title: Toxicogenomic effects of sub-lethal exposures of organophosphates on mouse liver cells [mRNA Expression]

city: Washington

first: Baochuan

last: Lin

state: DC

address: 4555 Overlook Avenue, S. W.

department: Center for Bio/Molecular Science & Engineering

institute: US Naval Research Laboratory

summary: In order to examine the long term effects of the OPs, murine liver cells (BNL CL.2, ATCC® TIB-73) have been exposed to sub-lethal doses of three OPs: diisopropylfluorophosphate (DFP) representative of sarin and soman, O,S-diethyl methylphosphonothioate (OSD) serving as a simulant for VX, and paraoxon as an example of OP insecticides.  Dosing levels of these compounds was set at 20% of the IV LD50 for each, with a 4 hour exposure time.  Gene arrays and physiological tests were run at three time points following exposure; 2 hours, 2 days, and 2 weeks.  The physiological results showed little to no effect upon exposure to sub-lethal dose of OPs.  Gene expression and microRNA (miRNA) profiles using GeneChip Mouse Gene 1.0 ST arrays and miRNA arrays (Affymetrix, Santa Clara, CA) found that the OPs did alter expression of genes related to several systems previously implicated in OP exposure with no long term effects.  In addition, a significant number of sRNA/snRNA and ribosomal RNA were found to be affected suggesting the need for further study of the changes in these regulators.

overall_design: Three biological replicates of liver cells were exposed to three representative OPs and then harvested at three time points (2 hours, 72 hours, and two weeks) following exposure.  These time points were designed for a determination of both early and late effects as well as identification of persistent, chronic changes.  The RNAs from the collected cells were extracted and processed on commercial microarrays to determine the gene expression patterns and miRNA profiles associated with response to exposure to the OPs.

first: Thomas

middle: J

last: O’Shaughnessy

first: Anthony

last: Malanoski

first: Robert

last: Rubin

first: Nina

middle: C

last: McAuliff


title: Toxicogenomic effects of sub-lethal exposures of organophosphates on mouse liver cells

status: Public on Feb 24 2016

country: USA

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

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

platform_organism:
Mus musculus
synthetic construct

overall_design: Refer to individual Series


title: Grainyhead-like 2 (GRHL2) maintains the epithelial status of ovarian cancer through miR-200-ZEB1 regulatory networks (expression)

status: Public on Feb 25 2016

city: Singapore

first: Tuan Zea

last: Tan

address: 14 Medical Drive, #11-01, Singapore

department: Cancer Science Institute Singapore

country: Singapore

institute: National University of Singapore

summary: Epithelial ovarian cancer (EOC) is clinically heterogeneous, comprising different histological and biological subtypes. Multiple studies have implicated epithelial-mesenchymal transition (EMT), a biological process by which polarized epithelial cells convert into a mesenchymal phenotype, to contribute significantly to this molecular heterogeneity of EOC. From gene expression analyses of a collection of EMT-characterized EOC cell lines, we found that the expression of the transcription factor Grainyhead-like 2 (GRHL2) correlates with E-cadherin expression and the epithelial phenotype. EOC tumors with lower levels of GRHL2 are associated with the Mes (mesenchymal) molecular subtype and show poorer overall survival in patients. Here, we demonstrate that shRNA-mediated knockdown of GRHL2 in EOC cells with an epithelial phenotype resulted in EMT changes, with increased cell migration, invasion and motility. By ChIP-sequencing and gene expression microarray, we identified a variety of target genes regulated by GRHL2, including protein-coding and non-coding genes. Our data suggest that GRHL2 maintains the epithelial phenotype of EOC cells through the regulatory networks of miR-200b/a, ZEB1 and E-cadherin. These findings support GRHL2 as a crucial player in the molecular heterogeneity of EOC.

overall_design: 7 samples were analyzed (shNon control in duplicates; shGRHL2 #10 in duplicates, shGRHL2 #12 in triplicates)

first: Vin-Yee

last: Chung

first: Tuan-Zea

first: Ming

first: Meng-Kang

last: Wong

first: Kuee-Theng

last: Kuay

first: Zhe

last: Yang

first: Jieru

last: Ye

first: Julius

last: Muller

first: Cheryl-Mei-Yi

last: Koh

first: Ernesto

last: Guccione

first: Jean-Paul

last: Thiery

first: Ruby-Yun-Ju

last: Huang


title: RNA-seq of male and female control cortex

status: Public on Feb 23 2016

city: San Francisco

first: Donna

middle: M

last: Werling

state: CA

address: 1550 4th St., Room RH 447

institute: UCSF

type: Expression profiling by high throughput sequencing

summary:
Purpose: The goal of this study was to compare gene expression patterns in the male and female human cortex
Methods: We performed RiboZero Gold (rRNA depleted) 50bp PE RNA-seq in a set of control samples of both sexes to identify sexually dimorphic gene expression patterns.
Results: Within these samples, we corroborated findings from a discovery set of RNA-seq data from adult human cortex tissue from the BrainSpan consortium which demonstrated male-biased expression of astrocyte marker genes and a gene co-expression module found to be up-regulated in the adult autistic cortex.
Conclusions: These findings suggest that sex-differential risk for autism spectrum disorder is not the result of sex-differential regulation of ASD risk genes, but of naturally occurring sexually dimorphic processes that modulate the impact of risk variants for autism spectrum disorder.

overall_design:
13 cerebral cortex samples from 10 individuals (7 samples from 5 males, 6 samples from 5 females). Three Samples are included in this study from Series GSE64018.

**PLEASE NOTE: Raw data has been submitted to dbGAP**

first: Daniel

middle: H

last: Geschwind


title: Expression data from U-937 cells exposed to nanosecond duration electrical pulses

status: Public on Feb 16 2016

city: San Antonio

first: Caleb

last: Roth

state: Texas

address: 7703 Floyd Curl

department: Radiology

institute: UTHSCSA

summary:
It is unclear how nanosecond electrical pulses affect gene expression.
We used microarrays to identify how cells respond to this specific type of stress

overall_design: U-937 cells were exposed to 100, 10 nanosecond duration pulses at 150 kV/cm.  Gene expression was analyzed 4 hrs post exposure

first: Bennett

middle: L

last: Ibey


title: Expression data from Jurkat Clone E-6 cells exposed to nanosecond duration electrical pulses

overall_design: Jurkat cells were exposed to 100, 10 nanosecond duration pulses at 150 kV/cm.  Gene expression was analyzed 4 hrs post exposure


title: Influence of Set7/9 on hESC differentiation

status: Public on Feb 17 2016

city: Barcelona

first: Stephanie

last: Boue

address: Dr Aiguader 88

country: Spain

institute: CMRB

summary: We analyzed the role of the histone lysine methyltransferase Set7/9 in the differentiation of human embryonic stem (ES) cells. Human ES cell lines expressing a control short hairpin and a short hairpin against Set7/9 were established and the genome wide expression profile was compared between both cell lines at different days during differentiation. Analysis of both profiles indicates that in the absence of Set7/9 there is a delay in the silencing of self-renewal factors as well as in the induction of differentiation markers. These results indicate that Set7/9 plays an active role in the differentiation of human ES cells.

overall_design: control and set7/9 shRNA hESCs were differentiated, and profiling was realized at days 0, 8 and 15.

first: Maria

last: Barrero

first: Stéphanie

last: Boué

first: Julio

last: Castaño

first: Borja

last: Sese

first: Juan-Carlos

last: Izpisúa-Belmonte


title: Identification of the gene expression in IPF lung fibroblasts after demethylation

city: Los Angeles

first: ting

last: Xie

address: 127 San Vicente Blvd

department: Pulmonary

institute: Cedars-Sinai Medical Center

summary: Idiopathic pulmonary fibrosis (IPF) is a progressive lung disease. Although the pathogenesis is poorly understood, evidence suggests that genetic and epigenetic alterations, such as DNA methylation, may play a key role. We used microarrays to see the gene expression in IPF fibroblasts after demethylation agent 5'-azacytidine treatment.

overall_design: Human IPF lung fibroblasts were cultured and then treated with 5'-azacytidine 5uM 24 hours. RNA were extracted and hybridized on Affymetrix microarrays.

first: Ting

last: Yang

first: Dianhua

last: Jiang


title: Analyses of ILC3s from the mesenteric lymph nodes (LN)

status: Public on Feb 15 2016

city: New York

first: Gregory

middle: F

last: Sonnenberg

state: NY

address: 413 East 69th Street, Belfer Research Building 512

institute: Weill Cornell Medical College

summary:
Analyses of ILC3s in Rorc floxed control and Id2iΔRORγt mice following daily treatments of tamoxifen for two weeks.
Cells were sort purified as lineage negative, CD127+ CD90.2+ CCR6+ ST2-

overall_design: CCR6+ ILCs were sorted from the mesenteric LN of Rorc floxed control and Id2iΔRORγt mice following daily treatments of tamoxifen for two weeks.


title: Expression data from HDFA cells exposed to nanosecond duration electrical pulses

overall_design: HDFA cells were exposed to 100, 10 nanosecond duration pulses at 150 kV/cm.  Gene expression was analyzed 4 hrs post exposure


title: Expression analysis of gastric cancer cells treated with periplocin

city: shijiazhuang

first: li

last: lei

address: jiankang road

country: China

institute: hebei medical university

summary: To further analyze the change of differential gene expression between SGC-7901 cells treated with 100ng/ml periplocin and untreated cells, respectively. We employed whole genome microarray expression profiling as a discovery platform to identify genes.

overall_design: Gene expression in SGC-7901 cells treated with 100ng/ml periplocin for 24h at 37 ºC in a humidified incubator with 5% CO2.

first: Lei

last: Li

first: Lianmei

last: Zhao


title: Endometrial methylome of patients without endometriosis

city: Tartu

first: Triin

last: Laisk-Podar

address: Puusepa 8

department: Obstetrics and Gynecology

country: Estonia

institute: University of Tartu

type: Methylation profiling by genome tiling array

summary: Alterations in endometrial DNA methylation profile have been proposed as one potential mechanism initiating the development of endometriosis. However, the normal endometrial methylome is influenced by the cyclic hormonal changes and the menstrual cycle phase-dependent epigenetic signature should be considered when studying endometrial disorders. So far, no studies have been performed to evaluate the menstrual cycle influences and endometriosis-specific endometrial methylation pattern at the same time. Therefore, we used Infinium HumanMethylation 450K BeadChip arrays to explore DNA methylation profiles of endometrial tissues from various menstrual cycle phases.

overall_design: Infinium HumanMethylation 450K BeadChip arrays were used to explore DNA methylation profiles of endometrial tissues from mid secretory cycle phase from 17 patients without endometriosis

first: Merli

last: Saare

first: Vijayachitra

last: Modhukur

first: Marina

last: Suhorutshenko

first: Balaji

last: Rajashekar

first: Kadri

last: Rekker

first: Deniss

last: Sõritsa

first: Helle

last: Karro

first: Pille

last: Soplepmann

first: Andrei

first: Cecilia

last: Lindgren

first: Nilufer

last: Rahmioglu

first: Alexander

last: Drong

first: Christian

last: Becker

first: Krina

middle: T

last: Zondervan

first: Andres

last: Salumets

first: Maire

last: Peters


title: The influence of menstrual cycle and endometriosis on endometrial methylome

first: Triin


title: The fusion protein SS18-SSX1 employs core Wnt pathway transcription factors to induce a partial Wnt signature in synovial sarcoma

city: Torino

first: Paolo

last: Provero

address: Via Nizza 52

department: Molecular Biotechnology and Health Sciences

country: Italy

institute: University of Turin

summary: Expression of the SS18/SYT-SSX fusion protein is believed to underlie the pathogenesis of synovial sarcoma (SS). Recent evidence suggests that deregulation of the Wnt pathway may play an important role in SS but the mechanisms whereby SS18-SSX might affect Wnt signaling remain to be elucidated. Here, we show that SS18/SSX tightly regulates the elevated expression of the key Wnt target AXIN2 in primary SS. SS18-SSX is shown to interact with TCF/LEF, TLE and HDAC but not β -catenin in vivo and to induce Wnt target gene expression by forming a complex containing promoter-bound TCF/LEF and HDAC but lacking β -catenin. Our observations provide a tumor-specific mechanistic basis for Wnt target gene induction in SS that can occur in the absence of Wnt ligand stimulation.

