title: Expression data of 10-day-old wild-type and chl1-5 plants exposed to 25 mM nitrate for 0h or 0.5h

status: Public on Oct 01 2007

city: Taipei

first: Yi-Fang

last: Tsay

address: 128 Sec. 2, Academia Rd, Nankang

department: Institute of Molecular Biology

country: Taiwan

institute: Academia Sinica

summary:
CHL1 is one of major nitrate transporters responsible for nitrate uptake and some studies suggest that it may be also play a role in regulating the nitrate response, its influence was analyzed in a global transcriptome study using Affymetrix ATH1 array.
Keywords: Time course

overall_design: Three biological replicates of 10-day-old Arabidopsis root tissue from wild-type and chl1-5 plants were performed to explore differences  in gene expression between the wild-type and chl1-5 mutants exposed to 25 mM nitrate for 0h (T0) or 0.5h (T0.5) using Affymetrix ATH1 microarray.

first: Heng-Cheng

last: Hu


title: Identification of IL-1 and IL-6-responsive genes in human monocyte-derived macrophages

status: Public on Sep 15 2007

city: Krakow

first: Marcin

last: Piechota

address: Smetna 12

department: Molecular Neuropharmacology

country: Poland

institute: Institute of Pharmacology PAS

summary:
Using whole-genome Affymetrix microarrays (HG-U133A), we characterized the transcriptome profile of cultured human macrophages stimulated for 4 h with interleukin 1 (IL-1) or interleukin 6 (IL-6). We found that, in distinction to liver cells, IL-1 is much more potent than IL-6 in modifying macrophage gene expression, although considerable heterogeneity in response of macrophages deriving from individual blood donors was observed. The obtained results permitted to identify a large number of cytokine-responsive genes. coding for proteins of unknown function that are now being studied in our laboratory. They may represent novel targets in the anti-inflammatory therapy.
Keywords: Cytokine response

overall_design: Analysis of the transcriptome of human monocyte-derived macrophages stimulated in vitro by low doses of IL-1 or IL-6.

first: Aleksander

last: Koj

first: Jolanta

last: Jura

first: Michal

last: Korostynski


title: A Comparison of microarray and MPSS Technology Platforms for Expression Analysis of Arabidopsis

status: Public on Sep 14 2007

city: Manchester

first: Junfeng

last: Chen

address: Kilburn Building, Oxford Road

department: School of Computer Science

country: United Kingdom

institute: University of Manchester

summary:
A comparison of microarray and MPSS technologies can help to establish the metrics for data comparisons across these technology platforms and determine some of the factors affecting the measurement of mRNA abundances using different platforms. Here,  different Treatments/Conditions based on different Arabidopsis tissues were used for three different platforms include MPSS, Affymetrix and Agilent.
Keywords: MPSS, Affymetrix, Agilent

overall_design: For the comparison, 11 different samples were used: Callus, Inforescence, Leaf, Root, Silique, Afamous Inflorescence, Ap1-10 Inflorescence, Ap3-6 Inflorescence, Sup/Ap1 Inflorescence, Leaves SA 4 hr and Leaves SA 52 hr. For details about samples, see Meyers Lab (http://mpss.udel.edu/at). All RNA samples were created in Meyers Lab. MPSS experiments were performed in Meyers Lab. Affymetrix experiments were performed in St. Clair Lab (http://stclairlab.ucdavis.edu/). Agilent experiments were performed by Sean J Coughlan from Agilent (http://www.agilent.com/). Two replicates for each samples were used in Affymetrix platform except Silique sample. Two replicates for each samples were used in Agilent platform.

first: Vikas

last: Agrawal

first: Magnus

last: Rattray

first: Marilyn

middle: A

last: West

first: Dina

first: Richard

middle: W

last: Michelmore

first: Sean

middle: J

last: Coughlan

first: Blake

middle: C

last: Meyers


title: Expression data from heart failure vs control peripheral blood mononuclear cells.

status: Public on Sep 22 2007

city: Rome

first: diego

last: arcelli

address: Via delle Messi d'Oro 156

country: Italy

institute: Regina Elena National Cancer Institute

summary:
Inflammatory mediators play a role in the pathogenesis/progression of chronic heart failure (CHF). The aim of the present study was to identify diagnostic/prognostic markers and gene expression profiles of CHF vs control.
Keywords: CHF patients profiling vs controls.

overall_design: Gene expression profiling was performed in three patients' groups: 1) Ischemic cardiomyopathy (ICM)- (n=12) and 2) Non ischemic cardiomyopathy (NICM)- (n=12) NYHA III-IV CHF patients ; 3) Age- and gender matched controls (n=12) by Affymetrix microarrays. Data were then subjected to informatic analysis.

first: Monica

last: Napolitano

first: Maurizio

last: Capogrossi


title: A screen to identify novel tumor suppressor genes silenced by methylation in melanoma

status: Public on Sep 21 2007

city: Burlington

first: Viswanathan

last: Muthusamy

state: VT

address: 323A HSRF, 149 Beaumont Ave

department: Pathology

country: USA

institute: University of Vermont

summary:
Malignant melanoma is a common and frequently lethal disease. Current therapeutic interventions have little effect on survival, emphasizing the need for a better understanding of the genetic, epigenetic, and phenotypic changes in melanoma formation and progression. We identified genes that were not previously known to be silenced by methylation in melanoma using a microarray-based screen following treatment of melanoma cell lines with the DNA methylation inhibitor 5-Aza-2'-deoxycytidine.
Keywords: Expression changes following pharmacological reversal of epigenetic silencing

overall_design: RNA was isolated following 0 and 48 hours of 5AzadC  treatment of melanocytes and six melanoma cell lines (MelJuSo, UACC 903, C8161, Neo6  C8161, WM1205, and WM35) and used for the reexpression microarray  analysis.

first: Sekhar

last: Duraisamy

first: Matthew

last: Bradbury

first: Cara

last: Hobbs

first: David

last: Curley

first: Betsy

last: Nelson

first: Marcus

last: Bosenberg


title: Identification of differentially expressed genes in brm-101 and syd-2 mutants

status: Public on Sep 10 2007

city: Philadelphia

first: Doris

last: Wagner

state: PA

department: Biology

institute: University of Pennsylvania

summary:
Global analysis of gene expression in 10 day old brm-101 and syd-2 mutant seedlings compared to wild type Landsberg erecta seedlings.
Keywords: mutant analysis

overall_design: 3 genotypes (2 mutant, 1 wild type), 2 replicates each


title: Transcriptional responses to UV irradiation in CS-B cells

city: Osaka-Sayama

first: Toshiro

last: Matsuda

state: Osaka

address: 377-2 Ohno-Higashi

department: Biochemistry

country: Japan

institute: Kinki University School of Medicine

summary:
Cockayne syndrome B (CSB) protein is a member of the SWI/SNF family and has DNA-dependent ATPase and ATP-dependent chromatin remodeling activities.  The CSB protein is missing or altered in CS-B cells.  CS-B cells are hypersensitive to UV light and defective in transcription-coupled DNA repair (TCR). TCR efficiently removes a variety of lesions from the transcribed strand of active genes.  It has been shown that lesions specifically in the transcribed strand of active genes trigger the induction of apoptosis following UV irradiation.  Several DNA damage signaling cascades, including the ATR/Chk1, p38 kinase, p53, and jun N-terminal kinase pathways are activated following UV irradiation.  However, the role of TCR in cellular global transcriptional responses to UV irradiation remains to be elucidated.  Using oligonucleotide microarray technology, we analyzed the time course of responses of CS-B cells (CS-B) and CS-B cells complemented with wild-type CSB cDNA (CS-B wt).
Keywords: UV response, time course, disease state analysis

overall_design: In order to investigate the global transcriptional responses to UV damage in TCR-proficient or TCR-deficient cells, CS-B wt and CS-B cells were irradiated with 10 J/m2 of UV light and incubated for 2 or 12 hours.  All experiments were performed in triplicate.

first: Yuki

last: Nagata

first: Seiji

last: Takeuchi

first: Takanori

middle: T

last: Tomura

first: Kiyoji

last: Tanaka


title: A two-gene classifier for predicting response to the farnesyltransferase inhibitor tipifarnib in acute myeloid leukemia

status: Public on Sep 12 2007

city: San Diego

first: Jack

last: Yu

state: CA

address: 3210 Merryfield Row

institute: Veridex, LLC

summary:
Currently there is no method available to predict response to farnesyltransferase inhibitors (FTI). We analyzed gene expression profiles from the bone marrow of patients from a phase 2 study of the FTI tipifarnib, in older adults with previously untreated acute myeloid leukemia (AML). The RASGRP1:APTX gene expression ratio was found to predict response to tipifarnib with the greatest accuracy. This two-gene ratio was validated by quantitative PCR (QPCR) in the newly diagnosed AML cohort. We further demonstrated that this classifier could predict response to tipifarnib in an independent set of 54 samples from relapsed or refractory AML, with a negative predictive value (NPV) and positive predictive value (PPV) of 92% and 28%, respectively (odds ratio of 4.4). The classifier also predicted for improved overall survival (154 vs 56 days, p = 0.0001), which was shown to be independent of other prognostic factors including a previously described gene expression classifier predictive of overall survival. Therefore, these data indicate that a two-gene expression assay may have utility in categorizing a population of AML patients who are more likely to respond to tipifarnib.
Keywords: classification

overall_design: 34 samples from 34 patients

first: Mitch

last: Raponi


title: Toll-like receptor triggering of a vitamin D-mediated human antimicrobial response

status: Public on Sep 01 2007

city: Los Angeles

first: Philip

middle: T.

last: Liu

address: 611 Charles E Young Dr. East, 522 MBI

department: Department of Medicine, Divison of Dermatology

institute: University of California at Los Angeles

summary:
In innate immune responses, activation of Toll-like receptors (TLRs) triggers direct antimicrobial activity against intracellular bacteria, which in murine, but not human, monocytes and macrophages is mediated principally by nitric oxide. We report here that TLR activation of human macrophages up-regulated expression of the vitamin D receptor and the vitamin D-1-hydroxylase genes, leading to induction of the antimicrobial peptide cathelicidin and killing of intracellular Mycobacterium tuberculosis. We also observed that sera from African-American individuals, known to have increased susceptibility to tuberculosis, had low 25-hydroxyvitamin D and were inefficient in supporting cathelicidin messenger RNA induction. These data support a link between TLRs and vitamin D-mediated innate immunity and suggest that differences in ability of human populations to produce vitamin D may contribute to susceptibility to microbial infection.

Keywords: timecourse, cell type comparison

overall_design:
The monocyte microarrays were generated using primary human monocytes stimulated with a TLR2/1L or media at 0, 3, 6, 12, 24 hour timepoints.  A total of 10 donors were used with time 0 h samples prepared for each. For time points, we used cells from 4 of the 10 donors to prepare media and TLR2/1-stimulated samples.

Dendritic cells were generated by culturing primary human monocytes with GM-CSF (800 U/ml) and IL-4 (1000 U/ml) for 7 days.  The cells were then harvested and recultured for 12 hours with TLR2/1L or media.  A total of four donors were used.

