAs were amplified and labeled following the Whole Transcript (WT) Sense Target Labeling Assay (Affymetrix). Labeled ssDNA was hybridized to Mouse Gene 1.0 ST Affymetrix GeneChip arrays (Affymetrix). The chips were scanned with a GeneChip Scanner 3000 (Affymetrix) and subsequent images analyzed using Affymetrix Expression Console Software (Affymetrix). A transcriptome analysis was performed using BRB-ArrayTools developed by Dr. Richard Simon and BRB-ArrayTools Development Team (http://linus.nci.nih.gov/BRB-ArrayTools.html).

first: Christoph

last: Wiegreffe

first: Katharina

last: Peschkes

first: Ruth

last: Simon

last: Strehle

first: Jin

last: Cheng

first: Swathi

last: Srivatsa

first: Pentao

last: Liu

first: Nancy

last: Jenkins

first: Neal

middle: G

last: Copeland

first: Victor

last: Tarabykin

first: Stefan

last: Britsch

first: Carolin

last: Kling


title: The genetic control of left atrial gene expression determined by RNA sequencing

status: Public on Jun 16 2015

city: Cleveland

first: Jeff

last: Hsu

state: OH

address: 9500 Euclid Ave

department: Cellular and Molecular Medicine

institute: Cleveland Clinic Lerner Research Institute

type: Expression profiling by high throughput sequencing

summary: Purpose: Genome wide association studies (GWAS) have identified 14 loci for atrial fibrillation, but the mechanisms responsible for these associations as well as the causal genetic variants remain enigmatic.  Genetic variants altering expression levels of nearby genes is one such plausible mechanism.

overall_design: Methods:  We performed polyA+ RNA sequencing of left atrial appendages from a biracial cohort of 265 subjects.  Approximately 50 million read fragments mapped to the transcriptome using TopHat aligner to hg19 and fragments counted against Ensembl 71 reference transcriptome with htseq.  We also obtained genotypes using Illumina Hap550v3 and Hap610-quad SNP microarrays.  Genotypes were then imputed to 1000 Genomes using IMPUTE.   Expression surrogate variables were calculated using the R package sva and used as covariates in a genome-wide eQTL scan.  Provision of raw data for this study, even to dbGaP, was not permitted per the study IRB. Therefore, raw data are not available for this study.

first: Jonathan

last: Smith


title: Expression data from human HT29, HDFa cell lines after normal and tumor tissue derived DNA treatment

status: Public on Jun 11 2015

city: Budapest

first: Wichmann

last: Barna

address: Szentkirály

country: Hungary

institute: SOTE

summary: Gene expression profile based on human HT29, HDFa cell lines after normal and tumor tissue derived DNA treatment

overall_design: Total RNA was extracted from human HT29, HDFa cell lines after normal and tumor tissue derived DNA treatment were hybridized on Affymetrix HGU133 Plus 2.0 microarrays

first: Istvan

last: Furi

first: Sandor

last: Spisak

first: Alexandra

last: Kalmár

first: Barnabas

last: Wichmann

first: Bela

last: Molnar


title: Expression data from diploid and aneuoploid human pluripotent stem cells-derived teratomas

status: Public on Jun 10 2015

city: Jerusalem

first: Yishai

last: Avior

state: Israel

address: Edmond J. Safra Campus, Givat Ram

department: Genetics

country: Israel

institute: Hebrew University of Jeursalem

summary: Teratoma formation is the gold standard assay for testing the capacity of human stem cells to differentiate into all embryonic germ layers. Although widely used, little effort has been made to transform this qualitative assay into a quantitative one. Using gene expression data from a wide variety of cells, we created a gene scorecard representing tissues from all three germ layers as well as an extraembryonic tissue. A calculated grade using this gene list successfully distinguishes pluripotent stem cell-initiated teratomas from malignant tumors, thereby translating cell potency into a quantitative measure. This new methodology, named TeratoScore, thus assesses the pluripotency of human cells, and is easily performed using an open-source code. The new teratoma database also allowed us to examine the gene expression differences between tumors with a diploid karyotype and those initiated by aneuploid cells. We found that while teratomas originating from aneuploid cells pass the TeratoScore benchmark for pluripotency, they exhibit aberrant gene expression congruent with human chromosomal syndromes (such as Down syndrome). This gene expression signature is significantly different from that of teratomas originating from diploid cells, particularly in central nervous system-specific genes, suggesting aberrant teratomas may be beneficial for in vivo disease modeling. Teratoma formation followed by TeratoScore analysis can rapidly assess cell potency and allows comparison between different pluripotent cell lines.

overall_design: Total RNA was extracted from hPSC (diploid or aneuploid)-derived teratomas using RNeasy mini kit (Qiagen), according to the manufacture instruction. RNA was subjected to Human Genome U133 Plus 2.0 microarray platform (Affymetrix); washing and scanning were performed according to the manufacturer’s protocol

first: Juan

last: Biancotti

first: Nissim

last: Benvenisty


title: Identification of neurexophilin 3 as a novel maturation factor for induced pluripotent stem cell-derived dopaminergic neuron progenitors

status: Public on Jun 12 2015

first: Kaneyasu

last: Nishimura

address: 53 Shogoin-Kawahara-cho

department: CiRA

institute: Kyto University

summary: To develop more potent cell transplantation therapy for neurodegenerative disorder such as Parkinson’s disease (PD), the condition of the host brain environment should be considered to improve the outcome of grafted neurons. However, we never know which condition of host brain environment is suitable and supportive for the donor cells. In addition, what endogenous factor(s) do contribute to improve the engraftment of donor cells in host brain? Therefore, the identification of such effective factor(s) strongly contribute to improve the overcome of cell transplantation therapy. Here, we constructed the experimental approach to identify the effective soluble factor(s) for cell-grafting by comparison between various parkinsonian mouse brain condition and transplantation outcome using induced pluripotent stem cell (iPSC)-derived dopaminergic (DA) neuron progenitors. According to our experimental approach, we have identified secreted peptide, neurexophilin 3 (NXPH3) that enhance the survival of grafted-iPSC-derived DA neurons. Grafted-iPSC-derived DA neurons were increased by local supplement of NXPH3 protein. In addition, the expression level of NXPH3 in putamen of PD patients was significantly decreased than that of normal controls by using postmortem samples. These findings would be expected to contribute the new experimental strategy to indentify the endogenous effective factors for cell-grafting as in vivo application of stem cell technology.

overall_design: Mice were divided into three groups as follows: (i) 1 week after acute administration (four times by every 2 h) of free base MPTP HCl (20 mg/kg, 80 mg/kg in total, intraperitoneally). (ii) 8 weeks after chronic administration (once a day for 20 consecutive days) of free base MPTP HCl (4 mg/kg per day, 80 mg/kg in total). (iii) 1 week after injection (four times by every 2 h) of saline (control).

first: Jun

last: Takahashi


title: MAF1 Represses CDKN1A through a Pol III-Dependent Mechanism

city: Taipei

first: Ming-Ta

address: No.155, Sec.2, Linong Street

country: Taiwan

institute: National Yang Ming University

summary: MAF1 represses Pol III-mediated transcription by interfering with TFIIIB and Pol III. Herein, we found that MAF1 knockdown induced CDKN1A transcription and chromatin looping concurrently with Pol III recruitment. Simultaneous knockdown of MAF1 with Pol III or BRF1 (subunit of TFIIIB) diminished the activation and looping effect, which indicates that recruiting Pol III was required for activation of Pol II-mediated transcription and chromatin looping. ChIP analysis after MAF1 knockdown indicated enhanced binding of Pol III and BRF1, as well as of CFP1, p300, and PCAF, which are factors that mediate active histone marks, along with the binding of TBP and POLR2E to the CDKN1A promoter. Simultaneous knockdown with Pol III abolished these regulatory events. Similar results were obtained for GDF15. Our results reveal a novel mechanism by which MAF1 and Pol III regulate the activity of a protein-coding gene transcribed by Pol II.

overall_design: Knockdown assay was performed using siRNA obtained from MISSION®RNA (Sigma). Inhibition of expression of Pol III (SASI_Hs01_00046568) and MAF1 (SASI_Hs01_00135954) was achieved by transfection with LipofectamineTM RNAiMax (Invitrogen) according to the manufacturer’s protocol. MISSION® siRNA Universal Negative Control (Sigma) was used as knockdown control. Cells were transfected in serum-free medium. After 8 h, the siRNA containing medium was replaced with complete medium.

