title: Upregulation of Expression of Matrix Metalloproteinases in Alveolar Macrophages of HIV1+ Smokers with Early Emphysema

city: New York

first: Yael

last: Strulovici-Barel

state: NY

address: 1300 York Avenue

department: Department of Genetic Medicine

institute: Weill Cornell Medical College

summary:
HIV1+ smokers develop emphysema at an earlier age and with a higher incidence than HIV1- smokers. Based on the knowledge that human alveolar macrophages (AM) are capable of producing proteases that degrade extracellular matrix components, we hypothesized that upregulation of AM matrix metalloproteinases may be associated with the emphysema of HIV1+ smokers. To test this hypothesis, microarray analysis was used to screen which MMP genes were expressed by AM isolated by bronchoalveolar lavage (BAL) of HIV1+ smokers with early emphysema. For each of the MMP genes observed to be expressed (MMP-1, -2, -7, -9, -10, -12 and -14), TaqMan PCR was used to quantify the relative expression in AM from 4 groups of individuals: HIV1 healthy nonsmokers, HIV1- healthy smokers, HIV1- smokers with early emphysema and HIV1+ smokers with early emphysema. Strikingly, while AM gene expression of MMPs was higher in HIV1- individuals with emphysema in comparison with HIV1- healthy smokers, for the majority of the MMPs (-1, -7, -9, -10, -12), AM expression from HIV1+ smokers with early emphysema was significantly higher than HIV1- smokers with early emphysema. Consistent with these observations, HIV1+ individuals with early emphysema had higher levels of epithelial lining fluid MMPs (-2, -7, -9,-12) than the 3 HIV1 groups. Interestingly, the active forms of MMP-2, -9 and -12 were detected in epithelial lining fluid from HIV1+ individuals with early emphysema, but not in any of the other groups. Considering that the substrate specificity of the upregulated AM MMPs includes collagenases, gelatinases, matrilysins and elastase, these data suggest that upregulated AM MMP genes and activation of MMP proteins may contribute to the emphysema of HIV1+ individuals who smoke.
Keywords: expression study

overall_design: Asymptomatic HIV+ smokers with early emphysema

first: Robert

last: Kaner

first: Francisco

last: Santiago

first: Ronald

middle: G

last: Crystal


title: Exosomal Transfer of Stromal Cell-Derived miR21 Confers Taxol Resistance in High-grade Serous Ovarian Cancer Cells Through Down-Regulation of APAF1.

status: Public on Mar 21 2016

city: Houston

first: Tsz-Lun

last: Yeung

state: TX

address: 1515 Holcombe Blvd. Unit 1362

department: Gynecologic Oncology and Reproductive Medicine

country: USA

institute: University of Texas MD Anderson Cancer Center

summary: Advanced ovarian cancer usually spreads to the visceral adipose tissue of the omentum.  However, the stromal cell-derived molecular determinants that modulate ovarian cancer growth have not been characterized. Here, we identified significantly higher levels of miR21 in exosomes and tissue lysate isolated from cancer associated adipocytes (CAA) and fibroblasts (CAF) compared to those from ovarian cancer cells. Functional studies and transcriptome analysis on miR21 transfected SKOV3 ovarian cancer cells revealed that miR21 could be transferred from CAA or CAF to ovarian cancer cells and modulate ovarian cancer apoptosis and chemoresistance through binding to its direct target APAF1.  These data suggest that malignant phenotype of metastatic ovarian cancer cells can be modulated by miR21 delivered by exosomes derived from neighboring stromal cells in the omental tumor microenvironment.

overall_design: SKOV3 cells were transfected with either 5 nM miR21 precursor or negative control precursor miRNA for 24 h; and total RNAs were isolated using TRI reagent (Molecular Research Center). Purified RNA samples were amplified and labeled using MessageAmp™ Premier RNA Amplification Kit (Ambion) and then hybridized onto Affymetrix GeneChip Human Genome U133 Plus 2.0 microarrays (Affymetrix, Santa Clara, CA), according to the manufacturer’s protocol. The arrays were washed and stained using Affymetrix Fluidics Station 450 and GeneChip® Hybridization, Wash, and Stain Kit (Affymetrix). Scanning of the arrays were done at the Cancer Genomics Core Lab at MD Anderson Cancer Center using the GeneChip Scanner 3000 7G (Affymetrix).

first: Chloe

last: Co

first: Samuel

middle: C

last: Mok

first: Tsz

middle: L


title: Human induced pluripotent stem cell–derived cardiomyocytes recapitulate the predilection of breast cancer patients to doxorubicin-induced cardiotoxicity

status: Public on Mar 22 2016

city: Chicago

first: Paul

middle: W

last: Burridge

state: IL

address: 320 E Superior St Searle 8-525

department: Pharmacology

institute: Northwestern

summary:
Microarray data on H9 hESC-derived cardiomyocytes (d30) treated with 0, 0.1, 1, or 10 uM of doxorubicin for 24 h
Establish effects of increasing doses of doxorubicin on control H9 hESC-derived cardiomyocytes

overall_design: Monolayers of cells in a 24-well plate were treated for 24 h


title: CCL4 Secretion By Interleukin-15 Dendritic Cells Directs Superior Recruitment Of Cd56+ Cytolytic Lymphocytes

status: Public on Mar 17 2016

city: Edegem

first: Heleen

middle: Hugo

last: Van Acker

address: Wilrijkstraat 10

department: Faculty of Medicine and Health Sciences

country: Belgium

institute: University of Antwerp

summary: A key requisite for the success of a dendritic cell (DC)-based vaccine in treating malignancies is the capacity of the DCs to attract immune effector cells for further interaction and activation, considering crosstalk with DCs is partially regulated by cell-contact-dependent mechanisms. Although critical for therapeutic efficacy, immune cell recruitment is a largely overlooked aspect regarding optimization of DC therapy. In this paper we examine if the so-called interleukin (IL)-15 DC vaccine provides a favorable chemokine milieu for recruiting T cells, natural killer (NK) cells and gamma delta (γδ) T cells, in comparison with the IL-4 DCs used routinely for clinical studies, as well as the underlying mechanisms of immune cell attraction by IL-15 DCs. Chemokine signaling is studied both at the RNA level, using microarray data of mature DCs, and functional level, by means of a transwell chemotaxis assay. Important to note, the classic IL-4 DC vaccine falls short to attract the required immune effector lymphocytes, whereas the IL-15 DCs provide a favorable chemokine milieu for recruiting all cytolytic effector cells. The elevated secretion of the chemokine (C-C motif) ligand 4 (CCL4), also known as macrophage inflammatory protein-1β (MIP-1β), by IL-15 DCs underlies the enhanced migratory responsiveness of T cells, NK cells and γδ T cells. Namely, neutralizing its receptor CCR5 resulted in a significant drop in migration of the aforementioned effector cells towards IL-15 DCs. These findings should be kept in mind in the design of future DC-based cancer vaccines.

overall_design: Total RNA extracted from mature IL-15 DCs and IL-4 DCs from 3 independent healthy donors

middle: H

first: Ottavio

last: Beretta

first: Sébastien

last: Anguille

first: Lien

last: De Caluwé

first: Angela

last: Papagna

first: Johan

middle: M

last: Van den Bergh

first: Yannick

last: Willemen

first: Herman

last: Goossens

first: Zwi

middle: N

last: Berneman

first: Viggo

middle: F

last: Van Tendeloo

first: Evelien

last: Smits

first: Maria

last: Foti

first: Eva

last: Lion


title: Expression profiles in Zbtb20-overexpressed neural precursor cells

city: Tokorozawa

first: Motoshi

last: Nagao

state: Saitama

address: 4-1 Namiki

department: Department of Rehabilitation for the Movement Functions

country: Japan

institute: Research Institute, National Rehabilitation Center for Persons with Disabilities

summary: Neural precursor cells (NPCs) are multipotent cells that can generate neurons, astrocytes, and oligodendrocytes in the mammalian central nervous system. Although Zbtb20 was expressed in NPCs, its functions in neural development are not fully understood. We performed microarray analysis to examine changes in gene expression between control and Zbtb20-overexpressed NPCs.

overall_design: NPCs derived from E11.5 mouse forebrains were infected with control or Zbtb20 retrovirus in the presence of fibroblast growth factor 2 (FGF2) and epidermal growth factor (EGF). Three days after infection, the virus-infected NPCs were harvested or dissociated and seeded on poly-D-lysine -coated dishes, and subsequently the cells were cultured for 1 day or without  FGF2 and EGF.

first: Toru

last: Ogata

first: Yasuhiro

last: Sawada

first: Yukiko

last: Gotoh


title: Mechanisms and disease associations of haplotype-dependent allele specific DNA methylation: Methylation array data for the identification of mQTL

city: hackensack

first: Benjamin

last: Tycko

state: NJ

address: 40 prospect avenue

department: Epigenetics

institute: HUMC

type: Methylation profiling by genome tiling array

summary: Haplotype-dependent allele-specific methylation (hap-ASM) can impact disease susceptibility, but maps of this phenomenon using stringent criteria in disease-relevant tissues remain sparse. Here we apply array-based and Methyl-seq approaches to multiple human tissues and cell types, including brain, purified neurons and glia, T lymphocytes, and placenta, and identify 795 hap-ASM differentially methylated regions (DMRs) and 3,082 strong methylation quantitative trait loci (mQTLs), most not previously reported. More than half of these DMRs have cell type-restricted ASM, and among them are 188 hap-ASM DMRs and 933 mQTLs located near GWAS signals for immune and neurological disorders. Targeted bis-seq confirmed hap-ASM in 12/13 loci tested, including CCDC155, CD69, FRMD1, IRF1, KBTBD11, and S100A*-ILF2, associated with immune phenotypes, MYT1L, PTPRN2,CMTM8 and CELF2, associated with neurological disorders, NGFR and HLA-DRB6, associated with both immunological and brain disorders, and ZFP57, a trans-acting regulator of genomic imprinting. Polymorphic CTCF and transcription factor (TF) binding sites are over-represented among hap-ASM DMRs and mQTLs, and analysis of the human data, supplemented by cross-species comparisons to Macaca mulattamacaques, indicates that CTCF and TF binding likelihood predicts the strength and direction of the allelic methylation asymmetry. These results show that hap-ASM is highly tissue-specific; an important trans-acting regulator of genomic imprinting is regulated by this phenomenon; variation in CTCF and TF binding sites is an underlying mechanism in primary tissues, and maps of hap-ASM and mQTLs reveal regulatory sequences underlying supera- and sub-threshold GWAS peaks in immunological and neurological disorders.

overall_design: Bisulfite converted DNA from 54 T cells, 44 brains (temporal cortex), 18 neuron nuclei, 22 non-neuronal nuclei (referred as glia), 37 fetal placentas samples were hybridised to the Illumina Infinium 450k Human Methylation Beadchip.  Illumina Infinium 450k Human Methylation Beadchip were performed by the Genomics Shared Resource supported by Roswell Park Cancer Institute and National Cancer Institute (NCI). The isolation of neuron and glia nuclei was performed by fluorescence-activated nuclear sorting (FANS) after incubarion with anti – NeuN- Alexa 488 conjugated antibody (Millipore MAB377X) .To identify mQTL (methylation quantitative trait loci), these methylation data were used in combination with genotyping data obtained using Illumina HumanOmni2.5-8v1.1 (Omni2.5) BeadChip.

first: Catherine

last: Do

first: Charles

last: Lang

first: John

last: Lin

first: Huferesh

last: Darbary

first: Izabela

last: Krupska

first: Aulona

last: Gaba

first: Lynn

last: Petukhova

first: Jean-Paul

last: Vonsattel

first: Mary

middle: P

last: Gallagher

first: Robin

middle: S

last: Goland

first: Raphael

middle: A

last: Clynes

first: Andrew

last: Dwork

last: Kral

last: Monk

last: Christiano


title: Regulation of casodex-dependent AR activity by NCOR1

status: Public on Mar 15 2016

first: Leif

middle: E

last: Peterson

address: 6565 Fannin, Suite MGJ6-031

department: Center for Biostatistics

institute: HMRI

summary: Proliferation of prostate cancer cells, LNCaP, is suppressed by casodex. This suppression requires expression of AR coregulator, NCOR1.

