title: Human inositol polyphosphate multikinase regulates transcript-selective nuclear mRNA export to preserve genome integrity

city: Cambridge

first: Vihandha

last: Wickramasinghe

address: Hills Road

institute: MRC Cancer Unit, Hutchison/MRC Research Centre

summary: Messenger (m)RNA export from the nucleus is essential for eukaryotic gene expression. Here, we identify a transcript-selective nuclear export mechanism affecting certain human transcripts, enriched for functions in genome duplication and repair, controlled by inositol polyphosphate multikinase (IPMK), an enzyme catalyzing inositol polyphosphate and phosphoinositide turnover. We studied transcripts encoding RAD51, a protein essential for DNA repair by homologous recombination (HR), to characterize the mechanism underlying IPMK-regulated mRNA export. IPMK depletion or catalytic inactivation selectively decreases the nuclear export of RAD51 mRNA, and RAD51 protein abundance, thereby impairing HR. Recognition of a sequence motif in the untranslated region of RAD51 transcripts by the mRNA export factor ALY requires IPMK. Phosphatidylinositol (3,4,5)-trisphosphate (PIP3), an IPMK product, restores ALY recognition in IPMK-depleted cell extracts, suggesting a mechanism underlying transcript selection. Our findings implicate IPMK in a transcript-selective mRNA export pathway controlled by phosphoinositide turnover that preserves genome integrity in humans.

overall_design: We used gene expression profiling to compare the abundance of cytoplasmic RNAs after IPMK depletion

first: Jane

last: Savill

first: Ashok

last: Venkitaraman


title: Nfix is a novel regulator of murine hematopoietic stem and progenitor cell survival

status: Public on Sep 05 2013

city: Memphis

first: David

last: Finkelstein

state: TN

address: 332 N. Lauderdale St.

department: Computational Biology

country: USA

institute: St Jude Children's Research Hospital

summary: Hematopoietic stem cells are both necessary and sufficient to sustain the complete blood system of vertebrates.  Here we show that Nfix, a member of the nuclear factor I (Nfi) family of transcription factors, is highly expressed by hematopoietic stem and progenitor cells (HSPC) of murine adult bone marrow.  Although shRNA mediated knockdown of Nfix expression in Lineage-Sca-1+c-Kit+ HSPC had no effect on in vitro cell growth or viability, Nfix-depleted HSPC displayed a significant loss of colony forming potential, as well as short- and long-term in vivo hematopoietic repopulating activity.  Analysis of recipient mice 4-20 days post-transplant revealed that Nfix-depleted HSPC establish in the bone marrow but fail to persist due to increased apoptotic cell death. Gene expression profiling of Nfix-depleted HSPC reveals that loss of Nfix expression in HSPC is concomitant with a decrease in the expression of multiple genes known to be important for HSPC survival, such as Erg, Mecom, Mpl and Prdm16.  These data reveal that Nfix is a novel regulator of HSPC survival post-transplantation and establish, for the first time, a role for Nfi genes in the regulation of this cellular compartment.

overall_design: 3 NFIX depleted samples are compared to 3 wt samples

first: Per

last: Holmfeldt

first: Jennifer

last: Pardieck

first: Satish-Kumar

last: Nandakumar

first: John

middle: T

last: Gray

first: Shannon

last: McKinney-Freeman


title: Transcriptomic profiling in childhood H1N1/09 influenza reveals reduced expression of protein synthesis genes

city: London

first: Jethro

middle: A

last: Herberg

address: Norfolk Place

department: Section of Paediatrics

country: United Kingdom

institute: Imperial College London

summary:
In order to understand the immunopathogenesis of severe influenza H1N1/09, we compared the whole blood RNA transcriptome of children hospitalised with H1N1/09 infection with that of children hospitalised with RSV or bacterial infection
Blood was collected into PAX gene tubes (PreAnalytiX). Total RNA integrity was assessed using an Agilent 2100 Bioanalyzer (Agilent, Palo Alto, CA). Labeled cRNA was hybridized to Illumina Human HT-12 v3 Beadchips.

overall_design: Observational, prospective study. Patients were recruited at or after presentation to hospital. Main inclusion criteria were presence of illness of sufficient severity to warrant blood tests for clinical reasons, in child aged <17 years. Patient numbers recruited were as follows: H1N1/09 infection (n=25) RSV (n=34) (n=21), and healthy paediatric controls (n=33). After exclusion of children with co-infections, numbers of arrays analysed in were as follows: H1N1/09 n=19; RSV n=22; bacterial infection n=18; controls n=33


title: Expression profiling of human foreskin fibroblasts cultured in media supplemented with human sera

status: Public on Sep 04 2013

city: Trieste

first: Danilo

last: Licastro

department: Genomica Funzionale

country: Italy

institute: CBM

summary: Treatment of cultured cells with serum collected from humans on long-term calorie restriction enhances stress resistance in vitro.

overall_design: RNA expression was compared in human foreskin fibroblasts cultured in media supplemented with human sera obtained from: 1) healthy lean and weight-stable volunteers who were consuming calorie-restricted diets, for an average of 7 years, and 2) age-, sex-matched individuals eating a Western Diet.

first: Daniela

middle: D

last: Omodei

first: Seth

last: Crosby

first: Luigi

middle: L

last: Fontana


title: A Common Docking (CD) Domain in Progesterone Receptor-B Links MKP3-Dependent Rapid Signaling Events to JAK/STAT Regulation of Gene Expression Required for Breast Cancer Cell Proliferation

status: Public on Sep 06 2013

city: Minneapolis

first: Todd

middle: P

last: Knutson

state: MN

address: 117 Pleasant St SE

department: Minnesota Supercomputing Institute

institute: University of Minnesota

summary: Progesterone receptors (PRs) are critical context-dependent transcription factors required for normal uterine (PR-A) and mammary gland (PR-B) development. Progesterone is proliferative in the breast, where PR-target genes include paracrine factors that mediate mammary stem cell self-renewal. In the context of altered signal transduction that typifies breast tumorigenesis, dysregulated (i.e. hyper-phosphorylated) PRs likely contribute to tumor progression by promoting cancer cell pro-survival and proliferation. Notably, in breast cancer cells, progestin-bound PRs induce rapid MAPK activation leading to selective regulation of growth-promoting genes by phosphorylated PR species. Functional domains within PR that interact with c-Src and estrogen receptors (ER) have been identified as indirect routes to MAPK activation. Herein, we describe a common docking (CD) domain located within the PR-B N-terminus, a motif first described in MAPKs that facilitates direct interactions between MAPKs and MEK1 or MAPK-phosphatases (MKPs). Mutation of negatively-charged amino acids, previously determined to be critical for CD domain function in MAPKs, within PR-B (mCD PR) did not alter MEK-binding or progestin-induced rapid signaling (i.e. MAPK activation) and PR transcriptional activity as measured by PRE-luciferase (reporter) assays. Microarray gene-expression analysis revealed that endogenous genes regulated by wt PR, but not mCD PR, are involved in critical cellular pathways regulating growth, proliferation, survival, and cancer. mCD PR failed to undergo ligand-induced phosphorylation on Ser81, a ck2-dependent site required for progestin-regulation of select growth-promoting genes (BIRC3, HSD11β2, HbEGF). Progestin-induced PR Ser81 phosphorylation mapped to CD domain-dependent binding of PR-B to MKP3, but did not require phosphatase activity. Receptors containing either mutant CD domains (mCD PR) or point mutations of Ser81 (S79/81A PR) failed to upregulate STAT5 and Wnt1, key PR-target gene products that act as critical mediators of mammary stem cell expansion. Inhibition of JAK/STAT signaling blocked progestin-induced STAT5 and Wnt1 expression. ChIP assays demonstrated that wt, but not phospho-mutant (S79/81A), PR-B was co-recruited to a PRE-containing enhancer region of the Wnt1 gene along with MKP3, ck2 and STAT5. Our studies reveal a novel scaffolding action of MKP3 mediated by interaction with the PR CD domain and required for ck2-dependent PR Ser81 phosphorylation. Co-regulation of select target genes by phospho-Ser81 PR and phospho-STAT5 is likely a global mechanism required for the activation of growth promoting programs active during normal mammary gland development and relevant to mechanisms of breast cancer progression.

overall_design: The study contains 6 different sample groups measured in triplicate, for a total of 18 individual samples (18 arrays). From parental T47D-Y human breast cancer cell lines, we created three stable clones expressing (1) an empty vector (pSG5), (2) the wild type progesterone receptor isoform B (pSG5-PR-B), or (3) a mutant mutant CD domain PR-B. These cell lines were treated with either (1) vehicle control (ethanol) or (2) R5020 10e-8 M for 6 hours before total RNA harvest. Thus, the experiment contains three cell lines, and two treatments (6 sample groups) treated and analyzed in triplicate (18 microarrays). Standard Illumina HT-12v4 chip controls were used during hybridization.

first: Christy

middle: R

last: Hagan

first: Carol

last: Lange


title: Responses of Arabidopsis immune signaling mutants to Alternaria brassicicola infection

status: Public on Sep 03 2013

city: Saint Paul

last: Glazebrook

address: 1500 Gortner Avenue

department: Plant Biology

summary: A major part of plant immune response is mediated by signaling pathways controlled by three hormnes,  jasmonate, ethylene, and salicylate. The involvement of each of these hormone signaling pathways in Arabidopsis thaliana was investigated in response to infection of a necrotrophic fungal pathogen, A. brassicicola. Arabideopsis mutants deficient in these hormone signaling pathways were compared to wild type.

overall_design:
Expression profiles were obtained from leaves of wild-type (Col-0), dde2-2, ein2-1, and sid2-2 plants at 9 and 24 hours after A. brassicicola inoculation. In addition, expression profiles were obtained from wild-type at 9 and 24 hours after mock inoculation. The replicates were made from three independent experiments (i.e., biological replicates).
Please note that 'Col-0 at 24 hpi with A. brassicicola, biological rep 3' was excluded from data processing because the data did not pass a QC based on affyPML of Bioconducter.

first: Chris

last: Botanga


title: Whole-genome gene expression profiling of normal melanocytes and melanoma cell lines

city: Houston

first: HAI

last: LONG

state: TX

address: 1515 Holcombe Blvd., Unit 425

department: Leukemia

institute: University of Texas MD Anderson Cancer Center

summary: Aberrant DNA methylation and histone modifications both contribute to carcinogenesis, but how these two epigenetic factors interact to impact gene expression remain unclear. To address this issue, we studied gene expression profiles, DNA methylation and two key histone modifications (H3K4me3 and H3K27me3), in two normal melanocytes (HEMn and HEMa) and two melanoma cell lines SK-MEL-28 and LOXIMVI. Using these data, we analyzed the relationship between epigenetic factors and gene expression status in both normal and melanoma cells, and the impact of epigenetic switches on gene expression change during melanomagenesis.

overall_design: Each of the two normal melanocytes (HEMn and HEMa) and the two melanoma cell lines SK-MEL-28 and LOXIMVI was cultured in triplicate. For each cell line, the same culture conditions and cell density were applied to the triplicates. Total RNA was extracted and microarray analysis was performed for genome-wide gene expression profiling.  Using the Sentrix Human-HT12 v4 Beadchip, all four cell samples, each in triplicate, were examined in 12 individual arrays on a same beadchip. Thus, together with the data on DNA methylation and histone modifications, we could not only analyze the epigenetic regulation of gene expression in each cell sample, but also investigate the expression change associated with epigenetic changes in melanoma when compared to normal melanocytes.