first: Yu-Ling

last: Lee

first: Yuan-Ching

last: Li


title: Expression analysis of big neurospheres generated in vitro

city: St lucia Brisbane

first: Zong-Hong

last: Zhang

state: Queensland

address: QBI Building (#79)

country: Australia

institute: QBI

summary: Expression analysis of neurospheres generated in vitro treated by potassium chloride (KCl) and norepinephrine

overall_design: Neurospheres generated in vitro were treated with norepinephrine or potassium chloride. Gene expression analysis was then carried out to identify genes that are up or down regulated due to chemical treatment.


title: Somatic cell fusions reveal extensive heterogeneity in basal-like breast cancer [methylation450]

city: Boston

first: Kornelia

last: Polyak

state: MA

address: 450 Brookline Ave

department: Medical Oncology

institute: Dana-Farber Cancer Institute

summary: Basal-like and luminal breast tumors have distinct clinical behavior and molecular profiles, yet the underlying mechanisms are poorly defined. To interrogate processes that determine these distinct phenotypes and their inheritance pattern, we generated somatic cell fusions and performed integrated genetic and epigenetic (DNA methylation and chromatin) profiling. We found that the basal-like trait is generally dominant and it is largely defined by epigenetic repression of luminal transcription factors. Definition of super-enhancers highlighted a core program common in luminal cells but high degree of heterogeneity in basal-like breast cancers that correlates with clinical outcome. We also found that protein extracts of basal-like cells is sufficient to induce luminal-to-basal phenotypic switch implying a trigger of basal-like autoregulatory circuits. We determined that KDM6A might be required for luminal-basal fusions, and identified EN1, TBX18, and TCF4 as candidate transcriptional regulators of luminal-to-basal switch. Our findings highlight the remarkable epigenetic plasticity of breast cancer cells.

overall_design: Bisulphite converted DNA from 20 breast cancer cell lines were hybridized to the Illumina Infinium HumanMethylation450 BeadChip.

first: Reo

last: Maruyama

first: Mary

last: Fackler


title: Expression data from CD4+ naïve T cells under Treg-inducing condition in the presence or absence of butyrate

city: Toyama

first: yukihiro

last: furusawa

address: Kurokawa

institute: Toyama Prefectural University

summary: Commensal bacteria shape the gut immune system. Colonization bacteria increase the frequency of regulatory T cells, however, the molecular mechanisms are not yet known. To reveal the mechanism, we isolated naïve CD4+ T cells from the spleen of C57BL/6 mice and cultured the cells under Treg-inducing condition culture in the presence or absence of butyrate, a metabolite produced by commensal bacteria.

overall_design: Naïve T cells were isolated from spleen and were cultured in the presence of IL-2, TGF-beta and in the presence or absene of Butyrate. RNA was extracted at Day 2.

first: Koji

last: Hase

first: Yukihiro

last: Furusawa

first: Yuuki

last: Obata


title: Blood Illumina Inf 450 DNA methylation samples from HIV+ and HIV- human subjects

status: Public on Jun 09 2015

city: Los Angeles

first: Steve

last: Horvath

address: 695 Charles E. Young Drive South, Box 708822

department: Human Genetics

institute: University of California, Los Angeles

summary: Genome wide DNA methylation profiles of cerebellum from HIV positive and HIV negative human subjects. The Illumina Infinium 450k Human DNA methylation Beadchip v1.2 was used to obtain DNA methylation profiles across approximately 486,000 CpGs. Dataset included 92 subjects from the USA.  The epigenetic clock software (Horvath 2013) was used to measure epigenetic age acceleration effects and to relate them to HIV status.

overall_design: Bisulphite converted DNA from the 92 samples were hybridised to the Illumina Infinium 450k Human Methylation Beadchip. HIV-1 status was related to an epigenetic measure of age acceleration.

first: Andrew

last: Levine


title: Whole blood DNA methylation samples from HIV positive men [2012 study]

summary: Genome wide DNA methylation profiles of whole blood from HIV positive men. The Illumina Infinium 450k Human DNA methylation Beadchip v1.2 was used to obtain DNA methylation profiles across approximately 480,000 CpGs. Dataset included 24 subjects from the USA. This data set was used as validation set for studying the effect of HIV viral load on host DNA methylation levels.

overall_design:
Bisulphite converted DNA from the 24 samples were hybridised to the Illumina Infinium 450k Human Methylation Beadchip. Subjects had different levels of HIV viral load.

This dataset reports DNA methylation data set on 24 subjects that were generated in 2012 (while the other data set of 120 subjects reports DNA meth data generated in 2013).

Details on what each sample characteristics and their values represent are provided in the 'characteristics_readme.txt' file.


title: Cerebellum Illumina Inf 450 DNA methylation samples from HIV+ and HIV- human subjects

summary: Genome wide DNA methylation profiles of cerebellum from HIV positive and HIV negative human subjects. The Illumina Infinium 450k Human DNA methylation Beadchip v1.2 was used to obtain DNA methylation profiles across approximately 486,000 CpGs. Dataset included 20 subjects from the USA.  The epigenetic clock software (Horvath 2013) was used to measure epigenetic age acceleration effects and to relate them to HIV status.

overall_design: Bisulphite converted DNA from the 20 samples were hybridised to the Illumina Infinium 450k Human Methylation Beadchip. 8 HIV+ subjects were compared to 12 HIV- subjects.


title: Effect of high-fat diet (HFD) on gene expression in brown adipose tissue (BAT)

status: Public on Jun 06 2015

city: Odense

first: Jan-Wilhelm

last: Kornfeld

state: Fyn

address: Campusvej 55

country: Denmark

institute: University of Southern Denmark

summary:
C57BL/6 male mice were fed a standardized NCD or HFD after weaning (4 weeks of age) over a course of 12 weeks.
Normal chow diet (NCD) fed animals served as Controls

overall_design: Biotin-labeled cDNA was synthesized using GeneChip Whole Transcript Sense Labeling Assay (Affymetrix) according to vendor’s instructions. After fragmentation, cDNAs were hybridized for 17h at 45°C on Affymetrix Mouse Gene 1.0 ST Arrays. The Arrays were washed and stained in the GeneChip Fluidics Station 450 and scanned on a GeneChip Scanner 3000 7G (Affymetrix). Data intensities were log transformed and normalized with a quantile normalization method using Affymetrix Power Tools. Differentially expressed genes were identified according to statistical evidence indicated by Student's t-test and fold change statistics

first: Jens

last: Brüning


title: Gene expression profile in the liver of BALB/c mice infected with Fasciola hepatica

status: Public on Jun 05 2015

city: Salamanca

first: Jose

last: Rojas-Caraballo

state: Salamanca

address: C/Licenciado Mendez Nieto s/n

department: Molecular Parasitology and Immunology

institute: University of Salamanca

summary:
Background: Fasciola hepatica infection still remains one of the helminthic neglected tropical diseases (NTDs). It has a huge worldwide distribution, affecting mainly cattle and, sometimes, human beings. In addition to data reported about the immunological response induced by helminthic infections and that induced by Fasciola hepatica, little is known about the gene expression profile in its organ target, the liver, which is where adult worms are established and live for long periods of time, causing its characteristic pathology. In the present work, we study both the early and late gene expression profiles in the livers of mice infected with Fasciola hepatica metacercariae using a microarray-based methodology.

Methodology: A total of 9 female-6-week-old BALB/c mice (Charles River Laboratories, Barcelona, Spain) weighing 20 to 35 g were used for the experiments. Two groups of BALB/c mice were orally infected with seven F. hepatica metacercariae, and the other group remained untreated and served as a control. Mice were humanely euthanized and necropsied for liver recovery, histological assessment of hepatic damage, RNA isolation, microarray design and gene expression analysis on the day of infection (t0), seven days post-infection (t7) and twenty-one days post-infection (t21).

Results: We found that Fasciola hepatica infection induces the differential expression of 128 genes in the liver in the early stage of infection and 308 genes in the late stage, and most of them are up-regulated. The Ingenuity Pathway Analysis revealed significant changes in the pathways related to metabolism, biosynthesis and signaling as well as genes implicated in inducing liver-toxicity, injury and death.

