title: DNA methylation differences between human regulatory T cells and conventional T cells

status: Public on Sep 09 2013

city: Parkville

first: Jovana

last: Maksimovic

state: Victoria

address: Royal Children's Hospital, Flemington Road

institute: Murdoch Childrens Research Institute

summary: Regulatory T cells (Treg) prevent the emergence of autoimmune disease. Prototypic natural Treg (nTreg) are programmed by Forkhead-box P3 (FOXP3) and can be reliably identified by demethylation at the FOXP3 locus. To explore the nTreg methylation landscape we performed genome-wide methylation studies on human naïve resting nTreg (rTreg) and conventional naïve CD4+ T cells (Naïve). We detected 2,315 differentially methylated CpGs between these two cell types, many of which clustered into 127 regions of differential methylation (RDMs). T cell activation induced changes in 466 individual CpGs and 18 RDMs in naïve CD4+ T cells, but did not alter DNA methylation in rTreg. Expression of mRNA for TIGIT, an immune suppressive receptor demethylated in rTreg, was upregulated in nTreg and reduced in peripheral blood mononuclear cells of individuals at risk for autoimmune (type 1) diabetes.  Gene-set testing of the 127 RDMs revealed enrichment of common Treg signature genes, FOXP3 bound genes and genes directly upregulated by FOXP3, which was primarily driven by the subset of demethylated RDMs. A putative Forkhead-binding motif overrepresented in promoter-associated RDMs suggests methylation regulates gene expression by influencing FOXP3 binding. Our findings provide new insights into epigenetic regulation of human nTreg and the potential to exploit differential methylation as an immune biomarker in human diseases.

overall_design: Naïve and rTreg cells were sorted from buffy coats of 3 healthy male donors (M28, 29, 30) and then activated for 6 days with anti-CD3 and anti-CD28 antibodies, supplemented with IL-2 at day 4. DNA was harvested and bisulfite converted for methylation analysis on illumina HM450 array from 2-3 biological replicates of each cell type: rTreg (M28, M30), naïve (M28, M29, M30), Act-naïve (M28, M29, M30) and Act-rTreg (M29, M30).

first: Yuxia

last: Zhang

first: Gaetano

last: Naselli

first: Junyan

last: Qian

first: Marnie

last: Blewitt

first: Alicia

last: Oshlack

first: Leonard

last: Harrison

first: Michael

last: Chopin


title: Lamin B1 Depletion in Senescent Cells Triggers Large-Scale Changes in Gene Expression and in the Chromatin Landscape [ expression array ]

city: Philadelphia

first: Gregory

last: Donahue

state: PA

address: 3400 Civic Center Blvd, Bldg 421

department: Cell & Developmental Biology

country: USA

institute: The University of Pennsylvania

summary: Cellular senescence is a stable proliferation arrest in response to stress, associated with an altered secretory pathway (Senescence Associated Secretory Phenotype (SASP)). Senescence-associated proliferation arrest and the SASP are thought to act in concert to promote tumor suppression and tissue aging.  While chromatin regulation and down regulation of lamin B1 have been implicated as effectors of cell senescence, functional interactions between them are poorly understood.  We compared the genome-wide distributions of H3K4me3 and H3K27me3 between proliferating and senescent primary human cells and found dramatic differences, including large-scale domains of H3K4me3- and H3K27me3-enriched “mesas” and H3K27me3-depleted “canyons” in senescent cells.  Senescent mesas form at the sites of lamin B1-associated domains (LADs) in proliferating cells.  Mesas also overlap with regions that exhibit DNA hypomethylation in cancer, suggesting that chromatin changes in pre-malignant senescent cells foreshadow epigenetic changes in cancer.  Proliferating fibroblasts from Hutchinson-Gilford Progeria Syndrome patients expressing mutant lamin A (progerin) also show evidence of H3K4me3 mesas, suggesting a link between premature chromatin changes and accelerated cell senescence and tissue aging.  In contrast, canyons form mostly in between LADs and are enriched in genes, gene promoters and enhancers.  Strikingly, H3K27me3 loss in canyons is correlated with upregulation of key senescence genes, including genes comprising the SASP, indicating a link between global changes in chromatin structure and local regulation of gene expression.  Finally, premature reduction of lamin B1 in midlife proliferating cells triggers formation of senescence-associated mesas and canyons and accelerated senescence.  Together, our data illustrate a profound reorganization of chromatin during senescence, and suggest that down regulation of lamin B1 in senescence is a key trigger of global and local chromatin changes that impact gene expression, aging and cancer.

overall_design: Two samples, proliferating and senescent, five replicates each

first: Parisha

middle: P

last: Shah

first: Greg

first: Gabriel

last: Otte

first: Brian

last: Capell

first: David

middle: M

last: Nelson

first: Kajia

last: Cao

first: Varun

last: Aggarwala

first: Hazel

last: Cruickshanks

first: Taranjit

middle: S

last: Rai

first: Tony

last: McBryan

middle: D

last: Gregory

first: Davinder

last: Sandhu

first: Peter

last: Adams

first: Shelley

middle: L

last: Berger


title: Global mRNA gene expression analysis profiling control HEK293 cell and cells expressing  HSP70K71E

status: Public on Sep 24 2013

city: Bethesda

first: Jung

last: Byun

state: MD

address: 37 convent drive, Bldg 37,  Rm 1042

institute: NCI/NIH

summary:
This is global mRNA gene expression data for HEK293  and cells expressing  HSP70K71E ; most genes were down-regulated for HSP70K71E compared to the control
Keywords: Global mRNA expression

overall_design: We overexpressed pCI1-EGFP (control) and Hsp70K71E-EGFP to HEK293 and collected total RNA from each condition to analyze global mRNA expression

first: Kevin

last: Gardner


title: expression data from Zbtb17 cKO mouse heart after pressure overload

status: Public on Sep 06 2013

city: London

first: Byambajav

last: Buyandelger

address: Du Cane Road

country: United Kingdom

institute: Imperial College London

summary:
whole gene expression analysis for ZBTB17 cKO mice after transverse aortic constriction (TAC)
We used microarrays to detail the global programme of gene expression underlying hypertrophy and heart failure process upon pressure overload

overall_design: 16 male mice, 4 mice per group, were selected at 8-10 weeks old for 4 weeks of TAC and SHAM and collected samples for RNA extraction and hybridization on Affymetrix microarrays. We included corresponding controls.

first: Sylvia

last: Gunkel

first: Nathalie

last: Lambie


title: Differences in DNA methylation between human neuronal and glial cells are concentrated in enhancers and non-CpG sites [methylation array]

status: Public on Sep 13 2013

city: Bronx

first: Stella

last: Dracheva

state: New York

address: James J. Peters VA Medical Center,130 W Kingsbridge Rd

department: Dept. of Psychiatry

institute: Icahn School of Medicine at Mount Sinai

type: Genome binding/occupancy profiling by genome tiling array

summary: We applied Illumina Human Methylation450K array to perform a genomic-scale single-site resolution DNA methylation analysis in neuronal and nonneuronal (primarily glial) nuclei separated from the orbitofrontal cortex of postmortem human brain. The findings were validated using enhanced reduced representation bisulfite sequencing. We identified thousands of sites differentially methylated (DM) between neuronal and nonneuronal cells. The DM sites were depleted within CpG island–containing promoters but enriched in predicted enhancers. Classification of the DM sites into those undermethylated in neurons (neuronal type) and those undermethylated in nonneuronal cells (glial type), combined with findings of others that methylation within control elements typically negatively correlates with gene expression, yielded large sets of predicted neuron-specific and non– neuron-specific genes. These sets of predicted genes were in excellent agreement with the available direct measurements of gene expression in human and mouse. We also found a distinct set of DNA methylation patterns that were unique for neuronal cells. In particular, neuronal-type differential methylation was overrepresented in CpG island shores, enriched within gene bodies but not in intergenic regions, and preferentially harbored binding motifs for a distinct set of transcription factors, including neuron-specific activity-dependent factors. Finally, non-CpG methylation was substantially more prevalent in neurons than in nonneuronal cells.

overall_design: Genomic DNA was isolated from FACS-sorted human brain neuronal and nonneuronal nuclei. DNA was bisulfite converted and hybridised to the Illumina Infinium 450K Human Methylation Beadchip array. Six subjects in two technical replicate expriments were analyzed.

first: Alexey

last: Kozlenkov


title: miR-146a-5p expression effect on human mesenchymal stem cell

status: Public on Sep 05 2013

city: Taipei

first: Jui-Yu

last: Hsieh

address: No. 155, Sec 2, Li-Nong Street

country: Taiwan

institute: National Yang-Ming University

summary: Analysis of human mesenchymal stem cells (MSC) from bone marrow and the Wharton's jelly of the umbilical cord after manupulating miR-146a-5p expression. miR-146a-5p is involved in controlling the proliferation and migration of MSCs. Results provide miR-146a-5p-regulating genes in MSCs.

overall_design: In this study, BM-MSCs transduced with miR-146a-5p expression vector or pCDH-CMV-MCS-EF1-copGFP vector only, as well as two WJ-MSCs transfected with short interfering RNAs targeting miR-146a or a GFP control.

first: Shing-Jyh

last: Chang

first: Tse-Shun

last: Huang

first: Shu-Meng

last: Cheng

first: Cheng-Chung

first: Tsung-Neng

last: Tsai

first: Oscar

middle: K

last: Lee

first: Hsei-Wei

last: Wang


title: Expression data from sorted control and Pygo2-null mouse mammary stem/basal cells

city: Houston

first: Bingnan

last: Gu

address: 1515 Holcombe Blvd

institute: The University of Texas MD Anderson Cancer Center

summary:
Skin-mammary specific knockout (SSKO) of Pygo2 (K14-cre; Pygo2 flox/-) , a WNT signaling co-activator, results in defective mouse mammary gland development.
The FACS sorted mammary stem cell (MaSC)/basal population from Pygo2 SSKO mammary gland displays biased differentiation towards luminal/alveolar lineage in vitro, and reduced regeneration rate of new mammary gland in vivo

overall_design: To gain the insight into gene expression profiles in control and Pygo2 SSKO mammary epithelial cells (MECs), we sorted the freshly isolated mouse MECs into MaSC/basal (Lin-CD29hiCD24+) and mature luminal population (Lin-CD29lowCD24+CD61-), and extract total RNA for cDNA microarray analysis

first: Xing

last: Dai


title: BRCA1-related gene signature in breast cancer: the role of ER status and molecular type

city: Gliwice

first: Katarzyna

middle: Marta

last: Lisowska

address: ul. Wybrzeże Armii Krajowej 15

department: Center for Translational Research  and Molecular Biology of Cancer

country: Poland

institute: MSC Memorial Cancer Center and Institute of Oncology, Gliwice Branch

summary: We have analyzed, using DNA microarrays, putative differences in gene-expression level between hereditary BRCA1 mutation-linked and sporadic breast cancer. Our results show that a previously reported marked difference between BRCA1-mutation linked and sporadic breast cancer was probably due to uneven stratification of samples with different ER status and basal-like versus luminal-like subtype. We observed that apparent difference between BRCA1-linked and other types of breast cancer found in univariate analysis was diminished when data were corrected for ER status and molecular subtype in multivariate analyses. In fact, the difference in gene expression pattern of BRCA1-mutated and sporadic cancer is very discrete. These conclusions were supported by the results of Q-PCR validation. We also found that BRCA1 gene inactivation due to promoter hypermethylation had similar effect on general gene expression profile as mutation-induced protein truncation. This suggests that in the molecular studies of hereditary breast cancer, BRCA1 gene methylation should be recognized and considered together with gene mutation.

