title: Sperm DNA methylation

status: Public on Jun 02 2011

city: Providence

first: Sara

last: Pacheco

state: RI

address: 70 Ship Street, Room 510

department: Pathology and Lab Medicine

institute: Brown University

summary: BACKGROUND: In previous studies using candidate gene approaches, low sperm count (oligospermia) has been associated with altered sperm mRNA content and DNA methylation in both imprinted and non-imprinted genes. We performed a genome-wide analysis of sperm DNA methylation and mRNA content to test for associations with sperm function. METHODS AND RESULTS: Sperm DNA and mRNA were isolated from 21 men with a range of semen parameters presenting to a tertiary male reproductive health clinic.  DNA methylation was measured with the Illumina Infinium array at 27,000 CpG loci.  Unsupervised clustering of methylation data differentiated the 21 sperm samples by their motility values. Recursively partitioned mixture modeling (RPMM) of methylation data resulted in four distinct methylation profiles that were significantly associated with sperm motility (P=0.01).  Linear models of microarray analysis (LIMMA) was performed based on motility and identified 9,189 CpG loci with significantly altered methylation (Q<0.05) in the low motility samples, with many loci located in genes associated with subfertility and epigenetic regulation. In the low motility samples, the majority of disrupted CpG loci (80%) were hypomethylated.  Of the aberrantly methylated CpGs, 194 were associated with imprinted genes almost equally distributed into hypermethylated (predominantly paternally expressed) and hypomethylated (predominantly maternally expressed) groups. Sperm mRNA was measured with the Human Gene 1.0 ST Affymetrix GeneChip Array. LIMMA analysis based on motility identified 20 candidate transcripts as differentially expressed in low motility sperm, including HDAC1 (NCBI 3065), SIRT3 (NCBI 23410), and DNMT3A (NCBI 1788).  Altered expression of these epigenetic regulatory genes was associated with RPMM DNA methylation class. CONCLUSIONS:  Using integrative genome-wide approaches to study epigenetic and gene expression patterns in human sperm we identified CpG methylation profiles and mRNA alterations associated with low sperm motility, and that low motility sperm may have aberrant genome-wide hypomethylation due to excess HDAC1 activity.

overall_design: See summary above

first: Kim

last: Boekelheide


title: Genome-scale analysis of aberrant DNA methylation in colorectal cancer

status: Public on Jun 03 2011

city: Los Angeles

first: Toshinori

last: Hinoue

state: CA

address: 1450 Biggy Street, NRT G511

country: USA

institute: USC Epigenome Center

summary: To characterize DNA methylation-based subgroups in colorectal cancer, we performed genome-scale DNA methylation profiling of 125 colorectal tumor samples and 29 histologically normal-adjacent colonic tissue samples 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 four DNA methylation-based subgroups of CRC using model-based cluster analyses. Each subtype shows characteristic genetic and clinical features, indicating that they represent biologically distinct subgroups.

overall_design: Bisulfite converted DNA from fresh frozen 125 colorectal tumors and 29 adjacent normal tissues were hybridized to the Illumina Infinium 27k Human Methylation Beadchip v1.2

first: Daniel

middle: J

last: Weisenbuerger

first: Fei

last: Pan

first: Peter

middle: W

last: Laird


title: ChIP-on-chip of H2A variants and H3 from normal Prostate epithelial cells (PrEC) and the LNCaP cancer cell line

status: Public on Jul 13 2011

city: Darlinghurst

first: Aaron

last: Statham

state: NSW

address: 384 Victoria St

department: Cancer Department

country: Australia

institute: Garvan Institute of Medical Research

type: Genome binding/occupancy profiling by genome tiling array

summary: H2A.Z is an evolutionarily conserved H2A variant implicated in the regulation of gene expression, however its role in transcriptional deregulation in cancer remains poorly understood. Using genome-wide studies, we investigated the role of promoter-associated H2A.Z and acetylated H2A.Z (acH2A.Z) in gene deregulation and its relationship with DNA methylation and H3K27me3 in prostate cancer. Our results reconcile the conflicting reports of positive and negative roles for histone H2A.Z and gene expression states. We find that H2A.Z is enriched in a bimodal distribution at nucleosomes surrounding the transcription start sites (TSSs) of both active and poised gene promoters, whereas acH2A.Z is only localized at the TSSs of actively expressed genes. Interestingly, H2A.Z spreads across the entire promoter of inactive genes in a de-acetylated state. Gene deregulation in cancer is also associated with a reorganization of acH2A.Z and H2A.Z nucleosome occupancy across the promoter region and TSS of genes. Notably, in cancer cells we find that a gain of acH2A.Z at the TSS occurs with an overall decrease of H2A.Z levels in concert with oncogene activation. Furthermore, underacetylated H2A.Z at TSSs is increased with silencing of tumour suppressor genes. We also demonstrate that acH2A.Z anti-correlates with promoter H3K27me3 and DNA methylation. For the first time, we show that acetylation of H2A.Z is a key modification involved in gene activity in normal cells and in epigenetic gene deregulation in tumourigenesis.

overall_design: ChIP samples against histones amplified and hybridised to Affymetrix Human Promoter 1.0R arrays, normalised to Input samples hybridised alongside

first: Fátima

last: Valdés-Mora

first: Jenny

middle: Z

last: Song

middle: L

first: Dario

last: Strbenac

first: Mark

middle: D

last: Robinson

first: Shalima

middle: S

last: Nair

first: Kate

middle: I

last: Patterson

first: David

last: Tremethik

first: Clare

last: Stirzaker

first: Susan

last: Clark


title: DNA methylation represents one of the key regulator that transcriptional control of highly expressed genes in gastric cancer.

status: Public on May 31 2011

city: Daejeon

first: Han-Chul

last: Lee

address: 111 Gwahangno, Yuseong-gu

department: Medical Genome Research Center

country: South Korea

institute: KRIBB

summary: We used microarray approach to establish demethylated specific genes profiles in early gastric cancer.

overall_design: We analyzed 11 gastric cancer cell lines and 32 pairs of gastric cancer and normal samples to discover methylation signatures specific to gastric cancer cells.

first: KYU-SANG

last: SONG

first: SEUNG-MOO

last: NOH


title: Smad2/3 binding sites in HaCaT, HepG2, and Hep3B cells determined by an Affymetrix promoter array

status: Public on Jun 08 2011

city: Tokyo

first: Daizo

last: Koinuma

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

department: Pathology

country: Japan

institute: University of Tokyo

summary: Specific regulation of target genes by transforming growth factor-β (TGF-β) in a given cellular context is determined in part by transcription factors and cofactors that interact with the Smad complex. In the present study, we determined Smad2 and Smad3 (Smad2/3) binding regions in the promoters of known genes in HepG2 hepatoblastoma cells, and compared them to those in HaCaT epidermal keratinocytes to elucidate the mechanisms of cell-type- and context-dependent regulation of transcription induced by TGF-β. Our results show that 81% of the Smad2/3 binding regions in HepG2 cells were not shared with those found in HaCaT cells. Hepatocyte nuclear factor 4α (HNF4α) is expressed in HepG2 cells, but not in HaCaT cells, and the HNF4α binding motif was identified as an enriched motif in the HepG2-specific Smad2/3 binding regions. ChIP-sequencing analysis of HNF4α binding regions under TGFα stimulation revealed that 32.5% of the Smad2/3 binding regions overlapped HNF4α bindings. MIXL1 was identified as a new combinatorial target of HNF4α and Smad2/3, and both the HNF4α protein and its binding motif were required for the induction of MIXL1 by TGF-β in HepG2 cells. These findings generalize the importance of binding of HNF4α on Smad2/3 binding genomic regions for HepG2-specific regulation of transcription by TGF-β, and suggest that certain transcription factors expressed in a cell-type-specific manner play important roles in the transcription regulated by the TGF-β-Smad signaling pathway.

overall_design: We determined and analyzed cell-line-specific Smad2/3 binding sites by ChIP-chip. HaCaT, HepG2, and Hep3B cells were treated with TGF-β for 1.5 h. anti-Smad2/3 ChIP samples and their input DNAs were hybridized to the arrays. Each bed file contains Smad2/3 binding sites determined by two-sample analysis (NCBIv36/hg18, p<10-4).

first: Anna

last: Mizutani

first: Shuichi

last: Tsutsumi

first: Naoko

last: Kamimura

first: Masato

last: Morikawa

first: HiroshiI

last: Suzuki

first: Kohei

last: Miyazono

first: Hiroyuki

last: Aburatani


title: Novel aspects of transcriptional regulation in the winter survival and maintenance mechanism of perennial woody plants, poplar.

status: Public on May 19 2011

city: Yongin

first: Jae-Heung

last: Ko

state: Gyeonggi

address: 1 Seocheon-dong, Giheung-gu

department: Plant & Environmental Resources

institute: Kyung Hee University

summary: Winter survival and maintenance strategy is crucial in temperate woody plants. Here, we demonstrate novel aspects of the transcriptional regulations adopted by perennial tree species in winter/dormancy, employing a biochemical and whole transcriptome analysis. As expected, genes related to cold hardiness and defense are over-represented. Interestingly, carbohydrate biosynthesis and transport-related genes were very actively expressed in winter/dormancy. Further biochemical analyses verified the dormancy/winter transcription phenotype. Furthermore, dormancy/winter preferential expression of genes involved in the cell wall biosynthesis/modification, circadian rhythm, the indirect transcriptional regulation (RNA metabolism), and chromatin modification/remodeling were identified. Taken together, regulation of gene expression in the winter survival and maintenance may include not only controlled by promoter binding transcription factors but may also be regulated at the post-transcriptional and chromatin levels.

overall_design: In the first step towards the understanding of molecular mechanisms underlying the winter survival and maintenance of perennial trees, we examined the characteristics of transcription phenotype of the dormancy/winter stem compared to the active growth/summer stem by using a whole transcriptome analysis (GeneChip Poplar Genome Array; Affymetrix). Poplar Genome Array has a total of 61,251 probe sets, representing 57,423 poplar gene models, and allows us to interrogate a total of 41,558 unique gene models because of the probe set redundancy. Slight redundancy of the probe sets within a single chip gave us a unique opportunity to have internal comparisons of the particular genes. Very high reproducibility (R2 > 0.97) between the replicated samples was found. Further confirmation of the GeneChip data was made by semi-quantitative RT-PCR analysis using several genes showing the summer or winter biased expression. Based on these results, further analysis of winter stem transcriptome against summer stem was performed.

first: Kyung-Hwan

last: Han


title: Classical Hodgkin lymphoma shows epigenetic features of an abortive plasma cellular differentiation: acetyl H3 K9/14 ChIP-chip

status: Public on May 05 2011

city: Berlin

first: Volkhard

last: Seitz

address: Hindenburgdamm 30

department: Institute of Pathology

country: Germany

institute: Charité Universitätsmedizin

summary:
Background
Epigenetic changes are involved in the extinction of the B-cell gene expression program of classical Hodgkin lymphoma. However, little is known regarding epigenetic similarities between classical Hodgkin lymphoma and plasma cell myeloma cells, both of which share an extinction of the gene expression program of mature B-cells.

Design and methods
Global histone H3 acetylation patterns were determined in cell lines derived from classical Hodgkin lymphoma, plasma cell myeloma and B-cell lymphoma by chromatin immunoprecipitation and subsequent hybridization onto promoter tiling arrays. H3K27 trimethylation was analyzed by chromatin immunoprecipitation and real-time DNA-PCR for selected genes. Epigenetic modifications were compared to gene expression data.

