title: Untimely expression of gametogenic genes in vegetative cells causes uniparental disomy (ChIP-chip)

status: Public on Feb 25 2017

city: Bethesda

first: Shiv

last: Grewal

state: MD

address: NCI bldg 37 Rm 6068 9000 Rockville Pike

department: LBMB

country: USA

institute: NCI

type: Genome binding/occupancy profiling by genome tiling array

summary:
Occupancy profiling of lysine 9 dimethylated histone H3 in fission yeast.
Occupancy profiling of Psc3, Rec8, Rad21 and Rec11 proteins in fission yeast.

overall_design: Agilent 60mer array was used to analyze DNA recovered by immunoprecipitation of  lysine 9 dimethylated histone H3 from asynchronous culture of fission yeast.

first: H

middle: D

last: Folco

first: Tomoyasu

last: Sugiyama

first: Venkata

last: Chalamcharla

first: Gobi

last: Thillainadesan

first: Martin

last: Zofall

first: Vanivilasini

last: Balachandran

first: Jothy

last: Dhakshnamoorthy

first: Takeshi

last: Mizuguchi

middle: I


title: MiRNA biomarkers for eribulin response

status: Public on Feb 20 2017

city: Rotterdam

first: Erik

last: Wiemer

address: Wytemaweg 80

department: Medical Oncology

country: Netherlands

institute: Erasmus University Medical Center

summary: Background: Recent phase II and III clinical trials demonstrated antitumor activity of eribulin, a tubulin-interacting cytotoxic agent, in patients with metastatic soft tissue sarcoma (STS). In this exploratory study we aimed to identify putative microRNA biomarkers that associate with eribulin sensitivity or resistance in STS.  Materials and methods: Archival tumor tissue from primary tumors or metastatic lesions was collected prior to eribulin treatment, from 65 consenting patients involved in the EORTC trial 62052. This phase II study (ClinicalTrials.gov identifier NCT00413192) included multiple subtypes of STS. Tissue was available from 21 leiomyosarcomas, 14 adipocytic sarcomas, 9 synovial sarcomas and 21 other sarcoma histotypes. Total RNA was isolated from formalin fixed, paraffin embedded tumor samples and analyzed using Taqman® Low Density Arrays to determine microRNA expression profiles. The expression of a total of 756 microRNAs was assessed. Progression free survival at week 12 (RECIST 1.0) measured as a binary variable, was the primary endpoint of the clinical trial and used as a primary response measure for correlative studies. Seventeen out of 53 (32.1%) evaluable patients in the analyzed subset had non-progressive disease at week 12 and were defined as responders.  Results: The expression of 26 individual microRNAs (p<0.05) differed significantly between non-responders and responders. Additional microRNAs of potential relevance were identified when considering the different histological subgroups.   Conclusions: The expression level of particular microRNAs in STS tissue samples may predict response to eribulin. Further validation studies as well as a preclinical assessment of the underlying molecular mechanisms are required.

overall_design: The miRNA expression profiles were determined of 65 archived tumor samples derived from patients with different soft tissue sarcomas. All patients were treated with eribulin in the context of the EORTC 62052 phase II clinical study. MiRNAs of which the expression correlated best with response to eribulin were identified.

middle: A

first: Agnieszka

last: Wozniak

first: Herman

last: Burger

first: Marcel

last: Smid

first: Giuseppe

last: Floris

first: Axelle

last: Nzokirantevye

first: Raf

last: Sciot

first: Stefan

last: Sleijfer

first: Patrick

last: Schöffski


title: Ontogenetic onset of immune-relevant genes in the common sole (Solea solea)

status: Public on Feb 14 2017

city: Legnaro (PD)

first: Serena

last: Ferraresso

state: Padova

address: Viale dell'Università

department: Dept of Comparative Biomedicine and Food Science

country: Italy

institute: University of Padova

summary: A microarray platform for Solea solea was employed to study gene expression profiles of common sole developmental stages.

overall_design: Characterization of the transcriptome of S. solea, focusing on larval and juvenile stages.   Pooled samples of 10–5 individuals (depending on larval age) were sampled and RNA extracted at 1, 4, 6, 8, 11, 13, 15, 18, 24 and 33 days post-hatching (dph). The number of biological replicates was four for each sampling point. Gene expression profiling was performed using the Agilent-036353 Solea solea oligo microarray (GPL16124) based on single-colour detection (Cyanine-3 only).

first: S

first: L

last: Bargelloni


title: Long non-coding RNA expression profile in the kidney of male low birth weight rats exposed to maternal protein restriction at postnatal day 10

status: Public on Feb 13 2017

city: SuZhou

first: Yanhong

last: Li

address: Jingde road 303

department: Department of nephrology, Institute of pediatric research

country: China

institute: Children’s Hospital affiliated to Soochow University

type:
Expression profiling by array
Non-coding RNA profiling by array

summary: To investigate the lncRNA profiles in low birth weight rats with reduced nephron endowment induced by restriction of maternal protein intake. Low birth weight by reduced nephron endowment is a risk factor for hypertension and end-stage renal disease in adulthood.

overall_design: Kidneys at postnatal day 10 were obtained from low birth weight male rats (n=3) fed a low-protein diet throughout gestation and lactation and normal control male rats (n=3) born from normal protein diet dams. LncRNA expression profiles were analyzed by sequencing and screening using the Agilent Rat lncRNA Array.

first: Xiaozhong

first: Xing

last: Feng


title: Host-parasite transcriptomics during immunostimulant enhanced rejection of salmon lice Lepeophtheirus salmonis by Atlantic salmon Salmo salar

status: Public on Feb 26 2017

city: Victoria

first: Ben

middle: F

last: Koop

state: BC

address: PO Box 3020 STN CSC

department: Biology

country: Canada

institute: The University of Victoria

summary: We investigate the effect of a functional feed for immunostimulation (peptidoglycan extract from bacterial cell wall with nucleotide formulation) on L. salmonis infection levels on Atlantic salmon Salmo salar, and on host and parasite gene expression profiles. Atlantic salmon smolts (~95 g) were fed a control diet, or a low or high dose immunostimulant diet, and then exposed to L. salmonis copepodids in three subsequent exposures. The transcriptome of salmon lice late in the infection attached to either the low dose diet or control diet hosts were compared using a 38K oligonucleotide microarray.

overall_design: Atlantic L. salmonis copepods were used to infect Atlantic salmon on an immunostimulant diet, and upon development to the adult stage the lice were collected and profiled. Lice are either feeding on immunostimulant-fed or control-fed salmon. Lice samples are equal numbers of males and females.

middle: J

last: Sutherland

first: Jennifer

middle: M

last: Covello

first: Sarah

middle: E

last: Friend

first: Jordan

last: Poley

first: Kim

middle: W

last: Koczka

first: Sara

middle: L

last: Purcel

first: Tara

last: MacLeod

first: Bridget

middle: R

last: Donovan

first: Jorge

last: Pino

first: Jose

last: González Vecino

first: Javier

last: Gonzalez

last: Troncoso

first: Simon

last: Wadsworth

first: Mark

last: Fast


title: MicroRNA expression profiling of one rhesus macaque at day 0 and day 7 post-exposure to aerosolized Ebola virus

city: Frederick

first: Janice

last: Duy

address: 1425 Porter St.

department: Diagnostics Systems Division

institute: U.S. Army Medical Research Institute of Infectious Diseases

summary: MicroRNA expression data were obtained from archived plasma from one rhesus macaque exposed to aerosolized Ebola virus.

overall_design: MicroRNA expression profiling using RT-PCR with the Exiqon microRNA Ready-to-Use PCR, Human panel I+II, V3.R (catalog number 203612). Plasma was obtained from one rhesus macaque challenged with aerosolized Ebola virus. Archived plasma from day 0 and day 7 post-exposure were used. Three technical replicates were run at each time point.

first: Jeffrey

last: Koehler

first: Anna

last: Honko

first: Timothy

last: Minogue


title: Differentiation of mammary epithelial cells with/without exposure to RANKL.

status: Public on Feb 12 2017

city: Hospitalet de Llobregat

first: Eva

last: González-Suárez

state: Barcelona

address: Hospital Duran i Reynals - 3a planta -Gran Via de l'Hospitalet, 199

department: Epigenetics and Cancer Biology

country: Spain

institute: Institut d'Investigació Biomèdica de Bellvitge

summary: In order to investigate the mechanisms underlying defective alveologenesis caused by RANK over-expression in mice, global gene expression profiles from primary acinar cultures of mammary epithelial cells were analyzed.

overall_design:
Mammary epithelial cells from gestation day 16.5 WT and MMTV-RANK females were obtained. Cultures were established in the presence of prolactin, which induces differentiation into milk secreting acini, and with or without RANKL (Receptor Activator of NFkB Ligand) to precisely determine the role of RANK signaling at midgestation. Global gene expression profiling at 8 hours (h), 24 h and 72 h from WT, and MMTV-RANK 3D acinar cultures was obtained.

Please note that experiments were performed technically as dual channel (e.g., Cy3 and Cy5-labeled samples hybridized to the same array; total 72 hybridizations) but the results were processed as though they were single channel. Rosetta Resolver ratio split algorithm was used to parse individual Cy3 (Ch1) or Cy5 (Ch2) intensity values and then to combine 4 replicate values for each sample into a single intensity value. Therefore, the normalized_combined_data.txt  (available on the Series records) contains 36 data columns [i.e. (72array X 2 channel)/4 replicates; 2 genotype (WT or TG)  X 3 replicates X 3 timepoints (8 ,24 ,72hr) X 2 treatments (w/&w/o RANKL)].

last: Gonzalez-Suarez

first: Alex

last: Cordero

first: Chetan

last: Deshpande


title: An integrated genomic approach for the study of mandibular prognathism in the European seabass (Dicentrarchus labrax) II

first: Serena

last: Ferraresso

summary: A sea bass oligo microarray platform was used to profile gene expression in mandibles of 58 days-old sea bass affected by prognathism, a skeletal malformation that strongly affects sea bass production. Two different conditions: i) protruding jaws, and ii) normal jaws were used for gene expression analysis. For each condition, total RNA was extracted from five (5) independent biological replicates, each consisting of pools of five (5) jaws.

overall_design:
In this study, we analyzed ten (10) samples, five (5) pools of jaws dissected from normal sea bass and five (5) pools of jaws dissected from individuals affected by prognathism. Gene expression profiling was performed using the GPL9663 Dicentrarchus labrax Oligo Microarray platform (10 arrays, no replicate) based on single-colour detection (Cyanine-3 only).

