title: Epigenetic Programming Alterations in Alligators from Environmentally Contaminated Lakes

city: Pullman

first: Michael

last: Skinner

state: WA

address: Abelson 507

department: SBS

institute: WSU

summary: Previous studies examining the reproductive health of alligators in Florida lakes indicate that a variety of developmental and health impacts can be attributed to environmental quality and exposures to environmental contaminants. A number of these environmental contaminants have been shown to disrupt normal endocrine signaling. The potential that these environmental toxicants may influence epigenetic status and correlate to the health abnormalities was investigated in the current study.  The red blood cell (RBC) (erythrocyte) in the alligator is nucleated so was used as an easily purified marker cell to investigate epigenetic programming.  RBCs were collected from adult male alligators captured at three sites in Florida, each characterized by varying degrees of contamination. While Lake Woodruff (WO) has remained relatively pristine, Lake Apopka (AP) and Merritt Island (MI) convey exposures to different suites of contaminants. DNA was isolated and methylated DNA immunoprecipitation (MeDIP) was used to isolate methylated DNA that was then analyzed in a competitive hybridization using a genome-wide alligator tiling array for a MeDIP-Chip analysis.  Pairwise comparisons of alligators from AP and MI to WO revealed alterations in the DNA methylome.  The AP vs. WO comparison identified 85 differential DNA methylation regions (DMRs) with ≥3 adjacent oligonucleotide tiling array probes and 15,451 DMRs with a single oligo probe analysis.  The MI vs. WO comparison identified 75 DMRs with the ≥3 oligo probe and 17,411 DMRs with the single oligo probe analysis.  There was negligible overlap between the DMRs identified in AP vs. WO and MI vs. WO comparisons. In both comparisons DMRs were primarily associated with CpG deserts which are regions of low CpG density (1-2 CpG/100bp).  Although the alligator genome is not fully annotated, gene associations were identified and correlated to major gene functional categories and pathways. Observations demonstrate that environmental quality is associated with epigenetic programming and status in the alligator. The epigenetic alterations may provide biomarkers to assess the environmental exposures and health impacts on these populations of alligators.

overall_design: The current study was designed to investigate potential alterations in the epigenome of alligators living in contaminated and non-contaminated lakes in Florida. The experimental design involved the collection of blood samples from adult male alligators from Lake Apopka and Merritt Island National Wildlife Refuge as contaminated lakes and Lake Woodruff as a reference lake. The epigenome analysis in the RBC involved the isolation of DNA followed by a methylated DNA immunoprecipitation (MeDIP).  The MeDIP was then analyzed using a genome-wide alligator tiling array chip set (Chip) to identify differential DNA methylation regions (DMRs). Comparative hybridizations between the Lake Apopka alligator samples versus Lake Woodruff alligator samples and Merritt Island National Wildlife Refuge alligator versus Lake Woodruff alligator samples were made with two independent experiments with different sets of multiple animals from each site.

first: Louis

last: Guillette Jr.

first: Benjamin

last: Parrott

first: Eric

last: Nilsson

first: M

last: Haque


title: Carbon starvation along the maize leaf gradient

status: Public on Aug 24 2016

city: Vienna

first: Angelika

middle: B

last: Czedik-Eysenberg

address: Dr-Bohr-Gasse 3

country: Austria

institute: Gregor-Mendel-Institute

summary:
gene expression profiling in different zones along the gradient of the growing maize leaf balde aover a time course of dirunal cycle and carbon starvation by extension of the night
Plants assimilate carbon in their photosynthetic tissues in the light. However, carbon is required during the night, and in non-photosynthetic organs. It is therefore essential that plants manage their carbon resources spatially and temporally and coordinate growth with carbon availability. In growing maize (Zea mays) leaf blades a defined developmental gradient facilitates analyses in the cell division, elongation and mature zones. We investigated the responses of the metabolome and transcriptome and polysome loading, as a qualitative proxy for protein synthesis, at dusk, dawn and 6, 14 and 24 hours into an extended night, and tracked whole leaf elongation over this time course. Starch and sugars are depleted by dawn in the mature zone, but only after an extension of the night in the elongation and division zones. Sucrose recovers partially between 14 and 24 h into the extended night in the growth zones but not the mature zone. The global metabolome and transcriptome track these zone-specific changes in sucrose. Leaf elongation and polysome loading in the growth zones also remain high at dawn, decrease between 6 and 14 h into the extended night and then partially recover indicating that growth processes are determined by local carbon status. The level of sucrose-signaling metabolite trehalose-6-phosphate, and the trehalose-6-phosphate:sucrose ratio are much higher in growth than mature zones at dusk and dawn but fall in the extended night. Candidate genes were identified by searching for transcripts that show characteristic temporal response patterns or contrasting responses to carbon starvation in growth and mature zones.

overall_design: 3 repliucates per time point and leaf region, each pooled form 5 indiviual plants

first: Stéphanie

last: Arrivault

first: Marc

middle: A

last: Lohse

first: Regina

last: Feil

first: Nicole

last: Krohn

first: Beatrice

last: Encke

first: Adriano

last: Nunes-Nesi

first: Alisdair

middle: R

last: Fernie

first: John

middle: E

last: Lunn

first: Ronan

last: Sulpice

first: Mark

last: Stitt


title: Covalent targeting of remote cysteine residues to develop CDK12 and CDK13 inhibitors [Affymetrix]

status: Public on Aug 29 2016

city: Cambridge

first: Richard

last: Young

state: MA

address: 9 Cambridge Center

country: USA

institute: Whitehead Institute for Biomedical Research

summary: Cyclin-dependent kinases 12 and 13 (CDK12 and CDK13) play critical roles in the regulation of gene transcription. However, the absence of CDK12 and CDK13 inhibitors has hindered the ability to investigate the consequences of their inhibition in healthy cells and cancer cells. Here we describe the rational design of a first-in-class CDK12 and CDK13 covalent inhibitor, THZ531. Co-crystallization of THZ531 with CDK12–cyclin K indicates that THZ531 irreversibly targets a cysteine located outside the kinase domain. THZ531 causes a loss of gene expression with concurrent loss of elongating and hyperphosphorylated RNA polymerase II. In particular, THZ531 substantially decreases the expression of DNA damage response genes and key super-enhancer-associated transcription factor genes. Coincident with transcriptional perturbation, THZ531 dramatically induced apoptotic cell death. Small molecules capable of specifically targeting CDK12 and CDK13 may thus help identify cancer subtypes that are particularly dependent on their kinase activities.

overall_design: Gene expression for Jurkat T-ALL and HAP1 cells treated with transcriptional inhibitors.

first: Tinghu

last: Zhang

first: Nicholas

last: Kwiatkowski

first: Calla

middle: M

last: Olson

first: Sarah

last: Dixon Clarke

first: Brian

middle: J

last: Abraham

first: Ann

middle: K

last: Greifenberg

first: Scott

last: Ficarro

first: Jonathan

last: Elkins

first: Yanke

last: Liang

first: Jarrod

last: Marto

first: Matthais

last: Geyer

first: Alex

middle: N

last: Bullock

first: Nathanael

middle: S

last: Gray

first: Mingfeng

last: Hao

first: Nancy

last: Hannett

first: Theresa

last: Manz

first: Bartlomiej

last: Bartkowiak

first: Arno

middle: L

last: Greenleaf


title: High-specificity bioinformatics framework for epigenomic profiling of discordant twins reveals specific and shared markers for ACPA and ACPA-positive rheumatoid arthritis.

status: Public on Nov 24 2016

city: Solna

first: David

last: Gomez-Cabrero

state: Stockholm

address: Karolinska University Hospital Solna

department: Department of Medicine

country: Sweden

institute: Karolinska Institutet

type: Methylation profiling by genome tiling array

summary: Study of changes in DNA Methylation in monozygotic Rheumatoid Arthritis discordant twins and ACPA+/- discordant twins

overall_design: Five healthy twin pairs discordant for presence of antibodies to citrullinated protein antigens (ACPA). Secondly, profiling seven twin pairs discordant for ACPA-positive RA.

first: Tomas

last: Ekstrom


title: Interference with ethylene perception at receptor level sheds light on auxin and transcriptional circuits associated with climacteric ripening of apple fruit (Malus x domestica Borkh.)

status: Public on Aug 23 2016

city: San Michele all'Adige

first: Fabrizio

last: Costa

state: N/A = Not Applicable

address: Via Mach 1

department: Center Agriculture Food Environment

country: Italy

institute: University of Trento

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

overall_design: Refer to individual Series


title: Interference with ethylene perception at receptor level sheds light on auxin and transcriptional circuits associated with the climacteric ripening of apple fruit (Malus x domestica Borkh.)

summary: Apple (Malus x domestica Borkh.) is a model fruit species to study the metabolic changes occurring at the onset of ripening as well the physiological mechanism governed by the hormone ethylene. In this survey, to dissect the climacteric interplay in apple, a multidisciplinary approach was employed. To this end, a comprehensive analysis of gene expression together with the investigation of several physiological entities (texture, volatilome and polyphenolic compounds) was carried out throughout fruit development and ripening. The transcriptomic profiling was conducted with two microarray platforms, a custom array dedicated to fruit ripening pathways (iRIPE) and a whole genome array specifically enriched of ripening related genes for apple (WGAA). The transcriptomic and phenotypic changes following the application of 1-methylcyclopropene (1-MCP), an ethylene inhibitor, were also highlighted. The suppression of ethylene modified and delayed the ethylene receptors turnover, leading to important modifications in the overall fruit physiology. The integrative comparative network analysis showed both negative and positive correlations between ripening related transcripts and accumulation of specific metabolites or texture components. The ripening distortion caused by the inhibition of the ethylene perception besides affecting the ethylene and texture control, stimulated the de-repression of auxin related genes, transcription factors and photosynthethic genes. In the end, the comprehensive repertoire of results obtained here step forwards in the elucidation of the multi-layered control of ethylene, hypothesizing a possible hormonal cross-talk coupled with a transcriptional regulation.

overall_design: whole genome array specifically enriched of ripening related genes for apple (WGAA) with two cultivars (Golden Delicious and Granny Smith)

first: Alice

last: Tadiello

first: Sara

last: Longhi

first: Marco

last: Moretto

first: Alberto

last: Ferrarini

first: Paola

last: Tononi

first: Brian

last: Farneti

first: Nicola

last: Busatto

first: Urska

last: Vrhovsek

first: Riccardo

last: Velasco

first: Franco

last: Biasioli

first: Luca

last: Cappellin

first: Matthias

last: Sholz

first: Livio

last: Trainotti

first: Massimo

last: Delledonne


overall_design: 48 samples analyzed; 8 stages have been identified over the fruit development and ripening (from flower to post harvest ripening) of apple fruit belonging to two apple cultivars (Golden Delicious and Granny Smith), ending with 16 samples (3 replacates for each sample)


title: Microarray expression profile of long noncoding RNAs in EGFR-TKI resistance of lung adenocarcinoma

city: Nanjing

first: Ying

last: Wu

address: Baiziting 42

country: China

institute: Nanjing Medical University Affiliated Cancer Hospital Cancer Institute of Jiangsu Province

summary: Lung adenocarcinoma cells harboring epidermal growth factor receptor (EGFR) mutations are sensitive to EGFR tyrosine kinase inhibitors (TKIs). Prolonged cancer treatment will induce the development of acquired resistance to EGFR TKI. To gain insight into the molecular mechanisms of EGFR-TKIs resistance, we generate EGFR-TKI-resistant HCC827-8-1 cells to be analyzed by microarray with their parental HCC827cells.

