title: Expression data from periphereal blood lymphocytes of metastatic renal cell carcinoma patients pre and post therapy as well as 9 healthy controls

status: Public on Feb 01 2013

city: Tübingen

first: Benita

last: Wolf

address: Quenstedtstrasse 12

department: Medical Clinic 1

institute: University Hospital Tübingen

summary:
Gene expression of periphereal blood lymphocytes (PBLs) of patients with metastatic renal cell carcinoma pre and post immunotherapy was accessed and pre therapy gene expression was compared to PBL gene expression of healthy volunteers
Microarray gene expression was confirmed by RT-PCR and compared to results from flow cytometry and serum cytokine analysis.

overall_design: PBLs of 17 patients pre therapy and 13 patients post therapy could be included in the study as well as PBLs from 9 healthy donors.


title: Expression data from HeLa cells after MBD2 and MBD3 knock down

status: Public on Feb 08 2013

city: Giessen

first: Marek

last: Bartkuhn

state: Hessen

address: Aulweg 132

department: Biomedical Informatics and Systems Medicine

country: Germany

institute: Justus-Liebig-University Giessen

summary: The heterogeneous collection of NuRD complexes can be grouped into the MBD2 or MBD3 containing complexes MBD2-NuRD and MBD3-NuRD. MBD2 is known to bind to methylated CpG sequences in vitro in contrast to MBD3. Although functional differences have been described, a direct comparison of MBD2 and MBD3 in respect to genome-wide binding and function has been lacking. Here we show when depleting cells for MBD2, the MBD2 bound genes increase their activity, whereas MBD2 plus MBD3 bound genes reduce their activity. Most strikingly, MBD3 is enriched at active promoters, whereas MBD2 is bound at methylated promoters and enriched at exon sequences of active genes. This suggests a functional connection between MBD2 binding to chromatin and splicing.

overall_design: 9 Total samples were analysed. Three individual replicates for HeLa cells treated with siRNA against MBD2, MBD3 or scrambled siRNA were performed. We calculated the fold change of gene expression of cells treated with MBD2- or MBD3-siRNA over cells treated with scrambled siRNA.

first: Katharina

last: Guenther

first: Rainer

last: Renkawitz


title: Deregulation of microRNAs by HIV-1 Vpr protein leads to the development of neurocognitive disorders.

status: Public on Feb 12 2013

city: Philadelphia

first: Bassel

middle: E

last: Sawaya

state: PA

address: 3307 N. Broad Street

department: Neurology

country: USA

institute: Temple University

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

summary: Studies have shown that HIV-infected patients develop neurocognitive disorders characterized by neuronal dysfunction. The lack of productive infection of neurons by HIV suggests that viral and cellular proteins, with neurotoxic activities, released from HIV-1-infected target cells can cause this neuronal deregulation. The viral protein R (Vpr), a protein encoded by HIV-1, has been shown to alter the expression of various important cytokines and inflammatory proteins in infected and uninfected cells; however the mechanisms involved remain unclear. Using a human neuronal cell line, we found that Vpr can be taken up by neurons causing: (i) deregulation of calcium homeostasis, (ii) endoplasmic reticulum-calcium release, (iii) activation of the oxidative stress pathway, (iv) mitochondrial dysfunction and v- synaptic retraction. In search for the cellular factors involved, we performed microRNAs and gene array assays using human neurons (primary cultures or cell line, SH-SY5Y) that we treated with recombinant Vpr proteins. Interestingly, Vpr deregulates the levels of several microRNAs (e.g. miR-34a) and their target genes (e.g. CREB), which could lead to neuronal dysfunctions. Therefore, we conclude that Vpr plays a major role in neuronal dysfunction through deregulating microRNAs and their target genes, a phenomenon that could lead to the development of neurocognitive disorders.

platform_organism:
Homo sapiens
Mus musculus
Rattus norvegicus
Human alphaherpesvirus 1
Human betaherpesvirus 5
Murid betaherpesvirus 1
human gammaherpesvirus 4
JC polyomavirus
Human immunodeficiency virus 1
Murid gammaherpesvirus 4
Human gammaherpesvirus 8
Betapolyomavirus hominis
Betapolyomavirus macacae

overall_design: Using primary cultures and neuronal cell lines, we examined the impact of a viral protein (HIV-1 Vpr) on the expression of miRNAs and mRNAs.

first: R

last: Mukerjee

first: J

middle: R

last: Chang

first: L

last: Del Valle

first: A

last: Bagashev

first: M

middle: M

last: Gayed

middle: B

last: Lyde

first: B

middle: J

last: Hawkins

first: E

last: Brailoiu

last: Cohen

first: C

last: Power

first: S

middle: A

last: Azizi

last: Gelman


title: A p53-like like transcription factor similar to Ndt80 controls the response to nutrient stress in the filamentous fungus, Aspergillus nidulans

status: Public on Jan 31 2013

city: Armidale

first: Margaret

middle: E.

last: Katz

state: NSW

address: McClymont Building

department: Molecular and Cellular Biology

country: Australia

institute: University of New England

summary: The xprG gene encodes a putative transcriptional activator involved in the regulation of extracellular proteases in response to nutrient stress in Aspergillus nidulans.  To investigate whether XprG is required for expression of other genes in response to carbon starvation, we used microarrays provided by the PFGRC.  These experiments indicate that the expression of many genes, including the sterigmatocystin gene cluster and other secondary metabolism genes, genes involved in asexual and sexual development and genes induced during autolysis, is altered in an xprGdelta mutant.  Many of these genes are known to be regulated in response to carbon starvation.  The results indicate that XprG may play a major role in the response to carbon limitation.

overall_design: An xprG+ (wt) strain and xprGdelta gene knockout strain (ko) were compared after transfer to medium containing 1% glucose (C)  or carbon-free medium (NC) for 16 hours.  The effect of the two nutrient conditions on each strain were also investigated.

first: Cedric

last: Gondro

first: Katharyn

last: Braunberger


title: Oncostatin M effects in IMR90 cells

status: Public on Jan 29 2013

city: Vienna

first: Martin

last: Bilban

country: Austria

institute: Medical University of Vienna

summary: The JAK2 mutation V617F is detectable in a majority of patients with Ph-negative myeloproliferative neoplasms (MPN). Enforced expression of JAK2 V617F in mice induces myeloproliferation and bone marrow (BM) fibrosis suggesting a causal role for the JAK2 mutant in the pathogenesis of MPN. However, little is known about mechanisms and effector molecules contributing to JAK2 V617F-induced myeloproliferation and fibrosis. Here we show that JAK2 V617F promotes expression of oncostatin M (OSM) in neoplastic myeloid cells. Correspondingly, OSM was found to be overexpressed in the BM and elevated in the serum of patients with JAK2 V617F+ MPN. In addition, OSM secreted by JAK2 V617F+ cells stimulated growth of fibroblasts and microvascular endothelial cells and induced the production of angiogenic and profibrogenic cytokines (HGF, VEGF, and SDF-1) in BM fibroblasts. All effects of MPN cell-derived OSM were blocked by a neutralizing anti-OSM antibody, whereas the production of OSM in MPN cells was effectively suppressed by a pharmacologic JAK2 inhibitor or RNAi-mediated knockdown of JAK2. In summary, JAK2 V617F-mediated upregulation of OSM may contribute to fibrosis, neoangiogenesis, and the cytokine storm observed in JAK2 V617F+ MPN, suggesting that OSM could serve as a novel therapeutic target molecule in these neoplasms.

overall_design: IMR90 cells were treated with a single dose of rh Oncostatin M (10ng/ml).

first: Gregor

last: Hörmann

first: Matthias

last: Mayerhofer


title: Expression data from inflamed PANC1 cells

status: Public on Jan 26 2013

city: Rehovot

first: Tomer

last: Cooks

address: 250 Herzel

country: Israel

institute: WIS

summary:
The effects of mutant p53 on TNFa stimulated PANC1 cells was tested.
PANC1 cell harbor endogenous mutation in p53 (R273H). We knocked down this mutp53 (using sirna for p53) and then treated with low doses of TNFa to detect any differential transcription regulation governed by mutp53.

overall_design: A total of 7 samples, 3 of them were duplicated

first: Moshe

last: Oren


title: Global Identification of SYT-SSX2 Downstream Genes using Human Pluripotent Stem Cells

status: Public on Jan 30 2013

city: kyoto

first: Junya

last: Toguchida

address: 53 kawahara-cho, shogoin

department: Center for iPS Cell Research and Application(CiRA)

country: Japan

institute: Kyoto University

summary: We established human pluripotent stem cell (PSC) lines expressing Synovial Sarcoma-specific oncogene, SYT-SSX2, under the control of doxycycline with dose- and time-dependent manner. Gene expression profiles were analyzed to identify early response genes of SYT-SSX2.

overall_design: SYT-SSX2-inducible PSC lines including two hESCs and one hiPSC were analyzed at several time points (0, 6, 12, 18, 24 hours) after doxycycline treatment.


title: Sodium metavanadate exhibits carcinogenic tendencies in vitro in immortalized human bronchial epithelial cells [DEG.C]

status: Public on Jan 19 2013

city: Tuxedo

first: Lisa

last: Passantino

state: New York

address: 57 Old Forge Road

department: School of Medicine

institute: New York University

summary: Pentavalent vanadium compounds induce intracellular changes in vitro that are consistent with those of other carcinogenic substances, including alteration of transcription factor levels, promotion of oxidative stress, inflammation, DNA damage, stimulation of mitogenic signals, and suppression of apoptosis. While there is no clear evidence that vanadium compounds cause cancer in humans, vanadium pentoxide causes lung cancer in rodents after long-term inhalation exposures and in turn IARC has categorized it as a group 2B possible human carcinogen. The goal of this study was to investigate the carcinogenicity of NaVO3 in the human immortalized bronchial epithelial cell line, Beas-2B.  Cells were treated with 10 µM NaVO3 for 5 weeks, with or without recovery time, followed by gene expression microarray analysis. In a separate experiment, cells were exposed to 1-10 µM NaVO3 for 4 weeks and then grown in soft agar to test for anchorage-independent growth. A dose-dependent increase in the number of colonies was observed. NaVO3-transformed clones could repair a wound faster than controls during the scratch test. In a gene expression microarray analysis of soft agar clones there were 2010 differentially expressed genes (DEG) (adjusted p-value ≤ 0.05) in NaVO3-transformed clones relative to control clones. DEG from this experiment were compared with the DEG of 5 week NaVO3 exposure with or without recovery, all with adjusted p-values <0.05, and 469 genes were altered in the same direction for transformed clones, 5 week NaVO3-treated cells, and the recovered cells; a subset of these changes were validated by QRT-PCR. The data from this study imply that chronic exposure to NaVO3 causes changes that are consistent with cellular transformation including anchorage- independent growth, enhanced migration ability, and gene expression changes that were epigenetically inherited through cell division.

overall_design: Beas-2B cells were chronically exposed to sodium metavanadate in growth media for 4 weeks. Then exposed cells and unexposed control cells were grown in soft agar for 3 weeks in the absence of vanadate. Transformed colonies (arising from vanadate-exposed cells) and control colonies (spontaneously grew from unexposed cells) were extracted from soft agar and expanded in the absence of vanadate, then processed for gene expression analysis on Affymetrix GeneChip Human Exon 1.0 ST array. 5 transformed clones, 3 control clones, 1 parental Beas-2B cell sample, and acute 24 hour vanadate exposed cell samples were analyzed.