overall_design: We analyzed 35 breast cancer specimens. Surgical samples obtained during mastectomy were flash-frozen in liquid nitrogen and stored at -80°C. Only samples from patients without neoadjuvant chemotherapy were used in this study as chemotherapy may seriously affect gene expression profile. All tissue samples were collected at the Pomeranian Medical University in Szczecin. Seventeen tumor samples were collected from patients with hereditary breast cancer: 12 were derived from tumors affecting women with hereditary BRCA1 mutation, the only one from a woman with BRCA2 mutation, while another eight cases had familial history of breast/ovarian cancer, but were negative for the BRCA1/2 mutations (so called BRCAx cases). Proportion of BRCA1 and BRCA2 mutated tumors was typical for the Polish population. Ten samples were derived from patients with apparently sporadic disease (no familial history of cancer) while 4 patients had a history of familial cancer aggregation (FCA) but without prevalence of breast/ovarian cancers. Thus, these samples were merged with sporadic samples in most of the analyses.  All BRCA1 mutation-linked tumors in our study were negative for estrogen receptor (by immunohistochemistry, standard procedures for ER, PGR and HER2 staining were applied), while the only BRCA2-mutated tumor was ER-positive. There were 26 ductal and 5 medullary carcinomas within the study group, which is consistent with the distribution of histopathological types in BRCA1 mutation carriers. Patients were diagnosed at stage T1-2, N0-1 and M0. Caution: this submission contains the data from 6 microarrays done on the normal/pathologically unchanged breast tissue from breast cancer patiets. The data from normal tissues was not analyzed in the paper BRCA1-related gene signature in breast cancer is strongly influenced by ER status and molecular type by Lisowska et al., 2011, Front Biosci (Elite Ed). 2011 Jan 1;3:125-36


title: Expression data from N/Tert-HPV E6 cells in the presence and absence of mitomycin C treatment

first: Elizabeth

middle: A

last: White

address: 3610 Hamilton Walk

department: Otorhinolaryngology

institute: University of Pennsylvania

summary:
HPV E6 from the genus alpha 'high risk' types such as HPV16 recruit the ubiquitin ligase E6AP to ubiquitinate p53 and target it for proteasome-mediated degradation.  This results in the functional inactivation of p53 in HPV16-E6 expressing cells.
To test what patterns in gene expression might change as a result of HPV16 E6 protein functions and to test whether HPV E6 proteins from genus beta virus types also inactivate p53, we profiled gene expression using Affymetrix arrays before and after stimulating p53 activity via DNA damage in a panel of N/Tert-E6 cell lines.

overall_design: N/Tert-1 human keratinocyte cell lines were cultured in K-SFM (Invitrogen) and treated with 2 ug/ml mitomycin C or with vehicle control for 18 hours.  RNA isolated from frozen cell pellets was analyzed on Affymetrix arrays.  Each cell line was grown and processed on arrays in 3-5 separate experiments.

first: Johanna

last: Walther

first: Hassan

last: Javanbakht

first: Peter

last: Howley


title: Microarray to find CHOP/ATF5 dependent genes in response to proteasome inhibition

city: Indianapolis

first: Ron

last: Wek

state: IN

address: 635 Barnhill Dr. MS4065

department: Biochemistry & Molecular Biology

institute: Indiana University School of Medicine

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

overall_design: Refer to individual Series


title: PGN induced transcriptional changes in human neonatal neutrophils

status: Public on Sep 04 2013

city: Hong Kong

first: Kathy

middle: YY

last: Chan

address: Rm84041, 6/F, Clinical Science Building, Prince of Wales Hospital, Shatin, N.T.

department: Paediatrics

country: Hong Kong

institute: The Chinese University of Hong Kong

summary: We have employed whole genome microarray expression profiling to identify genes differentially expressed in cord blood purified neutrophils after a short-term exposure to peptidoglycan (PGN).

overall_design: PGN induced gene expressions of neonatal neutrophils were measured at 4 hours. Three biological replicates were performed for each treatment group.

first: Karen

last: Li

middle: Y


title: Microarray to find ATF5 dependent genes in response to proteasome inhibition

summary: Environmental stresses that disrupt protein homeostasis induce phosphorylation of eIF2, triggering repression of global protein synthesis coincident with preferential translation of ATF4, a transcriptional activator of the Integrated stress response (ISR). Depending on the extent of protein disruption, ATF4 may not be able to restore proteostatic control and instead switch to a terminal outcome that features elevated expression of the transcription factor CHOP (GADD153/DDIT3). The focus of this study was to define the mechanisms by which CHOP directs gene regulatory networks that determine cell fate.  We find that in response to proteasome inhibition, CHOP induces the expression of a collection of genes encoding transcription regulators, including ATF5, which is preferentially translated during eIF2 phosphorylation.  Transcriptional expression of ATF5 is directly activated by both CHOP and ATF4.   Knock-down of ATF5 increased cell survival in response to proteasome inhibition, supporting the idea that both ATF5 and CHOP have pro-apoptotic functions.  Transcriptome analyses of ATF5-dependent genes revealed targets involved in apoptosis, including, NOXA, which is important for inducing cell death during proteasome inhibition. This study suggests that the ISR features a feed-forward loop of stress induced transcriptional regulators, each subject to transcriptional and translational control that can switch cell fate towards apoptosis.

overall_design: 8 plates (10cm)  of WT and and 8 plates (10cm) of ATF5-KD MEF cells were subject to no stress (4 each for a total of 8) or treated for 8 hours with 1uM MG132 (4 each for a total of 8).  Unstressed cells were harvested at the same time as the stressed cells

first: Brian

middle: F

last: Teske

first: Michael

middle: E

last: Fusakio

first: Donghui

last: Zhou

first: Jixiu

last: Shan

first: Jeanette

middle: N

last: McClintick

last: Kilberg

first: Ronald

middle: C


title: Expression data from wound skin taken at three time points post wounding

status: Public on Sep 01 2013

city: New York

first: Denise

last: Gay

address: 550 1st avenue

institute: NYU langone

summary:
The full complement of hair follicles is generated during embryogenesis. Normally, no new hair is created after this time. Large full thickness skin excision wounding can result in the generation of new hair in the adult. Placodes can be observed following complete reepithelialization at wound day 14.  The events leading to hair neogenesis following wounding remain poorly understood. Late healing events (from wound day 10 to wound day 14) provide a possible window of induction for hair regeneration.
We used microarrays to analyse changes in gene expression during late skin healing to provide candidates for factors involved in hair neogenesis following wounding.

overall_design: 6 week old C57Bl/6 mice received large full thickness skin excisions. Healing wound tissue was excised at wound day 10, 12 or 14 and analyzed for gene expression.

first: George

last: Cotsarelis


title: Knock-down of BCL6 expression in human Diffuse Large B-Cell Lymphoma cell lines

first: Mariano

middle: Javier

last: Alvarez

state: NY

address: 1130 St. Nicholas ave.

department: Systems Biology

institute: Columbia University

summary:
This dataset was used to benchmark the Virtual Inference of Protein-activity by Regulon Readout algorithm (VIPER). Despite recent advances in molecular profiling, proteome-wide assessment of protein activity in individual samples remains a highly elusive target. In stark contrast, protein activity quantitation is increasingly critical to the dissection of key regulatory processes and to the elucidation of biologically relevant mechanisms. Importantly, its value extends to the study of drug activity, as most small molecules inhibit activity of their cognate protein substrates without affecting the protein’s or associated mRNA’s abundance.
VIPER leverages the increasingly accurate and context specific knowledge of regulatory networks. Specifically, it uses the expression of the transcriptional targets most directly regulated by a given protein in an individual sample as a reporter for the computational inference of its activity.

overall_design: BCL6 knock down experiments were performed in OCI-Ly7 and Pfeiffer GCB-DLBCL cell lines. Both cell lines were maintained in 10% FBS supplemented IMDM medium and transiently transfected with either a BCL6-specific or a non-target control siRNA oligo in triplicate. Total RNA was isolated 48h after transfection and gene expression was profiled on H-GU133plus2 Affymetrix gene chips.

first: B

middle: H

last: Ye

middle: B

last: Ding


title: Genome-wide transcription profile of CpG-activated peritoneal macrophages

status: Public on Sep 07 2013

city: Boston

first: Alexander

last: Poltorak

state: Massachusetts

address: 150 Harrison avenue

institute: Tufts University

summary: To compare up-regulation of genes following CpG activation, we performed microarray analysis of activated macrophages from B6 and F1(B6xMOLF) mouse strains. Cells were activated for 0, 2 and 4 hrs with 200nM of type B CpG. Levels of mRNA for many genes differened dramatically between the strains

overall_design: Peritoneal macrophages were elicited from pertoneal cavity of mice 3 days after thioglycollate injection. The cells were plated overnight at a density of 5 million cells per 100 mm dish and activated the next day with 200 nM CpG. Total RNA was isolated with TRIZOL followed by  reverse transcrition, fragmentation and labeling accroding the manufacture's (Affymetrix) recommendations

first: Annie

last: Moseman


title: Epigenome analysis of uterin leiomyoma and myometrium with or without leiomyoma

city: Ube

first: Ryo

last: Maekawa

address: Minami-Kogushi 1-1-1

department: Department of Obstetrics and Gynecology

country: Japan

institute: Yamaguchi University School of Medicine

type: Methylation profiling by genome tiling array


title: Epigenome analysis of uterin leiomyoma and myometrium with or without leiomyoma [Methylation data]

summary: Profiles of genome-wide DNA methylation were investigated in leiomyomas and in myometrium with and without leiomyomas.  Profiles of DNA methylation in the myometrium with and without leiomyomas were quite similar while those in leiomyomas were distinct.

overall_design: Bisulphite converted DNA from the three uterine leiomyoma, three myometrium with leiomyoma and three myometrium without leiomyoma were hybridised to the Illumina infinium HumanMethylation450 BeadChip.

first: Shun

last: Sato

first: Yoshiaki

last: Yamagata

first: Hiromi

last: Asada

first: Isao

last: Tamura

first: Maki

last: Okada

first: Hiroshi

first: Norihiro

last: Sugino


title: Effects of neonatal stress and morphine on murine hippocampal gene expression

status: Public on Aug 30 2013

city: Seattle

first: James

middle: William

last: MacDonald

state: WA

address: 4225 Roosevelt Way NE

department: Environmental and Occupational Health Sciences

institute: University of Washington

summary: Critically ill preterm infants experience multiple stressors while hospitalized. Morphine is commonly prescribed to ameliorate their pain and stress. We hypothesized that neonatal stress will have a dose-dependent effect on hippocampal gene expression, and these effects will be altered by morphine treatment. Male C57BL/6 mice were exposed to 5 treatment conditions between postnatal day 5 and 9: 1) Control, 2) mild stress + saline, 3) mild stress + morphine, 4) severe stress + saline and 5) severe stress + morphine. Hippocampal RNA was extracted and analyzed using Affymetrix Mouse Gene 1.0 ST Arrays. Single gene analysis and gene set analysis were used to compare groups with validation by qPCR. Stress resulted in enrichment of genes sets related to fear response, oxygen carrying capacity and NMDA receptor synthesis. Morphine downregulated gene sets related to immune function. Stress plus morphine resulted in enrichment of mitochondrial electron transport gene sets, and down-regulation of gene sets related to brain development and growth. We conclude that neonatal stress alone influences hippocampal gene expression, morphine alters a subset of stress-related changes in gene expression and influences other gene sets. Stress plus morphine show interaction effects not present with either stimulus alone. These changes may alter neurodevelopment.

