title: Gene expression signature as a predictor of recurrence in stage II Colorectal cancer

city: Yokohama-shi, Tsurumi-ku

first: Ryo

last: Matoba

state: Kanagawa-ken

institute: DNAChipResearchInc

summary:
We have been attempting to stratify the stage II CRC patients into good or poor prognoses based on gene expression signatures of resected specimen. We collected more CRC stage II cases up to 300, and analyzed gene expression for those samples. We selected a set of 3,023 probes (1,978 genes) for extracting metastasis-related discriminator genes. These genes consisted of 491 prognosis related genes identical to the probes on another platform array, and other probes for hybridization and quality control. Using these 3,023 probes, we attempted to select discriminator genes, with the 150 training sample set, resulting 55 markers. We then applied the discriminator set to the second, 150 samples set in a blind test for predictive accuracy and prognostic validity.
The multivariate Cox analyses showed the significant parameters to predict the prognosis with a hazard ratio of 3.5 (95% confidence interval, 0.12-0.67; p=0.004). This personalized prognosis is crucial with CRC patients, the predictive performance may deserve serious consideration for possible application to clinic.

overall_design:
The study subjects were a total of 300 patients with advanced CRC who underwent curative surgery between 2003 and 2006 at the following institutions.
The first set of patients consists of 150 cases, including 110 recurrent-free (follow-up median, 60 months) and 40 recurrent patients who underwent surgery before December 2004. This set of 150 cases was assigned to a retrospective training study. The second set consists of 150 cases in which curative surgery was undertaken after January 2005.

first: Ichiro

last: Takemasa

first: Masakazu

last: Miyake

first: Masataka

last: Ikeda

first: Hirofumi

last: Yamamoto

first: Mitsugu

last: Sekimkoto

first: Motohiko

last: Tanino

first: Morito

last: Monden

first: Yuichiro

last: Doki

first: Kenichi

last: Matsubara

first: Masaki

last: Mori


title: Compared performance of Affymetrix HTA arrays and Illumina RNAseq for the analysis of tumours [Affymetrix]

status: Public on Jun 09 2017

city: Luxembourg

first: Arnaud

last: Muller

address: 84 Val Fleuri

department: DONC

country: Luxembourg

institute: LIH

summary: Here we compared the performance of Affymetrix HTA 2.0 microarray and Illumina 2000 RNA-sequencing techniques on the clinical samples collected from patients with lung squamous cell carcinoma.

overall_design: Comparison of transcriptome (9 tumor and 9 adjacent tissue samples) in RNA-seq and microarray.

first: Petr

middle: V

last: Nazarov

first: Tony

last: Kaoma

first: Nathalie

last: Nicot

first: Christelle

last: Ghoneim

first: Laurent

last: Vallar


title: Global expression analysis of the trabecular meshwork, cornea, sclera and trabecular meshwork-derived mesenchymal stem cells (TM-MSC)

city: Singapore

first: Padmapriya

last: Sathiyanathan

address: Genome, 60 Biopolis Street

department: Stem Cell & Regenerative Biology

country: Singapore

institute: Genome Institute of Singapore

summary: Microarray study comparing the trabecular meshwork (TM) with TM-MSC, corneal and scleral tissues

overall_design: Illumina humanRef-8 v3.0 expression beadchip was used to transcriptionally profile 3 biological replicates each of the TM, cornea, sclera and cultured TM-MSC.

first: P

first: L

middle: W

last: Stanton


title: Role of Histone Deacetylase 4 on cardiac expression after exercise

status: Public on Jun 07 2017

city: Mannheim

first: Carsten

last: Sticht

address: Theodor-Kutzer-Ufer

department: ZMF

country: Germany

institute: University Heidelberg

summary:
Physiological exercise leads to an activation of an distinct genetic program in the heart. During this process, we identified histone deacetlyase 4 (HDAC4) as an epigentic modifier, that regulates this adaptive process. To identify HDAC4 dependent genes that can are regulated after physiological stress, we investigated the cardiac gene expression in cardiomyocyte specific HDAC4 knockout animals and control animals after running exercise.
We used microarrays to detail the global programme of gene expression underlying physiological cardiac adaption on exercise and identified distinct, histone deacetylase 4 dependent up-regulated genes during this process.

overall_design: Cardiac tissue was collected after a 2 weeks forced running exercise protocol in mice. We compared cardiac RNA of cardimoyocyte specific HDAC4 knockout animals to control littermates. In both groups we included 3 replicates and included 3 replicates from non running littermates (HDAC4 knockout and wildtype animals.

first: Johannes

last: Backs

first: Lorenz

middle: H

last: Lehmann


title: Modulating the gut microbiota by dietary guar gum protects against diet-induced obesity but promotes non-alcoholic steatohepatitis in mice

status: Public on Jun 06 2017

city: Wageningen

first: Guido

last: Hooiveld

address: HELIX, Stippeneng 4

department: Div. Human Nutrition & Health

country: Netherlands

institute: Wageningen University

summary: Non-alcoholic fatty liver disease (NAFLD) is rapidly becoming the most common liver disease worldwide, yet the pathogenesis of NAFLD is only partially understood. Here, we investigated the role of the gut bacteria in NAFLD by stimulating the gut bacteria via feeding mice the fermentable dietary fiber guar gum and suppressing the gut bacteria via chronic oral administration of antibiotics. Guar gum feeding profoundly altered the gut microbiota composition, in parallel with reduced diet-induced obesity and improved glucose tolerance. Strikingly, despite reducing adipose tissue mass and inflammation, guar gum enhanced hepatic inflammation and fibrosis, concurrent with markedly elevated plasma and hepatic bile acid levels. Consistent with a role of elevated bile acids in the liver phenotype, treatment of mice with taurocholic acid stimulated hepatic inflammation and fibrosis. In contrast to guar gum, chronic oral administration of antibiotics effectively suppressed the gut bacteria, decreased portal secondary bile acid levels, and attenuated hepatic inflammation and fibrosis. Neither guar gum or antibiotics influenced plasma lipopolysaccharide levels. In conclusion, our data indicate a causal link between changes in gut microbiota and hepatic inflammation and fibrosis in a mouse model of NAFLD, possibly via alterations in bile acids.

overall_design: Mice were fed a high-fat, high-cholesterol diet, together with a 20% fructose solution as drinking water, or the same diet in which 10% corn starch (w/w) was replaced by the dietary fiber guar gum. After 18 wks of intervention, livers were removed and used for gene expression profiling.

first: Aafke

last: Janssen

first: Tom

last: Houben

first: Saeed

last: Katiraei

first: Lily

last: Boutens

first: Nieke

last: van der Bolt

first: Zeneng

last: Wang

first: Jonathan

middle: M

last: Brown

first: Stanley

middle: L

last: Hazen

first: Ronit

last: Shiri-Sverdlov

first: Ko

last: Willems van Dijk

first: Jacques

last: Vervoort

first: Rinke

last: Stienstra

middle: J

first: Sander

last: Kersten


title: Bile salts in Acinetobacter baumannii clinical strains with lack of AdeABC efflux pump

city: A Coruña

first: Maria

last: Tomas-Carmona

address: As Xubias, 84

department: Microbiology Department

country: Spain

institute: Instituto de Investigación Biomédica de A Coruña (INIBIC) / Complexo Hospitalario Universitario de A Coruña (CHUAC)

summary: Few are the studies that analyzed the molecular features implicated to the tolerance to bile salts by A.baumannii clinical strains. Interestingly, Ab421 GEIH-2010 strain (belonging to ST79/PFGE-HUI-1 clone constitute by isolates with lacking of the AdeABC efflux pump) and A.baumannii ∆adeB ATCC 17978  showed higher tolerance to bile salts by the expression of the  glutamate/aspartate transporter as well as virulence factors (Type VI Secretion System, twitching motility and biofilm) associated to the activation of the Quorum Sensing system.

overall_design: The studies of gene expression were carried out by microarrays which were designed (Bioarray Genetic Diagnosis, Alicante) using eArray (Agilent) from the complete genome of A. baumannii ATCC 17978 strain. The High Pure RNA Isolation Kit (Roche, Germany) was used to obtain Dnase-treated RNA from late log-phase cultures (OD=0.4-0.6) in absence and presence of 0.5% bile salts (the physiological concentrations in the human intestine are 0.1%-1.3%). The RNA samples were quantified in a NanoDrop ND-1000 Spectrophotometer (NanoDrop Technologies). Quality and integrity analysis of the samples was carried out in an Agilent 2100 Bioanalyzer with the RNA 6000 Nano reagents and the RNA Nano Chips (Agilent Technologies).

last: Lopez

first: Lucia

last: Blasco

first: Eva

last: Gato

first: Margarita

last: Poza

first: German

last: Bou

last: Tomas


title: Gene expression of LNCaP cells grown in androgen deprived conditions in the presence of 10nM insulin and/or 1nM R1881.

city: Brisbane

first: Colleen

last: Nelson

state: Queensland

address: 199 Ipswich Road

department: Institute of Health and Biomedical Innovation; Vancouver Prostate Centre

country: Australia

institute: Queensland University of Technology; University of British Columbia

summary: Analysis of LNCaP cell molecular differences and their response to insulin compared to control or R1881. Insulin differentially regulated genes, as did R1881, though the treatments had a very different profile, with some overlaps. These results provide insights into the effect of insulin on cancer related pathways in an androgen deprived setting.

overall_design: 4 treatment groups with biological replicates - EtOH (Control), Insulin 10nM+EtOH, R1881 1nM, R1881+ Insulin

first: Amy

middle: A

last: Lubik

first: Melanie

last: Lehman

first: Jennifer

last: Gunter

middle: C


title: Genome profiling of fibrolamellar carcinoma [CGH]

city: New York

first: Jeffrey

last: Zhao

state: NY

address: 1275 York Avenue

department: Genomics Core

country: USA

institute: Memorial Sloan Kettering Cancer Center

type: Genome variation profiling by genome tiling array

summary: Fibrolamellar hepatocellular carcinoma (FL-HCC) is a rare variant of HCC that most frequently affects young adults. Because of its rarity and an absence of preclinical models, the molecular biology of FL-HCC remains unclear. Our objective was to analyze chromosomal alterations and dysregulated gene expression in tumor specimens collected at a single center during two decades of experience with FL-HCC.

overall_design: We analyzed 38 specimens from 26 patients by array comparative genomic hybridiziation (aCGH)

first: Eric

last: Sorenson

first: Raya

last: Khanin

first: Zubin

last: Bamboat

first: Michael

last: Cavnar

first: Teresa

middle: S

last: Kim

first: Eran

last: Sadot

first: Shan

last: Zeng

middle: B

last: Greer

first: Adrian

last: Seifert

first: Noah

last: Cohen

first: Megan

last: Crawley

first: Benjamin

last: Green

first: David

last: Klimstra

first: Ronald

middle: P

last: DeMatteo


title: Microarray expression data from WT and Irf4-/- CD4+ T cells after activation

status: Public on Jun 01 2017

city: Houston

first: wenhao

last: chen

state: TX

address: 6670 Bertner Street, R7-216

institute: Houston Methodist Research Institute

summary: To define molecular basis underlying dysfunction of Irf4-deficient T cells. We found that Irf4-deficient T cells were dysfunctional and unable to infiltrate and reject heart allografts, and then investigated the molecular basis underlying dysfunction of Irf4-deficient T cells. Irf4-deficient and wild type B6 CD4+ T cells were activated in vitro for two days, followed by microarray analysis. We found that dysfunction of Irf4-deficient T cells is not only due to impaired effector differentiation, but also involves an altered transcriptional programme that allows the expression of essential negative regulators of T-cell function.