overall_design: SS18SSX expressing C3H cells vs control: no replicates. WNT-stimulated C3H cells vs controls: 3 replicates per condition

first: Luisa

last: Cironi

first: Tanja

last: Petricevic

first: Victor

last: Fernandes Vieira

first: Carlo

last: Fusco

first: Sandrine

last: Cornaz

first: Giulia

last: Fregni

first: Igor

last: Letovanec

first: Michel

last: Aguet

first: Ivan

last: Stamenkovic


title: Endometrial methylome of patients with endometriosis

last: Laisk-Podar

overall_design: Infinium HumanMethylation 450K BeadChip arrays were used to explore DNA methylation profiles of endometrial tissues from various menstrual cycle phases from 24 patients with endometriosis

first: Merli

last: Saare

first: Vijayachitra

last: Modhukur

first: Marina

last: Suhorutshenko

first: Balaji

last: Rajashekar

first: Kadri

last: Rekker

first: Deniss

last: Sõritsa

first: Helle

last: Karro

first: Pille

last: Soplepmann

first: Andrei

first: Cecilia

last: Lindgren

first: Nilufer


title: Gene expression data from human tonsillar B lymphocytes

city: Montreal

first: Bruce

middle: David

last: Mazer

state: Quebec

address: 1001 boul. Décarie

department: RESP

country: Canada

institute: RI-MUHC

summary:
B lymphocytes are important mediators of adaptive immunity. They drive naïve T cells to different T-helper profiles. Th2 responses are implicated in allergic reactions.
The goal of this study was to characterize the gene expression profile of B cells under Th2-skewing conditions.

overall_design:
B lymphocytes were isolated from human tonsils and cultured for 24 hours under Th2-skewing stimulation (anti-CD40 and IL4 treatment) or with no stimulation.
RNA was isolated from 4 biological replicates for each condition. 8 samples in total were hybridized to Affymetrix gene expression microarrays.
variable: treatment: antiCD40-IL4: antiCD40-IL4_1, antiCD40-IL4_2, antiCD40-IL4_3, antiCD40-IL4_4
variable: treatment: unstimulated: Control_1, Control_2, Control3, Control_4
repeat: biological replicate: antiCD40-IL4_1, antiCD40-IL4_2, antiCD40-IL4_3, antiCD40-IL4_4
repeat: biological replicate: Control_1, Control_2, Control3, Control_4

first: Gabriel

middle: N

last: Kaufman

first: Salem

last: Al-Tameni

middle: D


title: New molecular insights into modulation of platelet reactivity in aspirin-treated patients using a network-based approach

status: Public on Feb 18 2016

city: Lausanne

first: Mark

last: Ibberson

address: Genopode building

department: Vital-IT

country: Switzerland

institute: SIB Swiss Institute of Bioinformatics


title: Retrospective and prospective validation of a 33-gene signature to predict recurrence of lung cancer after surgery.

status: Public on Feb 11 2016

city: Hoesholm

first: Anker

last: Hansen

address: Venlighedsvej 1

country: Denmark

institute: Medical Prognosis Institute A/S

summary: We developed a 33-gene signature that is strongly correlated to the time to recurrence in non-small cell lung cancer (NSCLC). The signature was validated retrospectively in 5 cohorts of 972 NSCLC patients and in one prospective study of 111 NSCLC Stage IA patients. In all cohorts, and all stages of the disease, the signature identified a rare, aggressive tumor type that had a high proportion of recurrence after surgery and a median survival of 35 months (95% C.I.: 19-58). This tumor type forms a separate cluster in an analysis of the expression of the 33 genes in patient tumors. The signature is associated with cellular processes required by rapidly growing and spreading tumors: cell migration and invasion, vascularization, and response to hypoxia. The signature also identifies patients with good prognosis (median survival 114 months, (95% C.I.: 85-160), and intermediate prognosis (median survival 61 months (95% C. I.: 50-73). The signature is quite robust and works on tumor samples archived in RNAlater, Tissue-Tek, or formalin-fixed and paraffin embedded.

overall_design:
156 samples
--------------------------------
*** Submitter has not provided information such as time to recurrence.  Thus, the data is incomplete.

first: Steen

last: Knudsen

first: Thomas

last: Jensen

first: Mette

last: Pøhl

first: Ida

last: Buhl

first: Robert

last: Cerfolio

first: Ayesha

last: Bryant

first: Sai

last: Yendamuri

first: Hans

last: Pilegaard

first: Henrik

last: Vad

first: Niels

last: Katballe

first: Erik

last: Jakobsen

first: Peter

middle: B

first: Jon

last: Askaa

first: Jesper

last: Dahlgaard

first: Wiktor

last: Mazin

first: Kåre

last: Hornbech

last: Ravn

first: Jens

last: Sørensen


title: Effect of EglN1 knockdown on smooth muscle expression

city: Boston

first: William

middle: James

last: Gibson

state: Massachusetts

address: 34 Fairfield St #1

institute: Harvard Medical School

summary:
Ischemic preconditioning is the phenomenon whereby brief periods of sublethal ischemia protect against a subsequent, more prolonged, ischemic insult. In remote ischemic preconditioning (RIPC), ischemia to one organ protects other organs at a distance. We developed mouse models to ask if inhibition of EglN1, which senses oxygen and regulates the HIF transcription factor, could suffice to mediate local and remote ischemic preconditioning.
We used microarrays to detail the global expression changes induced when the oxygen sensor EglN1 is genetically deleted from skeletal muscle cells. We also used microarrays to assess the transcriptome alterations that occur in mouse hearts with pharmacologic inhibition of EglN1, using the EglN inhibitor FG-4497.

overall_design: We generated mice with a tamoxifen-inducible model of EglN1 loss using a floxxed EglN1 locus with skeletal muscle-specific CRE recombinase. WT mice and mice with the floxxed EglN1 locus were exposed to tamoxifen. Mouse skeletal muscle was isolated for RNA extraction and hybridization on Affymetrix microarrays. In a related experiment, mice were treated with the EglN inhibitor FG-4497, and RNA from their heart tissue was analyzed by microarray for transcriptome alterations compared to control hearts.

first: Benjamin

last: Olenchock


title: Expression data from SGBS human cells before and after 24 hours of stimulation with differentiation cocktail, with or without Scrambled (Scr) or Tenomodulin (TNMD) siRNA to knockdown the genes of interest.

city: Worcester

first: Michael

middle: P

last: Czech

state: MA

address: 373 Plantation St., Biotech II, Suite 100

department: Program in Molecular Medicine

institute: University of Massachusetts Medical School

summary:
In a screen for upregulated adipocyte genes in insulin resistant versus insulin sensitive subjects matched for BMI, we identified the type II transmembrane protein tenomodulin (TNMD), previously implicated in glucose tolerance in gene association studies. TNMD expression was greatly increased in human preadipocytes during differentiation, while silencing TNMD blocked adipogenic gene induction and adipogenesis.
We used microarrays to identify genes of interest that are differentially expressed after the addition of siRNA to tenomodulin or scrambled siRNA, in both preadipocytes and partially differentiated adipocytes.

overall_design: SGBS preadipocytes were treated with scrambled or siTNMD. Cells either were kept undifferentiated or stimulated for 24 hours with differentiation cocktail. Cells were prepared with this protocol on three different occasions and total RNA was isolated to provide three biological replicates per sample.

first: Senol-Cosar

last: Ozlem

first: Juerg

last: Straubhaar

first: Sarah

last: Nicoloro


title: The histone variant H2A.X is a regulator of Epithelial–Mesenchymal Transition

status: Public on Feb 10 2016

city: Bethesda

first: Urbain

middle: S

last: Weyemi

state: MD

address: 9000 Rockville Pike

department: National Cancer Institute

institute: National Institutes of Health

summary: The epithelial-mesenchymal transition (EMT), considered essential for metastatic cancer, has been a focus of much research, but important questions remain. Here, we show that silencing or removing H2A.X, a histone H2A variant involved in cellular DNA repair and robust growth, induced mesenchymal-like characteristics including activation of  EMT transcription factors, Slug and ZEB1, in HCT116 human colon cancer cells. Ectopic H2A.X re-expression partially reversed these changes; as did silencing Slug and ZEB1. In an experimental metastasis model, the HCT116 parental and H2A.X-null cells exhibited similar metastases levels, but the cells with re-expressed H2A.X exhibited substantially elevated levels. We surmise that H2A.X re-expression led to partial EMT reversal and increased robustness in the HCT116 cells, permitting them to both form tumors and to metastasize. In a human adenocarcinoma panel, H2A.X levels correlated inversely with Slug and ZEB1 levels. Together, these results point to H2A.X as a novel regulator of EMT.

overall_design: 9 samples in total including 4 replicates of control shRNA and 5 replicates of shH2A.X.

first: U

first: C

middle: E

last: Redon

first: R

last: Choudhuri

first: T

last: Aziz

first: D

last: Maeda

first: M

last: Boufraqech

first: P

middle: R

last: Parekh

middle: K

last: Sethi

last: Kasoji

first: N

last: Abrams

first: A

last: Merchant

first: V

last: Rajapakse

first: W

last: Bonner


title: The Long-HER Study

city: Madrid

first: Juan Ángel

last: Fresno Vara

state: Madrid

address: Paseo de la castellana 261

department: INGEMM

institute: Hospital La Paz

summary:
Trastuzumab improves survival outcomes in patients with HER2+ metastatic breast cancer. Some of these patients may become long-term survivors. The Long-Her study was designed to identify clinical and molecular markers that could differentiate long-term survivors from patients having early progression to trastuzumab.
103 patients were registered in the Long-HER study, of whom 71 had obtained a durable complete response. Median age was 58 years. Metastatic disease was diagnosed after a median of 24.7 months since primary diagnosis. Sixty-five per cent of tumours were poorly differentiated ductal carcinomas and hormonal receptors were present in 47%. Metastases were present in the liver (25%), lungs (25%), bones (23%) and soft tissues (23%), with 20% of patients having multiple locations of metastases. Median progression-free survival was 10.6 years after the diagnosis of metastatic disease. Absence of trastuzumab as part of adjuvant therapy was the only clinical factor associated with long-term survival . Gene ontology analysis demonstrated that genes involved in HIF activation, EGF receptor signalling pathway, PI3 kinase pathway, apoptosis signalling pathway and p53 pathway significantly correlated with response.  The PI3K pathway was the most strongly associated with poor response to trastuzumab-based therapy: tumours in the control group usually had four or five alterations in this pathway, whereas tumours in the Long-HER group had two alterations at most. These findings support that trastuzumab may provide a substantial long-term survival benefit in a selected group of patients. Whole genome expression analysis comparing long-term survivors vs. a control group predicted early progression to trastuzumab-based therapy. Multiple alterations in genes related to the PI3K-mTOR pathway seem to be required to confer resistance to this therapy.

overall_design: 53 FFPE samples, which passed the RNA quality control criteria, were analyzed (45 primary tumours and 8 metastases). Among these 53 samples, 35 samples corresponded to long-term responders and 18 to the control group.

