title: Gene expression comparison between two human cancer cell Lines: Oral squamous cell carcinoma SASL1m and adenoid cystic carcinoma ACC2

status: Public on Oct 25 2011

city: Toon

first: Alejandro

last: Mayorca-Guiliani

state: Ehime

address: Shitsukawa

department: Oral and Maxillofacial Surgery

institute: Ehime University Graduate School of Medicine

summary: SASL1 is highly metastatic to lymph nodes. ACC2 is not metastatic. We compared gene expression on cultured cells to identify genes associated to metastatic spread patterns.

overall_design: SASL1m cells and ACC2 cells were cultured to confluence in 10 100mm dishes (5 per cell type). Total RNA was extracted (ISOGEN, Nippongene, Japan), purified by centrifugation, pooled and checked for quality (Eukaryote Total RNA Series II, Agilent, Sta Clara, USA) . Two samples of 2ɥg of Total RNA from SASL1m and ACC2 cells were labeled with biotin (3'IVT Labeling Kit, Affymetrix, USA) and hybridized (GeneAtlas Hybridization, Wash, and Stain Kit for 3' IVT Arrays, Affymetrix). The Microarray platform used was Affymetrix HG U219 Array Strip. The arrays were scanned in a GeneAtlas scanner controlled by GeneAtlas Software (Affymetrix, Sta. Clara, USA). No replicates were made. Genes were later filtered according to expression fold change (GeneSpring GX Software, Agilent, Sta Clara USA) and later organized in hypothetical networks (Ingenuity Pathway and Analysis Software, Ingenuity Systems, Redwood, USA). No control or reference samples were included. The expression of genes of interest was confirmed with qrt-PCR in the samples studied and four additional samples from cell cultures (Lightcycler, Roche, Switzerland).

middle: M

last: Guiliani

first: Hajime

last: Yano

first: Koh-Ichi

last: Nakashiro

first: Hiroyuki

last: Hamakawa

first: Junya

last: Tanaka


title: Transcriptional profiling of liver tissue from mice with wild-type, N750F mutant or exon 19 deleted RB1, after treatment with diethylnitrosamine.

status: Public on Dec 01 2011

city: PHILADELPHIA

first: Adam

last: Ertel

state: PA

address: 233 S 10TH ST

department: Cancer Biology

country: USA

institute: Thomas Jefferson University

summary: The LXCXE peptide motif facilitates interaction between the RB tumor suppressor and a large number of cellular proteins that are expected to impinge on diverse biological processes.  In vitro and in vivo analyses demonstrated that LXCXE-binding function is dispensable for RB promoter association and control of basal gene expression.  Dependence on this function of RB is unmasked after DNA damage, wherein LXCXE-binding is essential for exerting control over E2F3 and suppressing cell cycle progression in the presence of genotoxic stress.  Gene expression profiling revealed that the transcriptional program coordinated by this specific aspect of RB is associated with progression of human hepatocellular carcinoma and poor disease outcome.  Consistent with these findings, biological challenge revealed a requirement for LXCXE-binding in suppression of genotoxin-initiated hepatocellular carcinoma in vivo.  Together, these studies establish an essential role of the LXCXE-binding motif for RB-mediated transcriptional control, response to genotoxic insult, and tumor suppression.

overall_design: Mice transgenic for Cre-recombinase under the albumin promoter contain indicated combinations of loxP sites flanking exon 19 of Rb1 (f), N750F mutation (NF) or wild-type (plus) genotypes.  For gene expression microarray analysis, mice were aged to 14 days and treated for 24 hours with diethylnitrosamine (DEN) or saline as an “untreated” control.  Liver tissue was obtained from DEN treated livers and compared to normal liver tissue of saline treated littermates.

first: Ryan

middle: J

last: Bourgo

first: Erik

middle: S

last: Knudsen

middle: A


title: Expression data from control and COUP-TFII siRNA treated HUVEC cells

status: Public on Oct 28 2011

city: Houston

first: Xinpu

last: Chen

address: One baylor Plaza

institute: Baylor College of Medicine

summary: COUP-TFII plays a critical role in angiogenesis during development. It has also been shown to suppress Notch signaling pathway to confer vein identity. However, the downstream targets and the mechanism mediate COUP-TFII function to regulate these processes remain elusive. To identify the downstream targets and the mechanism by which COUP-TFII regulates agiogenesis and vein specification, we knocked down COUP-TFII in HUVEC cells using COUP-TFII specific siRNA and used microarray analysis to identify downstream targets. Interestingly, we found the expression of many genes in the cell cycle pathway and Notch signaling pathway are significantly altered in the COUP-TFII depleted cells.

overall_design: HUVEC Cells were transfected with siRNA  (Control or COUP-TFII siRNA) duplexes (50 nM) and total RNA was isolated 48 hours later.

first: Sophia

middle: Y

last: Tsai

first: Ming-Jer


title: Gene expression profiling of negative-pressure-treated split-thickness skin graft donor site wounds reveals novel effects on epithelialization

city: Helsinki

first: Kristo

middle: Juhana

last: Nuutila

address: Haartmaninkatu 8, Biomedicum 1

department: Institute of Biomedicine

country: Finland

institute: University of Helsinki

summary: Negative-pressure wound therapy (NPWT) is widely used to improve skin wound healing and to accelerate wound bed preparation. Although NPWT has been extensively studied as a treatment for deep wounds, its effect on epithelialization of superficial dermal wounds remains unclear. To clarify the effect of NPWT on reepithelialization, we applied NPWT on split- thickness skin graft donor sites from the first postoperative day (POD) to the seventh POD. Six patients took part in the study and two samples were obtained from each. The first biopsy sample was taken at elective surgery before split-thickness skin grafting and the second one during reepithelialization on the seventh POD. In all 12 samples (eight from four NPWT patients, and four from two control patients) were collected for this study. From each sample, we carried out a comprehensive genome-wide microarray analysis. Data from patients receiving NPWT were compared groupwise with data from those not receiving NPWT.

overall_design: Overall 12 samples were analyzed

first: Antti

last: Siltanen

first: Matti

last: Peura

first: Ari

last: Harjula

first: Tapio

last: Nieminen

first: Jyrki

last: Vuola

first: Esko

last: Kankuri

first: Pertti

last: Aarnio


title: Modulation of mRNA in human T-cell development (expression)

status: Public on Oct 27 2011

city: Padova

first: Alberto

last: Corradin

state: PD

address: via Tiepolo

department: Dipertimento di Ingegneria dell'Informazione

country: Italy

institute: Università degli Studi di Padova

summary: Gene expression of Double Positive, and Single Positive CD4+ human thymocytes

overall_design: We used microarrays to identify genes involved in T cell maturation

first: M

last: Ghisi

first: A

first: K

last: Basso

first: C

last: Frasson

first: S

last: Mukherjee

first: L

last: Mussolin

first: V

last: Serafin

last: Ruggero

last: Guffanti

first: G

last: De Bellis

last: Gerosa

last: Stellin

first: D

last: D'Agostino

last: Bronte

last: Indraccolo

last: Amadori

first: P

last: Zanovello


title: Modulation of mRNA in human T-cell development

last: Corradin

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

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

overall_design: Refer to individual Series


title: Expression data from C2C12 cells with or without Smad3 overexpression

status: Public on Oct 21 2011

city: Madison

first: Michael

last: Hoffmann

state: WI

address: 1400 University Ave

institute: University of Wisconsin-Madison

summary: The goal of this study was to identify genes in C2C12 myoblasts whose expression was altered by overexpression of Smad3.

overall_design: Four total samples were analyzed. Two biological replicates were prepared from C2C12 cells infected with retroviral vector encoding wildtype Smad3 and exposed for 24 hours to 100 pM TGF-β.  Two biological replicates were prepared from C2C12 cells infected with a control retrovirus that did not encode Smad3 (empty vector, EV) and exposed for 24 hours to 100pM TGF-β.  To identify genes with altered expression between empty vector controls and cells overexpressing wild-type Smad3, we first pre-processed the four arrays using robust multiarray averaging as implemented in the R software package ‘xps’, version 1.10.2 (http://www.bioconductor.org/packages/release/bioc/html/xps.html). This preprocessing corrects for background noise and array effects, and aggregates probe data to 28,836 genes. Duplicates were averaged on the base-2 logarithm scale, and then we took differences between the averages to obtain logarithm-scale fold changes. Genes were selected which showed at least a two-fold change (raw scale) between wild-type and empty vector expressing cells. Due to the limited sample size, we did not apply any statistical tests to estimate false-discovery rate.  This resulted in 79 genes that were at least two-fold higher in the wild-type Smad3-expressing C2C12 cells compared to empty vector cells and 25 genes that were at least two-fold lower in the wild-type Smad3-expressing cells than the in the empty vector cells.

first: F

first: Michelle

last: Schiro


title: The redox-sensitive transcription factor, Nrf2, regulates murine hematopoietic stem cell survival

status: Public on Oct 22 2011

city: Baltimore

first: Biswal

last: Shyam

state: MD

address: 615 N Wolfe Street

department: EHS

institute: Johns Hopkins University

summary:
To better understand the differentiation and survival defect of Nrf2-/- HSPC, we performed gene expression studies on KSL cells isolated by FACS from Nrf2+/+ and Nrf2-/- mice.
Gene expression data suggests that loss of Nrf2 leads to global defects in cytokine signaling, and the administration of the exogenous granulocyte colony-stimulating factor (G-CSF) improved HSPC survival despite increasing intracellular ROS.

overall_design: Bone marrow cells from young healthy Nrf2+/+ and Nrf2-/- mice (n=5 per genotype ) were pooled, stained with KSL cell marker and FACS.  Total RNA was isolated from the pooled KSL cells, quantified, amplified and profiled. One pooled RNA sample from each genotype (Nrf2+/+ and Nrf2-/-) was profiled using Affymetrix GeneChip Mouse Gene ST 1.0 chips.

first: Akil

last: Merchant

first: Anju

last: Singh

first: William

last: Matsui

first: Shyam

last: Biswal


title: Gene expression changes in human neural cells exposed to VX (O-ethyl S-[2-(diisopropylamino)ethyl] methylphosphonothiolate)

city: Silver Spring

first: Xiugong

last: Gao

address: 503 Robert Grant Ave

institute: Walter Reed Army Institute of Research

summary:
Organophosphorus compounds may induce neurotoxicity through mechanisms other than the cholinergic pathway, which need to be unraveled by a comprehensive and systematic approach such as genome-wide gene expression analysis.
We used microarrays to study gene expression changes in human neural cells after exposure to VX, and identified pathways underlying these changes.

overall_design: Human neural cells were exposed to sublethal concentrations (0, 0.1, 10 μM) of VX. RNA were extracted at different timepoints (0, 6, 24, 72 h) after VX exposure and hybridized to Affymetrix microarrays. Four biological repeats were used for each condition.