See manuscript for specific details on data analysis and experimental design and reagents.

first: Stephan

middle: R

last: Krutzik

first: Belinda

middle: H

last: Tan

first: Huiying

last: Li

first: Robert

middle: L

last: Modlin


title: Blood Leukocyte Microarrays to Diagnose Systemic Onset Juvenile Idiopathic Arthritis and Follow IL-1 blocade

city: Dallas

first: Florence

last: Allantaz

state: TX

address: 3434 Live Oak Street

institute: Baylor Institute for Immunology Research

summary:
Systemic onset Juvenile Idiopathic Arthritis (SoJIA) represents up to 20% of Juvenile Idiopathic Arthritis (JIA). We have previously reported that this disease is Interleukin 1 (IL1)-mediated, and that IL-1 blockade results in clinical remission in the majority of patients. The diagnosis of SoJIA, however, still relies on clinical findings as no specific diagnostic tests are available, which leads to delays in the initiation of specific therapy. To identify specific diagnostic markers, we analyzed gene expression profiles in 19 pediatric patients with SoJIA during the systemic phase of the disease (fever and/or arthritis), 25 SoJIA patients with no systemic symptoms (arthritis only or no symptoms), 39 healthy controls, 94 pediatric patients with acute viral and bacterial infections (available under GSE6269), 38 pediatric patients with Systemic Lupus Erythematosus (SLE), and 6 patients with a second IL-1 mediated disease known as PAPA syndrome. Statistical group comparison and class prediction identified genes differentially expressed in SoJIA patients compared to healthy children. These genes, however, were also changed in patients with acute infections and SLE. By performing an analysis of significance across all diagnostic groups, we generated a list of 88 SoJIA-specific genes (p<0.01 in SoJIA and >0.5 in all other groups). A subset of 12/88 genes permitted us to accurately classify an independent test set of SoJIA patients with systemic disease. We were also able to identify a group of transcripts that changed significantly in patients undergoing IL-1 blockade. Thus, analysis of transcriptional signatures from SoJIA blood leukocytes can help distinguishing this disease from other febrile illnesses and assessing response to therapy. Availability of accurate diagnostic markers for SoJIA patients may allow prompt initiation of effective therapy and prevention of long-term disabilities.
Keywords: Disease state analysis

overall_design: 123 RNA samples extracted from PBMCs were studied. For more details on the clinical information, please refer to the paper (PudMed ID...).

first: Damien

last: Chaussabel

first: Dorothee

last: Stichweh

first: Lynda

last: Bennett

first: Windy

last: Allman

first: Asuncion

last: Mejias

first: Monica

last: Ardura

first: Wendy

last: Chung

first: Carol

last: Wise

first: Karolina

last: Palucka

first: Octavio

last: Ramilo

first: Marilynn

last: Punaro

first: Jacques

last: Banchereau

first: Virginia

last: Pascual


title: Chronic lymphocytic leukemia cells induce changes in gene expression of CD4 and CD8 T cells.

status: Public on Aug 22 2007

city: Boston

first: Gullu

last: Gorgun

state: MA

address: 44 Binney Street

department: Medical Oncology

institute: Dana-Farber Cancer Institute

summary:
To examine the impact of tumors on the immune system, we compared global gene expression profiles of peripheral blood T cells from previously untreated patients with B cell chronic lymphocytic leukemia (CLL) with those from age-matched healthy donors. Although the cells analyzed were not part of the malignant clone, analysis revealed differentially expressed genes, mainly involved in cell differentiation in CD4 cells and defects in cytoskeleton formation, vesicle trafficking, and cytotoxicity in CD8 cells of the CLL patients. In coculture experiments using CLL cells and T cells from healthy allogeneic donors, similar defects developed in both CD4 and CD8 cells. These changes were induced only with direct contact and were not cytokine mediated. Identification of the specific pathways perturbed in the T cells of cancer-bearing patients will allow us to assess steps to repair these defects, which will likely be required to enhance antitumor immunity.
Gene expression profiling was performed to determine whether CLL cells induce changes in T cells in patients with CLL.
Keywords: comparative gene expression profiling analysis.

overall_design: CD4 T cells and CD8 T cells were obtained from peripheral blood mononuclear cells of previously untreated patients with CLL and healthy individuals. Gene expression profiling was performed using total RNA and the data were analysed to compare gene expression profile of T cells from patients with CLL to healthy individuals .

first: Güllü

last: Görgün

first: Tobias

last: Holderried

first: David

last: Zahrieh

first: Donna

last: Neuberg

first: John

middle: G

last: Gribben


title: Contrasting infection strategies in generalist and specialist wasp parasitoids of Drosophila melanogaster.

status: Public on Sep 11 2007

city: Atlanta

first: Todd

last: Schlenke

state: GA

address: 1510 Clifton Road NE

department: Department of Biology

institute: Emory University

summary:
Although host-parasitoid interactions are becoming well characterized at the organismal and cellular levels, much remains to be understood of the molecular bases for the host immune response and the parasitoids’ ability to defeat this immune response.  Leptopilina boulardi and L. heterotoma, two closely related, highly infectious natural parasitoids of Drosophila melanogaster, appear to use very different infection strategies at the cellular level.  Here, we further characterize cellular level differences in the infection characteristics of these two wasp species using newly derived, virulent inbred strains, and then use whole genome microarrays to compare the transcriptional response of Drosophila to each.  While flies attacked by the melanogaster group specialist Leptopilina boulardi (strain Lb17) up-regulate numerous genes encoding proteolytic enzymes, components of the Toll and JAK/STAT pathways, and the melanization cascade as part of a combined cellular and humoral innate immune response, flies attacked by the generalist L. heterotoma (strain Lh14) do not appear to initiate an immune transcriptional response at the time points post-infection we assayed, perhaps due to the rapid venom-mediated lysis of host hemocytes (blood cells).  Thus, the specialist parasitoid appears to invoke a full-blown immune response in the host, but suppresses and/or evades downstream components of this response.  Given that activation of the host immune response likely depletes the energetic resources of the host, the specialist’s infection strategy seems relatively disadvantageous.  However, we uncover the mechanism for one potentially important fitness tradeoff of the generalist’s highly immune suppressive infection strategy.
Keywords: Time series of transcriptional responses against pathogens.

overall_design: The parasitoid wasps L. boulardi and L. heterotoma were allowed to attack late second instar D. melanogaster larvae (72 hrs old at 22˚C) in the following manner.  Nine petri dishes containing 60 fly larvae were each exposed to six experienced L. boulardi (strain Lb17) female wasps for 2 hrs, another nine plates were exposed to five L. heterotoma (strain Lh14) females, and nine control plates were left uninfected.  For each of three time points post-infection (2-5 hrs, 9-12 hrs, 21-24 hrs), 40 larvae from three replicate plates were removed and frozen at -80˚C for RNA extraction and microarray analysis (3 treatments x 3 time points x 3 replicates = 27 samples total).

first: Jorge

last: Morales

first: Shubha

last: Govind

first: Andrew

last: Clark


title: Identification of hypoxia-inducible genes in Arabidopsis mesophyll cells

status: Public on Aug 17 2007

first: Elena

last: Baena-Gonzalez

address: Simches Research Building, 185 Cambridge Street, CPZN7250

department: Molecular Biology (MGH) and Department of Genetics (HMS)

institute: Massachusetts General Hospital and Harvard Medical School

summary:
The goal of this experiment was to investigate the early transcript changes (6h) induced by hypoxia treatment in mesophyll protoplasts. A single pair (control & hypoxia) of GeneChips® was used to confirm that hypoxia treatment altered the expression of an overlapping set of genes controlled by KIN10 (At3g01090) in Arabidopsis mesophyll protoplasts.
Keywords: KIN10, KIN11, darkness, hypoxia, starvation, stress, sugar signalling, Arabidopsis, SnRK1

overall_design: For the hypoxic treatment protoplasts were submerged in mannitol buffer and the hypoxia condition was confirmed by the activation of the well-established early marker genes ADH (alcohol dehydrogenase, At1g77120) and PDC1 (pyruvate decarboxylase-1, At4g33070) based on RT-PCR and GeneChip® analyses. Results show a clear overlap in genes induced under hypoxic conditions and those induced by KIN10 expression in protoplasts. The overlap of the gene expression profiles was confirmed by triplicated real-time quantitative RT-PCR analyses of selected marker genes.

first: Filip

last: Rolland

first: Johan

middle: M

last: Thevelein

first: Jen

last: Sheen


title: Identification of KIN10-target genes in Arabidopsis mesophyll cells

summary:
The goal of this experiment was to explore the extent of KIN10 (At3g01090) transcriptional regulation and identify its early target genes in Arabidopsis mesophyll protoplasts. Results suggest that KIN10 targets a remarkably broad array of genes that orchestrate transcription networks, promote catabolism and autophagy, and suppress anabolism and ribosome biogenesis. The transient expression condition ruled out secondary or long-term effects of metabolism and growth, and circumvented experimental limitations caused by redundancy and embryonic lethality observed in mammals and plants.
Keywords: KIN10, KIN11, darkness, hypoxia, starvation, stress, sugar signalling, Arabidopsis, SnRK1

overall_design:
Analysis of the transcript changes induced by transient KIN10 (At3g01090) expression (6h) in Arabidopsis mesophyll protoplasts using protoplasts similarly transfected with control plasmid DNA for comparison. To maximize the significance of the duplicated experimental data for defining differentially expressed genes, the biologically independent experiments were carefully performed by two individuals using different soil, plants, growth chambers, DNAs and microarray facilities for hybridization and scanning to cover potential technical and biological variations. For each pair (control & KIN10) of large-scale protoplast transfection experiments, about 3 million protoplasts were isolated from the fifth and sixth leaves of 36 randomly picked plants and pooled.
RNA samples isolated from control and KIN10-transfected protoplasts were subjected to quality controls, including RNA quality and quantity inspection by gel electrophoresis and staining as well as consistent gene expression changes by duplicated real-time quantitative RT-PCR analyses of selected marker genes.


title: Effects of urocanic acid on primary human keratinocytes

status: Public on Aug 16 2007

city: London

first: Kazuyo

last: Kaneko

address: 9th floor of Guy's Tower

department: St John's Institute of Dermatology

institute: King's College London

summary:
Urocanic acid (UCA) is a major epidermal chromophore that undergoes trans to cis photoisomerisation following exposure to solar ultraviolet radiation (UVR). Although there is considerable evidence that cis-UCA suppresses cell-mediated immune response in mouse skin, the molecular events are not fully understood. In this study, we examined involvement of gene transcription in the immunomodulatory effects of cis-UCA on primary human keratinocytes.
The results showed that about 400 genes were induced by UVR, 16 of which also up-regulated by cis-UCA. In contrast, trans-UCA had no effect on gene expression. The genes up-regulated by both cis-UCA and UVR were associated with apoptosis, cell growth arrest, cytokines and oxidative stress.
Keywords: Agent response

overall_design: RNA was extracted from primary human keratinocytes treated with trans-, cis-UCA (10ug/ml) or solar simulated UVR (12J/cm2 ~ 2-3 minimal erythema doses for fair skin), or untreated. At 24hr, the transcriptional profiles were assessed by Affymetrix HG-U133A microarray.

first: Ulli

last: Smetana-Just

first: Mary

last: Matsui

first: Antony

last: Young

last: Norval

first: Susan

last: Walker


title: Endogeneous mRNA level fluctuations in various brain tumor cells

status: Public on Aug 07 2007

city: Santa Barbara

first: Tsunglin

last: Liu

address: R5157, BIO II, UCSB

institute: Neuroscience Research Institute

summary:
Background:  microRNAs (miRNAs) are approximately 21 nucleotide non-coding transcripts capable of regulating gene expression.  The most widely studied mechanism of regulation involves binding of the miRNA to a target mRNA, usually in its 3’ untranslated region (UTR).  As a result, translation of the target mRNA is inhibited and sometimes the mRNA itself can be de-stabilized.  The inhibitory effects of miRNAs have been linked to many diverse cellular processes including malignant proliferation and apoptosis, development and differentiation, metabolic processes and neural plasticity.  We asked whether endogenous fluctuations in a set of mRNA and miRNA profiles contain correlated changes that are statistically distinguishable from the many other fluctuations in the data set.