overall_design: We employed DNA microarrays to determine changes in casodex regulated gene expression with and without NCOR1

first: Sandra

last: Lopez

first: Anna

last: Frolov

first: Rile

last: Li

first: Michael

last: Ittmann

first: Nancy

last: Weigel

first: Irina

middle: U

last: Agoulnik


title: Expression data from cultured mouse macrophages treated with fatty acids or LPS

status: Public on Mar 18 2016

city: San Francisco

first: Charlie

last: Kim

state: CA

address: 1001 Potrero Ave

department: Medicine

institute: University of California, San Francisco

summary:
The goal of this study was to compare the transcriptional responses of mouse macrophages treated with unsaturated or saturated fatty acids to macrophages treated with LPS to stimulate classical inflammatory activation.
Microarray profiling was performed on total RNA isolated from primary mouse bone marrow-derived macrophages (BMDMs) treated with fatty acids (C18:1 oleic acid or C18:0 stearic acid), BSA vehicle, or LPS at two time points.

overall_design: RNA was extracted from n=3-4 biological replicates of BMDMs derived from wild type C57Bl/6 mice treated with 250 μM oleic acid (OA) or stearic acid (SA) for 5 h or 20 h, 125 μM BSA for 4 h (vehicle control), or 1 ng/mL LPS for 4h.

first: Megan

last: Robblee

first: Charles

first: Jess

last: Porter Abate

first: Suneil

middle: K

last: Koliwad


title: Loss of ZEB2 in basal breast cancer cells

city: Leuven

first: Rekin's

last: Janky

address: Herestraat 49 Box 816

department: Nucleomics Core

institute: VIB

summary: Study of loss of ZEB2 in breast cancer cells in vitro and in vivo: gene expression and phenotypic switch to more benign behavior of the cancer cells. Morphological, functional and gene microarray analysis following ZEB2 knockdown in MDAMB231 cells reveals gain of epithelial differentiation, reduction of migration, invasion and metastatic capability. The measurement of ZEB2 transcriptional activity in tumor cells efficiently predicts the probability of breast cancer patient survival.

overall_design: Global gene expression profiles were measured using Affymetrix U133 plus2 microarrays in MDAMB231 cells (control and ZEB2 shRNA and siRNA knockdown cells on plastic)

first: Eric

last: Raspé

first: Cindy

last: Vandewalle

first: Bram

last: De Craene

first: Geertrui

last: Denecker

first: Zeynep

last: Seflek

first: Peter

last: Vermeulen

first: Luc

last: Dirix

first: Steven

last: Van Laere

first: Frans

last: van Roy

first: Els

last: Goetghebeur

first: Geert

last: Berx


title: Identification of DNA methylation-independent epigenetic events underlying clear cell renal cell carcinoma

city: Los Angeles

first: Gangning

last: Liang

address: 1441 Eastlake Ave, NOR 7344

department: Urology

institute: University of Southern California

summary: Genome-wide analysis of endogenous and exogenous methylation in human ccRCC tumor and adjacent normal tissue to determine DNA methylation and chromatin structure states in ccRCC.

overall_design: Nuclei from the 6 patient kidney tumor and normal samples were either treated or not-treated with M.SssI enzyme, DNA was extracted and bisulfite-converted, then hybridised to the Illumina HumanMethylation450 BeadChip (HumanMethylation450_15017482)

first: Elinne

last: Becket

first: Sameer

last: Chopra

first: Christopher

last: Duymich

first: Justin

middle: J

last: Lin

first: Jeung

last: You

first: Kurinji

last: Pandiyan

last: Nichols

first: Kimberly

last: Siegmund

first: Jessica

last: Charlet

first: Daniel

last: Weisenberger

last: Jones


title: HDAC1 and 2 repress lineage inappropriate expression of Flt3 and Ptprf in B cells via Pax5 and Grg4

status: Public on Mar 16 2016

city: Basel

first: Tim

last: Roloff

address: Maulbeerstrasse 66

department: Functional Genomics

country: Switzerland

institute: FMI

summary:
Total RNA was isolated from pre BI (early lymphcytes) cells sorted by FACS with the following markers: B220+, CD25-, C-kit+,IgM-, CD19+.
The animals used carried floxed Hdac1 & 2 either in combination with mb1-cre (refered to as DKO) or not (WT).

overall_design: 6 samples of FACS-sorted pre BI cells were analyzed, corresponding to 6 individual female animals, 8 week of age, 3 per genotype DKO and WT.

first: Patrick

last: Matthias

first: Nina

last: Reichert

first: Stéphane

last: Thiry


title: Gene-expression profiles after siRNA knockdown and overexpression of bromodomian containing 1 (BRD1) in HEK293T cells

city: Aarhus

first: Tue

last: Fryland

state: Aarhus

address: Bartholins Allé 6

department: Biomedicine

country: Denmark

institute: Aarhus University

summary:
Background: The bromodomain containing 1 (BRD1) gene has been implicated with transcriptional regulation, brain development and susceptibility to schizophrenia and bipolar disorder.
Results: To advance the understanding of BRD1 and its role in mental disorders, we characterized the protein and chromatin interactions of the BRD1 isoforms, BRD1-S and BRD1-L, by a series of investigations and integration of functional molecular data with human genetic data. We present several novel protein interactions of BRD1, including proteins previously implicated with mental disorders. By BRD1-S and BRD1-L chromatin immunoprecipitation followed by next generation sequencing we identified binding to promoter regions of 1540 and 823 genes, respectively, and showed correlation between BRD1-S and BRD1-L binding and regulation of gene expression. The identified BRD1 interaction network was found to be predominantly co-expressed with BRD1 mRNA in human brain and enriched for pathways involved in gene expression and brain function. By interrogation of large data sets from genome-wide association studies, we further demonstrate that the BRD1 interaction network is enriched for schizophrenia risk.
Conclusion: Our results show that BRD1 interacts with chromatin remodeling proteins, e.g. PBRM1, as well as histone modifiers, e.g. MYST2 and SUV420H1. We find that BRD1 primarily binds in close proximity to transcription start sites and regulates expression of numerous genes, many of which are involved with brain development and susceptibility to mental disorders. Our findings indicate that BRD1  acts as a regulatory hub in a comprehensive schizophrenia risk network which plays a role in many brain regions throughout life,   implicating e.g.striatum, hippocampus, and amygdala at mid fetal stages.

overall_design: 9 expression arrays performed in HEK293T cells


title: Transcriptome expression profile of embryonic liver and placenta tissue from BAHD1+/+ (WT)  and BAHD1-/- (KO) mice at embryonic day E16.5

city: Jouy-en-Josas

first: Helene

last: Bierne

address: Domaine de Vilvert, bat 442, INRA Micalis

department: Micalis Institute

country: France

institute: INRAE - University PARIS SACLAY

summary: Comparisons of embryonic liver and placenta gene expression profiles of BAHD1-KO mice to those of wild-type littermate mice

overall_design: We used DNA microarrays to identify the repertoire of genes differentially expressed by ablation of the BAHD1 gene in embryos.

first: Olivia

last: Wendling

first: Guillaume

last: Soubigou

first: Emanuele

last: Libertini

first: Tania

last: Sorg

first: Jean-Yves

last: Coppee


title: Transcriptome expression profile of tissue from BAHD1+/+ (WT)  and BAHD1-/- (KO) mice

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

overall_design: Refer to individual Series


title: Derivation and differentiation of haploid human embryonic stem cells [methylation array]

city: Jerusalem

first: Ido

last: Sagi

address: Givat Ram

department: Genetics

country: Israel

institute: The Hebrew University of Jerusalem

summary: Diploidy is a fundamental genetic feature in mammals, in which haploid cells normally arise only as post-meiotic germ cells that serve to insure a diploid genome upon fertilization. Gamete manipulation has yielded haploid embryonic stem (ES) cells from several mammalian species, but as of yet not from humans. Here we analyzed a large collection of human parthenogenetic ES cell lines originating from haploid oocytes, leading to the successful isolation and maintenance of human ES cell lines with a normal haploid karyotype. Haploid human ES cells exhibited typical pluripotent stem cell characteristics such as self-renewal capacity and a pluripotency-specific molecular signature. Although haploid human ES cells resembled their diploid counterparts, they also displayed distinct properties including differential regulation of X chromosome inactivation and genes involved in oxidative phosphorylation, alongside reduction in absolute gene expression levels and cell size. Intriguingly, we found that a haploid genome is compatible not only with the undifferentiated pluripotent state, but also with differentiated somatic fates representing all three embryonic germ layers, despite a persistent dosage imbalance between the autosomes and X chromosome. We expect that haploid human ES cells will provide novel means for studying human functional genomics, development and evolution.

overall_design: Genome-wide DNA methylation profiling by Illumina Infinium HumanMethylation 450K Beadchip was performed on a total of 12 samples, including undifferentiated haploid and diploid human parthenogenetic embryonic stem cells in either G1 or G2/M, as well as 3 in vitro fertilization (IVF) control embryonic stem cell lines.

first: Dieter

last: Egli

first: Nissim

last: Benvenisty


title: Blockade of the neogenin-RGMb-BMP signaling hub inhibits allergen-induced airway hyperreactivtiy

status: Public on Mar 14 2016

city: Stanford

first: Rosemarie

last: DeKruyff

address: Stanford University

institute: Department of Medicine

summary:
Bronchial asthma is associated with type 2 immune responses induced by components of adaptive as well as innate immunity.  Although innate cytokines such as IL-25 have been shown to play key roles in development of airway hyperreactivity (AHR), little is known of innate molecules that regulate IL-25-mediated airway inflammation. We found that blockade of repulsive guidance molecule b (RGMb) in an experimental murine model of asthma blocked the development of AHR, a cardinal feature of asthma, and that RGMb is expressed on F4/80+CD11b+CD11cneg macrophages (RGMb+ macrophages), which accumulated in the lungs of OVA-sensitized and challenged mice, but not in naïve mice. Moreover, we found that a large fraction of the RGMb+ macrophages expressed the IL-25 receptor IL-17RB and produced IL-13.   IL-25 was critical for the development of AHR in our model, since mice deficient in IL-17RB did not develop AHR.  Finally, treatment with anti-RGMb mAb during the challenge phase of the protocol after allergen sensitization effectively prevented the development of AHR and airway inflammation, suggesting for the first time that RGMb+ cells, including RGMb+ macrophages, play critical roles in allergen-induced asthma.
We used microarrays to compare the gene expression patterns in WT mice sensitized and challenged with OVA that were treated with either RGMb mAb or an isotype control.

overall_design: First replicate: 3 control samples (mice sensitized and challenged with saline), 3 RGMb mAb samples, 3 isotype samples; 2nd replicate: 3 control samples, 3 RGMb mAb samples, 2 isotype samples.  Lung tissues were harvested at the same treatment time point in all groups.

first: Sanhong

last: Yu

first: Krystle

last: Leung

first: Hye-Young

last: Kim

first: Yanping

last: Xiao

first: Lee

last: Albacker

first: Hyun-Jun

last: Lee

first: Dale

middle: T

last: Umetsu

first: Gordon

last: Freeman


title: Jurkat T cell gene expression with IKKe gene knockdown and PMA and ionomycin stimulation

status: Public on Mar 11 2016

city: Wuhan

first: Junjie

last: Zhang

state: Hubei

address: Donghu Road, No. 115

department: Medical Research Institute

country: China

institute: Wuhan University

summary: We used microarray to monitor the differentially expresed genes during Jurkat T cell activaiton.