overall_design: Male mice were exposed to 5 treatment conditions between postnatal day (P)5 and P9 (n=3/group), with birth recorded as P1. Litters were culled to n=7 maximum per dam. Groups included: 1) Untreated controls (CC), 2) mild stress + saline (MSS), 3) mild stress + morphine (MSM), 4) severe stress + saline (SSS) and 5) severe stress + morphine (SSM).

first: Theodor

last: Bammler

first: Sandra

last: Juul

first: Frederico

last: Farin

first: Richard

middle: P

last: Beyer

first: Christine

last: Gleason


title: Deterministic direct reprogramming of somatic cells to pluripotency [Microarray/Expression]

status: Public on Sep 12 2013

city: Rehovot

first: Asaf

last: Zviran

address: 234 Herzl Street

department: Molecular Genetics

country: Israel

institute: Weizmann Institute of Science

summary: Somatic cells can be directly reprogrammed to pluripotency by exogenous expression of transcription factors, classically Oct4, Sox2, Klf4 and c-Myc. While distinct types of somatic cells can be reprogramed with varying efficiencies and by different modified reprogramming protocols, induced pluripotent stem cell (iPSC) induction remains inefficient and stochastic where a fraction of the cells converts into iPSCs. The nature of rate limiting barrier(s) preventing majority of cells to convert into iPSCs remains elusive. Here we show that neutralizing Mbd3, a core member of the Mbd3/NURD co-repressor and chromatin-remodeling complex, results in deterministic and synchronized reprogramming of multiple differentiated cell types to pluripotency. 100% of Mbd3 depleted mouse and human somatic cells convert into iPSCs after seven days of reprogramming factor induction. Our findings delineate a critical pathway blocking the reestablishment of pluripotency, and offer a novel platform for future dissection of epigenetic dynamics leading to iPSC formation at high resolution.

overall_design: Samples include Mbd3+/+, Mbd3flox/- and Mbd3-/- cells from mouse ES cells and mouse embryonic fibroblast (MEF) before and after DOX induction (initiating reprogramming by OSKM factors). Cells were expanded on irradiated mouse MEFs.

first: Yoach

last: Rais

first: Noa

last: Novershtern


title: Identification of  DNA methylation changes in monocytes to osteoclast differentiation

city: Badalona, Barcelona

first: Esteban

last: Ballestar

state: N/A = Not Applicable

address: Ctra de Can Ruti, Camí de les Escoles s/n

country: Spain

institute: Josep Carreras Research Institute (IJC)

summary: Conversion of monocytes to osteoclasts is a unique terminal differentiation process within the hematopoietic system involving differentiation and massive cell fusion. Here we focused on DNA methylation changes during osteoclastogenesis. Hypermethylation and hypomethylation changes took place in several thousand genes, including all relevant functional categories in osteoclast differentiation and function.

overall_design: Comparison between the DNA methylation levels of  CD14+ monocytes and derived osteoclast from 3 female donors. Bisulphite converted DNA from the 6 samples was hybridised to the Illumina Infinium 450k Human Methylation Beadchip

first: Lorenzo

last: de la Rica

first: Mireia

last: García

first: Javier

last: Rodríguez-Ubreva

first: Abul

last: Islam

first: José

middle: M

last: Urquiza

first: Henar

last: Hernando

first: Jesper

last: Christensen

first: Kristian

last: Helin

first: Carmen

last: Gómez-Vaquero


title: Selective Requirement for Mediator MED23 in Ras-active Lung Cancer

status: Public on Aug 31 2013

city: Shanghai

first: Xu

last: Yang

address: 320 Yueyang Road

country: China

institute: Insititute of biochemistry and cell biology

summary:
K-RAS activating mutations occur frequently in non-small cell lung cancer (NSCLC), leading to aberrant activation of Ras-MAPK signaling pathway that contributes to the malignant phenotype. However, the development of Ras-targeted therapeutics remains challenging. Here, we show that MED23, a component of the multisubunit Mediator complex that is known to integrate signaling and gene activities, is selectively important for Ras-active lung cancer. By screening a large panel of human lung cancer cell lines with or without a Ras mutation, we found that Med23 RNAi specifically inhibits the proliferation and tumorigenicity of lung cancer cells with hyperactive Ras activity. Med23-deficiency in fibroblasts selectively inhibited the oncogenic transformation induced by Ras but not by c-Myc. Transcription factor ELK1, which is phosphorylated by MAPK for relaying the Ras signaling to MED23, was also required for the Ras-driven oncogenesis. Transcriptiome analysis revealed that MED23 and ELK1 co-regulate a common set of target genes enriched in regulating cell cycle and proliferation to support the Ras-dependency. Furthermore, correlated with the strength of Ras signaling as indicated by the ELK1 phosphorylation level, MED23 was up-regulated by Ras-transformation, and was found to be overexpressed in both Ras-mutated lung cancer cell lines and primary tumor samples. Remarkably, lower Med23 expression predicts better survival in Ras-active lung cancer patients and xenograft mice. Collectively, our findings demonstrate a critical role for MED23 in enabling the “Ras-addiction” of lung carcinogenesis, thus providing a vulnerable target for the treatment of Ras-active lung cancer.
To gain a genome-wide understanding of how MED23 and ELK1 control gene expression in Ras-active lung cancer cells, we performed gene profiling experiments to analyze the transcriptomes from control, si-Med23, or si-Elk1 A549 cells.

overall_design: The si-Ctrl, si-Med23 and si-Elk1 A549 cells were cultured in the normal condition. Then the cells were harvested for RNA extraction and hybridization on Affymetrix microarrays. The analysis contain 9 samples. si-Ctrl cells have three replicates (si-Ctrl#1, si-Ctrl#2 and si-Ctrl#3), and the si-Med23 or si-Elk1 group contains three different cell lines that harbor three different RNAi oligos against Med23 or Elk1 (si-Med23A, B, C and si-Elk1A, B, C).

first: Gang

last: Wang


title: Usp44 binds centrin to regulate centrosome positioning and suppress tumorigenesis

city: Rochester

first: Alexey

middle: Aleksandrovich

last: Leontovich

state: MN

address: 200 First street

department: Health Science Research

institute: Mayo Clinic

summary: Most human tumors have abnormal numbers of chromosomes, a condition known as aneuploidy. The mitotic checkpoint is an important mechanism that prevents aneuploidy through restraining the activity of the anaphase-promoting complex (APC). USP44 was identified as a key regulator of APC activation that maintains the association of MAD2 with the APC co-activator Cdc20. However, the physiological importance of USP44 and its impact on cancer biology are unknown. Here, we show that USP44 is required to prevent tumors in mice and is frequently down-regulated in human lung cancer. USP44 inhibits chromosome segregation errors independently of its role in the mitotic checkpoint by regulating proper centrosome separation, positioning, and mitotic spindle geometry, functions that require direct binding to the centriole protein, centrin. These data reveal a new role for the ubiquitin system in mitotic spindle regulation and underscore the importance of USP44 in the pathogenesis of human cancer.

overall_design: Study included 100 non-neoplastic (N) lung samples, and 69, 12, and 13 stage I, II, and II lung adenocarcinoma (AD) frozen tissues, respectively.  Expression levels of Usp44 in different stages of AD was compared against N.

first: Dennis

last: Wigle

first: George

last: Vasmatzis


title: Gene expression in human umbilical cord vein and artery endothelial cells under physiological chronic normoxia (3% O2, PCN) and standard culture normoxia (21% O2, SCN)

city: Madison

first: Yizhou

last: Jiang

state: Wi

address: 202 S. Park st PAB1

institute: University of Wisconsin-madison

summary: Endothelial cells, and many other types of cells too, physiologically reside in low O2 environments (~ 2-13% O2 or 15-60 mmHg pO2; [PCN]) relevantly to atmospheric O2 (~ 21% or 160 mmHg pO2 at sea level) in vivo.  Such PCN is critical for endothelial functions. The majority of our current knowledge regarding the cellular and signaling mechanisms governing endothelial functions, however, is built on endothelial models established under atmospheric O2 (~21% O2).  Herein, we comapred the transcriptional profiles  between HUVE and HUAE cells cultured and expanded under  PCN (3% oxygen) and standard culture normoxia (21% O2).

overall_design: We established human umbilical vein (HUVE) and artery (HUAE) endothelial cell cultures under PCN (3% O2; 20-25 days) and SCN (21% O2), and examined the global gene expression using Affymetrix U133 plus 2.0 microarray chips.

first: Yi-Zhou

first: Jing

last: Zheng


title: The study of the differential expression profile in bone tissues between Tnni2del175k mutant mice and their wild-type littermates using mRNA array.

city: beijing

first: xiaoquan

last: zhu

address: N01 dahua road dongdan beijing

institute: beijing hospital

overall_design: 3 paires of  newbone mice bones from Tnni2del175k mutant mice and their wild-type littermates

first: Xiaoquan

first: Shaorong

last: gao

first: Ze

last: yang


title: HIF orchestrated metabolic shift confers protection against Acute Kidney Injury (AKI)

city: Berlin

first: Michael

last: Fähling

address: Charitéplatz 1

department: Institut für Vegetative Physiologie

country: Germany

institute: Charité - Universitätsmedizin Berlin

summary:
Renal hypoxia is widespread in acute kidney injury (AKI) of various aetiologies. Hypoxia adaptation, conferred through the hypoxia-inducible factor (HIF), appears to be insufficient. Here we show that HIF activation in renal tubules through Pax8-rtTA-based inducible knockout of von Hippel-Lindau protein (VHL-KO) protects from rhabdomyolysis-induced AKI. In this model, histological observations indicate that injury mainly affects proximal convoluted tubules, with 5% necrosis at d1 and 40% necrosis at d2. HIF-1alpha up-regulation in distal tubules reflects renal hypoxia. However, lack of HIF in proximal tubules suggests insufficient adaptation by HIF.
AKI in VHL-KO mice leads to prominent HIF activation in all nephron segments, as well as to reduced serum creatinine, serum urea, tubular necrosis, and apoptosis marker caspase-3 protein. At d1 after rhabdomyolysis, when tubular injury is potentially reversible, HIF mediated protection in AKI is associated with activated glycolysis, cellular glucose uptake and utilization, autophagy, vasodilation, and proton removal as demonstrated by qPCR, pathway enrichment analysis and immunohistochemistry. Together, our data provide evidence for a HIF-orchestrated multi-level shift towards glycolysis as a major mechanism for protection against acute tubular injury.

overall_design: All experiments were carried out in transgenic mice in which selective renal tubular VHL knockout (VHL-KO) was inducible by doxycycline (Reference: Mathia S, Paliege A, Koesters R, Peters H, Neumayer HH, Bachmann S, Rosenberger C. Action of hypoxia-inducible factor in liver and kidney from mice with Pax8-rtTA-based deletion of von Hippel-Lindau protein. Acta Physiol (Oxf). 2013; 207(3):565-76.). Four groups of animals were used: 1) controls: untreated mice; 2) VHL-KO: injected with doxycycline (0.1 mg per 10 g body weight SC), 4 days prior to sacrifice; 3) AKI: rhabdomyolysis; 4) VHL-KO/AKI: doxycycline plus rhabdomyolysis. To induce AKI, 50% glycerol (0.05 ml per 10 g body weight) was injected IM into the left hind limb under isoflurane narcosis. Drinking water was withdrawn between 20 h prior and 24 h after glycerol injection.

first: Susanne

last: Mathia

first: Alexander

last: Paliege

first: Robert

last: Koesters

first: Ralf

last: Mrowka

first: Harm

last: Peters

first: Pontus

last: Persson

first: Hans

last: Neumayer

first: Sebastian

last: Bachmann

first: Christian

last: Rosenberger


title: Methylation profiles in non-alcoholic fatty liver disease

city: Durham

first: Cynthia

last: Moylan

state: NC

address: 595 LaSalle Street, GSRB1, DUMC 3256

department: Gastroenterology

institute: Duke University Medical Center

summary:
Background & Aims: Cirrhosis and liver cancer are potential outcomes of advanced nonalcoholic fatty liver disease (NAFLD). It is not clear what factors determine whether patients will develop advanced or mild NAFLD, limiting non-invasive diagnosis and treatment before clinical sequelae emerge. We investigated whether DNA methylation profiles can distinguish patients with mild disease from those with advanced NAFLD, and how these patterns are functionally related to hepatic gene expression.

