title: Genome wide expression responses of Fusarium oxysporum wt and ΔhapX mutant to iron depleted and iron replete conditions.

status: Public on Jul 14 2012

city: Cordoba

first: David

last: Turrá

address: Campus de Rabanales

institute: University of Cordoba

summary: Soilborne fungal pathogens cause devastating yield losses, are highly persistent and difficult to control. To culminate infection, these organisms must cope with limited availability of iron. Here we show that the bZIP protein HapX functions as a key regulator of iron homeostasis and virulence in the vascular wilt fungus Fusarium oxysporum. Deletion of hapX does not affect iron uptake, but causes derepression of genes involved in iron-consuming pathways, leading to impaired growth under iron-depleted conditions. F. oxysporum strains lacking HapX are reduced in their capacity to invade and kill tomato plants and immunodepressed mice. The virulence defect of ΔhapX on tomato plants is exacerbated by coinoculation of roots with a biocontrol strain of Pseudomonas putida, but not with a siderophore-deficient mutant, indicating that HapX contributes to iron competition of F. oxysporum in the tomato rhizosphere. These results establish a conserved role for HapX-mediated iron homeostasis in fungal infection of plants and mammals.

overall_design: Iron dependent gene expression in Fusarium oxysporum wt and ΔhapX mutant was measured 10 hour after shifting the mycelia to minimal medium with or without 50 μM Fe2(SO4)3. Three independent experiments were performed.

first: Manuel

last: López-Berges

first: Javier

last: Capilla

last: Turrà

first: Lukas

last: Schafferer

first: Sandra

last: Matthijs

first: Christoph

last: Jöchl

first: Pierre

last: Cornelis

first: Josep

last: Guarro

first: Hubertus

last: Haas

first: Antonio

last: Di Pietro


title: Molecular insights into the progression of crystalline silica-induced pulmonary toxicity in rats

status: Public on Jun 30 2012

city: Morgantown

first: Rajendran

last: Sellamuthu

state: WV

address: 1095 Willowdale Rd

department: HELD

country: USA

institute: National Institute for Occupational Safety and Health

summary: Identification of molecular target(s) and mechanism(s) of silica-induced pulmonary toxicity is important for the intervention and/or prevention of diseases associated with occupational exposure to crystalline silica. Rats were exposed to crystalline silica by inhalation (15 mg/m3, 6 h/day, 5 days) and global gene expression profile was determined in the lungs by microarray analysis at 1, 2, 4, 8, and 16 weeks following termination of silica exposure. The number of significantly differentially expressed genes (>1.5 fold change and <0.01 FDR p value) detected in the lungs during the post-exposure time intervals analyzed exhibited a steady increase in parallel with the progression of silica-induced pulmonary toxicity noticed in the rats. Quantitative real-time PCR analysis of a representative set of 10 genes confirmed the microarray findings. The various biological functions, canonical pathways, and molecular networks affected by silica exposure, as identified by the bioinformatics analysis of the significantly differentially expressed genes, also exhibited a steady increase similar to the silica-induced pulmonary toxicity. Genes involved in oxidative stress, inflammation, respiratory diseases, cancer, and tissue remodeling and fibrosis were significantly differentially expressed in the rat lungs; however, unresolved lung inflammation was the single most significant biological response to pulmonary exposure to crystalline silica. Excessive mucus production, as implicated by significant overexpression of the pendrin coding gene, SLC26A4, was identified as a novel mechanism for silica-induced pulmonary toxicity. Collectively, the findings of our study provided insights into the molecular mechanisms underlying the progression of crystalline silica-induced pulmonary toxicity in the rat and these findings may be useful in future to develop strategies to prevent occupational silicosis.

overall_design: A total of 60 rat lung samples were analyzed in this gene expression experiment. Rats were exposed to crystalline silica at a concentration of 15 mg/m³, 6-hours/day for 5 consecutive days. Rats exposed simultaneously to filtered air served as the controls. The control (n=4) and silica exposed (n=8) rats were sacrificed at post-exposure time intervals of 1, 2, 4, 8, and 16 weeks following termination of silica exposure and lung gene expression profile was determined.

first: Christina

last: Umbright

first: Jenny

middle: R

last: Roberts

first: Amy

last: Cumpston

first: Walter

last: McKinney

first: Bean

last: Chen

last: Frazer

first: Shengqiao

last: Li

first: Michael

last: Kashon

first: Pius

last: Joseph


title: Identification of a New Chemical Class of Antimalarials, ACT-213615

status: Public on Jul 20 2012

city: Singapore

first: Zbynek

last: Bozdech

address: 60 Nanyang Drive

country: Singapore

institute: Nanyang Technological University

summary: The increasing spread of drug-resistant malaria strains underscores the need for new antimalarial agents with novel modes of action (MOAs). Here, we describe a compound representative of a new class of antimalarials. This molecule, ACT-213615, potently inhibits in vitro erythrocytic growth of all tested Plasmodium falciparum strains, irrespective of their drug resistance properties, with IC(50) values in the low single-digit nanomolar range. Like the clinically used artemisinins, the compound equally and very rapidly affects all three asexual erythrocytic parasite stages. In contrast, microarray studies suggest that the MOA of ACT-213615 is different from that of the artemisinins and other known antimalarials. ACT-213615 is orally bioavailable in mice, exhibits activity in the murine P. berghei model and efficacy comparable to that of the reference drug chloroquine in the recently established P. falciparum SCID mouse model.ACT-213615 represents a new class of potent antimalarials that merits further investigation for its clinical potential.  Histone deacetylase (HDACs) inhibitors are being intensively pursued as potential new antimalarial drugs, and are also emerging as valuable tools for investigating transcriptional control in malaria parasites. In this study, the genome-wide transcriptional effects of three structurally related hydroxamate HDAC inhibitors were profiled in Plasmodium falciparum, the most lethal of the malaria parasite species that infects humans.

overall_design: Trophozoite-stage P. falciparum cells were treated with ACT-213615 for increasing amount of time at IC50 concentration and cells were harvested in parralled with DMSO treated controls for microarray-based transcriptional profiling.

first: R

last: Brunner

first: H

last: Aissaoui

first: C

last: Boss

first: Z

last: Brun

first: O

last: Corminboeuf

first: S

last: Delahaye

last: Fischli

first: B

last: Heidmann

first: M

last: Kaiser

first: J

last: Kamber

last: Meyer

first: P

last: Papastogiannidis

last: Siegrist

first: T

last: Voss

last: Welford

last: Wittlin

last: Binkert


title: A Systematic Comparison and Evaluation of High Density Exon Arrays and RNA-seq technology in Unraveling the Peripheral Blood Transcriptome of Sickle Cell Disease.

status: Public on Jul 06 2012

city: Bethesda

first: Jennifer

last: Barb

state: MD

address: 12 South Drive Bldg 12A Room 2001

department: DCB

institute: NIH

summary: Sickle cell transcriptome was analyzed using whole blood clinical specimens on the Affymetrix Human Exon 1.0 ST arrays and Illumina’s deep sequencing technologies. Data analysis indicated a strong concordance (R=0.64) between exon array and RNA-seq in both gene level and exon level expression of transcripts. The magnitude of fold changes in the expression levels for the differentially expressed genes (p<0.05) was found to be higher in RNA-seq than microarrays. However, the arrays outperformed the sequencing technology in the detection of low abundant transcripts.  In addition to examining the expression level changes of transcripts, RNA-seq technology was able to identify sequence variation in the expressed transcripts. We also demonstrate herein the ability of RNA-seq technology to discover novel expression outside of the annotated genes.

overall_design:
This Series contains only the Exon array data.
10 patients and 10 healthy subjects participated in this study. Gene chip experiments were carreid out on 6 patients and 4 healthy controls
Human Exon 1.0 ST Arrays

first: Nalini

last: Raghavachari

first: Yanqin

last: Yang

first: Poching

last: Liu

first: Peter

middle: J

last: Munson

first: Gregory

last: Kato


title: M. smegmatis vapBC::aphA-3 ΔvapBC mutant (JR121) harboring tetracycline inducible vector pMind containing the vapBC operon (pJR230) and the pMind vector containing the vapC toxin gene (pJR29)

status: Public on Jun 15 2012

city: Dunedin

last: Robson

address: 720 Cumberland Street

department: Microbiology and Immunology

country: New Zealand

institute: University of Otago

summary: Transcriptional profiling of M. smegmatis JR121 expressing VapC and VapBC grown in flasks on Hartmans de Bont medium supplemented with 0.2% glycerol

overall_design: Comparing transcriptional response of strain JR121 to conditional expression of VapC toxin compared with the expression of VapBC complex. Biological replicates: 4 independently grown and harvested. One replicate per array.

first: Joanna

middle: L

last: McKenzie

middle: M

last: Cook

first: Vickery

last: Arcus


title: pCREB-dependent transcriptional activation is a mediator of molecular neuroadaptations induced by methamphetamine self-administration in the rat dorsal striatum

status: Public on Jun 01 2012

city: Baltimore

first: Jean Lud

last: Cadet

address: 251 Bayview Blvd, Suite 200

department: Molecular Neuropsychiatry Research Branch

institute: NIDA, IRP

summary: Neuroplastic changes in the dorsal striatum participate in the transition from casual drug use to habitual and compulsive drug taking. These alterations might also play a critical role in the development of methamphetamine (METH) addiction. Nevertheless, the molecular substrates that underlie habitual METH consumption have yet to be elucidated. Therefore, in the present study, we examined the influence of METH self-administration on the expression of genes and proteins of interest, as potential substrates of METH-induced neuronal plasticity in the dorsal striatum. Rats self-administered METH (0.1 mg/kg/injection, i.v.) during 15 h sessions for 8 d and were euthanized after 2 h, 24 h, or 1 month of abstinence. Compared to yoked saline control, METH self-administration induced increases in the mRNA expression of the transcription factors, c-fos and fosb, the neurotrophic factor, Bdnf, and of the synaptic protein, synaptophysin (Syp) at 2 h after cessation of drug exposure. METH self-administration also caused changes in FosB, BDNF and TrkB protein levels, with increases at 2 and 24 h but decreases observed after 1 month of drug abstinence. Importantly, METH exposure caused increases in the levels of H3K4me3 and pCREB after 2 and 24 h of abstinence. Chromatin immunoprecipitation followed by qPCR was used to clarify the role of these proteins in the regulation of gene expression. We found that METH self-administration caused enrichment of pCREB, but not of H3K4me3, on the promoters of c-fos, fosb, Bdnf and Syp at 2 h after drug cessation. These data indicate that METH-induced activation of their transcription is mediated, in part, by pCREB-dependent epigenetic phenomena. Thus, METH self-administration might trigger epigenetic changes that caused alterations in the expression of genes and proteins serving as substrates for addiction-related synaptic plasticity.

overall_design: Animals were trained to self-administer METH for 8 d as described in the paper, dorsal striata were isolated 2 h, 24 h and 1 month after the final self-administration session. RNA extraction, RNA labeling and microarray hybridization were performed. In brief, total RNA was isolated from the samples using RNeasy Mini Kit (QIAGEN, Valencia, CA). RNA concentration and integrity was determined using Agilent BioAnalyzer (Agilent, Santa Clara, CA). Samples were stored at -80ºC. Microarray hybridization was done using RatRef-12 Expression BeadChips arrays (22 523 probes) (Illumina Inc., San Diego, CA). A 600 ng of total RNA from each sample was amplified using Illumina RNA Amplification kit (Ambion, Austin, TX). Single-stranded RNA (cRNA) was generated and labeled by incorporating biotin-16-UTP (Roche Diagnostics, Indianapolis, IN). 750 ng of each cRNA sample were hybridized to Illumina arrays at 55°C overnight according to the Gene Expression Protocol for BeadStation (Illumina Inc.). Hybridized cRNA was detected with cyanine3-streptavidin (GE Healthcare, Piscataway, NJ) and quantified using Illumina's BeadStation 500GX scanner.

