title: Upstream regulators of human T cell-associated diseases (dataset 1)

status: Public on Dec 12 2015

city: Xuzhou

first: Hui

last: Wang

state: Jiangsu

address: 209 Tongshan Rd

institute: Xuzhou Medical University

summary: Medical research focuses on disease-specific genes. By contrast, here we systematically examined the roles of shared genes for disease susceptibility and as therapeutic and diagnostic targets. Meta-analysis of all published disease-related genome-wide association studies (GWAS) showed that T helper (Th) cell differentiation was the most shared pathway. Expression profiling data from highly diverse CD4+ T cell-associated diseases revealed shared disease-associated genes, which were enriched for Th cell differentiation, but also metabolic and proliferative pathways. This pleiotropy suggested that altered functions of shared genes could generally increase disease susceptibility. Indeed, compared to specific genes, the shared genes were enriched for disease-associated SNPs identified by all published disease-related GWAS. To examine if the shared genes induced disease-relevant pathways, we focused on transcription factors (TFs) that induced Th differentiation. Those TFs were enriched among the shared genes, as well as for disease-associated SNPs identified by GWAS, and disease-phenotypes in mice knock-out studies. Original GWAS and profiling data from patients with multiple sclerosis and allergy confirmed enrichment of disease-associated SNPs in the TFs, and that the TFs were differentially expressed at early disease stages, and their targets increased in parallel with disease development. From a clinical perspective, the shared genes were significantly enriched for known diagnostic and therapeutic targets. Prospective clinical studies of multiple sclerosis and allergy showed that shared or specific genes could be used to stratify patients for individualized medicine. Our findings show that shared disease genes generally increase disease susceptibility and are important therapeutic and diagnostic targets.

overall_design: Naïve CD4+ T cells were isolated from buffy coat from four healthy subjects using the naïve CD4+ T cell isolation kit (Miltenyi, Bergisch-Gladbach, Germany). Naïve CD4+ T cells were stimulated with plate-bound anti-CD3 (500 ng/mL), soluble anti-CD28 (500 ng/mL), in the presence of IL-12 (5 ng/ml), IL-2 (10 ng/mL) and anti-IL-4 (5 ug/mL) for Th1 cells, IL-4 (10 ng/ml), IL-2 (10 ng/mL) and anti-IL-12 (5 ug/mL) and anti-IFN-g (5 ug/mL) for Th2 cells. Gene expression microarray analysis was performed using SurePrint G3 Human Gene Expression 8x60K microarrays according to the manufacturer's instructions (Agilent Technologies, Palo Alto, Calif).

first: Mika

last: Gustafsson

first: Måns

last: Edström

first: Fredrik

last: Barrenäs

first: Sören

last: Bruhn

first: Ingrid

last: Kockum

first: Tomas

last: Olsson

first: Colm

last: Nestor

last: Ernerudh

first: Mikael

last: Benson


title: Identification of mir-342-3p functionally associated with transcriptional activity of MYC in lung cancer

status: Public on Jan 06 2016

city: Nagoya

first: Takashi

last: Takahashi

state: Aichi

address: 1-1 Kanokoden, Chikusa-ku

country: Japan

institute: Aichi Cancer Center

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

overall_design: Refer to individual Series


title: C646, a Novel p300/CREB-Binding Protein-Specific Inhibitor of Histone Acetyltransferase, Attenuates Influenza A Virus Infection

status: Public on Jan 07 2016

city: Minato

first: Yoshihiro

last: Kawaoka

state: Tokyo

address: Shirokanedai 4-6-1

department: ERATO Influenza-induced Host Responses Project

institute: Japanese Science and Technology Agency

summary: Whole-genome data was developed from influenza virus infected A549 cells to better characterize the effect of C646 on influenza virus infection

overall_design: A549 cells were treated with C646 or DMSO for 10 h, and then were infected with A/WSN/33 virus (WSN; H1N1) at a multiplicity of infection (MOI) 2. A549 cells for microarray studies were collected at different times. The gene expression in A549 cells was compared between C646-treated group and DMSO-treated group.

first: Dongming

last: Zhao

first: Satoshi

last: Fukuyama

first: Jason

middle: E

last: Shoemaker


title: Upstream regulators of human T cell-associated diseases

country: China


title: Muscle expression of SOD1G93A modulates microRNA and mRNA expression pattern associated with the myelination process in the spinal cord of transgenic mice [RT-PCR]

status: Public on Dec 31 2015

city: Roma

first: Camilla

last: Bernardini

address: L.go F.Vito 1

country: Italy

institute: Università Cattolica del Sacro Cuore

summary: Expression profile of microRNA in lumbar spinal cord from MLC/SOD1G93A using Applied Biosystem Array Mouse MicroRNA A Card

overall_design: Lumbar Spinal Cord Ventral samples were collected from mice MLC/SOD1[G93A] and control FVB age matched at 4 month-old. Samples were collected  for RNA extraction and analyzed on Taqman Array Mouse MicroRNA Card A version 3.0

first: Gabriella

last: Dobrowolny

first: Martina

last: Martini

first: Mirko

last: Baranzini

first: Marta

last: Barba

first: Antonio

last: Musarò


title: Identification of mir-342-3p functionally associated with transcriptional activity of MYC in lung cancer [cell culture]

summary:
Accumulating evidence indicates that altered miRNA expression is crucially involved in lung cancer development, but only little has been elucidated about how MYC, an archetypical oncogene, is regulated by miRNAs, especially through a mechanism involving the MYC cofactor(s). In this study, we aimed at identifying miRNAs involved in the regulation of MYC transcriptional activity in lung cancers. To this end, we have taken an integrative approach with combinatorial usage of miRNA and mRNA expression profile datasets of patients’ tumor tissues as well as those of MYC-inducible cell lines in vitro. We report here that in addition to miRNAs previously reported to be directly regulating or regulated by MYC including let-7 and miR-17-92, our strategy allowed us to identify miR-342-3p as the one capable of indirectly regulating MYC activity through direct repression of a MYC-cooperating molecule, E2F1. Furthermore, the miR-342-3p module activity, which we defined as a gene set reflecting experimentally substantiated influence of miR-342-3p on mRNA expression, was found to be inversely correlated with MYC activity reflected in the MYC module activity in three independent datasets of lung adenocarcinoma patients obtained by the Director’s Challenge Consortium of the United States (P=1.94x10-73), the National Cancer Center of Japan (P=9.05x10-34) and our own in this study (P=3.37x10-6). Our integrative approach thus appears to be useful to elucidate inter-regulatory relationships between miRNAs and a protein coding-gene of interest, even those present in tumor tissues in patients, which still remains a challenge to better understand the pathogenesis of this devastating disease.
Microarray analysis using a SurePrint G3 Human GE 8 x 60K Microarray G4851A (Agilent) was conducted.

overall_design: Tai, MeiChee

first: Taisuke

last: Kajino

first: Masahiro

last: Nakatochi

first: Yukako

last: Shimada

first: Chinatsu

last: Arima

first: Shohei

last: Ito

first: Hiroyuki

last: Miyoshi

first: Tomoya

last: Yamaguchi

first: Kiyoshi

last: Yanagisawa

first: Motochi

last: Suzuki


title: Cell cycle and P53 gate the direct conversion of human fibroblasts to dopaminergic neurons

status: Public on Dec 02 2015

city: Buffalo

first: Jian

last: Feng

state: NY

address: 955 Main Street, Room 3102

department: Department of Physiology and Biophysics

country: USA

institute: State University of New York at Buffalo

type: Genome variation profiling by genome tiling array

summary: Suppression of P53 in conjunction with cell cycle arrest at G1 and appropriate extracellular environment markedly increases the efficiency in the transdifferentiation of human fibroblasts to iDA neurons bt Ascl1, Nurr1, Lmx1a and miR-124.

overall_design: MRC-5 cells were used as control, iN cells generated from MRC-5 were analyzed.

first: Houbo

last: Jiang

first: Zhimin

last: Xu

first: Ping

last: Zhong

first: Yong

last: Ren

first: Gaoyang

last: Liang

first: Haley

middle: A

last: Schilling

first: Zihua

last: Hu

first: Yi

last: Zhang

first: Xiaomin

last: Wang

first: Shengdi

last: Chen

first: Zhen

last: Yan


title: Reconstruction of microRNA/genes transcriptional regulatory networks of multiple myeloma through in silico integrative genomics analysis

status: Public on Dec 15 2015

city: MILAN

first: Luca

last: Agnelli

address: Venezian 1

department: Department of Advanced Diagnostics

institute: IRCCS Istituto Nazionale dei Tumori

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

platform_organism:
Homo sapiens
synthetic construct


title: Gene expression analysis of Stabilin-1 positive human monocytes

status: Public on Nov 30 2015

city: Turku

first: Kati

last: Elima

address: Tykistökatu 6

department: MediCity

country: Finland

institute: University of Turku

summary: Stabilin-1/CLEVER-1 is a multidomain protein present in lymphatic and vascular endothelial cells and in M2 immunosuppressive macrophages. Stabilin-1 functions in scavenging, endocytosis and leukocyte adhesion to and transmigration through the endothelial cells. We analyzed the putative functions of Stabilin-1 in blood monocytes. We found that in healthy individuals 60-80% of both CD14+CD16- and CD14+C16+ monocytes, but not CD14dimCD16+ monocytes, expressed Stabilin-1 on the surface. Microarray analysis was performed to study these monocytes subtypes in more detail.

overall_design: Human peripheral blood CD14+ monocytes were sorted with FACS into Stabilin-1high and Stabilin-1low positive cells. Cells were sorted from 4 healthy individuals. Total RNA was extracted and used for microarray analysis.

first: Senthil

last: Palani

first: Eeva

last: Ekholm

first: Sirpa

last: Jalkanen

first: Marko

last: Salmi


title: Reconstruction of microRNA/genes transcriptional regulatory networks of multiple myeloma through in silico integrative genomics analysis [PCL, gene]

status: Public on Dec 08 2015

summary: The identification of deregulated miRNA in multiple myeloma (MM) has progressively added a further level of complexity to MM biology. In the present study, we take virtue of in silico integrative genomics analysis to generate an unprecedented global view of the transcriptional regulatory networks modulated in MM to define microRNAs impacting in regulatory circuits with potential functional and clinical relevance. miRNA and gene expression profiles in two large representative MM datasets, available from retrospective and prospective clinical trials and encompassing a total of 249 patients at diagnosis, were analyzed by means of two robust computational procedure to identify (i) relevant miRNA/transcription factors/target gene circuits in the disease and (ii) highly modulated miRNA-gene networks in those pathways enriched with miRNA-target gene interactions in specific MM subgroups. The analysis reinforced the pivotal role the miRNA cluster miR-99b/let-7e/miR-125a, specifically deregulated in MM patients with t(4;14) translocation, and disentangled its major relationships with transcriptional relevance. Integrated pathway analyses performed on the expression data of the MM patients stratified according to t(4;14) further allowed to define the pathway composed by the interactions that mainly characterize this MM subset and unravel connected pathways with putative role in the tumor biology.

overall_design:
miRNA and transcripts expression data were analyzed using MAGIA2, to identify mixed circuits (triplets) involving miRNA/gene/transcription factor (TF; http://gencomp.bio.unipd.it/magia2/), as previously described [Bisognin A et al., 2012, Nucl Acid Res]. Specifically, Targetscan was used as target prediction algorithm, and Pearson coefficient was used to measure relationships between microRNA and target mRNA expression profiles. Only the most variable 75% genes according to the coefficient of variation were considered. Lower threshold for absolute correlation coefficients within circuits was set to 0.2; 0.4 was used for miRNA/target binary relationships. Micrographite pipeline allows integrating pathway topologies with predicted and validated miRNA-target interactions, to perform integrated analyses of miRNA and gene expression profiles, for the identification of modulated regulatory circuits involved in the disease in terms of both expression variations and differential strength of inferred interactions [Calura E et al., 2014, Nucl Acid Res]. Micrographite has two steps: i) the extension of pathway annotation using miRNA-target interaction and ii) recursive topological pathway analysis on these networks. We considered network topologies derived from KEGG database by Graphite package [Sales G et al., 2012, BMC Bioinformatics] and miRNA-target gene interactions identified by the above-described MAGIA2 analysis. Specifically, a miRNA was added to a pathway-derived network only if one (or more) of its validated or predicted target genes is a pathway component. Then, a modified recursive version of CliPPER topological pathway analysis [Martini P et al., 2013; Nucl Acid Res] was applied to the composite network, as previously described [Calura E et al., 2014, Nucl Acid Res] in order to identify the most important and non-redundant circuit modulated across groups. Briefly, (i) in the first step, the most significant pathways were selected using P<0.1 as cut-off value for significance; (ii) for each dataset, the upper-scored 10th percentile of the portion of these previously selected pathways (i.e. paths, calculated over a 10,000-permutation step) mostly associated with phenotype were selected; and (iii) for each dataset a meta-pathway was assembled using the paths extracted from previous step and finally re-analyzed.