overall_design: Jurkat T cells with control shRNA or IKKe shRNA were treated with solvent or PMA and ionomycin for 3 h, and then RNA was extracted and applied to microarray analysis

first: Pinghui

last: Feng


title: Expression data from gemcitabine treated pancreatic CAFs

status: Public on Mar 09 2016

first: Paul

last: Toste

institute: UCLA

summary:
Pancreatic ductal adenocarcinoma (PDAC) has a characteristically dense stroma comprised predominantly of cancer associated fibroblasts (CAFs). CAFs promote tumor growth, metastasis and treatment resistance. We aimed to investigate the molecular changes and functional consequences associated with chemotherapy treatment of PDAC CAFs.
Chemoresistant immortalized CAFs (R-CAFs) were generated by continuous incubation in 100nM gemcitabine. Gene expression differences between treatment naïve CAFs (N-CAFs) and R-CAFs were compared by array analysis.

overall_design: Immortalized human pancreatic CAFs were grown for 30 days in either control media or media containing 100nM gemcitabine. RNA was then isolated and hybidized on U133 Plus 2.0 Affymetrix arrays.

first: Andrew

last: Nguyen

first: Brian

last: Kadera

first: Mindy

last: Duong

first: Nanping

last: Wu

first: Irmina

last: Gawlas

first: Linh

last: Tran

first: Mihir

last: Bikhchandani

first: Luyi

last: Li

first: Sanjeet

middle: G

last: Patel

first: David

last: Dawson

first: Timothy

middle: R

last: Donahue


title: Genome wide mapping of NR4A binding reveals cooperativity with ETS factors to promote epigenetic activation of distal enhancers in acute myeloid leukemia cells [array]

first: Orla

last: Conneely

address: One Baylor Plaza

institute: Baylor College of Medicine

summary: NR4As are critical tumor suppressors of acute myeloid leukemia (AML) whose expression is broadly silenced in leukemia initiating cell enriched populations from human patients relative to normal hematopoietic stem/progenitor cells. Rescued NR4A expression in human AML cells inhibits proliferation and reprograms AML gene signatures via transcriptional mechanisms that remain to be elucidated. By intersecting an acutely regulated, NR4A1 dependent transcriptional profile with genome wide NR4A binding distribution, we now identify an NR4A targetome of 685 genes that are directly regulated by NR4A1. We show that NR4As regulate gene transcription primarily through interaction with distal enhancers that are co-enriched for both NR4A1 and ETS transcription factor motifs. Using a subset of NR4A activated genes, we demonstrate that the ETS factors ERG and FLI-1 are required for activation of NR4A bound enhancers and NR4A target gene induction. NR4A1 dependent recruitment of ERG and FLI-1 promotes binding of p300 histone acetyl transferase to activate NR4A bound enhancers. These findings disclose novel epigenetic mechanisms by which NR4As and ETS factors cooperate to drive NR4A dependent gene transcription in human AML cells.

overall_design: Transcriptome analysis in triplicate 6hr after exogenous NR4A1 expression compared to GFP transfection control.

first: Ryan

last: Duren

first: Seth

last: Boudreaux


title: DNA methylation profiling in human Huntington's Disease brain

city: Vancouver

first: Michael

middle: S.

last: Kobor

state: BC

address: 950 West 28th Avenue

department: Medical Genetics

country: Canada

institute: Centre for Molecular Medicine and Therapeutics / University of British Columbia

summary: Despite extensive progress in Huntington’s Disease (HD) research, very little is known about the association of epigenetic variation and HD pathogenesis in human brain tissues. Moreover, its contribution to the tissue-specific transcriptional regulation of the huntingtin gene (HTT), in which HTT expression levels are highest in brain and testes, is currently unknown. To investigate the role of DNA methylation in HD pathogenesis and tissue-specific expression of HTT, we utilized the Illumina HumanMethylation450K BeadChip array to measure DNA methylation in a cohort of age-matched HD and control human cortex and liver tissues. In cortex samples, we found minimal evidence of HD-associated DNA methylation at probed sites after correction for cell heterogeneity but did observe an association to age of disease onset. By contrast, comparison of matched cortex and liver samples revealed tissue-specific DNA methylation of the HTT gene region at 38 sites (FDR < 0.05). Importantly, we identified a novel differentially methylated binding site in the HTT proximal promoter for the transcription factor CTCF. This CTCF site displayed increased occupancy in cortex, where HTT expression is higher, compared to liver. Additionally, CTCF silencing reduced the activity of a HTT promoter-reporter construct, suggesting that CTCF plays a role in regulating HTT promoter function. Overall, although we were unable to detect HD-associated DNA methylation alterations at queried sites, we found that DNA methylation may be correlated to age of disease onset in cortex tissues. Moreover, our data suggest that DNA methylation may, in part, contribute to tissue-specific HTT transcription through differential CTCF occupancy.

overall_design: The Illumina Infinium HumanMethylation450 Beadchip was used to obtain genome-wide DNA methylation measures in human cortex tissue (n = 13), with a subset of matched liver tissues (n = 5) , from a cohort of HD (n = 7)  and control (n = 6) individuals in order to identify potential HD-related DNA methylation aberration in the brain as well as tissue-specific DNA methylation variation at the HTT gene locus.

first: Rebecca

last: De Souza

first: Sumaiya

last: Islam

first: Lisa

last: McEwen

first: Anthony

last: Mathelier

first: Austin

last: Hill

first: Sarah

last: Mah

first: Wyeth

last: Wasserman

first: Blair

last: Leavitt


title: SMARCB1-deficient rhaboid tumors of the kidney and renal medullary carcinomas.

status: Public on Mar 08 2016

city: Paris

first: Wilfrid

last: Richer

address: 26 rue d'Ulm

institute: Institut Curie

summary: We used microarrays to compared gene expression profilings in various tumors of the kidney.

overall_design: [human mRNA] 8 human RTK, 5 human RMC.

first: Franck

last: Bourdeaut

first: Julien

last: Masliah Planchon


title: Effect of Kurozu on hippocampal gene expression profiles in SAMP8

city: Aomori

first: Yuji

last: Nakai

state: Aomori

address: 2-1-1, Yanagawa

department: Institute of Regional Innovation

institute: Hirosaki University

summary: Kurozu is a traditional Japanese rice vinegar. During fermentation and aging of the Kurozu liquid in an earthenware jar over 1 year, solid residue called Kurozu Moromi is produced. In the present study, we evaluated whether concentrated Kurozu or Kurozu Moromi could ameliorate cognitive dysfunction in the senescence accelerated P8 mouse. Senescence accelerated P8 mice were fed 0.25% (w/w) concentrated Kurozu or 0.5% (w/w) Kurozu Moromi for 4 or 25 weeks. Kurozu suppressed cognitive dysfunction and amyloid accumulation in the brain, while Kurozu Moromi showed a tendency to ameliorate cognitive dysfunction, but the effect was not significant. We hypothesize that concentrated Kurozu has an antioxidant effect, however, the level of lipid peroxidation in the brain did not differ in senescence accelerated P8 mice. DNA microarray analysis indicated that concentrated Kurozu increased HSPA1A mRNA expression, a protein that prevents protein misfolding and aggregation. The increase in HSPA1A expression by Kurozu was confirmed using quantitative real-time PCR and immunoblotting methods. Therefore, the suppression of amyloid accumulation by concentrated Kurozu may be associated with HSPA1A induction. However, concentrated Kurozu could not increase HSPA1A expression in mouse primary neurons, suggesting it may not directly affect neurons.

overall_design: Ten-times concentrated Kurozu (CK) was made from Kurozu liquid (Sakamoto Kurozu, Fukuyama, Kagoshima, Japan) by repeated vacuum distillation. The CK diet included 0.25% (w/w) CK in CE-2 basic rodent diet (Nihon CLEA, Tokyo, Japan). Senescence resistance (R1) and senescence accelerated P8 (P8) mice were purchased from Japan SLC (Shizuoka, Japan). Mice were housed at 25±2°C with 55±10% humidity on a 12-h light/dark cycle (lighting time 08:00-20:00). All mice were housed in independent cages and had free access to food and water. All procedures were compliant with the guidelines of the Kagoshima University Animal Ethics Committee (A10030). Ten-week old R1 mice (n=16) were fed a control CE2 diet and P8 mice were divided into three groups as follows: control CE2 diet group (n=9), KM diet group (n=9) or CK diet group (n=9). Feeding of the experimental diet started from 12 weeks of age until sacrificed. All mice were sacrificed under anesthesia at 17 weeks old (4 months old). The left side of the hippocampus region was excised from brains of 4 mice selected at random in each group, and then subjected to microarray analysis.

first: Hiroaki

last: Kanouchi

first: Toshiaki

last: Kakimoto

first: Mitsuharu

last: Matsumoto

first: Masanobu

last: Nagano


title: Longitudinal DNA Methylome analysis from saliva sample of adolescents with anxiety disorders and controls to anxiety disorders

city: Porto Alegre

first: Andressa

last: Bortoluzzi

state: RS

address: Ramiro Barcelos, 2350

department: Psychiatric

country: Brazil

institute: Universidade Federal do Rio Grande do Sul -UFRGS

summary: A cohort of adolescents and young adults took part in this longitudinal 5-year follow-up study. We selected four groups of subjects from the same community sample carefully paired by age and gender: (1) Typically Developing Adolescent (n=14); (2) Incident Anxiety Disorder (n=11); (3) Persistent Anxiety Disorder (n=14); (4) Remittent Anxiety Disorder (n=8).

overall_design: Bisulphite converted DNA from the 96 samples (2 replicated) were hybridized to the Illumina Infinium 450K Human Methylation Beadchip

first: Gisele

last: Manfro

first: Giovanni

last: Salum

first: Eduarda

middle: D

last: da Rosa

first: Mauro

last: Castro

first: Edenir

middle: I

last: Palmero

first: Lidia

last: Arantes

first: Vinícius

last: Chagas


title: MCT1 modulates cancer cell pyruvate export and growth of tumors that co-express MCT1 and MCT4

first: Nicholas

middle: Alexander

last: Graham

address: 570 Westwood Blvd, CNSI 4338

department: Molecular and Medical Pharmacology

institute: University of California, Los Angeles

summary: Many cancers rely on glycolytic metabolism to fuel rapid proliferation.  This has spurred interest in designing drugs that target tumor glycolysis such as AZD3965, a small molecule inhibitor of Monocarboxylate Transporter 1 (MCT1) currently undergoing Phase I evaluation for cancer treatment.  Since MCT1 mediates proton-linked transport of monocarboxylates such as lactate and pyruvate across the plasma membrane (Halestrap and Meredith, 2004), AZD3965 is thought to block tumor growth through disruption of lactate transport and glycolysis.   Here we show that MCT1 inhibition impairs proliferation of glycolytic breast cancer cells that express MCT4 via disruption of pyruvate rather than lactate export.  We found that MCT1 expression is elevated in glycolytic breast tumors and cell lines as well as in malignant breast and lung tissues.  High MCT1 expression predicts poor prognosis in breast and lung cancer patients.  Stable knockdown and AZD3965-mediated inhibition of MCT1 promote oxidative metabolism.  Acute inhibition of MCT1 reduces pyruvate export rate but does not consistently alter lactate transport or glycolytic flux in breast cancer cells that also express MCT4.  Despite the lack of glycolysis impairment, MCT1 loss-of-function decreases breast cancer cell proliferation and blocks growth of mammary fat pad xenograft tumors. Our data suggest that MCT1 expression is elevated in glycolytic cancers to promote pyruvate export, which when inhibited enhances oxidative metabolism and reduces proliferation.  This study presents an alternative molecular consequence of MCT1 inhibitors that further supports their use as anti-cancer therapeutics.

