title: Expression Profiling of Extracellular Microvesicles Reveals Intercellular Transmission of Oncogenic Pathways

city: padova

first: silvia

last: bresolin

state: padova

address: via giustiniani 3

department: department of women's and children's health

institute: università di padova

summary:
Circulating microvesicles (MVs) have been described as important players in cell-to-cell communication carrying biological information both in normal and pathologic condition. MVs released by cancer cells may incorporate biomolecules such as active lipids, proteins and RNA, which can be delivered and internalized by recipient cells potentially altering gene expression of receiving cells eventually impacting disease progression. In this study, we took advantage of a leukemia in vitro model to investigate MVs as vehicles of protein coding messages. Leukemic cell lines (K562, REH and SHI-1) carrying recurrent translocations were analyzed. In the leukemic cells these translocations are transcribed into oncogenic fusion transcripts. Here, using gene expression microarrays we monitored leukemic fusion transcripts as hallmarks of leukemic cells transcriptome to track mRNA transfer from parental cells to MVs. Transcriptome analysis of K562 cells and released MVs disclosed MVs as not just “small scale cells”. In fact, a number of transcripts related to membrane activity, cell surface receptors and extracellular communication were enriched in the MVs pool. On the other hand, sets of transcripts related to the basal cellular functions and transcripts of the BCR-ABL oncogenic pathway downstream of the fusion protein were detected in MVs as well as in parental K562 cells. Moreover, through co-culture analyses uptake of leukemic MVs in receiving cells was confirmed and an MV-dosage dependent increase of target cell proliferation was demonstrated.
Our study provides novel understanding of tumor-derived MVs as carrier of protein coding messages. For the first time a whole transcriptome gene expression analysis has been performed comparing K562 parental cells and released MVs, showing an enrichment of transcripts coding for oncogenic proteins and for proteins involved in key cellular pathways.

overall_design: Gene expression was measured on Affymetrix in 5 independent experiments of K562  cell lines and microvesicles derived from theK563 cell line

first: Silvia

last: Bresolin

first: Gloria

last: Milani


title: Validation of the MethylationEPIC BeadChip for fresh-frozen and formalin-fixed paraffin-embedded tumours (450K)

status: Public on Apr 01 2017

city: Gothenburg

first: Helena

last: Carén

address: Medicinaregatan 1F

country: Sweden

institute: Gothenburg University

summary: DNA methylation is the most studied epigenetic modification due to its role in regulating gene expression and aberrations in methylation involved in the pathogenesis of cancer and several diseases. The method of choice to evaluate genome-wide methylation has been the Illumina HumanMethylation450 BeadChip (450K), but it was recently replaced with the MethylationEPIC BeadChip (EPIC). We therefore sought to validate the EPIC array in comparison to the 450K array for both fresh-frozen (FF) and formalin-fixed paraffin-embedded (FFPE) pediatric brain tumors. We also performed analysis on the EPIC array with paired FF and FFPE samples, to adapt to a clinical setting where FFPE is routinely used. Further, we compared two restoration methods, REPLI-g and Infinium, for FFPE-derived DNA on the EPIC array.

overall_design: 9 fresh-frozen (FF) pediatric brain tumor samples (tumors T01-T09) were processed on the Illumina 450K and EPIC array to compare the platforms. 9 formalin-fixed paraffin-embedded (FFPE) samples paired to the FF samples (tumors T01-T09) were analyzed on the EPIC array to assess the correlation between FF and FFPE and thereby the suitability of the array in a clinical setting (FFPE samples). Four of the FFPE samples (tumors T01, T06, T08, T09) were restored with both the REPLI-g and Infinium protocol to enable comparison between the methods. Three FFPE samples (tumors T10-T12), restored with REPLI-g, were analyzed with the 450K as well as the EPIC array to compare the platforms for FFPE samples.

first: Teresia

last: Kling

first: Anna

last: Wenger


title: Validation of the MethylationEPIC BeadChip for fresh-frozen and formalin-fixed paraffin-embedded tumours

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

overall_design: Refer to individual Series


title: PRDM16 binding in brown adipocyte precursors [ChIP-seq]

status: Public on Apr 10 2017

city: Cincinnati

first: Hee-Woong

last: Lim

state: Ohio

address: 3333 Burnet Ave. MLC 7024

department: Division of Biomedical Informatics

country: USA

institute: Cincinnati Children's Hospital Medical Center

type: Genome binding/occupancy profiling by high throughput sequencing

summary: PRDM16 is an important transcriptional regulator of brown and beige adipocyte gene programs. We discovered that PRDM16 also represses type I Interferon-stimulated genes (ISGs) in brown and beige adipocytes. ChIP-seq demonstrated that PRDM16 binds proximal to many of the regulated ISGs and this correlates with reduction in the amount of the activating mark, H3K27Ac. Together this data shows PRDM16 represses ISG expression through direct binding at promoter regions to block transcription.

overall_design: Immortalized adipocyte precursors derived from Prdm16 KO brown adipose were infected with control or PRDM16 expressing plasmids. ChIP-seq was performed for PRDM16 and H3K27Ac to determine PRDM16 binding in adipocyte precursors.

first: Megan

last: Kissig

first: Jeff

last: Ishibashi

first: Matthew

middle: J

last: Harms

first: Rachel

middle: R

last: Stine

first: Kyoung-Jae

last: Won

first: Patrick

last: Seale


title: Epigenetic reprogramming in naïve CD4+ T cells favoring T cell activation and Th2 differentiation as an early event in lupus flares

city: OKC

first: Jonathan

middle: Daniel

last: Wren

state: OK

address: 825 NE 13th St

department: Arthritis & Clinical Immunology

institute: Oklahoma Medical Research Foundation

type: Methylation profiling by high throughput sequencing

summary: Systemic lupus erythematosus is a relapsing autoimmune disease that affects multiple organ systems. T cells play an important role in the pathogenesis of lupus, however, early T cell events triggering disease flares are incompletely understood. We studied DNA methylation in naïve CD4+ T cells from lupus patients to determine if epigenetic landscape change in CD4+ T cells is an early event in lupus flares.

overall_design: A total of 74 lupus patients with disease activity ranging from 0-18 as measured by the systemic lupus erythematosus disease activity index (SLEDAI) were included in this study. Naïve CD4+ T cells were isolated from peripheral blood samples and DNA extracted for genome-wide methylation assessment. RNA was also extracted from a subset of patients to determine the relationship between epigenetic changes and transcriptional activity using RNA sequencing.

last: Coit

middle: D

first: Amr

middle: H

last: Sawalha


title: Canadian Prostate Cancer GEnome NEtwork – HuGene RNA expression

status: Public on Apr 15 2017

city: Toronto

first: Nicholas

last: Harding

state: ON

address: 101 College St

department: Informatics and Biocomputing Platform

country: Canada

institute: OICR

summary: The goal of the Canadian Prostate Cancer Genome Network (CPC-GENE) is to use genomic data to predict treatment failure for intermediate risk prostate cancers so that we can provide better treatment pathways

first: Paul

middle: C

last: Boutros

first: Robert

middle: G

last: Bristow

first: Michael

last: Fraser


title: Epigenetic silencing of triple negative breast cancer hallmarks by Withaferin A

status: Public on Apr 06 2017

city: Antwerp (Wilrijk)

first: Ken

last: Declerck

address: Universiteitsplein 1

country: Belgium

institute: University of Antwerp

type: Methylation profiling by genome tiling array

summary: Triple negative breast cancer (TNBC) is characterized by poor prognosis and a DNA hypomethylation profile. Withaferin A (WA) is a plant derived steroidal lactone which holds promise as a therapeutic agent for treatment of breast cancer (BC).  We determined genome-wide DNA methylation changes in weakly-metastatic and  aggressive, metastatic BC cell lines, following 72h treatment to a subcytotoxic  concentration of WA. In contrast to the DNA demethylating agent 5-aza-2’-  deoxycytidine (DAC), WA treatment of MDA-MB-231 cells rather tackles an epigenetic  cancer network through gene-specific DNA hypermethylation of tumor promoting  genes including ADAM metallopeptidase domain 8 (ADAM8), urokinase-type  plasminogen activator (PLAU), tumor necrosis factor (ligand) superfamily, member  12 (TNFSF12), and genes related to detoxification (glutathione S-transferase mu 1,  GSTM1), or mitochondrial metabolism (malic enzyme 3, ME3). Gene expression and  pathway enrichment analysis further reveals epigenetic suppression of multiple cancer  hallmarks associated with cell cycle regulation, cell death, cancer cell metabolism,  cell motility and metastasis. Remarkably, DNA hypermethylation of corresponding  CpG sites in PLAU, ADAM8, TNSF12, GSTM1 and ME3 genes correlates with receptor  tyrosine-protein kinase erbB-2 amplification (HER2)/estrogen receptor (ESR)/  progesterone receptor (PR) status in primary BC tumors. Moreover, upon comparing  differentially methylated WA responsive target genes with DNA methylation changes in  different clinical subtypes of breast cancer patients in the cancer genome atlas (TCGA),  we found that WA silences HER2/PR/ESR-dependent gene expression programs to  suppress aggressive TNBC characteristics in favor of luminal BC hallmarks, with an  improved therapeutic sensitivity. In this respect, WA may represent a novel and  attractive phyto-pharmaceutical for TNBC treatment.

overall_design: Bisulfite converted DNA from the breast cancer cell lines MCF-7 and MDA-MB-231, left untreated or exposed for 72h to Withaferin A were hybridised to the Illumina Infinium HumanMethylation450 BeadChip

first: Katarzyna

last: Szarc vel Szic

first: René

middle: A

last: Crans

first: Jolien

last: Diddens

first: David

middle: B

last: Scherf

first: Clarissa

last: Gerhäuser

first: Wim

last: Vanden Berghe


title: Effect of S534A substitution in the p65 subunit of Nfkb on response to 1mg LPS

status: Public on Apr 05 2017

city: New York

middle: F

last: Schwabe

state: NY

address: 1150 st Nicholas Av

department: Medicine

institute: Columbia University

summary:
WT mice and Nfkb/p65 S534A were exposed to 1mg/kg LPS and their gene expression measured.
Affymetrix Mouse 1.0ST chips were used to measure gene expression.

overall_design:
Gene expression of the following mouse livers were characterized
WT untreated (n=4).
WT treated with 1mg/kg LPS (n=4).
S534A treated with 1mg/kg LPS (n=4).
S534A untreated 1mg/kg LPS (n=4).

first: Jean-Philippe

last: Pradère

first: Céline

last: Hernandez

first: Richard

last: Friedman


title: PROTEIN KINASE C EPSILON COOPERATES WITH PTEN LOSS FOR PROSTATE TUMORIGENESIS THROUGH THE CXCL13-CXCR5 PATHWAY

city: La Plata

first: Martin

middle: Carlos

last: Abba

state: Buenos Aires

country: Argentina

institute: School of Medical Sciences - UNLP

summary: PKCe, an oncogenic member of the PKC family, is aberrantly overexpressed in epithelial cancers. To date, little is known about functional interactions of PKCe with other genetic alterations and the effectors of this kinase that contribute to its tumorigenic and metastatic phenotype. Here we demonstrate that PKCe cooperates with the loss of the tumor suppressor Pten for the development of prostate cancer in a mouse model. Mechanistic analysis revealed that PKCe overexpression and Pten loss individually and synergically cause a remarkable up-regulation in the production of the chemokine CXCL13. Notably, targeted disruption of CXCL13 or its receptor CXCR5 in prostate cancer cells impaired their migratory and tumorigenic properties. In addition to providing evidence for an autonomous vicious cycle driven by PKCe, our studies identified a compelling rationale for targeting the CXCL13:CXCR5 axis for prostate cancer treatment.