first: Hai

last: Long

first: Jean-Pierre

middle: J

last: Issa


title: Specific extracellular matrix remodeling signature of colon hepatic metastases [HG-U133A]

status: Public on Sep 01 2013

city: Montpellier Cedex 5

first: Pierre

last: Martineau

address: 208 Rue des Apothicaires

department: IRCM

country: France

institute: Inserm

summary: To identify genes implicated in metastatic colonization of the liver in colorectal cancer, we collected pairs of primary tumors and hepatic metastases before chemotherapy in 13 patients. We compared mRNA expression in the pairs of patients to identify genes deregulated during metastatic evolution. We then validated the identified genes using data obtained by different groups. The 33-gene signature was able to classify 87% of hepatic metastases, 98% of primary tumors, 97% of normal colon mucosa, and 95% of normal liver tissues in six datasets obtained using five different microarray platforms. The identified genes are specific to colon cancer and hepatic metastases since other metastatic locations and hepatic metastases originating from breast cancer were not classified by the signature. Gene Ontology term analysis showed that 50% of the genes are implicated in extracellular matrix remodeling, and more precisely in cell adhesion, extracellular matrix organization and angiogenesis. Because of the high efficiency of the signature to classify colon hepatic metastases, the identified genes represent promising targets to develop new therapies that will specifically affect hepatic metastasis microenvironment.

overall_design: 57 samples of patients with stage IV colorectal cancer. We compared using Affymetrix chips gene expression profiles between primary tumors and hepatic metastases

first: Maguy

last: Del Rio

first: Caroline

last: Mollevi


title: A Kinetic Analysis of Auxin-mediated Changes in Transcript Abundance in Arabidopsis Reveals New Mediators of Root Growth and Development

city: WINSTON SALEM

first: Gloria

middle: Kressin

last: Muday

state: North Carolina

address: 1834 Wake Forest Road

department: Biology

institute: Wake Forest University

summary: Auxin-dependent transcript abundance was assayed by transferring 6 day old Arabidopsis grown on a a nylon mesh to IAA-containing or control media

overall_design:
Seedling roots were harvested 0, 0.5, 1, 2, 4, 8, 12, or 24 hours after treatment and the resultant RNA was used for microarray analysis to determine the kinetic profiles of auxin-responsive gene expression.
8 timepoints after control or IAA treatment done in triplicate

middle: K

first: Daniel

last: Lewis

first: Amy

last: Olex

first: Jacquelyn

middle: S

last: Fetrow


title: A spatiotemporal understanding of growth regulation during the salt-stress response (Affymetrix)

city: Stanford

first: Jose

middle: Ramon

last: Dinneny

state: United States

address: 260 Panama St

institute: Carnegie Institution for Science, Department of Plant Biology

summary:
Cell-type specific transcriptional profiles were generated by FACS (Fluorescence Activated Cell Sorting) sorting of roots that express cell-type specific GFP-reporters.  Four different GFP-reporter lines were utilized allowing us to obtain transcriptional profiles for cells in major radial zones of the root.  FACS cell populations were isolated from roots grown under standard conditions or roots that had been transfered to media supplemented with 140 mM NaCl for 1 hour, 3 hours, 8 hours, 20 hours, 32 hours and 48 hours.
Plant environmental responses involve dynamic changes in growth and signaling, yet little is understood as to how progress through these temporal events is controlled.  In this study we explore the phenotypic and transcriptional events involved in the acclimation of the Arabidopsis seedling root to a rapid change in salinity.  Using live-imaging analysis, we show that growth is dynamically regulated with a period of growth quiescence followed by growth recovery and homeostasis.  Through the development and analysis of a new high-resolution spatiotemporal transcriptional map, we have identified the key hormone signaling pathways that regulate specific transcriptional programs, predict their spatial domain of action and link the activity of these pathways to the control of specific phases of growth control. Through the use of tissue-specific approaches to suppress the ABA pathway, we demonstrate that ABA signaling likely acts in select tissue layers to control spatially localized transcriptional programs and promote growth recovery.  In addition to the biological pathways directly affecting growth, we show that salt also controls many tissue-specific and time-point specific transcriptional responses that are expected to modify water transport, Casparian strip formation and protein translation.  Together, our data reveal a sophisticated assortment of regulatory programs acting together to coordinate spatially patterned biological changes involved in the immediate and long-term response to a stressful shift in environment.

overall_design: 4 different GFP reporter lines were used to isolate specific populations of cells from the Arabidopsis root using FACS sorting of protoplasted cells.  GFP-reporter lines were grown under standard conditions before protoplasting and sorting or they were transfered to media supplemented with 140mM NaCl for a series of time: 1 hour, 3 hours, 8 hours, 20 hours, 32 hours and 48 hours before hand, as well as standard controls for 1 hour and 48 hours. 3 replicates for each condition was used.

first: Yu

last: Geng

first: Rui

last: Wu

first: Choon-Wei

last: Wee

first: Fei

last: Xie

first: Xueliang

last: Wei

first: Cliff

last: Tham

first: Lina

last: Duan


title: Gene expression analysis of H9 hESC derived cardiomyocytes (CM) and neuron stem cells (NSC)

status: Public on Aug 31 2013

city: La Jolla

last: Yi

state: CA

address: 10010 North Torrey Pines Road

institute: Salk Institute

summary: In this study, we generated wildtype H9 hESC derived cardiomyocytes (CM) and neural stem cells (NSC) by in vitro differentiation. Global gene expression profiles were compared among undifferentiated H9 hESC and the derived CM and NSC.

overall_design: Comparison of global gene expression profiles of undifferentiated H9 hESC and the derived CM and NSC populations.

first: Ying

last: Gu

first: Guang-hui

last: Liu

first: Juan-Carlos

last: Izpisua-Belmonte


title: The role of membrane fluidity in low temperature perception

status: Public on Aug 30 2013

city: Loughborough

last: Nottingham Arabidopsis Stock Centre (NASC)

address: Sutton Bonington Campus

department: School of Biosciences, University of Nottingham

summary:
The aim of this work is to investigate whether A. thaliana senses low temperature by perceiving changes in membrane fluidity. To this end, we have performed an experiment to test whether mutant or transgenic plants with altered membrane lipid composition, regulate their gene expression in the same manner as wild type plants in response to cold.
Previous work has demonstrated that a change in the expression levels of a number of genes is important in acquiring tolerance to low temperatures. Chemicals which rigidify cell membranes in such a way as to mimic the effects of cold have been shown to be able to induce the expression of such genes. However, because of the non-specific nature of such chemical treatments, it has not been possible to demonstrate unequivocally that the changes in gene expression observed were the result of changes in membrane fluidity.
All of the mutants used in our experiment,  fab1, fad2-2 and the fad3/fad7/fad8 mutant, have increased lipid saturation levels compared to wild type plants and are thought to have reduced membrane fluidity. The fab1 mutant is also known to be sensitive to chilling. In the fab1 mutant the elongation of 16:0 fatty acids to 18:0 is reduced. The fad2-2 mutant has reduced 18:1 desaturase activity and hence reduced amounts of polyunsaturated phospholipids. The fad3/fad7/fad8 triple mutant is deficient in 18:2 desaturase activity and consequently unable to synthesise trienoic fatty acids. The transgenic line used contained a 35S::FAD3 transgene and in contrast to the mutants tested, should have increased lipid desaturation and increased membrane fluidity. A. thaliana ecotype Col-0 was used as the wild type control for the fab1 and fad2-2 mutants, in addition to the 35S::FAD3 line. The fad3/fad7/fad8 mutant had previously been transformed with the 35S::apoaequorin transgene and a Columbia line expressing apoaequorin under the control of the same promoter, was included to control for the presence of aequorin.
Nine day old seedlings grown in petri-dishes on MS were transferred from their growth room (20 oC, 16 h photoperiod, 100 E m-2 s-1) to a growth cabinet (20 oC, 16 h photoperiod,160 m-2 s-1) 24 hours before the experiment began. The next day, one petri-dish of seedlings from each line of plants used was transferred to a cabinet running at 5 oC (16 h photoperiod,160 E m-2 s-1). Control plates remained at 20 oC. Seedlings were harvested after three hours and frozen in liquid nitrogen.

overall_design: 12 samples were used in this experiment

first: Nicola

last: Evans


title: Co-regulated gene expression by estrogen receptor-α and liver receptor homolog-1 is a feature of the estrogen response in breast cancer cells

first: Simak

last: Ali

address: Du Cane Road

department: Department of Surgery & Cancer

summary: Estrogen receptor α (ERα) is a nuclear receptor that is the driving transcription factor expressed in the majority of breast cancers. Recent studies have demonstrated that the liver receptor homolog-1 (LRH-1), another nuclear receptor, is ERα-regulated in breast cancer cells. Further, LRH-1 stimulates proliferation and promotes motility and invasion of breast cancer cells. To determine the mechanisms of LRH-1 action in breast cancer cells, we carried out gene expression microarray analysis following siRNA-mediated LRH-1 knockdown. Interestingly, gene ontology (GO) category enrichment analysis of the genes differentially regulated in the presence or absence of LRH-1 identified estrogen responsive genes as the most highly enriched GO categories. To further define LRH-1 target genes, we performed chromatin immunoprecipitation coupled to massively parallel sequencing (ChIP-seq) to identify genomic targets of LRH-1. Remarkably, ChIP-seq showed LRH-1 binding at many ERα binding sites. Analysis of select binding sites confirmed regulation of ERα-regulated genes by LRH-1 through binding to estrogen response elements, as exemplified by the TFF1/pS2 gene. Finally, LRH-1 over-expression stimulated ERα recruitment, whilst LRH-1 knockdown reduced ERα recruitment to ERα binding sites. Taken together, our findings establish a key role for LRH-1 in the regulation of ERα target genes in breast cancer cells and identify a mechanism in which co-operative binding of LRH-1 and ERα at estrogen response elements controls the expression of estrogen-responsive genes.

overall_design: MCF-7 cells were transfected with LRH-1 siRNA #2, #3, or with a non-targeting siRNA (siControl) for 72 hours. Following assessment of RNA integrity, four biological replicates for each siRNA treatment were used for microarray analysis.

first: Chun

middle: F

last: Lai

first: Paul

last: Thiruchelvam

first: Silvia

last: Ottaviani


title: Characterizing the wound healing response that drives human epidermal maturation on transcriptome level

city: Helsinki

first: Kristo

middle: Juhana

last: Nuutila

address: Haartmaninkatu 8, Biomedicum 1

department: Institute of Biomedicine

country: Finland

institute: University of Helsinki

summary: We collected biopsies from patients undergoing split-thickness skin graft harvesting. The first biopsy was collected from the intact skin before wounding and the second and third from the donor site wound on 14th and 21st day post-operatively. A genome-wide microarray was then executed from each sample, and the gene profiles of each time point were compared.

overall_design: 12 samples from 4 patients were analyzed

first: Matti

last: Kankainen

first: Ari

last: Harjula

first: Jyrki

last: Vuola

first: Esko

last: Kankuri


title: Comparison of Genome-Wide Binding of MyoD in Normal Human Myogenic Cells and Rhabdomyosarcomas Identifies Regional and Local Suppression of Promyogenic Transcription Factors (expression)

status: Public on Aug 29 2013

city: Seattle

first: Stephen

last: Tapscott

state: WASHINGTON

address: 1100 Fairview N. Ave

department: Human Biology

institute: Fred Hutch Cancer Research Center

summary: Rhabdomyosarcoma is a pediatric tumor of skeletal muscle that expresses the myogenic basic helix-loop-helix protein MyoD but fails to undergo terminal differentiation. Prior work has determined that DNA binding by MyoD occurs in the tumor cells, but myogenic targets fail to activate. Using MyoD chromatin immunoprecipitation coupled to high-throughput sequencing and gene expression analysis in both primary human muscle cells and RD rhabdomyosarcoma cells, we demonstrate that MyoD binds in a similar genome-wide pattern in both tumor and normal cells but binds poorly at a subset of myogenic genes that fail to activate in the tumor cells. Binding differences are found both across genomic regions and locally at specific sites that are associated with binding motifs for RUNX1, MEF2C, JDP2, and NFIC. These factors are expressed at lower levels in RD cells than muscle cells and rescue myogenesis when expressed in RD cells. MEF2C is located in a genomic region that exhibits poor MyoD binding in RD cells, whereas JDP2 exhibits local DNA hypermethylation in its promoter in both RD cells and primary tumor samples. These results demonstrate that regional and local silencing of differentiation factors contributes to the differentiation defect in rhabdomyosarcomas.

