title: Diurnal transcriptome dynamics of Japanese cedar in summer and winter

status: Public on Sep 29 2014

city: Hitachi

first: Mine

last: Nose

state: Ibaraki

address: 3809-1 Ishi, Juo

institute: Forest Tree Breeding Center

summary:
Investigation of transcriptome dynamics of Japanese cedar (Cryptomeria japonica) in winter (Dec. 22-23, 2011) and summer (July 30-31, 2012).

We investigated seasonal and diurnal transcriptome dynamics of Japanese cedar (Cryptomeria japonica) by analyzing shoot samples collected at four-hour interval for two days in winter and summer, respectively. We first collected sequence data of expressed genes from shoots to designed microarray probes. Microarray analysis revealed the significant difference of transcripts between summer and winter, and the diurnal transcriptome dynamic in summer.Statistical analysis indicated that about 7.7 % of unique genes showed diurnal rhythms with more than two-fold of peak-to-trough amplitude in summer.

overall_design: Summer samples were collected at four-hour interval for two days (12 time points) from three different cuttings as biological repeats (total 36 samples). Winter samples were collected at 4:00/8:00/12:00/16:00/20:00/24:00 on Dec 22 and 12:00/24:00 on Dec 23 (total eight samples).

first: M

first: A

last: Watanabe


title: Genome-wide methylation profiling of multiple sporadic colorectal cancer

status: Public on Sep 01 2014

city: Barcelona

first: Juanjo

last: Lozano

address: C/ Rosselló 153

department: Plataforma de Bioinformatica

country: Spain

institute: CIBEREHD

summary:
Background an Aim: Epigenetics are thought to play a major role in the carcinogenesis of patients that develop multiple colorectal cancers (CRC) in the non-hereditary setting. Previous studies have suggested concordant DNA hypermethylation between tumor pairs. However, only a few methylation markers have been analyzed. This study was aimed at describing the underlying epigenetic signature that differentiates multiple from solitary colorectal cancer tumors using a genome-scale DNA methylation profiling.
Patients and Methods: We used a population-based cohort (EPICOLON II) of 12 patients with synchronous CRC and 29 age- sex- and tumor location-paired solitary CRC patients. DNA methylation profiling was performed using the Illumina Infinium HM27 DNA methylation assay.  The most significantly hypermethylated CpG sites results were validated by Methylight. Tumors samples were also analyzed for the CpG Island Methylator Phenotype (CIMP) using the Infinium DNA methylation data; KRAS and BRAF mutations; microsatellite instability; and immunohistochemistry for MLH1/MSH2/MSH6/PMS2. Functional annotation clustering of differentially methylated genes between multiple and solitary CRCs was performed.
Results: We identified 102 CpG sites that showed significant DNA hypermethylation in multiple versus solitary tumors (difference in β value >0.1 and p<0.05). Methylight assays validated the array results for 4 selected significantly hypermethylated genes (MAP1B, HTRA1, ALOX15, TIMP3) identified in the profiling (p=0.0002). Based on the Infinium data, 8/12 (66.6%) of multiple tumors were classified as CIMP-high, as compared to 5/29 (17%) solitary tumors (p=0.004). CIMP-high tumors displayed significant hypermethylation in 301 CpG sites (difference in β value >0.1; p value <0.05). Interestingly, 76/102 (74.5%) of the hypermethylated CpG sites found in multiple vs. solitary tumors were also seen to be hypermethylated in CIMP-H tumors. Functional analysis of hypermethylated genes found in multiple vs. solitary tumors showed the presence and enrichment of genes involved in different tumorigenic functions.
Conclusions: Multiple colorectal cancers are associated with a distinct methylation phenotype, with a close association between tumor multiplicity and CIMP-high. Our results may be important to unravel the underlying mechanism of tumor multiplicity in the non-hereditary scenario, and provide novel potential biomarkers for identifying high-risk patients and tailoring surveillance strategies.

overall_design: We used a population-based cohort (EPICOLON II) of 12 patients with synchronous CRC and 29 solitary CRC patients. DNA methylation profiling was performed using the Illumina Infinium HM27 DNA methylation assay.

first: V

last: Gonzalo

last: Alonso

first: J

middle: J

first: F

last: Balaguer


title: Opposing Effects of HIF1α and HIF2α on Chromaffin Cell Phenotypic Features and Tumor Cell Proliferation: Insights from MAX [rat]

status: Public on Sep 18 2014

city: Madrid

first: Mercedes

last: Robledo

state: Madrid

address: C/ Melchor Fernández Almagro, 3

department: Human Cancer Genetics Program

institute: Spanish National Cancer Research Centre (CNIO)

summary: Pheochromocytomas and paragangliomas (PPGLs) are catecholamine-producing tumors with diverse phenotypic features reflecting mutations in numerous genes, including MYC-associated factor X (MAX). To establish whether PPGL phenotypic differences reflect a MAX-mediated mechanism and opposing influences of HIF2α and HIF1α, we combined observational investigations in PPGLs and gene-manipulation studies in two pheochromocytoma cell lines. In cell lines lacking Max, re-expression of the gene resulted in maturation of phenotypic features and decreased cell cycle progression. In cell lines lacking Hif2α, overexpression of the gene led to immature phenotypic features, failure of dexamethasone to induce differentiation and increased proliferation. HIF1α has opposing actions to HIF2α. These model systems explain the features observed in PPGLs due to mutations of MAX and other PPGL susceptibility genes.

overall_design: PC12 cell lines were cultured, one transfected with an emply vector (PC12wt) and the other transfected with an expression plasmid coding the MAX gene. In total four samples were hybridized, each experimental condition had two biological replicates obtained at two different cell passages (8 and 13).

last: Qin

first: Aguirre

last: Andres de Cubas


title: A functional portrait of Med7 and the Mediator complex in Candida albicans [ChIP-chip]

city: Québec

first: Faiza

last: Tebbji

address: 2705 Boulevard Laurier

country: Canada

institute: CHU Québec

type: Genome binding/occupancy profiling by genome tiling array

summary: In this study, we have investigated Mediator function in the human fungal pathogen C. albicans. An initial screening of conditionally regulated Mediator subunits showed that the Med7 of C. albicans was not essential, in contrast to the situation noted for Saccharomyces cerevisiae. While loss of CaMed7 did not lead to loss of viability under normal growth conditions, it dramatically influenced the pathogen’s ability to grow in different carbon sources, to form hyphae and biofilms, and to colonize the gastrointestinal tracts of mice. We used location profiling to determine Mediator binding under yeast and hyphal morphologies characterized by different transcription profiles. We observed a core set of specific and common genes bound by Med7 under both conditions; this specific core set is expanded considerably during hyphal growth, supporting the idea that Mediator binding correlates with changes in transcriptional activity and that this binding is condition specific. Med7 bound not only in the promoter regions of active genes but also of inactive genes and within coding regions and at the 3’ ends of genes. By combining genome-wide location profiling, expression analyses and phenotyping, we have identified different Med7 regulons including genes related to glycolysis and the Filamentous Growth Regulator family.

overall_design: We performed genome-wide occupancy experiments (YPD, 30oC and YPD, 37oC) with Med7p to determine its binding sites.

first: Yaolin

last: Chen

first: Julien

middle: R

last: Albert

first: Kearney

middle: T

last: Gunsalus

first: Carol

middle: A

last: Kumamoto

first: André

last: Nantel

first: Adnane

last: Sellam

first: Malcolm

last: Whiteway


title: A functional portrait of Med7 and the Mediator complex in Candida albicans [expression]

overall_design:
We performed a transcription profile with an med7 Grace strain under yeast and hyphae conditions (YPD +/- tet, 30oC and YPD +10% serum +/- tet, 37oC, respectively).
We used the Med7 tetracycline-repressible mutant to determine the transcriptional consequence of Med7 depletion by tetracycline; we measured the transcriptional differences between Med7 cells growing in YPD at 30°C in the presence and absence of tetracycline using whole-genome microarrays. Using a statistical-significance analysis with an estimated false-discovery rate of 5%, in addition to a cutoff of 1.5-fold, we identified 140 genes that require Med7p for their proper expression; 56 genes were up-regulated and 84 were down-regulated. Because of the wrinkled colony morphology and the evidence for changes in the expression of gene sets implicated in the hyphal transition, we also investigated the impact of the tet-repressed allele of MED7 on gene expression under hyphal growth conditions. We performed a Med7 conditional mutant expression profiling under the hyphal-inducing conditions of 37°C in the presence of 10% serum. Using a statistical-significance analysis with an estimated false-discovery rate of 5%, in addition to a cutoff of 1.5-fold, we identified 521 genes that require Med7p for their proper expression, including 261 up-regulated genes and 260 down-regulated genes.


title: A functional portrait of Med7 and the Mediator complex in Candida albicans

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

overall_design: Refer to individual Series


title: Modulation of miR-29 Expression by Alpha-fetoprotein is linked to the Hepatocellular Carcinoma Epigenome

status: Public on Sep 23 2014

city: Bethesda

first: Xin

middle: Wei

last: Wang

state: MD

address: 37 Convent Drive

department: Laboratory of Human Carcinogenesis

country: USA

institute: National Cancer Institute

type: Methylation profiling by genome tiling array

summary: Globally, hepatocellular carcinoma (HCC) accounts for 70-85% of primary liver cancers and ranks second in the leading cause of male cancer death. Serum alpha-fetoprotein (AFP), normally highly expressed in the liver only during fetal development, is reactivated in 60% of HCC tumors and associated with poor patient outcome. We hypothesize that AFP+ and AFP- tumors differ biologically. Using microarray-based global microRNA profiling in 223 HCC patients, we found that members of the miR-29 family were the most significantly (p<0.001) down-regulated miRNAs in AFP+ tumors. Consistent with miR-29's role in targeting DNA methyltransferase 3A (DNMT3A), a key enzyme regulating DNA methylation, we found a significant inverse correlation (p<0.001) between miR-29 and DNMT3A gene expression suggesting that they might be functionally antagonistic. Moreover, global DNA methylation array profiling reveals that AFP+ and AFP- HCC tumors have distinct global DNA methylation patterns and that increased DNA methylation is associated with AFP+ HCC. Interestingly, miR-29 family physiological expression is low in mouse embryonic livers but gradually increases after birth. This is in contrary to AFP expression, which dramatically decreases after birth. Experimentally, we demonstrated that increased AFP expression, or conditioned media from AFP expressing HCC cells, inhibits miR-29a expression in AFP- HCC cells. AFP also inhibited transcription of the miR-29a/b-1 locus and this effect is mediated through c-MYC binding to the miR-29a/b-1 promoter. Our findings indicate that tumor biology differs considerably between AFP+ HCC and AFP- HCC and that AFP is a functional antagonist of miR-29, which may contribute to global epigenetic alterations and poor prognosis in HCC.

overall_design: Illumina Human BeadChip Methylation microarrays were completed on 48 tumor HCC tissues.


