title: Identification of tissue microRNAs predictive of sutinib activity in patients with metastatic renal cell carcinoma

status: Public on Sep 30 2014

city: Pamplona

first: Alfonso

last: Calvo

state: Navarra

address: Pio XII, 55

department: Oncology

country: Spain

institute: CIMA

summary:
Purpose: To identify tissue microRNAs predictive of sunitinib activity in patients with metastatic renal-cell carcinoma (MRCC) and to validate them in a cellular model. Selected microRNAs were studied in serum from MRCC patients and healthy individuals.

Methods: We screened 673 microRNAs using TaqMan Low-density Arrays (TLDAs) in tumors from MRCC patients with extreme phenotypes of marked efficacy and resistance to sunitinib, selected from an identification cohort (n=41). Differentially expressed microRNAs were selected using bioinformatics-based target prediction analysis and quantified by qRT-PCR in tumors from patients presenting similar phenoytpes selected from an independent cohort (n=117). Results were validated in a cellular model of sunitinib resistance and studied in serum from healthy individuals and MRCC patients.

Results: TLDAs identified 64 microRNAs differentially expressed in the identification cohort. Seven candidates were quantified by qRT-PCR in the independent series. MiR-942 was the most accurate predictor of sunitinib efficacy (p=0.0074). High expression of miR-942, miR-133a, miR484, and miR-628-5p was significantly associated with decreased time-to-progression and overall survival. These microRNAs were overexpressed in the sunitinib resistant cell line Caki-2 in comparison with the sensitive parental cell line. Serum levels of miR-942, miR-133a, miR-484, miR-146a-5p, miR-374a and miR-486-5p were significantly reduced in MRCC patients compared to healthy controls.

Conclusions: Our strategy identified differentially expressed microRNAs in MRCC patients presenting marked sensitivity and resistance to sunitinib. Mir-942 was the best predictor of efficacy. Results were confirmed in a cellular model of sunitinib resistance. We also identified exosome derived serum microRNAs differentially expressed in MRCC patients and healthy individuals.

overall_design: Taqman Low Density Array for 6 FFPE tissues obtained from extreme phenotype MRCC patients, (n=3 marked resistance to sunitinib treatment patients and n=3 marked sensitivity to sunitinib treatment patients), was performanced to screen 667 microRNAs.

first: Celia

last: Prior

first: Jose

middle: L

last: Perez-Gracia

first: Jesús

last: García-Donás

first: Cristina

last: Rodriguez-Antona

first: Elizabeth

last: Guruceaga


title: miRNA expression profiles of peripheral monocytes and glioblastoma-infiltrating macrophages

status: Public on Sep 23 2014

city: Houston

first: Amy

middle: B

last: Heimberger

state: TX

address: 1400 Holcombe Blvd., FC7.2000

department: Neurosurgery

country: USA

institute: The University of Texas MD Anderson Cancer Center

summary: MicroRNAs (miRNAs) are non-coding molecules involved in post-transcriptional gene regulation that have been shown to modulate tumor cell proliferation and apoptosis and to act as oncogenes or tumor-suppressor genes. Although miRNAs have been linked to tumor progression, the connection between tumor-mediated immune modulation and miRNAs has yet to be explored. Specifically, how the miRNA dysregulation affects the monocyte-derived glioblastoma-infiltrating macrophages, the most abundant immune cell population within the glioblastoma microenvironment, and their immune suppressive properties has not been evaluated to date. Here we managed to purify the glioblastoma-infiltrating macrophages from the tumor microenvironment and compared their miRNA expression profile with the matched peripheral monocytes from the peripheral blood of the same GBM patient as well as with healthy donors. Of note, several most down-regulated miRNA candidates revealed in this study, including miR-142-3p, were also known for their role in mediating tumor-associated immunosuppression. These results suggest a novel approach to identify miRNA immune therapeutics using a two-step process: 1) screen miRNA expression from tumor-associated immune cells relative to normal immune cell, and 2) select and prioritize potential candidates on the basis of binding to immunosuppressive pathways or mechanisms.

overall_design: In the study presented here, 12 samples, including peripheral monocyte samples from 4 healthy donors, peripheral monocytes from 4 GBM patients and matched tumor-infiltrating macrophages extracted from the glioblastoma microenvironment, were used to acquire the miRNA expression profiles of 1732 unique mature miRNA sequences via the Phalanx Human miRNA OneArray Microarray v3 Platform.

first: Jun

last: Wei

first: Shuo

last: Xu


title: Prefrontal cortex gene expression in WSP and WSR male and female mice following chronic ethanol exposure during peak withdrawal at 8hr

status: Public on Sep 17 2014

city: Portland

first: Marina

last: Guizzetti

state: OR

address: 3710 SW US Veterans Hospital Rd

department: Behavioral Neuroscience

institute: Oregon Health & Science University; Portland VA Research Service

summary: While women are more vulnerable than men to many of the medical consequences of alcohol abuse, the role of sex in the response to ethanol is controversial. Neuroadaptive responses that result in the hyperexcitability associated with withdrawal from chronic ethanol likely reflect gene expression changes. We have examined both genders for the effects of withdrawal on brain gene expression using mice with divergent withdrawal severity that have been selectively bred from a genetically heterogeneous population. A total of 295 genes were identified as ethanol regulated from each gender of each selected line by microarray analyses. Hierarchical cluster analysis of the arrays revealed that the transcriptional response correlated with sex rather than with the selected withdrawal phenotype. Consistent with this, gene ontology category over-representation analysis identified cell death and DNA/RNA binding as targeted classes of genes in females, while in males, protein degradation, and calcium ion binding pathways weremore altered by alcohol. Examination of ethanol regulated genes and these distinct signaling pathways suggested enhanced neurotoxicity in females. Histopathological analysis of brain damage following ethanol withdrawal confirmed elevated cell death in female but not male mice. The sexually dimorphic response was observed irrespective of withdrawal phenotype. Combined, these results indicate a fundamentally distinct neuroadaptive response in females compared to males during chronic ethanol withdrawal and are consistent with observations that female alcoholics may be more vulnerable than males to ethanol-induced brain damage associated with alcohol abuse.

overall_design: A total of 32 microarrays were run with 4 biological replicates per treatment, line, and sex.  Selection replicates (i.e. WSP-1 and WSP-2) for each treatment, line, and sex were collapsed to improve statistical power (n=4) and to facilitate in the identification of phenotype related effects and exclude selection artifacts.  For comparisons, EtOH regulation was determined by comparing 4 arrays from (for example) Male WSR EtOH treated versus 4 arrays from Male WSR Air treated arrays.

first: Kristine

middle: M

last: Wiren

first: Joel

middle: G

last: Hashimoto


title: MiR-34a is dispensable for normal development but its loss accelerates medulloblastoma formation

status: Public on Sep 22 2014

city: Neuherberg

first: Martin

last: Irmler

state: Bayern

address: Ingolstaedter Landstrasse 1

department: Institute of Experimental Genetics

country: Germany

institute: Helmholtz Zentrum München GmbH

summary: Previous studies have evaluated the role of miRNAs in the initiation and progression of cancer. MiR-34a was found to be downregulated in several tumors, including medulloblastoma. We here analysed the function of miR-34a in vivo by targeted transgenesis to generate mice with constitutive deletion of the miR-34a gene, which resulted in the absence of mir-34a in all analysed tissues. Nevertheless, these mice were viable and fertile. A comprehensive standardized phenotypic analysis including more than 300 single parameters performed by the German Mouse Clinic revealed no apparent phenotype. Analysis of miR-34a expression in human medulloblastomas and medulloblastoma cell lines revealed significant downregulation as compared to human cerebellum. Re-expression of mir-34a in human medulloblastoma cells in vitro reduced cell viability, cell proliferation and induced apoptosis. Among the targets downregulated by miR-34a in human medulloblastoma cells were NMYC and SIRT1. Activation of the Shh pathway by targeted overexpression of SmoA1 causes medulloblastoma in mice, which is dependent on the presence and upregulation of NMYC. Analysis of miR-34a in ND2:SmoA1-derived medulloblastomas revealed significant suppression of miR-34a compared to normal cerebellum. Crossbreeding these mice with miR-34a knockout mice significantly accelerated medulloblastoma growth in mice deficient for miR-34a. Interestingly, NMYC and SIRT1 were highly expressed in medulloblastomas derived from these mice. We here demonstrate that miR-34a is dispensable for normal development, but that its loss accelerates medulloblastoma. Strategies aiming to re-express miR-34a in tumors could therefore represent an efficient therapy option.

overall_design: For genome-wide expression analysis total RNA from brain and thymus of three or four male miR34a and four control mice was isolated using RNeasy Midi kit (Qiagen, Hilden, Germany). The cDNA microarrays were generated, hybridized and analysed as described (Horsch et al 2009). Two chip hybridizations were performed with total RNA for each individual mutant mouse against a reference RNA pool of the same organ.

first: Johannes

last: Beckers

first: Marion

last: Horsch


title: Temporal gene expression profiling of myeloid cells during the peritoneal foreign body response

city: St. Lucia

first: Othmar

last: Korn

state: Queensland

address: University of Queensland

country: Australia

institute: Australian Institute for Bioengineering and Nanotechnology

summary: This study dermined the temporal gene expression profile of myeloid subpopulations recruited to the peritoneal cavity to encapsulate implanted foreign material.

overall_design: Sterile foreign objects  were inserted into the peritoneal cavities of MacGreen mice (in which the Csf1r promoter directs myeloid-specific EGFP expression).  At various time-points post-surgery (days 2, 4, 7, 14), mice were euthanased, and peritoneal exudate cells removed by lavage.  Peritoneal exudate cells from MacGreen mice that had not received implants were used as controls (day 0; 'unstimulated').  Free-floating objects encapsulated with tissue were removed from the peritoneal cavities of different mice at days 7, 14, 21, 28 days, and single cell suspensions obtained by collagenase digestion.  Single-cell suspensions from peritoneal exudate or tissue capsules  were separated on the basis of size/granularity and EGFP  fluorescence using FacsVantage SE Diva. Total RNA was extracted from FACS-sorted EGFP-hi cells.

first: Jane

middle: E

last: Mooney

first: Kim

last: Summers

first: Sean

last: Grimmond

first: Milena

last: Gongora

first: Julie

middle: H

last: Campbell

first: David

middle: A

last: Hume

first: Barbara

last: Rolfe


title: Sodium arsenite induced changes in A549 human epithelial lung carcinoma cells

city: Maastricht

first: Simone

last: van Breda

state: Limburg

address: Universiteitssingel 50

department: Toxicogenomics

country: Netherlands

institute: Maastricht University

type: Methylation profiling by genome tiling array

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

overall_design: Refer to individual Series


title: The pyruvate-tricarboxylic acid cycle node: a focal point of virulence control in the enteric pathogen Yersinia pseudotuberculosis [crp mutant]

city: Braunschweig

first: Ann

middle: Kathrin

last: Heroven

state: Niedersachsen

address: Inhoffenstr. 7

department: Molecular Infection Biology

institute: Helmholtz Centre for Infection Research

summary: Whole transcriptome assessment of the Yersinia pseudotuberculosis strain YPIII. The Y. pseudotuberculosis crp regulon was determined in Yersinia minimal minimum developed for the study. Crp is a key regulator coordinating virulence and metabolism.

