title: Aberrant DNA methylation profiling of classic Philadelphia Negative Myeloproliferative Neoplasms

status: Public on Nov 29 2013

city: Pamplona

first: Xabier

last: Agirre

state: Navarra

address: Pio XII, 55

institute: CIMA

summary: Since most DNA methylation studies in Classic Philadelphia-negative myeloproliferative neoplasms (MPNs) – polycythaemia vera (PV), essential thrombocythaemia (ET), and primary myelofibrosis (PMF) - have been performed on a gene-by-gene basis, a more comprehensive methylation profiling is needed to know the real implication of this alteration. In order to investigate the DNA methylation profile in chronic and transformed phase MPNs, we performed genome-wide DNA methylation arrays in 71 chronic (24 PV, 23 ET and 24 PMF) and 13 transformed MPNs. The three types of chronic MPNs showed the same aberrant DNA methylation pattern when compared to controls. Differentially methylated genes (DMG) were enriched in a gene network centered on the NF-κB pathway, indicating that they may be involved in the pathogenesis of these diseases. In the case of transformed MPNs we detected an increased number of DMGs with respect to chronic MPNs. Interestingly, these genes were enriched in a list of DMGs in primary AMLs and in a gene network centered around the IFN pathway. Further studies are clearly needed to elucidate the role of DMGs in MPNs, but our results suggest that this alteration plays an important role in the pathogenesis and transformation of MPNs and that modulation of these pathways would allow us to improve the quality of life of these patients.

overall_design: The methylation profile of 24 PBMCs samples from patients diagnosed with Policytemia Vera, 23 from Essential Thrombocythemia and  24 from primary myelofibrosis was assessed.  We also included 13 secondary acute myeloid leukaemia (AML): 5 transformed PMF,4 transformed TE and 4 transformed PV. As reference,4 healthy donor PBMCs samples from whole peripheral blood and 4 PBMCs samples from bone marrow were used.

first: Cristina

last: Pérez

first: Marien

last: Pascual

first: José

last: Martín-Subero

first: Beatriz

last: Bellosillo

last: Segura

first: Eric

last: Delabesse

first: Sara

last: Alvarez

first: María

middle: J

last: Larrayoz

last: Rifon

first: Juan

last: Cigudosa

first: Carles

last: Besses

last: Calasanz

first: Nicholas

last: Cross

first: Felipe

last: Prósper


title: The human AlkB homologue 4 interacts with proteins associated with transcription (methylation)

status: Public on Dec 01 2013

city: Oslo

first: Leonardo

middle: A.

last: Meza-Zepeda

address: Ullernchausseen 70

department: Dept. of Tumor Biology

country: Norway

institute: The Norwegian Radium Hospital

summary: The Fe(II)- and 2-oxoglutarate (2OG)-dependent dioxygenase AlkB from E. coli is a demethylase which repairs alkyl lesions in DNA, as well as RNA, through a direct reversal mechanism. Humans possess nine AlkB homologues (ALKBH1-8 and FTO). ALKBH2 and ALKBH3 display demethylase activities corresponding to that of AlkB, and both ALKBH8 and FTO are RNA modification enzymes. The biochemical functions of the rest of the homologues are still unknown. To increase our knowledge on the functions of ALKBH4 and ALKBH7 we have here performed yeast two-hybrid screens to identify interaction partners of the two proteins. While no high-confidence hits were detected in the case of ALKBH7, several proteins associated with chromatin and/or involved in transcription were found to interact with ALKBH4. For all interaction partners, the regions mediating binding to ALKBH4 comprised domains previously reported to be involved in interaction with DNA or chromatin. Furthermore, some of these partners showed nuclear co-localization with ALKBH4. However, the global gene expression pattern was only marginally altered upon ALKBH4 over-expression, and larger effects were observed in the case of ALKBH7. Although the molecular function of both proteins remains to be revealed, our findings suggest a role for ALKBH4 in regulation of gene expression or chromatin state and support the previous association of ALKBH7 with spermatogenesis.

overall_design: Comparison of DNA methylation patterns in cells over expressing ALKBH4 and ALKBH7

first: Linn

middle: G

last: Bjornstad

first: Trine

last: Meza

first: Marit

last: Otterlei

first: Solveig

middle: M

last: Olafsrud

middle: A

first: Pal

middle: O

last: Falnes


title: Desai OD00079_HCP3_N2_LTEMB

status: Public on Oct 30 2013

city: Toronto

first: DCC

last: modENCODE

state: Ontario

address: MaRS Centre, South Tower, 101 College Street, Suite 800

country: Canada

institute: Ontario Institute for Cancer Research

type: Genome binding/occupancy profiling by genome tiling array

summary:
modENCODE_submission_3542
This submission comes from a modENCODE project of Jason Lieb. For full list of modENCODE projects, see http://www.genome.gov/26524648
Project Goal: The focus of our analysis will be elements that specify nucleosome positioning and occupancy, control domains of gene expression, induce repression of the X chromosome, guide mitotic segregation and genome duplication, govern homolog pairing and recombination during meiosis, and organize chromosome positioning within the nucleus. 126 strategically selected targets include key histone modifications, histone variants, RNA polymerase II isoforms, dosage-compensation proteins, centromere components, homolog-pairing facilitators, recombination markers, and nuclear-envelope constituents.
We will integrate information generated with existing knowledge on the biology of the targets, perform ChIP-chip analysis on mutant and RNAi extracts lacking selected target proteins, use extrachromosomal arrays to assess the ability of candidate identified sequence motifs to recruit targets in vivo, identify tissue-specific patterns of selected targets, and create integrated, quantitative models of transcription and whole-chromosome functions.
For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODEDataReleasePolicyFinal2008.pdf

overall_design: EXPERIMENT TYPE: CHIP-chip. BIOLOGICAL SOURCE: Strain: N2; Developmental Stage: Late Embryos; Genotype: wild type; Sex: Hermaphrodite;  NUMBER OF REPLICATES: 2;  EXPERIMENTAL FACTORS: Developmental Stage Late Embryos; temp (temperature) 20 degree celsius; Antibody OD00079 HCP3 (target is HCP-3); Strain N2

first: Reto

last: Gassmann

first: Arshad

last: Desai


title: Characterization of the DNA methylation patterns in oxaliplatin chemosensitive and chemoresistant human colorectal cancer cell lines

status: Public on Nov 26 2013

city: L'Hospitalet de Llobregat

first: Manel

last: Esteller

state: Barcelona

address: Hospital Duran i Reynals Av. Gran Via s/n km, 2.7

department: PEBC

country: Spain

institute: IDIBELL

summary: Genome wide DNA methylation profiling of LoVo oxaliplatin sensitive (LoVo_S) and LoVo 10 fold oxaliplatin resistant (LoVo_R) cell lines. The Illumina Infinium 27k Human DNA methylation Beadchip v1.2 was used to obtain DNA methylation profiles across approximately 27,000 CpGs in cell lines genomic DNA samples.

overall_design: Bisulphite converted DNA from the LoVo_S and LoVo_R samples were hybridised to the Illumina Infinium 27k Human Methylation Beadchip v1.2

first: Cátia

last: Moutinho


title: Transcriptome analysis of Escherichia coli under various stress conditions

status: Public on Nov 04 2013

city: Tsukuba

first: Bei-Wen

last: Ying

state: Ibaraki

address: 1-1-1 Tennoudai

country: Japan

institute: University of Tsukuba

type: Expression profiling by genome tiling array

summary: A genome reduced E. coli strain MDS42ΔgalK::Ptet-gfp-kan were applied for the comparative transcriptome analysis. Genome-wide transcriptional changes under high osmotic prresure, high temperature condition and starvation were evaluated.

overall_design: Exponentially growing cells from recoverying stress response were collected for the transcriptome analysis. High osmotic prresure, high temperature condition and starvation were chosen as stressor. In each kind of stress, three level of stresses were applied. Every 3 biological replications were performed.

first: Yuki

last: Matsumoto

first: Tetsuya

last: Yomo


title: Transcriptomic response of zebrafish embryos to Polyamidoamine (PAMAM) dendrimers

status: Public on Nov 12 2013

city: Barcelona

first: Eva

middle: Lima

last: Oliveira

address: Carrer Jordi Girona 18-26

department: Environmental Chemistry

institute: IDAEA CSIC

summary: We are presenting here the application of toxicogenomics to perform the evaluation of toxic effects of two polyamidoamine dendrimers (Generation3 and Generation4) on the developing zebrafish embryo. They are nanomaterials of special concern under the toxicological point of view because of their relatively high solubility in water and bioavailability. Zebrafish embryo toxicity assays (zFET) showed that G3 was more toxic to zebrafish than G4, and that both compounds were several orders of magnitude more toxic than other carbonaceous nanomaterials, like carbon fullerenes or nanotubes. The results suggest a variety of MoA for different dendrimers, probably related to the nature and number of the chemical groups attached to their surface. They also confirm the relatively high bioavailability of these compounds, a key factor for the assessment of the risk associated to their use and release into the environment. About 5% genes were affected by the treatment. Gene ontology (GO) analyses show that these genes are involved in the oxidation-reduction process and also in the nervous system development. Representatives of each GO functional groups were selected and quantified by real-time PCR to validate the microarray data and to differentiate the action of generations of dendrimers studied.

overall_design: Two different treatments were performed in this study. Zebrafish fertlized eggs were exposed to PAMAM dendrimer G3 and G4 during 48h. 3 biological replicates per studied dendrimer are included such as each control sample.

first: Marta

last: Casado

first: Melissa

last: Faria

first: Amadeu

last: Soares

first: Jose

last: Navas

first: Carlos

last: Barata

first: Benjamín

last: Piña


title: Comparison of DNA methylation profilings between hESCs and hiPSCs

status: Public on Dec 03 2013

city: Kyoto

first: Shinya

last: Yamanaka

address: 53 Kawahara-machi, Shogoin, Sakyo-ku

institute: Center for iPS Cell Research and Applicaton (CiRA), Kyoto University

summary: It remains controversial whether human induced pluripotent stem cells (hiPSCs) are distinct from human embryonic stem cells (hESCs) in their molecular signatures and differentiation properties. We examined the gene expression and DNA methylation of 49 hiPSC and 10 hESC lines and identified no molecular signatures that distinguished hiPSCs from hESCs. Comparisons of the in vitro directed neural differentiation of 40 hiPSC and four hESC lines showed that most hiPSC clones were comparable to hESCs. However, in seven hiPSC clones, significant amount of undifferentiated cells persisted even after neural differentiation and resulted in teratoma formation when transplantated into mouse brains. These differentiation-defective hiPSC clones were marked by higher expression of several genes, including those expressed from long terminal repeats of human endogenous retroviruses. These data demonstrated that many hiPSC clones are indistinguishable from hESCs, while some defective hiPSC clones need to be eliminated prior to their application for regenerative medicine.

overall_design: Bisulphite converted DNA from 10 hESCs, 49 hiPSCs, 2 hECCs, 6 somatic cells and 3 cancer cell lines were hybridized to the Illumina Infinium 27k Human Methylation Beadchip.