overall_design: gefitinib resistant HCC827-8-1 cells with three replications; gefitinib-sensitive HCC827 cells with three replications

first: Jifeng

last: Feng

first: Yong

last: Hu

first: Haixia

last: Cao

first: Siwen

last: Liu


title: The multifaceted RisA regulon of Bordetella pertussis

status: Public on Aug 20 2016

city: Lille

first: David

last: Hot

address: 1 rue du professeur Calmette

department: Center for Infection and Immunity of Lille

country: France

institute: Institut Pasteur de Lille

summary: Bordetella pertussis, the etiological agent of whooping cough, regulates the expression of its virulence factors by the well-defined BvgA/S two-component regulatory system. Phosphorylated BvgA activates the virulence activated genes (vags) and represses via the activation of the bvgR gene the expression of the virulence repressed genes (vrgs). In the presence of MgSO4, known as modulating condition, the BvgA/S system is inactive, and the vrgs are expressed. Here, we show that, except for 6 genes of unknown function, the expression of all the vrgs depends on RisA, another transcriptional two-component regulator. In addition to the vrgs, RisA also regulates the expression of a  many other genes. Whereas the expression of most vags was not affected by the deletion of risA, some vags, including the genes coding for pertactin, filamentous hemagglutinin, fimbriae and adenylate cyclase toxin, were surprisingly no longer modulated by MgSO4 in the risA- background. Yet another set of genes, mostly of unknown function, were modulated only in the risA- background. Finally, a large group of genes were up-regulated under modulating conditions only in the risA- background. They comprise genes of the chemotaxis and flagellar operons, iron-regulated genes, some of which are under the control of BvgA/S, while others are not. We identified RisK as the cognate RisA kinase, and found that most of the RisA-dependent genes also required RisK for expression, whereas a few genes were independent of RisK. These results were confirmed by the replacement of RisA with the phosphoablative RisAD60N analog and the phosphomimetic RisAD60E analog. Thus, according to its phosphorylation state, RisA regulates the expression of many genes, which may or may not also be regulated by the BvgA/S system, adding a new layer of complexity of B. pertussis gene regulation.

overall_design: Comparison of mutant strains with their corresponding parental wild type strains using 2 to 4 Biological replicates.

first: Loic

last: Coutte

first: Ludovic

last: Huot

first: Camille

last: Locht


title: Expression analysis of Staphylococcus aureus Mu50 delta-SAV1322 mutant

status: Public on Aug 19 2016

city: Cheongju

first: Jung Wook

last: Kim

address: Osong Health Technology Administration Complex, 187

department: Division of Antimicrobial resistance

country: South Korea

institute: Korea National Research Institute of Health

summary:
Investigation of mRNA expression level changes in a Staphylococcus aureus Mu50 delta-SAV1322 mutant, compared to the wild-type strain.
A comparison of the wild-type and the mutant transcription profiles

sample_organism: Staphylococcus aureus subsp. aureus Mu50

overall_design: Total RNA recovered from four separate wild-type culture of Staphylococcus aureus Mu50 and four separate culture of a mutant strain, Mu50 delta-SAV1322, in which 689bp deleted of SAV1322 locus. Each chip measures the expression level of 967 genes from Staphylococcus aureus Mu50 with 11 probe pairs per genes (total probes 10,637).

first: Jung

middle: W

first: Jae

middle: I

last: Yoo


title: Comprehensive Genomic Characterization of Five Canine Lymphoid Tumor Cell Lines

city: Raleigh

first: Steven

last: Suter

state: NC

address: 1051 William Moore Drive

department: Department of Clinical Sciences

institute: NC State University

summary:
Background  Leukemia/lymphoma cell lines have been critical in the investigation of the pathogenesis and therapy of hematological malignancies. While human LL cell lines have generally been found to recapitulate the primary tumors from which they were derived, appropriate characterization including cytogenetic and transcriptional assessment is crucial for assessing their clinical predictive value.   Results  In the following study, five canine LL cell lines, CLBL-1, Ema, TL-1 (Nody-1), UL-1, and 3132, were characterized using extensive immunophenotyping, karyotypic analysis, oligonucleotide array comparative genomic hybridization (oaCGH), and gene expression profiling. Genome-wide DNA copy number data from the cell lines were also directly compared with 299 primary canine round cell tumors to determine whether the cell lines represent primary tumors, and, if so, what subtype each most closely resembled.   Discussion  Based on integrated analyses, CLBL-1 was classified as B-cell lymphoma, Ema and TL-1 as T-cell lymphoma, and UL-1 as T-cell acute lymphoblastic leukemia. 3132, originally classified as a B-cell lymphoma, was reclassified as a histiocytic sarcoma based on characteristic cytogenomic properties. In combination, these data begin to elucidate the clinical predictive value of these cell lines which will enhance the appropriate selection of in vitro models for future studies of canine hematological malignancies.
GEP using GeneChip Canine Genome 2.0 array (Affymetrix, Santa Clara, CA)

overall_design: Five canine lymphoid cell lines analyzed

first: Matthew

last: Breen


title: Human tandem repeat custom custom microarray ChIP-chip with anti-CTCF and anti-CTCFL/BORIS antibodies in K562 cell line

status: Public on Aug 17 2016

city: Guangzhou

first: Alexander

middle: V.

last: Strunnikov

state: Guangdong

address: 190 Kai Yuan Avenue

institute: GIBH

type: Genome binding/occupancy profiling by array

summary: A common aberration in cancer is the activation of germline-specific proteins. The DNA-binding proteins among them generate novel chromatin states, not found in normal cells. The chromatin architecture protein CTCF has a germline-specific paralog BORIS/CTCFL, which is often erroneously activated in cancers. Another common feature of malignancies is the changed expression and epigenetic states of genomic repeats. The investigation of BORIS and CTCF binding to DNA repeats in cancer cell lines by ChIP-chip revealed three classes: elements cohabited by BORIS and CTCF, CTCF-bound only, or BORIS-only.

overall_design: The two-channel experiment included 3 biological replicas for each protein, 6 datasets in total. The input was labeled with Cy3 and ChIP DNA was labeled with Cy5. The custom arary design (OID24708_Human) was done at Nimblegen based on Tandem Repeat Finder (TRF) database generated with human genome release hg18

middle: V


title: Reading between the lines: molecular characterization of five widely used canine  lymphoid tumor cell lines

summary:
Molecular characterization of tumour cell lines is increasingly regarded as a prerequisite for defining  their validity as models of in vivo neoplasia. We present the first comprehensive catalogue of  genomic and transcriptional characteristics of five widely used canine lymphoid tumour cell lines.  High-resolution microarray-based comparative genomic hybridization defined their unique profiles  of genomic DNA copy number imbalance. Multicolour fluorescence in situ hybridization identified  aberrant gains of MYC, KIT and FLT3 and deletions of PTEN and CDKN2 in individual cell lines, and also  revealed examples of extensive structural chromosome reorganization. Gene expression profiling  and RT-PCR analyses defined the relationship between genomic imbalance and transcriptional  dysregulation in each cell line, clarifying their relevance as models of discrete functional pathways  with biological and therapeutic significance. In combination, these data provide an extensive  resource of molecular data for directing the appropriate use of these cell lines as tools for studying  canine lymphoid neoplasia.
GeneChip Canine Genome 2.0 array (Affymetrix) which is comprised of 18,000 Canis familiaris mRNA transcripts and over 20,000 non-redundant predicted genes was used

overall_design: 5 widely used canine lymphoid cell lines underwent immunophenotypic, genomic, and transcriptome characterization


title: Array CGH analysis for intravascular large B-cell lymphoma (IVLBCL)

status: Public on Aug 13 2016

city: NAGOYA

first: KAZUYUKI

last: SHIMADA

address: 65, Tsurumai-cho, Showa-ku

department: HEMATOLOGY AND ONCOLOGY

country: Japan

institute: NAGOYA UNIVERSITY

type: Genome variation profiling by genome tiling array

summary: IVLBCL is a rare distinct disease entity of extranodal large B-cell lymphoma . The disease is characterized by selective growth of tumor cells in the lumina of small vessels and by the absence of remarkable lymphadenopathy. We have developed patient derived xenograft IVLBCL mouse models from primary patient bone marrow samples. This dataset includes the array CGH analysis of IVLBCL tumor cells from the mouse xenograft models.

overall_design: DNA was extracted from spleens or a liver of the four xenograft mouse models (IVLBCL #1, #2, #3, and #4). For one of the four models (IVLBCL #3), additional DNA was obtained from a kidney, a bone marrow and an adrenal grand of the mouse model.    Total seven DNA samples were then analyzed to identify copy number alterations for IVLBCL.

first: Kazuyuki

last: Shimada

first: Kyoko

last: Hirano

first: Ichiro

last: Takeuchi

first: Miyuki

last: Suguro

first: Masao

last: Seto


title: A High-Content, Phenotypic Screen Identifies Fluorouridine as an Inhibitor of Pyoverdine Biosynthesis and Pseudomonas aeruginosa Virulence

status: Public on Aug 10 2016

city: Houston

first: Natalia

last: Kirienko

state: TX

address: 6100 Main St. MS140

department: BioSciences

institute: Rice University

summary: Pseudomonas aeruginosa is an opportunistic pathogen that causes severe health problems. Despite intensive investigation, many aspects of microbial virulence remain poorly understood. We used a high-throughput, high-content, whole-organism, phenotypic screen to identify small molecules that inhibit P. aeruginosa virulence in C. elegans. Approximately half of the hits were known antimicrobials. A large number of hits were non-antimicrobial bioactive compounds, including the cancer chemotherapeutic 5-fluorouracil. We determined that 5-fluorouracil both transiently inhibits bacterial growth and reduces pyoverdine biosynthesis. Pyoverdine is a siderophore that regulates the expression of several virulence determinants and is critical for pathogenesis in mammals. We show that 5-fluorouridine, a downstream metabolite of 5-fluorouracil, is responsible for inhibiting pyoverdine biosynthesis. We also show that 5-fluorouridine, in contrast to 5-fluorouracil, is a genuine anti-virulent compound, with no bacteriostatic or bacteriocidal activity. To our knowledge, this is the first report utilizing a whole-organism screen to identify novel compounds with antivirulent properties effective against P. aeruginosa.

overall_design: There are 6 samples total that comprise three biological replicates of N2 animals exposed to DMSO or 5-fluorouracil for 8 hours at 25°C. Each biological replicate consists of N2 C. elegans animals in the young adult developmental stage.


title: Comparison of the pre-passage wild-type strain H99W with two mouse-passaged strains

status: Public on Aug 11 2016

city: Murfreesboro

first: Erin

last: McClelland

state: TN

address: 1301 East Main Street, P.O. Box 60

department: Biology

institute: Middle Tennessee State University

summary: Changes in gene expression of the serotype A pre-passage wild-type strain H99W with two mouse-passaged strains were examined during log-phase growth at 37 ºC.