This series contains re-analyzed samples from GSE19001 and two new samples.

first: Massimo

last: Milan

first: Luca

last: Bargelloni


title: Real-time quantitative PCR analysis of PP2C genes in Brachypodium distachyon of different tissues and under multiple stresses

city: Shanghai

first: Zhaoqing

last: Chu

address: 3888 Chenhua Road, Songjiang

institute: Shanghai Chenshan Plant Science Research Center, CAS

summary: PP2C genes responding to 13 stresses were screened using qPCR. All sampes were repeated with 3 times and ACTIN were regarded as house keeping gene.The stresses including heavy metal treatments, environmental factors,phytohormones and biotic treatments.

overall_design: qPCR gene expression profiling. The 2 weeks-seedlings were used and 2 µg of total RNA were used for cDNA synthesis by using PrimeScript Reverse Transcriptase (TAKARA).

first: Jianmei

last: Cao


title: Pseudomonas aeruginosa PAO1 response to sphingomyelin

city: Fukuoka

first: Nozomu

last: OKINO

state: Fukuoka

address: 6-10-1 Hakozaki, Higashi-ku

department: Department of Bioscience and Biotechnology, Graduate School of Bioresource and Bioenvironmental Sciences

country: Japan

institute: Kyushu University

summary: Analysis of Pseudomonas aeruginosa PAO1 treated with 200 µM sphingomyelin. Results provide insight into the response to sphingomyelin in P. aeruginosa.

overall_design: P. aeruginosa PAO1 was cultured in the presence and absence of sphingomyelin. The orginal culture was divided into two parts. One was treated with 200 μM sphingomyelin and the other served as a control. The experiment was performed in tripricates.


title: Zebrafish gonadal transcriptome analysis in response to heat

city: Singapore

first: Woei Chang

last: Liew

address: 1 Research Link, NUS

country: Singapore

institute: Temasek Life Sciences Laboratory

summary: High temperature can induce masculinization in many fish species including zebrafish (Ospina-Alvarez & Piferrer PLoS One 3:e2837). Juvenile zebrafish exposed to high temperature during gonad differentiation period will result in male bias adult sex ratio. This experiment compared the zebrafish gonadal transcriptome between fishes that were exposed to high (36 oC) and control (28 oC) temperatures. Gene expression analysis using microarray were performed at juvenile (37 dpf) and adult (90 dpf) stages.

overall_design: Juvenile zebrafish (18 dpf) were exposed to either high (36 oC) or control (28 oC) temperature treatment for 14 days. After the treatment both groups of fish were reared at 28 oC until 37 or 90 dpf. For analysis of the juvenile (37 dpf) 10 biological replicates (unknown sex) from each temperature treatment groups were compared. For the adult (90 dpf) female, 4 biological replicates from each temperature treatment groups were compared. For the adult (90 dpf) male, 10 biological replicates from each temperature treatment groups were compared.

first: Woei

middle: C

first: Laszlo

last: Orban


title: Retinoic acid specifically enhances embryonic stem cell metastate marked by Zscan4

city: Baltimore

first: Minoru

last: Ko

address: 251 Bayview Blvd, Suite 100, 10C

department: National Institute on Aging

institute: NIH

summary: Pluripotency confers Embryonic Stem Cells (ESCs) the ability to differentiate in ectoderm, endoderm, and mesoderm derivatives, producing the majority of cell types. Although the majority of ESCs divide without losing pluripotency, it has become evident that ESCs culture consists of multiple cell populations with different degrees of potency that are spontaneously induced in regular ESC culture conditions. Zscan4, a key pluripotency factor, marks ESC subpopulation that is referred to as high-level of pluripotency metastate. Here, we report that in ESC cultures treated with retinoic acid (RA), Zscan4 ESCs metastate is strongly enhanced. In particular, we found that induction of Zscan4 metastate is mediated via RA receptors (RAR-alpha, RAR-beta, and RAR-gamma), and it is dependent on phosphoinositide-3-kinase (PI3K) signaling. Remarkably, Zscan4 metastate induced by RA lacks canonical pluripotency genes Oct3/4 and Nanog but retained both self-renewal and pluripotency capabilities. Finally we demonstrated that the conditional ablation of Zscan4 subpopulation is dispensable for both endoderm and mesoderm but is required for ectoderm lineage. In conclusion, our research provides new insights about the role of RA signaling during ESCs high pluripotency metastate fluctuation.

overall_design: emeral+/-, retinoic acid cell sorting

first: Geppico

last: Falco


title: Chimeric-competent, embryo-derived stem cell lines unveil the plasticity of pluripotency in rabbits

city: Jouy-en-Josas

first: Jouneau

last: Luc

address: Domaine de Vilvert

country: France

institute: INRA

summary: Conventional rabbit embryonic stem cell (ESC) lines are derived from the inner cell mass (ICM) of pre-implantation embryos using methods and culture conditions established for primate ESCs (partial dissociation with collagenase and culture with FGF2). In the present work, we explored the capacity of rabbit ICM to give rise to ESC lines using conditions similar to those utilized to generate ESCs in mice.

overall_design: In the present work, we explored the capacity of rabbit ICM to give rise to ESC lines using conditions similar to those utilized to generate ESCs in mice. Especially we compared the transcriptomes of rabbit ES cell lines obtained using (i) different dissociation protocoles : either partial dissociation with Collagenase or single cell dissociation with accutase and (ii) different culture conditions: 20% KOSR with FGF2, 10% KOSR and 10% FCS,  10% KOSR and 10% FCS with FGF2, or 10% KOSR and 10% FCS with LIF. Because we wanted to compare these transcriptomes to those of the pluripotent cells present in the embryo, we also analyzed the transcriptomes of Rabbit Day 4 Inner Cell Masses (ICM) , and Rabbit Day 6 Epiblasts. These two embryonic compartments were isolated from in vivo developped embryos using immunosurgery for Day 4 ICM, and microdissection for Day 6 Epiblasts. At Day 6 in the Rabbit, the Epiblast forms a monolayered epithelium of cuboid and polarized cells.

first: Pierre

last: Osteil

first: Anaïs

last: Moulin

first: Luc

last: Jouneau

first: Yann

last: Tapponnier

first: Catherine

last: Archilla

first: Barbara

last: Schmaltz-Panneau

first: Jérome

last: Lecardonnel

first: Véronique

last: Duranthon

first: Marielle

last: Afanassieff

last: Savatier


title: Circulating miR-223 in Oral Cancer: Its Potential as a Novel Diagnostic Biomarker and Therapeutic Target

status: Public on Feb 11 2017

city: Kamakura

first: Satoshi

last: Kondo

state: Kanagawa

address: Tebiro 6-10-1

department: New Projects Development Division

institute: Toray Industries,Inc.

summary:
The current study used an ultra-sensitive genome-wide miRNA array to investigate changes in circulating miRNAs in plasma from patients with oral cancer and healthy individuals. Results indicated that there were only a few circulating miRNAs, including miR-223, miR-26a, miR-126, and miR-21, that were up-regulated in patients with oral cancer.
A subsequent validation test indicated that circulating miR-223 levels were significantly higher (~2-fold, P< 0.05) in patients with oral cancer than in those without cancer. Moreover, in vitro studies revealed that miR-223 functions as a tumor suppressor.

overall_design: Circulating levels of a total of 1,211 genome-wide miRNAs were measured with a microarray assay using pooled plasma samples from 5 patients with gingival squamous cell carcinoma (GSCC) and pooled normal plasma samples from 10 age- and sex-matched healthy controls. The circulating miRNA profile for patients with oral cancer was compared with that for controls.

first: Hirohiko

last: Tachibana

first: Ri

last: Sho

first: Yuji

last: Takeda

first: Xuhong

last: Zhang

first: Yukie

last: Yoshida

first: Mitsuyoshi

last: Iino


title: Cells released from Staphylococcus epidermidis biofilms interact differently from biofilm or planktonic cells with murine host immune system.

status: Public on Feb 22 2017

city: Braga

first: Ângela

last: França

address: Campus de Gualtar

department: Biological Engineering

country: Portugal

institute: University of Minho

summary: S. epidermidis ability to form biofilms on indwelling medical devices and its association with the emergence of chronic infections is its main virulence factor. Nevertheless, it has been shown that the cells released from these biofilms are associated with the advent of serious acute infections with bacteraemia as one of the major clinical manifestations. Despite their clinical relevance, very little is known about the impact of biofilm-released cells in pathogenesis. Hence, herein, we characterized the murine immune response to the presence of cells released from S. epidermidis biofilms analysing spleen cells transcriptome by microarrays. These findings may help to explain the recurrent inflammatory symptoms presented by patients with colonization of indwelling medical devices.

overall_design: In order to assess the role of the cells released from S. epidermidis biofilms in pathogenesis, an in vivo murine model of hematogenously disseminated infection was used. Planktonic and biofilm cells were used for comparative purposes. In brief, 1 × 108 planktonic, biofilm and biofilm-released cells were intravenously injected via lateral tail vein of 8-12 weeks old BALB/c females and 2 hours post infection, spleens were collected and prepared for microarrays analysis.

first: Angela

first: Begoña

last: Pérez-Cabezas

first: Alexandra

last: Correia

first: Manuel

last: Vilanova

first: Nuno

last: Cerca


title: An integrated genomic approach for the study of mandibular prognathism in the European seabass (Dicentrarchus labrax) I

first: Serena

last: Ferraresso

summary: A sea bass oligo microarray platform was used to profile gene expression in whole heads of 38 days-old sea bass affected by prognathism, a skeletal malformation that strongly affects sea bass production. Two different conditions: i) prognathous individuals, and ii) normal individuals were analyzed. For each condition, total RNA was extracted from three (3) independent biological replicates, each consisting of pools of five (5) heads.

overall_design:
In this study, we analyzed six (6) samples, three (3) pools of heads dissected from normal sea bass and three (3) dissected from individuals affected by prognathism. Gene expression profiling was performed using the GPL9663 Dicentrarchus labrax Oligo Microarray platform (6 arrays, no replicate) based on single-colour detection (Cyanine-3 only).