Results
B-cell characteristic genes were hypoacetylated in classical Hodgkin lymphoma and plasma cell myeloma cell lines, as demonstrated by comparison of their histone H3 acetylation patterns to those of B-cell lines. However, the number of genes jointly hyperacetylated and expressed in classical Hodgkin lymphoma and plasma cell myeloma cell lines, such as IFR4/MUM1 and RYBP, is limited. Moreover, H3K27 trimethylation for selected B-cell characteristic genes revealed that this additional epigenetic silencing is much more prevalent in classical Hodgkin lymphoma as compared to plasma cell myeloma.

Conclusion
Our epigenetic data support the view that classical Hodgkin lymphoma is characterized by an abortive plasma cell differentiation with a down-regulation of B-cell characteristic genes but without activation of most plasma cell typical genes.

overall_design: Three Hodgkin lymphoma cell lines (L1236, KM-H2, L428; referred to as cHL cell lines), three plasma cell myeloma cell lines (L363, U266, LP-1; referred to as PCM cell lines) and three B-cell lymphoma cell lines (SU-DHL4, SU-DHL6 [diffuse large B-cell lymphoma; DLBCL], Namalwa [Burkitt lymphoma; BL]; referred to as B-cell lines) were used for ChIP following the protocol developed by the group of Young (PMID 17406303) with minor modifications. For each ChIP experiment, 10 µg of anti-acetyl-histone H3 (Lys9 + Lys14) antibody was employed.  All experiments were performed in duplicates or triplicates. A detailed protocol is provided as supplementary information in the publication linked to this Series.

first: Philippe

last: Thomas

first: Karin

last: Zimmermann

first: Ulrike

last: Paul

first: Anke

last: Ehlers

first: Maria

last: Joosten

first: Lora

last: Dimitrova

first: Dido

last: Lenze

last: Sommerfeld

first: Elisabeth

last: Oker

first: Ulf

last: Leser

first: Harald

last: Stein

first: Michael

last: Hummel


title: FT1 and FT2 network analysis in poplar

status: Public on May 23 2011

city: Monticello

first: Joshua

last: Adams

state: AR

address: PO Box 3468

department: Forest Resources

institute: University of Arkansas-Monticello

summary: We conducted microarray experiments by comparing constitutive and inducible Flowering Locus T1 (FT1) and FT2 constructs with appropriate controls, followed by the identification of common targets of Pro35S:FT1 and ProHSP:FT1 or Pro35S:FT2 and ProHSP:FT2.

sample_organism:
Populus tremula x Populus tremuloides
Populus tremula x Populus alba

overall_design: Independent samples of leaf tissues were collected from 1- to 2-year-old plants. Each replication represents an individual plant from one of the treatment lines. RNA was extracted from tissues and hybridized on the Affymetrix GeneChip Poplar Genome Array.

first: Chuan-Yu

last: Hsu

first: Hyejin

last: Kim

first: Kyoungok

last: No

first: Caiping

last: Ma

first: Steven

last: Strauss

first: Jenny

last: Drnevich

first: Norman

last: Wickett

first: Lindsay

last: Vandervelde

first: Jeffery

last: Ellis

first: Brandon

last: Rice

first: Lee

last: Gunter

first: Amy

last: Brunner

first: Grier

last: Page

first: John

last: Carlson

first: Claude

last: dePamphilis

first: Dawn

last: Luthe

first: Cetin

last: Yuceer


title: Progression Free Survival in Ovarian Cancer is Reflected in Epigenetic DNA-Methylation Profiles

status: Public on May 04 2011

city: Aachen

first: Qiong

last: Lin

state: NRW

address: Universitatsklinikum Aachen, RWTH

department: Cell Biology

institute: Institute for Biomedical Engineering

summary:
Objective: Many patients with ovarian cancer disease relapse within 6 months after adjuvant chemotherapy, with a limited prognosis. Epigenetic modifications have been shown to play an important role in tumor development and formation. Therefore, global analysis of DNA methylation patterns might reveal specific CpG sites that correlate with progression-free interval (PFI) after therapy. Methods: Twenty samples of advanced ovarian cancer with a predominantly serous papillary histological subtype were subjected to DNA methylation profiling. Illumina HumanMethylation27 BeadChip technology was used for simultaneous analysis of 27,578 CpG sites in 114,000 genes. Results: Differential DNA methylation of various cytosines correlated with PFI. However, this becomes only significant by classification according to PFI with a cutoff of 128 months. Longer survival was
associated with hypomethylation at specific CpG sites (e.g. GREB1, TGIF and TOB1) and hypermethylation in other genes (e.g. TMCO5, PTPRN and GUCY2C). Gene ontology analysis revealed that differentially methylated genes were significantly overrepresented in the categories telomere organization, mesoderm development and immune regulation. Conclusion: Epigenetic modifications at specific CpG sites correlate with PFI in ovarian cancer. Therefore, such analysis might be of prognostic value.

overall_design: Bisulphite converted DNA from the 20 samples were hybridised to the Illumina Infinium 27k Human Methylation Beadchip

first: Dirk

middle: O

last: Bauerschlag

first: Ole

last: Ammerpohl

first: Karen

last: Bräutigam

first: Christian

last: Schem

first: Marion

middle: T

last: Weigel

first: Felix

last: Hilpert

first: Norbert

last: Arnold

first: Nicola

last: Maass

first: Ivo

last: Meinhold-Heerlein

first: Wolfgang

last: Wagner


title: Clone History Shapes Populus Drought Responses

status: Public on May 01 2011

city: Toronto

first: Malcolm

middle: M.

last: Campbell

state: ON

address: 25 Willcocks Street

department: Cell & Systems Biology

country: Canada

institute: University of Toronto

summary: Just as animal monozygotic twins can experience different environmental conditions by being reared apart, individual genetically-identical trees of the genus Populus can also be exposed to contrasting environmental conditions by being grown in different locations.  As such, clonally-propagated Populus trees provide an opportunity to interrogate the impact of individual environmental history on current response to environmental stimuli.  To test the hypothesis that current responses to an environmental stimulus, drought, are contingent on environmental history, the transcriptome-level drought responses of three economically important hybrid genotypes: DN34 (Populus deltoides x P. nigra); Walker (P. deltoides var. occidentalis x (P. laurifolia x P. nigra)); and, Okanese (‘Walker’ x (P. laurifolia x P. nigra)) derived from two different locations were compared. Strikingly, differences in transcript abundance patterns in response to drought were based on differences in geographic origin of clones for two of the three genotypes. This observation was most pronounced for the genotypes with the longest time since establishment and last common propagation.  Differences in genome-wide DNA methylation paralleled the transcriptome level trends, where the clones with the most divergent transcriptomes and clone history had the most marked differences in the extent of total DNA methylation, suggesting an epigenetic basis for the clone-history-dependent transcriptome divergence. The data provide insights into the interplay between genotype and environment in the ecologically and economically important Populus genus, with implications for both the industrial application of Populus trees, and the evolution and persistence of these important tree species.

sample_organism:
Populus x canadensis
Populus sp. cv. 'Walker'
Populus sp. cv. 'Okanese'

overall_design: 72 arrays total. 2 time points. 2 water regimes. 3 biological replicates per treatment

first: Sherosha

last: Raj

first: Katharina

last: Braeutigam

first: Erin

last: Hamanishi

first: Olivia

last: Wilkins

first: Barbara

last: Thomas

first: William

last: Schroeder

first: Shawn

last: Mansfield

first: Aine

last: Plant

middle: M


title: Isolation of poplar genes involved in xylem vessel differentiation

city: Ikoma

first: Misato

last: Ohtani

address: 8916-5 Takayama-cho

department: Graduate School of Biological Sciences

institute: NAIST

summary: Downstream genes of PtVNS genes were explored with inducible expression system using glucocorticoid receptor (GR). Transgenic poplar plants expressing 35S:AtVND7-VP16-GR were treated with dexamethazone (DEX). A number of genes related to the formation of xylem vessels were induced by DEX.

overall_design: Total RNAs of the transgenic plants carrying 35S:AtVND7-VP16-GR treated with and without DEX were compared.

first: Nobuyuki

last: Nishikubo

first: Taku

last: Demura


title: Depolymerization of plant cell wall glycans by symbiotic human gut bacteria (Bacteroides thetaiotaomicron)

city: Ann Arbor

first: Eric

middle: Charles

last: Martens

state: MI

address: 1150 West Medical Center Drive

department: Dept. of Microbiology and Immunology

institute: University of Michigan Medical School

summary: Symbiotic bacteria inhabiting the distal human gut have evolved under intense pressure to utilize complex carbohydrates, predominantly plant cell wall glycans abundant in our diets. These substrates are recalcitrant to depolymerization by digestive enzymes encoded in the human genome, but are efficiently targeted by some of the ~103-104 bacterial species that inhabit this niche. These species augment our comparatively narrow carbohydrate digestive capacity by unlocking otherwise unusable sugars and fermenting them into host-absorbable forms, such as short-chain fatty acids. We used phenotype profiling, whole-genome transcriptional analysis and molecular genetic approaches to investigate complex glycan utilization by two fully sequenced and closely related human gut symbionts: Bacteroides thetaiotaomicron and Bacteroides ovatus. Together these species target all of the common glycosidic linkages found in the plant cell wall, as well as host polysaccharides, but each species exhibits a unique ‘glycan niche’: in vitro B. thetaiotaomicron targets plant cell wall pectins in addition to linkages contained in host N- and O-glycans; B. ovatus uniquely targets hemicellulosic polysaccharides along with several pectins, but is deficient in host glycan utilization.

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

overall_design: Growth of Bacteroides thetaiotaomicron in vitro in minimal medium plus different purified complex glycans. Observation of increased gene expression was used to determine genes that are involved in metabolism of each glycan. Two biological replicates each.

middle: C

first: Jeffrey

last: Gordon


title: Depolymerization of plant cell wall glycans by symbiotic human gut bacteria

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

sample_organism:
Bacteroides thetaiotaomicron
Bacteroides ovatus

platform_organism:
Bacteroides thetaiotaomicron
Phocaeicola vulgatus
Parabacteroides distasonis
Methanobrevibacter smithii
Lachnospira eligens
Agathobacter rectalis
Bacteroides thetaiotaomicron VPI-5482
Bacteroides sp. WH2
Blautia obeum ATCC 29174
[Ruminococcus] torques ATCC 27756
Dorea longicatena DSM 13814
[Clostridium] scindens ATCC 35704
Bacteroides ovatus ATCC 8483
Bacteroides uniformis ATCC 8492
Faecalibacterium prausnitzii M21/2
Bacteroides caccae ATCC 43185
Collinsella aerofaciens ATCC 25986
Thomasclavelia spiroformis DSM 1552
Phocaeicola vulgatus ATCC 8482
Parabacteroides distasonis ATCC 8503
Agathobacter rectalis ATCC 33656

overall_design: Refer to individual Series


title: DNA methylation profiling reveals novel biomarkers and important roles for DNA methyltransferases in prostate cancer

status: Public on Apr 19 2011

city: Stanford

first: Yuya

last: Kobayashi

address: 259 Campus Dr

department: Genetics

institute: Stanford University

summary:
Genome wide DNA methylation profiling of normal and tumor prostate samples, as well as cultured primary prostate cells overexpressing DNA Methyltransferases (DNMTs) and EZH2
Candidate gene based studies have identified a handful of aberrant CpG DNA methylation events in prostate cancer. However, DNA methylation profiles have not been compared on a large scale between prostate tumor and normal prostate, and the mechanisms behind these alterations are unknown. In this study, we quantitatively profiled 95 primary prostate tumors and 86 healthy prostate tissue samples for their DNA methylation levels at 26,333 CpGs representing 14,104 gene promoters by using the Illumina HumanMethylation27 platform. A 2-class Significance Analysis of this dataset revealed 5,912 CpG sites with increased DNA methylation and 2,151 CpG sites with decreased DNA methylation in tumors (FDR < 0.8%). Prediction Analysis of this dataset identified 87 CpGs that are the most predictive diagnostic methylation biomarkers of prostate cancer. By integrating available clinical follow-up data, we also identified 69 prognostic DNA methylation alterations that correlate with biochemical recurrence of the tumor. To identify the mechanisms responsible for these genome-wide DNA methylation alterations, we measured the gene expression levels of several DNA methyltransferases (DNMTs) and their interacting proteins by TaqMan qPCR and observed increased expression of DNMT3A2, DNMT3B, and EZH2 in tumors. Subsequent transient transfection assays in cultured primary prostate cells revealed that DNMT3B1 and DNMT3B2 overexpression resulted in increased methylation of a substantial subset of CpG sites that also showed tumor-specific increased methylation.