first: M

last: Koyanagi-Aoi

first: Y

last: Sato


title: Desai OD00079_HCP3_N2_EEMB

first: DCC

last: modENCODE

summary:
modENCODE_submission_3540
This submission comes from a modENCODE project of Jason Lieb. For full list of modENCODE projects, see http://www.genome.gov/26524648
Project Goal: The focus of our analysis will be elements that specify nucleosome positioning and occupancy, control domains of gene expression, induce repression of the X chromosome, guide mitotic segregation and genome duplication, govern homolog pairing and recombination during meiosis, and organize chromosome positioning within the nucleus. 126 strategically selected targets include key histone modifications, histone variants, RNA polymerase II isoforms, dosage-compensation proteins, centromere components, homolog-pairing facilitators, recombination markers, and nuclear-envelope constituents.
We will integrate information generated with existing knowledge on the biology of the targets, perform ChIP-chip analysis on mutant and RNAi extracts lacking selected target proteins, use extrachromosomal arrays to assess the ability of candidate identified sequence motifs to recruit targets in vivo, identify tissue-specific patterns of selected targets, and create integrated, quantitative models of transcription and whole-chromosome functions.
For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODEDataReleasePolicyFinal2008.pdf

overall_design: EXPERIMENT TYPE: CHIP-chip. BIOLOGICAL SOURCE: Strain: N2; Developmental Stage: Early Embryo; Genotype: wild type; Sex: mixed Male and Hermaphrodite population;  NUMBER OF REPLICATES: 2;  EXPERIMENTAL FACTORS: Developmental Stage Early Embryo; temp (temperature) 20 degree celsius; Antibody OD00079 HCP3 (target is HCP-3); Strain N2

first: Reto

last: Gassmann


title: Recurrent inactivation of STAG2 in bladder cancer is not associated with aneuploidy [GPL6984]

status: Public on Oct 24 2013

city: Madrid

first: Enrique

last: Carrillo de Santa Pau

address: C/ Melchor Fernández Almagro, 3

department: Cancer Cell Biology Programme

institute: Spanish National Cancer Research Centre (CNIO)

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

summary: STAG2 is a novel UBC tumor suppressor acting through mechanisms that are different from its role to prevent aneuploidy

overall_design: Gene copy number analyses of STAG2 in urinary bladder tumors. R values were extracted from beadstudio and normalised using the pounds method. Log R Ratios were calculated using an average value of R from 200 cases and controls from the Epicuro study. WaviCGH was used to generate copy number calls and log R ratios in the region of STAG2 on the X chromosome were also visualised manually to determine STAG2 loss.

first: Francisco

middle: X

last: Real

first: Stephen

last: Chanock

first: Daniel

last: Rico

first: Kevin

last: Jacobs

first: Julie

last: Earl

first: David

last: Pisano

first: Alfonso

last: Valencia

first: Nuria

last: Malats


title: DNA methylation data from nasal epithelial cells of human smokers and nonsmokers

status: Public on Oct 01 2013

city: Chapel Hill

first: Rebecca

middle: Catherine

last: Fry

address: 1213 MHRC

department: Environmental Sciences and Engineering

country: USA

institute: UNC-Chapel Hill

summary:
We are investigating the methylation profiles associated with cigarette smoke exposure.
We used arrays to compare the DNA methylation profiles in healthy human smokers and nonsmokers.

overall_design: Nasal epithelial cells were extracted from 12 volunteers (6 smokers, 6 nonsmokers), and grown until fully differentiated. DNA was extracted from samples, and bisulfite converted, hybridized, and scanned to IlluminaMethylation27 BeadChip arrays.

first: Julia

middle: E

last: Rager

last: Bauer

first: Johnny

middle: L

last: Carson

first: Luisa

last: Brighton

first: Ilona

last: Jaspers

middle: C


title: Epigenome analysis of HCC samples with paired adjacent tissue

status: Public on Sep 27 2013

city: Stony Brook

first: Jinyu

last: Li

state: NY

address: 101 Nicolls Rd

department: Cancer Center

institute: Stony Brook University

summary: Genome wide DNA methylation profiling of paired adjacent and hepatocellular samples and 8 non-diseased liver samples. The Illumina Infinium 27k Human DNA methylation Beadchip v1.2 was used to obtain DNA methylation profiles across approximately 27,000 CpGs. Samples included 12 paired adjacent and 12 hepatocellular samples.

overall_design: Bisulphite converted DNA from the 24 samples were hybridised to the Illumina Infinium 27k Human Methylation Beadchip v1.2

first: Kate

last: Revill

first: Tim

last: Wang

first: Scott

last: Powers

first: Richard

middle: S

last: Finn

first: Xintong

last: Chen

first: Kensuke

last: Kojima

first: Yujin

last: Hoshida

first: Josep

last: Llovet


title: Genome-wide methylation analyses in glioblastoma multiforme (GBM)

status: Public on Oct 18 2013

city: Los Angeles

first: Rose

middle: K

last: Lai

state: CA

address: 1441 Eastlake Ave NTT Rm 3407

department: Neurology

institute: U of Southern California

summary: Our main objective was to study genome-wide differential methylation in de novo glioblastoma multiforme (GBM, grade IV glioma). We evaluated CpG sites in gene promoters of 26,000+ genes using an array-based chip. We retrieved 54 GBM from biorepositories of two institutions(40 from Columbia University and 14 from Case Western Reserve University) and 24 control brain tissues from the New York Brain Bank, which collected control brain tissues from consented subjects without history of neurological diseases at autopsy.

overall_design: Bisulfite modified DNA was extracted from 54 GBM and 24 control brain tissue. The HumanMethylation27 Analysis Bead-Chips (Illumina) were used to interrogate 26,486 informative CpG sites in the autosomes.

first: Yanwen

first: Xiaowei

last: Guan

first: Charu

last: Sharma

first: Darryl

last: Nousome

first: Peter

last: Canoll

first: Jeffrey

last: Bruce

first: Andrew

last: Sloan

first: Etty

last: Cortes

first: Jean-Paul

last: Vonsattel

first: Tao

last: Su

first: Lissette

last: Delgado-Cruzata

first: Irina

last: Gurvich

first: Regina

last: Santella

first: Quinn

last: Ostrom

first: Annette

last: Lee

last: Gregersen

first: Jill

last: Barnholtz-Sloan


title: Aberrant silencing of cancer-related genes by CpG hypermethylation occurs independently of their spatial organization in the nucleus

status: Public on Aug 30 2013

city: BALTIMORE

first: hari

last: easwaran

state: MD

address: 1650 Orleans Street, CRB1, Room 530

department: Oncology

institute: Johns Hopkins University

type:
Expression profiling by array
Methylation profiling by array

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

overall_design: Refer to individual Series

first: H

middle: P

last: Easwaran

first: S

middle: B

last: Baylin


title: Genome-wide DNA methylation profiling in cultured eutopic and ectopic endometrial stromal cells (methylation)

status: Public on Sep 07 2013

city: Ube

first: Yoshiaki

last: Yamagata

state: Yamaguchi

address: Minamikogushi 1-1-1

department: Obstetrics and Gynecology

institute: Yamaguchi University School of Medicine

summary: Profiles of genome-wide DNA methylation were investigated in isolated endometrial stromal cells from eutopic and ectopic endometrium. DNA methylation profiles were quite different between eutopic ESC and ectopic ESC, whereas no clear dfference were recognized between eutpic ESC with and without endometriosis.

overall_design: Bisulphite converted DNA from three cultured endometrial stromal cells (ESCs) from eutopic endometria without endometriosis, three ESCs with endometriosis and three ESCs from chocolate cysts were hybridised to the Illumina infinium HumanMethylation27 BeadChip.

first: Koichiro

last: Nishino

first: Eiichi

last: Takaki

first: Shun

last: Sato

first: Ryo

last: Maekawa

first: Akira

last: Nakai

first: Norihiro

last: Sugino


title: MGMT-STP27 methylation status as Predictive Marker for Response to PCV in Anaplastic Oligodendrogliomas and Oligoastrocytomas. A report from EORTC study 26951 [27K]

status: Public on Aug 26 2013

city: Rotterdam

first: Pim

last: French

address: Dr Molewaterplein 50

country: Netherlands

institute: Erasmus MC

summary:
Purpose: The long-term follow-up results from the EORTC-26951 trial showed that the addition of PCV after radiotherapy increases survival in anaplastic oligodendrogliomas/oligoastrocytomas (AOD/AOA). However, some patients appeared to benefit more from PCV treatment than others.

Experimental Design: We performed genome-wide methylation profiling of 115 samples included in the EORTC-26951 trial and extracted the CpG island hypermethylated phenotype (CIMP) and MGMT promoter methylation (MGMT-STP27) status.

Results: We first demonstrate that methylation profiling can be performed on archival tissues with a performance that is similar to snap frozen tissue samples. We then performed methylation profiling on EORTC-26951 clinical trial samples. Univariate analysis indicated that CIMP+ or MGMT-STP27 methylated tumors had an improved survival compared to CIMP- and/or MGMT-STP27 unmethylated tumors (median overall survival (OS) 1.05 v. 6.46 years and 1.06 v. 3.8 years, both P<0.0001 for CIMP and MGMT-STP27 status respectively). Multivariable analysis indicates that CIMP and MGMT-STP27 are significant prognostic factors for survival in presence of age, sex performance score and review diagnosis in the model.Multivariate analysis indicates that CIMP and MGMT-STP27 status are prognostic factors for survival independent of age, sex, performance score and review diagnosis. CIMP+ and MGMT-STP27 methylated tumors showed a clear benefit from adjuvant PCV chemotherapy: the median OS of CIMP+ samples in the RT and RT-PCV arms was 3.27 and 9.51 years respectively P=0.0033; for MGMT-STP27 methylated samples it was 1.98 and 8.65 years. There was no such benefit for CIMP- or for MGMT-STP27 unmethylated tumors. MGMT-STP27 status remained significant in an interaction test (P=0.003). Statistical analysis of microarray (SAM) identified 259 novel CpGs associated with treatment response.

Conclusions: MGMT-STP27 may be used to guide treatment decisions in this tumor type.

overall_design:
Bisulphite converted DNA from the 58 samples were hybridised to the Illumina Infinium 27k Human Methylation Beadchip

The following sample characteristics are provided;
OS: overall survival; PFS: progression free survival; CIMP: CpG Island Methylator phenotype; IGS: Intrinsic Glioma subtype; MGMT: O6-methylguanine-DNA-methyltransferase; OR diagn: original diagnosis; Rev diag: review diagnosis; Tum loc: Tumor location; Perf: Performance score; TRT: treatment
Performance is based on the ECOG performance status
Tum loc: tumor location indicated by 1: Biopsy; 2: Partial Resection; 3: Total Resection.
The MGMT promoter methylation status was determined previously (van den Bent et al, J. Clin Oncol 27: 5881-6, 2009) using MS-MLPA and may differ from the MGMT-SPT27 status.

first: Martin

last: van den Bent

first: Lale

last: Erdem-Eraslan

first: Ahmed

last: Idbaih

first: Johan

last: de Rooi

first: Paul

middle: H

last: Eilers

first: Wim

last: Spliet

first: Wilfred

middle: F

last: den Dunnen

first: Cees

last: Tijssen

first: Pieter

last: Wesseling

first: Peter

last: Sillevis Smitt

last: Kros

first: Thierry

last: Gorlia


title: Genome-wide DNA methylation profiles of human hepatocellular carcinoma

city: Dallas

first: Yujin

last: Hoshida

state: TX

address: 5323 Harry Hines Blvd

institute: University of Texas Southwestern Medical Center

summary:
Introduction: Hepatocellular carcinoma (HCC) is one of the most aggressive solid tumors and oncogenic pathways (e.g Akt, IGF signaling) are often activated in high proliferating HCC. Among several genetic alterations, epigenetic changes seem to be involved in the development and progression of HCC. DNA hypermethylation of promoter regions is almost always associated with transcriptional silencing and can lead to inactivation of tumor suppressor genes (TSG) in cancer cells.
Aim: (1) To identify genes differently methylated in a subclass of HCC associated with proliferation and, (2) To correlate methylation changes with activation of molecular pathways.
Methods: gDNA of 20 HCC, 8 cirrhotic and 8 normal liver samples was extracted and the methylation status was detected by the Illumina HumanMethylation27 BeadChip and immunohistochemistry of p-AKT, pIGF IR, p-S6 was analyzed.
Results: Unsupervised clustering clearly classified normal livers, cirrhosis and HCC in 3 different groups. 961 genes were significantly hypermethylated in HCC compared to cirrhotic and 3942 genes showed hypermethylation in cirrhotic compared to normal liver tissue. 163 genes showed stepwise significant hypermethylation from normal to cirrhotic to HCC, including well  described (p16, SOCS2, SFRP5, RBP1) and potential (SRD5A2, PCDH8, IGF-1R, UCHL1) TSGs,  and the miR-10a. 133 genes were specifically hypermethylated in HCC. Among them the transcription factors GATA2, DLX1, and KLF14, all significantly inversely correlated to gene expression (p=0.003, p=0.03, and p=0.007, respectively). The methylation status of SOCS2 (p=0.025) and DLX1 (p=0.025) was significantly correlated to phosphorylation of IGFR1. Samples with RBP1 hypermethylation showed significantly higher AFP serum levels (p=0.018). Conclusion: Whole genome methylation analysis markedly classifies normal, cirrhotic and HCC samples. 8 TSGs play a key role in this stepwise progression of hypermethylation in the development of HCC and could be a promising point of action in anticancer therapy.

