title: Calibration of a custom designed microarray for European Fire Salamander

status: Public on Jun 20 2015

city: Ploen

first: Till

last: Czypionka

address: August-Thienemann-Strasse 2

department: Evolutionary Genetics

country: Germany

institute: MPI for Evolutionary Biology

summary: A custom 8x60 k expression microarray for larvae of European fire salamander (Salamandra salamandra) was designed based on transcriptome sequencing. It is known the fact, that oligonucleotide probes differ in the binding behavior towards their target sequences. Therefore, we performed a calibration of our microarray where we assessed the binding behavior of the individual probes empirically. This information was used to normalize gene expression data measurements with the same microarray in another experiment. Please refer to the accompanying publication (Czypionka et al. 2015." Ecological transcriptomics – a non-lethal sampling approach for endangered fire salamanders" Methods in Ecology and Evolution) for more information.

overall_design:
Labeled cRNA was prepared from Salamander larvae kept at 9°C and 17°C. A cRNA calibration pool was prepared with equimolar amounts of cRNA prepared from (a) a larvae (temperature: 9°C:  source: pond KOE), (b) a larvae (temperature: 17°C:  source: pond KOE), (c) a larvae (temperature: 9°C:  source: stream KoGB (Klufterbach) and (d) a larvae (temperature: 17°C:  source: stream KoGB (Klufterbach). See Steinfartz et al. (2007) (doi: 10.1111/j.1365-294X.2007.03490.x) for information of the source populations. Increasing amounts of labeled cRNA (75 ng, 150 ng, 300 ng, 600 ng, 1000 ng, 1400 ng, 1800 ng, 2200 ng), corresponding to (1/8, 1/4, 1/2, 1, 1 2/3, 2 1/3, 3 and 3 3/3 times the recommended amount of 600 ng) were hybridized to 8 microarrays (one microarray per dilution). The change in observed signal intensity in relation to the change in amount of labeled cRNA was used to infer the target-binding behavior of the individual probes. This information was extracted, to be used for a normalization procedure in another experiment with the same microarray (see Czypionka et al. 2015." Ecological transcriptomics – a non-lethal sampling approach for endangered fire salamanders" Methods in Ecology and Evolution).
The current study provides only raw data for a calibration experiment, to validate the binding behavior of the different probes on a newly designed microarray for a non model organism (European Fire salamander). This calibration is based only on raw data. More information on targeted genes is provided in a different GEO dataset (currently submitted), where biological meaningful analysis are performed with data which are normalized based on this calibration.

first: Tamar

last: Krugman

first: Janine

last: Altmueller

first: Leon

last: Blaustein

first: Sebastian

last: Steinfartz

first: Alan

middle: R

last: Templeton

first: Arne

middle: W

last: Nolte


title: Potential Mechanism of Action of 3'-Demethoxy-6-O-Demethylisoguaiacin on Methicillin-resistant Staphylococcus aureus

status: Public on Jun 27 2015

city: Monterrey

first: Aldo

middle: Francisco

last: Clemente soto

state: Nuevo Leon

address: Vicente Guerrero

department: Farmacia

country: Mexico

institute: UNIVERSIDAD AUTONOMA DE NUEVO LEÓN

summary: Methicillin-resistant Staphylococcus aureus is one of the major causative agents associated to infections with a high morbidity and mortality in hospitals worldwide. In previous studies, we reported that lignan 3'-demethoxy-6-O-demethylisoguaiacin isolated and characterized from Larrea tridentata showed the best activity towards methicillin-resistant S. aureus. Understanding of mechanism of action of drugs allows design drugs in a better way. Therefore, we employed microarray to obtain gene expression profile of methicillin-resistant S. aureus after exposure to 3'-demethoxy-6-O-demethylisoguaiacin. The results showed that lignan had an effect on cell membrane affecting proteins of the ATP-binding cassette (ABC) transport system causing bacteria death.

sample_organism: Staphylococcus aureus subsp. aureus MRSA252

overall_design: This study consisted of comparison of isolated RNA of MRSA not treated and MRSA treated with lignan 3'-demethoxy-6-O-demethylisoguaiacin. Both RNAs samples were differentially dyed with Cy3 and Cy5 during cDNA synthesis and hybridized on DNA chip. Afterwards, the chip was scanned in a GenePix 4000B scanner. The resulting gene expression profile was analyzed in databases for functional annotations to find a potential mechanism of the lignan in MRSA.

first: Juan

middle: M

last: Favela-Hernández

middle: F

last: Clemente-Soto

first: Isaias

last: Balderas-Rentería

first: Elvira

last: Garza-González

first: María

last: Camacho-Corona


title: Illumina Infinium whole-genome SNP-CN data from cell lines originating from patients with multiple myeloma

status: Public on Jun 30 2015

city: Atlanta

first: Jeanne

last: Kowalski

address: 1365-B Clifton Rd. NE.

department: Winship Cancer Institute

country: USA

institute: Emory University

summary: We performed Illumina Infinium whole-genome SNP-CN profiling of KMS11, MM.1S, and RPMI8226 multiple myeloma cell lines to detect gene copy number variants distinct to each cell line

overall_design: Three multiple myeloma cell lines (KMS11, MM.1S, and RPMI8226)

first: Lawrence

middle: H

last: Boise

first: Sagar

last: Lonial

first: Michael

last: Rossi


title: Light and rhythmic regulation of gene expression in pineal gland of the chicken

city: Nashville

first: Xiaofei

last: Wang

state: TN

address: 3500 John A Merritt blvd

department: Biological Sciences

institute: Tennessee State University

summary: Light is the primary environmental cue in resetting the phase of circadian pacemaker in vertebrates. In birds, the effect of light is partly mediated by modulating the levels of circadian genes in the pineal gland. To further elucidate the mechanism by which light resets the circadian clock, we studied gene expression in the chicken pineal gland under acutely extended light period.

overall_design: Three paradigms of treatments were used in this study. For each paradigm, chicks were assigned at random to control treatment (control groups) or light treatment (light groups). All birds in control groups were given 12 h light and 12 h dark period (LD 12:12). Light-on time is referred to as Zeitgeber Time 0 (ZT0). In paradigm 1, birds in the light group (n =25 for each of the groups in each paradigm) were acclimated to LD 12:12 for one week in the same light scheme as were the control birds, then exposed to light for 2 h during the subjective late night (ZT22 to ZT24) on the last day. All birds (including the controls) were sacrificed at ZT0. Pineal glands were dissected and 5-6 pineal glands were pooled for the preparation of one RNA sample. In paradigm 2, birds in the light group were acclimated as in paradigm 1 for one week, then exposed to light for 2 h during the early subjective night (ZT12 to ZT14) on the last day. All birds (including controls) were sacrificed at ZT14. The pineal glands were also pooled as before. In paradigm 3, birds in the light group (n = 25) were kept in LD 15:9 cycle all the time, and all birds (including controls) were sacrificed at ZT14. Similarly, 5-6 pineal glands in the same treatment were pooled.

first: Kontip

middle: C

last: Mahautmr


title: Type II JAK2 Inhibitor NVP-CHZ868 is Active in Vitro and in Vivo Against JAK2-Dependent B-cell Acute Lymphoblastic Leukemias

status: Public on Jun 18 2015

city: Boston

first: Loretta

last: Li

state: MA

address: 450 Brookline Ave

department: Medical Oncology

institute: Dana-Farber Cancer Institute

summary: Gene expression profiling was performed to define transcriptional programs associated with response to type II JAK2 inhibitor NVP-CHZ868 alone or in combination with dexamethasone in vitro and in vivo.

overall_design:
MHH-CALL4 cells harboring a CRLF2 rearrangement and JAK2 I682F mutation were treated with vehicle, CHZ868, dexamethasone, or CHZ868 + dexamethasone combination for 12 hours in triplicate. RNA was then extracted for hybridization on Affymetrix microarrays.
CRLF2+ patient-derived xenografts (05-412, 05-440, and 05-537) were treated in vivo for 3 days with vehicle, CHZ868, dexamethasone, or CHZ868 + dexmathasone combination for 3 days and then sacrificed. Transcriptional profiling was performed on unselected splenocytes from these animals.

middle: S

first: Bjoern

last: Chapuy

first: David

last: Weinstock


title: Comprehensive expression analysis of primary hepatocytes under four different culture conditions

status: Public on Jun 25 2015

city: Saitama

first: Ryosuke

last: Takahashi

address: 2520 Hatoyama

department: Central Research Laboratory

country: Japan

institute: Hitachi, Ltd.

summary: Primary hepatocytes have been widely explored as cell sources for the study of in vitro drug metabolism and pharmacokinetics (DMPK). Aiming toward establishing an in vitro drug screening method, the current study illustrated a comprehensive increase in the DMPK-related gene expression of nanopillar (NP)-cultured 3D-spheroid. To examine the expressional changes in DMPK-related genes under four different conditions, namely, NP-, sandwich (SW)-, monolayer (ML)-cultured rat hepatocytes, and freshly isolated hepatocytes, genome-wide gene-expression analysis using a DNA microarray was performed. Among the DMPK-related genes, cytochrome P450, UDP-glucuronosyltransferase, and transporter genes were focused on. Principal component analysis showed that the global gene expression profile in sample from NP culture is closer to that from freshly isolated hepatocytes than that from SW culture. The expressions of almost all Cyp 1 to 3 and Ugt genes of NP-cultured 3-D spheroid were higher than those of ML and SW. The expression of Abcc2 gene whose translation product has a critical role in excretion of metabolized bile acids in hepatocyte to bile canaliculi was three times higher in NP than in ML. From these results, 3-D spheroid formed by the NP culture was suggested to possess higher ability of metabolism and excretion than conventional 2-D monolayer culture. The NP culture has a potential as an alternative culturing technique for evaluating metabolism and toxicity toward the development of new drugs.

overall_design: Gene expression in rat hepatocyte was measured under four different conditions, namely, Nanopillar (NP)-, sandwich (SW)-, monolayer (ML)-cultured rat hepatocytes, and freshly isolated hepatocytes. Three independent experiments were performed at 95 hours of post-seeding.

first: Akiko

last: Hisada

first: Hiroshi

last: Sonoda


title: Ecological transcriptomics: a non-lethal sampling approach for endangered fire salamanders

first: Till

last: Czypionka

summary: The analysis of transcriptomes is well-established and increasingly affordable in studies at the interface of ecology and evolution. Expression analysis of thousands of genes in parallel reveals functions and pathways involved in relevant phenotypic differentiation. The application of such methods typically involves the sacrifice of the analysed organisms, which is potentially subject to ethical and legal constraints. As an alternative to lethal sampling, transcriptome analyses can be performed using small biopsies of dispensable tissues. It has to be verified, however, to what extent such results are representative of the whole organism. Here, we use a custom microarray to compare transcriptomes of tail-clip samples with those of the remaining whole-body of fire salamander larvae (Salamandra salamandra). The microarray was calibrated using target RNA to validate the performance of each probe. We varied water temperature to test whether the thermal response in gene expression can be characterized in both types of sample. A large fraction (51 %) of the differentially expressed genes showed parallel changes for both tail clips and whole bodies in response to temperature. While sets of differentially expressed were not identical, they largely belonged to the same functional categories. The gene functions thus revealed a common thermal response of larvae irrespective of the sampled tissue. This included an overexpression of mitochondrial transcripts, an expected thermal acclimatization response of ectotherms. Hence, ecological transcriptomics based on small biopsies represent an alternative to the analysis of lethally sampled tissues in situations where the sacrifice of individuals is not an option.