overall_design: Total RNA samples were collected from primary human muscle cells (myoblasts and myotubes). Each sample has three biological replicates.

first: Kyle

last: MacQuarrie

first: Zizhen

last: Yao

first: Abraham

last: Fong

first: Scott

last: Diede

first: Erin

last: Rudzinski

first: Douglas

last: Hawkins


title: Bisphosphonate effect on murine whole draining lymph nodes before and 8 hours after VSV infection

city: Milan

first: Elena

last: Tonti

address: Via Olgettina 58

institute: San Raffaele Scientific Institute

summary: Bisphosphonates are a class of drugs that are widely used to inhibit loss of bone mass in patients. We show that the administration of clinically relevant doses of bisphosphonates in mice increases antibody responses to live and inactive viruses, proteins, haptens and existing commercial vaccine formulations. Bisphosphonates exert this adjuvant-like activity in the absence of CD4+ and γδ T cells, neutrophils or dendritic cells and their effect does not rely on local macrophage depletion nor does it depend upon Toll-like receptor signaling or the inflammasome. Rather, bisphosphonates target directly B cells and enhance B cell expansion and antibody production upon antigen encounter. These data establish bisphosphonates as a novel class of adjuvants that boost humoral immune responses.  Of note, gene-expression profile analysis shows that bisphosphonate treatment up-regulates a number of B cell-specific transcripts and gene sets associated with B cell function, suggesting that bisphosphonates might directly target B cells.

overall_design: C57Bl/6 mice received intrafoodpad injections of Clodronate (CLD, 2mg) or vehicle control (PBS) 3 and 1 day prior to infection with VSV serotype Indiana in the same footpad. Popliteal lymph nodes were harvested immediately before or 8 hours after the infection. Total RNA was extracted and prepared for hybridization on Affymetrix microarrays.

first: Nicolas

last: Chevier

first: Luca

middle: G

last: Guidotti

first: Ulrich

middle: H

last: von Andrian

first: Matteo

last: Iannacone


title: Gene expression changes resulting from the stable loss of BAP1 in uveal melanoma cell lines

city: Miami

last: Harbour

state: FL

address: 900 N.W. 17th Street

institute: University of Miami

summary: Uveal melanoma is a highly aggressive cancer with a strong propensity for metastasis, yet little is known about the biological mechanisms underlying this metastatic potential. We recently showed that most metastasizing uveal melanomas, which exhibit a class 2 gene expression profile, contain inactivating mutations in the tumor suppressor BAP1.  The aim of this study was to investigate the role of BAP1 in uveal melanoma progression.  To that end, uveal melanoma cells were studied following stable shRNA-mediated depletion of BAP1.

overall_design: RNA was isolated from three independent uveal melanoma cell lines each stably depleted using shRNA for either BAP1 or the control gene GFP.  Two biological replicates were performed for each cell line.

first: J

middle: W

first: Katie

last: Matatall

first: Michael

last: Onken


title: Effect of Alloantibody and Complement on Endothelial Cells

status: Public on Aug 28 2013

city: New Haven

first: Dan

last: Jane-wit

state: CT

address: 10 Amistad St

department: Immunobiology

institute: Yale University School of Medicine

summary:
Examine the possible pro-inflammatory gene effects of alloantibody and complement on endothelial cells
Microarray 3

overall_design: Experiment performed three times on three separate microarrays using three separate HUVEC and PRA donors. In each experiment, there are four groups of HUVEC with three replicates per group treated for 4 hours in gelatin veronal buffer containing either complement-inactivated PRA serum, vehicle (gelatin veronal buffer), PRA serum, or non-PRA serum

first: D

last: Pober


title: Gene expression in a three dimensionally cultivated human hepatocytes

city: Ilmenau

first: Uta

last: Fernekorn

department: Nano-Biosystem Technology

country: Germany

institute: Ilmenau Technical University

summary: The development of more complex but reliable systems for compound testing in a pharmaceutical context is a challenging task to date. Three dimensional (3D), organ mimetic cell culture is aiming to become an alternative to common two dimensional (2D) cell culture or animal testing in that field. We developed a biocompatible 3D cell culture environment for a 3D hepatocyte cell culture that enables cellular maintenance in a polycarbonate scaffold structure.  Our data indicate that an actively perfused three dimensional cell culture displays a more pronounced metabolic genotype than statically cultivated hepatocytes.

overall_design: Human hepatocytes of three donors were cultivated for five days under 2D and 3D statical and perfused conditions. Cultivation was started with 0.25 x106 in 2D and with 1x 106 vital cells for the 3D experiments. The day of seeding was defined as d0. The groups were classified as follows: 2D i.e.monolayer cultures,  3D i.e. statical 3D culture and BR denotes perfused 3D culture of hepatocytes. The perfusable bioreactor system was operated using a peristaltic pump. It houses the MatriGrid, a polycarbonate based microporous cellular support. For 3Dstatic cultivation, cell- inoculated MatriGrids were placed in wells of a 24 wells plate. Microarray experiments of three 2D (i.e. control), three 3D statically and three actively perfused 3D cultivations, respectively, were performed at SIRS-Lab GmbH (SIRS-Lab GmbH, Jena, Germany) according to the manufacturer’s instructions (Illumina, San Diego, CA). Altogether, 8 RNA samples of hepatocyte cultures and an internal control RNA were hybridized on two HumanHT-12 v4 Expression BeadChips.

first: Jörg

last: Hampl

first: Caroline

last: Augspurger

first: Christian

last: Hildmann

first: Frank

last: Weise

first: Maren

last: Klett

first: Annette

last: Läffert

first: Karin

last: Friedel

last: Gebinoga

first: Andreas

last: Schober


title: Genetic mapping with multiple levels of phenotypic information reveals new determinants of lymphocyte glucocorticoid sensitivity

city: Chicago

first: Joseph

middle: C

last: Maranville

state: IL

address: 920 E. 58th Street

institute: 920 E. 58th Street

summary: Clinical response to glucocorticoids (GCs), steroid hormones widely used as pharmaceuticals, varies extensively, with many patients (~30%) showing a weak response to treatment. Although little is known about the molecular basis of this variation, regulatory polymorphisms are likely to play a key role as GCs act largely through activation of a transcription factor, the GC receptor. In an effort to characterize the molecular basis of variation in GC sensitivity, we measured in vitro lymphocyte GC sensitivity (LGS) and transcriptome-wide response to GCs in peripheral blood mononuclear cells (PBMCs) from African-American healthy donors. We found that variation in LGS was correlated with transcriptional response at 27 genes (FDR<0.1). Furthermore, a genome-wide association scan revealed a quantitative trait locus (QTL) for LGS (rs11129354, P=4x10-8) that was also associated with transcriptional response at multiple genes, including many (14 of 27) where transcriptional response was correlated with LGS. Using allelic imbalance assays, we show that this QTL is a GC-dependent cis-regulatory polymorphism for RBMS3, which encodes an RNA-binding protein known as a tumor suppressor. We found that siRNA-mediated knockdown of RBMS3 expression increases cellular proliferation in PBMCs, consistent with the role of the gene as a negative regulator of proliferation. We propose that differences in LGS reflect variation in transcriptional response, which are influenced by a GC-dependent regulatory polymorphism that acts in cis relative to RBMS3 and in trans to affect the transcriptional response of multiple distant genes.

overall_design: Total RNA was obtained from paired aliquots of peripheral blood mononuclear cells treated with dexamethasone and phytohemagglutinin, vehicle (EtOH) and phytohemagglutinin, or blank (no treatment) for 6 hours.

first: Shaneen

last: Baxter

first: David

middle: B

last: Witonsky

first: Meredith

last: Chase

first: Anna

last: Di Rienzo


title: LHX2 in neural differentiation from hESCs H9

city: Taipei

first: pei-shan

last: Hou

address: No. 155, Sec. 2, Linong St., Beitou dist.

country: Taiwan

institute: Institute of Anatomy and Cell Biology, School of Medicine, National Yang-Ming Chiao-Tung University.

summary: In order to explore the role of LHX2 in neural fate determination, we performed knockdown and overexpression studies in H9.

overall_design:
--doxycycline induced LHX2 overexpression in H9--
GFP as a control
3 days doxycyline treatment was performed
samples was collected 1 day (Day4) and 13 days (Day16) post doxycyline treatment

--shLHX2 in H9--
shLuc as a control
samples were collected 12 days of neural induction

all samples were biological duplicate

first: Pei-Shan

first: Hung-Chih

last: Kuo

first: Chung-Liang

last: Chien


title: Current injection and distal wound response in Arabidopsis thaliana

status: Public on Aug 21 2013

city: Lausanne

first: Seyed

middle: Ali Reza

last: Mousavi

state: Vaud

address: Route de Sorge

department: DBMV

country: Switzerland

institute: University of Lausanne

summary: These data represent two experiments, one on wounding leaves and one based on injecting current into leaves. We first analyzed transcript levels in leaf 13 when leaf 8 was wounded. Transcripts levels in leaf 8 were then analyzed after current injection. Sample handling and normalisations were identical between experiments.

overall_design: Leaf 8 was wounded with forceps. 1 h later, leaf 13 was harvested. Unwounded leaf 13 was used for controls. For current injected (40 μA, 10 s) versus non-current injected leaves, samples were harvested 1h after current injection. Non-current injected leaves used as control. In each case leaf 8 was used.

middle: A

first: Adeline

last: Chauvin

first: Francois

last: Pascaud

first: Stephan

last: Kellenberger

first: Edward

middle: E

last: Farmer


title: Comparison of cellular and transcriptional responses to 1,25-dihydroxyvitamin D3 and glucocorticoids in peripheral blood mononuclear cells

summary: Glucocorticoids (GC) and 1,25-dihydroxyvitamin D3 (1,25(OH)2 D3) are steroid hormones with anti-inflammatory properties with enhanced effects when combined. We previously showed that transcriptional response to GCs was correlated with inter-individual and inter-ethnic cellular response. Here, we profiled cellular and transcriptional responses to 1,25(OH)2 D3 from the same donors. We studied cellular response to combined treatment with GCs and 1,25(OH)2 D3 in a subset of individuals least responsive to GCs. We found that combination treatment had significantly greater inhibition of proliferation than with either steroid hormone alone. Overlapping differentially expressed (DE) genes between the two hormones were enriched for adaptive and innate immune processes. Non-overlapping differentially expressed genes with 1,25(OH)2 D3 treatment were enriched for pathways involving the electron transport chain, while with GC treatment, non-overlapping genes were enriched for RNA-related processes. These results suggest that 1,25(OH)2 D3 enhances GC anti-inflammatory properties through a number of shared and non-shared transcriptionally-mediated pathways.

overall_design: Total RNA was obtained from aliquots of peripheral blood mononuclear cells treated with 1,25-dihydroxyvitamin D3 (1,25(OH)2 D3) for 8 and 24 hours. These data were analyzed together with previously published data from expression analysis of PBMC aliquots collected in parallel to these and treated with dexamethasone or vehicle (EtOH).

