title: The effect of TuMV on translation initiation in Arabidopsis

status: Public on Mar 11 2011

city: Ames

first: PLEXdb Curator

middle: Sudhansu

address: 1023  Crop Genomes Informatics Lab (Iowa State University)

department: Virtual Reality Application Center

institute: Iowa State University

summary: Arabidopsis ecotype Col-0 expressing RPL18 fused to His & Flag epitopes (RPL18-HF) under 35S control was used to discern the effects of Turnip mosaic virus (TuMV) infection on host translation initiation.  Plants were grown in LC-1 soil in 12 hour days and infected by TuMV-GFP or mock-inoculated just prior to sending up bolts.  Samples were taken from rosette leaves 10 days after inoculation.  Only tissue fluorescing GFP was selected from the virus-infected samples.  Similar tissue was sampled from mock-infected leaves.  FLAG antibody was used to isolate RPL18-HF. The RNA co-immunoprecipitated with RPL18-HF is fully translation-initiated. This translation-initiated RNA, also referred to as polysomal RNA, was isolated and compared to total RNA under both mock and TuMV-infected states to find TuMV-induced changes in host translation initiation.   ****[PLEXdb(http://www.plexdb.org) has submitted this series at GEO on behalf of the original contributor,  Jackson Moeller.  The equivalent experiment is AT42 at PLEXdb.]

overall_design: pathogen infection: TuMV inoculated - RNA fraction: polysomal RNA(3-replications);  pathogen infection: TuMV inoculated - RNA fraction: total RNA(3-replications);  pathogen infection: mock inoculated - RNA fraction: polysomal RNA(3-replications);  pathogen infection: mock inoculated - RNA fraction: total RNA(3-replications)

first: Jackson

last: Moeller


title: The effects of EBV transformation on gene expression and methylation levels

status: Public on Mar 01 2011

city: Philadelphia

first: Minal

last: Caliskan

state: PA

address: 415 Curie Blvd., Room 540

department: Genetics

country: USA

institute: University of Pennsylvania

type:
Expression profiling by array
Methylation profiling by array

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

overall_design: Refer to individual Series


title: Fine scale genetic mapping of a Hybrid Male Sterility factor between Drosophila simulans and D. mauritiana

status: Public on Mar 07 2011

city: Cambridge

first: Bernardo

last: Lemos

state: MA

address: 16 Divinity Avenue, Room 2105

institute: Harvard University

summary: see publication, arrays from 4 sterile genotypes containing homozygous segments with a Hybrid Male Sterility factor and 1 fertile strain in which the region is a Drosophila simulans and D. mauritiana heterozygous

overall_design: Dye swaps, loop design.

first: Luciana

last: Araripe


title: The effects of EBV transformation on gene expression

summary: Epstein-Barr virus (EBV)-transformed lymphoblastoid cell lines (LCLs) provide a conveniently accessible and renewable resource for functional studies in humans. The ability to accumulate multidimensional data pertaining to the same individual cell lines, from complete genomic sequences to detailed gene regulatory profiles, further enhances the utility of LCLs as a model system. A lingering concern, however, is that the changes associated with EBV transformation of LCLs reduce the usefulness of LCLs as a surrogate model for primary tissues. To evaluate the validity of this concern, we compared global gene expression profiles between CD20+ primary B cells and CD3+ primary T cells sampled from six individuals. Six independent replicates of transformed LCLs were derived from each sample.

overall_design: The study included 96 RNA samples: 8 different types (B cell + T cell + 6 independent LCLs per individual) x 6 individuals x 2 technical replicates (each RNA sample hybridized in duplicate).

first: Darren

last: Cusanovich

first: Carole

last: Ober

first: Yoav

last: Gilad


title: Expression data from human MSI colorectal cancer and normal colonic mucosa

city: Helsinki

first: Pia

last: Vahteristo

address: Haartmaninkatu 8

country: Finland

institute: University of Helsinki

summary: Microsatellite instability (MSI), caused by defective mismatch repair, is observed in a subset of colorectal cancers (CRCs). We evaluated somatic mutations in microsatellite repeats of genes chosen based on reduced expression in MSI CRC and existence of a coding mononucleotide repeat.

overall_design: Expression profiling of  34 MSI colorectal cancers and 15 normal colonic mucosas was performed in 2002. Comparison of malignant and healthy tissue.

first: Lauri

middle: A

last: Aaltonen

first: Torben

middle: F

last: Ørntoft

first: Diego

last: Arango

last: Alhopuro


title: T-Cells from CLL patients

status: Public on Mar 24 2011

city: Stockholm

first: Håkan

last: Mellstedt

department: Oncology & Pathology

country: Sweden

institute: Karolinska Institutet

summary: T cells may have a role in sustaining the leukemic clone in chronic lymphocytic leukemia (CLL). In this study, we have examined the ability of T cells from CLL patients to support the survival of the leukemic B cells in vitro. Additionally, we compared global gene expression of T cells from indolent CLL patients with healthy individuals and multiple myeloma (MM) patients. Apoptosis of purified CLL cells was inhibited in vitro when cocultured with increasing numbers of autologous T cells (p<0.01) but not with normal donors. The anti-apoptotic effect exceeded that of the antiapoptotic cytokine IL-4 (p=0.02) and was greater with CD8+ T cells than with CD4+ cells (p<0.05). The effect depended mainly on cell-cell contact although a significant effect was observed in transwell experiments (p<0.05). Additionally, about 356 genes involved in different cellular pathways were deregulated in T cells of CLL patients compared to healthy individuals and MM patients. The results of gene expression profiling was verified for 7 genes (KLF6, TRAF1, CCL4, CCL5, RANTES, XCL1 and XCL2) using qRT-PCR and immunoblotting. Our results demonstrate that CLL-derived T cells can prevent apoptosis of leukemic cells and have altered expression of genes that may facilitate survival of the leukemic clone.

overall_design: Peripheral blood was collected by venipuncture from CLL patients, multiple myeloma (MM) patients and age-matched healthy individuals with informed consent and approval of the local Ethics Committee in keeping with the Helsinki declaration on the use of human subjects for research.

first: Shahryar

last: Kiaii

first: Parviz

last: Kokhaei

first: Fariba

last: Mozaffari

first: Eva

last: Rossman

first: Ali

last: Moshfegh

first: Marzia

last: Palma

first: Lotta

last: Hansson

first: Kaveh

last: Mashayekhi

first: Mohammad

last: Hojat-Farsangi

first: Anders

last: Österborg

first: Aniruddha

last: Choudhury


title: Copy number variation: the balance between gene dosage and expression in Drosophila melanogaster

status: Public on Mar 03 2011

first: Jun

last: Zhou

address: 16 Divinity Ave. Rm2112

department: Organismic and Evolutionary Biology

summary: Copy number variants (CNVs) reshape gene structure, modulate gene expression, and contribute to significant phenotypic variation. Previous studies have revealed CNV patterns in natural populations of Drosophila melanogaster and suggested that selection and mutational bias shape genomic patterns of CNV. While previous CNV studies focused on heterogeneous strains, here we established a number of second-chromosome substitution lines to uncover CNV characteristics when homozygous. The percentage of genes harboring CNVs is higher than found in previous studies. More CNVs are detected in homozygous than heterozygous substitution strains, suggesting the comparative genomic hybridization arrays underestimate CNV owing to heterozygous masking. We incorporated previous gene expression data collected from some of the same substitution lines to investigate relationships between CNV gene dosage and expression. Most genes present in CNVs show no evidence of increased or diminished transcription, and the fraction of such dosage-insensitive CNVs is greater in heterozygotes. More than 70% of the dosage-sensitive CNVs are recessive with undetectable effects on transcription in heterozygotes. A deficiency of singletons in recessive dosage-sensitive CNVs supports the hypothesis that most CNVs are subject to negative selection. On the other hand, relaxed purifying selection might account for the higher number of protein-protein interactions in dosage insensitive CNVs than in dosage-sensitive CNVs. Dosage-sensitive CNVs that are up-regulated and down-regulated coincide with copy number increases and decreases. Our results help clarify the relation between CNV dosage and gene expression in the D. melanogaster genome.

overall_design: To determine copy number variation, the genomic DNA  from five homozygous and two heterozygous second chromosome substitution lines were extracted and compared to another second chromosome substitution line. Gene expression levels can be referred to at Series GSE12191 (Lemos et al. (2008) PMID:18791071).

first: Bernardo

last: Lemos

first: Erik

middle: B

last: Dopman

first: Daniel

middle: L

last: Hartl


title: Poorly metastatic HCT116 vs metastatic E1 colon cancer cell lines

city: Singapore

first: Puei Nam

last: Tay

address: Yong Loo Lin School of Medicine, Blk MD9, 2 Medical Drive

department: Physiology

country: Singapore

institute: National University of Singapore

summary: Comparison of gene expression between poorly metastatic HCT116 colon cancer cell line and the in-vivo derived metastatic E1 cell line, which has EMT (epithelial to mesenchymal transition) features.

overall_design: Each cell line has triplicate chips.

first: Puei-Nam

first: Patrick

last: Tan

first: Shing-Chuan

last: Hooi


title: HNI9/IWS1 mutant transcriptome in nitrogen-contrasted environments

city: Montpellier

first: Gabriel

last: Krouk

address: 2 Place Pierre Viala

department: Biology

country: France

institute: CNRS

summary: Effect of the high nitrogen insensitive 9 (hni9) mutation in contrasted nitrogen environments.

overall_design: hni9 vs. WT, and Low Nitrogen vs. High Nitrogen environments. 3 biological replicates per genotype/environment.

first: Marc

last: Lepetit

first: Alain

last: Gojon

first: Gloria

last: Coruzzi

first: Thomas

last: Widiez

first: Sandrine

last: Ruffel


title: Expression data from Drosophila female or male genital discs at different time points during morphogenesis

status: Public on Feb 25 2011

city: New York

first: Mark

last: Siegal

state: NY

address: 100 Washington Sq E

department: Department of Biology, Center for Genomics and Systems Biology

institute: New York University

summary:
The Drosophila genitalia develop from an imaginal disc that is patterned during the larval period and undergoes morphogenesis during the pupal period. Although the genetic hierarchy that controls sexual identity in Drosophila is well characterized, the downstream genes that effect sexually dimorphic development of the genitalia are largely unknown.
We used microarrays to profile gene expression in female and male genital imaginal discs at three time points during development: late third-instar larvae (L3), pupae approximately 6 hours after puparium formation (P6) and pupae approximately 20 hours after puparium formation (P20). We identified genes that are sex-differentially expressed in the developing genital disc, including three genes encoding transcription factors that are expressed in the genital disc of one sex but not the other. Through genetic analysis, we showed how the master regulator of sexual identity, Doublesex, limits expression of each of these three genes to one sex. We also determined which genital structures fail to develop properly in the absence of each of the three genes.