Methods: We collected frozen liver biopsies and clinical data from patients with biopsy-proven NAFLD (56 in the discovery cohort and 34 in the replication cohort). Samples were divided into groups based on histologic severity of fibrosis: F0?1 (mild) and F3?4 (advanced). DNA methylation profiles were determined and coupled with gene expression data from the same biopsies; differential methylation was validated in subsets of the discovery and replication cohorts. We then analyzed interactions between the methylome and transcriptome.

Results: Clinical features did not differ between patients known to have mild or advanced fibrosis based on biopsy analysis. There were 69,247 differentially methylated CpG sites (76% hypomethylated, 24% hypermethylated) in patients with advanced vs mild NAFLD (P<.05). Methylation at FGFR2, MAT1A, and CASP1 was validated by bisulfite pyrosequencing and the findings were reproduced in the replication cohort. Methylation correlated with gene transcript levels for 7% of differentially methylated CpG sites, indicating that differential methylation contributes to differences in expression. In samples with advanced NAFLD, many tissue repair genes were hypomethylated and overexpressed, whereas genes in certain metabolic pathways, including 1-carbon metabolism, were hypermethylated and under-expressed.

Conclusions: Functionally relevant differences in methylation can distinguish patients with advanced vs mild NAFLD. Altered methylation of genes that regulate processes such as steatohepatitis, fibrosis, and carcinogenesis indicate the role of DNA methylation in progression of NAFLD.

overall_design: Three technical replicates were included for quality control along with 35 mild NAFLD (33 unique samples) and 24 advanced NAFLD (23 unique sample). One sample per technical duplication was randomly included for a total of 56 NAFLD samples used for study.

first: Susan

last: Murphy

first: Hyuna

last: Yang

first: Herbert

last: Pang

first: Andrew

last: Dellinger

first: Manal

last: Abdelmalek

first: Melanie

last: Garrett

first: Allison

last: Ashley-Koch

first: Ayako

last: Suzuki

middle: L

last: Tillmann

last: Hauser

first: Anna

last: Diehl


title: The Human Oviductal Transcriptome Reveals An Anti-inflammatory, Anti-angiogenic, Secretory and Matrix-stable Environment During Embryo Transit

city: San Francisco

first: Linda

last: Giudice

state: CA

address: 513 Parnassus Ave. HSE 1619

department: OBGYN and RS

institute: University of California, San Francisco

summary: Human oviduct serves as a conduit for sperm in the peri-ovulatory phase and to nurture and facilitate transport of the developing embryo en route to the uterus for subsequent nidation during the luteal phase of the cycle. Interactions between the embryo and oviductal epithelial surface proteins and secreted products during the four day embryo transit are largely undefined. Herein, we have investigated gene expression in human oviduct in the early luteal vs. follicular phase to identify candidate genes and biomolecular processes that may participate in maturation and transport of the embryo as it traverses this tissue. Oviductal RNA was isolated, processed, and hybridized to oligonucleotide arrays. Resulting data were analyzed by bioinformatic approaches and revealed that 650 genes were significantly downregulated and 683 genes were significantly upregulated in the luteal vs. follicular phase. Real-time RT-PCR, immunoblot analysis, and immunohistochemistry confirmed select gene expression and cellular protein localization. The data demonstrate downregulation of genes involved in macrophage recruitment, immunomodulation, and matrix-degeneration and upregulation of ion transport and secretions as well as anti-angiogenic and early pregnancy recognition genes in luteal vs. follicular phase oviduct. Together, these data suggest a unique hormonally regulated environment during embryo development, maturation and transport through human oviduct.

overall_design: We have investigated gene expression in human oviduct in the early luteal vs. follicular phase. Oviductal RNA was isolated, processed, and hybridized to oligonucleotide arrays. Resulting data were analyzed by bioinformatic approaches and revealed that 650 genes were significantly downregulated and 683 genes were significantly upregulated in the luteal vs. follicular phase. Real-time RT-PCR, immunoblot analysis, and immunohistochemistry confirmed select gene expression and cellular protein localization.

first: Alexandra

last: Hess

first: Said

last: Talbi

first: Amy

last: Hamilton

first: Dunja

last: Baston-Buest

first: Mette

last: Nyegaard

first: Jan

middle: S

last: Krussel

first: Fatima

last: Barragan

first: Ariane

last: Germeyer


title: Expression data from striatum of a mouse model of Huntington´s disease (HD) (HdhQ111/Q111) crossed with mGluR5  knockout mice (mGluR5-/-) and their respective controls (HdhQ20/Q20 and mGluR5+/+).

status: Public on Aug 28 2013

city: London

first: Stephen

middle: Sean Gilbert

last: Ferguson

state: ON

address: 100 Perth Drive

department: Molecular Neurobiology

country: Canada

institute: Robarts Research Institute

summary:
To try to investigate the mechanism behind the adaptive phenotypes observed in a mice model model of HD crossed with mGluR5 knockout, we analyzed whether mutated huntingtin (Htt) expression in a mGluR5 null background could be altering the expression of genes that might be involved in the pattern of Htt aggregation and HD-related locomotor alterations.
In this data set, we include analysis of gene expression in striatum of mice with four different genotypes: HdhQ20/Q20/mGluR5+/+; HdhQ20/Q20/mGluR5-/- ; HdhQ111/Q111/mGluR5+/+ ; HdhQ111/Q111/mGluR5-/-

overall_design: 12 samples were analyzed. We used Partek Genomics Suite v6.5 (Partek, St. Louis, MO) to determine differences in gene expression levels. Genotype effects were considered significant based of the following criteria: (i) ANOVA p-values< 0.05 and (ii) 1.5 fold increase or decrease.

first: D

last: Carter

first: S

last: Cregan


title: Glioma stem cell treatment with MELK-signaling inhibitors

city: Los Angeles

first: Giovanni

last: Coppola

address: 1524 Gonda, 695 Charles Young Drive South

department: Psychiatry and Neurology

institute: UCLA

summary: Glioblastoma multiforme (GBM) is a highly lethal brain tumor. Due to resistance to current therapies, patient prognosis remains poor and development of novel and effective GBM therapy is crucial. Glioma stem cells (GSCs) have gained attention as therapeutic target in GBM due to their relative resistance to current therapies and potent tumor-initiating ability. Recent studies including our own identified that the mitotic kinase, maternal embryonic leucine-zipper kinase (MELK), is highly expressed in GBM tissues, specifically in GSCs, and its expression is inversely correlated with the post-surgical survival period of GBM patients. In addition, patient-derived GSCs depend on MELK for their survival and growth both in vitro and in vivo. Here, we provide evidence that the kinase activity of MELK is essential for the action of MELK in GSCs and vital for GBM growth. We utilized in silico structure-based analysis for protein-compound interaction to predict that a recently identified small molecule, Compound 1 (C1), binds to the kinase-active site of MELK protein and eliminates MELK kinase activity in nanomolar concentrations. When treated with C1, GSCs undergo mitotic arrest and subsequent cellular apoptosis in vitro, a phenotype identical to that observed using MELK shRNA-mediated knockdown. C1 treatment strongly induces tumor cell apoptosis in slice cultures of GBM surgical specimens and attenuates growth of mouse intracranial tumors derived from GSCs in a dose-dependent manner. Lastly, C1 treatment sensitizes GSCs to radiation treatment. Collectively, these data indicate that targeting MELK kinase activity is a promising approach to attenuate GBM growth by eliminating GSCs in tumors.

overall_design: Microarray-based expression analysis of glioma stem cells treated with MELK-signaling inhibitors

first: Mutsuko

last: Minata

first: Chunyu

last: Gu

first: Kaushal

last: Joshi

first: Mariko

last: Nakano-Okuno

first: Christopher

last: Hong

first: Chi-Hung

last: Nguyen

first: Harley

middle: I

last: Kornblum

first: Annie

last: Molla

first: Ichiro

last: Nakano


title: Red blood cells from mice on high fat diet induce macrophage activation during phagocytosis

city: Cincinnati

first: Bruce

middle: J

last: Aronow

state: OH

address: 240 Albert Sabin Way

department: Biomedical Informatics, Developmental Biology

institute: Cincinnati Children's Hospital Medical Center

summary:
We studied macrophage gene expression from mice fed chow diet (C) or 60% high fat diet (HF), that phagocytized C-RBC, HFD-RBC, or no RBC.
Macrophages from mice on HF diet were activated toward a pro-inflammatory phenotype.  In macrophages isolated from CD mice, RBC phagocytosis yielded a gene expression pattern similar to HF macrophages. Incubation of HF-RBC with macrophages resulted in a significantly more pronounced upregulation of pro-inflammatory chemokines as compared to C-RBC.

overall_design: Peritoneal macrophages were obtained from C57BL/6 mice fed either C or HF diet.  Phagocytosis was performed in vitro with C-RBC or HF-RBC; macrophages not exposed to RBC served as a control.  Affymetrix Mouse Gene 1.0 ST microarray chips were used to assess the gene expression profile.

first: Ramprasad

last: Srinivasan

first: Vladimir

last: Bogdanov


title: Effects of gene scilencing of USP2 on expression profiles of HL60 cells

status: Public on Aug 27 2013

city: Ebetsu

first: Hiroshi

last: Kitamura

address: 582 Midorimachi, Bunkyodai

department: School of Veterinary Medicine

institute: Rakuno Gakuen University

summary:
So far, we have found PMA induced USP2b isoform in myeloid leukemia cell lines such as HL60, THP-1, and U937.
To explore molecular function of USP2 in the cells, we assess expression profiles of HL60-derivatives continuously expressing shRNA for USP2 and control shRNA.

overall_design: HL60 derivatives continuously expressing shRNA for USP2 and control shRNA were treated with PMA (30nM) for 0, 1, 2, and 3 days. Total RNA was extracted from the cells and subjected to microarray experiments using Human Genome U133 GeneChips.