overall_design: Analysis included two replicates of each comparison with a Cy3-Cy5 dye swap


title: A Gene Expression-based Blood Diagnostic for Symptomatic Transthyretin Amyloidosis Revealing Male and Female-specific Signatures

status: Public on Aug 09 2016

city: La Jolla

first: Sunil

last: Kurian

state: CA

address: 10550 N Torrey Pines Road

department: Molecular and Experimental Medicine

institute: The Scripps Research Institute

summary: Early diagnosis of transthyretin (TTR) amyloid diseases remains challenging because of variable disease penetrance. Currently, patients must have an amyloid positive tissue biopsy to be eligible for disease modifying therapies. Early diagnosis is often difficult because the patient exhibits apparent symptoms of polyneuropathy or cardiomyopathy, but has a negative amyloid biopsy. Thus, there is a pressing need for more objective, quantitative diagnostics and biomarkers of TTR-aggregation-associated polyneuropathy and cardiomyopathy. This is especially true in the context of clinical trials demonstrating significant disease modifying effects, e.g. when the TTR tetramer stabilizer tafamidis was administered to familial amyloid polyneuropathy (FAP) patients early in the disease course. When asked if the findings of the tafamidis registration trial were “sufficiently robust to provide substantial evidence of efficacy for a surrogate endpoint that is reasonably likely to predict a clinical benefit” the advisory committee said yes, but the FDA rejected the tetramer stabilization surrogate biomarker required for orphan tafamidis approval–hence, acceptable biomarkers are badly needed. Herein, we explored whether peripheral blood cell mRNA expression profiles could differentiate symptomatic from asymptomatic V30M FAP patients, and if such a profile would normalize upon tafamidis treatment. We demonstrate that blood cell gene expression patterns reveal sex-independent as well as male and female specific inflammatory signatures in symptomatic FAP patients, but not in asymptomatic carriers, that normalize in FAP patients 6 months after tafamidis treatment. Thus these signatures have potential both as an early diagnostic and as a surrogate biomarker for measuring response to treatment in FAP patients.

overall_design: Study Subjects: Tafamidis-treated and untreated V30M FAP patients, asymptomatic V30M carriers, and healthy, age- and sex-matched controls without TTR mutations had whole blood drawn. RNA was extracted from a total of 309 peripheral blood samples collected in PAXgene tubes (Qiagen).   RNA Extraction and Microarray Processing: RNA was extracted with the PAXgene RNA Whole Blood Kit. Each RNA sample (100ng) was amplified and labeled with the Ambion WT Express Kit and hybridized to Affymetrix HuGene 1.1 ST Arrays using the Affymetrix GeneTitan Multi-Channel (MC) platform. Normalized signals were generated using Robust Multichip Average (RMA) in Partek Genomics Suite software version 6.6. Probesets on the DNA microarrays with low expressed signals were determined using a kernel density plot, and signals <Log2 of 6 were excluded from analysis.


title: mRNA microarray analysis of gene changes in Huh7 cells treated with IFN-λ4, IFN-λ1 and IFN-α

status: Public on Aug 08 2016

city: Shanghai

first: Weiguo

last: Fan

address: 320 Yueyang Road

department: Institut Pasteur of Shanghai

institute: Chinese Academy of Sciences

summary: The change of gene expression in Huh7 cells treated with IFN-λ4, IFN-λ1 and IFN-α was analyzed at 0h, 6h and 16h after different interferon treatments.

overall_design: Huh7 cells that had been treated with IFN-α (10 IU/ml), IFN-λ1 (20 ng/ml) and IFN-λ4 (20 ng/ml). Time points of 6 h and 16 h after stimulation were selected.

first: Shiqi

last: Xie

first: Xinhao

last: Zhao

first: Bing

last: Sun


title: Mesenchymal stem cell-derived exosomes stimulate cycling quiescence and early breast cancer dormancy in bone marrow

city: Newark

first: Pranela

last: Rameshwar

state: NJ

address: 185 South Orange Avenue

department: Medicine

institute: Rutgers NJ Medical School

summary: Transwell cultures were established in 6-well plates with 0.4 micron inserts. Equal amounts (6x10e4) of BCCs and MSCs were added to the outer and inner wells, respectively, in DMEM with 10% exosome-free FCS. After 24 h, the inner wells with BCCs were discarded. The MSCs were washed with PBS and then incubated with DMEM with 2% exosome-free FCS. At 48 h, exosomes were isolated from the MSC media. The exosomes from triplicate wells were added to duplicate naïve BCCs at 2.5x105/well of 6-well plates.

overall_design: qPCR miRNA expression profiling. RNA from MSCs-Exosomes were analyzed as indicated in the summary. The PCR was run on the 7300 Real-Time PCR System using the following thermal-cycling parameters: 94 0C for 15 min, 40 cycles at 940 C for 10 sec, 550 C for 30s, 700 C for 30 sec followed by a melting curve analysis.

first: Khadidiatou

last: Guiro

first: Oleta

last: Sandiford


title: Transcriptomic responses of copepodid sea lice (Lepeophtheirus salmonis) exposed to cypermethrin (Betamax®)

city: Victoria

first: Ben

middle: F

last: Koop

state: BC

address: PO Box 3020 STN CSC

country: Canada

institute: The University of Victoria

summary: This study investigates transcriptomic responses of Atlantic salmon lice, Lepeophtheirus salmonis exposed to cypermethrin, a commonly used antiparasitic agent used in aquaculture. Copepodid L. salmonis were exposed to cypermethrin (Betamax®) at a concentration of 1.0ppb

overall_design: An in vitro bioassay experiment was conducted using cypermethrin exposures on copepodid (larvae) sea lice (F1 generation) collected from BMA-2a New Brunswick, Canada in 2014. The bioassay exposed copepodids to 1.0 μg/L cypermethrin or a sea water control for 24 hours in glass beakers (VWR) at 12 ± 1oC. Each condition had a total volume of 500mL with six replicates and approximately 500 lice per beaker. After 24 hours, pools of ~500 copepodids were flash frozen for RNA extractions. Post 24-hours, lice were assessed for survival similarly to the technique used for staging and enumeratio first

first: Jordan

middle: D

last: Poley

first: Laura

last: Braden

first: Shona

last: Whyte

first: Amber

last: Messmer

first: Mark

last: Fast


title: Genes in Inflammatory Bowel Disease-Associated Risk Loci Demonstrate Genotype-, Tissue-, and Inflammation-Specific Patterns of Expression in Terminal Ileum and Colon Mucosal Tissue

city: Boston

first: Ramnik

last: Xavier

address: 185 Cambridge Street

institute: Massachusetts General Hospital

summary: With a greater understanding of the genetic risk variants associated with inflammatory bowel disease, there is a need to prioritize candidate genes within risk loci leading to the disease-SNP association. We created a custom NanoString probeset to capture 678 genes of interest in IBD (including 440 genes encoded within IBD risk loci and 15 housekeeping genes) - 22% of genes were not captured on traditional microarray platforms. Total RNA extracted from terminal ileum and colon tissues (uninflamed and inflamed) was used from patients with Crohn's disease and ulcerative colitis and healthy controls. We studied differential expression and performed an eQTL analysis to prioritize candidate genes within the risk loci.

overall_design: Gene expression profiles were generated for uninflamed and inflamed, colon and TI tissues from patients with inflammatory bowel disease and healthy controls on the NanoString platform.

first: J

last: Peloquin

first: G

last: Goel

first: R


title: Expression data from rat peripheral blood mononuclear cells (PBMCs)

status: Public on Aug 04 2016

city: London

first: Jacques

last: Behmoaras

address: Du Cane Road

country: United Kingdom

institute: Imperial College London

summary:
The effect of cafeteria (CAF) diet in PBMC gene expression was analyzed in two inbred rat strains
the Wistar Kyoto(WKY) and Lewis (LEW) rat PBMCs were isolated following a CAF or standard diet and subjected to whole genome expression analysis

overall_design: Rats from each strain were either fed with standard chow diet (n=5) or CAF (n=5). After 7 weeks of the indicated diet, rats were fasted for 9 hours, culled and PBMCs isolated from whole blood collected from the abdominal aorta

first: Neus

last: Martinez-Micaelo


title: Standardized whole-blood transcriptional profiling enables the deconvolution of complex induced immune responses

city: Paris

first: Vincent

last: Rouilly

state: Paris

address: 25 rue Dr Roux

institute: Institut Pasteur

summary: The study employs a standardized whole-blood stimulation systems to test the hypothesis that responses to Toll-like receptor ligands or whole microbes can be defined by the combined transcriptional signatures of key effector cytokines.

overall_design: The study encompasses the analysis of 21 distinct whole blood stimulations from 25 healthy donors from the Milieu Interieur Cohort (www.clinicaltrials.gov identifier: NCT01699893)

first: Alejandra

last: Urrutia

first: Darragh

last: Duffy

first: Lluis

last: Quintana-Murci

first: Matthew

last: Albert


title: Bile's chronic effect on the Cystic Fibrosis lung pathogen Pseudomonas aeruginosa

status: Public on Aug 01 2016

city: Cork

first: Fergal

last: O'Gara

address: UCC, Western Rd

department: Microbiology Dept, Univerisity College Cork

country: Ireland

institute: BIOMERIT Research Centre

summary:
Many patients with Cystic Fibrosis suffer from Gastroeosphgeal Refux Disease (GERD).  This disease may lead to the aspiration of bile into the lungs.  We invesigated the effect of bile on the CF lung pathogen P. aeruginosa.
We analysed gene expression profiles, comparing bile treated and untreated cells to identified distinct classes of up/down-regulated genes.

overall_design: P. aeruginosa PAO1 was grown to log stage for RNA extraction and hybridization on Affymetrix microarrays. We conducted three biological replicates as to increase the resolution of expression profiles.

first: David

last: Woods

first: F

last: Reen


title: Biological function of antisense RNAs that are synthesized by RNA-dependent RNA polymerases under rehydration

status: Public on Jul 31 2016

city: Yokohama

first: Akihiro

last: Matsui

state: Kanagawa

address: 1-7-22 Suehiro-cho, Tsurumi-ku

department: Center for Sustainable Resource Science

institute: RIKEN

summary: To identify RDR1/2/6-dependent antisense RNA loci under 2hr drought stress and 2hr rehydration, expression profiles of Poly (A+) RNA between rdr1/2/6 and wild-type using the custom microarray (GPL19830) were analyzed.

overall_design: rdr1/2/6 and wild-type plants (Arabidopsis thaliana ecotype Columbia) were grown on MS medium for 2 weeks. Then, the plants were transferred to plastic dish and kept for 2hr. Poly (A+) RNA  from 100μg total RNA by treating with Ambion Poly A purist twice.5 ng of Poly (A+) RNA were used for the expresion profiling using the custom array (GPL19830).

first: Kayoko

last: Mizunashi

first: Maho

last: Tanaka

first: Kei

last: Iida

first: Motoaki

last: Seki


title: Copy number analysis by low coverage whole genome sequencing using ultra low-input DNA from formalin-fixed paraffin embedded tumour tissue

status: Public on Aug 02 2016

city: Melbourne

first: TANJINA

last: KADER

state: VIC

address: 305 Grattan Street

department: Cancer Genomics

country: Australia

institute: The Sir Peter MacCallum Cancer Centre

summary: We analysed a cohort of Lifepool IDC cases treated only with wide local excision for genome-wide copy number and loss of heterozygosity using Affymetrix OncoScan® MIP arrays. Cases included IDC (n=4).Benign cases were available for 2 cases. We have analysed copy number calling from the same samples using low-coverage whole genome sequencing in order to investigate the concordance between the two techniques.