first: Hsiuling

last: Lin

first: Radharaman

last: Ray

first: Prabhati


title: Human embryonic stem cells derived from embryos at different stages of development share similar transcription profiles

city: Reno

first: Gnanaratnam

last: Giritharan

state: Nevada

address: 645 Sierra Rose Drive, Suite 205

institute: Nevada Center for Reproductive Medicine

summary: We have derived hESC from biopsied blastomeres of cleavage stage embryos under virtually the same conditions we used for the derivation of hESC lines from inner cell mass of blastocyst stage embryos.  Blastomere-derived hESC lines exhibited all the standard characteristics of hESC including undifferentiated proliferation, genomic stability, expression of pluripotency markers and the ability to differentiate into the cells of all three germ layers both in vitro and in vivo.  To examine whether hESC lines derived from two developmental stages of the embryo differ in gene expression, we have subjected three blastomere-derived hESC lines and two ICM-derived hESC lines grown under identical culture conditions to transcriptome analysis using gene expression arrays.  Unlike previously reported comparisons of hESC lines which demonstrated, apart from core hESC-associated pluripotency signature, significant variations in gene expression profiles of different lines, our data show that hESC lines derived and grown under well-controlled defined culture conditions adopt nearly identical gene expression profiles.  Moreover, blastomere-derived and ICM-derived hESC exhibited very similar transcriptional profiles independent of the developmental stage of the embryo from which they originated.  Furthermore, this profile was evident in very early passages of the cells and did not appear to be affected by extensive passaging.  These results suggest that during derivation process cells which give rise to hESC acquire virtually identical stable phenotype and are not affected by the developmental stage of the starting cell population.

overall_design: we investigated whether human stem cell lines derived from late totipotent blastomeres of the cleavage stage embryo develop a more “primitive” phenotype than ICM-derived lines by profiling their respective gene expression, molecular regulation and signaling pathways.  In this study, we examined whether the inherent differences in the development stage of the starting embryonic cell population are maintained in the derived hESC lines by evaluating the stemness, differentiation capacity and gene expression profiles of blastomere- and ICM-derived hESC lines.

first: Dusko

last: Ilic

first: Matthew

last: Gormley

first: Ana

last: Krtolica


title: Biology of human melanoma

status: Public on Oct 31 2011

city: Sao Paulo

first: Waleska

middle: Kerllen

last: Martins

state: Sao Paulo

address: Rua Antonio Prudente, 211

country: Brazil

institute: Hospital A.C. Camargo

summary: In normal skin, interactions between melanocytes and keratinocytes, and between melanocytes and the basal membrane are functionally relevant for maintenance of homeostasis and epidermal melanin unit whose deregulation may trigger a continuous proliferation of the melanocytes. In order to further elucidate the molecular events related to cell-cell and cell-ECM interactions in relation to the biology of melanomas, we analyzed the expression profile of 64 human melanomas, 21 primary samples and 43 independent metastasis.

overall_design: Tissue samples melanomas were obtained at Hospital A. C. Camargo.  All patients signed an informed consent and the study was approved by our internal ethics committee. Tissue samples obtained by surgery were snap-frozen in liquid nitrogen and biopsy samples were collected in RNAlaterTM (Ambion, Austin, TX). Non-tumor areas were removed by handy dissection and only samples represented by at least 70% of tumors cells within their natural stroma were selected for RNA extraction. Total RNA was extracted using RNeasy Midi-Kit® and amplified by a T7-based protocol. An indirect cDNA-labeling was performed as described by Cox et al. (2004). We used dual-label system in which two RNA samples (test and reference) were separately reverse-transcribed, labeled, mixed, and hybridized together to each array.  Each sample was hybridized in duplicate, with dye swap between sample and reference. As reference RNA we used a pool of equal amounts of total RNA from 5 human cutaneous melanoma cell lines (SK-MEL 05; 17; 28; 37 and 188, kindly provided by Dr. Alan Houghton, MSKCC, New York, NY, USA). We used glass arrays containing 4.800 cDNA sequences (Brentani et al.  2003) were prepared in our lab with the aid of the Flexys robot17 (Genomic Solutions, Cambridgeshire, United Kingdom). The list of immobilized genes can be obtained at GEO, accession number GPL1930. Pre-hybridization, hybridization and washing were performed as previously described (Gomes et al. 2003; 2005), and slides were scanned on a laser scanner (ScanArray Express, PerkinElmer Life Sciences, Boston, MA). Data were extracted with ScanArray Express software (PerkinElmer Life Sciences, Boston, MA) using the histogram method.

first: Gustavo

last: Esteves

first: Otávio

last: Almeida

first: Gilles

last: Landman

first: Sarah

last: Marques

first: Luiz

last: Camargo

first: Helena

last: Brentani

first: Alex

last: Carvalho

first: João

last: Duprat

first: Eduardo

last: Neves

last: Reis


title: The transcription factors Snail and Slug activate the TGF-B signaling pathway in breast cancer

city: Durham

first: Dhiral

last: Phadke

state: NC

address: Research Triangle Park

institute: SRA International Inc

summary:
Gene expression profiling to determine transcriptome changes following Snail or Slug expression in MCF-7 breast cancer cells
Samples were isolated in three biological replicates for microarray analysis.

overall_design: Four MCF-7 breast cancer cell subsets:  MCF-7(untreated), MCF-7 (with Control adenovirus), MCF-7 (with Snail adenovirus) and MCF-7 (with Slug adenovirus). RNA was purified on Day 0 for untreated, and on days 1,2 and 4 for the remaining three subsets for gene expression profiling on microarray.

first: Archana

last: Dhasarathy

first: Deepak

last: Mav

first: Ruchir

middle: R

last: Shah

first: Paul

last: Wade


title: Activity of SigB Modulates Virulence Gene Expression in a Murine Staphylococcus aureus Infection Model but Does Not Influence the Host Kidney Gene Expression

status: Public on Oct 24 2011

city: Greifswald

first: Maren

last: Depke

address: Friedrich-Ludwig-Jahn-Straße 15a

department: Functional Genomics

country: Germany

summary: Background.  Infections caused by Staphylococcus aureus are associated with significant morbidity and mortality and are an increasing threat not only in hospital settings. The expression of the staphylococcal virulence factor repertoire is known to be affected by the alternative sigma factor B (SigB). However, its impact during infection still is a matter of debate.  Methods.  Kidney tissue of controls or mice infected with S. aureus HG001 or its isogenic sigB mutant was analyzed by transcriptome profiling to monitor the host response, and additionally expression of selected S. aureus genes was monitored by RT-qPCR.  Results.  Direct transcript analysis by RT-qPCR revealed significant SigB activity in all mice infected with the wild type strain (WT), but not in its isogenic sigB mutant (p<0.0001). Despite a clear cut difference in the SigB-dependent transcription pattern of virulence genes (clfA, aur, and hla), the host reaction to infection (either WT or sigB mutant) was almost identical.  Conclusions.  Despite its significant activity in vivo, loss of SigB did not have an effect on the outcome of infection as well as on murine kidney gene expression pattern. Thus, these data support the role of SigB as virulence modulator rather than being a virulence determinant by itself.

overall_design: Murine kidney gene expression pattern of 3 groups were compared: 1) after infection with S. aureus HG001 (wild type); 2) after infection with S. aureus HG001 ΔsigB; 3) sham control (injection of physiological saline solution). The infection was performed twice (2 biological replicates), and the array analysis included 4 or 5 mice (independent samples) per group. In total, the study consisted of 24 arrays.

first: Marc

last: Burian

first: Tina

last: Schäfer

first: Knut

last: Ohlsen

first: Uwe

last: Völker


title: Epigenetic portraits of human breast cancers (various cell lines expression data)

status: Public on Oct 19 2011

city: Toronto

first: Benjamin

last: Haibe-Kains

state: Ontario

address: 610 University Avenue

department: Princess Margaret Research

country: Canada

institute: Princess Margaret Cancer Centre

summary: Breast cancer is a molecularly, biologically and clinically heterogeneous group of disorders. Understanding this diversity is essential to improving diagnosis and optimising treatment. Both genetic and acquired epigenetic abnormalities participate in cancer, but information is scant on the involvement of the epigenome in breast cancer and its contribution to the complexity of the disease. Here we used the Infinium Methylation Platform to profile at single-CpG resolution (over 14,000 genes interrogated) the methylomes of 119 breast tumours. It emerges that many genes whose expression is linked to the ER status are epigenetically controlled (or/ we show that the two major phenotypes of breast cancers determined by ER status are widely involving epigenetic regulatory mechanisms), offering the prospect of a novel approach to treating ER-positive tumours. We have distinguished methylation-profile-based tumour clusters, some coinciding with known “expression subtypes” but also new entities that may provide a meaningful basis for refining breast tumour typology. We show that methylation patterns may reflect the cellular origins of tumours. Having highlighted an unexpectedly strong epigenetic component in the regulation of key immune pathways, we show that a set of immune genes have high prognostic value in specific tumour categories. By laying the ground for better understanding of breast cancer heterogeneity and improved tumour taxonomy, the precise epigenetic portraits drawn here should contribute to better management of breast cancer patients.

overall_design: Gene expression profiling  cell lines. Study of epigenetic variation (methylation) linked to gene expression. No replicate, no reference sample.

last: Dedeurwaerder

first: Christine

last: Desmedt

first: Emilie

last: Calonne

first: Sandeep

middle: K

last: Singhal

first: Judith

last: Luciani

first: Pascale

last: Putmans

first: Françoise

last: Lallemand

first: Denis

last: Larsimont

first: Jérôme

last: Toussaint

first: Sandy

last: Haussy

last: Rothé

first: Ghizlane

last: Rouas

first: Otto

last: Metzger

first: Michel

last: Georges

first: Christos

last: Sotiriou

first: François

last: Fuks


title: Roles of  EMT regulator in colon cancer

city: Taipei

first: Wei-Lun

last: Hwang

address: No.155, Sec.2, Linong Street

department: Department of Biotechnology and Laboratory Science in Medicine

country: Taiwan

institute: National Yang Ming Chiao Tung University

summary: Isolation and enrichment of cancer stem cells in colorectal carcinoma to study role of epithelial-mesenchymal transition regilators in tumor malignancy.

overall_design:
Genome-wide comparision in sphere cells and parental control cells revealed potential regulators involved tumor malignancy .
Overexpression of these key regulators drafted cellular context toward therapy resistance


title: Expression data analyzing ID3 (Inhibitor of DNA binding 3)-affected mouse T cells

status: Public on Oct 16 2011

city: Budapest

first: Zoltan

last: Pos

address: 4 Nagyvarad ter

department: Dept. of Genetics, Cell- and Immunobiology

country: Hungary

institute: Semmelweis University

summary: Mouse CD8+ T cells affected by ID3 (Inhibitor of DNA binding 3) display patterns of gene expression suggesting enhanced persistance and survival. In this study, we identified genes differentially expressed between ID32a transduced and mock transduced, and ID32a knockout and wild type mouse CD8+ T cells. Most prominent functions of differentially expressed genes include DNA replication-associated repair, maintenance of chromosome stability and mitotic cell divison machinery. Overall, these data suggest that ID3 acts in favor of maintained survival in CD8+ mouse T cells.

overall_design: Two independent microarray experiments were carried out using separate array batches, one comparing Id32aThy1.1 (ID32a transduced) with Thy1.1 pmel-1 (mock transduced) CD8+ T cells sorted 5 days after infection, and a second experiment comparing Id32a-/- (Id32a knockout)CD8+ T cells with Id32a+/+ (Id32a wild type) controls, both in an upaired design. Individual array samples were generated by pooling equal amounts of total RNA derived from purified T cells of four individual mice. Each experimental group consisted of four such microarrays (statistical group size n=4, pooled samples derived from 16 mice per assay group total).