overall_design:
Bisulfite converted DNA from 193 samples were hybridized to the Illumina Infinium 27k Human Methylation Beadchip v1.2.
The tissue samples (first 181) and the cultured cell samples (last 12) were normalized independently.

first: Devin

last: Absher

first: James

last: Brooks

first: Richard

last: Myers

first: Gavin

last: Sherlock


title: Poplar cultivars Soligo and Carpacio

status: Public on Apr 01 2011

city: Beaucouze

first: sandrine

last: balzergue

address: Rue G. Morel

country: France

institute: INRA

summary:
affy_genomic_poplar - affy_genomic_poplar - The project aims to identify genes of interest for water deficit acclimation in poplar. We look for genes and gene expression networks related to drought stress in two hybrid cultivars, differing in their drought tolerance in field. Affymetrix poplar genome array was designed on several Populus species. In order to deal with comparative approaches, we checked the convenience of the array by hybridizing genomic DNA of the two hybrid cultivars (Populus deltoides × Populus nigra, namely ‘cv Carpaccio’ and ‘cv Soligo’). This point is important as transcript sequence might have diverged in the two genomes (Fossati et al, 2005), which could lead to absence of hybridization without physiological meaning. -Two poplar cultivars, Soligo (S) and Carpacio (C) were grown in controlled conditions. Mature leaves were collected and genomic DNA was extracted from leaves in CTAB buffer. gDNA was fragmented with DNAse1. DNA fragments were labelled with Biotin N6-ddATP and hybridized on Affymetrix poplar genome array. Two technical replicates per genotype were performed.

Keywords: genomic comparison,gain of fuction epimutation

overall_design: 4 arrays - poplar

first: Sandrine

last: Balzergue

first: Marie-Béatrice

last: Bogeat-Triboulot

first: David

last: Cohen

first: Marie-Laure

last: Martin-Magniette


title: DNA Methylation Dynamics in Human Induced Pluripotent Stem Cells over Time

status: Public on Apr 14 2011

city: Setagaya-ku

first: Akihiro

last: Umezawa

state: Tokyo

department: Center for Regenerative Medicine

institute: National Center for Child Health and Development

summary: We examined genome-wide DNA methylation with 22 human iPSC lines derived from different cell types and human ESC lines using Illumina’s Infinium HumanMethylation27 and focused on aberrant methylation sites in iPSCs for up to 42-week continuous cultivation. The iPSCs exhibited distinct epigenetic distances from ESCs at early passage. Continuous passaging of the iPSCs diminishes these differences between iPSCs and ESCs.

overall_design: Bisulphite converted DNA from the 47 samples were hybridised to the Illumina Infinium 27k Human Methylation Beadchip v1.2

first: Koichiro

last: Nishino

first: Masashi

last: Toyoda

first: Mayu

last: Yamazaki-Inoue

first: Yoshihiro

last: Fukawatase

first: Emi

last: Chikazawa

first: Hironari

last: Sakaguchi

first: Hidenori

last: Akutsu


title: Epigenome analysis of male identical twin pairs discordant for sexual orientation, age 21 to 55.

status: Public on Apr 21 2011

first: Sven

last: Bocklandt

state: California

address: Gonda 5524, 695 Charles Young Drive S

department: Department of Human Genetics

institute: UCLA

summary: Genome wide DNA methylation profiling of saliva samples from male identical twins discordant for sexual orientation, age 21 to 55. The Illumina Infinium 27k Human DNA methylation Beadchip v1.2 was used to obtain DNA methylation profiles across approximately 27,000 CpGs in bisulfite converted DNA. Samples included 34 pairs of identical twins and one set of identical triplets, and 13 hybridisations were technical replicates of a selection of those samples.

overall_design: Bisulphite converted DNA isolated from saliva of identical twin pairs were hybridised to the Illumina Infinium 27k Human Methylation Beadchip v1.2


title: Expression data from an in vitro growth of Methanobrevibacter smithii PS

status: Public on Mar 30 2011

city: St Louis

first: Federico

middle: E

last: Rey

state: MO

address: 4444 Forest Park Blvd

institute: Washington University

summary:
RNA-sequencing is a powerful tool for exploring expression profiles of microbial species that does not require the production of a custom genechip.
We used microarrays to compare our quantitative RNA-sequencing method to the standard expression quantification methods

overall_design: Methanobrevibacter smithii PS cultures were grown to stationary phase under 80% hydrogen, 20% CO2, with varying amounts of formate.  RNA was extracted and purified, then divided into two aliquots per sample.  One aliquot was prepared for hybridization on Affymetrix gene chips, the other was prepared for microbial RNA-sequencing.

first: Elizabeth

last: Hansen


title: EQUIVALENCE OF CONVENTIONALLY-DERIVED AND PARTHENOTE-DERIVED HUMAN EMBRYONIC STEM CELLS

status: Public on Mar 15 2011

city: Irvine

first: Julie

middle: V

last: Harness

address: 845 Health Sciences Rd.

department: Anatomy & Neurobiology

institute: University of California Irvine

summary: Parthenote lines proliferated more slowly than conventional hESC lines, and yielded lower quantities of less mature differentiated cells in a neural progenitor cell (NPC) differentiation protocol. However, the cell lines performed  similarly in a RPE differentiation protocol. The DNA methylation analysis showed similar general profiles, but the two cell types differed in methylation of imprinted genes. There were no major differences in gene expression between the lines before differentiation, but when differentiated into NPCs, the two cell types differed in expression of extracellular matrix (ECM) genes. Conclusions/Significance: These data show that hESC and phESC are similar in the undifferentiated state, and both cell types are capable of differentiation along neural lineages. The differences between the cell types, in proliferation and extent of differentiation, may be linked, in part, to the observed differences in ECM synthesis and methylation of imprinted genes.

overall_design: hESC and phESC were exposed to the same expansion conditions and subsequent neural and retinal pigmented epithelium (RPE) differentiation protocols. Growth rates and gross morphology were recorded during expansion.  RTPCR for developmentally relevant genes and global DNA methylation profiling were used to compare gene expression and epigenetic characteristics.

first: Nikolay

middle: A

last: Turovets

first: Magdalene

last: Seiler

first: Gabriel

last: Nistor

first: Gulsah

last: Altun

first: Larisa

last: Agapova

last: Ferguson

first: Louise

last: Laurent

first: Jeanne

middle: F

last: Loring

first: Hans

last: Keirstead


title: Prognostic Gene Expression Signature of Carcinoma Associated Fibroblasts in Non-Small Cell Lung Cancer [methylation profiling]

status: Public on Apr 08 2011

first: Ming-Sound

last: Tsao

institute: Ontario Cancer Institute/ Princess Margaret Hospital

summary:
The tumor microenvironment strongly influences cancer development, progression and metastasis. The role of carcinoma-associated fibroblasts (CAFs) in these processes and their clinical impact has not been studied systematically in non-small cell lung carcinoma (NSCLC). We established primary cultures of CAFs and matched normal fibroblasts (NFs) from 15 resected NSCLC. We demonstrate that CAFs have greater ability than NFs to enhance the tumorigenicity of lung cancer cell lines. Microarray gene expression analysis of the 15 matched CAF and NF cell lines identified 46 differentially expressed genes, encoding for proteins that are significantly enriched for extracellular proteins regulated by the TGF-beta signaling pathway. We have identified a subset of 11 genes that formed a prognostic gene expression signature, which was validated in multiple independent NSCLC microarray datasets. Functional annotation using protein-protein interaction analyses of these and published cancer stroma-associated gene expression changes revealed prominent involvement of the focal adhesion and MAPK signalling pathways. Fourteen (30%) of the 46 genes also were differentially expressed in laser-capture micro-dissected corresponding primary tumor stroma compared to the matched normal lung. Six of these 14 genes could be induced by TGF-beta1 in NF. The results establish the prognostic impact of CAF-associated gene expression changes in NSCLC patients.
Methylation profiles of 5 pairs of  were included in a molecular characterization of NSCLC fibroblast cell lines (CAFs) vs. normal lung fibroblasts (NFs).

overall_design: Methylation profiles of 5 paired primary NSCLC fibroblast cell lines (CAFs) and normal lung fibroblasts (NFs) were generated. Genes were determined to be hyper- and hypo-methylated based on paired analysis.

first: Roya

last: Navab

first: Dan

last: Strumpf


title: Bisphenol A Induced the Expression of DNA Repair Genes in Human Breast Epithelial Cells (methylation data)

status: Public on Mar 10 2011

city: Charlottesville

first: Yong

last: Huang

state: VA

address: 1340 Jefferson Park Ave

department: Medicine

institute: University of Viginia

type: Methylation profiling by genome tiling array

summary: Xenoestrogens are part of a group of agents termed endocrine disruptors because of their capacity to perturb normal hormonal actions. It has been suggested that xenoestrogens may contribute to the development of hormone-dependent cancers, such as breast and endometrial cancers. Bisphenol A (BPA) is polymerized to manufacture polycarbonate plastic and epoxy resins. Human exposure occurs when BPA leaches from plastic-lined food and beverage cans. In the present work we are aiming to determine if BPA has carcinogenic properties by using an in vitro system. For this purpose the human breast epithelial cells MCF-10F were treated with 10-3M to 10-9M BPA continuously for two weeks. The MCF-10F cells treated with 10-3M and 10-4M BPA died, indicating that these concentrations were toxic for the human breast epithelial cells. The cells treated with 10-5M to 10-9M BPA were evaluated for formation of solid masses in collagen and invasion capacity, both phenotypes that are indicators of cell transformation. MCF-10F treated with 10-5M, 10-6M, 10-7M, 10-8M and 10-9M BPA formed a high percentage of solid masses (34.6%, 20%, 42.4%, 31.8% and 32.2%, respectively). Ten passages after BPA treatments, the invasive capacities of the cells were evaluated using Boyden chambers. The invasion capacity was lower in the cells treated at high concentrations of BPA (10-5M and 10-6M), and there was an increased invasion for the cells treated at low BPA concentration (10-9M) although, in all the cases the differences were not significant to the controls. Expression and DNA methylation analyses were performed with the cells treated with 10-5M and 10-6M BPA. We found that these cells showed an increased expression of BRCA1, BARD1, CtIP, RAD51 and BRCC3, all genes involved in DNA repair, and downregulation of PDCD5 and BCL2L11 (also known as BIM), both involved in apoptosis. The upregulation of CtIP was related to hypomethylation of the promoter/exon1 of this gene. Furthermore, BPA induced silencing of BCL2L11 by hypermethylation. This is the first demonstration that BPA induces neoplastic transformation of breast epithelial cells and that aberrant DNA methylation of genes involved in DNA repair and apoptosis could be involved in the initiation of the neoplastic process.