overall_design: Since MCT1 levels are elevated in glycolytic and malignant breast tumors, we hypothesized that MCT1 may contribute to the Warburg effect metabolic phenotype.  To test this hypothesis, we generated whole genome microarray data from breast cancer cell lines either a) expressing a short hairpin (sh)RNA-mediated stable knockdown of MCT1; or b) treated for 24 hours with an MCT1 inhibitor (AZD3965).  Scramble shRNA or DMSO were used as controls, and all conditions were analzed in triplicate.  The cell lines used – HS578T, SUM149PT, and SUM159PT – are among the most glycolytic in a panel of 31 breast cancer cell lines.

first: Candice

last: Hong

first: Thomas

last: Graeber

first: Heather

last: Christofk


title: Temporal analysis of RNA turnover in Interferon Gamma treated bone marrow-derived macrophages

status: Public on Mar 07 2016

city: Edinburgh

first: Peter

last: Ghazal

state: Lothian

address: 49 Little France Crescent

department: Division of Infection and Pathway Medicine

country: United Kingdom

institute: University of Edinburgh

summary:
Interferon gamma treatment of macrophages results in hundreds if not thousands of alterations in gene expression and an antiviral state being established in these cells. Little is known about relationship between transcript synthesis, abundance and decay in macrophages during the first hours after interferon gamma treatment and how these factors influence the antiviral cellular phenotype.
Microarrays were used to analyse alterations in transcript synthesis and abundance in BMDM treated with Interferon Gamma for 8h.

overall_design: Bone Marrow derived macrophages (BMDM) were grown using L929 conditioned medium. On day 7, BMDM were mock-treated (16x 15cm dishes) or treated (16x 15cm dishes) with 10U/ml interferon gamma at time zero. 4-thiouridine (4sU) was then used to label newly transcribed RNA every 30 minutes for 8h (0 to 30, 30 to 60 etc. to give 16 discrete successive labellings) in mock and interferon gamma-treated samples. 16x Mock and 16x treated total samples were then isolated (32 in total) and newly transcribed RNA isolated from each total RNA sample using a protocol described in Dolken et al (PMID: 18658122). For analysis, 32 (16x mock and 16x treated) newly-transcribed RNA samples (every 30 minutes for complete 8h time course) and 16 (8x mock and 8x treated) total RNA samples (every hour for 8h time course) were hybridized to Affymetrix GeneST v1.0 arrays.

first: Kevin

last: Robertson


title: A Preclinical Model for ERα-Positive Breast Cancer Points to the Epithelial Microenvironment as Determinant of Luminal Phenotype and Hormone Response [BT20 & HCC1806]

status: Public on Mar 03 2016

city: Lausanne

first: George

last: Sflomos

address: SV 2815, Batiment SV, Station 19

department: ISREC

institute: EPFL

summary: A high percentage of potential oncology drugs fail in clinical trials, partly because preclinical models used to test them are inadequate. Breast cancer is the leading cause of cancer-related death among women worldwide but we lack appropriate in vivo models for the ER+ subtypes, which represent more than 75% of all cases. We address these issues by xenografting tumor cells to their site of origin, the milk ducts. All ER+ cell lines and patient-derived xenografts grow mimicking their clinical counterparts. Disease progresses with invasion and metastasis, which become amenable to study. The action of hormones, important in breast carcinogenesis, can now be studied in a relevant context. Importantly, these open opportunities for development and evaluation of therapies.

overall_design: Eight- to twelve-week-old female SCID Beige mice (Charles River) were injected with 5x10e5 BT20-GFP/luc2 cells (n=3) or 5x10e5 HCC1806-GFP/luc2 cells (n=3) either into the mammary fat pad or 2x10e5 BT20-GFP/luc2 cells (n=3) or 2x10e5 HCC1806-GFP/luc2 cells intraductally (n=3). Xenografted BT20 and HCC1806 basal breast cancer cells were sorted by FACS based on GFP expression; total RNA was extracted using Trizol Reagent (Invitrogen), purified with the miRNeasy Mini Kit (Qiagen), quantity and quality were assessed by NanoDrop®ND-1000 spectrophotometer and RNA 6000 NanoChips with the Agilent 2100 Bioanalyzer (Agilent, Palo Alto, USA). Only samples with RIN score >7.0 were included. For each sample, 300 ng of total RNA were amplified using the message amp II enhanced kit (AM1791, Ambion). 12.5 μg of biotin-labelled cRNA were chemically fragmented. Affymetrix GeneChip Human Genome U133A 2.0 Arrays (Affymetrix, Santa Clara, CA, USA) were hybridized with 11μg of fragmented target, at 45°C for 17 hours, washed and stained according to Affymetrix GeneChip® Expression Analysis Manual (Fluidics protocol FS450_0007). Arrays were scanned using the GeneChip® Scanner 3000 7G (Affymetrix) and raw data was extracted from the scanned images and analyzed with the Affymetrix Power Tools software package (Affymetrix). All statistical analyses were performed using R and Bioconductor packages (http://www.Bioconductor.org). Hybridization quality was assessed using the Expression Console software (Affymetrix). Normalized expression signals were calculated from Affymetrix CEL files using RMA. Differential hybridized features were identified using Bioconductor package “limma” that implements linear models for microarray data (Smyth, 2004). P values were adjusted for multiple testing with Benjamini and Hochberg’s method to control false discovery rate (FDR) (Benjamini et al., 2001). Probe sets showing ≥2-fold change and a FDR ≤0.05 were considered significant.


title: Effect of 4-hydroxytamoxifen and Shld1 on mouse embryonic stem cells (RW4)

status: Public on Mar 04 2016

city: St. Louis

first: Zongtai

last: Qi

state: Missouri

address: 4515 Mckinley Ave

institute: Washington University in St Louis

summary: Two induction systems, one based on the destablization domain (FKBP) and the other based on mutated ligand-binding domain of the estrogen receptor, require constant application of Shld1 and 4-hydroxytamoxifen (4OHT) to cells respectively, so we sought to quantify the extent to which these chemical inducers affect transcriptional networks. RW4 mouse ES cells were treated with Shld1 and 4-OHT respectively for 2 days and then subjected to gene expression profiling by microarray. Cells mock-treated with 95% ethanol as vehicle were used as controls. For each condition, two biological replicates were performed .

overall_design: RW4 ESCs were treated with 1 μM 4-hydroxytamoxifen (4-OHT, Sigma) for the ERT2 based induction system and 1μM Shld1 (Clontech) for FKBP based induction system, respectively.


title: Altered DNA methylation of glycolytic and lipogenic genes in liver from obese and type 2 diabetic patients [methylome analysis]

city: Huddinge

first: Karin

last: Dahlman-Wright

address: Blickagången 16

department: Department of Biosciences and Nutrition

country: Sweden

institute: Karolinska Institutet

summary: Type 2 diabetes is a complex disease associated with many underlying pathomechanisms. Epigenetic regulation of gene expression by DNA methylation has become increasingly recognized as an important component in the etiology of type 2 diabetes. We performed genome-wide methylome and transcriptome analysis in liver from severely obese patients with or without type 2 diabetes to discover aberrant pathways underlying the development of insulin resistance. We identified hypomethylation of five key genes involved in hepatic glycolysis, de novo lipogenesis and insulin resistance with concomitant increased mRNA expression and protein content. The CpG-site within the ATF-motif was hypomethylated in four of these genes in liver of non-diabetic and type 2 diabetic obese patients, suggesting epigenetic regulation of transcription by altered ATF-DNA binding.  In conclusion, severely obese non-diabetic and type 2 diabetic patients have distinct alterations in the hepatic methylome and transcriptome and genes controlling glucose and lipid metabolism are hypomethylated at a regulatory site. Thus, obesity may epigenetically reprogram the liver towards increased lipid production and exacerbate the development of insulin resistance.

overall_design: To better understand the molecular mechanisms underlying the development of hepatic insulin resistance and type 2 diabetes at a molecular level, we performed a genome-wide methylome and transcriptome analysis of liver from non-obese metabolically healthy, obese non-diabetic and obese type 2 diabetic patients. Distinct DNA methylation and gene expression profiles were identified in liver from the obese and type 2 diabetic patients compared with the non-obese participants.

first: Henriette

last: Kirchner

first: Indranil

last: Sinha

first: Hui

last: Gao

first: Maxwell

last: Ruby

first: Milena

last: Schönke

first: Jessica

middle: M

last: Lindvall

first: Romain

last: Barres

first: Anna

last: Krook

first: Erik

last: Näslund

first: Juleen

last: Zierath


title: Altered DNA methylation of glycolytic and lipogenic genes in liver from obese and type 2 diabetic patients

type:
Methylation profiling by array
Expression profiling by array


title: Insulin receptor substrate adaptor proteins mediate prognostic gene expression profiles in breast cancer

status: Public on Mar 05 2016

city: Rochester

first: Marc

last: Becker

state: MN

address: 200 First St SW

department: Medical Oncology

institute: Mayo Clinic

summary: Therapies targeting the type I insulin-like growth factor receptor (IGF-1R) have not been developed with predictive biomarkers to identify tumors with receptor activation.  We have previously shown that the insulin receptor substrate (IRS) adaptor proteins are necessary for linking IGF1R to downstream signaling pathways and the malignant phenotype in breast cancer cells.  The purpose of this study was to identify gene expression profiles downstream of IGF1R and its two adaptor proteins.  IRS-null breast cancer cells (T47D-YA) were engineered to express IRS-1 or IRS-2 alone and their ability to mediate IGF ligand-induced proliferation, motility, and gene expression determined. Global gene expression signatures reflecting IRS adaptor specific and primary vs. secondary ligand response were derived (Early IRS-1, Late IRS-1, Early IRS-2 and Late IRS-2) and functional pathway analysis examined. IRS isoforms mediated distinct gene expression profiles, functional pathways, and breast cancer subtype association. For example, IRS-1/2-induced TGFb2 expression and blockade of TGFb2 abrogated IGF-induced cell migration. In addition, the prognostic value of IRS proteins was significant in the luminal B breast tumor subtype. Univariate and multivariate analyses confirmed that IRS adaptor signatures correlated with poor outcome as measured by recurrence-free and overall survival.  Thus, IRS adaptor protein expression is required for IGF ligand responses in breast cancer cells. IRS-specific gene signatures represent accurate surrogates of IGF activity and could predict response to anti-IGF therapy in breast cancer.

overall_design: Microarrays were employed to elucidate IGF ligand regulated global transcription in IRS isogenic breast cancer cells and identify differentially expressed genes in IRS-1 vs. IRS-2 lines.

first: Doug

last: Yee


title: Gene Expression Profiles of 4 CRC PDX models treated by RSPO3 antagonist.

city: Redwood City

first: Ann

last: Kapoun

address: 800 Chesepeake Drive

department: Translational Medicine

institute: Oncomed Pharmaceuticals

summary:
RSPO is a WNT pathway activator and functions as a potent regulator of stem cell growth in colon. RSPO family members were produced by several human tumors representing multiple tumor types including ovarian, pancreatic, colon, breast and lung cancer.  Specific monoclonal antibody antagonists of RSPO family members were developed. In human patient-derived tumor xenograft models, anti-RSPO treatment markedly inhibited tumor growth either as single agents or in combination with chemotherapy. Furthermore, blockade of RSPO signaling reduced the tumorigenicity of cancer cells based on serial transplantation studies.
In order to assess the impact of RSPO3 inhibition and gain insight in the anti-RSPO3 treatment mechanism of action, the global gene expression profiles of 4 human colorectal cancer patient derived models (PDX) were performed using Affymetrix microarray for the xenografts treated by the anti-RSPO3 antibody.