first: Irina

last: Krasnova

first: Margarit

last: Chiflikyan

first: Zuzana

last: Justinova

first: Michael

middle: T

last: McCoy

first: Bruce

last: Ladenheim

first: Jayanthi

last: Subramaniam

first: Cynthia

last: Quintero

first: Chanel

last: Barnes

first: Jordan

middle: E

last: Adair

first: Elin

last: Lehrmann

first: Firas

last: Koveissy

first: Mark

middle: S

last: Gold

first: Kevin

last: Becker

first: Steven

last: Goldberg

first: Jean


title: Effect of LIF and IL-6 on gene expression in JEG-3 and HTR-8/SVneo trophoblastic cells

city: New Delhi

first: Satish

middle: Kumar

last: Gupta

state: Delhi

address: Aruna Asaf Ali Marg

country: India

institute: National Institue of Immunology

summary: Both leukemia inhibitory factor (LIF) and interleukin-6 (IL-6) increase the invasiveness of JEG-3 and HTR-8/SVneo cells. This study examines the effect of LIF and IL-6 on gene expression in trophoblastic cell models viz. JEG-3 and HTR-8/SVneo cells to decipher the molecular basis of the increase in invasiveness.

overall_design: JEG-3 and HTR-8/Svneo cells were stimulated with LIF (50 ng/ml) and IL-6 (100 ng/ml) for 24 h in plain medium keeping untreated cells as a control. After 24 h of stimulation, total RNA was isolated from these cells and used for microarray experiments. These experiments were performed once.

first: Pankaj

last: Suman

middle: K


title: Genome wide expression analysis of the Hypothalamic control of Mammalian Puberty

status: Public on May 25 2012

city: Beaverton

first: Alejandro

last: Lomniczi

state: OR

address: 505 NW 185th Ave

department: Neuroscience

institute: Oregon National Primate Research Center - OHSU

summary: Gene expression analysis of hypothalami from female animals at different juvenil developmental reproductive stages. Results provide insight into the role of the hypothalamus in controlling the onset of puberty.

overall_design: SD rats were housed (4/cage) in a controlled environment and euthanized at different ages (Early Juvenile: 21 days, Juvenile: 26 days, Late Juvenile: 29 days, Early Proestrus (before ovulation): 29-31 days, Late Proestus (the day of first ovulation): 31 days.  Rats were anesthetized and brains were rapidly removed. The hypothalamus was dissected away from the rest of the brain and flash frozen. Total RNA was isolated from each sample using Qiagen's RNeasy Mini Kit (Valencia, CA). Samples were bioanalyzed on a RNA 6000 Nano chip kit to check for integrity and concentration before sending it to the GMSR-Illumina-Core.

first: Sergio

last: Ojeda


title: Skeletal Muscle Contraction Reduces Effects of Unloading on Bone Independently from the Central Nervous System:  Studies Using Functional Electrical Stimulation after Spinal Cord  Transection

status: Public on Jun 28 2012

city: Bronx

first: Weiping

last: Qin

state: NY

address: 130 West Kingsbridge Road, Room 1E-02

department: Center of SCI

institute: James J. Peters Veterans Affairs Medical Center

summary: Spinal cord injury (SCI) causes severe bone loss and disrupts connections between higher centers in the central nervous system (CNS) and bone.  Muscle contraction elicited by functional electrical stimulation (FES) partially protects against loss of bone but cellular and molecular events by which this occurs are unknown. Here, using a rat model, we characterized effects of 7 days of contraction-induced loading of tibia and fibula due to FES when begun 16 weeks after SCI.  SCI reduced tibial and femoral BMD by 12-17% and promoted bone resorption, as indicated by increased serum CTX; SCI-related changes in CTX were reversed by FES. In cultures of bone marrow cell-derived cells, SCI increased the number of osteoclasts and mRNA levels of the several osteoclast differentiation markers; these changes were significantly reversed by FES.  The number of osteoblasts was also reduced by SCI as was the ratio of OPG/RANKL mRNAs therein; the unfavorable change in OPG/RANKL ratio was partially reversed by FES. cDNA microarray analysis revealed that alterations in genes involved in signaling through Wnt, FSH/LH, PTH and calcineurin/NFAT pathways may be linked to the favorable action of FES on SCI-induced bone resorption. In particular, SCI increased levels of the Wnt inhibitors DKK1, sFRP2 and SOST in osteoblasts, These effects were completely or partially reversed by FES.  Our results demonstrate an anti-bone resorptive activity of acute FES in bone loss after SCI and suggest potential underlying mechanisms, among them involving increased Wnt signaling to cause more favorable ratios of OPG and RANKL for the inhibition of osteoclastogenesis. The present study indicates that the effects of bone reloading on SCI- related bone remodeling occurred independently of the effects of higher CNS centers on bone.

overall_design: Implantation of the FES microstimulators was performed 14 weeks after SCI.  The FES was begun during the 16th week following spinal cord transection.  Stimulation was provided for 60 minutes on each training day and consisted of brief periods of contraction (2 seconds) at 40 Hz at 1.5 V with longer periods of rest (18 seconds).   Animals received FES on 7 consecutive days; collection of blood and tissues occurred at day at after initiating FES, as described below. The SCI-Sham FES animals received the implant surgery and gastrocnemius ablation during the 14th week after the spinal cord transection, but did not have a stimulator unit inserted; samples were collected from these animals at week 17.  To provide age-matched non-SCI controls, additional animals underwent a sham-SCI surgery identical to that for the SCI animals, except that the spinal cord was not transected.  Tissues were collected from these animals at 12-14 weeks after surgery.  Of note, at this age, animals were sexually mature and their growth minimal.  To collect blood and tissues, animals were anesthetized by inhalation of isofluorane followed by removal of the soleus and plantaris muscles after careful dissection and collection of blood by ventricular puncture and aspiration.  Animals were euthanized by aortic transaction and tibia and femur were removed as a single piece, leaving the knee joint intact, and placed in a-MEM for isolation of bone marrow cells.  Muscles were weighed; weights are expressed after being normalized to body weight before SCI or sham-SCI surgeries to control for individual variations in size.

first: Lauren

last: Collier

first: Yuanzhen

last: Peng

first: Yong

last: Wu

first: Li

last: Sun

first: Graham

last: Creasy

first: Jianghua

last: Li

first: Yiwen

first: Jay

last: Cao

first: William

middle: A

last: Bauman

first: Jonathan

last: Jarvis

first: Mone

last: Zaidi

first: Christopher

last: Cardozo


title: Expression data from HEK293T cells infected with Shigella or treated with Rapamycin

status: Public on May 19 2012

city: Toronto

first: Stephen

last: Girardin

address: 1, King's College Circle

country: Canada

institute: University of Toronto

summary: Shigella is an intracellular bacterial pathogen known to activate numerous innate immunity and inflammatory signaling pathways. Many of these pathways are also involved in mTOR signaling. We used HEK293T cell cultures and sought to understand how Shigella infection and rapamycin treatment affect the transcriptome and in particular whether there were commonly affected pathways in the two experimental conditions.

overall_design: 8 samples were used - 2 control that were uninfected/untreated -- 1 sample lost due to RNA degradation, 3 infected with Shigella for 4 hours, and 3 treated with Rapamycin (50 ug/mL) for 4 hours. All samples were from independent experiments. We used the program AltAnalyze to perform pairwise comparisons between Uninfected with Infected, and Uninfected with Rapamycin using default parameters.

first: A

last: Ling

first: S


title: Transcriptomic study of the impact of iron toxicity on rice plant

status: Public on May 15 2012

city: Louvain-la-Neuve

first: Stanley

last: Lutts

address: Croix du sud 4-5 bte L7.07.13

department: Earth and Life Institute

country: Belgium

institute: Université catholique de Louvain

summary:
transcriptomic study of the impact of iron toxicity on rice plant (Oryza sativa L.; cv ‘I Kong Pao’ ) after short term (3 days) or long term (3 weeks) exposure to ferrous iron (125 ppm).
Twenty five days old rice seedlings were exposed to 0 or 125 mg/L ferrous iron for 3 days and 3 weeks in hydroponic culture.  Comparison between control and iron stressed plants were done at the shoot and the root levels. The assays were replicated twice on two independent plant cultures.

overall_design: 8 samples, Two-condition experiment, control (0 ppm ferrous iron) vs. iron treated (125 ppm ferrous iron). Biological replicates: 2 replicates for comparison shoot 3 days of stress, root 3 days of stress, shoot 3 weeks of stress and root 3 weeks of stress.

first: Muriel

last: Quinet

first: Delphine

last: Vromman

first: André

last: Clippe

first: Pascal

last: Hols

first: Pierre

last: Bertin

first: Hélène

last: Lequeux

first: Inès

last: Dufey

first: Isabelle

last: Lefèvre


title: Microarray analysis of differentially expressed genes engaged in fruit development between Prunus mume and Prunus armeniaca

status: Public on May 13 2012

city: Nanjing

first: Jinggui

last: Fang

address: tongwei road 6

department: college of Horticulture

country: China

institute: Nanjing Agricultural University

summary: Microarray analysis is a technique that can be employed to provide expression profiles of single genes and a new insight to elucidate the biological mechanisms responsible for fruit development.  To evaluate expression of genes mostly engaged in fruit development between P. mume and P. armeniaca, we first identified differentially expressed transcripts along the entire fruit life cycle by using microarrays spotted with 10,641 ESTs collected from P. mume and other Prunus EST sequences.  A total of 1,418 ESTs were selected after quality control of microarray spots and analyzed for differential gene expression patterns during fruit development of P. mume and P. armeniaca.  Among them, 707 up-regulated and 711 down-regulated differentially expressed genes showing more than 2.0-fold differences in expression level were annotated by GO based on biological processes, molecular functions and cellular components.  These differentially expressed genes were found to be involved in several important pathways of carbohydrate metabolism, galactose metabolism, starch and sucrose metabolism, and biosynthesis of other secondary metabolites via KEGG, which could provide detailed information on the fruit quality differences during development and ripening.  With the obtained results, we provide a practical database for comprehensive understanding of molecular events during fruit development and also lay the theoretical foundation for the cloning of genes involved in a series of important rate-limiting enzymes in the vital metabolic pathways during the fruit development.

sample_organism:
Prunus armeniaca
Prunus mume

platform_organism:
Prunus persica
Prunus armeniaca
Prunus salicina
Prunus mume

overall_design: Fruits from 4 cultivar at different stages, replicated 2 times

first: Xiaoying

last: Li

first: Nicholas

last: Korir

first: Lili

last: Liu

first: Lingfei

last: Shangguan

first: Yuzhu

last: Wang

first: Yujuan

first: Ming

last: Chen


title: Transcriptomics of coping strategies in free-swimming Lepeophtheirus salmonis (Copepoda)

city: Victoria

first: Ben

middle: F

last: Koop

state: BC

address: PO Box 3020 STN CSC

department: Biology

institute: The University of Victoria

summary: To understand the sensitivity of larval lice to changing environmental parameters we applied a 38K oligo microarray and characterized transcriptome responses after 24 hour exposures to reduced salinity (30-10 parts per thousand (ppt)) or varied temperature (16-4ºC). To further characterize the effects of salinity, we profiled expression changes over a range of seawater with single increment differences (30-25 ppt).