overall_design: Larvae of European Fire salamander were exposed to two different temperatures (9°C &  17°C; n(cold) = 6, n(warm) = 6, n(total) = 12). The transcriptome response to temperature was assessed based on RNA extracted from tail tips, which can be sampled without sacrificing the individual, and based on RNA extracted from the remaining whole body. Results from the analysis of both tissues were compared.

first: Tamar

last: Krugman

first: Janine

last: Altmueller

first: Leon

last: Blaustein

first: Sebastian

last: Steinfartz

first: Alan

last: Templeton

first: Arne

last: Nolte


title: Tracking the elusive function of Bacillus subtilis Hfq (NimbleGen)

status: Public on Jun 22 2015

city: Jouy-en-Josas

first: Tatiana

last: Rochat

address: Domaine de Vilvert

country: France

institute: INRA

type: Expression profiling by genome tiling array

summary:
Transcriptomic analysis of Bacillus subtilis hfq mutant in exponential phase of growth. Wild-type strain and hfq mutant cells in exponentially growth phase were subjected to tiling array gene expression analysis.
RNA-binding protein Hfq is a key component of the adaptive responses of many proteobacterial species. In these organisms, the importance of Hfq largely stems from its participation to regulatory mechanisms involving small non-coding RNAs. In contrast, the function of Hfq in Gram-positive bacteria has remained elusive. Hfq does not appear to influence B.subtilis RNA patterns during the exponential phase to any significant extent, at least in cells grown in rich medium.

sample_organism: Bacillus subtilis subsp. subtilis str. 168

overall_design: This data set contains 4 samples. Expression profiles of Bacillus subtilis prototype strain (BSB1, a tryptophan-prototrophic derivative 168 strain) and a ∆hfq mutant were examined at OD ~0.5 in LB medium. Two biological replicates were analyzed.

first: Etienne

last: Dervyn

first: Pierre

last: Nicolas


title: aCGH in paired blood/tumor samples in Wilms Tumors

status: Public on Jun 19 2015

city: MADRID

first: LARA

last: RODRIGUEZ

address: PASEO DE LA CASTELLANA 261

department: GEF

country: Spain

institute: INGEMM

type: Genome variation profiling by genome tiling array

summary: Array CGH analysis of paired blood and tumor DNA samples from 14 patients with sporadic Wilms tumor. Previously array CGH studies in WT have only been performed in tumor tissue samples. We herein describe a novel set of constitutional abnormalities and point to candidate genes that might be associated with WT development.

overall_design: 28 paired DNA samples of peripheral blood/fresh tumor tissue from 14 patients (10 males, 4 females) with histologically confirmed WT. All tumor samples were collected from primary tumors from patients treated with the same neoadjuvant chemotherapy following the International Society of Paediatric Oncology (SIOP) WT 2001 trial protocol.

first: Victor

last: Martinez-Glez

first: Leila

last: Cabral de Almeida Cardoso

first: Lara

last: Rodriguez-Laguna


title: Tracking the elusive function of Bacillus subtilis Hfq (Agilent)

summary:
Transcriptomic analysis of Bacillus subtilis wild-type strain and hfq mutant in stationary phase of growth using to tiling array gene expression analysis.
RNA-binding protein Hfq is a key component of the adaptive responses of many proteobacterial species. In these organisms, the importance of Hfq largely stems from its participation to regulatory mechanisms involving small non-coding RNAs. In contrast, the function of Hfq in Gram-positive bacteria has remained elusive. 97 transcription units (representing 134 genes) were found significantly different between the wild-type and the ΔhfqBs strains in the stationary cultures performed in rich LB medium.

platform_organism: Bacillus subtilis subsp. subtilis str. 168

overall_design: This data set contains 4 samples. Expression profiles of Bacillus subtilis prototype strain (BSB1, a tryptophan-prototrophic derivative 168 strain) and a ∆hfq mutant were examined 5 h after the onset of stationary phase in LB medium. Two biological replicates were analyzed.

first: Ulrike

last: Mäder

first: Cyprien

last: Guérin


title: Tracking the elusive function of Bacillus subtilis Hfq

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

overall_design: Refer to individual Series


title: ncRNA (non-coding RNA) signature in endothelial cells during hypoxia [array]

city: Hannover

first: Jan

last: Fiedler

address: Carl-Neuberg-Str. 1

department: Institute of Molecular and Translational Therapeutic Strategies (IMTTS), IFB-Tx

institute: Hannover Medical School

summary:
To define ncRNA expression in hypoxic endothelial cells, we applied pro-angiogenic hypoxia to cultured endothelial cells.
Afterwards total RNA was isolated and underwent genechip analysis.

overall_design: HUVECs were subjected to normoxic or hypoxic (0.1-0.2% O2) cell culture conditions.

first: Robert

last: Geffers


title: CGH analyses for the Chinese indigenous pig breeds and commercial pig breeds [Agilent]

status: Public on Jun 29 2015

city: Beijing

first: Huimin

last: Kang

state: Beijing

address: Beijing

country: China

institute: China Agriculture University

summary:
Since CNVs play a vital role in genomic studies, it is an imperative need to develop a comprehensive, more accurate and higher resolution porcine CNV map with practical significance in follow-up CNV functional analyses
To detect CNV of pigs, we performed high density aCGH data of diverse pig breeds in the framework of the pig draft genome sequence (Sscrofa10.2)

overall_design:
9 Chinese indigenous pig, one Chinese wild boar and 2 commercial pigs were detected using one pig of Duroc as reference.
These 12 animals include 1 wild pig, 2 pigs each from Yorkshire and Landrace as the representatives of modern commercial breeds and 9 unrelated individuals selected from 6 Chinese indigenous breeds (2- Tibetan pig, 2- Diannan small-ear pig, 2-Meishan pig, 1- Min pig, 1-Daweizi pig, and 1-Rongchang pig).

first: Jianfeng

last: Liu

first: Jiying

last: Wang

first: Jicai

last: Jiang


title: Expression data from bovine nucleus pulposus interverteral disc cells

city: Athens

first: Eleni

last: Mavrogonatou

address: Patriarchou Grigoriou & Neapoleos

department: Institute of Biosciences and Applications

country: Greece

institute: NCSR "Demokritos"

summary:
Assessment of the putative differential gene expression profiles in high osmolality-treated bovine nucleus pulposus intervertebral disc cells for a short (5 h) and a long (24 h) time period. Identification of novel genes up- or down-regulated as an early or a late response to hyperosmotic stress.
A 5 and 24 h-hyperosmotic treatment of nucleus pulposus cells led to transcriptional changes in >100 and 200 genes, respectively.

overall_design: Nucleus pulposus intervertebral disc cells were exposed to hyperosmotic stress for 5 and 24 h before RNA extraction and transcriptomics analysis. Three biological replicates were tested for each condition. Selected genes found to be differentially expressed were validated by RT-qPCR. Functional experiments were performed in order to assess the role of specific proteins encoded by genes found to be up-regulated in the osmo-reguatory response of intervertebral disc cells.

first: Konstantinos

last: Papadimitriou

first: Jill

middle: P

last: Urban

first: Vassilios

last: Papadopoulos

first: Dimitris

last: Kletsas


title: Phosphoproteome analysis from BCR-ABL, MYC and CD22DE12 transgenic mouse models

city: St. Peter

first: Sanjive

last: Qazi

state: MN

address: 800 west College Av

department: Biology

institute: Gustavus Adolphus College

summary: Leukemic splenocytes from these commercial transgenic mice that developed fatal leukemia with massive splenomegaly were isolated at the time of the necropsy and subjected to gene expression profiling and phosphoprotein profiling in side by side comparison with CD22DE12-Tg BPL or CD22DE12_BCR-ABL double transgenic cells.

platform_organism:
Homo sapiens
Mus musculus
Rattus norvegicus

overall_design: Mouse leukemia cells were isolated from markedly enlarged spleens of CD22DE12-Tg, BCR-ABL-Tg, Eµ-MYC Tg mice, and Splenocytes from wildtype healthy C57BL/6 mice served as controls (2 samples and 2 relpicates per mouse genotype).

first: Fatih

last: Uckun


title: CGH of stage 13 amplifying follicle cells to measure changes in replication fork progression in DNA damage checkpoint and double-strand break repair mutants

city: Cambridge

first: Terry

middle: L.

last: Orr-Weaver

address: 9 Cambridge Center

institute: Whitehead Institute for Biomedical Research

summary: Comparative genomic hybridization was performed to compare amplification gradients of stage 13 follicle cells from several DNA damage checkpoint and double-strand break repair mutants to wild-type (OrR) gradients. Two-three replicates were done for each genotype.

overall_design: Stage 13 egg chamber genomic DNA from each genotype was measured relative to diploid genomic DNA from 0-2 hour wild-type (OrR) embryonic DNA.

first: Jessica

middle: L

last: Alexander


title: Regulation of PTSBio by transcriptional repressor NigR

city: Miami

first: Dragana

last: Ajdic

state: Florid

address: 1600 NW 10th Ave, RMSB 2023

department: Dermatology

institute: University of Miami

summary: In this study we analyzed the transcriptional regulation of the operon (OBio) encoding the PTSBio and showed that it was repressed by NigR, a LacI-like transcriptional regulator. To elucidate the role of NigR in regulation of S. mutans carbohydrate transporters we performed full genome expression microarrays using custom Affymetrix chip. Expression microarray analysis was performed with ΔnigR grown in CDM supplemented with glucose and compared to that of WT grown under identical conditions. Deletion of the nigR gene did not exert broad transcription changes in S. mutans under tested conditions. OBio was the only operon that was significantly upregulated in the ΔnigR strain (Supplemental Table 1). This data confirmed that NigR is the repressor of OBio and that OBio is its only PTS target under tested condition.

overall_design: Streptococcus mutans UA159 wild-type cells and ΔnigR strains were grown in a chemically-defined medium supplemented with glucose until the mid-log phase.  The transcriptional profile of the whole genome was examined with microarray.

first: Milos

last: Vujanac


title: Expression profiling of invasive breast carcinoma samples from Institut Curie

city: Paris

first: Tatiana

last: Popova

address: 26, rue d'Ulm

institute: Institute Curie

type: Expression profiling by high throughput sequencing

summary:
Genomic hallmarks of homologous recombination deficiency in invasive breast carcinomas to appear in Internationa Journal of Cancer
Transcriptome analysis of 243 (plus 12 duplicates) primary breast invasive carcinoma samples of various molecular subtypes.

overall_design: This dataset contains 255 arrays for 243 primary breast tumor samples obtained from 243 patient; 12 duplicated cases. Data production involved different array batches and hybridation series.

first: Marc-Henri

last: Stern

first: Anne

last: Vincent-Salomon


title: Comparative trascriptomic analysis between early-blastocyst and Hatched blastocyst

status: Public on Jun 21 2015

city: Edmonton

first: chi

last: zhou

state: Alberta

address: 114 street 90 ave NW.