overall_design: Y. pseudotuberculosis YPIII or the isogenic crp mutant strain  were cultivated at 25°C under aeration on a rotary shaker. First pre-cultures were grown in a 1:1 mixture of HAM’s F-12 Nutrient Mixture (Invitrogen, Carlsbad, US) and liquid DMEM medium (Biochrom, Berlin, DE). Second pre-cultures and main cultures were grown in a Yersinia minimal medium (YMM). The analysis comprised three biological replicates for each strain. In addition, samples, taken at three different time points of the exponential growth phase, were used to validate constant expression during the cultivation. Total RNA was extracted using SV Total RNA Isolation System (Promega). The samples were treated with RNase-free DNase (Roche Applied Science) and the quality of the RNA was confirmed by the lack of PCR amplification of the hns gene and by using an Agilent 2100 Bioanalyzer.

middle: K

first: René

last: Bücker


title: The pyruvate-tricarboxylic acid cycle node: a focal point of virulence control in the enteric pathogen Yersinia pseudotuberculosis [csrA mutant]

summary: Whole transcriptome assessment of the Yersinia pseudotuberculosis strain YPIII. The Y. pseudotuberculosis csrA regulon was determined in Yersinia minimal minimum developed for the study. CsrA is a key regulator coordinating virulence and metabolism.

overall_design: Y. pseudotuberculosis YPIII or the isogenic csrA mutant strain  were cultivated at 25°C under aeration on a rotary shaker. First pre-cultures were grown in a 1:1 mixture of HAM’s F-12 Nutrient Mixture (Invitrogen, Carlsbad, US) and liquid DMEM medium (Biochrom, Berlin, DE). Second pre-cultures and main cultures were grown in a Yersinia minimal medium (YMM). The analysis comprised three biological replicates for each strain. In addition, samples, taken at three different time points of the exponential growth phase, were used to validate constant expression during the cultivation. Total RNA was extracted using SV Total RNA Isolation System (Promega). The samples were treated with RNase-free DNase (Roche Applied Science) and the quality of the RNA was confirmed by the lack of PCR amplification of the hns gene and by using an Agilent 2100 Bioanalyzer.


title: The pyruvate-tricarboxylic acid cycle node: a focal point of virulence control in the enteric pathogen Yersinia pseudotuberculosis


title: Drosophila COP9 Signalosome Subunit 7 interacts with multiple genomic loci

city: Tel Aviv

first: Danny

last: Chamovitz

address: Ramat aviv

country: Israel

institute: Tel Aviv University

type: Genome binding/occupancy profiling by genome tiling array

summary: The COP9 signalosome protein complex has a central role in the regulation of development of multi-cellular organisms. While the function of this complex in ubiquitin-mediated protein degradation is well established, results over the past few years have hinted that the COP9 signalosome may function more broadly in the regulation of gene expression. Here, using DamID technology, we show that COP9 signalosome subunit 7 functionally associates with a large number of genomic loci in the Drosophila genome, and show that the expression of many genes within these loci is COP9 signalosome-dependent. This association is likely direct as we show CSN7 binds DNA in vitro. The genes targeted by CSN7 are preferentially enriched for transcriptionally active regions of the genome, and are involved in the regulation of distinct gene ontology groupings including imaginal disc development and cell-cycle control.

overall_design: DamID experiments were done in Drosophila Kc167 cells. Samples were hybridized to 380k NimbleGen arrays with 300 bp probe spacing. The experiment contains 4 samples, three biological replicates and one reverse dye orientation. For each sample Dam-fusion material was hybridized over Dam-only material.

first: Ruth

last: Singer

first: Amir

last: Orian

first: Daniel


title: Prokaryote whole-genome tiling microarray design and validation

status: Public on Sep 25 2014

city: Ames

first: Hui-Hsien

last: Chou

state: IA

address: 503 Science II

department: Genetics, Development and Cell Biology

institute: Iowa State University

type: Expression profiling by genome tiling array

sample_organism: Escherichia coli str. K-12 substr. MG1655


title: Integrated assessment of coding and non-coding expression in intrahepatic cholangiocarcinoma: Their potential biological significance as prognostic cancer biomarkers

city: HANGZHOU

first: wang

last: jianguo

state: ZHEJIANG

address: 79 Qingchun Road

department: Department of Surgery, First Affiliated Hospital, Zhejiang University School of Medicine

country: China

institute: zhejiang university

summary: Recent studies show that long non-coding RNAs (lncRNAs) play crucial roles in human cancers. However, functional lncRNAs and their downstream mechanisms are largely unknown in the molecular pathogenesis of intrahepatic cholangiocarcinoma (ICC) and its progression. In the present study, we performed transcriptomic profiling of five ICC and paired adjacent noncancerous tissues (N) using lncRNA and mRNA microarrays to identify relevant biomarkers in ICC. Quantitative real-time polymerase chain reaction (qRT-PCR) was used to validate the microarray results. We sought correlations between the expression levels of lncRNAs and those of target genes. Clinicopathological characteristics and overall survival  were compared using the t-test and the Kaplan–Meier method, respectively. A total of 3,054 and 2,111 lncRNAs were significantly up- and down-regulated(fold change≧2, p﹤0.05) in ICC tissues  compared to the adjacent NT samples. Bioinformatic analysis indicated that most such genes were related to carcinogenesis, hepatic system disease, and signal transduction. Positive correlations were evident between four pairs of lncRNAs and target mRNAs (RNA43085 and SULF1, RNA47504 and KDM8, RNA58630 and PCSK6, and RNA40057 and CYP2D6). In addition, some lncRNAs and mRNAs were significantly associated with clinicopathological characteristics. The cumulative overall survival rate was significantly associated with low-level expression of CYP2D6 (p=0.005) and PCSK6 (p=0.038). And patients with high expression levels of CYP2D6 and RNA40057 have significant better prognosis (p=0.014). Our results suggested that lncRNA expression profile in ICC tissues is profoundly different from that in NT samples. The lncRNA signature could be used as a biomarker for the prognosis of patients with ICC. Furthermore, the combination of lncRNA and mRNA can reliably predict the survival.

overall_design: The lncRNA expression profiles of cancer and adjacent normal tissues form 5 ICC patients were studied by microarray and an combination of lncRNA and mRNA could be used as a biomarker for the prognosis of patients with ICC

first: Xiao

last: Xu

first: Jianguo

last: Wang

first: Shusen

last: Zheng


title: Hepatitis B virus pre-S2 mutant LHBS induced DNA breakages and genomic instability.

status: Public on Sep 13 2014

city: Tainan

first: Wenya

last: Huang

address: No.1, University Road

department: Department of Medical Laboratory Science and Biotechnology

country: Taiwan

institute: National Cheng Kung University

type: Genome variation profiling by genome tiling array

summary: Although hepatitis B virus (HBV) has been established to cause hepatocellular carcinoma (HCC), the exact mechanism remains to be clarified. Type II ground glass hepatocytes (GGH) harboring the HBV pre-S2 mutant large surface protein have been recognized as morphologically distinct hallmark of HCC in advanced stages of chronic HBV infection. Considering its pre-neoplastic nature, we hypothesized that type II GGH may exhibit high genomic instability, which is important for the carcinogenic process in chronic HBV carriers. In this study we found that pre-S2 mutant LHBS directly interacted with importin 1, the key factor that recognizes cargos undergoing nuclear transportation mediated by the importin 1 associated nuclear pore complex (NPC). By interacting with importin 1, which inhibits its function as an NPC factor, pre-S2 mutant LHBS blocked nuclear transportation of an essential DNA repair and recombination factor Nijmegen breakage syndrome 1 (NBS1) upon DNA damage, thereby delaying formation of nuclear foci at the sites of DNA double strand breaks. Pre-S2 mutant LHBS was also found to block NBS1-mediated homologous recombination repair and induce multi-nucleation of cells. In addition, pre-S2 mutant LHBS transgenic mice showed genomic instability indicated by increased global gene copy number variations (CNV), which were significantly higher than those in hepatitis B virus X mice, indicating that pre-S2 mutant LHBS is the major viral oncoprotein inducing genomic instability in HBV-infected hepatocytes. Consistently, the human type II GGHs in HCC patients exhibited increased DNA double-strand breaks representing significant genomic instability. In conclusion, type II GGH harboring HBV pre-S2 mutant oncoprotein represents a high-risk marker for the loss of genome integrity in chronic HBV carriers and explains the complex chromosome changes in HCCs.

overall_design: Non-tumorous liver sections from four each the HBx and pre-S2 mutant LHBS transgenic mice and 3 double transgenic mice between 9 and 22 months old were examined for gene gain and loss.

first: Yi-Hsuan

last: Hsieh

first: Yu-Ying

last: Chang

first: Ih-Jen

last: Su


title: Effects of Acute Exposure to the Non-steroidal Anti-inflammatory Drug Ibuprofen on the Developing North American Bullfrog (Rana catesbeiana) Tadpole

city: Victoria

first: Nik

last: Veldhoen

state: BC

address: PO Box 3055 STN CSC

department: Biochemistry & Microbiology

country: Canada

institute: University of Victoria

summary: An anthropogenic chemical contaminant commonly identified in aquatic receiving environments is the non-steroidal anti-inflammatory drug (NSAID), ibuprofen(IBF). While the role of ibuprofen in target organisms is known, there exists a paucity of data on the impact of exposure to non-target wildlife species. In the case of frog species, normal development and environmental fitness involves the actions of the thyroid hormones (THs), particularly at key points in the life cycle. We investigated whether exposure of premetamorphic North American bullfrog (Rana catesbeiana) tadpoles to IBF altered their response to treatment with an exogenous dose of thyroid hormone (T3).

platform_organism:
Xenopus laevis
Aquarana catesbeiana
Lithobates pipiens

overall_design: Six animals randomly selected from each treatment were examined for the status of the hepatic transcriptome using MAGEX DNA array analysis.

middle: J

first: Graham

last: van Aggelen

first: Caren

middle: C

last: Helbing


title: Copy number variation analysis on a non-Hodgkin lymphoma case-control study identifies an 11q25 duplication associated with diffuse large B-cell lymphoma

city: Birmingham

first: Christine

middle: F

last: Skibola

state: AL

address: 1665 University Boulevard

institute: University of Alabama at Birmingham

summary: Recent GWAS have identified several susceptibility loci for NHL. Despite these successes, much of the heritable variation in NHL risk remains to be explained. Common copy-number variants are important genomic sources of variability, and hence a potential source to explain part of this missing heritability. In this study, we carried out a CNV analysis using GWAS data from 681 NHL cases and 749 controls to explore the relationship between common structural variation and lymphoma susceptibility. Here we found a novel association with diffuse large B-cell lymphoma (DLBCL) risk involving a partial duplication of the C-terminus region of the LOC283177 long non-coding RNA that was further validated by quantitative PCR. For chronic lymphocytic leukemia/small lymphocytic lymphoma (CLL/SLL), known somatic deletions were identified on chromosomes 13q14, 11q22-23, 14q32 and 22q11.22. Our study shows that GWAS data can be used to identify germline CNVs associated with disease risk for DLBCL and somatic CNVs for CLL/SLL.