This series contains samples reanalyzed from GSE19041.

first: Massimo

last: Milan

first: Luca

last: Bargelloni


title: Transcriptomic and proteomic analysis of Oenococcus oeni adaptation to wine stress conditions

city: Tarragona

first: Cristina

last: Reguant

state: Tarragona

address: Marcel·lí Domingo 1

department: Biochemistry and Biotechnology

institute: University Rovira i Virgili

summary: The correct development of malolactic fermentation depends on the capacity of Oenococcus oeni to survive under harsh wine conditions.  In this study it was characterized the transcriptomic response of O. oeni PSU-1 during the adaptation to wine-like medium (WLM). The period evaluated was from the inoculation into WLM  (12% v/v pH 3.4) until the beginning of malolactic fermentation (8h after inoculation).

overall_design: Oenococcus oeni PSU-1 was grown in rich medium and after inoculated into wine-like medium (12% v/v, pH 3,4) . Samples were taken at different times after inoculation up to 8 hours (start of malolactic fermentation). Total RNA was analysed using a custom designed expression microarray.

first: Mar

last: Margalef-Català

first: Albert

last: Bordons

first: Joaquín

last: Bautista


title: Plasma miRNAs expression in acute ischemic stroke patients with or without recombinant tissue plasminogen activator treatment.

status: Public on Feb 23 2017

city: guangzhou

first: Zhen

last: Deng

state: Guangdong

address: Nanfang Hospital,  #1838 Guangzhou Da dao North

department: Neurology

institute: southern medical university

summary:
To determine the expression of circulating miRNAs in AIS patients with thrombolysis and without thrombolysis.

Grant ID: 81100882
Grant title: The relation between transcription of miR-497 and neurons apoptosis after ischemic stroke
Funding source: Chinese National Natural Science Foundation
Grantee First Name: Zhen
Grantee Last Name:Deng

platform_organism:
Homo sapiens
Mus musculus
Rattus norvegicus

overall_design: Fifteen AIS patients with thrombolysis treatment and fifteen AIS patients (admission after 8h of onset) without thrombolysis were collected blood sample on the onset of 24h. Fifteen age-match healthy person were as control group. We used miRNA microarrays to detect plasma miRNA expression profiles and real-time PCR verified miRNA expression. Totally, there 3 sample in each group.

first: Wei

last: Xiang


title: Inhibition of CDK8 Mediator Kinase Suppresses Estrogen Receptor Signaling and Growth of Estrogen Receptor Positive Breast Cancer

city: Columbia

first: Martina

middle: SJ

last: McDermott

state: SC

address: 715 Sumter Street

department: Dept of Drug Discovery and Biomedical Sciences

institute: University of South Carolina

summary: Hormone therapy targeting estrogen receptor (ER) is the principal treatment for ER-positive breast cancers but many cancers develop resistance to anti-estrogens. Cyclin-dependent kinase 8 (CDK8) is a transcriptional regulator of several oncogenic pathways. Expression levels of CDK8 and ERα are inversely correlated in breast cancers suggesting a functional association between CDK8 and ER. CDK8 inhibition by selective small-molecule inhibitors, by shRNA knockdown or by CRISPR-Cas9 knockout suppressed estrogen-induced transcription, with no significant effects on ERα protein expression or phosphorylation. CDK8 inhibition also abrogated the mitogenic effect of estrogen on ER-positive breast cancer cells and potentiated growth inhibition by the ER antagonist fulvestrant. In vivo, administration of a CDK8 inhibitor suppressed ER-positive breast cancer xenograft growth and augmented the effects of fulvestrant with no apparent toxicity. CDK8 inhibitors also suppressed the development of estrogen independence in ER-positive breast cancer cells. These results identify CDK8 as a novel drug target for breast cancer therapy.

overall_design: Examining the effects of  2.5 µM Senexin A for 24 hr followed by 10 nM E2 for 12 hours compared to single agent treatments in estrogen-deprived MCF7 cells

middle: S

first: Alexander

last: Chumanevich

first: Chang-uk

last: Lim

first: Jiaxin

last: Liang

first: Mengqian

last: Chen

last: Altilia

first: David

last: Oliver

first: James

last: Rae

first: Michael

last: Shtutman

first: Hippokratis

last: Kiaris

first: Balázs

last: Győrffy

first: Igor

middle: B

last: Roninson

first: Eugenia

middle: V

last: Broude


title: Transcriptomic profiling of Arabidopsis thaliana mutants in response to combined abiotic stress

city: Bangalore

first: Genotypic

last: technology

state: Karnataka

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

country: India

institute: Genotypic Technology

summary: Identification of differentially expressed genes in Arabidopsis thaliana mutants in response to combined abiotic stress treatment through Microarray experiment.

overall_design: Agilent one-color experiment,Organism: Arabidopsis thaliana ,Agilent Custom Arabidopsis 8x60k Microarray designed by Genotypic Technology Private Limited (AMADID: 48015)

first: Deepak

last: Kumar

first: Sharmila

last: Chattopadhyay


title: An integrated genomic approach for the study of mandibular prognathism in the European seabass

first: Serena

last: Ferraresso

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

overall_design: Refer to individual Series


title: Transcriptional and Behavioral Responses of Zebrafish Larvae to Microcystin-LR Exposure

status: Public on Feb 16 2017

city: Ioannina

first: Katerina

middle: Periklis

last: Soupsana

address: Dourouti

department: Medical School

country: Greece

institute: University of Ioannina

summary: Microcystin-LR (MC-LR), the most toxic member of microcystin family, inhibits protein phosphatase PP2A, triggers oxidative stress and induces hepatotoxicity. Gene expression profiling of MC-LR treated larvae using DNA microarray analysis revealed effects in the retinal visual cycle and pigmentation synthesis pathways that have not been previously associated with MC-LR. Liver-related genes were also differentially expressed. The microarray data were confirmed by quantitative real-time PCR. Our findings provide new evidence that microcystin-LR exposure of zebrafish larvae modulates the retinal visual cycle and pigmentation synthesis pathways and ultimately alter larval zebrafish behavior

overall_design: MC-LR treatment vs. control

first: Eleni

last: Tzima

first: Iliana

last: Serifi

first: Ioanna

last: Tsikari

first: Ainhoa

last: Alzualde

first: Ioannis

last: Leonardos

first: Thomais

last: Papamarcaki


title: FSH and Testosterone treated Infant Monkey Sertoli cells vs. FSH and Testosterone treated  pubertal Monkey Sertoli cell

city: New Delhi

first: Sayon

last: Basu

state: Delhi

address: Aruna Asaf Ali Marg

institute: National Institute of Immunology

summary: Transcriptional profiling of Sertoli cells of Monkey origin comparing infant Sertoli cells with pubertal Sertoli cells, isolated from Monkeys in which puberty was induced by extrinsic GnRH administration. Both Infant and pubertal cells were treated with FSH and Testosterone in vitro.

overall_design: Two condition experiment, infant Sertoli cells vs Pubertal Sertoli cells. 1 set  infant sertoli cells, 1 set pubertal sertoli cells. One color experiment.

first: Subeer

last: Majumdar

first: Mukkesh

last: Gautam


title: Brain ischemia suppresses immunity in the periphery and brain via different neurogenic innervations

city: Tianjin

first: Fu-Dong

last: Shi

address: 154 Anshan Rd.

institute: Tianjin Medical University General Hospital

summary: Brain ischemia inhibits immune function systemically, with resulting infectious complications. Whether in stroke different immune alterations occur in brain and periphery and whether analogous mechanisms operate in these compartments remains unclear. Here we show that in patients with ischemic stroke and in mice subjected to middle cerebral artery occlusion, natural killer (NK) cells display remarkably distinct temporal and transcriptome profiles in the brain as compared to the periphery. The activation of catecholaminergic and hypothalamic-pituitary-adrenal axis leads to splenic atrophy and contraction of NK cell numbers in the periphery through a modulated expression of SOCS3, whereas cholinergic innervation-mediated suppression of NK cell responses in the brain involves RUNX3. Importantly, pharmacological or genetic ablation of innervation preserved NK cell function and prevented post-stroke infection. Thus, brain ischemia compromises NK cell-mediated immune defenses through mechanisms that differ in the brain versus the periphery, and targeted inhibition of neurogenic innervation limits post-stroke infection.

overall_design: NK cells were isolated from pooled splenocytes and brain tissues of B6 mice at days 1 or 3 after MCAO (n=3 at each time point) or sham-operations(n=3). RNA of FACS-sorted brain-infiltrating NK cells was obtained from pooled brain tissues of MCAO mice. RNA of FACS-sorted NK cells in spleens was obtained from single mouse spleens of MCAO mice. RNA samples for each data point were harvested from four individual experiments. The purity of FACS-sorted NK cells was >99%. RNA was purified using TRIzol reagent (Ambion, Grand Island, NY, USA) according to the manufacturer’s protocol. RNA samples were analyzed by nCounter gene expression analysis and quantified using nCounter Digital Analyzer (NanoString Technologies, Tucson, AZ, USA).

