title: Methylation data from CD4+ cells at birth and 12 months from a cohort of children who were diagnosed with IgE food allergy to either egg milk or peanut at 12 months (n=12) and healthy controls (n=12).

city: NEDLANDS

first: David

last: Martino

state: Western Australia

address: Perth Childrens Hospital, 15 Hospital Avenue

institute: Telethon Kids Institute

summary:
DNA methylation data derived from total CD4+ T-cells from a cohort of paediatric food allergy. There are 12 food allergic samples (6 activated and matched control), 12 non-allergic samples (6 activated and matched control) collected at birth and resample at 12-months, total 48 samples.
Mononuclear cells were either activated with anti-CD3 (0.5 ug/mL) + IL2(20U) or rested in media alone for 24 hours. CD4+ cells were purified and DNA was harvested and bisulphite converted for methylation analysis on illumina HM450K array.

overall_design: This is a pooled design. Each sample is bisulphite converted gDNA pooled in equimolar amounts from n=2 individuals. There are 6 allergic pools and 6 non allergic pools. Each pool is sampled at two time points, birth and 12 months, and either treated or untreated at each time point.


title: CD69-dependent gene expression in activated CD4 T cells from the spleen of Mus musculus

status: Public on Dec 29 2011

city: Ulm

first: Karlheinz

last: Holzmann

address: Helmholtzstreet 8/1

department: Medical Faculty

country: Germany

institute: Ulm University

summary:
CD69 is a transmembrane protein expressed on the surface of activated leukocyte. The ligand for CD69 and the intracellular signaling pathway of this molecule are yet unknown. It is widely used as a marker of activated lymphocyte, but its function in immune system is not known.
We used micro-array to define genes whose expression is regulated by activation antigene CD69.

overall_design: CD4 T cells were isolated from the spleen of wt B6 and CD69-deficient B6 mice and in vitro activated with anti-CD3/anti-CD28 coated beads. On one groupe of wt B6 cells, CD69 was activated using a anti-CD69 and secoundary antibody. RNA extraction and hybridization on Affymetrix microarrays was performed for wt B6, CD69-activated wt B6 and CD69-deficient B6 CD4 T cells.

first: Jan

middle: H

last: Niess

first: Katarina

last: Radulovic


title: Gene Expression in Three Early Human Hypertrophic Scar Samples

status: Public on Dec 31 2011

city: Ames

first: Oliver

last: Couture

state: IA

address: 2255 Kildee

country: USA

institute: Iowa State University

summary: The goal was to obtain expression data from the deep cones in early human hypertrophic scars to be used to confirm expression data obtained in a porcine model.

overall_design: Three samples of early human hypertrophic scar were obtained and processed with the Affymetrix Human GeneChip® Human Genome U133 plus 2.0. Sample demographics were Black 2, White 1; upper extremity 2, neck 1; times since injury 6.7 months and 10.8 months; and patient ages were 19 and 54.

first: Loren

last: Engrav


title: Gene expression profiles of human blood classical monocytes (CD14++CD16-), CD16 positive monocytes (CD14+16++ and CD14++CD16+), and CD1c+ CD19- dendritic cells [human data]

status: Public on Dec 17 2011

city: München

first: Olivia

last: Prazeres da Costa

state: Bavaria

address: Trogerstr. 30

department: Medical Microbiology, Immunology and Hygiene

institute: Technische Universität München

summary:
In this study gene expression of human blood classical monocytes (CD14++CD16-), CD16 positive monocytes  (consisting of non-classical CD14+16++ and intermediate CD14++CD16+ monocytes) and CD1c+ CD19- dendritic cells from healthy subjects were investigated.
Keywords: expression profiling by array

overall_design: The two major monocyte subsets and the CD1+ blood dendritic cells (DCs CD1c+ CD19-) were isolated from venous heparinized blood of three apparently healthy human volunteers (donors 1, 2 and  3) using MACS technology with all reagents and tools from Miltenyi Biotec. RNA was isolated and 1 µg was labeled using the Affymetrix One-Cycle Target Labeling Kit and the biotinylated cRNA used to perform Affymetrix U133 Plus 2.0 expression arrays. The data sets for CD14++CD16- classical monocytes are tagged CD16neg, the data sets for CD16 positive monocytes are tagged CD16pos and the data sets for the CD1c+CD19- DCs are tagged CD1cpos.

first: L

last: Ziegler-Heitbrock

first: O


title: Expression data of HGF/cMET pathway in prostate cancer DU145 cell line

status: Public on Dec 16 2011

city: Rotterdam

first: Guido

last: Jenster

department: Urology

country: Netherlands

institute: Erasmus MC

summary:
DU145 prostate cancer cells were treated with 25 ng/ml hepatocyte growth factor (HGF) or vehicle for 2, 8, or 24 hours. HGF stimulates the cMET protein, a tyrosine kinase transmembrane protein.
The aim of this study is to determine the role of the HGF/cMET pathway in immature cells of established prostate cancer. HGF stimulation of DU145 prostate cancer cell line led to cell migration in culture, formation of sprouts in Matrigel and inhibition of growth. These biological effects went together with induction of a stem-like phenotype as defined by up-regulation of CD49b, CD49f, CD44 and SOX9, and down-regulation of CD24 on gene-expression arrays and quantitative PCR. The shift towards a stem-like phenotype was reflected by protein modifications on FACS, Western blot, and enhanced rapid adhesion to collagen I. Small molecules SU11274 and PHA665752 were able to inhibit both morphologic and molecular HGF effects.

overall_design: DU145 cells were stimulated for 2, 8 and 24 hours with 25 ng/ml HGF or vehicle. For each time point two arrays analyses were performed. One for cells stimulated with a vehicle and one for the HGF stimulated cells. Six arrays were performed in total in this study.

first: Geert

middle: J

last: van Leenders

first: Rajesh

last: Sookhlall


title: Gene expression profile of myoepithelial progenitor cells

status: Public on Dec 15 2011

city: Omaha

first: Gautam

last: Malhotra

state: NE

address: 985805 Nebraska Medical Center

institute: UNMC

summary: There is increasing evidence that breast and other cancers originate from and are maintained by a small fraction of stem/progenitor cells with self-renewal properties. Whether such cancer stem/progenitor cells originate from normal stem cells based on initiation of a de novo stem cell program, by reprogramming of a more differentiated cell type by oncogenic insults or both remains unresolved.  A major hurdle in addressing these issues is lack of immortal human stem/progenitor cells that can be deliberately manipulated in vitro.  Here we discribe Myoepithelial Progenitor Cells (MPCs) that show properties of EMT and claudin low subtype of breast cancers. Through microarray analysis, we have found that these K5-/K19- cells show similar gene expression pattens of the claudin-low subtype of breast cancer.

overall_design: Normal human mammary epithelial cells (hMECs)  were isolated from Reduction Mammoplasty and immortalized by human telomerase (hTERT).  Type III- K5-/K19- cell colonies were isolated from K5+/K19- immortalized hMECs and cultured in MEGM medium for self-renewal and differentiation. Total RNA isolated from Type III cells were used on Affymetrix microarray.

first: Vimla

last: Band


title: A microRNA regulon that mediates endothelial recruitment by metastatic human breast cancer cells.

city: New York

first: Nils

last: Halberg

state: NY

address: 1230 York Avenue

institute: Rockefeller University

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

overall_design: Refer to individual Series


title: Gene expression-based dentification of microRNA-9-3 target genes in breast epithelial cells

city: Columbus

first: Pei-Yin

last: Hsu

state: OH

address: BRT836, 460W 12th Ave

institute: OSU

summary: In current study, DES could effectively suppress the expression of miR-9-3 through the ERa-dependent epigenetic machinery in MDECs and MCF-7 cells. We want to figure out the biological significance and the potential targets of miR-9-3 and the related signaling cascades.

overall_design: MCF-7 cells were transfected with two pre-designed maturated mimics of miR-9-3, miR-9 and miR-9*. After 48hr of transfection, total RNA was collected for gene expression analysis to figure out the potential targets of miR-9-3.

first: Sandya

last: Liyanarachchi

first: Benjamin

middle: A

last: Rodriguez


title: Whole-exome sequencing identifies mutations of BCOR in acute myeloid leukemia with normal karyotype

first: Hans-Ulrich

last: Klein

department: Neurology

institute: Columbia University Medical Center

summary:
Among acute myeloid leukemias (AML) with normal karyotype (CN-AML), NPM1 and CEBPA mutations define WHO provisional entities accounting for ~60% of cases, but the remaining ~40% remains poorly characterized. By whole exome-sequencing (WES) of one CN-AML patient lacking mutations in NPM1, CEBPA, FLT3, MLL-PTD and IDH1, we newly identified a clonal somatic mutation in BCOR (BCL6 co-repressor), a gene located in chromosome X. Further analyses showed that BCOR mutations occurred in 11/262 (4.2%) CN-AML cases and represented a substantial fraction (14/82, 17.1%) of CN-AML patients showing the same genetic background as the index patient subjected to WES.
BCOR somatic mutations were: i) disruptive events similar to germline BCOR mutations causing the oculo-cranio-facial-dental (OCFD) genetic syndrome; ii) associated with markedly decreased BCOR mRNA levels, absence of full-length BCOR and absent or low expression of a truncated BCOR protein; iii) almost mutually exclusive with NPM1 mutations and frequently associated with DNMT3A and RUNX1 mutations, pointing to a cooperation between these events. Finally, BCOR mutations correlated with poor outcome among a cohort of 160 CN-AML patients (28% versus 66% overall survival at 2 yrs, P=0.024). Our results implicate for the first time BCOR in the pathogenesis of CN-AML without NPM1 mutations.

overall_design: AML samples with normal karyotype were studied. Molecular analyses were performed for BCOR mutations. 12 BCOR wild-type cases and 12 BCOR mutated cases were hybridized to gene expression micro-arrays.

first: Vera

last: Grossmann

first: Enrico

last: Tiacci

first: Antony

last: Holmes

first: Alexander

last: Kohlmann

first: Maria

middle: P

last: Martelli

first: Wolfgang

last: Kern

first: Ariele

last: Spanhol-Rosseto

first: Martin

last: Dugas

first: Sonja

last: Schindela

first: Vladimir

last: Trifonov

first: Susanne

last: Schnittger

first: Claudia

last: Haferlach

first: Renato

last: Bassan

first: Victoria

last: Wells

first: Orietta

last: Spinelli

first: Joseph

last: Chan

first: Roberta

last: Rossi

first: Stefano

last: Baldoni

first: Luca

last: De Carolis

first: Katharina

last: Goetze

first: Hubert

last: Serve

first: Rudolf

last: Peceny

first: Karl-Anton

last: Kreuzer

first: Daniel

last: Oruzio

first: Giorgina

last: Specchia

first: Francesco

last: Di Raimondo

last: Fabbiano

first: Marco

last: Sborgia

first: Arcangelo

last: Liso

first: Laurent

last: Farinelli

first: Alessandro

last: Rambaldi

first: Laura

last: Pasqualucci

first: Raul

last: Rabadan

first: Torsten

first: Brunangelo

last: Falini


title: Expression data from DMSO and SP600125 treated neurons

status: Public on Dec 18 2011

city: Basel

first: Dirk

last: Schuebeler

address: Fabrikstrasse 24

country: Switzerland

institute: Friedrich Miescher Institute for Biomedical Research

summary:
Expression profiling of from DMSO and SP600125 treated glutamatergic neurons reveals JNK target genes that are transcriptionally regulated by JNK signaling.
SP600125 is a known JNK signaling inhibitor and therefore, we used this to test whether the expression of JNK bound genes is affected upon inhibition of JNK kinase activity.