overall_design: Naive CD4+ T cells (CD62L+CD44−) were sorted by flow cytometry Irf4-/- and wild type B6 mice, then 1×10e5 cells per well were activated with mAb to CD3e (1 μg/ml; 2C11; Biolegend) plus equal numbers of syngeneic mitomycin C-treated antigen-presenting cells in 96-well round bottom tissue-culture plates at 37 ºC in a humidified incubator with 5% CO2. Two days later, living CD4+ T cells were sorted by Flow Cytometry for RNA isolation. The total RNA samples were then used for microarray analysis. Two independent experiments for WT and Irf4-/- were performed.

first: Jie

last: Wu

first: Wenhao

last: Chen


title: Chinese lung ADC adjacent normal sample exon-level expression

status: Public on Jun 10 2017

city: Shanghai

first: Hongbin

last: Ji

address: YueYang Rd

country: China

institute: SIBCB

overall_design: In order to search for novel gene fusions which may play important roles in lung ADC initiation and progression, we performed Exon array on lung ADC and adjacent normal samples.

first: Fei

last: Li

first: Zhaoyuan

last: Fang


title: Identification of aberrant miRNA expression in multiple myeloma

status: Public on Jun 05 2017

city: Kuala Lumpur

first: Ivyna

middle: PN

last: Bong

state: Kuala Lumpur

address: Jalan Pahang

department: Cancer Research Centre

country: Malaysia

institute: Institute for Medical Research

summary: To identify aberrant miRNAs involved in the pathogenesis of multiple myeloma, we performed miRNA expression profiling of a total of 27 samples consisting of 19 clinical specimens, 8 myeloma cell lines and 3 normal peripheral blood samples. The microarray data were analysed by GeneSpring Software v13.0. We had identified 1799 miRNAs, which were differentially expressed by >2.0 fold change at p<0.05.  Out of 1799 miRNAs, 1791 and 8 of them were up-regulated and down-regulated, respectively in myeloma group compared to the normal control group. Expression of 2 miRNAs (miR-150-5p and miR-4430) were verified by real-time PCR using the same RNA samples (20-22 samples were used) using SYBR Green. The real-time PCR confirmed that the expression of the miRNAs were consistent with microarray data.

overall_design: Bone marrow aspirates of 19 clinical specimens and 8 myeloma cell lines were compared against 3 peripheral bloods from healthy individuals.

first: C

last: Ng

first: Puteri

last: Baharuddin

first: Z

last: Zakaria


title: Cxcl1 antagonist on UVB-induced skin inflammation leading to inhibitory effects on photo-skin tumorigensis in Xeroderma pigmentosum type A deficient mice

city: Kobe

first: Makoto

last: Kunisada

address: 7-5-2 Kusunoki-cho

department: Dermatology

country: Japan

institute: Kobe university of medicine

summary: Xeroderma pigmentosum type A (XP-A) is a hereditary disease characterized by early onset of skin cancers development by ultraviolet (UV) exposure. Although etiology of susceptible to skin tumor of XP-A is well investigated as a repair deficiency by UV-induced DNA damage, the mechanism of unusual strong and prolonged skin inflammation caused by UV in XP-A and whether UV-induced inflammatory response relates to skin tumor-prone phenotype remains to be elucidated. Among up-regulated inflammatory response related genes in Xpa mice compared with wild-type by gene profiling study, Cxcl1 in Xpa mice was significantly different from wild-type and blood level of Cxcl1 was increased with UVB exposed on even small area of skin in Xpa mice. We administered Cxcl1 neutralizing antibody or antioxidant agent n-acetylcysteine for Xpa mice after UVB irradiation, showing that blood levels of Cxcl1, ear swelling and skin redness as an inflammatory response were significantly suppressed. Xpa mice with chronic UVB exposure and Cxcl1 neutralizing antibody or n-acetylcysteine administered Xpa mice yields much less skin tumors compared with control group. Those results indicate that highly inflammatory response of Xpa mice by UVB plays a role of skin tumor development that could be suppressed by chemokine as Cxcl1 through antioxidant mechanism.

overall_design: UVB exposed with 1kJ/m^2 on Xpa mice and wild-type and back skin were collected 3 and 24 hr after UVB irradiation.

first: Chieko

last: Hosaka

first: Chihiro

last: Takemori

first: Eiji

last: Nakano

first: Hideki

last: Enomoto

first: Chikako

last: Nishigori


title: Comparative phenotypic and genome-wide expression analysis of ancestral Saccharomyces cerevisiae and a strain with higher flux through the pentose phosphate pathway

city: MONTPELLIER

first: Sylvie

last: Dequin

address: 2 PLACE PIERRE VIALA

country: France

institute: INRA

summary: By an evolutionary approach based on long-term culture on gluconate as the sole carbon source, a Saccharomyces cerevisiae wine strains with enhanced flux through the pentose phosphate (PP) pathway were obtained. One of these evolved strains, ECA5, exhibited several novel properties with great potential for wine making, including a higher than wild-type fermentation rate and altered production of acetate and aroma compounds. To describe the mechanisms underlying this complex phenotype, we performed a comparative analysis of transcriptomic profiles between ECA5 and its ancestral strain, EC1118, under low nitrogen, wine fermentation conditions.

overall_design: Analysis used RNA collected at 45g of CO2 realesed (stationary phase) for comparison of ECA5 and EC1118 strains

first: Axelle

last: Cadiere

first: Isabelle

last: Sanchez


title: tRNA level in HeLa, CFBE41o- and primary HBE cells

status: Public on May 24 2017

city: Glasgow

first: Sebastian

last: Kirchner

address: 120 University Place

department: Wellcome Centre for Molecular Parasitology

country: United Kingdom

institute: University of Glasgow

type:
Other
Non-coding RNA profiling by array

summary: Comparison of overall tRNA level between HeLa, cystic fibrosis (CF) bronichal epithelial (CFBE41o-) cells and primary CF patient derived human bronchial epithelial (HBE) cells, estimation of absolute HeLa tRNA levels.

overall_design: HeLa, CFBE41o- and primary HBE cells were compared to HEK cells, No. Biological repeats: 4, HeLa vs. HEK; 3, CFBE41o- vs. HEK; 4, primary HBE vs. HEK, 4, HEK vs. HEK, HeLa absolute levels, 2

first: Melanie

last: Anding

first: Andreas

last: Czech


title: In vitro murine embryonic microRNA expression signatures predicting the non-genotoxic carcinogenic potential of chemicals

city: Maastricht

first: Kasper

last: Derks

state: Limburg

address: P. Debyelaan 25

department: Clinical Genetics

institute: Maastricht University Medical Center

summary: The human body is continuously exposed to various compounds that could initiate or accelerate cancer development. Such carcinogenic compounds can be classified into a genotoxic and non-genotoxic group. Especially carcinogenicity of non-genotoxic compounds is difficult to determine with current in vitro assessments and therefore has to be improved urgently. Here, we used a toxicogenomics-based approach by genome-wide microRNA expression profiling of mouse embryonic stem (mES) cells to identify microRNA classifiers for genotoxic carcinogens (GTXC), non-genotoxic carcinogens (NGTXC) and oxidative (Ox) compounds. We exposed mES cells to four different NGTXC, four GTXC and four Ox compounds. Differential microRNA expression was determined 4, 8 and 12 hours after exposure and was used to assess its discriminative power for NGTXC and GTXC. We generated an accurate classifier set, which was discriminative for NGTXC using a tiered approach. In conclusion, our study indicates that microRNA expression profiles can discriminate between NGTXC, GTXC and Ox compounds with high accuracy.

platform_organism:
Homo sapiens
Mus musculus
Rattus norvegicus

overall_design: 146 mES samples in total, 2 control mock treatments, replicates per treated group n=3-4

first: Joost

last: Melis

first: Tessa

last: Pronk

first: Giel

last: Hendriks

first: John

last: Meerman

first: Erik

last: Danen

first: Bob

last: van de Water

first: Wilfred

middle: F

last: van Ijcken

first: Harry

last: van Steeg

first: Jan

last: Hoeijmakers

last: Vrieling

first: Mirjam

last: Luijten

first: Joris

last: Pothof


title: Methylation Profiling of IGHV Unmutated vs mutated CLL

status: Public on May 29 2017

city: New Delhi

first: Ritu

last: Gupta

state: Delhi

address: Dr. B.R.A.IRCH, Ansari Nagar

department: Laboratory Oncology

country: India

institute: All India Institute of Medical Sciences, New Delhi

type: Methylation profiling by high throughput sequencing

summary: In the present study, the methylation profiling (MeDIP) was carried out in 14 treatment-naive, early stage (Rai stage 0-2)  CLL patients and pooled 19+ normal controls. To find an association of methylation with IGHV mutation status, CLL patients were further segregated into IGHV unmutated (n=9) and  IGHV mutated (n=5) subgroups. The methylation signature obtained for CLL versus nornal controls and; unmutated versus mutated CLL was integrated with gene expression profile of these patients and the results were correlated with clinical outcome.

overall_design: Methylation profiling was carried out in 14 treatment naïve early stage CLL samples and pooled samples (n=3) from 10 healthy subjects. The CLL patients were further seggregated into unmutated (n=9) and mutated (n=5) on the basis of IGHV mutation status and methylation profile of these two groups were also compared.

first: Nitin

last: Mathur

first: Lata

last: Rani

first: Ajay

last: Gogia

first: Jaspreet

middle: K

last: Dhanjal

first: Durai

last: Sundar

first: Lalit

last: Kumar

first: Atul

last: Sharma


title: microRNA profiling of recurrent high grade ovarian carcinoma compared to primary ovarian cancer and normal ovary

city: Seoul

first: Eun Ji

last: Nam

address: 50 Yonsei-ro

department: Obstetrics and Gynecology

country: South Korea

institute: Yonsei University College of Medicine

summary: To determine microRNA expression in chemoresistant ovarian cancer, we have employed whole microRNA microarray expression profiling as a discovery platform to identify genes with the potential to distinguish recurrent ovarian cancer. 8 recurrent ovarian cancer tissue and 8 primary ovarian cancer tissue and 4 normal ovarian tissue was used to identify miRNA profiling.

overall_design: microRNA profilinf of recurrent high grade ovarian carcinoma compared to primary ovarian cancer and normal ovary

first: Eun


title: Differences of miRNA expression associated with ΔNp63β overexpressing OSCC cell line SQUU-B

city: Fukuoka

first: Yuma

last: Hashiguchi

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

department: Division of Maxillofacial Diagnostic and Surgical Sciences

institute: Kyushu University Faculty of Dental Science

summary: Recent reports have revealed that EMT is involved in cancer invasion and progression including oral squamous cell carcinoma (OSCC). Previously, we have also studied on the association of p63 gene, a homolog of the p53 tumor suppressor gene, with EMT in OSCC cells. Furthermore, we also demonstrated that down-regulation of ΔNp63 accompanied with EMT and that re-expression of ΔNp63β by stable cDNA transfection in OSCC cell lines reverted the EMT phenotype.  However, the detail mechanisms of ΔNp63β-mediated EMT remain to be unclear. Recent studies have shown that several microRNAs (miRNAs) are also involved in EMT process of human cancer by targeting EMT-related transcription factors. We thus sought to identify responsible miRNA associated with ΔNp63β-mediated EMT using miRNA microarray analyses.