first: Sonia

last: Kupfer

first: Yong

last: Huang


title: Dynamic expression profiling of type I and type III interferon-stimulated hepatocytes.

status: Public on Aug 22 2013

first: Christopher

last: Bolen

address: 300 George Street, Suite 505

department: Pathology

institute: Yale University

summary:
This dataset details the time-dependent response of human Huh7 hepatoma cells to type I and type III IFN.
Despite activating similar signaling cascades, the type I and type III interferons (IFNs) differ in their ability to antagonize viral replication. However, it is not clear whether these cytokines induce unique antiviral states, particularly in the liver, where the clinically important hepatitis B and C viruses cause persistent infection. Here, microarray-based gene expression analysis is combined with mechanistic studies of signaling pathways to dynamically characterize the transcriptional responses induced by these cytokines in Huh7 hepatoma cells and primary human hepatocytes. Type I and III IFNs differed greatly in their level of interferon-stimulated gene (ISG) induction with a clearly detectable hierarchy (IFN-β > IFN-α > IFN-λ3 > IFN-λ1 > IFN-λ2). This hierarchy resulted in widely varying numbers of differentially expressed genes when quantified using common statistical thresholds, even though individual IFNs did not appear to regulate unique sets of genes. The kinetic profiles of IFN-induced gene expression were also qualitatively similar with the important exception of IFN-α. While stimulation with either IFN-β or IFN-λs resulted in a similar long-lasting ISG induction, IFN-α signaling peaked early after stimulation then declined due to a negative feedback mechanism. The quantitative expression hierarchy and unique kinetics of IFN-α suggest different roles for individual IFNs in the immune response, and help explain previously observed differences in antiviral activity.

overall_design: Huh7 cells were seeded into 6-well plates at the density of 3x10^5 cells/well and cultured overnight before stimulation with either 500 U/ml of IFN-α or IFN-β, or 10 ng/ml of IFN-λ1, IFN-λ2, or IFN-λ3. Total RNA was harvested and isolated at 0.5, 1, 2, 4, 6, 12 and 24 hours post-incubation using RNeasy Mini Kit (Qiagen) following the Affymetrix GeneChip protocol of the Keck Affymetrix Resource facility at Yale University. IFN incubation at each time point was performed in duplicate. All subsequent processing, hybridization to the Illumina HumanHT-12 microarray, and quality control analyses were carried out by the Yale Center for Genome Analysis using standard protocols.

first: Siyuan

last: Ding

first: Michael

middle: D

last: Robek

first: Steven

last: Kleinstein


title: Foam cell specific LXRα ligand

city: Berlin

last: Weidner

address: Ihnestraße 63

department: Otto Warburg Laboratory

institute: Max Planck-Institute for Molecular Genetics

summary:
OBJECTIVE:
The liver X receptor α (LXRα) is a ligand-dependent nuclear receptor and the major regulator of reverse cholesterol transport in macrophages. This makes it an interesting target for mechanistic study and treatment of atherosclerosis.
METHODS AND RESULTS:
We optimized a promising stilbenoid structure (STX4) in order to reach nanomolar effective concentrations in LXRα reporter-gene assays. STX4 displayed the unique property to activate LXRα effectively but not its subtype LXRβ. The potential of STX4 to increase transcriptional activity as an LXRα ligand was tested with gene expression analyses in THP1-derived human macrophages and oxLDL-loaded human foam cells. Only in foam cells but not in macrophage cells STX4 treatment showed athero-protective effects with similar potency as the synthetic LXR ligand T0901317 (T09). Surprisingly, combinatorial treatment with STX4 and T09 resulted in an additive effect on reporter-gene activation and target gene expression. In physiological tests the cellular content of total and esterified cholesterol was significantly reduced by STX4 without the undesirable increase in triglyceride levels as observed for T09.
CONCLUSIONS:
STX4 is a new LXRα-ligand to study transcriptional regulation of anti-atherogenic processes in cell or ex vivo models, and provides a promising lead structure for pharmaceutical development.

overall_design:
2 treatment groups (STX4 vs. DMSO in foam cells), 3 biological replicates per treatment (6 samples in total), each representing one well from cell culture plate
2 treatment groups (STX4 vs. DMSO in macrophages), 4 biological replicates per treatment (8 samples in total), each representing one well from cell culture plate
2 treatment groups (T0901317 vs. DMSO in foam cells), 3-4 biological replicates per treatment (7 samples in total), each representing one well from cell culture plate
2 treatment groups (T0901317 vs. DMSO in macrophages), 4 biological replicates per treatment (8 samples in total), each representing one well from cell culture plate

first: Radmila

last: Feldmann

first: Anne

last: Geikowski


title: Lost miRNA surveillance of NOTCH, IGFR pathway-road to sarcomagenesis [Illumina]

city: Silver Spring

first: BIJU

last: ISSAC

state: MD

address: 503 Robert Grant Ave, Rm 2W123

department: Military HIV Research Program

institute: Walter Reed Army Institute of Research

summary: The goal of this study was comparative analysis of differentially expressed miRNA and their targets in human chondrosarcoma JJ012 and chondrocytes C28 cell line(control) to elucidate the major signal transduction pathways deregulation in sarcomagenesis. Total RNA extraction was followed by the analysis of RNA quality and integrity, Exiqon human miRNA panel of 743 unique miRNA assays, Illumina microarray HT12 platform and qRT-PCR verification of targets were performed.189 downregulated and 147 upregulated miRNAs were detected when comparing chondrosarcoma cell line to control C 28 chondrocytes cell line using human Exiqon arrays with biological triplicates.3045 target genes in total were detected woth 587 common and 2458 unique target genes between upand downregulated miRNAs. The upregulated miRNAs were linked to the promotion of aggressive phenotype and the majority of the downregulated miRNAs were oncosuppressors. Among upregulated targtes for upregulated miRNAS were the cluster of cancer testis antigen (CTA) genes, located on X chromosome the major signal transduction pathways leading to sarcomagenesis.

overall_design: compare in triplicates the miRNA expression profile with Exiqon, followed by Illumina microarrays for target mRNA expression  validation between  human JJ012 chondrosarcoma cell l ine and C28 control chondrocytes

first: Karina

last: Galoian

first: Toumy

last: Guettouche

first: Biju

last: Issac

first: Loida

last: Navarro

first: H

middle: T

last: Temple


title: Adult human brain stem cells 4

status: Public on Aug 19 2013

city: Oslo

first: Wayne

middle: George

last: Murrell

address: Sognsvannsveien 20

department: Institute for Surgical Research

country: Norway

institute: Oslo University Hospital

summary: Tissue repair using cell transplantation holds popular appeal. This underlines the need to understand stem cells within the target organ. Our laboratory works on the human brain. Using neurosphere methods, we and others have only been able to passage stem/progenitors a very few times with little expansion of numbers. Now we describe an efficient method for the establishment and propagation of human brain stem cells from whatever tissue samples we have tried. We describe virtually unlimited expansion of an authentic stem cell phenotype. Pluripotency markers Sox2 and Oct4 are expressed without artificial induction. For the first time, multipotency of adult human brain-derived stem cells is demonstrated beyond tissue boundaries. We characterize these cells in detail in vitro including microarray and proteomic approaches. Whilst clarification of these cells' behavior is ongoing, results so far portend well for the future repair of tissues by transplantation of an adult patient's own-derived stem cells.

overall_design:
Adult human brain stem cells from the subventricular zone, hippocampus, grey matter and white matter.
Total RNA from five adult human brain biopsy sources: 3 subventricular-derived cell lines, 3 hippocampus-derived cell lines, 3 grey matter-derived cell lines and 3 white matter-derived cell lines.

first: Emily

last: Pelmero


title: Adult human brain stem cells 3

overall_design:
Brain stem cells and glioblastoma stem cells: adherent compared to sphere culture.
Total RNA from three adult human brain biopsy sources and three brain tumour samples. Derived stem cell lines were grown as spheres and adherently. Comparison of cells under these culture conditions.


title: SLIT3-ROBO4 Activation Promotes Vascular Network Formation in Human Engineered Tissue and Angiogenesis in Vivo

status: Public on Aug 18 2013

first: Kareen

middle: L

last: Kreutziger

state: WA

address: 850 Republican Street

institute: University of Washington

summary: Successful implantation and long-term survival of engineered tissue grafts hinges on adequate vascularization of the implant. Endothelial cells are essential for patterning vascular structures, but they require supportive mural cells such as pericytes/mesenchymal stem cells (MSCs) to generate stable, functional blood vessels.1-5 While there is evidence that the angiogenic effect of MSCs is mediated via the secretion of paracrine signals,6,7 the identity of these signals is unknown.  Here, by utilizing two functionally distinct human MSC clones, we found that so-called “pericytic” MSCs secrete the pro-angiogenic neurovascular guidance molecule SLIT3,8 which guides vascular development by directing ROBO4-positive endothelial cells to form networks in engineered tissue. In contrast, “non-pericytic” MSCs exhibit reduced activation of the SLIT3/ROBO4 pathway and do not support vascular networks.  Using live cell imaging of organizing 3D vascular networks, we show that knockdown of SLIT3 in MSCs leads to disorganized clustering of ECs, and knockdown of its receptor ROBO4 in ECs abolishes the generation of functional human blood vessels in an in vivo xenogenic implant. These data suggest that the SLIT3/ROBO4 pathway regulates MSC-guided vascularization in engineered tissues. Heterogeneity of SLIT3 expression may underlie the variable clinical success of MSCs for tissue repair applications.

overall_design: 4 samples with 2 replicates each

first: David

last: Smith

first: Charles

last: Murry


title: Cancers originate preferentially in adult tissue stem cells

city: Memphis

last: Finkelstein

address: 332 N. Lauderdale St.

department: Computational Biology

institute: St Jude Children's Research Hospital

summary: Stem cells have long been regarded as a potential origin of cancer.  But cancers could also arise from mutated, differentiated cells that reacquire stem cell properties.  Here, in mice harboring conditional oncogenic and lineage tracing alleles, we show that cancers develop from Prom1+ (CD133) cells, only in organs where these cells operate as stem cells.  Allograft assays demonstrated that these cancers are not necessarily propagated by Prom1+ cancer stem cells, even when initiated in Prom1-lineages that maintain the normal organ.  Normal and transformed Prom1+ stem cells in our mice, maintained the gastric mucosa and gastric adenocarcinomas, respectively.  Comparison of these cells identified the latent sodium channel gene Nalcn as a novel gastric cancer suppressor that regulates the differentiation of stomach stem cell daughters.  Our data provide new evidence that cancers are initiated preferentially within stem cells, and important insights into how these cells are deregulated to initiate and maintain cancers

overall_design: Prom1 conditional mutants in mice that develped tumors and normal from cells various tissues in mice are compared.  117 samples were studied.