overall_design:
Genomic DNA extracted from fresh frozen tissue specimens and cell lines was hybridized to genome-wide mthylation beadarray after bisulphite treatment.
Keywords: DNA methylation, hepatocellular carcinoma, tissue, cell line

first: Anja

last: Lachenmayer

first: Augusto

last: Villanueva

first: Sasan

last: Roayaie

first: Myron

last: Schwartz

first: Jordi

last: Bruix

first: Vincenzo

last: Mazzaferro

first: Josep

last: Llovet


title: Differential DNA methylation with age displays both common and dynamic features across human tissues that are influenced by CpG landscape [muscle]

status: Public on Aug 16 2013

city: Huntsville

first: Devin

last: Absher

address: 601 Genome Way

institute: HudsonAlpha Institute for Biotechnology

summary:
Genome wide DNA methylation profiling of 4 human tissues of various ages: 51 vastus lateralis samples.The Illumina Infinium 27k Human DNA methylation Beadchip v1.2 was used to obtain DNA methylation profiles across approximately 27,000 CpGs.
Sentrix barcode provided for batch normalization

overall_design: 500ng of genomic DNA was bisulfite converted using EZ-96 DNA Methylation Kit from ZymoResearch, and hybridized to beadcheaps according to Illumina Infinium 27k Human DNA methylation standard procedures.

first: Kenneth

last: Day

first: Lindsay

last: Waite

first: Anna

last: Thalacker-Mercer

first: Andrew

last: West

first: Marcas

last: Bamman

first: James

middle: D

last: Brooks

first: Richard

last: Myers


title: Effect of cigarette smoke on gene expression in mammary epithelial cells [methylation]

status: Public on Aug 12 2013

city: Baltimore

first: Francescopaolo

last: Di Cello

address: 1650 Orleans Street

institute: The Johns Hopkin University School of Medicine

summary: Recent epidemiological studies demonstrate that both active and involuntary exposure to tobacco smoke increases the risk of breast cancer. Little is known, however, about the molecular mechanisms by which tobacco smoke contributes to breast carcinogenesis. To investigate these mechanisms we have analyzed gene expression and methylation in MCF 10A mammary epithelial cells chronically exposed to aqueous cigarette smoke extract (CSE).

overall_design: CSE was prepared weekly and added to the cell cultures at a concentration equivalent to 0.001 cigarettes/ml for 21 weeks. Mock-treated samples were prepared in parallel.

first: Cynthia

last: Zahnow


title: Methylation analysis of normal lymphocytes, HCT116, RKO and SW480

first: hari

last: easwaran

overall_design: In vitro methylated DNA (IVD) generated from normal lymphocytes, HCT116, RKO and SW480 genomic DNA was subjected to sodium bisulfite treatment and the DNA was analyzed for CpG methylation using the Infinium Methylation Array.

first: H

last: Easwaran

first: S

last: Baylin


title: Differential DNA methylation with age displays both common and dynamic features across human tissues that are influenced by CpG landscape [blood]

summary:
Genome wide DNA methylation profiling of 4 human tissues of various ages: 71 human buffy coat samples. The Illumina Infinium 27k Human DNA methylation Beadchip v1.2 was used to obtain DNA methylation profiles across approximately 27,000 CpGs.
Sentrix barcode provided for batch correction

overall_design: Buffy coats obtained from Conversant Bio and genomic DNAs isolated by Agencourt Genfind v2; 1ug of genomic DNA was bisulfite converted using EZ-96 DNA Methylation Kit from ZymoResearch; samples hybridized to beadchips according to Illumina Infinium 27k Human DNA methylation standard procedures


title: Differential DNA methylation with age displays both common and dynamic features across human tissues that are influenced by CpG landscape [brain]

summary:
Genome wide DNA methylation profiling of 4 human tissues of various ages: 78 samples from Brodmann area 19 of the cerebral cortex.The Illumina Infinium 27k Human DNA methylation Beadchip v1.2 was used to obtain DNA methylation profiles across approximately 27,000 CpGs.
Sentrix barcode included for batch normalization

overall_design: 1ug of genomic DNA was bisulfite converted using EZ-96 DNA Methylation Kit from ZymoResearch, and hybridized to beadchips according to Illumina Infinium 27k Human DNA methylation standard procedures


title: Expression data from poplar roots under nitrogen limitation

status: Public on Jul 17 2013

city: Houghton

first: Victor

last: Busov

state: MI

address: 1400 Townsend Drive

department: Forest Resources and Environmental Science

institute: Michigan Technological University

summary: We study the effect of nitrogen limitation on the growth and development of poplar roots. We used microarrays to detail the global program of gene expression underlying morphological and developmental changes driven by low nitrogen in the growth media. We report the effect of nitrogen limitation on the growth and development of poplar roots. Low nitrogen concentration led to increased root elongation followed by lateral root proliferation and finally increased root biomass. These morphological responses correlated with high and specific activation of genes encoding regulators of cell cycle and enzymes involved in cell wall biogenesis, growth and remodeling. Comparative analysis of poplar and Arabidopsis root transcriptomes under nitrogen deficiency indicated many similarities and diversification in the response in the two species. A reconstruction of genetic regulatory network (GRN) analysis revealed a sub-network centered on a PtaNAC1-like transcription factor. Consistent with the GRN predictions, root-specific upregulation of PtaNAC1 in transgenic poplar plants increased root biomass and led to significant changes in the expression of the connected genes specifically under low nitrogen. PtaNAC1 and its regulatory miR164 showed inverse expression profiles during response to LN, suggesting of a micro RNA mediated attenuation of PtaNAC1 transcript abundance in response to nitrogen deprivation.

overall_design: Poplar roots from low nitrogen treated and untreated from in vitro condition was selected for RNA extraction and hybridization on Affymetrix microarrays. Roots were sampled at 6, 12, 24, 48, 96 and 504h after transfer to control and low nitrogen media and RNA was extacted.

first: Yordan

last: Yordanov


title: Expression analysis of uninfected Boechera stricta and infected Boechera stricta with Puccinia monoica forming pseudoflowers using an Arabidopsis thaliana gene expression 4x72K array design from NimbleGen.

status: Public on Sep 01 2013

city: Norwich

first: Liliana

middle: Maria

last: Cano

state: Norfolk

address: Norwich Research Park

country: United Kingdom

institute: The Sainsbury Laboratory

summary: The expression of 30362 plant genes from uninfected flowers of Boechera stricta, uninfected steam and leaves of B. stricta and infected B. stricta with Puccinia monoica forming pseudoflowers. We hybridized cDNA from each sample to an Arabidopsis thaliana gene expression 4x72K format NimbleGen array (ATH6_60mer_expr).

overall_design: We used a eukaryotic gene expression array design No.5048 from NimbleGen (Cat No. A4511001-00-01). Each 5048 array measures the expression level of 30,362 target genes from Arabidopsis thaliana in a 4-plex format 4x72K with with 72,000 probes per array, a total of two probes per target gene, and 60-mer probe length. Total RNA samples recovered from infected leaves of Boechera stricta with Puccinia monoica (pseudoflowers) and uninfected stem and leaves of B. stricta. Experiments included three/two biological repllicates from each sample. We carried out total RNA extractions for all samples using RNAesy Plant Mini Kit (Qiagen, Cat No. 74904). cDNA synthesis was performed by NimbleGen.

first: Sophien

last: Kamoun

first: Sylvain

last: Raffaele


title: poplar estradiol study-TRANSCRIPTOMIC ANALYSIS OF POPLAR STEM ACCOMMODATION TO REPEATED BENDING Species: Populus tremula x Populus aba

status: Public on Jul 01 2013

city: evry

first: stephanie

last: huguet

address: 2 rue gaston cremieux

country: France

institute: inra

summary: affy_pop_2011_08 - poplar estradiol study - genes regulated by PtaZFP2 in absence of mechanical stress - genes regulated by PtaZFP2 after one bending.Species: Populus tremula x Populus alba-The laboratory previously established a poplar transgenic line overexpressing PtaZFP2 under the control of an estradiol-inducible promoter. - the experiment, conducted on 3-month-old hydroponically-grown poplars, consists in the comparison of WT poplars treated with estradiol and the PtaZFP2-overexpressing line treated with estradiol. We also compared unbent and bent PtaZFP2-overexpressing poplars. The applied strain is quantitatively controlled (Coutand & Moulia, 2000, JExpBot; coutand et al., 2009, Plant Physiology)

overall_design: 9 arrays - poplar; time course

first: Stephanie

last: Huguet

first: Alberto

last: Macho

first: Mélanie

last: Decourteix

first: Nathalie

last: Leblanc-fournier

first: Sandrine

last: Balzergue

first: Marie-Laure

last: Martin-Magniette


title: Differential DNA methylation with age displays both common and dynamic features across human tissues that are influenced by CpG landscape

first: Devin

last: Absher

first: Kenneth

last: Day

first: Lindsay

last: Waite

first: Anna

last: Thalacker-Mercer

first: Andrew

last: West

first: Marcas

middle: M

last: Bamman

first: James

last: Brooks

first: Richard

last: Myers


title: Integrated Genetic and Epigenetic Analysis of Childhood ALL Reveals a Synergistic Role for Structural and Epigenetic Lesions In Determining Disease Phenotype [186 samples]