overall_design: As samples for miRNA microarray, we used two clones established from an OSCC cell line SQUU-B, which lacks ΔNp63 expression and displays EMT phenotypes.  One is SQUU-BO cell overexpressing ΔNp63β, and another is SQUU-BC cell transfected with empty vector. In addition, SQUU-B EL cells with low expression of E-cadherin were also  used to identify the miRNA associated with E-cadherin expression strongly.

first: Masayo

last: Morifuji

first: Yuichi

last: Goto


title: Blood samples as a surrogate of brain methylation

city: Donostia

first: Borja

last: Calvo

state: Gipuzkoa

address: Paseo Manuel de Lardizabal, 1

department: Computer Science and Artificial Intelligence

institute: University of the Basque Country

summary: Epigenomic landscapes are variable between cells and tissue types and, fluctuate in time according to a number of factors such as the age related, environmental or nutritional factors among others. Existing biobanks that archive longitudinally assessed and correctly phenotyped samples have not stored exposure-disease relevant target tissue but DNA from peripheral sources such as the whole blood or buccal cells. Thus, a key question for the current epigenetic studies concerns the degree to which easily accessible peripheral tissues (such as blood) can be used to ask questions about the epigenomic changes taking place in inaccessible tissues such as the brain. In the current study we have compared the methylation profiles in brain (cortex and hippocampus) and blood samples within the same individuals in order to create an inventory of epigenetic marks for which measurements in blood are informative for the brain tissue.

overall_design: Bisulphite converted DNA from 13 cortex, hipocamppus and whole blood matched samples and 10 paired peripheral blood mononuclear cells (PBMCs) and whole blood samples were hybridised to the Illumina Infinium 27k Human Methylation Beadchip v1.217

first: Marian

last: de Pancorbo

first: Naiara

middle: G

last: Bediaga

first: Xabier

last: Elcoroaristizabal


title: Transcriptome profiling of murine aortic endothelium deleted for the transcription factor Mef2c

status: Public on May 31 2017

city: Albany

first: John

last: Schwarz

address: 47 New Scotland Ave.

department: Department of Molecular and Cellular Physiology

institute: Albany Medical College

summary: Laminar flow on endothelial cells in vitro activates MEF2 transcription factors to induce expression of atheroprotective genes. Here we sought to establish in vivo MEF2 functions in the endothelium through endothelial-specific deletion of Mef2c. Our results show that endothelial Mef2c regulates migration of vascular smooth muscle from the tunica media into the intima through fenestrations in the internal elastic lamina. Moreover, Mef2c regulates actin stress fiber formation in the endothelium. To investigate Mef2c-dependent targets in the endothelium, we perform transcriptome profiling on RNA isolated from the aortic endothelium with or without Mef2c deletion.

overall_design: Endothelial-specific, inducible-deletion of Mef2c was mediated by Cdh5-CreERT2 through 5 daily tamoxifen injections (Mef2cCdh5EKO) in 10 weeks old mice. Littermates who received vehicle injection served as controls. Thoracic aortas from these mice were harvest 14 days after the first injection. Endothelial RNA from individual aortas was isolated by flushing TRIzol through the aortic lumen and processed for Mouse Transcriptome Array 1.0 (Affymetrix). Each sample was from a single aorta.

first: Yao-Wei

last: Lu


title: Long recovery after heat shock

city: Potsdam

first: Isabel

last: Bäurle

address: Karl-Liebknecht-Str. 24-25

department: Institut für Biochemie und Biologie

institute: Universität Potsdam

summary:
Abiotic stress is a major factor for crop productivity, a problem likely to be exacerbated by climate change. Improving the tolerance to environmental stress is one of the most important goals of crop breeding programmes. While the early responses to abiotic stress in plants are well studied, plant adaptation to enduring or recurring stress conditions has received little attention. This project investigates the molecular mechanism of the maintenance of acquired thermotolerance as a model case of stress memory in Arabidopsis. Arabidopsis seedlings acquire thermotolerance through a heat treatment at sublethal temperatures. To investigate the underlying mechanisms, we are investigating changes in the transcriptome at two timepoints after a heat acclimation treatment using Arabidopsis thaliana seedlings.
Microarrays were used to compare gene expression at two timepoints after a heat acclimation treatment.

overall_design: RNA from three biological replicates per genotype and treatment (4 h after acclimation 52 h after acclimation, and 4 h non-treated control) was purified over an RNeasy Plant RNA extraction column (Qiagen) and processed for hybridization of Affymetrix ATH1 GeneChips (NASC microarray facility). The times were chosen to harvest all samples at the same time of day.

first: Anna

last: Stief

first: Simone

last: Altmann

first: Karen

last: Hoffmann


title: Comparative toxicogenomic effects of three IMX-101 constituents DNAN, NTO and NQ on C. elegans

city: Vicksburg

first: Ping

last: Gong

state: Mississippi

address: 3909 Halls Ferry Road

department: Environmental Laboratory

institute: U.S Army Engineer Research and Development Center

summary: We used the soil nematode Caenorhabditis elegans, a well-characterized genomics model organism, as the test organism and a species-specific, genome-wide 44K-oligo probe microarray for gene expression analysis. Our goal was to discern toxicological mechanisms for three insensitive munitions formulation IMX-101 constituents 2,4-dinitroanisole (DNAN), nitroguanidine (NQ) and nitrotriazolone (NTO) at the molecular level.

overall_design: Gene expression profiling was performed immediately after the 24-hr exposure for each chemical at the lowest, medium and highest sublethal concentrations plus the control with four replicates per treatment. Six 8 x 60K formatted slides (each 60K array containing 44K control and non-control probes, i.e., 27% spots empty) were used. Total RNA samples were randomized when hybridized to the arrays.

first: Keri

last: Donohue

first: Anne

last: Mayo

first: Mitchell

last: Wilbanks

first: Natalie

middle: D

last: Barker

first: Xin

last: Guan

first: Kurt

last: Gust


title: Tonic Signaling Controls Gene Expression in T Lymphocytes

status: Public on May 23 2017

city: San Francisco

first: Jeroen

last: Roose

state: CA

address: 513 Parnassus Ave, HSW 1330A

department: Anatomy

institute: University of California, San Francisco

summary:
To determine the role of tonic signals through the adapter LAT in controling helper T cell function, we performed microarray analysis of splenic CD4+ T cells from mice that are WT for LAT, are deficient in LAT (KO), and have a point-mutated version of LAT that abrogates PLCg1 binding (Y136F). These mouse models allow for inducible perturbation or deletion of LAT (using floxed alleles and the Cre-ER system), so we compared gene expression after both 1 and 4 weeks of tamoxifen treatment.
We identified a cluster of genes that are downregulated when LAT is perturbed, and these genes are also putative targets of the histone deacetylase HDAC7. We explored this mechanistic link between LAT, HDAC7, and genes in this cluster in CD4+ T cells

overall_design: Mice that are CRE ER+ and either LAT WT, LAT f/- (KO), or LAT Y136F/- were treated with tamoxifen for 1 or 4 weeks to inducibly delete or point-mutate LAT. Naïve CD44low CD4+ T cells were sorted from mouse spleens from three mice per genotype and analyzed by Agilent Mouse GE 4x44k arrays.

first: Darienne

middle: R

last: Myers

first: Tannia

last: Lau

first: Evan

last: Markegard

first: Andrea

last: Barczak

first: David

last: Erle


title: Dissecting Low Atmospheric Pressure Stress: Transcriptome Responses to the Components of Hypobaria in Arabidopsis

status: Public on May 11 2017

city: Gainesville

first: Robert

middle: J.

last: Ferl

state: Florida

address: 1301 Fifield Hall PO Box 110690

department: Horticultural Sciences

institute: University of Florida

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

overall_design: Refer to individual Series


title: Dissecting Low Atmospheric Pressure Stress: Transcriptome Responses to the Components of Hypobaria in Arabidopsis [Experiment 2]

summary: Controlled hypobaria presents biology with an environment that is never encountered in terrestrial ecology, yet the apparent components of hypobaria are stresses typical of terrestrial ecosystems. High altitude, for example, presents terrestrial hypobaria always with hypoxia as a component stress, since the relative partial pressure of O2 is constant in the atmosphere. Laboratory-controlled hypobaria, however, allows the dissection of pressure effects away from the effects typically associated with altitude, in particular hypoxia, as the partial pressure of O2 can be varied. In this study, whole transcriptomes of plants grown in ambient (97 kPa/pO2 = 21 kPa) atmospheric conditions were compared to those of plants transferred to five different atmospheres of varying pressure and oxygen composition for 24 h: 50 kPa/pO2 = 10 kPa, 25 kPa/pO2 = 5 kPa, 50 kPa/pO2 = 21 kPa, 25 kPa/pO2 = 21 kPa, or 97 kPa/pO2 = 5 kPa. The plants exposed to these environments were 10 day old Arabidopsis seedlings grown vertically on hydrated nutrient plates. In addition, 5 day old plants were also exposed for 24 h to the 50 kPa and ambient environments to evaluate age-dependent responses. The gene expression profiles from roots and shoots showed that the hypobaric response contained more complex gene regulation than simple hypoxia, and that adding back oxygen to normoxic conditions did not completely alleviate gene expression changes in hypobaric responses.

overall_design: The transcriptional profiles of Arabidopsis growing in atmospheric pressures of 50 kPa or 25 kPa, either with or without supplemental oxygen, were used to evaluate the consequence of removing the hypoxic stress component from the hypobaric environment. The 10 day old plants were transferred to The Low Pressure Growth Chambers (LPGC) (the Controlled Environment Systems Research Facility (CESRF) at University of Guelph, Ontario, Canada) and exposed to the following six treatments for 24 hours: 1) 97 kPa, 2) 50 kPa, 3) 25 kPa, 4) 50 kPa with oxygen supplemented to a partial pressure of 21 kPa (defined as 50kPa/NormOx), 5) 25 kPa with oxygen supplement to a partial pressure of 21 kPa (defined as 25kPa/NormOx) and 6) 97 kPa with reduced oxygen to a partial pressure of 5 kPa (defined as 97kPa/HypOx). At the same time, 5d plants were transferred to LPGCs and exposed to 97 kPa, 50 kPa, and 50 kPa with oxygen supplemented to a partial pressure of 21 kPa (50kPa/NormOx) for 24 hours. The carbon dioxide was held constant at a partial pressure of 0.05 kPa in all treatments. Nitrogen was used as a balance of remaining gas for oxygen treatments. The light, temperature and humidity remained the same as mentioned above. Each atmospheric treatment was replicated in three different chambers, and each chamber held 10 individual plates comprised of 12 plants each. At the completion of each atmospheric treatment, plants were harvested from media surface directly to RNAlater (Ambion). For each treatment, there were three chambers each containing 10 plates of plants in total. Approximately 12 plants from each plate were harvested to a separate tube and were immediately stored as previously described (Paul and Ferl, 2011). One tube was selected from each LPGC replicate, for a total of three tubes per treatment group. The plants were dissected into shoots (entire aerial portion of the plant including hypocotyl) and roots and the total RNA was extracted and subjected to the The Affymetrix GeneChip® Arabidopsis ATH1 Genome Arrays.