overall_design: Gene expression in the SP600125 treated neurons was compared to the DMSO treated neurons. a to e suffixes indicate biological replicates. Batch indicates different batches of the drug SP600125.

first: Vijay

last: Tiwari

first: Michael

middle: B

last: Stadler

first: Christiane

last: Wirbelauer

first: Renato

last: Paro

last: Schübeler

first: Christian

last: Beisel


title: Expression data comparing the effect of IKK2 KO on a KRAS mouse model

city: Charlottesville

first: Eugene

last: Ke

state: Virginia

address: P.O. Box 800734, 1340 Jefferson Park Avenue

department: MIC

institute: University of Virginia

summary:
Given that the NF-κB pathway plays an important role in tumor development and that IKK2 is the seminal kinase responsible for NF-κB pathway activation, we were particularly interested in exploring the therapeutic potential of IKK2 inhibition in non-small cell lung cancers.
We crossed IKK2fl/fl and KrasG12D mice so that we could simultaneously activate KrasG12D to initiate tumor formation and inactivate IKK2, upon transduction by Cre lentiviral vectors.

overall_design: RNA isolated from finely dissected tumor nodules and tumor cell lines (4A3 and1D3) was applied to microarray analysis using Affymetrix Mouse Gene 1.0 STArrays according to the manufacturer’s instructions.

first: Yifeng

last: Xia

first: Narayana

last: Yeddula

first: Inder

last: Verma


title: Expression data from in vitro and ex vivo Th1- and Th17-polarized TRP1 TCR transgenic CD4+ cells

city: Bethesda

first: Steven

last: Kern

state: MD

address: 10 Center Drive

department: Critical Care Medicine Department

institute: National Institutes of Health

summary: Serial comparison between Th1 and Th17 tumor-specific cells cultured in vitro and ex vivo after transferred into sublethaly irradiated B6.PL mice. Th17-derived cells acquire Th1-like properties in vivo but maintain a distinct molecular profile.

overall_design: TRP1 CD4+ T cells were peptide stimulated under Th1 and Th17 conditions for 7 days. mRNA was collected on the day of adoptive transfer and from multiple replicates on day 5 and 15 after adoptive transfer from pooled spleens and inguinal lymph nodes. Tissues were enriched for CD4 by negative selection and sorted by flow cytometry for the expression of Thy1.2.

first: Pawel

last: Muranski

first: Gabriela

last: Ferreyra

first: Zachary

last: Borman

first: Robert

middle: L

last: Danner

first: Nicholas

last: Restifo


title: Human skeletal muscle transcriptional response to exercise

city: Ann Arbor

first: GORDON

last: PAUL

state: MI

address: 325 E Eisenhower

institute: University of Michigan

summary: The aim of this investigation was to evaluate the effect of training on the global transcriptional response of skeletal muscle to an acute bout of resistance exercise.

overall_design: Seven young healthy men and women underwent a 12-week supervised progressive unilateral arm resistance exercise (RE) training program. One week after the last session of training, subjects performed an acute bout of bilateral arm RE in which the trained and the untrained arm exercised at the same relative intensity. A muscle biopsy was obtained 4h post exercise from the biceps brachii of the trained and untrained arm. Trained and untrained muscle samples were analyzed for mRNA levels of over 20,000 annotated genes using Affymetrix U133 Plus 2.0 microarrays.

first: Paul

last: Gordon

first: Dongmei

last: Liu

first: Maureen

last: Sartor

first: Heidi

last: IglayReger

first: Emidio

last: Pistilli

first: Laurie

last: Gutmann

first: Gustavo

last: Nader

first: Eric

last: Hoffman


title: Evaluation of the Infinium Methylation 450K technology

city: Bruxelles

first: Matthieu

last: Defrance

address: CP614 route de Lennik 808

country: Belgium

institute: Université Libre de Bruxelles

type: Methylation profiling by genome tiling array

summary: Genome-wide DNA methylation profiling of HCT116 WT, HCT116 DNMT1 and DNMT3B double KO, and breast cancer tumors by next generation Infinium assay

overall_design: Bisulfite converted DNA from 22 samples were hybridized to the Illumina's HumanMethylation450 BeadChip

first: Sarah

last: Dedeurwaerder

first: Emilie

last: Calonne

first: Hélène

last: Denis

first: Christos

last: Sotiriou

first: François

last: Fuks


title: Gene expression profiles along the tonotopic axis of the mouse cochlea during neonatal development

status: Public on Dec 13 2011

city: Seoul

first: Heejei

last: Yoon

address: 134 Shinchondong, Seodaemoongu

department: Anatomy

country: South Korea

institute: Yonsei University

summary: The cochlear duct is tonotopically organized, such that the basal cochlea responds more sensitively to high frequency sounds and the apical cochlea to low frequency sounds. In effort to understand how the tonotopic organization is established in mammals, we searched for genes that are differentially expressed along the tonotopic axis during neonatal development.

overall_design: Eighty temporal bones were dissected from C57BL/6 mice at P0 and P8. Two biological replicates were performed. The cochlear tissues were divided into three equal pieces representing the basal, middle and apical turns, and pooled separately. Twelve total RNA from the pooled samples were applied to 12 GeneChips.

first: Eun

last: Son

first: Ling

last: Wu

first: Sunny

last: Kim

first: Hyunjoo

first: Jinwoong

last: Bok


city: Erlangen

first: Roland

last: Lang

address: Wasserturmstr. 3-5

institute: University Hospital Erlangen

summary: Controlled decay of cytokine and chemokine mRNAs restrains the time and amplitude of inflammatory responses. Tristetraprolin (TTP) binds to AU-rich elements in 3´ untranslated regions of mRNA and targets the bound mRNA for degradation. We have addressed here the function of TTP in balancing the macrophage activation state by a comprehensive analysis of TTP-dependent mRNA decay in LPS-stimulated macrophages from WT and TTP-deficient mice.

overall_design: We compared mRNA stability in LPS-treated BMDMs from WT and TTP-/- mice by microarray-based measurement of the remnant mRNA after transcriptional blockade with actinomycin D (act D). To increase the sensitivity of the mRNA decay profiling we inhibited the LPS-activated p38 MAPK with the specific inhibitor SB203580 since p38 MAPK negatively regulates the mRNA-destabilizing activity of TTP. LPS stimulation was for 3h before addition of act D. RNA was harvested at 0', 45' and 90' thereafter.

first: Franz

last: Kratochvill

first: Pavel

last: Kovarik


title: Patients with Activated B-cell-like Diffuse Large B-cell Lymphoma (ABC DLBCL) in high and low infectious disease areas have different inflammatory gene signatures

city: Stockholm

first: Therese

last: Hogfeldt

address: Cancer Centre Karolinska, R:8

country: Sweden

institute: Karolinska Institutet

summary: DLBCL accounts for approximately 40% of newly diagnosed lymphomas worldwide. Several etiological mechanisms have been proposed. Among these are viral infections and chronic inflammation which may be associated with the initiation and progression of lymphoma.

overall_design: Paraffin-embedded specimens from Egyptian and Swedish DLBCL patients were studied using gene expression. RNA from patients were pooled together and arrays were performed in triplicates.


title: Overexpression of Gfi1b in a pro-B Abelson murine leukemia virus transformed cell line

first: Danae

last: Schulz

address: 1230 York Ave.

summary: We have conducted a screen for factors that downregulate expression of the genes encoding the V(D)J  recombinase (RAG1 and RAG2) during B cell development.  We have identified the transcription factor Gfi1B as being one of the proteins capable of decreasing RAG transcription when overexpressed in Ableson transormed ProB cell lines.  We have yet to determine whether the overexpression of Gfi1B downregulates the RAGs directly, or whether it initiates a signalling programme that results in RAG downregulation.  We hypothesize that by comparing global gene expression patterns in cells that overexpress Gfi1B and those that do not, we can distinguish between these possibilities and additionally gain insight into the broader genetic program that may be influenced by Gfi1B during hematopoiesis.

overall_design: Abelson pro-B cells were infected with a retrovirus encoding Gfi1b fused to the estrogen receptor domain.  Gfi1b expression was induced by adding tamoxifen to the culture medium for 12h.  Three biological replicates of untreated and treated cells were analyzed.


title: Evolution of gene expression during long term coexistence in a bacterial evolution experiment

status: Public on Jan 01 2012

city: Grenoble

first: Mickael

last: Le Gac

address: Institut Jean Roget

country: France

institute: CNRS

summary: We used microarrays to study the evolution of gene expression in two bacterial ecotypes that coexisted for more than 35000 generations of experimental evolution in an extremely simple environment

overall_design: We sampled four clones from each of two lineages at generations 6,500, 17,000 and 40,000 from the polymorphic Ara-2 population of the E. coli long-term evolution experiment. The four clones from each lineage and generation were mixed equally and used for global expression profiling, growth assays and competition experiments. Global expression profiles and growth assays were also performed on the ancestral strain. RNA extractions were done using cells in mid-exponential growth in the same glucose-limited minimal medium used in the evolution experiment. Global expression profiles were obtained by using Affymetrix arrays, with 5 or 6 biological replicates for each lineage-generation sample.

first: Jessica

last: Plucain

first: Thomas

last: Hindré

first: Richard

middle: E

last: Lenski

first: Dominique

last: Schneider


title: Gene Expression Profiling of Peripheral Blood Mononuclear Cells from Children With Active Hemophagocytic Lymphohistiocytosis

status: Public on Dec 12 2011

city: Cincinnati

first: Michael

last: Barnes

address: 3333 Burnet Ave

department: Rheumatology

institute: Cincinnati Childrens Hospital Medical Center

summary: Familial hemophagocytic lymphohistiocytosis (FHL) is a rare, genetically heterogeneous autosomal recessive immune disorder that results when the critical regulatory pathways that mediate immune defense mechanisms and the natural termination of immune/inflammatory responses are disrupted or overwhelmed. In order to advance the understanding of FHL, we performed gene expression profiling of peripheral blood mononuclear cells (PBMCs) from 11 children with untreated FHL. Total RNA was isolated and gene expression levels were determined using microarray analysis. Comparisons between patients with FHL and normal pediatric controls (n = 30) identified 915 down-regulated and 550 up-regulated genes with 2.5-fold difference in expression (P = 0.05). The expression of genes associated with natural killer cell functions, innate and adaptive immune responses, pro-apoptotic proteins, and B- and T-cell differentiation were down-regulated in patients with FHL. Genes associated with the canonical pathways of IL-6, IL-10 IL-1, IL-8, TREM1, LXR/RXR activation, and PPAR signaling and genes encoding of anti-apoptotic proteins were overexpressed in patients with FHL. This, first study of genome-wide expression profiling in children with FHL demonstrates the complexity of gene expression patterns, which underly the immunobiology of FHL.

overall_design: 11 Patients and 33 controls

first: Janos

last: Sumegi

middle: G

first: Susan

last: Molleran-Lee

first: Joyce

last: Villaneuva

first: Kejian

last: Zhang

first: Shawnagay

middle: V

last: Nestheide

first: Kimberly

last: Risma

first: Alexei

last: Grom

first: Alexandra

last: Filipovich


title: Direct Signaling Between Platelets and Cancer Cells Induces an Epithelial-Mesenchymal-Like Transition and Promotes Metastasis

city: Cambridge

first: Charles

middle: Arthur

last: Whittaker

state: MA

institute: Koch Institute

summary: Interactions of cancer cells with the primary tumor microenvironment are important determinants of cancer progression towards metastasis but it is unknown whether additional prometastatic signals are provided during the intravascular transit to the site of metastasis. Here, we show that transient platelet-tumor cell interactions are sufficient to prime tumor cells for subsequent metastasis. Platelet-derived TGF-beta and direct platelet-tumor cell contacts synergistically activate the TGF-beta/Smad and NF-kappaB pathways in cancer cells, resulting in their transition to an invasive mesenchymal-like phenotype and enhanced metastasis in vivo. Inhibition of NF-kappaB signaling in cancer cells or ablation of TGF-beta1 expression solely in platelets protects against lung metastasis in vivo. Thus, cancer cells rely on platelet-derived signals outside of the primary tumor for efficient metastasis.

overall_design:
MoEx-1_0-st:  Five replicates of Ep5 tumor cells cultured alone, five replicates of tumor cells cultured in combination with platelets, and three replicates of tumor cells combined with platelets just prior to RNA isolation to control for the presence of platelet RNAs.