Conclusion: The present study provides us insights at the molecular level about the underlying mechanisms used by Fasciola hepatica, leading to liver damage and its subsequent pathophysiology. The expression pattern obtained here could also be used to explain the lack of association between infection with F. hepatica and cholangiocarcinoma. However, more studies should be performed to confirm this hypothesis.

overall_design: We used three experimental groups each containing 3 mice. Group 1 remains untreated and served as control. Group 2 was infected with Fasciola hepatica metacercariae on day 0 and humanely necropsied at 7 days post-infection. Group 3 was infected with Fasciola hepatica metacercariae on day 0 and humanely necropsied at 21 days post- infection. At the time of necropsy, liver of each mice were removed and the RNA was isolated. We compared the gene expression profile in the liver of mice infected with Fasciola hepatica.

first: Julio

last: Lopez-Aban

first: Pedro

last: Fernandez-Soto

first: Belen

last: Vicente

first: Francisco

last: Collía

first: Antonio

last: Muro


title: Microarray analysis of HK-2 cells treated with cisplatin

city: Suwon

first: Sangdun

last: Choi

address: Woncheon-dong, Yeongtong-gu

department: Department of Molecular Science and Technology

institute: Ajou University

summary:
Chemotherapeutic use of cisplatin is limited by its severe side effects. In this study, we demonstrated that cisplatin induces cell death in a proximal tubular cell line by suppressing glycolysis- and tricarboxylic acid (TCA)/mitochondria-related genes. HK-2 cells were cultured to confluence in 100mm dishes. Total RNA was extracted (QIAGEN, Valencia, CA, USA), and the concentration in the samples was measured using a Micro UV-Vis fluorescence spectrophotometer (Malcom, Tokyo, JAPAN). Sample of 10ɥg of Total RNA from HK-2 cells were labeled with biotin (3'IVT Labeling Kit, Affymetrix, USA) and hybridized (GeneAtlas Hybridization, Wash, and Stain Kit for 3' IVT Arrays, Affymetrix).
The Microarray platform used was Affymetrix HG U219 Array Strip. The arrays were scanned in a GeneAtlas scanner controlled by GeneAtlas Software (Affymetrix, Sta. Clara, USA). Genes were later filtered according to expression fold change (Affymetrix Expression Console software, Affymetrix)

overall_design: Using Affymetrix GeneAtlas System, we determined the gene expression profiles of HK-2 cells treated with cisplatin. Two replicates were made for each timepoints (control, 6h and 24h).


title: DNA methylation levels of various brain regions from HIV+ and HIV- subjects

summary:
Genome wide DNA methylation profiles of various human brain regions (cerebellum, occipital lobe, etc). The Illumina Infinium 450k Human DNA methylation Beadchip v1.2 was used to obtain DNA methylation profiles across approximately 480,000 CpGs. The dataset includes 130 samples. Multiple brain regions were assessed per subject. The goal was to evaluate the effect of HIV infection on DNA methylation levels.
Genome wide DNA methylation profiles of various brain regions from HIV positive and negative subjects. The Illumina Infinium 450k Human DNA methylation Beadchip v1.2 was used to obtain DNA methylation profiles across approximately 480,000 CpGs. Dataset included 130 samples: 99 samples from HIV+ subjects and 31 samples from HIV- subjects.

overall_design: The Illumina Infinium450 platform was applied to various brain regions from HIV+ and HIV- subjects. We evaluated 130 brain samples from 84 different subjects. Specifically, we considered cerebellum (20 HIV+ samples and 4 controls), frontal lobe (2 cases, 4 controls), hippocampus (4 controls), medial frontal cortex (18 cases), occipital cortex (59 cases, 13 controls), temporal cortex (4 controls). In total, there were 99 samples from HIV+ subjects and 31 samples from HIV- controls of similar ages. The subjects were recruited from the National Neurological AIDS Bank study or Multicenter AIDS Cohort study in Los Angeles. Informed consent and all study procedures were approved by the UCLA Medical IRB. DNAm data from HIV+ cases and HIV- controls were generated at the same time and randomized across plates and chips. HIV viral load information was available for blood (measured at the last blood draw) and for cerebrospinal fluid (CSF).


title: FoxM1 is essential for quiescence and maintenance of hematopoietic stem cell

status: Public on Jun 15 2015

city: CHICAGO

first: Yu

last: Hou

state: Illinois

address: 909 S wolcott AVE. COMRB Rm:5040

department: medicined

institute: university of illinois at chicago

summary: FoxM1, a mammalian Forkhead Box M1 protein, is known as a typical proliferation-associated transcription factor that regulates of G1/S and G2/M transition in the proliferating cells. However, the in vivo function of FoxM1 in adult stem cells remains unknown. Here, we  found that FoxM1 is highly expressed in hematopoietic stem cells (HSCs) and is essential for maintaining quiescence and self-renewal of HSCs in vivo. FoxM1-deficient mice developed leukopenia, thrombocytopenia and neutropenia with an approximately 6-fold decrease in HSC pool size, which is associated with a failure of G0 cell cycle regulation and increased cell cycling in HSCs.  FoxM1 absence did not affect lineage commitment of HSCs and progenitors. However, FoxM1 loss significantly reduced the repopulating capacity and self-renewal of long-term HSC in a cell-autonomous manner. Mechanistically, FoxM1 loss markedly down-regulates the expression of orphan nuclear receptor Nurr1, known to regulate HSC quiescence.   We found that FoxM1 directly bound the promoter region of Nurr1 and induced transcriptional activity of Nurr1 promoter in vitro, and forced expression of Nurr1 rescued FoxM1-deletion-induced G0 loss of HSC-enriched population in vitro.  Thus, our studies show a previously unrecognized role of FoxM1 as a critical regulator of HSC quiescence and self-renewal by controlling Nurr1-mediated pathways.

overall_design: The Hematopoietic Stem Cells (HSCs) were sorted from FoxM1[fl/fl]  and Tie2-Cre FoxM1[fl/fl] mice, then amplified with Ovation® Pico WTA System V2 before microarray analysis. There are 3 samples from FoxM1[fl/fl]mice and 3 samples from  Tie2-Cre FoxM1[fl/fl] mice.

first: Zhijian

last: Qian


title: Lead exposure induces changes in 5-hydroxymethylcytosine clusters in CpG islands in human embryonic stem cells and umbilical cord blood [Pb_hESC]

status: Public on Jun 08 2015

city: Detroit

first: Douglas

last: Ruden

state: Michigan

address: 275 E. Hancock Ave., Room  291.1

department: Department of Obstetrics and Gynecology

institute: Wayne State University

summary: Prenatal exposure to neurotoxicants such as lead (Pb) may cause stable changes in the DNA methylation (5mC) profile of the fetal genome. However few studies have examined its effect on the DNA de-methylation pathway, specifically the dynamic changes of the 5-hydroxymethylcytosine (5hmC) profile. Therefore, in this study, we investigate the relationship between Pb exposure and 5mC and 5hmC modifications during early development. To study the changes in the 5hmC profile, we use a novel modification of the Infinium™  Human methylation 450K assay (Illumina, Inc.), which we named HMeDIP-450K assay, in an in vitro human embryonic stem cell model of Pb-exposure. We model Pb-exposure associated 5hmC changes as clusters of correlated, adjacent CpG sites, which are co-responding to Pb. We further extend our study to look at Pb-dependent changes in high density 5hmC regions in umbilical cord blood DNA from 48 mother-infant pairs from the Early Life Exposure in Mexico to Environmental Toxicants (ELEMENT) cohort. For our study, we randomly selected UCB from 24 male and 24 female children from the 1st and 4th quartiles of Pb levels. Our data show that Pb-associated changes in the 5hmC and 5mC profiles can be divided into sex-dependent and sex-independent categories. Interestingly, differential 5mC sites are better markers of Pb-associated sex-dependent changes compared to differential 5hmC sites. In this study we identified several 5hmC and 5mC genomic loci, which we believe might have some potential as early biomarkers of prenatal Pb-exposure.

overall_design: Human Methylation 450K array coupled with 5-hydroxymethylcytosine (5hmC) IP or HMeDIP-450K array, was used to determine the high density 5hmC profile of H9 hESCs treated with Pb at 3 concentration 0ug/dl, 16ug/dl,32ug/dl

first: Arko

last: Sen

first: Pablo

last: Cingolani

first: Adriana

last: Mercado-Garcia

first: Martha

last: Tellez-Rojo

first: Andrea

last: Baccarelli

first: Robert

middle: O

last: Wright


title: Regulatory RNA Apela Is a Component of a Negative Feedback Loop Regulating p53-Mediated Apoptosis in Embryonic Stem Cells (I)

city: Bethesda

first: Jing

last: Huang

institute: National Cancer Institute

summary: p53-repressed transcripts have recently been shown to play important roles in various biological processes, such as stem cell differentiation and cancer. We identified a transcript named Apela that is repressed by p53 and highly expressed in mouse ES cells. To see which transcripts are affected by Apela knockdown, we performed gene expression microarray using Affymetrix Gene ST 1.0 array. Two short hairpin RNAs (shRNAs) targeting Apela were used to decrease the RNA levels of Apela to about 20% of the control (a shRNA target luciferase, shLuc).