title: Madin-Darby canine kidney cells expression array

status: Public on Aug 14 2014

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

institute: IDIBELL

summary:
cDNA expression array of epithelial phenotype untreated MDCK cells; after 30 days of TGFb treatment, which induces a mesenchymal phenotype; TGF-b-treated cells that are treated with 5-AZA for 72 h; and 30 days after TGFb withdrawal
Gene expression was analyzed in a genome-wide manner, to asses those changes occurring upon TGF-b-induced epithelial to mesenchymal transition (EMT), those that are stimulated by treatment with a demethylating agent, and which are restored after TGF-b withdrawal

overall_design: Two replicates for untreated and TGFb treated, and one sample for 5-AZA and TGFb withdrawal

last: Carmona

middle: M

last: Davalos

first: M


title: Gene expression profile after injection of rhabdoviral recombinant protein NV

status: Public on Aug 11 2014

first: Julio

last: Coll

address: crt Coruna km7

department: Biotechnology

institute: INIA

summary: Due to the common presence of a non-virion NV gene absent from other fish rhabdoviruses, NV-coding rhabdoviruses, such as the viral haemorrhagic septicemia (VHSV), were placed into a new Novirhabdovirus genus. Because conflicting results do exist on the importance of NV for VHSV trout pathogenicity and the NV function is still unclear, the effects of intraperitoneal injection of recombinant NV protein were studied by using home-designed immune-related microarrays from rainbow trout Oncorhynchus mykiss.  The results were compared with parallel experiments using bacterial flagellins, a well know mammalian agonist of toll receptors (tlr5) with adjuvant activity recently described also in fish

overall_design: Four experimental groups were formed with four biological replicates each, 16 samples in total. First one was injected with NV recombinant protein in PBS, second one was a control group injected with PBS, the third group was injected with bacterial flagellins in PBS and the fourth group was injected with polihistidine peptide as a reference group because the recombinant proteins have a polihistidine tail. There is a technical replicate within each array.


title: A database of circadian and diel rhythmic gene expression in the yellow fever mosquito Aedes aegypti

status: Public on Aug 19 2014

city: Notre Dame

first: Matthew

last: Leming

state: IN

address: 100 Galvin Life Sciences Center

department: Biological Sciences

institute: University of Notre Dame

summary: The mosquito Ae. aegypti is responsible for the transmission of many diseases including yellow fever and Dengue fever. This species exhibits many behaviors that are under diel and circadian control. However, there has been little reporting on gene expression rhythmicity. To study how gene expression is globally regulated by diel and circadian mechanisms, we have undertaken a DNA microarray analysis of Ae. aegypti head and bodies under 12:12 light:dark cycle (LD) and constant dark (DD, free-running) conditions. Zeitgeber Time (ZT) with ZT12 defined as the initiation of the one hour dusk period under the light:dark cycle, and ZT0 defined as beginning of the one hour dawn period. Circadian Time (CT) with CT0 defined as subjective dawn, inferred from ZT0 of the previous light:dark cycle.

overall_design: This is a 12-plex high definition NimbleGen array design. The Higgs White Eye (Wh) strain of Aedes aegypti was investigated for rhythmic expression during the light/dark phase and constant darkness. Samples were collected every 4 hours for 44 hours in each treatment, and RNA collected from whole head tissue of females that were presumed mated.

first: S

middle: C

last: Rund

middle: K

last: Behura

first: G

middle: E

last: Duffield

last: O'Tousa


title: Differential expression analysis between litR (TTHB100) deletion mutant and wild-type of Thermus thermophilus HB8 under the dark condition.

status: Public on Aug 17 2014

city: Hyogo

first: Akeo

last: Shinkai

address: 1-1-1, Kouto, Sayo

department: SPring-8 Center

country: Japan

institute: RIKEN Harima Institute

summary: We observed the expression profile of the total mRNA of litR (TTHB100) deletion mutant of T. thermophilus HB8 strain grown in a rich (TM) medium at 60 °C under the dark condition compared with that of wild-type.

overall_design: Three wild-type strain of T. thermophilus HB8 were pre-cultured at 60 °C for 16 hours in 100 mL of TM medium containing 0.8% polypeptone, 0.4% yeast extract, 0.2% NaCl, 0.4 mM CaCl2, and 0.4 mM MgCl2, which was adjusted to pH 7.5 with NaOH. The cells (1 mL) were inoculated into 100 mL of the synthetic medium and then cultivated at 60°C for 8 hours under dark condition. Then the 1.0 mM of ZnSO4 was added into the medium, and continued cultivation. Cells were collected, and then, the expression of each mRNA was analyzed.

first: Hideaki

last: Takano

first: Yoshihiro

last: Agari

first: Kenji

last: Ueda

first: Seiki

last: Kuramitsu


title: Nucleosome positioning in A549 cells before/after NME2 induction

status: Public on Aug 04 2014

city: Delhi

first: Vinod

middle: Kumar

last: Yadav

state: Delhi

address: Mall Road

department: Bioinformatics

country: India

institute: IGIB

summary: Previous studies have analyzed patterns of transcription, transcription factor (TF) binding or mapped nucleosome occupancy across the genome. These suggest that the three aspects are genetically connected but the cause and effect relationships are still unknown.  For example, physiologic TF binding studies involve many TFs, consequently, it is difficult to assign nucleosome reorganization to the binding site occupancy of any particular TF. Therefore, several aspects remain unclear: does TF binding influence nucleosome (re)organizations locally (in close vicinity of their binding sites) or impact the chromatin landscape at a more global level; are all or only a fraction of TF binding a result of reorganization in nucleosome occupancy; finally, do all TF binding and associated nucleosome occupancy changes result in altered gene expression? With these in mind, we sought to study a single TF that induces physiological changes, and following characterization of the two states (before and after induction of the TF) we determined: (a) genomic binding sites of the TF, (b) promoter nucleosome occupancy and (c) transcriptome profiles, independently in both conditions. Results demonstrate that TF binding influences expression of the target gene only when it is coupled to nucleosome repositioning at or close to its binding site, and not when transcription factor binding occurs without local associated nucleosome reorganization.

overall_design: The nature of interaction between TF binding and nucleosomes and what extent it influences transcription

first: Aradhita

last: Baral

first: Ram

last: Thakur

first: Ankita

last: Singh

first: Akinchan

last: Kumar

first: Shantanu

last: Chowdhury


title: DNA methylation profile in well-differentiated cancer uncoves another source of diagnostic and prognostic markers

status: Public on Jul 31 2014

first: Mercedes

last: Robledo

summary: By characterizing at the genome-wide level the DNA methylation patterns of the largest series of well-differentiated thyroid tumors described to date, we provide novel insights into the biology underlying on the one hand the histological heterogeneity, and on the other differential patient outcomes of this disease. We describe distinct subtype- and mutational-specific methylation profiles as well as novel markers associated with recurrence-free survival, which could provide an improved classification of patients.

overall_design: Bisulphite converted DNA from the 83 primary thyroid tumor samples and 8 adjacent normal tissue samples were hybridized to the Illumina Infinium 27k Human Methylation Beadchip v1.2

first: Veronika

last: Mancikova

first: Raquel

last: Buj


title: Methylation analysis of locally advanced breast tumors treated with two drugs-doxorubicin and 5-fluorouracil

status: Public on Jul 25 2014

city: Oslo

first: Jovana

last: Klajic

address: Ullernchauseen 70

department: Genetics

country: Norway

institute: OUS/Radium Hospital

summary: Genome wide DNA methylation profiling of locally advanced breast tumors before and after treatment with doxorubicin and 5-fluorouracil Mitomycin C

overall_design: Bisulphite converted DNA from the 33 paired tumor samples and 9 normal samples were hybridised to the Illumina Infinium 27k Human Methylation Beadchip v1.2. After preprocessing, seven paired samples treated with doxorubicin were excluded due to low methylation levels, resulting in 26 paired tumor samples that were further analyzed.


title: Regulation of DNA methylation by CK2-mediated phosphorylation of DNMT3A (Beadchip)

status: Public on Jul 17 2014

city: Bruxelles

first: Matthieu

last: Defrance

address: CP614 route de Lennik 808

country: Belgium

institute: Université Libre de Bruxelles

summary: DNA methylation is a central epigenetic modification that has essential roles in cellular processes including chromatin structure, gene regulation, development and disease. The de novo DNA methyltransferases are responsible for the generation of genomic methylation patterns, but the underlying mechanisms are still poorly understood. Here, we show that phosphorylation of DNMT3A by the CK2 protein kinase regulates the establishment of DNA methylation patterns. We find that DNMT3A is phosphorylated by CK2 at two key residues located near its PWWP domain. We observed that, through phosphorylation of these residues, CK2 negatively regulates DNMT3A’s ability to methylate DNA and consistent with this, CK2 was found to decrease overall genomic level of 5-methylcytosine. Further, genome-wide DNA methylation analysis in CK2-depleted cells revealed that CK2 affects primarily CpG methylation of several heterochromatin repeats as well as Alu elements. Along these lines, we found that CK2-mediated phosphorylation of DNMT3A was required for its proper heterochromatin localization. Our results define phosphorylation as a new mode of regulation of de novo DNA methyltransferase function. These findings further uncover a previously unrecognized mechanism for the regulation of methylation at repetitive elements. They shed new light into the origin of DNA methylation patterns.

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

first: Rachel

last: Deplus

first: Loïc

last: Blanchon

first: Arumugam

last: Rajavelu

first: Halim

last: Boukaba

first: Judith

last: Luciani

first: Sarah

last: Dedeurwaerder

first: Arie

middle: B

last: Brinkman

first: Femke

last: Simmer

first: Fabian

last: Müller

first: Maria

last: Berdasco

first: Pascale

last: Putmans

first: Emilie

last: Calonne

first: David

middle: W

last: Litchfield

first: Yvan

last: de Launoit

first: Tomasz

middle: P

last: Jurkowski

first: Hendrik

middle: G

last: Stunnenberg

first: Christoph

last: Bock

first: Mario

middle: F

last: Fraga

first: Manel

last: Esteller

first: Albert

last: Jeltsch

first: François

last: Fuks


title: Transcriptomic analysis of F. oxysporum Δcon7-1 mutant during in vitro growth

status: Public on Jul 10 2014

city: Cordoba

first: Carmen

last: Ruiz Roldan

address: Campus de Rabanales

institute: University of Cordoba

summary: Previous studies have demonstrated the essential role of morphogenetic regulation in Fusarium oxysporum pathogenesis, including processes such as cell-wall biogenesis, cell division and differentiation of infection-like structures. We identified three F. oxysporum genes encoding predicted transcription factors showing significant identities to Magnaporthe oryzae Con7p, Con7-1, plus two identical copies of Con7-2. Targeted deletion of con7-1 produced non-pathogenic mutants with altered morphogenesis, including defects in cell wall structure, polar growth, hyphal branching and conidiation. By contrast, simultaneous inactivation of both con7-2 copies caused no detectable defects in the resulting mutants. Comparative microarray-based gene expression analysis indicated that Con7-1 modulates the expression of a large number of genes involved in different biological functions, including host-pathogen interactions, morphogenesis and development, signal perception and transduction, transcriptional regulation and primary and secondary metabolism. Taken together, our results points to Con7-1 as general regulator of morphogenesis and virulence in F. oxysporum.