overall_design: Drosophila female or male genital discs were dissected at the L3, P6 or P20 time points, total RNA was extracted, and labeled cDNA was produced for hybridization to Affymetrix microarrays. To aid in identifying genital discs, and thereby to avoid loss or contamination of tissue, we used animals expressing GFP in all imaginal discs (esgGAL4.B, UAS-GFP.nls/CyO). To collect discs of specific developmental ages, short-duration sex-nonspecific morphological features were used. L3 discs were dissected from wandering third-instar larvae and sexed by gonad size. For the two pupal time points, each sex-sorted larva was observed until it reached the white prepupa stage (0 hours after puparium formation, APF), which lasts 15-20 minutes. This short duration improves synchronization of the following stages. An air bubble forms mid-dorsally on the puparium at around 4 hours APF, peaks in size at 6-6.5 hours APF and disappears at 9-11 hours APF. We therefore used this morphological feature to collect P6 samples, rather than merely timing 6 hours since the white prepupa. Each animal was observed every 20 minutes from 5 hours APF, until peak bubble size was evident, at which time its genital disc was dissected. We followed a similar protocol for P20. We noted that GFP expression in an oval patch in the eye disc becomes faintly visible at around 20 hours APF. We observed each pupa every 20 minutes from 18 hours APF, until GFP appeared in the eye, at which time its genital disc was dissected. Morphologies of P6 and P20 discs collected this way showed little within-sex variation. For each combination of sex and time point, four biological replicates were performed.

first: Sujash

middle: S

last: Chatterjee

first: Locke

middle: D

last: Uppendahl

first: Moinuddin

last: Chowdhury

first: Pui-Leng

last: Ip


title: Interactions between reactive oxygen species stress and brassinosteroid hormone signaling in Arabidopsis seedlings

status: Public on Feb 28 2011

city: Urbana

first: Steven

middle: C.

last: Huber

state: IL

address: 1201 W. Gregory Drive, 197 ERML

institute: USDA-ARS

summary: We were interested in investigating the transcriptome responses to exogenous applications of brassinosteroid hormone when Arabidopsis seedlings are pre-stressed with a reactive oxygen species, hydrogen peroxide. We were interested in seeing which subsets of BR-responsive gene transcripts were most affected and how BR-responsive gene transcripts responded to increasing concentrations of hydrogen peroxide both as a whole and individually.

overall_design: Liquid culture Arabidopsis seedlings are grown under standard conditions. Hydrogen peroxide is added at various concentrations to pre-stress the seedlings. Following this pretreatment, the seedlings are then treated with brassinosteroid (BR) hormone (epi-brassinolide, BL). Following this treatment, seedlings are harvested and total RNA is extracted for genome-wide transcriptome analysis.

first: Clayton

middle: T

last: Larue

middle: C


title: Gene expression profiles elicited by estradiol and endoxifen in MCF7 parental and ER-beta expressing breast cancer cells

status: Public on Feb 18 2011

city: Rochester

first: John

last: Hawse

state: MN

address: 200 1st St. SW

department: Biochemistry and Molecular Biology

institute: Mayo Clinic

summary: We have previously demonstrated that endoxifen is the most important tamoxifen metabolite responsible for eliciting the anti-estrogenic effects of this drug in breast cancer cells expressing estrogen receptor-alpha.  However, the relevance of estrogen receptor-beta in mediating endoxifen action has yet to be explored.  Therefore, the goals of this study were to determine the differences in the global gene expression profiles elicited by estradiol treatment and endoxifen between parental MCF7 breast cancer cells (expressing estrogen receptor alpha only) and MCF7 cells stably expressing estrogen receptor beta.

overall_design: Total RNA was isolated from parental or estrogen-receptor beta expressing MCF7 cells following 24 hour treatments with either ethanol vehicle, 1nM 17-beta-estradiol or 1nM estradiol plus 40nM endoxifen.  All studies were conducted in biological replicates of 2.

first: Xianglin

last: Wu

middle: R


title: Expression data from third instar Drosophila eye discs

status: Public on Feb 22 2011

city: Charlestown

first: Brandon

last: Nicolay

address: Building 149, 13th Street

department: Cancer Center

institute: Massachusetts General Hospital

summary:
Third instar larval eye discs provide an in vivo model for cell cycle exit studies.  Posterior to the Second Mitotic Wave proliferation is absent in a wild type eye disc.  Inactivating mutations in tumor suppressor-like genes can lead to genome wide changes in gene expression that allow for inappropriate bypass of cell cycle exit signals posterior to the Second Mitotic Wave.
In a mosaic tissue comprised of two wild type (Canton) populations (distinguished by presence or absence of GFP)  there is roughly a 50/50 distribution of both populations in the tissue.  Using the same method but comparing Warts (wts) to wild type you see that Warts mutant tissue is ~70-80% of the eye disc and the rest is wild type tissue.  In the comparison of rbf1120a v rbf1120a+wts using the same method for mosaic creation we were able to see a similar ~80-85% of the eye disc as rbf1120a+wts.  rbf1120a cells have relatively little advantage over wild type cells, but we were able to use entirely homozygous mutant discs for RNA extraction.
We used microarrays to detail the global program of gene expression underlying cell cycle exit and identified distinct classes of up-regulated and down-regulated genes during this process.

overall_design: Drosophila third instar larvea were selected and the eye discs from these animals were prepared for RNA extraction and hybridization on Affymetrix microarrays. We used mosaic larval discs but the majority of the tissue was comprised of the mutant allelic combination we desired due to the proliferative advantage of these mutant cells over wild type cells.

middle: N

first: Maxim

middle: V

last: Frolov


title: Expression data from wild-type and AtERF73/HRE1 knock-down line under hypoxia in Arabidopsis seedlings

status: Public on Feb 24 2011

city: Taipei

first: Yang

last: Chin-Ying

address: No. 128, Sec. 2, Academia Road, Nankang

country: Taiwan

institute: Agriculture Biotechnology Research Center Academia Sinica

summary:
To mimic natural flooding conditions, we have adopted an “open system” treatment, in which only roots are subjected to hypoxia treatment.  Using microarray analysis, we identified a number of AP2/ERF genes in Arabidopsis that are induced at different stages of hypoxia treatment.
we performed microarray analysis to compare gene expression profiles of wild-type and AtERF73/HRE1-RNAi20 upon normaxic or hypoxic condition, in which AtERF73/HRE1 expression was severely knocked down.

overall_design: Arabidopsis Affymetrix GeneChip arrays were probed with RNAs isolated from roots of untreated plants (controls) and plants treated with hypoxia for 6 h.

first: Chin-Ying

last: Yang


title: Gene expression analysis of miR-663 knockdown under shear stress in HUVEC

status: Public on Mar 10 2011

city: Atlanta

first: Hanjoong

last: Jo

state: GA

department: Biomedical Engineering

institute: Emory University

summary: The mechanisms by which oscillatory shear (OS) induces, while high laminar shear stress (LS) prevents, atherosclerosis are still unclear. Here, we examined the hypothesis that OS induces inflammatory response, a critical atherogenic event, in endothelial cells by a miRNA-dependent mechanism. In particular, miR-663 mediated OS-induced inflammation through monocyte adhesion to endothelial cells. The potential targets of miR-663 were examined by knockdown of miR-663 and then the gene expression profiles were determined under shear stress conditions.

overall_design: To determine the potential targets of miR-663, HUVEC were transfected either with miR-663-LNA (inhibitor of miR-663) or control-LNA and then subjected to OS or LS for 24hr. Total RNA were collected from these four groups and microarray studies (Illumina HumanHT-12 v3 beadchip) were performed.

first: Chih-Wen

last: Ni


title: Effects of altered levels of Cyp6g1 and of Dhr96 on gene expression in Drosophila

status: Public on Feb 17 2011

city: RTP

first: Sheetal

last: Shah

state: NC

address: 3054E Cornwallis Road

institute: Syngenta


title: The gene regulatory cascade linking proneural specification with differentiation in Drosophila sensory neurons

city: Edinburgh

first: Ian

last: Simpson

address: 10 Crichton Street

department: Institute for Adaptive and Neural Computation

country: United Kingdom

institute: University of Edinburgh

summary:
A challenge in systems biology is to understand the gene regulatory networks that connect early cellular specification to terminal differentiation of specific cell types. In neurogenesis, neural specification has been well studied, but the link between the proneural transcriptional regulators of specification and the genes that must be activated to construct differentiated neurons is obscure. High resolution temporal profiling of gene expression reveals the events downstream of Atonal (Ato) proneural gene function in Drosophila sensory neurons. Unexpectedly, many differentiation genes are activated soon after specification, even before cell cycle exit and overt neuronal differentiation. Prominent among them are genes required for construction of the ciliary dendrite. Ato activates differentiation both directly and indirectly via several intermediate transcriptional regulators, including Rfx and a new Forkhead family factor. Our analysis of these factors and their regulation provides insight into how proneural factors regulate neuronal subtype differentiation.
Investigating the molecular mechanisms of peripheral nervous sytem development in Drosophila melanogaster.

overall_design: Affymetrix Drosophila version 2.0 chips used to measure gene expression from GFP+ and GFP- cells from embryos expressing GFP under the control of the atonal gene enhancer in both wild type and mutant embryos. Data generated for three developmental time-points in quadruplicate.

first: T

middle: I

first: Sebastian

last: Cachero

first: Petra

last: ZurLage

first: Andrew

middle: P

last: Jarman


title: Expression data from Drosophila melanogaster adults which contain transgenes to deliver a knockdown effect of Dhr96 expression, or over-expression of Dhr96, compared to control flies.

summary:
To investigate the systemic molecular changes occurring as a result of Dhr96 knockdown or over-expression, a comparison between knockdown or overexpression lines and their genetic controls were performed.   0-3 day old adult males or females were reared on 3 separate batches of diet (this was the standard diet we used for culturing Drosophila melanogaster and  was made up of 10L water, 100g agar (USP #7060 Bio-serve), 350g Brewer’s dried yeast (Sunshine Health), 300g black treacle (Lyles), 150g sucrose (Tate & Lyle), 300g Difco dextrose (Becton Dickinson), 150g cornmeal (#1151, Bioserve), 100g wheatgerm (#1659, Bioserve), 200g soya bean flour (#S9633 Sigma Aldrich), 10g methyl-4-hydroxybenzoate (#H3647 Sigma Aldrich) in 10ml ethanol, 50ml proprionic acid (#P5561  Sigma Aldrich)). Each of these 3 batches was considered to represent independent biological replication.  The RNA samples were hybridized to the Affymetrix Drosophila GeneChip 2.
Previous Q-PCR analysis had indicated that there was differential Dhr96 gene expression in the knockdown or overexpression strains compared to their controls. (This was also inferred from phenotypes resulting from other distinct crosses.) However the first analysis carried out on these samples was to verify the levels of differential  Dhr96 gene expression. From this analysis we found no evidence that Dhr96 is down-regulated in the knockdown line compared to its control for either Males or Females, as the confidence intervals for the fold change include the value of one and the p-values are large. Therefore the knockdown line and its control samples were excluded from further analysis. The overexpression line did however show significant up-regulation of Dhr96 expression relative to its control in both Males and Females, and was further analyzed.