overall_design: We designed two lentivirus-based shRNAs against Apela and used shRNA against luciferase as a control. Lentiviruses were made and used to transduced mouse ES cells. For each shRNA, three repeats were done.


title: Lead exposure induces changes in 5-hydroxymethylcytosine clusters in CpG islands in human embryonic stem cells and umbilical cord blood [ELEMENT]

overall_design: Human Methylation 450K array coupled with 5-hydroxymethylcytosine (5hmC) IP or HMeDIP-450K array, was used to determine the high density 5hmC profile of 46 Umbilical cord blood samples from the ELLEMENT cohort. HM450K array, without IP was used to determine the 5-methylcytosine(5mC) plus 5hmC profile. The 5hmC region detected from the HMeDIP-450K array was subtracted from the HM450K(without IP) to get putative high density 5mC regions.


title: Gene expression in human orbit

city: Portland

first: James

last: Rosenbaum

state: OR

address: 3181 SW Sam Jackson Park Road

department: Casey Eye Institute

institute: Oregon Health & Science University

summary:
Diagnosis of inflamed human orbit tissue with standard clinical and histopathology evaluation data is imprecise.  A large number of these patients are diagnosed with the catch-all classification of nonspecific orbital inflammation (NSOI).
We utilized gene expression analysis of orbit biopsies to assist in the classification of sarcoidosis, granulomatosis with polyangiitis (GPA), thyroid eye disease (TED), IgG4-associated disease, and subdivisions of NSOI.  As part of this process, we are investigating correlations between gene expression levels and disease characteristics.

overall_design: Anterior orbit and lacrimal gland tissues were collected for RNA extraction and analysis with Affymetrix microarrays.  Biopsy samples were obtained from subjects with inflammatory diseases such as NSOI, sarcoidosis, GPA, and TED as wells as from normal controls.  In some cases, more than one sample was obtained for a subject and some cases the samples were analyzed twice.

middle: T

first: Stephen

middle: R

last: Planck

first: Dongseok

first: Christina

last: Harrington


title: Lead exposure induces changes in 5-hydroxymethylcytosine clusters in CpG islands in human embryonic stem cells and umbilical cord blood

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

overall_design: Refer to individual Series


title: Identification of gene expression changes induced by ligands for RXR and its partners in differentiating human monocyte-derived dendritic cells

status: Public on Jun 04 2015

city: DEBRECEN

first: LAJOS

last: SZELES

address: Egyetem tér

institute: UNIVERSITY OF DEBRECEN

summary: Differentiating human dendritic cells were stimulated for 12 hours with RXR agonists (LG268, 9CRA, R- and S-9CDHRA) or agonists for RXR partners including GW3965 (LXRα/β panagonist), RSG (PPARγ agonist), and GW1516 (PPARδ agonist) and AM580 (RARa agonist). The gene expression changes were detected globally by Affymetrix Human Genome U133 Plus 2.0 Arrays.

overall_design: Human monocytes were obtained by Ficoll gradient centrifugation followed by immunomagnetic cell separation, and were cultured in the presence of GM-CSF and IL-4. Differentiating DCs were stimulated 18 h after plating by various nuclear receptor agonists or vehicle (DMSO:EtOH) for 12h. The ligands were used in the following concentrations: 10 μM R-9CDHRA, 10 μM S-9CDHRA, 1 μM 9cisRA, 100 nM LG100268 (LG268), 1 μM GW3965, 1 μM Rosiglitazone (RSG), 1 μM GW1516, 100 nM AM580. Experiments were performed in biological triplicates.

first: Lajos

last: Széles

first: László

last: Nagy

first: Ralph

last: Rühl


title: Identification of TLR3 regulated genes in CD8 positive Dendritic cell line

summary:
CD8 positive dendritic cell line , stimulated with or without TLR3 ligand polyI:C
We used microarray to obtain global gene expression data of TLR3 regulated genes

overall_design: CD8 positive dendritic cell line , stimulated with or without TLR3 ligand polyI:C 5ug/ml  for 0h (ctrl), 2h, 6h or 18h in biological triplicates

last: Szeles

first: Walter

last: Reith

first: Hans

last: Acha-Orbea


title: Expression arrays of inflammatory Ly6C+ monocytes in mice primary or secondary challenged with Listeria monocytogenes

city: Bronx

first: Gregoire

middle: S

last: Lauvau

state: NY

address: 1301 Morris park

department: M&I

institute: Albert Einstein College of Medicine

summary:
In this study we investigated the mechanisms involved in memory T-cell mediated protection using mice vaccinated with the intracellular bacterium Listeria monocytogenes. Our working hypothesis was that rapid activation of cells of the innate immune system, in particular inflammatory Ly6C+ monocytes, were essential in effective protection, in a memory T cell-dependent manner. Thus we generated a comprehensive comparison of the genetic program of activated Ly6C+ monocytes during a primary or a secondary infection with Listeria monocytogenes, at 8 hours post challenge infection.
Abstract of corresponding publication: Cells of the innate immune system are essential for host defenses against primary microbial pathogen infections, yet their involvement in effective memory responses of vaccinated individuals has been poorly investigated. Here we show that memory T cells instruct innate cells to become potent effector cells in a systemic and a mucosal model of infection. Memory T cells controlled phagocyte, dendritic cell and NK or NK T cell mobilization and induction of a strong program of differentiation, which included their expression of effector cytokines and microbicidal pathways, all of which were delayed in non-vaccinated hosts. Disruption of IFN-gamma-signaling in Ly6C+ monocytes, dendritic cells and macrophages impaired these processes and the control of pathogen growth. These results reveal how memory T cells, through rapid secretion of IFN-gamma, orchestrate extensive modifications of host innate immune responses that are essential for effective protection of vaccinated hosts.

overall_design: Overall design: Inflammatory monocytes were purified (see below for isolation method) from 4 groups of 3 individual mice each (triplicate): (i) uninfected mice, (ii) primary infected, (iii) secondary infected, (iv) secondary infected and T-cell depleted 1 day before. Isolation of cells was done on 3 different days for true biological replicates.

first: Saidi

last: Soudja


title: Histone architecture of stem-cell memory T cells reveals progressive remodeling of epigenetic landscape after activation of CD8 T cells

status: Public on Jun 03 2015

city: Doha

first: Francesco

middle: Maria

last: Marincola

address: Al Nasr Tower, AL Corniche Street, PO Box 26999

country: Qatar

institute: Sidra Medical and Research Center

summary: To better elucidate epigenetic mechanisms that correlate with the dynamic gene expression program observed after T cell activation, we investigated the genomic landscape of histone modifications in antigen-experienced CD8+ T cells. Using a ChIP-Seq approach coupled with global gene expression profiling, we generated genome-wide histone H3 lysine 4 (H3K4me3) and H3 lysine 27 (H3K27me3) trimethylation maps in distinct subsets of CD8+ T cells-naïve, stem cell memory, central memory, and effector memory-to gain insight into how histone architecture is remodeled during the differentiation of activated T cells. We show that H3K4me3 histone modifications are associated with activation of genes, while H3K27me3 is negatively correlated with gene expression at canonical loci and enhancers regions associated with T cell metabolism, effector function, and memory. Our results also reveal histone modifications and gene expression signatures that distinguish the recently identified stem cell memory T cell from other antigen-experienced CD8+ T cell subsets. Taken together, our results suggest that antigen-experienced T cells may undergo chromatin remodeling in a progressive fashion that may have implications for our understanding of peripheral T cell ontogeny and the formation of immunological memory.

overall_design: Gene expression profiles were analyzed in four subsets of peripheral CD8+ T cells: naive (TN; CD62L+CD44-), stem-cell memory (TSCM; CD62L+CD44-Sca1+), central memory (TCM; CD62L+CD44-), and effector memory (TEM; CD62L-CD44-) T cells. Each of the four subsets was done in triplicate, for a total of 12 arrays.