first: Mingqi

last: Zhou

first: Jordan

last: Callaham

first: Matthew

last: Reyes

first: Michael

last: Stasiak

first: Alberto

last: Riva

first: Agata

last: Zupanska

first: Mike

last: Dixon

first: Anna-Lisa

last: Paul


title: The histone H3 variant H3.3 regulates gene body DNA methylation in Arabidopsis thaliana

status: Public on Apr 25 2017

city: Singapore

first: Heike

last: Wollmann

address: 61 Biopolis Drive

institute: IMCB

summary: Gene bodies of vertebrates and flowering plants are occupied by histone variant H3.3 and DNA methylation. The origin and significance of these profiles remain largely unknown. The profiles of enrichments in DNA methylation and H3.3 over gene bodies are correlated and both depend similarly on gene transcription levels. This suggests a mechanistic link between H3.3 and gene body methylation. We engineered H3.3 knockdown in Arabidopsis and observed transcription reduction that predominantly affected genes responsive to environmental cues. When H3.3 levels were reduced, gene bodies showed a loss of DNA methylation correlated with transcription levels. To study the origin of changes in DNA methylation profiles when H3.3 levels are reduced, we examined genome-wide distributions of several histone H3 marks, H2A.Z, linker histone H1 and nucleosome densities. We observed that in absence of H3.3, H1 distribution increased in gene bodies. This depends on levels of gene transcription. We propose that H3.3 prevents recruitment of H1, which in turn promotes chromatin folding and antagonizes access to DNA methyltransferases responsible for gene body methylation. Thus, gene body methylation is likely shaped by H3.3 dynamics in relation with transcriptional activity.

overall_design: Examination of transcription in WT and H3.3 knockdown samples by microarray.

first: Hume

last: Stroud

first: Ramesh

last: Yelagandula


title: Transcriptome analysis of mycobacteria in sputum samples of pulmonary tuberculosis patients

status: Public on Apr 18 2017

city: Chandigarh

first: Indu

last: Verma

state: Outside U.S. & Canada

address: Dept. of Biochemistry, PGIMER

department: Biochemistry

institute: Post Graduate Institute of Medical Education and Research (PGIMER)

summary: Sputum expectorated by the pulmonary tuberculosis patients still remains a primary diagnostic specimen. The expression pattern of mycobacteria  in sputum will lead to an insight of bacterial adaptation at the most highly transmissible stage of infection and can also help in identifying newer diagnostic as well as drug targets. Further, the identification of crossreactive gene targets from the sputum samples of  other lung diseases will help to find the diagnostic candidates which will be highly specific to pulmonary tuberculosis.

sample_organism:
Mycobacterium tuberculosis
uncultured bacterium

overall_design: We compared  the global gene expression of mycobacteria in sputum of pulmonary TB patients in comparison to M. tb grown to log phase in Middlebrook 7H9 media.  Further, the global gene expression of sputum  from lung cancer patients was also compared to M. tb grown to log phase in Middlebrook 7H9 media for identifying crossreactive gene targets which could be eliminated from the list of  diagnostic candidates for PTB diagnosis

first: Sumedha

last: Sharma

first: Michelle

last: Ryndak

first: Ashutosh

middle: N

last: Aggarwal

first: Rakesh

last: Yadav

first: Sunil

last: Sethi

first: Shet

last: Masih

first: Suman

last: Laal


title: Dissecting Low Atmospheric Pressure Stress: Transcriptome Responses to the Components of Hypobaria in Arabidopsis [Experiment 1]

first: Robert

last: Ferl

first: Mingqi

last: Zhou

first: Jordan

last: Callaham

first: Matthew

last: Reyes


title: Coordinated Regulations of mRNA Synthesis and Decay during Cold Acclimation in Arabidopsis Cells.

status: Public on May 02 2017

city: Thuwal

first: Katsuhiko

last: Mineta

address: 4700 KAUST

country: Saudi Arabia

institute: King Abdullah University of Science and Technology

summary: Plants possess a cold acclimation system to acquire freezing tolerance through pre-exposure to non-freezing low temperatures. The transcriptional cascade of C-repeat binding factors (CBFs)/dehydration response element-binding factors (DREBs) is considered a major transcriptional regulatory pathway during cold acclimation. However, little is known regarding the functional significance of mRNA stability regulation in the response of gene expression to cold stress. The actual level of individual mRNAs is determined by a balance between mRNA synthesis and degradation. Therefore, it is important to assess the regulatory steps to increase our understanding of gene regulation. Here, we analyzed temporal changes in mRNA amounts and half-lives in response to cold stress in Arabidopsis cell cultures based on genome-wide analysis. In this mRNA decay array method, mRNA half-life measurements and microarray analyses were combined. In addition, temporal changes in the integrated value of transcription rates were estimated from the above two parameters using a mathematical approach. Our results showed that several cold-responsive genes, including Cold-regulated 15a, were relatively destabilized, whereas the mRNA amounts were increased during cold treatment by accelerating the transcription rate to overcome the destabilization. Considering the kinetics of mRNA synthesis and degradation, this apparently contradictory result supports that mRNA destabilization is advantageous for the swift increase in CBF-responsive genes in response to cold stress.

overall_design: To understand temporal changes in mRNA amount and stability in response to cold stress, we performed mRNA decay array using Arabidopsis T87 cells under the control condition (22°C) and 6 h, 12 h, 24 h, and 36 h after the start of cold treatment at 4°C. Cells were collected prior to the cordycepin treatment (0 h) and 0.5, 2, 4 h after cordycepin addition in the control cells. Incubation time after cordycepin addition was 4, 8 and 12 h in the cold treated cell.

first: Toshihiro

last: Arae

first: Shiori

last: Isai

first: Akira

last: Sakai

first: Masami

middle: Y

last: Hirai

first: Yuya

last: Suzuki

first: Shigehiko

last: Kanaya

first: Junji

last: Yamaguchi

first: Satoshi

last: Naito

first: Yukako

last: Chiba


title: Decreased DEPTOR expression is involved in enhanced cell motility and invasion capability of ASS1 (Argininosuccinate synthetase 1) -KO cells

status: Public on Apr 02 2017

city: Suita

first: Daisuke

last: Okuzaki

state: Osaka

address: Yamadaoka 3-1

department: Immunology Frontier Research Center

institute: Osaka univ.

summary: To elucidate the mechanisms underlying the enhanced sensitivity to arginine in the absence of ASS1 expression in endometrial cancer cells, we performed DNA microarray-based gene expression profiling using HEC1B harboring the empty vector (EV) and ASS1-knockout (KO) HEC1B cells. Since accumulating evidence has shown that arginine regulates mTORC1 activity, we focused on the expression patterns of genes related to the mTOR complex. ASS1-KO HEC1B cells had lower DEPTOR transcript abundance than EV cells, while no significant difference was observed in the expression levels of genes coding for other mTOR complex components such as mTOR, RAPTOR, or RICTOR. Indeed, immunoblot analysis confirmed that the expression level of DEPTOR protein was significantly decreased in ASS1-KO HEC1B cells, which were cultured in arginine-replete conditions.

overall_design: The labeled cRNAs were hybridized on a Whole Human Genome Oligo Microarray ver. 2 (G4845A) in two dye swap experiments, resulting in four individual microarrays.

first: Kenji

last: Ohshima

first: Eiichi

last: Morii


title: The B-cell receptor confers super competitor status to lymphoma cells via GSK3β inhibition II

status: Public on Apr 11 2017

city: Milan

first: Federica

last: Zanardi

address: via Adamello 16

country: Italy

institute: IFOM, the FIRC Institute of Molecular Oncology

summary:
Similar to resting mature B cells, where the B-cell antigen receptor (BCR) is essential for cellular survival, surface BCR expression is conserved in most mature B cell lymphomas. The identification of activating BCR mutations and the growth disadvantage upon BCR knockdown of cells of certain lymphoma entities has led to the view that BCR signaling is required for tumour cell survival. Consequently, the BCR signaling machinery has become a new target in the therapy of B cell malignancies. Here, we studied the effects of BCR ablation on MYC-driven mouse B cell lymphomas and compared them to observations in human Burkitt lymphoma. Whereas BCR ablation did not, per se, significantly affect lymphoma growth, BCR-negative (BCR-) tumour cells rapidly disappeared in the presence of their BCR-expressing (BCR+) counterparts in vitro and in vivo. This required neither cellular contact, nor factors released by BCR+ tumour cells. Instead, BCR loss induced the rewiring of central carbon metabolism increasing the sensitivity of receptor-less lymphoma cells to nutrient restriction. The BCR attenuated GSK3β activity to support MYC-controlled gene expression. BCR- tumour cells exhibited increased GSK3β activity and were rescued from their competitive growth disadvantage by GSK3β. BCR-negative lymphoma variants that restored competitive fitness, normalized GSK3β following constitutive activation of the MAPK pathway, commonly through Ras mutations. Similarly, in Burkitt lymphoma, activating RAS mutations may propagate Ig-crippled tumour cells, which usually represent a minority of the tumour bulk. Thus, while BCR expression enhances lymphoma cell fitness, BCR-targeted therapies may profit from combinations with drugs targeting BCR-less tumour cells.
In this dataset, we included the expression data obtained from BCR-positive (BCR+), BCR-negative (BCR-) and BCR-independent lymphoma cells co-cultured for four days in presence or absence of GSK3b inhibitor, CHIR99021. This data was used to a) identify genes regulated by the BCR through  GSK3b inhibition, and b) identify genes that confers BCR-independency to lymphoma variants resistant to BCR loss.

overall_design: BCR-positive lymphoma cells (BCR.POS) were co-culture with either BCR-negative lymphomas (BCR.NEG) or BCR-independent lymphoma variants (BCR.NEG. cl.x indep.) for four days in presence or absence of CHIR99021 (CT). BCR-positive and BCR-negative cells were sorted when counterselection of the latter population was observed (4 days). BCR-independent clones were not counterselected at the same time point. Total RNA was extracted and gene expression profiling was performed on Affymetrix Mouse Gene 1.1 ST Arrays

first: Gabriele

last: Varano

first: Simon

last: Raffel

first: Martina

last: Sormani

first: Silvia

last: Lonardi

first: Christin

last: Zasada

first: Laura

last: Perucho

first: Valentina

last: Petrocelli

first: Andrea

last: Haake

first: Albert

last: Lee

first: M

last: Bugatti

first: Ulrike

last: Paul

first: Eelco

last: Van Anken

last: Pasqualucci

first: Raul

last: Rabadan

first: Reiner

last: Siebert

first: Stefan

last: Kempa

first: Maurilio

last: Ponzoni

first: Fabio

last: Facchetti

first: Klaus

last: Rajewsky

first: Stefano

last: Casola


title: The B-cell receptor confers super competitor status to lymphoma cells via GSK3β inhibition

first: Federica

last: Zanardi


title: Acute (2 hr) response to rxLeptin injection in preoptic area/hypothalamus/pituitary of early prometamorphic (NF stage 54) Xenopus laevis tadpoles

status: Public on Mar 31 2017

city: Ann Arbor

first: Robert

last: Denver

state: Michigan

address: 1105 North University Ave

department: MCDB

institute: University of Michigan

summary:
Leptin binding to the leptin receptor (LepR) causes rapid signaling to the nucleus. We investigated the early (2 hr) transcriptional response to acute leptin injection (intracerebroventricular)
in the preoptic area/hypothalamus/pituitary of Xenopus tadpoles.

overall_design: Tadpoles were given i.c.v. injections of 0.6% saline or recombinant X. laevis leptin (rxLeptin; 20 ng/g BW) and 2 hrs later killed and the preoptic area/hypothalamus/pituitary dissected.