overall_design: Con7-1 dependent gene expression in Fusarium oxysporum wt and  Δcon7-1 mutant was measured after shifting the mycelia to PDB pH5.0 for 30 min and the transferred to PDB pH7.0 for 30 min. Three independent experiments were performed.

last: Ruiz-Roldán

first: Yolanda

last: Pareja-Jaime

first: José

last: González-Reyes

first: MIsabel

last: Roncero


title: Comprehensive Analysis of Preeclampsia-Associated DNA Methylation in the Placenta

status: Public on Jul 12 2014

city: Pittsburgh

first: David Peter

middle: G.

last: Peters

state: PA

address: 204 Craft Avenue

department: Department of Obstetrics, Gynecology and Reproductive Sciences

institute: University of Pittsburgh/Magee-Womens Research Institute

summary: Background: A small number of recent reports have suggested that altered placental DNA methylation may be associated with early onset preeclampsia. It is important that further studies be undertaken to confirm and develop these findings. We therefore undertook a systematic analysis of DNA methylation patterns in placental tissue from 24 women with preeclampsia and 24 with uncomplicated pregnancy outcome.   Methods: We analyzed the DNA methylation status of approximately 27,000 CpG sites in placental tissues in a massively parallel fashion using an oligonucleotide microarray. Follow up analysis of DNA methylation at specific CpG loci was performed using the Epityper MassArray approach and high-throughput bisulfite sequencing.  Results: Preeclampsia-specific DNA methylation changes were identified in placental tissue samples irrespective of gestational age of delivery. In addition, we identified a group of CpG sites within specific gene sequences that were only altered in early onset-preeclampsia (EOPET) although these DNA methylation changes did not correlate with altered mRNA transcription. We found evidence that fetal gender influences DNA methylation at autosomal loci but could find no clear association between DNA methylation and gestational age.   Conclusion: Preeclampsia is associated with altered placental DNA methylation. Fetal gender should be carefully considered during the design of future studies in which placental DNA is analyzed at the level of DNA methylation. Further large-scale analyses of preeclampsia-associated DNA methylation are necessary.

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


title: Methylomic analysis identifies epigenetically silenced genes and implies an activation of β-catenin signal in cervical cancer

status: Public on Jun 26 2014

city: Taipei

first: Hung-Cheng

last: Lai

address: No.250, Wuxing St.

department: Department of Obstetrics and Gynecology, School of Medicine, College of Medicine,

country: Taiwan

institute: Taipei Medical University

summary: Using the pools of DNA from squamous cervical carcinomas (SCC) and DNA from normal scraping cells discovered the abnormal changes of genomic wide methylation  by methylation BeadChip. The 61 genes were selected to validate by quantitative methylation specific PCR (qMSP) and bisulfite pyrosequencing in further processes. A CpG islands methylator phenotype (CIMP) was confirmed at 14 candidates in an independent set contained a spectrum of scraping cells form abnormal cervical lesions. In addition, we found among of 7 genes were announced to imply to potentially biological functions of β-catenin signal.

overall_design: A pool DNA collected from equal amount of DNA of 38 SCC, and the other pool collected from equal amount of DNA of 19 normal cervical scraping cells. Based on 40 percent of different methylation in two pools of samples, we selected 91 genes  showed abnormal methylation in SCC. After the confirmation of gene restored expression in cervical cell lines, there 61 genes showed upregulation in the treatment with demethylating drug.  In addition, gel based of MSP were contributed to confirm in a small size of samples, and quantitative MSP was contributed to validated in an independent set. The methylation status of qMSP was also confirmed by bisulfite pyrosequence. Finally, we selected 14 genes demonstrated clinical relevance in the high methylation of CIMP associated to a risk factor in  cervical intraepithelial neoplasia grade 3 (CIN3) and worse lesions. isk factor in  cervical intraepithelial neoplasia grade 3 (CIN3) and worse lesions.

first: Yu

last: Chen

first: Rui

middle: L

last: Huang

last: Laio

first: Po

middle: H

last: Su

first: Hui

last: Wang

first: Hung

first: Y


title: Epigenome analysis of normal colon mucosa samples

status: Public on Jul 01 2014

city: Basel

first: Faiza

last: Noreen

address: Mattenstrasse 28

department: Department of Biomedicine

country: Switzerland

institute: University of Basel

summary: To investigate whether lifestyle factors modulate the stability of gene promoter methylation in the normal aging colonic mucosa, we performed genome-scale DNA methylation profiling of 178 normal colon biopsies using the Illumina Infinium DNA methylation assay, which assesses the DNA methylation status of 27,578 CpG sites located at the promoter regions of 14,495 protein-coding genes. We identified Aspirin use and hormonal replacement therapy (HRT) suppress, whereas a high body mass index (BMI) and smoking promote age-related hyermethylation. Many of these loci modulated by lifestyle in the healthy colon mucosa coincide with loci hypermethylated in colorectal cancers and down-regulated in adenomas. The data show that lifestyle modulates the stability of DNA methylation in the aging colonic epithelium and thereby impacts the rate of evolution of cancer methylomes.

overall_design: Bisulphite converted DNA from the 178 samples were hybridised to the Illumina Infinium 27k Human Methylation Beadchip v1.2

first: Martin

last: Röösli

first: Pawel

last: Gaj

first: Jakub

last: Pietrzak

first: Stefan

last: Weis

first: Patric

last: Urfer

first: Jaroslaw

last: Regula

first: Primo

last: Schär

first: Kaspar

last: Truninger


title: Pesticide Methoxychlor Promotes the Epigenetic Transgenerational Inheritance of Adult-Onset Disease through the Female Germline

status: Public on May 30 2014

city: Pullman

first: Michael

last: Skinner

state: WA

address: Abelson 507

department: SBS

institute: WSU

summary: Environmental compounds including fungicides, plastics, pesticides, dioxin and hydrocarbons can promote the epigenetic transgenerational inheritance of adult-onset disease in future generation progeny following ancestral exposure during the critical period of fetal gonadal sex determination. This study examined the actions of the pesticide methoxychlor to promote the epigenetic transgenerational inheritance of adult-onset disease and associated differential DNA methylation regions (i.e. epimutations) in sperm. Gestating F0 generation female rats were transiently exposed to methoxychlor during fetal gonadal development (gestation days 8 to 14) and then adult-onset disease was evaluated in adult F1 and F3 (great-grand offspring) generation progeny for control (vehicle exposed) and methoxychlor lineage offspring. There were increases in the incidence of kidney disease, ovary disease, and obesity in the methoxychlor lineage animals. In females and males the incidence of disease increased in both the F1 and the F3 generations and the incidence of multiple disease increased in the F3 generation.  There was increased disease incidence in F4 generation reverse outcross (female) offspring indicating disease transmission was primarily transmitted through the female germline.  Analysis of the F3 generation sperm epigenome of the methoxychlor lineage males identified differentially DNA methylated regions (DMR) termed epimutations in a genome-wide gene promoters analysis. These epimutations were found to be methoxychlor exposure specific in comparison with other exposure specific sperm epimutation signatures. Observations indicate that the pesticide methoxychlor has the potential to promote the epigenetic transgenerational inheritance of disease and the sperm epimutations appear to provide exposure specific epigenetic biomarkers for transgenerational disease and ancestral environmental exposures.

overall_design: Methylated sperm DNA was isolated from rats ancestrally exposed to methoxychlor. Three independent samples from each treatment group were obtained.  Differential DNA methylation between treatment groups was determined using Nimblegen microarrays. Treated samples were paired with control samples and hybridized together on arrays, resulting in three arrays for the treatment.

first: Mohan

last: Manikkam

first: M

last: Haque

first: Carlos

last: Guerrero-Bosagna

first: Eric

last: Nilsson


title: Effect of temperature on gene expression profile of Aspergillus kawachii during a barley koji-making process

status: Public on Jun 14 2014

city: Kagoshima

first: Taiki

last: Futagami

address: Korimoto 1-21-24

department: Department of Agriculture

institute: Kagoshima University

summary: A koji mold Aspergillus kawachii is used for making a Japanese distilled spirit, shochu. During making shochu, A. kawachii is grown in a solid-state culture comprised of steamed grains such as rice or barley, termed koji, to convert the starch to glucose and also to produce citric acid. During this process, cultivation temperature of A. kawachii is generally controlled by raising to 40°C and then lowering to 30°C. The cultivation at 40°C and the following at lower temperature of 30°C has important roles in the elevated activity of amylase and starting an accumulation of a large amount of citric acid, respectively. In this study, we investigated the effect of temperature on the gene expression of A. kawachii when barley was used as ingredient for making koji. The results of DNA microarray and gene ontology analysis showed that the expression of genes involved in the metabolic processes of glycerol, trehalose, and pentose phosphate that branch from glycolysis was down-regulated by shifting the cultivation temperature from 40°C from 30°C. In addition, reduction in the expression of the genes related with heat shock responses and increasing in the expression of the genes related with amino acid transport after the temperature lowering were found to be significant change. These results suggested that the cultivation at 40°C is stressful event for the A. kawachii and the heat adaption lead to the depression of citric acid accumulation through activation of the branching pathways from glycolysis. The gene expression profile obtained in this study will help to understand the gene regulation during koji-making process to optimize A. kawachii as industrial microorganism.

overall_design: Gene expression of Aspergillus kawachii in barley koji was measured at 25, 26.5, and 44 hours at two different temperature control. Three independent experiments were performed at each time (25, 26.5, or 44 hours) using different barley koji for each expreriment.

first: Kazuki

last: Mori

first: Shotaro

last: Wada

first: Yasuhiro

last: Kajiwara

first: Hideharu

last: Takashita

first: Kosuke

last: Tashiro

first: Satoru

last: Kuhara

first: Masatoshi

last: Goto


title: Apple Atlas expression array

status: Public on Jun 04 2014

city: Beaucouzé

first: Jean-Marc

last: Celton

address: 42 rue Georges Morel

country: France

institute: INRA-IRHS

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

summary: Transcriptional profiling of various apple (Malus x domestica Borkh) organ systems using probes complementary to both sense and anti-sense transcripts.

overall_design: Eight apple organs/samples. Biological replicates: 2 for each sample, independently grown and harvested.