overall_design: We performed a genome-wide CNV analysis of 681 NHL cases and 749 controls from the San Francisco Bay Area, genotyped using the Illumina HumanCNV370-Duo BeadChip array. Signal intensity data in the form of log R ratio (LRR) and B allele frequency (BAF) values were obtained directly from the Beadstudio software. Quality control filtering was used to exclude unreliable samples, resulting in a final dataset of 619 NHL cases (205 FL, 242 DLBCL, 172 CLL/SLL) and 730 controls.

first: Lucia

last: Conde


title: Agrobacterium tumefaciens C58 whole-genome tiling microarray design and validation

summary:
This research focuses on the design, manufacturing and validation of a new Agrobacterium tumefaciens C58 whole-genome tiling microarray platform for novel RNA transcript discovery.
A whole-genome tiling microarray allows both annotated genes as well as previously unknown RNA transcripts to be detected and quantified at once.
The Agrobacterium tumefaciens C58 genome is re-acquired with next-generation sequencing and then used to design the tilinlg microarray with the thermodynamic analysis program Picky.
Validations are performed by subjecting Agrobacterium tumefaciens C58 under various growth conditions and then using the tling microarrays to verify expected gene expression patterns.

overall_design: Agrobacterium tumefaciens C58 was grown under 10 different conditions: a standard condition and 9 stressful conditions. 2 replications were measured for each condition.

first: Hyejin

last: Cho


title: Escherichia coli MG1655 whole-genome tiling microarray design and validation

summary:
This research focuses on the design, manufacturing and validation of a new E. coli whole-genome tiling micraorray platform for novel RNA transcript discovery.
A whole-genome tiling microarray allows both annotated genes as well as previously unknown RNA transcripts to be detected and quantified at once.
The E. coli MG1655 genome is re-acquired with next-generation sequencing and then used to design the tiling microarray with the thermodynamic analysis program Picky.
Validations are performed by subjecting E. coli under various growth conditions and then using the tiling microarrays to verify expected gene expression patterns.

platform_organism: Escherichia coli str. K-12 substr. MG1655

overall_design:
E. coli MG1655 was grown under 10 different conditions, including a standard condition and 9 stress condidtions.  2 replications were measured for each condition.
2 of the 20 resulted samples were lost due to large bubbles on the microarray surface, and are not included in this series.


title: Escherichia coli K-12: 5% isooctane treatment at four time points

city: Singapore

first: Aram

last: Kang

state: Singapore

address: 62 Nanyang Drive

department: School of Chemical and Biomedical Engineering

country: Singapore

institute: Nanyang Technological University

summary: Transcripitonal profiling of Escherichia coli K-12 BW25113 comparing cells with isooctane treatment at time point of 0, 10, 30 and 60 min with two biological replicates

overall_design: One-condition experiment, cells with isooctane treatment at incubation time of 0, 10, 30 and 60 min, respectively

first: A-Ram

first: Matthew

middle: W


title: Sodium arsenite induced gene expression changes in A549 human epithelial lung carcinoma cells

first: Simone

last: van Breda

summary: Arsenic is methylated during its metabolism, thereby depleting the intracellular methyl donor S-adenosyl-methionine, which may lead to disturbances in DNA methylation patterns which could lead to altered gene expression

overall_design: Cells were exposed to sodium arsenite (NaAsO2, Sigma) at concentrations of 0.08 µM, 0.4 µM and 2 µM for 1, 2 and 8 weeks.


title: Changes in brain gene expression profiles during sexual maturation of European eel (Anguilla anguilla) males.

status: Public on Sep 26 2014

city: Legnaro

first: Massimo

last: Milan

state: PD

address: Viale dell'Università 16

department: Dept. of Department of Public Health, Comparative Pathology,and Veterinary Hygiene

country: Italy

institute: University of Padova

summary: Gene expression analyses have been performed on brain tissue of sexually mature and immature males using microarrays. 60 eels were transferred to two independent temperature controlled recirculation water units connected to two 500 L cylindro-conical tanks (30 fish per tank) where the fish were acclimated to seawater (35 PSU salinity) over a 2 week period.Eel males in one of the seawater units were injected intramuscularly every week over a 140 day period with 2000 IU hCG/kg (human chorionic gonadotropin, Sigma–Aldrich Chemical) dissolved in 0.9% saline to induce sexual maturation. Eel males in the other recirculation unit were injected weekly over the same period with 0.9% NaCl (vehicle).At the end of the experiment, eels were anesthetized in a solution of 0.1mg/L tricaine methanesulfonate (MS-222, Sigma Aldrich) and blood samples collected into heparinized syringes. Tissues (brain, including the olfactory bulbs, telencephalon, diencephalon and mesencephalon, and gonads) were collected from sexually immature (n=12)  and sexually mature males (n=12).RNA was extracted from brain tissue of a total of 24 (12 mature and 12 immature) males. For each individual, RNA was extracted separately for olfactory bulb, telencephalon and diencephalon. Because RNA concentrations of olfactory bulb, telencephalon and diencephalon were below the amount needed for microarray analysis, a separate experiment for each part of the brain was not possible. Therefore, we combined equal concentrations of olfactory bulb, telencephalon and diencephalon as a single brain sample for each individual.Microarray analysis was conducted using an European eel-specific array consisting of a total of 14,913 probes based on a large collection of high-throughput transcriptomic sequences (Pujolar et al. 2012). Probe sequences and further details on the microarray platform can be found on the GEO database under accession number GPL15124. Data was normalized using a quantile normalization procedure using R (http://www.r-project.org)

overall_design: A comparative analysis of gene expression was conducted between sexually mature and immature males. Sample labelling and hybridization were conducted following the details in Pujolar et al. (2012). Hybridized slides were scanned at 5 µm resolution using an Agilent DNA microarray scanner. Slides were scanned at two different sensitivity levels (XDR Hi 100% and XDR Lo 10%) and the two linked images generated were analysed together. Data were extracted and background subtracted using the standard procedure in Agilent Feature Extraction (FE) software v. 9.5.1. Hybridization success was evaluated using flag values, excluding those intensities not equal to 1.

first: Milan

last: Massimo

first: Pujolar

last: Marti

first: Canário

last: Adelino


title: Differential gene expression in the skin of dogs sensitized to the house dust mite Dermatophagoides farinae

city: Lindau

first: Stefan

middle: Michael

last: Bauersachs

state: Zurich

address: Eschikon 27 EHB 23.1

department: Department for Farm Animals

country: Switzerland

institute: University of Zurich

summary: Atopic dermatitis is a multifactorial allergic skin disease in humans and dogs. Genetic predisposition, immunologic hyperreactivity, a defective skin barrier and environmental factors play a role in its pathogenesis. The aim of this study was to analyze gene expression in the skin of dogs sensitized to house dust mite antigens. Skin biopsies were collected from six sensitized and six non-sensitized Beagle dogs from normal, non-treated skin before and six and 24 hours after challenge using skin patches with allergen or saline as a negative control. Transcriptome analysis was performed by the use of DNA microarrays and expression of selected genes was validated by quantitative real-time RT-PCR. Expression data was compared between groups (unpaired design). After 24 hours 597 differentially expressed genes were detected, 361 with higher and 226 with lower mRNA concentration in allergen treated skin of sensitized dogs compared to their saline-treated skin and compared to the control specimens. Functional annotation clustering, pathway-and co-citation analysis showed, that the genes with increased expression were involved in inflammation, wound healing and immune response. In contrast, genes with decreased expression in sensitized dogs were associated with differentiation and barrier function of the skin. As the sensitized dogs did not show differences in the untreated skin compared to controls, inflammation after allergen patch test probably led to a decrease in the expression of genes important for barrier formation. Our results further confirm the similar pathophysiology of human and canine atopic dermatitis and revealed genes previously not known to be involved in canine atopic dermatitis.

overall_design: 60 canine (dog) skin tissue samples; six sensitized and six non-sensitized Beagle dogs; samples collected before (0h), 6h and 24h after challenge with allergen; samples collected from a skin area treated with saline and from an area treated with allergen

first: Paz

last: Schamber

first: Rachel

last: Schwab-Richards

first: Ralf

last: Müller


title: GEP of PMBCs during treatment with a gene-modified allogeneic tumor cell vaccine in advanced renal cell cancer (RCC) patients

status: Public on Sep 24 2014

city: Münster

first: Michael

last: Grau

state: Nordrhein-Westfalen

address: Albert-Schweitzer-Campus 1

department: Faculty of Medicine

institute: University of Münster

summary: Tumor-induced immunosuppression remains a major challenge for immunotherapy of cancer patients. To further elucidate why an allogeneic gene-modified (Interleukin-7(IL-7)/CD80 co-transfected) renal cell cancer vaccine failed to induce clinically relevant TH1-polarized immune responses, peripheral blood mononuclear cells (PBMCs) from enrolled study patients were analyzed by gene expression profiling (GEP) both prior and after vaccination. At baseline before vaccination, a profound downregulation of gene signatures associated with antigen presentation, immune response/T cells, cytokines/chemokines and signaling/transcription factors was observed in renal cell cancer patients as compared to healthy controls. Vaccination led to a partial reversion of preexisting immunosuppression, however, GEP indicated that an appropriate TH1 polarization could not be achieved. Most interestingly, our results suggest that the nuclear factor kappa B (NF-κB) signaling pathway might be involved in the impairment of immunological responsiveness and the observed TH2 deviation.   In summary, our data suggest that GEP might be a powerful tool for the prediction of immunosuppression and the monitoring of immune responses within immunotherapy trials.

overall_design: Gene expression was profiled using Affymetrix Human Gene v1.1 ST microarrays in the following settings: 9 RCC patients were profiled before and after vaccination (pairs of measurements) and additionally 9 healthy control samples were profiled.

first: Jörg

last: Westermann

first: Georg

last: Lenz


title: Transcriptome profile of wild type Azoarcus sp. BH72 grown under microaerobic condition (0.3% oxygen) compared with that grown under aerobic condition (21% oxygen), both in presence of combined nitrogen source, respectively

city: Bremen

first: Barbara

last: Reinhold-Hurek

department: Microbe-Plant-Interactions

institute: University Bremen

summary: Low oxygen tensions are often encountered in flooded soils of rice fields by root-associated, strictly respiratory, beta proteobacterium, Azoarcus sp. BH72 which fixes nitrogen only under microaerobic condition. In this study, genome wide oligonucleotide microarrays were used compare the global transcription profile of Azoarcus sp. BH72 under microaerobic condition with cells grown under aerobic condition, both with ammonia as sole nitrogen source. The outcome of this study will provide a better insight about the establishment of this endophyte in the microaerobic environment, probably prevailing inside of the rice root niche .

overall_design: RNA from cells grown under microaerobic condition with 0.3% oxygen (experiment) and aerobic condition with 21% oxygen (control), respectively  was used for two color whole genome microarray approach.

first: Abhijit

last: Sarkar


title: Sodium arsenite induced DNA methylation changes in A549 human epithelial lung carcinoma cells

summary: Arsenic is methylated during its metabolism, thereby depleting the intracellular methyl donor S-adenosyl-methionine, which may lead to disturbances in DNA methylation patterns

overall_design: Cells were exposed to sodium arsenite (NaAsO2, Sigma) at concentrations of 0.08 µM, 0.4 µM and 2 µM for 1, 2 and 8 weeks.  A549 arsenic dose time response study.