first: Yun

last: Ji

first: Mahadev

last: Rao

first: Christopher

last: Klebanoff

first: Zhiya

last: Yu

first: Madhusudhanan

last: Sukumar

first: Robert

middle: N

last: Reger

first: Douglas

middle: C

last: Palmer

first: Zachary

last: Borman

first: Pawel

last: Muranski

first: Ena

last: Wang

first: David

last: Schrump

first: Francesco

last: Marincola

first: Nicholas

middle: P

last: Restifo

first: Luca

last: Gattinoni


title: Gene expression data from cultured cells or from nude mice xenografts

status: Public on Oct 15 2011

city: Rochester

first: Alexey

middle: Aleksandrovich

last: Leontovich

state: MN

address: 200 First street

department: Health Science Research

institute: Mayo Clinic

summary: In this study we performed gene transcription analysis of parental MACF7 cell and MCF7 engineered to overexpress oncoprotein RAF1. We demonstrate that overexpression of RAF1 leads to development of ivasive phenotype.

overall_design: Total RNA was extracted from culturued cells or from nude mice xenografts.

first: Antonino

last: D'Assoro

first: Jeffrey

middle: L

last: Salisbury

first: James

last: Ingle

first: Evanthia

last: Galanis

first: Amy

last: Degnim


title: An eight-gene expression signature for the prediction of survival and time to treatment in chronic lymphocytic leukemia

status: Public on Oct 14 2011

city: Munich

first: Tobias

last: Herold

address: Marchioninistr. 15

department: Department of Internal Medicine III

institute: University Hospital Grosshadern, Ludwig-Maximilians-University (LMU)

summary: Chronic lymphocytic leukemia (CLL) is a common and heterogeneous disease. An accurate prediction of outcome is highly relevant for the development of personalized treatment strategies. Microarray technology was shown to be a useful tool for the development of prognostic gene expression scores. However, there are no gene expression scores which are able to predict overall survival in CLL based on the expression of few genes that are better than established prognostic markers. We correlated 151 CLL microarray data sets with overall survival using Cox regression and supervised principal component analysis to derive a prognostic score. This score based on the expression levels of eight genes and was validated in an independent group of 149 CLL patients by quantitative real time PCR. The score was predictive for overall survival and time to treatment in univariate Cox regression in the validation data set (both: p<0.001) and in a multivariate analysis after adjustment for 17p and 11q deletions and the IgVH-status. The score achieved superior prognostic accuracy compared to models based on genomic aberrations and IgVH-status and may support personalized therapy.

overall_design: Analysis of 151 samples of peripheral blood mononuclear cells (107 HGU-133plus2; 44 HGU-133A; 44 HGU-133B) from adult patients with chronic lymphocytic leukemia (CLL)

first: Vindi

last: Jurinovic

first: Klaus

last: Metzeler

first: Anne-Laure

last: Boulesteix

first: Manuela

last: Bergmann

first: Till

last: Seiler

first: Medhanie

last: Mulaw

first: Silvia

last: Thoene

first: Annika

last: Dufour

first: Zlatana

last: Pasalic

first: Markus

last: Schmidberger

first: Michael

last: Schmidt

first: Stephanie

last: Schneider

first: Purvi

last: Kakadia

first: Michaela

last: Feuring-Buske

first: Jan

last: Braess

first: Karsten

last: Spiekermann

first: Ulrich

last: Mansmann

first: Wolfgang

last: Hiddemann

first: Christian

last: Buske

first: Stefan

last: Bohlander


title: Expression analysis of genes located in the minimally deleted regions of 13q14 and 11q22-23 in chronic lymphocytic leukemia – unexpected expression pattern of the RHO GTPase activator ARHGAP20

first: Tobias

last: Herold

summary:
In chronic lymphocytic leukemia (CLL), 13q14 and 11q22-23 deletions are found in 2/3 of the cases. 11q22-23 deletions are associated with poor survival, whereas 13q14 deletions as single abnormality are often found in indolent disease forms. The molecular basis for this difference in prognosis is not known.
ARHGAP20 encodes an evolutionarily conserved protein. In the zebra fish (Danio rerio) genome the syntenic regions of human chromosomal bands 13q14 and 11q22-23 are juxtaposed. The similar expression profiles of ARHGAP20 in 13q14 and 11q22-23 deleted CLL cases suggest a molecular connection and an intriguing mechanism of regulation.

overall_design: Analysis of 154 samples of peripheral blood mononuclear cells (109 HGU-133plus2; 45 HGU-133A; 45 HGU-133B) from adult patients with chronic lymphocytic leukemia (CLL).

first: Vindi

last: Jurinovic


title: Nonlesional atopic dermatitis skin is characterized by broad terminal differentiation defects and variable immune abnormalities

status: Public on Oct 13 2011

city: New York

first: Mayte

last: Suarez-Farinas

state: NY

address: 1425 Madison Ave, L2-70C, Box 1077,

institute: Mount SinaiSchool of Medicine

summary: Atopic dermatitis (AD) is a common inflammatory skin disease with a T(H)2 and T22 immune polarity. Despite recent data showing a genetic predisposition to epidermal barrier defects in some patients, a fundamental debate still exists regarding the role of barrier abnormalities versus immune responses in initiating the disease. An extensive study of nonlesional AD (ANL) skin is necessary to explore whether there is an intrinsic predisposition to barrier abnormalities, background immune activation, or both in patients with AD. We sought to characterize ANL skin by determining whether epidermal differentiation and immune abnormalities that characterize lesional AD (AL) skin are also reflected in ANL skin.  We performed genomic and histologic profiling of both ANL and AL skin lesions (n = 12 each) compared with normal human skin (n = 10). We found that ANL skin is clearly distinct from normal skin with respect to terminal differentiation and some immune abnormalities and that it has a cutaneous expansion of T cells. We also showed that ANL skin has a variable immune phenotype, which is largely determined by disease extent and severity. Whereas broad terminal differentiation abnormalities were largely similar between involved and uninvolved AD skin, perhaps accounting for the background skin phenotype, increased expression of immune-related genes was among the most obvious differences between AL and ANL skin, potentially reflecting the clinical disease phenotype. Our study implies that systemic immune activation might play a role in alteration of the normal epidermal phenotype, as suggested by the high correlation in expression of immune genes in ANL skin with the disease severity index.

overall_design: Genomic profile of paired samples of  ANL and AL skin lesions from 12 patients compared with normal human skin (n = 8). For some patients, only 1 sample was available.

last: Suárez-Fariñas

first: Emma

last: Guttman-Yasky


title: b-AP15, a novel proteasome inhibitor

status: Public on Oct 17 2011

city: Uppsala

first: Mårten

last: Fryknäs

address: Akademiska sjh ingång 61

department: Medical sciencies

country: Sweden

institute: Uppsala university

summary: Microarray based mRNA profiling was used to identify the mechanism of action for the small molecule b-AP15.

overall_design: MCF7 cells were treated with b-AP15 (1µM) or vehicle for 6 hours, followed by RNA isolation and gene expression analysis.

first: Marten

last: Fryknas


title: Inferring transcriptional and microRNA-mediated regulatory programs in glioblastoma

status: Public on Oct 12 2011

city: Seattle

first: Manu

last: Setty

state: WA

address: 1100 Fairview Ave N

department: Basic Sciences Division

institute: Fred Hutchinson Cancer Center

summary: Large-scale cancer genomics projects are profiling hundreds of tumors at multiple molecular layers, including copy number, mRNA and miRNA expression, but the mechanistic relationships between these layers are often excluded from computational models.  We developed a supervised learning framework for integrating molecular profiles with regulatory sequence information to reveal regulatory programs in cancer, including miRNA-mediated regulation. We applied our approach to 320 glioblastoma profiles and identified key miRNAs and transcription factors as common or subtype-specific drivers of expression changes.  We confirmed that predicted gene expression signatures for proneural subtype regulators were consistent with in vivo expression changes in a PDGF-driven mouse model.  We tested two predicted proneural drivers, miR-124 and miR-132, both underexpressed in proneural tumors, by overexpression in neurospheres and observed a partial reversal of corresponding tumor expression changes.  Computationally dissecting the role of miRNAs in cancer may ultimately lead to small RNA therapeutics tailored to subtype or individual.

overall_design: miRNA mimetics were transfected to PDGFRA amplified neurosphere cell lines. Gene expression was measured 24 hours after transfection

first: Karim

last: Helmy

first: Aly

last: Khan

first: Aaron

last: Arvey

first: Frank

last: Neezen

first: Phaedra

last: Agius

first: Eric

last: Holland

first: Christina

last: Leslie


title: Beta-catenin Controls Metastasis in Braf-activated Pten-inactivated Melanomas

city: New Haven

first: William

last: Damsky

state: CT

address: 333 Cedar St, LCI 501

department: Dermatology

institute: Yale School of Meicine

summary: Malignant melanoma is characterized by frequent metastasis, however specific changes that regulate this process have not been clearly delineated. Although it is well known that Wnt signaling is frequently dysregulated in melanoma, the functional implications of this observation are unclear. By modulating beta-catenin levels in a mouse model of melanoma that is based on melanocyte-specific Pten loss and BrafV600E mutation, we demonstrate that beta-catenin is a central mediator of melanoma metastasis to lymph node and lung. In addition to altering metastasis, beta-catenin levels control tumor differentiation and regulate both MAPK/Erk and PI3K/Akt signaling. Highly metastatic tumors with beta-catenin stabilization are very similar to a subset of human melanomas; together these findings establish Wnt signaling as a metastasis regulator in melanoma.

overall_design:
MoGene-1_0-st-v1: Four samples total. Two biological replicates of uncultured Pten/Braf murine melanomas and two biological replicates of uncultured Pten/Braf/Bcat-STA murine melanomas.
MoEx-1_0-st-v1: Two samples total. Dissociated tumor and FACS-enriched Pten/Braf and Pten/Braf/Bcat-STA murine melanoma.

middle: E

first: David

last: Curley

first: Manjula

last: Santhanakrishnan

first: Lara

last: Rosenbaum

first: James

middle: T

last: Platt

first: Bonnie

middle: G

last: Rothberg

first: Makoto

last: Taketo

last: Dankort

last: Rimm

first: Martin

last: McMahon

first: Marcus

last: Bosenberg


title: Longitudinal analysis of gene expression and behaviour in the HdhQ150 mouse model of HD

status: Public on Nov 01 2011

city: CARDIFF

first: Peter

last: Giles

address: Heath Park

country: United Kingdom

institute: Cardiff University

summary: Transcriptional profiles in the HdhQ150 mouse model of HD and wild-type litter mates at 6, 12 and 18 months

first: Lesley

last: Jones


title: Gene expression data of endothelium exposed to heme

city: Atlanta

first: Tianwei

last: Yu

state: GA

address: 1518 Clifton Rd NE

department: Biostatistics

institute: Emory University

summary:
Sickle cell disease is characterized by hemolysis, vaso-occlusion and ischemia reperfusion injury. These events cause endothelial dysfunction and vasculopathies in multiple systems
However, the lack of atherosclerotic lesions has led to the idea that there are adaptive mechanisms that protect the endothelium from major vascular insults in SCD patients.
The molecular bases for this phenomenon are poorly defined. This study was designed to identify the global profile of genes induced by heme in the endothelium.