first: Enrique

last: Espinosa

first: Pilar

last: Zamora

first: Juan

middle: A

first: Angelo

last: Gamez-Pozo


title: Complex Interdependence Regulates Heterotypic Transcription Factor Distribution and Coordinates Cardiogenesis [microarray]

city: SAN FRANCISCO

first: Benoit

middle: G.

last: Bruneau

address: 1650 OWENS STREET

institute: GLADSTONE INSTITUTES

summary:
In the developing heart, heterotypic transcription factors (TFs) interactions, such as between the T-box TF TBX5 and the homeodomain TF NKX2-5 have been proposed as a mechanism for human congenital heart disease. In order to study the role of each TF during heart formation, embryonic stem (ES) cell-derived embryos were generated from KO ES cells for Tbx5, Nkx2-5 or both TFs.
We used microarrays to identify changes in the gene expression due to the lack of Tbx5, Nkx2-5 or both TFs during early heart formation.

overall_design: WT, Nkx2-5KO (NKO), Tbx5KO (TKO) and Tbx5KO;Nkx2-5KO (DKO) E8.75 mouse hearts were microdissected for RNA extraction and hybridization on Affymetrix microarrays.

first: Bogac

last: Kaynak

middle: G


title: Impact of Arylsulfatase B (ARSB) on gene expression

status: Public on Feb 09 2016

city: Chicago

first: Zarema

middle: H

last: Arbieva

state: IL

address: 835 S. Wolcott A301

department: RRC

institute: UIC

summary:
Arylsulfatase B (ARSB; N-acetylgalactosamine-4-sulfatase) null mouse hepatic gene expression was compared with control C57BL/6J mice
To determine if there were differences in gene expression between ARSB null mice and matched control mice.  ARSB is the enzyme that removes 4-sulfate groups from chondroitin 4-sulfate and dermatan sulfate and thereby regulates their degradation.

overall_design: comparison between ARSB-null mice on C57BL/6J background and control C57BL/6J mice matched for age and gender

first: Joanne

last: Tobacman

first: Sumit

last: Bhattacharyya

first: Leo

last: Feferman


title: Expression data from Mvt-1 clonal isolates over-expressing Ndn 50T or Ndn 50C

status: Public on Feb 08 2016

first: Nigel

last: Crawford

address: 50 South Drive, Room 5154

institute: Human Genome Research Institute

summary:
Ndn is a candidate metastasis suppressor gene that has been reported to regulate transcription.
We examined the changes in gene expression caused by the stable over-expression of allelic variants of Ndn, 50T or 50C, using lentiviral transduction in the mouse mammary tumor cell line Mvt-1.

overall_design: A total of 9 samples were analyzed. In pairwise comparisons using Partek, genes with a Benjamini-Hochberg corrected p-value <0.05 and a fold-change ≥abs(2.5) were selected.

first: Minnkyong

last: Lee

first: Niraj

last: Trivedi


title: Gene expression in ischemic, end-stage failing and non-failing human hearts

city: Ann Arbor

first: Margaret

middle: V

last: Westfall

state: MI

address: 2800 Plymouth Road

department: Cardiac Surgery

institute: University of Michigan

summary: A goal of this study was to identify and investigate previously unrecognized components of the remodeling process in the progression to heart failure by comparing gene expression in ischemic, failing (F) to non-failing (NF) hearts.  These results also were compared to the changes observed in a proteomic analysis of F and NF hearts.

overall_design:
RNA extracted from the left ventricle was hybridized to Affymetrix arrays to identify gene expression differences in ischemic, end-stage failing versus non-failing hearts.
biological replicate:  LV_NF_001, LV_NF002, LV_NF004, LV_NF005
biological replicate:  LV_F_003, LV_F005, LV_F009, LV_F006

first: Evelyn

last: Kim

first: Vladimir

middle: I

last: Galchev

first: Jin

middle: Y

first: Sean

last: Misek

first: Tamara

last: Stevenson

first: Matthew

last: Campbell

first: Francis

last: Pagani

first: Sharlene

middle: M

last: Day

first: T

middle: C

last: Johnson

first: Joseph

last: Washburn

first: Karen

middle: L

last: Vikstrom

first: Daniel

last: Michele

first: David


title: Molecular basis for remission and tolerance induction in pediatric ITP

status: Public on Feb 06 2016

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: Children with newly diagnosed ITP that after 12 month enter remission, shows molecular separate entities. The molecular basis for remission and tolerance induction is characterized by gene transcriptional profiling

overall_design: Global gene expression profile in isolated T-cells from 6 children with newly diagnosed ITP and after 12 month when they enter remission

first: Margareta

last: Jernås

first: Hans

last: Wadenik

first: Bob

last: Olsson

first: Karin

last: Mellgren

first: Frida

last: Celind


title: HER2 signaling drives DNA anabolism and proliferation through SRC-3 phosphorylation and E2F1-regulated genes

status: Public on Feb 02 2016

city: Houston

first: Suzanne

last: Fuqua

address: 1 Baylor Plaza

institute: Baylor College of Medicine

summary: Approximately 20% of early-stage breast cancers display amplification or overexpression of the ErbB2/HER2 oncogene, conferring poor prognosis and resistance to endocrine therapy. Targeting HER2+ tumors with trastuzumab or the receptor tyrosine kinase (RTK) inhibitor lapatinib significantly improves survival, yet tumor resistance and progression of metastatic disease can develop over time. While the mechanisms of cytosolic HER2 signaling are well studied, nuclear signaling components and gene regulatory networks that bestow therapeutic resistance and limitless proliferative potential are incompletely understood. Here, we use biochemical and bioinformatics approaches to identify effectors and targets of HER2 transcriptional signaling in human breast cancer. Phosphorylation and activity of the Steroid Receptor Coactivator-3 (SRC-3) is reduced upon HER2 inhibition, and recruitment of SRC-3 to regulatory elements of endogenous genes is altered. Transcripts regulated by HER2 signaling are highly enriched with E2F1 binding sites and define a gene signature associated with proliferative breast tumor subtypes, cell cycle progression, and G1 to S phase transition. We show that HER2 signaling drives proliferation in breast cancer cells through regulation of E2F1-driven DNA metabolism and replication genes together with phosphorylation and activity of the transcriptional coactivator SRC-3. Furthermore, our analyses identified a cyclin dependent kinase (CDK) signaling node that, when targeted using the CDK4/6 inhibitor Palbociclib, defines cooperative signaling pathways for expression of tumorigenic gene networks. Our findings suggest this proliferative gene signature is amendable to pharmacological targeting. These results have implications for rational discovery of pharmacological combinations in pre-clinical models of adjuvant treatment and therapeutic resistance

overall_design: 24 samples. BT-474 cell line. Genetic treatment: HER2 siRNA or Control siRNA. Hormone treatment:  10 nM Estrogen or Vehicle (0.001% Ethanol), Treatment time 4 and 24 hrs. Eight groups in total. Three samples in each grouo.

first: Bryan

last: Nikolai

first: Rainer

middle: B

last: Lanz

first: Brian

last: York

first: Nicholas

last: Mitsiades

first: Chad

middle: J

last: Creighton

first: Anna

last: Tsimelzon

first: Susan

last: Hilsenbeck

last: Lonard

first: Carolyn

last: Smith

first: Bert

middle: W

last: O’Malley


status: Public on Feb 03 2016

city: Illkirch

last: Chan

address: 1, rue Laurent Fries

country: France

institute: IGBMC

summary:
The experiment aimed at determining the genes that are under the control of the Ikaros transcription factor in mouse splenic B1 and B2 B lymphocyte subsets. To this aim, we used Ikf/f R26-CreERT2+ (Cre+) or Ikf/f R26-CreERT2- (Cre-) mice, which correspond to mice with floxed null alleles for Ikzf1 (Heizmann et al., JEM 210:2823-32, 2013) that were crossed with the R26-CreERT2 mice, which harbor a knock-in of the cDNA encoding the tamoxifen (TAM) inducible CreERT2 recombinase in the Rosa26 gene (Badea et al, J. Neurosci 23:2314-22, 2003). 6-8 week-old mice were injected daily with TAM for 3d (50mg/kg). Mice were sacrificed 10d after the first injection, and splenic B1 and B2 B cell populations sorted by flow cytometry.
Splenic B1 and B2 cells from mice with induced deletion of Ikaros

overall_design: 2 independent experiments were performed

first: Philippe

last: Kastner


title: Microarray data of mRNA exprssion in ERK/MAPK inactivated P14 mouse sensorimotor cortices

city: Tempe

first: Jason

last: Newbern

state: AZ

department: School of Life Sciences

institute: Arizona State University

summary: Inactivation of ERK/MAPK signaling in developing postmitotic cortical excitatory neurons results in a significent loss of Ctip2 positive layer 5 neurons and axon projections. Microarray dada revealed the reduced levels of a vast majority of layer V specific transcripts.

overall_design: ERK/MAPK signaling was inactivated by germline deletion of the gene Mek2 and conditional delection of the gene Mek1 using Nex:Cre driver. Sensorimotor cortices were dissected from 3 pair of mutant and control mice at the age of P14. Total RNAs were extracted using Qiagen miRNeasy kit and subjected to quality check and microarray analysis. Total 6 samples.

first: Lei

last: Xing

first: William

middle: D

last: Snider


title: A specialized mechanism of translation mediated by FXR1a-associated microRNP in cellular quiescence

city: BOSTON

first: Shobha

last: Vasudevan

address: 185 Cambridge Street

department: Cancer Center, Medicine

institute: Massachusetts General Hospital

summary:
MicroRNAs predominantly decrease gene expression; however, specific mRNAs are translationally upregulated in quiescent (G0) mammalian cells and immature Xenopus laevis oocytes by an FXR1a-associated microRNP (microRNA-protein complex) that lacks the microRNP repressor, GW182. We conducted global proteomic analysis  in THP1 cells depleted of FXR1 to globally identify activation targets of more than one microRNA, since FXR1 is required for microRNAmediated translation activation in THP1 G0 cells by FXR1-microRNPs.Since proteomic data changes could also be due to changes at the RNA level, total RNA levels in FXR1knockdown compared to control shRNA cells were examined in parallel by microarray analysis using Affymetrix Human GeneChip 2.0 ST.
We used microarrays to get total RNA levels from FXR1 knockdown and control shRNA cells, to normalize the mass spectrometry data in order to provide normalized protein data or translation efficiency.

overall_design: FXR1 knockdown and shRNA control cells were induced with 1ug/ml of doxycycline continually to cause knockdown of FXR1; the cells were grown in serum for 3 days to induce the shRNAs, followed by 2 days of serum-starvation to induce G0. After harvesting, the cells were lysed in proteinase K buffer (Truesdell et al., 2012) and total RNA was isolated using Trizol (Invitrogen) and hybridized on  Affymetrix Human GeneChip 2.0 ST microarray.

first: Syed

last: Bukhari

first: Samuel

middle: S

last: Truesdell

first: Sooncheol

last: Lee

first: Swapna

last: Kollu

first: Anthony

last: Classon

first: Myriam

last: Boukhali

first: Esha

last: Jain

first: Richard

last: Mortensen

first: Olivier

last: LeTonqueze

first: Akiko

last: Yanagiya

first: Ruslan

last: Sadreyev

first: Wilhelm

last: Haas


title: Flagellin-mediated effects of Salmonella enteritidis on gene expression in intestinal epithelial cells

status: Public on Feb 05 2016

city: Aberdeen

first: Denise

last: Kelly

address: Institute of Medical Sciences

country: United Kingdom

institute: University of Aberdeen

summary:
Analysis of gene expression in Caco-2 intestinal epithelial cells stimulated with flagellated or aflagellated S. enteritidis or recombinant flagellin. Results provide insight into how flagellin mediates innate immune responses in intestinal epithelial cells.
Keywords: Gene expression analysis

overall_design: Caco-2 cells were grown in 100 mm dishes to 3 days post-confluence. Cells were then incubated for 2 h with the following four treatments: medium alone (control); flagellated S. enteritidis; aflagellated S. enteritidis; or recombinant flagellin. Three independent experiments were performed to give an N=3 for each treatment. Caco-2 RNA was extracted and hybridized to the Affymetrix GeneChip Human Genome U133 Plus 2.0 Array.