first: Melissa

last: Bender


title: Methylome analysis of root-to-shoot transdifferentiation [58h]

status: Public on Mar 27 2017

city: Lyon

first: François

last: ROUDIER

address: 46 Allée d'Italie

department: Biologie

institute: Ecole Normale Supérieure de Lyon

type: Methylation profiling by genome tiling array

summary: DNA methylation profiling during root-to-shoot transdifferentiation

overall_design:
2 biological replicates in dye-swap - MeDIP-chip
58h treatment with 2iP

first: Francois

last: Roudier

first: Erwann

last: Caillieux

first: Vincent

last: Colot


title: Methylome analysis of root-to-shoot transdifferentiation [6h]

overall_design:
2 biological replicates in dye-swap - MeDIP-chip
6h treatment with 2iP


title: Methylome analysis of root-to-shoot transdifferentiation [34h]

overall_design:
2 biological replicates in dye-swap - MeDIP-chip
34h treatment with 2iP


title: High-throughput transcriptomics reveals uniquely affected pathways: AgNPs, PVP-coated AgNPs and Ag NM300K case studies

status: Public on Mar 24 2017

city: Aveiro

first: Susana

middle: Isabel Lopes

last: Gomes

address: Campus Universitário de Santiago, Departement of Biology, University of Aveiro

department: Biology

country: Portugal

institute: CESAM & University of Aveiro

summary:
Understanding the mode of action of nanomaterials (NMs) aids in improving predictions and environmental risk assessment. In the present study, a high-throughput (HTP) microarray was used to study Enchytraeus crypticus gene expression. Four Ag materials (Ag NM300K, PVP-coated AgNPs, AgNPs, and AgNO3) were tested at reproduction effect concentrations, EC20 and EC50, to anchor gene expression responses to higher effect level. The results showed that while PVP-AgNPs and AgNPs had similar responses, Ag NM300K caused effects via a differentiated transcriptomic profile, with uniquely affected processes (e.g. transcytosis). For the AgNPs, the EC50 negatively affected apoptosis, which can lead to accumulation of abnormal cells and cause apical damage (reproduction). Mechanisms which are known to be related to Ag toxicity and which were observed here for the various Ag forms included apoptosis regulation, cell redox homeostasis, impairment of energy production and response to DNA damage. This HTP genomic tool enabled discrimination between Ag materials, which is not possible via standard tests (i.e. survival and reproduction endpoints). Moreover, gene expression analysis provided information regarding the mechanisms of
toxicity of NMs and the pathways uniquely affected by NMs. An adverse outcome pathway (AOP) was drafted for the first time for Ag NMs; this AOP can and should be used as a basis for further research.

overall_design: Gene expression profile of Enchytraeus crypticus was analysed after 3 and 7 days of exposure to the EC20 and EC50 (effect concentrations on reproduction) of three silver nanomaterials (Ag-NPs PVP-Coated, Ag-NPs Non-Coated and Ag NM300K) and silver salt (AgNO3) in LUFA 2.2 soil. Three biological replicates per test treatment and controls (un-spiked LUFA soil for AgNO3, Ag-NPs PVP-Coated and Ag-NPs Non-Coated; and LUFA soil mixed with the NM300K dispersants _tween 20 for the Ag NM300K) were used.

middle: I

first: Carlos

last: Roca

first: Janeck

last: Scott-Fordsmand

first: Mónica

last: Amorim


title: Context-dependent miR-204 and miR-211 affect the biological properties of amelanotic and melanotic melanoma cells [array]

status: Public on Mar 26 2017

city: Pisa

first: Romina

last: D'Aurizio

state: PI

address: via Moruzzi 1

department: IIT

institute: CNR

summary:
Despite increasing amounts of experimental evidence depicting the involvement of non-coding RNAs in cancer, the study of BRAFV600E-regulated genes has thus far focused mainly on protein-coding ones. Here, we identify and study the microRNAs that BRAFV600E regulates through the ERK pathway.
By performing small RNA sequencing on A375 melanoma cells and a vemurafenib- resistant clone that was taken as negative control, we discover miR-204 and miR-211 as the miRNAs most induced by vemurafenib. We also demonstrate that, although belonging to the same family, these two miRNAs have distinctive features. miR-204 is under the control of STAT3 and its expression is induced in amelanotic melanoma cells, where it acts as an effector of vemurafenib’s anti-motility activity by targeting AP1S2. Conversely, miR-211, a known transcriptional target of MITF, is induced in melanotic melanoma cells, where it targets EDEM1 and consequently impairs the degradation of TYROSINASE (TYR) through the ER-associated degradation (ERAD) pathway. In doing so, miR-211 serves as an effector of vemurafenib’s pro-pigmentation activity. We also show that such an increase in pigmentation in turn represents an adaptive response that needs to be overcome using appropriate inhibitors in order to increase the ef cacy of vemurafenib.
In summary, we unveil the distinct and context-dependent activities exerted by miR-204 family members in melanoma cells. Our work challenges the widely accepted “same miRNA family = same function” rule and provides a rationale for a novel treatment strategy for melanotic melanomas that is based on the combination of ERK pathway inhibitors with pigmentation inhibitors.

overall_design: The expression levels of transcripts in 501 Mel cells transiently transfected with the control siRNA (si-CT), 211-mimic or 204-mimic for 24h were measured with the Illumina HT12_V4 array. Two independent replicates were analyzed for each condition.

first: Marianna

last: Vitiello

first: Andrea

last: Tuccoli

first: Laura

last: Poliseno


title: Comprehensive performance comparison of high-resolution array platforms for genome-wide Copy Number Variation (CNV) analysis in humans [Agilent022060]

status: Public on Mar 23 2017

city: St. Augustine

first: Rajini

last: Haraksingh

address: The University of the West Indies

department: Life Sciences

country: Trinidad and Tobago

institute: The University of the West Indies

summary:
Background: High-resolution microarray technology is routinely used in basic research and clinical practice to efficiently detect copy number variants (CNVs) across the entire human genome. A new generation of arrays combining high probe densities with optimized designs will comprise essential tools for genome analysis in the coming years. We systematically compared the genome-wide CNV detection power of all 17 available array designs from the Affymetrix, Agilent, and Illumina platforms by hybridizing the well-characterized genome of 1000 Genomes Project subject NA12878 to all arrays, and performing data analysis using both manufacturer-recommended and platform-independent software. We benchmarked the resulting CNV call sets from each array using a gold standard set of CNVs for this genome derived from 1000 Genomes Project whole genome sequencing data. Results: The arrays tested comprise both SNP and aCGH platforms with varying designs and contain between ~0.5 to ~4.6 million probes.  Across the arrays CNV detection varied widely in number of CNV calls (4 - 489), CNV size range (~40 bp to ~8 Mbp), and percentage of non-validated CNVs (0 - 86 %). We discovered strikingly strong effects of specific array design principles on performance. For example, some SNP array designs with the largest numbers of probes and extensive exonic coverage produced a considerable number of CNV calls that could not be validated, compared to designs with probe numbers that are sometimes an order of magnitude smaller. This effect was only partially ameliorated using different analysis software and optimizing data analysis parameters. Conclusions: High-resolution microarrays will continue to be used as reliable, cost- and time-efficient tools for CNV analysis. However, different applications tolerate different limitations in CNV detection. Our study quantified how these arrays differ in total number and size range of detected CNVs as well as sensitivity, and determined how each array balances these attributes. This analysis will inform appropriate array selection for future CNV studies, and allow better assessment of the CNV-analytical power of both published and ongoing array-based genomics studies. Furthermore, our findings emphasize the importance of concurrent use of multiple analysis algorithms and independent experimental validation in array-based CNV detection studies.
array Comparative Genome Hybridization of NA12878 versus NA10851 on Agilent platform

overall_design: We systematically compared the genome-wide CNV detection power of all 17 available array designs from the Affymetrix, Agilent, and Illumina platforms by hybridizing the well-characterized genome of 1000 Genomes Project subject NA12878 to all arrays in two technical replicates, and performing data analysis using both manufacturer-recommended and platform-independent software. We benchmarked the resulting CNV call sets from each array using a gold standard set of CNVs for this genome derived from 1000 Genomes Project whole genome sequencing data.


title: Comprehensive performance comparison of high-resolution array platforms for genome-wide Copy Number Variation (CNV) analysis in humans [Agilent023642]


title: ALK-TPM3 rearrangement in adult renal cell carcinoma: report of a novel case showing misleading TFE3 expression and loss of chromosome 3 and literature review

city: NICE

first: Thibault

last: FABAS

address: 28 av Valombrose

institute: CHU Nice

summary: We report a case of a 55 years old women who present a ALK associated renal cell carcinoma, with 3p deletion and measling of TFE3 expression. With CGH analysis and FISH we identify the rearrangment of ALK with TPM3

overall_design: 1 case

first: Y

last: Bodokh

first: F

last: Pedeutour


title: Comprehensive performance comparison of high-resolution array platforms for genome-wide Copy Number Variation (CNV) analysis in humans [Agilent021365]


title: Comprehensive performance comparison of high-resolution array platforms for genome-wide Copy Number Variation (CNV) analysis in humans [Agilent021850]


title: Comprehensive performance comparison of high-resolution array platforms for genome-wide Copy Number Variation (CNV) analysis in humans [Agilent021529]


title: Comprehensive performance comparison of high-resolution array platforms for genome-wide Copy Number Variation (CNV) analysis in humans [IlluminaHumanOmni5]

summary: Background High-resolution microarray technology is routinely used in basic research and clinical practice to efficiently detect copy number variants (CNVs) across the entire human genome. A new generation of arrays combining high probe densities with optimized designs will comprise essential tools for genome analysis in the coming years. We systematically compared the genome-wide CNV detection power of all 17 available array designs from the Affymetrix, Agilent, and Illumina platforms by hybridizing the well-characterized genome of 1000 Genomes Project subject NA12878 to all arrays, and performing data analysis using both manufacturer-recommended and platform-independent software. We benchmarked the resulting CNV call sets from each array using a gold standard set of CNVs for this genome derived from 1000 Genomes Project whole genome sequencing data. Results The arrays tested comprise both SNP and aCGH platforms with varying designs and contain between ~0.5 to ~4.6 million probes.  Across the arrays CNV detection varied widely in number of CNV calls (4 - 489), CNV size range (~40 bp to ~8 Mbp), and percentage of non-validated CNVs (0 - 86 %). We discovered strikingly strong effects of specific array design principles on performance. For example, some SNP array designs with the largest numbers of probes and extensive exonic coverage produced a considerable number of CNV calls that could not be validated, compared to designs with probe numbers that are sometimes an order of magnitude smaller. This effect was only partially ameliorated using different analysis software and optimizing data analysis parameters. Conclusions High-resolution microarrays will continue to be used as reliable, cost- and time-efficient tools for CNV analysis. However, different applications tolerate different limitations in CNV detection. Our study quantified how these arrays differ in total number and size range of detected CNVs as well as sensitivity, and determined how each array balances these attributes. This analysis will inform appropriate array selection for future CNV studies, and allow better assessment of the CNV-analytical power of both published and ongoing array-based genomics studies. Furthermore, our findings emphasize the importance of concurrent use of multiple analysis algorithms and independent experimental validation in array-based CNV detection studies.