first: Qiang

last: Liu


title: Macro ncRNAs are abundant in imprinted regions and directly regulated by DNA methylation [tiling array]

city: Klosterneuburg

first: Florian

last: Pauler

address: Am Campus 1

country: Austria

institute: IST Austria

type: Non-coding RNA profiling by genome tiling array

summary:
Imprinted macro ncRNAs such as Airn play an important role in silencing protein-coding genes in cis, macro ncRNAs could be a common feature in all imprinted gene clusters. By applying the RNA Expression on Tiling Array (RETA) technique, macro ncRNAs were found to be abundant in 26 known mouse genomic regions containing imprinted genes were detected.
All well-known imprinted macro ncRNAs were up-regulated upon depletion of DNA methylation.

overall_design: Surveying imprinted macro non-coding RNAs in 26 imprinted mouse regions from different mouse cells and tissues

first: Ru

last: Huang

first: Ido

last: Tamir

first: Denise

middle: P

last: Barlow


title: Recurrent aneuploidy patterns enable fitness gains in tumor metabolism

city: Los Angeles

first: Thomas

middle: G.

last: Graeber

state: CA

address: 570 Westwood Plaza, Bldg 114, Room 4341 CNSI

department: Mol & Med Pharmacology

institute: UCLA

type: Genome variation profiling by genome tiling array

summary: Copy number alteration (CNA) profiling of human tumors has revealed recurrent patterns of DNA amplifications and deletions. These patterns are indicative of conserved selection pressures, but cannot be fully explained by known oncogenes and tumor suppressor genes. Using integrative analysis of CNA data from patient tumors and experimental systems, we report that principal component analysis-defined CNA signatures are predictive of glycolytic phenotypes, including FDG-avidity of patient tumors, and increased proliferation. The primary glycolysis-linked CNA signature is associated with p53 mutation and shows coordinate amplification of glycolytic genes and other cancer-linked metabolic enzymes including TIGAR and RPIA. In contrast, alternative signatures involve both different mechanisms of tumor suppression loss (eg, MDM2 amplification) and different glycolysis enzyme isoforms. Furthermore, a cross-species CNA comparison identified 21 conserved CNA regions, containing 13 enzymes in the glycolysis and pentose phosphate pathways in addition to known cancer driving genes. In validation experiments, exogenous expression of hexokinase and enolase enzymes resulted in reduced propensities for amplifications at the corresponding endogenous loci. Our findings support metabolic stress as a selective pressure underlying the recurrent CNAs observed in human tumors, and further cast genomic instability as an enabling event in tumorigenesis and metabolic evolution.

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus

overall_design:
(i) There are 54 unique CD1 MEF sublines and 71 total CD1 MEF samples, including control diploid sample profiled at passage 1 and replicates of samples profiled at more than one passage. There is 1 DR4 MEF subline profiled at two different passages and 1 DR4 MEF diploid control sample profiled at passage 1. There are 29 unique p53-/- MEF sublines and 37 total MEF samples, including control diploid p53+/+ sample profiled at passage 2 and replicates of samples profiled at more than one passage.
(ii) 10 human breast cancer samples were profiled on Agilent 244K aCGH arrays per manufacturer's instructions. Either matched normal DNA or a pooled reference normal DNA was used as the reference.  The 10 aCGH samples are related to both this study and to GSE21217.  *** Raw data are unavailable ****

first: Nicholas

last: Graham

first: Aspram

last: Minasyan

first: Anastasia

last: Lomova

first: Sophie

last: Zhao

first: Adrian

last: Delgado

first: Shawna

last: Chan

first: Michael

last: Friedman

first: Nicolaos

last: Palaskas

first: Ingo

middle: K

last: Mellinghoff

first: Steven

last: Larson

first: Elisa

last: Port

first: Christian

last: Hurtz

first: Carina

last: Ng

first: Rong

last: Qiao

first: Hong

last: Wu

first: Markus

last: Müschen

middle: G


title: miRNAs in human subcutaneous adipose tissue: Effects of weight loss induced by hypo-caloric diet and exercise

status: Public on Feb 17 2017

city: Copenhagen

first: Malene

middle: Maag

last: Kristensen

address: Blegdamsvej 3

country: Denmark

institute: University of Copenhagen

summary: miRNA profiles were investigated in severely obese individuals before and after a weight loss induced by diet and moderate exercise.

platform_organism:
Homo sapiens
Mus musculus
Rattus norvegicus
Human alphaherpesvirus 1
Human alphaherpesvirus 2
Human betaherpesvirus 5
Murid betaherpesvirus 1
human gammaherpesvirus 4
JC polyomavirus
Human immunodeficiency virus 1
Murid gammaherpesvirus 4
Human gammaherpesvirus 8
Merkel cell polyomavirus
Mus musculus cytomegalovirus 2
Betapolyomavirus hominis
Betapolyomavirus macacae

overall_design: 13 severely obese individuals (seven women and six men) underwent a 15-week weight loss intervention including moderate daily exercise and a hypo-caloric diet.

first: Peter

last: Davidsen

first: Andreas

last: Vigelsø

first: Christina

middle: N

last: Hansen

first: Lars

last: Jensen

first: Niels

last: Jessen

first: Jens

last: Bruun

first: Flemming

last: Dela

first: Jørn

last: Helge


title: B lymphocytes signature is associated with the success of minimization therapy in kidney transplantation

city: Bergisch-Gladbach

first: Stefan

last: Tomiuk

address: Friedrich-Ebert-Str. 68

department: Bioinformatics

country: Germany

institute: Miltenyi Biotec GmbH

summary: The efficacy and safety of tacrolimus or sirolimus monotherapy after combined induction therapy with campath-1H and infliximab monoclonal antibodies in 20 kidney graft recipients were evaluated in single centre prospective randomized trial.  Campath-1H and infliximab induction followed by tacrolimus monotherapy spare tolerance asssociated naive B-cell related molecular markers and results in 36 months excellent renal graft function and normal histology.

overall_design:
The experiments were performed with total RNA derived from whole blood samples of twenty different patients who had undergone a kidney transplantation. After an initial administration of Campath, Infliximab, Methylprednisolone, and Tacrolimus, the participants of the trial were split into two arms, one of which was treated with the immunosuppressive Calcineurin inhibitor Tacrolimus, and the other was treated with the mTOR-Inhibitor Sirolimus (Rapamycin). As severe side effects were observed for the kidney recipients in the Sirolimus arm, this part of the study had to be stopped. Samples were collected before transplantation and at consistent time points (W3, M2, M3, M6, M12) after transplantation. As microarray platform, the RISET 2.0 microarray (GPL8136) was used.
classification of clinical samples

first: Ondrej

last: Viklicky

first: Petra

last: Hruba

first: Sabrina

last: Schmitz

first: Bernhard

last: Gerstmayer

first: Birgit

last: Sawitzki

first: Patrick

last: Miqueu

last: Hribova

first: Irena

last: Brabcova

first: Uwe

last: Janssen

first: Hans-Dieter

last: Volk

last: Reinke


title: miRNAs expression in HepG2 hepatocellular carcinoma cell lines: Vector Control vs. Twist1, Bcl-2, and Twist1/Bcl-2 Transfected

status: Public on Feb 10 2017

first: baocun

last: sun

address: No.22 Qixiangtai Road, Heping District

department: Department of Pathology

institute: Tianjin Medical University

summary: miRNAs profiling of HepG2 cells comparing vector-control treated HepG2 cells with HepG2 cells transfected with Twist1, Bcl-2, and Twist1/Bcl-2 plasmids. Microarray analysis revealed a panel of miRNAs with significant differential expression among these four HCC cell lines.

overall_design: In the study presented here, four HCC cell lines ( HepG2-Twist1, HepG2-Bcl-2, HepG2-Twist1/Bcl-2 HCC cell lines, and  HepG2-vector cell lines ) was used to analyze miRNA expression profiles. HepG2-Twist1, HepG2-Bcl-2, HepG2-Twist1/Bcl-2 HCC cell lines can stably express Twist1, Bcl-2, and Twist1/Bcl-2, respectively.

first: Baocun

last: Sun


title: Gene expression analysis of MCF12A human breast cultures exposed to ethanol or acetaldehyde [miRNA]

city: Torrance

first: Robert

last: Gelfand

address: 1124 W. Carson St

department: surgery

institute: LABiomed at Harbor UCLA,  and Charles Drew Univ

summary:
MCF12A monolayer cultures were exposed to ethanol or acetaldehyde for eiher 1 week or 4 weeks Total RNA samples were assayed for gene expression and for microRNA expression.
MicroRNA expression was accomplished using 2 experiments. The first experiment included untreated control, ethanol treated (4 weeks at 2.5 mM) and acetaldehyde treated (4 weeks at 1 mM). The data are presented in order of control1 for the ethanol and acetaldehyde treated samples followed by the ethanol and acetaldehyde treated samples, and then the control2 for the soft agar selected sample followed by the soft agar selected sample. The microRNA names are included in separate columns.

overall_design: Cells were cultured in DMEM/F12 in the presence of serum and growth factors. RNA was extracted using the miRVana kit and subjected to analysis of microRNAs.

middle: A

first: Dolores

last: Vernet

first: Kevin

last: Bruhn

first: Jaydutt

last: Vadgama

first: Nestor

middle: F

last: Gonzalex-Cadavid


title: Insights into the Staphylococcus aureus-host interface: global changes in host and pathogen gene expression in a rabbit skin infection model

city: Hamilton

first: Dan

last: Sturdevant

state: MT

address: 903 S 4th street

department: NIAID

institute: NIH

summary: Staphylococcus aureus is an important cause of human skin and soft tissue infections (SSTIs) globally. Notably, 80% of all SSTIs are caused by S. aureus, of which ~63% are abscesses and/or cellulitis. Although progress has been made, our knowledge of the host and pathogen factors that contribute to the pathogenesis of SSTIs is incomplete. To provide a more comprehensive view of this process, we monitored changes in the S. aureus transcriptome and selected host proinflammatory molecules during abscess formation and resolution in a rabbit skin infection model. Within the first 24 h, S. aureus transcripts involved in DNA repair, metabolite transport, and metabolism were up regulated, suggesting an increase in the machinery encoding molecules involved in replication and cell division. There was also increased expression of genes encoding virulence factors, namely secreted toxins and fibronectin and/or fibrinogen-binding proteins. Of the host genes tested, we found that transcripts encoding host IL-8, IL1β, oncostatin M-like, CCR1, CXCR1 (IL8RA), CCL4 (MIP-1β) and CCL3 (MIP1α)-like proteins were among the most highly up-regulated transcripts during S. aureus abscess formation. Our findings provide additional insight into the pathogenesis of S. aureus SSTIs, including a temporal component of the host response.  These results serve as a springboard for future studies directed to better understand how/why mild or moderate SSTIs progress to invasive disease.