first: Imke

middle: E

last: Mulder


title: Aberrant Methylated DNA Regions Lead to Low Activation of CD4+ T Cells with a Consequent Imbalance of the Th1/Th2 Polarization in IgA Nephropathy Patients

status: Public on Feb 01 2016

city: Bari

first: Fabio

last: Sallustio

state: Bari

address: Piazza G. Cesare N°11

institute: University of Bari

summary: To investigate alterations in the DNA methylation of CD4+ T cells in IgA nephropathy (IgAN), we performed an initial whole-genome DNA methylation screening on CD4+ T cells isolated from 6 IgAN patients and 6 healthy subjects (HS). We analyzed more than 485000 CpGs targeted across their promoters, 5'-untranslated regions (UTRs), first exons, gene bodies and 3'UTRs. Some of the most significant differentially methylated regions included genes specifically expressed in T cells and involved in the T cell receptor signaling. In particular, we found hypomethylation in the promoter region of DUSP3 and in the 3’UTR of TRIM27 (chr17:41840001-41845000; ∆β= -0.39; chr6:28876508-28893266; ∆β= -0.31). The products of these genes function as signal transductors of the T cell receptor. Moreover, in the chromosome 5 (chr5:135416205-135416475) we found the most strongly and extensively hypermethylated region in IgAN patients respect to HS (∆β=0.31) in the promoter region of VTRNA2-1 gene (known as precursor microRNA miR-886). The methylated region, 200 bp upstream of the transcription start site, it is also part of a CpG island.

overall_design: Bisulfite-converted DNA from the 12 samples (CD4+ T cells from 6 IgAN patients and 6 healthy subjects) were hybridised to the Illumina Infinium HumanMethylation450 BeadChip.

first: Grazia

last: Serino

first: Francesco

middle: P

last: Schena


title: The PGC-1α/ERRα Axis Represses One-Carbon Metabolism and Promotes Sensitivity to Anti-Folate Therapy in Breast Cancer [Microarray expression]

city: Québec City

first: Etienne

last: Audet-Walsh

state: QC

address: 2705 boulevard Laurier

department: Molecular Medicine

institute: Université Laval

summary:
Reprogramming of cellular metabolism plays a central role in fuelling malignant transformation, and AMPK as well as the PGC-1α/ERRα axis are key regulators of this process. Intersection of gene expression and binding event datasets in breast cancer cells shows that activation of AMPK significantly increases the expression of PGC-1α/ERRα and promotes the binding of ERRα to its cognate sites. Unexpectedly, the data also reveal that ERRα, in concert with PGC-1α, negatively regulates the expression of several one-carbon metabolism genes resulting in substantial perturbations in purine biosynthesis. This PGC-1α/ERRα-mediated repression of one-carbon metabolism promotes the sensitivity of breast cancer cells and tumors to the anti-folate drug methotrexate. These data implicate the PGC-1α/ERRα axis as a core regulatory node of folate cycle metabolism and further suggest that activators of AMPK could be used to modulate this pathway in cancer.
We used microarrays to detail the global program of gene expression following AMPK activation by AICAR in BT474 breast cancer cells.

overall_design: BT474 breast cancer cells were treated for 24h with vehicle or the AMPK activator AICAR and RNA was then purified for microarray analysis. Experiments were performed in duplicate for each condition.

first: David

last: Papadopoli

first: Julie

last: St-Pierre

first: Vincent

last: Giguère


title: Gene expression of CD11b+ and CD8+ spleen dendritic cells from NOD and B6 mice after in vivo CpG or PBS stimulation

first: Kristin

last: Tarbell

address: 10 Center Dr, Bldg 10 Rm 5-5832

department: Diabetes, Endocrinology, and Obesity Branch

institute: NIH/NIDDK

summary: Spleen conventional dendritic cells from NOD mice show a lower overall response to CpG-A compared to B6 cDCs.

overall_design: 8-10 week old NOD or B6 control mice were injected with either CpG-A or PBS. 12 hours later, CD8+ and CD11b+ DCs (CD11c+) were sorted from collagenase-digested spleen cells resulting in 24 samples with each condition having 3 replicates.

first: M

last: Rahman

first: Gwendoline

last: Rahir

first: Matthew

last: Dong

first: Yongge

last: Zhao

first: Kameron

last: Rodrigues

first: Chie

last: Hotta-Iwamura

first: Ye

last: Chen

first: Alan

last: Guerrero


title: Expression data from human dendritci cells that are transfected with piNC or td-piR(Glu)

city: guangzhou

first: xue

last: zhang

state: guangdong

address: 74 zhongshan 2 Rd

institute: sun yat sen university

summary: We used microarrays to detail the global gene expression in dendritic cells  transfected with piNC or td-piR(Glu)

overall_design: Human DCs transfected with piNC or td-piR(Glu) were for RNA extraction and hybridization on Affymetrix microarrays.

first: Xue

last: Zhang

first: Xin

last: He


title: An oncogenic MYB feedback loop drives alternate cell fates in adenoid cystic carcinoma

city: Jerusalem

first: Yotam

last: Drier

state: Israel

address: Faculty of Medicine, The Hebrew University, Ein Kerem

department: Immunology and Cancer Research

country: Israel

institute: The Hebrew University of Jerusalem

type: Genome binding/occupancy profiling by high throughput sequencing

summary: Translocation events are frequent in cancer and may create chimeric fusions or ‘regulatory rearrangements’ that drive oncogene overexpression. Here we identify super-enhancer translocations that drive overexpression of the oncogenic transcription factor MYB as a recurrent theme in adenoid cystic carcinoma (ACC). Whole-genome sequencing data and chromatin maps reveal distinct chromosomal rearrangements that juxtapose super-enhancers to the MYB locus. Chromosome conformation capture confirms that the translocated enhancers interact with the MYB promoter. Remarkably, MYB protein binds to the translocated enhancers, creating a positive feedback loop that sustains its expression. MYB also binds enhancers that drive different regulatory programs in alternate cell lineages in ACC, cooperating with TP63 in myoepithelial cells and a Notch program in luminal epithelial cells. Bromodomain inhibitors slow tumor growth in ACC primagraft models in vivo. Thus, our study identifies super-enhancer translocations that drive MYB expression and provides insight into downstream MYB functions in the alternate ACC lineages.

overall_design:
Examination of histone modifications in primary ACCs and primagrafts, MYB, BRD4, and P63 mapping in ACC primagrafts, H3K27ac of ACC cell line
Raw files have  been deposited at the European Genome-phenome Archive (EGA), which is hosted by the EBI, under accession number EGAS00001001457.

first: Birgit

last: Knoechel

first: Bradley

last: Bernstein


title: Expression signatures of dopaminergic neurons of ventral SNc (Pitx3-dependent), dorsal SNc (Pitx3-independent) and VTA

status: Public on Jan 31 2016

city: Montreal

first: Panojot

last: Bifsha

address: 3175 Chemin de la Côte Ste-Catherine

department: Pediatrics

institute: CHU Sainte-Justine

summary: Pitx3 is a transcription factor that is expressed in all midbrain dopaminergic (mDA) neurons during early development, but later becomes restricted in dopaminergic subsets of substantia nigra compacta (SNc) and of the ventral tegmental are (VTA) that are vulnerable to neurodegenerative stress (MPTP, 6-OHDA, rotenone, Parkinson's disease). Overall, in mice, Pitx3  is required for developmental survival of ventral SNc neurons and for postnatal survival of VTA neurons (after postnatal day 40). With the aim of determining the gene networks that distinguish Pitx3-vulnerable (Pitx3-positive) from Pitx3-resistant (Pitx3-negative) subsets of SNc and VTA, we performed a comparison at the transcriptome level between FAC-sorted mDA neurons of SNc and VTA that were obtained from wild-type and Pitx3-/- newborn mice. The latter mice have already lost the majority of their TH+Calb1- mDA neurons of ventral SNc (Pitx3-dependent), but their TH+Calb1+ neurons of dorsal SNc (Pitx3-independent), including all of VTA neurons (50% are Pitx3-dependent and 50% Pitx3-independent), are unaffected by Pitx3 deletion. At postnatal day 40, Pitx3-/- mice display a marked loss of dopaminergic subsets of VTA that normally co-express Pitx3 and Calb1 (Pitx3-dependent neurons of VTA).

overall_design: Ventral midbrains were dissected from Pitx3+/+;TH-EGFP+/- and Pitx3-/-;TH-EGFP+/- mouse pups (P1-P4). SNc and VTA were separated for both mouse genotypes (4 sample types: VTA WT, VTA KO, SNc WT and SNc KO) and then tissues were digested in papain solution. Propidium-iodide (PI) was then added to the single cell suspensions and EGFP+/PI- mDA neurons were sorted by flow cytometry into RNAlater solution (3000 cells per 30uL). Batches of EGFP+ cells in RNAlater were stored at -80°C until the necessary number of cells had been accumulated for enough total RNA (100ng) per sample type, as recommended by Affymetrix and Nugen companies. Prior to purification of total RNA, corresponding batches of cells were thawed from -80°C and pooled together in order to achieve the required amount of total RNA for each sample type (VTA WT, VTA KO, SNc WT and SNc KO) in duplicate (8 samples in total).

first: Aurelio

last: Balsalobre

first: Jacques

last: Drouin


title: Gene expression response to mitochondrial DNA depletion

city: Boston

first: Xiaoyan

middle: Robert

last: Bao

address: 185 Cambridge St. CPZN 6400

department: Molecular Biology

summary:
Mitochondrial defects are associated with a spectrum of human disorders, ranging from rare, inborn errors of metabolism to common, age-associated diseases such as diabetes and neurodegeneration. In lower organisms, genetic “retrograde” signaling programs have been identified that promote cellular and organism survival in the face of mitochondrial dysfunction. Here, we characterized the transcriptional component of the human mitochondrial retrograde response in an inducible model of mitochondrial dysfunction.
We used an HEK293-derived cell line that expresses a dominant negative DNA polymerase gamma (PolGdn) under tet repressor control. Upon induction with doxycycline, PolGdn inhibits replication of mitochondrial DNA (mtDNA), so that existing copies of mtDNA are progressively diluted as cells continue to divide. Upon removal of doxycycline, repression of PolGdn is re-established, and mtDNA copy number, as well as mitochondrial protein expression and oxidative phosphorylation complex abundance, recovers. We used microarrays to study transcriptional changes arising from mtDNA depletion. We found a robust transcriptional response that is partially mediated by ATF4, which appears to effect an adaptive rewiring of serine and one-carbon metabolism.

overall_design: We measured gene expression at 18 different time points during the mtDNA depletion / repletion process, as average mtDNA copy number fell approximately 40-fold and then recovered to baseline. In addition, we performed similar measurements in the parent cell line that does not express PolGdn, to rule out off-target effects of doxycycline treatment.

middle: R

first: Olga

last: Goldberger

first: Vamsi

middle: K

last: Mootha


title: Expression profiling in the human sclera

city: Setagaya-ku

first: Akihiro

last: Umezawa

state: Tokyo

department: Center for Regenerative Medicine

country: Japan

institute: National Center for Child Health and Development

summary: Global gene expression of RNA samples from the human sclera

overall_design: We analyzed scleral cells from 3 surgical specimens as a therapy for retinoblastoma using the Affymetrix GeneChip® Human Genome U133 plus 2.0 probe arrays. No techinical replicates were performed.