GSE73452 and GSE73454 Samples with the same patient number represent the same sample, profiled using two different Platforms.

first: Enrica

last: Calura

first: Andrea

last: Bisognin

first: Martina

last: Manzoni

first: Katia

last: Todoerti

first: Gabriele

last: Sales

first: Gareth

middle: J

last: Morgan

first: Antonino

last: Neri

first: Chiara

last: Romualdi

first: Stefania

last: Bortoluzzi

first: Elisa

last: Taiana

first: Nicola

last: Amodio

first: Pierfrancesco

last: Tassone

first: Giovanni

last: Tonon


title: Gene expression profiling of primary human hepatocytes after berberine chloride treatment

city: Taipei

first: Ting-fang

last: Lo

address: 128 Academia Road, Section 2, Nankang, Taipei 115, Taiwan

department: Institute of Biological Chemistry

country: Taiwan

institute: Academia Sinica

summary: Berberine, an isoquinoline alkaloid isolated from many medicinal herbs such as Coptis chinensis, has a wide range of pharmacological effects. Since xenobiotic drug-induced micoRNAs have recently emerged as key regulators in guiding their pharmacological effects and toxicity, we were interested in whether or not micoRNA expression was differentially altered by berberine treatment in liver. Here, we used miRNA microarray to analyze microRNA expression profiles of primary human hepatocytes after berberine chloride treatment or 0.08% DMSO as control.

overall_design: Comparing gene expression profiles of 40 M berberine-treated primary human hepatocytes to those of control cells sampled after 2, 4, or 8 hours treatment. A 50 mM stock solution of Berberine chloride was prepared in DMSO. Cells were treated with 40 M berberine chloride or 0.08% DMSO as control.

first: Ting-Fang

first: Shui-Tein

last: Chen


title: miRNA expression profile of mouse Lewis lung carcinoma LLC1 cell line cultivated in 2-dimensional or 3-dimensional cell culture enriched with laminin rich extracellular matrix proteins

status: Public on Dec 10 2015

city: Vilnius

first: Vaidotas

last: Stankevicius

state: Lithuania

address: Santariskiu 1

country: Lithuania

institute: National Cancer Institute

summary: The extracellular matrix (ECM), as one of the key components of tumor microenvironment has a high impact on cancer development and highly influences tumor cell features. ECM contribute not only structural support to growing tumor cells, but also affect other cellular functions such as cell differentiation, migration, survival or proliferation. Moreover, gene and protein expression levels are regulated in cell-ECM interaction dependent manner. MicroRNAs (miRNAs) act as key modulators of gene expression in various basic cellular processes where they can decrease protein synthesis through translational repression or RNA degradation. Despite miRNAs have recently emerged as important players involved in regulation of cell-ECM interactions molecular mechanisms of this phenomenon remains to be elucidated. To address this question we explored miRNA expression patterns in mouse Lewis lung carcinoma LLC1 cells growing in laminin rich ECM microenvironment.

overall_design: Total RNA enriched in small noncoding RNAs was isolated 48h after growing in two different cell culture systems

first: V

first: K

last: Suziedelis


title: Espression data of control and heat-stressed Arabidopsis WT, hd2c-3, brm-1 and brm-1 hd2c-3 plants

status: Public on Dec 04 2015

city: Warsaw

first: Daniel

last: Buszewicz

address: Pawińskiego 5A

department: Institute of Biochemistry and Biophysics

country: Poland

institute: Polish Academy of Sciences

summary:
Studies in yeast and animals have revealed that histone deacetylases (HDACs) often act as components of multiprotein complexes, including chromatin remodeling complexes (CRCs). In our group, we found evidence for the interaction between Arabidopsis HD2C deacetylase and a BRM-containing SWI/SNF chromatin remodeling complex. Moreover, we revealed a novel function of HD2C as a regulator of the heat stress response. HD2C transcript levels were strongly induced in plants subjected to heat treatment and the expression of selected heat-responsive genes was up-regulated in heat-stressed hd2c mutant, suggesting that HD2C acts to down-regulate heat-activated genes.
Microarray transcriptome analysis of brm and hd2c mutants identified a subset of commonly regulated heat-responsive genes, and the effect of the double brm hd2c mutation on the expression of these genes was non-additive. Moreover, heat treated hd2c, brm and brm hd2c mutants displayed similar rates of growth retardation. Taken together, our findings suggest that HD2C and BRM act in a common genetic pathway to regulate the Arabidopsis heat stress response.

overall_design: 3-week-old WT (Col-0), hd2c-3, brm-1 and brm-1 hd3c-3 plants were collected before and after 1 hour of heat (38°C) treatment.  For each variant, three biological replicates with similar expression levels of selected marker genes, were chosen for microarray analysis.

first: Buszewicz

last: Daniel

first: Fogtman

last: Anna

first: Iwanicka-Nowicka

last: Roksana

first: Koblowska

middle: K

last: Marta


title: Early Activation of Th2 Inflammatory and Pruritogenic Pathways in Acute Canine Atopic Dermatitis Skin Lesions

status: Public on Nov 02 2015

city: Collegeville

first: David

last: Mayhew

state: PA

address: 1250 South Collegeville Road

department: Target Sciences, Computation Biology, R&D

institute: GlaxoSmithKline

summary: To characterize the inflammatory events occuring during early experimental acute AD lesions, skin biopsies were collected 6, 24, and 48 h after epicutaneous application of Dermatophagoides farinae house dust mites (HDM) to sensitized atopic dogs.

overall_design: 8 dogs from each experimental group were examined.

first: Deepak

last: Rajpal


title: Reconstruction of microRNA/genes transcriptional regulatory networks of multiple myeloma through in silico integrative genomics analysis [MM, miRNA]

first: Luca

last: Agnelli

overall_design:
miRNA and transcripts expression data were analyzed using MAGIA2, to identify mixed circuits (triplets) involving miRNA/gene/transcription factor (TF; http://gencomp.bio.unipd.it/magia2/), as previously described [Bisognin A et al, 2012, Nucl Acid Res]. Specifically, Targetscan was used as target prediction algorithm, and Pearson coefficient was used to measure relationships between microRNA and target mRNA expression profiles. Only the most variable 75% genes according to the coefficient of variation were considered. Lower threshold for absolute correlation coefficients within circuits was set to 0.2; 0.4 was used for miRNA/target binary relationships. Micrographite pipeline allows integrating pathway topologies with predicted and validated miRNA–target interactions, to perform integrated analyses of miRNA and gene expression profiles, for the identification of modulated regulatory circuits involved in the disease in terms of both expression variations and differential strength of inferred interactions [Calura E et al, 2014, Nucl Acid Res]. Micrographite has two steps: i) the extension of pathway annotation using miRNA-target interaction and ii) recursive topological pathway analysis on these networks. We considered network topologies derived from KEGG database by Graphite package [Sales G et al, 2012, BMC Bioinformatics] and miRNA-target gene interactions identified by the above-described MAGIA2 analysis. Specifically, a miRNA was added to a pathway-derived network only if one (or more) of its validated or predicted target genes is a pathway component. Then, a modified recursive version of CliPPER topological pathway analysis [Martini P et al, 2013; Nucl Acid Res] was applied to the composite network, as previously described [Calura E et al, 2014, Nucl Acid Res] in order to identify the most important and non-redundant circuit modulated across groups. Briefly, (i) in the first step, the most significant pathways were selected using P<0.1 as cut-off value for significance; (ii) for each dataset, the upper-scored 10th percentile of the portion of these previously selected pathways (i.e. “paths”, calculated over a 10,000-permutation step) mostly associated with phenotype were selected; and (iii) for each dataset a meta-pathway was assembled using the paths extracted from previous step and finally re-analyzed

GSE70254 and GSE70319 Samples with the same patient number represent the same sample, profiled using two different Platforms.

first: Enrica

last: Calura

first: Andrea

last: Bisognin

first: Martina

last: Manzoni

first: Katia

last: Todoerti

first: Gabriele

last: Sales

first: Gareth

last: Morgan

first: Antonino

last: Neri

first: Chiara

last: Romualdi

first: Stefania

first: Elisa


title: Identification of a potent and selective chemical probe for exploring the role of Mediator complex-associated protein kinases CDK8 and CDK19 in human disease [LS-174-T]

status: Public on Oct 26 2015

city: Sutton

first: Robert

middle: te

last: Poele

state: Surrey

address: 15 Cotswold Road

department: Cancer Reserach UK Unit for Cancer Therapeutics

country: United Kingdom

institute: The Institute of Cancer Research

summary:
There is an unmet need for chemical tools to explore the role of the Mediator complex in human pathologies ranging from cancer to cardiovascular disease.  Here we determine that CCT251545
a WNT-pathway inhibitor discovered by cell-based screening
is a potent and selective chemical probe for the Mediator complex-associated protein kinases CDK8 and CDK19.  CCT251545 is an ATP competitive inhibitor with >100-fold selectivity over 291 other kinases. X-ray crystallography demonstrates Type 1 binding involving insertion of the CDK8 C-terminus into the ligand binding site.  In contrast to Type II inhibitors of CDK8/19
CCT251545 displays potent cell-based activity.  We show that CCT251545 and close analogues not only alter WNT-pathway regulated gene expression
but also other CDK8/19 targets including STAT1-regulated gene expression.   Consistent with this we find that phospho-STAT1SER727 is a biomarker of CDK8 kinase activity in vitro and in vivo.  Finally
we demonstrate in vivo activity of CCT251545 in WNT-dependent tumours.

overall_design:
LS-174-T colon cancer cells were treated with 715 nM of Compound 6 (IC90 of TCF dependent luciferase) for 0, 4 or 24h. Three samples with three biological repeats each. Sample were hybridized against human reference.
Compound 6 is a close analogue of a 3,4,5-trisubstituted pyridine series identified from a high-throughput cell-based reporter assay of WNT signalling. It was shown to be potent and selective inhibitor of the Mediator complex-associated protein kinases CDK8 and CDK19. Its is ATP competitive inhibitor with >100-fold selectivity over 291 other kinases. X-ray crystallography demonstrates Type 1 binding involving insertion of the CDK8 C-terminus into the ligand-binding site.