overall_design: Flies of the appropriate genotype (Dhr96 knockdown or over-expression and their genetic controls) were reared on 3 different batches of diet (same recipe, prepared on different days). 0-3 day old adults were collected (males and females stored seperately) and each sample was hybridised independently to a chip.

first: Carol

last: Yarrow


title: Dioxin exposure of human CD34+ hemopoietic cells induces gene expression modulation that recapitulates its in vivo clinical and biological effects

status: Public on Feb 15 2011

city: MILAN

first: Luca

last: Agnelli

address: Venezian 1

department: Department of Advanced Diagnostics

country: Italy

institute: IRCCS Istituto Nazionale dei Tumori

summary: 2,3,7,8-tetrachlorodibenzo-p-dioxin (TCDD) has a large number of biological effects, including skin, cardiovascular, neurologic disease, diabetes, infertility and cancer. We analysed the in vitro TCDD effects on human CD34+ cells and tested the gene expression modulation by means of microarray analyses before and after TCDD exposure. We identified 253 differentially modulated probe sets, identifying 217 well-characterized genes. A large part of these were associated with cell adhesion and/or angiogenesis and with transcription regulation. Synaptic transmission and visual perception functions, with the particular involvement of the GABAergic pathway, were also significantly modulated. Numerous transcripts involved in cell cycle or cell proliferation, immune response, signal transduction, ion channel activity or calcium ion binding, tissue development and differentiation, female or male fertility or in several metabolic pathways were also affected after dioxin exposure. The transcriptional profile induced by TCDD treatment on human CD34+ cells strikingly reproduces the clinical and biological effects observed in individuals exposed to dioxin and in biological experimental systems.

overall_design: This series of microarray experiments contains the gene expression profiles of highly purified human CD34+ cells separated from the leukapheresis of normal donors stimulated with G-CSF and analyzed before and after in vitro TCDD (20 nM, 12h) exposure. 3 micrograms of total RNA were processed and 15 micrograms of fragmented biotin-labelled cRNA were hybridized to the Affymetrix HG-U133A chip following the manufacturer's instructions.

first: Nicola

last: Fracchiolla

first: Katia

last: Todoerti

first: Pier

last: Bertazzi

first: Federica

last: Servida

first: Antonio

last: Colombo

first: Cristiana

last: Carniti

first: Paolo

last: Corradini

first: Antonino

last: Neri

first: Giorgio

last: Lambertenghi Deliliers


title: HDACI and DAC induce specific epigenetic profile in DLBCL

first: Matko

last: Kalac

address: 522 1st Avenue

department: NYU Cancer Institute

institute: NYU Medical Center

summary: Diffuse large B-cell lymphoma (DLBCL) is the most common type of lymphoid neoplasm in the world representing 30-40% of all lymphomas. Standard immunochemotherapy (cyclophosphamide, doxorubicin, vincristine, prednisone and rituximab) ensures cure in 60 to 65% of patients, while the rest progress or relapse. While advances have been made in the treatment of DLBCL, especially with the addition of rituximab, it is now apparent that there may be significant differences in prognosis that are related to the cell of origin, and that this disease is heterogeneous and novel treatment options are needed. It has been hypothesized that the combination of HDACI and hypomethylating agents might be a new approach to the treatment of relapsed or refractory DLBCL. This combination is thought to disrupt the transcription repressor complex consisting of methyl binding domain proteins (MBDP) and histone deacetylases (HDACs). We have explored the effect of different HDACI and decitabine combinations in in vitro and in vivo models of DLBCL. These data suggest a class effect, with all four HDACI (panobinostat, belinostat, vorinostat, depsipeptide) synergizing with decitabine in cytotoxicity assay across the spectrum of DLBCL cells. Synergy was validated in a number of other assays including a caspase 3 activation and apoptosis. Furthermore, the combination of panobinostat and decitabine induced markedly increased histone acetylation. The in vitro observations were confirmed in an in vivo murine xenograft experiment with the Ly1 DLBCL line. Genome wide methylation analysis and gene expression profiling demonstrated that the combination of these two epigenetic therapies produced a unique gene expression profile  compared to the samples treated with single drugs.  These data strongly support the potential therapeutic role of a combinatorial epigenetic platform for the treatment of B-cell lymphomas, in particular in patients with DLBCL. Clearly, future studies will need to focus on integrating the appropriate correlative studies, with an effort to identify and or validate biomarkers of activity with these combinations. The likelihood moving forward is that the mechanism of action of these combinations may vary from disease context to disease context.  Genome-wide array findings from these kinds of studies could be expanded to samples from patients on clinical trials to identify novel biomarkers of response, leading to the rational treatment of individual diseases based upon the underlying pathogenesis.

overall_design: We have used single samples from three DLBCL cell lines (biological replicates) which were treated with DMSO, decitabine alone, panobinostat alone and their combination for 48h - total of 12 samples

first: Luigi

last: Scotto

first: Enrica

last: Marchi

first: Jennifer

last: Amengual

first: Venkatraman

middle: E

last: Seshan

first: Govind

last: Bhagat

first: Netha

last: Ulahannan

first: Violetta

last: Leshchenko

first: Samir

last: Parekh

first: Benjamin

last: Tycko

first: Owen

last: O'Connor


title: Hedgehog/GLI signalling and hormone independence in prostate cancer (PCa) cell lines

status: Public on Feb 13 2011

city: london

first: sandeep

middle: k

last: Nadendla

address: 2 newark street

department: ccr

institute: qmul

summary: High levels of GLI (GLI1 and GLI2) mRNA and GLI luciferase reporter activity were detected in the androgen independent prostate cancer cell lines DU145 and PC-3 compared to the androgen-dependent LNCaP prostate cancer cell line. Subsequently, we observed that ectopic GLI1 promoted hormone independence in LNCaP cells (LNCaP-GLI1). We compared the gene expression profile of LNCaP-pBP (empty vector), LNCaP-GLI1, DU145, and PC-3 cells globally as well as to identify GLI1-regulated genes that may contribute to hormone independence.

overall_design: RNA was harvested and analysed from LNCap-pBP (control/reference sample), LNCaP-GLI1, DU145 and PC-3 cells

first: Sandeep

middle: K

first: Graham

middle: W

last: Neill


title: Expression of microRNAs and their gene targets are dysregulated in pre-invasive breast cancer (mRNA)

city: Boston

first: Bethany

last: Hannafon

address: 650 Albany Street

department: Medicine/Section of Hematology and Oncology

institute: Boston University School of Medicine

summary: Introduction: microRNAs (miRNAs) are short non-coding RNAs that negatively regulate gene expression and may play a causal role in invasive breast cancer. Since many genetic aberrations of invasive disease are detectable in earlier stages, we hypothesized that miRNA expression dysregulation and the predicted changes in gene expression would also be found in early breast neoplasias.   Methods: Expression profiling of 365 miRNAs by RT-qPCR was combined with laser-capture microdissection to obtain an epithelial specific miRNA expression signature of normal breast epithelium (n=9) and of paired samples of histologically normal epithelium (HN) and ductal carcinoma in situ (DCIS) (n=16). To determine how miRNAs may control the expression of co-dysregulated mRNAs we also performed gene expression microarray analysis in the same paired HN and DCIS samples and integrated this with miRNA-target prediction. We further validated several target pairs by modulating the expression levels of miRNAs in MCF7 cells and measured the expression of target mRNAs and proteins.  Results: Thirty-five miRNAs were aberrantly expressed between RM, HN and DCIS. Twenty-nine miRNAs and 420 mRNAs were aberrantly expressed between HN and DCIS. Combining these two datasets with miRNA-target prediction we identified two established target pairs (miR-195:CCND1 and miR-21:NFIB) and tested several novel miRNA:mRNA target pairs. Over-expression of the putative tumor-suppressor miR-125b, under-expressed in DCIS, repressed the expression of MEMO1, which is required for ErbB2-driven cell motility (also a target of miR-125b); and NRIP1/RIP140, which modulates the transcriptional activity of the estrogen receptor. Knockdown of the putative oncogenic miRNAs miR-182 and miR-183, both highly over-expressed in DCIS, increased the expression of CBX7 (which regulates E-cadherin expression), DOK4, NMT2, and EGR1. Augmentation of CBX7 by knockdown of miR-182 expression, in turn, positively regulated the expression of E-cadherin, a key protein involved in maintaining normal epithelial cell morphology which is commonly lost during neoplastic progression.   Conclusions: These data provide the first miRNA expression profile of normal breast epithelium and of pre-invasive breast carcinoma. Further, we demonstrate that altered miRNA expression can modulate gene expression changes that characterize these early cancers. We conclude that miRNA dysregulation likely plays a substantial role in early breast cancer development.

overall_design: Two total samples were analyzed via Affymetrix U133A.  Case numbers correspond to individual patients. Each sample is identified by case number, histologic lesion and corresponding microarray ID.

first: Carol

last: Rosenberg


title: Two different 4-week energy-restricted diets.

status: Public on Feb 09 2011

city: Paris

first: Edi

last: Prifti

state: IDF

address: 15, rue de l'école de Médecine

institute: INSERM UMRS-U872

summary:
The main aim of this experiment was to investigate gene expression on human adipose tissue after two different 4-week energy-restricted diets. Our questions consisted in understanding how gene expression was linked to clinical parameters of obese patients and whether the two diets were discriminated this data.
The subjects were randomly allocated, in a cross-over design, to two periods of 4 weeks of an energy restricted isocaloric diet of 1200 kcal as either a conventional diet (LC-CONV) or a special energy restricted diet compensated by proteins (LC-P-LGI). The two nutritional periods were separated by a wash-out interval of 8 weeks.  The samples who contain a K in their name correspond to the LC-P-LGI diet while those who contain a C correspond to LC-CONV diet.

overall_design: Total RNA obtained from isolated human adipose tissue of 12 subjects at 6 different time points (0, 5, 30, 90, 95 and 120 days).

first: Veronique

last: Pelloux

first: Maude

last: Vanpeene


title: Expression of microRNAs and their gene targets are dysregulated in pre-invasive breast cancer

type:
Expression profiling by array
Other

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

overall_design: Refer to individual Series


title: Expression data from Drosophila dLmo (EP1306 and BxJ) mutants

status: Public on Feb 01 2011

city: Emeryville

first: Amy

last: Lasek

state: CA

address: 5858 Horton Street, Suite 200

department: Neurology

institute: Ernest Gallo Clinic and Research Center/UCSF

summary:
The Drosophila gene dLmo encodes a transcriptional regulator involved in wing development and behavioral responses to cocaine and ethanol.
We were interested in discovering novel transcriptional targets of dLmo in the nervous system by examining gene expression changes in the heads of wild-type flies and flies carrying dLmo loss-of-function (EP1306) and gain-of-function mutants (BxJ).