platform_organism: Staphylococcus aureus subsp. aureus USA300

overall_design: Staphylococcus aureus inoculum vs. day 1 of abscess

first: Natalia

last: Malachowa

first: Scott

middle: D

last: Kobayashi

first: Daniel

middle: E

first: Dana

last: Scott

first: Frank

last: DeLeo


title: Genomic copy number aberrations in multiple synchronous lung cancer.

city: Shanghai

first: Yu

last: Liu

address: 1678 Dongfang Road, Pudong District

department: Pediatric Translational Medicine Institute

institute: Shanghai Children's Medical Center

summary: In current study, we applied array-CGH analysis to detect somatic copy number aberrations across tumor genome to help separate multiple primary lung cancers from metastasis cancers.

overall_design: Genomic analysis was carried out in 15 lung adenocarcinomas and one regional lymph node metastasis from 6 patients with multiple synchronous lung cancer. WGS/WES was applied to profile the somatic mutations in each tumor, while array-CGH data was analyzed to screen somatic copy number changes.

first: Jianjun

last: Zhang

first: Lin

last: Li

first: Guangliang

last: Yin

first: Jianhua

first: Shan

last: Zheng

first: Hannah

last: Cheung

first: Ning

last: Wu

last: Lu

first: Xizeng

last: Mao

first: Longhai

last: Yang

first: Jiexin

first: Li

first: Sahil

last: Seth

first: Huang

last: Chen

first: Xingzhi

last: Song

first: Kan

first: Yongqiang

last: Xie

first: Lina

last: Zhou

first: Chuanduo

last: Zhao

first: Naijun

last: Han

first: Wenting

first: Susu

first: Longyun

first: Wenjun

last: Cai

first: Miaozhong

last: Shen

first: Ningzhi

last: Xu

first: Shujun

last: Cheng

first: Huanming

first: J

last: Lee

first: Arlene

last: Correa

first: Junya

last: Fujimoto

first: Carmen

last: Behrens

first: Chi-Wan

last: Chow

first: William

last: William

first: John

last: Heymach

first: Waun

last: Hong

first: Stephen

last: Swisher

first: Ignacio

middle: I

last: Wistuba

first: Jun

last: Wang

first: Dongmei

last: Lin

first: Xiangyang

first: P

last: Futreal

first: Yanning


title: A novel feedback loop  that controls bimodal expression of genetic competence

city: Amsterdam

first: Martijs

last: Jonker

address: Science Park 904

department: Microarray Department

institute: University of Amsterdam

summary: Gene expression can be highly heterogeneous in clonal cell populations. An extreme type of heterogeneity is the so-called bistable or bimodal expression, whereby a cell can differentiate into two alternative expression states, and consequently a population will be composed of cells that are ‘ON’ and cells that are ‘OFF’. Stochastic fluctuations of protein levels, also referred to as noise, provide the necessary source of heterogeneity that must be amplified by autostimulatory feedback regulation to obtain the bimodal response. A classical model of bistable differentiation is the development of genetic competence in Bacillus subtilis. Noise in expression of the transcription factor ComK ultimately determines the fraction of cells that enter the competent state. Due to its intrinsic random nature, noise is difficult to investigate. We adapted an artificial autostimulatory loop that bypasses all known ComK regulators, to screen for possible factors that affect noise in the bimodal regulation of ComK. This led to the discovery of Kre, a novel factor that controls the bimodal expression of ComK. Kre appears to affect the stability of comK mRNA. Interestingly, ComK itself represses the expression of kre, adding a new double negative feedback loop to the intricate ComK regulation circuit. Our data emphasize that mRNA stability is an important factor in bimodal regulation.

overall_design: Comparing wild type Bacillus subtilis strain 168 (n=2) with Bacillus subtilis PG479 (Δkre, n = 3).

first: Pamela

last: Gamba

middle: J

first: Leendert

middle: W

last: Hamoen


title: Tissue-specific gene signatures of gilthead sea bream (Sparus aurata L.) after hyper- and hypo-osmotic challenges

city: Castellón

first: Josep

last: Calduch-Giner

address: Ribera de Cabanes

institute: Institute of Aquaculture Torre de la Sal (CSIC)

summary: Euryhaline teleosts can live in a wide range of environmental salinities. Transcriptomic analysis in important osmoregulatory and non-osmoregulatory tissues (liver, gills and hypothalamus) by means of a specific oligo-microarray revealed new aspects related to the osmoregulatory processes mediated by different canonical pathways after hypo- or hyper-omotic challenges in gilthead sea bream (Sparus aurata) juveniles. Liver was the most responsive tissue to salinity changes. In addition, around 24 %, 8 % and 12 % of the total genes differentially expressed were affected and regulated in the same way (up- or down-regulated) by both hyper- and hypo-osmotic challenges in liver, gills and hypothalamus, respectively. In liver and gills, functional analysis of the differentially expressed genes established 2 major clusters of canonical pathways related to i) Energy Metabolism and ii) Oxidative Stress: Damage and Repair, whereas for hypothalamus only a main clusters linked to Oxidative Stress: Damage and Repair was identified. Further, this common cluster presents different sub-nodes in all analyzed tissues, with a clear dualism between liver and gills in those pathways involved in nitrogenous turnover, as well as between gills and hypothalamus in cell stress processes. In addition, several sub-nodes related to cell and tissue architecture was only found in hypothalamus. Moreover, only genes involved in xenobiotic metabolism signaling canonical pathway were differentially regulated by both hypo- and/or hyper-salinity transfer in the three tissues considered. Our results indicated that hepatic, branchial and hypothalamic transcriptome of the sea bream clearly responded after 7 days in different environmental salinities, when mainly metabolic and different cell functions are activated to reach homeostasis, or even return to their basal levels.

overall_design: Immature males of gilthead sea bream (Sparus aurata L., 80-100 g body mass, n=36)  were acclimated for 10 days to experimental control sea water (SW, 38 ‰ salinity, 1049 mOsm·kg−1 H2O osmolality). Fish were randomly distributed in three 400-L tanks in an open system circuit (~ 2.5 kg·m−3 density), under natural photoperiod and constant temperature (18-19 °C). After the acclimation period, the animals were directly transferred, in duplicate, to the following environmental salinities: seawater (SW, 38 ‰ salinity, control group), low salinity water (LSW, 5 ‰ salinity, 139 mOsm·kg−1 H2O osmolality, hypoosmotic environment), and high salinity water (HSW, 55 ‰ salinity, 1439 mOsm·kg−1 H2O osmolality, hyperosmotic environment). On day 7 post-transfer, fish  were anesthetized with 2-phenoxyethanol (1 mL·L−1 at the specific salinity water). After blood extraction, hypothalamic lobules and representative samples of liver and gills were dissected.

first: Juan

last: Martos-Sitcha

middle: M

last: Mancera

first: Manuel

last: Yúfera

first: Gonzalo

last: Martínez-Rodríguez

first: Jaume

last: Pérez-Sánchez


title: Generation of neural crest cells by direct lineage conversion

city: Baltimore

first: Minoru

last: Ko

address: 251 Bayview Blvd, Suite 100, 10C

summary: Neural crest cells (NC cells) are multipotent cells that emerge from the dorsal region of a fusing neural tube and migrate throughout the developing embryo. Due to their multipotency and divergent roles during embryogenesis, the generation and differentiation of NC cells should be elucidated in more detail. However, difficulties have been associated with isolating and manipulating NC cells for investigation because a limited number of NC cells are generated in a short period of embryogenesis. To overcome this issue, we attempted to directly convert mouse fibroblasts into NC cells using transcription factors specifically expressed in NC cells. We analyzed the molecular profiles of NC cells and neural tube cells in 9.5-day mouse embryos, and identified the transcription factors that were strongly expressed in NC cells. Among these transcription factors, Sox10 together with c-Myc and Klf4 directly converted mouse fibroblasts into NC cells. The converted NC cells differentiated into neurons, glial cells, smooth muscle cells, adipocytes, and osteoblasts, exhibiting differentiation abilities similar to those of in vivo NC cells. They also displayed a self-renewal ability while maintaining their differentiation ability. In in ovo transplantation, the converted NC cells migrated along NC cell migration pathways. Therefore, directly converted NC cells can contribute to the progression of NC cell studies.

overall_design: 3 samples, duplicated. Sox10-positive cells were compared with Sox1-positive cells and/or whole embryo (control).

first: Tsutomu

last: Motohashi

first: Piao

last: Yulan


title: Methylation signature of pluripotent stem cells

city: Paris

first: Pierre

last: de la Grange

address: 29, rue du Faubourg Saint-Jacques

department: Paris Biotech Santé

institute: GenoSplice technology

type: Methylation profiling by genome tiling array

summary:
Two iPSC clones (iKCL004 and iKCL011) were compared with parental human neonatal foreskin fibroblasts BJ (ATCC, CRL-2522) as a negative and hESC line KCL034 as a positive control
Biological triplicates for each line were analyses for epigenome-wide methylation (>480,000 CpG sites) using Infinium Human Methylation 450 BeadChip Kit (Illumina).