first: Trevor

last: Dale

first: Paul

last: Clarke

first: Christina

last: Esdar

first: Dennis

last: Waalboer

first: Olajumoke

last: Adeniji-Popoola

first: Maria-Jesus

last: Ortiz-Ruiz

first: Aurelie

last: Mallinger

first: Rahul

last: Samant

last: Czodrowski

first: Djordje

last: Musil

first: Daniel

last: Schwarz

first: Klaus

last: Schneider

first: E

middle: V

first: A

last: Lammens

first: Mark

last: Stubbs

first: Ken

last: Ewan

first: Elizabeth

last: Fraser

middle: H

last: te Poele

first: Will

last: Court

first: Gary

last: Box

first: Melanie

last: Valenti

first: Alexis

last: de Haven Brandon

first: Sharon

last: Gowan

first: Felix

last: Rohdich

first: Florence

last: Raynaud

first: Richard

first: Oliver

last: Poeschke

first: Andree

last: Blaukat

last: Workman

first: Kai

last: Schiemann

first: Suzanne

last: Eccles

first: Dirk

last: Wienke

first: Julian

last: Blagg


title: Chlorella ingestion and suppression of resistin gene expression in borderline diabetics: a randomized, placebo-controlled study

status: Public on Oct 17 2015

city: Tsurumi-ku,

first: Michie

last: Kobayashi

state: Yokohama

address: 1-1-43, Suehirocho,

institute: DNA Chip Research Inc.

summary: Diabetes and Arteriosclerosis progression are frequently observed in borderline Type 2 diabetes cases. Onset of complications (arteriosclerosis and renal damage) due to Type 2 diabetes is well documented; it is extremely important to prevent or delay their progression. Type 2 diabetes onset and progression has been controlled through dietary habits and exercise, although these remain insufficient. Chlorella ingestion improves blood glucose and cholesterol concentrations in mice and humans, although no reports have evaluated Chlorella effects in borderline diabetics. Therefore, we conducted a randomized, placebo-controlled trial for borderline diabetics using laboratory results and comprehensive gene analysis as outcomes. Chlorella ingestion suppressed resistin gene expression, suggesting that Chlorella may be useful for preventing diabetes onset and ameliorating arteriosclerosis.

overall_design: Subjects were randomly divided into two groups: Chlorella group (n = 28) ingesting Chlorella powder (8.0 g/day) and placebo group (n = 29) ingesting lactose formulation (8.0 g/day) for 12 weeks. Blood and urine were collected every 4 weeks for laboratory tests. Gene expression analysis used RNA extracted from peripheral blood samples before and after 12 weeks of Chlorella or lactose ingestion.

first: Hiroshige

last: Itakura

first: Seiji

last: Nakamura


title: Valvular intersitial cell transcriptional response to culture platform

status: Public on Sep 30 2015

city: Boulder

first: Kristi

middle: S

last: Anseth

state: CO

address: 3415 Colorado Ave

institute: University of Colorado - Boulder

summary: Expression data from valvular interstitial cells cultured in 2D or 3D PEG hydrogel systems compared to culture on tissue culture polystyrene and freshly isolated cells

overall_design: 4 different conditions were analyzed, with 3 biological replicates each.

first: Kelly

middle: M

last: Mabry

first: Samuel

middle: Z

last: Payne

first: Wenhua

last: Ren

last: S Anseth


title: Genetically engineering self-organization of human pluripotent stem cells into a liver bud-like tissue using Gata6

status: Public on Nov 05 2015

city: Cambridge

first: Ron

last: Weiss

state: MA

address: 500 Technology sq. NE47-257

institute: MIT

summary: Human induced pluripotent stem cells (hiPSCs) have potential for personalized and regenerative medicine. While most methods of utilizing these cells have focused on deriving homogenous populations of specialized cells, there has been modest success in producing hiPSC-derived organotypic tissues or organoids. Here we present a novel approach for generating and then co-differentiating hiPSC-derived progenitors. With a genetically engineered pulse of GATA6 expression, we initiate rapid emergence of all three germ layers as a complex function of GATA6 expression levels and tissue context. Within two weeks we obtain a complex tissue that recapitulates early developmental processes and exhibits a liver bud-like phenotype, including haematopoietic and stromal cells, as well as a neuronal niche. Our approach addresses two major issues in derivation of tissues from hiPSCs: using a single autologous hiPSCs as source and generating a range of stromal cells that co-develop with parenchymal cells to form complex tissues.

overall_design: Gene expression profiling (microarray) of iPS cells (PGP1) at X days post- doxycycline induction of mouse Gata6. Either total cells or immunomagnetic isolation of cells with specific surface markers. Three samples per group.

first: Patrick

last: Guye

first: Mohammad

middle: R

last: Ebrahimkhani


title: Patterns of somatic uniparental disomy identify novel tumor suppressor genes in colorectal cancer

status: Public on Sep 02 2015

city: Barcelona

first: Jordi

last: Camps

state: Catalonia

address: c/Rosselló 149-153 4th floor, Center Esther Koplowitz

department: Gastroenterology

country: Spain

institute: IDIBAPS / Hospital Clinic

summary:
The aim of this study is to establish an integrative profiling of recurrent UPDs/UPPs, CNAs and genome-wide methylation status in sporadic CRC. Our results indicate that regions showing high frequencies of UPDs/UPPs mostly coincide with regions typically involved in genomic losses such as chromosome arms 1p, 5q, 8p, 14q, 17p, 18q, 20p, and 22q. Of these, chromosome arms 5q, 14q, 17p, and 20p preferentially showed UPDs/UPPs over genomic losses suggesting that tumor cells must maintain the disomic state of certain genes to favor cellular fitness. A meta-analysis using over 300 samples from The Cancer Genome Atlas confirmed our findings. In addition, the genes CSPG2, FLT4, SFRP1, DLK1, and GAS7 were frequently involved in regions of UPDs/UPPs and showed high levels of methylation revealing that UPDs/UPPs can result in the duplication of hypermethylated inactive genes.
This dataset includes the array CGH of 30 colorectal cancers.

overall_design: A total of 30 primary tumors from the colon and rectum were collected from the Hospital Clinic of Barcelona under the supervision of an experienced pathologist. DNA was extracted and labeled according to manufacturer's protocols. Matched patient DNA from normal mucosa  was used as a reference for these experiments.

first: Keyvan

last: Torabi

first: Rosa

last: Miró

first: Nora

last: Fernández-Jiménez

first: Isabel

last: Quintanilla

first: Laia

last: Ramos

first: Esther

last: Prat

first: Javier

last: del Rey

first: Núria

last: Pujol

first: Jonathan

last: Killian

first: Paul

last: Meltzer

first: Pedro

middle: L

last: Fernández

first: Thomas

last: Ried

first: Juan

last: Lozano

first: Immaculada

last: Ponsa


title: Nilotinib (Tasigna) in the Treatment of Early Diffuse Systemic Sclerosis: An Open-Label, Pilot Clinical Trial

status: Public on Aug 27 2015

city: Lebanon

first: Tammara

last: Wood

state: NH

address: WTRB 674

department: Biomedical Data Science

institute: Dartmouth Medical School

summary: To assess the safety, efficacy, and molecular change associated with treatment of patients with early, diffuse cutaneous systemic sclerosis (dcSSc) with nilotinib (Tasigna™).

overall_design: In this open-label pilot trial 6 adult patients with early dcSSc received nilotinib. Primary endpoints were safety and change in modified Rodnan Skin Score (MRSS) after 6 months. Lesional skin biopsies at baseline, 6 and 12 months of treatment were assessed by histopathology, immunohistochemistry, and DNA microarray.

first: Jessica

last: Gordon

first: Viktor

last: Martyanov

first: Cynthia

last: Magro

first: Horatio

last: Wildman

first: WeiTi

last: Huang

first: Mary

last: Crow

first: Michael

last: Whitfield

first: Robert

middle: F

last: Spiera


first: Jordi

last: Camps

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

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

overall_design: Refer to individual Series


title: Comparison of the Transcriptional Profiles of Melanocytes from Dark and Light Skinned Individuals under Basal Conditions and Following Ultraviolet-B Irradiation

status: Public on Aug 08 2015

city: London

first: Saioa

last: Lopez

address: Gower Street

institute: UCL

summary: We analysed the whole-genome transcriptional profile of 6 cell lines of dark melanocytes (DM) and 6 of light melanocytes (LM) at basal conditions and after UVB at different time points (6, 12 and 24h) to investigate the mechanisms by which melanocytes protect human skin from the damaging effects of ultraviolet-B radiation (UVB). Further, we assessed the effect of different keratinocyte-conditioned media (KCM+ and KCM-) on melanocytes.

overall_design: We analysed six lines of melanocytes isolated from lightly pigmented neonatal foreskin (LM), and six lines from darkly pigmented neonatal foreskin (DM), at 0, 6, 12 and 24 hours post UV irradiation. We also assessed the effect of different keratinocyte-conditioned media (KCM+ or KCM-)

first: Santos

last: Alonso

first: Isabel

last: Smith-Zubiaga


title: HT1080 WT or STAT deficient exposed to IFN beta or human trophoblast medium

status: Public on Aug 26 2015

city: PITTSBURGH

first: Yoel

last: Sadovsky

state: Pennsylvania

address: 204 Craft Ave

department: Obstetrics and Gynecology

institute: MAGEE WOMENS RESEARCH INSTITUTE

summary:
Previous microarray data indicated a significant increase in interferon (IFN) stimulated gene expression in cells exposed to conditioned medium from primary human trophoblasts compared to non conditioned medium. Here we want to compare the effects of conditioned media, non conditioned media, and non conditioned media spiked with 100 units of IFN beta in wild type HT1080 cells as well as in HT1080 cells deficient in STAT1 (a key signaling molecular in the IFN pathway).
Interferon stimulated genes (ISGs) target viruses at various stages of their infectious life cycles, including at the earliest stage of viral entry. Here we identify ArfGAP with dual pleckstrin homology (PH) domains 2 (ADAP2) as a gene upregulated by type I IFN treatment in a STAT1-dependent manner. ADAP2 functions as a GTPase-activating protein (GAP) for Arf6 and binds to phosphatidylinositol 3,4,5-trisphosphate (PI(3,4,5)P3) and PI(3,4)P2. We show that overexpression of ADAP2 suppresses dengue virus (DENV) and vesicular stomatitis virus (VSV) infection in an Arf6 GAP activity-dependent manner, while exerting no effect on coxsackievirus B (CVB) or Sendai virus (SeV) replication. We further show that ADAP2 expression induces macropinocytosis and that ADAP2 strongly associates with actin-enriched membrane ruffles and with Rab8a- and LAMP1-, but not EEA1- or Rab7-, positive vesicles. Utilizing two techniques—light-sensitive neutral red (NR)-containing DENV and fluorescence assays for virus internalization—we show that ADAP2 primarily restricts DENV infection at the stage of virion entry and/or intracellular trafficking and that incoming DENV and VSV particles associate with ADAP2 during their entry. Taken together, this study identifies ADAP2 as an ISG that exerts antiviral effects against RNA viruses by altering Arf6-mediated trafficking to disrupt viral entry.

overall_design: compare the cells exposed to CM and the cells exposed to NC media spiked with IFN to the control NC exposed cells, in wild type (2f-TGH) vs Stat -/- cells (HT1080U3A)

first: Yoe

last: l Sadovsky

first: Carolyn

last: Coyne


title: Genomic and functional characterization of human T cell responses to co-stimulation with an agonistic anti-CD27 mAb, 1F5 (Varlilumab)

status: Public on Jul 17 2015

city: Hampton

first: Venky

last: Ramakrishna

state: NJ

address: Perryville III Bldg., 53 Frontage Rd.

institute: Celldex Therapeutics

summary:
CD27, a member of the tumor necrosis factor receptor super family (TNFRSF7), is constitutively expressed on the majority of mature T cells, memory B cells, and a portion of NK cells. Here we report on the 1F5-induced immune modulation of isolated human T cells. In vitro activation of peripheral blood-derived T cells from different healthy volunteers with mAb 1F5 showed that crosslinking of CD27 in the presence of CD3 stimulation (OKT3 mAb) was essential to elicit proliferation and broad spectrum of cytokine release.
Analysis of this response on a multiplex cytokine array system revealed a Th1-biased cytokine profile (IFN-gamma, IL-2 and TNF-alpha). Transcriptional profiling by microarray RNA hybridization is underway to map specific and global gene expression changes following 1F5 modulation of T cells.