overall_design: 4 cases of lifepool  invasive ductal carcinoma (IDC) and 2 benign cases were microdissected from FFPE tissue and analysed by molecular inversion probe (MIP) copy number arrays. The data in this submission are CN values for the ~300,000 probes common to two batches performed.

first: Kylie

last: Gorringe


title: Density Gradients Separate Dormant and Treatment-Resistant Human Glioblastoma Cells

status: Public on Jul 01 2016

city: San Francisco

last: Quigley

address: 1450 Third St. Room 207

department: Helen Diller Comprehensive Cancer Center

institute: UCSF

summary: Glioblastoma (GBM) is among the most aggressive cancers. Despite aggressive radiotherapy and treatment with the alkylating agent temozolomide (TMZ), patients ultimately succumb to the disease. Although much interest has focused on highly tumorigenic GBM stem cells (GSCs), adaption of a concept from microbial research proposes that a minor population of dormant “persister” cells in cancer evade current therapies. To separate dormant and treatment-resistant tumor cells in human GBM tumorspheres, we have refined density gradient protocols previously used for separation of neurosphere-forming neural stem cells (NSCs). We find that a minor cell population in human GBM tumorsphere cultures and patient-derived tumor biopsies display increased cell density. These high-density GBM cells (HDGCs) display dormancy, variable expression of proposed GSC markers, and 10-100 fold higher levels of reprogramming gene expression compared to low-density GBM cells (LDGCs). Transcriptional profiling data confirmed the slow-cycling state of HDGCs. As a result, HDGCs show decreased tumorsphere formation capacity in vitro and reduced tumorigenicity in vivo. Using tumorspheres and xenografts, we demonstrated that HDGCs show increased treatment-resistance to ionizing radiation (IR) and temozolomide treatment compared to LDGCs. Similar to the NSC lineage, our data suggest that dormant HDGCs become increasingly sensitive to anti-proliferative therapies as they become activated and further differentiate. In conclusion, density gradients represents a marker-independent approach to separate dormant and treatment-resistant tumor cells in human GBMs and other solid cancers.

overall_design: 12 samples, no replicates, derived from 5 individual patients

first: Anders

last: Persson


title: Paracrine effects of estrogen on 231BR cells, through ER+ astrocytes

city: Aurora

first: Diana

last: Cittelly

state: CO

department: Pathology

institute: University of Colorado AMC

summary: The objective of this study was to determine the extent to which paracrine action of 17-beta-estradiol on ER+ mouse astrocytes, affect gene expression of MDA231-derived brain trophic 231BR cells.

overall_design: Microarray analysis was performed in triplicate samples from 231BR cells treated with vehicle (OH), 10nM Estradiol (E2), alone or in combination with mouse astrocytes.  231BR-EGFP cells were sorted after 24h co-culture.

first: Carol

last: Sartorius


title: Awaking from dormancy: Resuscitation of chlorotic Synechocystis sp. PCC 6803 cells reveals a highly orchestrated process

status: Public on Jun 15 2016

city: Freiburg

first: Jens

last: Georg

address: Schänzlestr. 1

country: Germany

institute: University of Freiburg

summary: Unicellular cyanobacteria that do not fix nitrogen can survive prolonged periods of nitrogen starvation as bleached cells in a non-growing, dormant state. Upon re-addition of a usable nitrogen source, bleached cultures re-green within 48 hours and the cells return to vegetative growth. Here we investigated the process of resuscitation at the physiological and molecular level. Almost immediately upon nitrate addition, the cells initiate an amazingly organized resuscitation program: they first turn on respiration, gaining energy and activating the genes of the entire translational apparatus, genes for ATP synthesis and nitrate assimilation. Only after about 12 hours, the cells rebuild the photosynthetic apparatus and switch on photosynthesis. Analysis of the transcriptome in recovering cells shows a perfect match to the physiological processes and reveals a paramount dynamics of non-coding RNAs in awaking cells. This genetically encoded program ensures rapid colonization of habitats, in which nitrogen starvation imposes a recurring growth limitation.

overall_design: Synechocstis PCC 6803 WT cells were subjected to nitrogen limitation for 14d, then nitrogen was re-added to monitor recovery of the cells. Samples were taken before nitrogen depletion, after 14d of nitrogen depletion and 4h, 13h, 24h and 48h after nitrogen re-addition. Samples were taken in biological replicates for all timepoints besides 48h nitrogen recovery.

first: Alexander

last: Klotz

first: Lenka

last: Bučínská

first: Satoru

last: Watanabe

first: Viktoria

last: Reimann

first: Roman

last: Sobotka

first: Dieter

last: Jendrossek

first: Wolfgang

last: Hess

first: Karl

last: Forchhammer


title: Transcriptome analysis of equine sarcoids

status: Public on Jun 18 2016

city: Balice

first: Ewelina

last: Semik-Gurgul

address: Krakowska 1

department: Department of Animal Molecular Biology

country: Poland

institute: National Research Institute of Animal Production

summary: The aim of this study was to identify changes in transcriptome of horse sarcoids - a locally invasive skin tumors of equids, which are considered to be the most common equine skin neoplasm. The global expression of genes was investigated in four tumour samples and in the tumour-distant skin samples, obtained from the same individual.

overall_design: One-condition experiment, sarcoid vs. tumour-distant skin. Biological replicates: 4 sarcoid replicates, 4 control tissue replicates.

last: Semik

first: Artur

last: Gurgul


title: Differential regulation of the two ferrochelatase paralogues in Shewanella loihica PV-4 in response to environmental stresses

status: Public on Jul 21 2016

city: Norman

first: Ming

last: Xie

state: Oklahoma

address: 101 L DAVID BOREN BLVD

department: Microbiology and plant biology

institute: Institute for Environmental Genomics

summary: The microarray experiment compare the transcriptome of PV-4 wild type versus the deltahemH1 mutant, a PPIX accumulating strain. Only part of the data is used in the manuscript and we are working on this dataset for future manuscripts

overall_design: The wild type and deltahemH1 cell were revived and then cultured into late log-phase for collection, when significant PPIX accumulation occurred. Three biological replicates for wild type and deltahemH1

first: Dongru

last: Qiu

first: Aifen

last: Zhou

first: Tong

last: Yuan

first: Joy

last: Van Nostrand


title: Real-time quantitative PCR analysis of human lung samples

first: Csaba

last: Galambos

address: 12700 East 19th Ave

institute: The University of Colorado Denver

summary: Human lung samples from control and Down Syndrome prenatal patients were examined for Angiogenic Factors

overall_design: qPCR gene expression profiling was performed to analyze the gene expression differences between human prenatal Down Syndrome patients and age matched control samples. Human lung tissue was obtained from the University of Maryland, Baltimore through its NICHD Brain and Tissue Bank for Developmental Disorders (NICH Contract #HHSN275200900011C, Ref. No. N01-HD-9-0011). The studies included in this report were examined by an institutional review board (IRB) of the University of Colorado School of Medicine and the Children’s Hospital Colorado and are supported through the Decedent Research Certification Program  All tissues were collected, stored and distributed while maintaining strict confidentiality, meeting appropriate HIPPA standards, with oversight provided by the University of Colorado IRB.  Accordingly, limited clinical data is available. Small numbers of tissue were available for study, including 5 DS and 4 control flash frozen samples for quantitative RT-PCR. Total RNA was extracted from human lung tissue using the RNAqueous Total RNA Isolation Kit (Life Technologies AM1912).  Samples were DNase I treated with the Ambion TURBO DNA-free kit (Invitrogen AM1907) and tested for quality with an Agilent 2100 Bioanalyzer. Samples were reverse-transcribed with RT2 First Strand Kit (Qiagen 330401). These samples were amplified using the RT2 Profiler PCR Array Human Angiogenesis (Qiagen PAHS-024Z).  Quantitative RT-PCR was performed on a LightCycler LC480 System (Roche).

first: Angela

last: Minic


title: microRNA profiles of nasopharyngeal carcinoma cell line and nasopharyngeal epithelial cell line

city: Guangzhou

first: ping

last: lan

address: 651 Dongfend East Road

institute: Sun Yat-sen University Cancer Center

summary: Exosomal and cellular miRNA expression levels were measured using a microRNA chip array or quantitative reverse transcription PCR (qRT-PCR). miR-24-3p was enriched in T-EXOs from the sera of NPC patients and NPC cells, which was correlated with worse disease-free survival (DFS). Exosomes (miR-24-3p-sponge-EXO) released from miR-24-3p-sponge-TW03 cells failed to inhibit T-cell proliferation and Th1 and Th17 differentiation or to induce Treg differentiation in vitro, compared with controlNC -sponge-EXO. Mechanistic analyses revealed that in miR-24-3p-sponge-EXO-treated T-cells, P-ERK, P-STAT1 and P-STAT3 were up-regulated, whereas P-STAT5 was down-regulated compared with controlNC-sponge-EXO-treated T-cells. FGF11 was identified as a direct target gene of miR-24-3p through in vivo and in vitro assessments. More importantly, the T-EXOs repressed FGF11 expression in T-cells during proliferation and differentiation. Interestingly, when FGF11 expression in T-cells was blocked, miR-24-3p-sponge-EXOs impeded shFGF11-T-cell proliferation and Th1 and Th17 differentiation but induced Treg differentiation, like controlNC-sponge-EXO. When FGF11 was knocked down in miR-24-3p-sponge-EXO-treated T-cells, neither P-ERK, P-STAT1 and P-STAT3 up-regulation or P-STAT5 down-regulation occurred. Interestingly, FGF11 expression in tumor-infiltrating lymphocytes (TILs) was significantly and positively correlated with the number of CD4+ and CD8+ TILs and predicted favorable DFS of the patients (p < 0.05).

platform_organism:
Homo sapiens
Mus musculus
Rattus norvegicus
Human alphaherpesvirus 1
Human alphaherpesvirus 2
Cytomegalovirus
Human betaherpesvirus 5
Lymphocryptovirus
Rhadinovirus
JC polyomavirus
Human immunodeficiency virus 1
Murid gammaherpesvirus 4
Merkel cell polyomavirus
Betapolyomavirus hominis
Betapolyomavirus macacae

overall_design: Two-condition experiment, one nasopharyngeal carcinoma cell line TW03 vs. one normal epithelium cell line NP69. Biological replicates: 1 nasopharyngeal carcinoma cell line TW03; 1 nasopharyngeal epithelial cell line NP69.

first: Jiang

last: Li

first: Shubiao

last: Ye


title: (CTA) expression after exposure to 5-aza-2'-deoxycytidine in HCT116 cells

status: Public on May 31 2016

city: Dallas

first: Min Soo

last: Kim

state: Texas

address: 5323 Harry Hines Blvd.

institute: University of Texas Southwestern

summary:
The expression of CTAs is normally restricted to gametogenic tissue but is often reactivated in the tumorigenic setting. This tumorigenic reactivation is thought to be due to global demethylation events during tumorigenesis. To test this, we employed an affymetrix microarray in the hypermethylated colorectal carcinoma tumor-derived cell line, HCT116, following 5-aza-2'-deoxycytidine treatment.
We used microarray analysis to uncover genes whose expression is modulated by DNA methylation in the colorectal carcinoma tumor derived cell line, HCT116.

overall_design: HCT116 cells were exposed to 5-aza-2'-deoxycytidine for 72 hours. Total RNA was isolated and hybridized on to Affymetrix microarrays.