first: Liqin

last: Zhu

first: Helen

last: Poppleton

first: Jay

last: Blundon

first: Stanislav

last: Zakharenko

first: Kirti

last: Gupta

first: Amy

last: Funk

first: Mohankumar

last: Murugesan

first: Cuilan

last: Gao

last: Wang

first: Spencer

last: Currle

first: Elisie

last: White

first: Stanley

last: Pounds

first: Geoffrey

last: Neale

first: Lei

last: Shi

last: Lu

first: Cyriac

last: Kandoth

first: Li

last: Ding

first: Jinghui

last: Zhang

last: Ellison

first: Arzu

last: Onar-Thomas

first: Richard

last: Gilbertson


title: Axl mediates acquired resistance of head and neck cancer cells to the epidermal growth factor receptor inhibitor erlotinib

status: Public on Aug 10 2013

city: Nedlands

first: Patrick

middle: Aaron

last: Candy

state: Western Australia

address: 6 Verdun St

department: Cancer Medicine

country: Australia

institute: Perkins Institute

summary: Elevated expression and activity of the epidermal growth factor receptor (EGFR) is associated with development and progression of head and neck cancer (HNC) and a poor prognosis. Clinical trials with EGFR tyrosine kinase inhibitors (TKIs; eg. erlotinib) have been disappointing in HNC. To investigate the mechanisms mediating resistance to these agents, we developed a HNC cell line (HN5-ER) with acquired erlotinib resistance. In contrast to parental HN5 HNC cells, HN5-ER cells exhibited an epithelial-mesenchymal (EMT) phenotype with increased migratory potential, reduced E-cadherin and epithelial-associated miRNAs, and elevated vimentin expression. Phosphorylated RTK profiling identified Axl activation in HN5-ER cells. Growth and migration of HN5-ER cells was blocked with a specific Axl inhibitor, R428, and R428 re-sensitized HN5-ER cells to erlotinib. Microarray analysis of HN5-ER cells confirmed the EMT phenotype associated with acquired erlotinib resistance, and identified activation of gene expression associated with cell migration and inflammation pathways. Moreover, increased expression and secretion of interleukin (IL)-6 and IL-8 in HN5-ER cells suggested a role for inflammatory cytokine signaling in EMT and erlotinib resistance. Expression of the tumor suppressor miR-34a was reduced in HN5-ER cells and increasing its expression abrogated Axl expression and reversed erlotinib resistance. Finally, analysis of 302 HNC patients revealed that high tumor Axl mRNA expression was associated with poorer survival (HR 1.66, p=0.007). In summary, our results identify Axl as a key mediator of acquired erlotinib resistance in HNC and suggest that therapeutic inhibition of Axl by small molecule drugs or specific miRNAs might overcome anti-EGFR therapy resistance.

overall_design: Differential gene expression between parental and acquired erlotinib resistant head and neck cancer cell lines of HN5.


title: Gene expression study in Neuroblastoma after BET inhibition

status: Public on Aug 23 2013

city: Collegeville

first: Gopinath

last: Ganji

state: PA

address: 1250 South Collegeville Road

institute: GSK

summary: We studied transcriptional changes by Illumina HumanHT-12 v4 microarrays in 2 Neuroblastoma cell lines after i-BET-726 treatment

overall_design: 2 neuroblastoma cell lines SK-N-SH and CHP-212 were treated with i-BET-726 at 100nM or 1uM concentrations for 16 hrs to study gene expression.

first: Caretha

last: Creasy

first: Anastasia

last: Wyce


title: Lost miRNA surveillance of NOTCH, IGFR pathway-road to sarcomagenesis

first: BIJU

last: ISSAC

type:
Expression profiling by array
Other

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

overall_design: Refer to individual Series


title: S100P is a metastasis-associated gene that facilitates transendothelial migration of pancreatic cancer cells [HG-U133B]

status: Public on Aug 15 2013

city: London

first: Claude

last: Chelala

state: London

address: Charterhouse square

department: Institute of Cancer

institute: Barts & The London School of Medicine (QMUL)

summary:
Pancreatic cancer is a devastating disease with both local invasion and distant metastasis. Identifying the genes expressed in liver metastases and signatures of metastatic progression would therefore be of particular importance as they could aid in both recurrence prediction as well as representing novel therapeutic targets.

Keywords: Gene expression profiling

overall_design: We have performed microarray gene expression analysis of normal pancreas, primary pancreatic ductal adenocarcinoma (PDAC), normal liver and pancreatic liver metastases to identify potential therapeutic targets.

first: Sayka

last: Barry

first: Tatjana

last: Crnogorac-Jurcevic


title: HT-29 cells treated with IFN-γ

status: Public on Aug 06 2013

city: Charlottesville

first: Byong

middle: Ha

last: Kang

state: VA

address: 415 Lane Road, MR5-Rm. 2225

department: Department of Biomedical Engineering

institute: University of Virginia

summary: Expression data from HT-29 human colon adenocarcinoma cells treated with IFN-γ for 24 hr

overall_design: Total RNA was isolated from HT-29 cells after 24h stimulation with 200 U ml-1 IFN-γ (Roche). The experiment was done on three biological replicates.

first: Karin

middle: J

last: Jensen

first: Jaime

last: Hatch

first: Kevin

last: Janes


title: Cell type-specific auxin responses in the Arabidopsis thaliana root

city: La Jolla

first: Bastiaan

middle: Otto Robert

last: Bargmann

address: 9500 Gilman Dr

institute: UCSD

summary: We performed an analysis of transcriptomic responses to auxin within four distinct tissues of the Arabidopsis thaliana root. This high-resolution dataset shows how different cell types are predisposed to react to auxin with discrete transcriptional responses. The sensitivity provided by the analysis lies in the ability to detect cell-type specific responses diluted in organ-level analyses. This dataset provides a novel resource to examine how auxin, a widespread signal in plant development, influences differentiation and patterning in the plant through tissue-specific transcriptional regulation.

overall_design: To analyze the effect of auxin in separate spatial domains of the root, early transcriptional changes in response to auxin treatment were assayed by means of fluorescence activated cell sorting (FACS) and microarray analysis in four tissues of the Arabidopsis root (wild type Col-0). The samples covered inner and outer as well as proximal and distal cell populations; including the stele (reporter line pWOL::GFP), xylem-pole (xp) pericycle (enhancer trap line E3754), epidermis/lateral root cap (reporter line pWER::GFP) and columella (enhancer trap line PET111). One-week-old seedlings of the individual lines were treated with auxin (two hours, 5µM indole-3-acetic acid [IAA]) or mock treated, after which roots were harvested and cells were dissociated by cell wall digestion (1 hour; including 5uM IAA) . GFP-positive cells were sorted and used for microarray transcriptome analysis (as in Bargmann and Birnbaum, Plant Phys. 2010). For comparison, transcriptional responses to auxin were also assayed in intact (undigested) roots.

middle: O

first: Kenneth

last: Birnbaum


title: Regulation of Gene Expression by Connective Tissue Growth Factor (CTGF) in Mesenchymal Stromal Cells (MSCs)

status: Public on Aug 05 2013

city: Houston

first: Wencai

last: Ma

address: 7455 Fannin st

institute: MD Anderson Cancer Center

summary: mRNA from bone marrow-derived MSCs stably expressing CTGF-specific shRNA (or empty vector control) was analyzed for differential gene expression. Significant differences were found in cell proliferation-related genes, especially genes related to the M phase of the cell cycle, which were down-regulated in CTGF-knockdown-MSCs compared to control MSCs.

overall_design: Bone marrow-derived MSCs were stably transduced with lentivirus expressing CTGF-specific shRNA or an empty vector control. After antibiotic selection, total RNA was amplified and hybridized to Illumina HT12 version 3 human whole-genome arrays (Illumina, San Diego, CA).

first: V

last: Battula

first: Zhiqiang

last: Wang

first: R

last: Davis

first: Michael

last: Andreeff


title: Characterization of Transcription Factor Networks Involved in Umbilical Cord Blood CD34+ Stem Cells-Derived Erythropoiesis

status: Public on Aug 02 2013

city: Augusta

first: Biaoru

last: Li

state: GA

department: Pediatrics

institute: MCG

summary: The characteristics of global gene expression patterns during umbilical cord blood (UCB)-CD34+ stem cell-derived erythropoiesis are not clearly elucidated. In this study, UCB-stem cells were grown in liquid culture as a model for this process. We observed a high proliferative capacity of UCB-stem cells producing over 10 billion viable cells in culture. Normal erythroid maturation was confirmed by increased expression of CD71 and CD235a biomarkers. Furthermore, the gamma- to beta-globin gene switch was observed around day 45 indicating extended gamma-globin gene expression in fetal erythroid cells. To study global gene expression patterns, microarray analysis was performed on days 21, 42, 49 and 56. Forty-five transcription factors were silenced during the culture period (Profile-1) including CUX1 and HES5 among others. Conversely, 30 transcription factors were activated by day 56 (Profile-2) such as KLF1, GATA1, and MAFB. Both datasets were analyzed further using the MIMI Cytoscape platform which defined transcription factor networks around KLF4 and GATA2 from Profile-1 genes and KLF1 and GATA1 for Profile-2 genes. The characteristics of UCB-CD34+ stem cells including high proliferative capacity and prolonged gamma-globin expression combined with novel transcription factor networks suggest novel mechanisms of fetal UCB-stem cell-derived erythropoiesis.

overall_design: Cd34 cell from umbilical cord blood were grown in three independent cultures using the one-phase protocol. Cells were cultured in aMEM containing 30% fetal bovine serum, 1% deionized BSA with penicillin (100 U/mL) and streptomycin (0.1 mg/mL) at 37°C and 5% CO2. The following growth factors were added on day 0: stem cell factor (50 ng/mL), interleukin-3 (10 ng/mL) and erythropoietin (4 U/mL).  Approximately 1.5 million cells were harvested from each culture (triplicate samples) on day 21, 42, 49 and 56 for microarray analysis on the whole-genome Illumina HumanWG-12 V4 Expression BeadChip.

first: Betty

middle: S

last: Pace

first: Kang

last: Baolin

first: Liu

last: Story

first: Lianghao

last: Ding

first: Yang

last: Chinrang


title: Expression data from Arabidopsis thaliana seedlings

city: Buenos Aires

first: Marcelo

last: Yanovsky

state: Ciudad Autonoma de Buenos Aires

address: Av. Patricias Argentinas 435

country: Argentina

institute: Fundación Instituto Leloir. IIBBA- CONICET

summary:
Light pulses at the end of the day or night be able to control the phase of the circadian clock. Pulses in the middle of the night has not effect on the circadian oscilations.
To understand how the circadian clock gate the light signal in the middle of the night we used microarrays to characterize the light effect in the whole expression profile.

overall_design:
Plants of Arabidopsis thalina (Columbia ecotype) were grown in 12/12 light/dark cicles for 15 days and then were tranfer to continuous dark .
Plants were slplit in two groups. First group recieved 1hr light pulse in the middle of the night (Night treatment), second group recieve 1hr light pulse in the middle of the subjective day (Day Treatment).
Samples of both groups were collected without light pulse named as a control.

first: Matias

last: Rugnone


title: Gene Expression Profile of 53 human T-ALL samples collected in human clinical trial E2993 (Marks et al., 2009)

city: New York

first: Alberto

last: Ambesi-Impiombato

state: NY

address: 1130 St. Nicholas Avenue

department: ICG

institute: Columbia University

summary: To analyze the prognostic relevance of transcriptional profiling in adult T-ALL, we analyzed a clinical series of 53 primary leukemia samples uniformly treated according to the ECOG E2993 protocol using gene expression oligonucleotide microarrays. Unsupervised analysis and consensus clustering of microarray gene expression data in this series revealed the presence of 2 stable gene expression clusters corresponding to early immature (n = 28) and cortical/mature (n = 25) adult T-ALLs respectively. Early immature T-ALLs show a gene expression signature related to hematopoietic stem cells and myeloid progenitors that was recently linked to a group of childhood T-ALLs with poor prognosis. Notably, univariate analysis in our patient series confirmed that early immature adult T-ALL is associated with poor prognosis and reduced overall survival compared with cortical/mature adult T-ALL (P = 0.0197)

overall_design: 53 adult T-ALL samples were analyzed

first: Pieter

last: Van Vlierberghe

first: Isaura

last: Rigo

last: Hadler

first: Elisabeth

last: Paietta

first: Peter

middle: H

last: Wiernik

first: Jacob

middle: M

last: Rowe

first: Montserrat

last: Rue

first: Adolfo

last: Ferrando


title: The effect of cell subset isolation method on gene expression in leukocytes.