overall_design: Affymetrix based gene expression profiles of 4 murine prostate epithelial cell lines (P8, CaP8, P8-PKCε and CaP8-PKCε) were generated (3 replicates in each case).

first: Marcelo

last: Kazanietz


title: Illumina M450 profiling of human prostate cancer tissue and benign prostate tissue

city: Huntsville

first: Marie

middle: K

last: Kirby

state: AL

address: 601 Genome Way NE

institute: HudsonAlpha Institute for Biotechnology

summary: Illumina M450 profiling was conducted on clinically-annotated human prostate cancer tissue and benign prostate tissue

overall_design: We measured genome-wide DNA methylation patterns in 73 clinically-annotated fresh-frozen prostate tissues and 63 benign prostate tissues using the Illumina Infinium HumanMethylation450 Beadchip array.

first: Ryne

last: Ramaker

first: Brian

middle: S

last: Roberts

first: Brittany

middle: N

last: Lasseigne

last: Gunther

first: Todd

last: Burwell

last: Davis

first: Zulfiquar

last: Gulzar

first: Devin

middle: M

last: Absher

first: Sara

last: Cooper

first: James

last: Brooks

last: Myers


title: Effect of S534A substitution in the p65 subunit of Nfkb on response to 1µg LPS

first: Robert

last: Schwabe

summary:
WT mice and Nfkb/p65 S534A were exposed to 1µg/kg LPS and their gene expression measured.
Affymetrix Mouse 1.0ST chips were used to measure gene expression

overall_design:
Gene expression of the following mouse livers were characterized
WT untreated (n=4).
S534A treated with 1µg/kg LPS (n=4).
WT treated with 1µg/kg LPS (n=4).

last: Pradère


title: Characterization of Notch transcription complex sequence paired sites

status: Public on Apr 07 2017

city: Boston

first: Eric

last: Severson

state: MA

address: 75 Francis Street

department: Pathology

institute: Brigham and Women's Hospital

summary: Notch transcription complexes (NTCs) drive target gene expression by binding to two distinct types of genomic response elements, NTC monomer-binding sites and sequence-paired sites (SPSs) that bind NTC dimers. SPSs are conserved and are linked to the Notch-responsiveness of a few genes, but their overall contribution to Notch-dependent gene regulation is unknown. To address this issue, we determined the DNA sequence requirements for NTC dimerization using a fluorescence resonance energy transfer (FRET) assay, and applied insights from these in vitro studies to Notch-“addicted” leukemia cells. We find that SPSs contribute to the regulation of approximately a third of direct Notch target genes. While originally described in promoters, SPSs are present mainly in long-range enhancers. Our work provides a general method for identifying sequence-paired sites in genome-wide data sets and highlights the widespread role of NTC dimerization in Notch-transformed leukemia cells.

overall_design: All samples were run in triplicate and all samples were treated either with DMSO or a gamma secretase inhibitor (GSI).  The samples were T6E cells transfected with the empty MigR1 vector, a dominant negative MAML (DNMAML), intracellular Notch 1 (ICN1), or a dimerization defective intracellular Notch 1(R1984A).

first: Kelly

last: Arnett

first: Hongfang

last: Wang

first: Chongzhi

last: Zang

first: Len

last: Taing

first: Liu

last: Hudan

first: Warren

last: Pear

first: Xiaole

last: Liu

first: Stephen

last: Blacklow

first: Jon

last: Aster


title: Epigenetic Contribution of the Myosin Light Chain Kinase Gene to Acute Respiratory Distress Syndrome

city: Chicago

first: Wei

last: Zhang

state: IL

address: 680 N. Lake Shore Drive, Suite 1400

institute: Northwestern University

summary: The nested case-control study included 39 ARDS cases, 75 non-ARDS ICU controls, and 30 healthy controls. Cytosine modification levels were profiled using the Illumina 450K BeadChip and genotypic data for 29 ARDS cases and 52 ICU controls were used in mQTL analysis

overall_design: Approximately 150 ng of bisulfite-converted DNA from each sample was used for profiling DNA methylation levels using the Illumina Infinium HumanMethylation 450 BeadChip (450K array)


title: Differential gene expression profiles in peripheral blood in Northeast Chinese Han people with acute myocardial infarction

status: Public on Apr 04 2017

city: Changchun

first: Bo

middle: Fan

last: Meng

address: Xiantai Street 126 of Changchun of Jilin Province

country: China

institute: the Department of Cardiology, China–Japan Union Hospital, Jilin University,

summary:
The genes had different expression between healthy people and acute myocardial infarction.We aimed to identify the differentially expressed genes involved in acute myocardial infarction in Northeast Chinese Han people.
We used microarrays to detail the global programme of gene expression to identify the differentially gene between the patients with acute myocardial infarction and healthy people in Northeast Chinese Han people

overall_design: Three patients with acute myocardial infarction and three healthy people in Northeast Chinese Han people were recruited,total RNA of each samples were extracted from peripheral blood to hybridize with Affymetrix microarrays.

first: Fanbo


title: Epigenetic signatures of gestational diabetes mellitus on ATP5A1, PRKCH, SLC17A4 and HIF3A cord blood methylation

status: Public on Mar 29 2017

city: Würzburg

first: Marcus

last: Dittrich

address: Biozentrum, Am Hubland

department: Biozentrum

country: Germany

institute: University of Würzburg

summary:
Background: Intrauterine exposure to gestational diabetes mellitus (GDM) confers a lifelong increased risk for metabolic and other complex disorders to the offspring. GDM-induced epigenetic modifications modulating gene regulation and persisting into later life are generally assumed to mediate these increased disease risks. To identify candidate genes for fetal programming, we compared genome-wide methylation patterns of fetal cord bloods (FCBs) from GDM and control pregnancies.
Methods and Results: Using Illumina's 450K methylation arrays and following correction for multiple testing, 65 CpG sites (52 of which are associated with genes) displayed significant methylation differences between GDM and control samples. Three of four candidate genes, ATP5A1, PRKCH, and SLC17A4, from our methylation screen and one, HIF3A, from the literature were validated by bisulfite pyrosequencing. The GDM effect on FCB methylation was more pronounced in women with insulin-dependent GDM who had a more severe metabolic phenotype than women with dietetically treated GDM. However, the effect remained significant after adjustment for the maternal BMI and gestational week in a multivariate regression model.
Conclusions: Our study supports an association between maternal GDM and the epigenetic status of the exposed offspring. Consistent with a multifactorial disease model, the observed FCB methylation changes are of small effect size but affect multiple genes/loci. The identified genes are primary candidates for transmitting GDM effects to the next generation. They also may provide useful biomarkers for the diagnosis and prognosis of adverse prenatal exposures and assessing the success of interventions during pregnancy.

overall_design:
Bisulphite converted DNA from the 38 samples were hybridised to the Illumina Infinium 450K Human Methylation Beadchip

Please note that the experiments were carried out as two batches (GSM2355316-GSM2355353 and GSM2355354-GSM2355447), and they were normalized and filtered independently.

first: Thomas

last: Haaf


title: Flicr, a long noncoding RNA modulating Foxp3 expression and autoimmunity

status: Public on Mar 28 2017

first: CBDM

last: Lab

address: 77 Avenue Louis Pasteur

department: Microbiology and Immunobiology

institute: Harvard Medical School

summary: Microarray profiles of splenic Tregs and Tconvs from Flicr WT and KO mice

overall_design: DAPI-CD4+TCRb+ CD25- (Tconvs) and CD25hi (top 50%) Tregs were single sorted from the spleen of male NOD mice. Total RNA was prepared using Trizol method followed by amplification and cDNA preparation. cDNA was hybridized to Affymetrix ST1.0 microarrays.

first: David

last: Zemmour

first: Diane

last: Mathis

first: Christophe

last: Benoist


title: DNA methylation landscape of hepatoblastomas reveals arrest at early stages of liver differentiation and cancer-related alterations

status: Public on Apr 03 2017

city: Campinas

first: Mariana

last: Maschietto

state: São Paulo

address: Rua Márcia Mendes, 619

department: Research Center

country: Brazil

institute: Boldrini Children's Hospital

summary: Hepatoblastomas carry few genetic alterations, and we hypothesize that epigenetic changes could be relevant to their onset. DNA methylation profile of hepatoblastomas was explored in relation to liver development using the HM450K platform. Seven paired samples of hepatoblastomas and adjacent non-tumoral livers were studied, with biologicaland results validation validated in an independent group (12 hepatoblastomas) that confirmed 1,359 differentiated methylated CpG sites (DMSs) in hepatoblastomas compared to controls, associated with 979 genes. Hepatoblastomas also exhibited a global low-level hypomethylation when compared with differentiated livers, especially at non-repetitive intergenic DNA (~55% of the hypomethylated CpGs); conversely, most of the hypermethylated CpGs were located in CpG islands. Functional analyses revealed an enrichment in signaling pathways involved in metabolism, negative regulation of cell differentiation, liver development, cancer, and the WNT pathway. Strikingly, an important overlap was observed between hepatoblastomas DMSs and the CpG sites reported to exhibit methylation changes through liver development.  Genes with differential methylation were related to maintenance of undifferentiated cell state, cell transformation and tumor progression, and the methylation profile of tumors resembled that of fetal livers. Altogether, our results suggest an arrest at early stages of liver cell differentiation, in line with the hypothesis that hepatoblastoma ontogeny involves the disruption of liver development.

overall_design: Bisulphite converted DNA from the 29 samples (19 hepatoblasmas and 10 livers) were hybridised to the Illumina Infinium 450k Human Methylation Beadchips.

first: Ana

last: Krepischi


title: Genome-wide methylation profiles of saliva

status: Public on Apr 02 2017

city: Seoul

first: Hwan Young

last: Lee

address: 103 Daehak-ro, Jongno-gu

department: Forensic Medicine

country: South Korea

institute: Seoul National University College of Medicine

summary: In order to investigate age-correlated DNA methylation changes in saliva, genome-wide DNA methylation profiling was performed for saliva from 54 males aged 18 to 73 years. The Illumina Infinium 450k Human DNA methylation Beadchip was used to acquire DNA methylation profiles across about 450,000 CpGs in bisulfite converted DNA.

overall_design: Bisulfite converted DNA from the 54 samples were hybridised to the Illumina Infinium 450k Human Methylation Beadchip

first: Sang-Eun

last: Jung

first: Eun Hee

first: Saerom

last: Hong


title: Expression data from human glioma cells U251 or LN-319 with stable expression of GFP control or sh-Circ-SHPRH

status: Public on Mar 30 2017

city: Guangzhou

first: Nu

state: Guangdong

address: NO.58, The Second Zhongshan Road，Yuexiu District

department: Neurosurgery

institute: The First Affiliated Hospital, Sun Yat-sen University

summary: The cDNA array of U251 or LN-319 cells stably infected with sh-Circ-SHPRH or control lenti-virus.

overall_design: To investigate the possible regulatory role of Circ-SHPRH, we did the expression microarray in U251 and LN-319 cell stably infected with sh-Circ-SHPRH or control lenti-virus. Total RNA extracted and hybridized on Affymetrix microarrays.