first: Angelique

last: Whitehurst


title: Transcriptional profile of Beijing/East-Asian Mycobacterium tuberculosis isolates

status: Public on Jun 24 2016

city: Montreal

first: Pilar

last: Domenech

state: Quebec

address: 1001 Décarie Boulevard

department: IDIGH Program

institute: Research Institute of McGill University Health Centre

summary: Transcriptional profile comparison among Beijing and non-Beijing M. tuberculosis isolates.

overall_design: Three M. tuberculosis strains were compared. The laboratory reference strain, H37Rv, belongs to the Euro-American or lineage 4. Two clinical isolates of the East-Asian or lineage 2: 98_1663 is a pre-Beijing or Group 1 isolate, and HN878 is a Beijing or Group 5 isolate. Three replicates were performed for each comparison using two different biological samples.

first: Michael

last: Reed


title: Gene expression in chronic heart failure patients

status: Public on May 25 2016

city: Vancouver

first: Bruce

middle: Maxwell

last: McManus

address: 1081 Burrard Street

department: UBC James Hogg Research Centre

institute: PROOF Centre of Excellence

summary: Measuring genome-wide changes in transcript abundance in circulating peripheral whole blood cells is a useful way to study disease pathobiology and may help elucidate biomarkers and molecular mechanisms of disease. The sensitivity and interpretability of analyses carried out in this complex tissue, however, are significantly affected by its heterogeneity. It is therefore desirable to quantify this heterogeneity, either to account for it or to better model interactions that may be present between the abundance of certain transcripts, some cell types and some indication. Accurate enumeration of the many component cell types that make up peripheral whole blood can be costly, however, and may further complicate the sample collection process. Many approaches have been developed to infer the composition of a sample from high-dimensional transcriptomic and, more recently, epigenetic data. These approaches rely on the availability of isolated expression profiles for the cell types to be enumerated. These profiles are platform-specific, suitable datasets are rare, and generating them is expensive. No such dataset exists on the Affymetrix Gene ST platform. We present a freely-available, and open-source, multiresponse Gaussian model capable of accurately inferring the composition of peripheral whole blood samples from Affymetrix Gene ST expression profiles. The model was developed on a cohort of patients with chronic obtructive pulmonary disease and tested in chronic heart failure patients.

overall_design: The chronic heart failure cohot includes prospectively enrolled HF patients presenting to St. Paul’s Hospital or Vancouver General Hospital (Vancouver, Canada). Subjects were approached during their visit to the heart function, pre-transplant, or maintenance clinics and those who consented were enrolled in the study. A blood sample was collected at the time of enrollment. Genome-wide transcript abundance profiles, based on total RNA extracted from PAXgene blood, and CBC differentials are available for 197 heart failure patients.


title: Expression data from human HSPCs

status: Public on Jun 17 2016

city: Lund

first: Alexandra

last: Rundberg Nilsson

address: Klinikgatan 26

department: Experimental Hematology

institute: Lund University

summary:
Aging within the human hematopoietic system associates with increased incidence of anemia and myeloid neoplasms, decreased bone marrow (BM) cellularity and reduced adaptive immune responses. Similar phenotypes have been observed in mice and shown, at least in part, to involve hematopoietic stem cells (HSCs). However, evidence supporting such an association within human hematopoiesis is still sparse and prompted us to detail characteristics of human hematopoietic stem and progenitor cells throughout ontogeny.
We used microarrays to detail the global programme of gene expression underlying the alterations of aged HSCs.

overall_design: Young human HSPC populations as well as aged HSCs were selected for RNA extraction and hybridization on Affymetrix microarrays. The different populations were isolated using FACS-purification.

first: Shamit

last: Soneji

first: Sofia

last: Adolfsson

first: David

last: Bryder

first: Cornelis

last: Pronk


title: Gene expression in chronic obstructive pulmonary disease (COPD) patients

summary: Measuring genome-wide changes in transcript abundance in circulating peripheral whole blood cells is a useful way to study disease pathobiology and may help elucidate biomarkers and molecular mechanisms of disease. The sensitivity and interpretability of analyses carried out in this complex tissue, however, are significantly affected by its heterogeneity. It is therefore desirable to quantify this heterogeneity, either to account for it or to better model interactions that may be present between the abundance of certain transcripts, some cell types and some indication. Accurate enumeration of the many component cell types that make up peripheral whole blood can be costly, however, and may further complicate the sample collection process. Many approaches have been developed to infer the composition of a sample from high-dimensional transcriptomic and, more recently, epigenetic data. These approaches rely on the availability of isolated expression profiles for the cell types to be enumerated. These profiles are platform-specific, suitable datasets are rare, and generating them is expensive. No such dataset exists on the Affymetrix Gene ST platform. We present a freely-available, and open-source, multiresponse Gaussian model capable of accurately inferring the composition of peripheral whole blood samples from Affymetrix Gene ST expression profiles. The model was developed on a cohort of patients with chronic obstructive pulmonary disease (COPD) and tested in chronic heart failure patients.

overall_design: The Rapid Transition Program (RTP) includes prospectively enrolled patients with chronic obstructive pulmonary disease (COPD), presenting either to St. Paul’s Hospital or Vancouver General Hospital (Vancouver, Canada). Subjects presenting to the emergency department or those attending the COPD clinic were approached for consent to participate in the study. Genome-wide transcript abundance, based on total RNA extracted from PAXgene blood, was available for 172 samples from this cohort. This data was used for method development and cross-validation. Complete blood counts (including leukocyte differentials) were available for all blood samples and used as an independent measure of blood composition (excluding lymphocyte subtypes).


title: The ubiquitin-dependent N-end rule pathway enhances pathogen responses in plants

status: Public on May 02 2016

city: Dublin

first: Frank

last: Wellmer

address: College Green

department: Genetics

institute: Trinity College Dublin

summary: Microarray experiments to compare gene expression profiles of ate1 ate2 double-mutant plants and the wild type at different developmental stages and after the infiltration with Pseudomonas syringae strain Pst AvrRpm1.

overall_design: Global gene expression in ate1 ate2 double mutant seedlings was compared to that in wild-type seedlings using Agilent whole-genome microarrays. In addition, the response of both ate1 ate2 mutant and wild-type plants to infection with Pseudomonas syringae strain Pst AvrRpm1 was tested at different time-points after infiltration.

first: Remi

last: de Marchi

first: Maud

last: Saurel

first: Brian

last: Mooney

first: Kevin

last: Goslin

first: Kamila

last: Kwasniewska

first: Patrick

last: Ryan

first: Susana

last: Rivas

first: Emmanuelle

last: Graciet


title: Response to Neoadjuvant Chemotherapy in Triple Negative Breast tumors.

status: Public on Mar 24 2016

city: PARIS

first: Fatima

last: Mechta-Grigoriou

address: 26 rue d'Ulm

department: INSERM U830

institute: Institut Curie

summary: In a cohort study of 7 women with primary invasive breast cancer, we obtained a tumor specimen before (biopsy) and after (tumorectomy) 4 cycles of NAC with epirubicine and cyclophosphamide, followed by 4 cycles of taxanes. Total RNA was extracted from tumor specimens and the whole transcriptome was quantified with Affymetrix HuGene1.1ST. Molecular functions changing during chemotherapy were searched.

overall_design: Whole genome expression of triple negative breast cancer tissues were measured before and after four cycles neoadjuvant chemotherapy

first: Tina

last: Gruosso

first: Yann

last: Kieffer


title: Gene Expression analysis of therapeutical response in Triple Negative Breast tumors.

summary: 10 biopsies before treatment from triple negative patients with complete response were collected. Total RNA was extracted from tumor specimens and the whole transcriptome was quantified with Affymetrix HuGene1.1ST. The biopsies were classified into Good (major or complete) or Poor (absent or minor) therapeutic response subgroup.

overall_design: Whole genome expression of triple negative breast cancer tissues were measured before neoadjuvant chemotherapy


title: Phytoplankton assemblage during the North Atlantic spring bloom assessed from functional gene analysis

status: Public on May 11 2016

city: Princeton

first: Bess

middle: B

last: Ward

address: Washington Road

department: Geosciences

institute: Princeton University

summary: The spring bloom in the North Atlantic develops over a few weeks in response to the physical stabilization of the nutrient replete water column and is one of the biggest biological signals on earth. The composition of the phytoplankton assemblage during the spring bloom of 2008 was evaluated, using a microarray, on the basis of functional genes that encode key enzymes in nitrogen and carbon assimilation in eukaryotic and prokaryotic phytoplankton. Oligonucleotide archetype probes representing RuBisCO, nitrate reductase and nitrate transporter genes from major phytoplankton classes detected a diverse assemblage. For RuBisCO, the archetypes with strongest signals represented known phytoplankton groups, but for the nitrate related genes, the major signals were not closely related to any known phytoplankton sequences. Most of the assemblage's components exhibited consistent temporal/spatial patterns. Yet, the strongest archetype signals often showed quite different patterns, indicating different ecological responses by the main players. The most abundant phytoplankton genera identified previously by microscopy, however, were not well represented on the microarray. The lack of sequence data for well-studied species, and the inability to identify organisms associated with functional gene sequences in the environment, still limits our understanding of phytoplankton ecology even in this relatively well-studied system.

sample_organism:
synthetic construct
seawater metagenome

overall_design: Two color array (Cy3 and Cy5): the universal standard 20-mer oligo is printed to the slide with a 70-mer oligo (an archetype).  Environmental DNA sequences (fluoresced with Cy3) within 15% of the 70-mer conjugated to a 20-mer oligo (fluoresced with Cy5) complementary to the universal standard will bind to the oligo probes on the array.  Signal is the ratio of Cy3 to Cy5.  Two replicate arrays were run on duplicate targets.

first: Nicolas

last: Van Oostende


title: Gene expression signature after abrupt glucose starvation in Lactococcus lactis

status: Public on Mar 04 2016

city: Kgs. Lyngby

first: Mogens

last: Kilstrup

address: Building 301 room 158

department: DTU Systems Biology

country: Denmark

institute: Technical University of Denmark

summary:
Stressed samples: Strain MG1363 was exposed to abrupt glucose depletion in SA medium after balanced growth.
Reference sample: Strain MG1363 was grown balanced in SA medium containing 1% glucose

sample_organism: Lactococcus cremoris subsp. cremoris MG1363

overall_design: Samples were taken from reference culture at OD450=0.15, and from glucose starved cultures 10 and 60 min after depletion.


title: Improved Fermentative Production of Gamma-Aminobutyric Acid via the Putrescine Route: Systems Metabolic Engineering for Production From Glucose, Amino Sugars, and Xylose

status: Public on May 21 2016

city: Bielefeld

first: João

middle: M. P.