overall_design: 4 CRC PDX models were treated by control anbodies, anti-RSPO3 antibodies, or anti-RSPO3 antibodies combined with standard-of-care. 4 weeks after the treatment, tumors were harvesed for the microarray analysis

first: Min

last: Wang


title: A Preclinical Model for ERα-Positive Breast Cancer Points to the Epithelial Microenvironment as Determinant of Luminal Phenotype and Hormone Response

first: George

last: Sflomos

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

overall_design: Refer to individual Series


title: Integrative functional genomic analysis identifies epigenetically regulated Fibromodulin as an essential gene for glioma cell migration

status: Public on Mar 12 2016

city: Toronto

first: Vikas

last: Patil

state: Ontario

address: 610 University Ave.

institute: Princess Margaret Cancer Center

summary: An integrative functional genomics of multiple forms of data is vital for discovering molecular drivers of cancer development and progression. Here, we present an integrated genomic strategy utilizing DNA methylation and transcriptome profile data to discover epigenetically regulated genes implicated in cancer development and invasive progression. More specifically, this analysis identified Fibromodulin (FMOD) as a glioblastoma (GBM) upregulated gene due to the loss of promoter methylation. Secreted FMOD promotes glioma cell migration through its ability to induce filamentous actin stress fiber formation. Treatment with Cytochalasin D, an actin polymerization inhibitor, significantly reduced the FMOD induced glioma cell migration. siRNA and small molecule inhibitor-based studies identified that FMOD-induced glioma cell migration is dependent on Integrin-FAK-Src-Rho-ROCK signaling pathway. FMOD lacking C terminus LRR11 domain (FMOD), which does not bind collagen type I, failed to induce integrin and promote glioma cell migration. Further, FMOD-induced integrin activation and migration was abrogated by a 9-mer wild type peptide from the FMOD C-terminus. However, the same peptide with mutation in two residues essential for FMOD interaction with collagen type I failed to compete with FMOD, thus signifying the importance of collagen type I-FMOD interaction in integrin activation. ChIP-PCR experiments revealed that TGF-ß1 regulates FMOD expression through epigenetic remodeling of FMOD promoter that involved demethylation and gain of active histone marks with a simultaneous loss of DNMT3A and EZH2 occupancy, but enrichment of SMAD2 and CBP. FMOD silencing inhibited the TGF-ß1 mediated glioma cell migration significantly. In univariate and multivariate cox regression analysis, both FMOD promoter methylation and transcript levels predicted prognosis in GBM. Thus, the present study identified several epigenetically regulated alterations responsible for cancer development and progression. Specifically, we found that secreted FMOD as an important regulator of glioma cell migration downstream of TGF-ß1 pathway and forms a potential basis for therapeutic intervention in GBM.

overall_design:
We used DNA isolated from 17 diffuse astrocytoma, 16 anaplastic astrocytoma, 36 glioblastoma and 9 control brain tissue for the array.
P53 status: All cases were subjected to histopathology and the diagnosis of GBM was confirmed. Paraffin sections (4 μm) from the tissues were collected on silane-coated slides, and the protein expression of p53 was assessed by immunohistochemistry (IHC). Antigen retrieval was done by heat treatment at 850W in citrate buffer or at 700W. After the initial processing steps, sections were incubated overnight with primary antibody for p53 (Mouse Monoclonal DO-7; Biogenex, USA)at 4°C with 1: 200 dilution.
MIB: Paraffin blocks of all the cases were retrieved, and histological features were reviewed on freshly cut and stained (hematoxylin and eosin) sections. After confirming the diagnosis of glioblastoma, 4 µm thick sections were collected on silane-coated slides, and IHC was performed using MIB-1 (anti Ki-67 monoclonal BGX 297, diluted to 1:30)
EGFR status: Paraffin blocks of all the cases were retrieved, and histological features were reviewed on freshly cut and stained (hematoxylin and eosin) sections. After confirming the diagnosis of glioblastoma, 4 µm thick sections were collected on silane-coated slides, and IHC was performed using EGFR (monoclonal E-30, diluted to 1:50)
GFAP status: Paraffin blocks of all the cases were retrieved, and histological features were reviewed on freshly cut and stained (hematoxylin and eosin) sections. After confirming the diagnosis of glioblastoma, 4 µm thick sections were collected on silane-coated slides, and IHC was performed using glial fibrillary acidic protein (GFAP, monoclonal GA-5, diluted to 1:100).

first: Baisakhi

last: Mondal

first: Shwetha

last: Shivayogi

first: Sravani

last: Kotha

first: A

last: Hegde

last: Arivazhagan

first: Vani

last: Santosh

first: Meena

last: Kanduri

first: Kumaravel

last: Somasundaram


title: A Preclinical Model for ERα-Positive Breast Cancer Points to the Epithelial Microenvironment as Determinant of Luminal Phenotype and Hormone Response [MCF7]

overall_design: Eight- to twelve-week-old female SCID Beige mice (Charles River) were injected with 2x10e5 MCF7-DsRed/luc2 cells (n=3) either into the mammary fat pad or 5x10e4 MCF7-DsRed/luc2 cells intraductally (n=3). Xenografted MCF7 were FACS sorting based on DsRed expression; total RNA was extracted using Trizol Reagent (Invitrogen), purified with the miRNeasy Mini Kit (Qiagen), quantity and quality were assessed by NanoDrop®ND-1000 spectrophotometer and RNA 6000 NanoChips with the Agilent 2100 Bioanalyzer (Agilent, Palo Alto, USA). Only samples with RIN score >7.0 were included. For each sample, 300 ng of total RNA were amplified using the message amp II enhanced kit (AM1791, Ambion). 12.5 μg of biotin-labelled cRNA were chemically fragmented. Affymetrix GeneChip Human Genome U133A 2.0 Arrays (Affymetrix, Santa Clara, CA, USA) were hybridized with 11μg of fragmented target, at 45°C for 17 hours, washed and stained according to Affymetrix GeneChip® Expression Analysis Manual (Fluidics protocol FS450_0007). Arrays were scanned using the GeneChip Scanner 3000 7G (Affymetrix) and raw data was extracted from the scanned images and analyzed with the Affymetrix Power Tools software package (Affymetrix). All statistical analyses were performed using R and  Bioconductor packages (http://www.Bioconductor.org). Hybridization quality was assessed using the Expression Console software (Affymetrix). Normalized expression signals were calculated from Affymetrix CEL files using RMA. Differential hybridized features were identified using Bioconductor package “limma” that implements linear models for microarray data (Smyth, 2004). P values were adjusted for multiple testing with Benjamini and Hochberg’s method to control false discovery rate (FDR) (Benjamini et al., 2001). Probe sets showing ≥2-fold change and a FDR ≤0.05 were considered significant.


title: Analysis of Mll1-deficiency identifies neurogenic transcriptional modules and Brn4 as a factor for direct astrocyte-to-neuron reprogramming

status: Public on Mar 06 2016

city: San Francisco

first: Daniel

last: Lim

address: 35 Medical Center Way RMB 933B

department: Neurological Surgery

institute: University of California, San Francisco

summary:
BACKGROUND: Mixed lineage leukemia-1 (Mll1) epigenetically regulates gene expression patterns that specify cellular identity in both embryonic development and adult stem cell populations. In the adult mouse brain, multipotent neural stem cells (NSCs) in the subventricular zone (SVZ) generate new neurons throughout life and Mll1 is required for this postnatal neurogenesis but not for glial cell differentiation. Analysis of Mll1-dependent transcription may identify neurogenic genes useful for the direct reprogramming of astrocytes into neurons.
OBJECTIVE: To identify Mll1-dependent transcriptional modules and determine whether genes in the neurogenic modules can be used to directly reprogram astrocytes into neurons.
METHODS: We performed gene coexpression module analysis on microarray data from differentiating wild-type and Mll1-deleted SVZ NSCs. Key developmental regulators belonging to the neurogenic modules were overexpressed in Mll1-deleted cells and cultured cortical astrocytes, and cell phenotypes were analyzed by immunocytochemistry and electrophysiology.
RESULTS: Transcriptional modules that correspond to neurogenesis were identified in wild-type NSCs. Modules related to astrocytes and oligodendrocytes were enriched in Mll1-deleted NSCs, consistent with their gliogenic potential. Overexpression of genes selected from the neurogenic modules enhanced the production of neurons from Mll1- deleted cells, and the overexpression of Brn4 (Pou3f4) in non-neurogenic cortical astroglia induced their transdifferentiation into electrophysiologically active neurons.
CONCLUSIONS: Our results demonstrate that Mll1 is required for the expression of neurogenic - but not gliogenic - transcriptional modules in a multipotent NSC population and further indicate that specific Mll1-dependent genes may be useful for direct reprogramming strategies.

overall_design: Comparison of gene expression changes during a differentiation time course between Mll1-deleted SVZ NSCs vs. control.

first: Matthew

middle: B

last: Potts

first: Jason

last: Siu


title: Expression data from Burkitt Lymphoma cell lines followed by expression or inhibition of ebv-BART6-3p microRNA

status: Public on Mar 02 2016

city: Siena

first: Mohsen

last: Navari

state: SI

address: Via delle Scotte 6

department: Medical Biotechnology

country: Italy

institute: University of Siena

summary:
Epstein-Barr virus is associated with several human malignancies, including Burkitt Lymnphoma. The virus encodes more than 40 microRNAs, which participate in its possible pathogenetic role.
We used microarrays to study the effect of the expression of an Epstein-Barr virus-encoded microRNA (ebv-BART6-3p) on the global gene expression profile of Burkitt Lymphoma cell lines.

overall_design: In order to determine the BART6-3p targets, EBV-negative Akata 2A8 or EBV-positive Akata cells were transiently transfected (in duplicates) with synthetic BART6-3p mimic or inhibitor (100 nM; Custom synthesized by Dharmacon- Thermo Scientific, Germany), respectively. For each treatment, a further transfection with corresponding negative control was performed as well (10 nM; I-300145-01, Dharmacon- Thermo Scientific, Germany). The transfection of 5,000,000 cells per treatment was performed by Amaxa nucleofector apparatus (Amaxa, Cologne-Germany), using the program G23 and the transfection solution V according to the manufacturer’s instructions. Transfection efficiency was assessed by means of a further treatment (2µg of pmaxGFP) and detection of both fluorescence and cell viability by flow cytometry. Twenty four hours post-transfection, cells were harvested and RNA was extracted using Trizol, and transfection efficiency was further confirmed by evaluating the expression level of BART6-3p using q-PCR by means of Taqman probes, employing RNU43 as housekeeping miRNA (Applied Biosystems, Cologne, Germany). RNA was further hybridized to HuGene-2.0-st array (Affymetrix, Santa Clara, CA) according to the manufacturer's instructions.

first: Fabio

last: Fulini

first: Maria

last: Laginestra

first: Maryam

last: Etebari

first: Lorenzo

last: Leoncini

first: Stefano

last: Pileri

first: Pier

last: Piccaluga


title: Expression of mRNAs in 230-238 B-cell line infected with a plasmid encoding the GFP protein or a plasmid encoding both the GFP and FOG1 proteins

city: Basel

first: Tim

last: Roloff

address: Maulbeerstrasse 66

institute: FMI

summary: The overexpression of Friend Of GATA1 (FOG1) in early B-cell stages may promote the proliferation of B-cells by changing the expression level of a certain number of key genes involved in cell cycle control.

overall_design: The 230-238 cell line was either infected with a plasmid encoding the GFP protein or a plasmid encoding both the GFP and FOG1 proteins. After infection, cells were put in culture in RPMI1640 medium for 3 days before to be sorted for being GFP+. They were put back again in culture for 4 days more after the sort. Then, RNA isolation was performed using the following QIAGEN kit: RNeasy micro without DNase treatment.

first: Aude

last: Versavel

first: Stephane

last: Thiry


title: Transcriptomic data of UCSF4 human embryonic stem cells (hESCs) and their neural derivatives

status: Public on Mar 01 2016

city: SAN FRANCISCO

first: Joshua

middle: F

last: Robinson

address: 513 Parnassus Ave HSE16

department: Obstretrics, Gynecology and Reproductive Sciences

summary: To compare transcriptomic profiles between UCSF4 hESCs and their neural derivatives, neural precursor cells (NPCs), we performed microarray analysis using the Affymetrix Human Gene 2.0 ST array platform.