first: Alexandra

last: Muñoz

first: Max

last: Costa


title: Reprogramming of human fibroblasts toward a cardiac fate

status: Public on Jan 18 2013

city: Dallas

first: young-jae

last: Nam

address: 5323 Harry Hines Blvd

institute: UT Southwestern Medical Center

summary: Reprogramming of mouse fibroblasts toward a myocardial cell fate by forced expression of cardiac transcription factors or microRNAs has recently been demonstrated.  The potential clinical applicability of these findings is based on the minimal regenerative potential of the adult human heart and the limited availability of human heart tissue.  An initial, but mandatory step toward clinical application of this approach is to establish conditions for conversion of adult human fibroblasts to a cardiac phenotype.  Toward this goal, we sought to determine the optimal combination of factors necessary and sufficient for direct myocardial reprogramming of human fibroblasts.  Here we show that four human cardiac transcription factors, including Gata4, Hand2, Tbx5, and myocardin, and two microRNAs, miR-1 and miR-133, activated cardiac marker expression in neonatal and adult human fibroblasts.  After maintenance in culture for 4-11 weeks, human fibroblasts reprogrammed with these proteins and microRNAs displayed sarcomere-like structures and calcium transients, and a small subset of such cells exhibited spontaneous contractility.  These phenotypic changes were accompanied by expression of a broad range of cardiac genes and suppression of non-myocyte genes.  These findings indicate that human fibroblasts can be reprogrammed to cardiac-like myocytes by forced expression of cardiac transcription factors with muscle-specific microRNAs and represent a step toward possible therapeutic application of this reprogramming approach.

overall_design: Human foreskin fibroblasts were transduced with 5 transcription factors and total RNA was obtained 4 weeks later.  total RNA was also obtained from human foreskin fibroblasts as a negative control and adult human heart tissue as a positive control. The expression level of genes in each sample was compared.

first: Young-Jae

first: Eric

middle: N

last: Olson


title: Clostridium thermocellum ATCC27405 Transcriptomic Profiles during growth on Populus and switchgrass

status: Public on May 16 2013

city: Oak Ridge

first: Dawn

middle: Marie

last: Klingeman

state: TN

address: 1 Bethel Valley Rd building 15056 Rm 366  MS 6038

department: Biosciences Division

institute: Oak Ridge National Lab

summary: The thermophilic anaerobe Clostridium thermocellum is a candidate consolidated bioprocessing (CBP) biocatalyst for cellulosic ethanol production.  It expresses enzymes for both cellulose solubilization and its fermentation to produce lignocellulosic ethanol.  To gain insights into the C. thermocellum genes, using an updated version of the C. thermocellum ATCC 27405 genome annotation, that are required for specific growth on the cellulosic feedstocks of either pretreated switchgrass or Populus, duplicate fermentations were conducted with a 5 g/L solid substrate loading.  High quality RNA was extracted using a method we report for C. thermocellum grown on solid substrates. Transcriptome profiles were obtained at two time points during actively growing fermentations (12 h and 37 h post inoculation).  A comparison of two transcriptomic analytical techniques, microarray and RNAseq, was performed and the data analyzed for statistical significance. When thresholds for genes passing significance of FDR>0.05 were applied, microarray (2351 genes) had a greater number of significant genes relative to RNA-seq (280 genes when normalized by KDMM).  When a 2-fold difference in expression threshold was applied, seventy-three genes were significantly differentially expressed in common between the two techniques.  We identified genes differentially expressed when C. thermocellum  ATC 27405 was grown on the two biomass substrates, with two putative efflux/transport systems highly differentially regulated (>5-fold).  This study has revealed consistency between these two transcriptomics analytical platforms that gives confidence in our switch from the DNA microarray platform to an RNAseq based platform for routine transcriptomics analyses.

first: Steven

middle: D

last: Brown

first: Charlotte

last: Wilson

first: Courtney

last: Johnson

first: Miguel

last: Rodriguez Jr.


title: Sodium metavanadate exhibits carcinogenic tendencies in vitro in immortalized human bronchial epithelial cells

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

overall_design: Refer to individual Series


title: Patient specific orthotopic glioblastoma xenograft models recapitulate the histopathology and biology of human glioblastomas in situ (gene expression)

city: Seoul

first: Jinkuk

last: Kim

address: 50 Irwon-dong, Gangnam-gu

country: South Korea

institute: Samsung Medical Center

summary: Frequent discrepancies between preclinical and clinical results of anti-cancer agents demand a reliable translational platform that can precisely recapitulate the biology of human cancers. Another critical unmet need is the ability to predict therapeutic responses for individual patients. Toward this goal, we have established a library of orthotopic glioblastoma (GBM) xenograft models using surgical samples of GBM patients. These patient-specific GBM xenograft tumors recapitulate histopathological properties and maintain genomic characteristics of parental GBMs in situ. Furthermore, in vivo irradiation, chemotherapy, and targeted therapy of these xenograft tumors mimic the treatment response of parental GBMs. We also found that establishment of orthotopic xenograft models portends poor prognosis of GBM patients and identified the gene signatures and pathways signatures associated with the clinical aggressiveness of GBMs. Together, the patient-specific orthotopic GBM xenograft library represent the preclinically and clinically valuable “patient tumor’s phenocopy” that represents molecular and functional heterogeneity of GBMs.

overall_design: Gene expression profiling experiments were conducted for 58 human glioblastoma samples using Affymetrix Human Gene 1.0 ST arrays according to manufacturer's protocol.

first: Kyeung-Min

last: Joo

first: Juyoun

last: Jin

first: Misuk

first: Ho-Jun

last: Seol

first: Do-Hyun


title: Human embryonic stem cells differentiated in dopaminergic neurons

status: Public on Jan 03 2013

city: Randwick

first: Jaemin

address: High

department: UNSW

institute: SCL

summary: Human embryonic stem cells have been a great interest due to its potential to provide a renewable source of surrogate dopamine neurons for transplantation into Parkinson’s disease patients. We have differentiated hESCs with a monolayer of PA6 cells under 2D and 3D systems for 28 days. Genome-wide microarray analysis showed that our 3D samples increased expression of genes that are involved in neuronal developments such as Wnt, hedgehog and mitogen-activated protein kinase (MAPK) signalling pathways. The results suggest that the 3D differentiation system may have affected the regulatory or signalling mechanisms which enhanced the rate of differentiation towards ectoderm.

overall_design: 3 biological replicates for 2D samples and 2 biological replicates for 3D samples.

first: Kuldip

middle: S

last: Sidhu


title: Patient specific orthotopic glioblastoma xenograft models recapitulate the histopathology and biology of human glioblastomas in situ

type: Genome variation profiling by genome tiling array


title: Expression data from FACS-sorted CD8+BTLA+ vs CD8+BTLA- Human Tumor-infiltrating Lymphocytes in Metastatic Melanoma

city: Houston

first: Laszlo

middle: G

last: Radvanyi

state: Texas

address: 1515 Holcombe Blvd

department: Melanoma Medical Oncology

institute: University of Texas M.D. Anderson Cancer Center

summary:
Adoptive T-cell Therapy (ACT) involves using tumor-infiltrating lymphocytes (TIL) isolated from metastatic melanoma and expanding them ex vivo prior to infusion into lympho-depleted patients.  This is one of the most promising approaches to treat metastatic melanoma, with the rates of clinical response between 48-50% based on studies done at NCI, M.D. Anderson Cancer Center (Houston, TX), and Sheba Medical Center (Tel Aviv, Israel). In the Phase II ACT Trial at M.D. Anderson Cancer Center , our group has uncovered an association between positive clinical response and the amount of CD8+ tumor-infiltrating lymphocytes expressing B and T Lymphocyte Attenuator (BTLA), a reported inhibitory receptor on T-cells.
We used microarrays to detail the differences in the global programme of gene expression between CD8+BTLA+ vs CD8+BTLA- TILs in order to understand the molecular basis of the clinical association.

overall_design: TILs were isolated by enzymatically digest the melanoma tumor fragments obtained from Stage IIIc/IV melanoma patients at M.D. Anderson Cancer Center.  The TILs were expanded with high-dose IL-2 for two weeks prior to sorting by FACS (fluoresecence-activated cell sorter) for CD8+BTLA+ and CD8+BTLA- susbets.  RNA was extracted from each sorted subsets and hybridized on Affymetrix microarrays

first: Richard

last: Wu

first: Cara

last: Haymaker

first: Hui

last: Liu

first: Ena

last: Wang

first: Francesco

last: Marincola

first: Patrick

last: Hwu


title: Effector cell signatures in peripheral blood after nasal allergen challenge: biomarkers of the allergic response

status: Public on Jan 16 2013

city: Bethesda

first: Sai

last: Kanaparthi

state: MD

address: 7500 Old Georgetown Rd

department: BiG

institute: Immune Tolerance Network

summary: This study investigated temporal transcriptomic changes in response to nasal allergen challenge of titrated timothy grass pollen.

overall_design: This is an open single-center observational study conducted outside the pollen season. Twelve participants with seasonal allergic rhinitis underwent a control (diluent) challenge followed by nasal allergen challenge after an interval of 14 days. On each challenge day, nasal challenge with control or titrated timothy grass pollen (Aquagen, phleum pratense; ALK) was administered. Peripheral blood was collected before nasal challenge (baseline) and at 3, 6 and 24 hours following challenge. RNA was extracted from whole blood and CD4 cells for microarray experiment using Affymetrix Human Gene 1.0 ST arrays.

first: Mohamed

middle: H

last: Shamji

first: Virginia

last: Bellido

first: Guy

middle: W

last: Scadding

first: Janice

last: Layhadi

first: Delica

middle: K

last: Cheung

first: Moises

last: Calderon

first: Adam

last: Asare

first: Zhong

last: Gao

first: Laurence

last: Turka

first: Alkis

last: Togias

first: Deborah

last: Phippard

first: Stephen

last: Durham


title: Differentially expressed genes in H2AX knockdown cells undergoing apoptosis

city: Beijing

first: Chengrong

last: Lu

address: Fucheng road 30

department: Aviation Medicine Research lab

country: China

institute: General Hospital of Air Force

summary:
H2AX has been characterized as a novel tumor suppressor protein. Difficiency of H2AX will result in apoptotic inhibition of cancer cells. However, how H2AX epigenetically regulates apoptosis of cancer cells is still unclear.
To reveal the genes expression regulated by H2AX and involved in apoptosis, the microarray profiling analysis was employed to identify differentially expressed genes in H2AX knockdown lung cancer cells and control ones after apoptotic induction. H2AX was knockdown by miRNA interfering system in human lung cancer originated cell A549 and the stable cell line named P1, while the control stable cell line named C. Genes with greater than 1.2-fold change and P-value ＜0.05 were identified as differentially expressed genes between C and P1 cells both with apoptosis induction.

overall_design: The two groups including control (C) and H2AX knockdown lung cancer cells (P1) were harvested 48 h after VP-16 treatment. Three independent experiments were performed for each group.


title: Expression data from HEK293 Flp-In cells constitutivly expressing FLAG-HA-tagged TRIM71 and that of the parental cell line

status: Public on Jan 22 2013

city: Basel

first: Tim

last: Roloff

address: Maulbeerstrasse 66

department: Functional Genomics

country: Switzerland

institute: FMI

summary:
We identify mammalian TRIM71 as repressor of mRNAs that inhibits translation and affects mRNA stability.
In this data set we compare the expression profile of human HEK293 Flp-In cells stably expressing TRIM71 to that of the parental cells, not expressing TRIM71 protein.

overall_design: Experiment was performed in triplicate.

first: I

last: Loedige

first: T

first: S

last: Thiry

first: W

last: Filipowicz


title: Lactate influences the gene expression profile of human mesenchymal stem cells (hMSC) in a dose dependent manner

status: Public on Jan 09 2013

city: Tuebingen

first: Michael

middle: H.