overall_design: Human pulmonary artery endothelial cells (PAECs), and human pulmonary microvascular endothelial cells (PMVECs) were grown to confluence, and treated with freshly prepared ferric heme every 48 hours for 7 days. Total RNA was extracted, used for microarray analysis, using an Affymetric U133 plus 2.0 chip

first: Samit

last: Ghosh

first: Fang

last: Tan

first: Yuhua

last: Li

first: Olufolake

last: Adisa

first: Mario

last: Mosunjac

first: Solomon

middle: F

last: Ofori-Acquah


title: CD4 on human monocytes

city: Los Angeles

first: Scott

middle: G.

last: Kitchen

state: CA

address: 615 Charles E.Young Dr. S.

institute: UCLA AIDS Institute

summary: We examined the efffects of ligating CD4 expressed by primary human peripheral blood monocytes with soluble MHC Class II.

overall_design: 3 replicates are included. Fresh blood monocytes, obtained through negative selection via magnetic activted cell sorting (Miltenyi, Auburn, CA), from three separate individual donors were treated with RPMI-1640 medium alone or with medium containing sMHC II (1 μg/ml) for three hours. Cells were harvested and RNA purified using the RNeasy procedure (Qiagen). RNA was then analyzed by the UCLA Clinical Microarray Core Laboratory using the Human U133 Plus 2.0 Array (Affimetrix). Data was analyzed using Dchip software. Visual inspection did not find any potential outliers or suspect areas. Data across all groups were normalized using the PM/MM difference.


title: The impact of aging on memory T cell phenotype and function in the human bone marrow

first: Dietmar

last: Herndler-Brandstetter

address: 300 Cedar Street

department: Immunobiology

institute: Yale University School of Medicine

summary: Recently, the bone marrow (BM) has been shown to play a key role in regulating the survival and function of memory T cells. However, the impact of aging on these processes has not yet been studied. We demonstrate that the number of CD4+ and CD8+ T cells in the BM is maintained during aging. However, the composition of the T cell pool in the aged BM is altered with a decline of naïve and an increase in effector-memory T cells. In contrast to the peripheral blood (PB), a highly activated CD8+CD28– T cell population, which lacks the late differentiation marker CD57, accumulates in the BM of elderly persons. IL-6 and IL-15, which are both increased in the aged BM, efficiently induce the activation, proliferation and differentiation of CD8+ T cell in vitro, highlighting a role of these cytokines in the age-dependent accumulation of highly activated CD8+CD28– T cells in the BM. Yet, these age-related changes do not impair the maintenance of a high number of polyfunctional memory CD4+ and CD8+ T cells in the BM of elderly persons. In summary, aging leads to the accumulation of a highly activated CD8+CD28– T cell population in the BM, which is driven by the age-related increase of IL-6 and IL-15. Despite these changes, the aged BM is a rich source of polyfunctional memory T cells and may thus represent an important line of defense to fight recurrent infections in old age.

overall_design: A total of 4 samples (bone marrow mononuclear cells) were analyzed (2 young and 2 elderly persons)


title: In vitro prednisolone resistance signature in MLL-rearranged infant ALL

city: Rotterdam

first: Jill

last: Spijkers-Hagelstein

address: Dr Molewaterplein 50

department: Pediatric Oncology

country: Netherlands

institute: ErasmusMC - Sophia's Childrens Hospital

summary: Acute Lymphoblastic Leukemia (ALL) in infants (<1 year of age) is characterized by a high incidence of MLL translocations which is associated with a poor prognosis. Contributing to this poor prognosis is cellular drug resistance, especially to glucocorticoids like prednisolone. Although in vitro prednisolone resistance mechanisms have been proposed in pediatric ALL, it has never been studied in MLL-rearranged infant ALL, which are highly resistant to glucocorticoids in vitro and in vivo.

overall_design: We analyzed primary MLL-rearranged infant ALL expression profiles, which were either in vitro prednisolone-resistant or prednisolone-sensitive, in order to study in vitro prednisolone resistance.

first: J

first: R

middle: W

last: Stam


title: Autism and increased paternal age related changes in global levels of gene expression regulation

status: Public on Oct 09 2011

city: Philadelphia

first: mark

last: alter

address: 125 S. 31st Street

department: Center for Neurobiology and Behvior

institute: University of Pennsylvania

summary: A causal role of mutations in genes encoding for multiple general transcription factors in neurodevelopmental disorders including autism suggested that alterations at the global level of gene expression regulation might also relate to disease risk in sporadic cases of autism. This premise can be tested by evaluating for global changes in the overall distribution of gene expression levels. For instance, in mice, we recently showed that variability in hippocampal-dependent behaviors was associated with variability in the pattern of the overall distribution of gene expression levels, as assessed by variance in the distribution of gene expression levels in the hippocampus. We hypothesized that a similar change in the variance in gene expression levels might be found in children with autism. Gene expression microarrays covering greater than 47,000 unique RNA transcripts were done on purified RNA from peripheral blood lymphocytes of children with autism (n=82) and controls (n=64). The variance in the distribution of gene expression levels from each microarray was compared between groups of children. Also tested was whether a risk factor for autism, increased paternal age, was associated with variance in the overall distribution of gene expression levels. A decrease in the variance in the distribution of gene expression levels in peripheral blood lymphocytes (PBL) was associated with the diagnosis of autism and a risk factor for autism, increased paternal age. Traditional approaches to microarray analysis of gene expression suggested a possible mechanism for decreased variance in gene expression. Gene expression pathways involved in transcriptional regulation were down-regulated in the blood of children with autism and children of older fathers. Thus, results from global and gene specific approaches to studying microarray data were complimentary and supported the hypothesis that alterations at the global level of gene expression regulation are related to autism and increased paternal age. Regulation of transcription, thus, represents a possible point of convergence for multiple etiologies of autism and other neurodevelopmental disorders.

overall_design:
The study was designed to compare gene expression profiles in peripheral blood lymphocytes of children with autism (n=82) and controls(n=64).
Expression profiling: Expression profiling was performed at Translational Genomics (TGen), a member of the NIMH Neuroscience Microarray Consortium. Total RNA was extracted from peripheral blood lymphocytes (PBL) within 30 minutes of the blood draw using the Qiagen Qiaquick kit (Germantown, MD). Isolated total RNA was double round amplified, cleaned, and biotin-labeled using Affymetrix’s GeneChip Two-Cycle Target Labeling kit (Santa Clara, CA) with a T7 promoter and Ambion’s MEGAscript T7 High Yield Transcription kit (Austin, TX) as per manufacturer’s protocol. Amplified and labeled cRNA was quantified on a spectrophotometer and run on a 1% TAE gel to check for an evenly distributed range of transcript sizes. Twenty micrograms of cRNA was fragmented to approximately 35-200bp by alkaline treatment (200 mM Tris-acetate, pH 8.2, 500 mM KOAc, 150 mM MgOAc) and run on a 1% TAE gell to verify fragmentation. Separate hybridization cocktails were made using 15 micrograms of fragmented cRNA from each sample as per Affymetrix’s protocol.
Two hundred microliters (containing 10 micrograms of fragmented cRNA) of each cocktail was separately hybridized to an Affymetrix Human Genome U133 Plus 2.0 Array for 16h at 45 degree Celsius in the Hybridization Oven 640. The Affymetrix Human Genome Arrays measure the expression of over 47,000 transcripts and variants, including 38,500 characterized human genes. Arrays were washed on Affymetrix’s GeneChip Fluidics Station 450 using a primary streptavidin phycoerythrin (SAPE) stain, subsequent biotinylated antibody stain, and secondary SAPE stain. Arrays were scanned on Affymetrix’s GeneChip Scanner 3000 7G with AutoLoader. Scanned images obtained by the Affymetrix GeneChip Operating Software (GCOS) v1.2 were used to extract raw signal intensity values per probe set on the array. A scaling factor of 150 was used to normalize array signal intensity in MAS 5.0.
Arrays were scanned over 1 day on 2 different machines. Arrays scanned on the same machine and in the same day were considered to be from the same scan batch. Rescanning of a limited number of samples indicated that there were no significant differences between machines, nonetheless, for all comparisons groups were balanced for the scan batch. Gene expression levels were not adjusted for possible batch effects as algorithms that attempt to adjust for batch effects also alter the gene expression distribution. When samples could not be prepped simultaneously they were balanced for group membership (autism vs. control). To statistically control for possible confounds related to scan batches in our analysis of gene expression variance, batch number was entered into an analysis of covariance. For traditional analysis of gene expression, experimental groups were balanced with respect to batch membership.
Microarray data analysis: Affymetrix .cel files were imported into Affymetrix Expression Console version 1.1.  Data was pre-processed and summarized by Microarray Analysis Suite (MAS) 5.0 and Robust Multiarray Analysis (RMA). For the analysis of gene expression distributions, MAS 5.0 was used because the algorithm does not alter the gene expression distribution, whereas, RMA utilizes quantile normalization of probes prior to summarization and, therefore, has the potential to remove group level differences in gene expression distributions. Because of the numerous advantages in its handling of noise in gene expression and background subtraction, RMA was used for traditional gene expression analyses looking for specific gene expression differences between groups. Because, we found group level differences in the distribution of gene expression levels between groups, for traditional gene expression analyses summarized gene expression levels were also quantile normalized after the summarization step. Quantile normalization adjusts all data sets such that they have identical distribution patterns. Probesets were then filtered for those that were called present in at least 50 out of the 146 subjects (n = 25,146 probesets). A p-value of .05 was used as a threshold for significance. A fold-change of 1.1 was used as a cut off for magnitude of change. All microarrays met manufacturers recommended quality control criteria. Present calls ranged from 37.4% to 49%, mean 43.7%, SD 2.7%. Actin 3’to5’ ratios ranged from .726 to 5.15, mean1.37, SD 0.5. There were no significant group level differences in quality control measures.

first: Mark

last: Alter


title: Individual aiEMT in surgical samples of esophageal cancer patients

status: Public on Oct 07 2011

city: Chuo-ku

first: Hiroki

last: Sasaki

state: Tokyo

country: Japan

institute: National Cancer Center Reseach Institute

summary:
Surgical samples have long been used as important subjects for cancer research. In accordance with an increase of neoadjuvant therapy, biopsy samples have recently become imperative for cancer transcriptome. On the other hand, both biopsy and surgical samples are available for expression profiling for predicting clinical outcome by adjuvant therapy; however, it is still unclear whether surgical sample expression profiles are useful for the prediction by the use of biopsy samples because little has been done about comparative gene expression profiling between the two kinds of samples.