overall_design: RNA was isolated from 3 pooled groups of 200 fly heads from each genotype (w;iso control, EP1306, and BxJ) and hybridized to triplicate Affymetrix Drosophila 2.0 oligonucleotide microarray chips at the Partners HealthCare Center for Personalized Genetic Medicine microarray facility (Harvard University).

first: Ulrike

last: Heberlein

first: Monica

last: Moore


title: Isolation and characterization of progenitor-like cells from human renal proximal tubules

city: Lund

first: David

last: Lindgren

address: Building 404 A3, Scheelevägen 2, Medicon Village

department: Dept of Laboratory Medicine

institute: Lund University

summary: The adult kidney has a remarkable capacity for self-renewal upon damage. Whether this regeneration is mediated by dedifferentiating surviving cells or as recently suggested by stem cells has not been unequivocally settled. The stem cell concept is however hampered by lack of consensus regarding the histological localization of and defining markers for these cells. Here, we demonstrate that aldehyde dehydrogenase (ALDH) activity may be used for isolation of cells with progenitor-like characteristics from adult human renal cortical tissue. Gene expression profiling of the isolated ALDHhigh and ALDHlow cell fractions followed by immunohistochemical interrogation of renal tissues enabled us to delineate a tentative progenitor cell population with a scattered distribution in the epithelial layer of the proximal tubules (PT). The cells differed from the surrounding cells by expression of CD133, CD24, vimentin, KRT7, KRT19, and BCL2, and were negative for PT-specific markers. Based on functional and bioinformatic analyses as well as an immunophenotypical resemblance to cells of regenerating tubules we suggest that these cells are endowed with a more robust phenotype, allowing increased resistance to acute renal injury, enabling rapid repopulation of the tubules. The rare intratubular cells also displayed marked transcriptional and immunophenotypical similarities to that of cortical adenomas and papillary renal cell carcinomas, indicating that these renal neoplasms arise through oncogenic transformation of this subset of PT cells.

overall_design: Total RNA extracted from three pairs of ALDH-high and ALDH-low cell fractions were hybridized to Illumina humanHT-12 v3.0 Expression BeadChips (Illumina Inc) at the SCIBLU Genomics Centre at Lund University Sweden (http://www.lth.se/sciblu).

first: Anna-Karin

last: Boström

first: Jennifer

last: Hansson

first: Kristina

last: Nilsson

first: Jonas

last: Sjölund

first: Christina

last: Möller

first: Karin

last: Jirström

first: Elise

first: Göran

last: Landberg

first: Håkan

last: Axelson

first: Martin

last: Johansson


title: Expression data from Drosophila melanogaster err mutant animals vs. wild type animals at a mid-second instar larval time

status: Public on Feb 02 2011

city: Richmond

first: Keith

last: Baker

state: VA

address: 1220 E. Broad St.

department: Biochemistry & Molecular Biology

institute: VCU School of Medicine

summary: Cancer cells utilize a unique form of aerobic glycolysis, called the Warburg effect, to efficiently produce the macromolecules required for proliferation.  Here we show that a metabolic program related to the Warburg effect is used during normal Drosophila development and regulated by the fly ortholog of the Estrogen-Related Receptor (ERR) family of nuclear receptors.  dERR null mutants die as second instar larvae with abnormally low ATP levels, diminished triacylglyceride stores, and elevated levels of circulating sugars. Metabolomic profiling revealed that the pathways affected in these mutants correspond to those used in the Warburg effect. The expression of active dERR protein in mid-embryogenesis triggers a coordinate switch in gene expression that drives a metabolic program supporting the dramatic growth that occurs during larval development. This study suggests that mammalian ERR family members may promote cancer by directing a metabolic state that supports proliferation.

overall_design: Drosophila larvae were staged at a mid-second instar time point and hand sorted for developmental progression. Individual pools of isogenic animals were collected for each replicate. Three replcates were assayed for each genotype. The two genotypes assayed were a control wild type strain (w1118) and a transheteroallelic combination of err mutant alleles (err1/err2). Labled RNA was then hybridized onto Affymetrix microarrays.

first: Geanette

last: Lam

first: Jason

middle: M

last: Tennessen

first: Carl

last: Thummel


title: Human thyroid adenomas, carcinomas, and normals

city: Ann Arbor

first: Rork

last: Kuick

state: MI

address: University of Michigan, SPH II, 1415 Washington Heights, Room M2533

institute: University of Michigan

summary: Human samples of various thyroid carcinomas, adenomas, and normals, each from a different patient, had mRNA assays performed using Affymetrix HG_U133A arrays, with 22283 probe-sets.  The 99 samples consisted of 4 normals, 10 follicular adenomas, 13 follicular carcinomas, 7 oncocytic adenomas, 8 oncocytic carcinomas, 51 papillary carcinomas (each typed as having classical, follicular or tall cell morphology), 4 anaplastic carcinomas, and 2 medullary carcinomas.  Interesting additional information on common mutations are provided including RAS mutation, BRAF mutation, RET/PTC rearrangements, and PAX8/PPARG translocations.  Details of those assays are provided in our linked publications, as well as additional details on the specific mutations in a few special cases.  No survival data is provided.  Information for 93 of the 99 samples was previously made available on the web.  The anaplastic and medullary carcinoma data were not previously shared.  A supplementary Excel spreadsheet holding the same processed data as the series matrix file is provided and is more compact.  The raw (.CEL) files are also provided.

overall_design: Human samples of various thyroid carcinomas, adenomas, and normals.  The 99 samples consisted of 4 normals, 10 follicular adenomas, 13 follicular carcinomas, 7 oncocytic adenomas, 8 oncocytic carcinomas, 51 papillary carcinomas (each typed as having classical, follicular or tall cell morphology), 4 anaplastic carcinomas, and 2 medullary carcinomas.  Additional information on common mutations are provided including RAS mutation, BRAF mutation, RET/PTC rearrangements, and PAX8/PPARG translocations.

first: Thomas

middle: J

last: Giordano

first: Amy

middle: Y

last: Au

first: Dafydd

middle: G

last: Thomas

first: Daniel

last: Rhodes

first: Kenneth

last: Wilhelm

first: Michelle

last: Vinco

last: Misek

first: Donita

last: Sanders

first: Zhaowen

last: Zhu

first: Raffaele

last: Ciampi

first: Samir

last: Hanash

first: Arul

last: Chinnaiyan

first: Roderick

last: Clifton-Bligh

first: Bruce

last: Robinson

first: Yuri

last: Nikiforov

first: Ronald

last: Koenig


title: Expression data from siliques of wild type and AtHb1-overexpressing plants under moderate hypoxia and standard conditions

city: Gatersleben

first: Johannes

last: Thiel

address: Corrensstrasse 3

country: Germany

institute: IPK-Gatersleben

summary:
Non-symbiotic hemoglobins are ubiquitously expressed proteins known to interact with nitric oxide, an inhibitor of mitochondrial respiration and an important signalling component. We evaluated the underlying molecular mechanisms of AtHb1 (also referred as AtGLB1 or AHb1) function, its effects on stress response and the interplay with nitric oxide. For this purpose, AtHb1 was overexpressed in Arabidopsis thaliana under control of the seed-specific promoter LeB4.
We performed comparative transcriptome analysis of developing siliques from wild type (WT, Col-0) and transgenic plants subjected to control and moderate hypoxic conditions. The experimental design was used to analyze the underlying molecular mechanisms of AtHb1 function and to assess differences in the hypoxic response between WT and AtHb1-overexpressing seeds/siliques.

overall_design: Hypoxic and control (normoxic) treatment was carried out with complete transgenic (T3) and WT plants 45 days after germination (DPG). Plants were aerated with a gas mixture containing 10.5% oxygen or ambient gas containing 21% oxygen for control samples in darkness. After one hour, plants were decapitated, immediately frozen in liquid nitrogen, and siliques were dissected in liquid nitrogen for RNA extraction and hybridization to Affymetrix microarrays. Hypoxic and control treatment runs with WT and AtHb1-overexpressing plants were repeated twice to provide 3 biological replicates (total number of samples = 12).

first: Hardy

last: Rolletschek


title: Genome wide gene expression profiles of Drosophila l(3)mbt larval brains and cultured tumors

city: Barcelona

first: David

last: Rossell

address: Baldiri Reixac 10

country: Spain

institute: IRB Barcelona

summary: Mutants in the Drosophila gene lethal (3) malignant brain tumor cause malignant growth in the larval brain. This data shows the changes in gene expression profile associated to mutations in l(3)mbt, both in situ in third instar larval brains and in tumors cultured for 1 5 and 10 (T1, T5, T10) rounds  of allograft culture

overall_design: We performed genome-wide gene expression profiling of l(3)mbt[E2] and l(3)mbt[ts1] homozygous and transheterozygous larval brains raised at restrictive temperatures (29º C). We obtained three replicates for l(3)mbt[E2]  at 17ªC (MBT_E2_17), l(3)mbt[ts1] at 17ºC (MBT_TS1_17), l(3)mbt[E2]  at 29ºC (MBT_E2_29) and the transheterozygous at 29ºC (MBT_TS1_ME2), and six replicates l(3)mbt[ts1] at 29ºC (MBT_TS1_29). We also obtained three replicates for l(3)mbt[ts1] tumors at the first (T1), fifth (T5) and tenth (T10) round of allograft culture in adult flies, and six replicates for wild type w[1118] flies (WT).

first: Ana

last: Janic

first: Cayetano

last: Gonzalez


title: Expression data from adult male Drosophila heads

city: Singapore

first: Jishy

last: Varghese

address: 1 Research Link

institute: TLL, Singapore

summary: A Drosophila microRNA (dme-miR-14) is involved in regulating the levels of insulin-like peptides (ilps) from the neuronal insulin-producing cells (IPCs). This is crucial for regulation of fat content in adult flies. Finding the target of this microRNA is crucial for understanding the regulation of ilp gene expression. We used microarrays to identify genes that are upregulated specifically in the neuronal IPCs in the microRNA mutants.

overall_design: Drosophila adult head RNA was extracted and hybridized on Affymetrix microarrays. We reared animals from early larval stages in controlled growth and feeding conditions. RNA was extracted from 5-day-old adult males. We collected RNA from control, homozygous dme-miR-14 mutants and mutants expressing dme-miR-14 microRNA specifically in the IPCs (rescue). We were interested in genes that were upregulated in the mutants and were restored or reduced to control levels in the rescue condition. Two biological replicates per sample type were performed.

first: Stephen

last: Cohen


title: Cleavage of NIK by the API2-MALT1 Fusion Oncoprotein Leads to Noncanonical NF-{kappa}B Activation

status: Public on Jan 30 2011

city: London

first: Rifat

last: Hamoudi

address: 67-73 Riding House Street

department: Surgery

institute: University College London

summary: Proper regulation of nuclear factor κB (NF-κB) transcriptional activity is required for normal lymphocyte function, and deregulated NF-κB signaling can facilitate lymphomagenesis. We demonstrate that the API2-MALT1 fusion oncoprotein created by the recurrent t(11;18)(q21;q21) in mucosa-associated lymphoid tissue (MALT) lymphoma induces proteolytic cleavage of NF-κB–inducing kinase (NIK) at arginine 325. NIK cleavage requires the concerted actions of both fusion partners and generates a C-terminal NIK fragment that retains kinase activity and is resistant to proteasomal degradation. The resulting deregulated NIK activity is associated with constitutive noncanonical NF-κB signaling, enhanced B cell adhesion, and apoptosis resistance. Our study reveals the gain-of-function proteolytic activity of a fusion oncoprotein and highlights the importance of the noncanonical NF-κB pathway in B lymphoproliferative disease.

overall_design:
This study compares nine t(11;18)-positive MALT lymphomas (8 from the stomach and 1 from lung) and eight translocation negative MALT lymphomas (all from the stomach) using gene set enrichment analysis (GSEA). All cases were subjected to Affymetrix U133A and U133B microarray analysis. The cases used in this study are the same cases used for the study by Hamoudi et al. (2010) entitled "Differential expression of NF-kB target genes in MALT lymphoma with and without chromosome translocation: insights into molecular mechanism" with GEO reference number: GSE18736

and

PubMed ID: http://www.ncbi.nlm.nih.gov/pubmed/20520640

All cases were subjected to non-specific filtering to eliminate non-variant probes, then the U133A and U133B probes were collapsed and the collapsed set was subjected to GSEA using the NF-kB target gene set as described in Hamoudi et al. (2010) study mentioned above.