title: Gene expression data in DLEU1 downregulated BL cell

city: Valhalla

first: Sanghoon

last: Lee

address: 40 Sunshine Cottage Road, Vos 145

department: Pediatrics

institute: New York Medical College

summary: Comparison of gene expression profiling between DLEU1 downregulated Raji BL cell and wild type Raji BL cell

overall_design: Transcription Activator-Like Effector Nucleases (TALENs) mediated DLEU1 downregulated Raji burkitt lymphoma (BL) cell clone and wild type (control) Raji cell clone were analyzed in duplicate. Four samples were hybridized to HGU133_plus_2 Genechip(Affymetrix) and scanned with the Scanner 3000 7G.

first: S

first: M

last: Cairo


title: MYC and CHK1 Dependent Cell Death in T-cell Lymphoma and Hodgkin Lymphoma Cell Lines and Human Xenograft Models Via Anti-Proteasomal Therapy (Affymetrix)

city: Mountain View

first: Afshin

last: Beheshti

address: Moffett Blvd

institute: NASA Ames Research Center

summary: We examined the biological effects of a potent second-generation proteasome inhibitor, ixazomib, in T-cell lymphoma and Hodgkin lymphoma cell lines and human xenograft models. Ixazomib resulted in time- and dose-dependent cytotoxicity and apoptosis in all cell lines (IC50’s <75nM). In vivo studies via SCID tumor xenografts showed significant inhibition of tumor growth (P<0.001) with significantly improved survival (P<0.001) in Jurkat and L540 models with ixazomib-treated mice versus controls. Through global transcriptome and network analyses, ixazomib-treated Jurkat and L540 cells showed significant overlap in biological functions involved in regulation of cell cycle, chromatin modification, and DNA repair processes with a lack of conservation observed in a relatively ixazomib-resistant cell line, L428. Moreover, the predicted activation and inhibition status of tumor suppressors and oncogenes strongly favored ixazomib inhibition of tumor progression. Most notably, ixazomib down-regulated protein levels of MYC and its target genes. Additionally, chromatin immunoprecipitation showed that histone H3 acetylation affected MYC levels and cell death response to ixazomib. Furthermore, inhibition of MYC with JQ1 resulted in synergistic cell death in L428, which was confirmed utilizing MYC knockout. Collectively, ixazomib down-regulated MYC and downstream substrates in TCL and HL, while resistance appeared mediated through MYC- and CHK1-dependent mechanisms.

overall_design: Jurkat (TCL)and L540 cells were treated with ixazomib for 24 hours, RNA was isolated using RNeasy Minikit (Qiagen), following instructions recommended supplied by the manufacturer. Purity and the yield of isolated RNA was determined using Bioanalyzer. These experiments were performed in biological triplicates. Microarray experiment with Jurkat and L540 was performed Affy Human Gene Chip 2.0, at UMASS Medical School Genomic Core facility. Data for Jurkat and L540 cell lines were background adjusted and quantile normalized using RMAExpress. Statistically relevant genes were determined by applying LIMMA with a FDR < 0.05 that resulted in 764 significant genes for the Jurkat experimental group and 5819 significant genes for the L540 experimental group.

first: Ravi

last: Dashnamoorthy

first: Nasséra

last: Abermail

first: Jaya

last: Sharma

first: Michael

last: Coyle

first: Athena

last: Kritharis

first: Irawati

last: Kandela

first: Lynn

last: Hlatky

first: Andrew

last: Mazar

first: Ronald

middle: B

last: Gartenhaus

last: Evens


title: Frontal lobe (brain) Illumina Inf 450 DNA methylation samples from HIV+ and HIV- human subjects

first: Steve

last: Horvath

summary: Genome wide DNA methylation profiles of Frontal Lobe from HIV positive and HIV negative human subjects. The Illumina Infinium 450k Human DNA methylation Beadchip v1.2 was used to obtain DNA methylation profiles across approximately 486,000 CpGs. Dataset included 33 subjects from the USA.  The epigenetic clock software (Horvath 2013) was used to measure epigenetic age acceleration effects and to relate them to HIV status.

overall_design: Bisulphite converted DNA from the 33 samples were hybridised to the Illumina Infinium 450k Human Methylation Beadchip. 8 HIV+ subjects were compared to 25 HIV- subjects.

middle: J

last: Levine


title: DNA methylation profiles of multiple human tissues


title: DNA methylation profiles of human bone samples

summary: The main goal of the study was to measure the epigenetic age (also known as DNA methylation age) of human bone tissue and to relate it to chronological age. Toward this end, we used the epigenetic clock software described in Horvath S (2013) DNA methylation age of human tissues and cell types. Genome Biology.2013, 14:R115. DOI: 10.1186/10.1186/gb-2013-14-10-r115 PMID: 24138928

overall_design: Human DNA methylation Beadchip v1.2 was used to obtain DNA methylation profiles across approximately 486,000 CpGs. The trabecular bone pieces were obtained from the central part of the femoral head of Spanish (Caucasian) patients with hip fractures (due to osteoporosis) or subjects with osteoarthritis. About 85% of the cell population in this bone tissue are osteocytes and the remainder are osteoblasts, bone marrow, etc.

first: Jose

middle: A

last: Riancho Moral


title: DNA methylation profiles of 30 tissues from a 112 year old woman

summary: The main goal of the study was to measure the epigenetic age (also known as DNA methylation age) of these tissues. Toward this end, we used the epigenetic clock software described in Horvath S (n=2013) DNA methylation age of human tissues and cell types. Genome Biology.2013, 14:R115. DOI: 10.1186/10.1186/gb-2013-14-10-r115 PMID: 24138928

overall_design: Human DNA methylation Beadchip v1.2 was used to obtain n=64 Illumina DNA methylation arrays from 30 tissues. For each of the following tissues, we obtained at least 2 replicates: adipose, adrenal gland, aorta, bone, bone-marrow, breast, buccal cells, cartilage, cerebellum, colon, diaphragm, esophagus , frontal cortex, kidney, heart, hippocampus, liver, lung, lymph node, midbrain,  muscle, occipital cortex, pancreas, pericardium skin, spleen, stomach, temporal cortex, thyroid, whole blood.

first: L

last: Coles


title: Neuronal DNA damage response-associated dysregulation of signalling pathways and cholesterol metabolism at th earliest stages of Alzheimer-type pathology

status: Public on Jun 02 2015

city: Sheffield

first: Paul

middle: Roy

last: Heath

state: S. Yorks

address: SITraN, 385a Glossop Road

department: Academic Neurology Unit

institute: University of Sheffield

summary:
High levels of oxidative stress and an associated neuronal DDR occur at the earliest stages of Alzheimer pathology (low Braak stage), and is associated with cognitive impairment.
The aim of the present study was to combine immuno-LCM and microarray analysis to characterize the neuronal transcriptome at low Braak stages (Braak 0-II), with respect to the neuronal DDR,  in post-mortem human frontal cortex  derived from the Medical Research Council Cognitive Function and Ageing Study (MRC-CFAS).

overall_design: Pyramidal neurones were isolated from age, sex and brain pH-matched cases derived from the MRC-CFAS cohort, using immuno laser capture microdissection.  The extracted RNA was amplified and applied to HGU133 Plus 2.0 Affymetrix gene arrays.  Genes were considered differentially expressed at p<0.001 in all 4 individual cases in each DDR group [8 cases in total: 4 cases high neuronal DDR & 4 cases low neuronal DDR].

first: Julie

middle: E

last: Simpson

last: Ince

first: Thais

last: Minett

first: Fiona

last: Matthews

first: Pamela

last: Shaw

first: Emily

last: Goodall

first: Claire

last: Garwood

first: Laura

last: Ratcliffe

first: Carol

last: Brayne

first: Magnus

last: Rattray

first: Stephen

last: Wharton


title: Expression data from human CD4 or CD8 T-cells isolated from PBMC cultured at a low cell density (LDC) or high cell density (HDC)

city: Würzburg

first: Claus

middle: Juergen

last: Scholz

address: Josef-Schneider-Str. 2

department: Core Unit SysMed

institute: University Hospital Würzburg

summary:
Research in human immunobiology is mainly based on working with peripheral blood mononuclear cells (PBMC). However, recent investigations have shown that circulating CD4+ T cells are less sensitive to several T-cell activating monoclonal antibodies (mAb) and to recall antigens as compared to tissue-resident cells or cells that were in-vitro cultured at a high cell density of 10^7 cells/mL for 2 days at 37°C and 5% CO2 (RESTORE protocol, Römer et al., Blood 2011, PMID: 21931118). To explain the increase in sensitivity of CD4+ T-cells to mAbs and recall antigens on a molecular level, we performed microarray hybridizations of total RNA from T-cells isolated from PBMC that were cultured at a low or high cell density. To avoid the detection of genes that are up- or down-regulated by the culture process itself, we used low cell density cultured PBMC, instead of freshly prepared PBMC.
We used microarrays to detail the global programme of gene expression underlying differences in the cell density of human PBMC and identified genes that are significantly up- or downregulated dependent on the cell density of PBMC.

