title: DNA methylation differences between Newborns and Nonagenarians [PBMNC]

city: L'Hospitalet de Llobregat

first: Manel

last: Esteller

state: Barcelona

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

department: PEBC

institute: IDIBELL

summary: Human aging implies many phenotypic modifications and an increased susceptibility to many common diseases, phenomena that cannot be fully explained by the constrained genetic setting. An alternative pathway that could explain the age-associated alterations is epigenetic drifts. To address this issue, we performed Whole Genome Bisulfite Sequencing (WGBS) of a newborn and of a centenarian. The centenarian DNA exhibited a significant loss in DNA methylation and a poor correlation in the methylation status of neighboring CpGs throughout the genome. From a gene-regulatory region standpoint, we observed that the DNA hypomethylation events occurred mainly at CpG-poor promoters and in tissue-specific genes, whereas a greater level of DNA methylation was observed in CpG island promoters. Most importantly, we extended the study to a larger cohort of newborn and nonagenarian samples using a 450,000 CpG-site DNA methylation microarray. The 450K DNA methylation approach enabled validation of the WGBS data and revealed additional age-related DNA methylation events. Interestingly, we also observed the DNA methylation fingerprint characteristic of a healthy aged cell in samples from patients with premature-aging disorders such as Hutchinson-Gilford progeria and Werner syndrome. Overall, we suggest that defects in the physiological DNA methylation profile contribute to the process of human aging. As the disease associated cells were immortalized B cells, the effect of EBV immortalization was determined in advance to the study using immortalized and naive B cells.

overall_design: DNA was quantified by Quant-iT PicoGreen dsDNA Reagent (Invitrogen) and the integrity was analyzed in a 1.3% agarose gel. Bisulfite conversion of 600 ng of each sample was perform according to the manufacturer's recommendation for Illumina Infinium Assay. Effective bisulphite conversion was checked for three controls that were converted simultaneously with the samples. 4 ul of bisulfite converted DNA were used to hybridize on Infinium HumanMethylation 450 BeadChip, following Illumina Infinium HD Methylation protocol. Chip analysis was performed using Illumina HiScan SQ fluorescent scanner. The intensities of the images are extracted using GenomeStudio (2010.3) Methylation module (1.8.5) software. Methylation score of each CpG is represented as beta value.

first: Holger

last: Heyn


title: Differential gene expression between skin and cervix induced by the E7 oncoprotein in a transgenic mouse model

status: Public on Jun 10 2012

city: Mexico

first: Sandra

middle: Lorena

last: Romero-Cordoba

state: Mexico

address: Periférico Sur No. 4809, Col. Arenal Tepepan, Delegación Tlalpan. México, D.F.

department: Cancer Genomics

country: Mexico

institute: National Instute of Genomic Medicine

summary: HPV16 E7 oncoprotein expression in K14E7 transgenic mice induces cervical cancer after 6 months of treatment with the co-carcinogen 17β-estradiol. In untreated mice, E7 also induces skin tumors late in life, albeit at low penetrance. These findings indicate that E7 alters cellular functions in cervix and skin so as to predispose these organs to tumorigenesis. Using microarrays, we determined the global genes expression profile in cervical and skin tissue of young adult K14E7 transgenic mice without estrogen treatment. In these tissues, the E7 oncoprotein altered the transcriptional pattern of genes involved in several biological processes, including immune response, intracellular signaling cascades, cell adhesion, cell migration, development, cell cycle, growth, response to wounding and regulation of apoptosis. Among the E7-dysregulated genes were ones not previously known to be involved in cervical neoplasia, including DMBT1, GLI1 and 17βHSD2 in cervix and MMP2, 12, 14, 19 and 27 in skin.

overall_design: The experiment consists of a total of 24 samples to evaluate the mRNA expression profiles in 4 different groups: skin biopsy of transgenic mice K14E7, cervix biopsy of transgenic mice K14E7, skin biopsy of FVB/N control virgin mice and cervix biopsy of  FVB/N control virgin mice. Each group has 6 samples that had been processed in 3 pools of two samples (biological replicates) for a total of 6 samples for each condition.

first: ELOÍSA

last: IBARRA SIERRA

first: JOSÉ

last: DE LA LUZ DÍAZ CHÁVEZ

first: ENOC

last: MARIANO CORTÉS MALAGÓN

first: LAURA

last: URIBE FIGUEROA

first: ALFREDO

last: HIDALGO MIRANDA

first: PAUL

middle: F

last: LAMBERT

first: PATRICIO

last: GARIGLIO VIDAL


title: DNA hypermethylation in intrahepatic cholangiocarcinomas and glioblastomas

city: Chapel Hill

first: Derek

last: Chiang

state: NC

address: UNC Lineberger Cancer Center, 450 West Drive, CB #7295

department: Department of Genetics

country: USA

institute: University of North Carolina

type: Methylation profiling by genome tiling array

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

overall_design: Refer to individual Series


title: Perilipin 2 improves insulin sensitivity in skeletal muscle despite elevated intramuscular lipid levels

status: Public on Jun 09 2012

city: Wageningen

first: Guido

last: Hooiveld

address: HELIX, Stippeneng 4

department: Div. Human Nutrition & Health

country: Netherlands

institute: Wageningen University

summary: Type 2 diabetes is characterized by excessive lipid storage in skeletal muscle. Excessive intramyocellular lipid storage exceeds intracellular needs and induces lipotoxic events ultimately contributing to the development of insulin resistance.  Lipid droplet (LD)-coating proteins may control proper lipid storage in skeletal muscle. Perilipin 2 (PLIN2/ADRP) is one of the most abundantly expressed LD-coating proteins in skeletal muscle. Here we examined the role of PLIN2 in myocellular lipid handling and insulin sensitivity by investigating the effects of in vitro PLIN2 knockdown and in vitro and in vivo overexpression. PLIN2 knockdown decreased LD formation and triacylglycerol storage, marginally increased FA oxidation, and increased incorporation of palmitate into diacylglycerols and phospholipids. PLIN2 overexpression in vitro increased intramyocellular TAG storage paralleled with improved insulin sensitivity. In vivo muscle-specific PLIN2 overexpression resulted in increased LD accumulation and blunted the high-fat diet-induced increase of OXPHOS protein content. Diacylglycerol levels were unchanged, while ceramide levels were increased. Despite the increased intramyocellular lipid accumulation, PLIN2 overexpression improved skeletal muscle insulin sensitivity. We conclude that PLIN2 is essential for lipid storage in skeletal muscle by enhancing the partitioning of excess FAs towards triacylglycerol storage in LDs thereby blunting lipotoxicity-associated insulin resistance.

overall_design: C2C12 cells (mouse myoblast cell line) were treated with fatty acids and effects of knockdown of Perilipin 2 by siRNA were studied by gene expression profiling.

first: Madeleen

last: Bosma

first: Matthijs

last: Hesselink

first: Lauren

last: Sparks

first: Silvie

last: Timmers

first: Maria

last: Ferraz

first: Frits

last: Mattijssen

first: Denis

last: van Beurden

first: Gert

last: Schaart

first: Marc

last: DeBaets

first: Fons

last: Verheyen

first: Sander

last: Kersten

first: Patrick

last: Schrauwen


title: Predict cytogenetic abnormalities with gene expression profiles

status: Public on Jun 12 2012

city: Little Rock

first: Yiming

last: Zhou

state: AR

address: 4301 West Markham St., Slot 776

institute: Myeloma Institute for Research and Therapy

type: Genome variation profiling by genome tiling array

summary: Cytogenetic abnormalities (CA) are important clinical parameters in various types of cancer, including multiple myeloma (MM). We developed a model to predict CA in patients with MM using gene expression profiling (GEP) and validated it by different cytogenetic techniques. The model was shown to have an accuracy up to 0.89. These results provide proof of concept for the hypothesis that GEP could serve as a one-stop data source for clinical molecular diagnosis and/or prognosis.

overall_design: 92 paired RNA-DNA samples were hybridized to Affy U133Plus2 and Agilent 244K aCGH arrays and used as training set. Another 23 paired samples as test set.

first: Qing

last: Zhang

first: John

last: Shaughnessy

first: Owen

last: Stephens

first: Bart

last: Barlogie


title: Hepatocytes treated with IFN-alpha or IFN-gamma and acute hepatitis C

city: Basel

first: Zuzanna

last: Makowska

address: Hebelstrasse 20

department: Biomedicine

country: Switzerland

institute: University of Basel

type:
Expression profiling by array
Third-party reanalysis


title: Mutations in IDH1 are associated with DNA hypermethylation in glioblastomas

status: Public on Jun 11 2012

first: Derek

last: Chiang

summary: We compared the DNA methylation profiles of 26 glioblastomas harboring mutations in IDH1 with 36 glioblastomas without these mutations on the Illumina HumanMethylation450 BeadChip.

overall_design: Genomic DNA from fresh frozen tumors was bisulfite converted with the Zymo Research EZ DNA Methylation kit, then hybridized to the Illumina HumanMethylation450 Beadchip

first: P

last: Wang

first: C

last: Kuan

first: J

middle: W

last: Kim

first: S

middle: M

last: Yourstone

middle: Y


title: Gene expression in germinal center light zone and dark zone B cells

status: Public on Jun 14 2012

city: Cambridge

first: Gabriel

middle: D

last: Victora

state: MA

address: 9 Cambridge Center

institute: Whitehead Institute

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus

first: David

last: Dominiguez-Sola

first: Riccardo

last: Dalla-Favera

first: Michel

middle: C

last: Nussenzweig


title: Escherichia coli BW25113 cobB/pCA24N-cobB vs. cobB/pCA24N under stress conditions

status: Public on Jun 06 2012

city: college station

first: Qun

last: Ma

address: 3122 TAMU

institute: Texas A&M University

summary: Acetylation of lysine residues is conserved in all three kingdoms; however, its role in prokaryotes is unknown.  Here we demonstrate that acetylation enables the reference bacterium Escherichia coli to withstand environmental stress. Specifically, the bacterium reaches higher cell densities and becomes more resistant to heat and oxidative stress when its proteins are acetylated, as shown by deletion of the gene encoding acetyltransferase YfiQ and the gene encoding deacetylase CobB, as well as by overproducing YfiQ and CobB. Furthermore, we show that the increase in oxidative stress resistance with acetylation is due to the induction of catalase activity through enhanced katG expression. We also found that two-component system proteins CpxA, PhoP, UvrY, and BasR are associated with cell catalase activity and may be responsible as the connection between bacterial acetylation and the stress response. This is the first demonstration of a specific environmental role of acetylation in prokaryotes.

overall_design: Overnight cultures of cobB/pCA24N-cobB and cobB/pCA24N were cultured to a turbidity of 0.05 at 600 nm and grown 2 h. Then, 0.1 mM IPTG was added for another 4 h to induce cobB expression, and then the cells were exposed to 20 mM H2O2 for 10 min. Cell pellets were collected and resuspended in RNAlater (Ambion Inc., Austin, TX), and total RNA was isolated using the RNeasy Mini Kit (Qiagen Inc., Valencia, CA). The E. coli GeneChip Genome 2.0 array (Affymetrix, P/N 900551) was used, and cDNA synthesis, fragmentation, and hybridizations were performed as described previously. If the gene with the larger transcription rate did not have a consistent transcription rate based on the 11-15 probe pairs (P-value less than 0.05), these genes were discarded. A gene was considered differentially expressed when the P-value for comparing two chips was lower than 0.05 (to assure that the change in gene expression was statistically significant and that false positives arise less than 5%) and if their fold change is higher than the standard deviation for the whole genome.