department: Agriculture Food and Nutritional Science

country: Canada

institute: University of Alberta

summary: Comparative trascriptomic analysis between porcine early-blastocyst and Hatched blastocyst collected around day 5-6

overall_design: direct comparison with dye-swap; two different arrays with 6 Samples each

first: Chi

last: Zhou


title: Transcriptomic responses of Fire Salamander larvae  to different temperature: patterns in whole body and peripheral tail tip tissues

first: Till

last: Czypionka


title: Day5-6 porcine blastocyst gene expression profile

summary: Day5-6 porcine blastocyst gene expression profiling

overall_design: dye-swaped loop design with 3 biological replicates of Day5-6 blastocyst


title: Leukemia Inhibitory Factor in C26 Cancer Cachexia

first: Robert

middle: William

last: Jackman

state: Massachusetts

address: 635 Commonwealth Avenue/rm 444

department: Health Sciences

institute: Boston University (BU)

summary: Cachexia is an exacerbating event in many types of cancer that is strongly associated with a poor prognosis. We have identified cytokine, signaling and transcription factors that are required for cachexia in the mouse C26 colon carcinoma model of cancer. C2C12 myotubes treated with conditioned medium from C26 cancer cells induced atrophy and activated a STAT-dependent reporter gene but not reporter genes dependent on SMAD, FOXO, C/EBP, NF-ĸB, or AP-1. Of the gp130 family members IL-11, IL-6, oncostatin M (OSM), and leukemia inhibitory factor (LIF), only OSM and LIF were sufficient to activate the STAT reporter in myotubes. A LIF blocking antibody abolished C26 CM-induced STAT reporter activation STAT3 phosphorylation and myotube atrophy, but blocking antibodies to IL-6 or OSM did not. JAK2 inhibitors also blocked the C26 CM-induced STAT reporter activation, STAT3 phosphorylation, and atrophy in myotubes. LIF at levels found in the C26 CM was sufficient for STAT reporter activation and atrophy in myotubes. In vivo, an increase in serum LIF preceded the increase in IL-6 in mice with C26 tumors. Overexpression of a dominant negative Stat3Cβ-EGFP gene in myotubes and in mouse muscle blocked the atrophy caused by C26 CM or C26 tumors, respectively. Taken together these data support an important role of LIF- JAK2-STAT3 in C26 cachexia and point to a therapeutic approach for at least some types of cancer cachexia.

overall_design: from three replicate wells of cells at each treatment, pools of total RNA were used to create cDNA which were evaluated on Affymetrix mouse gene 1.0 ST v.1 arrays.

first: Danielle

middle: N

last: Seto

first: Susan

last: Kandarian


title: Multiple sclerosis patient-derived CSF induces transcriptional changes in proliferating oligodendrocyte progenitors

city: Valencia

first: Angela

last: Riffo-Campos

state: Valencia

address: Avda. Blasco Ibáñes, 17

department: Department of Biochemistry and Molecular Biology

institute: University of Valencia, and INCLIVA

summary: This study provides an overview of the transcriptional signature of oligodendrocyte progenitor cells (OPCs) exposed to the CSF collected from multiple sclerosis patients with either a relapsing remitting disease course (RRMS) or a confirmed primary progressive diagnosis (PPMS).  Using an Affymetrix microarray we were able to detect a set of common and unique genes for each treatment group. Gene ontology analysis revealed a common group of genes involved in protein transport, actin dynamics and response to stress and DNA damage, while the RRMS-specific genes were grouped according to protein complex biogenesis, nuclear transport and RNA processing. The transcriptional signature of progenitors exposed to PPMS was characterized by an up-regulation of the pro-differentiation adhesion molecule Lgals3. We confirmed increased protein levels of its gene product,product; galectin-3 in proliferating OPCs incubated with CSF from PPMS patients and also found a four-fold increase in mRNA transcript levels of galectin-3 in human post-mortem normal-appearing white matter samples of primary progressive MS patients when compared to non-neurological controls. This study will help to better understand the common and specific transcriptional changes induced in the different subtypes of MS and therefore find more specific molecular targets for each disease subtype.

overall_design: Comparison of transcriptional signature by microarray analysis of OPCs treated with  RRMS and PPMS CSF.

first: Jeffery

middle: D

last: Haines

first: Oscar

middle: G

last: Vidaurre

first: Fan

last: Zhang

first: Ángela

first: Josefa

last: Castillo

first: Bonaventura

last: Casanova

first: Patrizia

last: Casaccia

first: Gerardo

last: Lopez-Rodas


title: Epigenome analysis of brain between human and chimpanzee

city: Wako-shi

first: Junko

last: Ueda

state: Saitama-ken

address: Hirosawa 2-1

department: BSI

institute: RIKEN

summary: Genome wide DNA methylation profiling of brain and liver from human and chimpanzee. The Illumina HumanMethylation27 DNA Beadchip v1.2 was used to obtain DNA methylation profiles across approximately 27,000 CpGs for each sample. Samples included liver and NeuN-positive/NeuN-negative/unsorted brain in three individuals from each of two species (human and chimpanzee).

sample_organism:
Pan troglodytes
Homo sapiens

overall_design: Bisulphite converted DNA from the 24 samples were hybridised to the Illumina HumanMethylation27 Beadchip (HumanMethylation27_270596_v.1.2)

first: Nakachi

last: Yutaka

first: Bundo

last: MIki

first: Nagae

last: Genta

first: Aburatani

last: Hiroyuki

first: Okazaki

last: Yasushi

first: Kato

last: Tadanari

first: Iwamoto

last: Kazuya


title: Differences in platelet miRNA profiles between patients with coronary artery disease and healthy controls.

city: Amsterdam

first: Perry

last: Moerland

address: Meibergdreef 9

department: Epidemiology and Data Science

country: Netherlands

institute: Amsterdam UMC

summary: Coronary artery disease (CAD) is the leading cause of human morbidity and mortality worldwide, underscoring the need to improve diagnostic strategies. Platelets play a major role, not only in the process of acute thrombosis during plaque rupture, but also in the formation of atherosclerosis itself. MicroRNAs are endogenous small non-coding RNAs that control gene expression and are expressed in a tissue and disease-specific manner. Therefore they have been proposed to be useful biomarkers. The aim of this study was to investigate whether differences in miRNA expression levels in platelets can be found (i) between patients with premature CAD and healthy controls and (ii) within healthy controls after and before aspirin and statin administration.

overall_design: In this case-control study we measured expression levels of platelet miRNAs using microarrays from 40 male patients with premature CAD and 40 age- and sex-matched healthy controls. Premature CAD was defined as a cardiac event before the age of 51 years. The patients were selected from the outpatient clinic of the Academic Medical Center (AMC) of Amsterdam, which is specialised in premature CAD. The control cohort was composed of 40 healthy Caucasian male volunteers, who were recruited by advertisement and who were matched with the cases for age and smoking habits. Individuals of this control cohort did not have a history of CVD, nor did they have a positive family history of CVD and they were not allowed to use any medication. Patients and controls were excluded when they suffered from diabetes.  Most CAD patients use aspirin and statins as secondary prevention. The influence of these drugs on miRNA profiles is unknown. To assess the possible influence of medication on miRNA expression and to control for medication as confounding factor, we asked 27 volunteers in our control cohort to also use these drugs. We administered simvastatin 40 mg, once daily, for 6 weeks  and during the last two weeks we added 100mg of acetyl salicylic acid, once daily. Blood samples including isolated platelets were collected at baseline in the absence of aspirin and statins and after six weeks of medication use.  We also assessed platelet function using the Multiplate® Analyzer (Roche) in the absence of aspirin and statin use. In short, 300 µl whole blood was diluted with 300 µl 0.9% saline and stirred for 3 minutes at 37 ºC. Adenosine diphosphate (ADP) was added in a final concentration of 2.5 μmol/L to initiate platelet aggregation. Aggregation was measured for 6 minutes and was reported in arbitrary aggregation units plotted against time. Also, the area under the aggregation curve (AUC) was measured. All samples were measured in the absence and presence of 200 μmol/L indomethacin (20 min incubation with blood) to mimic the effect of aspirin use. We calculated the percentage reduction in AUC after incubation with indomethacin as an in vitro measure of the effect of aspirin use on whole blood platelet aggregation.

first: Maayke

last: Kok

first: Sara-Joan

last: Pinto-Sietsma


title: Nucleosome Distribution Data for Methylphenidate Treatment

status: Public on Jun 26 2015

city: Tallahassee

first: Jonathan

last: Dennis

state: Florida

address: 319 Stadium Drive

department: Biological Science

institute: Florida State University

type: Genome binding/occupancy profiling by genome tiling array

summary: Jurkat T-leukemic cells at 0, 15, 45, and 240 minutes post MPH treatment. Chromatin structure depends highly on the position and density of nucleosomes in the genome. The distribution of these nucleosomes likely plays a critical role in all processes for which DNA is the template, including: gene expression, DNA replication, recombination and repair.  It has been proposed for more than half a century that although all the cells in a human body contain, essentially, the same genetic material, nucleosomes give access to different areas of the genome effectively giving access to cell-type specific areas of the genome. We hypothesized that alterations in nucleosome distribution might play a role in the MPH stimulated immune response. We measured chromatin structural changes in a human T-cell line (Jurkat T-leukemic) at high temporal resolution after MPH treatment. We mapped the nucleosome distribution at 4 different time points (0, 15, 45, 240 minutes). Nucleosomal DNA sequences were harvested via chromatin cross-linkage, MNase digestion and DNA extraction. Results were gathered by measuring differences in nucleosome distribution between the basal and the treated states at the different time points. We identified changes in nucleosome distribution.  Interestingly, these changes in nucleosome distribution were transient, returning to their basal positions.  Finally, these changes in nucleosome distribution exhibited different kinetics at different genes.   We propose that the changes in nucleosomal distribution help potentiate differences in gene activity. The results allow us to understand the direct affects of MPH on chromatin structure and help reveal certain mechanistic processes by which it performs.

first: Jose

last: Gil Jr


title: Disruption of mitochondrion-to-nucleus interaction in deceased cloned piglets

city: Pyeongchang

first: Joonghoon

last: Park

state: Kangwon

address: Pyeongchang daero 1447

department: International Agricultural Technology

country: South Korea

institute: Seoul National University

summary: Most animals produced by somatic cell nuclear transfer (SCNT) are heteroplasmic for mitochondrial DNA (mtDNA).  Oxidative phosphorylation (OXPHOS) in clones therefore requires the coordinated expression of genes encoded by the nuclear DNA and the two sources of mitochondria.  Such interaction is rarely studied because most clones are generated using slaughterhouse oocytes of unrecorded origin.  Here we traced the maternal lineages of seven diseased and five one-month-old live cloned piglets by sequencing their mtDNA (short SNP information in single mitochondrial gene).  Additionally by using a 13K oligonucleotide microarray, we compared the expression profiles of nuclear and mtDNA-encoded genes that are involved in mitochondrial functions and regulation between the cloned groups and their age-matched controls (n=5 per group).  We found that the oocytes used to generate the cloned piglets were of either the Large White or Duroc background, and oocyte genetic background was not related to the clones’ survival.  Expression profiles of mtDNA-encoded genes in clones and controls showed intermixed clustering patterns without treatment or maternal lineage-dependency.  In contract, clones and controls clustered separately for their global and nuclear DNA-encoded mitochondrial genes in the lungs for both the deceased and live groups.  Functional annotation of differentially expressed genes encoded by both nuclear and mtDNA revealed abnormal gene expression in the mitochondrial OXPHOS pathway in deceased clones.  Among the nine differentially expressed genes of the OXPHOS pathway, seven were down-regulated in deceased clones compared to controls, suggesting deficiencies in mitochondrial functions.  Together, these data demonstrate that the coordination of expression of mitochondrial genes encoded by nuclear and mtDNA is disrupted in the lung of diseased clones.