The 34 samples in this study are identical to the ones done in the previous series except that the gene set enrichment was done on just those 34 samples and not the complete set.

first: Shaun

last: Rosebeck

first: Lisa

last: Madden

first: Xiaohong

last: Jin

first: Shufang

last: Gu

first: Alex

last: Appert

first: Heidi

last: Noels

first: Xavier

last: Sagaert

first: Peter

last: Van Loo

first: Mathijs

last: Baens

first: Ming-Qing

last: Du

last: Lucas

first: Linda

last: McAllister-Lucas


title: Identification of STAT5 target genes in human CB HSC, CMP, GMP and MEP

status: Public on Jan 22 2011

city: Groningen

first: JJ

last: Schuringa

address: Hanzeplein 1

department: Experimental Hematology

country: Netherlands

institute: UMCG

summary: CB CD34+ cells were isolated by Miltenyi miniMACS column. Cells were prestimulated in HPGM with 100 ng/ml KITL, FLT#L and TPO for 48 hrs. Cells were transduced with control MiNR1 or STAT5A-ER in three rounds over 48 hrs. Hematopoietic stem cells (HSCs), common myeloid progenitors (CMPs), granulocyte/macrophage progenitors (GMPs), and megakaryocyte/erythroid progenitors (MEPs) were sorted (for details see Blood 2011, Fatrai et al). cells were stimulated with 100 ng/ml 4OHT for 24 hrs after which RNA was isolated for Illumina beadhchiop arrays HT12 v3

first: J


title: Female Drosophila melanogaster gene expression and mate choice: candidate genes underlying sexual isolation

status: Public on Feb 05 2011

city: Uppsala

first: Richard

middle: Ian

last: Bailey

address: Norbyvägen 18 D

department: Animal Ecology

institute: Uppsala University

summary:
Background  The evolution of female choice mechanisms favouring males of their own kind is considered as crucial  step during the early stages of speciation. However, although the genomics of mate choice may  influence both the likelihood and speed of speciation, the identity and location of genes underlying  assortative mating remain largely unknown.
Methods and Findings  We used mate choice experiments and gene expression analysis of female D. melanogaster to examine  three key components influencing speciation. We show that the 1,498 genes in Zimbabwean female  Drosophila melanogaster whose expression levels differ when mating with more (Zimbabwean) versus  less (Cosmopolitan strain) preferred males include many with high expression in the central nervous  system and ovaries, are disproportionately X-linked and form a number of clusters with low  recombination distance. Significant involvement of the brain and ovaries is consistent with the action  of a combination of pre- and postcopulatory female choice mechanisms, while sex linkage and  clustering of genes lead to high potential evolutionary rate and sheltering against the homogenizing  effects of gene exchange between populations.
Conclusion  Taken together our results imply favourable genomic conditions for the evolution of reproductive  isolation through mate choice in Zimbabwean D. melanogaster and suggest that mate choice may, in  general, act as an even more important engine of speciation than previously realized.

overall_design: We measured gene expression of adult female Drosophila melanogaster from a composite Zimbabwe (Z) strain population named SZ, produced by mixing the genomes of six Z strain isofemale lines, shortly after mating them with either SZ strain or cosmopolitan (M strain) males.    Data from four replicates of each of the two treatments (SZ mated with SZ; SZ mated with M) are presented, giving a total of eight arrays.

first: Paolo

last: Innocenti

first: Edward

middle: H

last: Morrow

first: Urban

last: Friberg

first: Anna

last: Qvarnström


title: JIL-1 RNAi in Drosophila S2 Cells

city: Martinsried

first: Tobias

last: Straub

address: Großhadener Str. 9

department: Biomedical Center, Bioinformatics

institute: LMU Munich

summary: Profiling of changes in steady state RNA levels upon RNAi-mediated knockdown of the chromosomal kinase JIL-1 in Drosophila S2 cells.

overall_design: Drosophila S2 cells were incubated 7 days after treatment with 10 µg of dsRNA directed against GST/EGFP or JIL-1, respectively. 5 biological replicates per target have been collected.

first: C

last: Regnard

first: T

first: A

last: Mitterweger

first: I

last: Dahlsveen

first: P

middle: B

last: Becker


title: Expression Data From Dietary Restriction, p53 Knockdown and sir2 Overexpression Mutants

status: Public on Jan 20 2011

city: Providence

first: Michael

last: Antosh

state: RI

address: Brown University Box 1843

institute: Michael Antosh

summary:
Expression data from four different lifespan-extending conditions: dietary restriction in two different genetic backgrounds (canton-s and a yw, w1118 combination), sir2 overexpression and p53 knockdown (+/-).
Comparison of significantly over and under-expressed genes reveals a signature for dietary restriction and lifespan extension.

Abstract
A major challenge in translating the positive effects of dietary restriction (DR) for the improvement of human health is the development of therapeutic mimics. One approach to finding DR mimics is based upon identification of the proximal effectors of DR life span extension. Whole genome profiling of DR in Drosophila shows a large number of changes in gene expression, making it difficult to establish which changes are involved in life span determination as opposed to other unrelated physiological changes. We used comparative whole genome expression profiling to discover genes whose change in expression is shared between DR and two molecular genetic life span extending interventions related to DR, increased dSir2 and decreased Dmp53 activity. We find twenty-one genes shared among the three related life span extending interventions. One of these genes, takeout, thought to be involved in circadian rhythms, feeding behavior and juvenile hormone binding is also increased in four other life span extending conditions: Rpd3, Indy, chico and methuselah. We demonstrate takeout is involved in longevity determination by specifically increasing adult takeout expression and extending life span. These studies demonstrate the power of comparative whole genome transcriptional profiling for identifying specific downstream elements of the DR life span extending pathway.

overall_design: 42 samples were used in the analysis. Sir2 overexpression flies and the yw, w1118 background DR flies had the same control. Flies were collected at ages 10 and 40 days. Tissue is whole body females.

first: Johannes

last: Bauer


title: Chromosomal kinase JIL-1 in Drosophila S2 Cells

type: Genome binding/occupancy profiling by genome tiling array


title: VCAM1 promotes outbreak from dormant bone metastasis

city: Princeton

first: Yibin

last: Kang

state: NJ

address: LTL 254, Washington Road

department: Molecular Biology

institute: Princeton University

summary:
A weakly bone metastatic variant of the breast cancer cell line MDA-MB-231, SCP6, gave rise to highly bone metastatic sublines (PD1, PD2A-E) after long time dormancy in vivo. These cell lines were subjected to microarray analysis with data drawn from previous studies (Kang et al., 2003; Minn et al. 2005; Lu and Kang 2009; Lu and Kang 2010).

Keywords: Cell type comparison

overall_design: 12 cell lines (parental MDA-MB-231 with biological repeats; weakly bone metastasis variants: SCP3, SCP4 and SCP6; post-dormancy sublines of SCP6: PD1, PD2A, PD2B, PD2C, PD2D, PD2E and PD2R) were cultured and subjected to Affymetrix microarray analysis. Data were analysed with Genespring software.

first: Xin

last: Lu


title: Microarray analysis of gene expression of ovarian cancer cells treated with 1,25-dihydroxyvitamin D3

status: Public on Jan 28 2011

city: Tampa

first: Xiaohui

last: Zhang

state: FL

address: 12901 Bruce B. Downs Blvd.

department: Pathology and Lab Medicine

institute: University of South Florida College of Medicine

summary: To profile the changes in the pattern of gene expression in human OCa cells induced by 1,25(OH)2D3, OVCAR3 cells were treated with 0.1 pM 1,25(OH)2D3 for 0, 8, 24 and 72 h.  The cells were harvested, RNA was extracted, and Affmetrix microarrays were hybridized.

overall_design: OVCAR3 cells were treated with 0.1 pM 1,25(OH)2D3 for 0, 8, 24 and 72 hours. 1,25(OH)2D3 was added at different times to allow the treated cells to be harvested at the same time. Ethanol was included as vehicle controls and all cells were exposed to the same amount of ethanol for the same length of time. Total RNA was extracted using Trizol reagent (Invitrogen) and purified using Qiagen Rneasy kit as recommended by Affymetrix. In the initial set of array analysis with U95 chips, GADD45 was identified to be a VD-induced gene in OVCAR3 cells, which was confirmed by a follow-up study to be a primary target gene. For the array analyses with U133A chips, the response to 1,25(OH)2D3 of the cells used for RNA isolation was ensured by Northern blotting analysis of GADD45. Three independent experiments were performed.

first: Pengfei

last: Li

first: Santo

last: Nicosia

first: Steven

last: Enkemann

first: Wenlong

last: Bai


title: Regulation of myogenic progenitor proliferation in human fetal skeletal muscle by BMP4 and its antagonist Gremlin.

status: Public on Jan 26 2011

first: Alvin

middle: T.

last: Kho

address: 320 Longwood Avenue

department: Informatics Program

institute: Boston Children's Hospital

summary: Analysis of the transcriptome of mononuclear side population (SP) and main population (MP) cells of human fetal skeletal muscle from 12 human subjects of gestational age 14-18 weeks.

overall_design: Total RNA was extracted and profiled from 12 human fetal skeletal muscle side population (SP) cells and 10 corresponding human skeletal muscle main population (MP) cells.