status: Public on Jun 27 2013

city: Memphis

first: Charles

middle: G

last: Mullighan

state: TN

address: 262 Danny Thomas Place

department: Pathology

institute: St Jude Children's Research Hospital

type: Methylation profiling by genome tiling array

summary: Acute lymphoblastic leukemia (ALL), the commonest childhood malignancy, is characterized by recurring gross and submicroscopic structural genetic alterations that contribute to leukemogenesis. Disordered epigenetic regulation is a hallmark of many tumors, and while analysis of DNA methylation of limited numbers of genes or ALL samples suggests epigenetic alterations may also be important, a large-scale integrative genome-wide analysis evaluating DNA methylation in ALL has not been performed. Here, we report an integrated epigenomic, transcriptional and genetic analysis of 167 childhood ALL cases, comprising B-progenitor ALL with hyperdiploidy (N=26), ETV6-RUNX1 (N=27), TCF3-PBX1 (N=9), BCR-ABL1 (N=19), rearrangement of MLL (MLLr) (N=20), rearrangement of CRLF2 (N=11, CRLF2r), deletion of ERG (N=11), miscellaneous or normal karyotype (N=14), and T-lineage ALL (N=30), including 4 MLLr cases and 7 cases with early T-cell precursor immunophenotype. Genome-wide profiling of structural DNA alterations was performed for all cases using Affymetrix 500K and SNP 6.0 arrays. Affymetrix U133A gene expression profiling data was available for 154 cases [GEO Series GSE26281]. Genome-wide methylation profiling was performed using the HELP microarray assay, which measures methylation at approximately 50,000 CpGs distributed among 22,722 Refseq promoters. Methylation data was compared to that of normal pro-B (CD34+CD19+sIg-), pre-B (CD34-CD19+sIg-) and mature B (CD34-CD19+sIg+) cells FACS-sorted from bone marrow of 6 healthy individuals. Unsupervised hierarchical clustering of the top 4043 most variable methylation probesets identified 9 B-ALL clusters with significant correlation to specific genetic lesions including ETV6-RUNX1, MLLr, BCR-ABL1, CRLF2r, TCF3-PBX1 and ERG deletion.  T-ALLs and hyperdiploid B-ALLs also defined specific DNA methylation clusters.  Supervised analysis including limma and ANOVA identified distinct DNA methylation signatures for each subtype. Notably, the strength of these signatures was subtype dependent, with more differentially methylated genes observed in ALL cases with genetic alterations targeting transcriptional regulators (e.g. ETV6-RUNX1 and MLLr) and fewer genes in cases with alterations deregulating cytokine receptor signaling (e.g. CRLF2r). Aberrant DNA methylation affected specific and distinct biological processes in the various leukemia subtypes implicating epigenetic regulation of these pathways in the pathogenesis of these different forms of ALL (e.g. TGFB and TNF in ERG deleted leukemias; telomere and centriole regulation in BCR-ABL1 ALL).  Aberrantly methylated genes were also enriched for binding sites of known or suspected oncogenic transcription factors that might represent cooperative influences in establishing the phenotype of the various B-ALL subtypes. Most importantly, an integrated analysis of methylation and gene expression of these ALL subtypes demonstrated striking inversely correlated expression of the corresponding gene transcripts.   The methylation signatures of each subtype exhibited only partial overlap with those of normal B cells, indicating that the signatures do not simply reflect stage of lymphoid maturation. In a separate approach, we discovered that 81 genes showed consistent aberrant methylation across all ALL subtypes, including the tumor suppressor PDZD2, HOXA5, HOXA6 and MSH2. Inverse correlation with expression was confirmed in 66% of these genes.  These data suggest the existence of a common epigenetic pathway underlying the malignant transformation of lymphoid precursor cells. Integrative genetic and epigenetic analysis revealed hypermethylation of genes on trisomic chromosomes that do not show increased expression, suggesting that epigenetic silencing may control genes within amplified regions and explain why only selected genes are overexpressed. Finally, analysis of individual genes targeted by recurring copy number alterations in ALL revealed a subset of genes also targeted by abnormal methylation, with corresponding changes in gene expression (e.g. ERG, GAB1), suggesting that such genes are inactivated far more frequently than suggested by genetic analyses alone.  Collectively, the data support a key role of epigenetic gene regulation in the pathogenesis of ALL, and point towards a scenario where genetic and epigenetic lesions cooperatively determine disease phenotype.

overall_design: 186 samples were analyzed by DNA methylation on the HELP array, including 167 Diagnostic ALL samples and 19 Normal Bone Marrow B cells. There are no replicates

first: Maria

last: Figueroa

first: Shann-Ching

last: Chen

last: Andersson

first: Letha

middle: A

last: Phillips

first: Yushan

last: Li

middle: R

last: Downing

first: Ari

last: Melnick


title: Fundamental differences in promoter CpG island DNA hypermethylation between human cancer and genetically engineered mouse models of cancer [Methylation profiling by array]

status: Public on Oct 10 2013

city: Seattle

first: Scott

middle: J.

last: Diede

state: WA

address: 1100 Fairview Avenue North, Mailstop c3-168

institute: Fred Hutchinson Cancer Research Center

summary: Genetic and epigenetic alterations are essential for the initiation and progression of human cancer. We previously reported that primary human medulloblastomas showed extensive cancer-specific CpG island DNA hypermethylation in critical developmental pathways. To determine whether genetically engineered mouse models (GEMMs) of medulloblastoma have comparable epigenetic changes, we assessed genome-wide DNA methylation in three mouse models of medulloblastoma. In contrast to human samples, very few loci with cancer-specific DNA hypermethylation were detected, and in almost all cases the degree of methylation was relatively modest compared to the dense hypermethylation in the human cancers. To determine if this finding was common to other GEMMs, we examined a Burkitt lymphoma and breast cancer model and did not detect promoter CpG island DNA hypermethylation, suggesting that human cancers and at least some GEMMs are fundamentally different with respect to this epigenetic modification. These findings provide an opportunity to both better understand the mechanism of aberrant DNA methylation in human cancer and construct better GEMMs to serve as preclinical platforms for therapy development.

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus

overall_design: Genome-wide DNA methylation profiles generated using the Denaturation Analysis of Methylation Differences (DAMD) assay of cancer versus normal samples.

middle: J

first: Zizhen

last: Yao

first: C

last: Keyes

first: Ashlee

last: Tyler

first: Joyoti

last: Dey

first: Christopher

last: Hackett

first: Katrina

last: Elsaesser

last: Kemp

first: Paul

last: Neiman

first: William

last: Weiss

last: Olson

first: Stephen

last: Tapscott


title: Methylation Profiling of Blood DNA from Sibling Discordant for Autism

status: Public on Dec 01 2013

city: Atlanta

first: Benjamin

last: Barwick

state: GA

address: 1365 Clifton Rd. NE WCI-C 4th Floor Benches 36-37

department: Hematology and Medical Oncology

institute: Emory University

summary: Analysis of the methylation level of 27,578 CpG dinucleotides in DNA derived from peripheral blood leukocytes from autistic children and unaffected siblings was conducted using the Illumina HumanMeth27 BeadChip

overall_design: DNA methylation association study for autistic and non-autistic siblings

first: Reid

last: Alisch

first: Pankaj

last: Chopra

middle: T

last: Warren


title: Differential DNA methylation with age displays both common and dynamic features across human tissues that are influenced by CpG landscape [kidney]

first: Devin

last: Absher

summary:
Genome wide DNA methylation profiling of 4 human tissues of various ages: 83 samples of normal adjacent resected kidney tissue .The Illumina Infinium 27k Human DNA methylation Beadchip v1.2 was used to obtain DNA methylation profiles across approximately 27,000 CpGs.
Sentrix barcode provided for batch normalization

overall_design: 1ug of genomic DNA was bisulfite converted using EZ-96 DNA Methylation Kit from ZymoResearch, and hybridized to beadcheaps according to Illumina Infinium 27k Human DNA methylation standard procedures

first: Kenneth

last: Day

first: Lindsay

middle: L

last: Waite

first: Anna

last: Thalacker-Mercer

first: Andrew

last: West

first: Marcas

last: Bamman

first: James

last: Brooks

first: Richard

last: Myers


title: Genome wide methylation array analysis in T-ALL

city: Umeå

first: Sofie

last: Degerman

state: Sweden

address: NUS, Blg 6M, 2nd floor

department: Medical Biosciensces

country: Sweden

institute: Umeå University

summary:
In short: Genome wide promoter DNA methylation profiling of 43 T-ALL samples and 5 T-cell controls (normal bone marrow and stimulated T-cells) . The Illumina Infinium 27k Human DNA methylation Beadchip v1.2 was used to obtain DNA methylation profiles across approximately 27,000 CpGs.
Manuscript abstract:
Background: Treatment of pediatric T-cell acute lymphoblastic leukemia (T-ALL) has improved, but there is a considerable fraction of patients experiencing a poor outcome. There is a need for better prognostic markers and aberrant DNA methylation is a candidate in other malignancies, but its potential prognostic significance in T-ALL is hitherto undecided.
Design and Methods: Genome wide promoter DNA methylation analysis was performed in pediatric T-ALL samples (n=43) using arrays covering >27000 CpG sites. Clinical outcome was evaluated in relation to methylation status and compared with a contemporary T-ALL group not tested for methylation (n= 32).
Results: Based on CpG island methylator phenotype (CIMP), T-ALL samples were subgrouped as CIMP+ (high methylation) and CIMP- (low methylation). CIMP- T-ALL patients had significantly worse overall and event free survival (p=0.02 and p=0.001, respectively) compared to CIMP+ cases. CIMP status was an independent factor for survival in multivariate analysis including age, gender and white blood cell count. Analysis of differently methylated genes in the CIMP subgroups showed an overrepresentation of transcription factors, ligands and polycomb target genes.
Conclusions: We identified global promoter methylation profiling as being of relevance for subgrouping and prognostication of pediatric T-ALL.

overall_design: Bisulphite converted DNA from the 48 samples were hybridised to the Illumina Infinium 27k Human Methylation Beadchip v1.2

first: Magnus

last: Borssen

first: Lars

last: Palmqvist

first: Kristina

last: Karrman

first: Jonas

last: Abrahamsson

first: Mikael

last: Behrendtz

first: Jesper

last: Heldrup

first: Erik

last: Forestier

first: Göran

last: Roos


title: Non-CpG island promoter hypomethylation and miR-149 regulate the expression of SRPX2 in colorectal cancer

status: Public on Jun 15 2013

city: Aarhus N.

first: Claus

middle: Lindbjerg

last: Andersen

address: Brenstrupgaardsvej 100

department: Dept. of Molecular Medicine (MOMA)

country: Denmark

institute: Aarhus University Hospital

summary: We used Illumina Infinium 27k Human DNA Methylation BeadChip v1.2 to assess genome-wide DNA methylation profiling of normal colon epithelial, adenomas and colorectal adenocarcinomas across approximately 27,000 CpGs in fresh frozen colorectal tissue samples. We found that cancer-associated methylation changes with impact on transcription occur nearly as frequent at non-CpG island as CpG island promoters in colorectal cancer (CRC).

overall_design: Samples included 6 normal colon epithelial tissue samples, 6 adenomas, and 30 colorectal adenocarcinomas. Bisulfite-converted DNA from the 42 samples were hybridised to the Illumina Infinium 27k Human Methylation Beadchip v1.2.