Methodology/Principal Findings:  Biopsies from 12 human primary brain tumors were used to extract RNA.  These samples were used to determine genome-wide mRNA expression levels by microarray analysis and a miRNA profile by real-time reverse transcription PCR (RT-PCR).  Correlation coefficients were determined for all possible mRNA-miRNA pairs and the distribution of these correlations compared to the random distribution.  An excess of high positive and negative correlation pairs were observed at the tails of these distributions.  Most of these highest correlation pairs do not contain sufficiently complementary sequences to predict a target relationship; nor do they lie in physical proximity to each other.  However, by examining pairs in which the significance of the correlation coefficients is modestly relaxed, negative correlations do tend to predict targets and positive correlations do tend to predict physically proximate pairs.  A subset of high correlation pairs were experimentally validated by over-expressing or suppressing a miRNA and measuring the correlated mRNAs.

Conclusions/Significance:  Sufficient information exists within a set of tumor samples to detect endogenous correlations between miRNA and mRNA levels.  Based on the validations of the correlations the causal arrow for these correlations is likely to be directed from the miRNAs to the mRNAs.  From these data sets, we inferred and validated a tumor suppression pathway linked to miR-181c.
Keywords: cell type comparison

overall_design: Microarray data were obtained from the 12 tumors using Affymetrics HG-U133A array platforms.  Tissue from glioma resections were obtained and collected at UCLA under approval from the Institutional Review Board. Categorization into high or low grade was based on the formal pathology report, with WHO grades III and IV being termed "high grade" and grades I and II termed "low grade".  Histological diagnoses fell into the following categories: two low grade anaplastic mixed gliomas, one low grade oligodendroglioma, six high grade glioblastomas, two high grade gliosarcomas, and one high grade glioblastoma/gliosarcoma.

first: Thales

last: Papagiannakopoulos

first: Kathy

last: Puskar

first: Shuping

last: Qi

first: Fernando

last: Santiago

first: William

last: Clay

first: Kaiqin

last: Lao

first: Yohan

last: Lee

first: Stanley

middle: F

last: Nelson

first: Harley

middle: I

last: Kornblum

first: Frank

last: Doyle

first: Linda

last: Petzold

first: Boris

last: Shraiman

first: Kenneth

middle: S

last: Kosik


title: Prediction of response and survival following chemotherapy in patients with advanced bladder cancer

status: Public on Aug 01 2007

city: Aarhus N

first: Lars

last: Dyrskjot

address: Brendstrupgaardsvej

department: Department of Molecular Medicine

country: Denmark

institute: Aarhus University Hospital, Skejby

summary:
BACKGROUND
Cisplatin-containing chemotherapy is the standard of care for patients with locally advanced and metastatic transitional cell carcinoma of the urothelium.
The response rate is around 50% and tumor derived molecular prognostic markers are needed for estimation of response and survival.
METHODS
Affymetrix GeneChip expression profiling was carried out using tumor material from 30 patients. A set of genes having an expression with high correlation to survival time after chemotherapy was identified.  Two of these genes were selected for validation by immunohistochemistry (IHC) in tumor tissue from 149 cisplatin treated patients having complete follow-up data.
RESULTS
Fifty-five differentially expressed genes correlated significantly to survival time. Two of these (Emmprin and Survivin) were validated using IHC, and multivariate analysis (n=145) identified Emmprin expression (hazard ratio 2.38; p<0.0001) and Survivin expression (hazard ratio 2.34; p<0.0001) as independent prognostic markers for poor outcome, together with the presence of visceral metastases (hazard ratio 2.72; p<0.0001). In the good prognosis group of patients without visceral metastases, both markers showed significant discriminating power as supplemental risk factors (p<0.0001). Within this group of patients, the subgroups of patients with no positive, one positive or two positive IHC stainings (Emmprin and Survivin) had estimated 5-year survival rates (+- SE) of 35.6+-?%, 6.3+-?%, and 0+?%, respectively. Response to chemotherapy could also be predicted with an OddsRatio of 4.60 (2.13-9.93) and 2.59 (1.25-5.38) for Emmprin and Survivin respectively.
CONCLUSION
Emmprin and Survivin proteins were identified as strong independent prognostic predictors for response and survival after cisplatin-containing chemotherapy in patients with bladder cancer.
Keywords: Analysis of gene expression differences between responders and non-responders to chemotherapy

overall_design: Tumors from 30 patients with advanced bladder cancer used in the study. A SAM analysis was used for identifying genes co-varying with treatment response.


title: Transcriptional Profile Analysis of the Lateral Geniculate Nucleus in Monocular Deprived Macaque Monkeys

status: Public on Jul 20 2007

city: Cleveland

first: Henry

middle: J.

last: Kaminski

state: OH

address: 11100 Euclid Avenue

department: Neurology

institute: Case Western Reserve University

summary:
Laser capture microdissection was used to obtain individual LGN layers for DNA microarray in macaque monkeys that underwent monocular eyelid suture at birth.
Keywords: parallel sample

first: Georgiana

last: Cheng

first: Bendi

last: Gong

first: Lan

last: Zhou

first: Denise

last: Hatala

first: Xiaohua

first: Michael

last: Mustari


title: Transcription profiling time series of finite life span and immortal non-malignant human mammary epithelial cell lines

status: Public on Jul 12 2007

city: Belmont

first: Katherine

last: Martin

address: 61 Carleton Rd

institute: Bioarray Consulting

summary:
Nonmalignant human mammary epithelial cells (HMEC) seeded in laminin-rich extracellular matrix (lrECM) form polarized acini and, in doing so, transit from a disorganized proliferating state to an organized growth-arrested state. We hypothesized that the gene expression pattern of organized and growth-arrested HMECs would share similarities with breast tumors with good prognoses. Using Affymetrix HG-U133A microarrays, we analyzed the expression of 22,283 gene transcripts in 184 (finite life span) and HMT3522 S1 (immortal nonmalignant) HMECs on successive days after seeding in a lrECM assay. Both HMECs underwent growth arrest in G0-G1 and differentiated into polarized acini between days 5 and 7. We identified gene expression changes with the same temporal pattern in both lines and examined the expression of these genes in a previously published panel of microarray data for 295 breast cancer samples. We show that genes that are significantly lower in the organized, growth-arrested HMEC than in their proliferating counterparts can be used to classify breast cancer patients into poor and good prognosis groups with high accuracy. This study represents a novel unsupervised approach to identifying breast cancer markers that may be of use clinically.
Keywords: time course

overall_design: We analyzed gene expression in 184 (finite life span) and HMT3522 S1 (immortal non-malignant) HMECs on successive days (3, 5, and 7) post-seeding in a laminin-rich extracellular matrix assay. Both HMECs underwent growth arrest in G0/G1 and differentiated into polarized acini between days 5 and 7.

first: Marcia

middle: V

last: Fournier

first: Paraic

last: Kenny

first: Kris

last: Xhaja

first: Irene

last: Bosch

first: Paul

last: Yaswen

first: Minna

last: Bissell


title: Microarray analysis of Multiples Sclerosis Brain tissue in comparison to control brain tissue

city: Dublin

first: Maureen

last: padden

address: Belfield

country: Ireland

institute: University College Dublin

summary:
MS is a primary demyelinating disease of the central nervous system. The cause is unknown and pathological hallmarks include plaque formation with immune cell infiltration. A microarray analysis of characterized brain tissue samples from three MS cases and a non-neurological control sample was performed containing over 22,000 genes. Real-time PCR analyses of 7 MS samples and 3 non-neurological control brain samples confirmed changes in expression in the chosen genes of interest.
Keywords: Disease state analysis

overall_design: Three MS cases and a non-neurological control sample were used.

last: Padden

first: Brenda

last: Brankin

first: Stephen

last: McQuaid


title: Inadequate protein intake affects skeletal muscle transcript profiles in older humans

status: Public on Jul 11 2007

city: West Lafayette

first: Wayne

last: Campbell

state: IN

address: 700 West State Street

department: Foods and Nutrition

institute: Purdue University

summary:
Inadequate dietary protein intake causes adverse changes in the morphology and function of skeletal muscle.  These changes may be reflected in early alterations in muscle mRNA levels.
Microarray analysis was used to assess whether inadequate protein intake differentially affects skeletal muscle transcript levels and expression profiles in older adults.
Keywords: dietary intake response

overall_design: 11 older males and females (aged 55-80 y) consumed controlled diets that contained 1.2 g protein•kg-1•d-1 (adequate protein) for one wk and then  0.5 g protein•kg-1•d-1 (inadequate protein; IP group; n=11) for a second wk.  RNA was isolated from fasting-state vastus lateralis biopsies obtained at the end of each period and the transcript levels were determined using the Affymetrix U133A array

first: Anna

middle: E

last: Thalacker-Mercer

first: James

last: Fleet

first: Bruce

last: Craig

first: Nadine

last: Carnell


title: Lithium-responsive neurological pathway (kitam-affy-droso-427260)

status: Public on Jun 30 2007

city: Phoenix

first: Winnie

last: Liang

state: AZ

address: 445 N. Fifth Street

institute: Translational Genomics

summary:
Lithium has been used for more than 50 years as the primary therapy for bipolar affective disorder (BPD) and is highly effective in its treatment.  However, the molecular and cellular mechanisms underlying the lithium’s therapeutic action still remains elusive.  The goal of the proposed study is to identify genes involved in the lithium-responsive neurological pathway using the fruit fly as a model organism.  Based on the fact that the fundamental molecular and cellular mechanisms are well conserved between the fruit fly and vertebrates, the outcomes of this project are expected to lead to the recognition of uncharacterized players or processes responsible for the lithium action in the vertebrates, which would open up the future possibility to develop novel and improved therapies for BPD.
The proposed gene-profiling experiment is designed to identify candidate genes and genetic pathways involved in the lithium-responsive biological process.  Specific aims of this project are; 1) identify genes whose expression levels are significantly different between the wild type and Shu, 2) identify genes whose expression levels are enhanced or suppressed after lithium treatment, and 3) identify genes whose expression is differentially regulated in the wild type and Shu after lithium treatment.  We expect that the genes identified through the proposed microarray analysis will provide important clues for elucidating the molecular and cellular processes responsible for the lithium action.
A Drosophila mutant Shudderer (Shu) exhibits various neurological phenotypes, including hyperactivity, uncoordinated movements, and sporadically occurring jerks.  Interestingly, many of these phenotypes are greatly suppressed by lithium with the internal concentrations used for treatment of human BPD patients.  In addition, Shu mutant is more resistant to the toxic effects of lithium than the wild type strain.  These data have led us to the hypothesis that the biological process responsive to lithium is affected in the Shu mutant.  We expect that we will be able to identify genes and genetic pathways involved in the lithium-responsive process by comparing the gene expression profiles between the wild type and the Shu mutant with or without lithium treatment.
Newly eclosed Canton-S (wild type) and Shu mutant females will be placed in vials containing fly food with or without 50mM LiCl.  They will be cultured at 25oC with 65% humidity for 5 days.  Three groups of fifty flies (150 flies in total) will be collected for each experimental condition (i.e., genotype and lithium treatment) and frozen on dry ice.  The head will be separated and total RNA will be extracted from each group using the TRIzol Reagent (Life Technologies) followed by an RNeasy (Qiagen) cleanup step and a DNase I digestion step.  The RNA will be resuspended in DEPC-treated water and the absorbance will be checked at 260 and 280 nm for determination of sample purity and concentration. The GeneChip Drosophila Genome 2.0 Arrays will be used to quantify the levels of transcripts in each sample.  The total number of samples will be 4 (2 genotypes and 2 treatments) X 3 (triplicate) = 12.
Keywords: dose response