overall_design: Two-condition experiment, Clones vs. age-matched controls, Biological replicates: 5 control replicates, 5-7 clone replicates, Technical replicates: dye-swap (10 control replicates, 10-14 clone replicates in total per age)

first: Liangxue

last: Lai

first: Melissa

last: Samuel

first: David

last: Wax

first: Randall

last: Prather

first: Xiuchun

last: Tian


title: Sphingosine-1-phosphate induces pro-remodelling response in airway smooth muscle cells

city: London

first: Grzegorz

last: Woszczek

state: London

address: 5th Floor, Tower Wing, Guy's Hospital

department: Division of Asthma, Allergy and Lung Biology

country: United Kingdom

institute: King's College London

summary:
Background: Increased proliferation of airway smooth muscle (ASM) cells leading to hyperplasia and increased ASM mass is one of the most characteristic features of airway remodelling in asthma. A bioactive lipid, sphingosine-1-phosphate (S1P), has been suggested to affect airway remodelling by stimulation of human ASM cell proliferation.
Objective: To investigate the effect of S1P on signalling and regulation of gene expression in ASM cells from healthy and asthmatic individuals.
Methods: ASM cells grown from bronchial biopsies of healthy and asthmatic individuals were exposed to S1P. Gene expression was analysed using microarray, real-time PCR and western blotting. Receptor signalling and function was determined by mRNA knockdown and intracellular calcium mobilisation experiments.
Results: S1P potently regulated the expression of more than 80 genes in human ASM cells, including several genes known to be involved in the regulation of cell proliferation and airway remodelling (HBEGF, TGFB3, TXNIP, PLAUR, SERPINE1, RGS4). S1P acting through S1P2 and S1P3 receptors activated intracellular calcium mobilisation and extracellular signal-regulated and Rho-associated kinases to regulate gene expression. S1P-induced responses were not inhibited by corticosteroids and did not differ significantly between ASM cells from healthy and asthmatic individuals.
Conclusion: S1P induces a steroid-resistant, pro-remodelling pathway in ASM cells. Targeting S1P or its receptors could be a novel treatment strategy for inhibiting airway remodelling in asthma.

overall_design: Airway smooth muscle cells from 3 healthy donors were cultured and stimulated for 4 h with sphingosine-1-phosphate (100 nM) or medium control. Total RNA was extracted and analysed using Affymetrix Human Exon 1.0 ST arrays.

first: Elisabeth

last: Fuerst

first: Holly

last: Foster

first: Jeremy

last: Ward

first: Christopher

middle: J

last: Corrigan

last: Cousins


title: caArray_green-00160: Initiating oncogenic event determines gene-expression patterns of human breast cancer models

city: Rockville

first: Mervi

last: Heiskanen

state: MD

address: 9609 Medical Center Drive, 1W378

department: CBIIT

institute: NCI

summary: Comparison of six well characterized mouse models of human breast cancer to determine the fundamental differences in gene expression between the normal mammary gland and mammary tumors and to define genes that are associated specifically with each oncogenic pathway.

overall_design:
green-00160
Assay Type*: Gene Expression
Provider*: GenePix
Array Designs: Mm-Incyte-v1px_16Bx24Cx23R
Organism*: Mus musculus (ncbitax)
Material Types: synthetic_DNA, organism_part, whole_organism, total_RNA


title: miRNA expression in myeloid-derived suppressor cells (MDSCs) treated with or without whole β-glucan particles (WGP)

city: zhenjiang

first: Jie

state: Jiangsu

address: Xuefu Road 301

department: School of Medicine

institute: Jiangsu University

summary: Murine MDSCs isolated from the spleens of Lewis lung carcinoma mice were treated with or without WGP, and then miRNA array was used to analyze the differentailly expressed miRNAs.

overall_design: Murine MDSCs were isolated from the spleens of Lewis lung carcinoma tumor-bearing mice, and the sorted MDSCs were stimulated with or without 100 µg/ml WGP for 24 h. Then, the total RNA was extracted to perform miRNA array to analyze the differentially expressed miRNAs in MDSCs treated with or without WGP

first: Shengjun

last: Wang


title: Detection of urinary microRNAs from epithelial ovarian cancer patients as biomarker

status: Public on Jun 17 2015

city: Changsha

first: Jun

last: Zhou

state: Hunan

address: 172 Tongzipo Road

department: Central South University

institute: urine

summary:
The Urine RNA from 5 ovarian cancer and 5 healthy control were analyzed with the Human miRNA Microarray and then validated with a quantitative reverse-transcription PCR assay with 29 individual samples, 20 benign gynecological disease and 26 age/sex-matched healthy control. This study determines the clinical value of urine miRNAs as biomarker for epithelial ovarian cancer.
Results: The miRNA microarray results demonstrate that the original 38 were identified that were significantly differentially expression in epithelial ovarian cancer compared with healthy control (P<0.01). A total of 1 miRNA was up-regulated in ovarian cancer, while 37 miRNA were down-regulated.

overall_design: the urine RNA from 5 ovarian cancer and 5 healthy women were analysised with Human mirRNA microarry

first: Xiaoying

last: Wu


title: Expression profiling of HeLa cell line treated with CDK9 inhibitor

city: emeryville

first: Zhenhai

last: Gao

state: California

address: 4560 Horton street

institute: Novartis Institute for Biomedical Research

summary:
CDK9 is the kinase subunit of P-TEFb that enables RNA polymerase (Pol) II to transit from promoter-proximal pausing to productive elongation. Although considerable interest exists in CDK9 as a therapeutic target, little progress has been made due to the lack of highly selective inhibitors. Here, we describe the development of i-CDK9 as such an inhibitor that potently suppresses CDK9 phosphorylation of substrates and causes genome-wide Pol II pausing. While most genes experience reduced expression, MYC and other primary response genes increase expression upon sustained i-CDK9 treatment. Essential for this increase, the bromodomain protein BRD4 captures P-TEFb from 7SK snRNP to deliver to target genes and also enhances CDK9’s activity and resistance to inhibition. Because the i-CDK9-induced MYC expression and binding to P-TEFb compensate for P-TEFb’s loss of activity, only the simultaneous inhibition of CDK9 and MYC can efficiently induce growth arrest and apoptosis of cancer cells, suggesting the potential of a combinatorial treatment strategy.
We used microarrays to examine the global impact on gene expression by imhibiting CDK9 at different time durations.

overall_design: HeLa cell lines treated with CDK9 inhibitor at different time points

first: Guoying

middle: K

last: Yu

first: Huasong

last: Lu

first: Qiang


title: Transcriptional co-factor Transducin beta-like (TBL) 1 acts as a checkpoint in pancreatic cancer malignancy

status: Public on Jun 16 2015

city: Mannheim

first: Carsten

last: Sticht

address: Theodor-Kutzer-Ufer

department: ZMF

institute: University Heidelberg

summary: Pancreatic ductal adenocarcinoma (PDAC) is the fourth leading cause of cancer fatalities in Western societies, characterized by high metastatic potential and resistance to chemotherapy. Critical molecular mechanisms of these phenotypical features still remain unknown, thus hampering the development of effective prognostic and therapeutic measures in PDAC.  Here we show that transcriptional co-factor Transducin beta-like (TBL) 1 was over-expressed in both human and murine PDAC. Inactivation of TBL1 in human and mouse pancreatic cancer cells reduced cellular proliferation and enhanced chemosensitivity, correlating with diminished glucose uptake, glycolytic flux, and PI3kinase signaling. TBL1 deficiency both prevented and reversed pancreatic tumor growth in mice, triggering transcriptional PI3kinase inhibition also in vivo. As TBL1 mRNA levels were also found to correlate with overall and disease-free survival in a cohort of human PDAC patients and to predict therapy responsiveness in these subjects, TBL1 expression may serve both as a novel prognostic marker and molecular target in the treatment of human PDAC.

overall_design: Capan-1 cells were transfected with control-siRNA (#1027292, Qiagen) or siRNA against human TBL1 (SI04329514, Qiagen) and RNA was isolated 24h later

first: Christian

last: Stoy

first: Maria

last: Muciek

first: Oliver

last: Strobel

first: Stephan

last: Herzig


title: TCDD and n-TiO2 induced mRNA changes in mussels

status: Public on Jun 15 2015

city: Chott-Mariem

first: Mohamed

last: Banni

state: Sousse

address: Route Touristique

department: Life sciences

country: Tunisia

institute: Higher Institut of Agronomy

summary:
Transcriptional profiling of the digestive gland tissue of female mussel Mytilus galloprovincialis exposed to TCDD, n-TiO2 and their binary mixture
Background: Exposure of marine organisms to pollutant mixtures  may affect the pattern of contaminant uptake/bioaccumulation, as well as of gene expression in the tissues. Despite the growing concern over the potential biological impact of nanoparticles (NPs) in the aquatic environment, little is known about their interactions with other pollutants.We have recently shown that in the marine  mussel Mytilus galloprovincialis exposure to n-TiO2, one of the most widespread type of NPs in use, in combination with 2,3,7,8-TCDD, chosen as model organic xenobiotic, can exert antagonistic or synergistic effects on different biomarkers from the molecular to the tissue level, depending on cell/tissue and type of measured response. An integrated approach involving immunhistochemical and transcriptomic analysis was employed to clarify the itteractive effects of n-TiO2 and TCDD in mussels digestive gland.  In particular,TCDD bioaccumulation was evaluated utilizing specific anti-TCDD fluorescent antibodies. Moreover, immunohistochemical evaluation of antioxidant and cytoskeletal components was performed.  To provide clues about how the molecular response to the investigated compounds is modulated, we used a cDNA microarray with1673 sequences. In animals exposed only to TiO2, functional genomics analysis of the microarray data (48 differentially expressed genes (DEGs)) highlighted three biological processes, largely dominated by the up-regulation of microtubule-based movement-related genes. Exposure to 2,3,7,8-TCDD yielded 49 DEGs exhibiting distinct patterns in terms of biological processes.  Finally,  exposure to the mixture rendered 62 GEGs characterized by the regulation of response to chemical stimulus, microtubule-based movement and intracellular signal transduction. Our data should be carefully considered in view of the biological effects of emerging pollutants, particularly in case of mixture chemicals.

first: Laura

last: Canesi

first: Susanna

last: Sforzini

first: Caterina

last: Oliveri

first: Aldo

last: Viarengo


title: M0191.bdl vs M0171.Col

city: saskatoon

first: daoquan

last: xiang

state: SK

address: 110 Gymnasium Place

institute: NRC Saskatoon

summary: Transcriptional profiling of  M0191xbdl vs M0171xCol-0 development embryos after 3 days and 6 days of fertilization

overall_design: Two conditional experiments: M0191xbdl vs M0171x Col-0, and two stages were compared: 3 days and 6 days after fertilization. 4 biological replicates for each experiment.

first: Daoquan

last: Xiang

first: Dolf

last: Weijers


title: Characterization of novel ovarian tumor cell lines that retain the phenotype of primary tumors [SNP]

first: Tan

middle: A

last: Ince

state: FL

address: 1501 NW 10th Avenue, Rm 926

department: Sylvester Cancer Center

institute: University of Miami - Miller School of Medicine

type:
SNP genotyping by SNP array
Genome variation profiling by SNP array

summary: The inability to establish stable cell lines from the vast majority of human tumors has limited the use of in vitro models to study human cancer. Currently available tumor cell lines fail to represent the biological diversity of human tumors. We have developed a cell culture medium that enabled us to routinely establish cell lines from diverse subtypes of ovarian tumors. Importantly, the twenty-five ovarian tumor cell lines described here retain the genomic landscape, histopathology, and molecular features of the original tumors. Furthermore, the molecular profile and drug response of these cell lines correlated with distinct groups of primary tumors with different outcomes. Thus, tumor cell lines derived using this methodology represent a significantly improved new platform to study human tumor biology and treatment.