status: Public on Aug 20 2013

first: Nadejda

middle: S.

last: Beliakova-Bethell

address: 9500 Gilman Dr.

department: Medicine

institute: University of California, San Diego

summary:
Analysis of the effect of isolation methods (fluorescence activated cell sorting (FACS), positive and negative immunomagnetic selection) on gene expression in human primary CD4+, CD8+ T cells, B cells and monocytes.
FACS incurs the least short-term changes in gene expression signature.

overall_design: This study evaluated the short-term effects on gene expression in four leukocyte subsets (CD4+, CD8+ T cells, B cells and monocytes) of the three commonly used isolation methods (FACS, positive and negative selection) in order to identify the optimal method for cell isolation for gene expression studies in patient samples where gene expression pertaining to a disease state or treatment is of interest and gene expression caused by cell handing is minimized.

first: Marta

last: Massanella

first: Christopher

last: Woelk


title: Expression data from fibroblasts cultured from normal and fibrotic human lung tissue

first: Carmel

last: Stock

address: 1b Manresa Road

department: Interstitial Lung Disease

institute: National Heart and Lung Institute

summary:
Pulmonary fibrosis develops as a consequence of environmentally induced lung injury and/or an inherent disease susceptibility causing fibroblast activation, proliferation and extracellular matrix deposition.
The study was undertaken to characterise global gene expression in pulmonary fibroblasts to better understand the mechanisms underlying the fibrotic fibroblast phenotype.

overall_design: Gene expression was evaluated in lung fibroblasts derived from ten controls (normal periphery of resected tumor), open lung biopsies from eight patients with interstitial lung disease associated with systemic sclerosis (fibrotic non specific interstitial pneumonia pattern on biopsy), and from three patients with usual interstitial pneumonia. Lung fibroblasts were grown to confluence in DMEM with 10% fetal calf serum. At confluence, lung fibroblasts were serum-deprived for 44 hours in the presence of fibroblast growth medium with the addition of 0.1% bovine serum albumin (Sigma).

first: Gisela

last: Lindahl

first: Xu

last: Shi-Wen

first: Andrew

middle: G

last: Nicholson

first: Michael

last: Dusmet

first: George

last: Bou-Gharios

first: David

last: Abraham

middle: P

last: Denton

first: Athol

middle: U

last: Wells

first: Elisabetta

last: Renzoni


title: RMST associates with SOX2 to regulate neurogenesis [Illumina expression data]

status: Public on Aug 01 2013

city: Cambridge

first: Shi Yan

last: Ng

state: MA

address: 7 Divinity Ave

institute: Harvard University

summary:
We report that knockdown of the lncRNA RMST changes the gene expression profile of neural stem cells.
RMST and SOX2 regulates a common subset of downstream targets.

overall_design: Examination of genome wide transcriptomic changes upon knockdown of the lncRNA RMST.

first: Shi-Yan

first: Lawrence

last: Stanton


title: Genome-wide analysis of gene expression in bladder cancer cell lines 253JB-V and UM-UC13 exposed to bortezomib

first: wei

last: Qi

state: TX

address: 7777 Knight Rd.

institute: UT MD Anderson Cancer Center

summary: We previously showed that the proteasome inhibitor bortezomib (Velcade) induces cell death in a subset of human bladder cancer cell lines. Heat shock protein 72 kDa (Hsp72) is the major cytosolic stress-inducible molecular chaperone, and is thought to protect cells from proteasome inhibition. Here, using whole genome mRNA expression profiling, we identify isoform-specific expression of Hsp72 within a heterogeneous panel of bladder cancer cell lines.  Bortezomib induced strong upregulation of both the HSPA1A and HSPA1B isoforms of Hsp72 in 253J B-V and SW780 (HSPA1A-high) cells, whereas only HSPA1B isoform expression was induced in UM-UC10 and UM-UC13 (HSPA1A-low) cells.  Bortezomib stimulated the binding of heat shock factor-1 (HSF1) to the HSPA1A promoter much more efficiently in 253JB-V cells than in UM-UC13, but other HSF1 transcriptional targets were induced in all of the cell lines, implicating a specific defect in HSPA1A induction.  Methylation-specific PCR revealed that the HSPA1A promoter was selectively methylated in the HSPA1A-low cell lines (UM-UC10 and UM-UC13), and exposure to the chromatin demethylating agent 5-aza-2'-deoxycytidine restored HSPA1A expression. Overexpression of Hsp72 promoted bortezomib resistance in the UM-UC10 and UM-UC13 cells, whereas transient knockdown of HSPA1B sensitized these cells to bortezomib.  Exposure to the chemical HSF1 inhibitor KNK-437 promoted bortezomib sensitivity in the 253J B-V cells.  Finally, shRNA-mediated stable knockdown of Hsp72 in 253J B-V promoted sensitivity to bortezomib both in vitro and in vivo.  Together, our results suggest that a subset of human bladder cancer cells possess epigenetic modifications that shut off the HSPA1A promoter and increases dependency on the HSPA1B isoform to maintain Hsp72 expression. Our data also support the targeting of HSF1 or Hsp72 for use as tools to enhance bortezomib sensitivity in solid tumors.

overall_design: RNA was isolated from cells using the TRIzol Reagent (Invitrogen/ Life Technologies, Grand Island, NY), followed by cleanup with RNeasy Mini kits (Qiagen, Germantown, MD). RNA was used for the synthesis of biotin-labeled cRNA, which was prepared using the Illumina RNA amplification kit (Ambion/ Life Technologies), and then hybridized to Illumina Human-HT12 (Illumina, Inc., Hayward, CA) chips. Washed chips were scanned with BeadStation 500x (Illumina) and the signal intensities quantified with BeadStudio (Illumina).

first: Wei

last: McConkey

first: Arlene

last: Siefker-Radtke


title: Genome wide analysis of differential gene expression of PFKFB3 under- or overexpression upon inhibition or activation of notch signaling in endothelial cells

city: Leuven

first: Bert

last: Cruys

address: Herestraat 49

country: Belgium

institute: Vesalius Research Center

summary: Analysis of gene expression profiles upon PFKFB3 under- or overexpression during inhibition or activation of notch signaling. With this experiment we aimed to identify whether alterations in PFKFB3 could influence the expression pattern of angiogenic genes in conditions that favor a tip- or stalk cell gene signature.

overall_design: Total RNA was collected of human umbilical vein endothelial cells either under- or overexpressing PFKFB3 and/ or have inhibited or activated notch signaling respectively. Cells were harvested 48h after manipulation of PFKFB3 and notch levels.

first: Peter

last: Carmeliet


title: Identification of p130Cas/ErbB2 dependent invasive signatures in transformed mammary epithelial cells.

city: Turin

first: antonio

last: lembo

state: Turin

address: Via Nizza, 52

department: Dept. of Genetics, Biology and Biochemistry

institute: University of Turin

summary: Understanding transcriptional changes during cancer progression is of crucial importance to develop new and more efficacious diagnostic and therapeutic approaches. It is well known that ErbB2 is over-expressed in about 25% of human invasive breast cancers. We have previously demonstrated that p130Cas over-expression synergizes with ErbB2 in mammary cell transformation and promotes ErbB2-dependent invasion in three-dimensional (3D) cultures of human mammary epithelial cells.  Here, by comparing coding and non-coding gene expression profiling, we define the invasive signatures associated with concomitant p130Cas over-expression and ErbB2 activation in 3D cultures of mammary epithelial cells. Specifically, we have found that genes involved in amminoacids synthesis (CBS and PHGDH), cell motility, migration (ITPKA, PRDM1), and angiogenesis (HEY1) are up-regulated while genes involved in the inflammatory response (SAA1, S100A7) are down-regulated. In parallel, we have shown that the expression of specific miRNAs is altered. Among these, mir-200b, miR-222, miR-221and miR-424 are up-regulated while miR-27a, miR-27b and miR-23b are down-regulated. Overall this study present, for the first time, gene expression changes underlying the invasive behaviour following p130Cas over-expression in an ErbB2 transformed mammary cell model.

overall_design: 12 samples were analyzed: 3 ErbB2, 3 Cas, 3 Cas/ErbB2, 3 Ctr MCF10A.B2

first: Enzo

last: Medico

first: Sara

last: Cabodi


title: Combinatorial treatment of DNMT inhibitor and LSD1 inhibitor results in cell growth inhibition and reexpression of epigenetically silenced genes (gene expression)

city: Los Angeles

first: Xiaojing

last: Yang

state: CA

address: 1441 Eastlake Ave, Room 7336

institute: USC/Norris Comprehensive Cancer Center

summary: A combinatorial treatment consisting of a DNMTi and a LSD1i shows synergistic effects in reactivating aberrantly silenced genes by enriching H3K4me2 and H3K4me.

overall_design: 24 Samples consisting of 3 cell lines hybridised to the Illumina HumanHT-12 V4.0 Beadchip.

first: Han

last: Han


title: miR-18a modulates gene transcription in breast cancer cells treated with Cobalt(II) chloride

status: Public on Jul 31 2013

first: Meiyun

last: Fan

address: 19 S. Manassas Street

institute: University of Tennessee

summary: Using the orthotopic breast cancer xenograft model of basal-like breast cancer MDA-MB-231 line, we have found that the expression of miRNAs encoded by MIR17HG was significantly decreased in cells isolated from spontaneous lung metastases compared to cells from primary tumors grown in orthotopic sites. We investigated the role of a MIR17HG family member, miR-18a, in primary tumor growth and pulmonary metastasis from the orthotopic site. We demonstrated that enforced expression of exogenous miR-18a, significantly limited continuous growth of primary tumors in mammary gland fat pads and reduced spontaneous lung metastasis. Further investigation on the mechanism of miR-18a action led to the finding that the expression of HIF1A, a key regulator of tumor metastasis, was regulated by miR-18a. Enforced miR-18a expression significantly decreased HIF1A expression at both mRNA and protein levels, resulting in altered transcriptional response and decreased survival of cells in response to Cobalt(II) chloride (CoCl2), a hypoxia-mimicking agent. Conversely, miR-18a knockdown significantly increased HIF1A expression levels and enhanced cell survival in response to CoCl2. Analysis of expression data of human breast tumor tissues showed that miR-18a expression is inversely correlated with HIF1A expression in basal-like breast tumors, supporting a role of miR-18a in restricting HIF1A expression in this subtype of breast cancer. In addition, we demonstrated that hypoxia inhibits miR-18a expression, likely through MYC inactivation. Furthermore, gene expression and functional analysis revealed that miR-18a also plays a role in regulating cell adhesion, migration and invasion. Taken together, this study provides evidence for a novel role of miR-18a to inhibit breast cancer metastasis. Our results suggest that miR-18a downregulation might provide tumor cells survival/growth advantage under hypoxic pressure in basal-like breast cancer.

overall_design: A lung metastatic subline,  designated as MB231RN-LM, was derived from MDA-MB-231 breast cancer cells through in vivo selection. The MB231RN-LM cells were stably transfected with has-miR-18a or control vector and treated with 200uM Cobalt(II) chloride (CoCl2, a hypoxia-mimicking agent) for 4 hr.   A total of 8 samples were subjected to microarray analysis, with two biological repeats for each experiment condition.