title: Comparison between wild type E. coli and adhE (alcohol dehydrogenase) mutants, grown under anaerobic condition

city: Daejeon

first: Seungwoo

last: Hwang

address: 52 Eoeun-dong Yuseong-gu

department: Korean Bioinformation Center

country: South Korea

institute: Korea Research Institute of Bioscience and Biotechnology

summary:
To characterize anaerobic stress-induced expression in adhE mutants, the microarray experiment was performed with two serotypes of wild type E. coli and their adhE mutants: (1) K-12 strain, wild type; (2) B strain, wild type; (3) BW25113, adhE mutants; (4) BL21(DE3), adhE mutants.
Under anaerobic growth condition in glucose-containing complex medium, the wild type strains 1 and 2 grew well whereas the mutant strains 3 and 4 experienced anaerobic stress and grew after 24 hours and 48 hours, respectively.

sample_organism:
Escherichia coli BL21(DE3)
Escherichia coli BW25113

overall_design: For each of the four strains, RNA sampling was done after six hours of growth under anaerobic condition. Only one replicate was obtained for each strain.

first: Sang Joon

last: Lee


title: The pyruvate-tricarboxylic acid cycle node: a focal point of virulence control in the enteric pathogen Yersinia pseudotuberculosis [rovA mutant]

first: Ann

last: Heroven

summary: Whole transcriptome assessment of the Yersinia pseudotuberculosis strain YPIII. The Y. pseudotuberculosis rovA regulon was determined in Yersinia minimal minimum developed for the study. RovA is a key regulator for Yersinia virulence.

overall_design: Y. pseudotuberculosis YPIII or the isogenic rovA mutant strain  were cultivated at 25°C under aeration on a rotary shaker. First pre-cultures were grown in a 1:1 mixture of HAM’s F-12 Nutrient Mixture (Invitrogen, Carlsbad, US) and liquid DMEM medium (Biochrom, Berlin, DE). Second pre-cultures and main cultures were grown in a Yersinia minimal medium (YMM). The analysis comprised three biological replicates for each strain. In addition, samples, taken at three different time points of the exponential growth phase, were used to validate constant expression during the cultivation. Total RNA was extracted using SV Total RNA Isolation System (Promega). The samples were treated with RNase-free DNase (Roche Applied Science) and the quality of the RNA was confirmed by the lack of PCR amplification of the hns gene and by using an Agilent 2100 Bioanalyzer.

first: René

last: Bücker


title: Prefrontal cortex gene expression in WSP and WSR male and female mice following 72h of chronic ethanol vapor exposure

city: Portland

first: Marina

last: Guizzetti

institute: Oregon Health & Science University; Portland VA Research Service

summary: Ethanol is the most common substance of abuse in the US, and abuse can lead to physical dependence, addiction, brain damage and premature death.  The cycle of alcohol addiction has been described as a composite consisting of three stages: intoxication, withdrawal and craving/abstinence.  As a complex brain disorder, there is evidence for both a genetic contribution to risk and sexually-dimorphic responses in alcoholism, but an overall understanding of the biological contributions and the neuroadaptive underpinnings of alcohol addiction is limited.  Utilizing novel genetic animal models with highly divergent withdrawal severity, Withdrawal Seizure-Resistant (WSR) and Withdrawal Seizure-Prone (WSP) selected lines of mice and by examining both sexes, the distinct or common contributions of response to alcohol genotype/phenotype and of sex to addiction stages over time were characterized.  Transcriptional profiling was performed to identify neuroadaptive changes as a consequence of chronic intoxication in the medial prefrontal cortex (mPFC). Significant expression differences were identified for each line and tracked over a behaviorally-relevant time course that covered each stage of alcohol addiction; i.e., after chronic intoxication, during peak withdrawal, and after a defined period of abstinence.  Females were more responsive to ethanol with higher fold expression differences.  Data structure was analyzed by bioinformatics, which showed a strong effect of sex with high similarity of male vs. female expression profiles during chronic intoxication and at peak withdrawal irrespective of genetic background.  However, during abstinence, striking differences were observed instead between the lines/phenotypes irrespective of sex.  Because sex was the strongest influence on neuroadaptive changes overall, confirmation analysis compared males vs. females.  Notably, results revealed distinct inflammatory signaling between males and females at peak withdrawal, with a pro-inflammatory inflammotoxic phenotype in females but in contrast overall suppression of immune signaling in males. Thus, the early response to chronic intoxication is strongly influenced by sex while pathways that are altered during a period of abstinence are dependent on genotype.  Combined, these results suggest that each stage of the addiction cycle is influenced differentially by sex vs. genetic background and support the development of distinct translational targets for stage- and sex-specific therapies for the treatment of alcohol withdrawal and the maintenance of sobriety.

overall_design: A total of 32 microarrays were run with 4 biological replicates per treatment, line, and sex.  Selection replicates (i.e. WSP-1 and WSP-2) for each treatment, line, and sex were collapsed to improve statistical power (n=4) and to facilitate in the identification of phenotype related effects and exclude selection artifacts.  For comparisons, EtOH regulation was determined by comparing 4 arrays from (for example) Male WSR EtOH treated versus 4 arrays from Male WSR Air treated arrays.

first: Kristine

last: Wiren

first: Joel

last: Hashimoto


title: Expression data from rhesus macaque blood CD8+ T cells

city: Davis

last: George

state: CA

address: 451 Health Sciences Drive

department: Medical Microbiology and Immunology

institute: University of California, Davis

summary:
Immunization of macaques with simian immunodeficiency virus with deletions in nef (SIVΔnef) has been shown to elicit protective immunity to infection by pathogenic SIV, yet our understanding of the mechanisms that orchestrate protection and prevent pathogenesis remains limited.  In the study, we utilize whole-genome transcriptional profiling to reveal molecular signatures of protective immunity in circulating CD8+ T cells of rhesus macaques vaccinated with SIVmac239Δnef and challenged with pathogenic SIVmac251.
Microarrays were used to characterize changes in gene expression in blood CD8+ T cells that occur following vaccination of rhesus macaques with attenuated SIV∆nef and subsequent challenge with pathogenic SIVmac251, in comparison to corresponding changes in healthy controls and unvaccinated animals infected with pathogenic SIVmac251

overall_design: CD8+ T cells were isolated by magnetic beads from the blood of healthy uninfected macaques, macaques vaccinated with SIV∆nef, and unvaccinated controls infected with SIVmac251, and used for RNA extraction and hybridization on Affymetrix microarrays. Blood samples from vaccinated animals were collected prior to vaccination, at 3, 20, and 40 weeks following vaccination. After the 40 week vaccination period, macaques were challenged with SIVmac251, and blood was again collected at 3 weeks following challenge. Blood was collected from the unvaccinated controls at 3 weeks following infection with SIVmac251

middle: D


title: Real-time quantitative PCR analysis of undifferentiated rat embryonic stem cells and induced pluripotent stem cells

city: Manhattan

first: Mark

middle: Louis

last: Weiss

state: KS

address: 1600 Denison Ave, 228 coles hall

department: Anatomy and Physiology

institute: Kansas State University

summary: Validation study of a focused microarray for evaluation of undifferentiated rat ESCs.Using a focused microarray, undifferentiated embryonic stem cells (ESCs) can be distinguished from differentiated ESCs and other cells derived from the early embryo since they have a unique gene expression pattern associated with pluripotency and lack of markers of differentiation.  To date, however, such an array has not been developed for the rat species and differences in genomes of rat and human or rat and mouse preclude the use of ESC focused human or mouse microarrays for the rat.  Here, we developed a focused microarray for screening rat ESCs and provide validation data that this array can distinguish undifferentiated rat ESCs from rat trophoblast stem cells (TS), rat extraembryonic endoderm cells (XEN), mouse embryonic fibroblast feeder cells (MEFs) and rat ESCs that have been differentiated in vitro.  We used this tool to compare rat ESCs which have been expanded in a conventional rat ESC medium containing two inhibitors, e.g., GSK3 and MEK inhibitors, and leukemia inhibitory factor (LIF), and found expression of Cdx2, a gene associated with trophoblast determination.  The rat ESC focused microarray described in this report has utility for rapid screening rat ESCs.  This will enable optimization of culture conditions in the future.

overall_design: qRT-PCR gene expression profiling of undifferentiated ESCs and iPS cells. Equal amounts (1000ng) total RNA from each cell line was used in independent trials conducted by two investigators, these are technical replicates.

first: He

last: Hong

first: Pavan

last: Rajanahalli

first: Hongzhou

last: Huang


city: Mol

first: Rob

last: Van Houdt

address: Boeretang 200

department: Interdisciplinary Biosciences

country: Belgium

institute: SCK-CEN

summary:
Metal resistant bacterium Cupriavidus metallidurans CH34 uses non-conventional proteins to combat oxidative stress
Keywords: Cupriavidus metallidurans; hydrogen peroxide; oxidative stress;

overall_design: Two-condition experiments. Comparing samples after challenging with oxidative stress versus non-induced samples. Biological triplicate. Each array contains 3 technical replicates.

first: Muhammad

middle: S

last: Islam

first: Pieter

last: Monsieurs

first: Paul

last: Janssen

first: Natalie

last: Leys


title: AR variant ARv567es induces carcinogenesis in a novel transgenic mouse model of prostate cancer.

status: Public on Sep 11 2014

city: Seattle

first: Ilsa

last: Coleman

state: WA

address: 1100 Fairview Ave N, E2-112

department: Human Biology

institute: Fred Hutchinson Cancer Center

summary: Androgen deprivation therapy remains the primary treatment modality for patients with metastatic prostate cancer but is uniformly marked by progression to castration-resistant prostate cancer (CRPC) after a period of regression. Continued activation of androgen receptor (AR) signaling is attributed as one of the most important mechanisms underlying failure of therapy. Recently, the discovery of constitutively active AR splice variants (AR-Vs) adds more credence to this idea. Expression of AR-Vs in metastases portends a rapid progression of the tumor. However, the precise role of the AR-Vs in CRPC still remains unknown. ARv567es is one of the two AR variants frequently found in human CRPC xenografts and metastases. Herein, we developed a probasin (Pb) promoter-driven ARv567es transgenic mouse, Pb-ARv567es, to evaluate the role of ARv567es in both autonomous prostate growth and progression to CRPC. We found that expression of ARv567es in the prostate results in epithelial hyperplasia by 16 weeks and invasive adenocarcinoma is evident by 1 year of age. The underlying genetic cellular events involved a cell cycle-related transcriptome and differential expression of a spectrum of genes that are critical for tumor initiation and progression. These findings indicate that ARv567es could induce tumorigenesis de novo and signifies the critical role of AR-Vs in CRPC. Thus, the Pb-ARv567es mouse could provide a novel model in which the role of AR variants in prostate cancer progression can be examined.

overall_design: Custom Agilent 44K whole mouse genome expression oligonucleotide microarrays were used to profile prostate tissue from probasin (Pb) promoter-driven ARv567es transgenic mice and control littermates. Total RNA was isolated and amplified prior to hybridization against a common reference pool of normal adult mouse tissues.