last: Jorge

address: Universitätsstraße 25

institute: University of Bielefeld

summary: Gamma-aminobutyric acid (GABA) is a non-protein amino acid widespread in Nature. Among the various uses of GABA, its lactam form 2-pyrrolidone can be chemically converted to the biodegradable plastic polyamide-4. In metabolism, GABA can be synthesized either by decarboxylation of L-glutamate or by a pathway that starts with the transamination of putrescine. Fermentative production of GABA from glucose by recombinant Corynebacterium glutamicum has been described via both routes. Putrescine-based GABA production was characterized by accumulation of by-products such as N-acetyl-putrescine. Their formation was abolished by deletion of the spermi(di)ne N-acetyl-transferase gene snaA. To improve provision of L-glutamate as precursor 2-oxoglutarate dehydrogenase activity was reduced by changing the translational start codon of the chromosomal gene for 2-oxoglutarate dehydrogenase subunit E1o to the less preferred TTG and by maintaining the inhibitory protein OdhI in its inhibitory formby changing amino acid residue 15 from threonine to alanine. Putrescine-based GABA  production by the strains described here led to GABA titers up to 63.2 g L-1 in fed-batch cultivation at maximum volumetric productivities up to 1.34 g L-11 h1-1, the highest volumetric productivity for fermentative GABA production reported to date. Moreover, GABA production from the carbon sources xylose, glucosamine, and N-acetyl-glucosamine that do not have competing uses in the food or feed industries was established.

overall_design: Two strains tested ABAL4 and GABA4. GABA4 is a GABA production strain, ABAL4 does not produce GABA and was used as control. Three technical replicates

first: Anh

middle: Q

last: Nguyen

first: Stefanie

last: Kind

first: Volker

last: Wendisch

first: Fernando

last: Pérez-García


title: Innate Immune Recognition of Bacterial Viability Instructs Human T follicular Helper Cell Differentiation

status: Public on Apr 06 2016

city: Wageningen

first: Guido

last: Hooiveld

address: HELIX, Stippeneng 4

department: Div. Human Nutrition & Health

country: Netherlands

institute: Wageningen University

summary: Live attenuated vaccines are often superior to dead vaccines, yet the immunological mechanisms remain largely obscure. We have recently uncovered an inherent capacity of antigen-presenting cells (APC) to discriminate live from killed bacteria by virtue of vita-PAMPs. Here we found that innate recognition of bacterial viability strongly promotes the differentiation of fully functional T follicular helper (TFH) cells. We identify TLR8 and its signaling adaptor MyD88 as critical sensor for bacterial viability in human APC, activation of which is required and sufficient to induce selective transcriptional remodeling and the production of TFH promoting signals like IL-12. Activators of other TLRs including licensed vaccine adjuvants fail to do so. Consequently, vita-PAMP receptors such as TLR8 represent promising targets for adjuvants to improve the efficacy of modern inanimate subunit vaccines.

overall_design: Human monocytes were infected with live or heat-killed E. coli for 6h.

first: Atijeh

last: Valai

first: Matteo

last: Ugolini

first: Jenny

last: Gerhard

first: Philipp

last: Georg

first: Elisa

middle: T

last: Helbig

first: Bastian

last: Opitz

first: Florian

last: Kurth

first: Mark

last: Boekschoten

first: Michael

last: Müller

first: Norbert

last: Suttorp

first: Leif

middle: E

last: Sander


title: Expression data from differentiating primary culture of equine satellite cells (ESC) incubated with gamma-oryzanol (GO)

status: Public on Feb 22 2016

city: Warsaw

first: Tomasz

last: Sadkowski

address: Nowoursynowska 159

department: Department of Physiological Sciences

institute: Warsaw University of Life Sciences - SGGW

summary: Transcriptional profiling of gamma-oryzanol-treated (24h) differentiating equine satellite cells (3rd day of differentiation) compared to control GO-untreated cells. Goal was to determine the effects of gamma-oryzanol influence on gene expression in equine satellite cells during in vitro myogenesis

overall_design: Two-condition experiment, GO-treated (24h) differentiating equine satellite cells (3rd day of differentiation) vs. differentiating equine satellite cells without GO treatment (control). Biological replicates: 4 reps of examined condition (Cy5), 4 control replicates (Cy3)

first: Anna

last: Ciecierska

first: Katarzyna

middle: A

last: Szcześniak


title: Expression data from fully-expanded leaflet of Bambara groundnut genotype (S19-3)

status: Public on Feb 10 2016

city: Nottingham

first: Venkata Suresh

last: Bonthala

address: Wollaton Road

department: School of Computer Science

institute: University of Nottingham

summary: Low temperature stress in a number of African countries, such as Botswana, at night can effect the growth and development of bambara groundnut, leading to losses in potential crop yield. Therefore, we made an attempt to identify and analyze the genes and gene modules associated with low temperature stress response in bambara groundnut using the cross-species microarray technique, as bambara groundnut has no microarray chip, coupled with network-based analysis.

overall_design: Three plants of the bambara groundnut genotype ‘S19-3’ were grown in controlled environment growth rooms at Sutton Bonington Campus, University of Nottingham under a 12 hour photoperiod and at a constant temperature of 27°C.  Plants were grown in soil columns containing a growing medium of 1 part John Innes 2 compost to 1 part sand, and were watered as required. A single, fully-expanded leaflet was sampled from each of the three plants growing at 27°C, snap frozen in liquid nitrogen and stored at -80°C. Plants were given a further 3 days at 27°C to recover from sampling before being moved to a controlled environment room at 23°C. On the fifth day at 23°C a single fully-expanded leaflet was sampled and stored, as described above. After 3 further days plants were moved to 18°C, and then five days later were sampled again.

first: Katie

last: Mayes

first: Sean

first: Festo

last: Massawe

first: Jamie

last: Twycross


title: Altered DNA methylation of glycolytic and lipogenic genes in liver from obese and type 2 diabetic patients [transcriptome analysis]

status: Public on Mar 08 2016

city: Huddinge

first: Karin

last: Dahlman-Wright

address: Blickagången 16

department: Department of Biosciences and Nutrition

institute: Karolinska Institutet

summary: Type 2 diabetes is a complex disease associated with many underlying pathomechanisms. Epigenetic regulation of gene expression by DNA methylation has become increasingly recognized as an important component in the etiology of type 2 diabetes. We performed genome-wide methylome and transcriptome analysis in liver from severely obese patients with or without type 2 diabetes to discover aberrant pathways underlying the development of insulin resistance. We identified hypomethylation of five key genes involved in hepatic glycolysis, de novo lipogenesis and insulin resistance with concomitant increased mRNA expression and protein content. The CpG-site within the ATF-motif was hypomethylated in four of these genes in liver of non-diabetic and type 2 diabetic obese patients, suggesting epigenetic regulation of transcription by altered ATF-DNA binding.  In conclusion, severely obese non-diabetic and type 2 diabetic patients have distinct alterations in the hepatic methylome and transcriptome and genes controlling glucose and lipid metabolism are hypomethylated at a regulatory site. Thus, obesity may epigenetically reprogram the liver towards increased lipid production and exacerbate the development of insulin resistance.

overall_design: To better understand the molecular mechanisms underlying the development of hepatic insulin resistance and type 2 diabetes at a molecular level, we performed a genome-wide methylome and transcriptome analysis of liver from non-obese metabolically healthy, obese non-diabetic and obese type 2 diabetic patients. Distinct DNA methylation and gene expression profiles were identified in liver from the obese and type 2 diabetic patients compared with the non-obese participants.

first: Henriette

last: Kirchner

first: Indranil

last: Sinha

first: Hui

last: Gao

first: Maxwell

last: Ruby

first: Milena

last: Schönke

first: Jessica

middle: M

last: Lindvall

first: Romain

last: Barres

last: Krook

first: Erik

last: Näslund

first: Juleen

middle: R

last: Zierath


title: Temporal analysis of physiological, metabolite and transcriptome responses during drought identifies distinct early and late phases in Arabidopsis

status: Public on Feb 29 2016

city: Norwich

first: Jonathan

middle: David

last: Moore

address: Norwich Research Park

department: Platforms and Pipelines

institute: The Genome Analysis Centre

summary: Water availability is the biggest single limitation on plant productivity worldwide. In Arabidopsis, adjustments to drought stress, involving changes in metabolism and gene expression drive increased drought tolerance and initiate diverse drought avoidance and escape responses. To address regulatory processes that integrate these complex responses we hypothesised that we needed to identify genes that govern early responses to drought. To this end, we produced a high-resolution time series transcriptomics dataset, coupled with detailed physiological and metabolic analyses of plants subjected to a slow transition from well-watered to the onset of drought conditions. 1825 differentially expressed genes (DEGs) were identified which showed no significant enrichment in gene ontology terms associated with dehydration responses and abscisic acid (ABA) regulation, confirming that the gene expression time series had targeted events prior to severe drought stress. Initial changes in gene expression coincided with a drop in carbon assimilation, not the later increase in foliar ABA content. Thus the early physiological and gene expression responses to drought were not driven by changes in leaf ABA content.  In order to identify gene regulatory networks (GRNs) linked to early events, we used Bayesian network modelling of differentially expressed transcription factor (TF) genes. This approach identified AGAMOUS-LIKE 22 as key hub gene in a TF GRN. AGL22 is involved in the transition from vegetative state to flowering. Loss of AGL22 expression affected flowering time and drying rate providing a link between early changes in metabolism and the subsequent initiation of developmental responses to stress that govern plant productivity.

overall_design:
A novel experimental design strategy (A Mead et al, in preparation), based on the principle of the “loop design”, was developed to enable efficient extraction of information about key sample comparisons using a two-color hybridization experimental system. With 108 distinct samples (four biological replicates, at each of 13 time points in control and droughted conditions, plus a shared time zero set) to be compared, the experimental design included 216 two-color microarray slides, allowing four technical replicates of each sample to be observed. One third of the slides were devoted to assessment of changes in gene expression between time points, using a simple loop design to link samples from time points across the sampled times, directly comparing samples collected on adjacent sampling times (i.e. day 1 with day 2, day 2 with day 3, etc.). With the remaining slides, four separate loops were constructed comparing treatments, biological replicates and sampling times.
All of the samples in the microarray experiment were Col-0.

first: Ulrike

last: Bechtold

first: Tracy

last: Lawson

first: Christopher

last: Penfold

first: Dafyd

last: Jenkins

first: Roxane

last: Legaie

first: Sunitha

last: Subramaniam

first: Neil

last: Baker

first: Hannah

last: Florance

first: Regina

last: Feil

first: John

last: Lunn

first: Nicholas

last: Smirnoff

first: Katherine

last: Denby

first: Vicky

last: Buchanan-Wollaston

first: Jim

last: Beynon

first: David

last: Wild

last: Rand

first: Sascha

last: Ott

first: Philip

last: Mullineaux


title: Peripheral Blood Gene Expression in Fibromyalgia Patients Reveals  Potential Biological Markers and Physiological Pathways

status: Public on Feb 01 2016

city: La Jolla

first: Sunil

last: Kurian

address: 10550 N Torrey Pines Road

department: Molecular and Experimental Medicine

institute: The Scripps Research Institute

summary: Fibromyalgia (FM) is a common pain disorder characterized by dysregulation in the processing of pain. Although FM has similarities with other rheumatologic pain disorders, the search for objective markers has not been successful. In the current study we analyzed gene expression in the whole blood of 70 fibromyalgia patients and 70 healthy matched controls. Global molecular profiling revealed an upregulation of several inflammatory molecules in FM patients and downregulation of specific pathways related to hypersensitivity and allergy. There was a differential expression of genes in known pathways for pain processing, such as glutamine/glutamate signaling and axonal development. We also identified a panel of candidate gene expression-based classifiers that could establish an objective blood-based molecular diagnostic to objectively identify FM patients and guide design and testing of new therapies. Ten classifier probesets (CPA3, C11orf83, LOC100131943, RGS17, PARD3B, ANKRD20A9P, TTLL7, C8orf12, KAT2B and RIOK3) provided a diagnostic sensitivity of 95% and a specificity of 96%. Molecular scores developed from these classifiers were able to clearly distinguish FM patients from healthy controls. An understanding of molecular dysregulation in fibromyalgia is in its infancy; however the results described herein indicate blood global gene expression profiling provides many testable hypotheses that deserve further exploration.