first: Bodil

last: Øster

first: Torben

last: Ørntoft


title: Integrated Genetic and Epigenetic Analysis of Childhood ALL Reveals a Synergistic Role for Structural and Epigenetic Lesions In Determining Disease Phenotype

first: Charles

last: Mullighan

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

overall_design: Refer to individual Series


title: Integrated Genetic and Epigenetic Analysis of Childhood ALL Reveals a Synergistic Role for Structural and Epigenetic Lesions In Determining Disease Phenotype [194 samples]

summary: Acute lymphoblastic leukemia (ALL), the commonest childhood malignancy, is characterized by recurring gross and submicroscopic structural genetic alterations that contribute to leukemogenesis. Disordered epigenetic regulation is a hallmark of many tumors, and while analysis of DNA methylation of limited numbers of genes or ALL samples suggests epigenetic alterations may also be important, a large-scale integrative genome-wide analysis evaluating DNA methylation in ALL has not been performed. Here, we report an integrated epigenomic, transcriptional and genetic analysis of 167 childhood ALL cases, comprising B-progenitor ALL with hyperdiploidy (N=26), ETV6-RUNX1 (N=27), TCF3-PBX1 (N=9), BCR-ABL1 (N=19), rearrangement of MLL (MLLr) (N=20), rearrangement of CRLF2 (N=11, CRLF2r), deletion of ERG (N=11), miscellaneous or normal karyotype (N=14), and T-lineage ALL (N=30), including 4 MLLr cases and 7 cases with early T-cell precursor immunophenotype. Genome-wide profiling of structural DNA alterations was performed for all cases using Affymetrix 500K and SNP 6.0 arrays. Affymetrix U133A gene expression profiling data was available for 154 cases. Genome-wide methylation profiling was performed using the HELP microarray assay, which measures methylation at approximately 50,000 CpGs distributed among 22,722 Refseq promoters. Methylation data was compared to that of normal pro-B (CD34+CD19+sIg-), pre-B (CD34-CD19+sIg-) and mature B (CD34-CD19+sIg+) cells FACS-sorted from bone marrow of 6 healthy individuals. Unsupervised hierarchical clustering of the top 4043 most variable methylation probesets identified 9 B-ALL clusters with significant correlation to specific genetic lesions including ETV6-RUNX1, MLLr, BCR-ABL1, CRLF2r, TCF3-PBX1 and ERG deletion.  T-ALLs and hyperdiploid B-ALLs also defined specific DNA methylation clusters.  Supervised analysis including limma and ANOVA identified distinct DNA methylation signatures for each subtype. Notably, the strength of these signatures was subtype dependent, with more differentially methylated genes observed in ALL cases with genetic alterations targeting transcriptional regulators (e.g. ETV6-RUNX1 and MLLr) and fewer genes in cases with alterations deregulating cytokine receptor signaling (e.g. CRLF2r). Aberrant DNA methylation affected specific and distinct biological processes in the various leukemia subtypes implicating epigenetic regulation of these pathways in the pathogenesis of these different forms of ALL (e.g. TGFB and TNF in ERG deleted leukemias; telomere and centriole regulation in BCR-ABL1 ALL).  Aberrantly methylated genes were also enriched for binding sites of known or suspected oncogenic transcription factors that might represent cooperative influences in establishing the phenotype of the various B-ALL subtypes. Most importantly, an integrated analysis of methylation and gene expression of these ALL subtypes demonstrated striking inversely correlated expression of the corresponding gene transcripts.   The methylation signatures of each subtype exhibited only partial overlap with those of normal B cells, indicating that the signatures do not simply reflect stage of lymphoid maturation. In a separate approach, we discovered that 81 genes showed consistent aberrant methylation across all ALL subtypes, including the tumor suppressor PDZD2, HOXA5, HOXA6 and MSH2. Inverse correlation with expression was confirmed in 66% of these genes.  These data suggest the existence of a common epigenetic pathway underlying the malignant transformation of lymphoid precursor cells. Integrative genetic and epigenetic analysis revealed hypermethylation of genes on trisomic chromosomes that do not show increased expression, suggesting that epigenetic silencing may control genes within amplified regions and explain why only selected genes are overexpressed. Finally, analysis of individual genes targeted by recurring copy number alterations in ALL revealed a subset of genes also targeted by abnormal methylation, with corresponding changes in gene expression (e.g. ERG, GAB1), suggesting that such genes are inactivated far more frequently than suggested by genetic analyses alone.  Collectively, the data support a key role of epigenetic gene regulation in the pathogenesis of ALL, and point towards a scenario where genetic and epigenetic lesions cooperatively determine disease phenotype.

overall_design: 194 samples were analyzed by DNA methylation on the HELP array, including 167 Diagnostic ALL samples, 19 Normal Bone Marrow B cell samples, and 8 Normal T lymphocyte cell samples. There are no replicates.

first: Maria

middle: E

last: Figueroa

first: Shann-Ching

last: Chen

first: Anna

last: Andersson

first: Letha

last: Phillips

first: Yushan

last: Li

first: Mondira

last: Kundu

last: Downing

first: Ari

last: Melnick


title: DNA methylation profiling of glioblastoma cancer stem cells

status: Public on May 28 2013

city: Cambridge

first: Esther

last: Rheinbay

state: MA

address: 7 Cambridge Center

institute: Broad Institute

summary: Glioblastoma (GBM) is thought to be driven by a sub-population of cancer stem cells (CSCs) that self-renew and recapitulate tumor heterogeneity, yet remain poorly understood. Here we present a comparative epigenomic analysis of GBM CSCs that reveals widespread activation of genes normally held in check by Polycomb repressors. These activated targets include a large set of developmental transcription factors (TFs) whose coordinated activation is unique to the CSCs. We demonstrate that a critical factor in the set, ASCL1, activates Wnt signaling by repressing the negative regulator DKK1. We show that ASCL1 is essential for maintenance and in vivo tumorigenicity of GBM CSCs. Genomewide binding profiles for ASCL1 and the Wnt effector LEF1 provide mechanistic insight and suggest widespread interactions between the TF module and the signaling pathway. Our findings demonstrate regulatory connections between ASCL1, Wnt signaling and collaborating TFs that are essential for the maintenance and tumorigenicity of GBM CSCs.

overall_design: Epigenomic profiling of glioblastoma stem cells

first: E

first: A

middle: S

last: Chi

first: B

last: Bernstein


title: Genome-wide Identification of Transcriptional Targets of RORA Reveals Direct Regulation of Multiple Genes Associated with Autism Spectrum Disorder

status: Public on May 31 2013

city: Washington

first: Valerie

middle: Wailin

last: Hu

state: DC

department: Biochemistry and Molecular Medicine

institute: The George Washington University School of Medicine and Health Sciences

summary: Background: We have recently identified the nuclear hormone receptor RORA (retinoic acid-related orphan receptor-alpha) as a novel candidate gene for autism spectrum disorder (ASD). Our independent cohort studies have consistently demonstrated the reduction of RORA transcript and/or protein levels in blood-derived lymphoblasts as well as the postmortem prefrontal cortex and cerebellum of individuals with ASD. Moreover, we have also shown that RORA has the potential to be under negative and positive regulation by androgen and estrogen, respectively, suggesting the possibility that RORA may contribute to the male bias of ASD. However, little is known about transcriptional targets of this nuclear receptor, particularly in humans.   Methods: Here we comprehensively identify transcriptional targets of RORA in human neuronal cells using chromatin immunoprecipitation (ChIP), followed by whole-genome promoter array (chip) analysis. Selected potential targets of RORA were then further validated by an independent chromatin immunoprecipitation, followed by qPCR analysis. To further demonstrate that reduced RORA expression results in aberrant transcription of RORA targets, we determined the expression levels of selected transcriptional targets in RORA-deficient human neuronal cells, as well as in postmortem brain tissues from individuals with ASD who exhibit reduced RORA expression.    Results: The ChIP-on-chip analysis reveals that RORA1, a major isoform of RORA protein in human brain, can be recruited to as many as 1,338 genomic locations corresponding to promoter regions of 1,274 genes across the human genome. Among the genes potentially directly regulated by RORA1 are genes known to have biological functions negatively impacted in individuals with ASD, including neuronal adhesion and survival, synaptogenesis, and development of the cortex and the cerebellum. Independent ChIP-qPCR analyses confirm binding of RORA1 to promoter regions of several ASD-associated genes, including A2BP1, CYP19A1, HSD17B10, ITPR1, NLGN1, and NTRK2, whose expression levels are also decreased in RORA1-repressed human neuronal cells and in prefrontal cortex tissues from individuals with ASD.  Conclusion: Findings from this study indicate that RORA transcriptionally regulates A2BP1, CYP19A1, HSD17B10, ITPR1, NLGN1, and NTRK2, and strongly suggest that reduction of this sex hormone-sensitive nuclear receptor in the brain causes dysregulated expression of these genes which, in turn, may contribute to the underlying pathobiology of ASD.

overall_design: Nuclear lysates from the human neuroblastoma cell line SH-SY5Y were chromatin-immunoprecipitated with goat anti-RORA1 antibody vs. normal goat IgG antibody

first: Tewarit

last: Sarachana

middle: W


title: Retained heterodisomy is associated with high gene expression in hyperhaploid inflammatory leiomyosarcoma (Illumina)

status: Public on May 22 2013

city: Lund

first: Karolin

middle: H

last: Nord

address: BMC C13

department: Dept of Clinical Genetics

institute: Lund University

summary: Inflammatory leiomyosarcoma (ILMS) is a soft tissue tumor that morphologically resembles conventional leiomyosarcoma (LMS) admixed with a prominent inflammatory infiltrate. Genetic data on ILMS are still limited but have suggested that this entity is characterized by hyperhaploidy (24-34 chromosomes). This low chromosome number is otherwise uncommon in neoplasia and has been found only in 0.2-0.3% of cytogenetically investigated tumors. Here, three ILMS were investigated using cytogenetic, SNP array and global gene expression analyses. All cases displayed a hyperhaploid origin. Combined with previously reported cases, hyperhaploidy has been found in six of seven cytogenetically investigated ILMS. The copy number distribution of individual chromosomes is clearly nonrandom; the hyperhaploid clones of all six cases displayed disomy for chromosomes 5 and 20, and two copies of chromosomes 18, 21 and 22 were also common. All chromosomes identified as disomic showed a biparental origin by SNP array analysis; whether this is of pathogenetic importance is not known. Compared with conventional LMS, ILMS had a distinct gene expression signature. Furthermore, the number of chromosome copies correlated well with gene expression levels, a finding which has not previously been reported for hyperhaploid tumors. Genes on disomic chromosomes showed higher expression levels in ILMS compared to LMS and disomic chromosomes showed higher average gene expression levels than monosomic chromosomes. Taken together, our findings suggest that disomy for some chromosomes, notably 5 and 20, as well as distorted gene expression balance achieved through massive loss of other chromosomes are essential for the development of ILMS.

overall_design: Tumor DNA was hybridized onto Illumina Human CNV370-Quad v3_C (case 1) and Illumina Human CNV370 v1_C (cases 2 and 3) BeadChips, containing ~370,000 markers, following standard protocols supplied by the manufacturer (Illumina). Data analysis was performed using the GenomeStudio software (Illumina), detecting imbalances by visual inspection.

first: Kajsa

last: Paulsson

first: Srinivas

last: Veerla

first: Johan

last: Wejde

first: Otte

last: Brosjö

first: Nils

last: Mandahl

first: Fredrik

last: Mertens


title: Expression data from two year old newly formed developing xylem and lignified xylem of Populus tomentosa

status: Public on May 16 2013

city: Canberra

first: xiaohui

last: yang

address: Ross

country: Australia

institute: CSIRO

summary: We take the two year old plant for sampling. Use the Affymetrix poplar gene chip to elucidate the gene functions and mechanisms in Populus tomentosa newly formed developing xylem and lignified xylem. We used microarrays to detail the global programme of gene expression in newly formed developing xylem and lignified xylem.

overall_design: Populus tomentosa newly formed developing xylem and lignified xylem were taken for RNA extraction and hybridization on Affymetrix microarrays. CB2009304-A and CB2009304-B from newly formed developing xylem, CB2009304-G and CB2009304-H from lignified xylem.

first: Deqiang

last: Zhang

first: Xiaohui

last: Yang

first: Lu

last: Wang


title: Expression data from Salix matsudana

status: Public on May 07 2013

city: Fuyang, Hangzhou

first: Mingying

last: Liu

state: Zhejiang

address: Daqiao Road 73

department: Research Institute of Subtropical Forestry

country: China

institute: Chinese Academy of Forestry

summary:
Salt responsive genes were identified in chinese willow (Salix matsudana) after the plants were treated with 100 mM NaCl. for 48 hours
We used microarrays to identify genes responsible for combating salt stress. Those up-regulated during the NaCl treatment may protect the plants from damages caused by salt stress.

overall_design: 2 month-old S. matsudana plants which were treated with 100 mM NaCl and control plants were used for RNA extraction and hybridization on Affymetrix microarrays. We sought to obtain salt responsive genes that protect the plants from stress injury.Those differentially expressed genes identified by the microarray would help to understand the mechanism of S. matsudana reacting to salt stress.