first: Gang

last: Liu

first: Cynthia

last: Sprenger

first: Shihua

last: Sun

first: Kathryn

last: Epilepsia

first: Kathleen

last: Haugk

first: Xiaotun

last: Zhang

first: Peter

last: Nelson

first: Stephen

last: Plymate


title: microRNA-7 modulates Rb1 and c-Myc expression in myeloid leukemias harboring c-Kit mutations

city: Takatsuki City

first: Masutani

last: Ryota

state: Osaka

address: Daigaku-machi

department: clinical central laboratory

country: Japan

institute: osaka medical college hospital

summary: The receptor tyrosine kinase, c-kit, plays a pivotal role in hematopoiesis and self-renewal. Aberrant activation of c-kit can be induced by genetic alterations and is thought to confer therapeutic resistance in leukemia. Significantly, the c-kit D816V mutation is a well-known indicator of poor prognosis in acute myeloid leukemias harboring t(8;21) chromosomal translocations; however, the mechanism by which this mutation promotes therapeutic resistance is still unclear. Our study identified that miR-7 directly targets Retinoblastoma-like Protein 1 (Rb1) and is regulated by the MEK pathway. In addition, we also found that c-Myc is upregulated by the D816V mutation, and is indirectly downregulated by miR-7.

platform_organism:
Homo sapiens
Mus musculus
Rattus norvegicus

overall_design: Sample: (1)Ba/F3 (2)Ba/F3 c-kit V814 (3)MEK inhibitor treated Ba/F3 c-kit V814  ((1)vs(2)), ((2)vs(3))  To screen candidate microRNAs, an array was used to identify differences in microRNA expression between Ba/F3 cells and V814+Ba/F3 cells, as well as V814+Ba/F3 cells in the presence or absence of MEK inhibitor.

first: Ryota

last: Masutani

first: Shinichiro

last: Kawamoto

first: Takayuki

last: Takubo


title: crr4_dyw1_col0-Comparative Arabidopsis Transcriptome -Sequencing

status: Public on Sep 10 2014

city: evry

first: Soubigou-Taconnat

last: Ludivine

address: 2 rue gaston crémieux

department: URGV

country: France

institute: INRA

summary: cat-seq - crr4_dyw1_col0 - A comparative assessment of the Arabidopsis sequencing approach High-throughput sequencing cDNA GAII or HiSeq2000 sequenceur (technology Solexa) and data on CATMA array hybridation (version 6). These different characteristics will be studied through the analysis of control samples but also samples from mutants in genes coding for cytosolic or nuclear PPR proteins - CRR4 and DYW1 are two PPR mutants. They have the same post-transcriptonnel molecular defect and their phenotype is very close. We will try to determine here if their transcriptome is similar or not.

overall_design: 4 dye-swap - genotype comparaison

first: Sandrine

last: Balzergue

first: Claire

last: Lurin

first: Marie-Laure

last: Martin-Magniette


title: ANGUSTIFOLIA 3 binds SWI/SNF chromatin remodeling complexes to regulate transcription during Arabidopsis leaf development

status: Public on Sep 09 2014

city: Zwijnaarde

first: Liesbeth

last: Vercruyssen

address: Technologiepark 927

department: Plant Systems Biology

institute: VIB / Ghent University

summary: The transcriptional coactivator ANGUSTIFOLIA 3 (AN3) stimulates cell proliferation during Arabidopsis leaf development, but the molecular mechanism is largely unknown. We show here that inducible nuclear localization of AN3 during initial leaf growth results in differential expression of important transcriptional regulators, including GROWTH REGULATING FACTORs (GRFs). Chromatin purification further revealed the presence of AN3 at the loci of GRF5, GRF6, CYTOKININ RESPONSE FACTOR 2 (CRF2), CONSTANS-LIKE 5 (COL5), HECATE 1 (HEC1), and ARABIDOPSIS RESPONSE REGULATOR 4 (ARR4). Tandem affinity purification of protein complexes using AN3 as bait identified plant SWITCH/SUCROSE NONFERMENTING (SWI/SNF) chromatin remodeling complexes formed around the ATPases BRAHMA (BRM) or SPLAYED (SYD). Moreover, SWI/SNF ASSOCIATED PROTEIN 73B (SWP73B) is recruited by AN3 to the promoter of GRF5, GRF3, COL5, and ARR4, and both SWP73B and BRM occupy the HEC1 promoter. Furthermore, we show that AN3 and BRM genetically interact. The data indicate that AN3 associates with chromatin remodelers to regulate transcription. In addition, modification of SWI3C expression levels increases leaf size, underlining the importance of chromatin dynamics for growth regulation. Our results place the SWI/SNF-AN3 module as a major player at the transition from cell proliferation to cell differentiation in a developing leaf.

overall_design: AN3-GR and wild-type (Col-0) plants were grown in vitro for 8 days and subsequently transferred to dexamethasone-containing medium for 8 hours. Developing leaves 1&2 of AN3-GR and wild-type plants were micro-dissected, and RNA was extracted. RNA from three biological repeats of dexamethasone-treated AN3-GR and dexamethasone-treated wild-type leaves was hybridized to Affymetrix ATH1 microarrays.

first: Nathalie

last: Gonzalez

first: Dirk

last: Inzé


title: Change of fate comitment in adult neural progenitor cells subjected to chronic inflammation

city: Stockholm

first: Ruxandra

last: Covacu

country: Sweden

institute: Karolinska Institutet

summary:
Neural progenitor cells (NPCs) have regenerative capabilities that are activated during inflammation. By measuring the global transcriptome and performing functional studies, we aimed at elucidating if and how NPCs from the non-germinal niche of the spinal cord differ from germinal niche NPCs, here represented by the subventricular zone (SVZ) NPCs. Moreover, we investigated how these cells are affected by chronic inflammation modeled by Experimental Autoimmune Encephalomyelitis (EAE). NPCs were isolated and propagated from the SVZ and cervical, thoracic and caudal regions of the spinal cord from healthy rats and rats subjected to EAE. Using Affymetrix microarray analyses, the global transcriptome was measured in the different NPC populations both in undifferentiated and differentiated cultures. These analyses were paralleled by differentiation studies and quantitative RT-PCR of differentiation-specific genes.
In NPCs isolated from healthy rats, transcriptional and functional analyses revealed a higher neurogenic potential in SVZ-derived NPCs compared to spinal cord NPCs. The neurogenicity of spinal cord NPCs was increased by exposure to the inflammatory environment. Concurrently, their gliogenicity was decreased which was supported by a decreased expression of glial differentiation signature genes and related signaling pathways. Differentiation analyses showed that spinal cord NPCs from EAE rats generated fewer oligodendrocytes and astrocytes than NPCs isolated from healthy controls.

overall_design: 54 samples were analysed. The transcriptome of NPCs isolated from healthy rats or rats with EAE was measured. The NPCs were isolated from the SVZ and the cervical, thoracic and caudal parts of the spinal cord. Pair wise student t-test analysis between the 3 EAE replicates and naive controls for each respective tissue type was performed. Genes with a signal value above the  cut-off of 50 and with FDR ≤ 5% and a foldchange of ≥1.2 or ≤-1.2 were selected for further analysis.

first: Cynthia

last: Perez Estrada

first: Lisa

last: Arvidsson

first: Mikael

last: Svensson

first: Lou

last: Brundin


title: TMPRSS2 Influences Prostate Cancer Metastasis

first: Ilsa

last: Coleman

summary: TMPRSS2 is an androgen-regulated cell surface serine protease expressed predominantly in prostate epithelium. TMPRSS2 is expressed highly in localized high-grade prostate cancers and in the majority of human prostate cancer metastasis. Through the generation of mouse models with a targeted deletion of Tmprss2, we demonstrate that the activity of this protease regulates cancer cell invasion and metastasis to distant organs. By screening combinatorial peptide libraries we identified a spectrum of TMPRSS2 substrates that include pro-hepatocyte growth factor (HGF). HGF activated by TMPRSS2 promoted c-Met receptor tyrosine kinase signaling, and initiated a pro-invasive EMT phenotype. Chemical library screens identified a potent bioavailable TMPRSS2 inhibitor that suppressed prostate cancer metastasis in vivo. Together, these findings provide a mechanistic link between androgen-regulated signaling programs and prostate cancer metastasis that operate via context-dependent interactions with extracellular constituents of the tumor microenvironment.

overall_design: Custom mouse cDNA microarrays were used to measure transcript levels in microdissected anterior prostate tumors from Tmprss2+/+;TRAMP mice, Tmprss2-/-;TRAMP mice or strain-matched benign epithelium. All samples were laser-capture microdissected and total RNA isolated and amplified prior to hybridization against a reference pool of normal adult mouse tissues.

first: Jared

last: Lucas

last: Heinlein

first: Tom

last: Kim

first: Susana

last: Hernandez

first: Muzdah

last: Malik

first: Lawrence

last: True

first: Colm

last: Morrissey

first: Eva

last: Corey

first: Bruce

last: Montgomery

first: Elahe

last: Mostaghel

first: Nigel

last: Clegg

first: Christopher

last: Brown

first: Eric

middle: L

last: Schneider

first: Charles

last: Craik

first: Julian

last: Simon

first: Tony

last: Bedalov

first: Peter

last: Nelson


title: plant rabt n°1-Plant RABT n°1

first: Soubigou-Taconnat

last: Ludivine

summary:
adt12-01_uprt - plant rabt n°1 - Impact of RNA labeling by Plant RABT on plant transcriptome - Determine the incidence of RNA marking by the RABT method Plantation on the plants transcriptome.
In several studies Clearly et al. have described a method referred as "4TU tagging" which can be use to study mRNA synthesis and decay either in a mixed population of cells or in a specific cell type (Cleary, Meiering et al. 2005, Zeiner, Cleary et al. 2008, Miller, Robinson et al. 2009, Rabani et al., 2011). Through the specific cell type expression in drosophila and mammalian cells of theToxoplasma gondii uracil PhosphoribosylTransferase activity and the metabolization of the uracil analog 4-thiouracil (4 TU), mRNA were selectively tagged, purified and used in microarray based analysis.

overall_design: 6 dye-swap - treated vs untreated comparison

first: Richard

last: Berthome

first: Sandrine

last: Balzergue

first: Ludivine

last: Taconnat

first: Marie-Laure

last: Martin-Magniette


title: Altering gene expression by aminocoumarin (novobiocin) treatment: Role of DNA supercoiling  in Staphylococcus aureus

status: Public on Sep 08 2014

city: Essen

first: Ludger

last: Klein-Hitpass

address: Virchowstr. 173

department: Universitaetsklinikum

institute: Institut fuer Zellbiologie

summary: For Staphylococcus aureus it was shown previously that aminocoumarinecoumarin antibiotics such as novobiocin lead to immediate down-regulation of recA expression and thereby inhibition of the SOS response, the mutation frequency and the recombination capacity.  Aminocoumarinecoumarin function by inhibition of the ATPase activity of the gyrase subunit B. Here we analysed the global impact of the DNA relaxing agent novobiocin on gene expression in S. aureus. By use of a novobiocin resistant mutant, it became evident that the change in recA expression is due to gyrase inhibition. Microarray analysis and Northern blot hybridization revealed that the expression of a distinct set of genes is increased (e.g. recF-gyrB-gyrA, rib operon and ure operon …)), or decreased (e.g. arlRS, recA, lukA, hlgC, fnbA) by novobiocin. The two-component ArlRS system was previously found to decrease the supercoiling level in S. aureus. Thus, down-regulation of arlRS might in part compensate for the relaxing effect of novobiocin. Novobiocin resulted in down-regulation of several of arlRS repressed target genes in an arl mutant. Global analysis and gene mapping of supercoiling sensitive genes did not give indications that they are clustered in the genome. Promoter fusion assays confirmed that responsiveness of a given gene is intrinsic to the promoter region but independent of the chromosomal location. The results indicate that molecular property of the spacers of a given promoter dictatesa given promoter rather than chromosomal topology dictates the responsiveness towards changes in supercoiling rather than chromosomal topology.