overall_design: Human PBMC of one healthy blood donor were cultured at a low cell density (10^6 cells/mL) or at a high cell density (10^7 cells/mL) for 2 days at 37°C and 5% CO2 and CD4 or CD8 T-cells of both cultures were isolated by MACSbeads. Expression profiles from total RNA extracts were generated by hybridization to Affymetrix microarrays.

first: Julia

last: Wegner

first: Heike

last: Weber

first: Thomas

last: Hünig


title: DNA methylation profiles of human brain tissue samples

first: Steve

last: Horvath

summary: The main goal of the study was to measure the epigenetic age (also known as DNA methylation age) of human tissues and to relate it to chronological age. Toward this end, we used the epigenetic clock software described in Horvath S (n=2013) DNA methylation age of human tissues and cell types. Genome Biology.2013, 14:R115. DOI: 10.1186/10.1186/gb-2013-14-10-r115 PMID: 24138928

overall_design: Human DNA methylation Beadchip v1.2 was used to obtain n=260 Illumina DNA methylation array from the following human Brain  regions: caudate nucleus (n=n=12), cingulate gyrus (n=n12), cerebellum (n=32), frontal cortex (n=41), hippocampus (n=25), midBrain  (n=18), motor cortex (n=33), occipital cortex (n=33), parietal lobe (n=23), sensory cortex (n=12), temporal cortex  (n=29), visual cortex (n=11).

first: Harry

middle: V

last: Vinters


title: Expression data from ADORA1 knockout and ADORA1 APOE double-knockout mice

city: Morgantown

first: Mary

last: Davis

state: WV

address: 1 Medical Center Drive

institute: West Virginia University Health Sciences Center

summary:
The goal of this study is to determine whether A1 adenosine receptor (ADORA1) plays a role in atherosclerosis development and its possible mechanisms. This dataset compares gene expression (aortas) of ADORA1 knockout mice to ADORA1+APOE double-knockout mice.

Mice deficient in both ADORA1 and APOE (DKO) demonstrated reduced atherosclerotic lesions in aortic arch (en face), aortic root, and innominate arteries when compared to (APOE-KO) of the same age. Treating APOE-KO with the ADORA1 antagonist DPCPX also achieved concentration-dependent reduction in lesions. The total plasma cholesterol and triglyceride levels were not different between DKO and APOE-KO, however, higher triglyceride was observed in DKO fed a high-fat diet. DKO also were heavier than APOE-KO. Plasma cytokine levels (IL-5, IL-6, and IL-13) were significantly lower in DKO. Proliferating cell nuclear antigen (PCNA) expression was also significantly reduced in the aorta from DKO. Despite smaller lesions in DKO, the composition of the innominate artery lesions and cholesterol loading and effusion [export] from bone-marrow-derived macrophages from DKO were not different from APOE-KO.

overall_design: DKO mice (n=3; ADORA1 -/- APOE -/-) were compared to ADORA1 KO mice (n=3). All mice are C57BL/6 background. For functional analysis (Ingenuity Pathways Analysis), ANOVA was used to compare genotype, with batch effects of microarray as a second factor (Partek). Significance Analysis of Microarrays (SAM) was used to determine genes with significant changes (also controlling for batch effects).

first: Bunyan

last: Teng

first: Jonathan

middle: L

last: Smith

first: Michael

last: Rosenfeld

first: Peggy

last: Robinet

first: Ray

last: Morrison

first: J

last: Mustafa


title: Array-based DNA-methylation analysis in individuals with developmental delay/intellectual disability and normal molecular karyotype

city: Ulm

first: Ole

last: Ammerpohl

address: Albert-Einstein-Allee 11

institute: UK Ulm

summary: We analyzed the DNA methylation of peripheral blood samples from 81 individuals with intellectual disability (ID) and compared this methylation pattern to 19 normal controls using the HumanMethylation450 BeadChip and bisulfite pyrosequencing for validiation. We could not show a global methylation pattern that separates the patients from the normal controls. But we detected in an individual approach DNA methylation changes in the genes COLEC11, SHANK2, GLI2 and KCNQ2, known to be associated with ID, in at least one patient. DNA methylation analysis of imprinted genes revealed patients with aberrant methylation pattern at the imprinted genes PPIEL, IGF2R, MEG3 and MCTS2/HM13. Our results suggest that imprinting disorders are under-diagnosed in ID patients moreover point to DNA methylation changes as potential alternative means to deregulated genes involved in the pathogenesis of ID.

overall_design: Bisulfite converted DNA of peripheral blood from 82 individuals with developmental delay/intellectual disability and 19 normal controls were hybridized to the Illumina Infinium HumaneMethylation450k BeadChip.

last: Kolarova


title: Th1/Th17 Immune Response in Rosacea

status: Public on Jun 01 2015

city: Sophia Antipolis

first: Isabelle

last: Carlavan

address: 2400 route des colles

department: Research

country: France

institute: Galderma R&D

summary: Rosacea is a common chronic inflammatory skin disease of unknown etiology. Our knowledge about an involvement of the adaptive immune system is very limited. We performed detailed transcriptome analysis, qRT-PCR, and quantitative immunohistochemistry on facial biopsies of rosacea patients, classified according to their clinical subtype. As controls, we used samples from healthy controls.   Our study shows significant activation of the immune system in all subtypes of rosacea, characterizing erythematotelangiectatic rosacea (ETR) already as a disease with significant influx of proinflammatory cells. The T cell response is dominated by Th1/Th17-polarized immune cells, as demonstrated by significant upregulation of IFNγ or IL-17, for example. Chemokine expression patterns support a Th1/Th17 polarization profile of the T cell response. Macrophages and mast cells are increased in all three subtypes of rosacea, while neutrophils reach a maximum in papulopustular rosacea. Our studies also provide evidence for activation of plasma cells with significant antibody production already in ETR, followed by a crescendo pattern towards phymatous rosacea.   In sum, Th1/Th17 polarized inflammation and macrophage infiltration is an underestimated hallmark in all subtypes of rosacea. Therapies directly targeting the Th1/Th17 pathway are promising candidates in the future treatment of this skin disease.

overall_design: Total of 58 chips. 19 patients and 10 healthy volunteers

last: Voegel

first: M

last: Steinhoff


title: Comparison of mouse cancer cell line global gene expression [MG1]

city: Munich

first: Georgios

last: Stathopoulos

state: Bayern

address: Max-Lebsche-Platz

department: Comprehensive Pneumology Center

institute: Helmholz Zentrum Munich

summary: We compared different mouse cancer cell lines to identify their unique cell signatures.

overall_design: Samples from different cancer cell lines were analyzed using Genespring 12.5 GX to obtain the  data.

first: Nikolaos

last: Kanellakis


title: SaOS-2 transfected with CD99 in differentiation medium for 14 days [total RNA]

city: Bologna

first: Andrea

last: Grilli

state: Italy

address: v. di Barbiano 1/10

department: Laboratory of Experimental Oncology

country: Italy

institute: Rizzoli Orthopaedic Institute

summary: We explored the transcriptional modification induced by CD99 transfection in the osteosarcoma cell lines SaOS-2 after 0, 7 and 14 days in differentiation medium.

overall_design: SaOS-2 cell lines transfected with CD99 molecule (Sa/CD99) were compared with parental SaOS-2. Cell lines were maintained in differentiation medium for 14 days. RNA was extracted at days 0, 7 and 14.

first: Marika

last: Sciandra

first: Katia

last: Scotlandi


title: Tumor-mast cell transcriptional interactions in malignant pleural effusion

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

overall_design: Refer to individual Series


title: SaOS-2 transfected with CD99 in differentiation medium for 14 days

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


title: STAT3 knockdown during transformation

city: Boston

first: Joseph

middle: Daniel

last: Fleming

state: Massachusetts

address: 240 Longwood Ave

department: Biological Chemistry and Molecular Pharmacology

institute: Harvard University

summary:
siSTAT3 knockdown of a tamoxifen initiated, transformation inducible, breast cancer model system (MCF10A-ER-Src), with associated controls of EtOH and siNEG treatments.
A description of MCF10A-ER-Src cells can be found here: www.encodeproject.org

overall_design: In order to determine the contribution of STAT3 to the gene expression profile of cells undergoing transformation, STAT3 was depleted prior to transformation.