overall_design: Three separate projects. Low resolution salinity (aka wide range or LR_SAL) contains 2 duplicate experiments, each with pools of lice (~500 copepodid lice per beaker; n=3 beakers per condition), incubated for 24 hr at 10ºC diluted to 30, 25, 20, or 10 parts per thousand (ppt). Temperature study conducted as above, but with a constant salinity of 30 ppt and changed temperature of 4, 10, or 16ºC. High resolution salinity conducted as above, but with no experiment replication, but with biological repication of n=6 beakers per condition, and with a range of 25, 26, 27, 28, 29, 30 ppt salinity. Please note that each experiment was normalized separately.

last: Sutherland

first: Stuart

middle: G

last: Jantzen

first: Motoshige

last: Yasuike

first: Dan

last: Sanderson

first: Simon

last: Jones


title: Gene expression of SLNs (Synthetic Lethal with Nutlin-3) on HCT116 cells

status: Public on Mar 20 2012

city: Cleveland

first: Jihye

last: Kim

state: Ohio

address: 9500 Euclid Ave.

department: Quantitative Health Sciences

institute: Cleveland Clinic

summary:
A subset of our SLNs would be upregulated by Nutlin-3 and down-regulated by 5-FU and that this differential regulation could potentially explain how cell fate choice is determined
SLNs as a group were largely members of pathways parallel to p53, in the sense that very few of them displayed significant changes in mRNA expression after Nutlin-3 or 5FU treatment

overall_design: RNA was harvested from cells treated with Nutlin-3, 5FU, or DMSO, for 12 hours using the RNeasy kit (Qiagen). cDNAs were synthesized and labeled with the Genechip Whole Transcript Sense Target Labeling Kit (Affymetrix) per the manufacturer’s instructions and hybridized to Human Exon 1.0 ST arrays (AffyMetrix)

first: Kelly

middle: D

last: Sullivan

first: Joaquin

last: Espinosa

first: Tan

last: Aik-Choon


title: Characterization of chemically induced malignant peripheral nerve sheath tumors (MPNSTs) in the rat by expression profiling

status: Public on Mar 29 2012

city: Essen

first: Andrea

last: Kindler-Röhrborn

address: Hufeland Str. 55

department: Patholpgy & Neuropathology

country: Germany

institute: University of Essen

summary: Identification of differentially expressed genes in ENU induced MPNSTs and normal tissue from rat  Nervus trigeminus  by expression profiling

overall_design: Gene expression of total RNA isolated from pooled, untreated trigeminal nerves from 85 days old rats compared to unpooled total MPNST tumor RNA  from BDIV, BDIX and hybrid strains.

first: Bernd

middle: U

last: Koelsch


title: Comparative gene expression profiling of P. falciparum malaria parasites exposed to three different histone deacetylase inhibitors

status: Public on May 01 2012

first: Archana

middle: P

last: Gupta

department: School Of Biological Sciences

summary:
Background
Histone deacetylase (HDACs) inhibitors are being intensively pursued as potential new antimalarial drugs, and are also emerging as valuable tools for investigating transcriptional control in malaria parasites. In this study, the genome-wide transcriptional effects of three structurally related hydroxamate HDAC inhibitors were profiled in Plasmodium falciparum, the most lethal of the malaria parasite species that infects humans.

Results
Following 2h exposure to trichostatin A (TSA), suberoylanilide hydroxamic acid (SAHA) or a 2-aminosuberic acid derivative (2-ASA-9), ~18-28% of genes in P. falciparum trophozoite-stage parasites were regulated greater than two fold. This global induction was transitory, with fewer genes (3-5%) regulated after removing the compounds and culturing for a further 2h. Just nine genes, including alpha-II-tubulin, were up-regulated by all three compounds. Despite structural similarity, the three inhibitors caused quite diverse transcriptional effects, possibly reflecting subtle differences in mode of action or cellular distribution.

Conclusions
Three structurally related HDAC inhibitors have been found to cause profound, genome-wide, transcriptional changes in P. falciparum parasites, but most effects were transitory. This highlights the dynamic and exquisitely controlled nature of transcription in these malaria parasites. We also identified a small subset of nine genes over-expressed by all three HDAC inhibitors that may represent the first recognized set of transcriptional markers that signify HDAC inhibition in malaria parasites. This data set is an important contribution to our understanding of gene regulation in malaria parasites and supports growing evidence for the potential of HDAC inhibitors as new antimalarial agents.

overall_design: Trophozoite-stage P. falciparum cells were treated with different compounds at IC90 concentrations (SAHA, 200nM, TSA 50nM, and 2-ASA-9 80nM) or DMSO vehicle control (<0.005%) for 2h, then harvested (termed 2h+). In parallel, after 2h exposure to compound, a second matched replicate was washed to remove the drug and cultured for a further 2h (termed 2h+/2h-). RNA extracted from these samples was processed for microarray analysis.

first: Archna

first: Katherine

last: Andrews

first: Zbynek

last: Bozdech


title: Comparative analysis of gene expression changes during differentiation in the Drosophila wing

status: Public on Mar 01 2012

city: Seattle

first: Laura

last: Buttitta

state: WA

address: 1100 Fairview Ave. N.

institute: Fred Hutchinson Cancer Research Center

summary:
Investigation of whole genome gene expression level changes in dissected Drosophila wings of the genotype w1118, at the wandering L3 larval stage, 2h, 6h, 18h, 24h and 36h After pupa formation. Stages after pupa formation were compared to the larval L3 stage to identify changes in gene expression.
The data included here is further discussed in O’Keefe, Thomas, Edgar and Buttitta (2012). Combinatorial control of temporal gene expression in the Drosophila wing by enhancers and core promoters Submitted to BMC Genomics

overall_design: A 24 chip study using total RNA recovered from three to four independently isolated samples of 10 dissected Drosophila wings at the indicated developmental stages from flies with the genotype w1118;+;+ (Bloomington Stock #3605). For sample 36BD, total RNA from sample 36B and 36D were pooled, labeled and hybridized independently.

first: David

last: O'Keefe

first: Bruce

last: Edgar


title: Environmental Toxicants Induce Epigenetic Transgenerational Inheritance of Ovarian Disease [Affymetrix]

city: Pullman

first: Michael

last: Skinner

address: Abelson 507

department: SBS

institute: WSU

summary:
The epigenetic transgenerational actions of environmental toxicants and relevant mixtures on ovarian disease was investigated with the use of a fungicide, a pesticide mixture, a plastic mixture, dioxin and a hydrocarbon mixture. After transient exposure of an F0 gestating female rat during embryonic gonadal sex determination, the F1, F2 and F3 generation progeny adult onset ovarian disease was assessed. Transgenerational disease phenotypes observed included an increase in cysts resembling human polycystic ovarian disease (PCO) and a decrease in the ovarian primordial follicle pool size resembling premature ovarian failure (POF).   The F3 generation granulosa cells were isolated and found to have a transgenerational effect on the transcriptome and epigenome (differential DNA methylation). Epigenetic biomarkers for environmental exposure and associated gene networks were identified. Epigenetic transgenerational inheritance of ovarian disease states were induced by different classes of environmental compounds suggesting a role of environmental epigenetics in ovarian disease etiology.
We used transcriptome microarray analysis to determine genes expressed differentially between F3 control and F3 vinclozolin lineage rat ovary granulosa cell and see which genes might be connected to or cause  observed ovary diseases

overall_design: RNA samples from  granulosa cell of 3 F3-control lineage groups are compared to granulosa cell of 3 F3-vinclozolin lineage groups

first: Eric

last: Nilsson

first: Ginger

last: Larsen

first: Mohan

last: Manikkam

first: Carlos

last: Guerrero-Bosagna

first: Marina

middle: I

last: Savenkova


title: Platelet-derived growth factor-alpha (PDGF-α) stimulates intestinal epithelial cell turnover after massive small bowel resection in a rat

status: Public on Feb 29 2012

city: Haifa

first: Igor

last: Sukhotnik

address: 47 Golomb St., P.O.B. 4940

department: Dept of Pediatric Surgery and Pathology,  Bnai Zion Medical Center, Haifa

country: Israel

institute: The Bruce Rappaport Faculty of Medicine, Technion-Israel Institute of Technology

summary: Numerous cytokines have been shown to affect epithelial cell differentiation and proliferation through epithelial-mesenchymal interaction. Growing evidence suggests that platelet-derived growth factor (PDGF) signaling is an important mediator of these interactions. The purpose of this study was to evaluate the effect of PDGF-α on enterocyte turnover in a rat model of short bowel syndrome (SBS). Male rats were divided into four groups: Sham rats underwent bowel transection, Sham-PDGF-α rats underwent bowel transection and were treated with PDGF-α, SBS rats underwent a 75% bowel resection, and SBS-PDGF-α rats underwent bowel resection and were treated with PDGF-α. Parameters of intestinal adaptation, enterocyte proliferation and apoptosis were determined at sacrifice. Illumina's Digital Gene Expression (DGE) analysis was used to determine PDGF-related gene expression profiling. PDGF-α and PDGF-α receptor (PDGFR-α) expression was determined using Real Time PCR. Western blotting was used to determine p-ERK, Akt1/2/3, bax and bcl-2 protein levels. SBS rats demonstrated a significant increase in PDGF-α and PDGFR-α expression in jejunum and ileum compared to sham animals. SBS-PDGF-α rats demonstrated a significant increase in bowel and mucosal weight, villus height and crypt depth in jejunum and ileum compared to SBS animals. PDGF-α expression in crypts increased in SBS rats (vs sham) and was accompanied by increased cell proliferation following PDGF-α administration.  A significant decrease in cell apoptosis in this group was correlated with lower bax protein levels. In conclusion, in a rat model of SBS, PDGF-α stimulates enterocyte turnover, which is correlated with up-regulated PDGF-α receptor expression in the remaining small intestine.

overall_design: Animals were divided randomly into two experimental groups of 6 rats each. Group A rats underwent bowel transection and re-anastomosis (Sham), Group B animals underwent 75% bowel resection (SBS). Due to  the quality of DNA, we performed final analysis from 5 jejunal samples (1 sham and 4 resected rats) and from 7 ileal samples (3 sham and 4 resected rats). Illumina's Digital Gene Expression (DGE) analysis using Illumina Rat Quad BeadChips was used to determine PDGF-related gene expression profiling.

first: Yulia

last: Pollak


title: Gene Bionetworks Involved in Epigenetic Transgenerational Inheritance of Environmentally Altered Sexual Selection:  Role of Epigenetics in Evolutionary Biology

summary:
Sexual selection involves mate preference behavior and is a critical determinant for natural selection and evolutionary biology. Previously an environmental compound (fungicide vinclozolin) was found to promote epigenetic transgenerational inheritance of modified mate selection characteristics in all progeny for three generations after exposure of a gestating female.  The current study investigated gene networks involved in various regions of the brain that correlated with the mate preference behavior altered in F3-Vinclozolin lineage animals.  Statistically significant correlations of differentially expressed gene clusters and modules were identified to associate with specific mate preference behaviors.  This novel systems biology approach identified critical gene networks involved in mate preference behavior and demonstrated the ability of environmental factors to promote epigenetic transgenerational inheritance of this altered evolutionary biology determinant.  Combined observations elucidate the potential molecular control of mate preference behavior and suggests environmental epigenetics can have a role in evolutionary biology.
We used Affymetrix Rat Gene 1.0 ST microarrays to determine genes expressed differentially in F3 Vinclozolin lineage male or female rats' 6 brain areas - amygdala (Amy), hippocampus (Hipp), olfactory bulb (OlfB), cingulate cortex (CngCtx), entorhinal cortex (EnCtx), and preoptic area-anterior hypothalamus (POAH) -  due to Vinclozolin treatments of their grand-grandmothers (F0).