overall_design: We analyzed S. aureus global gene expression changes to the treatment of novobiocin

first: W

last: Schröder

first: G

last: Marincola

first: L

first: J

last: Bernhardt

last: Krupp

first: A

last: Herbig

first: C

last: Wolz


title: FIR inhibition in HCC cells (Hep3B)

status: Public on Sep 03 2014

city: Mannheim

first: Carsten

last: Sticht

address: Theodor-Kutzer-Ufer

department: ZMF

institute: University Heidelberg

summary:
siRNA-mediated inhibition compared to untreated cells and cells transfected with nonsense siRNA
Together with far upstream element binding protein (FBP), the FBP-interacting repressor (FIR) represents a molecular tool for the transcriptional fine tune regulation of target genes. Previous evidence indicates that strong overexpression of FBP in human hepatocellular carcinoma (HCC) supports tumor growth and correlates with poor patient prognosis. However, the role of the transcriptional repressor FIR in hepatocarcinogenesis remains poorly delineated. We show that overexpression of FIR correlates with tumor dedifferentiation and tumor cell proliferation in about 60% of primary HCCs. Elevated FIR levels are associated with genomic gains of the fir gene locus at chromosome 8q24.3 in human HCC specimens. In vitro, nuclear enrichment of FIR supports HCC cell proliferation and migration. Expression profiling of HCC cells after siRNA-mediated silencing of FIR identified the transcription factor DP-1 (TFDP1) as a transcriptional target of FIR. Surprisingly, FIR stimulates the expression of FBP in a TFDP1/E2F-dependent manner. FIR splice variants lacking or containing exon 2 and/or exon 5 are expressed in the majority of HCCs. Specific inhibition of FIR isoforms with and without exon 2 revealed that all FIR splice variants facilitate tumor-supporting effects. This finding was confirmed in xenograft transplantation experiments with lentiviral-infected shRNA targeting all FIR variants as well as FIR with and without exon 2. In summary, high-level nuclear FIR does not facilitate repressor properties but supports tumor growth in HCC cells. Thus, the pharmacological inhibition of FIR might represent a promising therapeutic strategy for HCC patients.

overall_design: Expression profiling of cells transfected with scrambled/nonsense siRNA (control), and after siRNA-mediated FIR inhibition.

first: Mona

last: Malz

first: Michael

last: Bovet

first: Jana

last: Samarin

first: Uta

last: Rabenhorst

first: Michaela

last: Bissinger

first: Stephanie

last: Roessler

first: Justo

last: Bermajo

first: Marcus

last: Renner

first: Diego

last: Calvisi

first: Stephan

last: Singer

first: Matthias

last: Ganzinger

first: Achim

last: Weber

first: Norbert

last: Gretz

last: Schirmacher

first: Martin

last: Zörnig

first: Kai

last: Breuhahn


title: Methylation profiles of esophageal squamous cell carcinoma patients and cancer-free individual in Taiwan.

city: Tainan

first: Yi-Ching

last: Wang

address: No.1, University Road, Tainan 70101, Taiwan, R. O. C.

department: Department of Pharmacology, College of Medicine

institute: National Cheng Kung University

summary: Genome wide DNA methylation profiling of tumor and normal samples with esophageal squamous cell carcinoma patients. The Illumina GolodenGate methylation cancer panel I was used to obtain DNA methylation profiles across approximately 1,505 CpGs in esophageal squemous cell carcinoma samples. Samples included normal, tumors and plasma samples with esophageal squamous cell carcinoma, also inculding the plasma samples with cancer-free individual.

overall_design: Bisulfite converted DNA from the 288 samples were hybridised to the Illumina GolodenGate methylation cancer panel I

first: I

last: Kuo

first: Y


title: Zeb1 and Snail1 engage miR-200f transcriptional and epigenetic regulation during EMT

city: Madrid

first: Gema

last: Moreno-Bueno

state: Madrid

address: Arturo Duperier

department: Biochemistry

country: Spain

institute: IIB

summary:
Cell plasticity is emerging as a key regulator of tumor progression and metastasis. During carcinoma dissemination epithelial cells undergo epithelial to mesenchymal transition (EMT) processes characterized by the acquisition of migratory/invasive properties, while the reverse, mesenchymal to epithelial transition (MET) process, is also essential for metastasis outgrowth. Different transcription factors, called EMT-TFs, including Snail, bHLH and Zeb families are drivers of the EMT branch of epithelial plasticity, and can be post-transcriptionally downregulated by several miRNAs, as the miR-200 family. The specific or redundant role of different EMT-TFs and their functional interrelations are not fully understood. To study the interplay between different EMT-TFs, comprehensive gain and loss-of-function studies of Snail1, Snail2 and/or Zeb1 factors were performed in the prototypical MDCK cell model system. We here describe that Snail1 and Zeb1 are mutually required for EMT induction while continuous Snail1 and Snail2 expression, but not Zeb1, is needed for maintenance of the mesenchymal phenotype in MDCK cells. In this model system, EMT is coordinated by Snail1 and Zeb1 through transcriptional and epigenetic downregulation of the miR-200 family. Interestingly, Snail1 is involved in epigenetic CpG DNA methylation of the miR-200 loci, essential to maintain the mesenchymal phenotype. The present results thus define a novel functional interplay between Snail and Zeb EMT-TFs in miR200f regulation providing a molecular link to their previous involvement in the generation of EMT process in vivo.
Expression analysis of MDCK over-expression EMT-TF

overall_design: Analysis of 7 overexpression MDCK cells each of them using biological rpelicates (MDCK-E47, Snail2, Snail1, Twist1, Tiwst2, Zeb1, Zeb2)

first: Antonio

last: Dıaz-Lopez

first: Juan

last: Dıaz-Martın

first: Eva

middle: P

last: Cuevas

first: Vanesa

last: Santos

first: David

last: Olmeda

first: Francisco

last: Portillo

first: Jose

last: Palacios

first: Amparo

last: Cano


title: Time-Dependent miRNA Profiling Following Ischemia/Reperfusion Injury in Rat Retina

status: Public on Sep 04 2014

city: Louisville

first: Nigel

middle: G. F.

last: Cooper

state: KY

address: 500 S Preston St.

department: Anatomical Science and Neurobiology

country: USA

institute: University of Louisville

summary: The purpose of the present study was to investigate time-dependent changes in the expression profile of miRNAs, following induction of IR in the rat retina, and to characterize the affected pathways, networks and processes.

overall_design: 6 biological replicates with two treatments (Sham control and Ischemia reperfusion) and 5 time points (0h, 2h, 24h, 48h and 7day) with total of 60 samples.

first: Wei

last: Fan

first: Xiaohong

last: Li


title: Genome-wide analysis of stress-exposure-associated and exposure-related individual differences associated blood gene expression in males and females.

city: Belmont

first: Nikolaos

last: Daskalakis

state: MA

address: Oaks Building 328, Mailstop 212, 115 Mill Street

department: Department of Psychiatry

institute: McLean Hospital/ Harvard Medical School

summary: Delineating the molecular basis of individual differences in the stress response is critical to understanding the pathophysiology and treatment of posttraumatic stress disorder (PTSD). In this study, 7 d after predator-scent-stress (PSS) exposure, male and female rats were classified into vulnerable (i.e., “PTSD-like”) and resilient (i.e.,minimally affected) phenotypes on the basis of their performance on a variety of behavioral measures. Genome-wide expression profiling in blood and two limbic brain regions (amygdala and hippocampus), followed by quantitative PCR validation, was performed in these two groups of animals, as well as in an unexposed control group. Differentially expressed genes were identified in blood and brain associated with PSS-exposure and with distinct behavioral profiles postexposure. There was a small but significant between-tissue overlap (4–21%) for the genes associated with exposure-related individual differences, indicating convergent gene expression in both sexes. To uncover convergent signaling pathways across tissue and sex, upstream activated/deactivated transcription factorswere first predicted for each tissue and then the respective pathways were identified. Glucocorticoid receptor (GR) signaling was the only convergent pathway associatedwith individual differences when using the most stringent statistical threshold.

overall_design: Total RNA obtained from whole blood of female rats exposed to predator-scent-stress and showing extreme (n=8 males and n=8 females) or minimal (n=8 males and n=8 females) behavioral response compared to unexposed to stress and behaviorally tested controls (n=8 males and n=7 females).

first: Hagit

last: Cohen

first: Guiqing

last: Cai

first: Joseph

last: Buxbaum

first: Rachel

last: Yehuda


title: PTSD model

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

overall_design: Refer to individual Series


title: Molecular signatures of the evolving immune response in mice following a Bordetella pertussis infection.

status: Public on Sep 02 2014

city: Bilthoven

first: Jeroen

last: Pennings

address: A. van Leeuwenhoeklaan 9

institute: Natl. Inst. Public Health & Environment

summary:
Murine gene expression responses to Bordetella pertussis were determined in lung and spleen, between 0 and 28 days post infection.
Data were compared to other parameters such as microarray, flow cytometry, multiplex immunoassays, and lung clearance.

overall_design:
A 57 array study with 27 arrays for lung and 30 for spleen. For each tissue we used a common reference made from RNA samples of the same tissue.
Please note that the reference samples are made by pooling RNA of all samples used for a tissue (either infected or uninfected). Thus, Lung and spleen each have their own reference.


title: Genome-wide analysis of stress-exposure-associated and exposure-related individual differences associated amygdala gene expression in males and females.

overall_design: Total RNA obtained from amygdala of female rats exposed to predator-scent-stress and showing extreme (n=5 males and n=5 females) or minimal (n=5 males and n=5 females) behavioral response compared to unexposed to stress and behaviorally tested controls (n=5 males and n=5 females).


title: Comparison of gene expression profile of thymus samples from prednisolone-treated and control cows.

city: Legnaro (PD)

first: Serena

last: Ferraresso

state: Padova

address: Viale dell'Università

department: Dept of Comparative Biomedicine and Food Science

institute: University of Padova

summary: A bovine oligo microarray platform (GPL7053) was used to evidence differences in gene expression profiles from eight (8) thymus samples from prednisolone-treated cows and seven (7) from control animals. Significance analysis of microarray found 154 up-regulated and 234 down-regulated transcripts in the prednisolone-treated animal group respect to the controls.

overall_design: In this study, we analyzed fifteen (15) bovine thymus samples, eight (8) from prednisolone-treated cows and seven (7) from control animals. Gene expression profiling was performed using the Agilent-015354 Bos taurus Oligo Microarray platform (GPL7053) based on single-colour detection (Cyanine-3 only). Microarrays were scanned with Agilent scanner G2565BA (barcode on the left, DNA on the back surface, scanned through the glass) at a resolution of 5 microns; all slides were scanned twice at two different sensitivity settings (XDRHi 100% and XDRLo 10%); the scanner software created a unique ID for each pair of XDR scans and saved it to both scan image files. Feature Extraction (FE) 9.5 used XDR ID to link the pairs of scans together automatically when extracting data. The signal left after all the FE processing steps have been completed is ProcessedSignal that contains the Multiplicatively Detrended, Background-Subtracted Signal.