last: Walter

address: Calwer Str. 7

department: Department of Medical Genetics

institute: University of Tuebingen

summary: Wounds, especially non healing wounds are characterised by elevated tissue lactate concentrations. Lactate is known for being able to stimulate collagen synthesis and vessel growth. Lately it has been shown that lactate, in vivo, plays an important role in homing of stem cells. With this work we aimed to show the influence of lactate on the gene expressionprofil of human mesenchymal stem cells (hMSC).  hMSCs were obtained from bone marrow and characterised with fluorescence-activated cell sorting (FACS) analysis. Subsequently the hMSCs were treated with either 0, 5, 10  and 15 mM lactate (pH 7,4) for 24 hours. RNA Isolation from stimulated hMSCs and controls was performed. The Microarray analysis was performed using Affymetrix HuGene 1.0 ST Gene Chip. Selected targets were subsequently analysed using quantitative real time PCR (RTq-PCR). We were able to show that lactate in moderate concentrations of 5 respectively 10 mM leads to an anti-imflammatory, anti-apoptotic but growth and proliferation promoting gene expression after 24 h. In contrast, high latate concentrations of 15 mM leads to the opposed effect, namely promoting inflammation and apoptosis. Hypoxia induced genes did not not show any significant regulation. Contrary to expectation, we were not able to show any significant regulation of glycolysis associate candiadtes. We were able to show that lactate alters gene expression but does not change the cell phenotype, which might be helpful for further investigations of new treatment strategies for chronic non-healing wounds as well as tumor-therapy and neuronal plasticity.

overall_design:
Timecourse experiment with hMSCs treated with 5, 10, 15 mM lactic acid for 1, 3, 7 days.  hMSCs without lactate served as controls
*** CEL files lost due to hard disk crash

first: Carl

middle: C

last: Schneider

first: Atesch

last: Ateschrang

first: Ingmar

last: Königsrainer

first: Jörg

last: Glatzle

first: Hinnak

last: Northoff

first: Alfred

first: Stefan

last: Beckert

first: Sarah

last: Bühler

first: Markus

last: Löffler

first: Richard

last: Schaefer

first: Derek

last: Zieker


title: The global gene expression pattern between human fibroblasts and human neural stem cells

city: San Francisco

first: Saiyong

last: Zhu

address: 1650 Owens Street, GICD, 4P,

institute: The Gladstone Institute

summary:
Recent advances in direct reprogramming using cell type-specific transcription factors provide an unprecedented opportunity for rapid generation of desired human cell types from easily accessible tissues. However, due to the diversity of conversion factors that facilitate the process, an arduous screening step is inevitable to find the appropriate combination(s). Here, we show that under chemically defined conditions minimal pluripotency factors are sufficient to directly reprogram human fibroblasts into stably self-renewing neural progenitor/stem cells (NSCs), but without passing through a pluripotent intermediate stage. These NSCs can be expanded and propagated in vitro without losing their potential to differentiate into various neuronal subtypes and glia. Our direct reprogramming strategy represents a simple and advanced paradigm of direct conversion that will provide an unlimited source of human neural cells for cell therapy, disease modeling, and drug screening.

We used microarray to compare the global gene expression pattern between human fibroblasts and human neural epitheliums from human ESCs or directly from fibroblasts.

overall_design: We cultured cells and harvested them and then extracted total RNA for microarray.

first: Sheng

last: Ding

first: Janghwan

last: Kim


title: Gene expression propionic patients, carriers, and controls

status: Public on Jan 01 2013

city: Washington

first: Kimberly

last: Chapman

state: DC

address: 111 Michigan Ave NW

department: Genetics and Metabolism

institute: Children's National Medical Center

summary: Gene expression in LCLs from PA patients, their parents, and HapMap sex and age match controls at low glucose (9 mg/dL) and normal glucose growth conditions.

overall_design: 12 LCLs from Pa patients (coriell samples) 15 LCLs from parents of PA patient, 16 controls (HapMAp) who grown at low glucose (9mg/dL) and normal glucose for 24 hours.  Then  harvested for gene expression


title: Expression data of the parental and the induced radio-resistant colorectal cancer cell lines

status: Public on Dec 31 2012

first: Ye-Ah

address: Yongon-dong Jongno-gu

department: Seoul National University College of Medicine

institute: Cancer Research Institute

summary: We used microarray analysis to investigate differential gene expression on the induced radio-resistant colorectal cancer cell lines compared to the parental cell lines.

overall_design: Induced radio-resistant colorectal cancer cell lines were established in our lab to verify their cellular and genetic characteristics. They were exposed to Cesium-137 gamma-radiation up to a total 80 Gy.

first: Sang-Guen

last: Jang

first: Young-Kyoung

last: Shin

first: Ja-Lok

last: Ku


title: Expression data from siRNA knockdown of Ehf in primary human corneal epithelial cells

city: Irvine

first: Denise

last: Stephens

state: CA

address: 250 Sprague Hall

department: Biological Chemistry

institute: University of California, Irvine

summary: Ehf is a transcriptional regulator that is highly expressed and enriched in corneal epithelium. To gain insights into the role of Ehf in the corneal epithelium, we performed siRNA knockdown of Ehf in primary human corneal epithelial cells.

overall_design: Primary human corneal epithelial cells were transfected with siEhf or si controls, plated, and harvested at 72 hr.

first: Hsiang

last: Ho

first: Bogi

last: Andersen


title: ABBERANT GENE EXPRESSION BY EBERs IN EBV-NEGATIVE NPC HK1 CELL LINE

city: Kuala Lumpur

first: Lu Ping

last: Tan

address: Jalan Pahang

department: Molecular Pathology Unit

country: Malaysia

institute: Institute for Medical Research

summary:
Differential gene expression in RNA isolated from stably-transfected EBERs-negative versus EBERs-positive HK1 cell lines
We established stable transfection of EBERs in the EBV-negative NPC cell line, HK1,to elucidate the role of the EBERs in NPC pathogenesis.  Microarray gene expression profiling was carried out to investigate candidate genes which expression correlates with the expression of the EBERs.

overall_design: Total RNA was extracted from each cell line and processed using GeneChip® Whole Transcript (WT) Sense Target Labelling Assay and then analyzed with GeneChip® Human Gene 1.0 ST Array, with three repeats.  Candidate genes differentially expressed between the two transfected HK1 cell lines were identified using GeneSpring GX 10 (Agilent Technologies).

first: D

last: Maelinda

first: B

last: Saatheeyavaane

first: L

middle: P

first: A

last: Munirah

last: Khoo


title: Dissection of human embryonic stem cells-derived endoderm progenitors by  differential cell capture on antibody arrays

status: Public on Dec 29 2012

first: Yoav

last: Soen

address: Department of Biological Chemistry, Weizmann Institute of Science

institute: Weizmann Institute of Science

summary: Heterogeneity, shortage of material, and lack of progenitor-specific cell surface markers are major obstacles to elucidating the mechanisms underlying developmental processes. Here we report a proteomic platform that alleviates these difficulties and demonstrate its effectiveness in fractionating heterogeneous cultures of early endoderm derived from human embryonic stem cells. The approach, designated cell-capture antibody array, is based on highly parallel, comparative screening of live cell populations using hundreds of antibodies directed against cell-surface antigens. The results demonstrate the potential of the cell-capture antibody array as a powerful tool for detailed dissection of heterogeneous cellular systems.

overall_design: Genome-wide comparion of mRNA profile in hES-derived CD61+ cells versus CXCR4+ and CXCR4+/CD61- cells using Affymetrix arrays.

first: Revital

last: Sharivkin

first: Michael

last: Walker


title: Gene expression analysis of HepaRG cells that ectopically express miR-371-3 cluster

city: Evry

first: stefano

last: cairo

address: 4 rue Pierre Fontaine

country: France

institute: Xentech

summary: the immoratlized hepatic cell line HepaRG was transduced with a retroviral vector containing the miR-371-3 cluster. As a control, transduction was performed with the empty vector. Transcriptome analysis was performed by using the Affymetrix whole-transcript human gene 1.0 ST array. Each condition was analyzed in triplicate

overall_design: hierarchical unsupervised clustering of HB samples according to their miRNA expression profile identifies 2 tumor subgroups associated with different degree of differentiation, proliferation rate and invasive phenotype. As subset of these tumors is used as training set to build a mir classifier. When the signature is applied to an independent test set, an independent series of HB is classified patients into two groups associated with the clinical features identified in the first set of patients.

first: Stefano

last: Cairo

first: Marie-Annick

last: Buendia


title: Genome-wide expression profiling of SGTA knockdown in  C4-2B prostate cancer cells

city: Adelaide

first: Andrew

middle: Paul

last: Trotta

state: South Australia

address: 28 Woodville Road, Woodville South

department: Medicine

institute: University of Adelaide

summary:
Identifying the effect of the co-chaperone SGTA on global androgen receptor transcriptional activity in C4-2B prostate cancer cells with view to further elucidating the broader biological role of SGTA on other signaling pathways within prostate cancer cells
Knockdown of SGTA for 72 hours in C4-2B cells significantly altered the expression of approximately 1900 genes in both vehicle and DHT treated cells. The effect of SGTA knockdown was to suppress the expression of approximately 60% of those transcripts. The regulation of 35% of DHT target genes was also affected by SGTA knockdown, with gene-specific effects on basal, or DHT-induced expression, or both.

overall_design: C4-2B cells were transfected with 5nM non-specific control siRNA (NS) or with a pool of three commercially avaliable SGTA specific siRNA (SGTA) for 72hrs. Cells were subsequently treated with either ethanol vehicle control or 1nM DHT for 16hr.  Total RNA was extracted. Five independent vehicle and 2 DHT siNS and siSGTA samples were hybridized to Affymetrix Human Gene 1.0 ST array chips.

first: Grant

last: Buchanan


title: Feeder-Independent Derivation of Induced-Pluripotent Stem Cells From Peripheral Blood Endothelial Progenitor Cells

status: Public on Dec 16 2012

city: Ottawa

first: Wing

middle: Y

last: Chang

state: Ontario

address: 501 Smyth

country: Canada

institute: Ottawa Hospital Research Institute

summary: The objective of this study was to reprogram peripheral blood-derived late-endothelial progenitor cells (EPCs) to a pluripotent state under feeder-free and defined culture conditions. Late-EPCs were retrovirally-transduced with OCT4, SOX2, KLF4, c-MYC, and iPSC colonies were derived in feeder-free and defined media conditions. EPC-iPSCs expressed pluripotent markers, were capable of differentiating to cells from all three germ-layers, and retained a normal karyotype. Transcriptome analyses demonstrated that EPC-iPSCs exhibit a global gene expression profile similar to human embryonic stem cells (hESCs). We have generated iPSCs from late-EPCs under feeder-free conditions. Thus, peripheral blood-derived late-outgrowth EPCs represent an alternative cell source for generating iPSCs.

overall_design: Six samples were analyzed. The gene expression profile of four iPS clones were compared to the H9 human embryonic stem cell line and the parent endothelial progenitor cell line.