overall_design: For each of 6 brain areas of male or female rats (female: amygdala (F-Amy), cingulate cortex (F-CngCTX), enterorhinal cortex (F-EnCTX), hippocampus (F-Hipp), olfactory bulbs (F-OlfB), and preoptic area-anterior hypothalamus (F-POAH); male: amygdala (M-Amy), cingulate cortex (M-CngCTX), enterorhinal cortex (M-EnCTX), hippocampus (M-Hipp), olfactory bulbs (M-OlfB), and preoptic area-anterior hypothalamus (M-POAH)), RNA samples from 2 treatment groups - F3 Control lineage (Con) or F3 Vinclozolin lineage (Vin) - were compared to each other.  Each of treatment groups contained 4-6 biological replicas for each brain region.  RNA for each replica was isolated from an individual animal in order to compare to individual animal mate preference behavior studied with the same rats before sacrifice. Totally, 132 RNA samples from 24 animals (6 male F3 Control, 6 male F3 Vinclozolin,6 female F3 Control, and 6 female F3 Vinclozolin) were isolated and studied.

first: Bin

last: Zhang

first: Andrea

last: Gore

last: Crews


title: Mediator Complex Regulates Alternative mRNA Processing via the Med23 Subunit

status: Public on Feb 24 2012

city: Newark

first: Wencheng

last: Li

state: NJ

address: MSB-E501, 185 South Orange Ave.

institute: UMDNJ

summary: Mediator complex is an integrative hub for transcriptional regulation. Here we show that Mediator regulates alternative mRNA processing via its Med23 subunit. Combining tandem affinity purification and mass spectrometry, we identified a number of mRNA processing factors that bind to a soluble recombinant Mediator subunit MED23 but not to several other Mediator components. One of these factors, hnRNP L, specifically interacts with MED23 in vitro and in vivo. Consistently, Mediator partially colocalizes with hnRNP L and the splicing machinery in the cell. Functionally Med23 regulates a subset of hnRNP L-targeted alternative splicing (AS) and alternative cleavage and polyadenylation (APA) events as shown by minigene reporters and exon array analysis. ChIP-seq analysis revealed that Med23 can regulate hnRNP L occupancy at their co-regulated genes. Taken together, these results demonstrate a crosstalk between Mediator and the splicing machinery, suggesting a novel mechanism for coupling mRNA processing to transcription.

overall_design: We performed an exon array experiment using HeLa cells expressing Med23, hnRNP L or control siRNAs which were established by a virus-mediated siRNA technology. Each sample was done in three biological replicates. Total RNA of these cell lines was processed and hybridized to the Affymetrix human exon array.

first: Yan

last: Huang

first: Xiao

last: Yao

first: Qijiang

last: Lin

first: Jingwen

last: Yin

last: Liang

first: Monika

last: Heiner

last: Tian

first: Jingyi

last: Hui

first: Gang

last: Wang


title: Early Leaf Development: A not so gradual process

status: Public on Jan 17 2012

city: Zwijnaarde

first: Megan

last: Andriankaja

address: 927 Technologiepark

institute: VIB-PSB

summary: Early leaf growth is sustained by cell proliferation and subsequent cell expansion that initiates at the leaf tip and proceeds in a basipetal direction. Using detailed kinematic and gene expression studies to map these stages during early development of the third leaf of Arabidopsis thaliana we showed that the cell cycle arrest front did not progress gradually down the leaf, but rather was established and abolished abruptly. Interestingly, leaf greening and stomatal patterning followed a similar basipetal pattern, but proliferative pavement cell and formative meristemoid divisions were uncoordinated in respect to onset and persistence. Genes differentially expressed during the transition from cell proliferation to expansion were enriched in genes involved in cell cycle, photosynthesis, and chloroplast retrograde signaling. Proliferating primordia treated with norflurazon, a chemical inhibitor of retrograde signaling, showed inhibited onset of cell expansion. Hence, differentiation of the photosynthetic machinery is important for regulating the exit from proliferation.

overall_design:
GSM839070-GSM839081: Total RNA was extracted using RNeasy plant mini kit (Qiagen) from leaf 3 of Arabidopsis seedlings grown in vitro and treated or not treated with norflurazon (NF) at 8 days after stratification (DAS) and harvested 24 and 48 hours after treatment. RNA from three biological repeats of each timepoint and treatment were submitted to AGRONOMICS1 array hybridization.
GSM839082-GSM839099: Total RNAs were extracted using RNeasy plant mini kit (Qiagen) from leaf 3 of Arabidopsis seedlings 8, 9, 10, 11, 12, and 13 days after stratification (DAS) and grown in vitro. RNAs from three biological repeats of each timepoint were submitted to AGRONOMICS1 array hybridization.

first: Stijn

last: Dhondt

first: Stefanie

last: De Bodt

first: Hannes

last: Vanhaeren

first: Frederik

last: Coppens

first: Per

last: Mühlenbock

first: Aleksandra

last: Skirycz

first: Nathalie

last: Gonzalez

first: Gerrit

last: Beemster

first: Dirk

last: Inzé


title: Comparison of carboxysomal (ccmM) and photorespiratory (glcD1/D2) mutants of Synechocystis sp. PCC 6803 using metabolic and transcriptomic phenotyping

status: Public on Dec 30 2011

city: Amsterdam

first: Floyd

last: Wittink

address: Kruislaan 318

department: MAD

country: Netherlands

institute: Universiteit van Amsterdam

summary: The general acclimation of cyanobacteria to low carbon (LC) conditions includes coordinated alterations of gene expression and metabolism. To analyze possible signals for LC sensing and compensating reactions, we compared wild-type (WT) cells with two mutants of Synechocystis, the carboxysome-less mutant ccmM and the photorespiratory mutant ΔglcD1/D2. Metabolic phenotyping revealed that the mutant ΔccmM accumulated high 2-phosphoglycolate (2PG) levels while the ΔglcD1/D2 mutant accumulated glycolate, indicating oxygenase activity of RubisCO at high carbon (HC). The changes in the metabolite spectrum were compared to alterations in the global gene expression pattern. Cells of HC-grown mutants ΔccmM and ΔglcD1/D2 showed altered mRNA levels for many genes involved in photosynthesis, high light stress, and N-assimilation, while LC-specific genes such as those for inorganic carbon (Ci) transporters were not increased. After a shift to LC, mutant ΔglcD1/D2 revealed gene expression changes similar to WT cells, while mutant ΔccmM showed no differential expression of most LC-induced genes under identical conditions. In fact, none of the genes for Ci transporters or other components of the carbon concentrating mechanism (CCM) displayed higher transcript levels in the ΔccmM mutant. This finding renders a direct role for 2PG as a metabolic signal component for the induction of CCM during LC acclimation less likely. Because, the transcription pattern of ΔglcD1/D2 under LC showed specific differences compared to WT, a potential role for glycolate as a signal molecule that may trigger expression of parts of the CCM is proposed.

overall_design: Transcriptional profiling of carboxysomal and photorespiratory mutants of Synechocystis sp. PCC 6803 under high carbon (HC) and low carbon (LC) conditions relative to the wildtype response.

first: Claudia

last: Hackenberg

first: Jan

last: Huege

first: Annerose

last: Engelhardt

first: Michael

last: Laue

first: Hans

middle: C

last: Matthijs

first: Joachim

last: Kopka

first: Hermann

last: Bauwe

first: Martin

last: Hagemann


title: Identifying gene expression profiles in hypoplastic left heart syndrome and age-matched normal controls

status: Public on Dec 31 2011

city: Miami

first: Marco

last: Ricci

state: FL

address: 1611 NW 12th Ave, Holtz Center 3072

department: Pediatric Cardiac Surgery

institute: Jackson Memorial Hospital

summary: Affymetrix GeneChip Exon-1.0ST was used to study the differential gene profiles in RV (right ventricle) samples from neonates with HLHS (hypoplastic left heart syndrome) versus RV and LV (left ventricle) samples obtained from age-matched controls. Although few significant changes were observed in the genetic profiles between control LV and control RV, many genes passed the false discovery rate in comparing HLHS-RV to RV and LV control groups, with greater differential profiles noted between HLHS-RV and control RV.

overall_design: Myocardial samples were isolated from the RV of 6 HLHS neonates, diagnosed based upon clinical features including hypoplasia/atresia of the ascending aorta, various degrees of underdevelopment of the aortic valve, mitral valve, and LV cavity, and retrograde flow in the aortic arch as determined by conventional 2-D echocardiography. The mean gestational age at birth of all subjects was 38 weeks (range 36-39) and the mean body weight at surgery of 2.7 kg (range 2.1-3.4 kg) (3 males, 3 females). All subjects were undergoing stage 1 Norwood reconstruction. Children with HLHS and other complex cardiac anomalies entailing non-HLHS single ventricle circulation were excluded from our study. For control samples, RV and LV myocardial tissue was obtained from 5 newborns aged between 1-28 days (mean 18 days; 3 males and 2 females) with normal cardiac anatomy and expired from non-cardiac diseases processes.

first: Harriet

last: Hammond

first: Lubov

last: Nathanson

first: Maria

last: Rodriguez

first: Matteo

last: Vatta

first: Steven

last: Lipshultz

first: Joy

last: Lincoln


title: Ovarian transcriptomics over a complete breeding cycle in wild Largemouth bass (Micropterus salmoides) characterizes pathways underlying oocyte maturation and atresia

status: Public on Dec 20 2011

city: Gainesville

first: Christopher

middle: Joseph

last: Martyniuk

address: CEHT Mowry Road

department: Physiological Sciences

institute: UF

summary: Background: Follicular growth and maturation in semi-synchronously spawning fish involve numerous cell signaling cascades and different molecular cascades are activated or inhibited during specific stages of oocyte development. The objectives of the current study were to identify molecular pathways and temporal gene expression patterns throughout a complete breeding cycle in female wild LMB to characterize the molecular sequence of events underlying follicle and ovary development.  Methods: Microarray analysis was performed on eight morphologically distinct stages, from primary stages of oocyte growth to ovulation and atresia. Ovarian tissue histology, plasma vitellogenin, and sex steroids (E2 and T) were also measured to correlate molecular signaling cascades to higher levels of biological organization. Results: Global expression patterns revealed dramatic differences between early and late stages of ovarian follicle progression, with over 200 and 500 genes being differentially expressed during both ovulation and atresia respectively (p < 0.01). Time course analysis for all stages leading to ovulation and atresia identified increased expression of GABAA receptor subunits and peroxisome proliferator-activated receptor gamma during ovulation.  Gene set enrichment analysis (GSEA) revealed that early stages of oocyte growth involved increases in pathways of natural killer cell and mast cell activation, as well as gap junction regulation. GSEA revealed that arachidonic acid metabolism was significantly up-regulated while CD2, fibronectin, and neuropeptides Y receptor signaling cascades were down-regulated at ovulation.  Expression targets for LH signaling were decreased during vitellogenesis but increased at ovulation. GSEA revealed decreases in actin cytoskeleton regulation and receptor mediated signaling pathways involving TGFβ and ephrin receptor regulation at atresia. Conclusions: This study offers new insight into the molecular pathways involved in vitellogenesis, ovulation and atresia in LMB and provides new hypotheses about the cellular pathways involved in oocyte growth and maturation.