first: Maolei

first: Xuesong

last: Yang

first: Nunu

last: Huang


title: Gene expression in GSCs with shALKBH5

first: Sicong

address: 1230 York Avenue

institute: The Rockefeller University

summary:
Knocking down ALKBH5 in Glioma Stem Cells resulted in an altered gene expression profile
N6-methyl-adenosine (m6A) is the most prevalent internal chemical modification of mRNAs in eukaryotes. In mammals, m6A installed by m6A methyltransferases METTL3 and METTL14 is erased by two members of the AlkB family of nonheme Fe(II)/a-ketoglutarate (a-KG)-dependent dioxygenases, fat-mass and obesity associated protein (FTO) or ALKBH5. ALKBH5 affects nuclear RNA export and metabolism, gene expression and mouse fertility. To date, little is known about the biological significance of m6A in human cancer. We found that ALKBH5 is highly expressed in human glioblastoma stem cells which are resistant to conventional therapy and give rise to glioblastoma recurrence by sustaining long-term tumor growth. Global manipulation of the m6A modification by depleting ALKBH5 resulted in altered gene expression including subsets of genes enriched in "Cell Cycle", "DNA Replication, Recombination, and Repair" and "Cellular Assembly and Organization". Knockdown of ALKBH5 expression in human glioblastoma stem cells significantly reduced their self-renewal ability as a result of inhibition of cell cycle progression. This study demonstrated the important role of m6A modification in human glioblastoma development.

overall_design: GSCs expressing shRNAs for control and ALKBH5 were purimycin-selected for RNA extraction and hybridization on Affymetrix microarrays


title: Gene expression in germinal centre light zone and dark zone cells of high or low affinity

status: Public on Mar 27 2017

city: Zurich

first: Nike

last: Krautler

address: Vladimir-Prelog Weg1-5/10

department: Biology, Institute of Microbiology

country: Switzerland

institute: ETH Zurich

summary:
Gene expression analysis performed on FACS sort purified GC LZ and DZ cells of either high or low affinity to identify unique gene signatures.
Analysis revealed distinct transcription patterns.

overall_design: SwHEL B cells carrying the CD45.1 congenic marker were transferred into C57BL/6J mice (CD45.2) and immunized with sheep red blood cells conjugated to the hen egg lysozyme mutant HEL3x. Day 10 post immunization high and low affinity cells of either LZ (CD86 high, CXCR4 low) or DZ (CXCR4 high, CD86 low) were sort purified from donor-derived GC B cell population (CD45.1+, CD45.2-, IgG1+, CD38 low).

first: N

first: W

last: Kaplan

first: R

last: Brink


title: Effect of SETD8/PR-Set7 knockdown on gene expression profiles in human fibroblasts

city: Chuo-ku, Kumamoto

first: Mitsuyoshi

last: Nakao

state: Kumamoto

address: 2-2-1 Honjo

department: Department of Medical Cell Biology, Institute of Molecular Embryology and Genetics

country: Japan

institute: Kumamoto university

summary: Cellular senescence is an ireversible growth arrest with alterd metabolic potentials including DNA, RNA and protein dynamics. We found that loss of the SETD8/PR-Set7 methyltransferase, which catalyzes mono-methylation of histone H4 at lysine 20 (H4K20me1), induces senescence in human fibroblasts. To investigate the role of SETD8 in cellular senescence, we performed a microarray-based transcriptomic analysis in SETD8-knockdown cells. Our results demonstrate that SETD8 links the epigenomic gene regulation to senescence-associated metabolic remodeling.

overall_design: IMR-90 cells were transfected with Ctrl, SETD8-1 or SETD8-2 siRNAs for 24h.

first: Hiroshi

last: Tanaka

first: Shin-ichiro

last: Takebayashi

first: Shinjiro

last: Hino


title: Gene expression data of bone marrow mesenchymal stromal cells in myelofibrosis

status: Public on Mar 31 2017

first: Lei

last: Ding

state: New York

institute: Columbia University Medical Center

summary: Mesenchymal stromal cells are a critical component of the bone marrow hematopoietic stem cell niche. In myelofibrosis, these cells are the major source of fibrosis in the bone marrow. We performed gene expression analysis using microarrays to systematically elucidate the mechanisms leading to fibrogenic conversion of these cells.

overall_design: Myelofibrosis was induced in Cxcl12-DsRed/+ reporter mice using Tpo-overexpressing retrovirus. Mesenchymal stromal cells were flow cytometrically sorted and subjected to microarray analysis. Mesenchymal stromal cells sorted from control virus infected Cxcl12-DsRed/+ mice were used as controls.

first: Guannan

last: Wang


title: Zinc finger protein 521 overexpression is a feature of MLL-rearranged acute myeloid leukemia and contributes to the maintenance of myeloid differentiation block

city: padova

first: silvia

last: bresolin

address: via giustiniani 3

country: Italy

institute: università di padova

summary:
ZNF521 is a multiple zinc finger transcription factor previously identified because abundantly and selectively expressed in normal CD34+ hematopoietic stem and progenitor cells. From microarray datasets, aberrant expression of ZNF521 has been reported in both pediatric and adult acute myeloid leukemia (AML) patients with MLL gene rearrangements. However, a proper validation of microarray data is lacking, likewise ZNF521 contribution in MLL-rearranged AML is still uncertain. In this study, we show that ZNF521 is significantly upregulated in MLL translocated AML patients from a large pediatric cohort, regardless of the type of MLL translocations such as MLL-AF9, MLL-ENL, MLL-AF10 and MLL-AF6 fusion genes. Our in vitro functional studies demonstrate that ZNF521 play a critical role in the maintenance of the undifferentiated state of MLL-rearranged cells. Furthermore, analysis of the ZNF521 gene promoter region shows that ZNF521 is a direct downstream target of both MLL-AF9 and MLL-ENL fusion proteins. Gene expression profiling of MLL-AF9-rearranged THP-1 cells after depletion of ZNF521 reveals correlation with several expression signatures including stem cell-like and MLL fusion dependent programs. These data suggest that MLL fusion proteins activate ZNF521 expression to maintain the undifferentiated state and contribute to leukemogenesis.
ZNF521 is required to block differentiation in MLL-rearranged AML cells

overall_design: Gene expression was measured on Affymetrix in 3 independent experiments of THP-1 cells transfected with Lentiviral shRNA vector against ZNF521 (shZNF521) or control scrambled shRNA (shScram)

first: Silvia

last: Bresolin

first: Giuseppe

last: Germano


title: Transcriptome analysis of IMR-90 human fibroblasts following oncogene-induced and replicative senescence

summary: By transcriptome analysis of IMR-90 human fibroblasts following oncogene-induced senescence (OIS) and replicative senescence (RS), we identified commonly regulated genes in both conditions.

overall_design: Growing, OIS and RS cells were prepared for microarray analysis.

first: Nobuhiro

last: Sasai


title: Transcriptional Dynamics of Cultured Human Villous Cytotrophoblasts

city: SAN FRANCISCO

first: Joshua

last: Robinson

state: CA

address: 513 Parnassus Ave HSE16

department: Obstretrics, Gynecology and Reproductive Sciences

institute: University of California, San Francisco

summary: Transcriptomic characterization of cultured primary human cytrophoblasts (2nd trimester) undergoing differentiation/invasion in vitro.

overall_design:
Transcriptome of human villous cytotrophoblasts at 0h (following isolation) or 3, 15, or 39h after plating on Matrigel (in vitro).
Sample processing and hybridization was performed by the UCSF Gladstone Institute

first: J

first: M

last: Kapidzic

last: Gormley

first: S

last: Fisher


city: Munich

first: Matjaz

last: Rokavec

address: Thalkirchner Str. 36

department: Institute of Pathology

institute: Ludwig-Maximilians-University Munich

summary: DNA methylation profiling of four DLD1 colorectal cancer cell derivatives that recapitulate EMT/MET transitions during metastasis. The Illumina Infinium 450k Human DNA methylation Beadchip was used to obtain DNA methylation profiles across approximately 450,000 CpGs.

overall_design: Bisulphite converted DNA from four DLD1 colorectal cancer cell line derivatives were analyzed with the Illumina Infinium 450k Human Methylation Beadchip

first: Heiko

last: Hermeking


title: Gene expression data of Peyer's patch conventional dendritic cells  and macrophages at steady state and under TLR7 ligand stimulation

status: Public on Mar 21 2017

city: Marseille

first: Hugues

last: Lelouard

address: parc Scientifique de Luminy case 906

country: France

institute: CIML CNRS UMR 7280

summary: The initiation of the mucosal immune response in Peyer’s patch (PP) relies on the sampling, processing and efficient presentation of foreign antigens by dendritic cells (DC). PP DC encompass five subsets, among which CD11b+ conventional DC (cDC) and LysoDC have distinct progenitors and functions but share many cell surface markers. This has previously led to confusion between these two subsets. In addition, another PP DC subset, termed double-negative (DN), remains poorly characterized. Here, we have studied the genetic relatedness of  the different subsets of PP cDC at steady state and under TLR7 ligand stimulation. We also provide the transcriptional profiles of  subepithelial TIM-4- and interfollicular TIM-4+ macrophages.

overall_design: Three independent replicates of TIM-4- and TIM-4+ LysoMac, CD8a+ and DN dome cDC and five independent replicates of CD11b+ dome cDC were sorted from Peyer's patch of C57BL/6 mice at steady state. In addition, three and five independant replicates of CD11b+ and CD8a+ dome cDC, respectively were sorted from Peyer's patch of C57BL/6 mice 9 hours after R848 gavage. Total RNA of Peyer's patch sorted cells was extracted with a Qiagen RNeasy Plus Micro Kit. Quantity, quality and absence of genomic DNA contamination were assessed with a Bioanalyser (Agilent). Microarray experiments were performed by the Plateforme Biopuces of Strasbourg (France) using the Affymetrix GeneChip® Mouse Gene 1.0 ST Array.

first: Johnny

last: Bonnardel

first: Clément

last: Da Silva

first: Marion

last: Masse

first: Marc

last: Dalod

first: Jean-Pierre

last: Gorvel


title: Comparative expression data between ANGPTL4+/+ and ANGPTL4-/- mice whole colon tissue during DSS or SA-induced inflammation.

city: Singapore

first: Terri

last: Phua

state: Singapore

address: 60 Nanyang Drive

department: School of Biological Sciences

country: Singapore

institute: Nanyang Technological University

summary:
Protracted inflammatory responses are signatures common to many gastrointestinal disorders. Severe and chronic disorders often bring about extensive tissue damage, in turn leading to hypercytokinemia. Here, we show that stimuli like dextran sulphate sodium salt (DSS) and stearic acid (SA) cause acute colonic inflammation, and ANGPTL4 is an important regulator in mediating the extent of colonic inflammation.
Using comparative microarray gene expression analysis, we seek to identify genes whose expression are altered during inflammation between ANGPTL4+/+ and ANGPTL4-/- mice.

overall_design: C57BL/6J mice were kept on 5% DSS in (drinking water) or 15% SA (in ground maintenance-diet chow) for 8 days and fresh whole colon tissues were harvested. RNA was extracted with Trizol® (Thermo Scientific)  in accordance to manufacturer’s protocol. RNA samples were later processed using Applause® WT-Amp ST System (NuGEN), and subsequent microarray experiments were performed using GeneChip® Human Gene 1.0 ST arrays according to the manufacturer’s instructions.


title: The NCI-60 Methylome and Its Integration into CellMiner

city: Bethesda

first: Paul

last: Meltzer

address: 9100 Rockville Pike

institute: NCI/NIH

summary: Methylation assay of cell lines from 9 different cancer tissue of origin types (Breast, Central Nervous System, Colon, Leukemia, Melanoma, Non-Small Cell Lung, Ovarian, Prostate, Renal) from NCI-60 panel

first: William

last: Reinhold

first: Sudhir

last: Varma

first: Margot

last: Sunshine

first: Holly

last: Stevenson

first: Yonghong

last: Wang

first: Holger

last: Heyn

first: Vanesa

last: Trallero

first: David

last: Goldstein

first: James

last: Doroshow

first: Manel

last: Esteller

first: Yves

last: Pommier


title: Gene expression in germinal centre light zone and dark zone cells

first: Nike

last: Krautler

summary:
Gene expression analysis performed on FACS sort purified GC LZ and DZ cells of either high and low affinity to identify unique gene signatures.
In order to reveal differences between LZ and DZ independent of affinity, we compared a DZ data set (consisting of high and low affinity samples), to a LZ data set (consisting of high and low affinity samples). Analysis revealed distrinct transcription patterns.