overall_design: 41 samples were analyzed in singlicate. DNA was extracted from 16 OCI cell lines and the 16 uncultured tumor tissue samples from which they were derived.  DNA was also extracted from 9 standard ovarian cancer cell lines.

first: Aurea

last: Sousa


title: Expression profiles of 30-gene hepatocellular carcinoma molecular classification signature in surgically resected Japanese hepatocellular carcinoma patients

city: Dallas

first: Yujin

last: Hoshida

state: TX

address: 5323 Harry Hines Blvd

institute: University of Texas Southwestern Medical Center

summary:
Background & Aims:  Hepatocellular carcinoma (HCC) is the second most lethal cancer due to lack of effective therapies. Although promising, HCC molecular classification, which enriches potential responders to specific therapies, has not yet been assessed in clinical trials of anti-HCC drugs. We aimed to overcome these challenges by developing clinicopathological surrogate indices of HCC molecular classification.
Methods:  HCC classification defined in our previous transcriptome meta-analysis (S1, S2, and S3 subclasses) was implemented in an FDA-approved diagnostic platform (Elements assay, NanoString). Ninety-six HCC tumors (training set) were assayed to develop molecular subclass-predictive indices based on clinicopathological features, which were independently validated in 99 HCC tumors (validation set). Molecular deregulations associated with the histopathological features were determined by pathway analysis. Sample sizes for HCC clinical trials enriched with specific molecular subclasses were determined.
Results: HCC subclass-predictive indices were: steatohepatitic (SH)-HCC variant and immune cell infiltrate for S1 subclass, macrotrabecular/compact pattern, lack of pseudoglandular pattern, and high serum alpha-fetoprotein (>400 ng/mL) for S2 subclass, and microtrabecular pattern, lack of SH-HCC and clear cell variants, and lower histological grade for S3 subclass. Macrotrabecular/compact pattern, a predictor of S2 subclass, was associated with activation of therapeutically targetable oncogene YAP and stemness markers EPCAM/KRT19. BMP4 was associated with pseudoglandular pattern. Subclass-predictive indices-based patient enrichment reduced clinical trial sample sizes from 121, 184, and 53 to 30, 43, and 22 for S1, S2, and S3 subclass-targeting therapies, respectively.
Conclusions: HCC molecular subclasses can be enriched by clinicopathological indices tightly associated with deregulation of therapeutically targetable molecular pathways.

overall_design: 96 surgically resected hepatocellular carcinoma (HCC) tissue specimens from a cohort of 88 Japanese patients.

first: Poh

last: Tan

first: Anu

last: Venkatesh

first: Claudia

last: Canasto-Chibuque

first: Venugopalan

last: Nair

first: Xiaochen

last: Sun

first: Masahiro

last: Kobayashi

first: Hiromitsu

last: Kumada


title: DNA methylation profiles in primary cutaneous melanoma are associated with clinically significant pathologic features

city: Chapel Hill

first: Nathaniel

middle: Allen

last: Slater

state: North Carolina

address: 413 Mary Ellen Jones Building, 116 Manning Drive, CB#7287

institute: University of North Carolina School of Medicine

summary: We investigated whether methylation in primary melanomas is associated with tumor pathologic features or defines subgroups of primary melanomas

overall_design: 47 primary cutaneous melanomas were analyzed using the Illumina GoldenGate Cancer Panel I methylation array

first: Nancy

middle: E

last: Thomas

first: Sharon

last: Edmiston

first: Xin

last: Zhou

first: Pei

last: Kuan

first: Pamela

last: Groben

first: Craig

last: Carson

first: Honglin

last: Hao

first: Eloise

last: Parrish

first: Stergios

last: Moschos

first: Marianne

last: Berwick

first: David

middle: W

last: Ollila

first: Kathleen

last: Conway


title: Mapping and characterization of promoter-binding sites of protein phosphatase 1

city: Leuven

first: Rekin's

last: Janky

address: Herestraat 49 Box 816

department: Nucleomics Core

country: Belgium

institute: VIB

summary: Protein phosphatase 1 (PP1) is a Ser/Thr phosphatase that has been implicated in many key cellular functions including transcriptional regulation. Due to its involvement these many processes, it becomes difficult to directly link PP1 to transcriptional regulation on the chromatin level as no direct genomic binding sites have been identified. Previous work has failed to address this as the most common method used, namely chromatin immunoprecipitation (ChIP), is an antibody-dependent technique and currently no ChIP-grade PP1 antibodies have been developed. Using DamID, an alternative to ChIP, we have identified PP1 isoform-specific binding sites on the promoter regions of genes. We also identified the binding sites of three main PP1 regulatory subunits (R-subunits) in order to identify potential PP1 holo-enzymes binding sites. Our study revealed the full extent of PP1 isoform specific binding an allowed us to investigate the dependency of the R-subunits on PP1 for chromatin targeting. This data establishes PP1 as a chromatin interactor and allow for the identification of direct effects PP1 can have on the regulation of the genes on whose promoter it is bound.

overall_design: HeLa stable cell lines were created using constructs derived from pIND-(V5)-EcoDam. These constructs express trace amounts of Dam or C-terminal fusions with PP1α, PP1β, PP1γ and three R-subunits, PNUTS, NIPP1 and RepoMan, both wildtype (WT) and their PP1-binding mutants (RATA). Two independent stable cell lines were set up for each of the constructs. DamID-DNA was labeled and hybridized to a GeneChip Human Promoter 1.0R Array (Affymetrix, Santa Clara, CA, USA). The tiling array readouts were analyzed with the “model-based analysis of tiling arrays” (MAT) algorithm (version 1.0.0) against the hg19 reference genome. We normalized two biological replicates of each Dam-fusion over two Dam-only biological replicates. Each biological repeat consisted of 2 technical repeats pooled together prior to hybridization to the tiling array.

first: Toon

last: Verheyen

first: Janina

last: Görnemann

first: Aleyde

last: Van Eynde

first: Monique

last: Beullens

first: Mathieu

last: Bollen


title: Transcriptomic profiling of boars with high and low skatole levels

city: Aarhus

first: Lene

middle: Nagstrup

last: Conley

state: Denmark

address: Langelandsgade 140

department: Department of Chemistry

country: Denmark

institute: University of Aarhus

summary: Skatole is one of the compounds causing boar taint in meat of uncastrated male pigs. This study focuses on differences in gene expression of 50 Danish Landrace boars with high and low skatole levels. The animals were divided into 2 groups based on the skatole measurements, with animals having a skatole concentration of less than 0.01 ppm in one group, and above 0.275 ppm in the other group. Gene expression was assessed using porcine oligonucleotide microarrays. We report differential expression of CYP2E1, CYP2A13 and suggests involvement of FMO1, HSD17B13, CBR4 and several transcription factors.

overall_design: Gene expression study of liver, comparison of 25 boars with high and 25 boars with low skatole levels, using in-house printed porcine two-colour oligonucleotide microarrays.

first: Jakob

last: Hedegaard

first: Henrik

last: Hornshøj

first: Christian

last: Bendixen


title: Genome Profiling of Two Black Poplar (Populus nigra L.) Genotypes Differentially Adapted To Drought Stress Indicated Adaptation-Specific Transcripts

city: TOKAT

first: KUBILAY

last: YILDIRIM

address: TASLICIFTLIK

department: BIOENGINEERING

country: Turkey

institute: GAZIOSMANPASA UNIVERSITY

summary: Drought is one of the most important environmental fluctuations affecting tree growth and survival. Therefore, understanding of physiological and transcriptomic responses of trees to this stress factor will make important contributions to forest health and productivity. Here, we report comparative physiological and microarray based transcriptome analysis between drought resistant (N.62.191) and drought-sensitive (N.03.368.A) black poplar genotypes under well-watered (WWP), moderate drought (MD), severe drought (SD) and post drought re-watering (PDR) conditions. In the study, sensitive genotype exhibited a drought escape strategy with lower leaf water potential, higher reactive oxygen production, complete leaf abscission and subsequent terminal shoot necrosis under drought stress. On the other hand, resistant genotype had a dehydration tolerance indicating highly delayed leaf abscission under drought and fast growing capacity during re-watering conditions.  Gene ontology enrichment analysis attributed drought susceptibility of black poplar to significant up-regulation of genes functional in transcription regulation (AP2/ERF, NAC and WRKY), cell wall modification (Expansins), fatty acid metabolism (enoyl-ACP reductase, lipid transport protein particle), protein degradation (endopeptidases), ethylene synthesis (1-aminocyclopropane-1-carboxylate) and riboflavin synthesis (GTP cyclohydrolase II) under drought stress. Transcriptomic comparison indicated significant down-regulation of photosynthesis, electron transport and carbohydrate metabolism related genes under drought stress in sensitive genotype. Although, similar reduction in carbohydrate metabolism was also recorded for resistant genotype, genes related with photosynthesis and electron transport systems were not down regulated even under SD for this genotype. Resistant genotype specific up-regulation of small heat shock proteins (sHSP) and bark storage proteins revealed importance of protein protection and nitrogen remobilization under drought stress, respectively. This is the first study associating BSP production to delayed leaf abscission and drought tolerance in trees.

overall_design: For Microarray experiment total RNA was isolated from the leaves randomly selected from two balck poplar seedlings (two biological replicates) for resistant and sensitive genotypes at well watered period (WWP), moderate drought (MD), severe drought (SD) and post drought rewatering (PDR) periods. For each water availability regime total isolated RNA was loaded onto two Affymetrix poplar Gene Chips for each genotype. Totally 16 Affymetrix poplar GeneChips (2 genotypes × 4 water availability regimes × 2 biological replicates) were used for transcriptional analysis.

first: Kubilay

last: Yildirim

first: Zeki

last: Kaya


title: Chromatin-immunoprecipitant (ChIP) for CrdR binding site analysis in whole-genome tilling array

status: Public on Jun 13 2015

city: Sacramento

first: CHIU-LIEN

last: HUNG

state: CA

address: 4645 2nd Ave

institute: UCDMC

summary: The CrdR-ChIP profiling is comparing H. pylori gDNA without crdR interaction as control and CrdR interact with H. pylori gDNA (WT vs crdR). The goal was determine the crdR binding site on H. pylori genome, it provide possible crdR-regulated genes.

overall_design: 2 samples: H. pylori 26695 is control, and CrdR is experiment.

first: Chiu-Lien

last: Hung

first: Hsin-Hung

last: Cheng

first: Wan-Chen

last: Hsieh

first: Zing

middle: T

last: Tsai

first: Huai-Kuang

first: Chia-Han

last: Chu

first: Wen-Ping

first: Yi-Fan

last: Chen

first: Yu

last: Tsou

first: Chih-Ho

last: Lai

first: Wen-Ching

last: Wang


title: Dynamics of MBD2 deposition across methylated DNA regions during malignant transformation of human mammary epithelial cells (3)

city: LYON cedex

first: Robert

last: Dante

address: Centre Léon Bérard 28, rue Laennec

department: Tumoral escape

institute: Cancer Research Center of Lyon

type: Methylation profiling by genome tiling array

summary: DNA methylation is thought to induce a transcriptional silencing through the combination of two mechanisms: the repulsion of transcriptional activators that do not recognize their binding sites when methylated, and the recruitment of transcriptional repressors that specifically bind methylated DNA. Methyl CpG Binding Domain proteins MeCP2, MBD1 and MBD2 belong to the latter category. However, the exact contribution of each protein in the DNA methylation dependent transcriptional repression occurring during development and diseases remains elusive. Here we present MBD2 ChIPseq data generated from the endogenous protein in an isogenic cellular model of human mammary oncogenic transformation. In immortalized or transformed cells, MBD2 was found in one fourth of methylated regions and associated with transcriptional silencing. Depletion of MBD2 induces upregulations of genes bound by MBD2 and methylated in their transcriptional start site regions. MBD2 was partially redistributed on methylated DNA during oncogenic transformation, independently of DNA methylation changes. Genes downregulated during this transformation preferentially gained MBD2 binding sites on their promoter. Depletion of MBD2 in transformed cells induced the upregulation of some of these repressed genes, independently of the strategy used for the abrogation of oncosuppressive barriers. Our data confirm that MBD2 is a major interpret of DNA methylation, and show an unreported dynamic in this interpretation during oncogenic transformation.