first: William

middle: L

last: Stanford


title: The effect of IM and MSC treatment on gene expression in CML CD34+ cells

city: Duarte

first: Ravi

last: Bhatia

address: 1500 E Duarte Road

department: Hematopoietic Stem Cell and Leukemia Research

institute: City of Hope Beckman Research Institute

summary: Tyrosine kinase inhibitors (TKI) are highly effective in treatment of chronic myeloid leukemia (CML) but do not eliminate leukemia stem cells (LSC), which remain a potential source of relapse. TKI treatment effectively inhibits BCR-ABL kinase activity in CML LSC, suggesting that additional kinase-independent mechanisms contribute to LSC preservation. We investigated whether signals from the bone marrow (BM) microenvironment protect CML LSC from TKI treatment. Coculture with human BM mesenchymal stromal cells (MSC) significantly inhibited apoptosis and preserved CML stem/progenitor cells following TKI exposure, maintaining colony forming ability and engraftment potential in immunodeficient mice. We found that the N-Cadherin receptor plays an important role in MSC-mediated protection of CML progenitors from TKI. N-Cadherin-mediated adhesion to MSC was associated with increased cytoplasmic N-Cadherin-β-catenin complex formation, as well as enhanced β-catenin nuclear translocation and transcriptional activity. Increased exogenous Wnt-mediated β-catenin signaling played an important role in MSC-mediated protection of CML progenitors from TKI treatment. Our results reveal a close interplay between N-Cadherin and the Wnt-β-catenin pathway in protecting CML LSC during TKI treatment. Importantly, these results reveal novel mechanisms of resistance of CML LSC to TKI treatment, and suggest new targets for treatment designed to eradicate residual LSC in CML patients.

overall_design: RNA was obtained from CML CD34+ cells treated with or without IM (5μM) and MSC for 96 hours, amplified, labeled  and hybridized to GeneChip 1.0 arrays (Affymetrix, Santa Clara, CA). Microarray data analysis was performed using R (version 2.9) with genomic analysis packages from Bioconductor (version 2.4). The 33297 probes represented on the microarray were filtered by cross-sample mean, and for standard deviation of greater than the 25% quantile, yielding 18624 probes representing 12553 genes. Linear regression was used to model the gene expression with the consideration of a 2x2 factorial design and matched samples. Differentially expressed genes were identified by calculating empirical Bayes moderated t-statistic, and p-values were adjusted by FDR using the “LIMMA” package. Gene Set Enrichment Analysis (GSEA) was performed using GSEA software version 2.04 to detect enrichment of predetermined gene sets using t-scores from all genes for 1263 gene sets in the C2 (curated gene sets) category from the Molecular Signature Database (MsigDB).

first: Min

last: Li


title: The ets transcription factor ELF5 suppresses the estrogen sensitive phenotype and contributes to antiestrogen resistance in luminal breast cancer. [human]

status: Public on Dec 27 2012

city: Darlinghurst

first: Mark

last: Cowley

address: 384 Victoria St.

department: Genome Informatics & Clinical Genomics

institute: Garvan Institute of Medical Research

summary: The ets transcription factor ELF5 specifies the differentiation of mammary progenitor cells to establish the milk-secreting lineage. ER- and poor prognosis basal breast cancers arise from this progenitor cell and these cancers express high levels of Elf5. Knockdown of ELF5 expression in basal breast cancer cell lines, or forced expression in luminal breast cancer cell lines, resulted in reduced cell proliferation. Transcript profiling and chromatin immunoprecipitation revealed that the transcriptional activity of ELF5 specified the gene expression patterns that distinguish basal from luminal breast cancer, including suppression of FOXA1, GATA3 and ER, key estrogen-action genes. Tamoxifen treatment of luminal MCF7 cells upregulated Elf5 expression and cells that acquired resistance to Tamoxifen became dependent on ELF5 for proliferation. ELF5 is a regulator of breast cancer cell proliferation, transcriptionally specifies the basal molecular subtype and is utilised by ER+ breast cancer cells to escape proliferative arrest caused by Tamoxifen.

overall_design: Elf5 was knocked down via siRNA in basal HCC1937 cell lines, in triplicate. Elf5 was induced in luminal T47D and MCF7 cell lines via a doxycycline inducible expression vector, in duplicate.

first: Maria

last: Kalyuga

first: David

last: Gallego-Ortega

first: Heather

last: Lee

middle: J

first: Liz

last: Caldon

last: Stone

first: Stephanie

last: Allerdice

first: Fatima

last: Valdes-Mora

first: Rosalind

last: Launchbury

first: Aaron

last: Statham

first: Nicola

last: Armstrong

first: Chehani

last: Alles

first: Adelaide

last: Young

first: Andrea

last: Egger

first: Wendy

last: Au

first: Catherine

last: Piggin

first: Cara

last: Evans

first: Tilman

last: Brummer

first: Warren

last: Kaplan

first: Julia

middle: M

last: Gee

first: Robert

middle: I

last: Nicholson

last: Sutherland

first: Alex

last: Swarbrick

first: Matthew

last: Naylor

first: Susan

last: Clark

first: Jason

last: Carroll

first: Christopher

last: Ormandy


title: Ribosomal protein S3 regulates GLI2-mediated osteosarcoma invasion

status: Public on Dec 14 2012

city: Ann Arbor

first: Hiroko

last: Nagao-kitamoto

address: 1150 W Medical Center Dr,

institute: The University of Michigan Medical school

summary: It has been reported that GLI2 promotes proliferation, migration, and invasion of mesenchymal stem cell and osteosarcoma cells. To examine the molecular mechanisms of GLI2-mediated osteosarcoma metastasis, we performed a microarray analysis. The gene encoding ribosomal protein S3 (RPS3) was identified as a target of GLI2. Real-time PCR revealed that RPS3 was upregulated in osteosarcoma cell lines compared with normal osteoblast cells. Knockdown of GLI2 decreased RPS3 expression, whereas forced expression of a constitutively active form of GLI2 upregulated the expression of RPS3. RPS3 knockdown by siRNA decreased the migration and invasion of osteosarcoma cells. Although forced expression of constitutively active GLI2 increased the migration of human mesenchymal stem cells, knockdown of RPS3 reduced the up-regulated migration. In contrast, forced expression of RPS3 increased migration and invasion of osteosarcoma cells. Moreover, reduction of migration by GLI2 knockdown was rescued by forced expression of RPS3. Immunohistochemical analysis showed that RPS3 expression was increased in primary osteosarcoma lesions with lung metastases compared with those without. These findings indicate that GLI2–RPS3 signaling may be a marker of invasive osteosarcoma and a therapeutic target for patients with osteosarcoma.

overall_design: Negative siRNA(U-2OS) and GLI2 siRNA(U-2OS)

last: Nagao-Kitamoto

first: Takao

last: Setoguchi


title: Specific sequence determinants of miR-15/107 microRNA gene group targets

status: Public on Dec 11 2012

city: Chicago

first: Xiaowei

last: Wang

state: IL

address: 909 S Wolcott Ave, Rm 5137

institute: University of Illinois at Chicago

summary:
Using anti-Argonaute (anti-AGO) antibody co-immunoprecipitation, followed by microarray analyses and downstream bioinformatics, ‘RIP-Chip’ experiments enable direct analyses of miRNA targets. The analyses support four major findings: (i) RIP-Chip studies correlated with total input mRNA profiling provides more comprehensive information than using either RIP-Chip or total mRNA profiling alone after miRNA transfections; (ii) new data confirm that miR-107 paralogs target coding sequence (CDS) of mRNA; (iii) biochemical and computational studies indicate that the 3′ portion of miRNAs plays a role in guiding miR-103/7 to the CDS of targets; and (iv) there are major sequence-specific targeting differences between miRNAs in terms of CDS versus 3′-untranslated region targeting, and stable AGO association versus mRNA knockdown. For detailed protocol and for full discussion of the results please see Nelson PT et al, Nucleic Acids Res. 2011 Oct;39(18):8163-72.
Affymetrix microarrays which were performed 2 days following miRNA transfections: total lysate following miRNA-like transfections; and RNA from anti-Argonaute (2A8 monoclonal antibody) co-Ips

overall_design: RIP-ChIP studies (and parallel assessments of total input mRNA) were performed in cultured H4 cells after transfection with miRNAs corresponding to the miR-15/107 gene group (miR-103, miR-107, miR-16 and miR-195), another physiological miRNA (miR-320), miR-15b*, and three non-physiological additional miRNA-like molecules (miR-107-mut1, mir-107-mut2, and negative control miRNA from Ambion).  For details on transfected miRNA sequences, see Nelson PT et al, Nucleic Acids Res. 2011 Oct;39(18):8163-72.   Three biological replicates were run for each condition with a total of 54 separate human Affymetrix Human Gene 1.0 ST array replicates.  See Wang WX et al, RNA (2010) 16:394-404 for detailed protocol of RIP-ChIP.

first: Peter

middle: T

last: Nelson

first: Wang-Xia


title: Repression of genes for stimulators of glycolysis

status: Public on Dec 04 2012

city: Lund

first: Ram

last: Ajore

address: Klinikgatan 26

department: Hematology

country: Sweden

institute: Lund University

summary:
The overall aim of the present work was to identify MTG16 functions in leukemia cells. Alterations in quantity of the MTG16 co-repressor might affect gene regulation and cell metabolism in malignant cells. Differentiated cells secure energy for cellular homeostasis largely by mitochondrial oxidation. Whereas, mature cells, proliferating tumour cells including leukemia cells depend on glycolysis and mitochondrial respiration may be low even in oxygen–rich environments.The same signal transduction pathways that govern cell proliferation give instructions for nutrient uptake and co-regulate metabolic processes. In this manner, the metabolism of tumor cells, and other highly proliferating cells, is adapted to stimulate anabolic glycolysis–driven processes for incorporation of nutrients into nucleotides, amino acids and lipids to synthesize macromolecules required for growth and proliferation.
We used a doxycycline–regulated Tet-On gene expression system to achieve controlled expression of MTG16. A noticeable finding was that the expression of genes for key glycolytic regulators involved in aerobic tumor cell glycolysis was diminished by MTG16.

overall_design: Total cellular RNA was extracted from Raji/MTG16 Tet-On 3G cells after 8 hours of incubation with 1 mg/ml doxycycline. Cells were collected in triplicates as biological replicates. Total RNA was isolated using the RNeasy mini kit. The quality of RNA was examined by Bioanalyzer.RevertAidTM was used for synthesis of first strand cDNA from 1mg RNA using random primers.Microarray analysis was performed using Affymetrix expression system at SCIBLU Genomics.

first: Parveen

last: Kumar

first: Inge

last: Olsson

first: Srinivas

last: Veerla


title: Gene expression from Gaucher Disease iPSc

status: Public on Dec 07 2012

city: Barcelona

first: Erika

last: Lorenzo Vivas

address: Doctor Aiguader 88

country: Spain

institute: CMRB

summary: Gene expression data obtained from induced pluripotent stem cells derived from wild type fibroblasts (iPSc WT) and from Gaucher Disease type 2 fibroblasts (GD iPSc). Also, gene expression analysis from the initial fibroblasts was made (WT fibroblasts and GD- fibroblasts), as well as gene expression analysis from a human embryonic stem cell line (hES4).

overall_design: Two different iPSc cell lines derived from Gaucher Disease type 2 fibroblasts were analysed in order to be compared to iPSc derived from Wild Type fibroblasts (only one cell line) and human embryonic stem cells (only one cell line). The initial cells: two different wild type fibroblasts and one Gaucher disease type 2 fibroblasts were also analysed.