overall_design: MCF-10F, a normal-like Homo sapiens breast epithelial cell (HBEC) line that is ERa-negative PR-negative, was maintained in high calcium medium at 37°C and 5% CO2 until confluent. These cells were treated with different concentrations of BPA continuously for two weeks, adding fresh media every day. As controls, MCF-10F cells were not treated and maintained in the regular media or treated with 0.284% DMSO (vehicle). The cells treated with 10-5M or 10-6M BPA after the invasion assay were collected and expanded during 6 passages. DNA was isolated from the cells using a DNA extraction kit (Qiagen).

first: Sandra

last: Fernandez

first: Kara

last: Snider

first: Yan

last: Zhou

first: Jose

last: Russo


title: A Genome-wide Study of DNA Methylation Patterns and Gene Expression Levels in Multiple Human and Chimpanzee Tissues

status: Public on Feb 25 2011

city: Chicago

first: Athma

last: Pai

state: IL

address: 920 E. 58th Street

institute: University of Chicago

summary: It has long been hypothesized that changes in gene regulation have played an important role in primate evolution. However, despite the wealth of comparative gene expression data, there are still only few studies that focus on the mechanisms underlying inter-primate differences in gene regulation.  In particular, we know relatively little about the degree to which changes in epigenetic profiles might explain differences in gene expression levels between primates. To this end, we studied DNA methylation and gene expression levels in livers, hearts, and kidneys from multiple humans and chimpanzees.

sample_organism:
Pan troglodytes
Homo sapiens

overall_design: Genome wide DNA methylation profiling of heart, kidney, and liver samples from humans and chimpanzees.  The Illumina Infinium 27K Human DNA Methylation BeadChip v1.2 was used to compare DNA methylation profiles across approximately 10,575 CpG sites in human and chimpanzee tissue samples.  Samples included 6 human livers, 6 human kidneys, 6 human heart, 6 chimpanzee livers, 6 chimpanzee kidneys, and 6 chimpanzee hearts. Two techical replicates of bisulfite converted DNA from each of the 36 samples was hybridized to the Illumina HumanMethylation27 Beadchip. We limited our analysis to the  10,575 probes that were a perfect sequence match to both the human and chimpanzee genomes and which were associated with genes for which we had previously collected expression measurements across the three tissues.

first: Jordana

last: Bell

first: John

last: Marioni

first: Jonathan

middle: K

last: Pritchard

first: Yoav

last: Gilad


title: Epigenome analysis of normal and cancer tissues in prostate cancer

status: Public on Mar 01 2011

city: New Haven

last: Zhu

address: 60 collage street

institute: Yale Medical School

summary: Genome wide DNA methylation profiling of normal and cancer tissue samples in prostate cancer. The Illumina Infinium 27k Human DNA methylation Beadchip v1.2 was used to obtain DNA methylation profiles across approximately 27,000 CpGs. Samples are pool of 12 normal and 12 cancer tissues.

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

first: S

middle: J

last: Kim

first: W

last: Kelly

first: A

last: Fu

first: K

last: Haines

last: Hoffman


title: The effects of EBV transformation on methylation levels

city: Philadelphia

first: Minal

last: Caliskan

state: PA

address: 415 Curie Blvd., Room 540

institute: University of Pennsylvania

summary: Epstein-Barr virus (EBV)-transformed lymphoblastoid cell lines (LCLs) provide a conveniently accessible and renewable resource for functional studies in humans. The ability to accumulate multidimensional data pertaining to the same individual cell lines, from complete genomic sequences to detailed gene regulatory profiles, further enhances the utility of LCLs as a model system. A lingering concern, however, is that the changes associated with EBV transformation of LCLs reduce the usefulness of LCLs as a surrogate model for primary tissues. To evaluate the validity of this concern, we compared global promoter CpG profiles between CD20+ primary B cells and CD3+ primary T cells sampled from six individuals. Six independent replicates of transformed LCLs were derived from each sample.

overall_design: The study included 96 DNA samples: 8 different types (B cell + T cell + 6 independent LCLs per individual) x 6 individuals x 2 technical replicates (each DNA sample hybridized in duplicate).

first: Darren

last: Cusanovich

first: Carole

last: Ober


title: Wide ranging DNA methylation differences of primary trophoblast cell populations and derived-cell lines

status: Public on Jan 20 2011

city: Parkville

first: Richard

last: Saffery

state: Victoria

address: Flemington Rd

department: Cancer, Disease and Developmental Epigenetics

institute: Murdoch Children's Research Institute

summary: Difficulties associated with long term culture of primary trophoblasts have proven to be a major hurdle in their functional characterization. In order to circumvent this issue, several model cell lines have been established over many years using a variety of different approaches. Due to their differing origins, gene expression profiles, and behavior in vitro, different model lines have been utilized to investigate specific aspects of trophoblast biology. However, generally speaking, the molecular mechanisms underlying functional differences remain unclear. In this study, we profiled genome-scale DNA methylation in primary first trimester trophoblast cells and seven commonly used trophoblast-derived cell lines in an attempt to identify functional pathways differentially regulated by epigenetic modification in these cells. We identified a general increase in DNA promoter methylation levels in four choriocarcinoma (CCA)-derived lines and transformed HTR-8/SVneo cells, including hypermethylation of several genes regularly seen in human cancers, while other differences in methylation were noted in genes linked to immune responsiveness, cell morphology, development and migration across the different cell populations. Interestingly, CCA-derived lines show an overall methylation profile more similar to unrelated solid cancers than to untransformed trophoblasts, highlighting the role of aberrant DNA methylation in CCA development and/or long term culturing. Comparison of DNA methylation and gene expression in CCA lines and cytotrophoblasts revealed a significant contribution of DNA methylation to overall expression profile. These data highlight the variability in epigenetic state between primary trophoblasts and cell models in pathways underpinning a wide range of cell functions, providing valuable candidate pathways for future functional investigation in different cell populations. This study also confirms the need for caution in the interpretation of data generated from manipulation of such pathways in vitro.

overall_design: Purified primary trophoblast populations and trophoblast-derived cell lines were used

first: Jeffrey

last: Craig

first: Lavinia

last: Gordon

first: Ursula

last: Manuelpillai

first: Ashley

last: Moffett

first: Boris

last: Novakovic

first: Andrew

last: Sharkey

first: Nicholas

last: Wong


title: Comprehensive DNA methylation analysis of neuronal and non-neuronal nuclei in the human brain

status: Public on Feb 21 2011

city: Wako

first: Kazuya

last: Iwamoto

address: 2-1 Hirosawa

department: Brain Science Institute

institute: RIKEN

summary: We performed comprehensive DNA methylation analysis in neuronal and non-neuronal nuclei obtained from the human prefrontal cortex. This revealed that neuronal and non-neuronal nuclei manifest qualitatively and quantitatively distinctive DNA methylation patterns.

overall_design:
Profiling methylation pattern using methylated DNA enriched fraction by MethylCollector vs unmethylated DNA enriched fraction by McrBC treatment.
Bar files (see Sample supplementary files) were generated by MAT software and contain MAT scores in each probe.  Three bed files (see supplementary files linked below) contain high quality methylated regions in the neuronal, non-neuronal, or both fractions. After the consideration of effect of restriction enzymes, they are extracted based on the commonly methylated regions in all the relevant samples and that MAT score p values < 0.0001 in each sample.

first: Tadafumi

last: Kato


title: affy_popsec_nancy_leaves2008_poplar -Molecular bases of acclimatation and adaptation to water deficit in poplar

status: Public on Jan 15 2011

first: sandrine

last: balzergue

summary:
affy_popsec_nancy_leaves_poplar - affy_popsec_nancy_leaves2008_poplar  - This project aims to identify genes of interest for water deficit acclimation and/or adaptation in a tree species: poplar. We look for genes and gene expression networks related to drought stress. We intend to analyse the transcriptome in mature leaves, in two genotypes, Carpaccio and Soligo, at various stages and intensities of stress. During water deficit, leaves underwent many processes aiming to maintain cells integrity such as water status adjustment through osmoregulation or cell detoxication. These analyses intend to identify genes of interest involved in homeostasis maintenance. The comparison between medium and severe stress intensities and between early and long term stresses will power the selection of genes of interest. The co-analysis of two genotypes of contrasted tolerance to water deficit should help to discriminate genes presenting a potential adaptative character from genes responding passively to the constraint-In a first experiment, two poplar clones, Soligo (S) and Carpacio (C) were submitted to 4 treatments: control, mild water deficit, moderate water deficit (12-day long for both) and early-drought stress (about 36-h long). Growth and physiology was characterised on a batch of plants and samples collected on another batch of plants. In a second experiment, two poplar clones, Soligo (S) and Carpacio (C) were submitted to 2 treatments: control and moderate water deficit. Mature leaves were collected and total RNAs were extracted from each tree individually. Two pools of 3 (or 2) individuals were made using equimolar ratio. A pool is considered as one biological replicate and corresponds to one Affymetrix slide.

Keywords: treated vs untreated comparison

overall_design: 8 arrays - poplar

first: Sandrine

last: Balzergue

first: Marie-beatrice

last: Bogeat-triboulot

first: David

last: Cohen

first: Marie-Laure

last: Martin-Magniette


title: affy_popsec_nancy_leaves2007_poplar -Molecular bases of acclimatation and adaptation to water deficit in poplar

summary:
affy_popsec_nancy_leaves_poplar - affy_popsec_nancy_leaves2007_poplar  - This project aims to identify genes of interest for water deficit acclimation and/or adaptation in a tree species: poplar. We look for genes and gene expression networks related to drought stress. We intend to analyse the transcriptome in mature leaves, in two genotypes, Carpaccio and Soligo, at various stages and intensities of stress. During water deficit, leaves underwent many processes aiming to maintain cells integrity such as water status adjustment through osmoregulation or cell detoxication. These analyses intend to identify genes of interest involved in homeostasis maintenance. The comparison between medium and severe stress intensities and between early and long term stresses will power the selection of genes of interest. The co-analysis of two genotypes of contrasted tolerance to water deficit should help to discriminate genes presenting a potential adaptative character from genes responding passively to the constraint-In a first experiment, two poplar clones, Soligo (S) and Carpacio (C) were submitted to 4 treatments: control, mild water deficit, moderate water deficit (12-day long for both) and early-drought stress (about 36-h long). Growth and physiology was characterised on a batch of plants and samples collected on another batch of plants. In a second experiment, two poplar clones, Soligo (S) and Carpacio (C) were submitted to 2 treatments: control and moderate water deficit. Mature leaves were collected and total RNAs were extracted from each tree individually. Two pools of 3 (or 2) individuals were made using equimolar ratio. A pool is considered as one biological replicate and corresponds to one Affimetrix slide.