title: Comprehensive performance comparison of high-resolution array platforms for genome-wide Copy Number Variation (CNV) analysis in humans [IlluminaHumanOmni5Exome]


title: Methylome analysis of root-to-shoot transdifferentiation [0h]

overall_design:
2 biological replicates in dye-swap - MeDIP-chip
0h treatment with 2iP


title: Small chromosomal regions position themselves autonomously according to their chromatin class

status: Public on Mar 22 2017

city: Amsterdam

first: Bas

last: van Steensel

address: Plesmanlaan 121

department: division of Molecular Biology

institute: Netherlands Cancer Institute

type: Genome binding/occupancy profiling by genome tiling array

summary: The spatial arrangement of chromatin is linked to the regulation of nuclear processes. One striking aspect of nuclear organization is the spatial segregation of heterochromatin and euchromatin domains. The mechanisms of this chromatin segregation are still poorly understood. In this work we investigated the link between the primary genomic sequence and chromatin domains. We analyzed the spatial intranuclear arrangement of a human artificial chromosome (HAC) in a xenospecific mouse background and compared it to an orthologous region in the context of its native mouse chromosome. The two orthologous regions include segments that can be assigned to three major chromatin classes according to their gene abundance and repeat repertoire: (i) gene-rich and SINE-rich euchromatin, (ii) gene-poor and LINE/LTR-rich heterochromatin and (iii) gene-depleted and satellite DNA-containing constitutive heterochromatin. We show using FISH and 4C-seq technologies that chromatin segments ranging from 0.6 to 3 Mb cluster with segments of the same chromatin class. As a consequence, the chromatin segments acquire corresponding positions in the nucleus irrespectively of their chromosomal context, thus rendering this a chromosome segment autonomous property. Interactions with the nuclear lamina are also partially retained in the HAC but demonstrate less autonomy. Taken together, our results show that genomic segments autonomously fold and position themselves relative to other genomic parts, suggesting that the three major classes of chromatin constitute a blueprint for the overall nuclear architecture.

platform_organism:
Homo sapiens
Mus musculus

overall_design: DamID for LaminB1 was performed in primary mouse fibroblast cells containing a human artificial chromosome. Samples were hybridized on human and mouse microarrays, using 2 biological replicates, that were hybridized in a dye-swap design.

first: Ludo

last: Pagie

first: Wouter

last: Meuleman

first: Dominika

last: Bijos


title: Comprehensive performance comparison of high-resolution array platforms for genome-wide Copy Number Variation (CNV) analysis in humans [IlluminaHumanOmni2.5]

status: Public on Mar 21 2017


title: Methylome analysis of root-to-shoot transdifferentiation

first: François

last: ROUDIER

overall_design: Refer to individual Series


title: Comprehensive performance comparison of high-resolution array platforms for genome-wide Copy Number Variation (CNV) analysis in humans [IlluminaHumanOmni2.5Exome]


title: Comprehensive performance comparison of high-resolution array platforms for genome-wide Copy Number Variation (CNV) analysis in humans [IlluminaHumanCoreExome]

summary: Background: High-resolution microarray technology is routinely used in basic research and clinical practice to efficiently detect copy number variants (CNVs) across the entire human genome. A new generation of arrays combining high probe densities with optimized designs will comprise essential tools for genome analysis in the coming years. We systematically compared the genome-wide CNV detection power of all 17 available array designs from the Affymetrix, Agilent, and Illumina platforms by hybridizing the well-characterized genome of 1000 Genomes Project subject NA12878 to all arrays, and performing data analysis using both manufacturer-recommended and platform-independent software. We benchmarked the resulting CNV call sets from each array using a gold standard set of CNVs for this genome derived from 1000 Genomes Project whole genome sequencing data. Results: The arrays tested comprise both SNP and aCGH platforms with varying designs and contain between ~0.5 to ~4.6 million probes.  Across the arrays CNV detection varied widely in number of CNV calls (4 - 489), CNV size range (~40 bp to ~8 Mbp), and percentage of non-validated CNVs (0 - 86 %). We discovered strikingly strong effects of specific array design principles on performance. For example, some SNP array designs with the largest numbers of probes and extensive exonic coverage produced a considerable number of CNV calls that could not be validated, compared to designs with probe numbers that are sometimes an order of magnitude smaller. This effect was only partially ameliorated using different analysis software and optimizing data analysis parameters. Conclusions: High-resolution microarrays will continue to be used as reliable, cost- and time-efficient tools for CNV analysis. However, different applications tolerate different limitations in CNV detection. Our study quantified how these arrays differ in total number and size range of detected CNVs as well as sensitivity, and determined how each array balances these attributes. This analysis will inform appropriate array selection for future CNV studies, and allow better assessment of the CNV-analytical power of both published and ongoing array-based genomics studies. Furthermore, our findings emphasize the importance of concurrent use of multiple analysis algorithms and independent experimental validation in array-based CNV detection studies.


title: A Randomized Clinical Trial to Study the Effects of Single Doses of Corticosteroid on Response to Nasal Allergen Challenge in Patients

city: Boston

first: Vladislav

last: Malkov

state: MA

address: 33 Avenue Loius Pasteur

department: Human Genetics and Pharmacogenomics

institute: Merck Sharp & Dohme Corp

summary: We profiled genome-wide gene expression in nasal scrapes following grass pollen challenge and Prednisone treatment. It was a randomized, double-blind, placebo-controlled, three-period, cross-over trial to evaluate the effects of single oral doses of 10 mg and 25 mg of prednisone on inflammatory mediators measured in nasal exudates after nasal allergen challenge in susceptible individuals with allergic rhinitis. It examined the ability to quantify responses to allergen challenge and resolve dose responsive treatment effects of prednisone.

overall_design: This was a randomized, double-blind, placebo-controlled, three treatment period crossover study in 19 healthy patients with allergic rhinitis and allergy to grass pollen. Allergen was rapidly delivered using a nasal mist delivery system. Period 0 was a baseline in the absence of allergen challenge.


title: Comprehensive performance comparison of high-resolution array platforms for genome-wide Copy Number Variation (CNV) analysis in humans [IlluminaHumanOmniExpressExome]

status: Public on Mar 20 2017


title: Acute toxicity, bioaccumulation and effects of dietary transfer of silver from brine shrimps exposed to PVP/PEI-coated silver nanoparticles to zebrafish

city: Leioa

first: José María

last: Lacave

state: Bizkaia

address: Sarriena s/n

department: Zoology and Animal Cell Biology

institute: University of the Basque Country

summary: Silver nanoparticles (NPs) are extensively used due to their antimicrobial activity and, therefore, their input into the ecosystem will increase. Silver can be bioaccumulated by low trophic level organisms and, then, incorporated into the food chain, reaching high level predators. The objectives of this study were to test the acute toxicity of N-vynil-2-pirrolidone/polyethylenimine (PVP-PEI) coated Ag NPs of 5 nm to brine shrimp (Artemia sp) larvae and to assess bioaccumulation and effects of silver transferred by the diet. For the later, brine shrimps were exposed to two different concentrations of Ag NPs, 100 ng/L as an environmentally relevant concentration and 100 µg/L as a likely effective concentration, in parallel with an unexposed control group and, then, used to feed zebrafish during 21 days in order to simulate two trophic levels of a simplified food web. For brine shrimp larvae, EC50 values ranged from 7.39 mg Ag/L (48 h post hatch larvae (hph) exposed for 48 h) to 19.63 mg Ag/L (24 hph larvae exposed for 24 h. Silver accumulation was measured in brine shrimps exposed to 0.1 and 1 mg/L of Ag NPs for 24 h. In zebrafish fed with brine shrimps exposed to Ag NPs, intestine showed higher metal accumulation than liver, although both organs presented the same pattern of dose and time-dependent metal accumulation as revealed by autometallography. Feeding of zebrafish for 3 days with brine shrimps exposed to 100 ng/L of Ag NPs was enough to impair fish health as reflected by the significant reduction of the lysosomal membrane stability and the presence of several histopathological conditions in the liver. Overall, results showed that Ag NPs were able to exert toxic effects on zebrafish through dietary exposure, even at an environmentally relevant concentration, which should act as concern of the need of studies in further detail about real impact of nanomaterials in the environment.

overall_design: 20 samples per group, 5 replicates (4 liver or 4 intestine per replicate), 2 groups x 2 times, control and C1 (0.1 mg/L) of Ag NPs, 3 and 21 days of exposure

first: Jose

middle: M

first: Alvaro

last: Fanjul

first: Eider

last: Bilbao

first: Nerea

last: Gutierrez

first: Irantzu

last: Barrio

first: Inmaculada

last: Arostegui

first: Miren

last: Cajaraville

first: Amaia

last: Orbea


title: Comprehensive performance comparison of high-resolution array platforms for genome-wide Copy Number Variation (CNV) analysis in humans [IlluminaHumanOmniExpress]

first: Rajini

last: Haraksingh


title: Copy number profiling of 5-FU resistant gastric cancer cell line compared to the parental cell line

status: Public on Jun 09 2017

city: Tokyo

first: Takashi

last: Kobunai

address: 1-2-4, Uchikanda, Chiyoda-ku

institute: Taiho Pharmaceutical Co., Ltd.

summary: Copy number profiling of MKN45T 5-FU resistant gastric cancer cell lines and its parental cell line MKN45. We hypothesized that a detailed fine-scale survey of genomic CNAs might reveal the mechanism for acquired resistant to 5-FU in gastric cancer.

overall_design: Genomic DNA (1ug) was extracted from MKN45 and MKN45T cells using a Qiagen Qiamp DNA micro kit. The extracted DNA from MKN45 was labeled using an Agilent Genomic DNA Enzymatic Labeling Kit (Cy3-dUTP), while those DNA from MKN45T was labeled with Cy5-dUTP. The labeled DNA was hybridized to the Agilent Human Genome CGH Microarray Kit 244K and processed according to the manufacturer's protocol. Fluorescent array images were acquired with an Agilent DNA microarray scanner (Agilent Technologies). The log2 ratios were corrected for the GC content wave effect using 1 Mb windows for genome GC content. Outliers were smoothed and the normalized log2 ratios were segmented using circular binary segmentation analysis.

first: Ayako

last: Nakamura

first: Teiji

last: Takechi


title: Gene expression profiling of retrograde PAP-signaling and ABA-signaling mutants in response to ABA treatment

city: Brisbane

first: Peter

middle: A

last: Crisp

state: QLD

address: John Hines Building (62), The University of Queensland

department: School of Agriculture and Food Science

institute: The University of Queensland

summary: Chloroplast-nuclear retrograde signaling is viewed as a mechanism for inter-organelle communication. Here we show the SAL1-PAP (3′-phosphoadenosine 5′- phosphate) retrograde pathway functions more broadly in guard cells, interacting with abscisic acid (ABA) signaling at least in part via exoribonucleases. Unexpectedly, PAP bypasses the canonical signaling components ABA Insensitive 1 (ABI1) and Open Stomata 1 (OST1) by priming an alternative pathway that restores ABA-responsive gene expression, ROS bursts, ion channel function and stomatal closure in ost1-2. This alternative pathway up-regulates lowly expressed Calcium Dependent Protein Kinases (CDPKs) which have the capacity to activate the key slow anion channel SLAC1 in response to ABA-mediated and ost1-2 independent calcium release. The role of PAP in priming an alternative pathway to bypass components previously considered essential for stomatal closure demonstrates how a chloroplast signal can have broader roles as a secondary messenger to directly intersect with and tune hormone signaling.

overall_design: Gene expression responses in whole Arabidopsis leaves were compared between mock and ABA treated genotypes; Col-0 Ler, alx8, ost1-2 and alx8 ost1-2; in triplicate.

first: Gonzalo

last: Estavillo

first: Barry

middle: J

last: Pogson


title: Human ECFCs: Cord Blood vs Peripehral Blood ECFCs

city: Oxford

first: Cheen

last: Khoo

address: John Radcliffe Hospital Oxford

institute: NHSBT

summary:
miRNA profiling was carried out using the miRCURY LNA™ microRNA Array (5th gen - hsa, mmu & rno). microRNA profiling of CB and PB-derived ECFCs from 3 independent donors from each cell source.
To identify and understand the regulation of endothelial cell functions through comparing miRNA expression profiling of cord blood (CB) derived endothelial colony forming cells (ECFCs) and peripheral blood (PB) ECFCs

overall_design: Two condition experiment, CB vs PB-derived ECFCs. 3 independent donors per ECFC source.