overall_design: T cells were enriched using magnetic beads and stimulated with plate bound anti-CD3 mAb and anti-CD27 mAb, 1F5 (or control mAb) for 72 hours (late) or 4 hours (early) and characterized for functional responses that included cytokine release (ELISA), proliferation (CFSE dilution) and immunophenotyping (flow cytometry). Microarray analysis of treated T cells was used to further explore the universe of genes affected by costimulatory signals provided by mAb 1F5.

first: Tibor

last: Keler


title: Gene expression after Verticillium longisporum infection in a susceptible and a resistant A. thaliana near isogenic line

status: Public on Jun 30 2015

city: Berlin

first: Eva

last: Häffner

address: Albrecht-Thaer-Weg 6

department: Institut für Biologie

country: Germany

institute: Freie Universität Berlin

summary: Resistance against Verticillium longisporum is quantitative and multigenic. The vec1 QTL in Arabidopsis thaliana controlled resistance against systemic colonization by the fungus. Gene expression was studied to identify genes and pathways controlled by vec1. Near-isogenic lines derived from the resistant ecotype Bur and the susceptible ecotype Ler were compared. NIL9 contained Ler-alleles in the genomic region between 11753 and 12285 kb within vec1 on chromosome 2, tmNIL130 contained Bur-alleles. Microarrays were performed on samples containing the hypocotyl and the shoot basis because colonization is stopped in this region in resistant genotypes. Two developmental stages were studied: time-point (1) at the onset of flowering, when systemic colonization was shown to start and time point (2) at the onset of silique maturity, when extensive fungal proliferation was shown to occur. Two pathogen treatments were studied: (1) mock-inoculated controls, (2) plants inoculated with the V. longipsorum isolate 43 (VL).

overall_design: Gene expression was studied in two genotypes (NIL9-susceptible; tmNIL130-resistant), under two pathogen treatments (mock-inoculated; VL-inoculated) at two time points (at the onset of flowering, 13 days post inoculation [dpi]; at the onset of silique maturity, 27-29 dpi). Three biological replicates were used for each treatment (24 microarrays altogether).

first: Elke

last: Diederichsen


title: Gene expression profile of ATF6a and ATF6b overexpression in LS174T cells

status: Public on Aug 05 2015

city: Tokushima

first: Seiichi

last: Oyadomari

state: Tokushima

address: 3-18-15 Kuramoto

department: Division of Molecular Biology

institute: Institute for Genome Research

summary: To further development of our mRNA expression approach to ER stress, we have employed whole genome microarray expression profiling as a discovery platform to identify ER stress-responsible genes. LS174T cells were overexpressed with ER stress mediators, ATF6a or ATF6b. Genes responsible for each mediator were extracted and categorized by Gene Ontology.

overall_design: ATF6a and ATF6b were overexpressed in LS174T. Subsequently, cells were treated with 2 mM sodium butyrate, which induces LS174T cells to differentiate to mature goblet cells. Genes responsible for each mediator were extracted and categorized by Gene Ontology in GeneRanker program of Genomatix platform.

first: Kazuna

last: Takahara

first: Taiji

last: Ito

first: Tomoko

last: Mori

last: Zeng

first: Mari

last: Funahashi

first: Chinobu

last: Miyamoto

first: Seiko

last: Kagawa

first: Masato

last: Miyake

first: Miho

first: Eiji

last: Tanaka

first: Kazutoshi


title: Desmoplastic Melanoma

status: Public on Aug 07 2015

city: San Francisco

first: Alan

middle: Hunter

last: Shain

state: CA

address: 555 MISSION BAY SOUTH BLVD RM 282 # 3118

department: Pathology and Dermatology

institute: University of California San Francisco

summary: High resolution aCGH was performed on 10 primary Desmoplastic Melanomas (DMs). DMs are a rare subtype of melanoma known for their pronounced desmoplastic stroma and spindled melanocytes. 10 samples were hybridized to Agilent 1 Million feature two color arrays as compared to a panel of normal male DNA. 6 samples were hybridized to Agilent 244K feature two color arrays as compared to a panel of normal male DNA. 34 samples were hybridized to Agilent 180K feature two color arrays as compared to a panel of normal male DNA.

overall_design: 50 unique primary tumors were hybridized compared to normal male DNA.

first: A

first: Boris

middle: C

last: Bastian


title: Gene expression in human breast cancer cell lines regulated by CXCR6 gene

city: Shanghai

first: Gang

last: Xiao

address: 227 South Chongqing Road

institute: Shanghai Jiao-Tong University School of Medicine

summary: This study aimed to further our understanding of the role that CXCR6 plays in breast cancer progression. Microarrays were searched for some genes that had correlated expression with CXCR6 mRNA. According to fold-change screening between restoring expression of CXCR6 and its respective control cells in MDA-MB-231 and MCF-7 cells, both up-regulated and down-regulated genes were shown.

overall_design: The restoring of CXCR6 expression in MDA-MB-231 and MCF-7 cells were respectively noted as MDA-MB-231-CXCR6 and MCF-7-CXCR6 cells and the respective controls were noted as MDA-MB-231-GFP and MCF-7-GFP cells.

first: Xiao

last: Gang


title: HEK293T cells treated with a G9a small molecule inhibitor (UNC0638) or vehicle (DMSO), WIZ siRNA, G9a siRNA, or scrambled (control) siRNA

status: Public on Jul 15 2015

city: Chapel Hill

first: Sam

last: Pattenden

state: NC

address: 3015 Marsico Hall  125 Mason Farm Road  CB# 7363

department: Center for Integrative Chemical Biology & Drug Discovery

institute: University of North Carolina at Chapel Hill

summary: Transcriptional profiling of HEK293T cells following treatment with a small molecule inhibitor of catalytic activity of the G9a lysine methyltransferase (UNC0638, 1 micromolar, 48 hours), or siRNA against WIZ or G9a (72 hours treatment).

overall_design: Two condition experiment, UNC0638 vs DMSO, G9a siRNA vs control siRNA, or WIZ siRNA vs control siRNA.  Biological replicates: UNC0638 vs DMSO 5 biological replicates with 2 dye swap experiments; G9a siRNA vs control siRNA, 2 biological replicates; WIZ siRNA vs control siRNA, 2 biological replicates with 2 dye swap experiments.

first: Samantha

middle: G

first: Joel

last: Parker


title: Combined clinical and genomic signatures for the prognosis of early stage non-small cell lung cancer based on gene copy number alterations [Agilent]

status: Public on Aug 20 2015

city: San Sebastian

first: Angel

last: Rubio

state: GUIPÚZCOA

address: Paseo Mikeletegi, Nº 48

department: Bioinformatics

institute: CEIT

summary: Background: The development of a more refined prognostic methodology for early non-small cell lung cancer (NSCLC) is an unmet clinical need. An accurate prognostic tool might help to select patients at early stages for adjuvant therapies.  Results: A new integrated bioinformatics searching strategy, that combines gene copy number alterations and expression, together with clinical parameters was applied to derive two prognostic genomic signatures. The proposed methodology combines data from patients with and without clinical data with a priori information on the ability of a gene to be a prognostic marker. Two initial candidate sets of 513 and 150 genes for lung adenocarcinoma (ADC) and squamous cell carcinoma (SCC), respectively, were generated by identifying genes which have both: a) significant correlation between copy number and gene expression, and b) significant prognostic value at the gene expression level in external databases. From these candidates, two panels of 7 (ADC) and 5 (SCC) genes were further identified via semi-supervised learning. These panels, together with clinical data (stage, age and sex), were used to construct the ADC and SCC hazard scores combining clinical and genomic data. The signatures were validated in two independent datasets (n=73 for ADC, n=97 for SCC), confirming that the prognostic value of both clinical-genomic models is robust, statistically significant (P=0.008 for ADC and P=0.019 for SCC) and outperforms both the clinical models (P=0.060 for ADC and P=0.121 for SCC) and the genomic models applied separately (P=0.350 for ADC and P=0.269 for SCC).  Conclusion: The present work provides a methodology to generate a robust signature using copy number data that can be potentially used to any cancer. Using it, we found new prognostic scores based on DNA s that, jointly with clinical information, are able to predict overall survival (OS) in patients with early-stage ADC and SCC.

overall_design: Copy number analysis of Agilent 244K CGH arrays was performed for 64 early stage Non-Small Cell Lung Cancer (NSCLC) patients

first: Ignacio

last: Wistuba


title: Novel culture conditions facilitating the induction of naïve pluripotency in human embryonic stem cells

status: Public on Jun 08 2015

city: Gent

first: Pieter

last: mestdagh

address: De Pintelaan 185

country: Belgium

institute: Center for Medical Genetics

summary: It is now well recognized that human embryonic stem cells (hESCs)1 closely resemble mouse epiblast stem cells (mEpiSCs)2-5 exhibiting primed pluripotency unlike mouse ESCs (mESCs) which acquire a naïve pluripotent state4-8. Efforts have been made to trigger naïve pluripotency in hESCs9-11 for subsequent unbiased lineage-specific differentiation, a common conundrum faced by primed pluripotent hESCs due to heterogeneity in gene expression existing within and between hESC lines12. We report here a novel culture medium facilitating rapid induction of naïve pluripotency in established hESCs. Our medium also allows derivation of naïve mESCs from blastocyst stage which has not been shown earlier. The established naïve hESCs could survive long-term single cell passaging, maintain a normal karyotype, exhibit upregulation of naïve pluripotency genes and were dependent on signaling pathways similar to naïve mESCs. Also, they undergo global DNA demethylation, cluster together with previously described naïve hESCs13 and show a distinctive long non-coding RNA profile. Collectively, we demonstrate an alternate route to capture naïve pluripotency in hESCs which is fast, reproducible, can be employed to derive naïve mESCs and can induce efficient differentiation.

overall_design: Three primed and matching naive human embryonic stem cell lines were profiled in duplo.

last: Mestdagh

first: Jo

last: Vandesompele

first: Galbha

last: Duggal

first: Bjorn

last: Heindrix

first: Petra

last: De Sutter


title: Gene expression analysis of human bone marrow cells (hMSC-TERT) sorted from MCF7 and BT-20 co-culture

status: Public on Jun 23 2015

city: Riyadh

first: Nehad

last: Alajez

address: 1st floor College of Medicne

department: Anatomy

country: Saudi Arabia

institute: King Saud University College of Medicine

summary: We have employed whole genome microarray  to identify changes in gene expression in human bone marrow MSCs (hMSC-TERT) sorted from seven days co-cultures with breast cancer cell lines (MCF7) and (BT-20)

overall_design: Human MSC line (hMSC-TERT) were co-cultured with breast cancer cell lines MCF7 and BT-20 for seven days then were sorted using EpiCAM MACS beads. Subsequently, RNA was extracted using Norgen total RNA isolation kit. Extracted RNA was labeled and then hybridized to the one-color Agilent Human GE 8x60K Microarray chip.


title: Characterizing the interactions between a naturally-primed IgA (mAb 260.8) and its conserved Bacteroides thetaiotaomicron species-specific epitope in gnotobiotic mice [array]

status: Public on Jun 29 2015

city: St. Louis

first: Joseph

middle: D

last: Planer

state: Missouri

address: 4444 Forest Park Ave

department: Pathology

institute: Washington University School of Medicine

summary: Comparisons of gnotobiotic Rag1-/- mice, with and without subcutaneous 260.8 hybridomas, disclosed that this IgA does not affect B. thetaiotaomicron population density or suppress 260.8 epitope production but does affect bacterial gene expression in ways that are emblematic of a diminished host innate immune response.