first: Yuko

last: Seko

first: Noriyuki

last: Azuma

first: Tadashi

last: Yokoi

first: Sachiko

last: Nishina

first: Yoriko

last: Takahashi


title: Mycobacterium tuberculosis H37Ra-infected macrophages response to T0901317

first: David

last: Laperriere

address: 2950, chemin de Polytechnique

department: IRIC - Institut de recherche en immunologie et en cancerologie

institute: Université de Montréal

summary: Host macrophage transcriptional responses to intracellular pathogens remain poorly characterized. We screened transcriptional enhancers engaged in response to M. tuberculosis (Mtb) infection by ChIPseq analysis of histone H3 lysine 4 monomethylation (H3K4me1). De novo monomethylation during infection was associated with genes implicated in host defense and apoptosis. These regions were enriched for binding sites for ETS transcription factor family members and response elements for nuclear receptors, including liver X receptors (LXRs) and peroxisomal proliferator activated receptors (PPARs), many of which were encompassed by transposable elements. LXRa expression was strongly induced by infection, whereas that of PPARs was unaffected. LXR DNA binding and NCoR corepressor recruitment increased proportionately in infected cells but coactivator association was unchanged, consistent with a lack of induction of endogenous agonists. However, treatment of infected cells with LXR agonist T0901317 strongly increased coactivator recruitment and induced a gene expression program characterized by enhanced innate immune signaling and lipid metabolism. Remarkably, T0901317 treatment selectively induced apoptosis in infected macrophages, and was accompanied by Mtb death, reducing mycobacterial burden 18-fold relative to vehicle 5d after infection. These studies define macrophage transcriptional responses to Mtb infection, and suggest that tissue-specific LXRa agonists may be efficacious in clinical management of tuberculosis.

overall_design: THP-1 cells infected with H37Ra for 24h in the absence or presence of 20nM T0901317

first: Manuella

last: Bouttier

first: John

middle: H

last: White


title: Spatial and Temporal Homogeneity of Driver Mutations in Diffuse Intrinsic Pontine Glioma

status: Public on Jan 29 2016

first: Nada

last: Jabado

address: 1001 Décarie Boulevard

department: Department of Pediatrics

institute: McGill University

summary: Genome wide DNA methylation profiling of 35 samples from various neuroanatomical locations for four adult DIPGs

overall_design: Bisulphite converted DNA from 35 samples from four DIPGs were hybridised to the Illumina 450k Human Methylation Beadchip

first: Hamid

last: Nikbakht

first: Eshini

last: Panditharatna

first: Leonie

middle: G

last: Mikael

first: Rui

last: Li

first: Tenzin

last: Gayden

first: Matthew

last: Osmond

first: Cheng-Ying

last: Ho

first: Madhuri

last: Kambhampati

first: Eugene

last: Hwang

first: Damien

last: Faury

first: Alan

last: Siu

first: Simon

last: Papillon-Cavanagh

first: Denise

last: Bechet

first: Keith

last: Ligon

first: Benjamin

last: Ellezam

first: Wendy

last: Ingram

first: Andrew

last: Moore

first: Caedyn

last: Stinson

first: Katherine

last: Warren

first: Jason

last: Karamchandani

first: Roger

last: Packer

first: Jacek

last: Majewski

first: Javad

last: Nazarian


title: Mouse Smarcb1-deficient models recapitulate subtypes of human rhabdoid tumors.

status: Public on Jan 27 2016

city: Paris

first: Wilfrid

last: Richer

address: 26 rue d'Ulm

institute: Institut Curie

summary:
Rhabdoid Tumors (RT) are highly aggressive tumors that are frequently localized in the central nervous system (CNS) where they are termed atypical teratoid and rhabdoid tumors (ATRT). We generated conditional Smarcb1-deficient mouse model leads to CNS Smarcb1-deficient tumors.
We used microarrays to compared gene expression profilings of various human and mouse tumors. Our data demonstrate that the Smarcb1-deficient mouse model recapitulates the diversity of human RT.

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus

overall_design:
[human mRNA] 20 human MRT ( < 5 years), 30 human ATRT ( < 5 years), 4 human MB SHH.
[mouse mRNA] 8 Smarcb1-deficient mouse brain tumors, 15 Smarcb1-deficient T-Cell lymphomas, 3 Mb Shh  mouse tumors.

first: Franck

last: Bourdeaut

first: Zhi-Yan

last: Han


title: Gene expression profiling of KU812 CD25 shRNA vs KU812 control random shRNA

status: Public on Jan 26 2016

city: Vienna

first: Markus

last: Jeitler

address: Lazarettgasse 14

country: Austria

institute: Medical University Vienna

summary:
In chronic myeloid leukemia (CML) neoplastic stem cells (NCS) represent a critical target of therapy. However, little is known about markers and targets expressed in CML NSC.    We examined the phenotype and function of CD34+/CD38─/Lin─ CML LSC by a multi-parameter screen approach employing antibody-phenotyping, mRNA expression profiling, and functional studies, followed by marker-validation using diverse control-cohorts and follow-up samples of CML patients treated with imatinib.
We here show that in contrast to normal stem cells, CD34+/CD38− CML NSC express IL2RA (CD25), and that STAT5 induces expression of CD25 in Lin−/Sca-1+/Kit+ NSC (LSK) in C57/Bl6 mice. Correspondingly, expression of CD25 decreased in the human BCR/ABL1+ stem cell line KU812 upon shRNA-induced STAT5-depletion. The BCR/ABL1-inhibitors nilotinib and ponatinib were also found to decrease STAT5 activity and CD25-expression in KU812 cells and primary CML NSC. A CD25-targeting shRNA augmented the proliferation of KU812 cells in vitro and in vivo in NOD/SCID-IL2R-/- mice. In consecutive experiments the PI3K/mTOR-blocker BEZ235 was found to promote STAT5- and CD25 expression and to produce synergistic anti-neoplastic effects with nilotinib and ponatinib in CML cells. Together, CD25 is a novel STAT5-dependent marker and target in CML NSC.

overall_design: To define differences in mRNA expression patterns in KU812 cells transduced with a random control shRNA or a shRNA against CD25, gene array analyses were performed.

first: I

last: Sadovnik

first: P

last: Valent


title: Synovial biopsies of rheumatoid arthritis and healthy controls

city: Nijmegen

first: Mathijs

last: Broeren

address: Geert Grootplein 28

department: Department of Rheumatology

country: Netherlands

institute: Radboud university medical Center

summary:
Synovial biopsies were obtained from rheumatoid arthritis (RA) synovium and from subjects without a joint disease to find gene upregulated during RA.
The promoters of genes upregulated during RA compared to HC can be used to obtain disease-regulated gene therapy.

overall_design: 16 microarrays of end-stage RA synovial biopsies were compared to 7 microarrays of synovial biopsies from individuals without a joint disease. Genes with >1.2-fold upregulation and P<0.05 in RA VS HC were selected from the analysis.


title: The alterations of gene expression in aortic valve from calcific aortic valve disease patients

status: Public on Jan 28 2016

city: Seoul

first: Bongkun

last: Choi

address: Olympic-ro 43-gil

department: Department of Biomedical Sciences

country: South Korea

institute: Asan Medical Center, University of Ulsan College of Medicine

summary: Calcification of the aortic valve leads to increased leaflet stiffness resulting in development of calcific aortic valve disease (CAVD); however, the underlying molecular and cellular mechanisms of calcification are poorly understood. Here, we investigated gene expressions in relation to valvular calcification and promotion of CAVD progression.

overall_design: 3 samples of aortic valve from patients with calcific aortic valve disease (CAVD) were compared with 3 samples of aortic valve from age-matched normal subjects

first: Eun-Ju

last: Chang

first: Jae-Kwan

last: Song


title: Non-CG DNA methylation is a biomarker for assessing endodermal differentiation capacity in pluripotent stem cells

city: London

first: Lee

last: Butcher

address: 72 Huntley Street

institute: University College London

summary:
Illumina Infinium 450k Human DNA Methylation BeadChip was used to obtain DNA methylation profiles across approximately 470,000 CpG and 2,700 non-CG loci in 195 DNA extracts from iPSCs, ESCs and donor cell lines.
Non-CG methylation is an unexplored epigenetic hallmark of pluripotent stem cells.  Here we report that a reduction in non-CG methylation is associated with impaired differentiation capacity into endodermal lineages. Genome-wide analysis of 2,670 non-CG sites in a discovery cohort of 25 phenotyped human induced pluripotent stem cell (hiPSC) lines revealed unidirectional loss (Δβ = 13%, p<7.4x10-4) of non-CG methylation that correctly identifies endodermal differentiation capacity in 23 out of 25 (92%) hiPSC lines.  Translation into a simplified assay of only 9 non-CG sites maintains predictive power in the discovery cohort (Δβ = 23%, p<9.1x10-6) and correctly identifies endodermal differentiation capacity in nince out of ten pluripotent stem cell lines in an independent replication cohort consisting of hiPSCs reprogrammed from different cell types and different delivery systems, as well as human embryonic stem cell (hESC) lines.  This finding infers non-CG methylation at these sites as a biomarker when assessing endodermal differentiation capacity as a readout.

overall_design: 25 iPSC lines, 3 ESC lines and 7 donor cell lines (samples) were represented by multiple DNA extracts (2 < N < 6); 7 iPSC line samples were represented by a single DNA extract. Each DNA extract was bisulphite converted and hybridised to the Illumina Infinium 450k Human Methylation BeadChip. Raw data was fed through the ChAMP  analysis pipeline (Morris et al. 2013, Bioinformatics) and normalised using Subset-quantile Within Array Normalization (SWAN).


title: Methylation profiling of molar tissues caused by recessive maternal-effect NLRP7 mutations

city: L´Hospitalet de Llobregat

first: David

last: Monk

state: Barcelona

address: 199-203 Av. Gran Via de L' Hospitalet

department: PEBC

institute: IDIBELL

summary: Approximately 70% of women suffering with familial recurrent moles (RHM) are associated with recessive mutations of NLRP7, which cause the RHM by maternal-effect. It has been proposed that the phenotypes of molar pregnancies are associated with aberrant genomic imprinting. Using the Illumina Infinium HumanMethylation450 Beadchip arrays we characterize the genome-wide methylation profile of 4 molar samples and blood from the female patients. We confirm widespread loss-of-imprinting in the RHM samples but not in the blood-derived DNA from the asymptomatic female patients.  The aberrant methylation at imprinted loci was confirmed using bisulphite PCR and subcloning or pyrosequencing. Finally, by comparing the methylation patterns observed in the RHM with normal placenta biopsies we identify many candidate maternally methylated regions, consistent with novel imprinted genes.

overall_design: DNA was quantified by Quant-iT PicoGreen dsDNA Reagent (Invitrogen) and the integrity was analyzed in a 1.3% agarose gel. Bisulfite conversion of 600 ng of each sample was perform according to the manufacturer's recommendation for Illumina Infinium Assay. Effective bisulphite conversion was checked for three controls that were converted simultaneously with the samples. 4 ul of bisulfite converted DNA were used to hybridize on Infinium HumanMethylation 450 BeadChip, following Illumina Infinium HD Methylation protocol. Chip analysis was performed using Illumina HiScan SQ fluorescent scanner. The intensities of the images are extracted using GenomeStudio (2011.2) Methylation module (1.8.5) software. Methylation score of each CpG is represented as beta value.