first: Toshihiro

last: Kitamoto


title: Various human cell types

status: Public on Jul 17 2007

city: Setagaya-ku

first: Akihiro

last: Umezawa

state: Tokyo

department: Center for Regenerative Medicine

institute: National Center for Child Health and Development

summary:
We performed the GeneChip analysis to identify multiple extracellular determinants such as cytokines, cell membrane-bound molecules, and matrix responsible for cardiomyogenic differentiation, and evaluated the statistical significance of differential gene expression by the NIA array analysis (http://lgsun.grc.nia.nih.gov/ANOVA/) (Bioinformatics 21: 2548), a web-based tool for microarrays data analysis.
Keywords: Grem1-induced cardiogenesis via Wnt

overall_design: To identify cytokines and transcription factors responsible for cardiomyogenic differentiation, 69 human cells were clustered into 30 groups, depending on gene expression levels, by GeneSpringGX software. Among 30 groups, 21 groups includes cells with a cardiomyogenic potential. To identify genes specific for these groups, hierarchical clustering was employed; and Grem1 was nominated as one of the cluster-specific cardiomyocyte-promoting genes by NIA array analysis.

first: D

last: Kami

first: I

last: Shiojima

first: H

last: Makino

first: K

last: Matsumoto

first: Y

last: Takahashi

first: R

last: Ishii

last: Saito

first: M

last: Watanabe

last: Komuro

first: A


title: Gene expression in aortic aneurysms associated with tricuspid and bicuspid valves

status: Public on Jun 28 2007

city: Rochester

first: Ramanath

last: Majumdar

state: MN

address: 200 1st St, SW

institute: Mayo Clinic

summary:
Patients with bicuspid aortic valve (BAV) have increased risk of thoracic ascending aortic aneurysm (AscAA) and dissection compared to those with a normal tricuspid aortic valve (TAV). The present study was undertaken to evaluate whether differences in gene expression exist in aortas from BAV and TAV patients with AscAA.
Keywords: disease state analysis

overall_design: Aneurysmal tissue of ascending aorta was collected from 13 patients with bicuspid aortic valve (BAV) and 12 patients with tricuspid aortic valve (TAV). Patients were selected on the basis of aortic diameter, age and other disease conditions. Patients with giant cell aortitis, cardiovascular abnormalities, inherited connective tissue disorders such as Marfan and  Ehlers-Danlos syndrome were excluded from the study.  RNA was extracted using Invitrogen RNA extraction kit and shown to be of adequate quality before application to Affymetrix microarray U133A gene chips probing for over 16,000 genes per chip. Two different methods of data analysis were performed: a linear model and GeneSpring.


title: Abundant genetic variation in transcript level during early Drosophila development

status: Public on Aug 30 2007

city: Bloomington

first: Matthew

middle: W.

last: Hahn

institute: Indiana University

summary:
Variation in gene expression may underlie many important evolutionary traits.  However, it is not known at what stage in organismal development changes in gene expression are most likely to result in changes in phenotype.  One widely held belief is that changes in early development are more likely to results in changes in downstream phenotypes. In order to discover how much genetic variation for transcript level is present in natural populations, we studied zygotic gene expression in nine inbred lines of Drosophila melanogaster at two time points in development.  We find abundant variation for transcript level both between lines and over time: close to half of all expressed genes show a significant line effect at either time point.  We examine the contribution of maternally-loaded genes to this variation, as well as the contribution of variation in upstream genes to variation in their downstream targets in two well-studied gene regulatory networks.  Finally, we estimate the dimensionality of gene expression in these two networks and find that—despite large numbers of varying genes—there only appear to be two factors controlling this variation.
Keywords: Genetic variation and time course

overall_design: Two chips for each of nine isogenic lines sampled at two time points (=36 arrays).

first: Sergey

last: Nuzhdin

first: Danielle

last: Tufts


title: Protein 4.1B suppresses prostate cancer progression and metastasis

status: Public on Jul 02 2007

city: cambridge

first: steve

last: shen

address: 77 mass ave

institute: MIT

summary:
Protein 4.1B is a 4.1/ezrin/radixin/moesin (FERM) domain-containing protein whose expression is frequently lost in a variety of human tumors, including meningiomas, non-small-cell lung cancers and breast carcinomas. However, its potential tumor suppressive function under in vivo conditions remains to be validated. In a screen for genes involved with prostate cancer metastasis, we found that 4.1B expression is reduced in highly metastatic tumors. Downregulation of 4.1B increased the metastatic propensity of poorly metastatic cells in an orthotopic model of prostate cancer. Furthermore, 4.1B-deficient mice displayed increased susceptibility for developing aggressive, spontaneous prostate carcinomas. In both cases, enhanced tumor malignancy was associated with reduced apoptosis. As expression of Protein 4.1B is frequently downregulated in human clinical prostate cancer, as well as in a spectrum of other tumor types, these results suggest a more general role for Protein 4.1B as a negative regulator of cancer progression to metastatic disease.
Keywords: disease state

overall_design: primary cell line vs metastasis cell line

first: Sunny

last: Wong

first: Herbert

last: Haack

first: Steven

last: Shen

first: Charles

middle: A

last: Whittaker

first: Richard

middle: O

last: Hynes


title: XBP1 confers estrogen independence and antiestrogen resistance in breast cancer cell lines

status: Public on Aug 13 2007

city: Washington

first: Rebecca

middle: B.

last: Riggins

state: DC

address: E412 Research Building, 3970 Reservoir Rd. NW

department: Oncology, and Lombardi Comprehensive Cancer Center

institute: Georgetown University

summary:
Human X-box binding protein-1 (XBP1) is an alternatively spliced transcription factor that participates in the unfolded protein response (UPR), a stress signaling pathway that allows cells to survive the accumulation of unfolded proteins in the endoplasmic reticulum lumen.  We have previously demonstrated that XBP1 expression is increased in antiestrogen-resistant breast cancer cell lines, and is co-expressed with estrogen receptor alpha (ER) in breast tumors.  The purpose of this study is to investigate the role of XBP1 and the UPR in estrogen and antiestrogen responsiveness in breast cancer. Overexpression of spliced XBP1 (XBP1(S)) in ER-positive breast cancer cells leads to estrogen-independent growth and reduced sensitivity to growth inhibition induced by the antiestrogens Tamoxifen and Faslodex in a manner independent of functional p53. Data from gene expression microarray analyses imply that XBP1(S) acts through regulating the expression of ER, the anti-apoptotic gene BCL2, and several other genes associated with control of the cell cycle and apoptosis.
Keywords: genetic modification (effect of gene knock-in, stable transfection)

overall_design: Total RNA was isolated from six independent cultures (cell populations grown on different days from different stocks); three from MCF7/XBP1 cultures and three from the vector control cultures. MIAME 1.1 compliant data were collected as recommended by the Microarray Gene Expression Data (MGED) Society. RNA concentrations were determined by comparing the optical density ratios (260:280 nm) , and data on RNA quality was obtained using an Agilent 2100 Bioanalyzer and RNA 6000 LabChip kits (Agilent Technologies, New Castle, DE). RNA quality was assessed by visual inspection of the electropherograms from the Bioanalyzer data, and by the calculated RNA integrity numbers (RIN) and Degradometer values . Only high quality total RNA was labeled and hybridized to U133A Affymetrix GeneChips using manufacturer recommended procedures (Affymetrix, Santa Clara, CA). Standard “spiked-in” controls also were included in each hybridization.

first: Bianca

middle: P

last: Gomez

middle: B

first: Ayesha

middle: N

last: Shajahan

first: Uwe

last: Klimach

first: Aifen

last: Wang

first: Anatasha

middle: C

last: Crawford

first: Yuelin

last: Zhu

first: Alan

last: Zwart

first: Mingyue

first: Robert

last: Clarke


status: Public on Jul 07 2007

city: Cork

first: Fergal

last: O'Gara

address: College Road

department: Microbiology

institute: University College Cork

summary:
The purpose of this study was (1) to identify novel genes involved in the pathogenesis of Rheumatoid Arthritis (RA) disease, which may provide additional targets for therapeutic intervention and (2) to examine the molecular mechanisms associated with the response to anti-TNF treatment. Microarray analysis of LPS-stimulated whole blood from RA patients pre and post anti-TNF treatment was conducted. This study identified 818 transcripts, differentially expressed in RA patients pre-treatment compared to non-RA control samples. While a number of these genes were associated with RA in previous studies, validating our data, a number of novel genes with possible functions in RA disease were also identified. The number of transcripts (1051) significantly altered post anti-TNF treatment indicates the impact of anti-TNF therapy on systemic gene expression. A number of these transcripts were confirmed to be altered in a larger patient group and may represent potential genetic markers of a patient’s clinical response to anti-TNF treatment.
Keywords: Expression profiling in RA disease pre and post anti-TNF treatment

overall_design: Transcriptome profiling was performed on two RA patients, pre- and three months post-Enbrel therapy and two matched non-RA controls. The whole blood model described by Wang et al (2000) was used with minor modifications. Briefly, to EDTA anti-coagulated blood, LPS (30ng/ml) was added immediately after drawing, and incubated at 37oC for 4 hours, mixing at 80s. After 4 hours red blood cells were lysed and pelleted, white cells were washed once in PBS (Gibco) and frozen at –70oC for subsequent RNA extraction. Total RNA was extracted using the RNeasy kit (QIAGEN) as per manufacturer’s instructions. Samples were treated with DNA-Free (Ambion) to remove genomic DNA and checked using intron-overlapping primers prior to generating cRNA probes or cDNA (data not shown). Affymetrix array data was normalised (globally) and statistically (t-test) analysed using GeneSight software (Biodiscovery). Gene expression changes with a p value of < 0.05 and a fold change of 3 or greater were considered differentially expressed.