overall_design: Bisulphite converted DNA (500 ng/sample) from the 12 samples (3 biological replicates from 4 lines) were hybridized to the Infinium Human Methylation 450 BeadChip Kit (Illumina)

first: Dusko

last: Ilic

first: Laureen

last: Jacquet

first: Dimitra

last: Dafou


title: Combination of autoantibody signature with PSA level enables a highly accurate blood-based differentiation of prostate cancer patients from patients with benign prostatic hyperplasia

city: Homburg

first: Nicole

last: Ludwig

address: Kirrberger Strasse

department: Human Genetics

institute: Saarland University

summary: Although an increased level of the prostate-specific antigen can be an indication for prostate cancer, other reasons often lead to a high rate of false positive results. Therefore, an additional serological screening of autoantibodies in patients’ sera could improve the detection of prostate cancer. We performed protein macroarray screening with sera from 49 prostate cancer patients, 70 patients with benign prostatic hyperplasia and 28 healthy controls and compared the autoimmune response in those groups. We were able to distinguish prostate cancer patients from normal controls with an accuracy of 83.2%, patients with benign prostatic hyperplasia from normal controls with an accuracy of 86.0% and prostate cancer patients from patients with benign prostatic hyperplasia with an accuracy of 70.3%. Combining seroreactivity pattern with a PSA level of higher than 4.0 ng/ml this classification could be improved to an accuracy of 84.1%. For selected proteins we were able to confirm the differential expression by using Lluminex on 84 samples. We provide a minimally invasive serological method to reduce false positive results in detection of prostate cancer and according to PSA screening to distinguish men with prostate cancer from men with benign prostatic hyperplasia.

overall_design: Comparison of autoantibodies against 1827 E.coli expressed cDNA clones in patients with prostate cancer (n=49), benign prostate hyperplasia (n=70) and healthy controls (n=28)

first: Petra

last: Leidinger


title: The Rio1 kinase downregulates RNA polymerase I to promote rDNA stability and segregation

city: Milan

first: Peter

last: De Wulf

address: via Adamello 16

department: Department of Experimental Oncology

institute: European Institute of Oncology

summary: To sustain growth, budding yeast actively transcribes its ribosomal gene array (rDNA) in the nucoleolus to produce ribosomes and proteins. However, intense transcription during rDNA replication may provoke collisions between RNA polymerase I (Pol I) and the replisome, may cause replication fork instability, double-strand breaks, local recombinations and rDNA instability. The latter is manifested by rDNA array expansion or reduction and the formation of extrachromosomal rDNA circles, anomalies that accelerate aging in yeast. Transcription also interferes with the resolution, condensation and segregation of the sister chromatid rDNA arrays. As a consequence, rDNA segregation lags behind the rest of the yeast genome and occurs in late anaphase when rDNA transcription is temporarily shut off. How yeast promotes the stability and transmission of its rDNA array while satisfying a constant need for ribosomes remains unclear.  Here we show that the downregulation of Pol I by the conserved cell cycle kinase Rio1 spatiotemporally coordinates rDNA transcription, replication and segregation. More specifically, Rio1 activity promotes copy-number stability of the replicating rDNA array by curtailing Pol I activity and by localising the histone deacetylase Sir2, which establishes a heterochromatic state that silences rDNA transcription. At anaphase entry, Rio1 and the Cdc14 phosphatase target Pol I subunit Rpa43 to dissociate Pol I from the 35S rDNA promoter. The rDNA locus then condensates and segregates, thereby concluding the genome transmission process.  Rio1 is involved in ribosome maturation in the cytoplasm of budding yeast and human cells. Additional engagements in the cytoplasm or roles in the nucleus are unknown. Our study describes its first nuclear engagement as a Pol I silencing kinase. This activity may prove highly relevant as dysregulated RNA polymerase I activity has been associated with cancer initiation and proliferation.

overall_design: ChIP-on-chip analyses were carried out as described in Bermejo R. et al., Meth. Mol. Biol. 582: 103-18 (2009). Labelled probes were hybridized to Affymetrix S.cerevisiae Tiling 1.0 (P/N 900645) arrays and processed with TAS software.

first: Maria

last: Iacovella

first: Cristina

last: Golfieri

first: Lucia

last: Massari

first: Cinzia

last: Pagliuca

first: Valentina

last: Infantino

first: Sara

last: Busnelli

first: Marianna

last: Dal Maschio


title: Bifidobacterium breve UCC2003 metabolizes lacto-N-tetraose and lacto-N-neo-tetraose through overlapping, yet distinct pathways

status: Public on Feb 09 2017

city: Cork

first: Mary

last: O'Connell Motherway

address: Western Road

department: Department of Microbiology and Alimentary Pharmabiotic Centre

country: Ireland

institute: University College Cork

summary: Recent studies have begun to elucidate the mechanisms of utilisation of some human milk oligosaccharides (HMO) components by Bifidobacterium breve. However, this phenomenon is still relatively poorly understood, with little to no work to date in understanding a number of specific structures common to HMO.   In this study, we demonstrate that the prototype B. breve strain UCC2003 possesses specific metabolic pathways for the utilisation of Lacto-N-Tetraose and Lacto-N-neoTetraose, which represent the central moieties of Type I and Type II HMOs, respectively. Using a combination of experimental approaches, the enzymatic machinery involved in the metabolism of these two HMO structures was identified and characterised. Homologs of tWe also identified the key genetic loci involved in the utilisation of these HMO substrates in B. breve, B. bifidum and B. longum subsp. infantis using bioinformatic analyses were shown to be, and noted the relatively variably present among other members ofscant distribution of their homologs across the Bifidobacterium genus as a whole, withwhile noting a distinct pattern of conservation of LNB utilisation genes inamong human-associated bifidobacterial species.

overall_design: DNA-microarrays containing oligonucleotide primers representing each of the 1864 annotated genes on the genome of B. breve UCC2003 were designed by and obtained from Agilent Technologies (Palo Alto, Ca., USA). Methods for cell disruption, RNA isolation, RNA quality control, complementary DNA synthesis and labeling were performed as described previously (Pokusaeva et al., 2009). Labeled cDNA was hybridized using the Agilent Gene Expression hybridization kit (part number 5188-5242) as described in the Agilent Two-Color Microarray-Based Gene Expression Analysis v4.0 manual (G4140-90050). Following hybridization, microarrays were washed in accordance with Agilent’s standard procedures and scanned using an Agilent DNA microarray scanner (model G2565A). Generated scans were converted to data files with Agilent's Feature Extraction software (Version 9.5). DNA-microarray data were processed as previously described (Garcia De La Nava et al., 2003). Differential expression tests were performed with the Cyber-T implementation of a variant of the t-test (Long et al., 2001). A gene was considered differentially expressed when p < 0.001 and an expression ratio of >3 or <0.33 relative to the control.

first: Kieran

last: James


title: ChIP-chip assay on circular chromosome conformation capture (4C) genomic DNA sample from human telomerase-immortalized corneal epithelial (HTCE) cells with the specification of CTCF binding

first: luo

last: lu

address: 1124 W. Carson Street

department: molecular medicine

institute: LA BioMed

summary: Ability of CTCF binding on various gene promoters is essential to regulate their expression. It's been demonstrated that cornea-specific Pax6 expression is regulated conversely by CTCF (Li et al.). circular chromosome conformation capture (4C) and ChIP-chip profiling have been performed using HTCE cells. This approach is to elicit the epigenetic mechanism involving CTCF-mediated chromatin remodeling that regulates Pax6 and some target gene interactions.

overall_design: Compare CTCF interactions of gene promoters in HTCE cell

first: Jie

last: Wang

first: Luo

last: Lu


title: Methylation profiles of lung adenocarcinoma patients in Taiwan

city: Tainan

first: Yi-Ching

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

department: Department of Pharmacology, College of Medicine

country: Taiwan

institute: National Cheng Kung University

summary: Genome wide DNA methylation profiling of tumor samples with lung adenocarcinoma patients. The Illumina HumanMethylation27 BeadChip array was used to obtain DNA methylation profiles across approximately 27,578 CpGs in lung cancer samples. Samples included tumor samples with lung adenocarcinoma.

overall_design: Bisulfite converted DNA from the 39 adenocarcinoma samples were hybridised to the Illumina HumanMethylation27 BeadChip array.

first: I-Ying

last: Kuo

first: Jayu

last: Jen


title: Rhodobacter sphaeroides 2.4.1 pPos19 versus pBBR under singlet oxygen stress

city: Gießen

first: Gabriele

last: Klug

address: Heinrich-Buff-Ring 26-32

department: Molecular- and Microbiology

institute: Justus-Liebig University Gießen

summary: To learn more about the function of Pos19, we constructed an over-expression strain. For this purpose, the Pos19 gene together with its native RpoE promoter was cloned into the middle-copy plasmid pBBR1 and expressed in the R. sphaeroides wild-type 2.4.1 background. The corresponding strain consequently exhibits a singlet oxygen-induced Pos19 over-expression compared to an empty vector control. Total RNA from the over-expression (pPos19) and from the empty vector control (pBBR) strain was extracted after 7 min of singlet oxygen stress and used for microarray analysis to investigate Pos19-induced changes on transcriptome level.

overall_design: RNA samples collected after 7 min of singlet oxygen stress were analyzed by two-color microarrays. Each microarray contains a pool of three independent biological replicates for each sample.

first: Bork

last: Berghoff


title: Enrichment of pluripotent stem cell-derived hepatocyte-like cells

city: Matsumoto

first: Daihachiro

last: Tomotsune

state: Nagano

address: 3-1-1 Asahi

department: Institute for Biomedical Sciences

institute: Shinshu University

summary: The gene expression profiles of differentiating human pluripotent stem cells (hPSCs) were analyzed by DNA microarray. We identified differences and commonalities among six human pluripotent stem cell lines: the hESCs KhES1, KhES2, KhES3, and H1, and the iPSCs 201B7 and 243G1.  Analysis of DNA microarray data suggested that hepatocyte-like differentiation of EBs treated with ammonia in Lanford medium.