overall_design:
31 microarrays on 8 unique stages of ovary development; developmental profile
time course, development of LMB ovary

first: Melinda

last: Prucha

first: Nicholas

last: Doperalski

first: Philipp

last: Antczak

first: Kevin

last: Kroll

first: Francisco

last: Falciani

first: David

last: Barber

first: Nancy

last: Denslow


title: 81 human leukemia samples (affymetrix exon array)

status: Public on Jan 13 2012

city: chicago

first: chunjiang

last: he

state: il

address: 900 east 57th st

institute: university of chicago

summary: Intragenic microRNAs (miRNAs), including both intronic and exonic miRNAs, accounting approximately 50% of total mammalian miRNAs. Previous studies showed that intragenic miRNAs are often co-expressed with their host genes, and thus it was believed that intragenic miRNAs and their host genes are derived from the same primary transcripts. However, we provide evidence to show here that the observations from previous studies might be biased due to the small number and the predominance of "broadly conserved" intronic miRNAs they studied.

overall_design: In this Series, we analyzed 81 human leukemia samples using the Affymetrix Human Exon 1.0 ST platform. Array data was processed by Affymetrix Expression Console. No techinical replicates were performed.

first: Chunjiang

last: He

first: Zejuan

last: Li

first: Ping

last: Chen

first: Hao

last: Huang

first: Laurence

last: Hurst

first: Jianjun


title: Son Maintains Accurate Splicing of Pre-mRNAs Encoding Chromatin Modifiers

status: Public on Dec 22 2011

city: Dayton

first: Michael

last: Markey

state: OH

address: 3640 Colonel Glenn Hwy.

department: Biochemistry and Molecular Biology

institute: Wright State Unviersity

summary:
Exon and expression analysis of HeLa cells after knockdown of SON
Serine-arginine-rich (SR) proteins play a key role in alternative pre-mRNA splicing in eukaryotes. Our laboratory recently showed that a large SR protein called Son has unique repeat motifs that are essential for maintaining the subnuclear organization of pre-mRNA processing factors in nuclear speckles. Motif analysis of Son highlights putative RNA interaction domains that suggest a direct role for Son in pre-mRNA splicing.  A genome-wide screen was performed to identify putative human transcription and splicing targets of Son.

overall_design: HeLa cells were transfected with siRNA against SON or a control siRNA (siLuciferase) for 48 hours.  Five biological replicates were used for each condition.


title: Gene expression Microarray analysis for HEK293 WT and ELL KD with control and 1hr EGF stimulated conditions.

status: Public on Dec 09 2011

city: Bethesda

first: Jung

last: Byun

address: 37 convent drive, Bldg 37,  Rm 1042

institute: NCI/NIH

summary: Transcription is a multi-stage process that coordinates several steps within the transcription cycle including chromatin reorganization, RNA polymerase II recruitment, initiation, promoter clearance and elongation.  Recent advances have identified the super elongation complex (SEC), containing the eleven nineteen lysine rich leukemia protein (ELL), as a key regulator of transcriptional elongation.  We show here that ELL plays a diverse and kinetically distinct role prior to its assembly into the SEC by stabilizing Pol II recruitment/initiation and entry into the pause site.  Loss of ELL destabilizes the PIC complexes and results in disruption of early elongation and promoter proximal chromatin structure prior to recruitment of AFF4 and other SEC components. These changes result in significantly reduced transcriptional activation of rapidly induced genes.  Thus, ELL plays an early and essential role during rapid high amplitude gene expression that is required for both Pol II pause site entry and release.

overall_design:
Total RNA for unstimulated and for simulated with EGF (50 ng/mL) for 1hr from wild type and stably induced ELL KD in HEK293 cells were isolated and purified and submitted to LMT-Affymetrix microarray facility to obtain the raw data.
Affymetrix Human Exon ST1.0 platform was used for the microarray analysis. Raw data in CEL files were preprocessed using Affymetrix Expression Console software.

last: Gardner


title: Blood gene expression profile of control and crystalline silica exposed rats

status: Public on Dec 02 2011

city: Morgantown

first: Rajendran

last: Sellamuthu

address: 1095 Willowdale Rd

department: HELD

institute: National Institute for Occupational Safety and Health

summary: The present research aimed to investigate peripheral blood gene expression profiling as a minimally invasive surrogate approach to study silica-induced pulmonary toxicity. Rats were exposed to crystalline silica by inhalation (15 mg/m3, 6 hours/day, 5 days). Pulmonary damage and blood gene expression profiles were determined at various latency periods (0 - 16 weeks). Silica exposure resulted in pulmonary toxicity and this was evidenced by histological changes in the lungs and elevation of LDH activity, and total protein and albumin contents in the bronchoalveolar lavage fluid (BALF) of the rats. Microarray analysis of global gene expression profiles in the blood of the rats identified genes that were differentially expressed in response to silica exposure and toxicity. The number of significantly differentially expressed genes in the blood of silica exposed rats correlated with the severity of silica-induced pulmonary toxicity. Genes involved in biological functions such as inflammatory response, cancer, pulmonary damage, oxidative stress, energy metabolism, fibrosis, etc, were found differentially expressed in the blood of the silica exposed rats compared with the controls. Induction of pulmonary inflammation in the silica exposed rats, as suggested by differential expression of inflammatory response genes in the blood, was supported by significant increases in the number of macrophages and infiltrating neutrophils as well as the activity of pro-inflammatory chemokines – MCP1 and MIP2, observed in the BALF of the silica exposed rats. A silica-responsive blood gene expression signature developed using the gene expression data predicted with significant accuracy the exposure of rats to lower concentrations (1 and 2 mg/m3) of silica. Taken together our findings suggest the potential application of peripheral blood gene expression profiling as a minimally invasive and efficient surrogate approach to detect and study silica-induced pulmonary toxicity.

overall_design: 96 samples were analyzed in this experiment. The RNA from rat blood samples was isolated for gene expression studies. Rats (48) were exposed to crystalline silica by inhalation (15 mg/m3, 6 hours/day, 5 days) and air (24). Blood gene expression profiling was performed using rat blood samples, 8 each for silica exposed and 4 each for air exposed controls at various post-exposure time periods (0, 1, 2, 4, 8, and 16 weeks). A silica-responsive blood gene expression signature was developed using the gene expression data obtained from the 0 week post-exposure group and the control rats. The signature was tested for predicting silica exposure and resulting toxicity in the rats exposed to lower concentrations (1 and 2 mg/m3) of silica (8 rats per group) and air (8 rats).

first: Christina

last: Umbright

first: Jenny

last: Roberts

first: Rebecca

last: Chapman

first: Shih-Houng

last: Young

first: Diana

last: Richardson

first: Howard

last: Leonard

first: Walter

last: McKinney

first: Bean

last: Frazer

first: Shengqio

last: Kashon

first: Pius

last: Joseph


title: Transcriptome Profiling and Sequencing of differentiated Human Hematopoietic Stem cells Reveal Lineage Specific Expression and Alternative Splicing of Genes

status: Public on Nov 22 2011

first: Jennifer

last: Barb

address: 12 South Drive Bldg 12A Room 2001

department: DCB

institute: NIH

summary: Hematopoietic differentiation is strictly regulated by complex network of transcription factors that are controlled by ligands binding to cell surface receptors.  Disruptions of the intricate sequences of transcriptional activation and suppression of multiple genes cause hematological diseases, such as leukemias, myelodysplastic syndromes or myeloproliferative syndromes.  From a clinical standpoint, deciphering the pattern of gene expression during hematopoiesis may help unravel disease-specific mechanisms in hematopoietic malignancies. Herein, we describe a human in vitro hematopoietic model system where lineage specific differentiation of CD34+ cells was accomplished using specific cytokines.   Microarray and RNAseq based whole transcriptome and exome analysis was performed on the differentiated erythropoietic, granulopoietic and megakaryopoietic cells to delineate changes in expression of whole transcripts and exons. Analysis on the Human 1.0 ST exon arrays indicated differential expression of 172 genes (P< 0.0000001) and significant splicing of 86 genes during differentiation. Pathway analysis identified these genes to be involved in Rac/RhoA signaling, Wnt/B-catenin signaling and alanine/aspartate metabolism.  Comparison of the microarray data to next generation RNAseq analysis during erythroid differentiation demonstrated a high degree of correlation in gene (R= 0.72) and exon (R=0. 62) expression. Our data provides a molecular portrait of events that regulate differentiation of hematopoietic cells. Knowledge of molecular processes by which the cells acquire their cell specific fate would be beneficial in developing cell-based therapies for human diseases.

overall_design: Comparison of gene expression patterns between CD34, E, M and G groups

first: Poching

last: Liu

first: Peter

last: Munson

first: Nalini

last: Raghavachari


title: Whole transcriptome analysis identifies a subset of Group A var genes that encode the malaria parasite ligands for binding to human brain endothelial cells

status: Public on Nov 01 2011

city: Edinburgh

first: Antoine

last: Claessens

address: West Mains Road

department: Institute of Immunology and Infection Research

country: United Kingdom

institute: Edinburgh university

summary: Cerebral malaria is the most deadly manifestation of infection with Plasmodium falciparum. The pathology of cerebral malaria is characterised by the accumulation of infected erythrocytes in the microvasculature of the brain, due to parasite adhesins on the surface of infected erythrocytes binding to human receptors on microvascular endothelial cells.  The parasite and host molecules involved in this interaction are unknown.  We used the Human Brain Endothelial Cell line HBEC-5i to identify the malaria parasite ligands responsible for binding to human brain endothelial cells. Three P. falciparum strains (HB3, 3D7 and IT/FCR3) were selected for binding to HBEC5i and the whole transcriptome of selected and unselected parasites was analysed using a variant surface antigen-supplemented microarray chip. After selection, the only highly upregulated genes were a subset of group A-like var genes (HB3var3, 3D7_PFD0020c, ITvar7 and ITvar19), that showed 11 to >100-fold higher transcription levels in selected parasites. These genes are highly diverse in sequence, but do however show strong similarities in PfEMP1 architecture. Antibodies raised to the HB3var3 variant recognized the surface of infected erythrocytes and abolished the binding of infected erythrocytes to brain endothelial cells. The subset of Group A PfEMP1 variants identified here provides a new target for interventions to treat or prevent cerebral malaria.

overall_design: Unselected Plasmodium falciparum parasites (Uns) only poorly cytoadhere to human brain endothelial cells (HBEC-5i). Plasmodium falciparum HB3, 3D7 and IT/FCR3 strains were selected for binding to HBEC-5i (HB3-HBEC1, HB3-HBEC2, HB3-HBEC-TNF, 3D7-HBEC and IT-HBEC). HBEC-selected and unselected cultures were tightly synchronised before a timecourse experiment was performed. 6 samples, named time points 1 to 6, were taken every 8 hours. 12μg of RNA from the unselected parasites (HB3-Uns, 3D7-Uns or IT-Uns) at each of the 6 time points was combined together to form the reference pool. The pool and 12μg of each individual time point sample from both selected and unselectedparasites were then used for cDNA synthesis. For HB3-HBEC1 (pilot experiment), each HB3-HBEC1 time point (pilot experiment) was hybridised directly with HB3-Uns1 time points. For microarray hybridizations, each cDNA sample was coupled to Cy5 (red dye) while Cy3 (green dye) was added to the pool. Cy5-labelled time point samples were mixed with the same amount of Cy3-labelled pool sample. The solution was loaded on a microarray slide and hybridized for 14–16 h.