overall_design: SwHEL B cells carrying the CD45.1 congenic marker were transferred into C57BL/6J mice (CD45.2) and immunized with sheep red blood cells conjugated to the hen egg lysozyme mutant HEL3x. Day 10 post immunization high and low affinity cells of either LZ (CD86 high, CXCR4 low) or DZ (CXCR4 high, CD86 low) were sort purified from donor-derived GC B cell population (CD45.1+, CD45.2-, IgG1+, CD38 low)

first: N

first: W

last: Kaplan

first: R

last: Brink


title: Characterization of transcriptomes of human iPSC-derived retinal lineages

status: Public on Mar 22 2017

city: Taipei

first: Aliaksandr

last: Yarmishyn

address: No. 201, Section 2, Shipai Road, Beitou District

country: Taiwan

institute: Taipei Veterans General Hospital

summary: Retinal ganglion cells (RGCs) and retinal pigment epithelium (RPE) cells are two retinal cell types that are affected by the most prevalent retinal diseases leading to irreversible blindness, such as glaucoma affecting the former and age-related macular degeneration affecting the latter. One of the most promising approaches for the therapy of these diseases is via the autologous transplantation of RGC or RPE cells derived from the induced pluripotent stem cells (iPSCs). This emphasizes the importance of detailed characterization and understanding of the mechanisms of differentiation of iPSCs into retinal lineages on the genome-wide scale. Such information can be used to identify novel crucial regulators of differentiation, optimisation of differentiation protocols to make them more efficient and safe, identification of novel specific biomarker signatures of differentiated cells. In this study, we performed the genome-wide transcriptome analysis of terminally differentiated RGC and RPE lineages, as well as intermediate retinal progenitor cells (RPCs) of optic vesicles (OVs) derived from the human induced pluripotent stem cells (iPSCs). In our analysis we specifically focused on the classes of transcripts that encode regulators of gene expression, such as transcription factors, epigenetic factors, and components of signaling pathways.

overall_design: Total RNA was extracted from iPSCs, RPE cells and RGCs differentiated from the same iPSC cell line, as well as from optic vesicles (OVs), an intermediate stage of differentiation of iPSCs into RGCs. Thus, four RNA sample types were obtained for gene expression analysis. Two biological replicates were analyzed for each sample type.

first: A

first: J

last: Chuang

last: Wu

first: S

last: Chiou


title: Synthesis and activity of the salicylic acid ester of bakuchiol in psoriasiform keratinocytes and skin substitutes

status: Public on Mar 24 2017

city: Ann Arbor

first: William

last: Swindell

state: MI

address: 1500 E. Medical Center Drive

department: Dermatology

institute: University of Michigan

summary: Background: Topical retinoids are effective in retarding skin aging and restoring homeostasis in skin conditions, such as psoriasis.  However their adverse effects, which include irritation (retinoid dermatitis), photosensitivity and teratogenicity, limit their use level and patient compliance. Development of a retinoid analogue with minimal adverse effects would allow a broader and more compliant use. Objective: Here we report the synthesis of a novel molecule - bakuchiol salicylate (bakusylan) with the gene expression modulatory profile similar to retinoids, using as reference 3 prescription retinoids - tretinoin, tazarotene and adapalene. Methods: Having a structure entirely different from existing retinoids, we hypothesized that at least a partial uncoupling of retinoid adverse effects from retinoid skin normalizing activity may be obtained with bakuchiol salicylate. This hypothesis was tested in psoriasiform cultures of keratinocytes and organotypic skin substitutes by DNA microarrays and custom PCR arrays. Results: The evaluation of the bioactivity of bakuchiol salicylate revealed the elimination of several components of the retinoid-like proinflammatory response and teratogenic signature without a substantial loss of normalizing potential. A possible mechanism of action consisting in keratinocyte desensitization to cytokine signaling through the inhibition of the STAT1/3/interferon inflammatory signal transduction axis has also been identified. Conclusion: Bipartite materials obtained by merging two skin-active entities with specific, complementary bioactivities, such as bakuchiol and salicylic acid, may deliver a new class of functional retinoids.

overall_design: Psoriasiform epidermal keratinocyte cultures were generated by incubating keratinocytes with cytokines (IL-17A/IL-22/TNFα) for 24 hours (CnT-PCT media). Keratinocytes were then treated with control solvent (CS; 3% dimethyl isosorbide; 40% glycerin; 57% butylene glycol), control solvent supplemented with bakusylan (SE; 10ug/ml), or control solvent supplemented with all-trans-retinoic acid (ATRA; 0.1ug/ml). Two replicates were generated for each treatment group.

first: Krys

last: Bojanowski


title: Lysine 100 acetylation effect of CRP (catabolite activator protein)  in gene expression in Escherichia coli

city: ESPINARDO

first: ANA

last: ÉCIJA

state: MURCIA

address: CAMPUS ESPINARDO

department: BIOQUÍMICA Y BIOLOGÍA MOLECULAR B E INMUNOLOGÍA

country: Spain

institute: UNIVERSIDAD DE MURCIA

summary: cAMP receptor protein (CRP, also known as the catabolite activator protein [CAP]) is arguably the best-studied of the global transcription factors of E coli. CRP alone is responsible for regulating at least 283 operons. Upon binding cAMP, the CRP dimer binds DNA and directly interacts with RNA polymerase (RNAP). At Class II promoters, CRP binds near position -41,5 relative to the  transcription start site and contacts the amino-terminal domain of the RNAP α subunit (RNAPα-NTD). This interaction requires AR2, a patch of primarily positively charged residues (H19, H21, E96, and K101) that interact with negatively charged residues on RNAPα-NTD. Acetylome analyses consistently detect lysine 100 (K100) of CRP as acetylated. Since K100 is adjacent to the positively charged AR2, we hypothesized that the K100 positive charge may also play a role in CRP function. We further hypothesized that acetylation of K100 would neutralize this positive charge, leading to a potential regulatory mechanism

overall_design: To determine the effect of the K100 positive charge of CRP on promotes Class II transcription, we inset the K100R (named R) and K100Q (named Q) mutations into the chromosome. Since we were unable to insert these mutations into the native crp locus, we placed crp alleles (along with the native promoter region) into the paaH gene locus in a Δcrp background. Therefore, the insertion of native crp gene was also conducted into same position, and it was used as control, named as N. To this end, we performed RNA microarray on strains WT N, Q, or R variants of CRP grown in M9 minimal medium with 10mM glucose or 30mM acetate as sole carbon source and harvested during exponential growth or after entry into stationary phase. We used two biological replicates in this study and each condition (named 1 and 2).

last: Écija-Conesa

first: T

last: de Diego


title: Specific expression of microRNAs and snoRNAs characterize ERG-related B cell precursor acute lymphoblastic leukemia

city: Padova

first: Elena

last: Vendramini

address: Via Giustiniani, 3

department: Woman and Child's Health

institute: University of Padova

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

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

platform_organism:
Homo sapiens
synthetic construct

overall_design: Refer to individual Series


title: Specific expression of microRNAs and snoRNAs characterize ERG-related B cell precursor acute lymphoblastic leukemia [mRNA]

summary: ERG-related B cell precursor acute lymphoblastic leukemia (BCP ALL) is a recently described childhood ALL subtype characterized by aberrant ERG protein expression and highly recurrent ERG intragenic deletions. Several studies reported a remarkably favourable outcome for ERG-related BCP-ALL despite a high incidence of apparently inauspicious IKZF1 aberrations.  In this study we investigated by integrative genomic analysis the main features of the ERG-related group in a cohort of B-others BCP ALL patients enrolled in the AIEOP ALL 2000 therapeutic protocol. We report a specific microRNA and snoRNA signature that characterizes ERG-related patients with up-regulation of the miR-125b-2 cluster on chromosome 21 and several snoRNAs in the Prader-Willi locus at 15q11.2, including the orphan SNORD116 cluster.  Given the current lack of parameters for a comprehensive classification we suggest toexploit the noncoding RNAs signature for differential diagnosis of ERG-related patients.

overall_design: Gene expression profiling by array. Class comparison between ERG-related and non-ERG-related patient groups; class comparison between ERG-related patients with or without ERG intragenic deletion.

first: Geertruy

last: te Kronnie


title: Graded responses to variable TCR signaling are encoded in the affinities of AICE-containing enhancers responding to BATF and IRF4 [gene expression]

city: Chiba-shi

first: Arifumi

last: Iwata

state: Chiba

address: 1-8-1 Inohana, Chuou-ku

department: Department of Allergy and Clinical Immunology

institute: Chiba University

summary: Variable strengths of T cell receptor (TCR) signaling can produce divergent outcomes for T cell development and function. The mechanisms leading to different outcomes are incompletely understood, but may include distinct activation thresholds for different transcription factors as well as distinct sensitivities among target genes to transcription factors.  IRF4 is one transcription factor implicated in responses to variable TCR signal strength.  IRF4 expression increases uniformly with increasing TCR signal strength (i.e., analog), but it is unclear how IRF4 induced distinct genes at different levels, rather than different amounts of the same genes. Here, we analyzed global gene expression in TH2 cells and used ChIP-seq to define the relationship between TCR signal strength, enhancer occupancy and transcriptional activity for BATF/IRF4-dependent genes. We show that enhancers exhibit a spectrum of affinity for the BATF/IRF4 ternary complex mediate graded responsiveness of individual genes to increasing TCR signal strength. Differential gene induction by BATF and IRF4 occurs through interaction with enhancer elements of different affinity for BATF/IRF4 complexes. The increased resolution of factor binding site identified using ChIP-exo allowed the identification of a novel AICE2 motif binding BATF/IRF4 with higher affinity and that this may explain the protective role of a single nucleotide polymorphism in the CTLA-4 locus known to decrease the incidence of autoimmune diseases.

overall_design: Naïve CD4 T cells from 129SvEv genetic background or Batf1/3DKO mice were unsimulated or cultured under TH2 polalized condition for 2 days or 4 days with 2.2 ng/ml or 10 ng/ml of anti-CD3e.

first: Kenneth

last: Murphy


title: Bio-Electric Field Enhancement: The Influence on MDA-MB231 Cells in Vitro

city: Memphis

first: Marcy

middle: Cain

last: Purnell

state: TN

address: 4055 N. Park Loop

department: Loewenberg College of Nursing

institute: University of Memphis

summary: We grew MDA-MB231 cells in a media that had been reconstituted with water that was treated by the Bio-Electric Field Enhancement device generated direct current dielectrophoretic electromagnetic field (Treated group) and cells that were grown in media that was reconstituted with water that was not treated by the BEFE device dc DEP EMF. They were grown for 3 days in each of these media and then analyzed with Affymetrix 2.0 Microarrary Analyses. It was an experimental controlled design.

overall_design: 10,000 Cells were plated in triplicate in 6-well plates. The cells were grown for 24 hours in standard growth media (DMEM with 10% FBS).  Then the treated media was made by diluting a 10X DMEM with 9 parts of a hypotonic saline solution that was exposed to the dc DEP EMF from the BEFE unit for 30 minutes and 1 part 10X DMEM.  The control media was made by diluting the 10X media with a hypotonic saline solution that was not exposed to the dc DEP EMF from the BEFE unit.  The cells were grown in the treated/control media for 3 days and then analyzed with the Affymetrix 2.0 Human Genome Microarray. We looked at the changes in gene expression between the treated and control groups.