overall_design: Six biological samples, three biological replicates for each developmental cell stage (in vitro)

first: Susan

last: Fisher


title: Gene expression after knocking down of c-Met in breast cancer brain metastatic cell lines

city: Winston-Salem

first: fei

last: xing

state: North Carolina

address: 1 Medical Center Blvd

department: cancer biology

institute: wake forest baptist health

summary: The purpose of this study is to identify the target genes of c-Met signaling in breast cancer brain metastasis.

overall_design: 231BrM/Dox/shMet and SKBrM3/Dox/shMet cells were treated with or without doxycycline  for 48hrs.

first: F

last: Xing

first: Y

last: Lium

first: S

last: Sharma

first: K

last: Wu

last: Watanabe


title: EWS-FLI1-induced osteosarcoma model unveiled a crucial role of impaired osteogenic differentiation on osteosarcoma development [gene expression]

city: Tokyo

first: Yasuhiro

last: Yamada

address: 7-3-1 Hongo, Bunkyo-ku

department: Department of Molecular Pathology

institute: University of Tokyo

summary: EWS-FLI1, a multi-functional fusion oncogene, is exclusively detectable in Ewing sarcomas. However, previous studies reported that a subset of osteosarcomas also harbor EWS-ETS family fusion, suggesting that the fusion gene may be involved in the development of a particular type of osteosarcomas. Here using the doxycycline inducible EWS-FLI1 system, we established an EWS-FLI1-dependent osteosarcoma model from murine bone marrow stromal cells. We revealed that the withdrawal of EWS-FLI1 expression enhances the osteogenic differentiation of sarcoma cells, leading to mature bone formation. Taking advantage of induced pluripotent stem cell (iPSC) technology, we also showed that the sarcoma-derived iPSCs with cancer-related genetic abnormalities exhibited the impaired differentiation program of osteogenic lineage irrespective of the EWS-FLI1 expression. Finally, we demonstrated that EWS-FLI1 contributed to in vitro sarcoma development from the sarcoma-iPSCs after osteogenic differentiation. These findings demonstrated that modulating cellular differentiation is fundamental principle of the EWS-FLI1-induced osteosarcoma development. Furthermore, the in vitro cancer model using sarcoma-iPSCs should provide a novel platform for dissecting relationship between cancer genome and cellular differentiation.

overall_design: Microarray in mouse EWS-FLI1-induced osteosarcoma cell lines(SCOS#2 and SCOS#12) and sarcoma(SCOS#2)-derived iPSCs. Total 6 samples were analyzed.  We can induce EWS-FLI1 expression by Doxycycline-inducible expression system in SCOS#2 and #12. We investigaed EWS-FLI1 activated genes (Dox ON-High) and EWS-FLI1 repressed genes (Dox OFF-High) in SCOS#2 and #12 sarcoma cell lines. Also, we investigated global gene expression pattern of sarcoma-derived iPSCs (iPSC#2-A1 and #2-B5). A link to this sample file can be found below.

first: Shingo

last: Komura

first: Fumiaki

last: Itakura


title: Expression data comparing Hep3B Caveolin-1 (Cav1) knockdown cells with Hep3B non-target control cells

city: Hong Kong

first: Judy

middle: Wai Ping

last: Yam

address: Pokfulam

department: Department of Pathology

country: Hong Kong

institute: The University of Hong Kong

summary:
To identify genes regulated by Cav1
Affymetrix Human Genome U133 Plus 2.0 GeneChip

overall_design: Hep3B cells with or without knockdown of Cav1

middle: W


title: Global gene expression changes during immune complex-induced neutrophil activation (wild type and Card9‒/‒ cells)

status: Public on Feb 29 2016

city: Budapest

first: Attila

last: Mocsai

address: Tuzolto utca 37-47

department: Department of Physiology

country: Hungary

institute: Semmelweis University

summary:
--- Raw data of the Supplementary Table 1 of the Nature Communications article 'Neutrophil-specific deletion of the CARD9 gene expression regulator suppresses autoantibody-induced inflammation in vivo'
We used microarray to obtain global gene expression data of immobilised immune complex-activated mouse neutrophils in the presence and absence of the gene expression regulator molecule CARD9.

overall_design: Mouse neutrophils were isolated from the bone marrow and were plated on human serum albumin & anti-human serum albumin antibody-coated surfaces at a 4 x 106 cell concentration. Human serum albumin-coated surfaces served as controls. The cells were stimulated for 4 hours before RNA preparation. The experiments were done at 3 independent timepoints.

first: Tamás

last: Németh

first: Krisztina

last: Futosi

first: Cassian

last: Sitaru

first: Jürgen

last: Ruland

last: Mócsai


title: Similarity of PDXs between passages and lineages using Affymetrix mRNA expression data

city: Cambridge

last: Korn

state: MA

address: 250 Mass Ave

institute: Novartis

summary: PDX tumors at various passages post first implantation in nude mice

overall_design: PDX tumors were profiled at different passages when they reached ~400mm3

first: Hui

last: Gao

first: Tara

last: Naylor


city: Lund

first: Markus

last: Ringner

address: Sölvegatan 35

institute: Lund University

summary: We performed whole-genome methylation analysis using 450K Illumina BeadArrays on different human cell types. In total 24 experiments were performed. Dermal fibroblasts, three different epidermal melanocytes (dark, medium and light pigmentation), epidermal keratinocytes, mammary fibroblasts, mammary epithelial cells, mammary endothelial cells and mesenchymal stem cells were analyzed in technical duplicates. Unmethylated DNA were analyzed in technical duplicates. Two different normal breast tissue samples were analyzed. Finally peripheral blood leukocytes and an enzymatically methylated sample were analyzed.

overall_design: Genome-wide DNA methylation analysis of different cell types using Illumina Human Methylation 450K Beadchips.

last: Ringnér

first: Karolina

last: Holm

first: Johan

last: Staaf

first: Göran

last: Jönsson


title: DNA methylation profiling to assess pathogenicity of BRCA1 unclassified variants in breast cancer

city: London

first: Kirsty

last: Flower

address: Du Cane Road

institute: Imperial College London

summary: The Illumina Infinium 450k Human DNA methylation Beadchip was used to obtain DNA methylation profiles across  485,577 CpGs . Samples were restored FFPE DNA extracted from breast tumours in 3 groups; BRCA1 germline mutated tumours (BRCA1), BRCA1 germline wildtype tumours from women from high risk families (BRCAx) and the designated test variant tumours (BRCA1UV).

overall_design: Bisulphite converted DNA was hybridised to the Illumina Infinium 450k Human Methylation Beadchip

first: James

last: Flanagan


title: Expression data in liver from germ-free and conventional mice fed lard or fish oil for 11 weeks

city: Gothenbrug

first: Robert

last: Caesar

address: Gothenburg University

department: Wallenberg Laboratory

institute: Gothenburg University

summary: Dietary lipids and gut microbiota may both influence adipose tissue physiology. By feeding conventional and germ-free mice high fat diets with different lipid compositon we aimed to investigate how dietary lipids and the gut microbiota interact to influence inflammation and metabolism in the liver

overall_design: Wild-type C57Bl/6 male mice 11 weeks of age were fed isocaloric diets (45% kcal fat) with either menhaden fish oil (Research Diets, D05122102) or lard (Research Diets, D10011202) for 11 weeks. Liver samples were harvested at the end of the experiment and analyzed by microarray.

first: Fredrik

last: Bäckhed


title: Global gene expression profiles in whole blood total RNA from patients with lupus nephritis, before and after initiation of therapy

city: Brussels

first: Bernard

middle: Robert

last: Lauwerys

address: Avenue Hippocrate 10

department: Institut de Recherches Expérimentales et Cliniques

institute: Université catholique de Louvain

summary:
Patients with systemic lupus erythematosus are characterized by the spontaneous over-expression of interferon(IFN)-induced genes in peripheral blood RNA samples. In the present study, we wanted to study the evolution of the IFN gene signature in the peripheral blood of patients with lupus nephritis, before and after initiation of immunosuppressive therapy.
Strikingly, we found that immunosuppressive therapy did not strongly reduce the expression of IFN-induced genes in patients who responded to therapy, as indicated by decreased general and renal indices of disease activity. By contrast, the IFN gene signature decreased in patients developing renal failure.

overall_design: Global gene expression studies were performed in serial whole blood samples from SLE patients with a renal BILAG A prior to, 3 months, and 6 months after initiation of conventional immunosuppressive therapy (induction with high-dose corticosteroids, IV cyclophosphamide or oral mycophenolate during the first 3 months, followed by maintenance with moderate- to low-dose corticosteroids, azathioprine or mycophenolate). The expression of IFN-induced genes was analyzed, in comparison to global and renal indices of disease activity.

first: Julie

last: Ducreux

first: Frédéric

middle: A

last: Houssiau


title: Genome-wide DNA methylation analysis of breast cancer

summary: Aberrant DNA methylation is frequently observed in breast cancer. However, the relationship between methylation patterns and the heterogeneity of breast cancer has not been comprehensively characterized.    Whole-genome DNA methylation analysis using 450K Illumina BeadArrays was performed on 188 human breast tumors. Unsupervised bootstrap consensus clustering was performed to identify DNA methylation epigenetic subgroups (epitypes). The Cancer Genome Atlas data, incluing methylation profiles of 669 human breast tumors, was utilized for validation. The identified epitypes were characterized by integration with publicly available genome-wide data, including gene expression levels, DNA copy numbers, whole-exome sequencing data, and chromatin states.    We identified seven breast cancer epitypes. One epitype was distinctly associated with basal-like tumors and with BRCA1 mutations, one epitype contained a subset of ERBB2-amplified tumors characterized by multiple additional amplifications and the most complex genomes, and one epitype displayed a methylation profile similar to normal epithelial cells. Luminal tumors were stratified into the remaining four epitypes, with differences in promoter hypermethylation, global hypomethylation, proliferative rates and genomic instability. We observed two dominant patterns of aberrant methylation in breast cancer. One pattern, constitutively methylated in both basal-like and luminal breast cancer, was linked to genes with promoters in a Polycomb-repressed state in normal epithelial cells and displayed no correlation to gene expression levels. The second pattern correlated with gene expression levels and was associated with methylation in luminal tumors and genes with active promoters in normal epithelial cells.    Our results suggest that hypermethylation patterns in basal-like breast cancer may have limited influence on tumor progression and instead reflects the repressed chromatin state of the tissue of origin. On the contrary, hypermethylation patterns specific to luminal breast cancer influence gene expression, may contribute to tumor progression, and may present an actionable epigenetic alteration in some luminal breast cancers.

overall_design: Genome-wide DNA methylation analysis of 188 breast cancers using Illumina Human Methylation 450K Beadchips.


title: Down-regulation of Interferon signature in systemic lupus erythematosus patients by active immunization with Interferon alpha-Kinoid extended follow-up

summary:
Interferon-alpha Kinoid (IFN-K) is a therapeutic vaccine composed of IFN-alpha2b coupled to a carrier protein. In a phase I/II placebo-controlled trial, we observed that IFN-K significantly decreases the IFN gene signature in whole blood RNA samples from SLE patients (see GSE39088). Here, we analyzed extended follow-up data from IFN-K-treated patients, in terms of persistence of neutralizing anti-IFN± Abs, gene expression profiling and safety.
Follow-up analyses in six patients confirmed a significant correlation between neutralizing anti-IFNalpha Ab titers and decrease in IFN scores compared to baseline.  These analyses also revealed an inhibitory effect of IFN± blockade on the expression of B cell associated transcripts.