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

overall_design: C57BL/6 wildtype, C57BL/6J Rag1-/- , and C57BL/6J Rag1-/- mice harboring the 260.8 IgA producing hybridoma were colonized for 10 days with Bacteroides thetaiotaomicron VPI-5482.

first: Jeffrey

last: Gordon


title: OSCC whole genome expression by T stage

city: Ribeirao Preto

first: Joao Paulo

last: Oliveira-Costa

state: SP

address: Av Bandeirantes, 3900

country: Brazil

institute: University of Sao Paulo

summary: Differentially expressed genes between T4 and T1 stage human oral squamous cell carcinoma (OSCC)

overall_design: 36 OSCC samples separated by tumor size T stage, in dual color microarray, using a pool of human cell lines as control. Screening for differentially expressed genes was performed in a cohort of 36 patients randomly selected. Transcriptional profiles were performed using Agilent one color hybridizations in a G4851A platform.

first: Alfredo

last: Ribeiro-Silva


title: Integration of metabolic activation with a predictive toxicogenomics signature to classify genotoxic versus nongenotoxic chemicals in human TK6 cells [S9]

status: Public on May 14 2015

city: Ottawa

first: Julie

last: Buick

state: Ontario

address: 50 Colombine Driveway

department: Mechanistic Studies Division

country: Canada

institute: Health Canada

summary: The use of integrated approaches in genetic toxicology, including the incorporation of gene expression data to determine the molecular pathways involved in the response, is becoming more common. In a companion paper, a genomic biomarker was developed in human TK6 cells to classify chemicals as genotoxic or non-genotoxic. Because TK6 cells are not metabolically competent, we set out to broaden the utility of the biomarker for use with chemicals requiring metabolic activation. Specifically, chemical exposures were conducted in the presence of rat liver S9. The ability of the biomarker to classify genotoxic (benzo[a]pyrene, BaP; aflatoxin B1, AFB1) and non-genotoxic (dexamethasone, DEX; phenobarbital, PB) agents correctly was evaluated. Cells were exposed to increasing chemical concentrations for 4h and collected 0h, 4h and 20h post-exposure. Relative survival, apoptosis, and micronucleus frequency were measured at 24h. Transcriptome profiles were measured with Agilent microarrays. Statistical modeling and bioinformatics tools were applied to classify each chemical using the genomic biomarker. BaP and AFB1 were correctly classified as genotoxic at the mid- and high concentrations at all three time points, whereas DEX was correctly classified as non-genotoxic at all concentrations and time points. The high concentration of PB was misclassified at 24h, suggesting that cytotoxicity at later time points may cause misclassification. The data suggest that the use of S9 does not impair the ability of the biomarker to classify genotoxicity in TK6 cells. Finally, we demonstrate that the classifier is also able to accurately classify genotoxicity using a publicly available dataset derived from human HepaRG cells.

overall_design: This experiment examined the whole genome transcriptional response of TK6 cells exposed to 0.1 µM aflatoxin B1 (-S9), 10 µg/ml benzo[a]pyrene (-S9), 7.5 mM dexamethasone (-S9) and 24 µg/ml cisplatin (+S9) for 4 hours followed by a 0h, 4h and 20h recovery in fresh media (4h, 8h, and 24h time points, respectively), in addition to negative controls (±S9), vehicle controls (±S9), a direct-acting positive control, cisplatin (-S9) at 24 μg/ml and a positive control requiring metabolic activation, BaP (+S9) at 10 μg/ml. Each concentration and time point had 3 biological replicates, which were pooled for gene expression analysis. There were a total of 14 samples (28 arrays) included in the final analysis using a two-colour dye swap design.

first: Ivy

last: Moffat

first: Andrew

last: Williams

first: Carol

last: Swartz

first: Leslie

last: Recio

first: Daniel

last: Hyduke

first: Heng

last: Li

first: Albert

last: Fornace Jr.

first: Jiri

last: Aubrecht

first: Carole

last: Yauk


title: Synthetic mRNA switches for detection and purification of cardiomyocytes and endothelial cells derived from human pluripotent stem cells [mRNA]

status: Public on May 20 2015

city: Kyoto

first: Yoshinori

last: Yoshida

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

institute: Kyoto University

summary: We designed microRNA-responsive, modified mRNA switches (miR-switches) that quantitatively control their own translation level by determining the miRNA activities. We found that the three miR-switches (i.e., miR-1-, miR-208-, and miR-499-switches) enable to purify cardiomyocytes differentiated from hPSCs with high efficiency, accuracy, and safety. The purified cardiomyocytes were engrafted in mouse heart and did not form tumor. Simultaneous purification of two different cell types, cardiomyocytes and endothelial cells, was also performed by transfecting the mRNA responding to the both miR-208 and miR-126, into heterogeneous cell population derived from hPSCs. In addition, selective induction of apoptosis in noncardiomyocytes triggered by miR-1/208-Bim switch enriched cardiomyocytes without cell sorting. The mRNA switch could purify desired cell types and control cell death pathways by monitoring the miRNA expression dynamics during cell fate conversion.

overall_design:
MYH6-EIP4 iPSCs for mRNA, N=3
MYH6-EIP4 day18 cardiomyocytes (before transfection) for mRNA, N=3
MYH6-EIP4 day19 cardiomyocytes (miR-1-switch day1) for mRNA, N=3
MYH6-EIP4 day19 cardiomyocytes (without transfection) for mRNA, N=3
MYH6-EIP4 day25 cardiomyocytes (miR-1-switch day7) for mRNA, N=3
MYH6-EIP4 day25 cardiomyocytes (without transfection) for mRNA, N=3
201B7 d22 miR-208a-BFP sorted cells for mRNA, N=1
201B7 d22 miR-208a-BFP negative fraction sorted cells for mRNA, N=1
201B7 d22 SIRPA+LIN- sorted cells for mRNA, N=1
201B7 d22 SIRPA+LIN- negative fraction sorted cells for mRNA, N=1
201B7 d22 VCAM1+ sorted cells for mRNA, N=1
201B7 d22 VCAM1+negative fraction sorted cells for mRNA, N=1
MYH6-EIP4 day19 cardiomyocytes (miR-208a-Bim-switch day1) for mRNA, N=1
MYH6-EIP4 day19 cardiomyocytes (without transfection) for mRNA, N=1
MYH6-EIP4 day21 cardiomyocytes (miR-208a-Bim-switch day7) for mRNA, N=1
MYH6-EIP4 day21 cardiomyocytes (without transfection) for mRNA, N=1
MYH6-EIP4 day25 cardiomyocytes (miR-208a-Bim-switch day7) for mRNA, N=1
MYH6-EIP4 day25 cardiomyocytes (without transfection) for mRNA, N=1

first: K

last: Miki

first: M

last: Narita

first: H

last: Saito

first: Y


title: Integration of transcriptome and methylome analyses to dissect molecular pathogenesis of primary aldosteronism: comparision between aldosterone-producing adenomas and adjacent adrenal glands [transcriptome]

status: Public on May 09 2015

city: Setagaya

first: Kazuhiko

last: Nakabayashi

state: Tokyo

department: Department of Maternal-Fetal Biology

institute: National Research Institute for Child Health and Development

summary: Primary aldosteronism (PA) is the most common endocrine hypertension comprising 10% of hypertensive patients. A recent series of transcriptome analyses using DNA microarray has shown that neumerous genes are differentially expressed between aldosterone-producing adenoma (APA) and its adjacent adrenal gland (AAG) tissue from the same patient. However, the molecular mechanism(s) of pathogenesis of APA has not yet been fully clarified. Although growing body of evidence has shown that epigenetic abnormalities including DNA methylation play a key role in tumorigenesis, there are few studies with regard to DNA methylation in APA. In the present study, to elucidate the pathogenic relationship between gene expression and DNA methylation in PA, we conducted an integrated analysis of transcriptome and methylome data for paired APA-AAG samples from the same patient. Adrenal specimens were obtained from 7 Japanese patients with APA, who underwent adrenalectomy at Tokyo Medical and Dental University. RNA and DNA samples were extracted from those 7 paired APA and AAG tissues. Gene expression and genome-wide DNA methylation profiles were obtained using SurePrint G3 Human GE 8x60K Microarray (Agilent) and Infinium HumanMethylation450 Beadchip (Illumina), respectively. Transcriptome anlaysis identified 244 significantly (2 fold<) upregulated genes in APA compared to AAG. The upregulated genes include the previously studied genes such as PCP4, ALDH1A2, and CYP11B2, and other genes that have not been previously studied, such as HOXA9, HOXA11, and HOXB9. Gene ontology (GO) analysis for these upregulated genes identified the calcium signaling pathway to be most significantly enriched with the upregulated genes (8 genes). Methylome analysis revealed that APA was globally hypomethylated compared to AAG regardless of gene feature groups, namely, TSS1500, TSS200, 5’UTR, 1stExon, gene body, and 3’UTR. GO analysis for the genes showing hypomethylation at TSS1500/TSS200 regions in APA identified the term “cytokine-cytokine receptor interaction” to be most significantly enriched with hypomethylated genes (37 genes). Integrated analysis of gene expression and genome-wide DNA methylation profiles identified 18 genes that are upregulated and whose TSS1500/TSS200 regions are hypomethylated in APA compared to AAG. These genes include CYP11B2 and MC2R (ACTH receptor). In conclusion, this is the first genome-wide study for PA that integrated transcriptome and methylome data. Global DNA hypomethylation in APA and concordant transcriptional up-regulation of some key genes, such as CYP11B2 and MC2R, may play crucial roles in the pathophysiological significance in PA.

first: Masanori

last: Murakami

first: Takanobu

last: Yoshimoto

first: Ogawa

last: Yoshihiro


title: Integration of metabolic activation with a predictive toxicogenomics signature to classify genotoxic versus nongenotoxic chemicals in human TK6 cells [BaP 8hr]

status: Public on Apr 15 2015

first: Julie

last: Buick

summary: The use of integrated approaches in genetic toxicology, including the incorporation of gene expression data to determine the molecular pathways involved in the response, is becoming more common. In a companion paper, a genomic biomarker was developed in human TK6 cells to classify chemicals as genotoxic or non-genotoxic. Because TK6 cells are not metabolically competent, we set out to broaden the utility of the biomarker for use with chemicals requiring metabolic activation. Specifically, chemical exposures were conducted in the presence of rat liver S9. The ability of the biomarker to classify genotoxic (benzo[a]pyrene, BaP; aflatoxin B1, AFB1) and non-genotoxic (dexamethasone, DEX; phenobarbital, PB) agents correctly was evaluated.  Cells were exposed to increasing chemical concentrations for 4h and collected 0h, 4h and 20h post-exposure. Relative survival, apoptosis, and micronucleus frequency were measured at 24h. Transcriptome profiles were measured with Agilent microarrays. Statistical modeling and bioinformatics tools were applied to classify each chemical using the genomic biomarker. BaP and AFB1 were correctly classified as genotoxic at the mid- and high concentrations at all three time points, whereas DEX was correctly classified as non-genotoxic at all concentrations and time points. The high concentration of PB was misclassified at 24h, suggesting that cytotoxicity at later time points may cause misclassification. The data suggest that the use of S9 does not impair the ability of the biomarker to classify genotoxicity in TK6 cells. Finally, we demonstrate that the biomarker is also able to accurately classify genotoxicity using a publicly available dataset derived from human HepaRG cells.

overall_design:
This experiment examined the whole genome transcriptional response of TK6 cells exposed to BaP for 4 hours followed by a 4h in fresh media (8h time point) at 3 different concentrations, including a low (0.45 μg/ml), a medium (1.4 μg/ml), and a high (10 μg/ml) concentration, in addition to negative controls (±S9), vehicle controls (±S9) and a direct-acting positive control, cisplatin (-S9) at 24 μg/ml (PC-24).  Each concentration and time point had 3 biological replicates. There were a total 12 samples (24 arrays) included in the final analysis using a two-colour dye swap design.