first: Rosemary

last: Fisher


title: COPD lung tissue expression

status: Public on Jan 22 2016

city: Barcelona

first: Maria Rosa

last: Faner

address: C/Casanova 143, planta 2A,

department: Cellex

institute: Fundació Privada Clinic

summary: Comparison of emphysema vs non emphysema COPD lung tissue expression

first: Rosa

first: Susana

last: Kalko


title: Expression data from human unbilical endothelial cells (HUVEC) irradiated with X-ray

status: Public on Jan 21 2016

city: Toyama

first: yukihiro

last: furusawa

address: Kurokawa

institute: Toyama Prefectural University

summary: To understand the molecular mechanism underlying inflammatory reaction in vascular system post exposure to ionizing radiation, we carried out microarray analysis in HUVEC exposed with X-ray

overall_design: HUVEC were irradiated with X-ray (2.5 Gy) and then cultured for 6, 12, and 24 hr. Total RNA were extracted from the tissue by QIAGEN Rneasy mini kit.

first: Y

last: Furusawa


title: Expression data from Chinese renal cell carcinoma cells with FSTL1 knocked down

status: Public on Jan 20 2016

city: Shanghai

first: Xi

last: Chen

address: 8th Panshan Road

institute: Second Military Medical University

summary: Clear cell renal cell carcinoma (ccRCC), the major histotype of cancer derived from kidney, is lack of robust prognostic and/or predictive biomarker and powerful therapeutic target. We previously identified that follistatin-like protein 1 (FSTL1) was significantly down-regulated in ccRCC at the transcription level. In the present study, we characterized, for the first time, that FSTL1 immunostaining was selectively positive in the cytoplasm of distal convoluted tubules. The expression of FSTL1 was significantly lower in ccRCC tissues than in adjacent renal tissues (P<0.001), as measured using immunohistochemistry in 69 patients with paired specimens, and lower in most ccRCC cell lines than in human embryonic kidney cells, as measured by quantitative RT-PCR. Multivariate Cox regression analysis in 89 patients with follow-up data showed that FSTL1 expression in tumors conferred a favorable postoperative prognosis independently, with a hazard ratio of 0.325 (95% confidence interval: 0.118-0.894). FSTL1 knockdown promoted anchorage independent growth, mobility, and invasion of ccRCC cell lines and promoted cell cycle from G0/G1 phases into S phase; while over-expression of FSTL1 significantly attenuated cell migration ability in ACHN cells. FSTL1 knockdown resulted in decreased expression of E-cadherin and increased expression of N-cadherin in ccRCC cell lines significantly, indicating that FSTL1 may attenuate epithelial to mesenchymal transition in ccRCC. Microarray assay indicated that NF-κB and HIF-2α pathways were activated following FSTL1 knockdown in ccRCC cells. Our study indicates that FSTL1 serves as a tumor suppressor in ccRCC, up-regulation of FSTL1 in cancer cells may be a candidate target therapy for advanced ccRCC.

overall_design: RNA samples were collected from NRCC-shsiscramble, NRCC-shFSTL1-1 and NRCC-shFSTL1-2 cells. Then samples were hybridized to Affymetrix arrays for mRNA profiling.

first: Yan

last: Liu

first: Xiaojie

last: Tan

first: Wenbin

first: Xiaomei

last: Hou

first: Dan

last: Shen

first: Yibo

last: Ding

first: Jianhua

last: Yin

first: Ling

last: Wang

first: Hongwei

last: Zhang

first: Yongwei

last: Yu

first: Jianguo

first: Timothy

last: Thompson

first: Guangwen

last: Cao


title: Hepatocyte-like cells

city: Cambridge

first: Derek

last: Peters

address: 7 Divinity Ave

department: Stem Cell and Regenerative Biology

institute: Harvard University

summary:
Hepatocyte-like cells (HLCs) are derived from human pluripotent stem cells (hPSCs) in vitro, but differentiation protocols commonly give rise to a heterogeneous mixture of cells. This variability confounds the evaluation of in vitro functional assays performed using HLCs. We demonstrate the purification of a sub-population of functional HLCs differentiated from multiple hPSC lines using the hepatocyte surface marker Asialoglycoprotein Receptor 1 (ASGR1).
We analyzed the expression profile of ASGR1-positive cells by microarray, and tested their ability to perform mature hepatocyte functions (albumin and urea secretion, cytochrome activity). By these measures, ASGR1-positive HLCs are enriched for the gene expression profile and functional characteristics of primary hepatocytes compared to unsorted HLCs.

overall_design: We extracted and hybridized RNA to Affymetrix microarrays to obtain gene expression profiles from biological replicates of the following human cell types: hepatocyte-like cells (HLCs) differentiated in vitro from a hESC line and a hiPSC line, FACS-isolated ASGR1+ HLCs differentiated from the same hESC and hiPSC lines, cryopreserved primary human hepatocytes, HepG2 hepatoma cells. HLCs and FACS-isolated ASGR1+ HLCs differentiated from either hESCs or hiPSCs were collected as paired samples.

middle: T

first: Chad

middle: A

last: Cowan


title: Expression data from mammary epithelial HC11 cells stably transfected with NF1-C2 or FoxF1

status: Public on Feb 04 2016

city: Gothenburg

first: Jeanette

middle: Annika

last: Nilsson

address: Medicinaregatan 9C

department: Chemistry and Molecular Biology

country: Sweden

institute: Gothenburg university

summary:
NF1-C2 suppresses tumorigenesis and epithelial-to-mesenchymal transition by repressing FoxF1.
Forkhead Box F1 promotes breast cancer cell migration by upregulating lysyl oxidase and suppressing Smad2/3 signaling

overall_design: Biological replicates: 3 Wild type HC11 cells, 3 FoxF1-transfected HC11 cells and 3 NFI-C2-transfected HC11 cells, independently grown and harvested. One replicate per array.

first: Marie

last: Janson


title: Differential Gene expression in CCR5+ versus CCR5- OT-I T cells

status: Public on Jan 14 2016

city: Cleveland

first: David

last: Askew

state: OH

address: 2103 Cornell Road

country: USA

institute: CWRU

summary: OT-I T cells were exposed to CpG ODN-activated CCR5ko Lymph nodes for 6 h, stained for surface CCR5 and FACS-sorted into CCR5+ and CCR5- fractions

overall_design: In the study presented here freshly isolated OT1 T cells were exposed for 6h at 37oC to teased-out CpG ODN-activated CCR5ko LNs in 96-well plates and stained for surface CCR5 before sorting into CCR5+ (Hua2) and CCR5- (Hua1) fractions. High quality total RNA isolated from each cell fraction using TRIZOL and Qiagen RNEasy kit per manufacture's recommendation was subjected to microarray analysis using the Affymetrix Mouse Gene ST 1.0 array chip to discover differentially expressed genes.

first: Alex

last: Huang


title: Gene expression in the different stages of endometrial cancer

status: Public on Jan 18 2016

city: Hsin-Chu

first: Wei-Yun

address: 75 Bo-Ai Street

department: Department of Biological Science and Technology

country: Taiwan

institute: NCTU

summary:
Objectives: The aim of this study was to identify the dysregulated genes involved in tumorigenesis, invasion, and metastasis of endometrial endometrioid adenocarcinoma (EEC).

Materials and methods: Surgical specimens of endometrial tissues were obtained from 20 patients with normal endometrium (NEM), 20 patients with atypical endometrial hyperplasia (AEH), and 169 patients with EEC. The expression profiles of NEM, AEH, and EEC were compared by using GeneChip Array. The expression of dysregulated genes was first validated by semi-quantitative reverse transcriptase PCR (SQ RT-PCR). The gene expression levels were determined by real time reverse transcriptase PCR (RTQ RT-PCR) in 85 EEC patients as the training test and 84 EEC patients as the testing test. The protein expressions were then examined by immunohistochemical (IHC) staining. The correlations between the expression of dysregualted genes and clinico-pathologic parameters such as tumorigenesis, invasion, and metastasis of EEC were finally evaluated.

Results: Seven dysregulated genes were identified by SQ RT-PCR after microarray analysis.

Conclusions: uPA is a dysregulated gene in the tumorigenesis of endometrial carcinomas.

overall_design: The gene expression between tissues from NEM, AEH, and EEC were analyzed by microarray. The samples were grouped according to clinical stages but selected at random from our list of banked, frozen tissues. Ten NEM, 10 AEH, and 20 EEC of early and advanced stages were used for microarray experiments (Group 1: early-staged (stages I and II) EEC (n=10), Group 2: advanced-staged EEC (stages III and IV) (n=10)). Samples were pooled in equimolar amounts (10 samples / pool) for microarray analysis.


title: Comparative gene expression analyses of purified CD14+ monocytes from human umbilical cord blood, CD14+ monocytes from adult peripheral blood and the cell therapy product DUOC-01

status: Public on Jan 13 2016

city: Durham

first: Arjun

last: Saha

state: NC

address: 10 circuit dr, RP2

department: DTMI

institute: Duke University School of Medicine

summary: DUOC-01 is a macrophage-like cell therapy product manufactured from human umbilical cord blood (CB) mononuclear cells (MNCs) and intended for use in treatment of demyelinating diseases. During the 21-day manufacturing process, most initiating MNCs die in culture, but a highly active, adherent population of cells that resemble hematopoietic lineage macrophage in morphology, phagocytic activity, and antigen expression emerges; this population comprises the final DUOC-01 product [Kurtzberg et al. 2015]. Using the cuprizone-mediated murine demyelination model, we have found that DUOC-01 cells are capable of accelerating the remyelination process. In the same demyelination model, human cord blood-derived CD14+ cells (CBCD14) were less active. In another cellular therapy project, we have found that CBCD14 protects brain cells from oxygen-glucose-deprivation (OGD), but adult peripheral blood-derived CD14+ monocytes (PBCD14) did not. To address the functional differences between these cell types, we have analyzed differential gene expression by these three cell types.

overall_design: We used four cord blood (CB) samples (from Carolinas Cord Blood Bank) that were collected within 24hrs of delivery. Then, highly purified CB CD14+ monocytes were isolated by flow sorting. We collected the peripheral blood (PB) from four healthy volunteers and isolated the purified PB CD14+ monocytes by cell sorting. Three separate batches of cultured DUOC-01 cells were collected from Robertson Cell and Translational Cell Therapy cGMP facility. Total RNAs were isolated at the same time and kept frozen. RNA samples were given to Duke Microarray core facility to analyse the gene expression profile using Affymetrix GeneChip® Human Genome U133 Plus 2.0 Assay.

first: Susan

last: Buntz

first: Tracy

last: Gentry

first: Joanne

last: Kurtzberg

first: Andrew

last: Balber


title: Expression data from QY and QYRC cell lines

status: Public on Jan 12 2016

first: Huang

last: Qingshan

state: Shanghai

address: No 2005, Songhu Road

department: Genetics

institute: Fudan University

summary:
We superinfected a hepatocellular carcinoma (HCC) cell line (QGY-7703,QY) with oncolytic parvovirus H1 (H-1PV) and acquired a group of resistant cells QYRC. Previous studies suggested that cells surviving H-1PV superinfection should behave somewhat similarly to normal cells. When compared with the QGY-7703 cells, the QYRC cells indeed exhibited loss of colony formation in soft agar, and they didn’t form detectable tumors after being hypodermically injected into 5 nude mice.
In order to find out what cellular factors may be responsible for the loss of tumor cell phenotype, we compared the cDNA microarray profiles of the QGY-7703 and QYRC cells to find that a series of genes were upregulated in the H-1PV-resistant QYRC cells

overall_design: We investigated the expression profiles of QY and QYRC cell lines.