overall_design: Extended clinical (SLEDAI, BILAG, Physician Global Assessment) and biological (binding and neutralizing anti-IFNalpha Ab titers, C3 concentrations and anti double-stranded (ds)DNA Ab titers) follow-up data were collected in 6 IFN-K-treated patients. In these patients, whole blood samples were collected in PAXgene Blood RNA tubes (Qiagen) every 6 months after completion of the initial study. RNA was extracted from these samples, and was also re-extracted from baseline (month 0) and day 168 (month 6) PAXgene tubes stored at -80° from the same patients, and from 10 healthy volunteers.

first: Géraldine

last: Grouard-Vogel

first: Pierre

last: Vandepapeliere


title: Sex differences of leukocytes DNA methylation

city: Tokushima

first: Makoto

last: Kinoshita

state: Tokushima

address: 3-18-15, Kuramoto

department: Psychiatry

institute: Tokushima University Graduate School

summary: Genome wide DNA methylation profiling of peripheral blood samples. The Illumina Infinium 450k Human DNA methylation Beadchip was used to obtain DNA methylation profiles across approximately 450,000 CpGs. Samples included  63 of male samples,and 54 of female samples from peripheral leukocytes. All samples were healthy controls.

overall_design: Bisulphite converted DNA from the 117 samples were hybridised to the Illumina Infinium 450k Human Methylation Beadchip. Samples 1-93 were used in a pilot experiment and Samples 101-124 were used in a replicated experiment.

first: Shusuke

last: Numata


title: IFNalpha kinoid induces neutralizing anti-IFNalpha antibodies that decrease the expression of IFN-induced and B cell activation associated transcripts: analysis of extended follow-up data from the IFN-K phase I/II study

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

overall_design: Refer to individual Series


title: Transcriptome of human liver cells and culture-activated hepatic stellate cells

first: Adil

last: El Taghdouini

address: Laarbeeklaan, 103

department: Cell Biology

institute: Vrije Universiteit Brussel

summary:
The molecular determinants of a healthy human liver cell phenotype remain largely uncharacterized. In addition, the gene expression changes associated with activation of primary human hepatic stellate cells, a key event during fibrogenesis, remain poorly characterized. Here, we provide the transriptomic profile underpinning the healthy phenotype of human hepatocytes, liver sinusoidal endothelial cells (LSECs) and quiescent hepatic stellate cells (qHSCs) as well as activated HSCs (aHSCs)
We assess the transcriptome for purified, non-cultured human hepatocytes, liver sinusoidal cells (LSECs) and quiescent hepatic stellate cells (qHSCs) as well as culture-activated HSCs (aHSCs).

overall_design: Hepatocytes (n=2 donors), LSECs (n=3), qHSCs (n=3) and in vitro activated HSCs (n=3; from the same donors as the qHSCs and LSECs) were used for this study.

first: Anita

middle: L

last: Sørensen

first: Andrew

middle: H

last: Reiner

first: Mar

last: Coll

first: Stefaan

last: Verhulst

first: Inge

last: Mannaerts

first: Cristina

last: Øie

first: Bård

last: Smedsrød

first: Mustapha

last: Najimi

first: Etienne

last: Sokal

first: Aernout

last: Luttun

first: Pau

last: Sancho-Bru

first: Philippe

last: Collas

first: Leo

last: van Grunsven


title: BRG1/SMARCA4 is essential for neuroblastoma cell viability through modulation of cell death and survival pathways

city: Barcelona

first: Miguel

last: Segura

state: Barcelona

address: Passeig Vall d'Hebron 119-129. Collserola. Lab 207

department: Pediatric Oncology

country: Spain

institute: Vall d'Hebron Research Institute

summary: Neuroblastoma (NB) is a neoplasm of the sympathetic nervous system, and is the most common solid tumor of infancy. NBs are very heterogeneous, with a clinical course ranging from spontaneous regression to resistance to all current forms of treatment. High-risk patients need intense chemotherapy, and only 30-40% will be cured. Relapsed or metastatic tumors acquire multi-drug resistance, raising the need for alternative treatments. Owing to the diverse mechanisms that are responsible of NB chemoresistance, we aimed to target epigenetic factors that control multiple pathways to bypass therapy resistance. We found that the SWI/SNF-related, matrix-associated, actin- dependent regulator of chromatin, subfamily a, member 4 (SMARCA4/BRG1) was consistently upregulated in advanced stages of NB, with high BRG1 levels being indicative of poor outcome. Loss-of-function experiments in vitro and in vivo showed that BRG1 is essential for the proliferation of NB cells. Furthermore, whole genome transcriptome analysis revealed that BRG1 controls the expression of key elements of oncogenic pathways such as PI3K/AKT and BCL2, which offers a promising new combination therapy for high-risk NB

overall_design: Non-silencing control (NSC) or shBRG1 lentiviral vectors were transduced in the Neuroblastoma cell lines SK-N-BE(2) by triplicate. 48h post-infection, total RNA was extracted

first: Luz

last: Jubierre


title: Expression profiling of DLBCL subtypes PDX model

city: Shanghai

first: Zuguang

last: Xia

address: 270 Dong'an Road

institute: Shanghai Cancer Center

summary: Identify the PDX model of DLBCL subtypes by the microarray expression profiling

overall_design: Four samples without relplicates

first: Zhao

last: Liu

first: Junmin

last: Li


title: The expanded regulatory T cell population in chronic filarial infection is highly heterogeneous, activated and suppresses dendritic cell function indirectly through effector T cells.

status: Public on Feb 25 2016

city: Hamilton

first: Dan

last: Sturdevant

state: MT

address: 903 S 4th street

department: NIAID

institute: NIH

summary: Natural regulatory T cells (nTregs) are known to increase during chronic infection or at the site tumor, though the exact mechanisms that contribute to their accumulation and mode of action remain unclear. We used flow cytometry and microarray analyses to delineate the phenotype of nTregs and their role in modulating T cell and antigen presenting cell (APC) function in the setting of chronic infection. Using cells from 18 filaria-infected (Fil+) and 19 filaria-uninfected (Fil-) subjects, we found that the frequencies of nTreg expressing CTLA-4, GITR, LAG-3, and IL-10 were significantly higher in Fil+ compared with Fil- subjects. Microarray analysis revealed that, compared with those from Fil-, nTreg populations in Fil+ subjects were more heterogeneous and had higher expression of IL-10, CCL-4, IL-29 and CTLA-4, molecules that have been implicated in immune suppression. Moreover, the nTregs from Fil+ subjects had markedly upregulated activation-induced apoptotic genes with concomitant down regulation of cell survival genes. However, these activated nTregs from Fil+ subjects did not significantly affect cytokine production by APCs. To determine if nTregs directly modulate APC function, we modeled an in vitro culture system with cells from normal individuals. In this system, in response to antigen or anti-CD3, nTregs did inhibit APC production of IL-12-, CXCL-9, and CXCL-10, but did so indirectly through effector T cells. Taken together, our results suggest that in filarial infection, the expanded nTreg populations are heterogeneous, short-lived, activated and express regulatory molecules that modulate cytokine production by APC indirectly through an effector T cell-dependent mechanism.

overall_design: Control (nTREG-Lymphatic Filariasis negative) vs. test (nTREG-Lymphatic Filariasis positive)

first: Simon

last: Metenou

first: Yaya

last: Coulibaly

first: Daniel

first: Housseini

last: Dolo

first: Abdallah

last: Diallo

first: Lamine

last: Soumaoro

first: Michel

middle: E

first: Kishore

last: Kanakabandi

first: Stephen

last: Porcella

first: Amy

last: Klion

first: Thomas

last: Nutman


title: Maternal Weight Phenotype as a Predictor of Methylation of Obesity-Related CpG Sites in Saliva Samples from Latino Children

city: Nashville

first: Yan

last: Guo

state: TN

address: 639 Preston Research Bld

institute: Vanderbilt Cancer Center

summary: Epigenetics presents a dynamic approach to assess complex individual variation in obesity susceptibility. However, few studies have examined epigenetic patterns in preschool-age children, despite the relevance of this developmental stage to trajectories of weight gain, because of difficulties obtaining blood tissue samples. This proof of principle study examined DNA methylation in 92 saliva samples, comparing Latino preschool children of normal weight mothers (Body Mass Index [BMI] <27 kg/m2 and WC <90 cm) to children of obese mothers (BMI >30 kg/m2 and WC >100 cm). We hypothesized that salivary DNA methylation patterns in Latino preschool age children born of normal weight vs obese weight mothers would be: 1) associated with maternal BMI phenotype in continuous linear regression analysis; 2) saliva could demonstrate epigenetic variation across individuals; and 3) preschool child saliva would be differentially methylated when comparing those children with obese versus normal weight mothers.  One hundred and nineteen CpG sites were significantly (p-value <1.56 X 10-5, p-value adjusted <.05) associated with maternal BMI in linear regression models controlling for child’s age, gender, and BMI. Of these 119 CpG sites, 41 were found within the transcription start site, 5’ UTR, 3’ UTR, or another regulatory region outside of the gene body.  Saliva, a practical human tissue to obtain in naturalistic settings and in pediatric populations, was confirmed to be a viable medium for genome-wide epigenetic testing with maternal weight. Although not identical to results yielded from other human tissue types (i.e., cord blood samples), saliva findings indicate potential epigenetic differences in Latino preschool children at risk for pediatric obesity.

overall_design: This proof of principle study examined DNA methylation in 92 saliva samples, comparing Latino preschool children of normal weight mothers (Body Mass Index [BMI] <27 kg/m2 and WC <90 cm) to children of obese mothers (BMI >30 kg/m2 and WC >100 cm). Antropometry was measured objectively according to a standardized protocol.Saliva from preschool Latino children at risk for obesity (BMI>50% < 95% participating in WIC/SNAP programs) was collected using the Oragene DNA saliva kit following a strict data collection protocol. DNA extraction was performed as per DNA Genotek's recommendations using the PrepIT L2P reagent. Extracted DNA was stored in individually barcoded cryovials at –80 degrees Fahrenheit. For children, saliva was obtained using the “baby brush” approach, in which small sponges attached to plastic handles are inserted between cheek and gumline to absorb saliva .Arrays were processed using standard protocol [34], with 3 samples randomly selected to serve as duplicates and 1 sample run with HapMap DNA to test functionality of reagents. Duplicates were measured for high technique consistency with Pearson correlation coefficient (>.99). Methylation data were quality controlled using Illumina GenomeStudio (V2011.1), Methylation module (V1.9.0). Samples with lower than 98% call rate (i.e. <485,000 probes) were excluded. Any non-specific cross-reacting probes, probes carrying common SNPs (MAF >1%), or any probes with p-values greater than 0.05 for more than 20% of the sample were sequentially excluded. Validation via pyrosequencing was conducted.

first: Kathryn

last: Tully

last: Non

first: Shari

last: Barkin


title: Hepatocyte-specific knockout of Pten and of Pten and Tgfbr2 in mice

status: Public on Feb 26 2016

city: New York

first: Robert

last: Schwabe

state: NY

address: 1150 st Nicholas Av

department: Medicine

institute: Columbia University

summary:
Gene expression of hepatocyt-specific knockout of Pten and of Pten and Tgfbr2 in mice
as a model for human cholangiocarcinoma  was determined
Affymetrix Mouse 1.0ST chips were used to measure gene expression

overall_design:
Gene expression of the following mouse livers were characterized
A. WT  (n=3).
B. Pten-/- (n=4).
C. Pten-/- Tgfbr2-/- (n=4).