title: Gene expression profiles of Wnt-1 overexpressing melanoma

status: Public on Jun 05 2012

city: Vienna

first: Stefanie

last: Tauber

address: Dr. Bohr-Gasse 9

department: CIBIV

country: Austria

institute: MFPL

summary: We aimed to analyze the effects of Wnt-1 overexpression on the mRNA expression profile of human melanoma in a mouse xenograft model and correlated the results with then presence or absence of lymphangiogenesis and metastasis. Affymetrix gene expression analysis revealed activation of canonical and non-canonical targets genes in response to Wnt-1 as compared with controls. In regard to lymphangiogenic factors, the amount of VEGF-C was the single best marker to correlate with the amount of lymph-angiogenesis.

overall_design: mRNA expression array of human melanoma orthotopically grown in SCID mice. Comparison includes mRNA expression profile of   two melanoma cell-lines (A375 and M24met) stably overexpressing control vector or Wnt-1 treated with or without CsA. Comparison #1 comprised Wnt-1 versus control in A375 and M24met melanoma, respectively. Comparison #2 comprised Wnt-1 + Cyclosporine A (CsA) versus Wnt-1 without CsA.

first: Martin

last: Bilban

first: Heidi

last: Niederleithner

first: Peter

last: Petzelbauer


title: Dermal lymphatic endothelial cell response to type 2 diabetes [Homo sapiens]

status: Public on Jun 02 2012

first: Brigitte

last: Hantusch

address: Waehringer Guertel 18-20

department: Clinical Institute of Pathology

institute: Medical University of Vienna

summary:
Analysis of ex vivo isolated lymphatic endothelial cells from the dermis of patients to define type 2 diabetes-induced changes. Results preveal aberrant dermal lymphangiogenesis and provide insight into its role in the pathogenesis of persistent skin inflammation in type 2 diabetes.
The ex vivo dLEC transcriptome reveals a dramatic influence of the T2D environment on multiple molecular and cellular processes, mirroring the phenotypic changes seen in T2D affected skin. The positively and negatively correlated dLEC transcripts directly cohere to prolonged inflammatory periods and reduced infectious resistance of patients´ skin. Further, lymphatic vessels might be involved in tissue remodeling processes during T2D induced skin alterations associated with impaired wound healing and altered dermal architecture. Hence, dermal lymphatic vessels might be directly associated with T2D disease promotion.

overall_design:
Global gene expression profile of normal dermal lymphatic endothelial cells (ndLECs) compared to dermal lymphatic endothelial cells derived from type 2 diabetic patients (dLECs).Quadruplicate biological samples were analyzed from human lymphatic endothelial cells (4 x diabetic; 4 x non-diabetic).
subsets: 1 disease state set (dLECs), 1 control set (ndLECs)

first: Monika

last: Haemmerle

first: Thomas

last: Keller

first: Gerda

last: Egger

first: Dejan

last: Stokic

first: Carl-Walter

last: Steiner

first: Christoph

last: Neumayer

first: Dontscho

last: Kerjaschki


title: Expression data from primary human mammary fibroblasts purified from disease-free women of low and high mammographic density

city: San Francisco

first: RosaAnna

last: DeFilippis

state: CA

address: 513 Parnassus Ave

department: Pathology

institute: University of California San Francisco

summary:
Although high mammographic density (MD) is considered one of the strongest risk factors for invasive breast cancer, the genes involved in modulating this clinical feature are unknown.
Histologically, areas of high MD are associated with low adipocyte content and high matrix content, both stromal phenotypes. We hypothesized that fibroblasts purified from low and high MD tissues would show gene expression differences responsible for these histologic differences.

overall_design: Fibroblasts were purified from disease-free breast tissue from 6 women with low MD (MD quartile 2) and 7 women with high MD (MD quartile 4). The fibroblasts were cultured for 3 to 6 passages before cells pellets were collected for this study.

first: Thea

last: Tlsty


title: CD99 is a novel prognostic stromal marker in non-small cell lung cancer

city: Uppsala

first: Anders

last: Isaksson

address: Akademiska sjukhuset ing61 3tr

country: Sweden

institute: Uppsala University

summary:
The delicate interaction between cancer cells and the surrounding stroma plays an essential role in all stages of tumourigenesis. Despite the significance of this interplay, alterations in protein composition underlying tumour-stroma interactions are largely unknown. The aim of this study was to identify stromal proteins with clinical relevance in non-small cell lung cancer.
A list encompassing 203 stromal candidate genes was compiled based on gene expression array data and available literature. The protein expression of these genes in human NSCLC was screened utilising the Human Protein Atlas. Twelve proteins were selected that showed a differential stromal staining pattern. The corresponding antibodies were applied on a tissue microarray, including 190 NSCLC samples, and stromal staining was correlated with clinical parameters.
Higher stromal expression of CD99was associated with good prognosis in the univariate (p=0.037) and multivariate (p=0.039) analyses. The association was independent from the total proportion of tumour stroma, the fraction of inflammatory cells, and clinical and pathological parameters like stage, performance status and tumour histology. The prognostic impact of stromal CD99 protein expression was confirmed in an independent cohort of 240 NSCLC patients (p=0.008). Furthermore, double-staining confocal fluorescence microscopy showed that CD99 was expressed in stromal lymphocytes as well as in cancer associated fibroblasts.
Based on a comprehensive screening strategy the membrane protein CD99 was identified as a novel stromal factor with clinical relevance. The result supports the concept that stromal properties have a significant impact on tumourigenesis.

overall_design: Tissue from five tumors were compared to corressponding microdissected tissue from the same tissue sample

first: Patrick

last: Micke

first: Cecilia

last: Lindskog

last: Berglund

first: Fredrik

last: Pontén

first: Hanna

last: Göransson-Kultima

first: Mats

last: Lambe

first: Lars

last: Holmberg

first: Simon

last: Ekman

first: Michael

last: Bergkvist

first: Johan

last: Botling

first: Karolina

last: Edlund


title: Ewing's sarcoma tumor samples

city: Paris

first: Loredana

last: Martignetti

address: 26, rue d'Ulm

country: France

institute: Insitut Curie/ INSERM U900 / Mines Paris Tech

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


title: Myocardin-like Protein (MKL)-2 Regulates TGF-β Signaling in Embryonic Stem Cells and the Developing Vasculature

status: Public on Jun 01 2012

city: Philadelphia

first: Nina

middle: Michelle

last: Bowens

state: Pennsylvania

address: 3400 Spruce Street

department: Cardiology

institute: University of Pennsylvania

summary:
Signal transduction from the extracellular matrix to the arterial wall plays a critical role during development of the vasculature.  We now report the discovery of a Myocardin-like Protein (MKL)2/TGF-β signaling pathway that is required for maturation and stabilization of the vasculature.  Mkl2-/- null embryos exhibit profound derangements in the tunica media leading to aneurismal dilation, dissection and hemorrhage.
TGFβ expression, signaling and TGF-β-regulated genes are down-regulated in Mkl2-/- ES cells and in the vasculature of Mkl2-/- embryos.  Transcription of Tgfβ2 is activated via binding of a MKL 2/SRF complex to a conserved CArG element in the Tgfβ2 promoter. In this data set we include expression data from wild type and Mkl2-/- ES cells

overall_design: A total of 5 samples with mRNA of sufficient quality were analyzed.  Samples consisted of mRNA from independent cell culture of 2 wild-type and 3 Mkl2-/- undifferentiated Embryonic Stem Cells

first: Jian

last: Li

first: Lan

last: Cheng

first: Xiaohong

last: Zhu

first: Mary

last: Chen

first: Sridhar

last: Hannenhalli

first: Thomas

last: Cappola

middle: S

last: Parmacek


title: Gene expression profiling of 6 acute hepatitis C patients

first: Zuzanna

last: Makowska

summary:
Approximately 50% of patients with chronic hepatitis C (CHC) have a sustained virologic response (SVR) to treatment with pegylated interferon (pegINF)-α and ribavirin. Non-response to treatment is associated with constitutively increased expression of IFN-stimulated genes (ISGs) in the liver. Treatment of patients with acute hepatitis C (AHC) is more effective, with SVR rates >90%. We investigated mechanisms of the different responses of patients with CHC and AHC to pegIFN-α therapy. We analyzed IFN signaling and ISG expression in liver samples from patients with acute hepatitis C (AHC), patients with chronic hepatitis (CHC), and individuals without hepatitis C (controls) using microarray, immunohistochemical, and protein analyses. Findings were compared with those from primary human hepatocytes stimulated with IFN-α or IFN-γ, as reference sets. Expression levels of 100s of genes, primarily those regulated by IFN-γ, were altered in liver samples from patients with AHC compared with controls. Expression of IFN-γ–stimulated genes was induced in liver samples from patients with AHC, whereas expression of IFN-α–stimulated genes was induced in samples from patients with CHC. In an expression analysis of negative regulators of IFN-α signaling, we did not observe differences in expression of SOCS1 or SOCS3 between liver samples from patients with AHC and those with CHC. However, USP18 (another negative regulator of IFN-α signaling), was upregulated in liver samples of patients with CHC that did not respond to therapy, but not in AHC. In conclusion, differences in expression of ISGs might account for the greater response of patients with AHC, compared to those with CHC, to treatment with pegINF-α and ribavirin. Specifically, USP18 is upregulated in liver samples of patients with CHC that do not respond to therapy, but not in patients with AHC.

(Interferon-γ Stimulated Genes, but not USP18, are Expressed in Livers of Patients with Acute Hepatitis C; Dill MT, Makowska Z et al, Gastroenterology 2012 (in press))

overall_design:
Liver biopsy samples from 6 patients with acute hepatitis C virus infection were analyzed
CHC data and controls previously submitted as GSE11190

middle: T

last: Dill

first: Francois

last: Duong

first: Franzisca

last: Merkofer

first: Magdalena

last: Filipowicz

last: Baumert

first: Luigi

last: Tornillo

last: Terraciano

first: Markus

middle: H

last: Heim


title: New insights into key genes and pathways involved in the pathogenesis of HLA-B27-associated acute anterior uveitis

city: Beijing

first: Xiaofeng

last: Hu

address: No.8 South Gongti Road

department: Eye

country: China

institute: Beijing Chaoyang Hospital

summary:
HLA-B27-associated inflammatory diseases remains one of the strongest HLA-disease known to date. HLA-B27-associated acute anterior uveitis has wide-ranging medical significance due to its ocular, systemic, immunologic, and genetic features. To investigate the genes and signalling pathways located upstream of the inflammatory processes in HLA-B27-associated acute anterior uveitis will help to know the mechanism of this disease. HLA-B27-positive and -negative monocytes isolated from human peripheral blood were stimulated with Vibrio cholera lipopolysaccharide (LPS). Gene expression microarrays were used to identify the differentially expressed genes, and they were analysed by a series of bioinformatics-based techniques.
Gene expression microarray analysis revealed marked differences between B27-positive monocytes in the genes that are upregulated in response to LPS stimulation. Gene Ontology enrichment (GO) and pathway analysis indicated that genes participating in protein transport and folding were essential to the inflammatory process. The LPS receptor, TLR4, induced the Toll-like receptor signalling pathway and pathways related to Vibrio cholerae infection, which are located upstream of the network and contribute to the overall response. Among the DE genes, PIK3CA, PIK3CB, AKT3, and MAPK1 may play critical roles in inflammation.Equivalent LPS stimulation induces a different response in HLA-B27-positive monocytes compared to monocytes lacking this HLA protein, suggesting that the TLR pathway is involved in the pathogenesis of HLA-B27-associated AAU. Blocking this pathway and other pathways by siRNA interference of candidate genes may contribute to the development of a treatment for this type of AAU.