overall_design: MBD2 ChIP and input, Methylated DNA precipitation and input, in HMEC-hTERT and HMLER cell lines

first: Guillaume

last: Devailly

first: Mélodie

last: Grandin

first: Laury

last: Perriaud

first: Pauline

last: Mathot

first: Jean-Guy

last: Delcros

first: Anne-Pierre

last: Morel

first: Alain

last: Puisieux

first: Patrick

last: Mehlen


title: Murine hindlimb tissue: ischemic vs. control

status: Public on Jun 12 2015

city: Freiburg

first: Sebastian

last: Grundmann

address: Hugstetter Str. 55

institute: University Hospital Freiburg

summary:
Unilateral femoral artery occlusion (right side) and a sham operation on the contralateral (left) side was performed in C57BL/6J mice under anesthesia by double ligation of the superficial femoral artery proximal to the deep femoral artery and distal femoral artery. Animal numbers are stated with the different experimental results.
Total RNA was isolated from the distal adductor muscles by phenol-chloroform isolation (TRIzol, Invitrogen, Carlsbad, CA) at baseline and at 5 time points after femoral artery ligation (6h, 24h, 3 days, 7 days, 14 days) from 5 mice per time point. RNA was pooled in equal amounts, and microarray analysis for all identified murine miRNAs (miRBase 9.0) was performed by a service provider (LC Sciences, Houston, TX).

overall_design: 11 condition experiment. Biological replicates: 5 per condition, 5 pooled RNA replicates per array.


title: H. pylori 26695: wild-type vs nitro-oxide (NO) treated; knockout-crdS in H. pylori 26695 vs knockout-crdS with NO treatment

first: CHIU-LIEN

last: HUNG

summary: There are two transcription profiles. The first profiling is comparing control untreated H. pylori with H. pylori with NO treatment. And the second profiling is comparing knockout-crdS in H. pylori untreated with knockout-crdS with NO treatment. The goal was determine the effects of NO-responsive gene and crdS-regulated genes on H. pylori gene expression.

overall_design: Four-condition experiment, wild-type H. pylori untreated (WT –NO), H. pylori with NO treatment (WT +NO), knockout-crdS in H. pylori untreated (ΔcrdS -NO), ΔcrdS with NO treatment (ΔcrdS +NO)

first: Chiu-Lien

last: Hung

first: Hsin-Hung

last: Cheng

first: Wan-Chen

last: Hsieh

first: Zing

first: Huai-Kuang


title: Characterization of novel ovarian tumor cell lines that retain the phenotype of primary tumors [MIP]

city: Miami

first: Tan

last: Ince

type:
Genome variation profiling by SNP array
SNP genotyping by SNP array

overall_design: DNA was extracted from 25 OCI (human ovarian cancer) cell lines.

first: Marit

last: Krohn

first: Aurea

last: Sousa

first: Gordon

last: Mills


title: Bladder cancer analysis by antibody array

status: Public on Jun 11 2015

city: Daejeon

first: Myung-Shin

last: Lee

address: Yongdu-dong, Jung-gu

department: Microbiology and Immunology

institute: Eulji University School of Medicine

summary: Bladder cancer tissue from 11 patients diagnosed as superficial and muscle invasive and 7 normal bladder mucoa were analyzed by protein antibody array kit with 656 antibodies

overall_design: In this study, 18 tissue samples from bladder cancer or normal bladder mucosa were analyzed by protein antlbody array to investigate biomarker for bladder cancer. After the tissue samples were obtained intraoperatively, they were immediately frozen in liquid nitrogen and expressions of 656 proteins were analyzed using antibody microarray assay kit of Fullmoon Biosystems

first: Jinsung

last: Park


title: Crucial genes and pathways in chicken germ stem cell differentiation

city: yangzhou

first: zhentao

last: zhang

address: wenhui road

institute: yangzhou university

summary: The male germ cell differentiation is a subtle and complex regulation processes, currently its regulatory mechanism is not fully understood. In our experiment, we performed the first comprehensive genome  wide analyses of the crucial genes in three kinds of crucial cells (ESCs, PGCs and SSCs) associated with the male germ cells differentiation. We identified thousands of differentially expressed genes (DEGs) in this process andwe choosed 173 candidate genes involved in the differentiation and metabolic processes, like GAL9, AMH, PLK1, PSMD7 and so on. Further exploration found that the candidate genes express patterns were the same between in vitro induction experiments and transcriptome results. Our results clues to the mechanistic basis of male germ cell differentiation and provides an important reference for future studies.

overall_design: Gene expression in chicken germ stem cells was measured at different stages of development.  Three independent experiments were performed at each stage (ESCs, PGCs and SSCs).

first: Zhentao

last: Zhang

first: Bichun

last: Li


title: Effect of Sprouty2 Downregulation on MicroRNA Expression Profile in HCT116 Colon Cancer Cells

status: Public on Jun 09 2015

city: Columbia

first: Sharad

last: Khare

state: Missouri

address: CE447 Clinical and Educational Support Building

department: Division of Gastroenterology and Hepatology

institute: University of Missouri

summary: Sprouty proteins are evolutionarily conserved modulators of mitogen-activated protein kinase pathway. Sprouty2 appears to function as a tumor suppressor in cancers, whereas we reported earlier that Sprouty2 functions as an oncogene in colorectal cancer. To further understand the oncogenic potential of Sprouty2 in the colon, microRNA expression profile of colon cancer cells was investigated. Sprouty2 suppression in HCT116 colon cancer cells significantly increased MicroRNA 194-5p. Sprouty2 dependent regulation of microRNA194-5p and its biological targets were studied further for their tumor suppressive actions in reducing epithelial-mesenchymal transition in colorectal cancer.

overall_design: Sprouty2 knockdown was performed by infecting HCT116 cells with three different lentivirus expressing shRNAs against human Sprouty2 mRNA and a control non targeted non-silencing shRNA (Sprouty2 MISSION shRNA Lentiviral Transduction Particles; TRCN 0000007522, TRCN 0000231589, TRCN 0000231588 and a non-targeted shRNA control from Sigma) following lentiviral transduction protocols provided by Sigma. Due to the random integration of the lentivirus into the host genome, varying levels of Sprouty2 gene knockdown was expected in puromycin resistant colonies. Three colonies in triplicate that demonstrated highest to lowest level of Sprouty2 suppression, as assessed by western blotting, were selected. RNA samples from these colonies and one from non-targeted shRNA expressing colony were prepared for microRNA expression profile analysis. Pooled RNA samples from each group were shipped to Exiqon for microRNA profiling based on miRCURY LNATM array technology.

first: Helena

last: Palka-Hamblin


title: caArray_green-00001: Alterations in Gene Expression Profiles during Prostate Cancer Progression

city: Rockville

first: Mervi

last: Heiskanen

address: 9609 Medical Center Drive, 1W378

institute: NCI

summary: To identify molecular changes that occur during prostate tumor progression, we have characterized a series of prostate cancer cell lines isolated at different stages of tumorigenesis from C3(1)/Tag transgenic mice.

overall_design:
green-00001
Assay Type:  Gene Expression
Provider: GenePix
Array Designs: Mm-Incyte-v1px_16Bx24Cx23R
Organism: Mus musculus (ncbitax)
Tissue Sites: Prostate
Material Types: synthetic_DNA, organism_part, total_RNA
Cell Types: low grade prostatic intraepithelial neoplasia, invasive carcinoma, lung metastases, high grade prostatic intraepithelial neoplasia


title: A biphasic epigenetic switch controls immunoevasion, virulence and niche adapatation in non-typeable Haemophilus influenzae

city: St Lucia

first: Sean

middle: M

last: Grimmond

state: QLD

address: Research Rd

department: Genomics and Bioinformatics

country: Australia

institute: Institute of Molecular Bioscience, Uni of QLD

summary: Non-typeable Haemophilus influenzae (NTHi) contains an N6-adenine DNA-methyltransferase (ModA), that is subject to phase variable expression (random ON/OFF switching). Five modA alleles, modA2, 4, 5, 9 and 10, account for over two-thirds of clinical otitis media isolates surveyed. Single Molecule Real Time (SMRT) methylome analysis identified the DNA recognition motifs for all five of these modA alleles. Phase variation of these alleles regulated multiple proteins, including vaccine candidates. ON/OFF switching of modA alleles resulted in differential regulation of key virulence phenotypes, such as antibiotic resistance (modA2, 5, 10), biofilm formation (modA2) and immunoevasion (modA4). Analysis of the modA2 strain, 723, in the chinchilla model of otitis media showed a clear selection for switching from modA2OFF to ON in the middle ear. This is the first report of a biphasic epigenetic switch controlling bacterial virulence, immunoevasion and niche adaptation in an animal model system

overall_design: Direct comparison of biological triplicates of wild type and mutant strains

first: Yogitha

last: Srikhanta


title: Human p53 signaling qPCR primer Array

status: Public on Jun 05 2015

city: Beijing

first: Jie

state: HaiDian Qu

address: Taiping Road 27

department: Biochemistry and Molecular Biology

institute: Institute of Basic Medical Sciences

summary: H1299 cells were overexpressed miR-138 or silenced AGO2. The expression of 92 genes associated with p53 using the “Human p53 Signaling Pathway PCR Array”

overall_design: qPCR gene expression profiling. H1299 cells were transfected with NC mimics, AGO2 siRNA or miR-138 for 48h. Equal amount total RNA from each group was pooled prior to gene expression analysis.

first: J

first: N

last: Shao


title: MicroRNA expression data from H1299 cells

summary: We explored the biological effects of AGO2 downregulation on the expression of miRNAs in human NSCLC cells. Using AGO2 siRNA as a positive control, we overexpressed miR-138 in H1299 cells to observe changes in the miRNA profile using an miRNA microarray assay.

overall_design: Total RNAs were extracted from H1299 cells transfected with NC, AGO2 siRNA or miR-138  for 48h. Their microRNAs expression profiles were investigated using  LCSciences Human miRNA Array platform (LCSciences, Houston, TX; Sanger mirBase Release 19.0).

first: W

last: Xia


title: Growth arrest of human thyroid cancer cells 8505C after inhibition of TTF-1 transcriptional activity

city: Brussels

first: Frederick

last: Libert

address: 808 route de Lennik

department: IRIBHM

institute: ULB

summary:
Background: thyroid transcription factor-1 (TTF-1) is known to play key roles in thyroid organogenesis, in thyroid cell proliferation and in the expression of genes involved in thyroid differentiated function.   Objective: to understand why many human thyroid cancer cell lines keep producing TTF-1 despite the loss of differentiation.   Methods: a chimeric protein acting as a functional antagonist of TTF-1 transcriptional activity was expressed conditionally in 8505C cells originating from an undifferentiated thyroid carcinoma. The consequences of the inhibition of TTF-1 activity in the cells expressing the antagonist on cell proliferation, mRNA and miRNA expression were analyzed.
Results: we observed a growth arrest of 8505C thyroid cancer cells when the endogenous TTF-1 transcriptional activity was inhibited. It correlated with decreased levels of several mRNAs encoding positive effectors of cell proliferation like CDK1 and cyclinB1, and increased levels of various mRNAs encoding negative regulators of cell division like CDKN2B and DUSP6. By contrast, no significant change was observed in the miRNA population.  Conclusion: the persistence of TTF-1 expression observed in most dedifferentiated human thyroid cancer cell lines is likely to be explained by the fact that TTF-1 activity is still required for proliferation of these tumor cells as demonstrated here in the 8505C cell line.