MoGene-1_0-st:  Three replicates of tumor cells cultured alone, three replicates of tumor cells cultured in combination with platelets, three replicates of tumor cells cultured with centrifuged platelets and three replicates of tumor cells cultured with supernate (releasate) from centrifuged platelets.

first: Myriam

last: Labelle

first: Shahinoor

last: Begum

middle: O

last: Hynes


title: brain expression data from adult mice prenatally exposed to ethanol

status: Public on Dec 10 2011

city: London

first: Morgan

last: Kleiber

state: Ontario

address: Biological and Geological Sciences Building

department: Biology

country: Canada

institute: University of Western Ontario

summary:
Moderate alcohol consumption during pregnancy can result in a heterogeneous range of neurobehavioural and cognitive effects, termed fetal alcohol spectrum disorders (FASD).  We have developed a mouse moder of FASD that involves moderate ethanol exposure throughout gestation achieved by voluntary maternal consumption.  This model results in phenotypes relevant to FASD.  Since ethanol is known to directly affect the expression of genes in the developing brain leading to abnormal cell death, changes to cell proliferation, migration, and differentiation, and potential changes to epigenetic patterning, we hypothesize that this leaves a long-term footprint on the adult brain.  However, the long-term effects of prenatal ethanol exposure on brain gene expression, when behavioural phenotypes are apparent, are unclear.
We used two independent microarray experiments and focused on the genes identified by both to evaluate the genome-wide alterations to the adult brain transcriptome caused by prenatal ethanol exposure via moderate maternal drinking.

overall_design: To generate samples, two independent groups of female C57BL/6J mice were given access to 10% ethanol in water or water only.  Control females had access to water only.  Females were mated and continued to drink from gestational day 0 to pup postnatal day 10.  Whole brain RNA from adult (postnatal day 70) male ethanol-exposed offspring was extracted.  For experiment 1, RNA samples from three mice were pooled to reduce litter effects and the pooled samples were hybridized on Affymetrix arrays (2 control and 2 ethanol chips, total n=12 mice).  For experiment 2, RNA from two mice were pooled per chip and three arrays per treatment were used (3 control, 3 ethanol, total n=12 mice).

first: Benjamin

middle: I

last: Laufer

first: Eric

last: Diehl


title: Expression profile of shikonin resistant K562 cell line

city: Hangzhou

first: wu

last: hao

state: Zhejiang

address: 88, JieFang Road

department: Cancer Institute

country: China

institute: Zhejiang University

summary:
After over 25cycle and 18month's induction of shikonin, K562 cell show maginal resistance to shikonin but great change in gene expression
We use microarray to detect the global gene expression change of shikonin resistant cell

overall_design: K562 cell was treated by 4uM shikonin for 4hours, then allowed to die and grow back in fresh medium. Once recovered, cells were immidiatly subjected to another treatment.

first: Hao

last: Wu

first: Xun

last: Hu


title: Expression data from mouse cumulus cells

city: Adelaide

first: Maxime

last: Sasseville

state: SA

address: Level 6, Medical school, Frome Road

country: Australia

institute: The Robinson Institute, University of Adelaide

summary:
Follicle stimulating hormone (FSH) and epidermal growth factor (EGF) are currently used on cumulus-oocyte complexes to mimic the luteinizing hormone surge in vitro and induce oocyte maturation and cumulus expansion. We have previously shown that addition of exogenous recombinant growth differentiation factor 9 (GDF9) during oocyte in vitro maturation led to an improvement of oocyte quality, as shown by an increased blastocyst percentage and fetal survival.
Our objective was to characterize the effect of FSH/EGF and GDF9 treatments on mouse cumulus cells expression profile by microarray analysis.

overall_design: Cumulus-oocyte complexes (COCs) were recovered from 21 to 26 day old female 129/SV mice, 44 hours post equine chorionic gonadotropin treatment (eCG (5 IU)). For the microarray experiment whole COCs were treated with 293H control medium (0.125% v/v), with 20 ng/ml GDF9 or with a combination of 50 mIU/ml FSH and 10 ng/ml EGF. After 8 hours of in vitro maturation, COCs were denuded by gentle pipetting, the oocytes were removed and the cumulus cells centrifuged and extracted RNA analysed by microarray.

first: Melanie

last: McDowall

first: Jeremy

last: Thompson

first: Robert

last: Gilchrist


title: A sumoylation-dependent transcriptional subprogram is required for Myc-driven tumorigenesis

status: Public on Dec 08 2011

city: Houston

first: Chad

middle: A.

last: Shaw

state: TX

address: 1 Baylor Plaza

department: Molecular and Human Genetics

institute: BCM

summary: Myc is an oncogenic transcription factor frequently dysregulated in human cancer. To identify pathways supporting the Myc oncogenic program, we employed a genome-wide RNAi screen for Myc-synthetic-lethal (MySL) genes and uncovered a role for the SUMO-activating-enzyme (SAE1/2). Loss of SAE1/2 enzymatic activity drives synthetic lethality with Myc.  Mechanistically, SAE2 inhibition switches a transcriptional subprogram of Myc from activated to repressed. A subset of these SUMOylation-dependent Myc-switchers (SMS genes) governs mitotic spindle function and is required to support the Myc oncogenic program.

overall_design: comparison of 4 treatments: normal HMEC, High Myc in HMEC, SUMO depleted in HMEC, High Myc+Sumo Depleted in HMEC

first: Jessica

middle: D

last: Kessler

first: Kristopher

middle: T

last: Kahle

first: Tingting

last: Sun

first: Kristen

last: Meerbrey

first: Michael

middle: R

last: Schlabach

first: Earlene

middle: M

last: Schmitt

first: Samuel

last: Skinner

first: Qikai

last: Xu

first: Mamie

middle: Z

last: Li

first: Zachary

middle: C

last: Hartman

first: Mitchell

last: Rao

first: Peng

last: Yu

first: Rocio

last: Dominguez-Vidana

first: Anthony

last: Liang

first: Nicole

last: Solimini

first: Ronald

last: Bernardi

first: Bing

first: Tiffany

last: Hsu

first: Ido

last: Golding

first: Ji

last: Luo

first: C

middle: K

last: Osbourne

last: Creighton

first: Susan

last: Hilsenbeck

first: Rachel

last: Schiff

first: Stephen

last: Elledge

first: Thomas

middle: F

last: Westbrook


title: Invasion-mediating genes in breast cancer

city: Coleraine

last: Bjourson

state: Northern Ireland

address: Cromore Road

department: School of Biomedical Sciences

country: United Kingdom

institute: University of Ulster

summary:
From the parental breast cancer cell line MCF7 (weakly invasive), we progressively selected hyperinvasive subclones. We compared the gene expression between the parental MCF7-I0 and the hyper-invasive cells MCF7-I6.
We used Affymetrix U133 Plus 2 microarrays to detail the global programme of gene expression underlying weakly and highly invasive breast cancer cells derived from the human breast cancer cell line MCF7.

overall_design: The hyper-invasive subclones were selected using Matrigel invasion chambers as a model for the invasion process in vivo. The cells that invaded through the membrane were cultured and re-introduced into an additional invasion assay. This methodology was repeated to give rise to a subclone of MCF7 cells that had invaded six times; these were termed MCF7-I6 cells. The invasive capacity of MCF7-I6 cells was shown to be more than 11 times greater than the parental cells, which we denote as MCF7-I0. Thus, these hyper-invasive cells were present within the heterogeneous population, and we speculated that differences in gene expression between the MCF7-I6 cells and the parental cells MCF7-I0 may be involved in the invasion process.


title: Innate and adaptive immune responses associate with progressive histological damage of renal allografts

city: Stanford

first: Maarten

last: Naesens

address: Pasteur Drive

institute: Stanford University

summary: CONTEXT Slowly progressive chronic tubulo-interstitial damage jeopardizes long-term renal allograft survival. Both immune and non-immune mechanisms are thought to contribute, but the most promising targets for timely intervention have not been identified. OBJECTIVE In the current study we seek to determine the driving force behind progressive histological damage of renal allografts, without the interference of donor pathology, delayed graft function and acute graft rejection. DESIGN We used microarrays to examine whole genome expression profiles in renal allograft protocol biopsies, and analyzed the correlation between gene expression and the histological appearance over time. The gene expression profiles in these protocol biopsies were then compared with gene expression of biopsies with acute T-cell mediated rejection. PATIENTS Human renal allograft biopsies (N=120) were included: 96 rejection-free protocol biopsies and 24 biopsies with T-cell mediated acute rejection. RESULTS In this highly cross-validated study, we demonstrate the significant association of established, ongoing and future chronic histological damage with regulation of adaptive immune gene expression (T-cell and B-cell transcript sets) and innate immune response gene expression (dendritic cell, NK-cell, mast cell and granulocyte transcripts). We demonstrate the ability of gene expression analysis to perform as a quantitative marker for ongoing inflammation with a wide dynamic range: from subtle subhistological inflammation prior to development of chronic damage, over moderate subclinical inflammation associated with chronic histological damage, to marked inflammation of Banff-grade acute T-cell mediated rejection. CONCLUSION   Progressive chronic histological damage after kidney transplantation is associated with significant regulation of both innate and adaptive immune responses, months before the histological lesions appear. This study therefore corroborates the hypothesis that quantitative inflammation below the diagnostic threshold of classic T-cell or antibody-mediated rejection is associated with early subclinical stages of progressive renal allograft damage.

overall_design: We used microarrays to examine whole genome expression profiles in renal allograft protocol biopsies, and analyzed the correlation between gene expression and the histological appearance over time. The gene expression profiles in these protocol biopsies were then compared with gene expression of biopsies with acute T-cell mediated rejection. Human renal allograft biopsies (N=120) were included: 96 rejection-free protocol biopsies and 24 biopsies with T-cell mediated acute rejection.