overall_design: Undifferentiated pluripotent stem cells were prepared using the standard method with MEF-coated dishes (ML) or MEF-conditioned medium method with matrigel-coated dishes (MC).  EB were formed by transferring small clumps (200 µm diameter) of hPSCs to a non-adhesive 60-mm dish coated with Lipidure. Suspension cultures were maintained for 5 days.  Following EB formation, 1 µL/mL of 10% w/v aqueous ammonia (Wako) was added to fresh Lanford medium. This process was repeated every 2 days for 14 days total.

first: Katsunori

last: Sasaki


title: Difference in circulating microRNAs between grazing and grain-fed Japanese Black cattle

city: Tsukuba

first: Susumu

last: Muroya

state: Ibaraki

address: Ikenodai 2

department: Animal Products Research Division

institute: NARO Institute of Livestock and Grassland Science

summary: We aimed to elucidate the effects of feeding condition (indoor grain-feeding vs. grazing on pasture) on c-miRNAs in Japanese Black (JB) cattle (Wagyu). The cattle at 18 months old were divided into pasture feeding and conventional indoor grain feeding for 5 months. Microarray analysis of c-miRNAs from the plasma extracellular vesicles led to the detection of a total of 202 bovine miRNAs in the plasma, including 15 miRNAs that differed between the feeding conditions.

overall_design: miRNA expression in plasma extracellular vesicles (Evs) of the cattle was measured after 5 months of grazing or grain feeding. Plasma EV samples prepared from three cattle for each treatment were collected for microarray analysis .


title: Gene expression profiles of HEK293T cells following EBV-miR-BART6-3p mimics transfection

city: Changsha

first: Wei

last: Xiong

state: Hunan

address: 110 Xiangya Road

department: Cancer Research Institute

institute: Central South University

summary: EBV encodes 44 mature miRNAs, a number of which have been found to promote carcinogenesis by targeting host genes. To determine the biological functions of the BART cluster miRNAs, we singly transfected these miRNAs into HEK293T cells. Interestingly, we found that overexpression of EBV-miR-BART6-3p in HEK293T cells dramatically altered HEK293T cell shape. To explore the mechanism of EBV-miR-BART6-3p-mediated inhibition of cell migration and invasion, we attempted to identify its downstream host cellular genes by whole genome microarray, which contains probes to all known human protein coding genes (mRNAs) and long non-coding RNA genes (lncRNAs).

overall_design: EBV-miR-BART6-3p induced gene expression in human embryonic kidney cell line HEK293T was measured after transfected by EBV-miR-BART6-3p mimics.

first: Zhaoyang

last: Zeng

first: Baoyu

last: He

first: Guiyuan

last: Li


title: Large-scale microRNA expression profiling identifies retinal miRNA-mRNA signaling pathways underlying form-deprivation myopia in mice

city: New York

first: Andrei

last: Tkatchenko

state: NY

address: 160 Ft Washington Ave

department: Ophthalmology

country: USA

institute: Columbia University

summary: Development of myopia is associated with large-scale changes in ocular tissue gene expression. Although differential expression of coding genes underlying development of myopia has been a subject of intense investigation, the role of non-coding genes such as microRNAs in the development of myopia is largely unknown. In this study, we explored myopia-associated miRNA expression profiles in the retina and sclera of C57Bl/6J mice with experimentally induced myopia using microarray technology. We found a total of 53 differentially expressed miRNAs in the retina and no differences in miRNA expression in the sclera of C57BL/6J mice after 10 days of visual form deprivation, which induced -6.93 ± 2.44 D (p < 0.000001, n = 12) of myopia. We also identified their putative mRNA targets among mRNAs found to be differentially expressed in myopic retina and potential signaling pathways involved in the development of form-deprivation myopia using miRNA-mRNA interaction network analysis. Analysis of myopia-associated signaling pathways revealed that myopic response to visual form deprivation in the retina is regulated by a small number of highly integrated signaling pathways. Our findings highlight substantial involvement of miRNAs in the regulation of refractive eye development, and in the development of myopia through the retinal gene regulation.

overall_design: Differential expression of microRNAs was analyzed in the retina and sclera of C57BL/6J mice after 10 days of visual form deprivation. Visual form deprivation was carried out from P24 through P34. Three replicates were used per condition, i.e., myopia versus control.

first: Xiaoyan

last: Luo

first: Tatiana

first: Candida

last: Vaz

first: Vivek

last: Tanavde

first: Sebastian

last: Maurer-Stroh

first: Stefan

last: Zauscher

first: Pedro

last: Gonzalez

first: Terri

middle: L

last: Young


title: Comparison and analysis of gene expression between cattle and buffalo after infection with schistosoma japonicum

city: shanghai

first: yang

middle: jian

last: mei

address: minhang district ziyue road No.518

institute: shanghai veterinary research institute

summary: The microarray analysis of gene expression difference between cattle and buffalo, provide us a profiling as a new platform to discover the difference between their compatibility with schistosoma japonicum.

sample_organism:
Bos taurus
Bubalus bubalis

overall_design: Peripheral blood were collected from the cattle and buffalo before and after they infected at 49d (7weeks) with schistosoma japonicum. Three animals were perfused for each host.

first: Jianmei

last: Yang

first: Jiaojiao

last: Lin

first: Zhiqiang

last: Fu


title: Disabled-2 is a negative immune regulator of lipopolysaccharide-stimulated Toll-like receptor 4 internalization and signaling

city: Taoyuan

first: Ching-Ping

last: Tseng

address: No.259, Wenhua 1st Rd., Guishan Dist.

institute: Chang Gung University

summary: Toll-like receptor 4 (TLR4) plays a pivotal role in the host response to lipopolysaccharide (LPS), a major cell wall component of Gram-negative bacteria. Here we elucidated whether the endocytic adaptor protein Disabled-2 (Dab2) that is abundantly expressed in the macrophages plays a role in LPS-stimulated TLR4 signaling and trafficking. Molecular analysis and transcriptome profiling of the RAW264.7 macrophage-like cells expressing short-hairpin RNA of Dab2 revealed that Dab2 mainly regulated LPS-stimulated TRIF-dependent, but not MyD88-dependent TLR4 signaling. Consequently, knockdown of Dab2 augmented TRIF-dependent interferon regulatory factor 3 activation and the expression for the subsets of inflammatory cytokines and interferon-inducible genes. We further delineated that Dab2 acted as a “clathrin sponge” and sequestered clathrin from TLR4/MD2 complex in the resting stage of macrophages. Clathrin was released from Dab2 and associated with TLR4 to facilitate the internalization of TLR4/MD2 complex together with the bound ligand from the cell surface upon LPS stimulation. Dab2 thereby functions as a negative immune regulator of TLR4 endocytosis and signaling, supporting a novel role of Dab2-associated regulatory circuit in the control of inflammatory response of macrophage to endotoxin.

overall_design: In this study, RAW264.7 macrophage-like cells expressing short-hairpin RNA of Dab2 revealed that Dab2 mainly regulated LPS-stimulated TRIF-dependent, but not MyD88-dependent TLR4 signaling upon LPS stimulation.

first: Wei-Shan

last: Hung


title: Reduced genetic tumor heterogeneity after neoadjuvant chemotherapy is related to favorable outcome in patients with esophageal adenocarcinoma

city: Rotterdam

first: Askar

last: Obulkasim

state: Zuid Holland

address: Wytemaweg 80

department: Pediatric Oncology

country: Netherlands

institute: ErasmusMC - Sophia Children's Hospital

summary: The incidence of oesophageal adenocarcinoma (OeC) has been increasing rapidly in most Western countries during the last few decades. Although multimodal treatment combining pre-operative chemotherapy with radical surgical resection has become the standard of care in the UK for all patients with locally advanced resectable disease, the 5-year survival rate in this patient group is less than 25%. Only 30% of all patients will benefit from pre-operative chemotherapy. Hence, there is an urgent clinical need to identify genomic markers that allow stratification of patients for a more individualised therapy approach. The goal of this study is to use whole genome high-resolution array CGH to examine the DNA copy number profile of a subset of OeC patients recruited into the OE02 trial and establish it’s relationship with clinicopathological variables including pathological tumor regression and patient survival. High-resolution array CGH analysis was conducted on 84 formalin fixed paraffin embedded resection samples obtained from subjects enrolled in the Oe02 trial. We compared the DNA copy number profiles between patients treated with chemotherapy and surgery and those treated with surgery alone. DNA copy number entropy was assessed to identify differences in overall copy number aberrations between the two treatment groups. Furthermore, the association between DNA copy number aberrations and tumor regression grade was investigated. The genetic make-up of OeCs investigated in the current study proved to be highly complex reducing our ability to determine the background normal copy number level in a tumor sample. Using DNA copy number entropy as a measure to compare sample profiles, we identified significant treatment arm specific DNA copy number aberration patterns predominantly in chromosome 1 and 5. High DNA copy number entropy was associated with longer overall survival. Differential DNA copy number entropy was observed between the two treatment groups, and the positions of the driving DNA regions were identified. To our surprise, the differences between the treatment groups went unnoticed when a standard test was applied. We also found that the DNA copy number entropy was strongly correlated with patients’ overall survival and clinicopathological characteristics. To the best of our knowledge, this is the first study in OeC quantitatively showed that the tumor heterogeneity was reduced by chemotherapy. And, the observed tumor heterogeneity was shown to has prognostic value. However, further research is needed to narrow down these regions to a few driving genes/probes that may aid in predicting whether a new patient will benefit from chemotherapy.

overall_design: Two-condition experiment, CS vs. S patients. Biological replicates: 40 samples from pre-operative chemotherapy treated patients, 35 samples from surgery alone patients.