first: Gustavo

last: Tiscornia

first: Juan

last: Izpisua Belmonte


title: Analysis of Hepatoblastoma and normal fetal liver miRNA profiles and HepaRG cells that ectopically express miR-371-3 cluster

status: Public on Dec 13 2012

first: stefano

last: cairo

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

overall_design: Refer to individual Series


title: Gene expression profiling of neuroendocrine primary tumors: effect of Octreotide treatment

status: Public on Dec 12 2012

city: Brussels

first: Jean-Baptiste

last: Demoulin

address: av Hippocrate 75, B1.74.05

department: de Duve Institute

country: Belgium

institute: Université catholique de Louvain

summary:
The management of neuroendocrine tumors (NETs) is very variable, depending on many specific aspects, such as the type of tumor, spread and patient general health. Several advances have been made with the newly developed somatostatin analogues to cure this type of malignancies. Somatostain analogues such as octreotide have been used in clinic to treat patients with neuroendocrine tumors (NETs). However, the molecular mechanism leading either to successful therapy or acquired resistance to the analogues is still to large extent unclear. Patients develop drugs resistance during a long term treatment. Therefore, to identify the pivotal regulatory genes involved in the development of drug resistance is an actual challenge. We studied five human neuroendocrine tumor cell lines, CNDT2.5, KRJ1, QGP-1, NCI H720 and NCI H727. We also investigated a long-term treated CNDT2.5 by using octreotide. We performed gene expression profiling in all the human neuroendocrine cell lines.
Keywords: Gene Expression profiling, treatment comparison

overall_design: We investigated 5 human neuroendocrine cell lines, CNDT2.5 and KRJ1, established from ileum NETs, QGP1 by a pancreatic NET, NCI H720 and NCI H727 from bronchopulmonary NETs. CNDT2.5 cell were constantly treated with 1µM octreotide for 10 and 16 months. We isolated total RNA (Ambion, PARIS™ Kit) from 5 WT cell lines and CNDT2.5 treated with octreotide (Santostatin, Novartis). Total RNA was hybridized onto the Affymetrix Human Gene 1.0 ST Array by Affymetrix Uppsala Platform, UU. SE (Uppsala, Sweden). We first wanted to verify whether the different cell lines may become reliable models to study neuroendocrine signaling pathways. The main objective of this project aimed at understanding the mechanisms by which octrotide (Sandostatin, Novartis) alter cellular growth and differentiation of CNDT2.5 cells. We therefore focused on intermediate (10 months) and long stimulation (16 months) events triggered by sandostatin, which lead variation of CNDT.2.5 cells gene expression to identify potential pivotal genes involved in the development of drug resistance in neuroendocrine cells.

first: Su-Chen

last: Li

first: Ahmed

last: Essaghir

first: Valeria

last: Giandomenico


title: Critical role of SOX17 in the hematopoietic development from human embryonic stem cells

city: Yokohama

first: Takaho

middle: A.

last: Endo

state: Kanagawa

address: 1-7-22 Suehiro, Tsurumi

department: IMS

institute: RIKEN

type: Genome binding/occupancy profiling by genome tiling array

summary:
Human embryonic stem cells (hESCs) are a powerful tool for modeling regenerative therapy. To search for the genes that promote hematopoietic development from human pluripotent stem cell, we overexpressed a list of hematopoietic regulator genes in human pluripotent stem cell-derived CD34+CD43- endothelial cells (ECs) enriched in hemogenic endothelium. Among genes tested, only SOX17, a gene encoding a transcription factor of the SOX family, promoted cell growth and supported expansion of CD34+CD43+CD45-/low cells expressing a hemogenic endothelial maker VE-cadherin. SOX17 was highly expressed in CD34+CD43- ECs but at a low level in CD34+CD43+CD45- pre-hematopoietic progenitor cells (pre-HPCs) and CD34+CD43+CD45+ HPCs. SOX17-overexpressing cells formed sphere-like colonies and generated few hematopoietic progenies. However, they retained hemogenic potential and gave rise to hematopoietic progenies upon inactivation of SOX17. Global gene expression analyses revealed that the CD34+CD43+CD45-/low cells expanded upon overexpression of SOX17 are hemogenic endothelium-like cells developmentally placed between ECs and pre-HPCs. Of interest, SOX17 also reprogrammed both pre-HPCs and HPCs into hemogenic endothelium-like cells. Genome-wide mapping of SOX17 revealed that SOX17 directly activates transcription of key regulator genes for vasculogenesis, hematopoiesis, and erythrocyte differentiation. Depletion of SOX17 in CD34+CD43- ECs severely compromised their hemogenic activity. These findings suggest that SOX17 plays a critical role in priming hemogenic potential in ECs, thereby regulates hematopoietic development from hESCs.

This SuperSeries is composed of the SubSeries listed below.

overall_design:
ChIP on chip analysis was carried out using the Mouse Promoter ChIP-on-chip Microarray Set (G4490A, Agilent, Palo Alto, Calif., USA). MEFs were subjected to ChIP assay using a Ring1B antibody. Purified immunoprecipitated and input DNA was subjected to T7 RNA polymerase-based amplification. Labeling, hybridization and washing were carried out according to the Agilent mammalian ChIP-on-chip protocol (ver.9.0). Scanned images were quantified with Agilent Feature Extraction software under standard conditions.

Human ES cells were differentiated for 6 days in EBs, then CD34+CD43-CD45- endothelial cells were isolated, plated onto OP9 cells, and transduced with the 4OH-tamoxifen (4OHT)-inducible 3×FLAG-tagged Sox17-ERT retrovirus. The cells were seeded on OP9 stromal cells and cultured in the presence of 4OH-tamoxifen. At day 27 of  the co-culture with OP9 cells, CD34+CD43+CD45low hemogenic endothelium-like cells overexpressing Sox17-ERT were collected by CD34 magnetic-activated cell sorting (MACS) and subjected to a ChIP-chip analysis.
ChIP on chip analysis was carried out using the Mouse Promoter ChIP-on-chip Microarray Set (G4490A, Agilent, Palo Alto, Calif., USA). MEFs were subjected to ChIP assay using a Ring1B antibody. Purified immunoprecipitated and input DNA was subjected to T7 RNA polymerase-based amplification. Labeling, hybridization and washing were carried out according to the Agilent mammalian ChIP-on-chip protocol (ver.9.0). Scanned images were quantified with Agilent Feature Extraction software under standard conditions.

Human ES cells were differentiated for 6 days in EBs, then CD34+CD43-CD45- endothelial cells were isolated, plated onto OP9 cells, and transduced with the 4OH-tamoxifen (4OHT)-inducible 3×FLAG-tagged Sox17-ERT retrovirus. The cells were seeded on OP9 stromal cells and cultured in the presence of 4OH-tamoxifen. At day 27 of  the co-culture with OP9 cells, CD34+CD43+CD45low hemogenic endothelium-like cells overexpressing Sox17-ERT were collected by CD34 magnetic-activated cell sorting (MACS) and subjected to a ChIP-chip analysis.

first: Yaeko

last: Nakajima-Takagi

first: Atsushi

last: Iwama

first: Mitsujiro

last: Osawa


title: Effect of topographical micropatterning on human endothelial cells

status: Public on Nov 29 2012

city: Stanford

first: Ngan

middle: F

last: Huang

address: 300 Pasteur Drive

department: Cardiovascular Medicine

institute: Stanford University

summary:
Shear stress is known to regulate endothelial cell orientation along the direction of flow. We asked wither cellular patterning along, in the absence of shear could have similar biological effects as shear.
We used DNA microarrays to examine the effect of cellular patterning on their transcriptome.

overall_design: Human microvascular endothelial cells were cultured in parallel micropatterned channels (30um wide channels, 30um apart) composed of polydimethylsiloxane, followed DNA Microarray analysis (Affymetrix 1.0 ST array)


title: Influence of Interferon-beta on expression profile of memory T-cells

status: Public on Dec 01 2012

city: Boston

first: Vanessa

last: Beynon

address: 77 Avenue Louis Pasteur

institute: Brigham and Women's Hospital

summary: Inflammasomes are multi-protein complexes that control the production of pro-inflammatory cytokines such as IL-1beta. Inflammasomes play an important role in the control of immunity to tumors and infections, and also in autoimmune diseases, but the mechanisms controlling the activation of human inflammasomes are largely unknown. We found that human activated CD4+CD45RO+ memory T-cells specifically suppress P2X7R-mediated NLRP3 inflammasome activation, without affecting P2X7R-independent NLRP3 or NLRP1 inflammasome activation. The concomitant increase in pro-IL-1β production induced by activated memory T-cells concealed this effect. Priming with IFNβ decreased pro-IL-1β production in addition to NLRP3 inflammasome inhibition and thus unmasked the inhibitory effect on NLRP3 inflammasome activation. IFNβ did not suppress NLRP3 inflammasome activation by acting directly on monocytes. The inhibition of pro-IL-1β production and suppression of NLRP3 inflammasome activation by IFNβ-primed human CD4+CD45RO+ memory T-cells is partly mediated by soluble FasL and is associated with down-regulated P2X7R mRNA expression and reduced response to ATP in monocytes.  CD4+CD45RO+ memory T-cells from multiple sclerosis (MS) patients showed a reduced ability to suppress NLRP3 inflammasome activation, however their suppressive ability was recovered following in vivo treatment with IFNβ. Thus, our data demonstrate that human P2X7R-mediated NLRP3 inflammasome activation is regulated by activated CD4+CD45RO+ memory T cells, and provide new information on the mechanisms mediating the therapeutic effects of IFNβ in MS.

overall_design: Memory T-cells were cultured in the presence of monocytes with and without Interferon-beta, resorted and expression profile was determined

first: Francisco

last: Quintana

first: Howard

last: Weiner


title: Effects of EVI1 and EVI1Δ324 mild expression in HeLa cells

status: Public on Nov 14 2012

city: Singapore

last: Sayadi

state: Singapore

address: 61 biopolis

country: Singapore

institute: Genome Institute of Singapore

summary: We studied the variations of mRNA amounts after Flag-EVI1, Flag-EVI1Δ324, or Flag expression in HeLa cells.  Despites EVI1 discovery in 1988, its recognized role as a dominant oncogene in myeloid leukemia and more recently in epithelial cancers, only a few target genes were known and it was not clear why EVI1 was involved in cancer progression. Here we obtained the genomic binding occupancy and expression data for EVI1 in human cells. We identified numerous EVI1 target cancer genes and genes controlling cell migration and adhesion. Moreover, we characterized a transcriptional cooperation between AP1 and EVI1 that regulated proliferation and adhesion through a feed-forward loop. This study provides human genome-wide mapping and expression analyses for EVI1 that will be useful for the research community.

overall_design: 12 samples were collected. Each condition was done in 4 replicates, collected 24 hours after transfection (for mild expression of EVI1 or EVI1Δ324). Transfections with Flag-expressing vector were used as controls.

first: Emilie

middle: A

last: Bard-Chapeau

first: Justin

last: Jeyakani

first: A

first: Neal

last: Copeland

first: Guillaume

last: Bourque


title: Expression data from H226 squamous cell carcinoma cells

status: Public on Nov 06 2012

city: Boulder

first: Corrie

last: Gallant-Behm

state: CO

address: 347 UCB

department: Molecular, Cellular, and Developmental Biology

institute: University of Colorado at Boulder

summary:
To define the contribution of p53 versus DNp63a to gene expression control, we performed a series of microarray assays for cells where p53 was activated using Nutlin-3 or DNp63a was knocked down using a stably transduced tetracycline inducible shRNA.
We determined that p53 transcriptionally activates and DNp63a transcriptionally represses a non-overlapping subset of genes.

overall_design: Total RNA from H226 cells harvested using Tri reagent (Sigma-Aldrich) was used for gene expression analysis on Affymetrix HuGene 1.0 ST arrays following the manufacturer’s instructions. Differential gene expression was determined with Partek software using one-way ANOVA.