overall_design: HLA-B27-positive monocytes isolated from human peripheral blood were stimulated with Vibrio cholera lipopolysaccharide (LPS) for 12 hours.

first: Hong

last: Lu

first: Jing

last: Wang

first: Xiaosheng

last: Zhang

first: Xiaolong

first: Xuhui

last: Liu

first: Zhuozai

last: Xu

first: Junmin


title: Stem-like glioma-propagating cells contribute to molecular heterogeneity and survival outcome in oligodendroglial tumors

status: Public on Jun 03 2012

first: Felicia

last: Ng

address: Wellcome Trust/MRC Building, Addenbrooke's Hospital, Hills Road

country: United Kingdom

institute: Cambridge Institute for Medical Research

summary: Brain tumors are among the most malignant cancers and can arise from neural stem cells or oligodendrocyte progenitor cells (OPCs). Glioma-propagating cells (GPCs) that have stem-like properties have been derived from tumor variants such as glioblastoma multiforme (GBM) and oligodendroglial tumors, the latter being more chemosensitive with better prognosis. It has been suggested that such differences in chemosensitivity arise from the different profiles of OPCs versus neural stem cells. We thus explored if GPCs derived from these glioma variants can serve as reliable in vitro culture systems for studies. We utilized gene expression analyses, since GBM and oligodendrogliomas can be molecularly classified. Accordingly, we derived a gene signature distinguishing oligodendroglial GPCs from GBM GPCs collated from different studies, which was enriched for the Wnt, Notch and TGF-beta pathways. Using a novel method in glioma biology, the Connectivity Map, we mapped the strength of gene signature association with patient gene expression profiles in 2 independent glioma databases [GSE16011, http://caintegrator-info.nci.nih.gov/rembrandt]. Our gene signature consistently stratified survival in glioma patients. This data would suggest that in vitro low passage GPCs are similarly driven by transcriptomic changes that characterize the favorable outcome of oligodendrogliomas over GBM. Additionally, the gene signature was associated with the 1p/19q co-deletion status, the current clinical indicator of chemosensitivity. Our gene signature detects molecular heterogeneity in oligodendroglioma patients that cannot be accounted for by histology or the 1p/19q status alone, and highlights the limitation of morphology-based histological analyses in tumor classification, consequently impacting on treatment decisions.

overall_design: Total RNA obtained from primary neurosphere culture from brain tumor specimens of 6 patients were compared.  Replicate arrays were performed for all 6 neurosphere cultures.

first: Esther

last: Ting

first: Geraldene

middle: R

last: Koh

first: Mark

last: Phong

first: Swee

last: Wong

first: Siew

last: Leong

first: Oi

middle: L

last: Kon

first: Joan

last: Lee

first: Tan

middle: B

last: Toh

first: Greg

last: Tucker-Kellogg

first: Wai

first: Ivan

first: Carol

last: Tang

first: Beng

last: Ang


title: Expression data from three human DLD-1-derived colon cancer cell lines

city: Irvine

first: Marian

middle: L.

last: Waterman

address: 19182 Jamboree Blvd.

department: Microbiology and Molecular Genetics

institute: University of California, Irvine

summary:
The LEF/TCF family of transcription factors are downstream effectors of the WNT signaling pathway, which drives colon tumorigenesis.  LEF/TCFs have a DNA sequence-specific HMG box that binds Wnt Response Elements (WREs).  The “E tail” isoforms of TCFs are alternatively spliced to include a second DNA binding domain called the C-clamp.  We show that induction of a dominant negative C-clamp version of TCF1 (dnTCF1E) induces a p21-dependent stall in the growth of DLD1 colon cancer cells.  Induction of a C-clamp mutant did not induce p21 or stall cell growth.  Microarray analysis revealed that induction of p21 by dnTCF1EWT correlated with a decrease in expression of p21 suppressors that act at multiple levels from transcription (SP5, YAP1, RUNX1), to RNA stability (MSI2), and protein stability (CUL4A).  We show that the C-clamp is a sequence specific DNA binding domain that can make contacts with 5’-RCCG-3’ elements upstream or downstream of WREs.  The C-clamp-RCCG interaction was critical for TCF1E mediated transcriptional control of p21-connected target gene promoters.  Our results indicate that a WNT/p21 circuit is driven by C-clamp target gene selection.
Gene expression analysis of dnTCF and dnLEF induction in colon cancer cells.  Dominant negative LEF/TCFs interferes with endogenous Wnt signaling by binding to Wnt Response Elements of target genes and displacing beta-catenin.  Here we used induction of dnTCF-1 (wildtype and mutant forms of the C-clamp DNA binding domain) and dnLEF-1 to identify genes that change expression at 8 hours and 23 hours post-induction.

overall_design: Three DLD-1 clonal stable cell lines created by tetracycline-regulated expression (T-REx) system were treated with or without doxycycline for RNA extraction and hybridization on Affymetrix microarrays. One of the three cell lines is a mock cell line,a parental cell line that expresses only the Tet regulator and does not overexpress any protein when induced with doxycycline (Dox).  The other three cell lines can be induced by Doxycycline to overexpress wild-type dnTCF-1E or a mutant form of dnTCF-1E with five amino acid substitution mutations in the C-clamp of the E-tail, or dnLEF-1. The mock cell line and dnLEF-1 cell lines were treated with or without Dox for 23 hr. The wild-type and mutant dnTCF-1E cell lines were treated with or without Dox for 8 and 23 hr, and as well, wild-type dnTCF-1E was induced with maximal amounts of Dox (hi: 1ug/ml) for maximum expression and gene expression regulation.

first: Nate

middle: P

last: Hoverter

first: Ju-Hui

first: Suman

last: Sundaresh

first: Pierre

last: Baldi


title: Expression data from transfection of SW1783 and U87 glioma cells with miR-376a* for 24 and 72 hours

city: Singapore

first: Yukti

last: Choudhury

address: 31 Biopolis Way

country: Singapore

institute: Institute of Bioengineering and Nanotechnology, A*STAR


title: Transcriptome profiling identifies HMGA2 as a novel gene in melanoma progression

status: Public on Jun 08 2012

city: Nashville

first: Leon

last: Raskin

state: TN

address: 2525 West End Avenue, Suite 300

department: Medicine

institute: Vanderbilt University

summary:
The identification of novel tumor-specific markers may improve understanding of melanoma progression and prognostic accuracy. Whole genome expression profiling of 46 primary melanomas, 12 metastases, and 16 normal skin samples using Affymetrix U133 PLUS 2.0 array generated gene lists including both known and new melanoma genes.
The molecular genetic alterations contributing to the pathogenesis of melanoma are incompletely defined and few independent prognostic features have been identified beyond the pathologic characteristics of the primary tumor. Early stage melanoma is frequently curable, in contrast to the inferior prognosis of melanomas with regional lymph nodes involvement and the incurability of distant metastatic disease. The identification of novel tumor-specific markers may improve our understanding of melanoma progression and prognostic accuracy. To find differentially expressed genes that can distinguish melanoma from normal tissue, we performed a whole genome expression profiling of 46 primary melanoma samples, 12 regional or distant metastases, and 16 normal skin samples using Affymetrix U133 2.0 Plus array. Our study generated lists of differentially expressed genes in melanoma and identified novel prognostic marker HMGA2. It is  a novel, highly overexpressed melanoma gene associated with poor prognosis. The overexpression of HMGA2 is strongly associated with regional and distant metastases and serves as an independent predictor of disease-free survival and overall survival in melanoma.

overall_design: Melanoma samples were obtained through an IRB-approved protocol using informed consent at the University of Michigan Multidisciplinary Melanoma Clinic.  A portion of pigmented lesions clinically suspicious for melanoma and known melanoma were sampled by punch biopsy at the time of excision. The punch biopsy was bisected; half was sent to for clinical diagnosis and the other half along with adjacent normal skin when available immediately snap-frozen in liquid nitrogen. Snap-frozen tissue was embedded in OCT (TissueTek) followed by frozen sectioning and H&E slide preparation. The slides were evaluated by dermatopathologist who identified areas with greater than 70% tumor cellularity, which were sampled for RNA extraction. Primary melanomas and melanoma metastases were derived from different patients. Metastatic samples included lymph nodes (n=8), subcutaneous soft tissue (n=2), spleen (n=1), and small intestine (n=1).

first: Timothy

last: Johnson

first: Douglas

last: Fullen

first: Thomas

middle: J

last: Giordano

first: Stephen

last: Gruber


title: HIF1 is a master regulator of the adaptive gene expression to hypoxia.

status: Public on Jun 07 2012

city: Tokyo

first: Imari

last: Mimura

address: 4-6-1 Komaba Meguro-ku

department: Laboratory for Systems Biology and Medicine

country: Japan

institute: Research Center for Advanced Science and Technology

summary: Total 23 samples were derived from [1] HUVEC treated in the absence (0h) or presence of hypoxia (1, 2, 4, 8, 12, and 24 hrs) to determine hypoxia-regulated gene in endothelial cells, [2] control siRNA or HIF1α siRNA transfected HUVEC cells treated in the absence or presence of hypoxia, [3] control siRNA or KDM3A siRNA transfected HUVEC cells treated in the absence or presence of hypoxia, [4] ChIP-seq data for HIF1 binding sites and histone modifications under normoxia and hypoxia in endothelial cells.

overall_design:
This study represents 15 Samples from the gene expression part of the study described in 1,2, and 3 above.

The ChIP-Seq data mentioned above is available in GSE39089.

first: Masaomi

last: Nangaku

first: Yasuharu

last: Kanki

first: Shuichi

last: Tsutsumi

first: Hiroyuki

last: Aburatani

first: Tatsuhiko

last: Kodama


title: Expression data from transfection of U87 glioma cells with miR-376a* for 24 hours

summary:
Enforced expression of miRNAs in cells leads to down-regulation of several mRNAs, which harbour binding sites in their 3'UTRs for the overexpressed miRNA and represent potential target genes of the miRNA
We transfected unedited miR-376a* (376a*A) and edited miR-376a* (376a*G) into U87 cells to identify transcripts down-regulated by each in comparison to control  miRNA transfection. The aim was to identify target genes directly subject to regulation by miR-376a*A and by miR-376a*G

overall_design: U87 cells (100,000) were transfected with 50 nM of miR-376a*A, miR-376a*G or miR-control. Following incubation for 24 hours, total RNA was isolated from transfected cells. For each (miR-376a*A or miR-376a*G), genes differentially expressed upon miRNA transfection were determined based on comparison with miR-control-transfected samples. Biological triplicates were used for each sample type.


title: Expression data from transfection of SW1783 glioma cells with microRNA-376a* for 24 hours

summary:
Enforced expression of miRNAs in cells leads to down-regulation of several mRNAs which harbour binding sites in their 3'UTRs for the overexpressed miRNA and represent potential target genes of the miRNA
We transfected unedited miR-376a* (376a*A) and edited miR-376a* (376a*G) into SW1783 cells to identify transcripts down-regulated by each in comparison to control  miRNA transfection. The aim was to identify target genes subject to direct regulation by miR-376a*A and by miR-376a*G.

overall_design: SW1783 cells (100,000) were transfected with 50 nM of miR-376a*A, miR-376a*G or miR-control. Following incubation for 24 hours, total RNA was isolated from transfected cells. For each (miR-376a*A or miR-376a*G), genes differentially expressed upon miRNA transfection were determined based on comparison with miR-control-transfected samples. Biological triplicates were used for each sample type.