title: Comparative gene expression analysis of Porphyromonas gingivalis ATCC 33277 in planktonic and biofilm states

city: Madrid

first: Patricia

last: Romero Lastra

address: Plaza de Ramon y Cajal s/n

institute: Universidad Complutense de Madrid

summary: The aim of the present study was to compare the genome-wide transcription activities of P.gingivalis under both states, as biofilm and as planktonic growth, using microarray technology.

overall_design: P. gingivalis ATCC 33277 was incubated in multiwell culture plates at 37ºC for 96 hours in anaerobic conditions using an in vitro static model to to develop both the planktonic and biofilm states (the latter over sterile ceramic calcium hydroxyapatite discs). After incubation, the bacterial cells were harvested and total RNA was extracted, treated with DNase-I, and purified. Three biological replicates for each cell state were independently hybridized for transcriptomic comparison.

first: P

last: Romero-Lastra

first: M

middle: C

last: Sanchez

first: H

last: Vidal

first: A

last: Llama-Palacios

first: E

last: Figuero

first: D

last: Herrera

last: Sanz


title: Hypercholesterolemia increases the incidence of colorectal cancer by miR-101c-dependent downregulation of Tet1 in Hematopoietic Stem Cells

status: Public on Mar 18 2017

city: WORCESTER

first: Lyne

last: Khair

address: 368 PLANTATION STREET

department: SURGERY

institute: UMASS MEDICAL SCHOOL

summary:
To identify microRNAs which differentially expressed in hematopoietic stem cells from wt mice and ApoE KO mice
We used microRNA microarrays to identify miroRNAs which can directly regulate tet1 expression in hematopoietic stem cells

overall_design: The microRNAs expression in hematopoietic stem cells from wt mice and ApoE KO mice were measured

first: G

last: Tie

first: J

last: Yan

first: L

last: Messina

last: Deng

last: Kang

first: T

last: Fazzio


title: Protein disulfide isomerase inhibition synergistically enhances the efficacy of sorafenib for hepatocellular carcinoma [SNU761]

status: Public on Mar 19 2017

city: Seoul

first: Jae-Kyung

last: Won

address: 101 Daehak-ro

institute: Seoul National University Hospital

summary: Sorafenib is the only approved targeted drug for hepatocellular carcinoma (HCC), but its effect on patients’ survival gain is limited and varies over a wide range depending on patho-genetic conditions. Thus, enhancing the efficacy of sorafenib and finding a reliable predictive biomarker are crucuial to achieve efficient control of HCCs. In this study, we employed a systems approach by combining transcriptome analysis of the mRNA changes in HCC cell lines in response to sorafenib with network analysis to investigate the action and resistance mechanism of sorafenib. Gene ontology and gene set analysis revealed that proteotoxic stress and apoptosis modules are activated in the presence of sorafenib. Further analysis of the endoplasmic reticulum (ER) stress network model combined with in vitro experiments showed that introducing an additional stress by treating the orally active protein disulfide isomerase (PDI) inhibitor (PACMA 31) can synergistically increase the efficacy of sorafenib in vitro and in vivo, which was confirmed using a mouse xenograft model. We also found that HCC patients with high PDI expression show resistance to sorafenib and poor clinical outcomes, compared to the low PDI expression group. These results suggest that PDI is a promising therapeutic target for enhancing the efficacy of sorafenib and can also be a biomarker for predicting sorafenib responsiveness.

overall_design: Total RNA was extracted from cultured cells and subjected to RT-PCR analysis. HCC cell lines (SNU761, Huh7, Hep3B and HepG2) were treated with sorafenib 3 mM for 24 hours, while the control group was treated with only DMSO.

first: Su

last: Yu

first: Chae

last: Hwang

first: Jung-Hwan

last: Yoon

first: Kwang-Hyun

last: Cho


title: Comprehensive performance comparison of high-resolution array platforms for genome-wide Copy Number Variation (CNV) analysis in humans [IlluminaCytoSNP850K]

status: Public on Mar 17 2017

first: Rajini

last: Haraksingh


title: Saccharomyces cerevisiae deletion and DAmP collections chemogenomic screen with Selenomethionine

city: Paris

first: Cosmin

last: Saveanu

address: 25-28 rue du docteur Roux

department: Genomes and Genetics

institute: Institut Pasteur

summary: Growth assay in the presence of Selenomethionine that uses the barcoded collections of yeast gene modification (deletion or DamP) to identify strains that are hypersensitive to the presence of the aminoacid.

overall_design: Two-condition experiment – growth of a pool of strains in the presence or absence of Selenomethionine. Two or three independent biological replicates for each condition

first: Pierre

last: Plateau

first: Myriam

last: Lazard


title: Gene expression from embryoid bodies derived from HBG3 HB9 ES cells exposed to serum from a murine Huntington's disease model

city: Seattle

first: G. Adam

last: Whitney

state: WA

address: 401 Terry Ave.

department: Bioinformatics

institute: PreCyte

summary: We have established proof of principle for the Indicator Cell Assay Platformé (iCAPé), a broadly applicable tool for blood-based diagnostics that uses specifically-selected, standardized cells as biosensors, relying on their innate ability to integrate and respond to diverse signals present in patients' blood. To develop an assay, indicator cells are exposed in vitro to serum from case or control subjects and their global differential response patterns are used to train reliable, cost-effective disease classifiers based on a small number of features. In a feasibility study, the iCAP detected pre-symptomatic disease in a murine model of amyotrophic lateral sclerosis (ALS) with 94% accuracy (p-Value=3.81E-6) and correctly identified samples from a murine Huntington's disease model as non-carriers of ALS. In a preliminary human disease assay, the iCAP detected early stage Alzheimer's disease with 72% cross-validated accuracy (p-Value=3.10E-3). For both assays, iCAP features were enriched for disease-related genes, supporting the assay's relevance for disease research.

overall_design: Embryoid body derived motor neurons from HBG3 HB9 ES cells.

first: Jennifer

last: Smith

first: John

last: Aitchison

first: Leslie

last: Miller

first: Samuel

last: Danziger

first: Karanbir

last: Singh

first: Elaine

last: Peskind

first: Ge

last: Li

first: Robert

last: Lipshutz


title: Gene expression from embryoid bodies derived from HBG3 HB9 ES cells exposed to serum from mice carrying an ALS causing mutation, or non-carrier littermates.

summary: We have established proof of principle for the Indicator Cell Assay PlatformÈ (iCAPÈ), a broadly applicable tool for blood-based diagnostics that uses specifically-selected, standardized cells as biosensors, relying on their innate ability to integrate and respond to diverse signals present in patientsê blood. To develop an assay, indicator cells are exposed in vitro to serum from case or control subjects and their global differential response patterns are used to train reliable, cost-effective disease classifiers based on a small number of features. In a feasibility study, the iCAP detected pre-symptomatic disease in a murine model of amyotrophic lateral sclerosis (ALS) with 94% accuracy (p-Value=3.81E-6) and correctly identified samples from a murine Huntingtonês disease model as non-carriers of ALS. In a preliminary human disease assay, the iCAP detected early stage Alzheimerês disease with 72% cross-validated accuracy (p-Value=3.10E-3). For both assays, iCAP features were enriched for disease-related genes, supporting the assayês relevance for disease research.

overall_design: Embryoid bodies derived from HBG3 HB9 ES cells. 29 arrays are from sod1 hemizygous exposure, and 30 from non-carrier exposure.

first: G


title: WT and ENT3 KO MTA_2.0 Array

status: Public on Mar 14 2017

city: Columbus

first: Bhawana

last: Dikshit

state: OH

address: 500 W 12th Avenue

institute: Ohio State University

summary:
Gene expression analysis of liver from 6 Wildtype and 6 ENT3 knockout liver samples
We utilised microarrays to understand the global gene expression in Wildtype and ENT3 knockout mice liver

overall_design: We utilised age and gender matched mice (6 per group) for harvesting liver. Liver samples were utilised for RNA extraction and hybridization on Affymetrix microarrays


title: Gene expression from embryoid bodies derived from HBG3 HB9 ES cells

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

sample_organism:
Homo sapiens
Mus musculus


title: Time series micro RNA analysis of immature T-cells and reMAIT cells by microarrays

city: Koto-ku

first: Toutai

last: MITUYAMA

state: Tokyo

department: Artificial Intelligence Research Team

institute: National Institute of Advanced Industrial Science and Technology (AIST)

summary:
To explore the molecular mechanisms underlying selective differentiation of MAIT-derived iPSCs into reMAITs, we conducted micro RNAs profiling based on microarrays. We sampled reMAITs during the time course of differentiation from iPSCs as well as mature MAITs isolated from cord blood (CB MAITs). As control, we used immature T cells differentiated from hematopoietic stem cells (HSCs). For each of reMAITs and the immature T cells, we selected four time points: Start, Early, Middle, and Late.
MAITs isolated from CB were reprogrammed to iPSCs (PMID:23523177). The MAIT-derived iPSCs were cultured on OP9, and CD34+ CD43+ cells were isolated. These CD34+ CD43+ precursor cells were furthered cultured on OP9/DL1 for re-differentiation into MAITs. Based on the observation of the reported surface antigen profiles (PMID:23523177), reMAITs were harvested at four different time points: day 0 (Start), day 4 (Early), day 7-10 (Middle), and after day 30 (Late). For the immature T cells, CD34+ cells were isolated from CB using CD34 MicroBead Kit (Miltenyi Biotech). These CD34+ HSCs were cultured on OP9/DL1 for differentiation into T cell lineage as previously described (PMID:15494433). Based on the surface antigen profiles, the immature T cells were harvested at four different time points: CD34+ cells at day 0 (Start), CD4- CD8- double negative cells at day 21 (Early) and day 40 (Midlle), and CD4+ CD8+ double positive cells after day 50 (Late). Total RNA was extracted from each sample using RNeasy Kit (Quiagen). For micro RNA analysis, RNA was labeled with Cy3-pCp by ligation, and subjected to analysis using Human miRNA Microarray Release 19.0 8x60K (Agilent).

overall_design: Yutaka, Saito

first: Chie

last: Sugihara

last: Mituyama

first: Hiroshi

last: Wakao


title: Differential host gene responses from infection with neurovirulent and partially-neurovirulent strains of Venezuelan equine encephalitis virus

city: Bethesda

first: Paridhi

last: Gupta

state: MD

address: 4301 Jones bridge road

institute: USUHS

summary: Kinetics of the differential gene expression between a virulent and a partially-virulent strain of VEEV in mouse brain and spleen was evaluated by using whole genome microarray.

overall_design: Comparison between infection with 2 strains of VEEV at 3 different time points post infection in spleen and brain tissue samples. All infected samples compared with uninfected spleen and brain samples. 3 biological replicates for each condition were used.

first: Anuj

last: Sharma

first: Jing

last: Han

first: Amy

last: Yang

first: Manish

last: Bhomia

first: Barbara

last: Knollmann-Ritschel

first: Raj

last: Puri

first: Radha

last: Maheshwari


title: Functional characterization of a WRKY transcription factor involved in the regulation of vacuolar transport and flavonoid biosynthesis

status: Public on Mar 10 2017

city: VR

first: Alessandra

last: Amato

address: strada le grazie 15

institute: University of Verona

sample_organism:
Petunia x hybrida
Vitis vinifera

platform_organism:
Petunia x hybrida
Vitis vinifera


title: Gene expression from iPS derived neurons exposed to plasma from Alzheimer's (AD), pre-symptomatic AD, or control patients.