first: Masatoshi

last: Ito

first: Chisato

last: Kikuguchi

first: Osamu

last: Ohara


title: Expression data from normal B cells and chronic lymphocytic leukemia B cells -- with/without treatment of Wnt3a

status: Public on Aug 29 2013

first: Lili

last: Wang

state: MA

address: 77 Ave Louis Pasteur

institute: Dana Farber Cancer Instutute

summary:
Wnt pathway is dysregulated in CLL-We characterized Wnt pathway gene expression in normal B and CLL-B cells and identified Wnt targets in normal B and CLL-B cells through this data set.
In this dataset, we included normal B cells and CLL-B cells for Wnt pathway gene expression. This leads to the identification of 62 Wnt pathway components which are differnetially expressed between normal and CLl-B cells. We also included normal B cells and CLL-B cells with or without Wnt3a treatment and identified 468 and 676 Wnt regulated genes in normal and CLL B cells, respectively.

overall_design: 24 normal B cells and 179 CLL-B cells were used in the Wnt pathway gene expression analysis. Three normal and three CLL samples were included in the identification of Wnt regulated targets

first: Wandi

last: Zhang

first: Catherine

last: Wu

first: Bethany

last: Tesar

first: Jennifer

middle: R

last: Brown

first: Kristen

last: Stevenson

first: Donna

last: Neuberg

first: Nathalie

last: Pochet

first: Aviv

last: Regev


title: Expression data from control siRNA and β-catenin siRNA transfected cultured mouse dermal cells

status: Public on Sep 03 2013

city: Daegu

first: seung hyun

last: shin

address: 101 Dong-In-Dong, Jung-Gu

country: South Korea

institute: Department of Immunology and Hair Research Center, School of Medicine Kyungpook National University

summary:
β-catenin activity of dermal cells is crucial for hair follicle neogenesis and strongly suggest that transcriptional target genes of β-catenin pathway are essential for maintaining trichogenicity of dermal cells.
We used microarrays to identify genes targeted by the β-catenin pathway that are essential for maintaining the trichogenicity of dermal cells.

overall_design: Freshly isolated dermal cells from the dorsal skins of C57BL/6 neonates (P0) were cultured for 24 hours and transfected with either control siRNA or β-catenin specific siRNAs (β-catenin siRNA) at a final concentration of 10 nM for 48 hours followed by RNA extraction and hybridization on Affymetrix microarrays.

first: Seung

last: Shin

first: Young

middle: K

last: Sung


title: Expression data from human Th1 and Th1Th17 cells

status: Public on Aug 26 2013

city: Montréal

first: Jean-Philippe

last: Goulet

state: Québec

address: C.P. 6128, succursale Centre-ville

institute: Université de Montréal

summary:
We previously demonstrated that Th1Th17 cells are highly permissive to HIV-1, whereas Th1 cells are relatively resistant. Here, we investigated molecular mechanisms underlying these differences. Superior HIV replication in Th1Th17 vs. Th1 cells was regulated by entry and post-entry mechanisms.
We used microarrays to detail the gene expression signatures caracterizing Th1 cells from Th1Th17.

overall_design: Primary human Th1 (CXCR3+CCR6- phenotype) and Th1Th17 (CXCR3+CCR6- phenotype) CD4+ T-cells were isolated by flow cytometry from HIV-uninfected, healthy donors. Cells were stimulated via CD3/CD28 for 3 days. The RNA was extracted and hybridized on the GeneChip® Human Genome U133 Plus 2.0 Array (Affymetrix).

first: Annie

last: Bernier

first: Aurélie

last: Cleret-Buhot

first: Patricia

last: Monteiro

last: Gosselin

first: Sandrina

last: DaFonseca

first: Vanessa

last: Wacleche

first: Mohammad-Ali

last: Jenabian

first: Jean-Pierre

last: Routy

first: Cécile

last: Tremblay

first: Petronela

last: Ancuta


title: Expression data from human brain tumors and human normal brain

status: Public on Aug 25 2013

city: Aurora

first: Andrew

last: Donson

state: CO

department: Pediatrics

institute: CU Anschutz Medical Campus

summary:
The characteristics of immune cells infiltrating pediatric brain tumors is largely unexplored. A better understanding of these characteristics will provide a foundation for development of immunotherapy for pediatric brain tumors.
Gene expression profiles were used to identify immune marker gene that are differentially expressed between various brain tumor types.

overall_design: Gene expression profiles were generated from surgical tumor and normal brain samples (n=130) using Affymetrix HG-U133plus2 chips (Platform GPL570). Gene expression profiles of different types of brain tumors and normal brain were filtered to obtain gene expression of key immune cell markers. Comparative analyses between different brain tumors and normal brain was used to identifiy differential immune characteristics of these tumors.


title: Expression data from mouse CD3+ T-cells from WT and KLF13 KO mice

city: Bethesda

first: Seok-Joo

last: Kwon

address: 37 Convent Dr.

institute: NCI/NIH

summary: Kruppel-like factors are a subclass of zinc finger transcription factors that play important roles in different aspects of cell growth, development, and differentiation. Our group have identified KLF13 as an essential transcription factor for the late expression of chemokine RANTES in T lymphocytes. However, very little is known about the role of KLF13 in T cells and other potential transcriptional targets. To address this, we sought to identify genes that are regulated by KLF13 in mouse T cells. Using microarray analysis, we compared gene expression in activated CD3+ T lymphocytes from wild type and Klf13-/- animals.

overall_design: We isolated CD3+ T-cells from WT and KO mouse spleen. Isolated cells were activated with CD3 and CD28 for 4 days and RNA was extracted. All samples were hybrdized and gene expression were analyzed with Affymetrix microarrays.

first: Juan

last: Crespo-Barreto

first: Carol

last: Clayberger


title: Expression data for Nonalcoholic fatty liver disease patients

first: Cynthia

last: Moylan

summary:
Nonalcoholic fatty liver disease represents a spectrum of pathology that ranges from benign steatosis to potentially-progressive steatohepatitis and affects more than 30% of US adults. Advanced NAFLD is associated with increased morbidity and mortality from cirrhosis, primary liver cancer, cardiovascular disease and extrahepatic cancers.
Accurate identification of patients at risk for advanced NAFLD is challenging.  The aims of this study were to define the liver gene expression patterns that distinguish mild from advanced NAFLD and to develop a gene expression profile associated with advanced NAFLD.

overall_design: We analyzed total RNA from 72 patients with NAFLD (40 with mild NAFLD, fibrosis stage 0-1 and 32 with advanced NAFLD, fibrosis stage 3-4) and developed a gene profile associated with advanced NAFLD.

first: Anna

last: Diehl


title: Global analysis of NFATc1 targets in human vascular endothelial cells

city: Mitaka

first: Jun-ichi

last: Suehiro

state: Tokyo

address: 6-20-2, Shinkawa

department: Department of Pharmacology and Toxicology

institute: Kyorin University School of Medicine

summary: We performed the newly mapping of genome-wide NFATc1 binding events in VEGF-stimulated primary cultured endothelial cells, by chromatin immunoprecipitation followed by high-throughput sequencing (ChIP-seq). Combined NFATc1 ChIP-seq profile and the epigenetic histone marks revealed that predominant NFATc1-occupied peaks were overlapped with promoter marking but not silencer marking. DNA microarrays with NFATc1 expression or knockdown indicated the predominant NFATc1 binding targets were correlated with induced patterns.

overall_design: To determine NFATc1-regulated genes, a total of 5 samples were derived from human umbilical vein endothelial cells (HUVECs) stimulated with or without 50ng/mL VEGF (VEGF 60min and 0min, respectively), pretreated with cyclosporine A (VEGF 60min plus CsA) and infected with adenovirus expressing the control or constitutively active NFATc1 (Ad-control and Ad-NFATc1).

first: J

first: Y

last: Kanki

first: M

last: Miura

last: Manabe

first: H

last: Aburatani

first: T

last: Kodama


title: shRNA Screening Identifies JMJD1C as being required for Leukemia Maintenance

status: Public on Aug 22 2013

city: Copenhagen

first: Kristian

last: Helin

address: Ole Maaløes vej 5

department: BRIC

country: Denmark

institute: Copenhagen University

summary: We used a mouse model of human AML induced by the MLL-AF9 fusion oncogene, and an epigenetic shRNA library to screen for novel potential drug targets. One of the best candidate drug targets identified in these screens was Jmjd1c. Depletion of Jmjd1c impairs growth and colony formation of mouse MLL-AF9 cells in vitro, as well as establishment of leukemia after transplantation. Depletion of JMJD1C impairs expansion and colony formation of human leukemic cell lines, with the strongest effect observed in the MLL-rearranged ALL cell line, SEM. In both mouse and human leukemic cells, the growth defect upon JMJD1C depletion appears to be primarily due to increased apoptosis, which implicates JMJD1C as a potential therapeutic target in leukemia.

overall_design: To assess the effect of JMJD1C depletion on transcription, we compared the transcriptome of shJMJD1C- and shScr-transduced SEM cells soon after induction of shRNA expression by addition of IPTG to the growth medium. To ensure detecting early changes, 48h was selected as the earliest timepoint displaying JMJD1C depletion and detectable phenotype as monitored by PARP and Caspase 3 cleavage. These observations were consistent across triplicate samples. A total of 138 transcripts were detected as changing between the two conditions (FDR<0.05)

first: K


title: Regulation of endometrial bleeding by uNK cells

status: Public on Aug 23 2013

city: Edinburgh

first: Hilary

last: Critchley

address: 47 Little France Crescent

department: MRC Centre for Reproductive Health

institute: University of Edinburgh

summary: Uterine NK cells (uNK) play a role in the regulation of placentation but their functions in non-pregnant endometrium are not understood.  We have previously reported suppression of endometrial bleeding and alteration of spiral artery morphology in women exposed to asoprisnil, a progesterone receptor modulator (PRM).  We now compare global endometrial gene expression in asoprisnil-treated versus control women and demonstrate a statistically significant reduction of genes in the IL-15 pathway, known to play a key role in uNK development and function. Suppression of IL-15 by asoprisnil was also observed at mRNA level (p<0.05), and immunostaining for NK cell marker CD56 revealed a striking reduction of uNK in asoprisnil-treated endometrium (p<0.001). IL-15 levels in normal endometrium are progesterone-responsive. Progesterone receptor (PR) positive stromal cells transcribe both IL-15 and IL-15RA. Thus, the response of stromal cells to progesterone will be to increase IL-15 trans-presentation to uNK, supporting their expansion and differentiation. In asoprisnil-treated endometrium, there is a marked down-regulation of stromal PR expression and virtual absence of uNK.  These novel findings indicate that the IL-15 pathway provides a missing link in the complex interplay between endometrial stromal cells, uNK and spiral arteries affecting physiological and pathological endometrial bleeding.

overall_design: 39 Samples

middle: O

first: Nigel

last: Binns


title: Primary human hepatocytes treated with IL28B and the HCV JFH1 Genotype 2A clone.