first: Ashfaq

last: Ghumra

first: Cheryl

last: Andisi

last: Bull

first: Archana

last: Patkar

first: Sachel

last: Mok

first: Christian

last: Wang

first: Monica

last: Arman

first: Zbynek

last: Bozdech

first: J

last: Alexandra Rowe


title: Genome-wide time series analysis of gastrin induced gene expression in AR42J cells with and without protein synthesis

status: Public on Oct 17 2011

city: Trondheim

first: Arnar

last: Flatberg

address: Postboks 8905

department: Department of Cancer Research and Molecular Medicine

country: Norway

institute: Norwegian University of Science and Technology

summary: Genome-wide gene expression time series experiments are an important approach to studying a cells response to a given stimulus, as they enable capturing of the dynamics of the response. Moreover, information about the dynamics of the system is an important prerequisite for inferences on interactions between its components. We have performed extensive microarray-based genome-wide gene expression analyses up to 14h of the response to gastrin in AR42J adenocarcinoma cells. The gastrin reponse was also investigated in presence of the protein translation inhibitor cycloheximide. The rat cell line AR42J derived from pancreatic duct has the feature of pluripotency of the precursor cells of the gut endoderm. Furthermore, AR42J cells express gastrin receptors endogenously and are therefore frequently used as a model system to study gastrin responses. The hormone gastrin is the central regulator of gastric acid secretion and in addition plays a prominent role in regulation of growth and differentiation of gastric and colonic mucosa. Hypergastrinaemia has been linked to development of neuroendocrine gastrointestinal tumours (NE-GI) and, in conjugation with additional factors such as inflammation, to development of gastric adenocarcinoma (GA)

overall_design: Times series up to 14h treated with gastrin, gastrin and cycloheximide, cycloheximide and control at individual timepoints

first: Torunn

last: Bruland

first: Liv

last: Thommesen

first: Arne

last: Sandvik

first: Astrid

last: Lægreid

first: Jannicke

last: Holmseth

first: Sten

last: Erlandsen

first: Ingunn

last: Bakke

first: Christina

last: Sæten Fjeldbo


title: Increased mutability of staphylococci in biofilms as a consequence of oxidative stress

city: Leeds

first: Victoria

last: Ryder

state: West Yorkshire

address: Clarendon way

department: Faculty of Biological Sciences

institute: University of Leeds

summary: In this work we have demonstrated increased mutability of Staphylococcus aureus and S. epidermidis in biofilms and have explored the mechanisms underlying the enhanced mutability. A novel static biofilm model, utilising cellulose filter disks, was developed to support the formation of mature biofilms with sufficiently high cell densities to permit determination of mutation frequencies. The mutability of biofilm cultures increased up to 60 fold and 4 fold for S. aureus and S. epidermidis, respectively, compared with planktonic cultures. Incorporation of antioxidants into S. aureus biofilms reduced mutation frequencies, indicating that increased oxidative stress underlies increased mutability in the biofilm. Transcriptional profiling revealed upregulation of the superoxide dismutase gene, sodA, in early biofilm cultures, also suggesting enhanced oxidative stress in these cultures. However, loss of the genes encoding superoxide dismutases or peroxidases did not specifically exacerabate biofilm mutability. In S. aureus SH1000, hydrogen peroxide was found to contribute to biofilm mutability.

platform_organism: Staphylococcus aureus subsp. aureus NCTC 8325

overall_design: Three growth conditions (18 hr planktonic growth, 48 hr biofilm growth and 144 biofilm growth) of which there are three biological replicates of each

middle: J

first: Ian

last: Chopra

first: Alex

last: O'Neill


title: Effect of IL-11 on gene expression in JEG-3 and HTR-8/SVneo trophoblastic cells

status: Public on Nov 04 2011

city: New Delhi

first: Satish

last: Gupta

address: Aruna Asaf Ali Marg

institute: National Institute of Immunology

summary: IL-11 increases the invasiveness of JEG-3 cells while, reduces the invasiveness of HTR-8/SVneo cells. This study examines the effect of IL-11 on gene expression in trophobalstic cell models  viz. JEG-3 and HTR-8/SVneo cells to resolve the controversies associated with the IL-11 mediated regulation of the invasiveness of these two cell lines.

overall_design: JEG-3 and HTR-8/Svneo cells were stimulated with IL-11 (200 ng/ml) for 24 h in pain medium keeping un-treated cells as control. After 24 h of stimulation, total RNA was isolated from these cells and used for the microarray experiments. These experiments were performed once.

first: Pankaj

last: Suman


title: Methamphetamine administration causes differential alterations in gene expression and dynamic patterns of histone acetylation/hypoacetylation in the rat nucleus accumbens

status: Public on Aug 01 2011

city: Baltimore

first: Jean Lud

last: Cadet

address: 251 Bayview Blvd, Suite 200

department: Molecular Neuropsychiatry Research Branch

institute: NIDA, IRP

summary: Methamphetamine (METH) addiction is associated with a plethora of neuropsychiatric symptoms. In rodents, administration of the drug is accompanied by complex changes in gene expression in the dorsal striatum. Very little is known about the effects of the drug on gene expression and epigenetic modifications in the nucleus accumbens (NAc). The present study was conducted in order to investigate the effects of a single injection of METH on gene expression in that structure. We also queried whether changes in transcript levels were accompanied by alterations in histone acetylation as well as in the  expression of the histone acetyltransferase (HAT), ATF2, and of the histone deacetylases (HDACs), HDAC1 and HDAC2. Microarray analyses revealed that METH caused significant time-dependent increases in the expression of several genes that had previously been implicated in the acute and longterm effects of psychostimulants in the brain. These include several immediate early genes (c-fos, Egrs, c-jun, and Nurr1) and corticotropin-releasing factor (Crf). There were also increases in the levels of neuromedin U, Tnf-alpha, and Kcnk18, among others. In contrast, the METH injection caused decreases in the expression of many genes including Npas4 and cholecystokin (Cck). Pathway analyses showed that differentially affected genes participate in behavioral performance, cell-to-cell signaling and interactions, and regulation of gene expression. Other differentially affected genes are known to be involved in cellular compromise and death pathways. PCR analyses were used to confirm the changes in the expression of c-fos, fosB, c-jun, junB, Crf, NmU, Cck, and Npas4 transcripts. Western blot analyses also identified METH-mediated decreases in the acetylation of histone H3 at lysine 9 (H3K9) and lysine 18 (H3K18) as well as in histone 4 at lysine 16 (H4K16). In contrast, the METH injection caused time-dependent increases in the acetylation of H4K8 and H4K12. The changes in histone acetylation were also accompanied by decreased expression of HDAC1 but increased expression of ATF2 and of HDAC2. These results suggest that METH-induced alterations in global gene expression might be due, in part, to diverse effects of METH-induced histone acetylation secondary to changes in HAT and HDAC expression.

overall_design: At the indicated time after the METH or saline injections, rats (n = 5 per group) were euthanized and the NAc was dissected and immediately put on dry ice. The tissues were kept at -70 oC until RNA extraction. Total RNA was isolated from the nucleus accumbens according to the manufacturer’s manual using Qiagen RNeasy mini kit (Qiagen, Valencia, CA, USA). RNA integrity was detected using an Agilent 2100 Bioanalyzer (Agilent, Palo Alto, CA, USA).

first: Martin

last: Tracey

first: Jayanthi

last: Subramaniam

first: Brannock

last: Christie

first: Ladenheim

last: Bruce

first: Garrett

last: Tiffany

first: McCoy

last: Michael

first: Lehrmann

last: Elin

first: Becker

last: Kevin

first: Cadet

last: Jean Lud


title: Coupled pre-mRNA and mRNA dynamics unveil the operation  strategies underlying transcriptional responses

status: Public on Aug 31 2011

city: Rehovot

first: Amit

last: Zeisel

address: Weizmann Institute

department: Physics of complex systems

institute: Weizmann Institute of Science

summary: Transcriptional responses to stimuli are regulated by tuning rates of transcript production and degradation. Here we show that stimulation-induced changes in transcript production and degradation rates can be inferred from simultaneously measured precursor mRNA (pre-mRNA) and mature mRNA profiles. Our studies on the transcriptome-wide responses to extracellular stimuli in different cellular model systems revealed hitherto unanticipated dynamics of transcript production and degradation rates. Intriguingly, genes with similar mRNA profiles often exhibit marked differences in the amplitude and onset of their production. Moreover, we identify a group of genes, which take advantage of the unexpectedly large dynamic range of production rates to expedite their induction by a transient production overshoot. These findings provide an unprecedented quantitative view on processes governing transcriptional responses, and may have broad implications for understanding their regulation at the transcriptional and post-transcriptional levels.

overall_design: MCF10A cells stimulated with EGF

first: Wolfgang

last: Köstler

first: Natali

last: Molotski

first: Rita

last: Krauthgamer

first: Jasmine

last: Jacob-Hirsch

first: Gideon

last: Rechavi

first: Yoav

last: Soen

first: Steffen

last: Jung

first: Yosef

last: Yarden

first: Eytan

last: Domany


title: Role of miR-19b and its target mRNAs on 5-fluorouracil resistance in colon cancer cells

status: Public on Jul 27 2011

city: Tokushima-city

first: Toshihito

last: Tanahashi

address: Kuramoto-cho 3-18-15

country: Japan

institute: Tokushima University

summary: Despite the efforts in defining the molecular mechanisms for the drug resistance in colorectal cancers, little is known about the roles of microRNAs. With microarray containing 723 microRNAs, we examined effect of 5-fluorouracil (5-FU) on the microRNA expression. Respond to 5-FU, we identify two microRNAs, miR-19b and miR-21, that were differentially expressed in 5-FU resistant colon cancer cells derived from KM12C and DLD-1.

overall_design: DLD-1, DLD-1/R, KM12C, and KM12C/R cells were plated at 1 × 105 cells/well. After pre-culture, cells were treated with 60 uM of 5-FU for 72 h. This was the same condition as the analysis of cell cycle. RNAs were collected before (0 h) and after the treatment of 5-FU (72 h).


title: The CRE1 carbon catabolite repressor of the fungus Trichoderma reesei: a master regulator of carbon assimilation

status: Public on Jun 01 2011

city: Paris

first: Stéphane

last: LE CROM

address: 46 rue d'Ulm

department: Biology Institute - IBENS

country: France

institute: École normale supérieure

type: Expression profiling by genome tiling array

summary: The identification and characterization of the transcriptional regulatory networks governing the physiological behaviour and adaptation of microbial cells is a key step in understanding their behaviour. One such wide-domain regulatory circuit, essential to all cells, is carbon catabolite repression (CCR): it allows the cell to prefer some carbon sources, whose assimilation is of high nutritional value, over less profitable ones. This system has been investigated in bacteria, yeast and filamentous fungi. In the latter, the C2H2 zinc finger protein has been shown to act as the central transcriptional repressor in this process. Here, we deciphered the CRE1 regulon by profiling transcription in a wild-type and delta-cre1 mutant strains on glucose in the model cellulose and hemicellulose-degrading fungus Trichoderma reesei (anamorph of Hypocrea jecorina) at constant growth rates known to per se repress and derepress CCR-affected genes.