first: Terence

last: Skrinjar

first: Michael

last: Whitt


title: Gene expression profile of Baf3 cells conditionally expressing BCR-ABL in presence and absence of Growth factor IL-3

status: Public on Mar 20 2017

city: Cincinnati

first: Mohammad

last: Azam

state: OH

address: 3333 Burnet Avenue

department: Division of Experimental Hematology

institute: Cincinnati Childrens Hospital and Medical Center

summary: The Baf3 are dependent on IL-3 for grwoth however transformation by BCR -ABL oncogene causes BAf3 cells independent of IL-3. The BAf3 cells expressing BCR-ABL are dependent on continuous expression of BCR_ABL for growth. Inhibitionof BCR-ABL by its inhibitor Imatinib cause these cells to undergo apoptosis. When these cells are grown with IL-3  these cells do not respond to Imatinib mediated grwoth arrest.

overall_design: This experiment was  design to test the expression of genes driven by BCR-ABL and Growth factor that provides resistance to Imatinib treatment.


title: Expression profile of Imatinib treated BAF3 -BCR-ABL cells

summary: BAF3 cells harboring constitutively expressing BCR-ABL were grown with or without IL-3 supplement and treated with Imatinib and live cells from the IL-3 and without IL-3 were sorted by FACS.

overall_design: Cell growing without growth factor are sensitive to iamtinib and undergo apototis while cells grown with IL-3 are resistant. The expression profile of cells that will undergo death compared to that will survive was compared.


title: Platinum-based chemotherapy induces methylation changes in blood and tumour DNA at time of relapse that are associated with patient survival

status: Public on Mar 16 2017

city: London

first: James

last: Flanagan

state: London

address: Hammersmith Hospital, Du Cane Rd

department: Surgery and Cancer

country: United Kingdom

institute: Imperial College London

summary: The Illumina Infinium 450k Human DNA methylation Beadchip was used to obtain DNA methylation profiles across  485,577 CpGs . Samples included 11 clones of each of the four groups derived from the A2780/CP70 ovarian cancer cell line. Groups included MLH1 minus treated with 5uM Cisplatin (A), MLH1 plus treated with 5uM Cisplatin (B), MLH minus mock treated (C) and MLH1 plus mock treated (D).

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

first: Robert

last: Brown


title: HCT-8 human colorectal cancer (CRC) wild type cells (HCT8/WT) and its 5-FU-induced resistant cell line (HCT8/5-FU)

status: Public on Mar 15 2017

city: FuZhou

first: Guo

last: Zheng

state: FuJian

address: No.1 Xue Yuan Road

department: Department of Bioinformatics

institute: Fujian Medical University

type:
Expression profiling by array
Methylation profiling by array


title: Expression data from B-cell precursor acute lymphoblastic leukemia

city: Setagaya-ku

first: NOBUTAKA

last: KIYOKAWA

state: Tokyo

department: Pediatric Hematology & Oncology Research

institute: National Research Institute for Child Health & Development

summary:
B-cell precursor acute lymphoblastic leukemia (BCP-ALL) is a heterogeneous disease that can be subdivided according to primary recurrent genetic abnormalities that are strongly associated with characteristic biological and clinical features.  The detection of these abnormalities can facilitate diagnosis, risk stratification, and targeted therapy.
We identified an unexpectedly high incidence of fusion genes involving ZNF384 genes, including TCF3-ZNF384, EP300-ZNF384, and CREBBP-ZNF384, in BCP-ALL of our cohort.  We therefore used microarrays to evaluate the gene-expression characteristics of BCP-ALL harboring ZNF384-related fusion genes and compared with those of BCP-ALL with other types of conventional genetic abnormality.

overall_design: BCP-ALL samples with various genetic abnormalities were selected for RNA extraction and hybridization on Affymetrix microarrays.  In addition to BCP-ALL harboring ZNF384-related fusion genes, including TCF3-ZNF384 (10 cases), EP300-ZNF384 (5 cases), and CREBBP-ZNF384 (2 cases), BCP-ALL with conventional genetic abnormalities, such as BCR-ABL1 (19 cases), ETV6-RUNX1 (70 cases), high hyperdiploid (90 cases), MLL-AF4 (13 cases), and TCF3-PBX1 (19 cases), were included.  As a control, non-leukemic B-cell precursor samples (3 cases) were also selected.

first: Nobutaka

last: Kiyokawa

first: Kentaro

last: Ohki


title: Caloric-dose responsive genes in blood cells differentiate the metabolic status of obese men

status: Public on Mar 14 2017

city: Bern

first: Doreen

last: Gille

address: Schwarzenburgstrasse 161

institute: Agroscope

summary:
One current focus of nutrition research is the identification of biomarkers that reflect the impact of food on metabolic processes. As this approach mostly targets the prevention rather than the curing of diseases, novel biomarkers need to be identified. Those should be influenced by the diet already in healthy individuals and be nonetheless indicative, or even predictive, of the potential impact of specific food on the development of metabolic diseases such as obesity.
The blood cell transcriptome of two different population groups after the ingestion of different caloric doses of a high-fat meal was measured by microarray technology.

overall_design: A human intervention study was conducted including seven normal weight and seven obese subjects who consumed three caloric doses (500, 1000, 1500 kcal) of a high-fat meal. The blood cell transcriptome was measured before (0h) as well as 2h, 4h and 6h after the meal ingestion.

first: Nadine

last: Zangger

first: Charlotte

last: Soneson

first: Ueli

last: Buetikofer

first: Mauro

last: Delorenzi

first: Flurina

last: Schwander

first: Katrin

last: Kopf-Bolanz

first: Magali

last: Chollet

first: Barbara

last: Walther

first: Kurt

last: Laederach

first: Guy

last: Vergères


title: Mouse isolated kidney preglomerular arterioles: wild type vs conditional knockout of RBP-J in renin cells

status: Public on Mar 12 2017

city: Charlottesville

first: R. Ariel

last: Gomez

state: VA

department: Pediatrics

institute: University of Virginia

summary:
mRNA profiling of mouse kidney preglomerular arterioles comparing wild type arterioles vs.arterioles from mice having deletion of RBP-J in cells of the renin lineage
We used microarrays to detail the global program of gene expression in wild type and RBP-J conditional knockout (RPB-J cKO)  kidney arterioles which revealed upregulation of genes that belong to the immune response system.

overall_design: Two condition experiment: wild type vs RBP-J cKO. Replicates: wild type - pool of arteriole prparations from 3 animals and cKO - pool of arteriole preparations from 4 animals . One replicate per array.

first: R

first: Ellen

last: Pentz

first: Maria-Luisa

last: Sequeira-Lopez

first: Ruth

last: Castellanos-Rivera


title: Gene expression data from Terminal Effector and Memory Precursor CD8+ T cells during infection

status: Public on Mar 13 2017

city: Stanford

first: Howard

middle: Y

last: Chang

state: California

address: 269 Campus Drive

institute: Stanford University

summary:
Differentiation of naive T cells into effector and memory populations following infection is mediated by a network of transcription factors (TF) that translate environmental signals into regulatory circuits involving TF expression and binding activity as well as chromatin accessibility.
To delineate the transcriptional difference between effector subsets, we performed microarray on TE and MP subsets and found that TE and MP subsets reflect transcriptional differences between effector and memory CD8+ T cells

overall_design: KLRG1hiCD127lo Terminal Effector and KLRG1loCD127hi Memory Precursor CD8+ T cells were sorted into Trizol at day 8 of Lm-OVA infection. Two or more replicates per sample were analyzed

first: Bingfei

last: Yu

first: Ananda

middle: W

last: Goldrath


title: Methylation data from from HCT-8 human colorectal cancer (CRC) wild type cells (HCT8/WT) and its 5-FU-induced resistant cell line (HCT8/5-FU)

first: Guo

last: Zheng

summary:
Complete growth medium RPMI-1640 which contains 10% FCS, 1% Penicillin-Streptomycin Solution was used for cell culture.
Both cell lines were maintained at 37 °C in a humidified atmosphere containing 5% CO2. MTT assay was performed to determine the 5 ‑ FU resistance in both of HCT-8/WT and HCT-8/5-FU cell line.

overall_design: CRC wild type cell (HCT8/WT) and its 5-FU-induced resistant cell line (HCT8/5-FU) , both of which were treated with 5-fluorouracil (5-FU) for 0 and 72 hours, respectively. Three biological replicates of each condition were hybridised to the Illumina Infinium 450k Human Methylation Beadchip.

first: Zheng

last: Guo


title: A new molecular assay for the proliferation signature in mantle cell lymphoma applicable to formalin-fixed paraffin-embedded biopsies

status: Public on Mar 17 2017

first: Louis

middle: M.

last: Staudt

state: MD

address: 9000 Rockville Pike, Bldg 10, Rm 4N114

department: Lymphoid Malignancies Branch

institute: National Cancer Institute

summary: Mantle cell lymphoma (MCL) is an aggressive B-cell neoplasm displaying heterogeneous outcomes after treatment. In 2003, the Lymphoma/Leukemia Molecular Profiling Project described a powerful biomarker, the "proliferation signature", using gene expression in fresh frozen material. Here we describe the training and validation of a new assay that measures the proliferation signature in RNA derived from routinely available formalin-fixed paraffin-embedded (FFPE) biopsies.

overall_design: MCL specimens from 123 patients were investigated with Affymetrix HG U133 plus 2.0 gene expression arrays.


title: ChIP-seq from K562 (ENCSR700IEB)

first: ENCODE

last: DCC

address: 300 Pasteur Dr

institute: ENCODE DCC

summary:
Reverse Crosslink Control ChIP-seq on human K562 (fragmentation date 02-26-14)

For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODE_Data_Use_Policy_for_External_Users_03-07-14.pdf


title: ChIP-seq from HepG2 (ENCSR476TKW)

summary:
Reverse Crosslink Control ChIP-seq on human HepG2 (fragmentation date 02-20-14)

For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODE_Data_Use_Policy_for_External_Users_03-07-14.pdf


title: A new plant-derived compound, Hu-17, induces apoptosis and chemosensitization of ovarian cancer cells to platinum through activation of ROS-mediated JNK signaling

status: Public on Mar 11 2017

city: Shanghai

first: Jiansheng

last: Liu

state: Shanghai

address: No.845 LingShan Road, PuDong District

department: Renji Hospital

institute: Shanghai Jiao Tong University,School of Medicine.

summary: Platinum-based compounds exert their anti-neoplastic effect through direct binding to DNA, which blocks fundamental cellular process ultimately resulting in apoptotic cell death. However, many ovarian cancers become refractory to treatment with platinum-based compounds. To improve the existing therapies for ovarian cancer, we sought to identify potent, nontoxic and specific drug candidates that have anti-neoplastic effects towards cisplatin-sensitive and cisplatin-resistant ovarian cancer cells. Using a cell-based screening assay, we evaluated 56 compounds-derived from the Chinese medicinal plant, Phytolaccae, and one phytoaccagenin compound (Hu-17) was selected on the basis of its ability to dramatically decrease the viability of cisplatin-resistant SK-OV-3 cells.Using high-throughtput microarray system, we identified GO terms and pathway signatures enriched in Hu-17 and/or cisplatin treated SK-OV-3 cells.

overall_design: Ovarian cancer cells SK-OV-3 were cultured in McCoy's 5A medium supplemented with 10% fetal bovine serum, the cell were treated with Hu-17 and/or cisplatin for different time, and total RNA from SK-OV-3 cells was hybridized on Affymetrix U133 plus 2.0 genechip.