status: Public on Aug 16 2013

first: WeiPing

last: Chen

state: MD

address: Bldg 8, Room 1A11, NIDDK/NIH

department: GCL

institute: NIDDK/NIH

summary: Recent identification of IL28B gene polymorphisms associated with hepatitis C virus (HCV) clearance suggests a role for type III interferons (IFNs) in hepatitis C infection. The function of type III IFNs in intrinsic antiviral immunity is poorly understood. Here we show that HCV infection of primary human hepatocytes results in a robust induction of type III but not type I IFNs, leading to IFN- stimulated gene (ISG) expression. In addition, HCV infection elicits a much broader range of gene expression alterations in addition to ISG induction. The induction of type III IFNs is mediated by IRF3 and NFkB- dependent pathways. Type III IFN, aside from upregulating ISGs with a different kinetic profile, induces a distinct set of genes from type I IFN, potentially explaining the functional difference between the two types of IFNs. Chimpanzees undergoing experimental HCV infection demonstrated a prompt hepatic induction of IL28, associating with ISG upregulation, but minimal type I IFN induction. Analysis of liver biopsies from HCV-infected patients supported a close correlation among hepatic expression of IL28 and ISGs, but not with type I IFNs.  Our study demonstrates that HCV infection results predominantly in type III IFN induction in the liver and the level of induction correlates with hepatic ISG levels, thus providing a mechanistic explanation for the association between IL28, ISG levels and recovery from HCV infection as well as a potential therapeutic strategy for the treatment of non-responders.

overall_design: Samples were treated with JFHA, and IL28b respectively with three biological replication.

first: Emmanuel

last: Thomas

first: Veronica

middle: D

last: Gonzalez

first: Qisheng

last: Li

first: Ankit

middle: A

last: Modi

first: Mazen

last: Noureddin

first: Yaron

last: Rotman

first: Jake

last: Liang


title: Gene expression profiling of KMS11 parental (PAR), TKO and 8 reconstituted lines

city: Shanghai

first: Shannon

last: Chuai

state: Shanghai

address: Building 8, Lane 898 Halei Road, Pudong New Aera

institute: Novartis

summary:
NSD2, a histone lysine methyltransferase, is overexpressed as a result of the t(4;14) translocation that is associated with 15-20% of multiple myeloma. Earlier studies have indicated that NSD2 may be involved in myelomagenesis and suggested that it may be a target for myeloma therapy. Here we show that NSD2 is required for clonogenic growth, adherence and proliferation on bone marrow stroma, and tumorigenesis of t(4;14)+ but not t(4;14)- myeloma cells, in a methyltransferase activity dependent manner. Furthermore, we found that PHD domains are important for NSD2 cellular activity and biological functions by recruiting it to oncogenic gene loci and driving downstream transcription activation events. These results strengthened the disease link of NSD2 and provided a basis that targeting NSD2 may be a therapeutic strategy in multiple myeloma patients with t(4;14) translocation. Our data also revealed multiple domains in the protein for possible chemical modulation.
To elucidate the mechanisms underlying the oncogenic potential of NSD2 in myeloma, we performed microarray analysis on KMS11 parental (PAR), TKO and 8 reconstituted lines. Based on the whole-genome expression profile, the 10 samples clearly fell into 4 clusters – (1) PAR; (2) TKO; (3) WT, WT+MMSET I, 526-1240 and 526-1365; and (4) CDM, CDM+MMSET I, MMSET I and H762Y

overall_design: Biological triplicates of cell cultures of indicated lines were harvested in TRIzol (Invitrogen) and characterized by human U133 plus 2.0 Affymetrix GeneChip.  The gene expression data was normalized using the Robust Multiarray Averaging (RMA) method and log2 transformed before comparisons.

first: Haiping

last: Wu

first: Zheng

last: Huang

first: Min

last: Hu


title: Effect of ArhGAP30 on the gene expression profile of colorectal cancer cells

status: Public on Aug 20 2013

first: Jie

last: Xu

address: Shandong Rd 145

department: Shanghai Renji Hospital

institute: Shanghai Institute for Digestive Diseases

summary:
In order to determine the effect of ArhGAP30 on the gene expression profile of colorectal cancer cells, Lovo cells were infected with either ArhGAP30 or the control pcDNA3.1 empty vector.
The differentially expressed genes caused by ArhGAP30 ectopic expression suggests the underlying mechanism for ArhGAP30-induced cell apoptosis and cell cycle arrest.

overall_design: Total RNA from each sample was collected, amplified, labeled, and applied to Affymetrix HG U133 Plus 2 arrays.

first: Jilin

last: Wang

first: Jing-Yuan

last: Fang


title: Signal Transducer and Activator of Transcription 3 limits Epstein-Barr virus lytic-activation in B lymphocytes.

status: Public on Aug 21 2013

city: Stony Brook

first: Sumita

last: Bhaduri-Mcintosh

address: 020 Health Sciences Center

institute: Stony Brook University

summary: We used microarrays to identify genes differentially expressed in EBV-infected human B cells supporting lytic replication vs. those refractory to EBV lytic replication.

overall_design: We used serum from EBV-positive subject (compared to serum from EBV-negative subject) to FACS-separate lytic and refractory cells following treatment of HH514-16 cells with NaB, a lytic cycle inducing agent. RNA from sorted-lytic and sorted-refractory cells were hybridized to microarray.

first: Jizu

last: Zhi

last: Bhaduri-McIntosh


title: Effect of Twist-box mutation on gene expression induced by Twist1 overexpression

city: Baltimore

first: Russell

last: Williams

address: 1550 Orleans St

department: Radiation Oncology

institute: Johns Hopkins University

summary:
Twist1 is a transcription factor that induces EMT and drives metastasis in prostate cancer. We examined global gene expression in Myc-CaP mouse prostate cancer cells following overexpression
of Twist1 and the Twist1 mutants F191G, AQA, and DQD.

overall_design: 15 total samples were analysed, with 3 replicates of 5 groups: Twist1-WT, Twist1-AQA, Twist1-DQD, Twist1-F191G, and vector control. We performed the comparisons: WT > VEC, F191G > VEC. Samples were normalized by Twist1 expression in addition to normal

first: R

last: Gajula

first: P

last: Tran


title: Expression data from human ependymoma

first: Lindsey

middle: M.

last: Hoffman

state: Colorado

address: 12800 East 19th Avenue

department: Pediatric Neuro-Oncology

institute: University of Colorado Denver

summary:
We compared molecular characteristics of primary and recurrent pediatric ependymoma to identify sub-group specific differences.
Gene expression profiles were used to identify unique immunobiologic sub-types of posterior fossa pediatric ependymoma.

overall_design: Gene expression profiles were generated from surgical tumor (ependymoma) (n=65) using Affymetrix HG-U133plus2 chips (Platform GPL570). Normalization was performed on our entire cohort of ependymoma. Of the 65 samples, a sub-set of 58 were used in the corresponding manuscript. Excluded samples are noted. Gene expression profiles were filtered to obtain gene expression of key immune cell markers. Comparative analyses between tumor samples were used to identifiy unique immunobiology between posterior fossa sub-groups.


title: Methylome-Transcriptome Relationships in Nonalcoholic Fatty Liver Disease

first: Cynthia

last: Moylan

address: 595 LaSalle Street, GSRB1, DUMC 3256

institute: Duke University Medical Center

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

overall_design: Refer to individual Series


title: Divergent functions of hematopoietic transcription factors in lineage priming and differentiation during erythro-megakaryopoiesis

status: Public on Aug 09 2013

city: University Park

first: Ross

last: Hardison

state: PA

address: 303 Wartik Lab

institute: Pennsylvania State University

summary: Combinatorial actions of relatively few transcription factors control hematopoietic differentiation. To investigate this process in erythro-megakaryopoiesis, we correlated the genome-wide chromatin occupancy signatures of four master hematopoietic transcription factors (GATA1, GATA2, SCL/TAL1 and FLI1) and three diagnostic histone modification marks with the gene expression changes that occur during development of primary megakaryocytes (MEG) and erythroblasts (ERY) from murine fetal liver hematopoietic stem/progenitor cells. We identified a robust, genome-wide mechanism of MEG-specific lineage priming by a previously described stem/progenitor cell-expressed transcription factor heptad (GATA2, LYL1, SCL/TAL1, FLI1, ERG, RUNX1, LMO2) binding to MEG-specific cis-regulatory modules in multipotential hematopoietic progenitors. This is followed by genome-wide GATA factor switching that mediates further induction of MEG-specific genes following lineage commitment. Interaction between GATA and ETS factors appears to be a key determinant of these processes. In contrast, ERY-specific lineage priming occurs is biased toward GATA2-independent mechanisms. In addition to its role in MEG lineage priming, GATA2 plays an extensive role in late megakaryopoiesis as a transcriptional repressor at loci defined by a specific DNA signature. Our findings reveal important new insights into how ERY and MEG lineages arise from a common bipotential precursor via overlapping and divergent functions of shared hematopoietic transcription factors.

overall_design: Gene expression changes during the development of primary megakaryocytes (MEG) and erythroblasts (ERY) from murine fetal liver hematopoietic stem/progenitor cells

first: Maxim

last: Pimkin

first: Andrew

middle: V

last: Kossenkov

first: Tejaswini

last: Mishra

first: Christapher

last: Morrissey

first: Weisheng

first: Cheryl

last: Keller

first: Gerd

last: Blobel

first: Dongwon

last: Lee

first: Michael

last: Beer

middle: C

first: Mitchell

last: Weiss


title: S100P is a metastasis-associated gene that facilitates transendothelial migration of pancreatic cancer cells [HG-U133_Plus_2]

status: Public on Aug 15 2013

first: Claude

last: Chelala

state: London

address: Charterhouse square

department: Institute of Cancer

institute: Barts & The London School of Medicine (QMUL)

summary:
We and others have shown that S100P is highly upregulated during the progression of pancreatic cancer. We used microarrays to look at the target genes regulated by S100P in the pancreatic cancer cell line Panc1.

Keywords: Gene overexpression

overall_design: We generated stable cell lines by introducing control vector pcDNA3.1/V5-His or S100P-overexpressing vector pcDNA3.1/S100P-V5-His into the pancreatic cancer cell line Panc1, single cell clones were then isolated. RNA was extracted and hybridized on Affymetrix microarrays. We looked for new target genes regulated by S100P.

first: Sayka

last: Barry

first: Tatjana

last: Crnogorac-Jurcevic


title: Expression data from pancreatic cancer cell line MiaPaca2 [control]

city: Heidelberg

first: Matt

middle: Zbigniew

last: Rogon

address: Meyerhofstrasse 1

department: SCB

institute: EMBL

summary:
tumor-stroma crosstalk drives pancreatic carcinogenesis
we used time-resolved genome-wide transcriptional profiling to analyse changes caused by co-exposure of pancreatic tumor and stellate cells

overall_design: pancreatic tumor cell line MiaPaca2 was treated with a supernatant of pancreatic stellate cells and harvested hourly at 1-7, and 24 hours post exposure for RNA extraction and hybridization on Affymetrix microarrays.

first: Nathalia

last: Giese

first: Andrea

last: Bauer

first: Zbigniew


title: Expression data from pancreatic cancer cell line MiaPaca2

overall_design: pancreatic tumor cell line MiaPaca2 was treated with a supernatant of pancreatic stelalte cells, primed with cumulative TC-supernatant (of 8 tumor cell lines, TC) and harvested hourly at 1-7, and 24 hours post exposure for RNA extraction and hybridization on Affymetrix microarrays.