first: Jean-Pierre

last: Renou

first: Sandra

last: Pelletier

first: Sylvain

last: Gaillard

first: Maryline

last: Bruneau


title: Genome-wide analysis in Human Colorectal Cells reveals Ischaemia-mediated expression of motility genes via DNA hypomethylation (promoter array)

status: Public on Jul 07 2014

city: Guelph

first: Brenda

last: Coomber

state: Ontario

address: 50 Stone Road

department: Department of Biomedical Sciences

institute: University of Guelph

summary: DNA hypomethylation is an important epigenetic modification found to occur in many  different cancer types, leading to the upregulation of previously silenced genes and  loss of genomic stability. We previously demonstrated that hypoxia and  hypoglycaemia (ischemia), two common micro-environmental changes in solid tumors,  decrease DNA methylation through the downregulation of DNMTs in human colorectal  cancer cells. Here, we utilized a genome-wide cross-platform approach to identify  genes hypomethylated and upregulated by ischemia. Following exposure to hypoxia or  hypoglycaemia, methylated DNA from human colorectal cancer cells (HCT116) was  immunoprecipitated and analysed with an Affymetrix promoter array. Additionally, RNA  was isolated and analysed in parallel with an Affymetrix expression array. Ingenuity  pathway analysis software revealed that a significant proportion of the genes  hypomethylated and upregulated were involved in cellular movement, including PLAUR  and CYR61. A Matrigel invasion assay revealed that indeed HCT116 cells grown in  hypoxic or hypoglycaemic conditions have increased mobility capabilities. Confirmation  of upregulated expression of cellular movement genes was performed with qPCR. The  correlation between ischemia and metastasis is well established in cancer progression,  but the molecular mechanisms responsible for this common observation have not been  clearly identified. Our novel results suggest that hypoxia and hypoglycaemia may be  driving changes in DNA methylation through downregulation of DNMTs. This is the first  report to our knowledge that provides an explanation for the increased metastatic  potential seen in ischemic cells; i.e. that ischemia could be driving DNA  hypomethylation and increasing expression of cellular movement genes.

overall_design: Genomic DNA from the Human Colorectal cancer Cell line HCT116 cultured normally or in hypoxic or Hypoglycaemic conditions was enriched using Methylated DNA Immunoprecipitation, Amplified using whole genome amplification, and hybridized in triplicate (for each treatment) to Affymetrix Human promoter 1.0R arrays arrays.

first: Karolina

last: Skowronski

first: Joseph

last: Andrews

first: David

last: Rodenhiser


title: Carbon Redistribution from Surface Lipids into Triacylglycerols in Leaves of Arabidopsis by Introducing a Chlamydomonas Diacylglycerol Acyltransferase 2

status: Public on Jun 16 2014

city: East Lansing

first: Christoph

last: Benning

state: MI

address: 1066 Bogue St

department: Great Lakes Bioenergy Research Center

institute: Michigan State University

summary: Plants and microalgae have the ability to harness sunlight into energy dense molecules such as triacylglycerols (TAGs). TAGs hold great importance for human and animal nutrition, and are also a source for renewable energy. Acyl-CoA-dependent TAG synthesis by diacylglycerol acyltransferases (DGATs) in oilseeds has been well characterized, but how the ectopic introduction of TAG synthesis in vegetative tissues of plants affects metabolism is largely unknown. Here we report the identification and characterization of several Chlamydomonas reinhardtii Diacylglycerol Acyltransferase Type Two (DGTT) enzymes and their use in engineering TAG biosynthesis in plant vegetative tissues. Focusing on DGTT2 we demonstrate that it can accept a broad range of substrates. Production of DGTT2 in Arabidopsis results in distinct seedling phenotypes and accumulation of TAG with very long chain fatty acids (VLCFA), in both seedlings (23.4-fold increase) and in the leaves of soil-grown plants (13.3-fold increase). Levels of surface lipids, such as waxes and cutins, are decreased in DGTT2-producing lines, consistent with a decreased carbon/acyl flux to the surface lipid pathway. Global transcript analysis showed that very few genes had altered expression. Little to no change in the transcripts of wax/cutin pathway genes was observed in response to altered carbon partitioning into TAGs in the leaves suggesting that the supply of acyl groups for surface lipid biosynthesis is not transcriptionally adjusted in the transgenic lines. As an indication that the DGTT2-producing plants are richer in feed value, the generalist herbivore Spodoptera exigua reared on the transgenic plants gained more weight. Apparently, the substrate specificity of DGTT2 from Chlamydomonas when produced in the Arabidopsis cells leads to diversion of carbon from surface compounds in TAGs and enhances the nutritional value of leaves.

overall_design: 4 biological replicates DGTT2 transgenic plants are compared to 4 biological replicates of wild type

first: S

last: Sanjaya

first: Rachel

last: Miller

first: Timothy

last: Durrett

first: Dylan

last: Kosma

first: Bagyalakshmi

last: Muthan

first: Abraham

middle: J

last: Koo

first: Yury

middle: V

last: Bukhman

first: Gregg

last: Howe

first: John

last: Ohlrogge


title: Epigenome-Wide Scans Identify Differentially Methylated Regions for Age and Age-Related Phenotypes in a Healthy Ageing Population

status: Public on May 29 2014

city: London

first: Pei-Chien

last: Tsai

address: 3rd Floor South Wing Block D, St Thomas’ Campus, Lambeth Palace Road

department: Twin Research and Genetic Epidemiology

country: United Kingdom

institute: King's College London

summary: The Illumina Infinium 27k Human DNA methylation Beadchip v1.2 was used to obtain DNA methylation profiles across approximately 27,000 CpGs in whole blood samples from 172 normal female twins. See Bell, Tsai et al. Plos Genet. 2012;8(4):e1002629.

overall_design: Bisulphite converted DNA from the 172 samples were hybridised to the Illumina Infinium 27k Human Methylation Beadchip v1.2

first: Jordana

middle: T

last: Bell


title: Genome-wide analysis reveals DNA methylation markers that varies with both age and obesity

status: Public on Jul 09 2014

city: Uppsala

first: Markus

last: Sällman Almén

address: Box 593

department: Dept. of Neuroscience

country: Sweden

institute: Uppsala Universitet

summary: Background: The obesity epidemic and the aging population of many western countries together with their associated diseases are  major challenges for the healthcare. As obesity is a risk factor for many age related diseases, such as cancer, it is of importance to understand their interaction and the underlying molecular mechanisms. Lately, epigenetic programming in the form of DNA methylation and have been recognized for its importance in aging, obesity and several diseases.   Method: Herein, the methylation level was determined for around 27000 CpG-islands in 46 DNA samples from adult peripheral blood with microarrays. The dependence for each CpG island with age, obesity and their interaction was ascertained with a general linear model.  Results: The methylation level of more than 100 genomic sites were significantly altered with increasing age together with 10 additional sites that were differentially methylated with age in obese and lean individuals. The majority of the genomic sites were hypermethylated during aging, including the telomerase catalytic subunit (TERT). However, age dependent hypermethylation was prohibited or reverted in 8 of 10 regions in obese where an interaction between age and obesity was observed. Moreover, one region (LINC00304) was differentially methylated in obese and lean.  Conclusion: This study provides evidence for an obesity influence on age driven epigenetic changes, which provide a molecular link between aging and obesity.  This link and the identified markers may prove to be valuable biomarkers for the understanding of the molecular basis of aging, obesity and associated diseases.

overall_design: Bisulphite converted DNA from the 24 obese and 22 lean women were hybridised to the Illumina Infinium 27k Human Methylation Beadchip v1.2

first: Emil

last: Nilsson

first: Josefin

middle: A

last: Jacobsson

first: Ineta

last: Kalnina

first: Janis

last: Klovins

first: Robert

last: Fredriksson

first: Helgi

last: Schiöth


title: A familial disorder of altered DNA-methylation

city: Ulm

first: Ole

last: Ammerpohl

address: Albert-Einstein-Allee 11

country: Germany

institute: UK Ulm

summary: In a subset of imprinting disorders caused by epimutations, multiple imprinted loci are affected. We have investigated the clinical and molecular features of a familial DNA methylation disorder.

overall_design: Bisulphite converted DNA from the 60 samples were hybridised to the Illumina Infinium 27k Human Methylation Beadchip

first: Almuth

last: Caliebe


title: Transcriptional profiling of apple (Malus x domestica Borkh) pedicels abscission zone development

status: Public on May 20 2014

first: Jean-Marc

last: Celton

summary: Apple pedicel vascular development array

overall_design: Twelvet apple samples. Biological replicates: 2 for each sample, independently grown and harvested.

first: Jean-Pierre

last: Renou


title: Dietary fat quality, more than dietary fat quantity, impacts genome-wide DNA methylation patterns in Greek preadolescents

status: Public on May 09 2014

city: Footscray

first: Sarah

middle: Amandine Caroline

last: Voisin

state: VIC

address: Ballarat Road

department: Institute for Health and Sport

country: Australia

institute: Victoria University

summary: The type and the amount of dietary fat have a significant influence on the metabolic pathways involved in the development of obesity, metabolic syndrome, diabetes type 2 and cardiovascular diseases. However, it is unknown to what extent this modulation is achieved through DNA methylation. We assessed the effects of cholesterol intake, the proportion of energy intake derived from fat, the ratio of polyunsaturated fatty acids (PUFA) to saturated fatty acids (SFA), the ratio of monounsaturated fatty acids (MUFA) to SFA, and the ratio of (MUFA+PUFA) to SFA on genome-wide DNA methylation patterns in normal-weight and obese children. We determined the genome-wide methylation profile in blood of 69 Greek preadolescents (~10 y old), as well as their dietary intake for two consecutive weekdays and one weekend day. The methylation levels of four sites and a CpG island were significantly correlated with total fat intake. The methylation levels of 13 islands and 16 sites were significantly correlated with PUFA/SFA; of 35 islands and 158 sites with MUFA/SFA; and of 50 islands and 130 sites with (MUFA+PUFA)/SFA. We found significant gene enrichment in 26 pathways for PUFA/SFA, including the leptin pathway, and a significant enrichment in three pathways for (MUFA+PUFA)/SFA. Our results suggest that the quality, and to a lesser extent the quantity of fat intake, influences DNA methylation, including genes involved in metabolism. Thus, specific changes in DNA methylation may play an important role in the mechanisms involved in the physiological responses to different types of dietary fat.

overall_design: Bisulphite converted DNA from 22 boys were hybridised to the Illumina Infinium 27k Human Methylation Beadchip v1.2.Both obese and normal-weight indiviudals were included.

middle: S

last: Almén

first: George

last: Moschonis

last: Chrousos

first: Yannis

last: Manios


title: Stability of gene expression and epigenetic profiles highlights the utility of patient-derived paediatric acute lymphoblastic leukaemia xenografts for investigatoing molecular mechanisms of drug resistance (methylation)

status: Public on May 14 2014

city: Clayton

first: Nicholas

middle: C

last: Wong

state: Victoria

address: Wellington Road

department: Monash Bioinformatics Platform, Central Clinical School

institute: Monash University

summary: Background: Patient-derived tumour xenografts are an attractive model for preclinical testing of  anti-cancer drugs. Insights into tumour biology and biomarkers predictive of responses to  chemotherapeutic drugs can also be gained from investigating xenograft models. As a first step  towards examining the equivalence of epigenetic profiles between xenografts and primary tumours  in paediatric leukaemia, we performed genome-scale DNA methylation and gene expression  profiling on a panel of 10 paediatric B-cell precursor acute lymphoblastic leukaemia (BCP-ALL)  tumours that were stratified by prednisolone response.  Results: We found high correlations in DNA methylation and gene expression profiles between  matching primary and xenograft tumour samples with Pearson’s correlation coefficients ranging  between 0.85 and 0.98. In order to demonstrate the potential utility of epigenetic analyses in BCPALL  xenografts, we identified DNA methylation biomarkers that correlated with prednisolone  responsiveness of the original tumour samples. Differential methylation of CAPS2, ARHGAP21, ARX  and HOXB6 were confirmed by locus specific analysis. We identified 20 genes showing an inverse  relationship between DNA methylation and gene expression in association with prednisolone  response. Pathway analysis of these genes implicated apoptosis, cell signalling and cell structure  networks in prednisolone responsiveness.  Conclusions: The findings of this study confirm the stability of epigenetic and gene expression  profiles of paediatric BCP-ALL propagated in mouse xenograft models. Further, our preliminary  investigation of prednisolone sensitivity highlights the utility of mouse xenograft models for  preclinical development of novel drug regimens with parallel investigation of underlying gene  expression and epigenetic responses associated with novel drug responses.