first: Yanzhi

last: Du


title: MMTV-PyMT whole tumor gene expression with and without Class IIa HDAC inhibitor treatment

status: Public on Mar 08 2017

city: Cambridge

first: Scott

last: Davis

state: MA

address: 200 Technology Square, Suite 602

department: Tempero DPU

institute: GSK

summary: The aim of this study was to identify differential gene expression resulting from the inhibition of class IIa HDACs in the CD3+ or CD11b+ cells residing in MMTV-PyMT tumors.

overall_design: Prior to necropsy and collection of tumors from MMTV-PyMT mice, mice were treated with either vehicle (DMSO) or 50 mg/kg TMP195 for 2 weeks. One excised tumor from each of these mice was immediately snap frozen then stored at -80 C until processed for RNA extraction.  RNA samples were stored at -80 C until labeling and hybridization to Affymetrix arrays.

first: Jennifer

middle: L

last: Guerriero

first: Michael

last: Nolan

first: Holly

middle: E

last: Ponichtera


title: Expression data from ectopic PTHLH over-expression in Ca9-22 cells

first: Wei-Min

state: Not Applicable

address: 128 Academia Road, Section 2, Nankang,

institute: Academia Sinica

summary: To exmaine the PTHLH stimulated genes in Ca9-22 cells, we preformed the Affymetrix Human Genome U133 Plus 2.0 Array with  empty vector or PTHLH expression vector. The raw data were normalized by GeneSpring GX software and up-load with raw values.

overall_design: Total RNA was collected from empty vector or PTHLH expression Ca9-22 cells.

last: Hsiao

first: Sin-Gwo

last: Shiah


title: Gene expression profiles in preterm infants on continuous long-term oxygen therapy suggest reduced oxidative stress-dependent signaling during hypoxia

city: Oslo

first: Betty

last: Kalikstad

address: Oslo University Hospital, Institute of Clinical Medicine, Rikshospitalet

country: Norway

institute: 1University of Oslo

summary: Preterm infants are susceptible to neonatal inflammatory/infective diseases requiring drug therapy. The present study hypothesized that mRNA expression in the blood may be modulated by signaling pathways during treatment. The current study aimed to explore changes in global gene expression in the blood from preterm infants with the objective of identifying patterns or pathways of potential relevance to drug therapy. The infants involved were selected based on maternal criteria indicating increased risk for therapeutic intervention. Global mRNA expression was measured in 107 longitudinal whole blood samples using Affymetrix Human Genome U133 Plus 2.0 arrays; samples were obtained from 20 preterm infants. Unsupervised clustering revealed a distinct homogeneous gene expression pattern in 13 samples derived from seven infants undergoing continuous oxygen therapy. At these sampling times, all but one of the seven infants exhibited severe drops in peripheral capillary saturation levels below 60%. The infants were reoxygenated with 100% inspired oxygen concentration. The other samples (n=94) represented the infants from the cohort at time points when they did not undergo continuous oxygen therapy. Comparing these two sets of samples identified a distinct gene expression pattern of 5,986 significantly differentially expressed genes, of which 5,167 genes exhibited reduced expression levels during transient hypoxia. This expression pattern was reversed when the infants became stable, i.e., when they were not continuously oxygenated and had no events of hypoxia. To identify signaling pathways involved in gene regulation, the Database for Annotation, Visualization and Integrated Discovery online tool was used. Mitogen activated protein kinases, which are normally induced by oxidative stress, exhibited reduced gene expression during hypoxia. In addition, nuclear factor erythroid 2 related factor 2 antioxidant response element target genes involved in oxidative stress protection were also expressed at lower levels, suggesting reduced transcription of this pathway. The findings of the present study suggest that oxidative stress dependent signaling is reduced during hypoxia. Understanding the molecular response in preterm infants during continuous oxygenation may aid in refining therapeutic strategies for oxygen therapy.

overall_design: Gene expression levels from 107 longitudinal  whole-blood samples from 20 preterm born infants were analyzed from total RNA using NuGen Ovation amplification and Human-Genome-U133 Plus 2.0-arrays from Affymetrix.

first: Hanna

last: Kultima


title: Gene expression in MMTV-PyMT whole tumor, CD3+ lymphocytes or CD11b+ myeloid cells with and without Class IIa HDAC inhibitor treatment

country: USA

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

overall_design: Refer to individual Series


title: Time series transcriptome and DNA methylome analysis of immature T-cells and reMAIT cells

city: Koto-ku

first: Toutai

last: MITUYAMA

department: Artificial Intelligence Research Team

institute: National Institute of Advanced Industrial Science and Technology (AIST)


title: Expression data from primary adipocytes, ASCs, and ASC-adipocytes with or without IRF1 overexpression

first: Max

last: Friesen

address: 455 Main St

institute: Whitehead Institute

summary:
Through employing a comparative transcriptomics approach, we identified IRF1 as differentiatlly regulated between primary and in vitro derived genetically matched adipocytes.
We demonstrated IRF1 expression in adipocytes contributes to upregulation of inflammatory processes.

overall_design: Primary adipocytes and genetically matched ASCs were compared with in vitro derived ASC-adipocytes, with or without IRF1 expression.

first: Chad

last: Cowan


title: ChIP-seq from GM12878 (ENCSR136WQZ)

status: Public on Mar 09 2017

summary:
Reverse Crosslink Control ChIP-seq on human GM12878 (fragmentation date 02-20-14)

For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODE_Data_Use_Policy_for_External_Users_03-07-14.pdf


title: Time series DNA methylation analysis of immature T-cells and reMAIT cells by using methylation array

summary: To explore the molecular mechanisms underlying selective differentiation of MAIT-derived iPSCs into reMAITs, we conducted DNA methylation profiling based on a methylation array. We sampled reMAITs during the time course of differentiation from iPSCs as well as mature MAITs isolated from cord blood (CB MAITs). As control, we used immature T cells differentiated from hematopoietic stem cells (HSCs). For each of reMAITs and the immature T cells, we selected four time points: Start, Early, Middle, and Late.

overall_design: MAITs isolated from CB were reprogrammed to iPSCs (PMID:23523177). The MAIT-derived iPSCs were cultured on OP9, and CD34+ CD43+ cells were isolated. These CD34+ CD43+ precursor cells were furthered cultured on OP9/DL1 for re-differentiation into MAITs. Based on the observation of the reported surface antigen profiles (PMID:23523177), reMAITs were harvested at four different time points: day 0 (Start), day 4 (Early), day 7-10 (Middle), and after day 30 (Late). For the immature T cells, CD34+ cells were isolated from CB using CD34 MicroBead Kit (Miltenyi Biotech). These CD34+ HSCs were cultured on OP9/DL1 for differentiation into T cell lineage as previously described (PMID:15494433). Based on the surface antigen profiles, the immature T cells were harvested at four different time points: CD34+ cells at day 0 (Start), CD4- CD8- double negative cells at day 21 (Early) and day 40 (Midlle), and CD4+ CD8+ double positive cells after day 50 (Late). For DNA methylation analysis, Genomic DNA was extracted from each sample using Wizard Genomic DNA Purification Kit (Promega, Tokyo, Japan). DNA (1 micro gram) was subjected to bisulfite conversion using EZ DNA Methylation Kit (Zymo Research, CA, USA), and subjected to analysis using Infinium HumanMethylation450 BeadChip Kit (Illumina, Tokyo, Japan).

first: Yutaka

last: Saito

first: Chie

last: Sugimoto

last: Mituyama

first: Hiroshi

last: Wakao


title: Whole genome methylation profiling of melanoma-derived induced pluripotent cancer cells in comparison to the parental melanoma cells

city: Heidelberg

first: Jochen

last: Utikal

address: Im Neuenheimer Feld 280

department: Clinical Cooperation Unit Dermato-Oncology

institute: German Cancer Research Center

type: Genome binding/occupancy profiling by genome tiling array

summary: The Illumina Infinium HumanMethylation450 Bead Chip was used to obtain DNA methylation profiles. Samples included melanoma cell lines A375 and HT-144 as well as their reprogrammed progeny and melanoma-iPCC-derived fibroblasts. Pluripotent stem cells and normal human fibroblasts served as references.

overall_design: Genomic DNA from reprogrammed induced pluripotent cancer cells compared to parental melanoma cells, pluripotent stem cells and iPCC-derived fibroblasts as well as normal human fibroblasts.

first: Mathias

last: Bernhardt


title: Uniform Topographic Responses of the Small Airway Epithelium to Cigarette Smoking

city: New York

first: Yael

last: Strulovici-Barel

state: NY

address: 1300 York Avenue

department: Department of Genetic Medicine

institute: Weill Cornell Medical College

summary: Although smoking-induced lung disease tends to be more common in the upper lobe, it is not known if this results from the skewed distribution of inhaled cigarette smoke or increased susceptibility of the upper lobes to these disorders. The distribution of inhaled cigarette smoke within the lung is complex, depending on lung pressure-volume relationships, gravity, individual smoking habits and the properties of the individual components of cigarette smoke. With the knowledge that the small airway epithelium is the earliest site of smoking-induced lung disease, and that the small airway epithelium is acutely sensitive to inhaled cigarette smoke with significant changes in the up- and down-regulation of hundreds of genes, we compared upper vs lower lobe gene expression in the small airway epithelium of the same cigarette smokers to determine if the gene expression patterns were similar or different. Active smokers (n=11) with early evidence of smoking-induced lung disease (normal spirometry but low diffusing capacity) underwent bronchoscopy and brushing of the small airway epithelium to compare upper vs lower lobe genome-wide gene expression assessed by microarray. Interestingly, cluster and principal component analysis demonstrated that, for each individual, the expression of the known small airway epithelium smoking-responsive genes were remarkably similar as upper vs lower lobe pairs, although, as expected, there were differences in the smoking-induced changes in gene expression from individual to individual. Thus, while there may be topographic differences in the distribution of cigarette smoke, sufficient smoke reaches the upper vs lower lobe small airway epithelium so that, within each smoker, the upper vs lower lobe gene expression are similar. These observations support the concept that the topographic differences in the occurrence of the smoking-induced lung diseases are likely secondary to topographic differences in the susceptibility of the upper vs lower lobes to cigarette smoke, not the topographic differences in distribution of inhaled cigarette smoke.

overall_design: Gene expression of the small airway epithelium was assessed in the upper and lower lobe of 11 individuals with normal spirometry, but a low diffusing capacity of lung for carbon monoxide (DLCO).

first: Ben

last: Harvey

first: Jason

last: Mezey

first: Ramya

last: Raviram

first: Cynthia

last: Gordon

first: Jacqueline

last: Salit

first: Ann

last: Tilley

first: Augustine

last: Chung

first: Abraham

last: Sanders

first: Ronald

last: Crystal


title: Genome wide DNA methylation  in oral squamous cell carcinoma (OSCC) disease and adjacent normal tissue samples

city: Kolkata

first: Raghunath

last: Chatterjee

state: WB

address: 203 BT Road, HGU, Indian Statistical Institute

department: Human Genetics Unit

country: India

institute: Indian Statistical institute

summary: Genome wide DNA methylation profiling of normal and adjacent OSCC samples. The Illumina Infinium 450k Human DNA methylation Beadchip v1.2 was used to obtain DNA methylation profiles across approximately 4,50,000 CpGs in tissue samples. Total 21 samples were taken including 10 paired and 1 unpaired tissues. 6 were HPV Positive and 5 were HPV negative.