title: Network Analysis of HEK293T Gene Expression Profile Modulation During Nonviral Gene Delivery

city: Lincoln

last: Martin

state: NE

address: 32 Chase Hall

department: Biological Systems Engineering

institute: University of Nebraska-Lincoln

summary: The current understanding of the molecular factors underlying PEI-mediated transfection is largely unknown. The cationic polyethyleneimine (PEI) polymer gene delivery system was used to transfer the GFP gene to HEK293T cells. FACS separation of transfected (GFP positive), untransfected (GFP negative), and untreated cells enabled gene expression profiles to be obtained using Affymetrix® HG-U133A 2.0 microarrays for each cell population. Gene profiles were differentially compared for each population combination.

overall_design: Control (untreated), transfected (GFP positive), and untransfected (GFP negative) RNA samples were purified from HEK293T cells after FACS isolation. The experiment was repeated on triplicate days to run 3 microarrays for each cell population. Only 2 untreated replicates are included in this submission.

first: Sarah

last: Plautz

first: Angela

middle: K

last: Pannier


title: Molecular Evaluation of Patient-Derived Colorectal Cancer Explants as a Pre-clinical Mouse Model of Colorectal Cancer

city: Durham

first: David

last: Hsu

address: 905 S. LaSalle St. Rm 3008

department: Medical Oncology

institute: Duke University

summary: Mouse models have been developed to investigate colorectal cancer etiology and evaluate new anti-cancer therapies.  While genetically engineered and carcinogen-induced mouse models have provided important information with regard to the mechanisms underlying the oncogenic process, xenograft models remain the standard for the evaluation of new chemotherapy and targeted drug treatments for clinical use.  However, it remains unclear if drug efficacy data obtained from xenograft models translate into clinically-relevant treatment modalities.  In this study, we have generated a panel of 28 patient-derived colorectal cancer explants (PDCCEs), an extension of our previous work, by direct transplantation of human colorectal cancer (CRC) tissues into NOD-SCID mice.  A comprehensive histological and molecular evaluation of PDCCEs and their corresponding patient tumor demonstrates that PDCCEs maintain histological features and global biology through multiple passages.  Furthermore, we demonstrate that in vivo sensitivity of PDCCEs to oxaliplatin can predict patient outcomes. Our findings suggest that PDCCEs maintain similarity to the patient tumor from which they are derived and can serve as a reliable preclinical model that can be incorporated into future strategies to optimize individual therapy for patients with CRC.

overall_design: 28 human primary colorectal and 37 mouse derived colorectal explant tumors

first: Joshua

last: Uronis

first: Takuya

last: Osada

first: Shannon

last: McCall

first: Xiao

last: Yang

first: Christopher

last: Mantyh

first: Michael

middle: A

last: Morse

first: H

last: Lyerly

first: Bryan

last: Clary


title: Deep sequencing of small RNAs from Mouse brain during aging

city: NEW HAVEN

first: ALEXANDRE

last: DE LENCASTRE

address: 219 PROSPECT ST KBT 924

institute: YALE UNIVERSITY

type: Non-coding RNA profiling by high throughput sequencing

summary: MicroRNAs (miRNAs) are endogenous small RNA molecules that regulate gene expression post-transcriptionally. Work in Caenorhabditis elegans has shown that specific miRNAs function in lifespan regulation and in a variety of age-associated pathways, but the roles of miRNAs in the aging of vertebrates are not well understood. We examined the expression of small RNAs in whole brains of young and old mice by deep sequencing and report here on the expression of 233 known miRNAs and identification of 41 novel miRNAs. Of these miRNAs, 75 known and 18 novel miRNAs exhibit greater than 2.0-fold expression changes. The majority of expressed miRNAs in our study decline in relative abundance in the aged brain, in agreement with trends observed in other miRNA studies in aging tissues and organisms. Target prediction analysis suggests that many of our novel aging-associated miRNAs target genes in the insulin signaling pathway, a central node of aging-associated genetic networks. These novel miRNAs may thereby regulate aging-related functions in the brain. Since mouse miRNAs are conserved in humans, the aging-affected brain miRNAs we report here may represent novel regulatory genes that function during aging in the human brain.

overall_design: 2 samples examined: Mouse brain from two young (5 months) and two old animals (24-25 months).

first: Alexandre

last: de Lencastre

first: Sachi

last: Inukai

last: Turner

first: Frank

last: Slack


title: Oncogenic Activation Of FOXR1 by 11q23 Intrachromosomal Deletion-Fusions In Neuroblastoma

city: Amsterdam

first: Richard

last: Volckmann

state: Noord-Holland

address: van der Boechorststraat 6a

department: Laboratory of Experimental Oncology and Radiobiology

institute: msterdam UMC and University of Amsterdam

summary: Neuroblastoma tumors frequently show loss of heterozygosity of chromosome 11q with a shortest region of overlap in the 11q23 region.  These deletions are thought to cause inactivation of tumor suppressor genes leading to haploinsufficiency.  Alternatively, micro-deletions could lead to gene fusion products that are tumor-driving.  To identify such events we analyzed a series of neuroblastomas by comparative genomic hybridization (CGH) and single nucleotide polymorphism (SNP) arrays and integrated these data with Affymetrix mRNA profiling data with the bioinformatic tool R2 (http://r2.amc.nl).  We identified three neuroblastoma samples with small interstitial deletions at 11q23, upstream of the forkhead-box transcription factor FOXR1. Genes at the proximal side of the deletion were fused to FOXR1, resulting in fusion transcripts of MLL-FOXR1 and PAFAH1B2-FOXR1.  FOXR1 expression has only been detected in early embryogenesis.  Affymetrix microarray analysis showed high FOXR1 mRNA expression exclusively in the neuroblastomas with micro-deletions and rare cases of other tumor types, including osteosarcoma cell line HOS.  RNAi silencing of FOXR1 strongly inhibited proliferation of HOS cells and triggered apoptosis.  Expression profiling of these cells and reporter assays suggested that FOXR1 is a negative regulator of forkhead-box factor mediated transcription.  The neural crest stem cell line JoMa1 proliferates in culture conditional to activity of a MYC-ER transgene.  Over-expression of the wild-type FOXR1 could functionally replace MYC and drive proliferation of JoMa1.  We conclude that FOXR1 is recurrently activated in neuroblastoma by intrachromosomal deletion/fusion events, resulting in over-expression of fusion transcripts.  Forkhead-box transcription factors have not been previously implicated in neuroblastoma pathogenesis.  Furthermore, this is the first identification of intrachromosomal fusion genes in neuroblastoma.

overall_design: Time series Affymetrix U133p2 profiling of Osteosarcoma HOS cells transduced with FOXR1 targeted shRNAs or control shRNA

first: Evan

middle: E

last: Santo

first: Marli

last: Ebus

first: Jan

last: Koster

first: Johannes

last: Schulte

first: Arjan

last: Lakeman

first: Peter

middle: v

last: Sluis

first: Joelle

last: Vermeulen

last: Gisselsson

first: Ingrid

last: Ora

first: Sven

last: Lindner

first: Patrick

middle: G

last: Buckley

first: Raymond

last: Stallings

first: Jo

last: Vandesompele

first: Angelica

last: Eggert

first: Huib

middle: N

last: Caron

first: Rogier

last: Versteeg

last: Molenaar.


title: Expression data from DKAT breast cancer cell line pre- and post-EMT

first: Nicholas

last: D'Amato

address: MSRB Room 217, Research Dr.

department: Pharmacology and Cancer Biology

summary:
The DKAT cell line is a novel model of triple-negative breast cancer that was isolated from the pleural effusion of a 35 year-old caucasian woman with triple-negative breast cancer. When cultured in serum-free media (MEGM, Lonza) this cell line exhibits an epithelial morphology and gene expression pattern. However, when cultured in the presence of serum (SCGM, Lonza) it undergoes a reversible EMT.
We used microarrays to look at gene expression changes in the DKAT cell line when cultured in Mammary Epithelial Growth Media (MEGM, where DKAT cells have an epithelial morphology) vs Stromal Cell Growth Media (SCGM, where DKAT cells have a mesenchymal morphology).

overall_design: DKAT breast cancer cells (passage 10) grown in MEGM (Lonza) were split and cultured in T75 flasks in either in MEGM or SCGM for 14 days. RNA was isolated using Qiagen RNeasy kit and hybridization on Affymetrix microarrays was performed. Three separate cDNA reactions were performed and these were run as technical replicates.

middle: C

first: Julie

last: Ostrander

first: Michelle

last: Bowie

first: Victoria

last: Seewaldt


title: Phenotypic Plasticity in Aggressive Triple-Negative Breast Cancer: Human Biology is Recapitulated by a Novel Model System

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

overall_design: Refer to individual Series


title: Expression data from iPSCs generated with Yamanaka factors and miR-302 cluster

city: Stanford

first: Leng

last: Han

address: 265 Campus Dr

institute: Stanford University

summary: Baseline gene expression of adipose stem cell derived iPSCs generated by lentiviral Yamanaka 4 factors. We used microarrays to analyze the global gene expression of hACS derived iPSCs with KMOS and KMOS+miR-302.

overall_design: Compare the global gene expression of iPSCs with hESCs and adipose stem cells.

first: Shijun

last: Hu

first: Joseph

last: Wu


title: Genome-wide effects of Pbcas4 knockdown

status: Public on May 31 2012

city: Oxford

first: Ana

last: Marques

address: Oxford

institute: University of Oxford

summary: We tested the effect iof Pbcas4 knockdown using a specific shRNA on the expression of genes sharing miRNA binding sites in mouse N2A cells.

overall_design: 2 samples (shRNA and scramble), 3 biological replicates for each sample

first: Ana-Claudia


title: gene expression analyses of pediatric  lymphoblastic lymphomas and leukemias

city: Padua

first: Lara

last: Mussolin

address: via Giustiniani 3

country: Italy

institute: Department of Pediatrics

summary: T-cell acute lymphoblastic leukemia (T-ALL) and lymphoma (T-LBL) share common morphologic and immunophenotypic features and are treated with similar therapeutic approaches. Nonetheless, they show distinct clinical presentations suggesting that they may represent two different biological entities. In order to investigate T-LBL and T-ALL biological characteristics we used  transcriptional profiling approache. Genome-wide gene expression profiling, performed on 20 T-LBL and 10 T-ALL diagnostic specimens, showed that the two malignancies shared a large fraction of their transcriptional profile while a subset of genes appeared to be differentially expressed in T-LBL versus T-ALL. This gene signature included genes involved in chemotactic responses and angiogenesis which might play a role in the different tumor cell localization suggesting that T-LBL and T-ALL could be  two distinct diseases with unique transcriptional  characteristics.

overall_design: diagnostic bone marrow  aspirates from 10 T-ALL and 6 common-ALL pediatric patients and  tumor biopsies from 20 T-LBL  pediatric patients were analyzed by gene expression profiling

first: Katia

last: Basso


title: Sporadic vs. Post-Chernobyl Papillary vs. Anaplastic Thyroid Cancers

city: Brussels

first: Gil

last: Tomas

address: 808 route de Lennik

department: IRIBHM

country: Belgium

institute: ULB

summary:
We profiled the gene expression of anaplastic thyroid cancers of Belgian patients.
We compared these with the expression profile of a cohort of papillary thyroid tumors both from the Chernobyl Tissues Bank (CTB) and French patients with no history of exposure to radiations, along with their patient-matched healthy adjacent thyroid.

overall_design: A group of nine anaplastic thyroid carcinomas (ATCs), together with twenty papillary thyroid carcinomas (PTCs) paired with their respective adjacent tissues (N), were hybridized onto Affymetrix U133 Plus 2.0 arrays. PTCs were obtained from the Ambroise Paré Hospital (Boulogne, France; sporadic PTC, n=10) and from the Chernobyl Tissue Bank (CTB, www.chernobyltissuebank.com) (post-Chernobyl PTC, n=10). ATCs were obtained from the Jules Bordet Institute (Brussels) and the Ambroise Paré Hospital (France).