first: Purvesh

last: Khatri

first: Li

last: Li

first: Neeraja

last: Kambham

first: Tara

last: Sigdel

first: Amery

last: Chen

first: Rong

first: Atul

middle: J

last: Butte

first: Szu-Chuan

last: Hsieh

first: Oscar

last: Salvatierra

first: Minnie

last: Sarwal


title: Early dynamic transcriptomic changes as predictors of preoperative radiotherapy efficacy in patients with rectal cancer: a feasibility study.

city: Saint Herblain

first: Wilfried

last: Gouraud

address: bd Jacques Monod

department: Integrated Center of Oncology René Gauducheau

institute: ICO (Integrated Center of Oncology Nantes)

summary: With a view to developing novel biomarkers of the efficacy of radiotherapy in patients with rectal cancer, we measured gene expression profiles on biopsies taken before and during preoperative radiotherapy. Repeat biopsy did not increase toxicity. Radiotherapy induced the expression of genes involved in oxidative stress, signal transduction, apoptosis and immune response.

overall_design: Two rectum tumor biospsies for each patient (6 cases) : before RT and one hour after a dose of 7.2 Gy (4th fraction) during RT.

first: Stéphane

last: Supiot

first: Pascal

last: Jézéquel

first: Loïc

last: Campion

first: Bruno

last: Buecher

first: Josiane

last: Charrier

first: Marie-Françoise

last: Heymann

first: Marc-André

last: Mahé

first: Emmanuel

last: Rio

first: Michel

last: Chérel


title: Transcriptional profiling of 77 tissue samples from germ-free and conventionally raised mice.

city: Gothenburg

first: Erik

last: Larsson

address: Bruna stråket 16

department: Wallenberg Laboratory

institute: University of Gothenburg

summary:
Whole-transcriptome survey of gene expression differences between germ-free (GF) and conventionally raised (CONV-R) mice.
To assess the role of toll-like receptor signalling, both wild-type and Myd88 -/- mice were used.

overall_design: Four different tissues were harvested from 20 mice (5 WT CONV-R, 5 Myd88 -/- CONV-R, 4 WT GF, 6 Myd88 -/- GF) and expression profiles were determines using the Affymetrix Mouse Gene 1.0ST platform. 77 samples remained after quality control.

first: E

first: F

last: Bäckhed

first: C

last: Reigstad


title: Clinical significance of UNC5B Expression in Colorectal Cancer

status: Public on Dec 04 2011

city: Bunkyo-ku

first: Kaoru

last: Mogushi

state: Tokyo

address: 2-1-1 Hongo

department: Intractable Disease Research Center

country: Japan

institute: Juntendo University

summary: Purpose and Experimental Design: The purpose of this study is to find a methylation-related gene that could become a biomarker or therapeutic target in colorectal carcinoma (CRC). We screened candidate genes suspected to be silenced by DNA methylation using oligonucleotide microarray analysis. To investigate the clinical significance of one candidate gene (UNC5B), we analyzed the correlation between mRNA expression and clinicopathological features using clinical tissue samples. Finally, methylation specific PCR analysis was performed to reveal whether the promoter region was methylated in CRC cell lines.  Results: We found 75 candidate genes that were potentially suppressed by DNA methylation in CRC. We focused on UNC5B, a possible tumor suppressor gene and regulator of apoptosis known to be inactivated in CRC. The mRNA expression analysis using tissue samples revealed that UNC5B mRNA was down-expressed in about 20% of CRC patients, and the patients with low-UNC5B-expression tumors showed a significantly higher recurrence rate after curative surgery. According to the univariate and multivariate analysis, low UNC5B expression was an independent risk factor for postoperative recurrence in stage I, II, and III CRC patients. Furthermore, patients with low expression of UNC5B in tumors had significantly poorer prognosis than those with high expression of UNC5B. Although UNC5B mRNA expression was restored by the demethylation treatment in CRC cell lines, the promoter region of UNC5B was not methylated.  Conclusion: UNC5B is a potential biomarker for the selection of patients with high risk of postoperative recurrence and worse prognosis in CRC.

overall_design: Gene expression profiles for 17 pairs of cancer and non-cancerous tissues from colorectal cancer patients were measured by Affymetrix HG-U133 Plus 2.0 arrays. HT29 and HCT15 cells were also used to investigate genes upregulated after 5-aza-2'-deoxycytidine treatment. Normalization was performed by robust multi-array average (RMA) method under R 2.6.2 statistical software with affy package from BioConductor. The normalization procedure was separately performed for each data set of clinical samples, HT29 cells, and HCT15 cells. The normalized gene expression levels were presented as log2-transformed values by RMA.

first: S

last: Okazaki

first: T

last: Ishikawa

last: Iida

first: M

last: Ishiguro

first: H

last: Kobayashi

last: Higuchi

last: Enomoto

first: K

last: Mizushima

last: Tanaka

last: Uetake

last: Sugihara


title: Altered Hematopoietic Cell Gene Expression Precedes Development of Therapy-Related Myelodysplasia and Identifies Patients at Risk

city: Duarte

first: Ravi

last: Bhatia

state: CA

address: 1500 E Duarte Road

department: Hematopoietic Stem Cell and Leukemia Research

institute: City of Hope Beckman Research Institute

summary: Therapy-related myelodysplasia or acute myeloid leukemia (t-MDS/AML) is a lethal complication of cancer treatment. Although t-MDS/AML development is associated with known genotoxic exposures, its pathogenesis is not well understood and methods to predict risk of development of t-MDS/AML in individual cancer survivors are not available. We performed microarray analysis of gene expression in samples from patients who developed t-MDS/AML after autologous hematopoietic cell transplantation (aHCT) for Hodgkin lymphoma (HL) or non-Hodgkin lymphoma (NHL) and controls that did not develop t-MDS/AML after aHCT. CD34+ progenitor cells from peripheral blood stem cell (PBSC) samples obtained pre-aHCT from t-MDS/AML cases and matched controls, and bone marrow (BM) samples obtained at time of development of t-MDS/AML, were studied. Significant differences in gene expression were seen in PBSC obtained pre-aHCT from patients who subsequently developed t-MDS/AML compared to controls. Genetic alterations in pre-aHCT samples were related to mitochondrial function, protein synthesis, metabolic regulation and hematopoietic regulation. Progression to overt t-MDS/AML was associated with additional alterations in DNA repair and DNA-damage checkpoint genes. Altered gene expression in PBSC samples were validated in an independent group of patients. An optimal 63-gene PBSC classifier derived from the training set accurately distinguished patients who did or did not develop t-MDS/AML in the independent test set. These results indicate that genetic programs associated with t-MDS/AML are perturbed long before disease onset, and can accurately identify those at risk of developing this complication.

overall_design:
PBSC samples obtained pre-aHCT and BM samples at the time of development of t-MDS/AML post-HCT were studied. The training set consisted of 18 patients who developed t-MDS/AML (”cases”) after aHCT, matched with 37 controls who underwent aHCT, but did not develop t-MDS/AML. One to three controls were selected per case, matched for primary diagnosis (HL/NHL), age at aHCT (±10years), and ethnicity (Caucasians, African-Americans, Hispanics, other). The length of follow-up after aHCT for controls was longer than the time to t-MDS/AML in the corresponding case. The results of the training set were validated in an independent group of 36 patients (test set) consisting of 16 cases that developed t-MDS/AML post-aHCT and 20 matched controls.

In the test set, 55 PBSC samples from 18 cases and 37 matched controls were studied. BM samples from time of development of t-MDS/AML were available for 12 cases, and from 21 matched controls obtained at a comparable time from aHCT. For validation, 36 PBSC samples from 16 cases and 20 matched controls were studied. All samples had been cryopreserved as mononuclear cells. After thawing, samples were labeled with anti-CD34-APC and anti-CD45-FITC and CD34+CD45dim cells were selected using flow cytometry. Total RNA was extracted using the RNeasy kit. RNA from 1000 cells was amplified and labeled using GeneChip® Two-Cycle Target Labeling and Control Reagents from Affymetrix. 15 µg of cRNA each was hybridized to Affymetrix HG U133 plus 2.0 Arrays.

Microarray data were analyzed using R (version 2.9) with genomic analysis packages from Bioconductor (version 2.4). Data for PBSC and BM samples were normalized separately using robust multiarray averages with consideration of GC content (GCRMA). Probesets with low expression or variability were filtered. Expression of genes represented by multiple probesets was set as the median of the probesets. Using conditional logistic model (CLM) to retain matching between cases and controls, we analyzed the magnitude of association [expressed as odds ratio (OR)] between t-MDS/AML and i) gene expression levels in PBSC at the pre-aHCT time point; ii) gene expression levels in BM at time of t-MDS/AML; and iii) change of expression of individual genes from PBSC to time of t-MDS/AML. False discovery rate (FDR) was applied to adjust for multiple testing. Gene set enrichment analysis (GSEA) was performed on ranked lists of genes differentially expressed between cases and controls. Where multiple significant gene sets were related to each other, analysis was performed to identify a subset of common enriched genes. Average gene expression was calculated for each set and heatmaps plotted to show the contrasts between cases and controls. Gene Ontology (GO) and pathway analysis was performed using DAVID 2008 and Ingenuity IPA 7.5 respectively, retaining genes with z-scores ≥1.8 or ≤-1.8, and ≥1.5-fold change in OR between cases and controls.

The association between gene expression in the PBSC product and subsequent development of t-MDS/AML identified in the training set was validated in an independent test set of 36 PBSC sample procured from patients who developed t-MDS/AML after aHCT (16 cases) or did not (20 controls). Pre-processing, normalization and filtering procedures for the test set were identical to the training set. Differential expression between cases and controls was analyzed using CLM. GSEA analysis was performed on the ranked list of differentially expressed genes. Prediction analysis of microarray (PAM) was used to derive a prognostic gene signature from the training set to classify patients as case or control. PAM uses the “nearest shrunken centroid” approach and 10-fold cross-validation to select a parsimonious gene expression signature that can classify samples with minimal misclassification. PAM was applied to genes common to both datasets. Based on the misclassification error in cross-validation, a 63-gene signature was selected for prediction using the test data.

first: Smita

first: Liang

last: Li

first: Sierra


title: The effect of androgen deprivation on human prostate xenograft tumor LuCaP35

status: Public on Dec 06 2011

city: South San Francisco

first: Yuting

last: Sun

address: 1 DNA way

department: Research Oncology

institute: Genentech

summary: Androgen deprivation is a standard of care front-line therapy for human prostate cancer, however, majority of patients will eventally develop resistance to androgen deprivation. In this study, using a human prostate cancer xenograft model -LuCaP35, we examiend the gene expression changes after castration.

overall_design: We compare the gene expression of 5 LuCaP35 xenografts from non-treated mice (Control), and 5 androgen-deprived LuCaP35 xenografts from castrated mice (Castration).