overall_design: Microarrays hybridizations were performed on human thyroid cancer cells 8505C expressing a TTF1 antagonist (Engr HD –Dox) versus non-expressing cells (Engr HD +Dox) and versus cells expressing the control protein (Engr HDm – Dox).  After amplification and labelling, sample pairs were hybridized onto HS1100_Human_MI_ReadyArray (Microarrays Inc., Huntsville, AL, USA). The oligonucleotide set consists of 40,604 70-mer probes that were designed using a transcriptome-based annotation of exonic structure for genomic loci. Hybridizations were replicated with dye swap.

first: Christiane

last: Christophe-Hobertus

first: Manuel

last: Saiselet

first: Anne

last: Lefort

first: Jacques

last: Dumont

first: Carine

last: Maenhaut

first: Daniel

last: Christophe


title: The CrdRS two-component system in Helicobacter pylori responds to nitrosative stress

first: CHIU-LIEN

last: HUNG

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

overall_design: Refer to individual Series


title: Outer ECM-attached vs. inner cells of MCF10A acini at day 6 of morphogenesis

city: Charlottesville

first: Leen

last: Jamal

email: lj2p@virginia.edu, ljamal@ucsd.edu

state: VA

address: 415 Lane Road, MR5-Rm. 2225

department: Biomedical Engineering

institute: University of Virginia

summary:
Basal-like carcinoma is a subtype of breast cancer that is characterized by poor prognosis and high intratumor heterogeneity. Using a basal-like breast epithelial line, we have identified two anti-correlated gene-expression programs that arise among single extracellular matrix (ECM)-attached cells during organotypic 3D culture. The first program contains TGFBR3, a high-affinity receptor for transforming growth factor β (TGFβ) and other related ligands. The second program contains the JUND transcription factor together with the basal-like marker, KRT5. By disrupting the TGFBR3 and JUND programs individually, we reveal an important circuit for 3D morphogenesis that is wired together by four negative-feedback loops. Computational modeling of this circuit showed that it could exhibit damped, antiphase oscillations when excited with small impulses of TGFβ-like ligand. We directly visualize the circuit's spontaneous dynamics in organotypic cultures by using live-cell imaging with engineered pathway reporters. Importantly, we show that the essence of the JUND-TGFBR3 expression circuit holds true in early basal-like tumors that heterogeneously express KRT5. Correlated JUND-KRT5 expression depends critically on contact with stromal ECM and local expression of tenascin C. This work illustrates how complex tumor heterogeneities can be deconstructed into intrinsic single-cell expression circuits that are modulated by the microenvironment.

Gene expression analysis of outer ECM-attached vs. inner cells of MCF10A-5E clones grown in organotypic 3D culture at day 6.

overall_design: Total RNA was isolated from ~50 outer ECM-attached cells and ~50 inner cells, each separately microdissected from 8 micron sections of MCF10A structures at day 6 of morphogenesis. Total RNA was amplified in quadruplicate, and hybridized to HumanRef-8 v2.0 Expression BeadChips (Illumina).

first: Kevin

last: Janes


title: Development of micro RNA expression signatures for differential translation of protein isoforms.

status: Public on Jun 02 2015

city: Bangalore

first: Genotypic

last: technology

state: Karnataka

address: 259, Apoorva 4th cross,80 feet Road,RMV 2ND STAGE

country: India

institute: Genotypic Technology

summary: To identify differentially expressed miRNAs (“hits”) under differential expression of p53 isoforms RNA samples were sent for micro array. Some of the micro RNAs are shortlisted below depending on significant upregulation or downregulation. In this micro array we saw some miRNAs getting differentially regulated. 39 upreguated and 15 downregualted in case of p53 and 68 up and 9 downregulated in case of p47 with respect to the vector control.

overall_design: Agilent one-color experiment,Organism: Homo sapiens ,Agilent Human miRNA 8x15k Arrays AMADID: 021827

first: Aanchal

last: Katoch

first: Saumitra

last: Das


title: Responsive genes upon deletion of the dasR gene in Saccharopolyspora erythraea NRRL23338

city: Shanghai

first: Chengheng

last: Liao

address: 130 Meilong Road

department: State Key Laboratory of Bioreactor Engineering

institute: East China University of Science and Technology

summary: Transcription profile analysis between the wild-type strain NRRL23338 and the dasR null mutant to determine the overall transcription changes caused by the deletion of global regulatory gene dasR in S.erythraea.

overall_design: Transcription changes between the dasR mutant and the wild-type strain NRRL23338 were performed at two time points, 24,48h.

first: Ya

last: Xu

first: Sébastien

last: Rigali

first: Bang-Ce

last: Ye


title: Global transcriptome profile of S aureus treated with celecoxib and ampicillin in combination

city: HYDERABAD

first: Arunasree

middle: M.

last: Kalle

state: -- Please Select --

address: GACHIBOWLI

department: Department of Animal Sciences

institute: UNIVERSITY OF HYDERABAD

summary: We have previously shown that celecoxib, a selective COX-2 inhibitor, in combination with antibiotic sensitizes S aureus to antibiotic thereby decreasing the MIC of antibiotic. The present study is aimed at understanding the molecular mechanism of action of celecoxib on S aureus growth by microarray analysis. The results were analysed and the data clearly shows global change in the expression levels of S aureus genes in presence of celecoxib. Many virulence genes, essential genes and nonessential genes are down-regulated in presence of celecoxib in combination with ampicillin when compared to drug treatment alone.

overall_design: Agilent one-color experiment, Organism:  Staphylococcus aureus , Agilent Custom Staphylococcus aureus 8x15k designed by Genotypic Technology Private Limited (AMADID: 27491)

first: A

first: Yajarla

last: Varma

first: Kummari

last: Githavani


title: Posttransplant diffuse large B-cell lymphoma: new genetic findings

city: Leuven

first: Julio

last: Finalet

address: Herestraat 49

institute: KULeuven

summary:
Molecular pathogenesis of posttransplant (PT) lymphoproliferative disorder, including the most prevalent diffuse large B cell lymphoma (DLBCL), is largely unknown. We have recently showed that Epstein-Barr Virus (EBV)+ and EBV- PT-DLBCL are biologically different, but gene expression profile of the latter lymphoma is similar to that of immunocompetent (IC) DLBCL. To validate these findings on a genomic level, we performed array CGH analysis of 21 EBV+ and 6 EBV- PT-DLBCL, and 11 control IC-DLBCL. Genomic and transcriptomic data were subsequently integrated.
Notably, EBV+ and EBV- PT-DLBCL revealed only one shared recurrent imbalance, while EBV- PT-DLBCL displayed at least 10 aberrations recurrent in IC-DLBCL, among others gain of 3/3q and 18q, and loss of 6q23/TNFAIP3 and 9p21/CDKN2A. EBV+ PT-DLBCL showed distinct aberrations, including the most prevalent gain/amplification of 9p24.1 targeting PDCD1LG2/PDL2. Significant differential representation/expression of 3p13/FOXP1 and 9p21/CDKNA2 in EBV+ PT-DLBCL when compared with EBV- PT-/IC-DLBCL, suggests that the oncogene FOXP1 and the tumor suppressor gene CDKNA2 are not implicated in pathogenesis of EBV+ PT-DLBCL.  In summary, genomic profiling of PT-/IC-DLBCL confirmed biological distinctness of EBV+ and EBV- PT-DLBCL, and relationship between EBV- PT-DLBCL and IC-DLBCL. These findings support the hypothesis that EBV- PT-DLBCL are coincidental lymphomas in transplant recipients

overall_design: We performed a copy number alteration (CNA) analysis in combination with gene expression profiling of a series of thoroughly characterized PT-DLBCL and control IC-DLBCL.

last: Finalet Ferreiro

first: Julie

last: Morscio

first: Daan

last: Dierickx

first: Olivier

last: Gheysens

first: Gregor

last: Verhoef

first: Masoud

last: Zamani

first: Peter

last: Vandenberghe

first: Thomas

last: Tousseyn

first: Iwona

last: Wlodarska


title: Liver gene expression response to circadian rhythm disruption

status: Public on Jun 01 2015

city: Bilthoven

first: Jeroen

last: Pennings

address: A. van Leeuwenhoeklaan 9

institute: Natl. Inst. Public Health & Environment

summary: Frequent shift work causes disruption of the circadian rhythm and might on the long-term result in increased health risk. Current biomarkers evaluating the presence of circadian rhythm disturbance (CRD) require 24-hr (around the clock) measurements, which is not practical for use in large-scale (human) studies. The aim of the present study was to identify universal biomarkers for CRD independent of time of day using a transcriptomics approach. Female FVB mice were exposed to six shifts in a clockwise (CW) and counterclockwise (CCW) CRD protocol and sacrificed at baseline and after 1 shift, 6 shifts, 5 days recovery and 14 days recovery, respectively. At six time-points during the day, livers were collected for mRNA microarray analysis. Bioinformatics analysis identified a set of universal markers for CRD. These biomarkers might be useful to measure CRD and can be used later on for monitoring the effectiveness of intervention strategies aiming to prevent or minimize chronic adverse health effects.

overall_design: 120 samples, 2 or 4 replicates per group

first: Wendy

last: Rodenburg


title: Human embryonic stem cell based neuro-developmental toxicity assay: response to valproic acid and carbamazepine exposure

summary: Here we studied the effects of anticonvulsant drug exposure in a human embryonic stem cell (hESC) based neuro- developmental toxicity test (hESTn). During neural differentiation the cells were exposed, for either 1 or 7 days, to non-cytotoxic concentration ranges of valproic acid (VPA) or carbamazepine (CBZ), anti-epileptic drugs known to cause neurodevelopmental toxicity.

overall_design: 93 samples (multiple time points, multiple exposures, multiple concentrations, multiple replicates)


title: Assessing the exposure to nanosilver and silver nitrate on fathead minnow gill gene expression and mucus production

city: Vicksburg

first: Natalia

last: Vinas

state: MS

address: 3909 Halls Ferry Rd

institute: Mississippi State University

summary: Silver exposure is toxic to fish due to disturbances of normal gill function. A proposed toxicity mechanism of silver nanoparticles (AgNP) is derived from the release of silver ions, similar to silver nitrate (AgNO3). However, some datasets support the fact that AgNP can have unique toxic effects that are mediated at the gill. To determine if differences between AgNO3 and AgNP toxicities exist, fathead minnows were exposed to 20 nm PVP- or citrate-coated silver nanoparticles (PVP-AgNP; citrate-AgNP) at the nominal concentration of 200 μg/L or AgNO3 at nominal 6 μg/L for 96 hr. This nominal concentration was applied to approximate the dissolved fraction of Ag in the AgNP suspensions. Mucus production in the water was measured. While mucus production was initially significantly increased in the first 4 h of exposure in all silver treatments compared to control, a decrease in mucus production was observed following 24-96 h of exposure. To determine which genes/pathways are driving this shift in mucus production, gills were dissected and microarray analysis was performed. Hierarchal clustering of differentially expressed genes revealed that all samples distinctly clustered by treatment. There were 109 differentially expressed genes shared among all Ag treatments compared to controls. However, there were 185, 423, and 615 differentially expressed genes unique to AgNO3, PVP-AgNP, and citrate-AgNP, relative to control. While functional analysis indicated several common enriched pathways, such as aryl hydrocarbon receptor signaling, this analysis also indicated some unique pathways between nanosilver and AgNO3. Our results show that AgNO3, PVP-AgNP, and citrate-AgNP exposure affected mucus production in fish gills and also lead to common and unique transcriptional changes.