overall_design: Two biological pool by condition in dye switch. For the two biological replicates on each four experiments we apply on the pretreated results the linear modeling approach implemented by lmFit and the empirical Bayes statistics implemented by eBayes from the limma R package (Smyth 2004). We select the list of statistically regulated genes using a 5% significance threshold.

first: Stephane

last: Le Crom

first: Christian

last: Kubicek

first: Thomas

last: Portnoy

last: Linke

first: Antoine

last: Margeot

first: Bernard

last: Seiboth


title: Quantitative Analysis of Alternative Spliced Variants in HNSCC

status: Public on Jun 10 2011

city: Helsinki

first: Ping

last: Chen

address: PO Box 63 (Haartmaninkatu 8), 00014 University of Helsinki, Finland

country: Finland

institute: Research Programs Unit, Genome-Scale Biology and Institute of Biomedicine, Biochemistry and Developmental Biology

summary: Alternative splicing of pre-mRNA generates protein diversity and has been linked to cancer progression  and drug response. Exon microarray technology enables genome-wide quantication of expression levels  for the majority of exons and facilitates the discovery of alternative splicing events. Analysis of exon  array data is more challenging than gene expression data and there is a need for reliable quantication  of exons and alternative spliced variants. We introduce a novel, computationally efficient methodology,  MEAP, for exon array data preprocessing, analysis and visualization. We compared MEAP with other  preprocessing methods, and validation of the results show that MEAP produces reliable quantication  of exons and alternative spliced variants. Analysis of data from head and neck squamous cell carcinoma  (HNSCC) cell lines revealed several variants associated with 11q13 amplication, which is a predictive  marker of metastasis and decreased survival in HNSCC patients. Together these results demonstrate  the utility of MEAP in suggesting novel experimentally testable predictions. Thus, in addition to novel  methodology to process large-scale exon array data sets, our results provide several HNSCC candidate  genes for further studies.

overall_design: We analyzed 15 samples using the Affymetrix Human Exon 1.0 ST platform, of which 7 samples have 11q13 amplification. Array data was preprocessed by using Multiple Exon Array Processing (MEAP).

first: Tatiana

last: Lepikhova

first: Yizhou

last: Hu

first: Outi

last: Monni

first: Sampsa

last: Hautaniemi


title: tagF1-F2 and dlt mutant study

status: Public on May 01 2011

city: Ede

first: Michiel

last: Wels

address: Kernhemseweg 2

institute: NIZO food research

summary: Several strains of Lactobacillus plantarum are marketed as health-promoting probiotics. The role and interplay of specific cell-wall compounds like wall- and lipo-teichoic acids (WTA and LTA) in probiotic-host interactions remains obscure. Through genome mining and mutagenesis we constructed derivatives of L. plantarum WCFS1 that synthesize alternative WTA variants. The mutants were shown to completely lack WTA, or produce WTA and LTA that lack D-Ala substitution, or ribitol-backbone WTA instead of the wild-type glycerol-containing backbone. Transcriptome analysis revealed the genetic determinants involved in backbone switching. Human dendritic cells secreted drastically decreased levels of pro-inflammatory cytokines after stimulation with the WTA mutants, and indicated LTA contributes to TLR-2/6 signalling, whereas WTA attenuates TLR-2 and TLR-1/2 signalling in a backbone-alditol dependent manner. Overall, the engineering of WTA and its consequences for immune system interaction advances our molecular understanding of host-microbe communication, and underpins the strain-specificity of probiotics.

overall_design: All samples were hybridized twice (each dye once) in a triangular design, hybridizing all samples

first: M

first: P

last: Bron

first: D

last: Remus

first: R

last: Bongers

last: Kleerebezem


title: Dioxin effect on the pituitary and hypothalamic expression of genes in male fetal Wistar rats

status: Public on Oct 01 2011

city: Fukuoka

first: Tomoki

last: Takeda

address: 3-1-1 Maidashi, Higashi-ku

department: Pharmaceutical sciences

institute: Kyushu University

summary: 2,3,7,8-Tetrachlorodibenzo-p-dioxin (TCDD) causes the many forms of reproductive toxicity, such as defects in sexual behaviors, in pups of which mother is exposed to this substance at lower doses. However, the mechanism underlying these defects remains to be clarified in spite of many researches conducted so far. Our previous studies have revealed that maternal treatment with TCDD attenuates the production of pituitary gonadotropins [luteinizing hormone (LH) and follicle-stimulating hormone] in the late fetuses, leading to the impairment of sexual behavior in adulthood. To identify the target genes for a fetal reduction in gonadotropin β-subunit, we performed DNA microarray analysis using the fetal pituitary and its regulatory organ, the hypothalamus. The result showed that TCDD induced histone deacetylases (HDACs), and altered the expression of genes including gonadotropin-releasing hormone and activin signaling in the fetal pituitary. Moreover, our data indicated that the increased deacetylation of histone due to HDAC induction plays a critical role for a dioxin-induced attenuation of LHβ in the fetal pituitary. This study suggests a novel molecular mechanism explaining dioxin-produced reproductive toxicity.

overall_design: Pregnant Wistar rats were orally treated with TCDD (1 µg/kg in corn oil) at gestational day (GD)15. Then, the total RNA was extracted from the fetal pituitary and hypothalamus at GD20. To identify the target genes the alteration of which contributes to a reduction in fetal gonadotropin β-subunit, the profile of gene expression was analyzed using the Illumina RatRef-12 Expression BeadChip.

first: Misaki

last: Fujii

first: Hideyuki

last: Yamada


title: Crosstalk between gene body DNA methylation, H3K9me3 and H3K36me3 chromatin marks and transcription [HuEx-1_0-st]

status: Public on Mar 31 2011

city: Duarte

first: Xiwei

last: Wu

state: CA

address: 1500 E. Duarte Rd.

department: Computational and Quantitative Medicine

institute: City of Hope National Medical Center

summary: This is one of expressional parts of the study. These data were correlated to epigenetic changes and CG density of genes in analyzed cells. The whole study has a following summary: To elucidate possible roles of DNA methylation and chromatin marks in transcription, we performed epigenetic profiling of chromosome 19 in human bronchial epithelial cells (HBEC) and in the colorectal cancer cell line HCT116 as well as its counterpart with double knockout of DNMT1 and DNMT3B (HCT116-DKO). We found that H3K9me3 forms intragenic chromatin blocks along genes with low CpG density in the gene body. Analysis of H3K36me3 profiles indicated that this mark associates either with active genes with low CpG density and H3K9me3 in the gene body or with active genes with high CpG density and DNA hypermethylation in the gene body. In HCT116 cells with double knockout of DNMT1 and DNMT3B, transcription of genes with low CpG density in the gene body was highly elevated and associated with promoter DNA demethylation and rearrangement of H3K9me3 and H3K36me3 occupation. Our finding suggests that similar to DNA methylation, H3K9me3 may play a role in intragenic gene regulation. Further, we observed that a combination of low CpG density in gene bodies together with H3K9me3 and H3K36me3 marking is a specific epigenetic feature of zinc finger (ZNF) genes, which comprise 90% of all genes carrying both histone marks on chromosome 19. For high CpG density genes, transcription and H3K36me3 occupancy were not changed in condition of partial or intensive loss of DNA methylation in gene bodies in the HCT116-DKO cell line. siRNA experiments with SETD2 knockdown in both HBEC and HCT116-DKO cell lines failed to reduce DNA methylation in gene bodies under conditions of H3K36me3 depletion. Our study suggests that the H3K36me3 and DNA methylation marks in gene bodies are established independently from each other and points to similar functional roles of intragenic DNA methylation and intragenic H3K9me3 for CpG-rich and CpG-poor genes, respectively.

overall_design: To elucidate how a loss of DNA methylation affects a gene expression and epigenome we studied colon cancer cell line HCT116 and its derivative, HCT116 DNMT1-/- DNMT3b -/- (HCT116-DKO). According to previous studies HCT116-DKO is characterized by 95% of loss of DNA methylation. In HCT116 and HCT116-DKO cells, we profiled diverse epigenetic marks and gene expression. Further a crosstalk between epigenetic changes and transcriptional changes was analyzed. This is the expressional part of study.

first: Maria

last: Hahn

first: Arthur

middle: X

last: Li

first: Torsten

first: Gerd

last: Pfeifer


title: Exon level expression profiling of mutant U2AF35 transduced HeLa cells

status: Public on Sep 12 2011

city: Tokyo

first: Aiko

last: Sato-Otsubo

address: 7-3-1, Hongo, Bunkyo-ku

institute: University of Tokyo

summary: In this study, to obtain the biological impact of the mutated U2AF35, HeLa cells were retrovirally transduced with either mock, wild-type or S34F mutant of U2AF35, and Exon array was performed.

overall_design: Exon level analysis was performed for mock, wild-type U2AF35 or S34F mutant transduced HeLa in triplicate.

first: Kenichi

last: Yoshida

first: Masashi

last: Sanada

first: Yuichi

last: Shiraishi

first: Yasunobu

last: Nagata

first: Yusuke

last: Sato

first: Ayana

last: Kon

last: Shiosaka

first: Ryoichiro

last: Kawahata

first: Seishi

last: Ogawa


title: Gene Array Data from Human Annulus Disc Tissue

status: Public on Mar 01 2011

city: Charlotte

first: Helen

last: Gruber

state: NC

address: 1542 Graden Terrace

department: Orthopaedic Surgery

institute: Carolinas HealthCare System

summary:
Although it is well-recognized that apoptosis, senescence, and increased production of inflammatory cytokines and catabolic products are important factors in the degeneration of the human intervertebral disc, there is poor understanding of the underlying cause.
The objective of the present study was to analyze gene expression patterns in the human annulus disc tissue.

overall_design: Disc Tissue samples were obtained via the National Cancer Institute Cooperative Tissue Network (CHTN) as well as surgical disc procedures performed on patients with herniated discs and degenerative disc disease. Tissue was treated by one of the following methods: 1) fixed, paraffin embedded and standard laser capture microdissection (LCM) techniques used to collect cells or 2) homogenized in TRIzol reagent. Total RNA was isolated and analyzed via mircoarray.

first: Gretchen

middle: L

last: Hoelscher

first: John

last: Watts

first: Synthea

last: Bethea

first: Jane

last: Ingram

first: Natalia

last: Zinchenko

first: Edward

middle: N

last: Hanley Jr


title: Salmonella Typhimurium: control vs. cortisol treatment

status: Public on Jul 26 2011

city: Norwich

first: Neil

last: Shearer

state: Norfolk

address: Colney Lane

department: Gut Health and Food Safety

institute: Institute of Food Research

summary: Transcriptional profiling of log and stationary phases of S. Typhimurium, comparing untreated controls with cortisol-treated samples.

platform_organism: Salmonella enterica subsp. enterica serovar Typhimurium str. DT104

platform_organism: Salmonella enterica subsp. enterica serovar Typhimurium str. LT2

platform_organism: Salmonella enterica subsp. enterica serovar Enteritidis

platform_organism: Salmonella enterica subsp. enterica serovar Typhimurium str. SL1344

platform_organism: Salmonella enterica subsp. enterica serovar Gallinarum str. 287/91

overall_design: Each array used labelled cDNA against a common genomic DNA reference. Triplicate arrays were carried out for each of the 4 conditions: untreated log phase, untreated stationary phase, cortisol treated log phase and cortisol treated stationary phase.