first: Wei-Qiang

last: Gao

first: Jeffrey

last: Settleman

first: Leisa

last: Johnson


title: Down-regulation of PAX2 affects ovarian cancer cell growth and migration

status: Public on Dec 05 2011

first: Kwong-Kwok

last: Wong

address: T4-3900, 1515 Holcombe Boulevard

department: Gynecologic Oncology and Reproductive Medicine

institute: UT M. D. Anderson Cancer Center

summary:
PAX2 is one of nine PAX genes that regulate tissue development and cellular differentiation in embryos. PAX2 promotes cell proliferation, oncogenic transformation, cell lineage specification, migration, and survival. In our previous study, we found that PAX2 is highly expressed in low-grade ovarian serous carcinoma, but its expression in clear cell, endometrioid, and mucinous cell ovarian carcinomas have not been studied. More importantly, the functional role of PAX2 in ovarian cancer is not known.
Downregulation of PAX2 in PAX2-expressing ovarian cancer cells inhibits cell proliferation and migration. This growth inhibition is due to the upregulation of the tumor suppressor gene G0S2 and subsequent induction of apoptosis. The PAX2 pathway thus represents a potential therapeutic target for PAX2-expressing ovarian carcinomas.

overall_design: Knockdown PAX2 expression in these cell lines was achieved by lentiviral shRNAs targeting the PAX2 gene. PAX2 stable knockdown cells were characterized for cell proliferation, migration, apoptosis, and gene expression profiles.


title: Expression data of liver samples of dex or vehicle treated wildtype and HDAC6- knockout C57Bl/6 mice respectively

status: Public on Dec 07 2011

city: Basel

first: Tim

last: Roloff

address: Maulbeerstrasse 66

department: Functional Genomics

institute: FMI

summary:
In the present study, we investigated the importance of histone deacetylase 6 (HDAC6) for glucocorticoid receptor (GR) mediated effects on glucose metabolism, and its potential as a therapeutic target for the prevention of glucocorticoid (GC)-induced diabetes. Dexamethasone (dex)-induced hepatic glucose output and GR translocation were analysed in wildtype (wt) and HDAC6-deficient (HDAC6ko) mice. The effect of the specific HDAC6-inhibitor tubacin was analysed in-vitro. Wt and HDAC6ko mice were subjected to 3 weeks dex treatment before analysis of glucose and insulin tolerance. HDAC6ko mice showed impaired dex-induced hepatic GR translocation. Accordingly, dex induced expression of a large number of hepatic genes was significantly attenuated in mice lacking HDAC6 and by tubacin in-vitro. Glucose output of primary hepatocytes from HDAC6ko mice was diminished. A significant improvement of dex-induced whole-body glucose intolerance as well as insulin resistance in HDAC6ko mice compared to wt littermates was observed. The present study demonstrates that HDAC6 is an essential regulator of hepatic GC stimulated gluconeogenesis and impairment of whole body glucose metabolism through modification of GR nuclear translocation. Selective pharmacological inhibition of HDAC6 may provide a future therapeutic option against the pro-diabetogenic actions of GCs.
In this dataset, we include the expression data obtained from isolated RNA of dissected mouse livers using wildtype and HDAC6 deficient animals which were treated over a timespan of 3 weeks with 1mg/kg dexamethasone and vehicle respectively. These data are used to show the hdac6-deficiency mediated attenuation of several dexamethasone induced genes.

overall_design: 12 samples in total were analyzed. 3 samples of different animals of each group (wt vehicle, wt dexamethasone, hdac6ko vehicle and hdac6ko dexamethasone)

first: Robin

last: Winkler

first: Stephane

last: Thiry


title: CD133+ colon cancer cells are more interactive with the tumor microenvironment than CD133- cells

status: Public on Dec 01 2011

city: Galveston

first: Celia

last: Chao

address: 301 University Boulevard

department: Surgery

institute: Univ TX Medical Branch

summary: CD133-positive colorectal cancer cells exhibit enhanced tumorigenicity over CD133-negative cells. The CD133+ cells are more interactive with and responsive to their stromal microenvironment because they also express the cognate receptors, such as CXCR4, for ligands produced by their neighboring carcinoma-associated fibroblasts, such as SDF-1 (stromal-derived growth factor).

overall_design: we isolated and separately cultured both the carcinoma cells and CAF from the same patient tumor.  Three samples (CD133+, CD133-, Carcinoma associated fibroblasts) in triplicate for a total of 9 samples.

first: J

last: Carmical


title: Expression in irradiated MEFs exposed to murine acute lymphoblastic leukemia cells

city: Monrovia

first: Nora

last: Heisterkamp

address: 1218 S Fifth Avenue

department: Department of Systems Biology

institute: Beckman Research Institute City of Hope

summary: Primary pre-B acute lymphoblastic (ALL) cells do not proliferate long-term ex vivo without the presence of stromal support. We developed and use an ex vivo co-culture model, consisting of mouse leukemic pre-B Bcr/Abl-expressing ALL cells grown with mitotically inactivated mouse embryonic fibroblasts (MEFs). This system provides a generic type of environmentally-mediated protection to the ALL cells, because when the ALL cells are treated with a moderate dose of a therapeutic drug, drug-resistant ALL cells can be recovered after a 1-2 week period of culture. Some of the factors produced by stromal cells that provide protection to ALL cells have been identified. However, it is unclear if the presence of drug-treated ALL cells affects the stromal fibroblasts. The current study was initiated to examine this using expression profiling on the irradiated MEFs.

overall_design: We isolated RNA from irradiated wild-type MEFs after a 9-day culture period. MEFs had either been exposed to DMSO, to nilotinib, a drug that is not expected to affect them, or to ALL cells treated with DMSO or nilotinib. MEFs and ALL cells were physically separated by a Transwell membrane of a pore size that did not allow the ALL cells to migrate towards the MEFs, but allowed the exchange of diffusible molecules.

first: Sonia

last: Stoddard

first: Niklas

last: Feldhahn

first: Anna

last: Arutyunyan


title: Differential gene expression in thrombus-derived white blood cells of patients with acute coronary syndrome

city: Zurich

first: Stefan

last: Zoller

address: Universitatstrasse 16

department: Genetic Diversity Centre

institute: ETH Zurich

summary: Inflammatory mechanisms and immune cells are involved in acute coronary syndromes (ACS) and may lead to acute plaque rupture. However, the local expression of the different genes potentially involved is largely unknown. We therefore performed an Affymetrix analysis of genes expressed in white blood cells obtained from an occluding coronary thrombus or peripheral blood of patients with ST-elevation myocardial infarction.

overall_design: Thrombi of ACS patients were harvested from the site of coronary occlusion. Leukocytes were isolated by Ficoll centrifugation. Peripheral blood leukocytes (PBL) were treated in a similar fashion and mRNA was extracted from both cells.

first: Alexander

last: Akhmedov

first: Roland

last: Klingenberg

first: Keiko

last: Yonekawa

first: Christine

last: Lohmann

first: Christophe

last: Wyss

first: Roberto

last: Corti

first: Steffen

last: Gay

first: Christian

last: Matter

first: Willibald

last: Maier

first: Michel

last: Neidhart

first: Thomas

last: Lüscher


title: Expression data from epidermal stem cells isolated from dorsal skin of P19 Per1-Venus mice and Bmal1 epidermal knockout mice

city: Barcelona

first: Salvador

middle: Aznar

last: Benitah

address: Baldiri Reixac 10

department: Oncology

country: Spain

institute: Institute for Research in Biomedicine (IRB, Barcelona)

summary: Epidermal stem cells ensure that skin homeostasis is maintained. In murine skin, epidermal stem cells cluster at specific niches where, under steady-state conditions, they undergo cycles of dormancy and activation1. When cellular replenishment is required, epidermal stem cells egress from the niche and proliferate for a limited number of times to subsequently feed into the differentiated compartment1-3. However, only a subset of stem cells becomes active during each round of morphogenesis, suggesting that stem cells coexist in heterogeneous responsive states within the same niche. Using a circadian clock fluorescent reporter mouse model, we show that the dormant epidermal stem cell niche contains two coexisting populations of stem cells at opposite phases of the clock, which are differentially predisposed to respond to homeostatic cues. In dormant niches, the core molecular clock protein Bmal1 transcriptionally modulates the expression of stem cell regulatory genes, including modulators of Wnt and TGFb, to create two coexisting stem cell populations, one predisposed, and the other less prone, to activation. Unbalancing this equilibrium of epidermal stem cells, through conditional epidermal deletion of Bmal1, resulted in a long-term progressive accumulation of non-responsive stem cells, premature impairment of tissue self-renewal, and a significant reduction in the development of squamous cell carcinomas. Our results indicate that the molecular clock machinery fine-tunes the spatiotemporal behavior of epidermal stem cells within their niche, and that perturbation of this mechanism affects tissue homeostasis and the predisposition to neoplastic transformation. The goals of this study was to compare the transcriptome of epidermal stem cells according to their circadian rhythm phase. We isolated epidermal stem cells (bulge cells; alpha6bright/CD34+ population) from 19 days old Per1-Venus mice and separated them according to Venusbright (clock positive) and Venus dim (clock negative). The goals of this study was to compare the transcriptome of epidermal stem cells in which their circadian rhythm machinery has been perturbed by deleting the gene that encodes for Bmal1. We compared the transcriptomes of basal interfollicular epidermis cells (alpha6 integrin bright/CD34- cells) from the dorsal skin of 1 year old BmalKO mice and their respective control littermates. Each array corresponds to purified cells from approximately 5 mice.

overall_design: We profiled three samples of Venus bright and three of Venus dim epidermal stem cells. Each sample consisted of epidermal stem cells isolated from aproximately 20 mice (in order to obtain enough number of cells to perform high quality arrays). We profiled three WT samples and 3 KO samples. Each sample corresponds to basal interfollicular epidermis cells purified from 5 mice.

middle: A

first: Peggy

last: Janich


title: Human bronchial epithelial cells exposed to A. alternata spores

city: Blacksburg

first: Christopher

middle: B

last: Lawrence

address: Washington Street

institute: Virginia Bioinformatics Institute, Virginia Tech

summary: This present study is the first to investigate the global changes in host gene expression during the interaction of human bronchial epithelial cells and live Alternaria spores. Human bronchial epithelial cells (BEAS2-B) were exposed to spores or media alone for 24 hours. RNA was collected from three biological replicates/treatment and used to assess changes in gene expression patterns using Affymetrix Human Genome U133 Plus 2.0 Arrays. Interestingly, many cytokine/chemokine immune response genes were upregulated. Genes involved in cell death, retinoic acid signaling, TLR3, and interferon response pathways were also significantly upregulated.

overall_design: Three biological replicates for control (untreated cells) and treatment (5 x 10^5 A. alternata spores)

first: Mihaela

last: Babiceanu

first: Amanda

last: Rumore

first: Bradley

last: Howard

first: Hirohito

last: Kita


title: Down-regulation of ECRG4, a candidate tumor suppressor gene  in human breast cancer

status: Public on Dec 02 2011

city: Marseille

first: Pascal

last: FINETTI

state: BdR

address: 232 Bd Ste Marguerite

department: Centre de cancérologie de Marseille

institute: Institut Paoli-Calmettes

summary: ECRG4 is a promising tumor suppressor gene (TSG) recently identified in esophageal carcinoma. Its expression and prognostic value have never been explored in breast cancer. Using DNA microarray,  we examined ECRG4 mRNA expression in 353 invasive breast cancer samples. A meta-analysis was performed on a large public retrospective gene expression dataset (n=1,387) to analyze correlation between ECRG4 expression and histo-clinical features including survival.