overall_design: To explore the effects of silver and silver nanoparticles on fathead minnow gills, we explored cellular transcriptional responses following exposure of fathead minnow (Pimephales promelas) to either AgNO3, citrate or PVP-coated silver nanoparticles.   After 96h of exposure, total RNA was isolated from samples RNeasy (Qiagen, Valencia, CA, USA) for microarray analysis. Three to five replicates were used per treatment.

first: Cammi

last: Thornton

first: Adam

last: Hawkins

first: Lynn

last: Escalon

first: Alan

last: Kennedy

first: Jeffery

last: Steevens

first: Kristine

last: Willett


title: The tomato SlDREB2 transcription factor improves salt stress tolerance in tomato

city: Louvain-La-Neuve

first: IMENE

last: HICHRI

address: 5 (Bte 7.07.13) Place Croix du Sud

institute: UCL

summary: The tomato SlDREB2 transcription factor was overexpressed in cultivated tomato (Solanum lycopersicum) and transgenic plants tolerance to salinity was compared to that of wild-type plants.

overall_design: At least 4 plants were collected for RNA extraction. The aim of the experiment was to compare transcriptomes of 35::SlDREB2 plants and wild-type plants grown together and exposed to salt (125 mM) during 48h. A technical replicate (dye swap) was conducted.

first: Imène

last: Hichri

first: Yordan

last: Muhovski

first: André

last: Clippe

first: Eva

last: Žižková

first: Petre

middle: I

last: Dobrev

first: Vaclav

last: Motyka

first: Stanley

last: Lutts


title: Effect of 2-aryl benzimidazole (5a) on Gene Expression Profile of the Human Breast Cancer Cells

first: Chu

last: Bizhu

address: Haidian District, Beijing Tsinghua University

institute: Tsinghua Univercity

summary: To understand the mechanism of 2-aryl benzimidazole (5a) against breast cancer cells, we used microarray gene expression analyses to discover which target or signaling pathways were significant impact by 5a in MDA-MB-453 cells. We have investigated the mRNA expression patterns before and after 5a administration of breast cancer cells, we discovered that 5a had a significant impact on the cell cycle and MEK/Erk signaling pathways, and their p-Value were 5.62 × 10-21 and 2.04 × 10-17 respectively. We also searched for genes that exhibited the greatest differences in expression of the 5a-induced MDA-MB-453 cells relative to the control cells. Several of these genes, including FOS, JUN, TNFRSF10B (DR5), CDKN1A (p21), E2F1, E2F2 and CDC20, have been reported to relate to apoptosis and cell cycle arrest.

overall_design: Two-condition experiment, 5a treated vs. untreated MDA-MB-453 cells. Biological replicates: 3 control replicates, 3 treated replicates.

first: Bizhu

last: Chu

first: Lulu

last: Li


title: Four kinds of  ES cells and EB transcriptome analysis

city: Kamakura

first: Satoshi

last: Kondo

state: Kanagawa

address: Tebiro 6-10-1

department: New Projects Development Division

institute: Toray Industries,Inc.

summary: Analysis of wild type, PKm1 KI, 2TS22c and, ZHBTc4 ES cell lines and Embryoid Body from wild type ES cells.

overall_design: Each ES cells were cultured the medium containing LIF and EB were differentiated into three germ layer using embryoid body formation culture.

first: Masamitsu

last: Konno

first: Hideshi

last: Ishii


title: Saccharomyces cerevisiae ARO80 overexpression

city: Princeton

first: Megan

middle: Nicole

last: McClean

state: New Jersey

address: 120 Carl Ican

department: Lewis-Sigler Institute

institute: Princeton University

summary: The transcription factor ARO80 was overexpressed using the GEV system and gene expression assayed at T=0,30,90,180 minutes.

overall_design: Timecourse.  GEV strain (PGAL1-ARO80 vs control strain)


title: miRNA array on podocytes with the stimulation of TGF-b1

status: Public on May 31 2015

city: Kyoto

first: Kenichi

last: Koga

address: 54 Syogoin Kawahara-cho

department: Department of Nephrology, Kyoto University Graduate School of Medicine

institute: Kyoto University

summary: To identify miRNAs regulating CTGF at the downstream of TGF-β, we analyzed expression profiles of human miRNAs in immortalized human podocytes.

overall_design: TGF-b1 induced gene expression in human cultured podocytes were measured at 24 hours after the stimulation. Cells with PBS treatment were used as control.

first: Hideki

last: Yokoi


title: Thermospermine-induced transcriptomic changes in Populus stem

city: Oeiras

first: Ana

last: Milhinhos

state: Select a State or Province

address: Av Republica EAN Oeiras

department: Plant Sciences

country: Portugal

institute: IBET ITQB-UNL

summary: Thermospermine-induced transcriptomic changes were explored in Populus tremula x P. tremuloides. Transgenic hybrid aspen plants expressing 35S::POPACAULIS5 were compared to wild-type hybrid aspen under the influence of PGRs and depleted from PGRs.

overall_design: Total RNAs from stem tissues of transgenic plants carrying 35S::POPACAULIS5 either grown on auxin-containing and -depleted media were compared to wild-type grown also under the both conditions. Three biological replicates for each pair genotype/growth condition were performed.

first: Andreia

last: Matos

first: Célia

last: Miguel


title: Fetal programming of liver transcriptome in response to gestational diets varying in methylating micronutrients in pigs

city: Dummerstorf

first: Klaus

last: Wimmers

address: Wilhelm-Stahl-Allee 2

department: Genome Biology

country: Germany

institute: FBN Dummerstorf

summary: Pietrain gilts were fed a control diet (CON) or a methyl-enriched diet (MET) throughout their pregnancy. Liver transcriptome profiles of the offspring were analyzed at prenatal stages [35, 63, 91 days post-conception (dpc)].

overall_design: offspring of 5 - 6 gilts per stage were collected for expression profiling

first: Siriluck

last: Ponsuksili

first: Michael

last: Oster

first: Wirawan

last: Nuchchanart


title: Different Vitamin D Receptor Agonists Exhibit Differential Effects on Endothelial Function and Aortic Gene Expression in 5/6 Nephrectomized (NX) Rats

status: Public on May 29 2015

city: Chicago

first: J. Ruth

last: Wu-Wong

state: IL

address: 2201 W. Campbell Park Dr., Suite 13

country: USA

institute: Vidasym

summary: Vitamin D analogs alfacalcidol, paricalcitol, and VS-105 exhibit different effects on endothelial function and aortic gene expression in 5/6 NX uremic rats

overall_design: Uremic rats were treated with vehicle or test agent, i.p. 3x/week for 12 days. Each group consisted of 8-12 animals. Untreated, age-matched sham rats served as controls.  Five groups in this study: sham, NX-vehicle, NX-paricalcitol at 0.08 μg/kg, NX-alfacalcidol at 0.04 μg/kg, and NX-VS-105 at 0.01 μg/kg

first: J

middle: R

first: Xinmin

first: Yung-wu

last: Chen


title: Late lag phase Inhibitor tolerant NRRL Y-50049 vs WT Y-12632 against furfural and HMF challenge

status: Public on Apr 16 2015

city: Peoria

first: Z Lewis

last: Liu

address: 1815 N University

institute: USDA-ARS

summary: Adapted tolerant yeast strain Y-50049 is able to in situ detoxify furfural and HMF while the wild type control Y-12632 repressed to loss function under challenges of 20 mM each of furfural and HMF

overall_design: A time course study during the lag phase with cells harvested at 18, 24, 28, and 42 h after 20 mM furfural and 20 mM HMF treatment

first: Liu

last: Z. Lewis

first: Song

last: Joe


title: Sunitinib treatment exacerbates intratumoral heterogeneity in metastatic renal cancer (CGH)

status: Public on May 25 2015

city: Edinburgh

first: Fiach

last: O'Mahony

address: Crewe Road South

department: Pathology

institute: University of Edinburgh

summary: The aim of this study was to investigate the effect of VEGF targeted therapy (sunitinib) on intratumoral heterogeneity (ITH) in metastatic clear cell renal cancer (mRCC). To explore ITH in detail, multiple tumor samples were taken from the primary renal tumors of mRCC patients who were sunitinib treated (n=23) or untreated (n=23). ITH of pathological grade, DNA (using array-based comparative genomic hybridisation), RNA (Illumina Beadarray) and protein (reverse phase protein array) were evaluated. Tumor grade heterogeneity was greater in treated compared to untreated tumors (P=0.002). Unsupervised and supervised analysis, for renal cancer driver, hypoxia and stromal gene signatures, was then performed. In untreated patient tumor samples, significant ITH occurred in chromosomal aberrations, RNA and protein expression, with clustering of DNA and RNA correlating for individual patients. In unsupervised analysis sunitinib therapy was not associated with increased ITH in DNA or RNA. However there was an increase in ITH for the driver mutation and hypoxia gene signatures (DNA and RNA) as well as increasing variability of protein expression with treatment (p<0.05). Despite this variability, significant chromosomal and RNA changes to targets of sunitinib, such as VHL, PBRM1 and CAIX, occurred in the treated samples. Together these findings suggest that sunitinib treatment has significant effects on the expression and ITH of key tumor and treatment specific genes. The results do not support the hypothesis that resistant clones are selected and predominate after initiation of targeted therapy; instead it appears that an initial clonal diversification occurs, supporting the hypothesis of polyclonal drug resistance.

overall_design: 128 samples from patients with clear cell renal cell carcinoma, including biological replicates of nephrectomy samples. Source of samples includes both biopsy and nephrectomy. DNA extracted from FFPE and fresh frozen tissue samples.

middle: C

first: Grant

last: Stewart

first: Thomas

last: Powles

first: Alan

last: MacKay


title: Expression Profile of in vitro Expanded Human Tregs

status: Public on Apr 30 2015

city: Gainesville

first: Christopher

middle: A.

last: Fuhrman

address: 1275 Center Drive, BMSB J513

department: Pathology, Immunology and Laboratory Medicine

institute: University of Florida

summary:
Understanding human Regulatory T cell (Treg) heterogeneity may identify markers of disease pathogenesis and facilitate the development of optimized cellular therapeutics. Previous analysis revealed that the co-inhibitory receptor T-cell immunoglobulin and immunoreceptor tyrosine-based inhibitory motif domain (TIGIT) was highly expressed on tTreg. The negative regulator TIGIT and the co-stimulatory factor CD226 bind the common ligand CD155.
Human regulatory T cells (CD4+CD25+CD127-/lo) from adult peripheral blood were sub-fractionated  based on the markers CD226 and TIGIT and were subsequently expanded in vitro according to clinical expansion protocols.   The transcriptional profile of the final cell products uncovered considerable heterogeneity in terms of in vitro expansion and suppressive capacity. Most notably, the CD226+TIGIT- fraction adopted a transcriptional profile most similar to that of conventional T cells, including the capacity for effector cytokine production.

overall_design: Tregs and corresponding Tconv were expanded from peripheral blood of three normal healthy control male subjects.

first: Howard

last: Seay

first: Priya

last: Saikumar Lakshmi