title: Expression data from WT HL60 cells

city: St. John's

first: Touati

last: Benoukraf

state: NL

address: Craig L. Dobbin Genetics Research Centre,

department: Faculty of Medicine, Division of BioMedical Sciences

institute: Memorial University of Newfoundland

summary: We used the microarray analysis to detail the gene expression profile from the leukemic cell line HL-60

overall_design: Relationship between DNMT1-RNA interactions, DNA methylation and gene expression

first: Annalisa

last: Di Ruscio

first: Alexander

last: Ebralidze

first: Mengchu

last: Wu

first: Daniel

middle: G

last: Tenen


title: Constitutional Trisomy 8 Mosaicism as a Model for Epigenetic Studies of Aneuploidy (gene expression)

first: Josef

last: Davidsson

address: BMC B13

department: Clinical Genetics

summary:
To increase our understanding of epigenetic patterns associated with aneuploidy we used constitutional trisomy 8 mosaicism as a model, enabling analyses of single cell clones, harboring either trisomy or disomy 8, from the same patient.
We profiled gene and miRNA expression as well as genome-wide and promoter specific DNA methylation and hydroxymethylation patterns in trisomic and disomic fibroblasts, using microarrays and methylated DNA immunoprecipitation.

overall_design: comparison of trisomy 8 cells with disomic as well as reference fibroblasts

first: Bertil

last: Johansson


title: eQTL Analysis Identifies Novel Associations Between Genotype and Gene Expression in the Human Intestine

city: Toronto

first: Boyko

last: Kabakchiev

address: 60 Murray Street, Room L3-004

department: Samuel Lunenfeld Research Institute

institute: Mount Sinai Hospital

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


title: Characterizing the molecular spatial and temporal field of injury in early stage smoker non-small cell lung cancer patients after definitive surgery by expression profiling

city: Houston

first: Humam

last: Kadara

state: TX

address: 2130 W. Holcombe Blvd

institute: University of Texas MD Anderson Cancer Center

summary:
Gene expression alterations in response to cigarette smoke have been characterized in normal-appearing bronchial epithelium of healthy smokers and it has been suggested that adjacent histologically normal tissue display tumor-associated molecular abnormalities.
We sought to delineate the spatial and temporal molecular lung field of injury in smoker early stage non-small cell lung cancer (NSCLC) patients (n=19) who were accrued into a surveillance clinical trial for annual follow-up and bronchoscopies within one year after definitive surgery.

overall_design: Bronchial brushings and biopsies were obtained from six different sites in the lung at the time of inclusion in the study and at 12, 24 and 36 months after the first time point. Affymetrix Human Gene 1.0 ST arrays were used for whole-transcript expression profiling of airways (n=391). Mixed-effects models were performed to determine significant differential gene expression modulation by site from tumor and time following inclusion in the study within the molecular field of injury.

first: Ignacio

last: Wistuba


title: Constitutional Trisomy 8 Mosaicism as a Model for Epigenetic Studies of Aneuploidy

type: Methylation profiling by genome tiling array

platform_organism:
Homo sapiens
synthetic construct


title: Knockdown of mineralocorticoid receptor or glucocorticoid receptor on human endometrial stromal cells and decidualization

status: Public on Nov 28 2012

first: Scott

middle: Andrew

last: Ochsner

address: One Baylor Plaza

department: Molecular and Cellular Biology

institute: Baylor College of Medicine

summary: To clarify mineralcorticoid receptor and glucocorticoid receptor-dependent gene networks in decidualizing human endometrial stromal cells.

overall_design: Genome-wide microarray analysis was performed on primary cultures established from 4 different patients.  Stromal cell cultures were subjected to either GR or MR siRNA knockdown or control non-targeting siRNA then decidualized for four days before harvesting and RNA extraction for microarray analysis.

first: Keiji

last: Kuroda

first: Mark

last: Christian

first: Jan

last: Brosens


title: eQTL Analysis Identifies Novel Associations Between Genotype and Gene Expression in the Human Intestine (Expression)

summary: Genome-wide association studies (GWAS) have been pivotal to increasing our understanding of intestinal disease. However, the mode by which genetic variation results in phenotypic change remains largely unknown, with many associated polymorphisms likely to modulate gene expression. Analyses of expression quantitative trait loci (eQTL) to date indicate that as many as 50% of these are tissue specific. Here we report a comprehensive eQTL scan of intestinal tissue.

overall_design:
Subjects who had undergone ileal pouch anal anastomosis and closure of ileostomy at least one year prior to recruitment were prospectively enrolled at Mount Sinai Hospital in Toronto. Endoscopically and histologically normal tissue biopsies from the afferent limb of these individuals were obtained and preserved in RNAlater. Total RNA was extracted with the QIAGEN miRNeasy Kit and mRNA analysis was performed on Affymetrix Human Gene 1.0 ST arrays. DNA was obtained from whole-blood samples from the same individuals and genotyped using the Illumina beadchips. Cis- and trans-eQTL analyses were carried out on 173 subjects encompassing the expression levels of 19,047 unique autosomal genes listed in the NCBI database and over 580K dbSNPs (Call Rate  ≥ 95%; MAF  ≥ 5%; Hardy–Weinberg equilibrium (HWE) χ2 p-values  ≥ 10-6). This work was done in a custom software pipeline and the Kruskal-Wallis test was used to compare expression values across different genotypes. False discovery rate correction for multiple testing was applied at an alpha level of 5%.

This Series includes the Affymetrix data.

first: B

first: M

middle: S

last: Silverberg


title: Expression data from YAP-S127D DLD1 Xenografts

first: Fernando

last: Camargo

address: 1 Blackfan Circle

institute: Children's Hospital Boston

summary: We overexpressed YAP-S127D in DLD1 colorectal cancer cells for 21 days after sub-cutaneous (SubQ) injection into the flanks of nude mice.

overall_design: Mice were given dox for 21 days, sacrificed, and tumors were isolated for RNA extraction and analyzed by Affymetrix microarrays.

first: Evan

middle: R

last: Barry

middle: D


title: YAP Inhibition in HCC cells (Hep3B)

status: Public on Nov 01 2012

city: Mannheim

first: Carsten

last: Sticht

address: Theodor-Kutzer-Ufer

department: ZMF

institute: University Heidelberg

summary:
siRNA-mediated inhibition compared to untreated cells and cells transfected with nonsense siRNA.
Loss of contact inhibition and anchorage-independent growth are hallmarks of cancer cells. In this context, frequent inactivation of the Hippo pathway and subsequent nuclear enrichment of the transcriptional coactivator yes-associated protein (YAP) uncouple cell proliferation and anti-apoptosis from contact inhibition, associated with uncontrolled tumor growth and tumor cell dissemination. However, general molecular mechanisms of tumor-supporting YAP activity remain unclear. In this study, we show that overexpression and nuclear accumulation of YAP in hepatocytes and hepatocellular carcinoma (HCC) cells leads to an induction of the Notch pathways through transcriptional activation of the Notch ligand jagged-1 (Jag-1). This induction of Jag-1 strictly depends on binding of YAP to TEAD4 and does not rely on WNT/β-catenin pathway activity. Co-activation of YAP, TEAD4, Jag-1, and the Notch target gene Hes-1 was significantly higher in HCC from patients with poor prognosis. High-level expression and nuclear accumulation of YAP correlates with Jag-1/Notch activation not only in human HCC tissues, but also in colon and pancreatic cancer tissues. Thus, our data demonstrate that YAP-driven co-activation of the Jag-1/Notch pathway in part facilitates oncogenic properties of the oncogene YAP not only in HCC but also in different gastrointestinal malignancies.

overall_design: Expression profiling of untreated HCC cell lines (control 1), cells transfected with scrambled/nonsense siRNA (control 2), and after siRNA-mediated YAP inhibition.

first: Darjus

last: Tschaharganeh

first: Xin

last: Chen

first: Philipp

last: Latzko

first: Mona

last: Malz

first: Matthias

last: Gaida

first: Klaus

last: Felix

first: Stephan

last: Singer

first: Federico

last: Pinna

first: Norbert

last: Gretz

first: Salvatore

last: Delogu

last: Evert

first: Fan

last: Biao

first: Silvia

last: Ribback

first: Lijie

last: Jiang

first: Stefania

last: Brozzetti

first: Frank

last: Bergmann

last: Dombrowski

first: Peter

last: Schirmacher

first: Diego

last: Calvisi

first: Kai

last: Breuhahn


title: Expression data from A549 cells after treatment with flagellin and transforming growth factor beta 1

status: Public on Oct 31 2012

city: Nishihara

first: Hideyuki

last: Yamamoto

state: Okinawa

address: 207 Uehara

department: Faculty of medicine

institute: University of the Ryukyus

summary:
We have examined the changes in gene expression aftert reatment  of A549 cells, a cultured alveolar epithelial cells, with flagellin and transforming growth factor beta 1.
In this dataset, we include the expression data obtained from A549 cells after treatment with purified flagellin or transforming growth factor beta 1 receptor.  The analysis indicated that flagellin induced a change in gene expression that was similar to the changes induced by transforming growth factor 1.

overall_design: A549 cells were treated with flagellin or transforming growth factor 1 for 24 h. Total RNA was extracted and reverse transcribed to cDNA. Synthesized cDNA was fragmented and labeled with biotin.   The biotinylated cDNA was hybridized to to an Affymetrix GeneChip Array, and probe signal intensities were captured.

first: Y

last: Kondo

first: H


title: Expression data generated by syndecan-1 silencing in malignant mesothelioma STAV-AB cell line

city: Huddinge

first: Tünde

last: Szatmári

state: Stockholm

address: F42 Karolinska Universitetssjukhuset

department: Laboratory Medicine

institute: Karolinska Institute

summary:
The transcriptomic responses of syndecan-1 silencing in a human mesothelioma cell line was followed with microarray analysis. To project the transcriptome analysis on the full-dimensional picture of cellular regulation, we applied a novel method of network enrichment analysis which elucidated signalling relations between differentially expressed genes and pathways acting via various molecular mechanisms.
Our results suggest that syndecan-1 regulates cell proliferation in a highly complex way, although the exact contribution of the altered pathways necessitates further functional studies.

overall_design: Gene expression profiles (Human Gene 1.0 ST) of malignant mesothelioma cells were studied in cells silenced for syndecan-1  (N=3) and scrambled control cells (N=3)

first: T

first: F

last: Mundt

first: D

last: Brodin

first: K

last: Dobra


title: An epithelial-mesenchymal transition (EMT) gene signature predicts resistance to erlotinib and PI3K pathway inhibitors and identifies Axl as a novel EMT marker in non-small cell lung cancer.

status: Public on Oct 25 2012

first: Pierre

last: Saintigny

address: 1515 Holcombe

department: Thoracic / Head and Neck Medical Oncology

institute: The University of Texas M.D. Anderson Cancer Center

summary:
Epithelial/mesenchymal transition (EMT) is associated with loss of cell adhesion molecules, such as E-cadherin, and increased invasion, migration, and proliferation in epithelial cancers. In non-small cell lung cancer (NSCLC), EMT is associated with greater resistance to EGFR inhibitors. However, its potential to predict response to other targeted drugs or chemotherapy has not been well characterized. The goal of this study was to develop a robust, platform-independent EMT gene expression signature and to investigate the association of EMT and drug response in NSCLC.
A 76-gene EMT signature was derived in 54 DNA-fingerprinted NSCLC cell lines and tested in an independent set of cell lines and in NSCLC patients from the BATTLE clinical trial.  The signature classified cell lines as epithelial or mesenchymal independent of the microarray platform and correlated strongly with E-cadherin protein levels, as measured by reverse phase protein array.  Higher protein expression of Rab25 (in epithelial lines) and Axl (in mesenchymal lines), two signature genes associated with in EMT in other cancer types, was also confirmed. Mesenchymal cell lines demonstrated significantly greater resistance to EGFR inhibition, independent of EGFR mutation status and were more resistant to drugs targeting the PI3K/Akt pathway. We observed no association between EMT and response to cytotoxic chemotherapies, including cisplatin, pemetrexed, and docetaxel monotherapy and/or doublets (p-values ≥0.2).  In NSCLC patients, the EMT signature predicted 8-week disease control in the erlotinib arm, but not in other treatment arms.  In conclusion, we have developed a robust EMT signature that predicts resistance to EGFR inhibitors and PI3K/Akt pathway inhibitors.