overall_design: 20 samples were analysed using Illumina Infinium HM27K Bead arrays. This consisted of 10 matched primary tumour and low passage xenografts. Of which, 5 were prednisolone good responders and 5 were prednisolone poor responders

first: Vivek

last: Bhadri

first: Richard

last: Lock


title: Apple pedicel vascular development array

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

overall_design: Refer to individual Series


title: Estrogen deprivation alters epigenetic modifications in breast cancer cells - HOXC10 loss in endocrine resistance

status: Public on May 01 2014

city: Houston

first: Yuanxin

last: Xi

state: TX

address: 1400 Pressler St

department: Bioinformatics and Computational Biology

institute: The University of Texas MD Anderson Cancer Center

summary: Postmenopausal breast cancer patients benefit from aromatase inhibitors (AIs) that reduce the levels of estrogens critical for the growth of estrogen receptor (ER)-positive tumors.  Unfortunately, many tumors are resistant to AI, and we are only beginning to understand the complex mechanisms underlying treatment resistance. Here we set out to determine whether epigenetic changes could contribute to therapy resistance.   For AI-resistance models, we used previously established MCF-7 cell clones, termed C4-12 and long-term estrogen deprivation (LTED), that were isolated after being cultured in estrogen-free media for 9 months and 18–24 months, respectively. Methyl CpG Binding Domain (MBD) - pull down followed by affymetrix promoter array was used to detect promoter methylation patterns in these cell lines. These studies identified widespread genomic hyper- and hypomethylation events, with a significant enrichment of promoter hypermethylation of development-associated genes in both cell lines. A developmentally regulated gene that was heavily methylated and lost expression in both cell-line systems was HOXC10. Moreover, we found that HOXC10 is an estrogen-regulated gene and lack of ER regulation is associated with progressive epigenetic silencing through EZH2/H3K27me3 and DNA hypermethylation. Stable knockdown of HOXC10 in MCF-7 cells resulted in increased cell growth, reduced cell apoptosis, and increased cell motility.  A preliminary study using AI-treated breast tumors did not show significant associations, however, the numbers were small.  We identified HOXC10 methylation as a novel determinant of endocrine resistance. Also, we revealed that epigenetic reprogramming of genes involved in development may be a fundamental phenomenon in hormone resistance. Therefore, our study might provide the basis for the expansion of clinical markers for endocrine resistance and future clinical trials such as combination of endocrine and epigenetic therapies.

overall_design: Long-term estrogen deprived previously established MCF-7 cell clones termed C4-12 and LTED genomic DNA subjected to Methyl CpG Binding Domain (MBD) - pull down followed by affymetrix promoter array to detect promoter methylation patterns

first: Xi

last: Yuanxin

first: Pathiraja

last: Thushangi


title: DNA methylation profiling of whole blood DNA samples from BRCA1 wild-types without breast cancer and BRCA1 mutants with and without breast cancer (Prague Set 1)

status: Public on May 06 2014

first: Andrew

middle: E

last: Teschendorff

address: 72 Huntley Street

department: UCL Cancer Institute/Institute for Women's Health

institute: University College London

summary: The Illumina Infinium 27k Human DNA methylation Beadchip v1.2 was used to obtain DNA methylation profiles across approximately 27,000 CpGs in whole blood DNA samples from 84 women (42 BRCA1 wild-type and healthy, 7 BRCA1 mutants and healthy, 35 BRCA1 mutants with breast cancer)

overall_design:
whole blood DNA from women, with and without breast cancer, and with or without BRCA1 mutation
Bisulphite converted DNA from the whole blood samples were hybridised to the Illumina Infinium 27k Human Methylation Beadchip v1.2
The BRCA1 mutation status represent 0=healthy-brca1wt, 1=healthy-brca1mt, 2=breastcancer-brca1mt.

first: Martin

last: Widschwendter


title: Expression data from different photosynthetic rate in Populus.

status: Public on May 31 2014

city: Beijing

first: Bowen

last: Wang

address: Beijing Forest University

country: China

institute: Beijing Forest University

summary:
Despite the significance of nucleus genes in plant growth and development, little is known of the molecular bases of regulation of photosynthesis in woody plants.Hence discovering the genetic basis for photosynthesis related phenotypic variation and identifying the major genes controlling these complex traits in trees is essential.
Combining the microarray technique and bulked segregant analysis strategy, we used poplar as a model to detect the nucleus genes differentially expressed in segregation population of photosynthesis traits. We measured the F1 interspecific population and segregated the stable extrem samples into two groups including three pools containing five incividuals.Use the Affymetrix poplar gene chip to decrypt the gene functions and mechanisms in different photosynthetic rate.

sample_organism: (Populus alba x Populus glandulosa) x Populus tomentosa

overall_design: Leaves were taken from high and low  photosynthetic rate individuals for RNA extraction and hybridization on Affymetrix microarrays. H_A, H_B, H_C are from the high photosynthetic rate individuals. L_D,L_E, L_F are from the low photosynthetic rate incividuals.

first: Deqiang

last: Zhang

first: Qingzhang

last: Du


title: Genome-scale methylome profiling of adrenocortical carcinomas (ACC) and adenomas (ACA)

status: Public on Apr 29 2014

city: Paris

first: Nabila

last: Elarouci

address: 14 rue Corvisart

department: Recherche

institute: Ligue Nationale contre le Cancer

summary: Genome-scale DNA methylation was analyzed in a cohort of ACC and ACA to identify DNA methylation changes.

overall_design: Bisulfite converted DNA from 51 fresh frozen ACC and 30 ACA samples were hybridized to Illumina HumanMethylation27 BeadChips.

first: Eric

last: Letouzé

first: Aurélien

last: de Reyniès

first: Windy

last: Luscap

first: Olivia

last: Barreau

first: Guillaume

last: Assié

first: Jérome

last: Bertherat


title: Transcriptional profiling of apple (Malus x domestica Borkh) pedicels displaying abnormal additional amphivasal vascular bundles in the pith

first: Jean-Marc

last: Celton

overall_design: Eight apple samples. Biological replicates: 2 for each sample, independently grown and harvested.

first: Jean-Pierre

last: Renou


title: Identification of Type 1 Diabetes-Associated DNA Methylation Variable Positions That Precede Disease Diagnosis

status: Public on Apr 09 2014

first: Robert

last: Lowe

address: 4 Newark Street

department: Blizard Institute

institute: QMUL

summary: Monozygotic (MZ) twin pair discordance for childhood-onset Type 1 Diabetes (T1D) is ~50%, implicating roles for genetic and non-genetic factors in the aetiology of this complex autoimmune disease. Although significant progress has been made in elucidating the genetics of T1D in recent years, the non-genetic component has remained poorly defined. We hypothesized that epigenetic variation could underlie some of the non-genetic component of T1D aetiology and, thus, performed an epigenome-wide association study (EWAS) for this disease. We generated genome-wide DNA methylation profiles of purified CD14+ monocytes (an immune effector cell type relevant to T1D pathogenesis) from 15 T1D-discordant MZ twin pairs. This identified 132 different CpG sites at which the direction of the intra-MZ pair DNA methylation difference significantly correlated with the diabetic state, i.e. T1D-associated methylation variable positions (T1D-MVPs). We confirmed these T1D-MVPs display statistically significant intra-MZ pair DNA methylation differences in the expected direction in an independent set of T1D-discordant MZ pairs (P = 0.035). Then, to establish the temporal origins of the T1D-MVPs, we generated two further genome-wide datasets and established that, when compared with controls, T1D-MVPs are enriched in singletons both before (P = 0.001) and at (P = 0.015) disease diagnosis, and also in singletons positive for diabetes-associated autoantibodies but disease-free even after 12 years follow-up (P = 0.0023). Combined, these results suggest that T1D-MVPs arise very early in the etiological process that leads to overt T1D. Our EWAS of T1D represents an important contribution toward understanding the etiological role of epigenetic variation in type 1 diabetes, and it is also the first systematic analysis of the temporal origins of disease-associated epigenetic variation for any human complex disease.

overall_design: Bisulphite converted DNA from the 100 samples were hybridised to the Illumina Infinium 27k Human Methylation Beadchip v1.2

first: Vardhman

last: Rakyan


title: Heat acclimation memory: Does the de-acclimated transcriptome reveal epigenetic processes of transcriptional regulation?

status: Public on Mar 31 2014

city: Jerusalem

first: Michal

last: Horowitz

address: Hadassah Med Center

country: Israel

institute: The Hebrew University

summary:
Heat acclimation (AC) allows its faster re-induction following its decline. Constitutively preserved euchromatin state in hsp70 promoter during acclimation decline/regain pushed forward the hypothesis that acclimation decline is a period of “dormant memory” involving molecular program including epigenetic controlled transcriptional regulation leading to heat acclimation mediated cytoprotective memory.
We used microarray to uncover hallmark pathways in the induction of heat-acclimation-mediated memory, focusing on markers of epigenetic processes.

overall_design: Rats subjected to heat acclimation, deacclimation, reacclimation and untreated controls were used. We showed here that (i) AC2d provides the molecular switch for acclimation (ii) AC30 heart demonstrates qualitative adaptations (iii) specific molecular program encompassing up/down regulated gene during DeAC, of which epigenetic markers such as class A histones, chromatin modifiers and microRNA suggest epigenetic transcriptional regulation linked to acclimation memory (iv) constitutive upregulation of MAPK P38 module and targets as well as jak/stat and AKT associated pathways during DeAC imply its major role in this process. Noteworthy are players such as poly-(ADP-ribose)polymerase-1 (PARP1) and linker histones (histones H1 cluster in this process).

first: Anna

last: Tetievsky

first: Miri

last: Assayag

first: Rotem

last: Hamo

first: Sol

last: Efroni

first: Gal

last: Cohen

first: Atallah

last: Abbas


title: Expression data from leaf of (P. tomentosa x P. bolleana) x P. tomentosa under elevated CO2 concentrations

status: Public on May 24 2014

city: Bjing

first: Liu

last: Juanjuan

address: XiangShan Road, HaiDian District

department: Research Institute of Forestry

institute: Chinese Academy of Forestry

summary:
The atmosphere CO2 concentration keeps increasing every year. Use the Affymetrix poplar gene chip to confirm the expression changes in key genes in the triploid white poplar due to the influence of elevated CO2 concentrations.
We used microarrays to detail the global programme of gene expression under normal and elevated CO2 concentrations.

sample_organism: (Populus tomentosa x Populus bolleana) x Populus tomentosa

overall_design: Gene expression of triploid white poplar ((P. tomentosa × P. bolleana）× P. tomentosa) leaves were investigated by using the Affymetrix poplar genome gene chip, after grown in controlled environment chambers under three different CO2 concentrations. Poplar leaves were subjected to normal CO2 concentrations (T0) and elevated CO2 concentrations (T1, 550 ppm and T2, 720 ppm) treatments three months.

first: Juanjuan

last: Liu

first: Jianguo

last: Zhang


title: Epigenome analysis of irradiated and non-irradiated breast tumor tissue samples and normal controls

status: Public on Mar 26 2014

city: Oslo

first: Ann Rita

last: Halvorsen

address: Montebello

institute: OUS- The Norwegian Radium Hospital

summary: Genome wide DNA methylation profiling of irradiated and non-irradiated breast tumor samples and normal control tissue. The Illumina Infinium 27k Human DNA methylation Beadchip, Genome Build 36  was used to obtain DNA methylation profiles across approximately 27,000 CpGs in breast tumor samples. Samples included 20 non-irradiated tumor samples, 19 irradiated tumor samples and 9 normal controls.