first: Sara

last: Pegolo

first: Tiziana

last: Cannizzo


title: Electroacupuncture Improves Trinitrobenzene Sulphonic Acid-Induced Colitis, Evaluated by Transcriptomic Study

city: Taichung

first: Chien-Yun

last: Hsiang

address: 91 Hsueh-Shih Road

institute: China Medical University

summary: Inflammatory bowel disease is a chronic colonic inflammation that displays symptoms like diarrhea and weight loss. Acupuncture has been widely accepted by Western countries for the treatment of pain. In this study, we analyzed the efficacy and mechanism of electroacupuncture (EA) on trinitrobenzene sulphonic acid (TNBS)-induced colitis in mice. Mice were intrarectally administered 250 mg/kg TNBS and electroacupunctured at Quze (PC3) and Neiguan (PC6) acupoints, which have been applied for gastrointestinal disorders. Gene expression profiles in colons and spleens were analyzed by microarray for the elucidation of mechanism of EA. Our data showed that EA at PC3 and PC6 improved macroscopic and microscopic features of colitis, and the improvement displayed a frequency-dependent manner. Administration of TNBS upregulated the expression of most cytokine genes in colons, while EA downregulated the expression of TNBS-induced cytokine genes. Pathway analysis showed that EA significantly affected inflammatory pathways in colons and immunity-associated pathway in spleens. Immunohistochemical staining further showed that EA decreased the expression of interleukin-1β and nuclear factor-κB. In conclusion, this is the first study reporting the global gene expression profiles of EA on TNBS-induced colitis. Our findings suggested that inflammatory and immunity pathways were involved in the anti-inflammatory mechanism of EA on colitis induced by TNBS.


title: Transcriptional profile of bovine chorioallantoic membrane explants in response to wild type, ΔvirB2 or ΔbtpB Brucella abortus

city: Belo Horizonte

first: Alex

middle: FIORINI

last: Carvalho

state: MG

address: Avenida Antonio Carlos 6627

department: DMVP

country: Brazil

institute: UFMG

summary: In this study the transcription profile of bovine trophoblastic cells infected with Brucella samples was evaluated. Chorioallantoic membrane (CAM) explants inoculated with wild type (strain 2308), and to compare with the transcription profile of trophoblastic cells infected with mutant strains lacking virB2 or btpB.ΔvirB2 or ΔbtpB by microarray analysis at 4 hours post infection. Genes with significant variation in levels of transcripts (fold change > 2 and P < 0.05) were functionally classified, and transcripts related to defense and inflammation were assessed by quantitative real time RT-PCR.

overall_design: Chorioallantoic membrane explant culture (CAM) were obtained from 7 intact pregnant bovine uteruses at the final third of gestation. Three-condition experiment, wild type B. abortus 2308, DvirB2 or DbtpB in 4 control replicates and Microarray analysis.

first: Juliana

last: Mol

first: Erica

last: Costa

first: Reneé

middle: M

last: Tsolis

first: Tatiane

last: Paixão

first: Renato

last: Santos


title: Genome-wide analysis of stress-exposure-associated and exposure-related individual differences associated hippocampus gene expression in males and females.

overall_design: Total RNA obtained from hippocampus of rats exposed to predator-scent-stress and showing extreme (n=5 males and n=5 females) or minimal (n=5 males and n=5 females) behavioral response compared to unexposed to stress and behaviorally tested controls (n=5 males and n=5 females).


title: PCR array analysis of DNA repair gene expression in human vascular smooth muscle cells

status: Public on Sep 01 2014

city: Cambridge

first: Kelly

middle: Louise

last: Gray

state: Cambs

address: Addenbrookes Hospital, Hills Road

department: Medicine

country: United Kingdom

institute: University of Cambridge

summary:
cDNA from aortic and plaque VSMCs was isolated and subject to PCR array analysis
VSMCs were cultured from human tissue samples and used at passage number 5 or below.

overall_design: qPCR gene expression profiling. VSMCs from 9 donors ( 5 disease free aortic tissue as controls and 4 diseased carotid plaques). Equal amounts of RNA was used from each patient sample. RNA was not pooled.

first: Martin

last: Bennett


title: Molecular differences between mesenchymal populations from deciduous and permanent human teeth

city: New York

first: Paolo

last: Guarnieri

state: NY

address: 1130 St. Nicholas Avenue

department: Systems Biology

institute: Columbia University

summary: Deciduous and permanent human teeth represent a model system to study ageing of mesenchymal populations. Aging is tightly connected to self-renewal and proliferation and thus, mapping potential molecular differences in these characteristics between populations constitutes an important task. Specifically designed microarray panels were used. We have detected a number of molecules that were differentially expressed in dental pulp mesenchyme from deciduous and permanent teeth extracted from young children and adults, respectively. Among the differentially regulated genes HMGA2, a stem cell-associated marker, stood out as a remarkable example with a robust expression in deciduous pulp cells. In addition to this, we discovered that several proliferation-related genes, including CDC2A and CDK4, were up-regulated in deciduous pulp cells, while matrix genes COL1A1, fibronectin and several signaling molecules, such as VEGF, FGFr-1 and IGFr-1 were up-regulated in the pulp cells from permanent teeth. Taken together, our data suggest that deciduous pulp cells are more robust in self- renewal and proliferation, whereas adult dental pulp cells are more capable of signaling and matrix synthesis.

overall_design: The deciduous teeth were collected from 3-12-year-old children (N=8), whereas the permanent teeth were collected from adults, 19-52 years of age (N=8). The tooth was mechanically separated into two halves to remove all soft tissue in the pulp. The pulp tissue was digested and the dissociated cells were passed through cell strainer and plated with culture medium.  The cells were then passaged at 90% confluency to a 10 cm dish for expansion. RNA was extracted from passage one cells with the Qiagen RNeasy Mini Kit. Microarray analysis was performed using PIQORTM Stem Cell Microarray chip (Miltenyi Biotech), which is comprised of 942 relevant genes for stem/progenitor cells and key genes for cell differentiation, to identify gene sets that are differentially expressed between cells in the deciduous and adult teeth. A total of 1 μg RNA for each sample was used for amplification and further analysis with the PIQORTM stem cell microarray chip (Miltenyi Biotec), followed by detection with a laser scanner (Agilent Technologies). In total, 8 comparisons were performed with dataset consisting of two microarrays, each containing a total of 11 slides with signal intensities within the R/Bioconductor statistical framework. The Linear Model for Microarray Data package (Limma) was used to pre-process the raw data, perform quality controls and estimate statistical significance. Expression intensities were background-corrected using a convolution of normal and exponential distributions with an offset of 50, which were then normalized within every slide using loess normalization. We analyzed the red and green channels separately using the mixed model method and different groups were quantile-normalized separately. The correlation was computed between the two channels for the same spot. Differentially expressed genes were identified by computing the contrasts, fitting to a linear model, performing the hypothesis tests, and correcting for multiple testing by performing the false discovery rate using the Benjamini-Hochberg correction.

first: Nina

last: Kaukua

first: Mo

last: Chen

first: Jeremy

last: Mao

first: Kaj

last: Fried


title: State- and trait-specific gene expression in euthymia and mania

first: Carsten

last: Sticht

country: Germany

summary: Gene expression profiles of bipolar disorder (BD) patients were assessed during both a manic and a euthymic phase and compared both intra-individually, and with the gene expression profiles of controls.

overall_design: 11 BD patients were assessed in their manic as well as in their euthymic phase. Comparison of gene expression BD euthymic vs. controls, BD manic vs. controls, and intra-patient comparison BD euthymic vs. BD manic.

first: Stephanie

middle: H

last: Witt

first: Dilafruz

last: Juraeva

first: Jana

last: Strohmaier

first: Sandra

last: Meier

first: Jens

last: Treutlein

first: Helene

last: Dukal

first: Josef

last: Frank

first: Maren

last: Lang

first: Franziska

last: Degenhardt

first: Manuel

last: Mattheisen

first: Benedikt

last: Brors

first: Sven

last: Cichon

first: Markus

last: Nöthen

first: Christian

first: Marcella

last: Rietschel


title: Gene expression profile of in vitro produced bovine blastocyst with and without Thyroid hormone supplementation

city: Guelph

first: Tamas

last: Revay

state: ON

address: 50 Stone Rd E

department: Biomedical Sci

institute: University of Guelph

summary: Bovine IVP blastocysts (day 8) were produced with and without thyroid hormones and gene expression profiles were compared.

overall_design: The IVC media (SOF) was supplemented with 50ng/ml of each T3 and T4. Four independent IVF run, each gave 1 control and 1 treated sample. Each sample is a pool of 5 blastocyst. Total Rna was extracted from each sample, amplified, labeled (also with dye swap) and hybridized to the EmbryoGene custom Agilent array (GPL13226). FlexArray software was used for data analysis.

first: Fazl

last: Ashkar

first: Isabelle

last: Durfort

first: Claude

last: Robert

first: Allan

last: King


title: Transcript profiling reveals a molecular signature that distinguishes early versus late time to bud set phenotypes in a white spruce full-sib family.

city: Edmonton

first: Chelsea

last: Ju

state: Alberta

address: CW 405, Biological Sciences Centre

department: Biological Sciences

institute: University of Alberta

summary: It is crucial for north temperate tree species like white spruce to control timing of growth cessation and bud set in order to survive winter conditions.  While much work has examined both endogenous and exogenous mechanisms influencing this transition within angiosperms, the mechanisms underlying this transition in conifers; including photoperiod perception, growth cessation and development of endodormancy, have been less well-characterized. The objective of this research was to compare the genetic responses of spruce genotypes exhibiting an early transition from active growth to bud initiation with those that delay the transition, to tease apart the molecular mechanisms underlying these complex traits. In order to gain a deeper understanding of how genomic architecture influences bud phenology and related regulatory pathways, transcript levels were quantified using a 25,045 element spruce oligonucleotide microarray. Individuals exhibiting early versus late time to bud set were selected from a large unrelated full-sib family that had been phenotyped multiple years under natural and controlled environment conditions, and harvested at an early and mid stage of bud formation. Progeny designated as early time to bud set were more likely to undergo second flush, particularly under long day (16 h) and constant temperature (20°C) conditions. Approximately 5400 genes were differentially expressed in either or both of the early and late time to bud set phenotypic classes between time points, while ca. 1500 genes were differentially expressed between phenotypic classes at either or both time points. These analyses revealed about 400 genes with putative regulatory roles. The comparison between early and late time to bud set trees revealed a large number of specifically differentially expressed genes in the early developmental stage for bud formation (957 genes, including 53 putative regulators) relative to the later developmental stage (81 genes, including 4 putative regulators). Genes implicated in the circadian cycle, photoperiodic pathway and chromatin remodeling figured prominently in these lists, providing new insight into mechanisms that may regulate bud formation in determinate species such as white spruce.