Please note that each sample data table contains normalized data combined from two replicates and the sample-dye assignment information for each of the raw data files is included in the 'readme.txt' (available as Series supplementary file).

first: Ivy

last: Moffat

first: Andrew

last: Fornace Jr


title: Integration of metabolic activation with a predictive toxicogenomics signature to classify genotoxic versus nongenotoxic chemicals in human TK6 cells [BaP]

overall_design:
This experiment examined the whole genome transcriptional response of TK6 cells exposed to BaP for 4 hours followed by a 0h and 20h recovery in fresh media (4h and 24h time points, respectively) at 3 different concentrations, including a low (0.45 μg/ml), a medium (1.4 μg/ml), and a high (10 μg/ml) concentration, in addition to negative vehicle controls (±S9) and a direct-acting positive control, cisplatin (-S9) at 24 μg/ml (PC-1).  Each concentration and time point had 3 biological replicates. There were a total 23 samples (46 arrays) included in the final analysis using a two-colour dye swap design.

Please note that each sample data table contains normalized data combined from two replicates and the sample-dye assignment information for each of the raw data files is included in the 'readme.txt' (available as Series supplementary file).

first: Carol

last: Swartz

first: Leslie

last: Recio

last: Williams

first: Daniel


title: Gene expression profiling for human iPS-derived motor neurons from sporadic ALS patients reveals a strong association between mitochondrial functions and neurodegeneration

status: Public on Apr 25 2015

city: São Paulo

first: Chrystian

middle: Junqueira

last: Alves

address: Rua Dr Arnaldo 455

department: Neurology

institute: School of Medicine of Sao Paulo University

summary: Differentiated motor neurons from hiPSC derived from peripheral nerve fibroblasts of sporadic ALS patients and evaluated the gene expression profile by means microarray-linked to specific analysis tools.

overall_design: Two-condition experiment, ALS patients motor neurons vs. controls. Biological replicates: 3 ALS replicates, 3 control replicates.

first: Rafael

last: Dariolli

first: Matheus

last: Monteiro

first: Leonardo

last: Jensen

first: Frederico

last: Jorge

first: Jessica

last: Maximino

first: Roberto

last: Martins

first: Bryan

middle: E

last: Strauss

first: José

last: Krieger

first: Dagoberto

last: Callegaro

first: Gerson

last: Chadi


title: Efficient detection and purification of cell populations using synthetic microRNA switches

first: Yoshinori

last: Yoshida

summary: Isolation of specific cell types, including pluripotent stem cell (PSC)-derived populations, is frequently accomplished using cell surface antigens expressed by the cells of interest.  However, specific antigens for many cell types have not been identified, making their isolation difficult.  Here, we describe an efficient method for purifying cells based on endogenous miRNA activity. We designed synthetic mRNAs encoding a fluorescent protein tagged with sequences targeted by miRNAs expressed by the cells of interest. These miRNA switches control their own translation levels by sensing miRNA activities. Several miRNA switches (miR-1-, miR-208a-, and miR-499a-5p-switches) efficiently purified cardiomyocytes differentiated from human PSCs, and switches encoding the apoptosis inducer Bim enriched for cardiomyocytes without cell sorting. This approach is generally applicable, as miR-126-, miR-122-5p- and miR-375-switches purified endothelial cells, hepatocytes and INSULIN-producing cells differentiated from hPSCs, respectively. Thus, miRNA switches can purify cell populations for which other isolation strategies are unavailable.

overall_design:
MYH6-EIP4 day8 differentiated cells (EGFP+) for miRNA, N=1
MYH6-EIP4 day8 differentiated cells (EGFP-) for miRNA, N=1
MYH6-EIP4 day20 differentiated cells (EGFP+) for miRNA, N=1
MYH6-EIP4 day20 differentiated cells (EGFP-) for miRNA, N=1
HUVEC for miRNA, N=2
AoSMC for miRNA, N=2
Hepatocytes for miRNA, N=2
NHDF for miRNA, N=2
MYH6-EIP4 iPSCs for mRNA, N=3
MYH6-EIP4 day18 cardiomyocytes (before transfection) for mRNA, N=3
MYH6-EIP4 day19 cardiomyocytes (miR-1-switch day1) for mRNA, N=3
MYH6-EIP4 day19 cardiomyocytes (without transfection) for mRNA, N=3
MYH6-EIP4 day25 cardiomyocytes (miR-1-switch day7) for mRNA, N=3
MYH6-EIP4 day25 cardiomyocytes (without transfection) for mRNA, N=3
201B7 d22 miR-208a-BFP sorted cells for mRNA, N=1
201B7 d22 miR-208a-BFP negative fraction sorted cells for mRNA, N=1
201B7 d22 SIRPA+LIN- sorted cells for mRNA, N=1
201B7 d22 SIRPA+LIN- negative fraction sorted cells for mRNA, N=1
201B7 d22 VCAM1+ sorted cells for mRNA, N=1
201B7 d22 VCAM1+negative fraction sorted cells for mRNA, N=1
MYH6-EIP4 day19 cardiomyocytes (miR-208a-Bim-switch day1) for mRNA, N=1
MYH6-EIP4 day19 cardiomyocytes (without transfection) for mRNA, N=1
MYH6-EIP4 day21 cardiomyocytes (miR-208a-Bim-switch day7) for mRNA, N=1
MYH6-EIP4 day21 cardiomyocytes (without transfection) for mRNA, N=1
MYH6-EIP4 day25 cardiomyocytes (miR-208a-Bim-switch day7) for mRNA, N=1
MYH6-EIP4 day25 cardiomyocytes (without transfection) for mRNA, N=1


title: A nested case-control study to investigate drivers for metastatic disease in breast cancer (QC substudy)

status: Public on May 28 2016

city: Stockholm

first: John

last: Lövrot

address: Cancer Center Karolinska

department: Oncology-Pathology

country: Sweden

institute: Karolinska Institutet

type:
Expression profiling by array
Third-party reanalysis

summary:
This is a quality control (QC) substudy of GSE48091. The QC substudy comprises gene-expression profiling of re-extracted tumor RNA for a subset of the tumours in the full study. As background, a population-based cohort study of metastatic breast cancer patients was first designed. Thereafter, a case-control study nested in the corresponding population-based cohort of primary breast cancer patients was designed by selecting distant metastasis-free controls to each case. Tumor RNA was extracted in the same order. All RNA was profiled on microarrays in randomized order. For quality control, RNA was also re-extracted (new tumor piece) in a randomized order for randomly selected cases-controls sets and profiled with the rest.

Keywords: Expression profiling by array

overall_design:
The nested case-control study included 768 study subjects corresponding to 623 primary tumor samples. This QC substudy comprises 97 of the study subjects (all different primary tumor samples). Details concerning case-control status are given in the samples section.

This Series includes a re-analysis of 97 samples from GSE48091. The file "full_data_matrix.txt" includes the re-normalized values for the 97 samples from GSE48091 and the normalized values for the 97 new samples from the same patients that were analyzed together.

first: L

last: Lindström

first: J

first: A

last: Jauhiainen

first: K

last: Czene

last: Bergh


title: Integration of metabolic activation with a predictive toxicogenomics signature to classify genotoxic versus nongenotoxic chemicals in human TK6 cells [DEX]

first: Julie

last: Buick

overall_design:
This experiment examined the whole genome transcriptional response of TK6 cells exposed to Dexamethasone for 4 hours followed by a 0h, 4h and 20h recovery in fresh media (4h, 8h, and 24h time points, respectively) at 2 different concentrations, including 0.63 mM and 1mM, in addition to negative controls (±S9), vehicle controls (±S9) and a direct-acting positive control, cisplatin (-S9) at 24 μg/ml (PC-24).  Each concentration and time point had 3 biological replicates. There were a total 22 samples (44 arrays) included in the final analysis using a two-colour dye swap design.

Please note that each sample data table contains normalized data combined from two replicates and the sample-dye assignment information for each of the raw data files is included in the 'readme.txt' (available as Series supplementary file).

first: Ivy

last: Moffat

first: Carol

last: Swartz

first: Leslie

last: Recio

first: Andrew

last: Williams

first: Daniel

last: Hyduke

first: Heng

last: Li

first: Albert

middle: J

last: Fornace Jr

first: Jiri

last: Aubrecht

first: Carole

last: Yauk


title: Integration of metabolic activation with a predictive toxicogenomics signature to classify genotoxic versus nongenotoxic chemicals in human TK6 cells

overall_design: This experiment examined the whole genome transcriptional response of TK6 cells exposed to DMSO (+S9) and 10 μg/ml BaP (-S9) (both compared to DMSO (-S9)) for 4 hours followed by a 20h in fresh media (24h time point),  in addition to 7.5 mM dexamethasone (+S9) (compared to DMSO (+S9)).  Each condition had 3 biological replicates, which were pooled for gene expression analysis. There were a total 3 samples (6 arrays) included in the final analysis using a two-colour dye swap design.

middle: K

first: Heng-Hong

last: Fornace


title: Identification of a novel, recurrent MBTD1-CXorf67 fusion in low-grade endometrial stromal sarcoma (expression)

status: Public on Mar 31 2015

city: Stanford

first: Joanna

last: Przybyl

address: 300 Pasteur Drive

department: Department of Pathology

institute: Stanford University

summary:
Endometrial stromal sarcomas (ESSs) are a genetically heterogeneous group of rare uterine neoplasms that are frequently driven by recurrent gene rearrangements. In conventional low-grade ESSs, JAZF1-SUZ12, PHF1-JAZF1, EPC1-PHF1 and MEAF6-PHF1 chimeric fusions have been reported in >50% of cases. The recently described t(10;17)(q22;p13) translocation yields YWHAE-FAM22A/B chimeric proteins that are associated with histologically high-grade and clinically more aggressive ESS.
Integrating whole-transcriptome paired-end RNA sequencing with fluorescence in situ hybridization (FISH) and conventional cytogenetics, we identified MBTD1 (Malignant Brain Tumor Domain-containing 1) and CXorf67 (Chromosome X open reading frame 67) as the genes involved in the novel reciprocal t(X;17)(p11.2;q21.33) translocation in two independent low-grade ESS of classical histology. The presence of the MBTD1-CXorf67 fusion transcript was validated in both cases using RT-PCR followed by Sanger sequencing.
A specific FISH assay to be used on paraffin tissues was developed to detect the novel t(X;17) translocation, and resulted in identification of an additional low-grade ESS case positive for the MBTD1-CXorf67 fusion among 14 uterine stromal tumours [9 ESSs and 5 undifferentiated endometrial sarcomas (UESs)] that were negative for JAZF1 and YWHAE rearrangements.
Gene expression profiles of 3 ESSs with YWHAE- and 4 classical ESSs with JAZF1-rearrangements, and 4 UESs without known gene rearrangements, indicated clustering of tumours with MBTD1-CXorf67 fusion together with low-grade JAZF1-associated ESSs.
The chimeric MBTD1-CXorf67 fusion identifies yet another cytogenetically distinct subgroup of low-grade ESS and offers the opportunity to shed light on the functions of two poorly characterized genes.

overall_design: Total RNA was extracted from 11 frozen tumor samples from 4 low-grade ESS cases, 4 UES cases and 3 high-grade ESS cases; Agilent One-Color technology.