first: Kevin

last: Struhl

first: Elsa

last: Beyer


title: Expression data from glioblastoma stem-like cells

status: Public on May 31 2015

first: Nadiya

middle: M.

last: Teplyuk

address: 77 Avenue Louis Pasteur, HIM610

department: Neurology

institute: Brigham and Womens Hospital

summary:
The objective of this study is to determine how inhibition of microRNA 10b affects gene expression in neurospheres cultures of glioblastoma stem-like cells.
We used microarrays to detail the regulation of gene expression by microRNA 10b in glioblastoma.

overall_design: We used Affymetrix microarrays to profile genes expression in three GBM stem-like cells cultures, GBM4, GBM6 and GBM8 (Wakimoto H. et al., Cancer Research, 2009, PMID19351838) 24h after transfection with miR-10b antisense oligonucleotide, or non-specific control (control 1) or transfection reagent alone (control 2).

middle: M

first: Anna

last: Krichevsky


title: Expression data from M0505 (with and without PAX2) murine ovarian surface epithelial cell lines

status: Public on May 27 2015

city: Ottawa

first: Ensaf

last: Alhujaily

address: 501 Smyth road

country: Canada

institute: University of Ottawa

summary:
Our lab established the M0505 cell line from the ovarian surface epithelium (OSE) of FVB/N mice in May 2005 in order to study OSE biology. This cell line was infected with PAX2 to study the biological consequences of PAX2 expression in normal mOSE cells
We used microarrays to try to determine the downstream targets of PAX2 in mOSE (M0505) cells  to gain information that may lead to a greater understanding of its oncongenic potential.

overall_design: Two biological replicates of M0505+WPI, M0505+PAX2  and M0505+PAX2+Cre cells were collected for RNA extraction and subesequent hybridization on the Affymetrix MoGene-1_0-st-v1 platform.

last: Al-hujaily

first: Barbara

middle: C

last: Vanderhyden


title: Effect of siRNA knock-down of FTO on 3T3-L1 cell differentiation

status: Public on May 29 2015

city: Beijing

first: Zhao

last: Renbin

address: 61 Zhichun Road

department: Space Biology Research and Technology Center

country: China

institute: China Academy of Space Technology

summary: 3T3-L1 preadipocytes were treated with control siRNA and two siRNA to FTO: siFTO-1 and siFTO-2. 24 hours after transfection, cells were induced to differentiation with MDI cocktail. RNA were collected from non-treated cells, and those treated with control siRNA, siFTO-1 or siFTO-2 at 0, 6, 24 and 72 hours post induction. Three replicates were done for each data point.

overall_design: Time series of treatment and control

first: Meizi

last: Zhang

first: Ying

first: Jun

last: Ma

first: Feima

last: Guo

first: Qian

last: Cao

first: Yu

first: Bin

last: Zhou

first: Jijie

last: Chai

first: Wenqing

last: Zhao

first: Renbin


title: Age-related profiling of DNA methylation in CD8+ T cells reveals changes in immune response and transcriptional regulator genes

city: Tartu

first: Pärt

last: Peterson

address: Ravila 19

country: Estonia

institute: University of Tartu

summary: Human ageing affects the immune system resulting in an overall decline in immunocompetence. Although all immune cells are affected during aging, the functional capacity of T cells is most influenced and is linked to decreased responsiveness to infections and impaired differentiation. We studied age-related changes in DNA methylation and gene expression in CD4+ and CD8+ T cells from younger and older individuals. We observed marked difference between T cell subsets, with increased number of methylation changes and higher methylome variation in CD8+ T cells with age. The majority of age-related hypermethylated sites were located at CpG islands of silent genes and enriched for repressive histone marks. Specifically, in CD8+ T cell subset we identified strong inverse correlation between methylation and expression levels in genes associated with T cell mediated immune response (LGALS1, IFNG, CCL5, GZMH, CCR7, CD27 and CD248) and differentiation (SATB1, TCF7, BCL11B and RUNX3). Our results thus suggest the link between age-related epigenetic changes and impaired T cell function.

overall_design: The study includes 101 individuals, 50 young and 51 old, no replicates. From each individual there are CD4 and CD8 T-cell and peripheral blood samples extracted. The total number of samples is 296, of which 99 have CD4 T -cell, 100 have CD8 T-cell and 97 have peripheral blood data.

first: Lili

last: Milani


title: Ets factors regulate neural stem cell depletion and gliogenesis in Ras pathway-driven glioma

status: Public on May 28 2015

city: Houston

first: Xin

last: HU

state: TX

address: 1515 Holcombe Blvd

department: Genomic Medicine

institute: MD Anderson Cancer Center

summary: As the list of putative driver mutations in glioma grows, we are just beginning toAs the list of putative driver mutations in glioma grows, we are just beginning to elucidate the effects of dysregulated developmental signaling pathways on the transformation of neural cells.  We have employed a postnatal, mosaic, autochthonous, glioma model that captures the first hours and days of gliomagenesis in more resolution than conventional genetically engineered mouse models of cancer.  We provide evidence that disruption of the Nf1-Ras pathway in the ventricular zone at multiple signaling nodes uniformly results in rapid neural stem cell depletion, progenitor hyperproliferation, and gliogenic lineage restriction.  Abolishing Ets subfamily activity, which is upregulated downstream of Ras, rescues these phenotypes and blocks glioma initiation.  Thus, the Nf1-Ras-Ets axis might be one of the select molecular pathways that are perturbed for initiation and maintenance in glioma.

overall_design: Mouse Gene 1.0 ST Microarrays from Affimetryx were used for microarray analysis. For each experiment, total RNA was fluorescently labeled and hybridized.  3 cell lines derived from in vivo electroporated neural stem and progenitors were compared.

first: Joshua

last: Breunig

first: Rachelle

last: Levy

first: C

middle: D

last: Antonuk

first: Jessica

last: Molina

first: Marina

last: Dutra-Clarke

first: Hannah

last: Park

first: Aslam

last: Akhtar

first: Gi

last: Kim

last: Hu

first: Serguei

middle: I

last: Bannykh

first: Roel

middle: G

last: Verhaak

first: Moise

last: Danielpour


title: VLX60 characterization

city: Uppsala

first: Mårten

last: Fryknäs

address: Akademiska sjh ingång 61

department: Medical sciencies

country: Sweden

institute: Uppsala university

summary: Microarray based mRNA profiling was used to identify the mechanism of action for the small molecule VLX60.

overall_design: MCF7 cells were treated with the drug candidate VLX60 for 6h prior to RNA isolation

first: Marten

last: Fryknas


title: Gene expression profiling of human vaginal cells in vitro discriminates compounds with pro-inflammatory and mucosa-altering properties

status: Public on May 30 2015

city: Norfolk

first: Irina

last: Zalenskaya

state: Virginia

address: 601 Colley ave

department: Ob/Gyn

institute: Eastern Virginia Medical School

summary: Inflammation and immune activation of the cervicovaginal mucosa are considered factors that increase susceptibility to HIV infection. It is essential to screen candidate anti-HIV microbicides for potential mucosal immunomodulatory/inflammatory effects prior to further clinical development. The goal of this study was to develop an in vitro method for preclinical evaluation of the inflammatory potential of new candidate microbicides. We compared transcriptomes of human vaginal cells (Vk2/E6E7) treated with well-characterized pro-inflammatory (PIC) and non-inflammatory (NIC) compounds. Microarraray comparative analysis allowed us to generate a panel of 20 genes that were consistently deregulated by all PICs compared to NICs, thus distinguishing between these two groups.

overall_design: Vk2/E6E7 cells were treated with non-inflammatory compounds: carboxymethyl cellulose (9 samples), hydroxyethyl cellulose (9 samples), pro-inflammatory compounds: imiquimod  (6 samples), macrophage activating lipopeptide 2 (MALP2) (6 samples), nonoxynol 9 (N9) (9 samples), Pam3CSK4 (6 arrays), TNF-alpha (6 samples). Non-treated cells (GM) were used as controls (54 samples). Altogether 105 samples were analyzed.