first: Renying

last: Zhuo


title: DNA methylation and expression profiling study for bladder cancer [methylation]

status: Public on May 03 2013

city: Daejeon

first: Seon-Kyu

last: Kim

address: 125 Gwahak-ro, Yuseong-gu, Daejeon 305-806, Korea

department: Personalized Genomic Medicine Research Center

country: South Korea

institute: Korea Research Institutue of Bioscience & Biotechnology

summary: The DNA methylation patterns associated with the development and progression of cancer. The aim of the present study was to identify novel methylation markers that can discriminate between normal and Non-muscle-invasive bladder cancer (NMIBC), and between good and poor prognosis using microarray analysis of DNA methylation and RNA expression patterns in NMIBC patients. From the 24 matched microarray-based DNA methylation and gene expression profiling data set, tumor specific hypermethylated genes were selected and clinical relevance of these genes were verified by quantitative PQS analyses. Methylation statues of several genes were significantly associated with decreased gene expression levels and aggressive clinicopathological characteristics. In multivariate regression analyses, hypermethylation of these genes were the independent predictors of recurrence and progression.

overall_design: Genomic DNA was extracted by standard methods using the Wizard Genomic DNA Purification System (Promega, Madison, WI). Total RNA was extracted with TRIzol reagent (Life Technologies, NY) according to the manufacturer’s protocol. Methylation patterns were assayed using the genome-wide Illumina Infinium HumanMethylation27 BeadChip array (Illumina Inc., San Diego, CA). Methylation assays were carried out according to the manufacturer’s protocol. Bisulfite conversion of genomic DNA was performed using the EZ DNA Methylation Kit (Zymo Research, Orange, CA). Fluorescence signals corresponding to C or T nucleotides were measured and the data were used to assign a quantitative measure of methylation level (β value). The β value is a quantitative measure of DNA methylation levels of specific CpGs and ranges from 0 for completely unmethylated to 1 for completely methylated.

first: Hyung-Yoon

last: Yoon

first: Yong-June


title: Genome-wide promoter methylation analysis identifies epigenetic silencing of MAPK13 in primary cutaneous melanoma

status: Public on Apr 24 2013

city: Leiden

first: Linda

last: Gao

address: Einthovenweg 20

department: Dermatology

institute: Leids Universitair Medisch Centrum

summary: The implication of epigenetic alterations in the pathogenesis of melanoma is increasingly recognized. Here we performed genome-wide DNA methylation analysis of primary cutaneous melanoma and benign melanocytic naevus interrogating 14,495 genes using beadchip technology. This first genome-wide view of promoter methylation in primary cutaneous melanoma revealed an array of recurrent DNA methylation alterations with potential diagnostic applications. Among 106 frequently hypermethylated genes there were many novel methylation targets and tumor suppressor genes. Highly recurrent methylation of the HOXA9, MAPK13, CDH11, PLEKHG6, PPP1R3C and CLDN11genes was established. Promoter methylation of MAPK13, encoding p38?, was present in 67% of primary and 85% of metastatic melanomas. Restoration of MAPK13 expression in melanoma cells exhibiting epigenetic silencing of this gene reduced proliferation, indicative of tumor suppressive functions. This study demonstrates that DNA methylation alterations are widespread in melanoma and suggests that epigenetic silencing of MAPK13 contributes to melanoma progression.

overall_design: Bisulphite converted genomic DNA from 5 fresh-frozen benign naevus and 24 fresh-frozen primary melanoma biopsy samples were hybridised to Illumina's Infinium HumanMethylation27 Beadchips

first: Marjon

last: Smit

first: Joost

last: van den Oord

first: Jelle

last: Goeman

first: Els

last: Verdegaal

first: Sjoerd

last: van der Burg

first: Marguerite

last: Stas

first: Samuel

last: Beck

first: Nelleke

last: Gruis

first: Cornelis

middle: P

last: Tensen

first: Rein

last: Willemze

first: Daniel

last: Peeper

first: Remco

last: van Doorn


title: Genome-scale methylome profiling of pheochromocytomas and paragangliomas with Illumina Infinium 27k Human Methylation arrays

status: Public on May 06 2013

city: Paris

first: Eric

last: Letouzé

address: 15 rue de l'école de médecine

institute: Ligue Contre Le Cancer

summary: Genome-scale DNA methylation was analyzed in a large cohort of pheochromocytomas and paragangliomas (PCC/PGL). Consensus clustering identified 3 stable clusters significantly associated with expression subgroups, gene mutations, and clinical parameters.

overall_design: Bisulfite-converted DNA from 145 fresh frozen PCC/PGL and 3 normal adrenal medulla samples were hybridized to Illumina Infinium 27k Human Methylation BeadChips.

first: Anne-Paule

last: Gimenez-Roqueplo

first: Judith

last: Favier


title: Expression data from two year old shoot apex and mature xylem of Populus tomentosa

status: Public on Apr 23 2013

first: xiaohui

last: yang

summary:
We take the two year old plant for sampling.Use the Affymetrix poplar gene chip to elucidate the gene functions and mechanisms in Populus tomentosa shoot apex and mature xylem.
We used microarrays to detail the global programme of gene expression in shoot apex and mature xylem.

overall_design: Populus tomentosa shoot apex and mature xylem were taken for RNA extraction and hybridization on Affymetrix microarrays.CB2009304-C and CB2009304-D from shoot apex, CB2009304-G and CB2009304-H from mature xylem.

first: Deqiang

last: Zhang

first: Xiaohui

last: Yang

first: Lu

last: Wang


title: A family of secreted pathogenesis-related proteins in Candida albicans

status: Public on Mar 25 2013

city: Stuttgart

first: Steffen

last: Rupp

address: Nobelstr. 12

department: MBT

country: Germany

institute: Fraunhofer IGB

summary: Analyzing culture supernatants of yeast and hyphal cells of Candida albicans by mass spectrometry, we found two close homologues of pathogenesis-related (PR-) 1 proteins, Rbe1p and Rbt4p, in the secretome of this human pathogen. By sequence homology, we assigned three yet not characterized open reading frames, ORF19.6200, ORF19.2787 and ORF19.2336, in addition to Rbe1p and Rbt4p to a novel family of proteins. Correspondent with our secretome analysis RBE1 was expressed in blastospores and opaque cells, whereas transcription was down-regulated in hyphae. On the contrary, RBT4 was up-regulated in hyphae and down-regulated in opaque cells. Remarkably, transcription of RBT4 and RBE1 was each up-regulated in blastospores of ∆rbe1 or hyphae of ∆rbt4 deletion strains, respectively, indicating a compensatory function of both proteins.  In a ∆rbe1/∆rbt4 double deletion strain, genome-wide transcriptional analysis showed differential transcription of a limited set of genes that are also implicated in virulence and oxidative stress response. In this context, deletion of RBE1 or RBT4 in a clinical C. albicans isolate resulted in a moderate but significant attenuation in virulence in a mouse model for disseminated candidiasis. However, a synergistic effect was observed in the ∆rbe1/∆rbt4 double deletion strain, where virulence was strongly affected. Furthermore, the double deletion strain showed increased sensitivity to attack by polymorphonuclear leukocytes (neutrophils). Therfore, our data suggest that the crucial contribution of both C. albicans pathogenesis-related proteins for in vivo virulence results at least partially from reduced survival in phagocytes.

overall_design: Experiments were performed under blastospore (YPD) as well as hyphae (alpha-MEM)-inducing conditions. In total, three biological replicates were performed for each condition. All experiments were performed as dye swaps. Thus, in total six arrays have been hybridzed for each comparison (alpha-MEM and YPD, respectively). Hybridization experiments included a reference strain (C. albicans SC5314) and a double deletion strain (C. albicans MRC27). The array included one technical replicate of each probe.

first: Marc

last: Röhm

first: Elena

last: Lindemann

first: Ekkehard

last: Hiller

first: David

last: Ermert

first: Karin

last: Lemuth

first: Dijana

last: Trkulja

first: Ozlem

last: Sogukpinar

first: Herwig

last: Brunner

first: Constantin

middle: F

last: Urban

first: Kai

last: Sohn


title: Genome wide-DNA methylation analysis of articular chondrocytes reveals a cluster of osteoarthritic patients (methylation)

status: Public on Apr 01 2013

city: A Coruña

first: Juan

last: Fernandez Tajes

address: As Xubias

department: Genomics Area

institute: INIBIC

summary:
The aim of this study is to identify, for the first time, the genome-wide DNA methylation profiles of human articular chondrocytes from OA and healtly cartilage samples.
Genome wide DNA methylation profiling of normal and osteoarthritic samples. The Illumina Infinium 27k Human DNA methylation Beadchip v1.2 was used to obtain DNA methylation profiles across approximately 27,000 CpGs in cartilage knee samples. Samples included 18 healthy controls and 23 OA patients.

overall_design: Bisulphite converted DNA from the 31 samples were hybridised to the Illumina Infinium 27k Human Methylation Beadchip v1.2

first: Francisco

last: Blanco

first: Ignacio

last: Rego-Perez

last: Fernández-Tajes


title: Genome-Wide STAT5 binding sites in Kit225 leukemia cells

status: Public on Mar 21 2013

city: Debrecen

first: Zsuzsanna

middle: S.

last: Nagy

address: Nagyerdei krt. 98

department: Biochemistry and Molecular Biology

country: Hungary

institute: University of Debrecen

summary:
In order to systematically map STAT5 genomic binding sites and IL-2 mediated gene expression changes we mapped STAT5 binding sites using chip-on-ChIP in IL-2 dependent Kit225 cells that were either left un-stimulated or stimulated with IL-2 for 30 minutes.
Using MAT analysis we identified 1581 STAT5 binding sites.

overall_design: IL2-stimulated Kit225 cells ChIPed with STAT5 antibodies vs. Input


title: Intermediate- and low-methylation epigenotypes do not correspond to CpG island methylator phenotype (low and -zero) in colorectal cancer.

status: Public on Mar 08 2013

city: Tuebingen

first: Michael

middle: H.

last: Walter

address: Calwer Str. 7

department: Department of Medical Genetics

institute: University of Tuebingen

summary: We performed comprehensive genome-scale DNA methylation profiling by Illumina Infinium HumanMethylation27 of 18 DNA pools that represent 84 colorectal cancer (CRC) samples divided according to their high-, intermediate-, and low-methylation epigenotypes (HME, IME, and LME, respectively) and 3 pools representing 70 normal-adjacent colonic tissues.

overall_design: Bisulphite converted DNA from the 21 DNA pools were hybridised to the Illumina Infinium 27k Human Methylation Beadchip v1.2

first: Pawel

last: Karpinski

first: Elzbieta

last: Szmida

last: Ramsey

first: Blazej

last: Misiak

first: Joanna

last: Kozlowska

first: Marek

last: Bebenek

first: Zygmunt

last: Grzebieniak

first: Nikolaus

last: Blin

first: Lukasz

last: Laczmanski

first: Maria

middle: M

last: Sasiadek


title: ETV1 and ERG genome binding/occupancy profiling by genome tiling array

status: Public on Mar 01 2013

city: Boston

first: Esther

last: Baena

address: 300 Longwood Avenue

department: Hematology/Oncology

institute: Childrens Hospital Boston

summary: Chromosomal rearrangements involving ETS factors, ERG and ETV1, occur frequently in prostate cancer. How these factors contribute to tumorigenesis and whether they play similar in vivo roles remain elusive. We show that ERG and ETV1 control a common transcriptional network but in an opposing fashion. In mice with ERG or ETV1 targeted to the endogenous Tmprss2 locus, either factors cooperated with Pten-loss, leading to localized cancer, but only ETV1 supported development of advanced adenocarcinoma, likely through enhancement of androgen receptor signaling and steroid biosynthesis. Indeed, ETV1 expression promotes autonomous testosterone production, which may contribute to tumor progression to castration-resistant prostate cancer. Patient data confirmed association of ETV1 expression with aggressive disease. We conclude that despite many shared targets, ERG and ETV1 contribute differently to prostate tumor biology. Hence, prostate cancers with these fusions should be considered as distinct subtypes for patient stratification and therapy.