Keywords: treated vs untreated comparison

overall_design: 16 arrays - poplar


title: Genomic binding sites of non-metastatic 2 (NME2) across promoters in lung cancer A549 cells

status: Public on Feb 08 2011

city: Delhi

first: Vinod

middle: Kumar

last: Yadav

state: Delhi

address: Mall Road

department: Bioinformatics

country: India

institute: IGIB

summary: Non-metastatic 2 (NME2) is one of the first discovered suppressors of metastases. However, the molecular mechanisms underlying its anti-metatsic activity remain insufficiently characterized. We hypothesized that large scale transcriptional potential of NME2 might be at the core of this function. Using a combination of gene expression meta-analysis, and high throughput genomic assays, we explored the transcriptional targets of NME2. Specifically, we found >250 binding sites of NME2 across human gene promoters. Several of the novel targets identified in this way regulated cell adhesion and survival. We subsequently constructed NME2 target gene network which delineated a transcriptional program responsive to NME2 capable of restricting metastasis.

overall_design: Three sets of ChIP vs. mock-ChIP experiments were done. pcDNA plasmid was transfected to lung cancer, A549 cells to express NME2 tagged with MYC epitope which was subsequently immunoprecipitated using anti-MYC antibodies (after 48 hours of transfection). Non-specific IgG was used for mock immunoprecipitation.

first: Shantanu

last: Chowdhury


title: A Novel Approach Identifies New Differentially Methylated Regions (DMRs) Associated with Imprinted Genes

status: Public on Jan 26 2011

first: Rosanna

last: Weksberg

state: Ontario

address: 555 University Ave.

department: Genetics and Genome Biology

institute: The Hospital for Sick Children

summary: Imprinted genes are critical for normal human growth and neurodevelopment. We developed a strategy to identify new DNA differentially methylated regions (DMRs), a hallmark of imprinted genes. Using genome-wide methylation profiling, candidate DMRs were selected by identifying CpGs with putative allelic differential methylation in normal biparental tissues. In parallel, we looked for parent of origin-specific DNA methylation patterns in paternally derived human androgenetic complete hydatidiform mole (AnCHM), and maternally derived mature cystic ovarian teratoma (MCT).  Using this approach, we found known DMRs associated with imprinted genomic regions as well as new DMRs for known imprinted genes, NAP1L5 and ZNF597.  Most importantly, novel candidate imprinted genes were identified. The paternally methylated DMR for one candidate, AXL, a receptor tyrosine kinase, was validated by methylation analyses in humans. Further validation in mouse embryos showed that Axl was expressed preferentially from the maternal allele in a DNA methylation–dependent manner.

overall_design: We have analyzed 3 androgenetic complete hydatidiform mole (AnCHM), 16 white blood cell (WBC), 1 mature cystic ovarian teratoma (MCT), 5 placenta, and 1 lymphoblastoid cell line paternal UPD4 sample

first: Sanaa

last: Choufani

first: Jonathan

last: Shapiro

first: Martha

last: Susiarjo

first: Darci

last: Butcher

first: Daria

last: Grafodatskaya

first: Jose

last: Ferreira

first: Dalila

last: Pinto

first: Stephen

middle: W

last: Scherer

first: Lisa

middle: G

last: Shaffer

first: Philippe

last: Coullin

first: Isabella

last: Caniggia

first: Joseph

last: Beyene

first: Rima

last: Slim

first: Marisa

last: Bartolomei


title: Transcriptional signature of C/EBPBeta in Hep3B cells: Involvement of the LAP and LIP isoforms in hepatocarcinogenesis

status: Public on Jan 16 2011

city: ROUEN

first: Jean

middle: Philippe

last: SALIER

address: Bvd Gambetta

department: Inserm Unit 519

institute: Faculty of Medicine and Pharmacy

summary:
C/EBPβ plays a major role in numerous biological processes but unfortunately its precise role is not still clear and conflicting studies showed that this transcription factor could have contradictory functions. These latter arise from the complexity of mechanisms regulating C/EBPβ activity. Indeed, C/EBPβ encodes an intronless gene that generates a single mRNA that is alternatively translated into two major isoforms of 35kDa (liver-enriched activator protein: LAP) and 20kDa (liver-enriched inhibitory protein: LIP). LAP is the active isoform of this transcription factor whereas LIP, a truncated isoform negatively regulate C/EBPβ-LAP-mediated gene expression.   The main goal of our research was to understand how LAP and LIP isoforms governe C/EBPβ cellular functions with the identification of new genes and pathways regulated by these isoforms in the human Hep3B hepatoma cell line. For this purpose an original in vitro system characterized by a target genes induction with the activatory C/EBPß isoform LAP and a target genes repression with the inhibitory C/EBPß isoform (LIP) was used to identify the genuine C/EBPβ molecular signature. Using a cDNA microarray which provides a complete coverage of the liver transcriptome, we identified 676 genes inversely regulated by LAP and LIP. These selected genes are involved in many biological processes as the hepatic metabolism (cholesterol), detoxification, induction of apoptosis and negative regulation of the cell proliferation.   According to the involvement of C/EBPβ in hepatic carcinogenesis we focused on cell cycle regulation and apoptosis. Through functional studies, we proved for the first time that LIP plays in favor of the survival of the Hep3B cells whereas LAP makes the cells more sensitive to staurosporine-induced cell death. Moreover, a lot of studies demonstrated that the anti-proliferative action of C/EBPβ mainly depends on RB protein. By studying the rate of Hep3B cells proliferation which overexpress LAP, we brought to the fore that this isoform would be able to induce a repression of the Hep3B cells line proliferation - a RB- and p53- negative cell line. Thus, LAP seems able to induce the repression of proliferation by a different metabolic way from the RB one.

Keywords: comparison of cells expressing LAP or LIP

overall_design: RNA were extracted from 5 Hep3BLAPexpressing LAP,  5 Hep3BLAP control without expression of LAP, 5 Hep3BLIP expressing LIP and 5 Hep3BLIP control without epression of LIP. Each sample was hybridized once in 5 different nylon membranes.

first: Gaëlle

last: Saint-Auret

first: Martine

last: Hiron

first: Céline

last: Blache

first: Maryvonne

last: Daveau

first: Jean-philippe

last: Salier


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

first: sandrine

last: balzergue

summary:
affy_popsec_nancy_roots_poplar - This project aims to identify genes of interest for water deficit acclimation and/or adaptation in a tree species: poplar. We look for genes and gene expression networks related to drought stress. We intend to analyse the transcriptome in root apices, in two genotypes, Carpaccio and Soligo, at various stages and intensities of stress. Root apex is the location of root elongation and these analyses intend to identify genes involved in the control of cell expansion and thus of root elongation. Indeed, root growth maintenance in response to water shortage contributes to plant tolerance to water deficit. The comparison between medium and severe stress intensities and between early and long term stresses will power the selection of genes of interest. The co-analysis of two genotypes of contrasted tolerance to water deficit should help to better discriminate genes presenting a potential adaptative character from genes responding passively to the constraint.-Two poplar clones, Soligo (S) and Carpacio (C) were submitted to 4 treatments: control, mild water deficit, moderate water deficit (12-day long for both) and early-drought stress (about 36-h long). Growth and physiology was characterised on a batch of plants and samples collected on another batch of plants. Four to eight root apices (1 cm-long) were collected on each individual tree. Total RNAs were extracted from all roots for each tree individually. Two pools of 3 (or 2) individuals were made using equimolar ratio. A pool is considered as one biological replicate and corresponds to one Affymetrix slide. The two biological replicates originate from the same experiment.

Keywords: treated vs untreated comparison

first: Sandrine

last: Balzergue

first: Marie-beatrice

last: Bogeat-triboulot

first: David

last: Cohen

first: Marie-Laure

middle: L

last: Martin-Magniette


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

summary:
affy_popsec_nancy_pophydro_roots_poplar  - This project aims to identify genes of interest for control of root growth in response to water deficit in a tree species: poplar. We look for genes and gene expression networks related to drought stress. We intend to analyse the transcriptome in root apices of cuttings grown in hydroponics and osmotically stressed with PEG. Root apex is the location of root elongation and these analyses intend to identify genes involved in the control of cell expansion and thus of root elongation. Indeed, root growth maintenance in response to water shortage contributes to plant tolerance to water deficit.-Poplar cuttings (cv Soligo) were grown in hydroponics. A moderate water deficit was applied by adding PEG to the nutrient solution (200g/l). After 3 days, the apex (1 cm-long) of the roots of each cutting were collected. For control and stressed treatments, RNAs were extracted from two pools of 5 to 9 roots (issued from 2 to 5 cuttings). A pool is considered as one biological replicate and corresponds to one Affymetrix slide.

Keywords: treated vs untreated comparison

overall_design: 4 arrays - poplar

first: Marie-Béatrice-

last: BOGEAT-TRIBOULOT


title: delta-uvrY versus wild-type

status: Public on Jan 01 2011

city: Marburg an der Lahn

first: Jürgen

last: Lassak

state: Hessen

address: Karl-von-Frisch Strasse

department: Ecophysiology

institute: Max-Planck-Institute for Terrestrial Microbiology

summary: The BarA/UvrY two-component system is well conserved in numerous species of the γ-proteobacteria. However, the regulatory output of this system differs significantly between the species. In this study, we characterized the BarA/UvrY two-component system in Shewanella oneidensis MR-1. Sensor kinase BarA and the cognate response regulator UvrY were identified by bioinformatic analysis and subsequent in vivo interaction and phosphotransfer studies. The expression of two putative small regulatory RNAs (sRNAs), CsrB1 and CsrB2, was demonstrated to be dependent on UvrY. In contrast, a third predicted sRNA, CsrC, was expressed independently of UvrY. Transcriptomic analysis by microarrays revealed that UvrY is a global regulator and affects transcription of key enzymes of carbon metabolism such as ackA, aceAB, and pflAB. Subsequent growth experiments demonstrated that mutants lacking UvrY have a significant growth advantage over the wild type during aerobic growth on N-acetylglucosamine while under under anaerobic conditions the mutant grew more slowly. This effect was absent during growth with lactate as carbon source or in complex medium. Based on these results, we conclude that, in S.oneidensis MR-1, the global BarA/UvrY regulatory system is involved in central carbon metabolism processes.

overall_design: In the study presented, expression profiles of  three independent replicates of Shewanella oneidensis MR-1 ∆uvrY were compared to three independent replicates of Shewanella oneidensis MR-1 wild type cells. All samples were obtained from exponentially aerobically grown cells in LB  to stationary phase  (OD600nm=4.0)

first: Kai

last: Thormann


title: DNA Methylation Profiling of Glioblastoma: Impact on Gene Expression and Clinical Outcome (Illumina)

status: Public on Jan 19 2011

city: Rennes

first: Amandine

last: Etcheverry

address: 2 rue Henri Le Guilloux

institute: CNRS UMR 6290 - IGDR

summary: Genome-scale measurements of DNA methylation levels are necessary to decipher the epigenetic events involved in glioblastoma aggressive phenotype, and to guide new therapeutic strategies. In that purpose, we performed a whole genome integrative analysis of the methylation and expression profiles for 40 newly diagnosed glioblastoma patients. We have also screened for associations between CpG sites methylation levels and overall survival in a cohort of 50 patients uniformly treated with radiotherapy and chemotherapy with concomitant and adjuvant temozolomide (STUPP protocol).  The methylation analysis identified 616 CpG sites differentially methylated between glioblastoma and control brain, a quarter being differentially expressed in a concordant way. Among these concordant CpG sites, 13 genes displayed, within our glioblastoma cohort, an inverse correlation between promoter methylation and expression levels: B3GNT5, FABP7, ZNF217, BST2, OAS1, SLC13A5, GSTM5, ME1, UBXD3, TSPYL5, FAAH, C7orf13, and C3orf14. The expression of these genes may be tightly regulated by epigenetic mechanisms.   The survival analysis identified six CpG sites associated with overall survival. The SOX10 promoter methylation status (two CpG sites) stratifies the patients in a way similar to MGMT with improved performance based on Area Under the Curve criteria (0.78 vs. 0.71, p-value < 5.10-4). The methylation status of FNDC3B, TBX3, DGKI, and FSD1 promoters identify patients with MGMT methylated tumors non-responding to STUPP treatment (p-value < 1.10-4). These markers have a potential impact on therapeutic decision.