first: Hongyu

last: Wu

first: Wei

first: Jinjiang

first: Kuikui

last: Ge

first: Guodong

last: Li

first: Qingshan


title: Expression data of human tympanic membrane cells and epidermal keratinocytes

status: Public on Jan 08 2016

city: Lorenskog

first: Peder

last: Aabel

address: Sykehusvn. 27

department: ENT

country: Norway

institute: Akershus University Hospital

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

platform_organism:
Homo sapiens
synthetic construct

overall_design: Refer to individual Series


title: Genome-wide methylation analysis and gene expression profiling identifies genes silenced in non-seminoma cell lines [methylation]

status: Public on Jan 15 2016

city: Nottingham

first: Paul

last: Scotting

address: Queen's Medical Centre

department: School of Life Sciences

institute: University of Nottingham

summary: Germ cell tumours (GCTs) are a complex group of malignancies. They are unique in developing from a pluripotent progenitor cell. The initial lesion is believed to be the relatively benign precursor lesion (ICGNU), from which either highly chemosensitive seminomas or the more aggressive non-seminomas develop. Previous analyses of selected genes have suggested that non-seminomas exhibit much higher levels of DNA methylation than seminomas. However, the genomic targets that are methylated, the extent to which this results in gene silencing and the identity of the silenced genes most likely to play a role in the tumours’ biology have not yet been established.   Here genome-wide methylation and expression analysis of GCT cell lines was combined with gene expression data. This demonstrated that the seminoma cells exhibited very little aberrant DNA methylation while non-seminoma cells exhibited very high levels of DNA methylation. Large differences in the level of methylation of the CpG islands of individual genes between tumour cell lines correlated well with differential gene expression. Treatment of non-seminoma cells with 5-aza-2-deoxycytidine verified that methylation of all genes tested did indeed play a role in their silencing and many of these genes were also differentially expressed in primary tumours. Through this approach the genes silenced in the various GCT cell lines were identified.   Conclusions: Several pluripotency-associated genes, never before implicated in this type of cancer, were identified as a major functional group of silenced genes. Silencing of these factors that normally suppress somatic differentiation might play an important role in the progression to non-seminoma formation.

overall_design: Genomic DNA and RNA was extracted from cell lines representing four subtypes of GCT.  RNA was subjected to Affymetric expression array analysis while DNA was bisulfite treated and analysed using Illumina Infinium 450K arrays. Statistical approaches were used to correlate methylation and expression for each gene.

first: Dzul

last: Noor

first: Jennie

middle: N

last: Jeyapalan

first: Safiah

last: Alhazmi

first: Matthew

last: Carr

first: Benjamin

last: Squibb

first: Jaime

last: Hughes

first: Janet

last: Shipley

first: Denise

last: Sheer


title: Genome-wide methylation analysis and gene expression profiling identifies genes silenced in non-seminoma cell lines


title: Genome-wide methylation analysis and gene expression profiling identifies genes silenced in non-seminoma cell lines [gene expression]


title: Expression data of BRPF3 depletion from the human osteosarcoma U2OS cell line

city: Copenhagen

first: Anja

last: Groth

address: Ole Maaløes Vej 5, DK-2200 Copenhagen N

institute: Copenhagen University

summary:
The Bromo-domain and PHD-finger protein, BRPF3, forms a complex with HBO1 and regulates the initiation of DNA replication. BRPF3-dependent histone H3K14 enriched in chromatin surrounding a fraction of replication origins may play an important role in origin firing.
We used microarrays to evaluate whether replication defect due to the lack of BRPF3 is associated with transcriptional changes of replication genes.

overall_design: Human osteosarcoma U2OS cells depleted for BRPF3 were used for RNA extraction and hybridization on Affymetrix microarrays. Cells were treated with either scamble siRNA (Control_1_B1) or siRNA against BPRF3 (BRPF3_B1) for 48 hours. Two samples in a biological replica set were prepared in exactly the same way and labeled as Control_1_B2 and BRPF3_B2 respectively.


title: Characterization of CD57+PD1- CD4 T cells

city: Atlanta

first: Gregory

last: Tharp

state: GA

address: 954 Gatewood Dr

department: Developmental and Cognitive Neuroscience

institute: Yerkes National Primate Research Center

summary: We have identified a CD57+PD1- CD4 T cell phenotype at the time of transplantation that strongly correlates with subsequesnt development of belatacept-resistant rejection. In this study, we used microarray to determine which genes were upregulated in CD57+ compared to CD57- CD4 T cells.

overall_design: Peripheral blood obtained from 5 healthy controls was processed and sorted into CD4+CD57+PD1- and CD4+CD57-PD1- populations. Total RNA was extracted from the sorted populations and quality assessed. cDNA synthesis and amplification was performed, and fragmented and biotinylated samples were hybridized to the Affymetrix Human U133 plus 2.0 probe array. The arrays were scanned and probe intensity measurements were normalized across the samples using the robust multichip average (RMA) algorithm.

first: Jaclyn

last: Espinosa

first: Linda

last: Stempora

first: Steven

last: Bosinger

first: Allan

last: Kirk


title: Genome-wide analyses in neuronal cells reveal that USF transcription factors regulate lysosomal gene expression [Expression analysis]

city: Niigata

first: Tomoyuki

last: Yamanaka

address: 1-757 Asahimachidori, Chuo-ku

department: Brain Research Institute

institute: Niigata University

summary:
The upstream stimulating factors (USFs) USF1 and USF2 are ubiquitously expressed transcription factors characterized by a conserved basic helix-loop-helix leucine zipper DNA-binding domain. They form homo- or heterodimers and recognize E-box motifs to modulate gene expression. They are known to regulate diverse cellular functions including the cell cycle, immune response and glucose-lipid metabolism, but their roles in neuronal cells remain to be clarified. Here, we performed chromatin immunoprecipitation of USF1 from mouse brain cortex preparations. Subsequent promoter array analysis (ChIP-chip) indicated that USF1 exclusively bound to the CACGTG E-box motifs in the proximal promoter regions. Importantly, functional annotation of the USF1-binding targets revealed an enrichment of genes related to lysosomal functions. Gene expression arrays using a neuronal cell line subsequently revealed that knockdown of USFs deregulated lysosomal gene expression. Altered expression was validated by quantitative RT-PCR, supporting the conclusion that USFs regulate lysosomal gene expression. Furthermore, USFs knockdown slightly increased LysoTracker staining, implying a role for USFs in modulating lysosomal homeostasis. Together, our comprehensive, genome-scale analyses identified lysosomal genes as targets of USFs in neuronal cells, suggesting a potential additional pathway of lysosomal regulation.
Gene expression profiling of neuro2a cells knocking down USFs.

overall_design: To screen USFs-downstream genes, mouse neuro2a cells were transfected with vectors for USFs miR RNAi or an empty vector, and then subjected to microarray analysis using Affymetrix Mouse Gene 1.0 ST Array.

first: T

first: N

last: Nukina


title: Transcriptome Sequencing (RNAseq) enables utilization of Formalin-Fixed, Paraffin-Embedded Biopsies with Clear Cell Renal Cell Carcinoma for Exploration of Disease Biology and Biomarker Development

city: Bergen

first: Philipp

last: Strauss

address: Haukeland Universitetssykehus Laboratoriebygget, 7. etg. Heis øst

institute: University of Bergen

summary: Formalin-fixed, paraffin-embedded (FFPE) tissues are an underused resource for molecular analyses. This proof of concept study aimed to compare RNAseq results from FFPE biopsies with the corresponding RNAlater® (Qiagen, Germany) stored samples from clear cell renal cell carcinoma (ccRCC) patients, to enable the decision of whether or not it is feasible to apply RNAseq technology to archival tissue. Core biopsies were obtained with a 16g needle from 16 patients undergoing partial or full nephrectomy. The RNA sequencing libraries were generated applying the new Illumina TruSeq® Access library preparation protocol.

overall_design: *** Access to raw data can be requested from submitters ***

first: Oystein

last: Eikrem

first: Christian

last: Beisland

first: Karin

middle: M

last: Hjelle

first: Arnar

last: Flatberg

first: Andreas

last: Scherer

first: Lea

last: Landolt

first: Trude

last: Skogstrand

first: Sabina

last: Leh

first: Vidar

last: Beisvag

first: Hans-Peter

last: Marti


title: Strong Components of Epigenetic Memory in Cultured Human Fibroblasts Related to Site of Origin and Donor Age (Methylation)

status: Public on Jan 23 2016

city: Baltimore

first: Andrew

last: Jaffe

address: 855 N Wolfe St, Ste 300

department: Clinical Sciences

institute: Lieber Institute for Brain Development

summary: Differentiating pluripotent cells from fibroblast progenitors is a potentially transformative tool in personalized medicine. We previously identified relatively greater success culturing dura-derived fibroblasts than scalp-derived fibroblasts from postmortem tissue. We hypothesized that these differences in culture success were related to epigenetic differences between the cultured fibroblasts by sampling location, and therefore generated genome-wide DNA methylation and transcriptome data on 11 intrinsically matched pairs of dural and scalp fibroblasts from donors across the lifespan (infant to 85 years). While these cultured fibroblasts were several generations removed from the primary tissue and morphologically indistinguishable, we found widespread epigenetic differences by sampling location at the single CpG (N=101,989), region (N=697), “block” (N=243), and global spatial scales suggesting a strong epigenetic memory of original fibroblast location. Furthermore, many of these epigenetic differences manifested in the transcriptome, particularly at the region-level. We further identified 7,265 CpGs and 11 regions showing significant epigenetic memory related to the age of the donor, as well as an overall increased epigenetic variability, preferentially in scalp-derived fibroblasts -83% of loci were more variable in scalp, hypothesized to result from cumulative exposure to environmental stimuli in the primary tissue. By integrating publicly available DNA methylation datasets on individual cell populations in blood and brain, we identified significantly increased inter-individual variability in our scalp- and other skin-derived fibroblasts on a similar scale as epigenetic differences between different lineages of blood cells. Lastly, these epigenetic differences did not appear to be driven by somatic mutation - while we identified 64 probable de-novo variants across the 11 subjects, there was no association between mutation burden and age of the donor (p=0.71). These results depict a strong component of epigenetic memory in cell culture from primary tissue, even after several generations of daughter cells, related to cell state and donor age.

overall_design: We measured DNA methylation (DNAm) levels from scalp- and dura-derived cultured fibroblasts in 11 postmortem donors (22 samples) from across the lifespan, ranging from early infancy to 85 years using the Illumina HumanMethylation450 microarray (Illumina 450k). After data processing, normalization, and quality control with the minfi package, we obtained normalized data on 21 samples (one dura sample with lower quality was removed prior to across-sample normalization). The tissue donor demographics are tabulated in S1 Table in the publication. Briefly, 1 donor was female, the rest were male. 1 donor was African American, 1 was Hispanic, and the others were all Caucasian. 2 donors were diagnosed with Bipolar disorder, the diagnosis was unknown for 5 of the donors, and the remaining 4 donors were Controls.

first: Nikolay

last: Ivanov

first: Thomas

last: Hyde


title: Expression data from HeLa cell lines stably expressing shRNA targeting ctrl  or UHRF1

status: Public on Jan 05 2016

city: Rochester

first: Asha

last: Nair

address: 200 1ST ST SW

institute: Mayo Clinic

summary: We used microarrays to explore  the expression profile from cells expressing wild type and UHRF1 S674A mutant. HeLa cells expressing UHRF1 WT and S674A mutant showed similar gene expression pattern without significant affecting the  transcription of DNA repari genes.

overall_design: UHRF1 was depleted in HeLa cells by shRNA treatment. Total RNA was purified and used to determine the global gene transcription profiles by microarray assays. The UHRF1-related genes expression profiles were compared among control cells, UHRF1-depleted cells, UHRF1 WT reconstituting cells and UHRF1 S674A mutant reconstituting cells.