first: Arthur

last: Thompson

first: Elin

last: Verbrugghe


title: Sex-biased suppression of chemically induced neural carcinogenesis in congenic BDIX-BDIV-Mss4a rats

status: Public on Jul 01 2011

city: Essen

first: Andrea

last: Kindler-Röhrborn

address: Hufeland Str. 55

department: Patholpgy & Neuropathology

institute: University of Essen

summary: Gender specific expression profiling of congenic BDIX-BDIV-Mss4a rats vs. BDIX and BDIV parental strains using trigeminal nerve tissue

overall_design: Total RNA obtaines from pooled, isolated trigeminal nerves from untreated 85 days old males and females of inbred strains BDIX, BDIV and BDIX.BDIV-Mss4a were compared

first: Bernd

last: Koelsch


title: Exon-array profiling of Heat-shock stress response in HeLa cell line

first: Mitali

last: Mukerji

state: New Delhi

address: Sukhdev Vihar, Mathura Road

department: Functional Genomics and Molecular Medicine

institute: CSIR-Institute Of Genomics and Integrative Biology

summary:
The heat-shock stress response was studied at the level of exons using Affymetrix Exon-array profiling for both sense and anti-sense transcripts. Sense transcript profiling was done as per the protocol of Affymetrix Exon 1.0 ST array and anti-sense transcript array profiling was done using a modified protocol (Xijin Ge et al., BMC Genomics. 2008 Jan 22;9:27).
In short, for profiling antisense transcripts, first cycle cDNA synthesis and IVT step is skipped. This modified protocol starts directly from the second cycle cDNA synthesis step. The labelled target DNA fragments are in reverse orientation of original mRNAs. Thus the hybridization signals will represent transcripts from the same exonic regions but from the opposite DNA strand.

overall_design:
Study was undertaken with 2 biological replicates each for -
a) Heat-shock treated Sense
b) Heat-shock treated Anti-sense
c) Untreated control Sense
d) Untreated control Anti-Sense

first: Rajesh

last: Pandey


title: Tissue-specific genetic regulation of splicing and expression (exon-level)

status: Public on Jul 08 2011

city: New York

first: Erin

middle: L.

last: Heinzen

department: Institute for Genomic Medicine

institute: Columbia University

summary: Numerous genome-wide screens for polymorphisms that influence gene expression have provided key insights into the genetic control of transcription. Despite this work, the relevance of specific polymorphisms to in vivo expression and splicing remains unclear. We carried out the first genome-wide screen, to our knowledge, for SNPs that associate with alternative splicing and gene expression in human primary cells, evaluating 93 autopsy-collected cortical brain tissue samples with no defined neuropsychiatric condition and 80 peripheral blood mononucleated cell samples collected from living healthy donors. We identified 23 high confidence associations with total expression and 80 with alternative splicing as reflected by expression levels of specific exons. Fewer than 50% of the implicated SNPs however show effects in both tissue types, reflecting strong evidence for distinct genetic control of splicing and expression in the two tissue types. The data generated here also suggest the possibility that splicing effects may be responsible for up to 13 out of 84 reported genome-wide significant associations with human traits. These results emphasize the importance of establishing a database of polymorphisms affecting splicing and expression in primary tissue types and suggest that splicing effects may be of more phenotypic significance than overall gene expression changes.

overall_design: We evaluated 93 autopsy-collected cortical brain tissue samples with no defined neuropsychiatric condition and 80 peripheral blood mononucleated cell samples collected from living healthy donors. Affymetrix Human ST 1.0 exon arrays were used to assess exon and transcript expression levels for all samples used in the study. Replicate analyses were not performed.  Exon array sample preparation from total RNA was conducted based on standard Affymetrix protocols.  Data were normalized separately within PBMC and brain sets Affymetrix PLIER protocol with a sketch-quantile normalization procedure (Affymetrix Expression Console).  Normalized files include brain core transcripts (NABRAINSETCOMBplier-gene-core.summary), brain all transcripts (NABRAINSETCOMBplier-gene-full.summary), brain core exons (NABRAINSETCOMBplier-exon-core.summary), brain all exons (NABRAINSETCOMBplier-exon-all.summary), PBMC core transcripts (NAPBMCfullsetplier-gene-core.summary), PBMC all transcripts (NAPBMCfullsetplier-gene-full.summary), PBMC core exons (NAPBMCfullsetplier-exon-core.summary), PBMC all exons (NAPBMCfullsetplier-exon-all.summary).  all, full and core definitions are provided by Affymetrix.

first: David

middle: B

last: Goldstein


title: The Hace1 E3 Ligase Modulates the Activity of Multiple Tumor Suppressive CRL E3 Ligases by binding to CAND1

city: Vancouver

first: Tony

last: Ng

department: Molecular Oncology

institute: BC Cancer Research Centre

summary:
The Hace1 E3 ligase is a tumor suppressor in stressed cells. Through unknown mechanisms, Hace1 indirectly targets the cyclin D1 proto-oncogene for proteasomal degradation during nutrient depletion. We now show that Hace1 targets HIF1alpha for VHL-dependent degradation during hypoxia. To better understand these diverse actions we performed mass spectrometry to identify Hace1-interacting proteins. We show that Hace1 interacts with cullin-associated NEDD8-dissociated protein 1 (CAND1) under nutrient depletion and hypoxia. CAND1 binds cullins and prevents their entry into cullin ring E3 ligase (CRL) complexes, thus blocking CRL activity. Hace1 binding releases CUL1/2 from CAND1, facilitating assembly of CRL complexes to degrade cyclin D1 and HIF1alpha, respectively. These findings suggest a broad role for Hace1 in regulating tumor suppressive CRL E3 ligases.
In this study, we used gene expression profiling to characterize how Hace1 overexpression affect the transcriptional response to hypoxic stress

overall_design: Using Affymetrix exon-level microarrays, we compared the expression profile of HEK293 cells overexpressing either Hace1 or MSCV vector alone, under hypoxia or normoxia

first: Fan

last: Zhang

first: Elai

last: Davicioni

first: Poul

last: Sorensen


title: High-throughput sequencing of small RNAs in Chara corallina

status: Public on Apr 30 2011

city: Udine

first: Emanuele

last: De Paoli

state: UDINE

address: via delle Scienze 206

department: Agricultural, Food, Environmental and Animal Sciences

country: Italy

institute: University of Udine

type: Non-coding RNA profiling by high throughput sequencing

summary: Small RNAs (21-24 nt) are pivotal regulators of gene expression that guide both transcriptional and post-transcriptional silencing mechanisms in diverse eukaryotes, including most if not all plants. MicroRNAs (miRNAs) and short interfering RNAs (siRNAs) are the two major types, both of which have a demonstrated and important role in plant development, stress responses and pathogen resistance. In this work, we used a deep sequencing approach (Sequencing-By-Synthesis, or SBS) to develop sequence resources of small RNAs from Chara corallina thallus in different growing conditions. The high depth of the resulting datasets enabled us to examine in detail critical small RNA features, such as size distribution, tissue-specific regulation and sequence conservation between different organs in this species. We also developed database resources and a dedicated website (http://smallrna.udel.edu/) with computational tools for allowing other users to identify new miRNAs or siRNAs involved in specific regulatory pathways, verify the degree of conservation of these sequences in other plant species and map small RNAs on genes or larger regions of the maize genome under study.

overall_design: Small RNA libraries were derived from thallus of Chara corallina incubated in different growth conditions. Total RNA was isolated using the Plant RNA Purification Reagent (Invitrogen) and submitted to Illumina (Hayward, CA, http://www.illumina.com) for small RNA library construction using approaches described in (Lu et al., 2007) with minor modifications. The small RNA libraries were sequenced with the Sequencing-By-Synthesis (SBS) technology by Illumina. PERL scripts were designed to remove the adapter sequences and determine the abundance of each distinct small RNA. We thank John Boyer for providing the plant material, as well as Kan Nobuta and Gayathri Mahalingam for assistance with the computational methods.

first: Monica

last: Accerbi

first: Pamela

last: Green

first: Blake

last: Meyers


title: Misregulation of alternative splicing of BIN1 leads to T-tubule alterations and muscle weakness in myotonic dystrophy

status: Public on May 26 2011

city: Illkirch

first: Doulaye

last: Dembele

address: 1 rue Laurent Fries

department: Biopuces

institute: IGBMC

summary: Myotonic dystrophes (DM), the most common adult muscular dystrophy, are the first recognized examples of RNA-mediated diseases in which expression of mutant RNAs containing expanded CUG or CCUG repeats interfere with the splicing of other mRNAs. Using whole-genome microarrays, we found that alternative splicing of the BIN1 mRNA is altered in DM skeletal muscle tissues, resulting in the expression of an inactive form of BIN1 deprived of phosphoinositide-binding and membrane-tubulating activities. BIN1 is involved in tubular invaginations of the plasma membrane and is essential for biogenesis of the muscle T-tubules, which are specialized skeletal muscle membrane structures essential to correct excitation-contraction (E-C) coupling. Mutations in the BIN1 gene cause centronuclear myopathy (CNM) that shares some histopathological features with DM, and both diseases are characterized by muscle weakness. Consistent with a loss-of-function of BIN1, muscle T-tubules were altered in DM patients, and membrane tubulation was restored upon expression of the correct splicing form of BIN1 in DM muscle cells. By deciphering the mechanism of BIN1 splicing mis-regulation we demonstrate that the splicing regulator, MBNL1, which is sequestered by expanded CUG and CCUG in DM, binds the BIN1 pre-mRNA and regulates directly its alternative splicing. Finally, reproducing BIN1 splicing alteration in mice is sufficient to reproduce the DM features of T-tubule alterations and muscle weakness. We propose that alteration of BIN1 alternative splicing regulation leads to muscle weakness, a predominant pathological feature of DM.

overall_design: Exon-Array analysis of control and CDM1 muscle primary cultures 10 days of differentiation

first: Nicolas

last: Charlet-Berguerand


title: EMT is the dominant program in human colon cancer (Affymetrix)

status: Public on Apr 25 2011

city: West Point

first: Michael

last: Nebozhyn

state: PA

address: Mail Stop WP53B-120, 770 Sumneytown Pike, Building 53, P.O. Box 4

department: GpGx/Computational System biology

institute: Merck, Inc

summary:
mRNA profiling data for 67 colorectal cancer at baseline
Supporting data for PMID: 21251323

overall_design: mRNA profiles at baseline for 67 colorectal cancer cell lines

middle: V


title: Expression profiles of human primary keratinocytes differentiated with TPA

status: Public on Apr 12 2011

city: Berlin

first: Ulf

middle: Andersson

last: Ørom

address: Ihnestrasse 63-73

department: OWL

institute: Max Planck Institute for Molecular Genetics

summary: Human primary keratinocytes were left untreated or treated for 48 hr with 12-O-tetradecanoylphorbol-13-acetate (TPA) and expression profiles were compared to find long ncRNAs expressed and differentially regulated upon differentiation.

overall_design: 4 replicates of minus TPA and 3 of plus TPA with dye-swap. Custom-made microarray from Agilent.

first: Ramin

last: Shiekhattar