overall_design: 55 glioblastoma samples and 3 control brain samples were analysed.

last: Mosser


title: DNA methylation patterns associated with arsenicosis

status: Public on Dec 16 2010

city: Chapel Hill

first: Rebecca

middle: Catherine

last: Fry

address: 1213 MHRC

department: Environmental Sciences and Engineering

institute: UNC-Chapel Hill

summary:
DNA methylation patterns were analyzed in blood samples from humans unexposed or exposed to arsenic
Using a state-of-the-art technique to map the methylomes of our study subjects, we identified a large interactome of hypermethylated genes that are enriched for their involvement in arsenic-associated diseases, such as cancer, heart disease, and diabetes. Notably, we have uncovered an arsenic-induced “suppressorome” - a complex of 17 known and putative tumor suppressors silenced in human cancers. This finding represents a pivotal clue in unravelling a possible epigenetic mode of arsenic induced disease.

overall_design: DNA was extracted from 16 blood samples, 8 of which were from individuals showing signs of arsenicosis and 8 from individuals not showing signs of arsenicosis. CpG-methylated DNA was pulled down using a methyl binding domain protein. DNA samples were hybridized to Affymetrix Human Promoter 1.0R arrays, and chips were scanned using an Affymetrix scanner.

first: Lisa

last: Smeester

first: Julia

last: Rager

first: Kathryn

last: Bailey

first: Lu

last: Zhang

first: Xiaojun

last: Guan

first: Nikia

last: Smith

first: Gonzalo

last: Garcia-Vargas

first: Luz-Maria

last: Del Razo

first: Zuzana

last: Drobna

first: Hemant

last: Kelkar

first: Gary

last: Schroth

first: Miroslav

last: Styblo


title: Epigenome analysis of patients with various myeloid malignancies including differential levels of 5-hydroxymethylcytosine

status: Public on Dec 11 2010

city: Cleveland

first: Anna

last: Jankowska

state: Ohio

address: 9500 Euclid Ave.

department: THOR

institute: Cleveland Clinic,Taussig Cancer Institute

summary: TET2 is a close relative of TET1, an enzyme that converts 5-methylcytosine (5mC) to 5-hydroxymethylcytosine (5hmC) in DNA. The gene encoding TET2 resides at chromosome 4q24, in a region showing recurrent microdeletions and copy-neutral loss of heterozygosity (CN-LOH) in patients with diverse myeloid malignancies. Somatic TET2 mutations are frequently observed in myelodysplastic syndromes (MDS), myeloproliferative neoplasms (MPN), MDS/MPN overlap syndromes including chronic myelomonocytic leukaemia (CMML), acute myeloid leukaemias (AML) and secondary AML (sAML). We show here that TET2 mutations associated with myeloid malignancies compromise catalytic activity. Bone marrow samples from patients with TET2 mutations displayed uniformly low levels of 5hmC in genomic DNA compared to bone marrow samples from healthy controls. Moreover, small hairpin RNA (shRNA)-mediated depletion of Tet2 in mouse haematopoietic precursors skewed their differentiation towards monocyte/macrophage lineages in culture. There was no significant difference in DNA methylation between bone marrow samples from patients with high 5hmC versus healthy controls, but samples from patients with low 5hmC showed hypomethylation relative to controls at the majority of differentially methylated CpG sites. Our results demonstrate that Tet2 is important for normal myelopoiesis, and suggest that disruption of TET2 enzymatic activity favours myeloid tumorigenesis. Measurement of 5hmC levels in myeloid malignancies may prove valuable as a diagnostic and prognostic tool, to tailor therapies and assess responses to anticancer drugs.

overall_design:
Genome wide DNA methylation profiling of patients samples with various myeloid malignancies and diffrential levels of 5hmC.The Illumina Infinium 27k Human DNA methylation Beadchip v1.2 was used to obtain DNA methylation profiles across approximately 27,000 CpGs in bone marrow samples and occasionally peripheral blood samples. Samples included 28 control healthy bone marrows, 29 patients samples with low 5hmC levels (7 patients with wild-type TET2 and 22 mutant TET2) and 24 with high levels of 5hmC (22 with wild-type TET2 and 2 mutant TET2).
Bisulphite converted DNA from 81 samples was hybridised to the Illumina Infinium 27k Human Methylation Beadchip v1.2

last: Ganetzky

first: Jaroslaw

middle: P

last: Maciejewski


title: DNA methylation patterns associate with genetic and gene expression variation in HapMap cell lines

status: Public on Jan 05 2011

city: London

first: Jordana

last: Bell

address: St Thomas' Hospital, Westminster Bridge Rd

department: Department of Twin Research and Genetic Epidemiology

country: United Kingdom

institute: King's College London

summary: We measured the methylation status at 27,578 CpG sites using the Human Methylation27 DNA array in 77 HapMap Yoruba lymphoblastoid cell lines.

overall_design: Bisulphite converted DNA from 77 samples were hybridised to the Illumina Infinium 27k Human Methylation Beadchip

first: J

middle: T

first: A

last: Pai

last: Pickrell

first: D

last: Gaffney

first: R

last: Pique-Regi

last: Degner

first: Y

last: Gilad

last: Pritchard


title: DNA methylation titration data from two samples with known methylation differences

status: Public on Dec 01 2010

first: Pan

last: Du

address: 676 N ST Clair St, 1200#

institute: Northwestern University

summary: Two samples with known methylation differences. Sample A is NA 10923 from Coriell Institute for Medical Research. It is a B-Lymphocyte sample from a male donor. Sample B is HTB-38 cell line from ATCC (http://www.atcc.org). It is a colon cancer sample from a female donor. Sample A and B were normalized into the same concentration, and then mixed in five different titration ratios: 100:0, 90:10, 75:25, 50:50 and 0:100

overall_design: Sample A and Sample B were mixed in five different titration ratios: 100:0, 90:10, 75:25, 50:50 and 0:100

first: Simon

last: Lin

first: Lifang

last: Hou

first: Xiao

last: Zhang


title: Genome-Wide STAT3 binding sites in DU145 prostate cancer cells coupled to expression analysis

status: Public on Dec 09 2010

city: Washington

first: Olga

last: Timofeeva

state: DC

address: 3900 Reservoir Rd NW

department: Oncology

institute: Georgetown University Medical Center

summary:
Activation of Signal Transducer and Activator of Transcription 3 (STAT3) is common in prostate cancers. STAT3 may induce cell proliferation and resistance to apoptosis, as well as promote tumor angiogenesis, invasion, and migration by activating gene expression. Many STAT3-dependent transcriptional responses are mediated through protein-protein interactions that involve the amino-terminal domain (N-domain).
In this study, we found that inhibition of the STAT3 N-domain using novel inhibitor ST3-Hel2A-2 induces apoptotic death in prostate cancer cells. The cell death was accomponied by robust activation of pro-apoptotic gene. Using chromatin immunoprecipitation and tiling human promoter arrays (ChIP-chip), we have defined genome-wide targets of STAT3 in DU145 prostate cancer cells. We found that upregulated pro-apoptotic genes were bound by STAT3 in prostate cancer cells, and that STAT3 binding was decreased following inhibition of the STAT3 N-domain.

overall_design: Chromatin samples were ChIPed with STAT3 vs. IgG from DU145 cells  treated with ST3-Hel2A-2 for 3 hr or DMSO as a control.

first: O


title: Investigation of somatic copy number variation in MZ twins

city: San Antonio

first: August

middle: Nolan

last: Blackburn

state: Texas

address: 7702 Floyd Curl

department: Medicine - Clinical Epidemiology

institute: University of Texas Health Science Center at San Antonio

summary: There is growing evidence that genomic DNA sequence changes occur in individual somatic cells during the lifetime of an individual and accumulation of these changes may influence aging and disease. In light of this, and contradicting reports regarding discordant copy number profiles between MZ twins(BARANZINI et al. 2010; BRUDER et al. 2008), we set out to identify de novo somatic copy number mutations in DNA from blood for MZ twin pairs of Mexican American descent who were participants of the San Antonio Family Heart Study (SAFHS) or San Antonio Family Diabetes/Gallbladder study (SAFDGS). By applying circular binary segmentation (CBS) to B-allele ratio differences we determined that the 3 MZ twin pairs in this study had concordant copy number profiles. We also detected 2 de novo germ-line CNVs in 2 MZ twin pairs from the SAFHS.

overall_design: This study includes data for 4 monozygotic (MZ) twin pairs, and both parents of 2 of these MZ twin pairs. The purpose of this study was to compare concordance of copy number profiles between MZ twins.

middle: N

first: Angela

last: Dean

first: Harald

middle: H

last: Göring

first: Satish

last: Kumar

first: Melanie

last: Carless

first: Joanne

last: Curran

first: Ravindranath

last: Duggirala

first: John

last: Blangero

first: Donna

last: Lehman


title: Epigenome analysis in HPV(-) and HPV(+) squamous cell carcinoma cell lines

city: Ann Arbor

first: Jung

last: Kim

address: 1420 Washington Heights

institute: University of Michigan

summary: Human papillomavirus (HPV)-associated head and neck cancers (HNSCCs) have a distinct risk profile and appreciate a prognostic advantage compared to HPV-negative HNSCC. Promoter hypermethylation has been widely recognized as an important mechanism in the progression of HNSCC, but the extent to which this mechanism is consistent between HPV(+) and HPV(-) tumors is unknown. To assess the genome-wide methylation changes in HPV(+) and HPV(-) tumors, we analyzed DNA methylation and expression patterns in two HPV(+) and two HPV(-) cell lines. HPV(+) tumors have overall higher DNA methylation in genic and LINE1 regions than HPV(-) tumors, and polycomb repressive complex 2 (PRC2) targets tend to be much more highly methylated in HPV(+) cells.

overall_design: Bisulphite-converted DNA from 4 squamous cell carcinoma (SCC) cell lines were hybridized to the Illumina Infinium 27k Human Methylation Beadchip.

first: Maureen

last: Sartor

first: Dana

middle: C

last: Dolinoy

first: Thomas

middle: E

last: Carey

first: Tamara

last: Jones

first: Justin

last: Colacino

first: Laura

middle: S

last: Rozek


title: Altered DNA Methylation in Leukocytes with Trisomy 21

status: Public on Nov 18 2010

city: La Jolla

first: Ali

last: Torkamani

state: CA

address: 3344 North Torrey Pines Court Suite 300

institute: TSRI

summary:
The primary abnormality in Down syndrome (DS), trisomy 21, is well known, but how this chromosomal gain produces the complex DS phenotype, including immune system defects, is not well understood. We profiled DNA methylation in total peripheral blood leukocytes (PBL) and T-lymphocytes from adults with DS and normal controls and found gene-specific abnormalities of CpG methylation in DS, with many of the differentially methylated genes having known or predicted roles in lymphocyte development and function.