When gene expression profiles were compared between biopsy and surgical samples, artificially induced epithelial-mesenchymal transition (aiEMT) was found in the surgical samples. This study will evoke the fundamental misinterpretation including underestimation of the prognostic evaluation power of markers by overestimation of EMT in past cancer research, and will furnish some advice for the near future as follows: 1) Understanding how long the tissues were under an ischemic condition; 2) Prevalence of biopsy samples for in vivo expression profiling with low biases on basic and clinical research; and 3) Checking cancer cell contents and normal- or necrotic-tissue contamination in biopsy samples for prevalence.

overall_design: We used microarrays to compare gene expression profiles between 20 biopsy (BPY) and 20 surgical (OPE) samples derived from the cancerous portion of the esophagus of 20 esophageal cancer patients. One biopsy sample and one surgical sample was obtained from each patient; these sample pairs have the same number.

first: Keiko

last: Minashi


title: Expression data from sorted Id3-GFP hi Id2-YFP int and Id3-GFP lo Id2-YFP hi activated CD8 T cells

city: San Diego

first: John

middle: Adam

last: Best

state: California

address: 9500 Gilman Dr

institute: UCSD

summary: During an immune response, CD8 T cells fall along a gradient of memory potential, but the regulators of these fate decsisions are not well understood. We utlized Id3-GFP and Id2-YFP reporter mice to elucidate the role of Id3 and Id2 during early CD8 T cell differentiation by gene expression.

overall_design: Id3-GFP hi Id2-YFP int  or Id3-GFP lo Id2-YFP hi OT-I cells were sorted into trizol at day 6 of VSV-OVA infection and analyzed by microarray


title: Tenascin-C modifies expression levels and territories of key patterning genes during spinal cord astrocyte specification [mus musculus]

status: Public on Oct 20 2011

city: Aachen

first: Bernd

last: Denecke

state: NRW

address: Pauwelsstrasse 30

department: IZKF Aachen

institute: RWTH Aachen University

summary: We demonstrate for the first time that the extracellular matrix glycoprotein Tenascin-C regulates the expression of key patterning genes during late embryonic spinal cord development, leading to a timely maturation of gliogenic neural precursor cells. We first show that Tenascin-C is expressed by gliogenic neural precursor cells during late embryonic development. The loss of Tenascin-C leads to a sustained generation and delayed migration of Fibroblast growth factor receptor 3 expressing immature astrocytes in vivo. Furthermore, we could demonstrate an upregulation of Nk2 transcription factor related locus 2 (Nkx2.2) and its downstream target Sulfatase 1 in vivo. A dorsal expansion of Nkx2.2-positive cells within the ventral spinal cord indicates a potential progenitor cell domain shift. Moreover, Sulfatase 1 is known to regulate growth factor signalling by cleaving sulphate residues from heparan sulphate proteoglycans. Consistent with this possibility we observed changes in both Fibroblast growth factor 2 and Epidermal growth factor responsiveness of spinal cord neural precursor cells. Taken together our data clearly show that Tenascin-C promotes the astroglial lineage progression during spinal cord development.

overall_design: in total 6 probes: 3 replica of TNC_wt and 3 replica of TNC_ko

first: Michael

last: Karus


title: Expression data for Mobilized Peripheral Blood CD34+ cells with Wnt or BMP stimulation

city: Boston

first: Teresa

middle: Venezia

last: Bowman

state: MA

address: One Blackfan Circle, 7th floor

institute: Children's Hospital Boston

summary:
Analysis of mobilized peripheral blood CD34+ cells from a healthy volunteer under erythroid differentiation conditions with and without stimulation to the BMP or Wnt signaling pathways. For erythroid differentiation, expanded CD34+ cells were placed in Stemspan SFEM medium supplemented with 2% pen/strep, 20ng/ml SCF, 1U/ml Epo, 5ng/ml IL3, 2uM dexamethasone, and 1uM beta-estradiol. Arrays were performed 2 hours after addition of cytokines. For signaling pathway stimulation, cells were exposed to 0.5uM BIO (a GSK3 inhibitor) for Wnt pathway activation, 25ng/ml rhBMP4 for BMP pathway activation, or vehicle control for 2 hours. Three biological replicates were performed per treatment group.
We used microarrays to detail the global program of gene expression changes after Wnt or BMP pathway stimulation in human CD34+ hematopoietic progenitors under erythroid differentiation conditions.

overall_design: To investigate the changes to gene expression in human CD34+ hematopoietic progenitors following stimulation of the Wnt or BMP pathways during the early stages of erythroid differentiation. Three biological replicates were performed per treatment group.

first: Eirini

last: Trompouki

middle: V

first: Lee

last: Lawton

first: Zi

last: Fan

first: Dai-Chen

last: Wu

first: Anthony

last: DiBiase

first: Corey

middle: S

last: Martin

first: Jennifer

last: Cech

first: Anna

last: Sessa

first: Jocelyn

last: Leblanc

first: Pulin

first: Ellen

middle: M

last: Durand

first: Christian

last: Mosimann

first: Garrett

last: Heffner

first: George

middle: Q

last: Daley

first: Robert

last: Paulson

first: Richard

middle: A

last: Young

first: Leonard

middle: I

last: Zon


title: Dissecting the retinoid-induced differentiation of F9 embryonal stem cells by integrative genomics [mRNA profiling]

status: Public on Oct 11 2011

city: Illkirch; Strasbourg

first: Marco Antonio

last: Mendoza-Parra

address: 1, rue Laurent Fries

country: France

institute: IGBMC

summary: Retinoic acid (RA) triggers physiological processes by activating heterodimeric transcription factors comprising retinoic acid (RARa,b,g) and retinoid X (RXRa,b,g) receptors. How a single signal induces highly complex temporally controlled networks that ultimately orchestrate physiological processes is unclear. Using an RA-inducible differentiation model we defined the temporal changes in the genome-wide binding patterns of RARg and RXRa and correlated them with transcription regulation. Unexpectedly, both receptors displayed a highly dynamic binding, with different RXRa heterodimers targeting identical loci. Comparison of RARg and RXRa co-binding at RA-regulated genes identified putative RXRa-RARg target genes that were validated with subtype-selective agonists. Gene regulatory decisions during differentiation were inferred from transcription factor target gene information and temporal gene expression.  This analysis revealed 6 distinct co-expression paths of which RXRa-RARg is associated with transcription activation, while Sox2 and Egr1 were predicted to regulate repression. Finally, RXRa-RARg regulatory networks were reconstructed through integration of functional co-citations. Our analysis provides a dynamic view of RA signalling during cell differentiation, reveals RA heterodimer dynamics and promiscuity, and predicts decisions that diversify the RA signal into distinct gene-regulatory programs.

overall_design: Transcriptional activity in F9 cells treated with different retinoic acid receptor (RAR) agonists; like all-trans retinoic acid (ATRA), BMS961 (RARg-specific), BMS753 (RARa-specific) or BMS641(RARb-specific); has been evaluated at different time-points (2, 6, 24, 48h) and compared with that found under Ethanol-vehicle treatment conditions (48h treatment).

first: Marco

first: Mannu

last: Walia

first: Martial

last: Sankar

first: Hinrich

last: Gronemeyer


title: Artificially induced epithelial-mesenchymal transition in surgical subjects: its implications in clinical and basic cancer research

first: Hiroki

last: Sasaki

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

overall_design: Refer to individual Series


title: Intracellular Signaling Pathways in Nonviral Gene Delivery: Microarray Analysis of Gene Expression Profiles in Transfected Cells

status: Public on Oct 05 2011

city: Lincoln

first: Jean-Jack

middle: M.

last: Riethoven

state: NE

address: 1901 Vine Street

department: Beadle Center for Biotechnology

institute: University of Nebraska-Lincoln

summary: Analysis of gene expression changes due to nonviral gene delivery of DNA lipoplexes versus control in human HEK293T cells.

overall_design: Human HEK293T RNA was isolated from control, non-transfected cells (CTR), transfected (GFP), and untransfected (GFPMINUS) samples for analysis on microarrays with three to six biological replicates.

first: Sarah

last: Plautz

first: Gina

last: Boanca

first: Angela

middle: K

last: Pannier


title: Identification of a Potently Oncogenic CALM-AF10 Minimal-Fusion Mutant

city: Ulm

first: Karlheinz

last: Holzmann

address: Helmholtzstreet 8/1

department: Medical Faculty

institute: Ulm University

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

platform_organism:
Mus musculus
synthetic construct


title: Rapid and robust generation of functional oligodendrocyte progenitor cells from epiblast stem cells

status: Public on Oct 03 2011

city: Cleveland

first: Paul

last: Tesar

state: Ohio

address: 10900 Euclid Ave.

department: Genetics & Genome Sciences

institute: Case Western Reserve University

summary: Stem cell biology has garnered much attention due to its potential to impact human health through disease modeling and cell replacement therapy.  This is especially pertinent to myelin-related disorders such as multiple sclerosis and leukodystrophies where restoration of normal oligodendrocyte function could provide an effective treatment.  Progress in myelin repair has been constrained by the difficulty in generating pure populations of oligodendrocyte progenitor cells (OPCs) in sufficient quantities.  Pluripotent stem cells theoretically provide an unlimited source of OPCs but significant advances are currently hindered by heterogeneous differentiation strategies that lack reproducibility.  Here we provide a platform for the directed differentiation of pluripotent mouse epiblast stem cells (EpiSCs) through a defined series of developmental transitions into a pure population of highly expandable OPCs in ten days.  These OPCs robustly differentiate into myelinating oligodendrocytes both in vitro and in vivo.  Our results demonstrate that pluripotent stem cells can provide a pure population of clinically-relevant, myelinogenic oligodendrocytes and offer a tractable platform for defining the molecular regulation of oligodendrocyte development, drug screening, and potential cell-based remyelinating therapies.

overall_design: 6 total samples were analyzed.  Pluripotent epiblast stem cells (EpiSCs) were differentiated to patterned neural rosettes, oligodendrocyte progenitor cells (OPCs), and oligodendrocytes.  OPCs and oligodedrocytes were analyzed at two separate passages (3 and 11).


title: Dosage-dependent phenotypes in models of 16p11.2 lesions found in autism

city: Cold Spring Harbor

first: Guy

last: Horev

state: New York

address: 1 Bungtown Road

institute: Cold Spring Harbor Laboratory

summary: Recurrent Copy Number Variations (CNVs) of human 16p11.2 have been associated with a variety of developmental/neurocognitive syndromes. In particular, deletion of 16p11.2 is found in patients with autism, developmental delay, and obesity. Patients with deletions or duplications have a wide range of clinical features, and siblings carrying the same deletion often have diverse symptoms. To study the consequence of 16p11.2 CNVs in a systematic manner, we used chromosome engineering to generate mice harboring deletion of the chromosomal region corresponding to 16p11.2, as well as mice harboring the reciprocal duplication. These 16p11.2 CNV models have dosage-dependent changes in gene expression, viability, brain architecture, and behavior. For each phenotype, the consequence of the deletion is more severe than that of the duplication. Of particular note is that half of the 16p11.2 deletion mice die postnatally; those that survive to adulthood are healthy and fertile, but have alterations in the hypothalamus and exhibit a ‘behavior trap’ phenotype—a specific behavior characteristic of rodents with lateral hypothalamic and nigrostriatal lesions. Our findings indicate that 16p11.2 CNVs cause both brain and behavioral anomalies, providing new insight into human neurodevelopmental disorders.

overall_design: We analyzed gene expression profiles in the brain and determined whether expression corresponded with gene dosage. We measured mRNA intensities in 37 microarray hybridizations representing four brain regions (olfactory bulbs, cortex, cerebellum and brain stem; 5 samples were hybridized twice for estimation of technical errors) in two df/+ mice heterozyous for the deletion of the chromosomal region syntenic to human 16p11.2, three +/+ (wild type) mice and three dp/+ mice heterozyous for the duplication of the chromosomal region syntenic to human 16p11.2. All mice were F1 C57BL/6N: 129Sv hybrid males; therefore, other than the engineered CNV, their genomes were identical.