overall_design: Bisulphite converted DNA from the 21 samples were hybridised to the Illumina Infinium 450k Human Methylation Beadchip v1.2


title: Rapid and efficient generation of myelinating oligodendrocytes from human induced pluripotent stem cells using a combination of three transcription factors

status: Public on Mar 06 2017

city: Münster

first: Marc

last: Ehrlich

address: Röntgenstraße 20

institute: Max Planck Institute for Molecular Biomedicine


title: DNA methylome modifications in ME/CFS

city: Toronto

first: Patrick

last: McGowan

state: Ontario

address: 1265 Military Trail

department: Biological Sciences

country: Canada

institute: University of Toronto Scarborough

summary: Examination of DNA methylome patterns in a larger cohort of ME/CFS samples using the Illumina Infinium HumanMethylation450 Beadchip Array

overall_design: Bisulfite-converted DNA from 75 samples were hybridised onto the Illumina Infinium HumanMethylation450 Beadchip Array

first: Wilfred

middle: C

last: de Vega

first: Santiago

last: Herrera

first: Suzanne

middle: D

last: Vernon

middle: O


title: Characterization of Human Lung Airway APC Subsets

status: Public on Mar 07 2017

city: Oklahoma City

first: Jordan

last: Metcalf

state: Oklahoma

address: 800 Research Parkway, RP-1, Suite 425

institute: University of Oklahoma Health Sciences Center

summary: The respiratory system is a complex network of many cell types, including subsets of macrophages and dendritic cels, that work together to maintain steady-state respiration. Due to limitations in acquiring cells from healthy human lung, these subsets remain poorly characterized transcriptionally and phenotypically. We set out to systemically identify these subsets in human airways, by developing a schema of isolating large numbers of cells by whole lung bronchoalveolar lavage. Six subsets of phagocytic antigen presenting cells were consistently observed, which varied in their ability to internalize bacterial particles. Subsets could be further separated by their inherent capacities to upregulate CD83, CD86, and CCR7. Whole genome transcriptional profiling revealed a clade of “true dendritic cells” distinct from a “macrophage/monocyte” clade. Each clade, and each member of both clades, could be discerned by specific genes of increased expression, which would serve as markers for future studies in healthy and diseased states.

overall_design: 6 antigen presenting cell subsets were sorted from 7 different human lung donors. In addition, immature monocyte-derived dendritic cells and macrophages were generated from monocytes of 6 human blood donors. Monocyte-derived dendritic cells were generated by exposure to IL-4 and GM-CSF, while monocyte-derived macrophages were generated by exposure to GM-CSF alone. Immature macrophages and dendritic cells were sorted as the lung cells were. A fraction of the monocyte-derived cells from the same blood donors were further matured with LPS exposure prior to sorting. Samples were processed into purified total RNA, which was reverse transcribed into cDNA and further amplified. Reverse transcription and amplification occurred in two batches of samples. Positive and negative controls (composed of blood PBMC) for RT and amplification were included with both batches, but were not used in analysis. Samples were fragmented and biotinylated for hybridization with Human genome U133 Plus 2.0 arrays. Array data was log2 transformed and had batch effects removed for final analysis.

first: Vineet

middle: I

last: Patel

middle: P

first: Dennis

last: Burian

first: Mikhail

last: Dozmorov


title: Expression data from diagnostic samples of diffuse large B-cell lymphomas (DLBCL), follicular lymphoma (FL) and primary and relapsed transformed FL

city: Aalborg

first: Julie

middle: Støve

last: Bødker

address: Sdr. Skovvej 15

department: Department of Heamatology

country: Denmark

institute: Aalborg University Hospital

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


title: Expression data from human iENP

city: Taipei

first: pei-shan

last: Hou

address: No. 155, Sec. 2, Linong St., Beitou dist.

institute: Institute of Anatomy and Cell Biology, School of Medicine, National Yang-Ming Chiao-Tung University.

summary:
The early neural population that differentiates from human pluripotent stem cells (hPSCs) consists of various embryonic neural stem cells and progenitors (ENSCs/ENPs) with broad neural developmental propensity, and these cells are thus an excellent source for the development of novel clinical interventions. Here, we sought to directly convert human somatic cells into cells with ENP-like phenotypes through the use of hESC-derived NP-enriched neural transcription factors (hESC-NP-TFs).
Microarray was used to examine global gene expression profiling of human iENP versus hESC-derived neural progenitors.

overall_design: RNA was extracted from control hESC-NP and iENP using QIAquick kit. We sought to understand the characteristics in iENP with hESC-NP as a control.

first: Pei-Shan

first: Chan-Hsien

last: Yeh

first: Ching-Yu

last: Chuang

first: Wei

last: Chiang

first: Hsiao-Jung

last: Liu

first: Tan-Nan

last: Lin

first: Hung-Chih

last: Kuo


title: Expression data from diagnostic samples of diffuse large B-cell lymphomas (DLBCL), follicular lymphoma (FL) and primary and relapsed transformed FL [RNA]

summary: Comparison of gene expression profiles from diagnostic samples of diffuse large B-cell lymphoma (DLBCL) and follicular lymphoma (FL) to a patient case withsamples of primary and relapsed transformed FL

overall_design: Global gene expression data of diagnostic samples of diffuse large B-cell lymphoma (DLBCL), follicular lymphoma (FL) and primary and relapsed transformed FL

first: Marianne

middle: T

last: Severinsen

first: Tarec

last: El-Galaly

first: Rasmus

middle: F

last: Brøndum

first: Maria

middle: B

last: Laursen

first: Steffen

last: Falgreen

first: Mette

last: Nyegaard

first: Alexander

last: Schmitz

first: Victor

last: Iver

first: Preben

last: Johansen

first: Lasse

middle: H

last: Jakobsen

first: Anna

middle: A

last: Schönherz

first: Hanne

last: Rasmussen

first: Linn

last: Reinholdt

first: Martin

last: Bøgsted

first: Karen

last: Dybkær

first: Hans

last: Johnsen


title: Differentiation of human and murine induced pluripotent stem cells to microglia-like cells [human]

status: Public on Mar 02 2017

city: Bethesda

first: Kory

middle: R

last: Johnson

address: 10/3B01, 9000 Rockville Pike

department: DIR IT & Bioinformatics

institute: NINDS/NIH

summary: Microglia are myeloid-lineage inflammatory cells that activate innate and adaptive immune responses within the central nervous system (CNS). They also have important roles in CNS development and homeostasis and can modulate the course of a variety of CNS diseases. We report here the sequential differentiation of murine induced pluripotent stem cells (iPSC) into hematopoietic progenitor-like cells and then into cells with a phenotype and gene expression profile resembling that of primary brain-isolated microglia. Functionally, the iPSC-derived microglia (iPS-MG) produce inflammatory cytokines and reactive oxygen species, demonstrate phagocytic activity and migrate to areas of pathology within the brain following intracranial injection. The ability to readily generate iPS-MG in vitro will facilitate the study of normal and disease-specific microglia and be useful for the development of microglia-based treatments for CNS diseases.

overall_design: 21 human samples: 3 "NCRM-5" samples representing an iPS cell line established from cord-blood CD34+ cells (available at NIH CRM); 3 "iMG (NCRM-5)" samples representing microglia derived from the "NCRM-5" iPS cell line; 3 "iNC-012" samples representing an iPS cell line established from peripheral blood hematopoietic progenitor CD34+ cells (made available by Dr. Harry L. Malech lab at NIAID, NIH); 3 "iMG (iNC-012)" samples representing microglia derived from the "iNC-012" iPS cell line; 3 "fMG" samples representing fetal microglia (available from Clonexpress); 3 "DC" samples representing dendritic cells (available from AllCells); and 3 "Mac" samples representing bone marrow macrophages (also obtained from AllCells).

first: Hetal

last: Pandya

first: Michael

middle: J

last: Shen

first: David

middle: M

last: Ichikawa

first: Andrea

last: Sedlock

first: Yong

last: Choi

first: Gloria

last: Kim

first: Mason

last: Brown

first: Abdel

last: Elkhaloun

first: Dragan

last: Maric

first: Dorian

last: McGavern

first: Harry

last: Malech

first: John

middle: K

last: Park


title: Differential gene expression in either CD3+ lymphocytes or CD11b+ myeloid cells due to Class IIa HDAC inhibitor treatment

first: Scott

last: Davis

overall_design: Prior to necropsy and collection of tumors from MMTV-PyMT mice, 5 mice were treated with either vehicle (DMSO) or 50 mg/kg TMP195 for 5 days. Tumors from these 5 mice were pooled to generate the single cell suspensions taken to EPCAM depletion and FACS sorting.  Cells were sorted from the single cell populations based on viability (7-AAD negative) and the presence/absence of cell-surface antigens assess by flow cytometry (BD FACS Aria II).  CD3+ lymphocyte populations were 7-AAD-/CD45+/CD19-/CD3+/CD11b-; and CD11b+ myeloid cells were 7-AAD-/CD45+/CD19-/CD3-/CD11b+.  This was repeated 6 times (n=3 vehicle-treatment groups, n=3 TMP195 treatment groups).  All samples were immediately processed for RNA extraction, and stored at -80 C until labeling and hybridization to Affymetrix arrays.

first: Jennifer

middle: L

last: Guerriero

last: Nolan

first: Holly

last: Ponichtera


title: Wilms Tumor in Beckwith-Wiedemann Syndrome and Loss of Methylation at Imprinting Centre 2 [450K Methylation Array]

status: Public on Mar 01 2017

first: Jack

last: Brzezinski

state: ON

address: 555 University Avenue

institute: University of Toronto

summary: Beckwith-Wiedemann syndrome (BWS) is an overgrowth syndrome caused by a variety of molecular changes on chromosome 11p15.5. Children with BWS have a significant risk of developing Wilms tumours with the degree of risk being dependent on the underlying molecular mechanism. In particular, only a relatively small number of children with loss of methylation at the centromeric imprinting centre (IC2) were reported to have developed Wilms tumour. Discontinuation of tumour surveillance for children with BWS and loss of methylation at IC2 has been proposed in several recent publications. We report here three children with BWS reported to have loss of methylation at IC2 on clinical testing who developed Wilms tumour or precursor lesions.  Using multiple molecular approaches and multiple tissues, we reclassified one of these cases to paternal uniparental disomy for chromosome 11p15.5. These cases highlight the current challenges in definitively assigning tumour risk based on molecular classification in BWS. The confirmed cases of loss of methylation at IC2 also suggest that the risk of Wilms tumour in this population is not low as previously thought. Therefore, we recommend that for now, all children with a clinical diagnosis of BWS be screened for Wilms tumour by abdominal ultrasonography until the age of 8 regardless of the molecular classification.

overall_design: 2 blood samples (Case 1 and Case 2) are genotyped on the Illumina HumanOmni2.5M SNP array (GPL20641). 3 blood samples (Case 1, Case 2, and Case 3) have methylation measured on the Illumina HumanMethylation450 Bead Chip array (GPL13534). 21 Control blood samples were analyzed on the HumanMethylation BeadChip Array, there were no controls used for the HumanOmni2.5M SNP array. Pyrosequencing and MS-MLPA in cases and controls were done as described in the associated publication. There are no replications in this submission.