overall_design: To determine ECRG4 mRNA expression in breast cancer and normal breast, we first analyzed gene expression data generated by our laboratory (Institut Paoli Calmettes (IPC), Marseille, France) from cancer and normal mammary samples. Tumor tissues were from 353 patients with invasive adenocarcinoma who underwent initial surgery at IPC between 1987 and 2007. The study was approved by our institutional review board. Each patient gave a written informed consent for research use. Samples were macrodissected and frozen in liquid nitrogen within 30 min of surgical removal. All profiled specimens contained more than 60% of cancer cells (as assessed before RNA extraction using frozen sections adjacent to the profiled samples). After surgery, patients received an adjuvant multimodal treatment according to standard guidelines. Extraction of nucleic acids from frozen samples was done by using guanidium isothiocynanate and cesium chloride gradient. Expression profiles had been established for these 353 cancers pools with Affymetrix U133 Plus 2.0 human microarrays (Affymetrix®, Santa Clara, CA, USA).

first: R

last: Sabatier

first: P

last: Finetti

first: J

last: Adelaïde

first: A

last: Guille

first: L

last: Lane

first: D

last: Birnbaum

first: M

last: Chaffanet

first: F

last: Bertucci


title: The time-course transcriptomic responses of THP-1 human macrophage-like cells  to W-Beijing Mycobacterium tuberculosis strains of different sublineages

city: Bristol

first: Hai

last: Fang

address: Woodland Road

department: Department of Computer Science

institute: University of Bristol

summary: The W-Beijing family of Mycobacterium tuberculosis (Mtb) strains is known for its high-prevalence and -virulence, as well as for its genetic diversity, as recently reported by our laboratories and others. However, little is known about how the immune system responds to these strains. To explore this issue, here we used reverse engineering and genome-wide expression profiling of human macrophage-like THP-1 cells infected by different Mtb strains of the W-Beijing family, as well as by the reference laboratory strain H37Rv. Detailed data mining revealed that host cell transcriptome responses to H37Rv and to different strains of the W-Beijing family are similar and overwhelmingly induced during Mtb infections, collectively typifying a robust gene expression signature ("THP1r2Mtb-induced signature"). Analysis of the putative transcription factor binding sites in promoter regions of genes in this signature identified several key regulators, namely STATs, IRF-1, IRF-7, and Oct-1, commonly involved in interferon-related immune responses. The THP1r2Mtb-induced signature appeared to be highly relevant to the interferon-inducible signature recently reported in active pulmonary tuberculosis patients, as revealed by cross-signature and cross-module comparisons. Further analysis of the publicly available transcriptome data from human patients showed that the signature appears to be relevant to active pulmonary tuberculosis patients and their clinical therapy, and be tuberculosis specific. Thus, our results provide an additional layer of information at the transcriptome level on mechanisms involved in host macrophage response to Mtb, which may also implicate the robustness of the cellular defense system that can effectively fight against genetic heterogeneity in this pathogen.

overall_design:
THP-1 cells were infected by the reference laboratory strain H37Rv, and the infected cells at 4, 18 and 48h were collected (in duplicate). A total of 40 samples (including the 33 W-Beijing-infected samples, the 6 H37Rv-infected samples, and an uninfected sample at 0h as a control) were subjected to the RNA extraction for microarray hybridization.
RNA was treated for hybridization with HG-U133 Plus 2.0 Array according to the Affymetrix protocol. Then, arrays were scanned by a high-resolution scanner and the scanned images were converted to cell intensity file (.CEL files) using GeneChip Operating Software (GCOS). These CEL raw expression data were first normalized using Robust Multi-array Averaging (RMA) with quantile normalization in R (Bioconductor). Detection call-based filter was then applied to remove all the probesets whose expression values were consistently below an empirically determined value of minimum sensitivity. This value was calculated according to the 95th percentile of all the ‘Absent’ call-flagged signals of the entire dataset. Any expression values below this value are considered as being technically unreliable. Since the uninfected sample was served as a common control for the comparison, probesets with expression values less than this empirical value at the uninfected control were also removed. Finally, expression values of probesets in 39 infected samples were subtracted by their cognate values in the uninfected control (0h).
After the normalization and pre-filtering above, a gene expression matrix was constructed, containing 18,541 probesets (representing 10,315 unique Entrez Genes) across 39 samples, that is, time-courses (4h, 18h and 48h) of THP-1 cells infected by each of 11 Mtb W-Beijing strains as well as H37Rv (in duplicate). This matrix was first subjected to Cluster3.0/TreeView-1.0.8 with Euclidean distance for unsupervised sample classification. The pair-wise Pearson’s correlation coefficients were also calculated to show a high degree of similarity for different strains within the same time point. For gene clustering and visualization, the gene expression matrix was also subjected to component plane presentation integrated self-organizing map (CPP-SOM), an component of topology-preserving selection and clustering (TPSC) package (see http://www.cs.bris.ac.uk/~hfang/TPSC/). Specifically, the input data were first trained using the SOM algorithm with the Epanechikov neighborhood kernel. The trained map was then visualized by CPP to display sample-specific transcriptome changes.
Linear Models for Microarray Data (LIMMA) was applied to identify those differentially expressed genes between any two successive time points. LIMMA used linear models and empirical Bayes methods (the moderated t-statistic) in assessing differential expression. The criteria for identifying the top significant probesets for the designed contrast was based on adjusted P-value < 0.01, as corrected using Benjamini and Hochberg procedure. Under such criteria, all genes identified as being differentially expressed from 4h to 18h are expressed by 2-folds and more. These highly modulated genes were further divided into two groups: the induced group (cTHPr2Mtb-induced) and the other repressed (cTHPr2Mtb-repressed). The former overwhelmingly dominates the latter; those genes in the cTHPr2Mtb-induced group collectively typify a molecular signature of common host transcriptome responses to W-Beijing family strains.
Functional enrichment analysis using Gene Ontology (GO) and KEGG Pathways was conducted to interpret the gene set of interest (e.g., those genes in cTHPr2Mtb-induced signature). This analysis was implemented by Database for Annotation, Visualization and Integrated Discovery (DAVID) v6.7 for identifying enriched GO and KEGG pathway, based on Benjamini and Hochberg-derived FDR (<0.01). For regulatory enrichment analysis, PRomoter Integration in Microarray Analysis (PRIMA) was used to identify putative transcriptional regulators for a given gene set compared to background (entire Entrez Genes) (Bonferroni-corrected P-value < 0.01). Based on the known transcription factor binding sites (as represented by positional weight matrix, PWM), PRIMA scanned putative binding sites of promoter sequences spanning promoter regions from 2,000 bp upstream to 200 bp downstream of the transcription start site.

first: Kang

last: Wu

first: Kankan

last: Wang

first: Ji

last: Zhang


title: CHAC1 mRNA expression is a strong prognostic biomarker in breast and ovarian cancer

city: Bolzano

first: Johannes

last: Rainer

address: Via A. Volta 21

department: Institute for Biomedicine

country: Italy

institute: Eurac Researc

summary: Extracellular, cancer-specific methylated DNA has been shown to be a prognostic marker when detected in serum or plasma. In this study we investigated the effect of treating cancer cells with differentially methylated CpG DNA. When breast cancer cell lines were treated with methylated CpG DNA, a consistent upregulation of CHAC1 mRNA expression was observed. CHAC1 was recently described to be a novel component of the unfolded protein response pathway. To elucidate the role of CHAC1 mRNA expression in cancer in more detail, we analyzed expression of this gene in breast (n=107) and ovarian cancer (n=107) and found a strong correlation with tumor differentiation. Poorly differentiated tumors exhibited higher CHAC1 expression levels (p=0.004 for breast and p=0.031 for ovarian cancer). Additionally, hormone receptor (HR)-negative breast cancers (p<0.001) and advanced stage disease ovarian cancers (p=0.026) also demonstrated high CHAC1 mRNA levels. mRNA expression analysis of the two known CHAC1 isoforms showed a strong association of expression above the median with poor outcome in breast cancer patients in a multivariate analysis (isoform a: relative risk (RR) of death 3.2 (95% CI 1.6-6.5; p<0.01); RR of relapse 3.9 (95% CI 1.6-9.8; p<0.01); isoform b: relative risk (RR) of death 3.5 (95% CI 1.6-7.3; p<0.01); RR of relapse 6.6 (95% CI 2.4-18.5; p<0.01)). Univariate analysis in ovarian cancer showed that CHAC1 mRNA expression above the median was associated with a poor relapse free survival (p=0.03). In younger ovarian cancer patients (age < median age), a high CHAC1 mRNA expression was associated with overall survival (p=0.007) and relapse free survival (p=0.015). Finally, we show that downregulation of CHAC1 by small interfering RNA suppressed breast cancer cell migration and proliferation, whereas overexpression resulted in an observed increase in these cellular behaviours. This is the first report demonstrating that a gene (CHAC1) whose expression is triggered by methylated, but not unmethylated DNA, is involved in tumour biology.

overall_design: Human breast cancer cell lines (BT-20, Hs578T) were treated with methylated and unmethylated DNA oligos, and differentially expressed genes were identified between treatments with methylated and un-methylated oligos.

first: Georg

last: Goebel

first: Regina

last: Berger

first: Alexander

last: Strasak

first: Daniel

last: Egle

first: Elisabeth

last: Müller-Holzner

last: Presul

first: Stephan

last: Schmidt

first: Stefan

last: Lang

first: Allison

last: Jones

first: Ian

last: Jacobs

first: Martin

last: Widschwendter

first: Heidi

last: Fiegl


title: Expression data from p27WT, p27CK and KO MEFs cells in quiescence

first: oriol

last: bachs

email: obachs@ub.edu, raffaellapippa@ub.edu

address: Casanova 143

department: Cell Biology, Immunology and Neurosciences

institute: University of Barcelona

summary: Low levels of the cell cycle regulator p27Kip1 are associated with a worse outcome in many tumor types. We report here a new regulatory role of p27Kip1 as a transcriptional regulator. In association with transcriptional factors such as ETS and E2F4 and co-repressors like p130, HDACs and mSin3A, p27 binds to promoters of multiple genes leading to their repression. The p27-target genes participate in RNA processing, translation, respiration and cell cycle. Remarkably, p27-target genes are over-expressed in different human tumors in tight association with a poor clinical prognosis. We also observed a clear correlation between low levels of p27 and over-expression of p27-target genes in tumors. Overall, our findings indicate new tumor suppressor roles of p271 as a transcriptional regulator of genes relevant for oncogenesis.