middle: T

first: Natasha

last: Frank

first: Emanuela

last: Gussoni


title: Expression data from human blood from MELAS patients and controls

status: Public on Jan 24 2011

city: Dresden

first: Susanne

last: Mende

address: Fetscherstrasse 74

institute: University Clinic Dresden

summary:
Background: The heteroplasmic mitochondrial DNA (mtDNA) mutation A3243G causes the MELAS syndrome as one of the most frequent mitochondrial diseases. The process of reconfiguration of nuclear gene expression profile to accommodate cellular processes to the functional status of mitochondria might be a key to MELAS disease manifestation and could contribute to its diverse phenotypic presentation.
Objective: To determine master regulatory protein networks and disease-modifying genes in MELAS syndrome.
Methods: Analyses of whole blood transcriptomes from 10 MELAS patients using a novel strategy by combining classic Affymetrix oligonucleotide microarray profiling with regulatory and protein interaction network analyses.
Results and Interpretation: Hierarchical cluster analysis elucidated that the relative abundance of mutant mtDNA molecules is decisive for the nuclear gene expression response. Further analyses confirmed not only transcription factors already known to be involved in mitochondrial diseases (such as TFAM), but also detected the hypoxia-inducible factor 1α (HIF-1α)/HIF-1β complex, nuclear factor Y (NF-Y) and CREB-related transcription factors as novel master regulators for reconfiguration of nuclear gene expression in response to the MELAS mutation. Correlation analyses of gene alterations and clinico-genetic data detected significant correlations between A3243G-induced nuclear gene expression changes and mutant mtDNA load as well as disease characteristics. These potential disease-modifying genes influencing the expression of the MELAS phenotype are mainly related to clusters primarily unrelated to cellular energy metabolism, but important for nucleic acid and protein metabolism, and signal transduction. Our data thus provide a framework to search for new pathogenetic concepts and potential therapeutic approaches to treat the MELAS syndrome.

overall_design: Peripheral blood samples were collected from ten A3243G MELAS patients and twenty age- and sex-matched healthy controls (2 controls for each patient). The patient cohort consisted of 4 females and 6 males, mean±s.e.m. age was 44.1±11.9 years (range: 22–63 years), mean±s.e.m. age at disease onset was 27.1±4.9 years (range: 13–55 years), mean±s.e.m. disease duration was 19.0±4.7 years (range: 4–43 years), and disease severity measured by the ‘Newcastle Mitochondrial Disease Adult Scale’ (NMDAS) 8 ranging from 0.0 (no symptoms) to 1.0 (maximum score) was 0.26±0.05 (range: 0.02–0.54).

first: Loic

last: Royer

first: Alexander

last: Herr

first: Janet

last: Schmiedel

first: Marcus

last: Deschauer

first: Thomas

last: Klopstock

first: Vladimir

middle: D

last: Kostic

last: Schroeder

first: Heinz

last: Reichmann

last: Storch


title: Microarray analysis of R7 and R8 targeting

city: Los Angeles

first: S

middle: Lawrence

last: Zipursky

state: California

address: 675 Charles E. Young Drive South

department: Biological Chemistry

institute: Howard Hughes Medical Institute

summary:
The formation of neuronal connections requires the precise guidance of developing axons towards their targets.  In the Drosophila visual system, photoreceptor neurons (R cells) project from the eye into the brain. These cells are grouped into some 750 clusters comprised of eight photoreceptors or R-cells each. R cells fall into three classes, R1-R6, R7 and R8. Posterior R8 cells are the first to project axons into the brain. How these axons select a specific pathway is not known.
Here, we used a microarray-based approach to identify genes expressed in R7 and R8 neurons as they extend into the brain.

overall_design: We used microarray analysis to measure gene expression changes when the transcription factor Runt is misexpressed in eye discs and conversely when eye discs are rendered mutant for the Senseless transcription factor.

first: Kartik

middle: S

last: Pappu

first: Marta

last: Morey

first: Aljoscha

last: Nern

first: Bettina

last: Spitzweck

first: Barry

last: Dickson

middle: L


title: Systematic meta-analysis and replication of genome-wide expression studies of Parkinson’s disease: 4

city: Cambridge

first: Bin

last: Zheng

address: 65 Landsdowne Street

department: Center for Neurologic Diseases

institute: Brigham and Women's hospital

summary: Analysis of substantia nigra from postmortem brains of 4 patients with Parkinson’s disease (PD). Results provide insight into the molecular processes perturbed in the PD substantia nigra.

overall_design: Fresh frozen tissue blocks from cerebellar hemispheres of PD patients and controls were provided by the Queens Square Brain Bank for Neurological Disorders (London, UK). Total RNA was isolated from about 500 mg fresh frozen postmortem tissue from each subject by using Trizol reagent (Invitrogen, Carlsbad, CA, USA) according to the manufacturer's protocol and further purified using the RNeasy mini kit (Qiagen, Hilden, Germany). Quality of the extracted total RNA was assessed using an Agilent 2100 Bioanalyzer (Agilent Technologies, Boblingen, Germany). Cerebellar mRNA with the following criteria: two distinct visible peaks for 18 s and 20 s RNA with lack of multiple small peaks indicating major degradation in Agilent Bioanalyzer fluorograms and GAPDH 3′/5′ ratios smaller 5.0 and percentage present calls greater 40% for the parameter assessed by chip hybridization were hybridized on Affymetrix human U133A GeneChip Array. Sample labeling, hybridization to arrays and image scanning (Affymetrix® GeneChip® Scanner 2500, Agilent technologies, Boblingen, Germany) were performed using standard Affymetrix® protocol (Affymetrix® Expression Analysis Technical Manual) as described previously (Bonin et al,  Brain Res. Mol. Brain Res. 126, 2004). The Affymetrix .CEL files were normalized to “all probe sets” in a standardized matter, and scaled to 100 by the MAS5 algorithm implemented in the Bioconductor package.

first: Ullrich

last: Wüllner

first: Clemens

middle: R

last: Scherzer


title: Coexpression Networks of Phosphate Deficiency Genes

city: Berlin

middle: J.

last: Buckhout

address: Invalidenstrasse 42

department: Biology

institute: Humboldt University Berlin

summary:
Phosphate (Pi) deficiency triggers the differential expression of a large set of genes, which communally adapt the plant to low Pi bioavailability.
To infer functional modules in early transcriptional responses to Pi deficiency, we conducted time-course microarray experiments and subsequent coexpression-based clustering of Pi-responsive genes by pairwise comparison of a large number of genes against a customized data base.

overall_design: Arabidopsis were hydroponically grown in the presence (control) or absence of phosphate. Samples to be analyzed were collected at 0, 1, 6, and 24 h. Differentially expressed transcripts were determined at the respective time points. The experiment was conducted 3 times.

first: Wolfgang

last: Schmidt


title: A Gene Signature Predicting for Survival in Suboptimally Debulked Patients with Ovarian Cancer

city: Boston

first: Michael

last: Birrer

address: 70 Blossom Street

department: Medicine

institute: MGH

summary:
To identify a prognostic gene signature accounting for the distinct clinical outcomes in ovarian cancer patients
Despite the existence of morphologically indistinguishable disease, patients with advanced ovarian tumors display a broad range of survival end points. We hypothesize that gene expression profiling can identify a prognostic signature accounting for these distinct clinical outcomes. To resolve survival-associated loci, gene expression profiling was completed for an extensive set of 185(90 optimal/95 suboptimal) primary ovarian tumors using the Affymetrix human U133A microarray. Cox regression analysis identified probe sets associated with survival in optimally and suboptimally debulked tumor sets at a P value of <0.01. Leave-one-out cross-validation was applied to each tumor cohort and confirmed by a permutation test. External validation was conducted by applying the gene signature to a publicly available array database of expression profiles of advanced stage suboptimally debulked tumors. The prognostic signature successfully classified the tumors according to survival for suboptimally (P = 0.0179) but not optimally debulked (P = 0.144) patients. The suboptimal gene signature was validated using the independent set of tumors (odds ratio, 8.75; P = 0.0146). To elucidate signaling events amenable to therapeutic intervention in suboptimally debulked patients, pathway analysis was completed for the top 57 survival-associated probe sets. For suboptimally debulked patients, confirmation of the predictive gene signature supports the existence of a clinically relevant predictor, as well as the possibility of novel therapeutic opportunities. Ultimately, the prognostic classifier defined for suboptimally debulked tumors may aid in the classification and enhancement of patient outcome for this high-risk population.

overall_design: Gene expression profiling was completed for an extensive set of 185 primary ovarian tumors and 10 normal ovarian surface epithelium using the Affymetrix human U133A microarray


title: Systematic meta-analysis and replication of genome-wide expression studies of Parkinson's disease

status: Public on Feb 03 2011

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

overall_design: Refer to individual Series


title: Systematic meta-analysis and replication of genome-wide expression studies of Parkinson's disease: 3

summary:
Systematic meta-analysis and replication of genome-wide expression studies identifies molecular pathways of Parkinson's disease.
Analysis of substantia nigrae from postmortem brains of 6 patients with Parkinson's disease (PD). Results provide insight into the molecular processes perturbed in the PD substantia nigra.

overall_design: Substantia nigra samples from 6 PD and 5 control subjects were obtained. At autopsy, brain hemispheres were frozen in liquid nitrogen and stored at -80C in the Kathleen Price Bryan Brain Bank in the Alzheimer's Disease Research Center at Duke University. Using the RNAgents kit (Promega, Madison, Wis), RNA was extracted from SN and adjacent midbrain tissues. Double-stranded complementary DNA was made with a biotinylated T7(dT)-24 primer. Twenty micrograms of biotinylated complementary RNA was fragmented and hybridized to Affymetrix human genome U133A microarrays. The Affymetrix .CEL files were normalized to "all probe sets" in a standardized matter, and scaled to 100 by the MAS5 algorithm implemented in the Bioconductor package.

first: MIchael

middle: A

last: Hauser


title: Systematic meta-analysis and replication of genome-wide expression studies of Parkinson's disease: 2

summary:
Systematic meta-analysis and replication of genome-wide expression studies identifies molecular pathways of Parkinson's disease.
Examination of substantia nigra from postmortem brains of 8 patients with Parkinson's disease (PD).

overall_design: The substantia nigra samples from 8 PD subjects were obtained from the Human Brain and Spinal Fluid Resource Center, VAMC, Los Angeles, CA, the Mind Unit Brain Bank at the University of Rochester, Rochester, NY, and from Dr. E. Masliah at UCSD, San Diego, CA, and 9 control subjects were obtained from the University of Rochester Alzheimer's Disease Center brain bank. The RNA was extracted using Trizol reagent (Invitrogen), DNAse treated with Qiagen DNAse, and analyzed on a bioanalyzer. The complementary RNA was fragmented and hybridized to Affymetrix human U133A arrays. The total 17 Affymetrix .CEL files were normalized to "all probe sets" in a standardized matter, and scaled to 100 by the MAS5 algorithm implemented in the Bioconductor package.