overall_design: Genomic targets of ERG and ETV1 transcription factors were identified by antibody-mediated and biotin-mediated ChIP-chip in human VCaP and LNCaP cells, respectively.

first: Zhen

last: Shao

first: Zhe

last: Li

first: Stuart

last: Orkin


title: DNA Methylation Dynamics in Blood after Hematopoietic Cell Transplant

status: Public on Feb 27 2013

city: Oviedo

first: Ramon

last: Rodriguez

state: Asturias

address: Celestino Villamil s/n

department: Department of Immunology

institute: Hospital Universitario del Principado de Asturias (HUCA)

summary: Classically, epigenetic deregulation is considered a common hallmark of cancer. Nevertheless, recent publications have demonstrated its association with a large array of human diseases such as autoimmune disorders and environmental factors such as diet. Despite the increasing relevance of DNA methylation for the study of critical biological processes and for the development of novel biomarkers, DNA methylation analysis applied to the study of hematopoietic cell transplantation (HCT) has not yet been explored. Here, we analyzed global DNA methylation in blood samples by using a pyrosequencing based methylation assay of repetitive DNA elements (LINE1 and NBL2) in a cohort of 47 patients with allogenic HCT up to 12 months post-HCT. We observed that the recipients stably maintained the donor’s global methylation levels after transplant. Nonetheless, NBL2 methylation is affected by physiopathological events such as development of mixed chimerism. Microarray-based DNA methylation analysis of promoters revealed that methylation in more than 200 genes is altered 1 month post-HCT when compared with non-pathological methylation levels in the donor’s blood. Interestingly, this number dramatically decreased by 6 months post-HCT. Finally, based in the microarray data, we analyzed by pyrosequencing DNA methylation in IFN-γ, FASL, and IL-10 and found a statistically significant association between methylation in these immune genes and the severity of the acute graft-versus-host disease. In conclusion, our results provide strong evidence that DNA methylation changes in blood are linked to underlying physiological events and demonstrate that DNA methylation analysis is a viable strategy for the study of hematopoietic cell transplantation and for development of biomarkers.

overall_design: Bisulphite converted DNA from 6 blood samples were hybridised to the Illumina Infinium 27k Human Methylation Beadchip v1.2

first: R

first: C

last: López-Larrea


title: NID2 and HOXA9 promoter hypermethylation as biomarkers to prevent and detect Oral Cavity Squamous Cell Carcinoma

status: Public on Feb 13 2013

city: Baltimore

first: Rafael

last: Guerrero-Preston

address: 1550 Orleans Street, CRBII, Rm 5M

institute: Johns Hopkins School of Medicine

summary: Differentially methylated oral squamous cell carcinoma (OSCC) biomarkers, identified in-vitro and validated in well-characterized surgical specimens, have shown poor clinical correlation in cohorts with different risk profiles. To overcome this lack of relevance we used the HumanMethylation27 BeadChip, publicly available methylation and expression array data, and Quantitative Methylation Specific PCR to uncover differential methylation in OSCC clinical samples with heterogeneous risk profiles. A two stage-design consisting of Discovery and Prevalence screens was used to identify differential promoter methylation and deregulated pathways in patients diagnosed with OSCC and head and neck squamous cell carcinoma. Promoter methylation of KIF1A (k=0.64), HOXA9 (k=0.60), NID2 (k=0.60), and EDNRB (k=0.60) had a moderate to substantial agreement with clinical diagnosis in the Discovery screen. HOXA9 had 68% sensitivity, 100% specificity and a 0.81 AUC.  NID2 had 71% sensitivity, 100% specificity and a 0.79 AUC. In the Prevalence screen HOXA9 (k=0.82) and NID2 (k=0.80) had an almost perfect agreement with histologic diagnosis. HOXA9 had 85% sensitivity, 97% specificity and a 0.95 AUC.  NID2 had 87% sensitivity, 95% specificity and a 0.91 AUC.  A HOXA9 and NID2 gene panel had 94% sensitivity, 97% specificity and a 0.97 AUC. In saliva from OSCC cases and controls HOXA9 had 75% sensitivity, 53% specificity and a 0.75 AUC.  NID2 had 87% sensitivity, 21% specificity and a 0.73 AUC. This Phase I Biomarker Development Trial identified a panel of differentially methylated genes in normal and OSCC clinical samples from patients with heterogeneous risk profiles. This panel may be useful for early detection and cancer prevention studies.

overall_design: The 12 samples analyzed comprise equal numbers of three tissue-types: Primary oral squamous cell carcinoma, Oral leukoplakia and Normal oral mucosa.  Gender, age and smoking-status were approximately equally represented in these goups.  Normal oral mucosa served as a control.

first: Ethan

last: Soudry

first: Julio

last: Acero

last: Orera

first: Luis

last: Moreno-López

first: Germán

last: Macía-Colón

first: Andrew

last: Jaffe

last: Berdasco

first: Carmen

last: Ili-Gangas

first: Priscilla

last: Brebi-Mieville

first: Yumei

last: Fu

first: Christina

last: Engstrom

last: Irizarry

first: Manel

last: Esteller

first: William

last: Westra

first: Wayne

last: Koch

first: Joseph

last: Califano

first: David

last: Sidransky


title: Aberrant DNA methylation at genes associated with a stem cell-like phenotype in cholangiocarcinoma tumors

status: Public on Jan 01 2013

city: London

first: Wei

last: Dai

address: Du Cane Road

department: Sugery and Cancer

institute: Imperial College London

summary:
Genetic abnormalities of cholangiocarcinoma have been widely studied; however, epigenomic changes related to cholangiocarcinogenesis have been less well characterised. We have profiled the DNA methylomes of 28 primary cholangiocarcinoma and six matched adjacent normal tissues using Infinium’s HumanMethylation27 BeadChips with the aim of identifying gene sets aberrantly epigenetically regulated in this tumour type.
Using a linear model for microarray data we identified 1610 differentially methylated autosomal CpG sites with 809 CpG sites (representing 603 genes) being hypermethylated and 801 CpG sites (representing 712 genes) being hypomethylated in cholangiocarcinoma versus adjacent normal tissues (false discovery rate ≤ 0.05). Gene ontology and gene set enrichment analyses identified gene sets significantly associated with hypermethylation at linked CpG sites in cholangiocarcinoma including homeobox genes and target genes of PRC2, EED, SUZ12 and histone H3 trimethylation at lysine 27. We confirmed frequent hypermethylation at the homeobox genes HOXA9 and HOXD9 by bisulfite pyrosequencing in a larger cohort of cholangiocarcinoma (n = 102).
Our findings indicate a key role for hypermethylation of multiple CpG sites at genes associated with a stem cell-like phenotype as a common molecular aberration in cholangiocarcinoma. These data have implications for cholangiocarcinogenesis, as well as possible novel treatment options using histone methyltransferase inhibitors.

overall_design: Array-based methylation profiling was performed using the Infinium HumanMethylation27 BeadChip in 28 primary cholangiocarcinomas and six matched adjacent normal tissues. The reproducibility of the Infinium HumanMethylation27 BeadChips was evaluated using five technical replicates of the ovarian cancer cell line PEO1. Differential methylation cutoff was estimated from five technical replicates by bootstrap resampling and set at Δβ ≥ 0.15 corresponding to a FDR ≤ 0.05.

first: Ruethairat

last: Sriraksa

first: Constanze

last: Zeller

first: Afshan

last: Siddiq

last: Walley

first: Temduang

last: Limpaiboon

first: Robert

last: Brown


title: Using DNA methylation to detect dysplasia/early neoplasia in Barrett's carcinogenesis

status: Public on Jan 28 2013

first: Muhammad

middle: Abdullah

last: Alvi

address: Addenbrooke's site

institute: University of Cambridge

summary: Dysplasia and early cancer are hard to detect in endoscopic biopsies and hence this study was carried out to evaluate the biomarker potential of DNA methylation to detect dyspasia and early cancer in Barrett's esophaghus patients. Bisulfite converted genomic DNA was hybridized onto Illumina 27k methylation arrays.

overall_design: 22 Barrett's esophagus (BE) and 2 Duodenum vs. 24 esophageal adenocarcinoma (EAC)

middle: A

first: Rebecca

middle: C

last: Fitzgerald


title: Coordinated Chromatin Remodeling induced by Demethylation requires SRCAP mediated H2A.Z exchange [Methylation]

city: Detroit

first: Houtan

last: Noushmehr

address: 2799 W. Grand Blvd

institute: Henry Ford Health System

summary: Genome wide DNA methylation profiling of RKO cells with combination treatments of non-target siRNA or SRCAP siRNA and PBS or 1uM 5-Aza-CdR treatment. The Illumina Infinium 27k Human DNA methylation Beadchip v1.2 was used to obtain DNA methylation profiles across 27,578 CpGs in treated RKO cells. Samples included cells under 4 different treatments. The sample treated with non target siRNA and PBS serves as control sample.

overall_design: Bisulphite converted DNA from the 4 samples were hybridised to the Illumina Infinium 27k Human Methylation Beadchip v1.2

first: Xiaojing

last: Yang

first: Peter

last: Jones


title: affy_popsec_nancy_stomata_poplar -Molecular bases of acclimation and adaptation to water deficit in poplar

status: Public on Feb 28 2013

city: Beaucouze

first: sandrine

last: balzergue

address: Rue G. Morel

institute: INRA

summary:
affy_popsec_nancy_stomata_poplar  - This project aims to identify genes of interest for water deficit acclimation and/or adaptation in a tree species: poplar. We look for genes and gene expression networks related to drought stress. We intend to analyse the transcriptome in laser-microdissected stomata, in two genotypes, Carpaccio and Soligo, at various stages and intensities of stress. In response to water deficit, water loss is adjusted through stomatal conductance. Transcriptome of pure stomatal material should bring valuable information hardly reachable in whole leaf transcriptome analysis. The comparison between medium and severe stress intensities and between early and long term stresses will power the selection of genes of interest. The co-analysis of two genotypes of contrasted tolerance to water deficit should help to discriminate genes presenting a potential adaptative character from genes responding passively to the constraint.-Two poplar clones, Soligo (S) and Carpaccio (C) were submitted to 4 treatments: control, mild water deficit, moderate water deficit (12-day long for both) and early-drought stress (about 36-h long). Growth and physiology was characterised on a batch of plants and samples collected on another batch of plants. Five hundred stomata (one thousand five hundreds guard cells) were laser microdissected in mature leaves of each tree. Stomata from 3 trees (1500) were pooled for total RNAs extraction. A pool is considered as one biological replicate and corresponds to one Affymetrix slide. The two biological replicates originate from the same experiment.