NOTE 1: the analysis in Kerkel et al., PLOS Genet, 2010 was carried out after removing probes for genes on the X and Y chromosomes.  NOTE 2: these GEO data have been analyzed with this latest version of BeadStudio; the data in the supplementary tables of Kerkel et al., PLOS Genetics, 2010, were from these same Bead chips, but extracted using an earlier version of this software.  This re-extraction does not affect the conclusions in Kerkel et al., PLOS Genetics, 2010.

overall_design: Profiling of CpG methylation status in gene promoter regions using Illumina Infinium BeadChips.

first: Kristi

last: Kerkel

first: Benjamin

last: Tycko


title: Obesity related methylation changes in DNA of peripheral blood leukocytes

status: Public on Nov 29 2010

city: Augusta

first: Xiaoling

last: Wang

state: GA

address: 1120 15th street

department: Pediatrics

institute: Medical College of Georgia

summary: We performed a genome wide methylation scan using the Illumina HumanMethylation27 BeadChip on DNAs extracted from the leukocytes of 7 obese (BMI≥99th percentile for age and sex) and 7 lean (BMI≤10th percentile for age and sex) African American males aged 14-18 years.

overall_design: Bisulphite converted DNA from the 14 samples were hybridised to the Illumina Infinium 27k Human Methylation Beadchip v1.2


title: Genome-wide SF-1 (NR5A1) binding sites in NCI-H295R cells

status: Public on Dec 17 2010

first: Bruno

last: Ferraz-de-Souza

address: 30 Guilford St

department: Clinical & Molecular Genetics Unit

institute: UCL Institute of Child Health

summary:
The nuclear receptor steroidogenic factor-1 (SF-1, NR5A1) is a key regulator of adrenal and gonadal biology. We aimed to identify a novel subset of SF-1 target genes in the adrenal by performing ChIP-on-chip in NCI-H295R human adrenocortical cells using promoter tiling arrays. Analysis of ChIP-on-chip experiments with CisGenome identified 738 SF-1-binding regions that met criteria of an MA score more than 3.5 mean ± S.D. and a false discovery rate of <5%. Subsequent analysis focused on those regions that were located between 10 kb upstream and 3 kb downstream of the TSS of known genes, in keeping with the design of the Human Promoter 1.0R arrays. Using this approach, binding regions were annotated to 445 gene loci.
The supplementary bed file contains all 946 SF-1 binding sites identified by analysis with CisGenome using standard settings (MA>3.0)

overall_design: Unstimulated NCI-H295R cells ChIPed with Upstate Millipore 07-618 anti-SF-1 antibody vs input chromatin. Two full experiments were analysed (biological replicates): 2 SF-1 ChIP arrays, 2 input control arrays

first: Lin

last: Lin

first: Sonia

last: Shah

first: Nipurna

last: Jina

first: Mike

last: Hubank

first: Mehul

last: Dattani

last: Achermann


title: Ahringer AB15823_H4K8AC487128_N2_L3

city: Toronto

first: DCC

last: modENCODE

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

institute: Ontario Institute for Cancer Research

summary:
modENCODE_submission_2774
This submission comes from a modENCODE project of Jason Lieb. For full list of modENCODE projects, see http://www.genome.gov/26524648
Project Goal: The focus of our analysis will be elements that specify nucleosome positioning and occupancy, control domains of gene expression, induce repression of the X chromosome, guide mitotic segregation and genome duplication, govern homolog pairing and recombination during meiosis, and organize chromosome positioning within the nucleus. 126 strategically selected targets include key histone modifications, histone variants, RNA polymerase II isoforms, dosage-compensation proteins, centromere components, homolog-pairing facilitators, recombination markers, and nuclear-envelope constituents.
For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODEDataReleasePolicyFinal2008.pdf

overall_design: EXPERIMENT TYPE: CHIP-chip. BIOLOGICAL SOURCE: Strain: N2; Developmental Stage: L3 Larva; Genotype: wild type; Sex: mixed Male and Hermaphrodite population;  NUMBER OF REPLICATES: 2;  EXPERIMENTAL FACTORS: Developmental Stage L3 Larva; temperature 20; Antibody H4K8ac (target is H4K8ac); Strain N2

first: Isabel

last: latorre

first: Julie

last: Ahringer


title: Concomitant deletions of tumor suppressor genes MEN1 and AIP are essential for the pathogenesis of the brown fat tumor hibernoma

status: Public on Nov 24 2010

city: Lund

first: Karolin

last: Nord

address: BMC C13

department: Dept of Clinical Genetics

country: Sweden

institute: Lund University

summary: Hibernomas are benign tumors with morphological features resembling brown fat. They consistently display cytogenetic rearrangements, typically translocations, involving chromosome band 11q13. Here we demonstrate that these aberrations are associated with concomitant deletions of AIP and MEN1, tumor suppressor genes that are located 3 Mb apart and that underlie the hereditary syndromes pituitary adenoma predisposition and multiple endocrine neoplasia type I. MEN1 and AIP displayed a low expression in hibernomas whereas the expression of genes up-regulated in brown fat-PPARA, PPARG, PPARGC1A, and UCP1-was high. Thus, loss of MEN1 and AIP is likely to be pathogenetically essential for hibernoma development. Simultaneous loss of two tumor suppressor genes has not previously been shown to result from a neoplasia-associated translocation. Furthermore, in contrast to the prevailing assumption that benign tumors harbor relatively few genetic aberrations, the present analyses demonstrate that a considerable number of chromosome breaks are involved in the pathogenesis of hibernoma.

overall_design: Global copy number analysis was performed using single nucleotide polymorphism (SNP) array. Cases 1-14 were hybridized onto Illumina Human1M-Duo v3.0 (and Human CNV370-Quad v3.0) BeadChip (Illumina, San Diego, CA, USA), following standard protocols supplied by the manufacturer. Case 15 was analyzed using Illumina Human Omni-Quad BeadChip. Normal blood DNA was analyzed in cases 1, 2, 4 and 6 using the Human CNV370-Quad v3.0 BeadChip. Data analysis was done using the BeadStudio software (Illumina).

first: Linda

last: Magnusson

first: Margareth

last: Isaksson

first: Jenny

last: Nilsson

first: Henrik

last: Lilljebjörn

first: Henryk

middle: A

last: Domanski

first: Lars-Gunnar

last: Kindblom

first: Nils

last: Mandahl

first: Fredrik

last: Mertens


title: miR-193b Regulates Mcl-1 in Melanoma

status: Public on Oct 30 2010

city: Kingston

first: Harriet

last: Feilotter

address: 88 Stuart St

department: Pathology and molecular department

institute: Queen's University

summary: MicroRNAs (miRNAs) have important roles in gene regulation. Dysregulation of miRNAs has been associated with tumorigenesis. Recent studies suggest miR-193b is a tumor suppressor gene. In a previous study, we reported that miR-193b represses cell proliferation and regulates cyclin D1 (CCND1) in melanoma. Now we demonstrate that miR-193b regulates myeloid cell leukemia sequence 1 (Mcl-1) in melanoma cells. miRNA microarray profiling revealed the miR-193b level in malignant melanomas was significantly downregulated compared to benign nevi, while a tissue microarray demonstrated overexpression of Mcl-1 in malignant melanoma. The Mcl-1 expressions were inversely correlated with the miR-193b levels in melanoma tissue samples, suggesting a potential regulatory role of miR-193b. Overexpression of miR-193b repressed Mcl-1 in melanoma cell lines. It is well known that Mcl-1 knockdown confers cell sensitivity to ABT-737, a small molecular inhibitor of Bcl-2, Bcl-XL and Bcl-w. We found miR-193b, through repressing Mcl-1 expression, could also sensitize melanoma cells that were refractory to ABT-737. Furthermore, miR-193b directly regulates Mcl-1 by targeting the 3’ untranslated region (3’UTR) of Mcl-1 mRNA. Interestingly, miR-193b may recognize sequences on the 3’UTR that do not base pair with its seed region. In conclusion, our study suggests the downregulation of miR-193b could be an early event during melanoma progression, and demonstrates miR-193b directly regulates Mcl-1 by targeting both seed and seedless sequences of the 3’ UTR.

overall_design: 15 primary melanoma samples, 8 metastatic melanomas  and 8 benign nevi samples were profiled on Agilent miRNA array platform

first: Jiamin

last: Chen

first: Xiao

last: Zhang

first: Cindy

last: Lentz

first: Marie

last: Abi-Daoud

first: Victor

last: Tron


title: Expression profiling of cold-induced hybrid necrosis in triploid hybrids crossed between tetraploid wheat and Aegilops tauschii.

status: Public on Oct 07 2010

city: Kobe

first: Shigeo

last: Takumi

state: Hyogo

address: Rokkodai 1-1, Nada

department: Graduate School of Agricultural Science

institute: Kobe University

summary:
We have employed whole genome microarray expression profiling as a discovery platform to identify genes to alter the transcript accumulation levels in cold-induced hybrid necrosis lines, which are triploid hybrids crossed between tetraploid wheat and diploid wheat progenitor Aegilops tauschii. Of the up-regulated genes, defense-related genes were most frequently found in the leaves and shoot apical meristem (SAM) of type II necrosis line with low temperature. On the other hand, cell cycle-related genes were highly down-regulated in SAM of type II necrosis line under low temperature. To validate the microarray data, RT-PCR and quantitative RT-PCR analyses for 37selected genes were performed in total. Of the examined 21 up-regulated and 16 down-regulated genes, more than 75% of expression pattern were consistent with the microarray data.
Together with cytological analysis of the necrotic tissues, the microarray analysis strongly suggests that an autoimmune response-like reaction and repression of cell division might be triggered by intergenomic incompatibility between the AB and D genomes in type II necrosis.

overall_design: Expression patterns were compared between the two synthetic hexaploid lines showing the wild-type phenotype (as a reference) and cold-induced hybrid necrosis. Total RNA samples were isolated from the 3-week-old seedling leaves. In addition, total RNA were also extracted from the seedling leaves and shoot meristem with 12- and 6-weeks of low temperature, respectively. Two independent experiments were conducted in each exprement.

first: Nobuyuki

last: Mizuno


title: Aberrant global methylation patterns affect the molecular pathogenesis and prognosis of human multiple myeloma

status: Public on Oct 18 2010

city: Sutton

first: Brian

last: Walker

address: 15 Cotswold Road

department: Haemato-Oncology Research Unit

institute: The Institute of Cancer Research

summary: We have used genome-wide methylation microarrays to analyze differences in CpG methylation patterns in cells relevant to the pathogenesis of myeloma plasma cells, including B cells, normal plasma cells, MGUS, presentation myeloma, and plasma cell leukemia (PCL). We show that methylation patterns in these cell types are capable of distinguishing non-malignant from malignant cells and that the main reason for this difference is hypomethylation of the genome at the transition from MGUS to presentation myeloma. In addition, gene-specific hypermethylation was evident at the myeloma stage. Differential methylation was also evident at the transition from myeloma to PCL with re-methylation of the genome, specifically of genes involved in cell-cell signaling and cell adhesion, which may contribute to independence from the bone marrow microenvironment. There was a high degree of methylation variability within presentation myeloma samples and this was associated with the cytogenetic differences between samples. More specifically, we found that methylation subgroups were defined by translocations and hyperdiploidy, with t(4;14) myeloma having the largest impact on DNA methylation. Two groups of hyperdiploid samples were identified, based on unsupervised clustering, which had an impact on overall survival. Overall, DNA methylation has a large impact on disease progression and on myeloma cytogenetic subgroups.