first: Jacob

last: Ellegood

first: Jason

middle: P

last: Lerch

first: Young-Eun

last: Son

first: Lakshmi

last: Muthuswamy

first: Hannes

last: Vogel

first: Abba

last: Krieger

first: Andreas

last: Buja

first: R

last: Henkelman

first: Michael

last: Wigler

first: Alea

last: Mills


title: Expression data of Hmg20 knock down I/11 cells and controls

first: Sjaak

last: Philipsen

address: Dr molewaterplein

department: Cell Biology

institute: Erasmus MC

summary: We performed microarray analysis to investigate the gene expression profile changes induced by Hmg20b knock down in I/11 cells.

overall_design: Three normal and three Hmg20b knocked down I/11 cell Samples were examined.


title: Dietary heme stimulates epithelial cell turnover by downregulating feedback inhibitors of proliferation in murine colon (part 1)

status: Public on Oct 02 2011

city: Wageningen

first: Guido

last: Hooiveld

address: HELIX, Stippeneng 4

department: Div. Human Nutrition & Health

institute: Wageningen University

summary: The risk for colon cancer is associated with nutrition, especially with diets high in red meat. Red meat contains the iron porphyrin pigment heme, which induces cytotoxicity of the colon contents and epithelial hyperproliferation. Using a mouse model, we showed that heme caused damage to the colonic surface epithelium and induced compensatory hyperproliferation. Expression levels of heme- and stress-related genes show that heme affects surface cells and not directly crypt cells. Therefore, injured surface cells should signal to crypt TA cells to induce compensatory hyperproliferation. Surface-specific downregulated inhibitors of proliferation were Wnt inhibitory factor 1, Indian Hedgehog, Bone morphogenic protein 2 and possibly Interleukin-15.  Heme also upregulated Amphiregulin, Epiregulin and Cyclooxygenase-2 mRNA in the surface cells, however, their protein/metabolite levels were not increased as heme induced surface-specific translation repression by increasing 4E-BP1. Therefore, we conclude that heme induced colonic hyperproliferation and hyperplasia by repressing feedback inhibition of proliferation.

overall_design: C57BL/6 mice received a Westernized diet with or without heme (the polyporphyrin pigment of red meat). Mice received control or heme diet for 14 days. After 14 days, mice were sacrificed and colons were taken out. Swiss rolls were made from the middle 2 cm of the colon. These rolls were used for LCM, and surface cells and crypts cells were separately isolated. RNA was isolated from surface and crypt cells and subjected to gene expression profiling (n=4 control mice and n=3 heme-fed mice).

first: Noortje

last: IJssennagger

first: Anneke

last: Rijnierse

last: Müller

first: Roelof

last: van der Meer


title: Gene expression changes with induction of in-vitro platinum-resistance in ovarian cancer cell lines.

city: Tampa

first: Steven

last: Eschrich

state: FL

address: 12902 Magnolia Drive

department: Biostatistics & Bioinformatics

institute: Moffitt Cancer Center

summary: We treated 8 human ovarian cancer cell lines with cisplatin in treatment/recovery cycles to induce in-vitro resistance to the drug. Microarrays measured gene expression at baseline and after each dose schedule (after recovery).

overall_design: OVCA cells lines (T8, OVCAR5, OV2008, IGROV1, C13, A2780S, A2780CP, and A2008) were used in the study.  Cells were subject to sequential treatment with increasing doses of cis-diammine-dichloroplatinum (cisplatin, CIS), using three dosing schedules resulting in a total of 144 treatment/expansion cycles. Treatment schedules A, B and C included three treatments with 1, 2 and 3μg/ml CIS respectively, followed by three treatments with 3, 4 and 5μg/ml, respectively. Each CIS-treatment was followed by a cell recovery/expansion phase. Both CIS-resistance and genome-wide expression changes were measured serially in each cell line at baseline and after 3 and 6 CIS-treatment/expansion cycles. CIS-resistance was quantified using CellTiter-96, MTS proliferation assays (Fisher Scientific) and genome-wide expression was performed using Affymetrix Human U133 Plus 2.0 GeneChips as previously described.

first: Douglas

last: Marchion

first: Johnathan

last: Lancaster


title: Dietary heme stimulates epithelial cell turnover by downregulating feedback inhibitors of proliferation in murine colon


title: Gene expression profiles of Glioblastoma stem cells in which ALK or pleiotrophin expression was suppressed.

status: Public on Oct 01 2011

city: Tokyo

first: Tetsu

last: Akiyama

address: 1-1-1, Yayoi, Bunkyo-ku

department: Institute of Molecular and Cellular Biosciences

institute: Tokyo University

summary: Cancer stem cells are believed to be responsible for tumor initiation and development. Much current research on human brain tumors is focused on the stem-like properties of glioblastoma stem cells. Anaplastic lymphoma kinase (ALK) and its ligand pleiotrophin are required for maintaining the stem-like properties and tumorigenicity of glioblastoma stem cells.

overall_design: Human glioblastoma stem cells (GB2) were infected with a lentivirus expressing an shRNA targeting ALK or pleiotrophin.

first: Ryo

last: Koyama-Nasu

first: Kenzui

last: Taniue

first: Yuki

last: Katou

first: Katsuhiko

last: Shirahige


title: CD140a+ human oligodendrocyte progenitor cells

city: Buffalo

first: Fraser

middle: James

last: Sim

address: 3435 Main Street

department: Pharmacology

institute: University at Buffalo

summary: Glial progenitor cells (GPCs) pervade the human brain. These cells express gangliosides recognized by MAb A2B5, and some but not all can generate oligodendrocytes. Since some A2B5+ GPCs express PDGFa receptor (PDGFRa), which is critical to oligodendrocyte development, we asked if PDGFRa-directed sorting might isolate oligodendrocyte-competent progenitors. We used FACS to sort PDGFRa+ cells from the second trimester fetal human forebrain, based on expression of the PDGFRa epitope CD140a. CD140a+ cells could be maintained as mitotic progenitors that could be instructed to either oligodendrocyte or astrocyte phenotype. Transplanted CD140a+ cells robustly myelinated the hypomyelinated shiverer mouse brain. Microarray confirmed that CD140a+ cells differentially expressed PDGFRA, NG2, OLIG1/2, NKX2.2 and SOX2. Some expressed CD9, thereby defining a CD140a+/CD9+ fraction of oligodendrocyte-biased progenitors. CD140a+ cells differentially expressed genes of the PTN-PTPRZ1, wnt, notch and BMP pathways, suggesting the interaction of self-renewal and fate-restricting pathways in these cells, while identifying targets for their mobilization and instruction.

overall_design: 10 samples, 5 CD140a+, and 5 CD140a- sorted samples for individual fetal human brain

middle: J

first: Crystal

last: McClain

first: Tricia

middle: L

last: Protack

last: Schanz

first: Martha

last: Windrem

last: Goldman


title: Cereblon expression is required for the anti-myeloma activity of lenalidomide and pomalidomide [expression profiling]

city: Scottsdale

first: Esteban

last: Braggio

state: AZ

address: 13208 East Shea Boulevard, MCRB 3-024

department: Biochemistry

institute: Mayo Clinic

summary: The precise molecular mechanism of action and targets through which thalidomide and related immunomodulatory drugs (IMiDs) exert their anti-tumor effects remains unclear.  We investigated the role of cereblon (CRBN), a primary teratogenic target of thalidomide, in the anti-myeloma activity of IMiDs.  CRBN depletion is initially cytotoxic to human myeloma cells but surviving cells with stable CRBN depletion become highly resistant to both lenalidomide and pomalidomide, but not to the unrelated drugs bortezomib, dexamethasone and melphalan.  Acquired deletion of CRBN was found to be the primary genetic event differentiating isogenic MM1.S cell lines cultured to be sensitive or resistant to lenalidomide and pomalidomide.  Gene expression changes induced by lenalidomide were dramatically suppressed in the presence of CRBN depletion further demonstrating that CRBN is required for lenalidomide activity.  Downstream targets of CRBN include interferon regulatory factor 4 (IRF4) previously reported to also be a target of lenalidomide.  Patients exposed to and putatively resistant to lenalidomide had lower CRBN levels in paired samples before and after therapy.  In summary, CRBN is an essential requirement for IMiD activity, and a possible biomarker for the clinical assessment of anti-myeloma efficacy.

overall_design: We included 15 samples from multiple myeloma cell lines.

first: Braggio

last: Esteban

first: Zhu

middle: Y

last: Xiao

first: Stewart

last: Keith


title: Molecular profiling and gene expression analysis in cutaneous sarcoidosis (CS)

city: Radnor

first: Hongtao

last: Fan

state: PA

address: 145 King of Prussia Rd

department: RDI

institute: Centocor

summary: Cutaneous sarcoidosis skin provides relatively non invasive access to granulomatous sarcoidosis tissue.

overall_design: Twenty participants were enrolled: 15 with active CS and 5 healthy volunteers. Microarray analyses comparing non-LS and healthy volunteer skin with LS showed several thousand genes differentially expressed

first: Brodemerkel

last: Carrie


title: Gene expression in ovarian cancer

first: Steven

last: Eschrich


title: bFGF-selected Bone Marrow-derived Mesenchymal Stem Cells triggers the host response for bone regeneration

city: Genova

first: Roberta

last: Tasso

address: Largo Rosanna Benzi 10

institute: University of Genova

summary: The classical concept of bone marrow-derived mesenchymal stem cells (BM-MSC), intended as a uniform, broad potent population, is progressively being substituted by the idea that the bone marrow harbors heterogeneous populations of non-hematopoietic stem cells. This in vivo heterogeneity is also amplified by the different experimental strategies used to isolate/culture them. Among the exogenous factors described to affect MSC in vitro growth, basic-fibroblast growth factor (bFGF) is one of the most common growth factors used to expand stem cells. Moreover, it has been reported that its signaling is associated with the mainteinance of stemness of a variety of stem cells, included MSC. Using an ectopic model of bone regeneration, we have previously described that the implantation of cells with different commitment levels, differentially influences the capacity to recruit host cells, activating endogenous regenerative mechanisms. Due to its properties, we here demonstrate that the addition of bFGF to primary BM cultures, leads to the selection of specific subpopulations able to induce a different host regenerative response, when in vivo implanted in association with suitable ceramic scaffolds. Moreover, taking advantage of a multiparametric and comparative genomic and proteomic approach, it has been evaluated how different culture conditions combine to bring about appreciable changes in the secretome of the cells, that consequently influence their in vivo regenerative behaviour. The full comprehension of the regulatory mechanisms that rule the host response depending on the type and differentiative stage of the transplanted cells could help us to develop novel clinical strategies where host cells could directly contribute to regenerate the appropriate tissue.

overall_design: Comparison of bFGF effects on bone marrow mesenchymal stem cells.