overall_design: Samples from MEFs p27WT, p27CK and p27KO cells were analyzed

first: Raffaella

last: Pippa

first: Lluis

last: Espinosa

first: Gunes

last: Gundem

first: Ramón

last: García-Escudero

first: Ana

last: Domínguez

first: Cristina

last: Sainz

first: Arnaud

last: Besson

first: Maria

last: Pujol

first: Núria

last: López-Bigas

first: Jesus

last: Paramio

first: Oriol

last: Bachs


title: Expression data from isolated peritoneal macrophages treated with Histidine-rich glycoprotein

city: Uppsala

first: Sonia

last: Tugues

address: dag hammarsjöldsväg 20

department: Genetics and pathology

institute: Uppsala University

summary: Histidine-rich glycoprotein (HRG) is a 75 kDa heparin-binding plasma protein which has been implicated in regulation of tumor angiogenesis and growth. To exert some of its biological functions, HRG acts on macrophages.This study was performed to assess changes in gene expression in peritoneal macrophages treated with HRG using oligonucleotide microarrays

overall_design: A total of 8 samples were analyzed. Peritoneal macrophages were pooled from 10 wt C57/BL6 mice and treated with recombinant HRG (1ug/ml) for 6 and 24 hours in duplicates

first: Lena

last: Claesson-Welsh


title: NOTCH3 knockdown in non-transformed human esophageal cells

city: Philadelphia

first: Hiroshi

last: Nakagawa

state: PA

address: 415 Curie Blvd.

department: Gastroenterology Division

institute: University of Pennsylvania

summary:
To determine the role of NOTCH3 in human esophageal epitheila homeostasis/squamous cell differentiation
Zinc finger E-box binding (ZEB) proteins ZEB1 and ZEB2 are transcription factors essential in transforming growth factor (TGF)-β-mediated epithelial to mesenchymal transition (EMT), senescence and cancer stem cell maintenance through mutual negative regulation of the microRNA (miR)-200 family members. However, little is known as to how ZEB expressing tumor cells may emerge during invasive growth. We find that canonical Notch signaling prevents expansion of a unique subset of cells expressing ZEBs through NOTCH3 (N3). In primary esophageal squamous cell carcinoma (ESCC), ZEB1 is induced in tumor cells displaying EMT-like dedifferentiation at the invasive front of tumor nests with reciprocal downregulation of the miR-200. ZEB expression was associated with the lack of cellular capability of undergoing squamous differentiation through dysfunction of N3, implicated at the onset of normal esophageal squamous differentiation. Dominant-negative Mastermind-like1 (DNMAML1), a genetic pan-notch inhibitor, prevented CSL-dependent transcription, resulting in suppression of N3 expression and squamous differentiation while enriching EMT competent cells with robust upregulation of ZEBs and downregulation of the miR-200. Such a cell population demonstrated enhanced anchorage independent growth as well as tumor formation in nude mice. RNA interference (RNAi) experiments documented the requirement of ZEBs in TGF-β-mediated EMT. Invasive growth and impaired squamous differentiation was recapitulated upon Notch inhibition in organotypic 3D culture, a form of human tissue engineering. Finally, RNAi experiments revealed N3 as a key factor limiting the expansion of the ZEB expressing cells, providing novel mechanistic insights into the role of Notch signaling in ESCC cell fate regulation and disease progression.

overall_design: NOTCH3 was knockdown stably in immortalized human esophageal keratinocytes EPC2-hTERTstably by lentivirus-mediated gene transfer with shRNA directed against NOTCH3 (Open BiosystemsV2LHS_229748).  A scrambled shRNA (Open Biosystems RHS4346) served as acontrol. Cells were stimulated with 0.6 mM calcium chloride to induce squamous cell differentiation for 72 hrs (0.09 mM Calcium Chloride as a unstimulated control) as described in Gastroenterology. 2010 Dec;139(6):2113-23 by Ohashi et al.

first: Anil

last: Rustgi


title: p27Kip1 regulates transcription of genes involved in tumorigenesis

type: Genome binding/occupancy profiling by genome tiling array

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

overall_design: Refer to individual Series


title: Expression profiling of DNMT1 inhibitors in HCT116 cells

city: Waltham

first: Paul

last: Mason

address: 153 Second Ave

institute: Genzyme Corporation

summary: Epigenetic changes accompany tumorigenesis and are required for tumor maintenance. Modulation of DNA methylation state, histone acetylation, and histone methylation, as well as reversal of disease-associated epigenetic state aberrations, can be disruptive to malignant disease progression. We produced lipophilic prodrugs of decitabine, which is a DNA methyltransferase inhibitor and is efficacious in treatment of myelodysplastic syndromes when dosed subcutaneously. Comparison of parent and prodrug activities in vitro and in vivo revealed comparable effects and unveiled several novel features of nucleoside analog molecular activity in vitro.

overall_design: HCT116 were treated for 72 hour with Decitabine, Azacytidine and various prodrugs in duplicates at different dose concentrations. Cells were also treated with DMSO as control (quadrpulets), RNA was extracted and samples were hybridized to Affymetrix Hu133plus 2.0 arrays.

first: Mindy

last: Zhang

first: Shruti

last: Madhiwalla


title: Expression data from IFN alpha 2-treated macrophages infected with HIV

city: Quebec City

first: Frederic

last: Raymond

state: Quebec

address: 2440 Bd Hochelaga Suite 1710

department: École de nutrition

institute: Université Laval

summary:
Temporal changes of the expression levels of the complete human transcriptome during the first 24 hours following infection of IFN-pre-treated macrophages. This approach has allowed us to identify genes involved in the IFN signaling that have an impact on HIV-1 infection of macrophages
KEYWORDS: time course

overall_design:
Purified primary macrophages were treated with 1000 IU/ml of IFNα2, for 18 hours before infection. Pre-treated macrophages were infected with the Bal strain of HIV-1 at an MOI of 1. Uninfected and untreated cells were used for control. Aliquots of cells (3x106 cells) were taken at 0,2, 4, 8, 16 and 24 hrs after infection for RNA extraction and hybridization on Affymetrix microarrays.

*** No CEL file for Sample GSM757646  MDMs CTL at T0

first: Melissa

last: Sirois

first: Lynda

last: Robitaille

first: Mohak

last: Shah

first: Christopher

middle: H

last: Woelk

first: Jérôme

last: Estaquier

first: Jacques

last: Corbeil


title: Expression data of interferon-alpha treated Huh-7 cells

status: Public on Nov 30 2011

city: Sydney

first: Filip

last: Bebek

state: NSW

address: Molecular Microbiology Laboratory Rm 262, School of Biotechnology and Biomolecular Sciences (BABS), University of new South Wales

institute: Molecular Microbiology Laboratory

summary:
Hepatitis C virus (HCV) infection is primarily treated with a pegylated interferon alpha based therapy, a regime that induces antiviral effects through the upregulation of many interferon-stimulated genes (ISGs). Whilst a number of anti-HCV ISGs have previously been identified, others may also be involved.
Micorarrays were used to validate the presence of ISGs within subtracted libraries generated using the related techniques of suppression subtractive hybridisation and mirror orientation selection, which had  initally been impllemented to isolate clones of ISGs following the interferon-alpha treatment of Huh-7 cells.

overall_design: Microarray data was generated for both untreated and interferon-alpha treated Huh-7 cells. No replicates were performed, however the microarray data was verified via the use of non-parametric (spearman) correlation analysis with RT-PCR data that had been generated using the same Huh-7 cell total RNA samples as the microarray experiments earlier.

first: Laurent

middle: P

last: Rivory


title: Transcriptome analysis of adult retina cell types.

first: Sandra

last: Siegert

institute: Friedrich Miescher Institute

summary:
Brain circuits are assembled from a large variety of morphologically and functionally diverse cell types. It is not known how the intermingled cell types of individual brain regions differ in their expressed genomes. Here we describe an atlas of cell type transcriptomes of the adult retina. We found that each adult cell type expresses a specific set of genes, including a unique set of transcription factors, forming a “barcode” for cell identity. Cell type transcriptomes carry enough information to categorize cells into corresponding morphological classes and types. Surprisingly, several barcode genes are eye disease-associated genes that we demonstrate to be specifically expressed not only in photoreceptors but also in particular retinal circuit elements such as inhibitory neurons as well as in retinal microglia. Our data suggest that distinct cell types of individual brain regions are characterized by marked differences in their expressed genomes.
We assembled a library of 22 transgenic mouse lines in which each line had a group of retinal cells marked with fluorescent proteins. We built up the library with the purpose of having some mouse lines in which single retinal cell types and others in which combinations of types from a single class are labeled. The library had mouse lines with labeled cells representing each of the six retinal cell classes. Retinal cells were characterized by physiological recording and immunohistochemical staining. We isolated 200 fluorescent protein-labeled retinal cells (“cell groups”) from at least three different mice of each mouse line by fluorescence-activated cell sorting. The transcripts of each cell group of these biological triplicates were independently amplified in batches. Each batch contained an internal control cell group from the Arc-line.

overall_design: We performed gene expression analysis of 22 transgenic mouse lines. All experiments were performed in biological triplicates. Gene expression analysis was performed in 3 batches. Arc is the batch control (1st, 2nd, 3rd). B2 was repeated 3 times.

first: Botond

last: Roska

first: Erik

last: Cabuy


title: Linearity of amplification between gene expression values and the amounts of RNA in a retina cell group

summary:
Brain circuits are assembled from a large variety of morphologically and functionally diverse cell types. It is not known how the intermingled cell types of individual brain regions differ in their expressed genomes. Here we describe an atlas of cell type transcriptomes of the adult retina. We found that each adult cell type expresses a specific set of genes, including a unique set of transcription factors, forming a “barcode” for cell identity. Cell type transcriptomes carry enough information to categorize cells into corresponding morphological classes and types. Surprisingly, several barcode genes are eye disease-associated genes that we demonstrate to be specifically expressed not only in photoreceptors but also in particular retinal circuit elements such as inhibitory neurons as well as in retinal microglia. Our data suggest that distinct cell types of individual brain regions are characterized by marked differences in their expressed genomes.
To test whether amplifications were linear, we examined the relationship between gene expression values and the amounts of RNA in a cell group. We pooled together two retinas from the Chrnb4-GFP (cone) and six retinas from the ChAT-Cre × Rosa26-LSL-RFP (starburst amacrine cell) mouse lines. Five mixtures of GFP:RFP cells (“titration mixtures”) were then FACS-sorted with the following cone-starburst compositions: 0:200, 50:150, 100:100, 150:50 and 200:0. The total number of cells in each mixture was 200. Five mixtures from different mice were sorted 3 times to give biological triplicates. Next 20 genes with the highest specificity ratio for cones and another 20 for starburst cells were chosen and linear curves were fitted to the data pairs of expression value:cone number or expression value:starburst cell number. For both cone- and starburst-enriched genes, gene expression values increased linearly with an increase in the number of cones or starburst cells in the mixtures. The linear correlation coefficients were independent of the extent to which genes were expressed in the pure cone and starburst cell groups. This suggests that   A practical use of the finding that amplification is linear is to separate the transcriptome of a cell group that contains cells from different types into its cell-type components. Assuming, for example, a cell group (Group A) containing a mixture of two cell types, Type 1 and Type 2, as well as a futher cell group (Group B) containing only Type 1 (Supplementary Figure 10). We wish to determine the transcriptome of Type 2 but we have no cell group (Group C) that contains Type 2 only. Or more generally, assume a cell group (Group A) containing a mixture of cell types, Type 1, Type 2…Type N, as well as a further cell group (Group B) containing only Type 1. We wish to determine the mixed transcriptome of Group C that contains Type 2….Type N, without Type 1. This separation of cell-type transcriptomes is useful for two reasons. First, ~80% of mouse retinal cells are rods30 and it is expected that transcripts from rods will be present in the solution after retina dissociation, leading to rod contamination of the transcriptome of each cell group. We wished to eliminate rod contamination. Second, we found that cones in some mouse lines are labeled together with a type of amacrine cell and we needed to determine the amacrine cell transcriptome alone.    Due to linearity, the following procedure can be used to separate Type 1 from the rest of the cell types in a mixture (Group A). A set of cell type-specific genes for Type 1 is determined. This may be known a priori or from the dataset itself. The ratio of the expression value in Group A to the expression value in Group B is calculated for each Type 1-specific gene. The mean ratio is the estimate of the number of Type 1 cells in Group A. Next, the transcriptome (the expression values of all genes, which we treat as a vector) of Group B is multiplied by the mean ratio and the result is subtracted from the transcriptome of Group A. All negative numbers are then removed from this “unmixed” transcriptome by setting them to zero followed by normalization with the Group B (Type 1) transcriptome using quantile normalization. The quantile normalized “unmixed” transcriptome forms the prediction of the transcriptome of Group C. Note that if Group A contains only two cell types, Type 1 and Type 2, then the transcriptome of Group C is the transcriptome of Type 2 cells.    We have demonstrated and quantitatively evaluated this procedure for the cone:starburst mixtures described above. In addition to the titration mixtures, we also made three “test mixtures” consisting the following cone:starburst cell numbers: 157:43, 75:125 and 183:17. Cones served as the Type 1 cells and starburst cells as Type 2. In our experiment, we had one pure cone group (200:0) and one pure starburst cell group (0:200) as well as six mixtures (50:150, 100:100, 150:50, 157:43, 75:125 and 183:17. First, we predicted the mixture composition using different numbers of cone-specific genes. Since we chose 20 cone-specific genes, the use of single genes presents 20 possible ways of predicting the number of cones in the mixture. Using two genes for the prediction provides 190 possible ways of predicting the number of cones in the mixture. The number of possible predictions when using k genes is: 20!/((20-k)! k!). When more than one gene is used for the prediction, the prediction is the mean of the individual gene-based predictions. Error was calculated as the mean of the absolute values of the deviation from the cone cell numbers in the mixtures. The mean and standard deviation of the prediction error decrease with the use of increasing number of genes. With 10 genes used for the prediction, for example, the prediction error will be approximately 12±3% (s.d.), regardless of which 10 genes are chosen, as long as they are cell type-specific.