overall_design: Gene expression profiles were measured in 131 core biopsies from patients with refractory non-small cell lung cancer in the  Biomarker-integrated Approaches of Targeted Therapy for Lung Cancer Elimination (BATTLE) trial. We used the BATTLE dataset to test an EMT gene expression signature trained in cell lines and independant of the microarray platform.

first: Ignacio

last: Wistuba

first: John

middle: V

last: Heymach

first: Edward

last: Kim

first: Scott

last: Lippman

first: Roy

last: Herbst

first: Waun

middle: K

last: Hong

first: J

last: Lee

first: Kevin

last: Coombes

first: Li

last: Mao


title: Expression data from gingival tissue

status: Public on Oct 29 2012

city: Kiel

first: Robert

last: Haesler

address: Schittenhelmstr. 12

department: IKMB / 1st Dept. of Medicine

institute: University Clinic of Schleswig Holstein

summary: The experiment aims to identify transcriptional effects differences between periimplantitis, Parodontitis and healthy gingival tissue

overall_design: 8 controls, 7 periimplantitis patients, 7 Parodontitis patients

last: Häsler


title: Expression data from human iPS cells treated by a small molecule KY02111

status: Public on Oct 30 2012

city: Kyoto, Sakyo-ku

first: Itsunari

last: Minami

address: Yoshida Ushinomiya-cho

institute: iCeMS

summary:
Human pluripotent stem cells (hPSCs) such as embryonic stem cells and induced pluripotent stem cells are promising materials for cell-based regenerative therapies to heart diseases. However, until realization there are many hurdles such as high efficiency of cardiac differentiation of hPSCs and production of clinical-grade cardiac cells derived from hPSCs. Here, we show that a novel small molecule KY02111 robustly enhances differentiation to functional cardiomyocytes from hPSCs.
To reveal how KY02111 function on promoting cardiac differentiation of hPSCs, we analyzed the gene expression profiles in KY02111-treated IMR90-1 hiPSCs using the microarray technique.

overall_design: At Day3 of cardiac differentiation from hiPSCs, KY02111 or DMSO was added in the culture and then the cell population was harvested after 12 or 24 hours for RNA extraction.

first: Takuya

last: Yamamoto


title: The histotype-specific copy-number landscape of ovarian cancer (expression Japan)

first: Liang

last: Goh

address: College Road

institute: Duke-NUS graduate medical school

summary: Ovarian cancer is characterized by multiple structural aberrations; most are passenger alterations which do not confer tumor growth.  Like many cancers, it is a heterogeneous disease and till date, the histotype-specific copy number landscape has been difficult to elucidate.  To dissect the heterogeneity of ovarian cancer and understand the pathogenesis of its various histotypes, we developed an in silico hypothesis-driven workflow to identify histotype-specific copy number aberrations across multiple datasets of epithelial ovarian cancer.  In concordance with previous studies on global copy number changes, our study showed similar alterations.  However, when the landscape was de-convoluted into histotypes, distinct alterations were observed.  We report here a comprehensive histotype-specific copy number landscape of ovarian cancer and showed that there is genomic diversity between the histotypes; some involving well known cancer genes and some novel potential driver genes.  Besides preferential occurrence of alterations in some histotypes, opposite trends of alteration were observed; such as ERBB2 amplification in mucinous but deletion in serous tumors.  The landscape highlights the need for identifying histotype-specific aberrations in ovarian cancer and present potential to tailor management of ovarian cancer based on molecular signature of histotypes.

overall_design: 56 samples containing the 4 histotypes were used for this study.  It contained 12 clear cell carcinoma, 6 endometrioid adenocarcinoma, 2 mucinous adenocarcinoma, 5 mucinous-borderline tumors, 26 serous adenocarcinoma, and 5 serous-borderline tumors.


title: Expression data from human pancreatic islets

status: Public on Oct 23 2012

city: Malmo

first: Anders

last: Rosengren

address: CRC 91-11 SUS

institute: Lund University

summary: A gene co-expression network analysis has been conducted to identify T2D-associated gene modules. Donors 1-48 were used for the initial analysis and donors 49-80 for the replication and were normalized separately in this study

overall_design: Islets from cadaver donors (57 non-diabetic and 20 diabetic) were provided by the Nordic Islet Transplantation Programme (www.nordicislets.org), Uppsala University. The microarrays were performed using GeneChip® Human Gene 1.0 ST whole transcript according to Affymetrix standard protocol.

first: Leif

last: Groop

first: Erik

last: Renström


title: The histotype-specific copy-number landscape of ovarian cancer (expression Taiwan)

overall_design: 42 archived frozen tumor samples collected from Department of Obstetrics and Gynecology, Tri-Service General Hospital, Taiwan, containing 8 clear cell, 3 mucinous, and 31 serous.


title: Expression data from phenotypically discordant monozygotic twin lymphoblasts

status: Public on Oct 20 2012

city: Kobe-shi

first: Chihchieh

last: Yu

address: 7-5-1 kusunoki-cho, chuo-ku

institute: Kobe University

summary:
Human intelligence demonstrates one of the highest heritabilities among human quantitative traits. Phenotypically discordant monozygotic twins provide a way to identify loci responsible for normal-range intelligence.
We conducted array-based genome-wide gene expression analysis aiming to identify genes displaying significant difference among monozygotic twin pairs manifesting between-co-twins IQ differences.

overall_design: Total RNA was isolated from B-lymphoblastoid cell lines and applied to Affymetirx arrays after reverse transcription. 17 twin pairs (34 subjects) were recruited in this study.

first: Mari

last: Furukawa

first: Kazuhiro

last: Kobayashi

first: Chizuru

last: Shikizima

first: Juko

last: Ando

first: Tatsushi

last: Toda


title: Expression data from human cancer cells

status: Public on Oct 19 2012

city: Augusta

first: Keith

last: robertson

address: 1120 15th street

institute: Georgia Health Sciences University

summary: We used microarrays to profile gene expression of NCCIT cells to study the link between epigenetic modifications and gene transcription.

overall_design: Extract total RNA to examine gene expression of NCCIT cells in the undifferentiated and differentiated states.

first: Bilian

last: Jin

first: Justin

last: Choi

last: Roberterson


title: Control of breast cancer growth and initiation by the stem cell-associated transcription factor TCF3

city: Jerusalem

first: Ittai

last: Ben-Porath

address: Faculty of Medicine, Ein kerem

department: Developmental Biology and Cancer Research

institute: Hebrew University of Jerusalem

summary: Regulatory factors controlling stem cell identity and self-renewal are often active in aggressive cancers and are thought to promote their growth and progression. TCF3 (also known as TCF7L1) is a member of the TCF/LEF transcription factor family that is central in regulating epidermal and embryonic stem (ES) cell identity. We found that TCF3 is highly expressed in poorly differentiated human breast cancers, preferentially of the basal-like subtype. This suggested that TCF3 is involved in the regulation of breast cancer cell differentiation state and tumorigenicity. Silencing of TCF3 dramatically decreased the ability of breast cancer cells to initiate tumor formation, and led to decreased tumor growth rates. In culture, TCF3 promotes the sphere formation capacity of breast cancer cells and their self-renewal. We found that in contrast to ES cells, where it represses Wnt-pathway target genes, TCF3 promotes the expression of a subset of Wnt-responsive genes in breast cancer cells, while repressing another distinct target subset. In the normal mouse mammary gland Tcf3 is highly expressed in terminal end buds, structures that lead duct development. Primary mammary cells are dependent on Tcf3 for mammosphere formation, and its overexpression in the developing gland disrupts ductal growth. Our results identify TCF3 as a central regulator of tumor growth and initiation, and a novel link between stem cells and cancer.

overall_design: Cells infected with different shRNA vectors were either untreated, treated with control or Wnt3A condition medium. Condition medium treatments were done in biological repeats.

first: Michal

last: Slyper

first: Amit

last: Shahar

first: Anat

last: Bar-Ziv

first: Roy

middle: Z

last: Granit

first: Tamar

last: Hamburger

first: Bella

last: Maly

last: Peretz


title: Relevance of Chromosome 2p Gain in Early Binet Stage A Chronic Lymphocytic Leukemia (expression)

status: Public on Oct 12 2012

city: MILAN

first: Luca

last: Agnelli

address: Venezian 1

department: Department of Advanced Diagnostics

country: Italy

institute: IRCCS Istituto Nazionale dei Tumori

summary: Chronic lymphocytic leukemia (CLL) is a clinically heterogeneous disease characterized by chromosomal aberrations of prognostic significance. Recent studies showed that gain of chromosome 2p is a recurrent lesion in CLL. We investigated the 2p gain and its relationship with prognostic biomarkers in a prospective series of 287 early-stage CLLs (Binet A). The 2p gain was detected by FISH in 17 patients (6%) and further characterized by single nucleotide polymorphism-array. Overall, unfavorable cytogenetic deletions, i.e. del(11)(q23) and del(17)(p13) (P=0.002) as well as unmutated (UM) status of IGHV (P<1×10-4) and CD38 (P<1×10-4) and ZAP-70 positive expression (P=0.003) were significantly more prevalent in 2p gain cases. Furthermore, 2p gained patients showed a significantly higher occurrence of stereotyped HCDR3 sequences compared to 2p normal CLLs (P=0.009). Among the stereotyped subsets, the incidence of subset #1 in 2p positive patients was significantly higher than that found in the remaining CLLs (P=0.031). Finally, gene expression profiling analysis identified a number of genes significantly upregulated in 2p gain CLLs. Among those located at 2p, NCOA1 and ROCK2 are known for their involvement in tumor progression in several human cancers, whereas among those located in different chromosomes, CAV1 at 7q31.1 has been recently identified to play a critical role in CLL progression. Our study indicates that 2p gain is a recurrent lesion in early CLL, correlated with the major biological and cytogenetic risk markers of the disease. Moreover, we provide insights to define novel candidate genes that may play additional pathogenetic roles in CLL.

overall_design: This series of microarray experiments contains the gene expression profiles of purified B-cell chronic lymphocytic leukemia (B-CLL) cells obtained from 136 patients (Binet stage A) showing 2p gain alteration. Peripheral blood mononuclear cells from B-CLL patients were isolated by Ficoll-Hypaque density-gradient centrifugation and the proportion of CD5/CD19/CD23 triple positive B cells in the suspension was determined by direct immunofluorescence performed using a FACS-sort flow cytometer with antibodies to: CD19 FITC/PE, CD23 PE and CD5 Cy-Chrome. If B-CLL cells were less than 90%, T cells, NK cells and monocytes were removed by negative selection using CD3, CD56, CD16, and CD14 monoclonal antibody treatment followed by magnetic beads. 5.5 micrograms of single-stranded DNA target obtained from 100 ng of purified total RNA was fragmented and then labeled using the WT Terminal Labeling Kit according to the standard Affymetrix protocol (GeneChip® Whole Transcript (WT) Sense Target Labeling Assay Manual). The fragmented labeled single-stranded DNA target was hybridized for 16 hours and 30 minutes at 45°C on GeneChip® Gene 1.0 ST array according to the standard Affymetrix protocol. Washing and scanning were performed using GeneChip System of Affymetrix (GeneChip Hybridization Oven 640, GeneChip Fluidics Station 450 and GeneChip Scanner 7G). Log2-transformed expression values were extracted from CEL files and normalized using NetAffx Transcript Cluster Annotations, Release 31 and robust multi-array average (RMA) procedure in Expression Console software (Affymetrix Inc.). The expression values of transcript cluster ID specific for loci representing naturally occurring read-through transcriptions were summarized as median value for each sample.