first: G. Adam

last: Whitney

summary: We have established proof of principle for the Indicator Cell Assay Platformé (iCAPé), a broadly applicable tool for blood-based diagnostics that uses specifically-selected, standardized cells as biosensors, relying on their innate ability to integrate and respond to diverse signals present in patientsÕ blood. To develop an assay, indicator cells are exposed in vitro to serum from case or control subjects and their global differential response patterns are used to train reliable, cost-effective disease classifiers based on a small number of features. In a feasibility study, the iCAP detected pre-symptomatic disease in a murine model of amyotrophic lateral sclerosis (ALS) with 94% accuracy (p-Value=3.81E-6) and correctly identified samples from a murine HuntingtonÕs disease model as non-carriers of ALS. In a preliminary human disease assay, the iCAP detected early stage AlzheimerÕs disease with 72% cross-validated accuracy (p-Value=3.10E-3). For both assays, iCAP features were enriched for disease-related genes, supporting the assayÕs relevance for disease research.

overall_design: 18 assays from Alzheimer's patients, 20 assays each from pre-symptomatic Alzheimer's and control patients

first: Jennifer

last: Smith

first: John

last: Aitchison

first: Leslie

last: Miller

first: Samuel

last: Danziger

first: Karanbir

last: Singh

first: Elaine

last: Peskind


title: GATA4-dependent organ-specific endothelial differentiation controls liver development and embryonic hematopoiesis (3 of 3)

status: Public on Mar 09 2017

city: Mannheim

first: Carsten

last: Sticht

address: Theodor-Kutzer-Ufer

department: ZMF

institute: University Heidelberg

summary: Microvascular endothelial cells (EC) are increasingly recognized as organ-specific gatekeepers of their microenvironment. Microvascular EC instruct neighboring cells in their organ-specific vascular niches by angiocrine factors that comprise secreted growth factors/angiokines, but also extracellular matrix molecules and transmembrane proteins. The molecular regulators, however, that drive organ-specific microvascular transcriptional programs and thereby regulate angiodiversity, are largely elusive. Opposite to continuous barrier-forming EC, liver sinusoids are a prime model of discontinuous, permeable micro-vessels. Here, we show that transcription factor GATA4 controls liver sinusoidal endothelial (LSEC) specification and function. LSEC-restricted deletion of GATA4 caused transformation of discontinuous liver sinusoids into continuous capillaries. Capillarization was characterized by ectopic basement membrane deposition and formation of an abundantly VE-Cadherin expressing continuous endothelium. Correspondingly, ectopic expression of GATA4 in cultured continuous EC mediated downregulation of continuous EC transcripts and upregulation of LSEC genes. Regarding angiocrine functions, the switch from discontinuous LSEC to continuous EC during embryogenesis caused liver hypoplasia, fibrosis, and impaired colonization by hematopoietic progenitor cells resulting in anemia and embryonic lethality. Thus, GATA4 acts as master regulator of hepatic microvascular specification and acquisition of organ-specific vascular competence indispensable for liver development. The data also establish an essential role of the hepatic microvasculature for embryonic hematopoiesis.

overall_design: bEnd3 cells were transduced with mouse Gata4 or empty vector for RNA extraction and hybridization on Affymetrix microarrays.

first: Cyrill

last: Géraud

first: Philipp-Sebastian

last: Koch

first: Johanna

last: Zierow


title: GATA4-dependent organ-specific endothelial differentiation controls liver development and embryonic hematopoiesis (2 of 3)

overall_design: HUVEC were transduced with human GATA4 or empty vector for RNA extraction and hybridization on Affymetrix microarrays.


title: Octopamine Enhances Oxidative Stress Resistance Through the Fasting-Responsive Transcription Factor DAF-16/FOXO in C. elegans

status: Public on Mar 08 2017

city: Kyoto

first: Masaharu

last: Uno

address: Sakyo-ku

department: Graduate School of Biostudies

institute: Kyoto University

summary:
Dietary restriction regimens lead to enhanced stress resistance and extended lifespan in many species through the regulation of fasting and/or diet responsive mechanisms. The fasting stimulus is perceived by sensory neurons and causes behavioral and metabolic adaptations. Several studies have implicated that the nervous system is involved in the regulation of longevity. However, it remains largely unknown whether the nervous system contributes to the regulation of lifespan and/or stress resistance elicited by fasting. In this study, we first investigated the role of the nervous system in fasting-elicited longevity and stress resistance. We found that lifespan extension in Caenorhabditis elegans caused by an intermittent fasting (IF) regimen was suppressed by functional defects in sensory neurons. The IF-induced longevity was also suppressed in a mutant that lacks the enzyme required for the synthesis of an amine neurotransmitter, octopamine (OA), which acts in the absence of food, i.e., under fasting conditions. Although OA administration did not significantly extend the lifespan, it enhanced organismal resistance to oxidative stress. This enhanced resistance was suppressed by a mutation of the OA receptors, SER-3 and SER-6. Moreover, we found that OA administration promoted the nuclear translocation of DAF-16, the key transcription factor in fasting responses, and that the OA-induced enhancement of stress resistance required DAF-16. Altogether, our results suggest that OA signaling, which is triggered by the absence of food, shifts the organismal state to a more protective one to prepare for environmental stresses.
To investigate the involvement of DAF-16 and octopamine receptors (SER-3 and SER-6) in octopamine-induced genome-wide transcriptome alterations, we conducted transcriptome analysis.

overall_design: Synchronized animals (wild-type N2, daf-16, and ser-3;ser-6) were raised under normal conditions. Then, young adult animals were treated with or without 20 mg/mL octopamine for 2 days. After 2 days OA administration, we collected animals and isolated total RNA. The total RNAs were subjected to microarray analysis.

first: Haruka

last: Hoshikawa

first: Sakiko

last: Honjoh

first: Eisuke

last: Nishida


title: Comprehensive proteomic characterization of stem cell-derived extracellular matrices

status: Public on Mar 07 2017

city: Cambridge

first: Charles

middle: Arthur

last: Whittaker

institute: Koch Institute

summary: In the stem-cell niche, the extracellular matrix (ECM) serves as a structural support that additionally provides stem cells with signals that contribute to the regulation of stem-cell function, via reciprocal interactions between cells and components of the ECM. Recently, cell-derived ECMs have emerged as in vitro cell culture substrates to better recapitulate the native stem-cell microenvironment outside the body. Significant changes in cell number, morphology and function have been observed when mesenchymal stem cells (MSC) were cultured on ECM substrates as compared to standard tissue-culture polystyrene (TCPS). As select ECM components are known to regulate specific stem-cell functions, a robust characterization of cell-derived ECM proteomic composition is critical to better comprehend the role of the ECM in directing cellular processes. Here, we characterized and compared the protein composition of ECM produced in vitro by bone marrow-derived MSC, adipose-derived MSC and neonatal fibroblasts isolated from different donors, employing quantitative proteomic methods. Each cell-derived ECM displayed a specific and unique matrisome signature, yet they all shared a common set of proteins. We evaluated the biological response of cells cultured on the different matrices and compared them to cells on standard TCPS. The matrices lead to differential survival and gene-expression profiles among the cell types and as compared to TCPS, indicating that the cell-derived ECMs influence each cell type in a different manner. This general approach to understanding the protein composition of different tissue-specific and cell-derived ECM will inform the rational design of defined systems and biomaterials that recapitulate critical ECM signals for stem-cell culture and tissue engineering.

overall_design: Adipose mesenchymal stem cells (Ad MSC), Bone Marrow mesenchymal stem cells (Bm MSC) or dermal fibroblasts (NHDF) cultured for 3 days on substrates consisting of extracellular matrix deposited by the each different cell type or tissue culture plastic (TCPS) in triplicate with one exception that is duplicate instead.

first: Héloïse

last: Ragelle

first: Alexandra

last: Naba

first: Benjamin

middle: L

last: Larson

first: Fangheng

last: Zhou

first: Miralem

last: Prijic

first: Amanda

last: Del Rosario

first: Robert

last: Langer

first: Richard

middle: O

last: Hynes

first: Daniel

last: Anderson


title: The Grapevine Vegetative Color Locus Encompasses Three Closely Related R2R3-MYB Transcription Factors and Regulates Anthocyanin Synthesis with Different Specificities Compared to the Berry Color Locus

status: Public on Mar 11 2017

city: Verona

first: Erika

last: Cavallini

state: Verona

address: Strada Le Grazie, 15

department: Biotechnology

summary: The grape color locus 2 affects anthocyanin pigmentation of vegetative organs.

overall_design: For the genetic transformation of Vitis vinifera cv Maccabeu, the in vitro plantlets were grown for 90 days under light and temperature controlled. For overexpression of the MYB genes in Vitis vinifera cv Maccabeu hairy roots, the cDNA sequences were transferred into the binary vector pH2GW7 by site-specific recombination. The construct were then inserted into Agrobacterium tumefaciens A4 by electroporation and used for the grapevine transformation. The induction and culture of transgenic HRs in grapevine were performed as described by Torregrosa and Bouquet (1997), with modifications reported in Cutanda-Perez et al. (2009).

first: Josè

middle: T

last: Matus

first: Rodrigo

last: Loyola

first: Janine

last: Holl

first: Laura

last: Finezzo

first: Silvia

last: Santo

first: Sara

last: Zenoni

first: Sandrine

last: Vialet

first: Francisca

last: Godoy

first: Mauro

last: Commisso

first: Andrea

last: Schubert

first: José

last: Alcalde

first: Jochen

last: Bogs

first: Agnès

last: Ageorges

first: Giovanni

middle: B

last: Tornielli

first: Patricio

last: Arce-Johnson


title: Yeast heterozygous FHL1 deletion mutant

status: Public on Mar 02 2017

city: Nagahama

first: Yukio

last: Mukai

state: Shiga

address: 1266 Tamura-cho

department: Department of Bioscience

institute: Nagahama Institute of Bio-Science and Technology

summary: Forkhead transcription factor FHL1 gene was required for replicative lifespan as well as cell proliferation in yeast. In this study, to see how Fhl1p determines the lifespan, we performed a DNA microarray analysis of heterozygous diploid strain deleted for FHL1 and, from the Fhl1p-target genes, screened for a lifespan-related gene. Transcriptomic profiles showed large increases and moderate decreases in transcripts in the fhl1/FHL1 mutant. Pathway analysis suggested upregulation of most of carbon metabolisms (glycolysis, gluconeogenesis, and TCA cycle) and downregulation of translation (ribosomal proteins and translation factors) in the FHL1-deficient mutant. We found a remarkable downregulation of a set of phosphate metabolism genes and ribonucleotide reductase large subunit genes, RNR1 and RNR3. We demonstrated that Fhl1p regulates RNR1 gene transcription to maintain dNTP levels, modulating longevity against replication stress and genomic instability.

overall_design: Total RNA samples were prepared from wild-type BY4743 and its isogenic fhl1/FHL1 mutant cells grown in YPD medium at 30°C to OD600 of 1.0. Antisense RNA was synthesized and labeled with Cy3 for the fhl1/FHL1 mutant and with Cy5 for the wild type. Each mixture of Cy3- and Cy5-labeled antisense RNA was hybridized on a 3D-Gene Yeast Oligo Chip 6K (Toray, Kanagawa, Japan). The hybridized array was scanned with a 3D-Gene Scanner 3000 (Toray).

first: Akiko

last: Tai

first: Yuka

last: Kamei