first: Heidi

last: Mulcahy

first: Claire

last: Adams

first: Michael

last: Molloy


title: Transgenerational Stability of the Arabidopsis Epigenome Is Coordinated by CG Methylation

status: Public on Jun 27 2007

city: Genève

first: Jon

last: Reinders

state: Genève

address: 30 quai Ernest-Ansermet

department: Department of Plant Biology

country: Switzerland

institute: Universite de Geneve

summary:
Maintenance of CG methylation (mCG) patterns is essential for chromatin-mediated epigenetic regulation of transcription in plants and mammals. Using successive generations of an Arabidopsis thaliana mutant deficient in maintaining mCG, we found that mCG loss triggered genome-wide activation of alternative epigenetic mechanisms. However, these mechanisms involving RNA-directed DNA methylation, inhibiting expression of DNA demethylases, and retargeting of histone H3K9 methylation act in a stochastic and uncoordinated fashion. As a result, new and aberrant epigenetic patterns were progressively formed over several plant generations in the absence of mCG. Interestingly, the unconventional redistribution of epigenetic marks was necessary to ‘rescue’ the loss of mCG, since mutant plants impaired in rescue activities were severely dwarfed and sterile. Our results provide evidence that mCG is a central coordinator of epigenetic memory that secures stable transgenerational inheritance in plants.
Keywords: DNA methylation profiling, epigenetic inheritance, mCIP, H3K9 methylation, RdDM, demethylase expression

overall_design:
Per entry, two biological replicates of leaf tissue (approx. 12th true leaf) from 9-12 plants were frozen in liquid nitrogen. DNA was CTAB extracted and isopropanol precipitated, RNase A and Proteinase K treated, re-extracted and ethanol precipitated. Two replicate 3 µg genomic DNA samples of 2nd generation met1-3, 4th generation met1-3 and Col-0 were sheared by sonication and methylated DNA was immunoprecipitated, as previously described (Weber et al., 2005), and amplified following the chromatin immunoprecipitation assay protocol (Affymetrix). Two replicates per entry with 7.5 µg DNA were fragmented; end labeled, and hybridized on Affymetrix ATH1 arrays as recommended (Affymetrix). Microarray data analysis was performed using the following procedure. First, background adjustments were made using the gcRMA method available in the Bioconductor package of R. Next, background-adjusted values from the six ATH1 datasets were quantile normalized and average signal intensities were determined in log2 scale per probe set.
Contrast coefficient ratios for all pair-wise comparisons were calculated as follows: met1-3 2nd/Col-0, met1-3 4th/Col-0, and met1-3 4th/met1-3 2nd. Corrections for multiple comparisons at the 5% false discovery rate (FDR) were performed and significant differences were detected using Fisher’s test.  Contrast coefficient ratios and p values may be found in the Supplementary file at the foot of this record. For each probe set, three outcomes (significantly hypermethylated, no difference, and significantly hypomethylated) were possible per comparison, creating 27 possible methylation profiles analyzed at the 5% FDR level.

first: Olivier

last: Mathieu

first: Marian

last: Čaikovski

first: Chotika

last: Smathajitt

first: Jerzy

last: Paszkowski


title: RARα-PLZF overcomes PLZF-mediated repression of CRABPI contributing to retinoid resistance in t(11;17) APL

city: Belfast

first: Ken

last: Mills

address: 97 Lisburn Road

department: CCRCB

institute: Queens University Belfast

summary:
This study supports an active role for PLZF and RARα-PLZF in leukemogenesis, identifies upregulation of CRABPI as a novel mechanism contributing to retinoid resistance and reveals the ability of the reciprocal fusion gene products to mediate distinct
epigenetic effects contributing to the leukemic phenotype.
Keywords: Disease state analysis

overall_design: 5 patients with t(11;17) or t(7;17) translocations and with the RARA-PLZF status known were analysed for changes in expression related to the reciprocal status.   This is a rare disease.

first: Fabian

last: Guidez

first: Sarah

last: Parks

first: Henna

last: Wong

first: Jelena

last: Jovanovic

first: Ashley

last: Mays

first: Amanda

last: Gilkes

first: Kenneth

first: Marie-Claude

last: Guillemin

first: Pier-Paulo

last: Pandolfi

first: Hughes

last: de The

first: Ellen

last: Solomon

first: David

last: Grimwade


title: Candida-induced expression profile in HUVEC

status: Public on Jul 01 2007

city: Hannover

first: Dorothee

last: Viemann

state: Deutschland

address: Carl-Neuberg-Straße 1

department: Department of Pediatric Pulmonology, Allergy and Neonatology

country: Germany

institute: Hannover Medical School

summary:
Using oligonucleotide microarray analysis, we identified 56 genes that were transcriptionally up-regulated and 69 that were suppressed upon exposure of endothelial cells to C. albicans. Among the regulated genes those attributed to the categories ‘chemotaxis’, ‘signaling’, and ‘transcription and translation’ were remarkably overrepresented.
Keywords: endothelial stress response

overall_design: We performed 4 independent experiments comparing the expression profiles of untreated HUVEC monolayer with those of candida-infected HUVEC monolayer.

first: Verena

last: Müller

first: Marc

last: Schmidt

first: Nicole

last: Endres

first: Stephan

last: Ludwig

first: Martin

last: Leverkus

first: Johannes

last: Roth

first: Matthias

last: Goebeler


title: H295R human adrenocortical cells treated with Angiotensin II, Potassium or Forskolin

status: Public on Jul 09 2007

city: Jackson

first: Damian

middle: G.

last: Romero

state: MS

address: 2500 N. State St.

institute: University of Mississippi Medical Center

summary:
H295R human adrenocortical cells were cultured in H295R complete media containing DMEM:F12 (1:1) supplemented with 2% Ultroser G (Biosepra, Villeneuve-la-Garenne, France), ITS-Plus (Discovery Labware, Bedford, MA) and an antibiotic/antimycotic mixture (Invitrogen, Carlsbad, CA) in 175 cm2 flasks until subconfluente. Media was replaced with 40 ml fresh media containing different agents and cultured for 3 h.
Treatments: Angiotensin II (100 nM), potassium (16 mM) and forskolin (10 uM).
Total RNA extracted with RNAesy Midi Kit (Qiagen) with on-column DNase digestion
Keywords: Agent response

overall_design:
Controls, n=2
Angiotensin=1
Potassium=1
Forskolin=1
Same biological sample used for GPL96 and GPL97

first: Silvia

last: Rilli

first: Maria

middle: W

last: Plonczynski

first: Licy

middle: L

last: Yanes

first: Ming

middle: Y

last: Zhou

first: Elise

last: Gomez-Sanchez

first: Celso


title: Identification of genes responsive to paeoniflorin, a heat shock protein-inducing compound, in human leukemia U937 cells

status: Public on Jun 23 2007

city: Toyama

first: Yoshiaki

last: Tabuchi

state: Toyama

address: 2630 Sugitani

department: Life Science Research Center

institute: University of Toyama

summary:
Paeoniflorin (PF) isolated from paeony root (Paeoniae radix) has been used as an herbal medicine in East Asis for its anti-allergic, anti-inflammatory, and immunoregulatory effects. PF is known to be a chemical heat shock protein (HSP) inducer. The effects on the gene expression in human lymphoma U937 cells treated with PF were investigated using by an Affymetrix GeneChip system. PF treatment induced Hsp70 expression in U937 cells in a dose- and time-dependent manner as shown in Western blot analysis. When the cells were treated with PF (160 μg/ml; 30 min), 41 up-regulated and 23 down-regulated genes were identified.
Keywords: paeoniflorin, gene expression, Human lymphoma U937 cell

overall_design: U937 cells, a human lymphoma cell line, were treated with paeoniflorin (0.16 mg/ml; 30 min) and followed by incubation for 0, 3, and 6 h at 37°C. Non-treated cells were served as control. Total RNA samples were prepared from the cells. Gene expression was analyzed by an Affymetrix GeneChip® system with Human Expression Array U133A which was spotted with 22,283 probe sets. Sample preparation for array hybridization was carried out as described in the manufacture’s instructions.

first: Ichiro

last: Takasaki

first: Thucydides

last: Salunga

first: Takashi

last: Kondo


title: Gene expression profile of conjunctival epithelial cell lines

status: Public on Aug 03 2007

city: Singapore

first: Louis

last: Tong

address: 11, Third Hospital Avenue

country: Singapore

institute: Singapore National Eye Center

summary:
Human conjunctival cell lines are useful tools for modeling ocular surface disease and evaluation of ocular drugs. Here we demonstrate that the IOBA-NHC and the ChWK conjunctival epithelial cell lines show, using an unbiased gene microarray approach, unique gene expression signatures that differ from primary conjunctival epithelial cells (PCEC) and conjunctival tissue. Globally, the expression profile obtained with the Affymetrix U133A chip (>22000 genes) from PCEC was clustered more closely to conjunctival tissue than either of the 2 cell lines. However, when restricted to Gene Ontology sub-categories: cellular defense, viral replication/cycling, antigen presentation, anti-oxidant pathways and ubiquitin ligase complex, the cell lines correlated reasonably well to PCEC (r > 0.70). In the category response to inflammation, correlation of cell lines to PCEC was poor (r = -0.012 and –0.041 for IOBA-NHC and ChWK respectively).  In general, the expression profile in IOBA-NHC cells was better correlated to PCEC than the ChWK cells. This was statistically significant (p<0.05) when one considers all the genes on the chip, or for proteins in the extracellular region, response to wounding, stress, lipid, protein and organic acid metabolism, development and differentiation. Our results are useful for the choice of conjunctival cell lines, if necessary, in future experiments, to increase validity of extrapolation to clinical scenarios.
Keywords: Cell type comparison

overall_design:
Affymetrix U133A Genechip
Experimental samples:
IOBA-NHC cells (5 samples)
Chang conjunctival epithelial cells WK derivative (4 samples)
Primary conjunctival epithelial cells from explants (3 samples, obtained from cadaveric human explants)
Conjunctival tissue from pterygium study where small piece uninvolved conjunctiva harvested (4 patients' RNA pooled to form one sample, total number of samples: 4)
RT and hybridisation 16 hr according to Affymetrix protocol
Labeling with biotin
Washing microfluidics station 450
Analysis with Genespring GX 7.3.1
RMA normalisation following by normalisation to chip level median signal
These processed data used for correlation analysis
Further gene level normalisation to primary conjunctival epithelial cells samples for the purpose of fold change analysis to compare expression in IOBA or ChWK cells vs primary conjunctival epithelial cells.

first: Roger

last: Beuerman

first: Michael

last: Stern

first: Yolanda

last: Diebold

first: Margarita

last: Calonge

first: Jan-Peng

last: Gao


title: Rhythmic growth explained by coincidence between internal and external cues

status: Public on Jun 24 2007

city: Davis

first: Julin

last: Maloof

address: One Shields Ave

department: Plant Biology

institute: University of California, Davis

summary:
Plant hypocotyls elongate in response to darkness.  The response to darkness is gated by the circadian clock, such that wild-type plants (Col) only respond to darkness with growth once every 24 hours, whereas arrhythmic lines, such as CCA1-34, will respond to darkness with growth at any time of day.  The experiment here was designed to find genes whose expression was correlated with growth. It should also pick up other genes that are gated by the circadian clock or that are direct targets of CCA1.
Keywords: time course

overall_design: Two genotypes were uses, wild-type (Col) and the arrhythmic CCA1-34 line that overexpresses the CCA1 protein.  Plants were entrained in short day conditions for four days and then subjected light/dark pulses consisting of 160 minutes of light and 320 minutes of dark.  We collected samples 120 minutes into the first and last dark periods of the day, corresponding to 280 and 1240 minutes after dawn.  At the 280 minute time point Col plants are growing in response to darkness.  At the 1240 minute time point Col plants are not growing.  CCA1-34 plants are growing at both time points.  The collection regime was continued for three days for a total of three temporal replicates for each time point/genotype combination.