first: Renee

last: Miller

first: Howard

last: Federoff


title: Expression data from developing regulatory T cells

city: Munich

first: Iryna

last: Prots

address: Pettenkoferstrasse 8a

department: Rheumatology

institute: University of Munich

summary:
CD25+ regulatory T cells develop in the thymus (nTregs), but may also be generated in the periphery upon stimulation of naive CD4 T cells under appropriate conditions (iTregs). The mechanisms that regulate the generation of peripheral iTregs are largely unknown.
We used microarrays to gain insights into the molecular program of extrathymic Treg development

overall_design: Human iTregs were generated in vitro from CD4CD25- naive T cells in the presence of autologous feeder cells and interleukin (IL)-4. Total RNA was isolated at start and from purified CD25+ and CD25- T cells at days 3, 5, 7, and 10 of culture and used for DNA microarrays. CD25+ T cells generated in the absence of IL-4 constituted activated effector T cells (Teffs) lacking regulatory capacity and were therefore used to control for Treg-specific gene expression.

first: Alla

last: Skapenko


title: Systematic meta-analysis and replication of genome-wide expression studies of Parkinson's disease: 1

summary:
Systematic meta-analysis and replication of genome-wide expression studies identifies molecular pathways of Parkinson’s disease.
Snap-frozen human substantia nigras (SNs) of 16 individuals with a clinicopathological diagnosis of incidental Lewy body (ILB) disease with Lewy bodies detected in the brainstem nuclei of locus coeruleus and substantia nigra, but generally not in higher cortical regions consistent with Braak stage 3 criteria for Parkinson's disease (PD), and 17 age-, sex-, postmortem interval-, and RNA integrity number-matched controls, who were clinicopathologically within normal limits for age collected under the rapid-autopsy program of Sun Health Research Institute or by the Harvard Brain Tissue Resource Center at McLean Hospital, were used for gene expression analyses in stage 2. Protocols were approved by the Institutional Review Board of Brigham and Women’s Hospital.

overall_design:
RNA was isolated and quality-controlled as described by Agilent Bioanalyzer6. Only RNAs with preserved ribosomal peaks on electropherogram were forwarded for analysis, and RINs of cases and controls were matched. 350 ng of total RNA were reverse transcribed from each SN sample and hybridized to Illumina HumanHT-12v3 Expression BeadChips targeting more than 25,000 annotated genes with more than 48,000 probes derived from the National Center for Biotechnology Information (NCBI) Reference Sequence (RefSeq; Build 36.2, Rel 22) and UniGene (Build 99) databases, and scanned on a BeadArray Reader. Data were processed, normalized by “average normalization”, and quality-controlled using GenomeStudio.

The supplementary file 'GSE20159_non-normalized.txt' contains non-normalized data for Samples GSM505716-GSM505748.


title: comparison of powdery mildew-induced gene expression between Col-0 and the edr1 mutant

status: Public on Jan 19 2011

city: Bloomington

first: Roger

last: Innes

state: IN

address: 915 East Third Street

institute: Indiana University

summary: The edr1 mutant of Arabidopsis thaliana displays enhanced resistance to the powdery mildew Golovinomyces cichoracearum, resulting in cell death and an absence of visible disease symptoms.  To better characterize and understand the defense response of edr1, a time course of early signaling responses was performed after inoculation with powdery mildew and compared to the responses of wild-type Col-0.  These time points represent early stages in the infection process, before any signs of susceptibility or resistance are visible.

overall_design: Four-week-old Col-0 and edr1 plants were inoculated with powdery mildew and whole rosettes were collected at 0, 18, 36, and 96 hours post inoculation.  Each sample is a pool of four rosettes processed together.

middle: W

first: Katy

last: Christiansen


title: Effect of mitochondria on nuclear gene expression in Drosophila melanogaster

status: Public on Jan 09 2011

first: Paolo

last: Innocenti

address: Norbyvägen 18D

department: Dept. of Animal Ecology

institute: Uppsala university

summary: Five different mitochondrial strains were introgressed in male and female fruit flies with identical (w1118) nuclear genetic background.

overall_design: 40 samples: Five mitochondrial strains, two independent introgressions, two sexes, two biological replicates.

first: Edward

last: Morrow

first: Damian

middle: K

last: Dowling


title: Maternal influences on the transmission of leukocyte gene expression profiles in population samples (Red Cross Donors)

status: Public on Jan 01 2011

city: Chicago

first: Jinhee

last: Kim

address: 676 North St. Clair Street Arkes Suite 2330

department: Infectious Disease

institute: Northwestern University

summary: This is a companion study to (GSE21342).  Peripheral blood leukocyte samples were obtained with consent from 100 red cross blood donors sampled cross-sectionally across the city of Brisbane, Australia.  After correction for RNA integrity values, individuals fall into major profiles of expression variation suggesting environmental and cultural influences on immune gene expression.

overall_design: 100 individuals, 50 men and 50 women, were sampled with permission of the Red Cross Society of Australia and under informed consent. The age of individulas were between 18 and 68 (mean 44). BMI ranged from 17.7 to 51.3 with a mean of 26.6. Collection was carried out by EM at mobile Red Cross vans at 10 locations (Bellbowrie, Capalaba, Dayboro, Eagle Farm, Kenmore, Mount Ommaney, South Brisbane, St Lucia, Virginia, and Woolloongabba) distributed across the city.

first: Elizabeth

last: Mason

first: Graham

last: Tronc

first: Katia

last: Nones

first: Nick

last: Matigian

first: Russell

last: Wolfinger

first: Christine

last: Wells

first: Greg

last: Gibson


title: Maternal influences on the transmission of leukocyte gene expression profiles in population samples (mother and child)

summary: This study contrasts the expression profiles of peripheral blood leukocytes from third trimester pregnant mothers, with cord blood leukocytes from their newborn children.  It is a companion to (GSE21311).  After normalization for RNA integrity, major principal components of the variation were found to distinguish individuals.  Transmission of gene expression profiles from mother to child was documented, along with differences between gestational diabetic, obese, and normal weight mothers and their children.

overall_design: 56 individulas (Brisbane, Australia) were sampled for the mother-newborn study, under informed consent. 19 mothers sample were collected in the last month of pregnancy (between 30th and 36th week of pregnancy) and 37 cord blood samples were obtained at birth from newborn babies. Mothers having BMI values over 30 before pregnancy were classified as obese. From the 37 newborn babies, 10 were born to obese mothers, 8 to gestational diabetic mothers (with a wide range of body mass indices), and 19 to normal-weight mothers. There were 16 mother-newborn pairs in the dataset. RNA from each was hybridized to an Illumina HT12 array.


title: Maternal influences on the transmission of leukocyte gene expression profiles in population samples


title: NFAT5 is a critical regulator of rheumatoid inflammation

status: Public on Dec 31 2010

city: LA

first: Sungyong

last: You

address: Beverly Blvd 8400

institute: Cedars-Sinai Medical Center

summary: NFAT5 is an osmoprotective transcription factor whose DNA binding domain shares structural homology with NFkappaB and other member of NFAT family, but its role in chronic inflammatory diseases remains unclear. The mRNA profiling of synoviocytes and endothelial cells transfected with NFAT5-targeted siRNA reveals three major changes in cellular processes associated with the pathogenesis of rheumatoid arthritis: cell cycle and survival, angiogenesis, and cell migration.

overall_design: The cells were transfected with NFAT5-targeted siRNA or non-specific scrambled (control) siRNA.

first: Wan-Uk

first: Daehee

last: Hwang

first: Chul-Soo

last: Cho


title: Weight loss in obesity reduces colorectal inflammation

status: Public on Dec 30 2010

city: New York

first: Mayte

last: Suarez-Farinas

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

institute: Mount SinaiSchool of Medicine

summary: The hypothesis tested in the present study was  The effect fo weight loss by dietary intervention with very low calorie diet on colorectal inflammatory genes and genepathways. The study results have shown that a 10% weight loss in obese women down-regulated inflammatory and cancer gene pathways. In addition there was downregulation of transcription factors known to play an important role in colorectal cancer.

overall_design: Total RNA obtained from colorectal mucosal biopsy samples

first: Swaroop

last: Pendyala

first: Peter

last: Holt


title: Expression data from testes of CG3875 knockout and wildtype flies

city: Kunming

first: Yun

last: Ding

state: Yunnan

address: #32 Jiaochang Road

country: China

institute: Chinese Academy of Sciences

summary: CG3875 is a young duplicate gene of kep1 family originated recently in Drosophila melanogaster (D. melanogaster) species complex (including D. melanogaster, D. simulans, D. mauritiana and D. sechellia) after it split from D. yakuba. It encodes an RNA-binding protein containing a single maxi-KH domain. Characterization of loss-of-function phenotypes of CG3875 mutants generated by gene targeting demonstrated that CG3875 null males display a seriously reduced fertility compared with wildtype males and most of the null males are completely sterile. Further cytological identification of CG3875 null males suggested that CG3875 plays an important role in spermiogenesis processes including sperm individualization and sperm coiling. In addition, CG3875 is also essential for the formation of outer dynein arm of sperm axoneme. In order to identify the molecular mechanism responsible for the involvement of CG3875 in spermiogenesis and structural integrity of sperm axoneme, we performed microarray analysis to identify transcripts whose levels are altered in the testes of CG3875 null males.

overall_design: We compared gene expression profiles between testes of 0-2 day CG3875 null mutants and wildtype flies, respectively. For the sake of an identical genetic background between knockout flies and wildtype flies, the wildtype stock used here is wildtype recombinant line created during gene targeting. Seminal vesicles were removed from the testes during dissection. Two independent RNA extractions and hybridizations were conducted for each sample.

first: Wen

last: Wang


title: Gene expression in human oral mucosal fibroblasts and patient-matched skin fibroblasts

city: Cardiff

first: Philip

last: Stephens

state: South Glamorgan

address: Dental Drive, Heath Park

department: Dental School

institute: Cardiff University

summary:
Wound healing within the oral mucosa results in minimal scar formation compared to wounds within the skin. We have recently demonstrated distinct differences in the ageing profiles of cells (oral mucosal and patient-matched skin fibroblasts) isolated from these tissues. We hypothesize that the increased replicative potential of oral mucosal fibroblasts may confer upon them preferential wound healing capacities. Passage-matched early cultures of oral mucosal fibroblasts and skin fibroblasts demonstrated distinct gene expression profiles with a number of genes linked to wound healing/tissue repair.
We analyzed the gene expression profiles of oral mucosal and patient-matched skin fibroblasts for multiple patients both prior to (0h) and (6h) following a wounding stimulus.

overall_design: Differences in the gene expression profiles of oral mucosal and patient-matched skin fibroblasts were anlazyed for multiple patients both prior to (0h) and (6h) following a wounding stimulus. Serum starvation and subsequent stimulation provides a model for wounding and RNA extracted at 0h and 6h following this stimulus was hybridized to Affymetrix microarrays for analysis. We sought to compare the expression profiles both between oral and normal fibroblasts, in both serum depleted and stimulated conditions and also compare differences between patients.