title: Expression data from pancreatic stellate cells and cancer cell line MiaPaca2


title: Expression data from pancreatic stellate cells

overall_design:
Primary pancreatic Stellate cells (PSC) were treated with  a cumulative supernatant of pancreatic tumor cell lines (n=8) and harvested at 1-7, and 24 hours post exposure for RNA extraction and hybridization on Affymetrix microarrays.
The 8 tumor cell lines are pancreatic ductal adenocarcinoma lines: AsPC1, BxPC3, Capan1, Colo357, MiaPaca2, Panc1, Su8686, and T3M4


title: S100P is a metastasis-associated gene that facilitates transendothelial migration of pancreatic cancer cells


title: Identification of de-differentiation and re-development phases during post-pneumonectomy lung growth.

city: Boston

first: Alvin

middle: T.

last: Kho

address: 320 Longwood Avenue

department: Informatics Program

institute: Boston Children's Hospital

summary: The medial and cardiac lobes of the right lung and whole right lung of (initially) 10-12 week old C57BL/6 mice were transcriptome profiled at days 0, 3, 7, 14, 28 and 56 post left pneumonectomy, with day 0 being pre-pneumonectomy, and an additional day 56 post sham surgery to control for 8 week aging post left pneumonectomy.

overall_design: pneumonectomy time course

middle: T

first: Francis

last: Boudreault


title: p/CIP gene regulation in mouse embryonic stem cells

city: London

first: Joseph

last: Torchia

state: Ontario

address: 800 Commissioners Rd E

institute: LRCP

summary:
p/CIP binds to many nuclear receptors and plays a major role in hormone dependent transcription of genes. Recently, p/CIP was shown to affect mouse stem cell pluripotency.
Microarray gene expression analysis was conducted to assess the role of p/CIP in mouse embryonic stem cells.

overall_design:
p/CIP was downregulated using two different siRNAs and total RNA was extracted and hybridized to a microarray. As control, wild type cells were transfected with pooled non specific siRNAs. The expression difference was calculated between the control wild-type cells and cells having p/CIP downregulation.
The experiments were carried out at London Regional Genomic Centre (http://www.lrgc.ca/).

first: Jenny

last: Chitilian

first: Gobi

last: Thillainadesan


title: Cross-talk between E. coli strains and a human colorectal adenocarcinoma-derived cell line

city: Davis, CA

first: Carolyn

last: Slupsky

address: One Shields Ave

department: Department of Nutrition, Department of food science and technology

institute: University of California, Davis

summary: The deposit microarray data were generated in a study that comprehensively integrated gene expression profiles and metabolic responses of Caco-2 cells that incubated with either E. coli K-12 or O157:H7. The aim of this study is to examine the impact of colonic bacteria on the global gene expression regulation and metabolite levels of the host, and investigate the molecular mechanics of the E. coli/host interaction.

overall_design: Caco-2 cells were incubated with one of two strains of E. coli strains (K-12 or O157:H7). Gene expression measurements were analyzed at three time points: 60, 90, and 120 minutes after co-culture, and compared with the controls in the monoculture.

first: Xuan

last: He

first: Darya

last: Mishchuk

first: Jigna

last: Shah

first: Bart

last: Weimer

middle: M


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

city: Rotterdam

first: Pim

last: French

address: Dr Molewaterplein 50

department: Neurology

country: Netherlands

institute: Erasmus MC

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

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

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

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

overall_design:
Bisulphite converted DNA from the 59 samples were hybridised to the Illumina Infinium 450k Human Methylation Beadchip

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

***Please note that the non-normalized data provided for the records is incomplete, missing data for many probes***

first: Martin

last: van den Bent

first: Lale

last: Erdem-Eraslan

first: Ahmed

last: Idbaih

first: Johan

last: de Rooi

first: Paul

middle: H

last: Eilers

first: Wim

middle: G

last: Spliet

first: Wilfred

middle: F

last: den Dunnen

first: Cees

last: Tijssen

first: Pieter

last: Wesseling

first: Peter

last: Sillevis Smitt

last: Kros

first: Thierry

last: Gorlia


title: PINT lincRNA connects the p53 pathway with epigenetic silencing by the Polycomb Repressive Complex 2

city: Pamplona

first: Maite

last: Huarte

state: Navarra

address: c/ Avd Pio XII, 55

institute: Centro de Investigación Médica Aplicada

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus


title: DNA methylation analysis in non-alcoholic fatty liver disease suggests distinct disease-specific and remodeling signatures after bariatric surgery

status: Public on Aug 08 2013

city: Ulm

first: Ole

last: Ammerpohl

address: Albert-Einstein-Allee 11

institute: UK Ulm

summary: Non-alcoholic fatty liver disease (NAFLD) is the most common chronic liver disorder in industrialized countries. Liver samples from morbidly obese patients with all stages of NAFLD and controls were analysed by array-based DNA methylation and mRNA expression profiling.

overall_design: Bisulphite converted DNA from the 85 samples were hybridised to the Illumina Infinium 450k Human Methylation Beadchip

first: O

first: J

last: Hampe


title: Differential expression profiles of human primary endothelial cells (HUVECs) from umbilical cords of Gestational Diabetic mothers

city: Rome

first: Guido

last: Leoni

address: Via Pontina

department: Bioinformatics

country: Italy

institute: IRBM

summary: Primary endothelial cells from umbilical cord vein (HUVEC) obtained at delivery from gestational diabetic (GD) women, represent an expedient model for the study of the effects of chronic HG in vivo. In fetal tissues genome-wide epigenetic changes are likely to occur with specific long term and even trans-generational effects. We have utilized this model to study the effects of chronic hyperglycemia on the transcriptome and to verify the presence of specific epigenetic changes associated to chronic HG in vascular cells.

overall_design:
HUVEC cells from Umbilical cords of 3 Caucasian Gestational Diabetes women  were compared with HUVEC cells from umbilical of from 3 Caucasian non diabetic women matching for age and Body Mass Index.
[sample collection] Umbilical cords were obtained from 3 Caucasian Gestational diabetes  women (diagnosed not later than 28 th gestational week - gw) and from 3 Caucasian non diabetic women matching for age and Body Mass Index (BMI). All pregnants signed an informed consent. All donors were normotensive, and underwent a 100 g 3 hours Oral Glucose Tolerance Test (OGTT) between the 24 -34th gw. Each woman performed a 7 points-blood glucose monitoring on 3 days at week 34 -36th gw.

first: Roberto

last: Ambra


title: Circadian gene expression from wild type MEFs

city: Irvine

first: Paolo

last: Sassone-Corsi

address: 340 Sprague Hall

department: Center for Epigenetics and Metabolism. Dept. Biological Chemistry

institute: University of California

summary: Expression profiles in WT MEF at different circadian time point after dexamethasone synchronyzation.

overall_design: We used the Affymetrix expression microarrays to detail the circadian gene expression from wild type mouse embryonic fibroblasts during a 24 hour circadian cycle. For each circadian time point (CT), three biological replicates were analyzed.

first: Lorena

last: Aguilar-Arnal


title: Cycles in spatial and temporal chromosomal organization driven by the circadian clock

type:
Other
Expression profiling by array


title: Sorted normal bone marrow cells from healthy volunteers at Washington University

status: Public on Aug 07 2013

city: Los Angeles

middle: W.

last: Laird

state: California

address: 1450 Biggy St.

department: USC Epigenome Center

institute: USC/Norris Cancer Center

summary:
Normal healthy cells (monocytes, promyelocytes, polymorphonuclear cells, B cells, T cells, CD34+CD38- HSPCs) run as controls for TCGA AML marker publication.
Bone marrow cells collected from healthy donors were sorted and DNA extracted at Washington University in St. Louis, microarrays were then run at USC

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

first: P

middle: W

first: T

last: Triche


title: Identification and systematic annotation of tissue-specific differentially methylated regions using the Illumina 450k array

status: Public on Aug 06 2013

city: Leiden

first: Roderick

last: Slieker

address: PO Box 9600

department: Medical Oncology

institute: Leiden University Medical Center

summary:
Background
DNA methylation has been recognized as a key mechanism in cell differentiation. Various studies have compared tissues to characterize epigenetically regulated genomic regions, but due to differences in study design and focus there still is no consensus as to the annotation of genomic regions predominantly involved in tissue-specific methylation. We used a new algorithm to identify and annotate tissue-specific Differentially Methylated Regions (tDMRs) in Illumina 450k chip data on four peripheral (blood, saliva, buccal swab and hair follicles) and six internal tissues (liver, muscle, pancreas, subcutaneous fat, omentum, spleen with matched blood samples).

Results
The majority of tDMRs, in both relative and absolute terms, occurred in CpG-poor regions. Further analysis revealed that these regions were associated with alternative transcription events (alternative first exons, mutually exclusive exons and cassette exons). Only a minority of tDMRs mapped to gene-body CpG islands (13%) or CpG islands shores (25%) suggesting a less prominent role for these regions than indicated previously. Implementation of ENCODE annotations showed enrichment of tDMRs in DNase hypersensitive sites and transcription factor binding sites. Despite the predominance of tissue differences, inter-individual differences in DNA methylation in internal tissues were correlated with that in blood for a subset of CpG sites in a locus and tissue-specific manner.

Conclusions
We conclude that tDMRs preferentially occur in CpG-poor regions and are associated with alternative transcription. Furthermore, our data suggest the utility of creating an atlas cataloguing variably methylated regions in internal tissues that are marked by DNA methylation measured in easy accessible peripheral tissues.

overall_design: Comparison of four peripheral (blood, saliva, buccal swab and hair follicles in n=5) and six internal tissues (liver, muscle, pancreas, subcutaneous fat, omentum, spleen with matched blood samples in n=6).

first: R

first: S

last: Bos

middle: J

last: Goeman

last: Bovée

middle: P

last: Talens

last: van der Breggen

first: H

middle: E

last: Suchiman

first: E

last: Lameijer

last: Putter

middle: B

last: van den Akker

first: Y

last: Zhang

last: Jukema

last: Slagboom

first: I

last: Meulenbelt

first: B

last: Heijmans


title: Expression data from T lymphocytes derived from T-iPS and peripheral blood

city: New York

first: Michel

last: Sadelain

address: 1250 1st Ave

institute: Memorial Sloan-Kettering Cancer Center

summary: T lymphocytes can be generated from T-cell-derived induced pluripotent stem cells (T-iPS). We used microarrays to better elucidate their phenotype and compare their gene expression profile to that of known lymhoid subsets from peripheral blood.

overall_design: Total mRNA was extracted from T-iPS-derived T cells at day 30-35 of differentiation and from sorted peripheral blood lymphoid subpopulations. Total RNA was amplified and labelled following the standard Affymetrix protocol (Affymetrix, Santa Clara, CA, USA). The labeled complementary RNA was then fragmented and hybridized to Affymetrix GeneChip arrays HG-U133 plus 2.0.