first: Kazunari

last: Nozue

middle: F

last: Covington

first: Stacey

last: Harmer


title: Ethylene and auxin interactions in the roots of Arabidopsis seedlings

status: Public on Jul 13 2007

city: Raleigh

first: Jose

middle: M

last: Alonso

state: NC

department: Genetics

institute: North Carolina State University

summary:
Understanding how developmental and environmental signals are integrated to produce specific responses is one of the main challenges of modern biology. Hormones and, most importantly, interactions between different hormones serve as crucial regulators of plant growth and development, playing central roles in the coordination of internal developmental processes with the environment. Herein, a combination of physiological, genetic, cellular, and whole-genome expression profiling approaches has been employed to investigate the mechanisms of interaction between two key plant hormones, ethylene and auxin.
Quantification of the morphological effects of ethylene and auxin in a variety of mutant backgrounds indicates that auxin biosynthesis, transport, signaling and response are required for the ethylene-induced growth inhibition in roots but not in hypocotyls. Analysis of the activation of early auxin and ethylene responses at cellular level, as well as of global changes in gene expression in the wild type versus auxin and ethylene mutants, suggests a simple mechanistic model for the interaction between these two hormones in roots. This model not only implies existence of several levels of interaction but also provides a likely explanation for the strong ethylene response defects observed in auxin mutants.
Keywords: Genetic modification. Plant hormone response

overall_design:
The effect of ethylene on gene expression in Col-0 (wild-type) and aux1-7 (an auxin resistant mutant) seedlings' roots was investigated. Hydrocarbon-free air was used as control for the ethylene treatment. Two biological replicates were examined.
Similarly, the effect of auxin (IAA) on gene expression in Col (wild-type) and ein2-5 (an ethylene insensitive mutant) seedlings' roots was studied. Two biological replicates were employed.

first: Anna

last: Stepanova

first: Jeonga

last: Yun

first: Alla

last: Likhacheva


first: Yoshiaki

last: Tabuchi

summary:
Anisomycin is known as a potent apoptosis inducer by activating JNK/SAPK and inhibiting protein synthesis during translation. However, only few details are known on the mechanism of apoptosis induced by this compound. Genes in apoptosis induced by anisomycin in human leukemia U937 cells were investigated by using an Affymetrix GeneChip system. DNA fragmentation and phosphatidylserine externalization assays clearly demonstrated that anisomycin induced apoptosis in a time- and concentration- dependent manner. Of 22,283 probe sets analyzed, this compound down-regulated 524 probe sets and up-regulated 523 by a factor 1.5 or greater.
Keywords: anisomycin, gene expression, Human lymphoma U937 cell

overall_design: U937 cells, a human lymphoma cell line, were incubated with anisomycin (1 μM) for 0, 1, 2, 3, and 6 h at 37°C. Total RNA samples were prepared from the cells. Gene expression was analyzed by an Affymetrix GeneChip® system with Human Expression Array U133A which was spotted with 22,283 probe sets. Sample preparation for array hybridization was carried out as described in the manufacture’s instructions.

last: Takasaki

first: Takeshi

last: Hori


title: Gene expression data from prostate cancer samples

status: Public on Jun 22 2007

city: San Diego

first: Yipeng

last: Wang

institute: Vaccine Research Institute of San Diego

summary:
Prostate cancer gene expression profiles were studied in this project. A total RNA from 148 prostate sample with various amount of different cell types were hybridized to Affymetrix U133A arrays. The percentage of different cell types vary considerably among samples and were determined by pathologist. Cell type specific genes can be determined by linear regression using the methods of Stuart et al, PNAS, 2004.
Keywords: disease state analysis

overall_design: 148 prostate samples, with various amounts of tumor, stroma, BPH and atrophic gland, were used for this study.


title: Pooh cells

status: Public on Jun 14 2007

first: Akihiro

last: Umezawa

summary:
POU5F1 (more commonly known as Oct-4/3) is one of the stem cell markers and affects direction of differentiation in embryonic stem cells.  To investigate whether cells of mesenchymal origin acquire embryonic phenotype, we generated a human cell line of mesodermal origin with overexpression of the chimeric POU5F1 gene with physiological co-activator EWS, which is driven by the potent EWS promoter by translocation.  The cell line termed Pooh (POU5F1/Oct-4/3 overexpressing human) cells expressed embryonic stem cell genes such as Nanog and also non-translocated POU5F1, lost mesenchymal phenotypes, and exhibited embryonal stem cell-like alveolar structure when implanted into the subcutaneous tissue of immunodeficient mice.  Hierarchical analysis by microchip analysis and cell surface analysis revealed that Pooh cells are subcategorized into the group of human embryonic stem cells and embryonal carcinoma cells.  These results imply that cells of mesenchymal origin can partially be traced back to cells to embryonic phenotype by the POU5F1 gene in collaboration with the potent cis-regulatory element and the fused co-activator.
Keywords: Involvement of chimeric POU5F1 (Oct-4/3) with physiological co-activator EWS in mesenchymal-embryonic transition of human cells

overall_design: Pooh cells was generated from primary or first passage cells of pelvic tumor (Yamaguchi et al., Genes Chromosomes Cancer. 2005 Jun;43(2):217-22), and cultured in tissue culture dishes (100 mm, Becton Dickinson) in the G031101 medium (Med Shirotori, Tokyo). All cultures were maintained at 37°C in a humidified atmosphere containing 95% air and 5% CO2.

first: Hatsune

last: Makino


title: Identification of circadian-regulated genes of Arabidopsis thaliana.

status: Public on Jul 15 2007

address: One Shields Avenue, LS 1002

institute: University of California-Davis

summary:
Most higher organisms, including plants and animals, have developed a time-keeping mechanism that allows them to anticipate daily fluctuations of environmental parameters such as light and temperature.  This circadian clock efficiently coordinates plant growth and metabolism with respect to time-of-day by producing self-sustained rhythms of gene expression with an approximately 24-hour period.  The importance of these rhythms has in fact been demonstrated in both phytoplankton and higher plants: organisms that have an internal clock period matched to the external environment possess a competitive advantage over those that do not.
We used microarrays to identify circadian-regulated genes of Arabidopsis thaliana to elucidate how the clock provides an adaptive advantage by  understanding how the clock regulates outputs and determining which pathways and processes may be under circadian control.
Keywords: time course

overall_design: Groups of Arabidopsis seedlings were grown in light/dark cycles for 7 d before, transferred to constant light, and after 24 h in constant light 12 samples were harvested at 4-h intervals over the next 44 h for RNA extraction and hybridization on Affymetrix microarrays.


title: Gingival Epithelial Cell Transcriptional Responses to Commensal and Opportunistic Oral Microbial Species.

status: Public on Jun 21 2007

city: Gainesville

first: Martin

last: Handfield

state: FL

address: 1600 SW Archer Road, BOX 100424

department: Oral Biology

institute: University of Florida

summary:
Transcriptional profiling was utilized to define the biological pathways of gingival epithelial cells modulated by co-culture with the oral commensal S. gordonii and the opportunistic commensal F. nucleatum.
We used microarrays to detail the global programme of gene expression underlying infection and identified distinct classes of up- and down-regulated genes during this process.
Keywords: infection state

overall_design: Gingival epithelial HIGK cells were sham infected (CTRL) and infected with either the oral commensal S. gordonii (Sg) or the opportunistic commensal F. nucleatum (Fn). These samples were hybridized to Affymetrix microarrays. Understanding how host cells have adapted to commensals, and how barrier cells respond to limit their impact, provides a mechanistic biological basis of health in the mixed bacterial-human ecosystem of the oral cavity.

first: Richard

middle: J

last: Lamont

last: Hasegawa

first: Jeffrey

last: Mans

first: Henry

last: Baker


title: microRNA160 resistant AUXIN RESPONSE FACTOR10 (mARF10) germinating seeds

status: Public on Jun 17 2007

city: Corvallis

first: Hiro

last: Nonogaki

state: OR

address: 4017 ALS Bldg, Dept. of Horticulture, Oregon State University

department: Horticulture

institute: Oregon State University

summary:
The expression profiles were determined using Affymetrix ATH1 arrays. Comparisons among the Col-0, ARF10 and mARF10 sample groups allow the identification of genes regulated by ARF10.
Keywords: Potential upregulated and downregulated genes

overall_design: Germinating seeds (22 hr imbibition) from three independent biological replicates of Col-0, ARF10 and mARF10 samples, which contain three independent seed lots each, were analyzed.

first: Po-Pu

last: Liu

first: Taiowa

last: Montgomery

first: Noah

last: Fahlgren

first: Kristin

middle: D

last: Kasschau

first: Hiroyuki

first: James

last: Carrington


title: Gene expression profile during monocytes to macrophage differentiation

city: Chicago

first: Bo

last: Shi

state: IL

address: 240 E. Huran

department: Medicine

institute: Northwestern University

summary:
Macrophages play a critical role in the pathogenesis of many diseases, including rheumatoid arthritis, inflammatory bowel disease and atherosclerosis.  Monocytes recruited into tissues from peripheral blood differentiate into macrophages.  There is limited data concerning the global changes in the expression of genes during monocyte to macrophage, and how the patterns of change identify the mechanism contributing to differentiation or macrophage function.  Employing the microarray technology, we examined the transcriptional profile of in vitro adherence-induced differentiation of primary human monocytes into macrophages.  We found the significant up regulation of genes contributing to the functions of macrophage, including signature patterns defining the induction of genes contributing to immunity and defense; lipid, fatty acid and steroid metabolism; cell adhesion and; carbohydrate metabolism; amino acid metabolism and endocytosis.  In contrast, a variety of transcription factors were down regulated during monocyte to macrophage differentiation, suggesting that transcriptional repression may be important for the transition from monocytes to macrophages. However, a limited number of transcription factors were up regulated, among these was C/EBPA, which may contribute to differentiation by regulating down stream genes, which a characteristic of differentiated macrophages.  These observations suggest that examination of the transcriptional profile in monocytes and macrophages in patients may identify relevant therapeutic targets in diseases such as rheumatoid arthritis and atherosclerosis.
Keywords: Targeting differential gene expressions during monocyte to macrophage differentiation

overall_design: Total 9 samples were analyzed. Repeats of 3 total RNA samples from monocytes at 0 hour, 3 samples from monocytes at 16 hours, and other 3 samples of monocytes at 168 hours after differentiation were collected. Following the Affymetrix protocol, 5-10 mg of high quality RNA was used to make labeled cRNA. The size distribution of fragmented and unfragmented labeled cRNA were assessed by 2100 Bioanalyzer (Agilent Technologies). 20mg of fragmented labeled cRNA was hybridized to Human U133A GeneChip at 45C for 18 hours. Affymetrix fluidics station was used to perform the washing and staining of the chips. GeneChip 3000 scanner system was used to scan the chips. The data were normalized by dCHIP method.