overall_design: Blood samples were collected in PAXgene tubes and collected samples were stored at -80oC.  The RNA was isolated using the PAXgene RNA isolation kit according to standard protocols. Total RNA was quantified on a Nanodrop spectrophotometer and visualized for quality on an Agilent Bioanalyzer. Samples with an average RIN (RNA Integrity Number) >8, indicating good quality RNA, were processed. 200ng of total RNA was amplified and then hybridized to Affymetrix® Human Gene 1.1 ST Peg arrays using standard manufacturer’s protocols on a Gene Titan MC instrument. Data was analyzed using Partek Genomics Suite (version 6.6) using RMA normalization. All genes with Log2 signal intensity less than 4.8 were excluded from analysis based on low expression. Differential expression analysis was carried out using a one way ANOVA by using Method of Moments and Fisher's Least Significant Difference (LSD) tests with a threshold p-value <0.005 for the biological and molecular function analyses, and a more conservative threshold p-value <0.001 (FDR q-value range 0.002% to 13%) for candidate diagnostic signatures.


title: Gene expression profiling in human precision-cut liver slices upon treatment with the FXR agonist obeticholic acid [human]

status: Public on Jan 27 2016

first: Guido

last: Hooiveld

summary:
Background: The bile acid-activated farnesoid X receptor (FXR) is a nuclear receptor regulating bile acid, glucose and cholesterol homeostasis. Obeticholic acid (OCA; also known as INT-747 or 6α-ethyl-chenodeoxycholic acid), a promising drug for the treatment of non-alcoholic steatohepatitis (NASH) and type 2 diabetes, activates FXR. Mouse studies demonstrated that FXR activation by OCA (INT-747) alters hepatic expression of many genes. However, no data are available on the effects of OCA in human liver. Here, we generated gene expression profiles in human precision-cut liver slices (hPCLS) after treatment with OCA.

Methods: hPCLS were incubated with OCA for 24 h. WT or FXR -/- mice received OCA or vehicle by oral gavage for 7 days.

Results: Transcriptomic analysis showed that well-known FXR target genes, including NR0B2 (SHP), ABCB11 (BSEP), SLC51A (OSTα) and SLC51B (OSTβ) and ABCB4 (MDR3), are regulated by OCA in hPCLS. Ingenuity pathway analysis confirmed that 'FXR/RXR activation' is the most significantly changed pathway upon OCA treatment. Comparison of gene expression profiles in hPCLS and mouse livers identified 18 common potential FXR targets. ChIP-sequencing in mouse liver confirmed FXR binding to IR1 sequences of Akap13, Cgnl1, Dyrk3, Pdia5, PPP1R3B and Tbx6.

Conclusions: Our study shows that hPCLS respond to OCA treatment by upregulating well-known FXR target genes, demonstrating its suitability to study FXR-mediated gene regulation. We identified 6 novel bona-fide FXR target genes in both mouse and human liver. Finally, we discuss a possible explanation for changes in HDL/LDL observed in NASH and primary biliary cirrhosis patients treated with OCA based on the genomic expression profile in hPCLS.

overall_design: Precision-cut liver slices, prepared from liver biopsies obtained from obese subjects undergoing bariatric surgery, were incubated with the FXRα agonist obeticholic acid (OCA, INT-747, 6α-ethyl-chenodeoxycholic acid) or vehicle for 24hrs, after which gene expression was profiled by array.

first: Noortje

last: Ijssennagger

first: Aafke

last: Janssen

first: Saskia

last: van Mil

first: Sander

last: Kersten


title: Transcriptomic Analysis of Soil-Grown Arabidopsis thaliana Roots and Shoots in Response to a Drought Stress

status: Public on Feb 02 2016

city: Yokohama

first: Akihiro

last: Matsui

address: 1-7-22 Suehiro-cho, Tsurumi-ku

department: Center for Sustainable Resource Science

institute: RIKEN

summary: Gene expression profiles of drought-stressed roots and shoots was performed at 0, 1, 3, 5, 7 and 9 days were analyzed using the custom microarray Agilent-034592.

overall_design: Seeds of Arabidopsis thaliana (Col-0 ecotype) were grown on MS medium at 22°C under 16-h-light/8-h-dark for 9 days. Plantlets were then transferred to ceramics granular soil (size 2.5L, Sakatanotane, Japan) and grown for 8 days at 22°C. The drought treatment was then commenced by removing excess water from the trays and ceasing any subsequent watering. Roots and shoots were harvested separately at 0, 1, 3, 5, 7 and 9 days after the onset of drought treatment.

first: Sultana

last: Rasheed

first: Khurram

last: Bashir

first: Maho

last: Tanaka

first: Motoaki

last: Seki


title: The effect of maternal diets on transcriptome profiling of in vivo bovine pre-implantation embryos

status: Public on Jan 31 2016

city: Edmonton

first: Stephen

last: Tsoi

state: Alberta

address: 4-32G Agriculture/Forestry Cen

department: AFNS

institute: University of Alberta

summary: Early embryonic development is enhanced in Holstein cows fed diets enriched in specific polyunsaturated fatty acids. However, the molecular mechanisms affected by specific polyunsaturated fatty acids during early embryonic development in cattle are poorly understood. Therefore, our objective was to evaluate the maternal effects of diets enriched in linoleic or α-linolenic acid on transcriptome profiling of in vivo bovine pre-implantation embryos.

overall_design: Non-lactating Holstein cows were blocked by parity and body weight, and assigned to one of three diets supplemented with rolled oilseeds: canola (n=8, high in oleic acid; control; CAN), sunflower (n=7, high in linoleic acid; SUN) or flax (n=8, high in α-linolenic acid; FLX). n is the number of maternal cows involved in each group. After a minimum of 35 d diet adaptation, ovarian status was synchronized and superstimulated by follicle-stimulating hormone treatments. Cows were artificially inseminated twice, 12h apart, with semen of the same sire. Once initiated, cows remained on the same diet until the end of the experiment.

middle: C

first: Reza

middle: S

last: Karashk

first: Marcos

middle: G

last: Colazo

first: Michael

middle: K

last: Dyck

first: Divakar

last: Ambrose


title: Mother-specific composition of the maternal transcriptome in Zebrafish eggs

status: Public on Jan 22 2016

city: Amsterdam

first: Han

last: Rauwerda

state: Nederland

address: Sciencepark 904

department: SILS

institute: University of Amsterdam

summary: Microarray transcriptional analysis of 24 individual zebrafish eggs from five sibling mothers

overall_design: eggs from 5 clutches (mothers); from 4 clutches 5 eggs were profiled, from 1 clutch 4 eggs were profiled

first: Timo

last: Breit


title: Genome-wide profiling of inflammatory cistrome reveals AP-1/c-Jun as a key regulator of TNFalpha-mediated triple-negative breast cancer progression [microarray]

status: Public on Jan 20 2016

first: Karin

last: Dahlman-Wright

summary: Triple-negative breast cancer (TNBC) represents a highly aggressive form of breast cancer with limited treatment options. Proinflammatory cytokines such as TNFalpha can facilitate tumor progression and metastasis. However, our knowledge of the molecular mechanisms underlying TNBC progression mediated by inflammation is still limited. Here, we define the AP-1 transcription factor c-Jun cistrome, which is comprised of 13800 binding sites responsive to TNFalpha-induced signaling in TNBC cells. In addition, we show that c-Jun regulates nearly a third of the TNFalpha-elicited transcriptome. Expression of the c-Jun-regulated pro-invasion gene program is strongly associated with clinical outcomes in TNBCs. Mechanistically, we demonstrate that c-Jun drives TNFalpha-mediated TNBC tumorigenicity by transcriptional regulation of Ninj1. As exemplified by the c-Jun bound CXC chemokine genes clustered on chromosome 4, we demonstrate that NF-kB might be a pioneer factor and is required for the regulation of TNFalpha-inducible inflammatory genes, whereas c-Jun has little effect. Together, our results uncover AP-1 as an important determinant for inflammation-induced cancer progression, rather than inflammatory response.

overall_design: BT549 cells were cultured to 50% confluency and transfected with control or c-Jun siRNA for 72 hours, followed by treatment with or without TNFα for 6 hours.

first: Yichun

last: Qiao

first: Philip

last: Jonsson

first: Chunyan

last: Zhao

first: Indranil

last: Sinha


title: Genomic and transcriptomic data integration and its automated analysis in clear-cell renal cell carcinoma suggests population heterogeneity of causes and mechanism of the disease

status: Public on Dec 28 2015

city: Voronezh

first: Sergey

last: Solodskikh

address: Universitetskaya sq, 1

department: Genetics, Cytology and Bioengineering

country: Russia

institute: Voronezh State University

summary: Renal cell carcinoma (RCC) is one of the most widespread solid kidney tumors – it represents 90% of all malignant kidney tumors. Clear-cell RCC is the most widespread type of RCC.  It is characterized by 3-rd chromosome rearrangements, VHL inactivation due to mutations or promoter hypermethylation, 5p amplification, and mutations in KDM6A/UTX, SETD2, KDM5C/JARID1C and MLL2 genes. Molecular profile of ccRCC was characterized in a number of research papers using high-throughput platforms (microarray SNP-profiling, RNA-seq, whole exome and whole genome sequencing). Nevertheless, differences of observed mutations and gene expression levels among different populations suggest that causes and mechanism of the disease can also vary. In order to obtain such information about Western Russian population we have performed DNA resequencing and microarray expression profiling, and then integrated this data in a single dataset. We then analyzed DNA mutations and gene expression level simultaneously using standard molecular data analysis pipelines (gene set enrichment analysis, casual gene network generation, principle component analysis).

overall_design: Gene expression was analyzed in tumor and normal kidney tissues of patients 50 to 75 years old using Affymetrix Human Gene 1.1 ST arrays.


title: Genome-wide peripheral blood transcriptome analysis of Arab female Lupus and Lupus nephritis

status: Public on Jan 06 2016

city: Kuwait

first: Suad

last: AlFadhli

address: Jabriya

department: Medical laboratory Sciences

country: Kuwait

institute: Kuwait University

summary:
Genome-wide alternative splice analysis of RNA from lupus and its severe form lupus nephritis
We aimed to explore the genome-wide peripheral blood transcriptome of lupus (SLE) and its severe form lupus nephritis (LN) cases compared to healthy subjects (HC) using high density Affymetrix Human Exon1.0.ST arrays. Analysis revealed 15 splice variants that are differentially expressed between SLE/HC and 99 variants between LN/HC (p≤0.05,SI>or≤0.5,Benjamin Hochberg-False discovery rate correction). Comparison between LN/SLE revealed 7 variants that are differentially expressed with p≤0.05,SI>0.5,Benjamin Hochberg-FDR correction. Pathway analysis of differentially spliced genes revealed 11 significant pathways in SLE and 12 in LN (p<0.05). Analysis of peripheral blood transcriptome revealed signature causative genes that are alternatively spliced, signifying their clinical relevance in the pathophysiology of disease. The extent of differential splicing was found to be higher in LN than in SLE, signifying the need for further in-depth research in the same domain. Present study is the first to reveal the significance of alternative variants in susceptibility to SLE and LN.