first: Barbara

last: Dewaele

first: Anna

last: Quattrone

first: Julio

last: Finalet-Ferreiro

first: Vanessa

last: Vanspauwen

first: Ellen

last: Geerdens

first: Valentina

last: Gianfelici

first: Zeynep

last: Kalender

first: Agnieszka

last: Wozniak

first: Philippe

last: Moerman

first: Raf

last: Sciot

first: Sabrina

last: Croce

first: Frederic

last: Amant

first: Peter

last: Vandenberghe

first: Jan

last: Cools

first: Maria

last: Debiec-Rychter


first: Julie

last: Buick

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

overall_design: Refer to individual Series

first: Ivy

last: Moffat

first: Carol

last: Swartz

first: Leslie

last: Recio

first: Andrew

last: Williams

first: Daniel

last: Hyduke

first: Heng

last: Li

first: Albert

last: Fornace Jr

first: Jiri

last: Aubrecht

first: Carole

last: Yauk


title: Genome-Wide Gene Expression Profiles in the Pancreatic Lymph Nodes of At-Risk Autoantibody Positive Individuals

status: Public on Mar 03 2015

first: Keiichi

last: Kodama

address: 269 Campus Drive, Room 2225

department: Department of Medicine, Division of Immunology & Rheumatology

institute: Stanford Univeristy School of Medicine

summary: Type 1 diabetes (T1D) is a polygenic autoimmune disorder caused by autoreactive T cells that recognize pancreatic islet antigens and subsequently destroy insulin-producing β-cells. Pancreatic lymph nodes (PLN) are an essential site for the development of T1D, where tolerance to pancreatic self-antigens is first broken and the autoimmune responses are amplified. The purpose of this study was to identify candidate genes and pathways in the PLN that may contribute to the pathogenesis of T1D.

overall_design: Microarray analysis was performed on the PLN of human non-diabetic healthy controls (n=7) and at-risk autoantibody-positive subjects (n=13).

first: Linda

last: Yip

first: Rebecca

last: Fuhlbrigge

first: C

last: Fathman


title: Identification of DEK as a potential therapeutic target for Neuroendocrine prostate cancer

status: Public on Jan 15 2015

city: Vancouver

first: Shawn

last: Anderson

state: BC

address: 2660 Oak Street

institute: Vancouver Prostate Centre

summary: Introduction: Neuroendocrine prostate cancer (NEPC) is an aggressive subtype of prostate cancer, exhibiting rapid progression and is unresponsive to hormone therapy. Reliable prognostic assays and more effective treatments are critically required. However, the research of NEPC has been hampered by a lack of clinically relevant in vivo models. Recently, we successfully developed a first-in-field patient tissue-derived xenograft model of complete neuroendocrine transdifferentiation from prostate adenocarcinoma. By comparing gene expression profiles of the parental adenocarcinoma line (LTL331) and the NEPC subline (LTL331R), we identified DEK, a gene not previously reported in prostate cancer, as a potential biomarker and target for NEPC. Methods: DEK protein expression in patient tissue-derived xenograft models and clinical samples was assessed by immunohistochemistry. The function of DEK was determined by siRNA-induced reduction of DEK expression in PC-3 cells, a cell line with NEPC characteristics, followed by functional assays and gene expression profiling analysis. Results: Elevated DEK protein expression was observed in all clinical NEPC cases, which is distinct from their benign counterparts (0%), hormonal naïve prostate cancer (2.45%) and castration resistant prostate cancer (29.55%). Increased DEK expression is an independent clinical risk factor and is associated with shorter disease free survival in hormonal naïve prostate cancer patients. Reduction of DEK expression in PC-3 cells led to a marked reduction in cell proliferation, cell migration and invasion.  Conclusions: The results suggest that DEK may play an important role in the progression of prostate cancer, especially NEPC and provide a potential biomarker to aid risk stratification of prostate cancer and a novel therapeutic target for treating NEPC.

first: Dong

last: Lin

first: Alexander

middle: W

last: Wyatt

first: Sonal

last: Brahmbhatt

first: Anne

last: Haegert

middle: A


title: Identification of a novel, recurrent MBTD1-CXorf67 fusion in low-grade endometrial stromal sarcoma

first: Joanna

last: Przybyl


title: Integration of metabolic activation with a predictive toxicogenomics signature to classify genotoxic versus nongenotoxic chemicals in human TK6 cells [AFB1]

first: Julie

last: Buick

overall_design:
This experiment examined the whole genome transcriptional response of TK6 cells exposed to Aflatoxin B1 for 4 hours followed by a 0h, 4h and 20h recovery in fresh media (4h, 8h, and 24h time points, respectively) at 3 different concentrations, including a low (0.025 μM), a medium (0.075 μM), and a high (0.1 μM) concentration, in addition to negative controls (±S9), vehicle controls (±S9) and a direct-acting positive control, cisplatin (-S9) at 1 μg/ml (PC-1) and 24 μg/ml (PC-24).  Each concentration and time point had 3 biological replicates. There were a total 30 samples (60 arrays) included in the final analysis using a two-colour dye swap design.

Please note that each sample data table contains normalized data combined from two replicates and the sample-dye assignment information for each of the raw data files is included in the 'readme.txt' (available as Series supplementary file).

first: Ivy

last: Moffat

first: Carol

last: Swartz

first: Leslie

last: Recio

middle: H


title: Characterization of differentially expressed genes involved in pathways associated with gastric cancer

status: Public on Feb 11 2015

city: shanghai

first: hao

last: li

address: libing road

institute: school

summary: To explore the patterns of gene expression in gastric cancer, a total of 32 paired gastric cancer and noncancerous tissues from patients were collected for gene expression microarray analyses. Limma methods were applied to analyze the data, and genes were considered to be significantly differentially expressed if the False Discovery Rate (FDR) values < 0.01, P-value < 0.01 and the fold change >2. Subsequently, Gene Ontology (GO) analysis was used to analyze the main functions of the differentially expressed genes. According to the Kyoto Encyclopedia of Genes and Genomes (KEGG) database, we found pathways significantly associated with the differential genes. Gene-Act network and Co-Expression networks were built respectively based on the relationships among the genes, proteins and compounds in the database. There were 2371 differential mRNAs and 350 differential lncRNAs in our microarray data. The GO categories, pathway analyses and the Gene-Act network showed a consistent result that up-regulated genes were involved in tumorigenesis, migration, angiogenesis and microenvironment formation, while down-regulated genes were involved in metabolism. The results of this study provide some novel findings on genes, pathways and the co-expression network in gastric cancer which will be useful to guide further investigation and target therapy for this disease.

overall_design: 32 gastric cancer tissues and 32 paired  noncancerous tissues were collected for this microarray analysis.

first: Li

last: Hao

first: Yu

last: Beiqin

last: Jiangfang

first: Su

last: Liping

first: Yan

last: Min

first: Zhang

last: Jun

last: Chen

first: Zhu

last: Zhenggang

first: Liu

last: Bingya


title: LncRNA Expression Discriminates Karyotype and Predicts Survival in B-lymphoblastic Leukemia (Agilent)

status: Public on Feb 05 2015

city: LOS ANGELES

first: Dinesh

middle: S

last: Rao

address: 750 CHARLES E YOUNG DRIVE, 12-272 FACTOR

department: PATHOLOGY AND LABORATORY MEDICINE

institute: UCLA

summary: Long non-coding RNAs (lncRNAs) have been found to play a role in gene regulation with dysregulated expression in various cancers. The precise role that lncRNA expression plays in the pathogenesis of B-acute lymphoblastic leukemia (B-ALL) is unknown. Therefore, unbiased microarray profiling was performed on human B-ALL specimens and it was determined that lncRNA expression correlates with cytogenetic abnormalities, which was confirmed by RT-qPCR in a large set of B-ALL cases. Importantly, high expression of BALR-2 correlated with poor overall survival and diminished response to prednisone treatment. In line with a function for this lncRNA in regulating cell survival, BALR-2 knockdown led to reduced proliferation, increased apoptosis, and increased sensitivity to prednisolone treatment. Conversely, overexpression of BALR-2 led to increased cell growth and resistance to prednisone treatment. Interestingly, BALR-2 expression was repressed by prednisolone treatment and its knockdown led to upregulation of the glucocorticoid response pathway in both human and mouse B-cells. Together, these findings indicate that BALR-2 plays a functional role in the pathogenesis and/or clinical responsiveness of B-ALL and that altering the levels of particular lncRNAs may provide a future direction for therapeutic development.

overall_design: B-lymphoblastic leukemia is characterized by several translocations.  In this study, we hybridized patient bone marrow samples from a total of 44 patients including 14 patients with B-ALL carrying a TEL-AML1 translocation, 15 patients with E2A-PBX1 translocation, and 15 patients carrying MLL translocations.  The hybridizations were carried out in two sets, a discovery set and a validation set.  In addition, we utilized samples from a human cell line (NALM6) and control CD10+CD19+ cells from human bone marrow.

first: Thilini

last: Fernando

first: Norma

last: Rodriguez-Malave

first: Ella

middle: V

last: Waters

first: Weihong

last: Yan

first: David

last: Casero

first: Giuseppe

last: Basso

first: Martina

last: Pigazzi


title: Understanding toxicity pathways of gold nanoparticles: RNA expression study on Caco-2 human colon carcinoma cells

status: Public on Jan 22 2015

city: Varese (VA)

first: Marco

last: Fabbri

address: via dunant 5

institute: Università dell'Insubria

summary: A safer design and higher eficacy of nano-gold therapeutic formulations requires examination of cellular responses to gold nanoparticles (AuNPs). In this work we compared cellular uptake, cytotoxicity and RNA expression patterns induced in Caco-2 cells of citrate-stabilized Au NP of two different sizes (5 and 30 nm). The toxicity was measured with Colony Forming Efficiency (CFE) and Trypan Blue assays at 24 and 72 h after exposure to AuNPs in the 10 - 300 mM range. Toxicity was observed only in the CFE assay, at 200 and 300 mM exposure levels, and exclusively for smaller AuNPs size. Cellular internalization was dose and time-dependent for both AuNPs. The most pronounced changes in gene expression, evaluated with Agilent microarrays, were detected at 72 h (300 mM) for 5 nm AuNPs, with 103 up and 708 down regulated transcripts. For 30 nm AuNPs, only 4 gene transcripts were repressed under these conditions. The biological processes affected by 5 nm AuNPs were: RNA/zinc ion/transition metal ion binding (decreased), cadmium/copper ion binding and glutathione metabolism (increased). Some Nrf2 responsive genes (several metallothioneins, HMOX, G6PD, OSGIN1 and GPX2) were highly up regulated. Members of the selenoproteins (SELT, SELK, 15 kDa selenoprotein, SEPP1 and GPX2) were also differentially expressed. Our findings indicate that at high concentrations, smaller AuNPs can induce metal exposure and oxidative stress signaling pathways, and might influence selenium homeostasis. Therefore, some observed effects associated with nano-gold cytotoxicity can be further explored as potential enhancers of anti-cancer properties of already existing AuNPs based nanomedicin.

overall_design: Caco-2 cells were expoxed to spherical gold nanoparticles of two different sizes and concentrations (5 and 30 nm AuNPs, 100 and 300 microM). Cells were collected after 24 or 72 hours

first: Edyta

last: Bajak

first: Jessica

last: Ponti

first: Sabrina

last: Gioria

first: Isaac

last: Ojea-Jiménez

first: Angelo

last: Collotta

first: Valentina

last: Mariani

first: Douglas

last: Gilliland

first: François

last: Rossi

first: Laura

last: Gribaldo


title: The Assembly of miRNA-mRNA-protein Regulatory Networks Using High-throughput Expression Data

status: Public on Mar 01 2015

city: Pittsburgh

first: Jean-Francois

last: Mouillet

state: PA

address: 204 Craft Ave

department: MWRI - OBGYN and Reproductive Sciences

institute: University of Pittsburgh

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


title: The Assembly of miRNA-mRNA-protein Regulatory Networks Using High-throughput Expression Data (mRNA)

summary: Analyze gene expression levels in primary trophoblasts, derived from term human placenta and cultured under standard or hypoxic conditions

overall_design: Human placental trophoblasts were dispersed using a trypsin-deoxyribonuclease-dispase/Percoll method, plated in 6-well plates, and maintained in standard culture conditions (O2=20%). After 4 h (defined as time 0), the plates were divided to those in continued standard culture conditions, or to culture in hypoxia (O2=0%). Cells were then harvested at 6 h, 12 h, 24 h, 48 h and 72 h, and processed for mRNA arrays

first: Tianjiao

last: Chu

first: Thomas

middle: P

last: Conrads

first: Yoel

last: Sadovsky


title: Transcription profile of SSEA-3-positive population of MSCs

status: Public on Jan 07 2015

city: Tsukuba

first: Hisako

last: Ishimine

state: Japan Ibaraki

address: higashi1-1-1 Tsukuba central 4

department: Research Center for Stem Cell Engineering

institute: National Institute of Advanced Industrial Science and Technology

summary: Microarray analysis of the gene expression profile of SSEA-3-positive human adipose-derived MSCs were performed.