overall_design: Bone marrow aspirates were obtained after informed consent. B cells (n=6) from normal individuals were selected from peripheral blood using CD19. Plasma cells (PC) from non-myeloma patients (normal plasma cell controls, n=3) as well as MGUS (n=4) and presentation myeloma patients (n=161) were selected to a purity of >90% using CD138 microbeads and magnet-assisted cell sorting (Miltenyi Biotech, Bisley, UK). Samples from PCL patients (n=7) were not CD138 selected but contained >90% plasma cell infiltration as determined by microscopy. In order to achieve a sufficient quantity of DNA some normal plasma cell control samples were pooled.

first: Gareth

last: Morgan


title: An integrative multi-dimensional genetic and epigenetic strategy to identify aberrant genes and pathways in cancer: DNA methylation

status: Public on Nov 05 2010

city: Vancouver

first: Raj

last: Chari

state: BC

address: 675 West 10th Avenue

department: Cancer Genetics and Developmental Biology

institute: BC Cancer Research Centre

summary: Methylation profiles of a panel of breast cancer lines that were included in the integrative analysis of DNA copy number, allelic status, DNA methylation and gene expression.

overall_design: Methylation profiles of 9 breast cancer cell lines and one normal line were generated.  Genes were determined to be hyper and hypomethylation in a cell line with respect to the normal line, MCF10A.


title: Autocatalytic differentiation of epigenetic modifications within the Arabidopsis genome

status: Public on Sep 21 2010

city: Ikoma

first: Soichi

last: Inagaki

state: Nara

address: 8916-5, Takayama-cho

department: Graduate School of Biological Sciences

institute: Nara Institute of Science and Technology

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

overall_design: Refer to individual Series


title: DNA Methylation Analysis in Human Chorionic Villus and Maternal Blood Cells

status: Public on Jul 31 2010

city: Pittsburgh

first: Tianjiao

last: Chu

address: 204 Craft Ave

institute: Magee Womens Research Institute

summary: Comparative analysis of DNA methylation in 12 human chorionic villus samples and 12 human maternal blood cell samples

overall_design:
We performed a genome wide analysis of DNA methylation first trimester CVS samples and gestational age matched MBCs.  We analyzed DNA samples obtained from 12 CVS samples and 12 MBC samples. Data were generated using two high-throughput approaches: the Infinium “humanmethylation27” platform marketed by Illumina and a custom Agilent-based platform. We then compared these data with genome wide transcription data for the same tissues.

This Series covers only the Illumina HumanMethylation27 part of the study.

first: David

last: Peters


title: Genome-wide expression analysis in kyp and cmt3 mutants of Arabidopsis thaliana

summary: Investigation of genome-wide expression in the mutant of histone H3K9 methyltransferase KRYPTONITE (KYP) or DNA methyltransferase CHROMOMETHYLASE3 (CMT3) in Arabidopsis. These mutants showed decrease in H3K9 methylation and DNA methylation levels, and transcriptional activation at transposons and repeats. Using NimbleGen DNA microarray, global pattern of expression of genes and transposons were examined in these mutants.

overall_design: Total RNA from leaves was isolated using the RNeasy Plant Mini kit (Qiagen) and was treated with DNase I (TAKARA). Double-stranded cDNA was synthesized using the SuperScript Double Stranded cDNA Synthesis kit (Invitrogen) and oligo (dT)20 primer. cDNA was labeled by Cy3, hybridized to 4 x 72k array, and scanned according to manufacture's instructions (www.nimblegen.com).

first: Tetsuji

last: Kakutani


title: Comprehensive Analysis of Karyotypic Mosaicism between Trophectoderm and Inner Cell Mass

status: Public on Sep 28 2010

city: Stanford

middle: Scott

last: Johnson

address: 300 Pasteur Drive

department: Genetics

institute: Stanford University

summary: Aneuploidy has been well documented in blastocyst embryos, but prior studies have been limited in scale and/or lack mechanistic data. We previously reported preclinical validation of microarray 24-chromosome preimplantation genetic screening (PGS) in a 24-hour protocol. The method diagnoses chromosome copy number, structural chromosome aberrations, parental source of aneuploidy, and distinguishes certain meiotic from mitotic errors. In this study our objective was to examine aneuploidy in human blastocysts and determine correspondence of karyotypes between trophectoderm (TE) and inner cell mass (ICM). We disaggregated 51 blastocysts from seventeen couples into ICM and one or two TE fractions. The average maternal age was 31. Next, we ran 24-chromosome microarray molecular karyotyping on all of the samples, and then performed a retrospective analysis of the data. The average per-chromosome confidence was 99.95%. Approximately 80% of blastocysts were euploid. The majority of aneuploid embryos were simple aneuploid, i.e., one or two whole-chromosome imbalances. Structural chromosome aberrations, which are common in cleavage stage embryos, occurred in only three blastocysts (5.8%). All TE biopsies derived from the same embryos were concordant. Forty-nine of fifty-one (96.1%) inner cell mass (ICM) samples were concordant with TE biopsies derived from the same embryos. Discordance between TE and ICM occurred only in the two embryos with structural chromosome aberration. We conclude that trophectoderm karyotype is an excellent predictor of inner cell mass karyotype. Discordance between TE and ICM occurred only in embryos with structural chromosome aberrations.

overall_design: We thawed all fractions at 22°C, and then added Arcturus PicoPure Lysis Buffer (Molecular Devices, Sunnyvale, CA) to each of the biopsies. The tubes were incubated at 56°C for one hour, and then heat inactivated at 95°C for 10 minutes. DNA from the lysed biospsies was amplified using a commercial kit (GE Healthcare, Waukesha, WI) for multiple displacement amplification (MDA). MDA reactions were incubated at 30°C for 2.5 hours and then heat-inactivated at 65°C for five minutes. The amplified samples were genotyped using Illumina (San Diego, CA, USA) Infinium II genotyping microarrays (CytoSNP-12 chips) using a modified 24-hour protocol, as described previously*. Previously, we developed a genotyping microarray molecular karyotyping technology that uses parental genetic data to increase accuracy and determine mechanism and source of aneuploidy*. The algorithm uses parental genotypes and the observed distribution of unprocessed single cell microarray channel intensities to diagnose whole-chromosome imbalances and structural chromosome aberrations*. Because parental genotypes are available, the algorithm readily identifies parental source of whole-chromosome imbalances and structural chromosome aberrations. Additionally, the algorithm uses parental information, high confidence disomic single cell measurements on children, and recombination probabilities (genome.ucsc.edu) to determine the phase of the parental chromosomes. The phased data is then used to determine whether certain trisomies and uniparental disomies were mitotic or meiotic in origin*. *Johnson DS, Gemelos G, Baner J, Ryan A, Cinnioglu C, Banjevic M, Ross R, Alper M, Barrett B, Frederick J, Potter D, Behr B, Rabinowitz M. (2010). Preclinical validation of a microarray method for full molecular karyotyping of blastomeres in a 24-hour protocol. Human Reproduction January 24 [Epub ahead of print].


title: Transcriptomic response to aluminum stress in roots of aspen (Populus tremula L.)

status: Public on Aug 24 2010

city: Zurich

first: Stefan

last: Zoller

address: Universitatstrasse 16

department: Genetic Diversity Centre

country: Switzerland

institute: ETH Zurich

summary:
Background

Ionic aluminum (mainly Al3+) is rhizotoxic and can be present in acid soils at concentrations high enough to inhibit root growth. Many forest tree species grow naturally in acid soils and often tolerate high concentrations of Al. Previously, we have shown that aspen (Populus tremula) releases citrate and oxalate from roots in response to Al exposure. To obtain further insights into the root responses of aspen to Al, we investigated root gene expression at Al conditions that inhibit root growth.

Results

Treatment of the aspen roots with 500 µM Al induced a strong inhibition of root growth within 6 h of exposure time. The root growth subsequently recovered, reaching growth rates comparable to that of control plants. Changes in gene expression were determined after 6 h, 2 d, and 10 d of Al exposure. Replicated transcriptome analyses using the Affymetrix poplar genome array revealed a total of 175 significantly up-regulated and 69 down-regulated genes, of which 70% could be annotated based on Arabidopsis genome resources. Between 6 h and 2 d, the number of responsive genes strongly decreased from 202 to 26, and then the number of changes remained low. The responses after 6 h were characterized by genes involved in cell wall modification, ion transport, and oxidative stress. Two genes with prolonged induction were closely related to the Arabidopsis Al tolerance genes ALS3 (for Al sensitive 3) and MATE (for multidrug and toxin efflux protein, mediating citrate efflux). Patterns of expression in different plant organs and in response to Al indicated that the two aspen genes are homologs of the Arabidopsis ALS3 and MATE.

Conclusion

Exposure of aspen roots to Al results in a rapid inhibition of root growth and a large change in root gene expression. The subsequent root growth recovery and the concomitant reduction in the number of responsive genes presumably reflect the success of the roots in activating Al tolerance mechanisms. The aspen genes ALS3 and MATE may be important components of these mechanisms.

overall_design: Aspen roots were treated with Al in solution culture for 6 h, 54 h, 246 h to cover a broad range of exposure times. Transcriptomic changes were assessed by the Affymetrix GeneChip Poplar Genome Array. For each time point, root tips of three independant plants were analyzed.

first: Nadine

last: Grisel

first: Marzanna

last: Künzli-Gontarczyk

first: Thomas

last: Lampart

first: Martin

last: Münsterkötter

first: Ivano

last: Brunner

first: Lucien

last: Bovet

first: Jean-Pierre

last: Métraux

first: Christoph

last: Sperisen


title: Endogenous overexpression of Poplar MYB186 increases trichome density, improves growth rate and insect pest resistance

status: Public on Sep 01 2010

first: Sharon

last: Regan

address: Biosciences Complex, Queen's University

department: Department of Biology

summary: Trichomes are specialised epidermal cells that generally play a role in reducing transpiration and act as a deterrent to herbivory. In a screen of activation tagged Populus tremula x P. alba 717-1B4 trees, we identified a mutant line, fuzzy, with increased foliar trichome density. This mutant also had a 35% increase in growth rate and a 200% increase in the rate of photosynthesis as compared to wild-type poplar. The fuzzy mutant had significant resistance to feeding by larvae of the white spotted tussock moth (Orgyia leucostigma), a generalist insect pest of poplar trees.  The fuzzy phenotype is attributable to activation tagging and increased expression of the gene encoding PtaMYB186, which is related to Arabidopsis thaliana MYB106, a known regulator of trichome initiation.  The fuzzy phenotype can be recapitulated by overexpressing PtaMYB186 in poplar.  PtaMYB186 overexpression results in reconfiguration of the poplar transcriptome, with changes in the transcript abundance of suites of genes that are related to trichome differentiation.  It is notable that this gene responsible for trichome development also altered traits related to growth rate and pest resistance, suggesting that non-intuitive facets of plant development might be useful targets for plant improvement.

overall_design: 6 arrays total. 2 genotypes – WT, FUZZY – PtaMYB186 OE

first: Jonathan

middle: M

last: Plett

first: Olivia

last: Wilkins

first: Malcolm

last: Campbell

first: Steven

last: Ralph