first: Raisa

last: Krutilina

first: Wenlin

last: Sun

first: Tiffany

middle: N

last: Seagroves

last: Pfeffer

first: Tatyana

last: Ignatova


title: Gene expression profiles for paediatric brain tumours

status: Public on Jul 29 2013

first: Denise

last: Sheer

address: Blizard Institute, 4 Newark Street

department: Neuroscience & Trauma

institute: Barts & The London School of Medicine & Dentistry

summary: In this study, we screened a cohort of 57 paediatric brain tumours, with a wide range of pathologies to identify gene expression profiles

overall_design: We analysed gene expression in paediatric brain tumours as compared to normal adult brain in order to understand the molecular profiles. Our cohort included 14 pilocytic astrocytomas, 3 diffuse astrocytomas, 2 anaplastic astrocytomas, 5 glioblastomas, 14 ependymomas, 9 medulloblastomas, 5 atypical teratoid/rhabdoid tumours, 4 choroid plexus papillomas, 1 papillary glioneuronal, 8 adult brain and 8 foetal brain controls.


title: Germline Aberrations of PAX5 Cause Susceptibility to pre-B cell Acute Lymphoblastic Leukemia

first: Jeffery

last: Klco

state: TN

address: 262 Danny Thomas Place

institute: St Jude Children's Research Hospital

summary: A novel heterozygous germline variant, c.547G>A (p.Gly183Ser), in the paired box protein encoding gene, PAX5, was found to segregate with disease in two unrelated kindreds with autosomal dominant pre-B cell acute lymphoblastic leukemia (ALL). Leukemic cells from both families exhibited 9p deletion, with loss-of-heterozygosity and retention of the mutant PAX5 allele at 9p13. Two additional sporadic ALL cases with 9p loss demonstrated PAX5 Gly183 substitution in the leukemic cells. Functional and gene expression analysis of the PAX5 germline variants demonstrated reduced transcriptional activity. These data extend the role of PAX5 alterations in the pathogenesis of pre-B ALL, and implicate PAX5 in a novel syndrome of germline susceptibility to pre-B cell neoplasia.

overall_design: We analyzed 40 samples comprising sevenfold replicates of transductions with empty vector, wild type PAX5 and 4 mutant PAX5 constructs

first: Sohela

last: Shah

first: Kasmintan

middle: A

last: Schrader

first: Esmé

last: Waanders

first: Andrew

middle: E

last: Timms

first: Joseph

last: Vijai

first: Cornelius

last: Miething

first: Jeremy

last: Wechsler

first: Jun

first: James

last: Hayes

first: Robert

last: Klein

first: Jinghui

last: Zhang

first: Gang

last: Wu

first: Mike

last: Rusch

first: Panduka

last: Nagahawatte

first: Jing

last: Ma

first: Shann-Ching

last: Chen

first: Guangchun

last: Song

first: Lei

last: Wei

first: Paul

last: Meyers

first: Deepa

last: Bhojwani

first: Suresh

last: Jhanwar

last: Maslak

first: Martin

last: Fleisher

first: Jason

last: Littman

first: Lily

last: Offit

first: Rohini

last: Rau-Murthy

first: Megan

last: Harlan-Fleischut

first: Xiaoni

last: Gao

first: Christopher

last: Manschreck

first: Thomas

last: Kitzing

first: Vundavalli

middle: V

last: Murty

first: Susana

last: Raimondi

first: Roland

last: Kuiper

first: Annet

last: Simons

first: Joshua

middle: D

last: Schiffman

first: Sharon

last: Plon

first: Kenan

last: Onel

first: David

last: Wheeler

first: Deborah

last: Ritter

last: Ziegler

first: Kathy

last: Tucker

first: Rosemary


title: Cytokine and gene transcription profiles of immune responses elicited by HIV lipopeptide vaccine in HIV-negative volunteers

status: Public on Jul 30 2013

city: Creteil

first: hakim

last: hocini

address: Hopital Henri Mondor, 51, Avenue du Maréchal De Lattre De Tassigny

institute: inserm

summary: Successful development of HIV-vaccination strategies will also depend on the ability to use novel approaches to analyse and integrate immunogenicity data generated in vaccine trials. The ANRS VAC 18 trial evaluated the immunogenicity of HIV-LIPO-5 vaccine (5 HIV peptides coupled to a palmytoil tail) administered at W0, 4, 12 and 24 in healthy volunteers. 62-69% of vaccinees developed HIV-specific ELISpot responses by W26. Here we present extensive immunogenicity assessments in a subset of vaccinees using ELISpot, lymphoproliferation, intracellular cytokine staining (ICS), cytokine multiplex and transcriptomic analyses. Peripheral blood mononuclear cells from volunteers collected before and following vaccinations were stimulated with HIV LIPO 5 vaccine, Gag peptides contained or not in the vaccine as controls. Different time points and stimulation conditions were compared, using false discovery rate to control for test multiplicity. 74% and 30% of vaccinees had cultured ELISpot and lymphoproliferation responses at W14, respectively. Ex-vivo ICS showed mainly single IL-2 producing cells. Secretion of IFN-γ, TNF-α, IL-5, and IL-13 increased significantly in response to Gag stimulation after culture at W14 compared to W0. An induction of metallothionein genes was consistently detected after HIV-LIPO-5 stimulation at W0 and W14 related to the adjuvant effect of the lipid tail. After vaccination (W14), significant probes increased substantially (>1200 probes) including IFN-γ, CXCL9, IL2RA, TNFAIP6, CCL3L1 and IL-6 W14 (fold change > 100%). In conclusion, HIV LIPO-5 vaccination elicited memory precursor responses with a Th1 and Th2 profile. The signature profile before vaccination provides information about the adjuvant effect of the lipid tail. Consistently with cytokine responses, vaccination is associated with a modulation in gene expression. This combined approach allowed to identify new signatures of HIV vaccine response and indicates that HIV-LIPO-5 could be further developed as a prime component of heterologous prime boost strategies.

overall_design: PBMC mRNA of 12 healthy volunteers, stimulate in four different conditions (HIV-LIPO-5, Gag+, Gag-, NS) during 6 and 24 hours before and after vaccination (week 0 and week 14)

first: Yves

last: LEVY

first: Rodolphe

last: THIEBAUT


title: S100P is a metastasis-associated gene that facilitates transendothelial migration of pancreatic cancer cells [HG-U133A]

first: Claude

last: Chelala

address: Charterhouse square

institute: Barts & The London School of Medicine (QMUL)

summary:
Pancreatic cancer is a devastating disease with both local invasion and distant metastasis. Identifying the genes expressed in liver metastases and signatures of metastatic progression would therefore be of particular importance as they could aid in both recurrence prediction as well as representing novel therapeutic targets.

Keywords: Gene expression profiling

overall_design: We have performed microarray gene expression analysis of normal pancreas, primary pancreatic ductal adenocarcinoma (PDAC), normal liver, and pancreatic liver metastases to identify potential therapeutic targets.

first: Sayka

last: Barry

first: Tatjana

last: Crnogorac-Jurcevic


title: Genome-wide analysis of c-Myb-responsive gene expression in prostate cancer cells

status: Public on Jul 28 2013

first: Timothy

middle: C.

last: Thompson

state: Texas

address: 1515 Holcombe Blvd.

department: Genitourinary Medical Oncology

summary: Analysis of c-Myb-regulation of  gene expression. The hypothesis tested in the present study was that c-Myb influences the expression of specific sets of genes that are involved in cell cycle, DNA replication, recombination and repair. Results provide important information on c-Myb-responsive genes that may be crucial to the cell survival and the progression of prostate cancer.

overall_design: Total RNA obtained from c-Myb siRNA-transfected prostate cancer cells compared to negative control siRNA-transfected prostate cancer cells 48 h after siRNa transfection.

middle: C

first: Likun

last: Li

first: Wenjun

last: Chang

first: Hyun-Sung

last: Lee

first: Ju-Seog


title: AR and c-Myb depletion effects in prostate cancer cells

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

overall_design: Refer to individual Series


title: Genome-wide analysis of AR-responsive gene expression in prostate cancer cells

summary: Analysis of AR-regulation of  gene expression. The hypothesis tested in the present study was that AR influences the expression of genes that participate in important bioprocesses in  prostate cancer cells, including cell cycle, DNA replication, recombination and repair. Results provide important information on AR-responsive genes that may be crucial to the cell survival and the progression of prostate cancer.

overall_design: Total RNA obtained from AR siRNA-transfected prostate cancer cells compared to negative control siRNA-transfected prostate cancer cells 48 h after siRNa transfection.


title: PDK1 Signaling Towards PLK1-Myc Activation Confers Oncogenic Transformation and Tumor Initiating Cell Activation and Resistance to mTOR-targeted Therapy.

city: Singapore

first: Peiyong

last: Guan

address: 60 Biopolis Street, Genome, #02-01

country: Singapore

institute: Genome Institute of Singapore

summary: Although 3-Phosphoinositide-dependent protein kinase-1 (PDK1) has been predominately linked to PI3K-AKT pathway, it may also evoke additional signaling outputs to promote tumorigenesis. Here we report that PDK1 directly induces phosphorylation of Polo-like kinase 1 (PLK1), which in turn induces Myc phosphorylation and protein accumulation. We show that PDK1-PLK1-Myc signaling is critical for cancer cell growth and survival and small molecule inhibition of PDK1/PLK1 provides an effective approach for therapeutic targeting Myc-dependency. Intriguingly, PDK1-PLK1-Myc signaling induces an embryonic stem cell-like gene signature associated with aggressive tumor behaviors and is a robust signaling axis driving cancer stem cell (CSC) self renewal. Finally, we show that PLK1 inhibitor synergizes with mTOR inhibitor to induce synergistic anti-tumor effect in colorectal cancer by antagonizing a compensatory Myc induction. These findings identify a novel pathway in human cancer and CSC activation and provide a therapeutic strategy for targeting Myc-associated tumorigenesis and therapeutic resistance.

overall_design: Gene expression profiling of Human Embryonic Kidney Cells (HEK-TERV) under different conditions: PMN, PDK1, MYC and E545K

first: Jing

last: Tan

first: Zhimei

first: Puay

middle: L

first: Mei

middle: Y

last: Aau

first: Shuet

middle: T

first: Min

last: Feng

first: Cheryl

middle: Z

last: Lim

first: Eric

first: Zhen

last: Wee

first: Yaw

first: R

middle: K

last: Karuturi

first: Qiang

last: Yu


title: Similarities and differences between human activated macrophages I

status: Public on Jul 26 2013

city: Guildford

first: Fernando

middle: O

last: Martinez Estrada

state: Surrey

address: Stag Hill

department: Faculty of Health & Medical Sciences

institute: University of Surrey

summary: The human AA dataset 5 includes the gene expression profile of monocyte-derived macrophages isolated from blood donor buffy coats and plated on TCP in medium containing 10% autologous serum. Cells were stimulated for 120 hours with 50 ng/ml of IL-4, 50 U/ml of IFN-γ plus 12.5 ng/ml of TNF-α, 50 ng/ml of M-CSF or 50 ng/ml of IL-10. RNA samples were isolated using TriPure isolation reagent (Roche) and the RNeasy Mini Kit-Qiagen Clean up method. The transcriptional profile was evaluated in two independent cell preparations, each derived from a different single donor using the HT12 V4 R2 bead chip arrays from Illumina.

overall_design: Total RNA obtained from monocyte-derived macrophages exposed to representative polarizing cytokines

first: Viviana

last: Cobos Jimenez

last: Martinez

first: Siamon

last: Gordon

first: Jörg

last: Hamann

first: Neeltjee

last: Kookstra


status: Public on Aug 09 2013

city: Vienna

first: Sebastian

middle: M

last: Nijman

address: Lazarettgasse 14

country: Austria

institute: Research Center for Molecular Medicine

summary: Transcriptional response of KBM7 cells to IFN-gamma or TNF-alpha was investigated in control or cells with genetrap insertions in JAK2 or TNFRS1A, respectively. The experiment shows that, as expected, cells lacking JAK2 or TNFRS1A expression display a severly blunted response to the tested cytokines.