first: Maria

last: Themeli


title: PINT lincRNA connects the p53 pathway with epigenetic silencing by the Polycomb Repressive Complex 2 (MEF cells)

first: Maite

last: Huarte

summary: It has been recently shown that the transcription factor p53 induces the expression of multiple lincRNAs. However, relatively little is known about the role that lincRNAs play in this pathway. Here we characterize a lincRNA named PINT (p53 Induced Noncoding Transcript). We show that PINT is a ubiquitously expressed lincRNA that is finely regulated by p53. In mouse cells, PINT promotes cell proliferation and survival by regulating the expression of genes of TGF-beta, MAPK and p53 pathways. PINT is a nuclear lincRNA that directly interacts with Polycomb Repressive Complex 2 (PRC2), being required for PRC2 targeting of specific genes for repression. Furthermore, PINT functional activity is dependent on PRC2 expression, representing a connection between the p53 pathway and epigenetic regulation by PRC2. We have also identified PINT human ortholog (hPINT), which presents suggestive analogies with the mouse lincRNA. hPINT is similarly regulated by p53, and its expression correlates significantly with the same cellular pathways as the mouse ortholog, including the p53 pathway. Interestingly, hPINT is significantly downregulated in colon cancer, representing a novel tumor suppressor candidate. Our results not only help our understanding of the role of p53 and lincRNAs in cancer, but also contribute to the open debate regarding the utility of mouse models for the study of lincRNAs.

overall_design: Inhibition of PINT or p53 gene expression and subsequent treatment with 150 nM doxorubicine for 12h in MEF LSL p53 +/+ cells.

first: Oskar

last: Marín-Béjar

first: Alejandro

last: Athie


title: Cigarette Smoking Induces Small Airway Epithelial Epigenetic Changes with Corresponding Modulation of Gene Expression

status: Public on Aug 05 2013

first: Yael

last: Strulovici-Barel

state: NY

address: 1300 York Avenue

department: Department of Genetic Medicine

institute: Weill Cornell Medical College

summary: The small airway epithelium (SAE), the first site of smoking-induced lung pathology, exhibits genome-wide changes in gene expression in response to cigarette smoking. Based on the increasing evidence that the epigenome can respond to external stimuli in a rapid manner, we assessed the SAE of smokers for genome-wide DNA methylation changes compared to nonsmokers, and whether changes in SAE DNA methylation were linked to the transcriptional output of these cells. Using genome-wide methylation analysis of SAE DNA of nonsmokers and smokers, the data identified 204 unique genes differentially methylated in SAE DNA of smokers compared to nonsmokers, with 67% of the regions with differential methylation occurring within 2 kb of the transcriptional start site. Among the genes with differential methylation were those related to metabolism, transcription, signal transduction and transport. For the differentially methylated genes, 34 exhibited a correlation with gene expression, 53% with an inverse correlation of DNA methylation with gene expression and 47% a direct correlation. These observations provide evidence that cigarette smoking alters the DNA methylation patterning of the SAE and that, for some genes, these changes are associated with the smoking-related changes in gene expression.

overall_design: Small airway epithelium DNA was assessed for genome-wide methylation using the microarray-based high resolution HpaII tiny fragment enriched by ligation-mediated PCR (HELP) assay. Small airway epithelium transcriptome was also assessed for healthy nonsmokers (n=16) and healthy smokers (n=20) with Affymetirx HG-U133 Plus 2.0 arrays

first: Lauren

last: Buro-Auriemma

first: Neil

middle: R

last: Hackett

first: Jacqueline

last: Salit

first: Matthew

middle: S

last: Walters

first: Michelle

last: Staudt

first: Jennifer

last: Fuller

first: Melisa

last: Ho

first: Ronald

last: Crystal


title: Differential gene expression profiles between Parp-2-/- and wild-type hematopoietic stem/progenitors cell at basal and in response to 5 Gy gamma Irradiation (2.5 hours post-irradiation)

city: Barcelona

first: José

last: Yélamos

address: Dr. Aiguader, 88

department: Cancer Research Program

institute: Hospital del Mar Medical Research Institute (IMIM)

summary: Gene expression profile between Parp-2-/- and wild-type hematopoietic stem/progenitor cells at basal and to the early response (2.5 hours) to 5 Gy total body irradiation

overall_design: We analyzed 2 arrays from each condition. Each samples represent a pool of at least 3 mice

first: Jose

last: Yelamos

first: Juanjo

last: Lozano

first: Lara

last: Nonell

first: Eulalia

last: Puigdecanet


title: Expression data from Human CD40L+ Tcells

city: Berlin

first: Andreas

last: Thiel

address: Augustenburger Platz 1

institute: Berlin-Brandenburg Center for Regenerative      Therapies, Charite University Medicine

summary: To assess the nature of CD8+CD40L+ memory Tcells, we compared the gene expression to CD8+CD40L- and CD4+ counterparts, and found similarities in expression of genes encoding cytokines

overall_design: PBMCs were isolated from five healthy donors. The cells were stimulated with PMA/Ionomycin for 6 h, and subsequently sorted into the CD4+CD45RA-CD40L+, CD8+CD45RA-CD40L-, CD8+CD45RA-CD40L+ populations by FACS-sort

first: Marco

last: Frentsch

first: Regina

last: Stark


title: Differences in gene expression and cytokines levels between newly diagnosed and chronic pediatric immune thrombocytopenia (ITP)

city: Little Rock

first: Intawat

last: Nookaew

address: 4301 W Markham St

department: Department of Biomedical Informatics

institute: University of Arkansas for Medical Sciences

summary: Immune thrombocytopenia (ITP) is an autoimmune disease where platelets are destroyed prematurely. In the majority of children the disease resolves but in some it becomes chronic. To investigate whether the two forms of the disease are similar or separate entities we performed DNA microarray analysis of T-cells from newly diagnosed children and children with chronic ITP. We found complete separation of the expression files between the two forms of the disease. Furthermore, the gene expression of several cytokines differed between the two forms of the disease. This was also reflected in plasma with increased levels of IL-16 and TWEAK and lower levels of IL-4 in newly diagnosed compared with chronic ITP. Thus, our data indicate that the two forms of the disease may be separate entities.

overall_design: Microarray expression analysis of mRNA  in peripheral blood T-cell of Newly diagnosed ITP vs Chronic ITP

first: Margareta

last: Jernås

first: Hans

last: Wadenvik

first: Bob

last: Olsson

first: Yu

last: Hou

first: Frida

last: Strömberg

first: Linlin

last: Shao

first: Qian

last: Wang

first: Xiuli

last: Ju

first: Karin

last: Mellgren

first: Ming


title: KSHV vIRF4-mediated cellular genes alteration

status: Public on Aug 03 2013

first: Jae U

last: Jung

address: 1450 Biggy Street

department: Department of Molecular Microbiology and Immunology

institute: University of Southern California, Keck School of Medicine

summary: Approximately, KSHV vIRF4 deregulate 284 genes by two-folds

overall_design: Transient overexpression of vIRF4 into KSHV-infected PEL cells

first: Jae

middle: U

first: Hye-Ra

last: Lee


title: NOTCH3 is a master-regulator of motility in neuroblastoma and is essential for cell survival

city: Amsterdam

first: Richard

last: Volckmann

state: Noord-Holland

address: van der Boechorststraat 6a

department: Laboratory of Experimental Oncology and Radiobiology

institute: msterdam UMC and University of Amsterdam

summary: Migratory embryonal neuroblasts give rise to several tissues, including the sympathetic nervous system (SNS). Neuroblastomas are paediatric tumours of the peripheral SNS with a highly variable prognosis. We observed that high NOTCH3 expression in neuroblastomas correlated with a poor prognosis. Expression of a NOTCH3 transgene in neuroblastoma cells induced many motility genes and conferred a highly motile phenotype. Expression of these motility genes strongly correlated with NOTCH3 expression in neuroblastomas and many other tumours, suggesting a general role for NOTCH3 in regulation of these genes. Silencing of NOTCH3 or genes of the Notch-processing γ-secretase complex induced apoptosis in all neuroblastoma cell lines tested. These data suggest that NOTCH3 is a key-regulator of motility, and indispensable for survival of neuroblastoma cells.

overall_design: Time-course experiments of NOTCH3IC induction in two independent clones (c6 and c8), with 9 or 8 time points, respectively.

first: Johan

last: van Nes

first: Jan

last: Koster

first: Rogier

last: Versteeg


title: Effects of PP2Ac over-expression on mouse naïve CD4 T cell gene profile upon activation

status: Public on Aug 02 2013

first: Jose

middle: C

last: Crispin

address: 330 Brookline Ave, CLS-928

department: Medicine

institute: Beth Israel Deaconess Medical Center

summary: A transgenic mouse was generated using a CD2-driven transgene containing the cDNA of Ppp2ca to achieve over-expression of PP2Ac in T cells. Naïve CD4 T cells were isolated and lysed at times 0, 6, and 24 hours after stimulation with anti-CD3 and anti-CD28

overall_design: Naïve CD4 T cells from wild type mice were compared with naïve CD4 T cells from PP2Ac transgenic mice

first: Sokratis

middle: A

last: Apostolidis


title: MicroRNA regulate immune pathways in T-cells in multiple sclerosis (MS)

first: Intawat

last: Nookaew

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

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

platform_organism:
Homo sapiens
synthetic construct

overall_design: Refer to individual Series


title: MicroRNA regulate immune pathways in T-cells in multiple sclerosis (MS) mRNA

summary: MicroRNAs are small noncoding RNA molecules that are involved in the control of gene expression. To investigate the role of microRNA in multiple sclerosis (MS), we performed global microarray analyses of mRNA and microRNA in peripheral blood T-cells from relapsing-remitting MS patients and controls. We identified 2,452 regulated genes and 21 regulated microRNA that differed between MS patients and controls. By Kolmogorov-Smirnov test, 20 of 21 regulated microRNA were shown to affect the expression of their target genes, many of which are involved in the immune system. LIGHT (TNFSF14) was a microRNA target gene significantly decreased in MS. The down-regulation of mir-494 and predicted mRNA-target LIGHT was verified by real-time PCR and we could demonstrate decreased serum levels of LIGHT in MS. Thus, regulated microRNA were significantly associated with both gene and protein expression of a molecule in immunological pathways. These findings indicate that microRNA may be important regulatory molecules in T-cells in MS.

overall_design: Microarray expression analysis of mRNA and miRNA in peripheral blood T-cell of control andMS patients

first: Margareta

last: Jernas

first: CLAS

last: Malmestrom

first: MARKUS

last: Axelsson

first: Hans

last: Wadenvik

first: JAN

last: Lycke

first: Bob


title: Location of indigenous human HSCs reveals functional properties of HSCs that are dictated by anatomic and cellular architecture of bone marrow

status: Public on Aug 01 2013

city: Hamilton

first: Mickie

last: Bhatia

address: 1200 Main Street West

department: Stem Cell and Cancer Research Institute (SCC-RI)

institute: McMaster University


title: Expression data from H1299 human non-small cell lung carcinoma cell lines stably expressing CHES1 compared with H1299 infected with an empty vector

city: Montréal

first: Mathieu

last: Vernier

state: Quebec

address: 2900 Edouard Montpetit

department: Biochemistry

institute: Université de Montréal

summary:
The expression of the forkhead transcription factor CHES1, also known as FOXN3, is reduced in many types of cancers. In vitro, CHES1 expression suppresses cell proliferation in tumor cell lines but not in normal cells. Conversely shRNA-mediated depletion of CHES1 increases tumor cell proliferation.
We used microarrays to characterize the gene expression changes induced by CHES1 in H1299 cancer cells

overall_design: H1299 cells were infected with a retroviral vector that expresses CHES1 or an empty vector. After 5 days of infection, RNA was extracted from three independent replicas of each condition. Total RNA was send to Genome Quebec service for hybridization with Affymetrix microarrays.

first: Geneviève

last: Huot

first: Gerardo

last: Ferbeyre