first: Detours

last: Vincent


title: The H3K27 demethylase Utx facilitates somatic and germ cell epigenetic reprogramming to pluripotency [Affymetrix gene expression]

status: Public on May 30 2012

city: Rehovot

first: Noa

last: Novershtern

address: Weizmann Institute

department: Molecular Genetics

country: Israel

institute: Weizmann Institute of Science

summary: Pluripotency can be induced in somatic cells by ectopic expression of defined transcription factors, however the identity of epigenetic regulators driving the progression of cellular reprogramming requires further investigation. Here we uncover a non-redundant role for the JmjC-domain-containing protein histone H3 methylated Lys 27 (H3K27) demethylase Utx, as a critical regulator for the induction, but not for the maintenance, of primed and naïve pluripotency in mice and in humans. Utx depletion results in aberrant H3K27me3 repressive chromatin demethylation dynamics, which subsequently hampers the reactivation of pluripotency promoting genes during reprogramming. Remarkably, Utx deficient primordial germ cells (PGCs) display a cell autonomous aberrant epigenetic reprogramming in vivo during their embryonic maturation, resulting in the lack of functional contribution to the germ-line lineage.

overall_design: Samples include UTX+/Y (WT) and UTX-/Y (KO) cells from mouse ES cells and mouse embryonic fibroblast (MEF) before and after DOX induction (initiating reprogramming by OSKM factors). One sample is OSKM-induced Nanog-/- fibroblasts.

first: Ohad

last: Gafni


title: Expression data from human cord blood CD34+ CD38- cells

first: Taito

last: Nishino

address: 7-1, Kanda-nishikicyo 3-chome, Chiyodaku

institute: Nissan Chemical Industries, LTD

summary: We used microarrays to observe the global gene expression in hematopoietic stem and projenitor cells during ex vivo culture with DMSO (Blank) or with Garcinol (GAR) and identified distinct classes of up or down-regulated genes.

overall_design: CD34+ cells were cultured ex vivo with DMSO (Blank) or with Garcinol (GAR) for 7 days. CD34+ CD38- cells were sorted from cultured cells (blank and GAR) with a FACS and total RNA were extracted from the sorted cells (blank and GAR), respectively. Blank represents a control sample.

first: Nishino

last: Taito


title: Transcriptome analysis of E. coli in M9 minimal media supplemented with propylene glycol or glycerol

city: La Jolla

first: Bernhard

last: Palsson

address: 9500 Gilman Dr.

department: Bioengineering

institute: UCSD

summary:
The aim of this study is to investigate the changes of global gene expression in E. coli during a carbon source shift.
Expression profiling of an evolved strain of E. coli K12 MG1655 grown in M9 minimal media supplemented with propylene glycol or glycerol.

sample_organism: Escherichia coli str. K-12 substr. MG1655

overall_design: A six chip study under two separate culture conditions

first: Dae-Hee

last: Lee

first: Hojung

last: Nam

first: Nathan

last: Lewis

middle: O


title: Melanoma cell culture phenotypes II

status: Public on May 24 2012

city: Zürich

first: Daniel

middle: Simon

last: Widmer

address: Gloriastrasse 31

department: Dermatology

institute: University Hospital Zürich

summary:
These samples are part of a study that tries to find melanoma subgroups by the mean of gene expression analysis.
Recent trials with MAPK inhibitors have shown promising results in many patients with metastatic melanoma; however, nearly all responding patients experience disease relapse. We describe here how melanoma cells respond to MAPK inhibition in a phenotype-specific manner, suggesting that slow cycling invasive phenotype cells provide a treatment-resistant pool from which disease relapse may be derived. The implication is that while MAPK inhibition may successfully treat proliferating cells, another cell population needs to be addressed at the same time.

overall_design: 3 samples

middle: S


title: Mouse Myoblast Pax3, Pax7 overexpression and control

status: Public on May 23 2012

city: Ottawa

first: Theodore

last: Perkins

state: ON

address: 501 Smyth Rd.

department: Cellular and Molecular Medicine

country: Canada

institute: Ottawa Hospital Research Institute

summary: This data set contains 3 replicates each for a Pax7 overexpression, Pax3 overexpression and an empty vector Control

overall_design: Measurement of expression levels in Pax3, Pax3 overepxression and empty vector control

first: Vahab

middle: D

last: Soleimani

first: Vincent

last: Punch

first: Yoh-ichi

last: Kawabe

first: Andrew

last: Jones

first: Gareth

last: Palidwor

first: Christopher

last: Porter

first: Joe

middle: W

last: Cross

first: Jaime

last: Caravajal

first: Christel

last: Kockx

first: Wilfred

middle: F

last: van IJcken

first: Peter

last: Rigby

first: Frank

last: Grosveld

first: Michael

last: Rudnicki


title: Gene expression signatures modulated by epidermal growth factor receptor activation and their relationship to cetuximab resistance in head and neck squamous cell carcinoma

city: Baltimore

first: Elana

middle: Judith

last: Fertig

state: MD

address: 670 W. Baltimore Street, 3rd floor

department: Institute for Genome Sciences

institute: University of Maryland, Baltimore

summary: Aberrant activation of signaling pathways controlled in normal epithelial cells by the epidermal growth factor receptor (EGFR) has been linked to cetuximab (a monoclonal antibody against EGFR) resistance in head and neck squamous cell carcinoma (HNSCC). To infer relevant and specific pathway activation downstream of EGFR from gene expression in HNSCC, we generated gene expression signatures using immortalized keratinocytes (HaCaT) subjected to either ligand stimulation or pharmacological inhibition of the signaling intermediaries PI-3-Kinase and MEK or transfected with EGFR, RELA/p65, or HRASVal12.   The gene expression patterns that distinguished the various HaCaT variants and conditions were inferred using the Markov chain Monte Carlo (MCMC) matrix factorization algorithm Coordinated Gene Activity in Pattern Sets (CoGAPS). This approach inferred gene expression signatures with greater relevance to cell signaling pathway activation than the expression signatures inferred with standard linear models.  Furthermore, the pathway signature generated using HaCaT-HRASVal12 further associated with the cetuximab treatment response in isogenic cetuximab-sensitive (UMSCC1) and -resistant (1CC8) cell lines. Our data suggest that the CoGAPS algorithm can generate gene expression signatures that are pertinent to downstream effects of receptor signaling pathway activation and potentially be useful in modeling resistance mechanisms to targeted therapies.

overall_design: 58 total RNA collected from HaCaT cell lines with combinations of the following experimental conditions: forced expression of EGFR, RELA/p65, and HRAS-VAL12D; grown in PBS, serum starve, and media stimulated with TNF or EGF; treated with gefitinib, LY294002, and U1026.

first: C

middle: H

last: Chung

first: E


title: Regulation of interferon-inducible proteins by doxorubicin via IFN-alpha-JAK-STAT signaling in tumor cells

city: Greifswald

first: Sabine

last: Ameling

address: Felix-Hausdorff.Str 8

department: Interfakultäres Institut für Genetik und Funktionelle Genomforschung

country: Germany

institute: Universitätsmedizin Greifswald

summary: Activation of the immune system is a way for host tissue to defend itself against tumor growth. Hence, treatment strategies that are based on immunomodulation are on the rise. Conventional cytostatic drugs such as the anthracycline doxorubicin can also activate immune cell functions of macrophages and natural killer cells. In addition, cytotoxicity of doxorubicin can be enhanced by combining this drug with the cytokine IFN-alpha. Although doxorubicin is one of the most applied cytostatics, the molecular mechanisms of its immunomodulation ability are not investigated thoroughly.   In microarray analyses of HeLa cells, a set of 19 genes related to interferon signaling was significantly overrepresented among genes regulated by doxorubicin exposure including STAT-1, -2, IRF9, NMI, and caspase 1. Regulation of these genes by doxorubicin was verified with Real-Time PCR and immunoblotting. An enhanced secretion of IFN-alpha was observed when HeLa cells were exposed to doxorubicin as compared to untreated cells. IFN-alpha neutralizing antibodies and inhibitors of JAK-STAT signaling (ATA and AG490) significantly abolished doxorubicin-stimulated expression of interferon signaling-related genes. Furthermore, inhibition of JAK-STAT signaling significantly reduced doxorubicin induced caspase 3 activation and desensitized HeLa cells to doxorubicin cytotoxicity.   In conclusion, we demonstrate that doxorubicin induces interferon-responsive genes via IFN-alpha-JAK-STAT1 signaling and that this pathway is relevant for doxorubicin’s cytotoxicity in HeLa cells. As immunomodulation is a promising strategy in anticancer treatment, this novel mode of action of doxorubicin may help to further improve the use of this drug among different types of anticancer treatment strategies.

overall_design: One batch of HeLa Cell culture treated with doxorubicin and DMSO (control) were used for screening of global changes at the transcriptome level.

first: J

last: Hussner

first: S

last: Hammer

first: L

last: Steil

first: M

last: Schwebe

last: Niessen

first: H

last: Schroeder

last: Kroemer

last: Ritter

first: U

last: Voelker

last: Bien


title: Stem cell lines of the early mouse embryo

status: Public on May 22 2012

city: Toronto

first: Brian

middle: Joseph

last: Cox

state: Ontario

address: 1 King's College Circle, Rm 3360

department: Physiology

institute: University of Toronto

summary: Expression profiling of stem cell lines derived from the early embryo representing the trophoblast, primitive endoderm, early epiblast (inner cell mass E3.5) and late post-implantation epiblast (E5.5).

overall_design: Cells were grown without feeders and harvested. Comparisons were made to provide evidence of unique gene expression between the cell lines. Specifically, pre-implantation (ICM, epiblast and primitive endoderm, and trophoblast), as well as pre-implantation and post-implantation epiblasts.

last: Rugg-Gunn

first: Jant

last: Rossant


title: Hsp27 acts as a master molecular chaperones and plays an essential role in hepatocellular carcinoma metastasis

city: Hangzhou

first: cheng

last: jun

state: Zhejiang Province

address: 79 Qingchun Road

department: Department of Surgery

institute: Division of Hepatobiliary and Pancreatic Surgery

summary: Hsp27 can regulate multiply signaling pathway and protect HCC cells apoptosis by mediating interaction with its cochaperones

overall_design: 3 HepG2 samples stably transfected with Hsp27 ORF vectors, Hsp27 shRNA or control vectors

first: Jun

last: Cheng

first: Jian

last: Wu

first: Zhen

last: Lv

first: Sunyi

last: Ye

first: Kezhen

last: Shen

first: Mansheng

last: Li

first: Yunsheng

last: Qin

first: Chenxi

last: Zhang

first: Shusen

last: Zheng


title: Expression data from transfection of U87 glioma cells with miR-376a* for 72 hours

city: Singapore

first: Yukti

last: Choudhury

address: 31 Biopolis Way

institute: Institute of Bioengineering and Nanotechnology, A*STAR

summary:
Several biological pathways can be under the regulation of miRNAs. These pathways can be indentified by the enforced expression of a miRNA and analysing the expression data for enrichment of specific pathways represented among the genes differentially expressed upon miRNA overexpression.
We transfected unedited miR-376a* (376a*A) and edited miR-376a* (376a*G) into U87 cells to identify differentially regulated transcripts. List of differentially expressed genes were subject to pathway enrichment analysis to identify specific biological processes regulated by each of miR-376a*A and miR-376a*G.