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

first: Ann

middle: R

first: Åslaug

last: Helland

first: Hege

last: Edvardsen


title: Expression data from different tissues in different seasons  from P. tomentosa

status: Public on Mar 20 2014

city: Beiijing

last: Chao

state: Beijing

address: Beijing Haidian Distric Qinghua East Road 35

department: College of Bioscience and Biotechnology

institute: Beijing Forestry University

summary:
Different fuctional genes have different expression levels in various tissues. Along with the seasons changing, expression level also changes. One-year expression level for functional genes can be indicated by the four seasonal samples and respective time-course change can also be detected.
We use microarry chips to study the expression levels for specific genes and explore new functional genes involved in secondary metabolism

overall_design: Samples from four tissues (bud, root, xylem and phloem) were collected in different seasons in one year. April and May were the months in spring for collecting samples. June and July were the months in summer for collecting samples.  September and October were the months in autumn for collecting samples. December was the month for collecting samples in winter. RNA from each sample was extracted for hybridization.


title: Global DNA methylation: Uncommon event in Oral Lichenoid Disease [Illumina HumanMethylation27 BeadChip]

status: Public on Apr 30 2014

city: Adelaide

first: Naiara

last: Bediaga

state: South Australia

address: 4 North Terrace

department: Adelaide Centre for Epigenetics and the South Australian Immunogenomics Cancer Institute, Faculty of Health and Medical Sciences

institute: The University of Adelaide

summary: Purpose  Accumulating evidence indicates aberrant DNA methylation is closely related to oral carcinogenesis, and it has been shown that methylation changes might be used as prognostic biomarker in oral squamous cell carcinoma. Oral lichenoid disease (OLD) is the most common oral potentially malignant disorder in our region. In this study, we have performed a wide DNA methylation study of a series of oral lichenoid disease in order to assess the relevance of DNA methylation changes in this premalignant disorder.  Experimental Design  Discovery phase utilized HumanMethylation27 DNA Analysis BeadChip assay in 18 OLD and 5 control samples. The differently methylated loci and the global DNA methylation surrogate LINE-, were further validated in an independent sample set consisting in 158 OLD and 65 controls.  Results  DNA methylation profile of the OLD showed only minor significant differences when compared to controls. MGC40178, ADORA1 and LINE-1 were slightly hypomethylated in 23, 40 and 43 % of the OLD samples respectively, while only in 13, 18 and 15% of the controls.  Conclusions  In summary, our data indicates that the frequency of aberrant DNA alteration is very low in OLD, which support the low rate of malignization of this oral potentially malignant disorder.

overall_design: Bisulphite converted DNA from the 17 Oral lichenoid samples and 5 control samples were hybridised to the Illumina Infinium 27k Human Methylation Beadchip v1.217

first: Jose

middle: M

last: Aguirre-Urizar

first: Amelia

last: Acha-Sagredo


title: Global DNA Methylation: Uncommon Event in Oral Lichenoid Disease


title: Expression data from amiEBBB1 poplar apices

status: Public on Mar 12 2014

city: Charleston

first: Yordan

last: Yordanov

state: IL

address: 600 Lincoln ave

department: Department of Biological Sciences

institute: Eastern Illinois University

summary:
We study gene expression Populus amiEBB1  lines affecting dormancy. We used microarrays to detail the global program of gene expression underlying morphological and developmental changes droved by expression of artifical micro RNA (ami) targeting EBB1 gene.
By screening activation tagging population we identified the EARLY BUD-BREAK1 (EBB1) mutant. We positioned the tag, localized a putative candidate gene and verified transcription activation. The activated gene encodes an AP2/ERF  transcription factor similar to a small B1 gene-subfamily in Arabidopsis encoding strong regulators of meristem function and lateral organ outgrowth.  We fully recapitulated the phenotype by overexpression of the gene into the same genotype under strong constitutive promoter (P35S::EBB1).  We also found that EBB1 transcript abundance in wild type plants increases during the period prior to bud-break, and in response to the hormone cytokinin.  Down-regualtion of EBB1 influence negatively bud break. Our data indicates that EBB1 plays a important role in the process of bud-break.

overall_design: Poplar apex was selected  for RNA extraction and hybridization on Affymetrix microarrays. We used apices tissue from amiEBB1 grown greenhouse healthy plants.

first: Victor

middle: B

last: Busov


title: Gene expression in canine adipose stromal vascular fraction

status: Public on Mar 05 2014

city: Lexington

first: Donald

state: KY

address: 800 Rose Street

department: Microbiology, Immunology and Molecular Genetics

institute: Univ. of Kentucky

summary: Microarray studies were performed to identify expression patterns by cryopreserved adipose stromal vascular fraction (SVF) preparations that were prepared by three different veterinary stem cell companies from the same source of canine adipose tissue.

overall_design:
[Samples 1 - 3] Three equal samples of approximately 20 grams of adipose tissue were shipped on ice to 3 different companies which specialize in adipose-derived veterinary stem cell therapy.  All 3 SVF preparations were cryopreserved at their respective facilities.  Approximately one month later, cryopreserved samples were retrieved from all companies and transported frozen to the University of Kentucky for gene profiling and viability analysis.
[Samples 4 - 11] Groups of cells (samples 5, 7, 9, 11) were treated by the stem cell company with photo-activated platelet-rich plasma (PRP) according to their proprietary procedures in order to enhance regenerative properties of the adipose stem cells.  These PRP-treated cells were incubated in the investigator's lab for 6 hours at 37 degrees Celsius to allow for expression of genes that were induced by PRP treatment.


title: DNA methylation analysis of PBMC from HIV and HIV/TB co-infected patients

city: Philadelphia

first: Louise

last: Showe

address: 3601 Spruce St

institute: The Wistar Institute

summary: Genome wide DNA methylation profiling of PBMC from South African patients either infected with HIV only or coinfected with HIV and tuberculosis (TB). The Illumina Infinium 27k Human DNA methylation Beadchip was used to obtain DNA methylation profiles from PBMC samples. Samples included 19 HIV patients and 20 HIV/TB co-infected patients.

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

first: Noor

last: Dawany

first: Andrew

last: Kossenkov

first: Celia

last: Chang

first: Prudence

last: Ive

first: Francesca

last: Conradie

first: Wendy

last: Stevens

first: Ian

last: Sanne

first: Livio

last: Azzoni

first: Luis

last: Montaner


title: Single-cell derived clones from human adipose stem cells present different immunomodulatory properties.

status: Public on Mar 03 2014

city: Oviedo

first: Agustin

last: Fernandez

email: affernandez@hca.es, agusff@gmail.com

state: Asturias

address: Avenida de Roma s/n

department: IUOPA

institute: Oviedo University-HUCA

summary: Human adipose mesenchymal stem cells are a heterogeneous population, where cell cultures derived from single cell-expanded clones present varying degrees of differential plasticity. This work focuses on the immunomodulatory/anti-inflammatory properties of these cells. To this end, 5 single cell clones were isolated (1.X and 3.X) from 2 volunteers. Regarding the expression level of the lineage-characteristic surface antigens, clones 1.10 and 1.22 expressed the lowest amounts, while clones 3.10 and 3.5 expressed more CD105 than the rest and clone 1.7 expressed higher amounts of CD73 and CD44. Regarding cytokine secretion, all clones were capable of spontaneously releasing high levels of IL-6 and low to moderate levels of IL-8. Furthermore, clone 3.X produced the highest amounts of pro-inflammatory cytokines such as IL-1β, while clones 1.10 and 1.22 highly expressed IL-4 and IL-5. These differences can be explained in part by the distinct DNA promoter methylation profile exhibited by the clones. The results of this work indicates that this stem cell population is heterogeneous in its secretion profile, and that isolation, characterization and selection of the appropriate cell clone is a more exact method for the possible treatment of different patients or pathologies.

overall_design: Total DNA isolated by standard procedures from different clones of human dipose mesenchymal stem cells (hMSC)

first: José

last: Sempere

first: Pascual

last: Martínez-Peinado

first: María

middle: I

last: Arribas

first: Juan

last: Reig

first: Mari

last: De La Sen

last: Zubcoff

first: Mario

last: Fraga

first: Alfredo

last: Santana

first: Enrique

last: Roche


title: Photoperiod associated genes in the poplar bark

status: Public on Mar 01 2014

city: college park

first: rongshuang

last: lin

address: Plant Sci building

department: Plant sci

institute: Univ Maryland

summary: The role of bark storage proteins (BSPs) in seasonal N storage and cycling has been well documented. However, the regulatory mechanisms and pathways associated with this physiological process are poorly understood. The objective of this study is to investigate global patterns of gene expression associated with photoperiod regulated BSP accumulation and to identify candidate genes, pathways and regulatory factors governing N storage and cycling in poplar. In this study, differential expression of protease inhibitors, proteases, transcription factors, and other genes coincided with increased BSP gene expression, suggesting a complex regulatory network that might play an important role in BSP accumulation.

overall_design: Bark of Populus trichocarpa (Nisqually-1) was collected at weekly intervals for 6 weeks from plants treated with short-day (SD) photoperiods at 20°C as well as from long-day (LD) grown plants immediately before the SD treatment.

first: Rongshuang

last: Lin

first: Gary

last: Coleman

first: Ganesh

last: Sriram

first: Jianhua

last: Zhu


title: Detection of hypermethylated circulating serum DNA in metastatic breast cancer and confirmation by the cMethDNA assay

city: Baltimore

first: leslie

last: cope

address: 550 N. Broadway

institute: leslie cope

summary: The ability to consistently detect cell-free tumor-specific DNA in peripheral blood of patients with metastatic breast cancer provides the opportunity to detect changes in tumor burden and to monitor response to treatment. We developed cMethDNA, a quantitative multiplexed methylation specific PCR assay for a panel of ten genes, discovered through whole genome methylation array analysis of serum DNA.  Cancer-specific methylated DNA was detected in training and test sets of recurrent Stage 4 patient sera with a sensitivity of >90% and a specificity of >96%.  A core methylation signature was retained in serum, primary and metastatic tissues throughout the course of the disease, and the cMethDNA assay levels reflected patient response to chemotherapy. Together, our data suggest that the cMethDNA assay can provide a sensitive tool to detect minute levels of tumor DNA present in a vast excess of normal DNA in serum.