overall_design: We analyzed blood from 11 female subjects (5 lupus, 3 lupus nephritis and 3 healthy control) using the Affymetrix Human Exon 1.0 ST platform. Array data was processed by Alt Analyze and Genespring software. No techinical replicates were performed. One of the outiler sample (HC2)  was excluded from further analysis.

first: Rasheeba

last: Nizam


title: Blood transcriptional biomarkers for active TB among US patients: A case-control study with systematic cross-classifier evaluation.

status: Public on Nov 23 2015

city: Aurora

first: Nicholas

last: Walter

state: Colorado

address: 12700 East 19th Avenue

country: USA

institute: University of Colorado

summary: In a prospective case-control study, we identified novel transcriptional classifiers for TB among US patients and systematically compared their accuracy to other classifiers in published studies.

overall_design: Whole blood from US patients was collected to accurately diagnose active TB in racially and ethnically diverse populations for RNA extraction and hybridization on Affymetrix microarrays.


title: Transcriptomic analysis of Retinoic acid and 9 cis retinoic acid in zebrafish.

status: Public on Dec 31 2015

city: Barcelona

first: Eva

middle: Lima

last: Oliveira

state: Barcelona

address: Carrer Jordi Girona 18-26

department: Environmental Chemistry

country: Spain

institute: IDAEA CSIC

summary: We are presenting the application of toxicogenomics in the evaluation of the toxic effects of retinoic acid and one of its isoforms the 9-cis retinoic acid. The main goal is to distinguish the pattern of action of the both chemical compounds and their action in an extended exposure. The results suggest a different pattern within the days and the chemicals. Representatives of each GO functional groups were selected and quantified by real-time PCR to validate the microarray data and to differentiate the action of retinoic acid compounds studied.

overall_design: Two different treatments were performed in this study. Zebrafish fertlized embryos were exposed to retinoic acid and 9-cis retinoic acid, during 24h and 72h. 3 biological replicates were performed per treatment.

first: Marta

last: Casado

first: Amadeu

last: Soares

first: Carlos

last: Barata

first: Benjamín

last: Piña


title: The impact of PPARα activation on whole genome gene expression in human precision-cut liver slices

first: Guido

last: Hooiveld

summary:
Background: Studies in mice have shown that PPARα is an important regulator of lipid metabolism in liver and a key transcription factor involved in the adaptive response to fasting. However, much less is known about the role of PPARα in human liver. Here we set out to study the function of PPARα in human liver via analysis of whole genome gene regulation in human liver slices treated with the PPARα agonist Wy14643.

Results: Quantitative PCR indicated that PPARα is well expressed in human liver and human liver slices and that the classical PPARα targets PLIN2, VLDLR, ANGPTL4, CPT1A and PDK4 are robustly induced by PPARα activation. Transcriptomics analysis indicated that 617 genes were upregulated and 665 genes were downregulated by PPARα activation (q value<0.05). Many genes induced by PPARα activation were involved in lipid metabolism (ACSL5, AGPAT9, FADS1, SLC27A4), xenobiotic metabolism (POR, ABCC2, CYP3A5) or the unfolded protein response, whereas most of the downregulated genes were involved in immune-related pathways. Among the most highly repressed genes upon PPARα activation were several chemokines (e.g. CXCL9-11, CCL8, CX3CL1, CXCL6), interferon γ-induced genes (e.g. IFITM1, IFIT1, IFIT2, IFIT3) and numerous other immune-related genes (e.g. TLR3, NOS2, and LCN2). Comparative analysis of gene regulation by Wy14643 between human liver slices and primary human hepatocytes showed that down-regulation of gene expression by PPARα is much better captured by liver slices as compared to primary hepatocytes. In particular, PPARα activation markedly suppressed immunity/inflammation-related genes in human liver slices but not in primary hepatocytes. Finally, several putative new target genes of PPARα were identified that were commonly induced by PPARα activation in the two human liver model systems, including TSKU, RHOF, CA12 and VSIG10L.

Conclusion: Our manuscript demonstrates the suitability and superiority of human liver slices over primary hepatocytes for studying the functional role of PPARα in human liver. Our data underscore the major role of PPARα in regulation of hepatic lipid and xenobiotic metabolism in human liver and reveal a marked immuno-suppressive/anti-inflammatory effect of PPARα in human liver slices that may be therapeutically relevant for non-alcoholic fatty liver disease.

overall_design: Precision-cut liver slices, prepared from liver biopsies obtained from obese subjects undergoing bariatric surgery, were incubated with the peroxisome proliferator-activated receptor alpha (PPARα) agonist Wy14643 or vehicle for 24hrs, after which gene expression was profiled by array.

first: Aafke

middle: W

last: Janssen

first: Bark

last: Bretzel

first: Geert

last: Stoopen

first: Frits

middle: J

last: Berends

first: Ignace

first: Ad

last: Peijnenburg

first: Sander

last: Kersten


title: Early regulation of profibrotic genes in primary human cardiac myocytes by Trypanosoma cruzi

status: Public on Dec 09 2015

city: Nashville

first: Pius

middle: N

last: Nde

address: 1005 Dr. D.B. Todd Jr. Blvd

department: Microbiology and Immunology

institute: Meharry Medical College

summary: The molecular mechanisms of Trypanosoma cruzi induced cardiac fibrosis remains to be elucidated. Primary human cardiomyoctes (PHCM) exposed to invasive T. cruzi trypomastigotes were used for transcriptome profiling and downstream bioinformatic analysis to determine fibrotic-associated genes regulated early during infection process (0 to 120 minutes). The identification of early molecular host responses to T. cruzi infection can be exploited to delineate important molecular signatures that can be used for the classification of Chagasic patients at risk of developing heart disease. Our results show distinct gene network architecture with multiple gene networks modulated by the parasite with an incline towards progression to a fibrogenic phenotype. Early during infection, T. cruzi significantly upregulated transcription factors including activator protein 1 (AP1) transcription factor network components (including FOSB, FOS and JUNB), early growth response proteins 1 and 3 (EGR1, EGR3), and cytokines/chemokines (IL5, IL6, IL13, CCL11), which have all been implicated in the onset of fibrosis. The changes in our selected genes of interest did not all start at the same time point. The transcriptome microarray data, validated by quantitative Real-Time PCR, was also confirmed by immunoblotting and customized Enzyme Linked Immunosorbent Assays (ELISA) array showing significant increases in the protein expression levels of fibrogenic EGR1, SNAI1 and IL 6. Furthermore, phosphorylated SMAD2/3 which induces a fibrogenic phenotype is also upregulated accompanied by an increased nuclear translocation of JunB. Pathway analysis of the validated genes and phospho-proteins regulated by the parasite provides the very early fibrotic interactome operating when T. cruzi comes in contact with PHCM. The interactome architecture shows that the parasite induces both TGF-β dependent and independent fibrotic pathways, providing an early molecular foundation for Chagasic cardiomyopathy. Examining the very early molecular events of T. cruzi cellular infection may provide disease biomarkers which will aid clinicians in patient assessment and identification of patient subpopulation at risk of developing Chagasic cardiomyopathy.

overall_design: Primary Human Cardiomyoctes (low passage) were exposed to T. cruzi at different time points. The control was done in biological triplicates and the time points (60, 90 and 120 minutes) were done in biological duplicates.

first: Aniekanabassi

last: Udoko

first: Candice

last: Johnson

first: Andrey

last: Dykan

first: Girish

last: Rachakonda

first: Fernando

last: Villalta

first: Sammed

last: Mandape

first: Maria

middle: F

last: Lima

first: Siddharth

last: Pratap


title: Growth signals employ CGGBP1 to suppress transcription of Alu-SINEs [Affymetrix]

status: Public on Dec 21 2015

city: Gandhinagar

first: Umashankar

last: Singh

state: Gujarat

address: Acad Block 4 Room 317 IIT Gandhinagar Palaj

department: Biological Sciences and Engineering

country: India

institute: IIT Gandhinagar

summary:
Alu SINEs are the most numerous frequently occurring transcription units in our genome and possess sequence competence for transcription by RNA Pol III. However, through poorly understood mechanisms, the Alu RNA levels are maintained at very low levels in normal somatic cells with obvious benefits of low rates of Alu retrotransposition and energy-economical deployment of RNA Pol III to the tRNA genes which share promoter structure and polymerase requirements with Alu SINEs. Using comparative ChIP sequencing, we unveil that a repeat binding protein, CGGBP1, binds to the transcriptional regulatory regions of Alu SINEs thereby impeding Alu transcription by inhibiting RNA Pol III recruitment. We show that this Alu-silencing depends on growth factor stimulation of cells and subsequent tyrosine phosphorylation of CGGBP1. Importantly, CGGBP1 ensures a sequence-specific discriminative inhibition of RNA Pol III activity at Alu promoters, while sparing the structurally similar tRNA promoters. Our data suggest that CGGBP1 contributes to growth-related transcription by preventing the hijacking of RNA Pol III by Alu SINEs.
This study was used to find out the effect of CGGBP1 on serum-induced changes in gene expression and effect of serum on gene expression regulation by CGGBP1.

overall_design: Gene expression profiling of normal human fibroblasts under 4 different experimental perturbations: serum starvation or serum stimulation and CGGBP1 depletion or normal CGGBP1 levels.

first: Prasoon

last: Agarwal

first: Bengt

last: Westermark


title: The regulation of the AdcR regulon in Streptococcus pneumoniae depends both on Zn2+- and Ni2+- availability

status: Public on Nov 20 2015

city: STOCKHOLM

first: Sulman

last: Shafeeq

address: nobel vag 16

department: MTC

country: Sweden

summary:
By using the transcriptomic approach, we have elucidated the effect of Ni2+ on the global gene expression of S. pneumoniae D39 by identifying several differentially expressed genes/operons in the presence of a high extracellular concentration of Ni2+. The genes belonging to the AdcR regulon (adcRCBA, adcAII-phtD, phtA, phtB and phtE) and the PsaR regulon (pcpA, prtA and psaBCA) were highly upregulated in the presence of Ni2+. We have further studied the role of Ni2+ in the regulation of the AdcR regulon by using ICP-MS analysis, electrophoretic mobility shift assays and transcriptional lacZ-reporter studies, and demonstrate that Ni2+ is directly involved in the derepression of the AdcR regulon via the Zn2+-dependent repressor AdcR, and has an opposite effect on the expression of the AdcR regulon as compared to Zn2+.

This SuperSeries is composed of the SubSeries listed below.

overall_design: Refer to individual Series


title: Impact of adcR delation on the transcriptome of Streptococcus pneumoniae D39 in the presence of Ni2+

summary: Transcriptome comparison of the Streptococcus pneumoniae D39 wild-type to D39 ΔadcR grown in CDM with 0.3 mM Ni2+

overall_design: One condition design comparision of two strains including a dye swap.

first: Irfan

last: Manzoor

first: Oscar

middle: P

last: Kuipers


title: Transcriptome response of the Streptococcus pneumoniae D39 wild-type to Ni2+

summary: Transcriptome comparison of the Streptococcus pneumoniae D39 wild-type grownin CDM with 0.5 mM Ni2+ to grown in CDM with 0 mM Ni2+

overall_design: Two conditions design comparison of one strain including a dye swap.