overall_design: U87 cells (100,000) were transfected with 50 nM of miR-376a*A, miR-376a*G or miR-control. Following incubation for 72 hours, total RNA was isolated from transfected cells. For each (miR-376a*A or miR-376a*G), genes differentially expressed upon miRNA transfection were determined based on comparison with miR-control-transfected samples. Biological triplicates were used for each sample type.


title: Expression data from DKAT and other breast cancer cell lines under baseline growth conditions

first: Nicholas

last: D'Amato

institute: Duke University

summary:
The DKAT cell line is a novel model of triple-negative breast cancer that was isolated from the pleural effusion of a 35 year-old caucasian woman with triple-negative breast cancer.
We used microarrays to look at gene expression in the DKAT cell line compared to several other commonly-used breast cancer cell lines as well as a previously published data set in order to determine the molecular subtype of the DKAT cell line.

overall_design: DKAT, HMEC, and MDA-MB-231 cells were cultured in Mammary Epithelial Growth Media (MEGM, Lonza). RNA was isolated using Qiagen RNeasy kit and hybridization on Affymetrix microarrays was performed. Three separate cDNA reactions were performed and these were run as replicates.

first: Julie

last: Ostrander

first: Michelle

middle: L

last: Bowie

first: Victoria

last: Seewaldt


title: A Computational Profiling of Changes in Gene Expression and Transcription Factors Induced by vFLIP K13 in Primary Effusion Lymphoma

status: Public on May 21 2012

city: Los Angeles

first: Vasu

last: Punj

address: Biggy Street

institute: USC

summary:
Infection of Kaposi's sarcoma associated herpes virus (KSHV) has been linked to the development of primary effusion lymphoma (PEL), which is characterized by the loss of expression of  B cell markers and effusions in the body cavities. This unique clinical feature of PEL has been attributed to their distinctive  gene expression profile which shows overexpression of genes in various signaling pathways. KSHV-encoded latent protein vFLIP K13 has been  shown to promote the survival and proliferation of PEL cells. In this study, we have employed gene array analysis followed by bioinformatics analysis of coordinated transcriptional factors network as well as biological pathways  to characterize the effect of K13 on PEL-derived BCBL1 cells. We observed that genes associated with Cytokine signaling, Cell death, NF-kappaB and Cell adhesion pathways were differentially regulated by K13.
We used computational approach complemented with microarrays to detail the global gene expression and identified distinct classes of differentially regulated genes in various cellular processes.

overall_design: We employed gene array analysis followed by bioinformatics analyses of coordinated transcriptional factors network as well as biological pathways  to characterize the effect of K13 on in PEL-derived BCBL1 cells.

first: Hittu

last: Matta

first: Preet

middle: M

last: Chaudhary


title: Microarray analysis of Zbtb46 KO CD4+ splenic DCs and bone marrow erythroid progenitors

city: Saint Louis

first: Ansuman

last: Satpathy

state: MO

address: 660 S. Euclid Ave.

department: Pathology and Immunology

institute: Washington University in St. Louis

summary:
Zbtb46 represses G-CSFR and LifR in cDCs
Zbtb46 does not significantly affect gene expression in erythroid progenitors

overall_design: WT, Het, and KO cells were sorted from BM or spleen and analyzed.  Pre MegE cells were sorted as CD117+ CD150+ CD105-CD41-CD16/32-. Pre CFU-E cells were sorted as CD117+ CD150+ CD105lo CD41- CD16/32-.  CFU-E cells were sorted as CD117+ CD150- CD105+ Cd41- CD16/32-.  Splenic CD4+ DCs were sorted as B220- CD11c+ MHCII+ CD8- CD172+ CD11b+ CD4+.

first: Kenneth

last: Murphy


title: miR-129-3p control cilia assembly by regulating CP110 and actin dynamics [miR-129-3p overexpression]

city: New York

first: Jingli

last: Cao

state: NY

department: Cell & Developmental Biology

institute: Weill Cornell Medical College

summary:
Primary cilium serves as a cellular “antenna” to sense environmental signals. Ciliogenesis requires the removal of CP110 to convert the mother centriole into the basal body. Actin dynamics is also critical for cilia formation. How these distinct processes are properly regulated remains unknown. Here we show that miR-129-3p, a microRNA conserved in the vertebrates, controlled cilia assembly by down-regulating both CP110 and four proteins critical for actin dynamics, Arp2, Toca1, abLIM1, and abLIM3. Consistently, blocking miR-129-3p repressed cilia formation in cultured mammalian cells, whereas its overexpression potently induced ciliogenesis in proliferating cells and extraordinary cilia elongation. Moreover, inhibition of miR-129-3p in zebrafish embryos suppressed cilia assembly in the Kupffer’s vesicle and pronephric duct, leading to developmental abnormalities including curved body, pericardial oedema, and randomised left-right patterning. Our results thus unravel a novel mechanism that orchestrates both the centriole-to-basal body transition and subsequent cilia assembly via microRNA-mediated posttranscriptional regulations.
We want to find the targets of miR-129-3p by overexpressing miR-129-3p oligo or control oligo in hTERT-RPE1 cells. Through microarray analysis we could check the downregulated genes and these genes might be the targets of miR-129-3p.

overall_design: RPE1 cells were transfected with control (Ctrl) or miR-129-3p (M129) oligo for 72h, and harvested for RNA extraction and hybridization on Affymetrix microarrays. Two samples: RPE1-Ctrl, RPE1-M129

first: Yidong

first: Xiumin

last: Yan

first: Xueliang

last: Zhu


title: Zbtb46 expression distinguishes classical dendritic cells and their committed progenitors from other immune lineages

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

overall_design: Refer to individual Series


title: Clinical and Molecular Characteristics of  Congenital Glioblastoma Multiforme

city: Aurora

first: Diane

middle: K

last: Birks

state: CO

department: Neurosurgery

institute: University of Colorado, Denver - Anschutz Medical Campus

summary:
Congenital glioblastoma multiforme (cGBM) historically has been considered an aggressive tumor of infancy requiring extensive chemotherapy to achieve cure. We report on 4 patients at our institution with cGBMs who were treated with surgery and chemotherapy (carboplatin and etoposide every 21 days for 2-6 cycles).  Four of four patients are progression free at a median time of 27.5 months (22-103 months).  To characterize the molecular biology of cGBM, we compared the gene expression profiles of 3 cGBMs to 12 pediatric and 6 primary adult glioblastomas collected at our institution. Unsupervised hierarchical clustering showed cGBMs grouped together with other high-grade gliomas. cGBMs demonstrated marked similarity to both pediatric and adult GBMs, with only a total of 31 differentially expressed genes identified (FDR < 0.05). Unique molecular features of congenital GBMs identified included over-expression of multiple genes involved in glucose metabolism and tissue hypoxia pathways. Four tyrosine kinases were also mong the up-regulated genes (RET, RASGRF2, EFNA5, ALK). Thus, at our institution congenital GBMs, while similar both histologically and molecularly to other GBMs, appear to have a good prognosis with surgery in combination with relatively moderate chemotherapy. Further study is needed to determine if the few gene expression differences that were identified may contribute to the better survival seen in these tumors compared to pediatric or adult GBMs.
Key Words: glioblastoma; congenital; pediatric; gene expression; microarray

overall_design: Molecular profiling of 18 AT/RT patient tumor samples was performed using Affymetrix U133 Plus2 GeneChips. Data were background corrected and normalized using gcRMA (as implemented in Bioconductor). Unsupervised agglomerative hierarchical clustering was performed to identify subsets of AT/RTs with similar gene expression. Limma (moderated t-tests; Bioconductor) was used to identify signature genes for each cluster. Bioinformatics web tool DAVID was used to identify enriched biological processes for each cluster. Survival was analyzed using Kaplan-Meier curves and Cox Hazard Ratio.  Bioinformatics tools Gene Set Enrichment (GSEA) and Ingenuity Pathways Analysis were also used to gain further insight into cluster differences.

first: Margaret

last: Macy

first: Valerie

last: Barton

first: Andrew

last: Donson

first: Bette

last: Kleinschmidt-DeMasters

first: Michael

last: Handler

last: Foreman


title: Gene expression data from teratomas formed by human iPSCs (chiPS) in SCID (Severe combined immunodeficiency) mice and humanized SCID mice (HuSCID)

first: Tongbiao

last: Zhao

address: 9500 Gilman Dr

department: Biological Sciences

institute: University of California San Diego

summary:
Human fetal liver fibroblast were reprogrammed to chiPS without exogenous DNA integration using a single episomal vector. The chiPS were then transplanted into SCID mice and HuSCID to form teratomas.
We used microarrays to profile the gene expression differences between the teratomas formed by chiPS in SCID and HuSCID mice.

overall_design: Pooled total RNA from two teratomas formed by chiPS in SCID and HuSCID mice respectively were used for hybridization on Affymetrix microarrays.

first: Yang

last: Xu


title: Epigenetic reprogramming in relapsed childhood ALL

city: NY

first: Teena

last: Bhatla

address: 550 first avenue

institute: NYU medical center

summary:
Reversing gene expression signatures in relapsed patient may restore chemosensitivity.
We demonstrate that the histone deacetylase inhibitor vorinostat not only reprograms the aberrant gene expression profile of relapsed blasts but is synergistic when applied prior to chemotherapy in primary patient samples and leukemia cell lines

overall_design: Primary patient samples were collected from patients treated at the New York University Medical Center and from the Children’s Oncology Group (COG) cell bank,RNA was isolated from three primary patient samples and three B-lineage leukemia cell lines with or without treatment with vorinostat for 24 hours.

first: Jinhua

last: Wang

first: William

last: Carroll


title: Expression data from iPS cells

status: Public on May 16 2012

city: Tokyo

first: Keiki

last: Kumano

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

institute: University of Tokyo

summary:
We generated iPSCs from imatinib-sensitive chronic myelogenous leukemia (CML) patient samples.
We used microarrays tc ompare the gene expression pattern among CML-iPSCs and normal cord blood (CB) iPSCs.

overall_design: Two CML derived iPS cells and one CB derived iPS cells were selected  for RNA extraction and hybridization on Affymetrix microarrays.

first: Shunya

last: Arai


title: Gene expression analysis of THP-1 cells co-cultured with platelet-like particles

status: Public on May 18 2012

city: Boston

first: Antonina

last: Risitano

address: 700 Albany St.

department: Whitaker Cardiovascular Institute

institute: Boston University School of Medicine

summary: Abstract. The role of platelets in hemostasis and thrombosis is clearly established; however, the mechanisms by which platelets mediate inflammatory and immune pathways are less well understood.  Platelets interact and modulate the function of blood and vascular cells by releasing bioactive molecules. Although the platelet is anucleate, it contains transcripts that may mirror disease.  Platelet mRNA is only associated with low-level protein translation, however, platelets have a unique membrane structure allowing for the passage of small molecules, leading to the possibility that its’ cytoplasmic RNA may be passed to nucleated cells. To examine this question, platelet-like particles with labeled RNA were co-cultured with vascular cells. Co-culture of platelet-like particles with activated THP-1, monocytic, and endothelial cells led to visual and functional RNA transfer. Post-transfer microarray gene expression analysis of THP-1 cells showed an increase in HBG1/HBG2 and HBA1/HBA2 expression which was directly related to the transfer. Infusion of wild-type platelets into a TLR2 deficient mouse model established in vivo confirmation of select platelet RNA transfer to leukocytes.  By specifically transferring green fluorescent protein, it was also observed that external RNA was functional in the recipient cells. The observation that platelets possess the capacity to transfer cytosolic RNA suggests a new function for platelets in the regulation of vascular homeostasis.