overall_design: Samples used: 11 cancer sera,,4 pools of normal leukocytes (5 donors per pool), 6 normal breast tissues microdissected, adjacent to tumor, 15 normal breast tissues, organoid preparations

first: MaryJo

last: Fackler

first: Zoila

last: Bujanda

first: Christopher

last: Umbricht

first: WeiWen

last: Teo

first: Zhe

last: Zhang

first: Kala

last: Visvanathan

first: Stacie

last: Jeter

first: Pedram

last: Argani

first: Chenguang

last: Wang

first: Jaclyn

middle: P

last: Lyman

first: Marina

last: deBrot Andrade

first: James

middle: N

last: Ingle

first: Judy

last: Boughey

first: Kandace

last: McGuire

first: Tari

last: King

first: Lisa

last: Carey

first: Leslie

last: Cope

first: Antonio

last: Wolff

first: Saraswati

last: Sukumar


title: Gene expression of alveolar macrophages before and after allergen challenge

status: Public on Feb 01 2014

city: Chicago

first: Gye Young

last: Park

address: 840 S. Wood St

department: Medicine, Pulmonary

institute: University of Illinois at Chicago

summary: Mild asthmatics who met the criteria of the IRB approved protocol of Sub-segmental Bronchial Provocation with Allergen were recruited. The subjects were challenged with sensitive allergen through bronchoscopy. Bronchoalveolar lavage (BAL) fluids were collected before and at 48 hours after allergen challegen. From the BAL fluids, alveolar macrophages were purifed and their RNA was extracted. Total 138 genes including five house keeping genes were evaluated.

overall_design: Two samples of alveolar macrophages from single subject, before and 48 hours after allergen challenge, were directly compared in terms of the expression of inflammatory, chemokine, cytokine genes and their receptor genes.

first: Gye

first: Jong

last: Jeong


title: Aberrant methylation of gene associated CpG sites occurs in borderline personality disorder

city: Giessen

first: Marek

last: Bartkuhn

state: Hessen

address: Aulweg 132

department: Biomedical Informatics and Systems Medicine

institute: Justus-Liebig-University Giessen

summary:
Borderline personality disorder (BPD) is a complex psychiatric disease with an increased impact in the last years. While the diagnosis and therapy are well established, little is known on the pathogenesis of borderline personality disorder. Previously, a significant increase in DNA methylation of relevant neuropsychiatric genes in BPD patients has been reported.
In our study we performed genome wide methylation analysis and revealed specific CpG sites that exhibited increased methylation in 26 BPD patients compared to 11 healthy controls. Bead chip technology and quantitative bisulfite pyrosequencing showed a significantly increased methylation at CpG sites of APBA2 (1.1 fold) and APBA3 (1.1 fold), KCNQ1 (1.6 fold), MCF2 (1.1 fold) and NINJ2 (1.2 fold) in BPD patients. For the CpG sites of GATA4 an increase in DNA methylation was observed, but was only significant in the bead chip assay. Moreover genome wide methylation levels of blood samples of BPD patients and control samples are similar.
In summary, our results show a significant 1.26 fold average increase in methylation at the analyzed gene associated CpG sites in the blood of BPD patients compared to controls samples (p<0.001). This data may provide new insights into epigenetic mechanisms underlying the pathogenesis of BPD.

overall_design: Whole blood samples for 26 BPD patients and 11 controls were obtained from the Psychiatric Hospital in Münsterlingen, Switzerland. All patients signed informed consent at initial clinical investigation. The study was approved by the local ethic committee. Diagnosis of BPD was established by an experienced psychiatrist (Dr. G. W. Dammann). Clincopathological parameter of the patients and controls are summarized in table S1 (for details see (Dammann et al, 2011)). Genomic DNA from whole blood was isolated by Nucleo Spin XL Blood (Macherey and Nagel, Düren, Germany). For the bead chip array 500 ng of genomic DNA was treated with bisulfite (Dammann et al, 2011).

first: Stefanie

last: Teschler

first: Natascha

last: Künzel

first: Christian

last: Schmidt

first: Gerhard

last: Dammann

first: Reinhard

first: Steffen

last: Kiehl


title: Methylation profiles of COPD small airways

status: Public on Feb 28 2014

city: Vancouver

first: Wan

middle: L.

last: Lam

state: British Columbia

address: 675 West 10th Avenue

department: Integrative Oncology

institute: British Columbia Cancer Research Centre

summary:
Rationale: DNA methylation is an epigenetic modification that is highly disrupted in response to cigarette smoke and involved in a wide spectrum of malignant and non-malignant diseases, but surprisingly not previously assessed in small airways of patients with chronic obstructive pulmonary disease (COPD). Small airways are the primary sites of airflow obstruction in COPD. We sought to determine whether DNA methylation patterns are disrupted in small airway epithelia of COPD patients, and evaluate whether changes in gene expression are associated with these disruptions.
Methods: Genome-wide methylation and gene expression analysis were performed on small airway epithelial DNA and RNA obtained from the same patient during bronchoscopy, using Illumina's Infinium HM27 and Affymetrix's Genechip Human Gene 1.0 ST arrays. To control for known effects of cigarette smoking on DNA methylation, methylation and gene expression profiles were compared between former smokers (FS) with and without COPD matched for age, pack years and years of smoking cessation.
Results: Our results indicate that aberrant DNA methylation is i) a genome-wide phenomenon in small airways of patients with COPD and ii) associated with altered expression of genes and pathways important to COPD, such as the Nrf2 oxidative response pathway.
Conclusions: DNA methylation is likely an important mechanism contributing to modulation of genes important to COPD pathology. Since these methylation events may underlie disease-specific gene-expression changes, their characterization is a critical first step towards the development of epigenetic markers and an opportunity for developing novel epigenetic therapeutic interventions for COPD.

overall_design: Bisulphite converted DNA from small airway (airways less than <2 mm in diameter) from 38 former smokers: 15 subjects with COPD (post bronchodilator FEV1/FVC ratio <70% and FEV1 predicted ≤ 80%) and 21 with normal lung function, were hybridized to the Illumina Infinium 27k Human Methylation Beadchip.

first: Emily

last: Vucic


title: EYA4 is a non-small cell lung cancer tumor suppressor located in the susceptibility locus on chromosome 6q

status: Public on Feb 25 2014

first: Ian

middle: Michael

last: Wilson

state: BC

department: Cancer Genetics

type: Genome variation profiling by genome tiling array

summary: This study was undertaken to identify novel tumour suppressor genes in lung adenocarcinoma.  EYA4, located at 6q23.2 was identified as a frequently lost and hypermethylated gene in the analyzed samples.  EYA4 is underexpressed in addition to being deleted and hypermethylated.  Control of EYA4 expression by DNA methylation was assessed using 5'-azacytidine.  The role of EYA4 in apoptosis was assessed using a stable knock down of the gene which was assessed for apoptotis using FACS and qPCR.

overall_design:
Methylation profiling: 30 adenocarcinoma samples and 30 patient-matched non-malignant lung samples are included.  Non-malignant samples were used as references to identify hypermethylated probes.  For each normal/tumor pair, the sample numbers are paired but offset by one with the tumor being the lower of the two numbers.  For example, 85040001 is the adenocarcinoma tumor profile that pairs with non-malignant 85040002.
Genome variation (aCGH) profiling: 30 adenocarcinoma gene dosage profiles are included.  Values presented are log2 ratios of Cy3(sample)/Cy5(diploid reference)

first: I

first: E

first: R

last: Char

first: Y

last: Zhang

first: D

last: Starczynowski

first: T

last: Buys

first: A

last: Karsan

first: J

last: Yee

first: C

last: MacAulay

first: S

middle: L

middle: F

last: Gazdar

first: W


title: Epigenome study of normal human epithelial tissues

status: Public on Jan 14 2014

city: Zerifin

first: Ella

last: Evron

address: Oncology Department

department: Oncology

institute: Asaf Harofeh Medical Center Affiliated with Tel Aviv University

summary: Genome wide DNA methylation profiling of normal human epithelial tissues of breast colon lung and endometrial origin, WBC and sperm to identify breast-specific methylated gene promoter loci. The Illumina Infinium 27k Human DNA methylation Beadchip v1.2 was used to obtain DNA methylation profiles across approximately 27,000 CpGs. Breast tissues were pre-enriched for organoids and other epithelial tissues were carefully selected by the pathologist.

overall_design: Bisulphite converted DNA from the 23 samples were hybridised to the Illumina Infinium 27k Human Methylation Beadchip v1.2. Two arrays of 12 and samples each were run separately. Each array included a control of human sperm DNA treated with SssI CpG methylase and human sperm DNA not treated (one sample did not pass QC and was dicarded ) .

first: Ayelet

last: Avraham


title: Regulated expression of polysaccharide utilization and capsular biosynthesis loci in biofilm and planktonic Bacteroides thetaiotaomicron during growth in chemostats

status: Public on Jan 01 2014

city: Ithaca

first: Michaela

middle: Anne

last: TerAvest

state: New York

address: B45 Riley-Robb Hall

department: Biological and Environmental Engineering

institute: Cornell University

summary: We used Affymetrix GeneChips to determine the physiological differences between biofilm and planktonic cells of Bacteroides thetaiotaomicron strain VPI-5482 (ATCC 29148) by comparing gene expression. For this purpose, B. thetaiotaomicron cells were grown in sterile, continuous flow bioreactors fed with tryptone, yeast extract, glucose (TYG) medium. The bioreactors were controlled at a temperature of 37C using a water jacket and a recirculating water heater. After 8 hours post-inoculation, planktonic cells were harvested from the bulk solution in the bioreactor, and after 8 days post-inoculation, the biofilm was scraped from the carbon paper. RNA was harvested from both biofilm and planktonic populations. RNA was extracted by a phenol:chloroform method and purified with a Qiagen RNA Easy mini-kit.

platform_organism:
Bacteroides thetaiotaomicron
Phocaeicola vulgatus
Parabacteroides distasonis
Methanobrevibacter smithii
Lachnospira eligens
Agathobacter rectalis
Bifidobacterium longum

overall_design: Overall growth conditions are summarized above. The experimental conditions were: biofilm (BF), and planktonic (PL).

first: Zhen

last: He


title: A panel of CpG methylation patterns distinguishes human embryonic stem cells and induced pluripotent stem cells

city: Los Angeles

first: Kevin

last: Huang

state: CA

address: Gonda BLDG Rm. 6554, P.O.Box 957088

department: Human Genetics

institute: UCLA

summary: Genome wide DNA methylation profiling of normal human embryonic stem cells, induced pluripotent stem cells, and somatic cells. The Illumina Infinium 27k Human DNA methylation Beadchip v1.2 was used to obtain DNA methylation profiles across approximately 27,000 CpGs in 5 normal hESCs, 15 hiPSCs (vector-containing and vector-free), and 5 somatic cells.