first: Stuart

last: Enoch


title: Genome-wide analysis gene expression of MCF10A cells growing in the presence of EGF or AREG or without EGF or AREG for 24 hrs

status: Public on Dec 23 2010

city: Detroit

first: Andrea

last: Baillo

address: 4100 John R

institute: Wayne State University

summary: Results of growing MCF10A cells continuously in serum free media supplemented with EGF (MCF10A) or AREG (MCF10A+AREG) followed by 24 hours of ligand withdrawl and measuring gene expression provides information as to what genes are regulated by AREG and EGF in a normal mammary epithelial cell model

overall_design: MCF10A cells continuously in serum free media supplemented with 10ng/ml of EGF (MCF10A) or 20ng/ml of AREG (MCF10A+AREG) followed by 24 hours of ligand withdrawl. Total RNA was collected and genome-wide analysis of expression was performed on RNA from each cell line.

first: Stephen

middle: P

last: Ethier


title: Anti-microbial peptides increase tolerance to oxidant stress in Drosophila melanogaster

status: Public on Dec 21 2010

city: La Jolla

first: Dan

last: Zhou

address: CMG 103, 9500 Gilman Drive, MC0735

department: Pediatrics

institute: University of California, San Diego, School of Medicine

summary: It is well appreciated that reactive oxygen species (ROS) are deleterious to mammals, including humans, especially when generated in abnormally large quantities from cellular metabolism. Whereas the mechanisms leading to the production of ROS are rather well delineated, the mechanisms underlying tissue susceptibility or tolerance to oxidant stress remain elusive. Through an experimental selection over many generations, we have previously generated Drosophila melanogaster flies that tolerate tremendous oxidant stress and have shown that the family of antimicrobial peptides (AMP) is over-represented in these tolerant flies. Furthermore, we have also demonstrated that overexpression of even one AMP at a time (e.g. Diptericin) allows wild type flies to survive much better in hyperoxia. In the current study, we used a number of experimental approaches to investigate the potential mechanisms underlying hyperoxia tolerance in flies with antimicrobial peptide overexpression. We demonstrate that flies with Diptericin overexpression resist oxidative stress by increasing antioxidant enzyme activities and preventing an increase in ROS level after hyperoxia. Depleting the GSH pool using buthionine sulfoximine limits fly survival, thus confirming that enhanced survival observed in these flies is related to improved redox homeostasis. We conclude that a) AMPs play an important role in tolerance to oxidant stress; b) overexpression of Diptericin changes the cellular redox balance between oxidant and antioxidant, and c) this change in redox balance plays an important role in survival in hyperoxia.

overall_design: Expression profiles of Drosophila melanogaster with anti-microbial peptide over-expression (experimental sample; n=3) and controls (UAS-AMP alone not crossed to da-GAL4; n=3) were determined using Affymetrix Drosophila Genome 2.0 Arrays.

first: Huiwen

last: Zhao

first: Gabriel

last: Haddad


title: Global expression analysis of BAP1 knockdown in transfected 92.1 cells

status: Public on Jan 06 2011

city: St. Louis

first: Elisha

last: Roberson

state: MO

address: 660 South Euclid Ave., CB 8045

department: Internal Medicine & Genetics

institute: Washington University in St. Louis

summary: Analysis of the effect that reduced BAP1 levels have on global gene expression.The hypothesis tested was that reduction in BAP1 levels would produce changes in gene expression similar to changes observed in class 2 uveal melanomas. Data provided insight into genes that are disrupted with reduced BAP1 levels.

overall_design: Total RNA was isolated from 92.1 cells transfected with either control or BAP1 knockdown constructs for global expression analysis.

first: J

last: Harbour

first: Michael

last: Onken

first: Shenghui

last: Duan

first: Li

last: Cao

first: Lori

last: Worley

first: M

last: Council

first: Katie

last: Matatall

first: Cynthia

last: Helms

first: Anne

middle: M

last: Bowcock


title: Genome-wide analysis gene expression in SUM-149 cells expressing AREG shRNA

status: Public on Dec 15 2010

summary: Results of knocking-down AREG expression in SUM-149 cells by lenitviral infection of shRNA vectors and measuring gene expression provides information as to what genes are regulated by AERG in inflammatory breast cancer cells.

overall_design: SUM-149 cells were infected with a single AREG shRNA virus (sh4) or three AREG shRNA viruses (shPld) and the non-silencing vector (shNS). Total RNA was collected and genome-wide analysis of expression was performed on RNA from each cell line.


title: A Comparision of Gene Expression between Normal and Diseased Human Meibomian Glands

first: David

last: Sullivan

state: MA

address: 20 Staniford Street

institute: Schepens Eye Research Institute

summary: The objective of this study is to identify human meibomian gland genes that may promote the development and/or progression of meibomian gland dysfunction.

overall_design: Total RNA was isolated from normals (n=6) and patients with meibomian disease (n=6).   The RNA was then used in conjuction with HumanHT-12 v3 Expression BeadChips to assay differential gene expression between normal and diseased meibomian glands.

first: Shaohui

last: Liu

last: Richards


title: Drosophila expression data from larval, prepupal and pupal wings to identify targets of Hox protein Ultrabithorax (Ubx)

first: Anastasios

middle: Tassos

last: Pavlopoulos

address: Downing Street

department: Department of Zoology

institute: University of Cambridge

summary:
Hox genes regionalize the animal body axis by modifying complex morphogenetic and differentiation processes during development. The transformation of wings into halteres by the Hox gene Ultrabithorax (Ubx) in Drosophila melanogaster presents an excellent model system to study the transcriptional networks that control such complex developmental programmes.
We have employed an inducible misexpression system to switch on Ubx in the wing epithelium at successive larval, prepupal and pupal stages, and have used microarray expression profiling to identify the primary transcriptional responses to Ubx. We find that Ubx regulates hundreds of downstream genes, mostly in a subtle manner. These targets are largely distinct at the different stages of appendage development and diversification.

overall_design: We have generated an experimental fly line combining the nabGal4NP3537-driver, a tub-GAL80ts transgene, and a UAS-UbxIa transgene (the control line was carrying a UAS-eGFP transgene instead). Our core microarray analysis has involved comparison of the transcriptional profile of experimental wings carrying the UAS-UbxIa transgene with that of control wings carrying the UAS-eGFP transgene. Pairwise comparisons have been carried out at three successive developmental stages, in particular at (i) the third instar larval wandering stage, about 4hrs before puparium formation at 29˚C, (ii) the prepupal stage, 6hrs after puparium formation (APF) at 29˚C, and (iii) the early pupal stage, 16hrs APF at 29˚C. Moreover, pairwise comparisons have been carried out with samples developed exclusively at 19˚C (UbxIa or eGFP expression OFF), as well as with samples collected at 16hrs after the temperature shift from 19 to 29˚C (UbxIa or eGFP expression ON). This has allowed us to distinguish the Ubx-dependent effects from the intrinsic expression differences between the fly lines used, and from the temperature-induced responses. We have carried out 4 biological replicates for each condition making a total of 48 hybridizations to Affymetrix Drosophila Genome 2.0 arrays.

last: Akam


title: Effect of Mycophenolic Acid on renal transplant recipients

status: Public on Dec 22 2010

city: Bari

first: Paola

last: Pontrelli

address: Piazza G.Cesare 11

department: Dept. of Precision and Regenerative Medicine and Ionian Area (DIMEPRE-J)

institute: University of Bari

summary:
Mycophenolic acid (MPA), an immunosuppressive drug widely used in kidney transplantation, has been suggested to have anti-fibrotic effects.
To analyze at a genomic level these effects, we prospectively studied a group of stable kidney transplant recipients (n=35) on cyclosporine (CyA) and azathioprine treatment. Twenty patients were converted from azathioprine to MPA (MPA group) and 15 patients continued on azathioprine (AZA group). RNA was extracted by peripheral blood mononuclear cells at baseline and 3 months thereafter. Genomic analysis, performed on 5 randomly-selected MPA patients, revealed that 17 genes discriminated the transcriptomic profile after conversion. Neutral endopeptidase (NEP), an enzyme degrading angiotensin-II, was the most significant up-regulated gene. NEP expression level was inversely correlated to proteinuria at baseline and after conversion. Immunohistochemistry on graft biopsy of 33 independent patients demonstrated higher glomerular and tubular NEP protein expression in CyA+MPA (n=13) compared to CyA+AZA (n=12) and CyA alone (n=8). Glomerular NEP levels were inversely correlated to proteinuria and glomerulosclerosis. Tubular NEP expression was inversely correlated to interstitial fibrosis. Incubation of proximal tubular cells with MPA led to a dose- and time-dependent increase of NEP gene expression. The direct  influence of MPA on NEP expression may suggest a novel therapeutic effect of this drug.

overall_design: For microarray analysis, we studied 5 randomly selected patients included in the training group. Patients included in this group were, at the time of enrollment (T0), on standard maintenance immunosuppression with Cyclosporine (Neoral, Novartis, Basel, mean±SD of daily dose: 160.1±37.1mg), prednisone (5 mg daily) and Azathioprine (50 mg daily). Twenty patients, at T0, were switched from Azathioprine to EC-MPS (Myfortic, Novartis, Basel, 720 mg bid) for their need of allopurinol therapy (EC-MPS group). However, to avoid confounding factors, allopurinol treatment did not start until the end of our study (3 months). For the microarray analysis, we randomly selected 5 patients from the EC-MPS group. PBMC both at T0 and at T1 (3 months after the switching of the therapy) were immediately isolated from 20 ml of whole blood by Ficoll–Hypaque (Flow Laboratories, Irvine, UK) density gradient centrifugation. Total RNA was extracted by RNeasy mini kit (QIAGEN Inc., Valencia, CA) according the manufacturer’s instructions. Total RNA was processed and hybridized to the Affymetrix GeneChips Human Genome U133 Array Set HG-U133A (Affymetrix)(Affymetrix, Santa Clara, CA)


title: Transcription profiling of WT and dsr1 Arabidopsis seedlings treated with salicylic acid

status: Public on Dec 14 2010

city: Wembley

last: Gleason

state: WA

address: Private Bag #5

department: Plant Industry

country: Australia

institute: CSIRO

summary:
Reactive oxygen species such as hydrogen peroxide (H2O2) are important in biotic and abiotic stress responses in plants, but their source is often unclear. We have identified an Arabidopsis mutant that shows loss of stress responsive GSTF8 gene expression in response to the plant defence signal salicylic acid (SA) .  The mutant showed increased susceptibility to both fungal and bacterial pathogens. The dsr1 mutation was mapped to mitochondrial succinate dehydrogenase (SDH1-1) and dsr1 had reduced SDH activity and a lowered mitochondrial H2O2 production.
To better understand the loss of SA-response in dsr1, we performed ATH1 microarray analysis in WT and dsr1 10 hours after a 1 mM SA treatment, a point at which we observed maximal SA-induced GSTF8 promoter activity.

overall_design: 4 day old WT (a Columbia line containing a -800GSTF8::LUC reporter) and dsr1 seedlings (a mutant Columbia line containing a -800GSTF8::LUC) reporterwere treated with water (mock) or 1 mM SA for 40 min.  Ten hours after treatment, samples were collected.

first: Karam

last: Singh