overall_design: Liposuction aspirates were obtained from the abdomen and thighs. Stromal vascular fraction (SVF) was isolated from the aspirated fat. Muse cells that express human SSEA-3 were collected from SVF using anti SSEA-3 antibody conjugated with PE and anti-PE microbeads. SSEA-3-negative fraction was considered ‘Muse-poor population’.

first: Kahori

last: Kinoshita

first: Kanako

last: Watanabe-Susaki

first: Akira

last: Kurisaki

first: Noriyuki

last: Aoi

first: Harunosuke

last: Kato

first: Kentaro

last: Doi

first: Shinichiro

last: Kuno

first: Hiromu

last: Sugino

first: Kotaro

last: Yoshimura


title: The effect of MEK inhibition, Interferon beta, and their combination on transcription in melanoma

status: Public on Jan 01 2015

city: New York

first: Dana

last: Pe'er

state: NY

address: 1212 Amsterdam Ave.

department: Biological Sciences

institute: Columbia University

summary:
We examined the transcriptional effect of interferon beta, MEK inhibition or their combination on 6 melanoma cell lines
3 cell lines have high basal acitvity of the interferon pathway, and 3 have low basal activity

overall_design: Samples were treated with 50nM of the MEK inhibitor PD901, 1000Units/mL of interferon beta, or their combination and collected 8 hours after treatment

first: Oren

last: Litvin


title: The effect of MEK inhibition on transcription in melanoma


title: Time course IAA treatment Arabidopsis seedlings

status: Public on Jan 02 2015

city: Yokohama

first: Yukihisa

last: Shimada

state: Kanagawa

address: Maiokacho, Totsuka

department: Kihara Institute for Biological Science

institute: Yokohama City University

summary: 7-days-old Arabidopsis seedlings of wildtype (Col-0) were treated with 1 μM IAA for 15 minutes or 3 hours and gene expression of whole plant was analyzed using Affymetrix Gene 1.1 ST Array strips.

overall_design: Arabidopsis seedling (Col-0) 25 plants were grown in each plate (1/2 MS medium) under continuous light at 22 °C for 6 or 7 days. Ten seedlings were cultured in 50 ml plastic tube containing liquid medium (1/2 MS medium), and incubated with shaking. After 24 hours, samples were treated with 0.1% DMSO for 15 minutes or 3 hours (Mock treatments) and with 1 μM indole-3-acetic acid dissolved in DMSO for 15 minutes or 3 hours (IAA tretments). The plants were wiped on papertowels and sampled. Immediately after sampling of the plants, these plants were soaked in liquid nitrogen and stored at -80 °C. The experiment was repeated 3 times in 3 different days. Total RNA was extracted from the frozen samples using RNeasy Plant Mini Kit (Qiagen) following the protocol supplied by manufacturer. The quality of RNA was checked by 2100 Bioanalyzer system (Agilent) and 100 ng RNA of each experiment was applied to microarray analysis. The microarray analysis was carried out using Affymetrix gene 1.1 ST array strips and GeneAtlas (Affymetrix) following the protocol supplied manufacturer.

first: Yusuke

last: Kakei


title: The effect of MEK inhibition on transcription in melanoma [Batch 2]

summary: In order to reveal the downstream targets of MAPK in melanoma, we measured the expression of 14 melanoma cell lines pre and post MEK inhibition

overall_design: Samples were treated with 50nM of the MEK inhibitor PD901 and collected 8 hours after treatment


title: Expression profiling in primary and stem-cell derived Human Endothelial and Vascular Smooth Muscle Cells

status: Public on Dec 31 2014

city: Basel

first: Tobias

last: Heckel

address: Grenzacherstr. 124

department: pRED

country: Switzerland

institute: Roche

summary: Whole transcriptome gene expression profiling of Normal Human Endothelial and Vascular Smooth Muscle Cells

overall_design: A NimbleGen Homo sapiens Expression Array [100718_HG18_opt_expr] study using total RNA recovered from endothelial and vascular smooth muscle cells grown in cell culture. Each microarray measures the expression level of 23,611 genes using 45,033 probe sets with three 60-mer probes (PM) per probe set. Each probe set is represented once on the array.

first: Christoph

last: Patsch


title: The effect of MEK inhibition on transcription in melanoma [Batch 1]

summary: In order to reveal the downstream targets of MAPK in melanoma, we measured the expression of 12 melanoma cell lines pre and post MEK inhibition


title: Studying relative gene expression in Head and Neck (HNSCC) tumor under diverse culture conditions

status: Public on Nov 22 2014

city: Bangalore

first: Pradip

last: Majumder

address: Suite 202, Narayana Nethralaya, Narayana Hrudayalaya Health City, Hosur Main Road, Bangalore 99, Karnataka State.

country: India

institute: Mitra Biotech Pvt Ltd.

summary: To compare the gene expression profile in HNSCC tumor cultured under various conditions

overall_design: Primary human HNSCC tumor was cultured for upto 72 hours in presence of Autologous Serum and combination of Autologous Serum and Tissue metalloproteinases ; angiogeneesis and tissue associated microenvironment signatures were studied

first: Biswanath


title: HSP90 empowers evolution of resistance to hormonal therapy in human breast cancer models

status: Public on Dec 01 2014

city: Cambridge

first: Marc

last: Mendillo

state: MA

address: 9 Cambridge Center

institute: Whitehead Institute for Biomedical Research

summary: The efficacy of hormonal therapies for advanced estrogen receptor-positive breast cancers is limited by the nearly inevitable development of acquired resistance. Efforts to block the emergence of resistance have met with limited success, largely because the mechanisms underlying it are so varied and complex. Here, we investigate a new strategy, aimed at the very processes by which cancers evolve resistance.  From yeast to vertebrates, HSP90 plays a unique role amongst molecular chaperones by promoting the evolution of heritable new traits. It does so by regulating the folding of a diverse portfolio of metastable client proteins, many of which mediate adaptive responses that allow organisms to adapt and thrive in the face of diverse challenges, including those posed by drugs. Guided by our previous work in pathogenic fungi where very modest HSP90 inhibition impairs resistance to mechanistically diverse antifungals, we examined the effect of similarly modest HSP90 inhibition on the emergence of resistance to anti-estrogens in breast cancer models. Even though this degree of inhibition fell below the threshold for proteotoxic activation of the heat-shock response and had no overt anticancer activity on its own, it dramatically impaired the emergence of resistance to hormone antagonists both in cell culture and in mice. Our findings strongly support the clinical testing of combined hormone antagonist-low level HSP90 inhibitor regimens in the treatment of metastatic ER+ breast cancer.  At a broader level, they also provide promising proof-of-principle for a generalizable strategy to combat the pervasive problem of rapidly emerging resistance to molecularly targeted therapeutics.

overall_design: We used microarrays to examine the effect of tamoxifen (a widely used anti-estrogen), ganetespib (STA-9090; a synthetic second generation HSP90 inhibitor), and their combination on gene expression in MCF-7 breast cancer cells.  MCF-7 cells were treated for 10 days with the indicated drug or drugs.

first: Luke

last: Whitesell

first: Sandro

last: Santagata

first: Nancy

middle: U

last: Lin

first: David

last: Proia

first: Susan

last: Lindquist


title: Studying relative gene expression in primary and xenograft CRC samples

summary: To compare the gene expression profile in primary human colorectal cancer samples and samples passaged in mice for two generations

overall_design: Primary human CRC samples were implanted in mice and allowed to grow for 2 generations. The tumors were then excised and a relative expression profile was evaluated to see similarity/dissimilarity between the two.


title: Pharmacodynamic effects of GLP-1 agonist liraglutide in adolescent, prediabetic pigs

status: Public on Dec 31 2015

city: Munich

first: Stefan

last: Krebs

address: Feodor-Lynen-Str. 25

department: Gene Center

institute: Ludwig-Maximilian University

summary: GLP-1 agonists are potent glucose-lowering agents, however, their effect on adolescent organisms needs to be clarified

overall_design: Transgenic pigs expressing a dominant-negative GLP receptor randomly assigned for a 90 day treatment trial with liraglutide (0.6-1.8 mg per day)/placebo

first: Eckhard

last: Wolf

first: Elisabeth

last: Streckel

first: Maik

last: Dahlhoff

first: Barbara

last: Kessler

first: Andreas

last: Blutke

first: Nicole

last: Übel

first: Mathias

last: Ritzmann

first: Helmut

last: Blum

first: Simone

last: Renner

first: Christina

last: Braun-Reichhart

first: Andrea

last: Bähr

first: Nadja

last: Herbach

first: Natasha

middle: B

last: Michaelsen

first: Matthias

last: Eddicks

first: Rüdiger

last: Wanke


title: The effect on gene expression by shRNA-58335

city: Sapporo

first: Masashi

last: Idogawa

country: Japan

institute: Sapporo Medical University

summary: To evaluate the effect on gene expression by shRNA-58335, we evaluated gene expression by microarray analysis.

overall_design: Gene expression was measured in Huh-7 cells stably expressing shRNA-58335 or control shRNA after infection with adenovirus expressing p53 (Ad-p53) or LacZ (Ad-LacZ).


title: Gene expression analysis during adipocytic differentiation of human bone marrow cells (hMSC-TERT)

status: Public on Sep 09 2014

city: Riyadh

first: Nehad

middle: M

last: Alajez

address: 1st floor College of Medicne

institute: King Saud University College of Medicine

summary: We have employed whole genome microarray  to identify changes in gene expression in human bone marrow MSCs (hMSC-TERT) during adipocytic differentiation in culture for 7 days

overall_design: Human MSC line (hMSC-TERT) were subjectd to adipocytic differentiation for 7 days, subsequently, RNA was extracted using Norgen total RNA isolation kit. Extracted RNA was labeled and then hybridized to the one-color Agilent Human GE 8x60K Microarray chip.


title: A combined omics approach to generate the surface protein atlas of human naive CD4+ T cells during early TCR activaion

status: Public on Nov 01 2014

city: Muenchen

first: Kathrin

last: Suttner

address: Biedersteiner Str. 29

department: Helmholtz Zentrum und TU Muenchen

institute: ZAUM-Center for Allergy and Environment

summary: To increase the dataset of our proteomic naive CD4+ T cell surface atlas, we applied whole genome microarray expression analysis. The NCBI RefSeq accession number of all transcripts which were detected in naive and stimulated CD4+ T cells (aCD3/aCD28 for 3h) of four different donors, was mapped to the corresponding UniProtKB accession number. For these UniProtKB ACs, we extracted the subcellular localization (UniProt_SL) annotation from the UniProtKB/Swiss-Prot database or if not available the subcellular localization was predicted unsing LocTree3 and PolyPhobius. This led to the identification of 908 genes coding for proteins located on the surface of human naive and/or activated CD4+ T cells.

overall_design: Gene expression in human naive T cells and naive T cells which were stimulated with aCD3/aCD28 for 3h was measured. Naive T cells from four different human blood donors were analyzed.

first: Anke

last: Graessel