overall_design: Bisulphite converted DNA from the 25 samples were hybridised to the Illumina Infinium 27k Human Methylation Beadchip v1.2

first: Yin

last: Shen

first: Guoping

last: Fan


title: Comparison of the molecular profiles of human embryonic and isogenic induced pluripotent stem cells. [Illumina]

city: Bethesda

first: Kory

last: Johnson

state: MD

address: 10/3B01, 9000 Rockville Pike

department: DIR IT & Bioinformatics

institute: NINDS/NIH

summary: Many studies have compared the genetic and epigenetic profiles of human induced pluripotent stem cells (hiPSCs) to human embryonic stem cells (hESCs) and yet the picture remains unclear. To address this, we derived a population of neural precursor cells (NPCs) from the H1 (WA01) hESC line and generated isogenic iPSC lines by reprogramming. The gene expression and methylation profile of three lines were compared to the parental line and intermediate NPC population. We found no gene probe with expression that differed significantly between hESC and iPSC samples under undifferentiated or differentiated conditions. Analysis of the global methylation pattern also showed no significant difference between the two PSC populations. Both undifferentiated populations were distinctly different from the intermediate NPC population in both gene expression and methylation profiles. One point to note is that H1 is a male line and so extrapolation to female lines should be cautioned. However, these data confirm our previous findings that there are no significant differences between hESCs and hiPSCs at the gene expression or methylation level.

overall_design: 12 samples:  1 human NPC, 5 human ESC (UNDIFF), 6 human iPSC (UNDIFF)

first: Barbara

last: Mallon

first: Rebecca

last: Hamilton

first: Olga

last: Kozhich

first: Yang

last: Fann

first: Mahendra

last: Rao

first: Pamela

middle: G

last: Robey


title: Expression data from leaves of GA-deficient and GA-insensitive transgenic poplar

city: Houghton

first: Victor

last: Busov

address: 1400 Townsend Drive

department: Forest Resources and Environmental Science

institute: Michigan Technological University

summary:
We used whole-genome microarrays to identify differentially expressed genes in leaves of GA-deficient (35S::PcGA2ox) and/or GA-insensitive (35S::rgl1) transgenics as compared to WT poplar (717-1B4 genotype).
Our work suggests that the molecular machinery that reduces gibberellins (GAs) concentration and signaling is a major route for restraining growth under both immediate and imminent adverse conditions. We show that inhibition of growth as a result of water deprivation and short days (SDs) coincides with up-regulation of several DELLA and GA2ox encoding genes in poplar. Likewise, GA-deficient and GA-insensitive transgenics, with up-regulated GA2ox and DELLA domain proteins, elicited a hypersensitive growth inhibition in response to both drought and SDs. Because the GA-modified transgenic showed accelerated response to drought and SD, we hypothesized that the mechanisms associated with these responses are constitutively elevated even under control conditions (well-watered, long day photoperiod). Therefore, we used whole-genome poplar microarray to study transcriptome level changes in the leaves of transgenic compared to WT plants grown under control environment.

overall_design: Genetic background for all plants was INRA 717-1B clone (Populus tremula x Populus alba). Expression analysis was preformed on three individual genotypes; wild-type (WT, untransformed control), 35S::PcGA2ox and 35S::rgl1. Leaves from two independent biological replicates per genotype were used, each pooled from 20 clonally propagated plants.


title: Prenatal smoke exposure, DNA methylation, and childhood atopic disorders

status: Public on Dec 31 2013

city: Taipei

first: I-Jen

last: Wang

address: No. 1, Sec. 4, Roosevelt Road, Taipei

institute: Division of Allergy and Immunology, Department of Pediatrics, Taipei Hospital Department of Health, Taipei, Taiwan

summary:
Background: How prenatal smoke exposure affects DNA methylation leading to atopic disorders remains to be addressed. Epigenetic biomarkers informative of prenatal smoke exposure and atopic disorders are wanting. Since most children suffering from atopic dermatitis (AD) continue to develop asthma later in life, we explored whether prenatal smoke exposure e induces DNA methylation and searched for predictive epigenetic biomarkers for smoke related atopic disorders.   Methods: Methylation differences associated with smoke exposure were screened by Illumina methylation panel for children from the Taiwan birth panel study cohort initially. Information about development of atopic dermatitis (AD) and risk factors were collected. Cord blood cotinine levels were measured to represent prenatal smoke exposure. CpG loci that demonstrated a statistically significant difference in methylation were validated by methylation-dependent fragment separation (MDFS). Differential methylation in three genes (TSLP, GSTT1, and CYB5R3) was identified through the screen and their functions were investigated.
Results: Among these, only thymic stromal lymphopoietin (TSLP) gene displayed significant difference in promoter methylation percentage after being validated by MDFS (p=0.029). TSLP gene was further investigated in a larger sample of 92 children from the cohort. Methylation status of the TSLP 5′-CpG island (CGI) was found to be significantly associated with prenatal smoke exposure (OR=3.59, 95%CI=1.49-8.64; cotinine level 0.10 ng/ml, sensitivity= 77%; specificity = 61%) and with AD (OR=4.77, 95%CI=1.47-15.53). The degree of TSLP 5′CGI methylation inversely correlated with TSLP protein expression levels (per unit: β=－6.69 ng/ml; 95% CIs, －12.80~－0.59; p=0.032).   Conclusions: The effect of prenatal tobacco smoke exposure on the risk for AD may be mediated through DNA methylation. Cord blood methylated TSLP 5′CGI may be a potential epigenetic biomarker for environmentally-related atopic disorders.

overall_design: The buffy coat and plasma samples were separated and stored at −80°C. DNA (100 ng-500 ng) was extracted from cord white blood cells. Microarrays have been performed to investigate fourteen samples, which were classified as two groups according to cotinine exposure dosage (7 versus 7 : high exposure verses low exposure).

first: Tzu-Pin

last: Lu

first: Pau-Chung

last: Chen


title: Epigenome analysis of primary breast cancer tumors and different types of recurrences.

status: Public on Dec 24 2013

city: Paris

first: Matahi

last: MOARII

address: 70 Rue Mouffetard

institute: Mines Paristech

summary: Genome wide DNA methylation profiling of primary breast cancer tumors and their axillary metastasis and/or ipsilateral breast recurrence and/or contralateral breast recurrence. The Illumina Infinium 27k Human DNA methylation Beadchip v1.2 was used to obtain DNA methylation profiles across approximately 27,000 CpGs. Samples included 20 primary breast tumors and their matched axillary metastasis, 17 primary breast tumors and their matched ipsilateral breast recurrence, and 11 primary breast tumors and their matched contralateral breast recurrence.

overall_design:
Bisulphite converted DNA from the 96 samples were hybridised to the Illumina Infinium 27k Human Methylation Beadchip v1.2
contributed by Institut Curie  - Fabien Reyal


title: Genome-wide promoter methylation analysis associated with malignant melanoma progression

status: Public on Dec 20 2013

city: Boston

first: Byungwoo

last: Ryu

state: MA - Massachusetts

address: 609 Albany Street

department: Dermatology

institute: Boston University

summary: Epigenetic alterations play significant roles in the melanoma tumorigenesis and malignant progression. We profiled genome-wide promoter DNA methylation patterns of melanoma cells deribed from primary lesions of Radial Growrth phase (RGP) and Vertical Growth Phase (VGP), metastatic lesions, and primary normal melanocytes by interrogating 14,495 genes using Illumina bead chip technology. By comparative analysis of the promoter methylation profiles, we identified epigenetically silenced gene signatures that potentially associated with malignant melanoma progression.

overall_design: Bisulphite converted genomic DNA from a group of melanoma cells representing pathologic stages of melanoma progression (3 cell lines derived from RGP melanoma lesions, 4 cell lines derived from VGP lesions, and 3 melastatic melanomas) and normal human primary melanocytes isolated from lightly pigmented adult skin were hybridized to Illumina's Infinium HumanMethylation27 BeadChips

first: Hye-Eun

last: Kim

first: Soonyean

last: Hwang


title: The relationship between DNA methylation, genetic and expression inter-individual variation in untransformed human fibroblasts [genotyping]

status: Public on Dec 11 2013

city: Montreal

first: Tomi

middle: Markku

last: Pastinen

state: Quebec

address: 740, Dr. Penfield Avenue

institute: McGill University and Génome Québec Innovation Centre

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

summary: Background   DNA methylation has long been known to play an essential role in the epigenetic regulation of gene expression and other cellular functions, and has been in some cases linked to genetic variation. While its presence near the transcription start site of a gene has been associated with reduced expression, the variation in methylation levels across individuals, its environmental or genetic causes, and its association with gene expression remain poorly understood.   Results   We report the joint analysis of sequence variants, gene expression and DNA methylation in primary fibroblast samples derived from a set of 62 unrelated individuals. Approximately 2% of the most variable CpG sites are mappable in cis to sequence variation, usually within 5kb. However, only 5% of those mappable CpG sites also have methylation levels that correlate in cis with a gene's expression level. Methylation and gene expression are often correlated but not always in the expected direction (negative for promoter CpGs, positive for gene body CpGs). Population-level correlation between methylation and expression is strongest in a subset of developmentally significant genes, including all four HOX clusters. The presence and sign of this correlation are best predicted using specific histone marks or DNase hypersensitivity rather than position of the CpG site with respect to the gene, showing that other epigenetic markers are necessary to interpret downstream effects of individual methylation variants.   Conclusion  Our results indicate strong relationships between gene expression and DNA methylation in untransformed adult human fibroblasts, with considerable involvement of chromatin features and relatively modest involvement of sequence variation.

overall_design: 98 human skin fibroblast samples obtained from Coriell and McGill Cellbank, genotypes were obtained using Illumina HumanOmni 1M Beadchips.

first: Bing

last: Ge


title: Methylation status of OCI Ly3 SP vs. nonSP

status: Public on Dec 07 2013

city: Goettingen

first: Raphael

last: Koch

address: Robert Koch Str

department: Hematology

institute: University Medicine of Goettingen

summary: Promotor methylation status of Side Population cells of DLBCL cell line OCI Ly3 was compared to non Side Population Cells of OCI Ly3

overall_design: DLBCL Cell Line OCI Ly3 was cultured and stained using Hoechst33342. FACS analysis showed a distinct Side Population. Side Population Cells and non Side Population cells were sorted, gDNA was extracted and Methylation analysis was performed using Illumin 27k Bead Array.

first: Gerald

last: Wulf


title: Epigenome analysis of human brain gliomas (part 1)

status: Public on Dec 12 2013

city: Beijing

first: Tao

last: Jiang

address: Tiantan Xili No.6, Dongcheng District

department: Neurosurgery

institute: Beijing Tiantan Hospital, Capital Medical University

summary: Genome wide DNA methylation profiling of 112 human glioma samples. The Illumina Infinium 27k Human DNA methylation Beadchip v1.2 was used to obtain DNA methylation profiles across approximately 27,000 CpGs in glioma samples, including 55 WHO grade 2 glioma samples, 33 WHO grade 3 glioma samples and 24 WHO grade 4 glioma samples.

overall_design: Bisulphite converted DNA from the 112 glioma samples were hybridised to the Illumina Infinium 27k Human Methylation Beadchip v1.2

first: Zheng


title: OCI Ly3 SP vs. nonSP cells

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

overall_design: Refer to individual Series