first: Theresa

last: Joseph

first: Jasmin

last: Bavarva

first: Nazita

last: Yousefieh

first: Suzanne

middle: S

last: Jackson

first: Robert

last: Settlage

first: Gustavo

middle: F

last: Doncel


title: Transcriptomic profiling associated with temozolomide (TMZ) response of glioblastoma mouse model

city: LA TRONCHE

first: Michèle

last: EL ATIFI

address: Chemin fortuné ferrini

institute: INSERM

summary: The gene expression of an orthotopic mouse model developed from human glioblastoma neurospheres was compared between temozolomide treated and untreated mice.

overall_design: Sampling consisted of seven samples: 3 untreated cerebral tumors versus 4 cerebral tumors treated with Temodal.

first: Feriel

last: Tiar

first: Teodora

last: Perles-Barbacaru

last: El Atifi

first: Didier

last: Wion

first: Laurent

last: Pelletier

first: Hana

last: Lahrech

first: François

last: Berger


title: Expression data from pancreatic beta cells isolated from differentially weaned mice.

status: Public on May 26 2015

city: Jerusalem

first: Miri

last: Stolovich-Rain

address: Ein Karem

department: Department of Developmental Biology and Cancer Research

institute: The Hebrew University-Hadassah Medical School

summary: Transcriptome analysis reveals that in pancreatic beta cells weaning increases the expression of genes involved in replication licensing, suggesting a mechanism to increased responsiveness to the mitogenic activity of high glucose.

overall_design: β cells were sorted from dissociated islets of P25 insulin-Cre; Rosa26-LSL-YFP mice (Gannon et al., 2000; Srinivas et al., 2001) that were either suckling or prematurely weaned at P18. YFP+ FACS-sorted cells were subjected for RNA extraction and hybridization on Affymetrix microarrays

first: M

first: Y

last: Dor


title: The effect of age on the skeletal muscle transcriptome during hypertrophy

city: Lexington

first: Tyler

last: Kirby

state: Kentucky

address: 900 Rose Street

department: Physiology

institute: University of Kentucky

summary:
Transcriptome analysis of skeletal muscle during hypertrophic growth in aged mice
Global gene expression patterns were determined from microarray results on day 1, 3, 5, 7, 10 and 14 during plantaris muscle hypertrophy induced by synergist ablation in old adult mice (25 months).

overall_design: For each time point, two Affymetrix chips (Mouse Gene 1.0 ST) were used with 100 ng of total RNA derived from a pooled sample of either the right or left plantaris muscles from six animals.

first: Jonah

last: Lee

first: Jonathan

middle: H

last: England

first: Thomas

last: Chaillou

first: Karyn

last: Esser

first: John

last: McCarthy


title: Expression data of Sirt1-deficient and sufficient medullary thymic epithelial cells (mTECs)

status: Public on May 25 2015

city: Rehovot

first: Jakub

last: Abramson

address: Herzl 234

department: Immunology

institute: Weizmann Institute

summary:
Medullary thymic epithelial cells play essential role for induction of central self-tolerance. This functional capacity is mediated through a phenomenon known as promiscuous gene expression (pGE) of various tissue-restricted antigen (TRA) genes. pGE was previously shown to be mediated by a single factor called the Autoimmune regulator (Aire), which is specically expressed by mTECs. The aim of this study was to analyze the impact of  deacetylase Sirtuin1, which is also highly expressed by mTECs, on mTEC gene expression profile and compare it with the impact of Aire.
We used Affymetrix mouse 1ST arrays to analyze the impact of the Sirt1 gene on the gene expression profile of MHC-II high medullary thymic epithelial cells

overall_design: Mature MHC-II high mTECs were flow-sorted from thymi isolated from B6.Sirt1fl/fl, B6.Sirt1fl/flFoxn1-Cre and B6.Aire–/– 6weeks old mice. Typically, 3 mice were pooled to obtain 30-60 thousand sorted mTECs, which were then analyzed by gene expression profiling. Specifically, total RNA was extracted from ~30,000 pooled sorted cells using Trizol. Purified total RNA was then amplified using the MessageAmp RNA kit (Ambion). Biotinylated cRNA was then hybridized to Affymetrix Mouse Gene 1-ST arrays by the genomics core at the Weizmann Institute


title: Expression data from Escherichia coli strains with increased or decreased levels of Obg (ObgE, CgtA, YhbZ)

city: Leuven

first: Jan

last: Michiels

address: Kasteelpark Arenberg 20 - box 2460

department: Department of Microbial and Molecular Systems (M²S)

country: Belgium

institute: KU Leuven

summary: We measured transcriptional changes resulting from overexpression or downregulation of the GTPase Obg.

overall_design: Four samples were run in triplicate. Samples include a wild-type control (WT), a strain overproducing wild-type Obg (pBAD-obgWT), a strain overproducing Obg containing a G166V substitution (pBAD-obgG166V), and a strain displaying moderate depletion of Obg (pHN1009-obg).


title: Genome-wide methylation profiles of forensically relevant body fluids [Set3]

city: Seoul

first: Hwan Young

address: 103 Daehak-ro, Jongno-gu

department: Forensic Medicine

country: South Korea

institute: Seoul National University College of Medicine

summary: The ability to predict tissue type and donor’s age from molecular profiles of crime scene samples has practical implications in forensics. In order to identify body fluid- and age-associated DNA methylation changes, genome-wide DNA methylation profiling was carried out for body fluids including blood, saliva, semen, menstrual blood, and vaginal fluid obtained from individuals aged 20 to 59. The Illumina Infinium 450k Human DNA methylation Beadchip was used to obtain DNA methylation profiles across approximately 450,000 CpGs in bisulfite converted DNA. Samples included 12 of each blood, saliva and semen samples from 18 male donors aged 20 to 59, and 3 of each vaginal fluid and menstrual blood samples from 4 female donors in their twenties.

overall_design:
Genome-wide DNA methylation profiling of body fluids obtained from individuals aged 29 to 41. The Illumina Infinium 450K Human DNA methylation Beadchip was used to obtain DNA methylation profiles across approximately 450K CpGs from human body fluids including blood, saliva and semen.
Bisulfite converted DNA from the 6 samples were hybridised to the Illumina Infinium 450k Human Methylation Beadchip

first: Hwan

middle: Y


title: Genome-wide methylation profiles of forensically relevant body fluids [Set2]

overall_design:
Genome-wide DNA methylation profiling of body fluids obtained from individuals aged 37 to 48. The Illumina Infinium 450K Human DNA methylation Beadchip was used to obtain DNA methylation profiles across approximately 450K CpGs from human body fluids including blood, saliva and semen.
Bisulfite converted DNA from the 12 samples were hybridised to the Illumina Infinium 450k Human Methylation Beadchip


title: Genome-wide methylation profiles of forensically relevant body fluids


title: Genome-wide methylation profiles of forensically relevant body fluids [Set1]

overall_design:
Genome-wide DNA methylation profiling of body fluids obtained from young and old individuals. The Illumina Infinium 450K Human DNA methylation Beadchip was used to obtain DNA methylation profiles across approximately 450K CpGs from human body fluids including blood, saliva, semen, vaginal fluid and menstrual blood.
Bisulfite converted DNA from the 24 samples were hybridised to the Illumina Infinium 450k Human Methylation Beadchip


title: Atg7 deficiency induces a microbiome-influenced immune response and suppresses tumor growth to inhibit intestinal tumorigenesis

city: 91400 Orsay

first: Florent

last: Dumont

state: Ile de France

address: 17 avenue des sciences

institute: Université Paris-Saclay

summary: Here, we show that autophagy is activated in the intestinal epithelium in murine and human colorectal cancer and that the conditional inactivation of Atg7 in intestinal epithelial cells inhibits the formation of pre-cancerous lesions in Apc+/- mice by enhancing anti-tumor responses. The antibody-mediated depletion of CD8+ T cells showed that these cells are essential for the antitumoral responses mediated by the inhibition of autophagy. We show that Atg7 deficiency leads to intestinal dysbiosis and that the microbiota is required for anti-cancer responses. In addition, Atg7 deficiency resulted in a stress response accompanied by metabolic defects, AMPK activation and p53-mediated cell cycle arrest in tumor cells but not in normal tissue. This study reveals that the inhibition of autophagy within the epithelium may prevent the development and progression of colorectal cancer in genetically-predisposed patients.

overall_design: 6 samples analyzed corresponding to 3 normal duodenum of Apc+/- mice and 3 normal duodenum of Apc+/-Atg7-/- mice.

first: B

last: Romagnolo

first: J

last: Lévy