first: Erica

last: Molino

first: Claudia

last: Lo Sicco

first: Massimiliano

last: Monticone

first: Ranieri

last: Cancedda


title: Effects of long dsRNA expression in HeLa and HEK293 cells

city: Prague 4

first: Matyas

last: Flemr

address: Videnska 1083

country: Czech Republic

institute: Institute of Molecular Genetics

summary:
Double-stranded RNA (dsRNA) can enter different pathways in mammalian cells, including sequence-specific RNA interference, sequence-independent interferon response and editing by adenosine deaminases. To assess the potential of expressed dsRNA to induce interferon stimulated genes in somatic cells, we performed microarray analysis of HEK293 and HeLa cells transfected with a MosIR plasmid expressing an mRNA with a long inverted repeat structure in its 3’UTR (MosIR) or with a parental MosIR plasmid (without inverted repeat) as a control.
Clustering analysis based on differentially expressed genes suggested that there was no common transcriptome signature in cells expressing dsRNA. Overall, the number of genes with altered expression upon transfection of the MosIR plasmid was rather small and only 19 probe sets, corresponding to 17 genes, were changed more than two-fold in both cell lines.

overall_design: Total RNA from cultured HEK293 or HeLa cells was used in each sample. Two independent biological replicates were analyzed for each condition.

first: Petr

last: Svoboda

first: Witold

last: Filipowicz


title: Mycobacterium tuberculosis H37Rv (WT) versus Mut1 and Comp1

city: Bangalore

first: Genotypic

last: technology

state: Karnataka

address: 259, Apoorva 4th cross,80 feet Road,RMV 2ND STAGE

country: India

institute: Genotypic Technology

summary: Transcriptional profiling of H37Rv (WT), Mut1 and Comp1 bacteria under aerobic (Aer/0 day, i.e 0 D) and hypoxic conditions (Hyp/5 days standing culture, i.e  5 D). Mut1: H37Rv carrying devR gene disruption by in frame insertion of kanamycin resistance cassette and expressing DevRN-Kan fusion protein. Comp1: Mut1 complemented with low copy number plasmid carrying devR gene expressed from its native constitutive upstream promoter. (Reference: Majumdar et al., 2010, PLoS One 5:e9448). Goal is to compare transcriptional patterns of WT, Mut1 and Comp1 strains under aerobic (0 D) and hypoxic (5 D) conditions in vitro.

overall_design: Two color and One-color experiments,Organism: Mycobacterium tuberculosis, Genotypic Technology designed Custom Mycobacterium tuberculosis H37Rv Whole Genome 8x15k GE Microarray (AMADID-020181)

first: Shyamasree

last: De Majumdar

first: Jaya

last: Sivaswami Tyagi


title: Cereblon expression is required for the anti-myeloma activity of lenalidomide and pomalidomide

first: Esteban

last: Braggio

type: Genome binding/occupancy profiling by genome tiling array


title: Calcineurin/NFAT signaling inhibits myeloid hematopoiesis in mice.

city: Singapore

first: jinmiao

last: chen

address: Biopolis

country: Singapore

institute: Singapore Immunology Network

summary: Nuclear factor of activated T cells (NFAT) comprises a family of transcription factors that regulate T cell development, activation and differentiation. NFAT signaling can also mediate granulocyte and DC activation, but it is unknown whether NFAT influences their development from progenitors. Here we report a novel role for calcineurin/NFAT signaling as a negative regulator of myeloid hematopoiesis. Reconstituting lethally-irradiated mice with hematopoietic stem cells expressing an NFAT-inhibitory peptide resulted in enhanced development of the myeloid compartment. Culturing bone marrow cells with Flt3-L and Cyclosporin A, which inhibits NFAT signaling, increased numbers of differentiated DC. Global gene expression analysis of untreated DC and NFAT-inhibited DC revealed differential expression of transcripts that regulate cell cycle and apoptosis. Thus, calcineurin/NFAT signaling negatively regulates myeloid lineage development. The finding that NFAT acts as a negative regulator of myeloid development provides novel insight in understanding immune responses during treatment with calcineurin/NFAT inhibitors as Cyclosporin A.

overall_design: bone marrow cells from C57B/6 mice were stimulated in Flt3-L suplemented media in presence or absence of calcineurin/NFAT inhibitor Cyclosporin A, samples in 3 biological replicates

first: Jan

last: Fric

first: Clarice

last: Lim

first: Esther

last: Koh

first: Benjamin

last: Hofmann

first: Jinmiao

last: Chen

first: Siti

last: Isa

first: Alessandra

last: Mortellaro

first: Christiane

last: Ruedl

first: Paola

last: Ricciardi-Castagnoli


title: Changes in the Bone Marrow Microenvironment Impact Anabolic Actions of PTH

status: Public on Sep 30 2011

city: Ann Arbor

first: Amy

state: MI

address: 1011 N. University Ave.

department: POM

institute: University of Michigan

summary:
Irradiation induced bone marrow ablation ultimately enhanced PTH anabolic effects in bone.
B6 mice at 10 days of age were sub-lethally irradiated and treated with PTH 24h later for 5 days.  24h post last-injection, bone marrow was flushed with Trizol and RNA isolated and purified.  Microarray analyses was performed to determine differential differences in PTH effects in non-irradiated vs. irradiated bone marrow.

overall_design: Triplicates of 4 groups (total of 12 samples) which include:  Nonirradiated Vehicle, Nonirradiated PTH, Irradiated Vehicle and Irradiated PTH

first: Laurie

last: McCauley


title: Expression data from RKO cells transfected with SPARCL1 and vector control

city: Hangzhou

first: Hang

last: Zhang

address: 88 Jiefang Road

country: China

institute: Zhejiang University Cancer Institute

summary:
Colon cancer cell line RKO grown on Matrigel form a luminal-like structure after the transfection of SPARCL1 gene, which may imply the differentiation of the cells. To indentify genes regulated by SPARCL1, we built two stable cell lines: RKO with pLXSN-SPARCL1 plasmid (RKO-SPARCL1) and RKO with pLXSN plasmid (RKO-pLXSN). Then we cultured these two cell lines on both plastic dish and dish cover with a layer of Matrigel.
We used microarrays to undentify global gene expression change in RKO cells after the tranfection of SPARCL1.

overall_design:
Four samples including RKO-pLXSN cells cultured on plastic, RKO-pLXSN cells cultured on Matrigel, RKO-SPARCL1 cells cultured on plastic and RKO-SPARCL1 cells cultured on Matrigel were trypsinized and collected for RNA extraction and hybridization on Affymetrix microarray U133plus2.0.
Supplementary files:
* RLvsRP: up and down regulated genes comparing with RKO-SPARCL1(RL) and RKO-pLXSN(RP) cells cultured on plastic
* RLMvsRPM: up and down regulated genes comparing with RKO-SPARCL1(RL) and RKO-pLXSN(RP) cells cultured on Matrigel

first: Hanguang

last: Hu

first: Weiting

last: Ge


title: Identification of a Potently Oncogenic CALM-AF10 Minimal-Fusion Mutant (mRNA)

first: Karlheinz

last: Holzmann

summary: The t(10;11) p (13;q14) translocation, giving rise to CALM-AF10, is a recurring chromosomal translocation observed in several types of acute leukemias as well as in lymphoma. We have previously demonstrated that the expression of the human CALM/AF10 fusion gene in murine bone marrow stem and progenitor cells results in an aggressive acute myeloid leukemia in vivo. In this study, we have screened the various domains essential for CALM-AF10 function and leukemogenicity. Our study identifies a mutant of CALM-AF10 that greatly enhances the clonogenic potential of hematopoietic progenitors while retaining key characteristics of disease induced by the full length CALM-AF10 fusion.

overall_design: Global gene expression of bone marrow cells transduced with various constructs were compared. We used the empty vector, MIG, as a control and baseline. Four samples are tested with three biological replicates each.

first: Aniruddha

last: Deshpande

first: Arefeh

last: Rouhi

first: Yihui

last: Lin

last: Stadler

first: Philipp

last: Greif

first: Natalia

last: Arseni

first: Sabrina

last: Opatz

first: Leticia

last: Quintanilla-Fend

first: Wolfgang

last: Hiddemann

first: Guoliang

last: Xu

first: Scott

last: Armstrong

first: Stefan

last: Bohlander

first: Christian

last: Buske


title: Gene expression is differently affected by pimecrolimus and betamethasone in lesional skin of atopic dermatitis.

city: Kontiolahti

first: Andreas

last: Scherer

address: Pajutie 3A

institute: Spheromics

summary:
Topical corticosteroids and calcineurin inhibitors are well known treatments of atopic dermatitis (AD), but differ in their efficacy and side effects. A study in AD patients has demonstrated that betamethasone valerate (BM) though clinically more efficient impaired skin barrier repair in contrast to pimecrolimus. Objective: The present study elucidates the mode of action of topical BM and pimecrolimus cream in AD.
Methods: These two components were subjected to gene expression profile analysis in lesional AD skin after topical treatment.
Results: BM resulted in a significant reduction of mRNA levels of genes encoding for markers for dendritic cells, T cells, cytokines, chemokines and serine proteases, whereas pimecrolimus exerted minor effects only. This corroborates the clinical finding that BM reduces inflammation more effectively than pimecrolimus. Genes encoding molecules important for skin barrier function were differently affected. Both BM and pimecrolimus normalized the expression of filaggrin and loricrin. BM, but not pimecrolimus, significantly reduced the expression of rate-limiting enzymes for lipid synthesis and the expression of involucrin and small proline-rich proteins, which covalently bind ceramides. This may explain the lack of restoration of functional stratum corneum layers observed after BM treatment.
Conclusion: The gene expression profiles are consistent with previous findings that corticosteroids may exert a more potent anti-inflammatory effect but may impair the restoration of the skin barrier. Hence, this study confirms the hypothesis at the molecular level that corticosteroids are a suitable treatment for acutely exacerbated AD, but that pimecrolimus is preferable for long-term treatment and stabilization.

overall_design: Fifteen patients with mild-to-moderate AD (according to Hanifin and Rajka criteria) and a target lesion score (pEASI) of 3 to 8 (on a scale of 0-12) for both right and left target lesions, and symmetric AD lesions (not differing >1 point between the right and left sides) affecting the upper limbs by at least 10% were treated twice daily for 3 weeks on 1 upper limb with 1% pimecrolimus cream and on the other upper limb with 0.1% betamethasone valerate cream in a double blind manner. The clinical, biophysical, immuno-histological and electron-microscopical results have already been published. Biopsy samples have been obtained before and after the end of the treatments for gene expression profiling measurement from ten patients out of the group of 15. Of the ten patients there were seven women and three men. The average age was 23.8 ± 3.6 years. After three weeks of treatment with pimecrolimus and BM cream, the clinical score (pEASI) revealed a reduction of 0.9 ± 2.1 and 2.9 ± 3.1, respectively. The study was approved by the local ethics commission and the German Federal Institute for Pharmaceuticals and Medical Products (EudraCT-Nr. 2004-004824-11).