platform_organism:
Picea glauca
Picea sitchensis

overall_design: A clonally replicated QTL mapping population (cross C94-1-2516, ♀77111 × ♂2388), previously characterized by Pelgas et al. (2011), was used for this study.  Phenotypic data collected between 2006-2008 was used to identify extremes for time to bud set within the QTL population. Genotypes falling within the lower quartile for time to bud set for at least three of six experiments were designated as early time to bud set, while genotypes falling within the upper quartile for time to bud set for at least three of six experiments were designated as late time to bud set. Shoot tips from four ramets of each genotype were harvested for molecular analysis.  Two ramets were harvested at the first sign of bud formation (Time 1) and the remaining two ramets were harvested six weeks later at which time the majority of seedlings were at the mid stage of bud set (Time 2). Microarray hybridizations were conducted to make the following comparisons:  a comparison of bud development (Time 1 v. Time 2) in early time to bud set seedlings, a comparison of bud development (Time 1 v. Time 2) in late time to bud set seedlings, and a comparison of early and late time to bud set seedlings within early stages of bud formation or mid stage of bud formation. Each of two biological replicates for each time point and each phenotypic class was hybridized.

first: W

last: El Kayal

first: A

last: Gregoris

first: J

middle: A

last: Hamilton

first: C

middle: T

middle: G

last: Allen

first: M

last: Gros-Louis

first: B

last: Pelgas

first: P

last: Sylvestre

first: N

last: Isabel

middle: E

last: Cooke


title: The global response regulator RegR controls expression of denitrification genes in Bradyrhizobium japonicum

city: Zürich

first: Hans-Martin

last: Fischer

address: Vladimir-Prelog-Weg 4

department: Microbiology

institute: ETH Zürich

summary: Bradyrhizobium japonicum RegSR regulatory proteins belong to the family of two-component regulatory systems, and orthologs are present in many Proteobacteria where they globally control gene expression mostly in a redox-responsive manner. In this work, we have performed a transcriptional profiling of wild-type and regR mutant cells grown under anoxic denitrifying conditions. The comparative analyses of wild-type and regR strains revealed that almost 620 genes induced in the wild type under denitrifying conditions were regulated (directly or indirectly) by RegR, pointing out the important role of this protein as a global regulator of denitrification. Genes controlled by RegR included nor and nos structural genes encoding nitric oxide and nitrous oxide reductase, respectively, genes encoding electron transport proteins such as cycA (blr7544), or cy2 (bll2388), genes involved in nitric oxide detoxification (blr2806-09), copper homeostasis (copCAB), as well as two regulatory genes (bll3466, bll4130). Purified RegR interacted with the promoters of norC (blr3214), nosR (blr0314), a fixK-like gene (bll3466), and bll4130 which encodes a LysR-type regulator. By using fluorescently labeled oligonucleotide extension (FLOE), we were able to identify two transcriptional start sites located at about 35 (P1) and 22 (P2) bp upstream of the putative translational start codon of norC. P1 matched with the previously mapped 5’end of norC mRNA which we demonstrate in this work to be under FixK2 control. P2 is a start site modulated by RegR and specific for anoxic conditions. Moreover, qRT-PCR experiments, expression studies with a norC-lacZ fusion, and heme c-staining analyses revealed that anoxia and nitrate are required for RegR-dependent induction of nor genes, and that this control is independent of the sensor protein RegS.

overall_design: A total of eight Affymetrix GeneChips are included in this study. Per strain (wild-type B. japonicum 110spc4, delta regR mutant 2426) four biological replicates were processed and analyzed. Strains were grown under anoxic conditions in Bergersen minimal medium supplemented with succinate as carbon source and KNO3 as terminal electron acceptor. For comparison, a microarray expression dataset generated with B. japonicum wild-type (Hauser et al., Mol. Genet. Genomics 278:255-271, 2007) and delta regR mutant cells (Lindemann et al., J. Bacteriol. 189:8928-8943, 2007) was used.

first: Maria

middle: J

last: Torres

first: Montserrat

last: Argandoña

first: Carmen

last: Vargas

first: Eulogio

last: Bedmar

first: Socorro

last: Mesa

first: María

last: Delgado


title: Expression data from murine natural killer cell subsets based on Ly49 receptor expression in C57BL/6 mice (C/I+ versus Ly49G2+ NK cells)

city: Frederick

first: Stephen

middle: Kent

last: Anderson

state: MD

address: Building 560, room 31-33

department: CCR

institute: NCI-Frederick

summary:
Natural killer (NK) cells have differential expression of inhibitory and activating receptors. NK cells that express inhibitory receptors with high binding affinity to self are considered licensed and normally functional cells, while those with low affinity are unlicensed are considered hyporesponsive. Microarray analysis was performed to better understand gene expression differences between these two subpopulations of NK cells after culturing the NK cells with IL-2 from splenocytes isolated from C57BL/6 mice and then sorting for CD3-CD122+Ly49G2+Ly49C/I- or CD3-CD122+Ly49G2-Ly49C/I+.
Gene fold expression differences were compared between the Ly49G2+ and Ly49C/I+ NK cells to better understand the functional roles and characterisitics of these cells.

overall_design: A total of 6 samples were analyzed, 3 for the CD3-CD122+Ly49G2+Ly49C/I- NK cells and 3 for the CD3-CD122+Ly49G2-Ly49C/I+. Samples were obtained from C57BL/5 splenocytes that were T cells depleted through anti-Thy1.2 and complement mediated depletion and cultured for 7 days with IL-2. Fold changes greater than 1.5 were recorded.

first: Can

last: Sungur

first: Mingyi

last: Chen

first: Anthony

last: Zamora

first: Claire

last: Pomeroy

first: Ethan

last: Aguilar

first: Bruce

last: Blazar

first: Raymond

last: Lochhead

first: Dan

last: Longo

first: Juan

last: Du

middle: K

first: Trang

last: Nguyen

first: Jeffrey

last: Venstrom

first: Nicole

last: Baumgarth

first: William

last: Murphy


title: Hepatic transcriptome analysis of male and female Eastern Mosquitofish (Gambusia holbrooki) exposed to a progestin and anti-progesterone reveals the mode of action of endocrine disruption of synthetic steroids in an aquatic organism

city: Gainesville

first: Erica

middle: Karin

last: Brockmeier

state: FL

address: 2187 Mowry Road

institute: University of Florida

summary: Major classes of hormone mimics that have been studied include environmental estrogens and androgens, but recent studies have also demonstrated the significant impacts of natural and synthetic progesterones in the environment. The objective of this study was to evaluate the molecular and physiological impacts of progestin, anti-progestin, and mixture exposures in the Eastern Mosquitofish (G. holbrooki). By comparison of gene expression profiles and modulated biological processes in the three groups, it was determined that mifepristone acts more as a progestin than as an anti-progestin, as has also been demonstrated in other species of fish. This work contributes to the overall knowledge of the impacts of this class of chemical contaminats on aquatic organisms, which are a sentinel species for pollutants as aquatic ecosystems often become a reservoir for anthropogenic contaminants.

overall_design: G. holbrooki adult males and females were exposed to one of the following conditions: vehicle control (ethanol), 100 ng/L of levonorgestrel, 100 ng/L of mifepristone, or a mixture of both levonorgestrel and mifepristone. All exposures were conducted for 48 hours with water changed and chemicals renewed daily. Fish were anesthetized using 100 mg/L Benzocaine (Ethyl 4-aminobenzoate). Livers were removed and stored in RNAlater (Qiagen, Hilden, Germany) overnight at 4 C before storage at -80 C. RNA was isolated from the livers using TRIzol (Invitrogen, Grand Island, USA), hydrated using RNAsecure (Ambion, Grand Island, USA), and DNase treated using the Turbo DNA-free kit (Ambion, Grand Island, USA). Four oocyte-development stage-matched RNA samples per treatment were evaluated for RNA integrity using the 2100 BioAnalyzer (Agilent, Santa Clara, USA). The range of RIN values was 8.2-9.6

first: Brockmeier

last: Erica

first: Denslow

last: Nancy


title: RNA binding protein DDX1 promotes subset of primary miRNA processing

city: Houston

first: Cecil

last: Han

state: TX

address: 7777 knight road

department: Cancer Biology Department

institute: MD Anderson Cancer Center

summary: human miRNA expression profile from human U2OS cells which is treated by shDDX1 and control or DNA damage treated or nontreated

overall_design: Genome-wide miRNA expression profiling analyses were performed using microRNA Ready-to-Use PCR array (Human panel I+II, V2.M, Exiqon) according to the manufacturers’ instructions.

first: Xiongbin

last: Lu


title: Identification of grape genes regulated in response to resistance inducer treatments

city: Orsay

first: Stéphanie

last: Pateyron

address: Rue de Noetzlin _ Batiment 630

institute: IPS2_Institute of Plant Sciences Paris-Saclay


title: Transcriptome analyses of dhh1 mutants in yeast

city: Paris

first: frederic

last: devaux

address: 15 rue de l'ecole de medecine

institute: Universite Pierre et Marie Curie

summary: Previous experiments revealed that DHH1, a RNA helicase involved in the regulation of mRNA stability and translation, complemented the phenotype of a Saccharomyces cerevisiae mutant affected in the expression of genes coding for monocarboxylic-acids transporters, JEN1 and ADY2. In wild type cells, JEN1 expression had been shown to be undetectable in the presence of glucose or formic acid, and induced in the presence of lactate. In this work, we show that JEN1 mRNA accumulates in a dhh1 mutant, when formic acid was used as sole carbon source. Dhh1 interacts with the decapping activator Dcp1 and with the deadenylase complex. This led to the hypothesis that JEN1 expression is post-transcriptionally regulated by Dhh1 in formic acid. Analyses of JEN1 mRNAs decay in wild-type and dhh1 mutant strains confirmed this hypothesis. Microarray analyses of dhh1 mutant indicated that Dhh1 plays a large role in metabolic adaptation, suggesting that carbon source changes triggers a complex interplay between transcriptional and post-transcriptional effects.

overall_design: We compared gene expression between wild type and dhh1 deleted yeast strains grown either with formate or in glucose as sole carbon source. The experiments were replicated using biologically independant samples with dye swap. A total of four hybridizations were performed.

first: Sandra

last: Mota

first: Neide

last: Vieira

first: Sonia

last: Barbosa

first: Thierry

last: Delaveau

last: Torchet

first: Agnes

last: Le Saux

first: Mathilde

last: Garcia

first: Ana

last: Pereira

first: Sophie

last: Lemoine

first: Fanny

last: Coulpier

first: Xavier

last: Darzacq

first: Lionel

last: Benard

first: Margarida

last: Casal

first: Frederic

last: Devaux

last: Paiva


title: Effect of multiple longitudinal biopsy sampling in individual mice

city: Amsterdam

first: Oskar

last: Bruning

address: Science Park 904

department: SILS

country: Netherlands

institute: University of Amsterdam

summary:
Small scale study to asses the effects of taking multiple skinbiopts from individual mice in time.
Results showed no influence on expression levels in time from older samplings on newer samplings.

overall_design: skin biopts from 4 individual mice in taken at 6 points in time

first: Wendy

last: Rodenburg

first: Conny

last: van Oostrum

first: Martijs

last: Jonker

first: Mark

last: de Jong

first: Rob

last: Dekker

first: Han

last: Rauwerda

first: Wim

last: Ensink

first: Annemieke

last: de Vries

first: Timo

last: Breit