overall_design: THP-1, treated with Pam3CSK4, were co-cultured with platelet-like particles for 12 hours and 24 hours then collected and processed for RNA isolation. We also included as control THP-1 untreated and THP-1 treated with Pam3CSK4. A total of 4 samples were analyzed by microarray for gene expression.

first: Lea

last: Beaulieu

first: Olga

last: Vitseva

first: Jane

middle: E

last: Freedman


title: Differential gene expression profiles between SKOV3.ip1-S116A cells (Ser116 of PEA-15 substituted with alanine) and SKOV3.ip1-S116D cells (Ser116 of PEA-15 substituted with aspartic acid).

status: Public on May 12 2012

city: Houston

first: Xuemei

last: Xie

state: Texas

address: 1515 Holcombe Blvd

department: Breast Medical Oncology

institute: The University of Texas MD Anderson Cancer Center

summary: To dissect the molecular mechanisms of PEA-15-mediated paclitaxel sensitization in ovarian cancer cells, we performed cDNA microarray analysis using SKOV3.ip1-S116A cells (Ser116 of PEA-15 substituted with alanine) and SKOV3.ip1-S116D cells (Ser116 of PEA-15 substituted with aspartic acid). cDNA microarray data analysis showed that SCLIP (SCG10-like protein), also known as STMN3, was highly expressed in SKOV3.ip1-S116D cells and was involved in pPEA-15-mediated paclitaxel sensitization in ovarian cancer cells.

overall_design: SKOV3.ip1-S116A cells (Ser116 of PEA-15 substituted with alanine) and SKOV3.ip1-S116D cells (Ser116 of PEA-15 substituted with aspartic acid) were used. Total RNA was extracted and purified using RNeasy mini kit (Qiagen, Inc.) according to the manufacturer’s instructions. The integrity of the obtained RNA was assessed using an Agilent 2100 BioAnalyzer (Agilent Technologies). The Affymetrix HGU133 plus platform was used for hybridization, staining, and imaging of the arrays by following the manufacturer’s instructions. Gene expression analysis was performed in triplicate.

first: Naoto

middle: T

last: Ueno

first: Chandra

last: Bartholomeusz

first: Anna

last: Kazansky


title: Transcriptome profile in the human synovial MSC-aggregates

status: Public on May 13 2012

city: Setagaya-ku

first: Akihiro

last: Umezawa

state: Tokyo

department: Center for Regenerative Medicine

institute: National Center for Child Health and Development

summary: One of strategies to regenerate cartilage defect is transplantation of mesenchymal stem cells (MSCs). Improvements of therapeutic potential of MSCs are needed to achieve successful cartilage regeneration by transplantation of a limited number of cells. Aggregated culture is a popular method in ES and iPS cells to maintain or enhance their potentials. Here we investigated gene expression profile of aggregated MSCs. 621 genes were up-regulated and 409 genes were down-regulated more than 5-fold in MSC-aggregates compared with the number in MSCs in a monolayer culture. The most up-regulated gene was BMP2, which is one of the genes involved in chondrogenesis. Anti-inflammatory genes were also up-regulated in MSC-aggregates. The microarray data for selected genes were confirmed by real-time PCR.

overall_design: Human synovial MSCs was isolated from synovium of 3 distinct donors. The gene expression profile of MSC-aggregates cultured in hanging drop for 3days was compared with that of MSCs in a monolayer culture.

first: S

last: Shiro

first: T

last: Muneta

first: K

last: Tsuji

first: H

last: Makino

first: A

first: I

last: Sekiya


title: C/EBPa Regulates Protease/anti-protease Balance and Mediates Bronchiolar Cell Recovery After Injury

city: Cincinnati

first: Yan

last: Xu

state: OH

address: 3333 Burnet Ave

institute: Cincinnati Children's Hospital Medical Center

summary: In the present study, we hypothesized that C/EBPa (CCAAT/enhancer-binding protein alpha) plays a role in cell regeneration in response to bronchiolar epithelial cell injury. C/EBPa mediated ciliated cell regeneration after naphthalene bronchiolar epithelial cell injury in vivo. Furthermore, we demonstrated that C/EBPa regulates protease/anti-protease balance after lung injury, and intratracheal treatment with anti-protease (BPTI) restored ciliated cell regeneration after naphthalene injury in CebpaD/D mice.

overall_design: Cebpa d/d VS. Control mice 0hr, 3hr and 72hr after naphthalene injury. Three replicates each.

first: Atsuyasu

last: Sato

first: Jeffery

middle: A

last: Whitsett

first: Machiko

last: Ikegami


title: Mid-gestational gene expression profile in placenta and link to pregnancy complications

status: Public on May 11 2012

city: Perth

first: Sulev

last: Koks

state: Western Australia

address: 90 South Street

department: Centre for Molecular Medicine and Innovative Therapeutics

country: Australia

institute: Murdoch University

summary: Data on the temporal dynamics of human placental gene expression is scarce. We have completed the first whole-genome profiling of human placental gene expression dynamics (GeneChips, Affymetrix®) from early to mid- gestation (10 samples; gestational weeks 5 to 18) and report 154 genes with considerable change in transcript levels (FDR P<0.1). Functional enrichment analysis revealed >200 GO categories that are statistically over-represented among 105 genes with dynamically increasing transcript levels. Analysis in an extended sample (n=43; gestational weeks 5 to 41) conformed a highly significant (FDR P<0.05) expressional peak in mid-gestation placenta for ten genes: BMP5, CCNG2, CDH11, FST, GATM, GPR183, ITGBL1, PLAGL1, SLC16A10, STC1. A central hypothesis of our study states that the aberrant expression of genes characteristic to mid-gestation placenta may contribute to affected fetal growth, maternal preeclampsia (PE) or gestational diabetes (GD). The gene STC1 coding for Stanniocalcin 1 (STC1) was identified with a sharp placental expressional peak in mid-gestation, increased mRNA levels at term and significantly elevated STC1 protein levels in post-partum maternal plasma in all pregnancy complications. The highest STC1 levels were identified in women, who developed simultaneously PE and delivered an SGA baby (median 731 vs 418 pg/ml in controls; P=0.001). CCNG2 and LYPD6 exhibited significantly increased placental mRNA expression and enhanced intensity of immunohistochemistry staining in placental sections all studied in GD and PE cases. Aberrant expression of mid-gestation specific genes in pregnancy complications at term indicates the importance of the fine-scale tuning of the temporal dynamics of transcription regulation in placenta. Observed significantly elevated plasma STC1 in complicated pregnancies warrants further investigations of its potential as a biomarker. Interestingly, a majority of genes with high expression in mid-gestation placenta have also been implicated in adult complex disease. This observation promotes a recently opened discussion on the role of placenta in developmental programming.

overall_design: 4 samples; this submission is extension of our earlier study (accession GSE22490).

first: Liis

last: Uusküla

first: Jaana

last: Männik

first: Kristiina

last: Rull

first: Ave

last: Minajeva

last: Kõks

first: Pille

last: Vaas

last: Teesalu

first: Jüri

last: Reimand

first: Maris

last: Laan


title: Dynamic re-wiring of apoptotic signaling networks enhances tumor cell killing by DNA damage

status: Public on May 15 2012

city: Cambridge

first: Charles

middle: Arthur

last: Whittaker

state: MA

institute: Koch Institute

summary: Crosstalk and complexity within signaling pathways has limited our ability to devise rational strategies for using network biology to treat human disease. This is particularly problematic in cancer where oncogenes that drive or maintain the tumorigenic state alter the normal flow of molecular information within signaling networks that control growth, survival and death. Understanding the architecture of oncogenic signaling pathways, and how these networks are re-wired by ligands or drugs, could provide opportunities for the specific targeting of oncogene-driven tumors. Here we use a systems biology-based approach to explore synergistic therapeutic strategies to optimize the killing of triple negative breast cancer cells, an incompletely understood tumor type with a poor treatment outcome. Using targeted inhibition of oncogenic signaling pathways combined with DNA damaging chemotherapy, we report the surprising finding that time-staggered EGFR inhibition, but not simultaneous co-administration, can dramatically sensitize the apoptotic response of a subset of triple-negative cells to conventional DNA damaging agents. A systematic analysis of the order and timing of inhibitor/genotoxin presentation—using a combination of high-density time-dependent activity measurements of signaling networks, gene expression profiles, cell phenotypic responses, and mathematical modeling—revealed an approach for altering the intrinsic oncogenic state of the cell through dynamic re-wiring of oncogenic signaling pathways. This process converts these cells to a less tumorigenic state that is more susceptible to DNA damage-induced cell death, through re-activation of an extrinsic apoptotic pathway whose function is suppressed in the oncogene-addicted state.

overall_design: Three or 4 replicates of 3 different cell lines at time points 0minutes, 30minutes, 6 hours and 1 day after EGFR inhibition with erlotinib

first: M

middle: J

last: Lee

last: Ye

last: Gardino

last: Heijink

first: P

last: Sorger

first: G

last: MacBeath

middle: B

last: Yaffe


title: Breast cancer cells resistant to hormone deprivation maintain an estrogen receptor alpha-dependent, E2F-directed transcriptional program

status: Public on May 14 2012

city: Nashville

first: Todd

last: Miller

address: 2220 Pierce Ave, 777 PRB

department: Medicine

institute: Vanderbilt Univ

summary: A significant fraction of breast cancers exhibit de novo or acquired resistance to estrogen deprivation. To model resistance to aromatase inhibitor (AI) therapy, long-term estrogen-deprived (LTED) derivatives of MCF-7 and HCC-1428 cells were generated through culture for 3 and 7 months under hormone-depleted conditions, respectively. These LTED cells showed sensitivity to the ER downregulator fulvestrant under hormone-depleted conditions, suggesting continued dependence upon ER signaling for hormone-independent growth. To evaluate the role of ER in hormone-independent growth, LTED cells were treated +/- 1 uM fulvestrant x 48 h before RNA was harvested for gene expression analysis.

overall_design: MCF-7/LTED and HCC-1428/LTED cells were treated with 10% DCC-FBS with or without the estrogen receptor antagonist drug fulvestrant for 48 hrs prior to RNA harvest for array analysis. Three replicates per condition.

first: Carlos

last: Arteaga


title: A seven-gene signature aggregates a subgroup of stage II colon cancers with stage III.

city: Marseille

first: Sylviane

last: Olschwang

address: 232 boulevard Sainte-Marguerite

department: Centre de Recherches en Cancérologie de Marseille

institute: Institut Paoli-Calmettes

summary: Colorectal cancer is one of the most common cancers in the world. Histological staging is efficient but combination with molecular markers may improve tumors classification. Gene expression profiles have been defined as prognosis predictors among stage II and III tumors but their implementation in medical practice remains controversial. Stage-II tumors have been recognized as a heterogeneous group and high-risk morphologic features have been retained as justifying adjuvant chemotherapy. We propose here the investigation of clinical features and expression profiles from stage II and stage III colon carcinomas without DNA mismatch repair defect. A series of 130 colon cancer samples was retained. Expression profiles were established on oligonucleotide microarrays and processed in the R/Bioconductor environment. Hierarchical then supervised analyses were successively performed applying the data-sampling approach. A molecular signature of seven genes was found to cluster stage III tumors with an adjusted p-values lower than 10^-10. A subgroup of stage-II tumors aggregated this cluster in both series. No correlation was found between with the disease severity but the function of the discriminating genes suggests that tumors have been classified according to their putative response to adjuvant targeted or classic therapies. Further pharmacogenetic studies might document this observation.