first: Sonia

last: Fabris

first: Laura

last: Mosca

first: Giovanna

last: Cutrona

first: Marta

last: Lionetti

first: Gabriella

last: Ciceri

first: Marzia

last: Barbieri

first: Francesco

last: Maura

first: Serena

last: Matis

first: Massimo

last: Gentile

first: Anna

last: Recchia

first: Emanuela

last: Pesce

last: Di Raimondo

first: Caterina

last: Musolino

first: Marco

last: Gobbi

first: Nicola

last: Di Renzo

first: Francesca

last: Mauro

first: Maura

last: Brugiatelli

first: Fiorella

last: Ilariucci

first: Simonetta

last: Zupo

last: Angrilli

first: Gianni

last: Quintana

first: Ugo

last: Consoli

first: Giovanni

last: Bertoldero

first: Paolo

last: Di Tonno

first: Alberto

last: Fragasso

first: Stefano

last: Molica

first: Pellegrino

last: Musto

first: Maria

middle: C

last: Cox

first: Gianluca

last: Festini

first: Iolanda

last: Vincelli

last: Sacchi

last: Baldini

first: Agostino

last: Cortelezzi

last: Federico

first: Fortunato

last: Morabito

first: Manlio

last: Ferrarini

first: Antonino

last: Neri


title: Genome-wide DNA methylation and gene expression analyses of monozygotic twin discordant for intelligence levels

first: Chihchieh

last: Yu

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

overall_design: Refer to individual Series

first: Mari

last: Furukawa

first: Kazuhiro

last: Kobayashi

first: Chizuru

last: Shikizima

first: Juko

last: Ando

first: Tatsushi

last: Toda


title: Relevance of Chromosome 2p Gain in Early Binet Stage A Chronic Lymphocytic Leukemia

first: Luca

last: Agnelli

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


title: Vastus lateralis muscle gene expression after local physical deconditioning and exercise training

status: Public on Oct 15 2012

city: Nijmegen

first: Gerwen

last: Lammers

address: PO Box 9101

country: Netherlands

institute: Radboud University Nijmegen Medical Centre

summary:
The leg of healthy volunteers was locally deconditioned using three weeks of unilateral lower limb suspension (ULLS). The extremely deconditioned legs of subjects with a spinal cord injury (SCI) were trained using eight weeks of functional electrical stimulation (FES) exercise, 2-3 times per week (total 20 sessions).
These models for local (in)activity were used to study changes in gene expression level of: A) Long-term deconditioning: before FES versus before ULLS (=SCI versus control); B) Short-term deconditioning: after ULLS versus before ULLS; and C) Exercise training:  after FES versus before FES.

overall_design: RNA was isolated from six healthy subjects before and after ULLS deconditioning, and three subjects with SCI before and after FES exercise training.

first: Noortje

last: vanDuijnhoven

last: Hopman


title: Expression data from human primary keratinocytes

status: Public on Oct 01 2012

city: Taichung City

first: Hong-Lin

last: Su

address: 250, Kuo-Kuang Rd

department: Department of Life Sciences

country: Taiwan

institute: National Chung Hsing University

summary: The genetic expression profile of a Wnt signal agonist, BIO, was evaluated in human primary keratinocytes.

overall_design: Accelerating scaling up of primary keratinocytes benefits skin autografts for severely burned patients. Wnt signal, a conserved pathway controlling cell cycle and morphogenesis of embryo, has been postulated to promote the cell proliferation and tumorigenesis in adult. Here, the effects of Wnt signal on the growth of interfollicular keratinocytes were investigated. We demonstrated that recombinant Wnt3a significantly promoted the primary keratinocyte growth at a low cell density. A well-characterized GSK-3beta inhibitor, BIO, activated the Wnt signals and also enhanced the colony formation of keratinocytes dose-dependently. Gene expression profile of the BIO-treated keratinocytes revealed the linkage of the BIO with the cell mitosis and indicated that epithelial cell adhesion molecule (EpCAM), a Wnt target gene, was upregulated. Comparing to the EpCAM- keratinocytes, the EpCAM+ cells showed higher proliferation rate and efficacy of the colony formation. Especially, inhibiting the EpCAM expression by shRNA attenuated the proliferation effect of BIO and the growth advantage of the EpCAM+ keratinocytes. These evidences emphasize the positive role of canonical Wnt and EpCAM on the regulation of cell growth and self-renewal for human keratinocytes.

first: Ching-I

last: Shen


title: Genome wide DNA methylation analysis of leukemia and reprogrammed leukemia cells (gene expression)

first: Touati

last: Benoukraf

address: Craig L. Dobbin Genetics Research Centre,

institute: Memorial University of Newfoundland

summary: We analyzed the methylation pattern of a well characterized leukemia cell line, named K562. Furthermore, we decided to investigate how the malignant epiegenome change during the reprogramming process

overall_design: We used Affymatrix expression microarrays analysis to investigate the relation between expression and methylation in leukemia and reprogrammed leukemia (LiPS). We show that the erasure of the epigenetic aberrancies have functional consequences on leukemia phenotype

first: Giovanni

last: Amabile

first: Annalisa

last: Di Ruscio

first: Alexander

last: Ebralidze

first: Sarawut

last: Wongphayak


title: Regulation of Pattern Recognition Receptors by the Apolipoprotein A-I Mimetic Peptide 4F

status: Public on Sep 30 2012

city: Birmingham

first: Geeta

last: Datta

address: 1808 7th Ave S

country: USA

institute: University of Alabama at Birmingham

summary: The apolipoprotein A-I (apoA-I) mimetic peptide 4F displays prominent anti-inflammatory properties, including the ability to reduce vascular macrophage content.  Macrophages are a heterogenous group of cells, represented by two principal phenotypes, the classically activated M1 macrophage and an alternatively activated M2 phenotype. We recently reported that 4F favors the differentiation of human monocytes to an anti-inflammatory phenotype similar to that displayed by M2 macrophages. In the current study, microarray analysis of gene expression in monocyte-derived macrophages (MDMs) was carried out to identify inflammatory pathways modulated by 4F treatment. ApoA-I treatment of MDMs served as a control. Transcriptional profiling revealed that 4F and apoA-I modulated expression of 113 and 135 genes that regulate inflammatory responses, respectively. Cluster heat maps revealed that 4F and apoA-I induced similar changes in expression for 69 common genes.  Modulation of other gene products, including STAT1 and PPARG, were unique for 4F treatment. Besides modulating inflammatory responses, 4F was found to alter gene expression in cell-to-cell signaling, cell growth/proliferation, lipid metabolism and cardiovascular system development. These data suggest that the protective effects of 4F in a number of disease states may be due to underlying changes in monocyte/macrophage gene expression.

overall_design: 16 samples analyzed (four 4F+LPS, four 4F, four Controls+LPS, four Controls).

first: C

last: White

first: David

last: Crossman


title: Integrative Transcriptomic Profiling reveals Hepatic Stem-like Phenotype and Interplay of EMT and miR-200c in Intrahepatic Cholangiocarcinoma

status: Public on Sep 28 2012

city: Bethesda

first: Xin

middle: Wei

last: Wang

address: 37 Convent Drive

department: Laboratory of Human Carcinogenesis

institute: National Cancer Institute


title: Integrative Transcriptomic Profiling reveals Hepatic Stem-like Phenotype and Interplay of EMT and miR-200c in Intrahepatic Cholangiocarcinoma [mRNA]

summary:
We compared transcriptomic profiles of 23 ICC tumor specimens to hepatocellular carcinoma (HCC) specimens using Affymetrix mRNA array and the miRNA array platforms to search for unique gene signatures linked to patient prognosis.
ICC and HCC share common stem-like molecular characteristics and stem-like tumor features associated with poor prognosis.

overall_design: Gene expression profiling of 16 intrahepatic cholangiocarcinoma (ICC), 7 mixed type of combined HCC and ICC (CHC), 2 Hepatic Adenoma, 5 Focal Nodular Hyperplasia, and 7 Non-Tumor Tissues were performed.

first: Naoki

last: Oishi

middle: W


title: Methotrexate activates aspects of inflammation in EA.hy 926 cells

city: Philadelphia

middle: Steven

last: Whitehead

state: PA

address: 421 Curie Blvd, 8th floor BRB

department: Pharmacology

institute: University of Pennsylvania

summary: Methotrexate (MTX) is an anti-folate drug used to treat inflammatory diseases such as rheumatoid arthritis. The changes induced by MTX were profiled within EA.hy 926 cells grown in normal (Hi) and low (Lo) folate. Several inflammatory genes were up regulated and several mitosis related genes were down regulated.

overall_design: Hi and Lo cells were grown to confluence and maintained in fresh medium for 24 hours prior to treatment with 0.5uM MTX for 48 hours.

first: Carolyn

middle: M

last: Summers

first: Andrea

middle: L

last: Hammons

first: Jeanine

last: Jochems


title: Gene expression profiles of induced pluripotent mesenchymal stromal cells [Affymetrix]

status: Public on Sep 24 2012

city: Aachen

first: Wolfgang

last: Wagner

address: Pauwelsstrasse 20

department: Helmholtz Institute for Biomedical Engineering

country: Germany

institute: RWTH Aachen University

summary: Reprogramming of somatic cells into induced pluripotent stem cells (iPSC) is an epigenetic phenomenon. We have reprogrammed mesenchymal stromal cells (MSC) from human bone marrow by retrovirus-mediated overexpression of OCT-3/4, SOX2, c-MYC, and KLF4. This series summarizes gene expression profiles of eight iP-MSC clones derived from three different donors. These datasets were subsequently used for PluriTest analysis (Muller FJ, Schuldt B et al., Nat. Methods 2011; 8: 315-317) demonstrating that all iP-MSC clones were clearly associated with pluripotent cells.

overall_design: Eight iP-MSC clones derived from three different donors.

first: Kaifeng

last: Shao

first: Carmen

last: Koch

first: Qiong

last: Lin

first: Bernd

last: Denecke

first: Tomo

last: Saric


title: Long-term culture associated gene expression changes in MSC [Affymetrix]

summary: Mesenchymal stromal cells (MSC) were isolated from human bone marrow. Here, we have compared gene expression profiles of MSC at early and late passages. Long-term culture associated gene expression changes were then correlated with DNA-methylation profiles. The goal of this study was to determine if senescence-associated DNA-methylation (SA-DNAm) changes are reflected by differential gene expression. Overall, genes with SA-DNAm changes (particularly with SA-hypomethylation) were detected at low level and seemed to be scarcely expressed at early and late passages.

overall_design: MSC were isolated from three different donors and culture expanded until replicative senescence. Gene expression profiles were compared at early and late passage using GeneChip Humang Gene 1.0 ST arrays (Affymetrix). Six hybridizations are included in this series.

first: Gudrun

last: Walenda


title: FBP1 expression in basal-like breast cancer MDA-MB231 and Hs578T cells

status: Public on Sep 27 2012

city: Lexington

first: Binhua

middle: P

last: Zhou

state: KY

address: 789 South Limestone

department: Markey Cancer Center/Biochemistry

institute: University of Kentucky School of Medicine

summary: FBP1 is a rate limiting enzyme in glucogenogenesis and FBP1 expression changes cells to oxidative phosphorylation. Expressing FBP1 in basal-like breast cancer cells, which lack the expression of this enzyme, will identify the genes involved in glycolysis.

overall_design: FBP1 was expressed in MDA-MB231 and Hs578T cells, stable clones were selected, and RNA was prepared for microarray analysis.

first: Chenfang

last: Dong