first: Hongtao

first: Chiang-ching

last: Huang

first: Polikseni

last: Eksarko

last: Pope


title: Wilms' tumor 1 WT1(-KTS) isoform time course induction in U2OS cells

city: Bethesda

first: WeiPing

last: Chen

state: MD

address: Bldg 8, Room 1A11, NIDDK/NIH

department: GCL

institute: NIDDK/NIH

summary:
The Wilms' tumor suppressor gene (WT1) encodes a zinc finger transcription factor that plays important roles during development of several organs including metanephric kidneys. A number of WT1 target genes have been identified, but the detailed mechanisms by which WT1 orchestrates renal development remain elusive. To identify WT1 target genes relevant to development, genome-wide expression profiling was performed using oligonucleotide microarrays representing 39,000 human transcripts
Keywords: Wilms' tumor 1 (WT1) gene, -KTS isoform; time course

overall_design:
Sample_source_name: UB27 cells, U2OS cells with Tetracycline-repressible WT1(-KTS) expression

Sample_characteristics: U2OS cell line (osteosarcoma; female), Tetracycline-repressible WT1(-KTS) expression, time-course induction
of WT1(-KTS) expression

Sample_description: WT1(-KTS) expression was induced for 4, 8 or 12
hrs and the expression profile of each time-points was compared to the
uninduced sample (0 hr).

first: Ho-Shik

last: KIM

first: Myoung-Shin

last: Kim

first: Maggie

last: Cam

first: Karim

last: Malik

first: Sean-Bong

last: Lee


title: Transcript profiles of DCs of PLOSL patients show abnormalities in pathways of actin bundling and immune response

status: Public on Jun 01 2007

city: Uppsala

first: Anna

last: Kiialainen

address: University Hospital, Entrance 70

department: Deapartment of Medical Sciences

country: Sweden

institute: Uppsala University

summary:
This study was aimed to identify pathways associated with loss-of-function of the DAP12/TREM2 receptor complex and thus gain insight into pathogenesis of PLOSL (polycystic lipomembranous osteodysplasia with sclerosing leukoencephalopathy). Transcript profiles of PLOSL patients' DCs showed differential expression of genes involved in actin bundling and immune response, but also for the stability of myelin and bone remodeling.
Keywords: PLOSL patient samples vs. control samples

overall_design: Transcript profiles of in vitro differentiated DCs of three controls and five PLOSL patients were analyzed.

first: Ville

last: Veckman

first: Juha

last: Saharinen

last: Paloneva

first: Massimiliano

last: Gentile

first: Panu

last: Hakola

first: Dimitri

last: Hemelsoet

first: Basil

last: Ridha

first: Outi

last: Kopra

first: Ilkka

last: Julkunen

first: Leena

last: Peltonen


title: RhoGDIbeta-responsive genes in MDA-MB-231 cells

status: Public on Jun 13 2007

city: Halle (Saale)

first: Juergen

last: Dittmer

department: Clinic of Gynecology

institute: University of Halle

summary:
RhoGDIbeta (ARHGDIB) is often expressed in tumor cells. It negatively regulates Rho-GTPases, but may have other functions as well. To analyze its effect on gene expression, RhoGDIbeta was suppressed by RNA interference in MDA-MB-231 breast cancer cells and changes in gene expression monitored by cDNA microarrays.
Keywords: siRNA knock-down analysis

overall_design: MDA-MB-231 cells were either transfected with a RhoGDIbeta-specific siRNA or a control siRNA (siLuc), grown for three days, harvested and lysed for total RNA isolation. RNA was subjected to cDNA microarray analysis by using Affymetrix chip HG-U133A. A total of three independent transfection experiments were performed. The samples obtained from experiments 1, 2 and 3 were designated as siLuc_rep1, siLuc_rep2, siLuc_rep3 (siLuc transfected) and siARH_rep1, siARH_rep2, siARH_rep3 (siRhoGDIbeta transfected), respectively.

first: Pearl

last: Campbell


title: Changes in PBMC Gene Expression During Acute Measles

status: Public on Jun 07 2007

city: Atlanta

first: Michael

last: Zilliox

address: 1510 Clifton Road

department: Microbiology and Immunology

institute: Emory University School of Medicine

summary:
Children with acute measles were admitted to the University Teaching Hospital in Lusaka, Zambia.  Peripheral blood was collected at hospital entry, discharge and 1-month follow-up.  Control samples were also collected from uninfected children.  All children were HIV negative.
Keywords: Clinical timecourse

overall_design: There are five patients with acute measles.  Samples from entry, discharge and follow-up were run for each patient.  Three uninfected control samples are also included.

first: William

last: Moss

first: Diane

middle: E

last: Griffin


title: Strong Time Dependence of the 76-Gene Prognostic Signature

status: Public on Jun 11 2007

city: Toronto

first: Benjamin

last: Haibe-Kains

state: Ontario

address: 610 University Avenue

department: Princess Margaret Research

country: Canada

institute: Princess Margaret Cancer Centre

summary:
Background: Recently a 76-gene prognostic signature able to predict distant metastases in lymph node-negative (N-) breast cancer patients was reported. The aims of this study conducted by TRANSBIG were to independently validate these results and to compare the outcome with clinical risk assessment. Materials and Methods: Gene expression profiling of frozen samples from 198 N- systemically untreated patients was performed at the Bordet Institute, blinded to clinical data and independent of Veridex. Genomic risk was defined by Veridex, blinded to clinical data. Survival analyses, done by an independent statistician, were performed with the genomic risk and adjusted for the clinical risk, defined by Adjuvant!Online. Results: The actual 5- and 10-year time to distant metastasis (TDM) were 98% (88%-100%) and 94% (83%-98%) respectively for the good profile group and 76% (68%- 82%) and 73% (65%-79%) for the poor profile group. The actual 5- and 10-year overall survival (OS) were 98% (88%-100%) and 87% (73%-94%) respectively for the good profile group and 84% (77%-89%) and 72% (63%-78%) for the poor profile group. We observed a strong time-dependency of this signature, leading to an adjusted HR of 13.58 (1.85-99.63) and 8.20 (1.10-60.90) at 5 years, and 5.11 (1.57-16.67) and 2.55 (1.07-6.10) at 10 years for TDM and OS respectively. Conclusion: This independent validation confirmed the performance of the 76-gene signature and adds to the growing evidence that gene expression signatures are of clinical relevance, especially for identifying patients at high risk of early distant metastases.
Keywords: disease state analysis

overall_design: dataset of microarray experiments from primary breast tumors used to validate the 76-gene signature (VERIDEX). No replicate, no reference sample.

first: Christine

last: Desmedt

first: Fanny

last: Piette

first: Sherene

last: Loi

first: Yixin

last: Wang

first: Francoise

last: Lallemand

first: Giuseppe

last: Viale

first: Mauro

last: Delorenzi

first: Yhi

last: Zhang

first: Mahasti

last: Saghatchian

first: Jonas

last: Bergh

first: Rosette

last: Lidereau

first: Paul

last: Ellis

first: Adrian

last: Harris

first: Jan

middle: G

last: Klijn

first: John

last: Foekens

first: Fatima

last: Cardoso

first: Martine

last: Piccart

first: Marc

last: Buyse

first: Christos

last: Sotiriou


title: Differential gene expression in astrocytic tumours

status: Public on May 26 2007

city: Cambridge

first: Lawrence

last: Petalidis

institute: University of Cambridge

summary:
This study aims at investigating differential gene expression in human astrocytic tumours of grades I, II, III and IV. A total of 65 tumours were assessed using the Affymetrix U133A GeneChip. The study aims not only at discovering the main expression differences between astrocytic tumours of distinct histological grades but also wishes to correlate these findings with the known histopathological hallmarks of astrocytoma progression. Further, the study aims at correlating gene expression with previously obtained genomic information for several loci known to be involved in astrocytoma tumour progression.
Keywords: other

first: L

first: M

last: Wayland

first: T

last: Freeman

first: V

last: Collins


title: Breast cancer relapse free survival and lung metastasis free survival

status: Public on May 14 2007

first: Andy

last: Minn

address: 924 E. 57th Street

institute: University of Chicago

summary:
Validation of lung metastasis signature (LMS) and its association with risk of developing lung metastasis and with primary tumor size.
Keywords: Disease state analysis

overall_design: 58 tumor samples

first: Yixin

last: Wang

first: Joan

last: Massague


title: Expression data of an albino mutant DS 13-2198-1

status: Public on May 01 2007

city: Kurashiki

first: Takashi

last: Hirayama

state: Okayama

department: Institute of Plant Science and Resources

institute: Okayama University

summary:
The effect Ds insertion mutation in Ds13-2198-1 line on the gene expression profiles was investigated. The genes for photosynthesis and some transcriptional factors were upregulated while genes for metabolism were downregulated.
Keywords: strain comparison

overall_design: To investigate the effect of an strong albino mutation, the genome wide gene expression profiles of plants were examined. Segregants with normal phenotype and albino phenotype obtained from the heterotalic parental line were grown on the same 1/2 MS plate for 3 weeks.


title: Comparison of gene expression in SVG-A glial cells and SVGR2 glial cells

status: Public on May 25 2007

city: Providence

first: Kate

last: Manley

state: RI

address: 70 Ship St.

institute: Brown University

summary:
SVGR2 cells are glial cells which are derived from SVG-A cells. They were created by subjecting SVG-A cells to multiple rounds of lytic infection by the human polyomavirus JCV. SVGR2 cells are the cells that survived this process and are resistant to JCV infection. This experiment was designed to identify gene expression differences that may be responsible for SVGR2 resistance to JCV.
Keywords: Cell type

overall_design: SVG-A and SVGR2 cells are transformed cell lines. To eliminate gene expression differences that may have occurred due to genetic instability of these cell lines three subclones of each of the cell lines were created and used as a triplicate in the comparison. Total RNA was extracted from cells that had been left at 100% confluency for one day using the Qiagen RNeasy kit. cDNA was hybridized to the Affymetrix Human GeneChips U133A or U133B according to Affymetrix gudielines.

first: Walter

last: Atwood


title: Influence of TGFbeta on human resting CD4+ T cells

city: Bonn

first: Joachim

last: Schultze

state: NRW

address: Carl-Troll-Strasse 31

department: Genomics and Immunoregulation

institute: LIMES (Life and Medical Sciences Center Genomics and Immunoregulation)

summary:
Based on studies in knockout mice, several inhibitory factors such as TGF-beta, IL-10, or CTLA-4 have been implicated as gate keepers of adaptive immune responses. Lack of these inhibitory molecules leads to massive inflammatory responses mainly mediated by activated T cells. In humans, the integration of these inhibitory signals for keeping T cells at a resting state is less well understood. To elucidate this regulatory network we assessed early genome-wide transcriptional changes during serum deprivation in human mature CD4+ T cells. The most striking observation was a "TGF-beta loss signature" defined by downregulation of many known TGF-beta target genes. Moreover, numerous novel TGF-beta target genes were identified that are under the suppressive control of TGF-beta. Expression of these genes was upregulated once TGF-beta signaling was lost during serum deprivation and again suppressed upon TGF-beta reconstitution. Constitutive TGF-beta signaling was corroborated by demonstrating phosphorylated SMAD2/3 in resting human CD4+ T cells in situ, which were dephosphorylated during serum deprivation and re-phosphorylated by minute amounts of TGF-beta. Loss of TGF-beta signaling was particularly important for T cell proliferation induced by low-level T cell receptor and costimulatory signals. We suggest TGF-beta to be the most prominent factor actively keeping human CD4+ T cells at a resting state.
Keywords: time course, dose response

overall_design: Early genome-wide transcriptional changes during serum deprivation in human mature CD4+ T cells assessed using Affymetrix HGU133A and Illumina  Sentrix BeadChip arrays.