overall_design: We pooled together two adult retinas from the Chrnb4-GFP (cone) and six adult retinas from the ChAT-Cre × Rosa26-LSL-RFP (starburst amacrine cell) mouse lines. Five mixtures of GFP:RFP cells (“titration mixtures”) were then FACS-sorted with the following cone-starburst compositions: ChAT.200: cone 0, ChAT.150: cone 50, ChAT.100: cone 100, ChAT.50 : cone 150, ChAT.0: cone 200. The total number of cells in each mixture was 200. Five mixtures from different mice were sorted 3 times to give biological triplicates (indicated by _1, _2, _3). X1, X2 and X3 stand for the following ratios: X1: ChAT.43 : cone 157, ChAT.125 : cone 75, ChAT.17 : cone 183. Arc represents as internal batch control to compare with other gene arrays within our dataset.


title: Retina cells


title: MIWI catalysis is required for piRNA amplification-independent LINE1 transposon silencing [microarray]

city: Gneveva

first: Ramesh

last: Pillai

address: 30, Quai Ernest-Ansermet

department: Department of Molecular Biology

institute: University of Geneva

summary: Here we show that MIWI is a small RNA-guided ribonuclease (Slicer) that requires extensive complementarity for target cleavage in vitro. Disruption of its catalytic activity in mice by a single point mutation results in male infertility and displays increased accumulation of LINE1 transposon transcripts.

overall_design: Round spermatids were purified from adult mouse testes of indicated Miwi genotypes. Total RNA was extracted and subjected to microarray analysis for gene expression profiling.

first: Michael

last: Reuter

first: Philipp

last: Berninger

first: Shinichiro

last: Chuma

first: Hardik

first: Mihoko

last: Hosokawa

first: Charlotta

last: Funaya

first: Claude

last: Antony

first: Ravi

last: Sachidanandam

middle: S


title: KSHV regulation of gene expression in the human endothelial cell line EAHY

status: Public on Nov 29 2011

city: Bethesda

first: ombretta

last: salvucci

address: 37 Convent Drive

department: LCO

institute: NCI

summary:
KSHV promotes endothelia to mesenchymal transformation (EntMT) in EAHY cells
We have used Affymetrix Gene Arrays to investigate the patterns of regulation of gene expression in EAHY cells infected with KSHV in comparison to uninfected EAHY cells

overall_design: EAHY cells were infected with rKSHV.219 virus (derived from the virus-producing VERO cells). 12 days after infection and in puromycin selection to achieve greater than 90% infection RNA was exctrated from KSHV infected and control non-infected cells.

first: Paola

last: Gasperini

first: Ombretta

last: Salvucci


title: Mixed Culture Gene Expression of E. coli and Pseudomonas aeruginosa grown on defined media with N-acetyl glucosamine

city: San Marcos

first: Robert

middle: JC

last: McLean

address: 601 University Drive

department: Biology

institute: Texas State University-San Marcos

summary: Transcriptional profiles of Escherichia coli MG1655 in mixed culture with Pseudomonas aeruginosa PAO1 showed a number of E. coli genes to be upregulated including purA-F and other genes associated with purine synthesis. In contrast, genes associated with pyrimidine synthesis were unaffected. Competition experiments in both planktonic and biofilm cultures, using three purine synthesis mutants, purD, purH, and purT showed little difference in E. coli survival from the parent strain. As purines are components of the cell signals, cAMP and c-di-GMP, we conducted competition experiments with E. coli mutants lacking adenylate cyclase (cyaA), cAMP phosphodiesterase (cpdA), and the catabolite receptor protein (crp), as well as ydeH, an uncharacterized gene that has been associated with c-di-GMP synthesis. Survival of the cyaA and crp mutants during co-culture were significantly less than the parent strain. Supplementation of the media with 1mM cAMP could restore survival of the cyaA mutant but not the crp mutant. In contrast, survival of the cpdA mutant was similar to the parent strain. Survival of the ydeH mutant was moderately less than the parent, suggesting that cAMP has more impact on E. coli mixed culture growth than c-di-GMP. Addition of 1 mM indole restored the survival of both the cyaA and crp mutations. Mutants in genes for tryptophan synthesis (trpE) and indole production (tnaA) showed a loss of competition and recovery through indole supplementation, comparable to the cyaA and crp mutants. Overall, these results suggest indole and cAMP as major contributing factors to E. coli growth in mixed culture.

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

platform_organism:
Pseudomonas aeruginosa
Escherichia coli

overall_design: E. coli MG1655 and P. aeruginosa PAO1 were grown in a minimal defined medium containing N-acetyl glucosamine, overnight at 37C to an OD of 1.5, and then inoculated in fresh media at an OD of 0.001 and grown in pure or mixed culture for 4-5 hours to a final OD of 0.5. RNA was extracted, purified, reverse transcribed to cDNA and then analyzed on E. coli and P. aeruginosa chips from Affymetrix. Expression profiles of mixed culture-grown organisms were compared to pure culture E. coli and P. aeruginosa grown on the same defined medium.

first: Marvin

last: Whiteley


title: Human acute myelogenous leukemia-initiating cells treated with fenretinide

city: Shanghai

first: Hui

last: Zhang

address: 197 Ruijin Rd II

department: Shanghai Institute of Hematology

institute: Rui-Jin Hospital affiliated to Shanghai Jiao Tong University School of Medicine

summary: Transcriptional profiling of human acute myelogenous leukemia (AML) CD34+ cells treated with 5 μM fenretinide. Two timepoints included are 6h, 12h, covering the apoptosis-induction time window of AML CD34+ cells responsing to the fenretinide treatment. We studied gene expression series in human AML CD34+ cells with or without 5 μM fenretinide treatment by cDNA microarray analysis. Several signal transduction pathways are involve, including stress response, NF-kappaB inhibition and p53 inhibition (p<0.05). These findings indicate fenretinide may represent a promising candidate for targeting AML-initiating cells.

overall_design: 6-condition experiment, untreated AML CD34+ cells vs. fenretinide-treated AML CD34+ cells,including 2 time points, for each point the untreated and 5 μM fenretinide treated, independently grown and harvested. Untreated was used to counteracting the background.

first: Kankan

last: Wang

first: Lin

last: Wu

first: Huiyong

last: Fan


title: Expression data from mouse bone marrow adipocytes with age

city: Palo Alto

first: Li Fen

last: Liu

address: 3801 Miranda AVE

department: Medicine

institute: Stanford University

summary:
The aim of this study was to characterize the age-related gene expression profiles between bone marrow adipocytes and peripheral white adipocytes.
Alterations of gene expression with aging were analyzed in bone marrow and peripheral white adipocytes isolated from C57BL/6J male mice using Affymetrix Mouse Gene 1.0 ST arrays.

overall_design: Bone marrow adipocytes and peripheral white adipocytes (n=6-10 animals per group) were isolated from male C57BL/6J mice (6-months, 14-months and 18-months of age).  Samples were grouped into cell type (bone marrow adipocytes vs. peripheral adipocytes) and age (6-month (6M), 14-month (14M) and 18-month (18M)).

first: Liu

last: Li Fen

first: Fredric

last: Kraemer


title: Expanding the Pathways of Manganese Homeostasis: Role of a Small Manganese Chaperone Protein, MntS

first: Lauren

last: Waters

address: 18 Library Drive, Room 113

institute: National Institutes of Health

summary: Escherichia coli possesses >65 small proteins of <50 amino acids, many of which are uncharacterized. We have identified a new small protein, MntS, involved in manganese homeostasis. Manganese is a critical micronutrient, serving as an enzyme cofactor and protecting against oxidative stress. Yet manganese is toxic in excess and little is known about its function in cells. Bacteria carefully control intracellular manganese levels using the transcription regulator MntR. Before this work, mntH, which encodes a manganese importer, was the only gene known to respond to manganese via MntR repression in E. coli K12. We demonstrated that mntS is another member of the MntR manganese regulon. We also identified yebN, which encodes a putative manganese efflux pump, as the first gene positively regulated by MntR in Enterobacteria. Since MntS is expressed when manganese levels are low, causes manganese sensitivity when overexpressed, and binds manganese, we propose that MntS may be a manganese chaperone. This study reveals new factors involved in manganese regulation and metabolism and expands our knowledge of how small proteins function.

overall_design: Two E. coli strains, MG1655 (wild type) and GSO458 (Delta-mntR) were grown to OD600 ~ 0.5 in M9 glucose media at 37 ºC and treated with 10 microM MnCl2. In the first experiment, this incubation with 10 microM MnCl2 was for 60 min and in the second experiment, it was for 10 min.  RNA was extracted using the hot phenol method and cDNA prepared and hybridized according the manufacturer's instructions (Affymetrix).

first: L

first: G

last: Storz


title: Gene Array Analyzer (GAA): Alternative usage of gene arrays to study alternative splicing events

status: Public on Nov 28 2011

city: Bad Nauheim

first: Pascal

last: Gellert

address: Ludwigstr. 43

department: Cardiac Development and Remodelling

institute: Max Planck Institut for Heart and Lung Research