first: Brzezinski

last: Jack

first: Shuman

last: Cheryl

first: Choufani

last: Sanaa

first: Ray

last: Peter

first: Stavropolous

last: Dmitri

first: Basran

last: Raveen

first: Steele

last: Leslie

first: Parkinson

last: Nicole

first: Grant

last: Ronald

first: Thorner

last: Paul

first: Lorenzo

last: Armando

first: Weksberg

last: Rosanna


title: Adipose Precursor HO-1 prevents healthy visceral adipose tissue expansion during obesity [I]

city: Vienna

first: Markus

last: Jeitler

address: Lazarettgasse 14

country: Austria

institute: Medical University Vienna

summary: Excessive accumulation of white adipose tissue (WAT) is a hallmark of obesity. The expansion of WAT in obesity involves proliferation and differentiation of adipose precursors (APs), however, the underlying molecular mechanisms remain unclear. Here, we identify Heme Oxygenase-1 (HO-1) as selectively being upregulated in the AP fraction of WAT, upon high-fat diet (HFD) feeding. Specific conditional deletion of HO-1 in APs of Hmox1fl/fl-Pdgfra Cre mice enhanced HFD-dependent visceral AP proliferation and differentiation, upstream of Cebpα and PPARγ. Opposite effects on human preadipocyte proliferation and differentiation in vitro were observed following HO-1 overexpression. Mechanistically, HO-1 acts upstream of AKT2 via ROS thresholding in mitochondria. Deletion of HO-1 in APs is sufficient to lower blood glucose, insulin and free fatty acid levels as well as liver steatosis during obesity, an effect not seen when HO-1 was conditionally deleted at later stages of adipogenesis using AdipoQ-Cre. Together, our data identify HO-1 as a diet-induced regulator limiting visceral adipose tissue hyperplasia during obesity.

overall_design: Visceral adipose tissue from obese Hmox1fl/fl PdgfraCre or Hmox1fl/fl mice was digested after 8 weeks of high fat diet (HFD) and Adipose Progenitors were lysed directly in RLT lysis buffer after magnetic bead purification.

first: Martin

last: Bilban

first: Gabriel

last: Wagner


title: Adipose Precursor HO-1 prevents healthy visceral adipose tissue expansion during obesity[II]

overall_design: viWAT and scWAT of male C57BL/6J mice (aged 7-8 weeks) were digested after either 3 days of standard diet (SD) or high fat diet (HFD) and lysed directly in RLT lysis buffer after magnetic bead purification.


title: Wilms Tumor in Beckwith-Wiedemann Syndrome and Loss of Methylation at Imprinting Centre 2


title: Adipose Precursor HO-1 determines healthy visceral adipose tissue expansion during obesity


title: Integrated analysis of the molecular action of Vorinostat identifies epi-sensitised targets for combination therapy

city: Belfast

first: Ken

last: Mills

address: 97 Lisburn Road

department: CCRCB

institute: Queen's University Belfast

summary: Acute myeloid leukaemia (AML) is a highly heterogeneous entity of disorders in haematopoietic progenitors, characterised by an arrest in differentiation and an outgrowth of myeloid blasts in the bone marrow. AML is a disease of the aging, many patients are unable to withstand standard chemotherapy therefore novel approaches for anti-cancer agents has arisen in the understanding of epigenetic regulation in cancer cells, such as chromatin remodelling.  Acetylation of histones is a reversible process, whereby acetyl groups are transferred on the ε-amino groups of specific lysine residues by a specific group of enzymes, histone acetyltransferases (HATs) and removed by histone deacetylase complexes (HDACs).   HDACs are involved in regulating a number of processes in the cell, such as cell proliferation, differentiation as well as apoptosis.  Deregulation of the activity of these enzymes is associated with cancer; therefore it is important that the HAT and HDAC equilibrium is regained.  This equilibrium can be improved through the inhibition of HDAC enzymes using HDAC inhibitors.  Vorinostat is a HDAC inhibitor, clinically approved for the treatment of CTCL, and is in phase II clinical trials for AML and a number of haematological malignancies.  Studies have shown that some patients are non-responsive/resistant to Vorinostat; therefore a fuller characterisation of Vorinostat needs to be made so an adequate combination drug can be identified, as understanding of resistance is crucial to overcoming it.  The purpose of this study was to provide a comprehensive analysis of Vorinostat in AML cell lines and to identify potential synergistic therapies that could be used in combination with Vorinostat to provide a better outlook in AML. The global identification of genes associated with Vorinostat induced histone H3 lysine 9 (H3K9) acetylation, investigated using chromatin immunoprecipitation coupled with next generation sequencing (ChIP-SEQ), was integrated with data from gene expression studies to provide a comprehensive approach to understanding Vorinostat. This study has identified the sonic hedgehog homolog (SHH) as a rational and potential therapeutic target for combination therapy with Vorinostat

overall_design: Six samples: three controls treated with DMSO and three with 1 µM SAHA (Vorinostat) were hybridized to Affymetrix HG-U133 Plus 2.0 GeneChips

first: Jodie

last: Hay

first: Katrina

last: Lappin

first: Fabio

last: Liberante

first: Alex

last: Thompson


title: Overexpression of trophoblast stem cell-enriched microRNAs promote trophoblast fate in embryonic stem cells.

first: Brian

middle: Joseph

last: Cox

address: 1 King's College Circle, Rm 3360

department: Physiology

summary: The role of microRNAs (miRNA) in first cell fate choice of the preimplantation mouse embryo remains unresolved, as gene expression and knockout data are conflicting. This cell fate choice generates the extraembryonic lineage of the trophoblast and the embryonic lineage of the epiblast (inner cell mass). The trophoblast differentiates into polar and mural cells, where polar cells contribute to placental development and mural cells to the implantation process and Reichert’s membrane. The inner cell mass further differentiates into the epiblast and primitive endoderm. We used stem cell lines that can be derived from the trophoblast and epiblast lineages to address the role of miRNAs in early lineage cell fate specification and determination. Using embryonic stem cells (ESC) and trophoblast stem cells (TSC) as starting and ending states of cell development we identified a network of TSC expressed miRNAs that are enriched in ESC targets mRNA. We used constitutive and inducible expression of TSC enriched miRNAs in ESC and show that they can drive cell morphology and gene expression profiles similar to trophoblast. Additionally we show that this process required HDAC2 inhibition and is miRNA specific, as cardiac specific miR-1 could not induce trophoblast under these conditions. In contrast to embryo derived and Cdx2 induced trophoblast cells, miRNAs promote a mural TE like cell phenotype. Transplantation into preimplantation mouse embryos showed that miRNA-induced trophoblast preferentially contributes to the mural trophoblast in both the blastocyst and the Reichert’s membrane. Our data support a role for miRNAs and HDACs in the specification of the trophoblast and potentially the polar and mural cell types.

overall_design: TSC and ESC were used as references to cell fate states. Duplicate inducible clonally derived miR lines were tested. Only a single Cdx2 inducible line was availible.

first: Ursula

last: Nosi

first: Fredrik

last: Lanner


title: Expression data from human tendon-derived stem cells with nestin knockdown

city: hangzhou

first: Xiao

last: Chen

state: zhejiang

address: yu hang tang road 866#

department: School of Medicine

country: China

institute: Zhejiang University

summary: We have compared the gene expression profile of human tendon-derived stem cells with stable nestin knockdown.

overall_design: TSPC with stable nestin knockdown by using two different nestin shRNA. Total RNA was extracted and fragmented biotin-tagged cRNA was hybridized to Human Genome U133 Plus 2.0 Array.

first: Chen

last: Xiao


title: Gene expression profile (GEP) of miR-34a-5p-overexpressing CD34+ HPCs

city: Modena

first: Rossella

last: Manfredini

address: Via Gottardi 100

department: Life Sciences

institute: Centre for Regenerative Medicine

summary:
Primary Myelofibrosis (PMF) is a myeloproliferative neoplasm characterized by hyperplastic megakaryopoiesis and myelofibrosis. Through a gene expression profile (GEP) study we recently highlighted the upregulationof miR-34a-5p in PMF versus healthy donor (HD) CD34+ hematopoietic progenitor cells (HPCs). To shed some light into the role of miR-34a-5p in PMF pathogenesis, here we unravelled the effects of the overexpression of miR-34a-5p in HPCs forcing its expression in HPCs.
We showed that enforced expression of miR-34a-5p blocks proliferation and favours the megakaryocyte and monocyte/macrophage commitment of HPCs.  Interestingly, we identified lymphoid enhancer-binding factor 1 (LEF1) and nuclear receptor subfamily 4, group A, member 2 (NR4A2) transcripts as miR-34a-5p-targets  downregulated after miR-34a-5p overexpression in HPCs as well as in PMF compared with HD HPCs. Remarkably, the knockdown of NR4A2 in HPCs mimicked the antiproliferative effects of miR-34a-5p overexpression, while the silencing of LEF1 phenocopied the effects of miR-34a-5p overexpression in HPCs lineage choice, by stimulating the megakaryocyte and monocyte/macrophage commitment.

overall_design: Human CD34+ cells were transfected by using the 4D-Nucleofector™ System (Lonza). Briefly, starting from the day after CD34+ cells purification, each sample was electroporated twice, once every 24 hours, with 3 µg of mirVana™ miR-34a-5p mimic or mirVana™ miRNA mimic Negative Control (NegCTR mimic). For each electroporation, 4×105 CD34+ cells were resuspended in 100 µL of P3 Primary Cell Solution (Lonza) containing 3 µg of miR-34a-5p mimic or NegCTR mimic and pulsed with the program DS112. Gene expression profile (GEP) was performed on total RNA derived from three independent experiments at 24h after the last nucleofection.

first: Elisa

last: Bianchi

first: Samantha

last: Ruberti

first: Sebastiano

last: Rontauroli

first: Ruggiero

last: Norfo

first: Valentina

last: Pennucci

first: Chiara

last: Rossi

first: Roberta

last: Zini

first: Simona

last: Salati

first: Sergio

last: Ferrari

first: Enrico

last: Tagliafico


title: Gene expression in the mouse adult small intestinal epithelium

city: Milwaukee

first: Michele

last: Battle

state: WI

address: 8701 Watertown Plank Rd

department: Cell Biology, Neurobiology, and Anatomy

institute: Medical College of Wisconsin

summary: Gene expression was compared between adult wildtype (WT)  CD1 jejunual epithelium (J) and ileal epithleium (I). Gene expression was compared between adult control ileal epithleium and Gata4 conditional knockin (cKI) ileal epithelium. Gene expression was compared between adult wildtype CD1 jejunum and Gata4 conditional knockout (cKO) jejunal epithelium.

overall_design: Adult jejunal and/or ileal tissue was collected from wildtype CD1 mice, Gata4 conditional knockin mice, and Gata4 conditional knockout mice. Epithelial cells were isolated, and RNA was prepared.  Affymetrix Mouse Gene 1.0 gene arrays were used to interrogate gene expression.  Data was analyzed using Partek Genomic Suite.


title: Rapid and efficient generation of myelinating oligodendrocytes from human induced pluripotent stem cells using a combination of three transcription factors [brain]

first: Marc

last: Ehrlich

country: Germany

summary: We demonstrate that the induction of three transcription factors (SOX10, OLIG2, NKX6.2) in hiPSC-derived neural progenitor cells (hiPSC-NPC) is sufficient to rapidly generate O4+ oligodendrocytes with an efficiency of 60 to 70% within 28 days.

overall_design: Human brain biopsy from 3 different patients

first: Michael

last: Glatza


title: CRLF2 Over-expression is a Poor Prognostic Marker in Children With High Risk T-Cell Acute Lymphoblastic Leukemia

city: padova

first: silvia

last: bresolin

state: padova

address: via giustiniani 3

department: department of women's and children's health

institute: università di padova

summary: Seventeen T-ALL patients out of 120 (14.2%) presented CRLF2 expression 5 times higher than the median (‘CRLF2-high’) with a significantly inferior 5-y EFS and an increased CIR  compared to CRLF2-low patients.GEP of 15 T-ALL patients with  (‘CRLF2-high’) were compared to 15 CRLF2-low patients. GSEA identified cell cycle deregulating gene sets.

overall_design: RQ-PCR identified a range of expression of CRLF2 in BM samples of T-ALL patients. GEP was performed on 15 high CRLF2 vs 1 low CRLF2 expressing samples to identify specific deregulated pathways between these two groups.

first: Silvia

last: Bresolin

first: Geertruy

last: te Kronnie