Keywords: treated vs untreated comparison

overall_design: 16 arrays - poplar

first: Sandrine

last: Balzergue

first: Marie-beatrice

last: Bogeat-triboulot

last: Cohen

first: Marie-Béatrice

last: BOGEAT-TRIBOULOT

first: Marie-Laure

last: Martin-Magniette


title: Expression profiling in young spikes of pistillody wheat line compared with normal wheat line

status: Public on Dec 31 2012

city: Yokohama

first: Kanako

last: Kawaura

address: Maioka-cho 641-12

institute: Kihara Institute for Biological Research, Yokohama City University

summary: We have employed whole genome microarray expression profiling to identify genes conferring induction of pistillody, homeotic transformation of stamens into pistil-like structures. As a result, we identified five genes which show higher expression levels in pistillody line compared with normal line. Quantitative expression analysis using real-time PCR indicated that among five genes a calmodulin (CaM)-binding protein gene, WCBP1 (wheat calmodulin-binding protein 1), is obviously up-regulated in the young spikes of the pistillody line. The full-length cDNA sequence for WCBP1 showed it is a member of the ACBP60 family CaM-binding protein.

overall_design: Expression patterns were compared between the pistillody line and normal line. Total RNA samples were isolated from young spikes (3-10mm in length) at floret differentiation stage. Two independent experiments were conducted in each experiments.

first: Koji

last: Murai

first: Yasunari

last: Ogihara


title: Genome-scale DNA methylation profiling of TEL/AML positive childhood acute lymphoblastic leukaemia

city: Clayton

first: Nicholas

last: Wong

state: Victoria

address: Wellington Road

department: Monash Bioinformatics Platform, Central Clinical School

institute: Monash University

summary: DNA methylation profiling of 48 samples to determine a DNA methylation signature specific to leukaemic bone marrow samples. Matching Leukaemia bone marrow and day 28 remission bone marrow or post induction follow up (follow up up to 2 years post induction) genomic DNA were extracted from archived microscope smear slides from 11 children diagnosed with TEL/AML positive Acute Lymphoblastic Leukaemia (ALL). Unmatched bone marrow samples from an additional 8 children were also analysed. Primary tissue control samples from CD34+ and CD19+ bone marrow from adult and childhood samples as well as model cell lines (cancer and non cancerous) were compared to primary diseased samples. Disease specific DNA methylation changes were identified from these results and then verified using SEQUENOM EpiTYPER.

overall_design: A total of 48 samples were analysed by Infinium DNA methylation analysis. As per manufacturer's protocols. Replicates were performed on one primary tumour sample and one cell line sample.


title: Epigenome analysis of  primary uveal melanoma cells, normal uveal melanocytes, neural crest stem cells, embryonic stem cells and uveal melanoma cell lines

status: Public on Feb 14 2013

city: Cleveland

first: Li

last: Zhang

state: OH

address: 9500 Euclid Ave, JJN3

department: Quantitative Health Sciences

institute: CleveLAND CLINIC LERNER COL/MED-CWRU

summary: Genome wide DNA methylation profiling of  primary uveal melanoma cells, normal uveal melanocytes, neural crest stem cells, embryonic stem cells and uveal melanoma cell lines. The Illumina Infinium 27k Human DNA methylation Beadchip Rev B was used to obtain DNA methylation profiles across approximately 27,000 CpGs in the samples. Samples included 58 primary UM, 3 NUM and NCSC controls and 2 cell lines.

overall_design: Bisulphite converted DNA from the 63 samples were hybridised to the Illumina Infinium 27k Human Methylation Beadchip Rev B

first: Saunthararajah

last: Yogen


title: Array-based DNA-methylation profiling of fetal tissues obtained by routine invasive prenatal testing (chorionic and amniotic samples)

status: Public on Dec 14 2012

city: Ulm

first: Ole

last: Ammerpohl

address: Albert-Einstein-Allee 11

institute: UK Ulm

summary: Genome wide DNA methylation profiling of fetal DNA-methylation levels in 47 chorionic villi (CVS) and 16 amniotic cell (AC) samples. The Illumina Infinium 27k Human DNA methylation Beadchip was used to determine DNA methylation profiles across approximately 27,578 CpGs in fetal samples.

overall_design: Bisulphite converted DNA from the 61 samples were hybridised to the Illumina Infinium 27k Human Methylation Beadchip (2 sample in duplicate pairs)

first: O.

first: C

last: Eckmann-Scholz


title: Use of the B cell transcription program results in hypomethylation and overexpression of key genes in EBV-mediated conversion of resting to proliferative B cells

status: Public on Dec 20 2012

city: Cambridge

first: Fatima

last: Al-Shahrour

address: 7 Cambridge Center

department: Cancer program

institute: Broad Institute of MIT and Harvard

summary: We investigated the effects of experimental EBV infection of B cells on DNA methylation profiles by using high-throughput analysis. Remarkably, we observed hypomethylation of around 250 genes, but no hypermethylation. Hypomethylation did not occur at repetitive sequences, consistent with the absence of genomic instability in lymphoproliferative cells. Changes in methylation only occurred after cell divisions started, without the participation of the active demethylation machinery, and were concomitant with acquisition of B cells of the ability to proliferate. Gene ontology analysis, expression profiling, high-throughput analysis of the presence of transcription factor-binding motifs and occupancy revealed that most genes undergoing hypomethylation are active and display the presence of NFkB p65 and other B cell-specific transcription factors. Promoter hypomethylation associated with upregulation of genes relevant for the phenotype of proliferating lymphoblasts. Interestingly, pharmacologically-induced demethylation increased the efficiency of transformation of resting B cells to lymphoblastoid cells, suggesting the establishment of a productive cooperation between hypomethylation and lymphocyte proliferation.

overall_design: Bisulfite-converted DNA from 12 samples (6 Bcell, 6 Bcell immortalized) were hybridized to the Illumina Infinium 27k Human Methylation Beadchip v1.2.

first: Henar

last: Hernando

first: Claire

last: Shannon-Lowe

first: Abul

middle: B

last: Islam

first: Javier

last: Rodriguez-Ubreva

first: Virginia

last: Rodríguez-Cortez

first: Biola

last: Javierre

first: Cristina

last: Mangas

first: Agustín

last: Fernández

first: Maribel

last: Parra

first: Henri

middle: J

last: Delecluse

first: Manel

last: Esteller

first: Eduardo

last: López-Granados

first: Mario

last: Fraga

first: Nuria

last: López-Bigas

first: Esteban

last: Ballestar


title: Seasonal differences in expression patterns of LMPC-enriched poplar wood rays

status: Public on Dec 05 2012

city: Wuerzburg

first: Peter

last: Ache

address: Julius von Sachs Platz 2

institute: Julius von Sachs Institut

summary: Ray cells were enriched from wood samples of poplar (Populus x canescens) by LMPC and transcripts monitored by poplar whole genome microarrays. Results provided insight into molecular processes during the transition from dormancy to flowering in early spring in contrast to the active growth phase in summer.

overall_design: 4 samples of summer (July) 4 of early spring (February) from Populus x canescens field-culture


title: xyleme-Molecular bases of acclimation and adaptation to water deficit in poplar.

status: Public on Dec 15 2012

first: sandrine

last: balzergue

summary:
affy_popsec_orleans_poplar - xyleme - This project aims to identify candidate genes for water deficit acclimation and/or adaptation in a tree species: poplar. Due to compelling evidence that transcriptional regulation plays a major role in regulating many biological processes, we will look for genes and gene expression networks related to drought stress. We intend to analyse the transcriptome in two poplar genotypes of contrasted tolerance to water deficit, at various stages and intensities of stress and simultaneously in whole xylem and cambial zone from young trees. The co-analysis of two genotypes of contrasted tolerance to water deficit should allow to better discriminating genes presenting a potential adaptative character from genes responding passively to the constraint. The consideration of both whole xylem and cambial zone will enable us to discriminate between regulations events originating from very young xylem cells undergoing their first steps of xylem differentiation (cambial zone) compared to whole xylem sample enriched in more differentiated xylem cells and parenchyma ray cells.-Two poplar clones, named Soligo (S) and Carpaccio (C) were submitted to 4 treatments: non-stressed control, severe-drought stress, mild-drought stress and early-drought stress. Two pools of 2 or 3 trees were considered as biological replicates. Two different samples were collected on each individual tree: whole stem xylem (X) and cambial zone plus very young expanding xylem (Y). Total RNAs were extracted from each tree and assemble in pool of 3 or 2 individuals using equimolar ratio for each X and for Y. One affymetrix slide corresponds to one pooled RNA sample (X or Y). A total number of slides : 4 treatments x 2 clones x 2 tissues x 2 biological replicates (pool) = 32 slides, will be done.

Keywords: genotype and ecotype comparison,organ comparison,treated vs untreated comparison

overall_design: 32 arrays - poplar

first: Sandrine

last: Balzergue

first: Jean-Charles

last: Leple

first: Marie-Laure

middle: L

last: Martin-Magniette


title: Integrative analysis reveals relationships of genetic and epigenetic alterations in osteosarcoma [methylation]

status: Public on Dec 06 2012

city: Oslo

first: Leonardo

middle: A.

last: Meza-Zepeda

address: Ullernchausseen 70

department: Dept. of Tumor Biology

institute: The Norwegian Radium Hospital

summary: Osteosarcomas are the most common primary malignant tumours of bone, and almost all conventional osteosarcomas are high-grade tumours showing complex genomic aberrations. We have integrated genome-wide genetic and epigenetic profiles from the EuroBoNeT panel of 19 human osteosarcoma cell lines based on microarray technologies. The cell lines showed complex patterns of DNA copy number changes, where copy number gains were significantly associated with gene-rich regions of the genome and losses with gene-poor areas. Integration of the datasets showed that the mRNA levels were regulated by either alterations in DNA copy number or DNA methylation. Using a recurrence threshold of 6/19 (> 30 %) cell lines, 348 genes were identified as having alterations of two data types (gain or hypo-methylation/over-expression, loss or hyper-methylation/under-expression). These genes are involved in embryonic skeletal system development and morphogenesis, as well as remodelling of extracellular matrix. Several genes were hyper-methylated and under-expressed compared to normal osteoblasts, and expression could be reactivated by demethylation using 5-Aza-2’-deoxycytidine treatment for all four genes tested. Globally, there was as expected a significant positive association between gain and over-expression, loss and under-expression as well as hyper-methylation and under-expression, but gain was also associated with hyper-methylation and under-expression, suggesting that hyper-methylation may oppose the effects of increased copy number for some genes. Integrative analysis of genome-wide genetic and epigenetic alterations identified mechanistic dependencies and relationships between DNA copy number and DNA methylation in terms of regulating mRNA expression levels in osteosarcomas, contributing to better understanding of osteosarcoma biology.

overall_design: Comparison of DNA methylation patterns in 19 osteosarcoma cell lines and 6 normal samples (osteoblasts and bones)

first: Stine

last: Kresse

first: Halfdan

last: Rydbeck

first: Magne

last: Skårn

first: Heidi

last: Namløs

first: Ana

last: Barragan-Polania

first: Anne-Marie

last: Cleton-Jansen

first: Knut

last: Liestøl

first: Eivind

last: Hovig

first: Ola

last: Myklebost


title: Genome-Wide Analysis of DNA Methylation Differences in Muscle and Fat from Monozygotic Twins Discordant for Type 2 Diabetes

status: Public on Dec 10 2012

city: Copenhagen

first: Rasmus

last: Ribel-Madsen

address: Universitetsparken 1

institute: University of Copenhagen

summary: Monozygotic twins discordant for type 2 diabetes constitute an ideal model to study environmental contributions to type 2 diabetic traits. We aimed to examine whether global DNA methylation differences exist in major glucose metabolic tissues from twelve 53–80 year-old monozygotic discordant twin pairs.

overall_design: DNA methylation was measured by the Illumina HumanMethylation27 BeadChip in 22 (11 pairs) skeletal muscle and 10 (5 pairs) subcutaneous adipose tissue biopsies. No replicates were included.

first: Mario

last: Fraga

last: Jacobsen

first: Jette

last: Bork-Jensen

first: Ester

last: Lara

first: Vincenzo

last: Calvanese

first: Agustin

last: Fernandez

first: Martin

last: Friedrichsen

first: Birgitte

last: Vind

first: Kurt

last: Hojlund

first: Henning

last: Beck-Nielsen

first: Manel

last: Esteller

first: Allan

last: Vaag

first: Pernille

last: Poulsen