overall_design:
KBM7 genetrap mutant cells stimulated with TNF-alpha and IFN-gamma
Sample WT_1 corresponds with the control sample for the IFN-gamma stimulation; Sample WT_2 corresponds with the control sample for the TNF-alpha stimulation.
As the expected differences between the samples was large, only single replicates were performed for each condition

first: Tilmann

last: Buerckstuemmer


title: Nanotoxicogenomic study of ZnO and TiO2 responses

status: Public on Jul 25 2013

city: Turku

first: Soile

last: Tuomela

address: P.O. Box 123

department: Turku Centre for Biotechnology

institute: University of Turku


title: Expression data from white adipose tissue of adult mice with mutations in Regulator of sex-limitation genes

status: Public on Jul 23 2013

city: Ann Arbor

first: Christopher

middle: J

last: Krebs

state: MI

address: 1241 E. Catherine St

department: Human Genetics

institute: University of Michigan Medical School

summary:
Regulator of sex-limitation (rsl) is a recessive mouse phenotype in which the otherwise male-specific sex-limited protein (Slp) gene is expressed in females. Positional cloning in rsl mice led to the identification of mutations in two neighboring KRAB zinc finger transcriptional repressors, Rsl1 and Rsl2, and BAC transgenic rescue experiements verified their ability to repress male-specific genes in the liver.
Microarrays were used here to identify RSL-sensitive genes in mouse abdominal white adipose tissue.
Experiment type: sex comparison and genetic modification

overall_design: Total RNA was extracted from abdominal white adipose tissue of adult male and female wild type and Rsl-null mice. Equivalent amounts of RNA were pooled from five mice per sex and genotype. Two pools per sex and genotype were hybridized to the Affymetrix Mouse Genome 430 2.0 PM Array Strip.

first: Diane

last: Robins


title: Nanotoxicogenomic study of ZnO and TiO2 responses (Illumina)

summary: A comprehensive in vitro assessment of two commercial metal oxide nanoparticles, TiO2 and ZnO, was performed using human monocyte-derived macrophages (HMDM), monocyte-derived dendritic cells (MDDC), and T cell leukemia-derived cell line (Jurkat). TiO2 nanoparticles were found to be non-toxic whereas ZnO nanoparticles caused dose-dependent cell death. Subsequently, global gene expression profiling was performed to identify signaling pathways underlying the cytotoxicity caused by ZnO nanoparticles. Analysis was done with doses, 1µg/ml and 10µg/ml after 6 and 24 hours of exposure. Interestingly, 2703 genes were significantly differentially expressed in HMDM upon exposure to 10µg/ml ZnO nanoparticles, while in MDDCs only 12 genes were affected. In Jurkat cells, 980 genes were differentially expressed. It is noteworthy that the gene expression of metallothioneins was upregulated in all the three cell types. In addition to the common ZnO-inducible changes, a notable proportion of the genes were regulated in a cell type-specific manner. Using a panel of ZnO nanoparticles, we obtained an additional support that the cellular response to ZnO nanoparticles is caused by particle dissolution. Gene ontology analysis revealed that the top biological processes disturbed in HMDM and Jurkat cells were regulating cell death and growth. In addition, genes controlling immune system development were affected. Bioinformatics assessment showed that the top human disease category associated with ZnO-responsive genes in both HMDM and Jurkat cells was cancer. Overall, the study revealed novel genes and pathways for mediating ZnO nanoparticle-induced toxicity and demonstrated the value of assessing nanoparticle responses through combined transcriptomics and bioinformatics approach.

overall_design: Altogether 90 samples were analyzed originating from three biological replicates of HMDM, MDDC or Jurkat cells containg untreated control cells, ZnO or TiO2 treated cells with doses 1µg/ml and 10µg/ml. The sample timepoints were 6 hours and 24 hours.

first: Reija

last: Autio

first: Tina

last: Bürki-Thurnherr

first: Andrea

last: Kunzmann

first: Britta

last: Andersson-Willman

first: Peter

last: Wick

first: Osman

last: Arslan

first: Sanjay

last: Mathur

first: Annika

last: Scheynius

first: Harald

last: Krug

first: Bengt

last: Fadeel

first: Riitta

last: Lahesmaa


title: IkB-like protein NFKBIZ regulates NF-kB signaling and is critical for survival of ABC DLBCL (MLN inhibition)

status: Public on Jul 22 2013

city: Münster

first: Michael

last: Grau

state: Nordrhein-Westfalen

address: Albert-Schweitzer-Campus 1

department: Faculty of Medicine

institute: University of Münster

summary:
Constitutive activation of the nuclear factor-kappa B (NF-kB) pathway is a hallmark of the activated B-cell-like (ABC) subtype of diffuse large B-cell lymphoma (DLBCL). Recurrent mutations of NF-kB regulators that cause constitutive activity of this oncogenic pathway have been identified. However, it remains unclear how specific target genes are regulated. We identified the IkB-like protein NFKBIZ that binds NF-kB subunits and enhances transactivation of some NF-kB target genes while repressing others, to be upregulated in ACB compared to GCB DLBCL primary patient samples (p=5.1 x 10^-37). Knockdown of NFKBIZ by RNA interference was toxic to ABC but not GCB DLBCL cell lines. Gene expression profiling following NFKBIZ knockdown significantly downregulated a large number of NF-kB target genes, suggesting a central role in regulating NF-kB signaling. To further investigate the molecular mechanisms of how NFKBIZ mediates NF-kB signaling in ABC DLBCL, we performed immunoprecipitations and detected an interaction of NFKBIZ with both p50 and p52 NF-kB subunits, indicating that both the canonical and non-canonical NF-kB pathways are regulated by NFKBIZ. Collectively, our data imply that NFKBIZ is required for NF-kB signaling in ABC DLBCL and thus might represent a promising molecular target for future therapies.

The complete dataset is comprised of three experiments with the male HBL-1 ABC DLBCL cell line: a) 8 paired GEP measurements after NFKBIZ inhibition by shRNA, b) 6 paired GEP measurements after applying the MLN inhibitor and c) 4 two-color measurements after applying a MALT inhibitor.

overall_design: This dataset includes 6 paired GEP measurements after applying the MLN inhibitor.

first: Georg

last: Lenz


title: IkB-like protein NFKBIZ regulates NF-kB signaling and is critical for survival of ABC DLBCL


title: The mRNA levels of CD133 positive and CD133 negative cells after radiation exposure

status: Public on Jul 20 2013

city: Pohang

first: Taek-Kyun

last: Kim

state: Gyeongbuk

address: San 31, Hyoja-dong, Nam-gu

department: Interdisciplinary Bioscience and Bioengineering

country: South Korea

institute: POSTECH

summary: The cancer initiating cells (CICs) act as a tumor initiation source. Recent studies have shown that CICs contribute to chemoresistance and radioresistance. The aims of this study were to investigate the relationship of CD133+ liver CICs and radiation resistance and to define a possible mechanism for radioresistance in hepatocellular carcinoma (HCC).

overall_design: Total RNA is obtained from CD133 positive cells and CD133 negative cells at 0, 12 and 24 hours after radiation exposure.

first: Won-Hui

last: Heo

first: Daehee

last: Hwang

first: Seung-Gyu

last: Yun


title: IkB-like protein NFKBIZ regulates NF-kB signaling and is critical for survival of ABC DLBCL (NFKBIZ  inhibition)

overall_design: This dataset includes 8 paired GEP measurements after NFKBIZ inhibition by shRNA.


title: AtbZIP16 integrates light and hormone signaling pathways to regulate Arabidopsis early seedling development

city: Taipei

first: Wen-Ping

last: Hsieh

address: 128 Academia Road, Section 2, Nankang

institute: Academia Sinica

summary:
In response to environmental light signals, transcriptomic adjustment plays an important role in Arabidopsis seed germination and seedling development. G-box cis-element is commonly present in promoters of genes positively or negatively responding to the light signal. For the pursuit of additional transcriptional regulator modulating light-mediated transcriptome changes, we have identified AtbZIP16, a basic region/leucine zipper motif transcription factor, via G-box DNA affinity chromatography. We have confirmed that AtbZIP16 possesses G-box-specific binding activity. Analyses of atbzip16 mutants indicate that AtbZIP16 is a negative regulator in phyB-mediated inhibition of cell elongation, but a positive regulator in phytochrome-mediated seed germination process. Transcriptomic analysis supports that AtbZIP16 is primarily a transcriptional repressor regulating light-, GA- and ABA-responsive genes. Chromatin immunoprecipitation study revealed that AtbZIP16 could directly target RGL2, a DELLA gene, and indirectly repress the expression of PIL5 gene, which encodes a bHLH protein inhibiting seed germination in Arabidopsis. Our study indicated that, through repressing the expression of RGL2 and the antagonizing the expression of PIL5, AtbZIP16 functions to promote seed germination and hypocotyl elongation during early stages of Arabidopsis seedling development.
In response to environmental light signals, transcriptomic adjustment plays an important role in Arabidopsis seed germination and seedling development. G-box cis-element is commonly present in promoters of genes positively or negatively responding to the light signal. For the pursuit of additional transcriptional regulator modulating light-mediated transcriptome changes, we have identified AtbZIP16, a basic region/leucine zipper motif transcription factor, via G-box DNA affinity chromatography. We have confirmed that AtbZIP16 possesses G-box-specific binding activity. Analyses of atbzip16 mutants indicate that AtbZIP16 is a negative regulator in phyB-mediated inhibition of cell elongation, but a positive regulator in phytochrome-mediated seed germination process. Transcriptomic analysis supports that AtbZIP16 is primarily a transcriptional repressor regulating light-, GA- and ABA-responsive genes. Chromatin immunoprecipitation study revealed that AtbZIP16 could directly target RGL2, a DELLA gene, and indirectly repress the expression of PIL5 gene, which encodes a bHLH protein inhibiting seed germination in Arabidopsis. Our study indicated that, through repressing the expression of RGL2 and the antagonizing the expression of PIL5, AtbZIP16 functions to promote seed germination and hypocotyl elongation during early stages of Arabidopsis seedling development.

overall_design: Three biological replicates for 4-d-old seedlings grown under dark or red-light and long-day (0.5 μmole m-2 sec-1) contitions.

first: Shu-Hsing

last: Wu


title: Gene expression profiles from peripheral blood mononuclear cells (PBMCs) of osteoarthritis patients and healthy controls

status: Public on Jul 18 2013

city: Leiden

first: Yolande

middle: F. M.

last: Ramos

address: Einthovenweg 20

department: Molecular Epidemiology

country: Netherlands

institute: Leiden University Medical Center

summary: By performing a comprehensive exploration of peripheral blood by microarray analysis from a subset of the Genetics osteoARthritis and Progression (GARP) study in comparison with sex and age-matched healthy controls we have identified disease specific gene expression networks. Our data hint at the relevance of apoptosis as an etiological factor in osteoarthritis onset, thereby qualifying expression profiling of blood as a useful tool to understand the underlying molecular mechanisms of osteoarthritis.

overall_design:
Case-control study comparing gene expression profiles generated with total messenger RNA obtained from peripheral blood mononuclear cells of controls with that of osteoarthritis (OA) patients from the GARP study.
The GARP study consists in Dutch Caucasian sib pairs with symptomatic OA at multiple joint locations and has been described previously by Riyazi et al (Ann Rheum Dis 2005;64:438-43).

middle: F

first: Steffan

last: Bos

first: Nico

last: Lakenberg

first: Stefan

last: Böhringer

first: Wouter

last: den Hollander

first: Margreet

last: Kloppenburg

first: Eline

last: Slagboom

first: Ingrid

last: Meulenbelt