first: Haoxing

last: Zhang

first: Tongzheng

last: Liu

first: Min

last: Deng

first: Krishna

last: Kalari

first: Huadong

last: Pei

first: Zhenkun

last: Lou


title: Genome-wide profiling of the functional DNA methylation landscape at base-pair resolution in human cancer types [Methylation BeadChip]

city: L'Hospitalet de Llobregat

first: Manel

last: Esteller

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

country: Spain

institute: IDIBELL

summary: High-resolution DNA methylation array analysis of human cancer samples and normal control tissue types

overall_design: Analisys of Differential Methylation Regions (DMRs) of human cancer samples and normal control tissue types performing  high-resolution DNA methylation array analysis

first: Holger

last: Heyn


title: FGFR signature

status: Public on Jan 06 2016

city: Kamakura

first: Yoshito

last: Nakanishi

address: Kajiwara 200

institute: Chugai pharmaceutical

summary:
Drugs that target specific gene alterations have proven beneficial in the treatment of cancer. Because cancer cells have multiple resistance mechanisms, it is important to understand the downstream pathways of the target genes and monitor the pharmacodynamic markers associated with therapeutic efficacy.
We performed a transcriptome analysis to characterize the response of various cancer cell lines.

overall_design: We performed a transcriptome analysis to characterize the response of various cancer cell lines to a selective fibroblast growth factor receptor (FGFR) inhibitor (CH5183284/Debio 1347), a mitogen-activated protein kinase kinase (MEK) inhibitor, or a phosphoinositide 3-kinase (PI3K) inhibitor. We treated compounds for 24 hours and purified total RNA.

first: Hideaki

last: Mizuno


title: A molecular signature for MET-targeted therapy

first: Maria

middle: Libera

last: Ascierto

address: 5500 Orleans Street

department: Oncology

institute: Johns Hopkins

summary: Constitutive MET signaling promotes invasiveness in primary and recurrent GBM; however, current MET-targeting strategies lack of effective biomarkers for selecting suitable patients for treatment. Here, we identified a predictive signature potentially valuable for indicating vulnerability to MET-targeted therapy in GBM. The use of both human and mouse gene expression microarrays showed that MET inhibitors regulate tumor (human) and host (mouse) cells within the tumor via distinct molecular processes, but overall they impede tumor growth by inhibiting cell cycle progression. Notably, GBM tumors with EGFRamp that showed resistance to erlotinib treatment also showed activation of the MET pathway, suggesting that a combination of EGFR and MET inhibitors may overcome or prevent such resistance in patients with EGFRamp GBM.

overall_design: GBM cell lines (DBM2, U251M2, U87M2, U118, and SF295) were treated for 7 days with either vehicle (n=14) or V-4084 (n=14) (i.e. SF295 + vehicle (n=2), SF295 + V-4084 (n=2), U118 + vehicle (n=3), U118 + V-4084 (n=3), U87M2 + vehicle (n=3), U87M2 + V-4084 (n=3), DBM2 + vehicle (n=3), DBM2 + V-4084 (n=3), U251M2 + vehicle (n=3), U251M2 + V-4084 (n=3)). GBM cell lines (DBM2, U251M2, U87M2, U118, and SF295) were subcutaneously inoculated into the flank region of nude mice to initiate tumor growth. Subsequently mice were treated for 7 days with either vehicle (n=14) or V-4084 (n=14) (i.e. SF295 + vehicle (n=2), SF295 + V-4084 (n=3), U118 + vehicle (n=3), U118 + V-4084 (n=3), U87M2 + vehicle (n=3), U87M2 + V-4084 (n=3), DBM2 + vehicle (n=3), DBM2 + V-4084 (n=3), U251M2 + vehicle (n=3), U251M2 + V-4084 (n=2)).


title: Profiling placental and fetal DNA methylation in human neural tube defects

city: Vancouver

first: Wendy

last: Robinson

state: BC

address: 950 W 28th Ave

department: Medical Genetics

institute: University of British Columbia

summary: The incidence of neural tube defects (NTDs) declined by about 40% in Canada with the introduction of national folic acid (FA) fortification programs. However, NTDs persist despite the fact that few Canadians currently exhibit folate deficiency. FA fortification may have aided in reducing NTDs by overcoming abnormal one carbon metabolism cycling, the process which provides one carbon units for methylation of DNA. We considered that NTDs persisting in a folate replete population may also occur in the context of compromised one carbon metabolism, and that this might manifest as abnormal DNA methylation (DNAm). Second trimester human placental chorionic villi, kidney, spinal cord, brain and muscle were collected from 19 control, 22 spina bifida and 15 anencephaly fetuses in British Columbia, Canada. DNA was extracted, assessed for methylenetetrahydrofolate reductase (MTHFR) genotype and for genome-wide DNAm using repetitive elements, in addition to the Illumina Infinium HumanMethylation450 (450k) array. No difference in repetitive element DNAm was noted. Using a false discovery rate <0.05 and average group difference in DNAm >0.05, differentially methylated array sites were only identified in (i) the comparison of anencephaly to controls in chorionic villi (n=4 sites) and (ii) the comparison of spina bifida to controls in kidney (n=3,342 sites). We suggest that the distinctive DNAm of spina bifida kidneys may be consequent to the neural tube defect. Although other studies have provided data to support altered DNAm in NTDs, this was not a major feature of British Columbian cases on a genome-wide or site specific level.

overall_design: Tissue was collected from 2nd trimester (14-26 wks) human fetuses with spina bifida (SB, n=22) or anencephaly (AN, n=15) in addition to controls (CON, n=19), to explore DNAm using the Illumina Infinium HumanMethylation450 BeadChip (450k) platform. Whenever possible, a sample of chorionic villi, kidney, spinal cord, brain and muscle was obtained from each individual. DNAm was compared within a tissue, and spina bifida and anencephaly cases  were compared as separate NTD status groups to controls, as it has not been determined if they have a common or distinct etiology.

first: E

last: Price

last: Peñaherrera

first: Elodie

last: Portales-Casamar

first: Paul

last: Pavlidis

first: Margot

middle: I

last: Van Allen

first: Deborah

last: McFadden


title: Expression data from mouse differentiated Bhlhe40-GFPneg and Bhlhe40-GFPpos TH17 cells

status: Public on Jan 04 2016

city: St. Louis

first: Chih-Chung

last: Lin

state: MO

address: 660 S. Euclid Ave. Box 8118

department: Pathology and Immunology

institute: Washington University School of Medicine

summary:
Microarray data on TH17 cells from Bhlhe40-GFP reporter mice
We used microarrays to detail the global programme of gene expression in polarized Bhlhe40-GFPneg and Bhlhe40-GFPpos TH17 cells

overall_design: Purified naïve CD4 T cells from spleen were polarized under TH17 condition in vitro.  On day 4, cells were stimulated with PMA and ionomycin, and sorted by their Bhlhe40-GFP expression prior to microarray analysis

first: Brian

last: Edelson


title: Genome-scale profiling of the DNA methylation landscape in human neurological disorders (BeadChip)

summary: Genome-scale DNA methylation profiling using the Infinium DNA methylation BeadChip platform and samples from 4 human neurological disorders.

overall_design: DNA methylation analysis of brain samples from patient suffering from Down’s syndrome, Dementia of Lewy bodies or Alzheimer's and Parkinson's disease using the Infinium DNA methylation BeadChip platform .


title: Expression data from glioma patients

city: Kyoto

first: Ryuya

last: Yamanaka

address: 465 Kajii-cho, Kamigyoku

institute: Kyoto Prefectural University of Medicine

summary:
We used microarrays to select the genes associated glioma patients survival.
This study aimed to define genes associated with survival.  Expression profiling was performed on 50 gliomas. A gene classifier was developed.

overall_design: Fifty glioma patients were selected  for RNA extraction and hybridization on Affymetrix microarrays.

first: Atsushi

last: Kawaguchi


title: DNA methylation analyses in infants reveal signals correlated with fetal alcohol syndrome, maternal smoking, gender, and ethnicity

status: Public on Jan 29 2016

city: Bethesda

first: David

last: McGaughey

state: MD

address: 50 South Drive Rm 5317

department: NHGRI

institute: NIH

summary:
Alcohol exposure is known to impact several components of the one-carbon metabolism pathway, which is vital for providing methyl groups for DNA and peptide synthesis and for methylation modification of nucleotides and proteins.  Methylation patterning in DNA is known to be altered across generations in specific situations in humans, including nutrient deprivation and smoking during pregnancy. We were interested in seeing whether heavy alcohol exposure during pregnancy, which is associated with fetal alcohol syndrome, influences genome-wide infant methylation patterning.
From Guthrie card spots across over 100 infants of various genders, ethnicities, and maternal smoking and drinking status, we find two loci that are have significantly different methylation patterning associated with maternal drinking; cgXXX and cgYYY, the former near MCOLN3 and the latter in intergenic space. We also use available epidemiological information associated with our data set to replicate maternal smoking with infant methylation changes as well as replicate and expand upon methylation differences between genders and ethnicities.

overall_design: Case Control design with 72 cases and 73 controls. Our study sample of Guthrie card DNA from NY state infants contains 150 unique samples. Four samples were removed due to poor performance in the PCA analysis and another was removed because there is a set of identical twins in the study. As we were interested in studying the role ethnicity plays in methylation differences, we removed eight of the Hispanic and other ethnicity samples, leaving a total of 137 samples. The populations of the FAS cases and controls are matched for gender and ethnicity


title: Whole-genome saliva and blood DNA methylation patterns in individuals with a respiratory allergy

city: Mol

first: Sabine

last: Langie

state: Please Select…

address: Boeretang 200

country: Belgium

institute: Flemish Institute of Technological Research (VITO)

summary: It has been suggested that the etiology of respiratory allergies (RA) can be partly explained by DNA methylation changes caused by adverse environmental and lifestyle factors experienced early in life. Longitudinal, prospective studies can aid in the unravelment of the epigenetic mechanisms involved in the disease development. High compliance rates can be expected in these studies when data is collected using non-invasive and convenient procedures. Saliva is an attractive biofluid to analyze changes in DNA methylation patterns. We investigated in a pilot study the differential methylation in saliva of RA (n=5) compared to healthy controls (n=5) using the Illumina Methylation 450K BeadChip platform. We evaluated the results against the results obtained in mononuclear blood cells from the same individuals. Differences in methylation patterns from saliva and mononuclear blood cells were clearly distinguishable (PAdj<0.001 and |Δβ|>0.2), though the methylation status of about 96% of the cg-sites was comparable between peripheral blood mononuclear cells and saliva. When comparing RA cases with healthy controls, the number of differentially methylated sites (DMS) in saliva and blood were 485 and 437, respectively, of which 216 were in common. The methylation levels of these sites were significantly correlated between blood and saliva. Pyrosequencing analysis of 3 selected DMS in the PM20D1, STK32C, and FGFR2 genes, confirmed the absolute levels of methylation as well as the differences between cases and controls as observed from the array data. Our findings show that saliva can be used for genome-wide methylation analysis and that it is possible to identify DMS to distinguish RA cases from healthy controls. The results were replicated in blood cells of the same individuals and confirmed by selected pyrosequencing analysis. This study provides a proof-of-concept that the analysis of DNA methylation profiles in saliva may offer distinct opportunities for molecular epidemiology studies of RA.

overall_design: Bisulphite converted DNA from the 10 samples were hybridised to the Illumina Infinium 450k Human Methylation Beadchip

first: Katarzyna

last: Szarc vel Szic

first: Sophie

last: Traen

first: Ken

last: Declerck

first: Gudrun

last: Koppen

first: Guy

last: Van Camp

first: Greet

last: Schoeters

first: Wim

last: Vanden Berghe

first: Patrick

last: De Boever


title: Genome-wide analyses in neuronal cells reveal that USF transcription factors regulate lysosomal gene expression

first: Tomoyuki

type: Genome binding/occupancy profiling by genome tiling array

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

overall_design: Refer to individual Series