first: J

last: Jensen

first: A

first: C

last: Wanke

first: M

last: Braeutigam

first: S

last: Bongiovanni

last: Letzkus

first: F

last: Staedtler

last: Kehren

last: Zuehlsdorf

first: T

last: Schwarz

last: Weichenthal

first: R

last: Foelster-Holst

first: E

last: Proksch


title: Generation of feederless iPS cell from human cord blood cells using Sendai virus (SeV) vector

city: KOBE

first: Naoki

last: Nishishita

institute: Founbation for Biomedical Research and Innovation

summary: CD34+ fraction of cord blood (CB) cells can be reprogrammed on pronectinF-coated dish in serum free medium using Sendai virus (SeV) vector carrying reprogramming factors OCT3/4, SOX2, KLF4 and c-MYC. human ES cell-like colonies came to merge around 18 days after SeV infection on pronectin-coated dish in human ES cell medium supplemented with bFGF under normoxic culture (20% O2). After passages, dish like-shape colonies were seeded on pronectinF-coated 96 well-plate in a single cell and cultured in N2B27 based medium supplemented with LIF, FK, MAPKi, GSKi in hypoxic culture condition (5% O2) for cloning purpose. Emerged dome shape colonies were collected and cultured in human ES cell medium supplemented with bFGF under normoxic culture (20% O2) again. Dish shape and human ES cell-like colonies derived from single cell were picked up for further appraisal of reprogrammed cells such as expression of pluriotency–related molecules. Reprogrammed cells can be maintained for more than 20 passages without differentiation.

overall_design: We investigated that gene expression profile of generated feederless human iPS cells from cord blood cells using temperature sensitive sendai-virus vector.

first: Shin

last: Kawamata


title: Expression data from ALL diagnosis and relapse pediatric acute lymphoblastic leukemia cases

status: Public on Sep 23 2011

city: Stony Brook

first: Laura

middle: E.

last: Hogan

department: Department of Pediatrics

country: USA

institute: Stony Brook University

summary: There is a distinct signature of differentially expressed probes from diagnosis to relapse

overall_design: Gene expression profiles of pediatric patients with B-precursor ALL were compared to at 2 time points, diagnosis and relapse. The overall design was a comparison of gene expression at diagnosis and relapse within individual patients.  A subset analysis (comparing diagnosis to relapse expression within individuals), was done for early relapse (less than 36 months) cases only and late relapse (greater than 36 months) cases only.

middle: E

first: Jinhua

last: Wang

first: William

last: Carroll


title: Significant Effects of Antiretroviral Therapy on Global Gene Expression in Brain Tissues of Patients with HIV-Associated Neurocognitive Disorders

status: Public on Sep 25 2011

city: New York

first: Alejandra

last: Borjabad

state: NY

address: 432 West 58th, Street

department: Medicine

institute: St.Luke's-Roosevelt Hospital Center

summary: Antiretroviral therapy (ART) has reduced morbidity and mortality in HIV infection; however HIV-1-associated neurocognitive disorders (HAND) persist despite treatment. We used microarray analysis in post-mortem brain tissues to determine ART effectiveness in the brain and to identify molecular signatures of HAND under ART.

overall_design: We performed microarray analysis using Affymetrix Arrays in portmortem brain tissues from seven treated and eight untreated HAND patients and six uninfected controls.

first: David

last: Volsky


title: Comparisons between fully and partially reprogrammed iPS cells induced by pMX-Klf4, pMX-Oct4 and pMX-Sox2 retroviruses

status: Public on Sep 22 2011

city: Ottawa

first: Theodore

last: Perkins

state: ON

address: 501 Smyth Rd.

department: Cellular and Molecular Medicine

institute: Ottawa Hospital Research Institute

summary: Induced pluripotent stem (iPS) cell reprogramming is a gradual epigenetic process that reactivates the pluripotent transcriptional network by erasing and establishing heterochromatin marks.  Here, we characterize the physical structure of heterochromatin domains in full and partial mouse iPS cells by correlative Electron Spectroscopic Imaging (ESI). In somatic and partial iPS cells, constitutive heterochromatin marked by H3K9me3 is highly compartmentalized into chromocenter structures of densely packed 10 nm chromatin fibers.  In contrast, chromocenter boundaries are poorly defined in pluripotent ES and full iPS cells, and are characterized by unusually dispersed 10 nm heterochromatin fibers in high Nanog-expressing cells, including pluripotent cells of the mouse blastocyst prior to differentiation. This heterochromatin reorganization accompanies retroviral silencing during conversion of partial iPS cells by Mek/Gsk3 2i inhibitor treatment.  Thus, constitutive heterochromatin reorganization serves as a novel biomarker with retroviral silencing for identifying iPS cells in the very late stages of reprogramming.

overall_design: We compared the expression profiles of partially and fully reprogrammed iPS cell lines derived from CD1 mouse embryonic fibroblasts (MEFSs) by retroviral reprogramming (pMX-Oct4, pMX-Klf4 and pMX-Sox2). to the differentiated MEFS and the J1 embryonic stem cell line. We also studied the effect of a 2i cocktail treatment in partially reprogrammed iPS cells.

first: James

last: Ellis


title: Integrated Genomic Analysis of Relapsed Childhood Acute Lymphoblastic Leukemia reveals therapeutic strategies

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


title: Cooperative and redundant signaling of leukotriene B4 and leukotriene D4 in human monocytes

status: Public on Sep 21 2011

city: Bethesda

first: Jennifer

last: Barb

state: MD

address: 12 South Drive Bldg 12A Room 2001

department: DCB

institute: NIH

summary: LTB4, 50 nmol/L for 30 minutes, induced expression of 27 genes in cultured human elutriated monocytes comparred to vehicle (ethanol) treated control cells.

overall_design: Matched control versus treated cells

first: Li-Yuan

last: Chen

first: Michael

last: Eberlein

first: Sara

last: Alsaaty

first: Asuncion

last: Martinez-Anton

first: Peter

last: Munson

first: Robert

last: Danner

first: Yueqin

last: Liu

first: Carol

last: Logun

middle: H

last: Shelhamer

first: Grzegorz

last: Woszcze


title: High expression of BMP pathway genes distinguishes a subset of Atypical Teratoid/Rhabdoid Tumors associated with shorter survival

city: Aurora

first: Diane

last: Birks

state: CO

department: Neurosurgery

institute: University of Colorado, Denver - Anschutz Medical Campus

summary:
Molecular profiling of tumors has proven a valuable tool for identification of prognostic and diagnostic subgroups in medulloblastomas, glioblastomas and other cancers. However, the molecular landscape of atypical teratoid / rhabdoid tumors (AT/RTs) remains largely unexplored. To address this issue, we used microarrays to measure the gene expression profiles of 18 AT/RTs, and performed unsupervised hierarchical clustering to determine molecularly similar subgroups. Four major subgroups (clusters) were identified. These did not conform to gender, tumor location, or presence of monosomy 22. Clusters showed distinct gene signatures and differences in enriched biological processes, including elevated expression of choroid plexus genes in Cluster 4. In addition, survival differed significantly by cluster, with shortest survival (mean 4.7 months) in both Clusters 3 and 4 compared to Clusters 1 and 2 (mean 28.1 months). Analysis showed that multiple bone morphogenetic protein (BMP) pathway genes were up-regulated in the short survival clusters, with BMP4 showing the most significant up-regulation (270-fold). Thus, high expression of BMP pathway genes was negatively associated with survival in this dataset. Our study indicates that molecular subgroups exist within AT/RTs, and that molecular profiling of these comparatively rare tumors may be of diagnostic, prognostic and therapeutic value.
Key Words: atypical teratoid / rhabdoid tumor; bone morphogenetic protein pathway; BMP4; survival; 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: Andrew

last: Donson

first: Purvi

middle: R

last: Patel

first: Christopher

last: Dunham

first: Andrea

last: Muscat

first: Elizabeth

last: Algar

last: Ashley

first: Bette

last: Kleinschmidt-DeMasters

first: Rajeev

last: Vibhakar

last: Handler

first: Nicholas

last: Foreman


title: Expression data from mouse heart deficient of HDAC3

city: Houston

first: Zheng

last: Sun

state: TX

address: 1 Baylor Plaza

institute: Baylor College of Medicine

summary:
Gene expression changes in the heart of MCH3-KO mouse (HDAC3 f/f, Muscle Creatine Kinase-Cre) versus control WT mouse (HDAC3 f/f).
Histone deacetylases (HDACs) play important roles in cardiac development and function. We show here that mice deficient of HDAC3 in heart and skeletabl muscle are relatively normal on normal chow, but develop hypertrophic cardiomyopathy and heart failure that leads to death on high-fat diet. This microarray experiment is to explore the underlying molecular mechanism.

overall_design: Hearts from 6-weeks old WT and MCH3-KO C57BL/6 mice (n=4 in each group, male) on normal chow were subjected to RNA extraction and Affymetrix Mouse Gene 1.0ST analysis.

first: Mitchell

last: Lazar


title: Epigenome profiling of repressive histone modifications, DNA methylation and gene expression in normal and malignant urothelial cells

status: Public on Sep 20 2011

city: Sheffield

first: Ewa

last: Dudziec

address: Beech Hill Road

department: ICS

institute: The University of Sheffield

summary:
To gain a more depth knowledge of repressive epigenetic gene regulation in UCC, we have profiled H3K9m3 and H3K27m3 in normal and malignant urothelial cells. We matched these profiles to those 5-methylcytosine and gene expression. We hypothesized that differences represent pro-carcinogenic events within the urothelium.
We identified a panel of genes with cancer specific epigenetic mediated aberrant expression.

overall_design: Two repressive histone modifications (H3K9m3 and H3K27m3) , cytosine methylation and gene expression were compared between normal human urothelial cell line (NHU) and malignant urothelial cells (EJ and RT112).

first: Andreas

last: Gogol-Döring

first: Victoria

last: Cookson

first: Wei

last: Chen

first: James

last: Catto


title: Integrated epigenome profiling of DNA methylation and gene expression in normal and malignant urothelial cells

type: Methylation profiling by genome tiling array


title: Human keratinocytes have a response to injury that upregulates CCL20 and other genes linking innate and adaptive immunity

first: Mayte

last: Suarez-Farinas

address: 1425 Madison Ave, L2-70C, Box 1077,

institute: Mount SinaiSchool of Medicine

summary: In the early stages of wound healing, keratinocytes become “activated” and release inflammatory molecules such as interleukin-1 and interleukin-8 that are linked to innate immune responses and neutrophil recruitment. It is unclear, however, whether keratinocytes release molecules linked to adaptive immune responses, e.g. CCL20, in their early state of activation without signals from infiltrating T cells. This study aims to isolate the immediate alterations in protective and inflammatory gene expression that occur in epidermal keratinocytes, with a particular focus on molecules associated with cell-mediated immunity. We used dispase-separated epidermis, followed by intercellular disassociation by trypsinization, as a model for epidermal injury. We obtained a pure population of keratinocytes using flow cytometry. As a control for uninjured epidermis, we performed laser capture microdissection on normal human skin. Sorted keratinocytes had an early burst of upregulated gene expression, which included CCL20, IL-15, IL-23A, IFN-κ, and several antimicrobial peptides. Our results provide insight into the potential role of keratinocytes as contributors to cell-mediated inflammation, and expand knowledge about gene modulation that occurs during early wound healing. Our findings may be relevant to cutaneous diseases such as psoriasis, where micro-injury can trigger the formation of psoriatic plaques at the site of trauma.

overall_design: Compare keratinocyte response to cell disassociation with (1) epidermal samples isolated by laser caputre microscopy and (2) cultured KCs

middle: G

last: Krueger

first: Milene

last: Kennedy

last: Suárez-Fariñas