first: Sabine

last: Classen

first: Thomas

last: Zander

first: Daniela

last: Eggle


title: Expression data from 59 human colon tumor tissue samples

status: Public on Apr 21 2007

city: Pennington

first: Mark

middle: David

last: Ayers

state: NJ

address: 311 Pennington-Rocky Hill Rd.

department: Clinical Discovery Technologies

institute: Bristol-Myers Squibb

summary:
Transcriptional profiling was conducted on RNA from 59 human colon tumor tissue samples to identify genes whose expression level correlates VEGFR-2
Keywords: Identfication of genes coexpressed with a specific drug target

overall_design: Baseline gene expression profiling was performed using 59 human colon tumor tissue samples to identify genomic signatures highly correlated with VEGFR-2 gene


title: ATR1_like_Clade_OE_and_miR

status: Public on Apr 26 2007

city: Rehovot

first: Eyal

last: Blum

address: P.O. Box 26

department: Plant

country: Israel

institute: Weizmann Institute of Science

summary:
check the effect of over expression and down regulation of this clade of TFs
Keywords: TF OE miR ATR1 MYB

overall_design: each line have two replicate


title: eif3h/WT transcript level

city: Knoxville

first: Albrecht

last: von Arnim

state: TN

address: M407 Walters Life Science Building

department: Biochemistry, Cellular and Molecular Biology

institute: The University of Tennessee

summary:
Microarray comparisons of transcript level in wild-type Arabidopsis and eif3h mutant plants.
Goal:
To detect any change in transcript level between WT and eif3h mutant.
BACKGROUND: The eukaryotic translation initiation factor eIF3 has multiple roles during the initiation of translation of cytoplasmic mRNAs. However, the contributions of individual subunits of eIF3 to the translation of specific mRNAs remain poorly understood. RESULTS: Working with stable reporter transgenes in Arabidopsis thaliana it was demonstrated that the h subunit of
eIF3 contributes to the efficient translation initiation of mRNAs harboring upstream open reading frames (uORFs) in their 5’ leader sequence. uORFs, which can function as devices for translational regulation, are present in over 30% of Arabidopsis mRNAs, and are enriched among mRNAs for transcriptional regulators and protein modifying enzymes. Microarray comparisons of polysome loading in wild-type and eif3h mutant plants revealed that eIF3h generally helps to maintain efficient polysome loading of mRNAs harboring multiple uORFs. Independently, eIF3h also boosted polysome loading of mRNAs with long coding sequences. Moreover, the lesion in eIF3h revealed a concerted upregulation of translation for specific functional subgroups of mRNAs, including ribosomal proteins and proteins involved in photosynthesis.
CONCLUSIONS: The intact eIF3h protein contributes to efficient translation initiation on 5’ leader sequences harboring multiple uORFs, although mRNA features independent of uORFs were also implicated. Moreover, our data suggest that regulons of translational control can be revealed by mutations in generic translation initiation factors.
Keywords: mutant, total RNA

overall_design: Total RNA samples were isolated from 10-day-old wild-type and eif3h mutant plants

first: Byung-Hoon

last: Kim


title: Identif. of oscillatory genes in somitogenesis from functional genomic analysis of a human mesenchymal stem cell model

city: Tempe

first: Kenro

last: Kusumi

state: AZ

department: School of Life Sciences

institute: Arizona State University

summary:
During somitogenesis, oscillatory expression of genes in the notch and wnt signaling pathways plays a key role in regulating segmentation. These oscillations in expression levels are elements of a species-specific developmental mechanism. To date, the periodicity and components of the human clock remain unstudied. Here we show that a human mesenchymal stem/stromal cell (MSC) model can be induced to display oscillatory gene expression. We observed that the known cycling gene HES1 oscillated with a 5 hour period, consistent with available data on the rate of somitogenesis in humans. We also observed cycling of Hes1 expression in mouse C2C12 myoblasts with a period of 2 hours, consistent with previous in vitro and embryonic studies. Furthermore, we used microarray and quantitative PCR (Q-PCR) analysis to identify additional genes that display oscillatory expression both in vitro and in mouse embryos. We confirmed oscillatory expression of the notch pathway gene Maml3 and the wnt pathway gene Nkd2 by whole mount in situ hybridization analysis and Q-PCR. Expression patterns of these genes were disrupted in Wnt3atm1Amc mutants but not in Dll3pu mutants. Our results demonstrate that human and mouse in vitro models can recapitulate oscillatory expression observed in embryo and that a number of genes in multiple developmental pathways display dynamic expression in vitro.
Keywords: time series

overall_design: Synchronization of human umbilical cord blood derived stem/stromal cell (population 1) was carried out as follows: T-25 cm flasks were set up in parallel. These cells were grown to 90% confluence in DMEM supplemented with 10% FBS (UCB-MSC), then incubated in DMEM with only 0.2% FBS for 24 hours, and returned to DMEM supplemented with FBS. Samples were collected at 30 min. intervals from 0 to 8 hours, and then at 1 hour intervals from 9 to 24 hours.

first: Dilusha

middle: A

last: William

first: Biagio

last: Saitta

first: Joshua

last: Gibson

first: Jeremy

last: Traas

first: Vladimir

last: Markov

first: Dorian

last: Gonzalez

first: William

last: Sewell

first: Douglas

last: Anderson

first: Stephen

last: Pratt

first: Eric

last: Rappaport


title: Differential gene expression in diffusely infiltrating astrocytic

first: Lawrence

last: Petalidis

summary:
This study aims at investigating differential gene expression in human diffusely infiltrating astrocytic tumours, grades II, III and IV. A total of 63 tumours were assessed using the Affymetrix U133A GeneChip. Samples comprised in this GEO submission are identical to those in submission GSE1993 with the exception of two pilocytic astrocytoma tumours (grade I) that have not been included. The study aims not only at discovering the main expression differences between astrocytic tumours of distinct histological grades but also wishes to correlate these findings with the known histopathological and biological hallmarks of astrocytoma progression. Further, the study aims at correlating gene expression with previously obtained genomic information for several loci known to be involved in astrocytoma tumour progression.
Keywords: other

first: L

first: M

last: Wayland

first: T

last: Freeman

first: V

last: Collins


title: eif3h/WT polysome loading

first: Albrecht

last: von Arnim

summary:
Microarray comparisons of polysome loading in wild-type Arabidopsis and eif3h mutant
Goal:
To find the target mRNAs that are translationally regulated by eIF3h.
BACKGROUND: The eukaryotic translation initiation factor eIF3 has multiple roles during the initiation of translation of cytoplasmic mRNAs. However, the contributions of individual subunits of eIF3 to the translation of specific mRNAs remain poorly understood. RESULTS: Working with stable reporter transgenes in Arabidopsis thaliana it was demonstrated that the h subunit of
eIF3 contributes to the efficient translation initiation of mRNAs harboring upstream open reading frames (uORFs) in their 5’ leader sequence. uORFs, which can function as devices for translational regulation, are present in over 30% of Arabidopsis mRNAs, and are enriched among mRNAs for transcriptional regulators and protein modifying enzymes. Microarray comparisons of polysome loading in wild-type and eif3h mutant plants revealed that eIF3h generally helps to maintain efficient polysome loading of mRNAs harboring multiple uORFs. Independently, eIF3h also boosted polysome loading of mRNAs with long coding sequences. Moreover, the lesion in eIF3h revealed a concerted upregulation of translation for specific functional subgroups of mRNAs, including ribosomal proteins and proteins involved in photosynthesis.
CONCLUSIONS: The intact eIF3h protein contributes to efficient translation initiation on 5’ leader sequences harboring multiple uORFs, although mRNA features independent of uORFs were also implicated. Moreover, our data suggest that regulons of translational control can be revealed by mutations in generic translation initiation factors.
Keywords: mutant, polysome, non-polysome

overall_design: Polysomal and non-polysomal RNA samples were isolated from 10-day-old wild-type and eif3h mutant plants. The translation state (ratio between the polysome and non-polysome, PL/NP) for each gene in the WT and in the mutant was separately established, and then the translation states between the genotype were compared.

first: Byung-Hoon


title: Genome-wide gene expression analysis reveals a critical role for CRY1 in the Response of Arabidopsis to High Irradiance

status: Public on May 09 2007

city: Planegg

first: Tatjana

last: Kleine

address: Großhaderner Straße 2

department: Biologie I, Botanik

institute: Ludwig-Maximilians-Universität München

summary:
Exposure to high irradiance results in dramatic changes in nuclear gene expression in plants. However, little is known about the mechanisms by which changes in irradiance are sensed and how the information is transduced to the nucleus to initiate the genetic response. To investigate whether the photoreceptors are involved in the response to high irradiance, we analyzed expression of ELIP1, ELIP2, APX2 and LHCB2.4 in the phyA, phyB, cry1 and cry2 photoreceptor mutants and hy5 and hyh transcription factor mutants. Following exposure to high intensity white light for 3 h (HL, 1000 micro mol quanta m-2 s-1) expression of ELIP1/2 and APX2 was strongly induced and LHCB2.4 expression repressed in wild type. The cry1 and hy5 mutants showed specific mis-regulation of ELIP1/2 and we show that the induction of ELIP1/2 expression is mediated via CRY1 in a blue light intensity-dependent manner. Furthermore, using the Affymetrix Arabidopsis 24K Gene-Chip we showed that 77 of the HL responsive genes are regulated via CRY1, and 26 of those genes were also HY5 dependent. As a consequence of the mis-regulation of these genes the cry1 mutant displayed a high irradiance-sensitive phenotype with significant photoinactivation of PSII, indicated by reduced Fv/Fm. Thus, we describe a novel function of CRY1 in mediating plant responses to high irradiances that is essential to the induction of photoprotective mechanisms. This indicates that high irradiance can be sensed in a chloroplast-independent manner by a cytosolic/nucleic component.
Keywords: photoreceptor, transcription factor, cytosolic/nuclear component, chloroplast, stress response, photoprotection

overall_design:
All samples were done in biological triplicates (named A, B, C): Arabidopsis Col-O: growth conditions (7 d continuous white light; 100 micro mol quanta m-2 s-1, 22 °C), growth conditions followed by high light (3 hours 1000 micro mol quanta m-2 s-1, 22 °C)  and growth conditions followed by blue light (3 hours; HQI-T 400 W lamps were filtered through color filter #74, 400-540 nm, absorption maximum: 470 nm (Night Blue; Rosco International))
cryptochrome 1 (cry1) mutant: growth conditions and growth conditions followed by 3 hours high light
long hypocotyl 5 (hy5) mutant: growth conditions and growth conditions followed by 3 hours high light

first: Asa

last: Strand

first: Peter

last: Kindgren

first: Catherine

last: Benedict

first: Luke

last: Hendrickson


title: Dioxin-induced gene expression changes in MCF-7 human breast cancer cells

status: Public on May 12 2007

city: Los Angeles

first: Oliver

last: Hankinson

state: CA

department: Pathology and Laboratory Medicine

institute: UCLA

summary:
MCF7 cells were treated with DMSO or 100 nM Dioxin for 16 hr.  Gene expression changes were quantified by microarray analyses.
Keywords: dose response

overall_design: HU133A and B arrays were used to quantify differences in RNA after treatment with 100 nM dioxin for 16 h.  The experiment was repeated 3 times.

first: Diana

last: Yoon