first: Xueru

last: Mu

first: Jean-Philippe

last: Pradere

first: Dianne

last: Dapito

first: Richard

last: Friedman

first: Jay

last: Lefkovitch


title: Genome-wide DNA methylation levels and altered cortisol stress reactivity following childhood trauma in humans

city: Utrecht

first: Marco

last: Boks

state: Nederland

address: Heidelberglaan 100, PO box 85500, Huispostnr A01.146

department: Department of Psychiatry

country: Netherlands

institute: University Medical Center Utrecht

summary: DNA methylation likely plays a role in the regulation of human stress reactivity. In a genome-wide analysis of blood DNA methylation in 85 healthy individuals a locus in the Kit ligand (KITLG) gene (cg27512205) had the strongest association with cortisol stress reactivity (p=5.8x10-6). Replication was obtained in two independent samples, one using blood (N=45, p=0.001) and the other using buccal cells (N=255,p=0.004). KITLG methylation strongly mediated the relationship between childhood trauma and cortisol stress reactivity (32% mediation). Its genomic location (CpG island shore within an H3K27ac enhancer mark) provide further evidence that KITLG methylation is functionally relevant for the programming of stress reactivity. Our results extend preclinical evidence for epigenetic regulation of stress reactivity to humans and provide leads to enhance our understanding of the neurobiological pathways underlying stress vulnerability.

overall_design: Bisulphite converted DNA from whole blood of 85 healthy controls exposed to psychosocial stress task (TSST-G) was hybridised to the Illumina Infinium 450k Human Methylation Beadchip

middle: P

first: Christiaan

last: Vinkers


title: Cerebral gene expression changes in Pdgfc and Pdgfra mutant

status: Public on Feb 24 2016

city: Uppsala

first: L.

last: He

address: Dag Hammarskjölds Väg 20

institute: Uppsala University

summary: Platelet-derived growth factor-C (PDGF-C) is one of three known ligands for the tyrosine kinase receptor PDGFRα. Analysis of Pdgfc null mice has demonstrated roles for PDGF-C in palate closure and the formation of cerebral ventricles, but redundancy with other PDGFRα ligands might hide additional functions. In search of further developmental roles for PDGF-C, we generated mice that were double mutants for Pdgfc -/- and Pdgfra GFP/+. These mice display a range of severe phenotypes including cerebellar malformation, neuronal over-migration in the cerebral cortex, spina bifida and lung emphysema. We focused our analysis on the central nervous system (CNS), where PDGF-C was identified as a critical factor for the formation of meninges and assembly of the glia limitans basement membrane.

overall_design: Meninges freely dissected and released from P0 cerebrum. RNA was isolated using RNeasy micro kit (Qiagen) and quality checked in a 2100 BioAnalyzer (Agilent Technologies, Santa Clara, CA, USA). Transcription profiling was performed with Gene Chip Mouse Gene 1.0 ST array. We compared Pdgfc-/-; Pdgfra GFP/+ mice, with a control group consisting of all littermates (Pdgfc+/+, Pdgfc+/-, Pdgfc-/-, Pdgfc+/+; Pdgfra GFP/+ and Pdgfc+/-; Pdgfra GFP/+). One litter was used, including 4 mutants and 9 controls

first: Johanna

last: Andrae


title: Gene expression data from CNS-PNETs and various other brain tumor samples

city: Heidelberg

first: Marcel

last: Kool

address: Im Neuenheimer Feld 280

department: Pediatric Neurooncology

country: Germany

institute: German Cancer Research Center DKFZ

summary: Primitive neuroectodermal tumors of the central nervous system (CNS PNETs) are highly aggressive, poorly differentiated embryonal tumors occurring predominantly in young children. Using DNA methylation and gene expression profiling we have demonstrated that a significant proportion of institutionally diagnosed CNS PNETs display molecular profiles indistinguishable from those of various other well defined CNS tumor entities, facilitating diagnosis and appropiate therapy for children with these tumors. From the remaining fraction of CNS PNETs, we have identified four distinct new CNS tumor entities extending to other neuroepithelial tumors, each associated with a recurrent genetic alteration and particular histopathological and clinical features. These molecular entities, designated “CNS Neuroblastoma with FOXR2 activation (CNS NB FOXR2)”, “CNS Ewing sarcoma family tumor with CIC alteration (CNS EFT CIC)”, “CNS high grade neuroepithelial tumor with MN1 alteration (CNS HGNET MN1)”, and “CNS high grade neuroepithelial tumor with BCOR alteration (CNS HGNET BCOR)”, will enable meaningful clinical trials and the development of therapeutic strategies for patients affected by these poorly differentiated CNS tumors.

overall_design: 182 brain tumor samples were selected for RNA extraction and hybridization on Affymetrix Affymetrix Human Genome U133 Plus 2.0 Arrays.


title: Expression data from LNCaP cells

status: Public on Feb 23 2016

city: Beijing

first: Chong

last: Li

address: 15 Datun Road

institute: Institute of Biophysics, Chinese Academy of Sciences

summary: Prostate Cancer Stem Cells (CSCs) are considered one of the main reasons the tumor recurrence after chemotherapy. Here we employed a chemoresistant xenograft prostate cancer model in NOD/SCID mice and found CD54 is a reliable new marker for prostate CSCs. Gene expression profile were utilized to analyze stemness-related genes in cancer stem cells.

overall_design: 12 Male NOD/SCID mice were obtained from the Animal Center of the Chinese Academy of Medical Science (Beijing, China). For xenograft generation, 1×106 LNCaP cells were subcutaneously injected into the backs of NOD/SCID mice (n=24). When tumors reached a diameter of 5 mm after 3 d, mice were randomly divided into two groups without castration (12 per group). Mice in the treatment group were administered with cisplatin at a dose of 5 mg/kg every 3 d for 30 d. Mice in the control group were treated with vehicle PBS. Tumors were taken out for microarray assay after 30 d.


title: New molecular insights into modulation of platelet reactivity in aspirin-treated patients using a network-based approach [Affymetrix]

status: Public on Feb 18 2016

city: Lausanne

first: Mark

last: Ibberson

address: Genopode building

department: Vital-IT

institute: SIB Swiss Institute of Bioinformatics

summary: Platelet reactivity (PR) in cardiovascular (CV) patients is variable between individuals and modulates clinical outcome. However, the determinants of platelet reactivity are largely unknown. Integration of data derived from high-throughput omics technologies may yield novel insights into the molecular mechanisms that govern platelet reactivity. The aim of this study was to identify candidate genes modulating platelet reactivity in aspirin-treated cardiovascular patients PR was assessed in 110 CV patients treated with aspirin 100mg/d by aggregometry using several agonists. 12 CV patients with extreme high or low PR were selected for transcriptomics, proteomics and miRNA analysis.

overall_design: 2 extreme patient groups, 6 samples per group

first: A

last: Zufferey

first: M

first: J

last: Reny

first: S

last: Nolli

first: D

last: Schvartz

last: Docquier

first: I

last: Xenarios

last: Sanchez

first: P

last: Fontana


title: Immune and HCT116 RNA mixtures

city: Seattle

first: Etienne

last: Becht

address: 1100 Fairview Ave N

country: USA

institute: Fred Hutchison Cancer Research Center

summary: These experiments were designed as a benchmark tool for deconvolution methods. 5 immune cell populations were sorted from 3 healthy donors' peripheral bloods. Peripheral Blood Mononuclear Cells (PBCMs) and PolymorphoNuclear Cells (PMN) were separated using gradient centrifugation. T cells (DAPI-/CD3+/CD14-/CD19-/CD56-), monocytes (DAPI-/CD3-/CD14+/CD19-/CD56-), B cells (DAPI-/CD3-/CD14-/CD19+/CD56-) and NK cells (DAPI-/CD3-/CD14-/CD19-/CD56+) were FACS-sorted from PBMCs and neutrophils (DAPI-/CD66b+/CD19-/CD3-/CD56-/CD14-) were sorted from PMNs. RNA was extracted from the purified cell population, as well as from the HCT116 colon cancer cell line. RNAs from pure populations were then mixed in various proportions.

overall_design: RNA from HCT116 cells and FACS-sorted T cells (DAPI-/CD3+/CD14-/CD19-/CD56-), monocytes (DAPI-/CD3-/CD14+/CD19-/CD56-), B cells (DAPI-/CD3-/CD14-/CD19+/CD56-), NK cells (DAPI-/CD3-/CD14-/CD19-/CD56+), and neutrophils (DAPI-/CD66b+/CD19-/CD3-/CD56-/CD14-) were mixed in various proportions.

first: Nicolas

last: Giraldo

first: Benedicte

last: Buttard

first: Laetitia

last: Lacroix

first: Aurélien

last: de Reyniès

first: Catherine

last: Sautès-Fridman

first: Wolf

last: Fridman


title: Genome-Wide Chromatin Landscape Transitions Identify Novel Pathways in Early Commitment to Osteoblast Differentiation (microarray)

status: Public on Feb 20 2016

city: Bethesda

first: Songjoon

last: Baek

state: MD

address: 41 Library Drive

department: CCR

institute: NCI / NIH

summary: DHS enahncers identify novel pathways in OB differentiation

overall_design: We examined gene expression and compared to DHS on promoters and enhancers during OB differentiation

first: Lyuba

last: Varticovski

first: Bethtrice

last: Thompson

first: Gordon

last: Hager


title: RNA-seq of pre-treatment and post-relapse matched samples from melanoma patients

city: Rehovot

first: Itay

last: Tirosh

address: Herzl 234

institute: WEIZMANN INSTITUTE OF SCIENCE

type: Expression profiling by high throughput sequencing

overall_design:
RNA-seq was performed for matched samples before treatment and after relapse from six patients that have been treated with RAF or RAF+MEK inhibitors.

Submitter declares that raw sequence data will be submitted to dbGaP due to patient privacy concerns.

first: Eliezer

last: Van Allen


title: miR-182 modulates myocardial hypertrophic response induced by angiogenesis in heart

status: Public on Feb 17 2016

city: New Haven

first: Daniela

last: Tirziu

state: CT

address: 300 George Street

department: Internal Medicine/Cardiology

institute: Yale University School of Medicine

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

platform_organism:
Mus musculus
synthetic construct


title: Expression data from CD1d tetramer-sorted b-GL122/LGL1–specific human T cells or iNKT cells

status: Public on Feb 16 2016

first: Rakesh

last: Verma

address: 333 Cedar St.

department: Yale Cancer Center

institute: Yale University

summary: The ability to detect and isolate bGL1-22/LGL1–specific human type II NKT cells allowed us to compare the global gene expression profiles of these cells with type I NKT cells using microarray analysis. Principal component analysis revealed that the gene expression profile signature for bGL1-22 and LGL1-specific T cells both before and after activation with anti-CD3/CD28 beads is distinct from that of type I NKT cells.

overall_design: RNA from CD1d tetramer-sorted b-GL122/LGL1–specific T cells or iNKT cells was amplified, labeled, and hybridized on the Affymetrix Human Genome U133 Plus 2.0 microarray chips. The data were analyzed with GeneSpring GX 12.5 (Agilent Technologies)


title: miR-182 modulates myocardial hypertrophic response induced by angiogenesis in heart (MoGene)

summary:
Angiogenesis induced by placental growth factor (PlGF) in heart promotes myocardial hypertrophy through the paracrine action of endothelium-derived nitric oxide which triggers the degradation of RGS4 and subsequent the activation of Akt/mTORC1 pathway in cardiomyocytes. However, whether alterations in miRNAs contribute to the development of hypertrophy is largely undetermined.
We found that miR-182 contributed to the hypertrophic response and activation of Akt/mTORC1 pathway by suppressing the expression of Bcat2, Pink1, Adcy6, Foxo3.

overall_design: miR-182 targeted genes  were investigated in the mouse model of myocardial angiogenesis induced by conditional, cardiac specific expression of PlGF. We also induced angiogenesis, but blocked hypertrophy by concomitant expression of PlGF and RGS4 (PlGF/RGS4 mice). The mRNA expression profiling in PlGF and PlGF/RGS4 mice were assessed after 6 weeks of transgene expression, concurent with the development of myocardial hypertrophy.

last: Li