overall_design: Expression profile of stage-II colon carcinomas distinguishes two patterns of tumors based on a 7-gene signature. One pattern is very similar to that of stage-III tumors and the corresponding tumors aggregate into a single cluster. Genes function suggests possible tumor determinism in drug response more than in prognosis evolution.


title: Reduced Retinal Microvascular Density, Improvement in Forepaw Reach, Comparative Microarray and Gene Set Enrichment Analysis using DNA Enzyme Targeting c-jun mRNA

city: Darlinghurst

first: Warren

last: Kaplan

state: NSW

address: 384 Victoria Street

department: Peter Wills Bioinformatics Centre

institute: Garvan Institute of Medical Research

summary: Retinal neovascularization is a critical component in the pathogenesis of common ocular disorders that cause blindness, and treatment options are limited. We evaluated the therapeutic effect of a DNA enzyme targeting c-jun mRNA in mice with pre-existing retinal neovascularization. A single injection of Dz13 in a lipid formulation containing N-[1-(2,3-dioleoyloxy)propyl]-N,N,N-trimethylammonium methyl-sulfate and 1,2-dioleoyl-sn-glycero-3-phosphoethanolamine inhibited c-Jun expression and reduced retinal microvascular density. The DNAzyme inhibited retinal microvascular density as effectively as VEGF-A antibodies. Comparative microarray and gene expression analysis determined that Dz13 suppressed not only c-jun but a range of growth factors and matrix-degrading enzymes. Dz13 in this formulation inhibited microvascular endothelial cell proliferation, migration and tubule formation in vitro. Moreover, animals treated with Dz13 sensed the top of the cage in a modified forepaw reach model, unlike mice given a DNAzyme with scrambled RNA-binding arms that did not affect c-Jun expression. These findings demonstrate reduction of microvascular density and improvement in forepaw reach in mice administered catalytic DNA.

overall_design: Total RNA from pooled eyes was used to prepare labeled probes for microarrays. Pooled samples included a Control, Vehicle, Dz13 and Dz13_scrambled.

first: Cecilia

last: Chan

first: Christopher

middle: R

last: Parish

first: Levon

last: Khachigian


title: MiR-23b suppresses IL-17 associated autoimmune pathogenesis

city: Shanghai

last: Shen

address: 145 Shan Dong Middle Road

department: Department of Rheumatology

institute: Renji Hospital, JiaoTong University School of Medicine

type:
Expression profiling by RT-PCR
Expression profiling by array

summary:
MicroRNAs (miRNAs) have been implicated as fine-tuning  regulators controlling diverse biological processes at the level of posttranscriptional repression. Dysregulation of miRNAs has been described in various disease states, including inflammatory autoimmune diseases.

By using high-throughput microRNA profiling analysis, we identified a series of miRNAs dysregulated in local inflammatory lesions of human patients with autoimmune diseases such as SLE.

This SuperSeries is composed of the SubSeries listed below.

first: Wen

last: Pan

first: Shu

last: Zhu

first: Youcun

last: Qian


title: Transcriptional profiling of clinically relevant SERMs and SERM/estradiol complexes in a cellular model of breast cancer

status: Public on May 09 2012

city: Palo Alto

first: Dmitri

last: Kazmin

state: CA

address: 240 Pasteur Dr

department: Institute for Immunity, Transplantation and Infection

institute: Stanford University

summary:
In this study, we have utilized microarray analysis to directly compare a subset of structurally distinct, clinically relevant SERMs in the presence and absence of estradiol, using a high replicate number (10) to ensure detection of modestly regulated genes.
Tested compounds included 4-hydroxytamoxifen, ICI-182,780, Raloxifene, Bazedoxifene and Lasofoxifene.

overall_design: MCF-7 cells were treates with indicated SERMs in the presence of E2 or vehicle; RNA was isolated and used for preparation of label for 3' expression analysis.

first: Donald

middle: P

last: McDonnell

first: Suzanne

last: Wardell


title: RD effect on PC-3 cells

status: Public on May 08 2012

city: Philadelphia

first: Zhongyi

last: Hu

state: Pennsylvania

address: 421 Curie Blvd

institute: University of Pennsylvania

summary:
RD induced DNA damage and suppressed DNA repair in PC-3 cells.
Expression profiling of PC-3 cells treated with 10 umol/L RD for 24 hours.

overall_design: Total RNA was extracted from PC-3 cells exposed to RD for 24 h using an RNAiso plus kit (TaKaRa). Microarray analysis was performed on separate samples on the Affymetrix HG-U133 plus 2 chip.

first: Huiqing

last: Yuan


title: Knock-down and Over-expression of JMJD6 in MCF-7 and/or MDA-MB231

status: Public on May 10 2012

city: Singapore

first: Yi Fang

last: Lee

address: 60 Biopolis Street

institute: Genome Institute of Singapore

summary: By survival analysis of breast cancer patients, JMJD6 was found to be significantly associated with poor prognosis. Over-expression and knock-down of JMJD6 in breast cancer cell lines suggested a role in proliferation. In order to study the transcriptional events that occur following JMJD6 expression changes, siRNA-mediated knock-down of JMJD6 was performed in MCF-7 and MDA-MB231 and stable over-expression of JMJD6 was performed in MCF-7.

overall_design: There are 2 different siRNA-mediated knock-downs of JMJD6 with 2 biological replicates in MCF-7 and MDA-MB231; 3 clones of JMJD6 over-expression with 3 biological replicates in MCF-7. The control for the knock-downs is scrambled siRNA-treated MCF-7 and MDA-MB231 and the control for JMJD6 over-expression is empty vector over-expression in MCF-7.

first: YiFang

first: Kartiki

middle: V

last: Desai


title: Recurrent Variations in DNA Methylation in Human Pluripotent Stem Cells and their Differentiated Derivatives [Illumina Infinium 450K DNA Methylation]

city: La Jolla

first: Kristopher

middle: L.

last: Nazor

address: 10550 North Torrey Pines Road

department: Regenerative Medicine

institute: The Scripps Research Institute

summary: Human pluripotent stem cells (hPSCs) are potential sources of cells for modeling disease and development, drug discovery, and regenerative medicine. However, it is important to identify factors that may impact the utility of hPSCs for these applications. In an unbiased analysis of 205 hPSC and 130 somatic samples, we identified hPSC-specific epigenetic and transcriptional aberrations in genes subject to X chromosome inactivation (XCI) and genomic imprinting, which were not corrected during directed differentiation. We also found that specific tissue types were distinguished by unique patterns of DNA hypomethylation, which were recapitulated by DNA demethylation during in vitro directed differentiation. Our results suggest that verification of baseline epigenetic status is critical for hPSC-based disease models in which the observed phenotype depends on proper XCI or imprinting, and that tissue-specific DNA methylation patterns can be accurately modeled during directed differentiation of hPSCs, even in the presence of variations in XCI or imprinting.

overall_design: To obtain a comprehensive view of hPSC-specific epigenomic patterns, we collected 136 hESC and 69 hiPSC samples representing more than 100 cell lines for analysis.  In order to establish expected variation in human tissues, we collected 80 high-quality and well-replicated samples representing 17 distinct tissue types from multiple individuals. Finally, we selected 50 additional samples from primary cell lines of diverse origin to control for any aberrations that may arise as a general, non-hPSC-specific, consequence of in vitro manipulation. With these samples, we performed genome-wide DNA methylation and mRNA expression profiling using the Illumina Infinium 27K and 450K DNA Methylation BeadChips as well as the Illumina HT12v3 Gene Expression BeadArray.

first: Gulsah

last: Altun

first: Candace

last: Lynch

first: Ha

last: Tran

first: Julie

last: Harness

first: Ileana

last: Slavin

first: Ibon

last: Garitaonandia

first: Franz-Josef

last: Müller

first: Yu-Chieh

last: Wang

first: Francesca

middle: S

last: Boscolo

first: Eyitayo

last: Fakunle

first: Sunray

first: Hyun

last: Park

first: Marina

last: Martynova

first: Tsaiwei

last: Ole

first: Darryl

middle: D

last: D'Lima

first: Ruslan

last: Semechkin

first: Mana

last: Parast

first: Vasiliy

last: Galat

first: Andrew

last: Laslett

first: Uli

last: Schmidt

first: Hans

last: Keirstead

first: Jeanne

last: Loring

first: Louise

middle: C

last: Laurent


title: Recurrent Variations in DNA Methylation in Human Pluripotent Stem Cells and their Differentiated Derivatives

first: Kristopher

last: Nazor

type:
Expression profiling by array
Methylation profiling by array

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

overall_design: Refer to individual Series

first: Gulsah

last: Altun

first: Candace

last: Lynch

first: Ha

last: Tran

first: Ileana

last: Slavin

first: Ibon

last: Garitaonandia

first: Franz

middle: F


title: Retinal light damage microarray

status: Public on May 05 2012

first: Joshua

last: Dunaief

state: PA

address: 422 Curie Blvd, 305 Stellar Chance labs

department: Ophthalmology

summary: Microarray analysis of murine retinal light damage reveals changes in iron regulatory, complement, and antioxidant genes in the neurosensory retina and isolated retinal pigment epithelium (RPE). With the advent of microarrays representing most of the transcriptome and techniques to obtain RNA from the isolated RPE monolayer, we have probed the response of the RPE and neurosensory retina (NSR) to light damage.

overall_design: Mice were exposed to 10,000 lux cool white fluorescent light for 18 hours and sacrificed 4 hours after photic injury. NSR and isolated RPE were collected, and RNA was isolated. DNA microarray hybridization was conducted as described in the Affymetrix GeneChip Expression Analysis Technical Manual. Microarray analysis was performed using probe intensity data derived from the Mouse Gene 1.0 ST Array. For the genes of interest, confirmation of gene expression was done using quantitative real-time PCR. Immunofluorescence assessed protein levels and localization.

first: Majda

last: Hadziahmetovic

first: Usha

last: Kumar

first: Steven

last: Grieco

first: Delu

last: Song

first: Yafeng

last: Li

first: John

middle: W

last: Tobias

middle: L


title: Expression data of Pioglitazone- or vehicle-treated CD4+FoxP3- T cells transduced with Foxp3+/- Pparg1 (or Pparg2)

status: Public on May 04 2012

first: CBDM

last: Lab

address: 77 Avenue Louis Pasteur

department: Microbiology and Immunobiology

institute: Harvard Medical School

summary: We identified Pparg as a major orchestrator of the phenotype of adipose-tissue resident regulatory T cells (VAT Tregs). To explore the contribution of Pparg1 and 2 in the generation of the VAT Tregs-specific gene signatures, CD4+FoxP3- T cells were transduced with Foxp3+/- Pparg1 (or Pparg2), treated with Pioglitazone or vehicle, and double sorted for microarray analysis.

overall_design: All gene expression profiles were obtained from highly purified (double-sorted) T cell populations sorted by flow cytometry. To reduce variability, cells from multiple mice were pooled. Triplicates were generated for all groups. Raw data were preprocessed with the RMA algorithm in GenePattern and averaged expression values were used for analysis.

first: Daniela

last: Cipolletta

first: Diane

last: Mathis

first: Christophe

last: Benoist


title: Expression data of Pioglitazone-, Rosiglitazone-, GW1929- and vehicle-treated CD4+FoxP3- T cells transduced with Foxp3+Pparg1

summary: Pioglitazone treatment of CD4+FoxP3- T cells transduced with Pparg and Foxp3 up-regulated a set of genes whose products have been implicated in lipid metabolism pathways. To verify the specificity of this treatment, we performed microarray analysis on Foxp3+Pparg1-transduced CD4+FoxP3- T cells after treatment with other PPARg agonists such as Rosiglitazone (TZD) and GW1929 (non-TZD).