first: Bauke

last: Ylstra

first: Hendrik

middle: B

last: van Essen

first: Christian

last: Benner

first: Sally

last: Stenning

first: William

middle: H

last: Allum

first: David

last: Cunningham

first: Imran

last: Inam

first: Nicholas

last: West

first: Gerrit

last: Meijer

first: Mark

last: van de Wiel

first: Heike

last: Grahsch


title: A map of mobile DNA insertions in the NCI-60 human cancer cell panel

first: John

last: Zampella

state: MD

address: 733 N Broadway

department: Dermatology

institute: Johns Hopkins University School of Medicine

summary: The National Cancer Institute-60 (NCI-60) cell lines are among the most widely used models of human cancer. They provide a platform to integrate DNA sequence information, epigenetic data, RNA and protein expression, and pharmacologic susceptibilities in studies of cancer cell biology. Genome-wide studies of the NCI-60 have included exome sequencing, karyotyping, and copy number analyses but have not targeted repetitive sequences. Interspersed repeats are a significant source of heritable genetic variation, and insertions of active elements can occur somatically in malignancy. To approach a functional understanding of these sequences in transformed cells, we used transposon insertion profiling (TIP) to map Long INterspersed Element-1 (LINE-1, L1) and Alu Short INterspersed Element (SINE) insertions in cancer genes in NCI-60 cells. As expected, this identified known insertions, polymorphisms shared in unrelated tumor cell lines, as well as unique, potentially tumor-specific insertions. Here, we report a map of these insertion sites and conduct association analyses relating individual insertions to a variety of cellular phenotypes.

overall_design:
60 cell lines representing nine different types of neoplasias were mapped for LINE-1 and Alu transposable elements using a TIP-CHIP microarray tiling known cancer genes
Please note that a technique called TIP-Chip was used to discover transposable elements (TE) in the NCI-60 cancer cell lines. The process uses labeled unique 3' DNA amplicons adjacent to these elements to map the TEs in the genome. These 3' amplicons are hybridized to the array and serve as a marker to identify a genomic coordinate. When the array scanner generate .gff output files as raw data output files on which clean-up algorithms and subsequent analysis were performed (resulting in peak files in text format).

first: Wan

middle: R

last: Yang

first: Nemanja

last: Rodric

first: Cheng

last: Huang

first: Jane

last: Welch

first: Veena

middle: P

last: Gnanakkan

first: Toby

last: Cornish

first: Jef

last: Boeke

first: Kathleen

last: Burns


title: Prenatal hyperbaric normoxia exposure alters gene expression in male and female Drosophila melanogaster

city: Seoul

first: Suyeun

last: Yu

address: 5-Ka, Anam-dong, Sungbuk-Ku

department: preventive medicine

country: South Korea

institute: Korea university medical college

summary: We investigated the hormetic effects of prenatal hyperbaric normoxia exposure on Drosophila healthspan related to molecular defense mechanisms. HN exposure had no disruptive effect on developmental rate or adult body weight. However, lifespan was clearly enhanced, as was resistance to oxidative and heat stress. In addition, levels of reactive oxygen species were significantly decreased and motor performance was increased. Furthermore, to determine the hormetic mechanism underlying these phenotypic and molecular changes, we performed a genome-wide profiling in HN-exposed and control flies. Genes encoding chitin metabolism were highly up-regulated in both sex, which could possibly serve to scavenge free radicals. These results identify prenatal HN exposure as a potential hormetic factor that may improve longevity and healthspan by enhancing defense mechanisms in Drosophila.

overall_design: After HA exposure during development, all newly born (F1) flies were maintained in a climate-controlled incubator. Each experiment was performed with 10-day-old flies.

first: Eunil

last: Lee


title: A microRNA driven epithelial differentiation model: primary culture and long-term expansion of intestinal epithelial cells

city: Berlin

first: Soroush

last: Sharbati

address: Oertzenweg 19b

department: Institute of Veterinary Biochemistry

institute: Freie Universitaet Berlin

summary: In this study, we put specific efforts in the development of primary intestinal colonic cells (CEC) in monolayer culture that can be expanded to phenotypically uniform and stable, finite cell lines. Morphological assessment showed that limited passaging had no obvious effect on phenotype and proliferation of CEC. For a fundamental verification of this observation we performed a whole transcriptome microarray study using isolates from 2 different animals and CEC culture passages 1 to 4. Data analysis did not reveal any effect of subcultivation on the global gene expression. When comparing the two different isolates, interindividual effects on expression profiles were not observed. Functional annotation of the genes showing robust expression in cell culture (log ratios ≥ 0, compared with native tissue) pointed to a high metabolic activity, migratory capacity and a stable degree of mesenchymal marker expression and supporting the crypt-like character.

overall_design: Intestinal epithelial cells (passage 1-4) originally isolated from ascending colon of 2 individual piglets were cultivated in 25 cm2 cell culture flasks until confluence. Additionally original colon tissues were used as the common reference. Number of samples: 8 samples plus 1 common reference; 2 merged replicate microarrays for CEC#11P2 sample; Reference sample: RNA from pooled whole tissue samples from ascending colon; Dye Swaps: none

first: Jutta

first: Carlos

last: Hanisch

first: Robert

last: Pieper

first: Ralf

last: Einspanier


title: In Silico transcriptional regulatory networks during tomato fruit ripening

city: Chania

first: Panagiotis

last: Kalaitzis

address: Alsyllio Agrokepio, 1 Makedonias str

department: Horticultural Genetics and Biotechnology

institute: Mediterranean Agronomic Institute of Chania (MAICh)

summary: The aim of this study is to generate gene regulatory networks by analyzing Affymetrix GeneChip expression datasets from four different stages of tomato fruit ripening, Breaker (Br), Turning (Tu), Pink (Pk) and Red Ripe (RR) with the LeMoNe algorithm in order to identify co expression modules and their putative regulatory TFs.

overall_design: 9 samples were analyzed in total, mainly 2 replicates for each developmental stage.

first: Andreas

last: Perrakis

first: Craita

last: Bita

first: Stilianos

last: Arhondakis


title: Circulating microRNAs reprogramming are involved in early acclimatization to high altitude in humans

city: Chongqing

first: bao

last: liu

address: 30 Gaotanyan street

department: Institute of Medicine and Hygienic Equipment for High Altitude Region

country: China

institute: 3rd Military Medical University

summary: Altitude acclimatization is the physiological process to restore oxygen delivery to the tissues and promote the oxygen application under high altitude hypoxia. High altitude illness could happen in individuals who did not get acclimatization. Unraveling the molecular underpinnings of altitude acclimatization would help people to understand the beneficial response of body to high altitude hypoxia and disturbed biological process in un-acclimatized individuals. Here, we measured physiological adjustments and circulating microRNAs (cmiRNAs) profiles of individuals exposed to high altitude to explore the altitude acclimatization in humans.

overall_design: In this study presented here, a total of 22 volunteers were enrolled in this study. Circulating microRNA (cmiRNAs) expression profiles were scanned by miRCURYTM LNA Array (v.18.0) (Exiqon) array in all individuals before and after exposure to high altitude. Eighty-six cmiRNAs (79 up-regulated and 7 down-regulated) showed differential expression with statistical significance after exposure to high altitude.

first: Bao

last: Liu

first: YuQi

last: Gao


title: microRNA profilling in dendritic cells of systemic lupus erythematosus

city: Shanghai

first: Yilun

last: Wang

address: No.12 Wulumuqi Zhong Road

institute: Fudan University

summary: Recent studies have shown that alterations in the function of dendritic cells (DCs) are involved in the pathogenesis of systemic lupus erythematosus (SLE). However, the role of DCs participating in SLE remains unclear. We profiled the microRNAs (miRNAs) of LPS-stimulated DCs in SLE patients and found diffentially expressed miRNAs in DCs of such group patients.

overall_design: Two-condition experiment, DC (as controls) vs. SLG (as patients with SLE group) cells. Biological replicates: 5 control replicates, 5 patient replicates.

first: Jinhua

last: Xu

first: Haihong

last: Qin

first: Qi

last: Zhang

first: Jun

last: Liang

first: Jinran

last: Lin


title: Aberrant methylation-mediated silencing of microRNAs contributes to HPV-induced anchorage independence [miR-Agilent]

city: Amsterdam

first: Saskia

last: Wilting

address: De Boelelaan 1117

institute: VU University Medical Center

summary: Cervical cancer and a subset of anogenital and head-and-neck carcinomas are caused by persistent infection with high-risk types of the human papillomavirus (hrHPV). Early stages of hrHPV-induced carcinogenesis can be faithfully mimicked in vitro. A major hallmark of hrHPV-transformed cells is their ability to grow anchorage independently, an oncogenic trait known to depend on inactivation of tumour suppressor genes. This study used an in vitro model of hrHPV-induced transformation to delineate in a longitudinal manner to what extent DNA methylation-mediated silencing of tumour suppressive microRNAs (miRNAs) contributed to hrHPV-induced anchorage independence.  Genome-wide miRNA expression profiles were yielded from anchorage dependent (n=11) and independent passages (n=19) of 4 hrHPV-immortalised keratinocyte cell lines with and without demethylating treatment (DAC). Unsupervised clustering analysis showed that overall miRNA expression patterns discriminated between anchorage dependent and independent cells. Ten miRNA genes potentially silenced by methylation were selected and validated by bisulfite sequencing and methylation-specific PCR. Hsa-mir-129-2, -137, -935, -3663, -3665, and -4281 showed increased methylation in both HPV-transformed keratinocytes and cervical cancer cell lines compared to primary keratinocytes. Mature miRNAs derived from hsa-mir-129-2, -137, -3663, and -3665 decreased anchorage independence in cervical cancer cell lines. Finally, significantly increased methylation of hsa-mir-129-2, -935, -3663, -3665, and -4281 was observed in cervical (pre)cancerous lesions, underlining the clinical relevance of our findings.    In conclusion, methylation-mediated silencing of tumour suppressive miRNAs contributes to the acquisition of anchorage independence, supporting the importance of miRNAs during early stages of carcinogenesis and underlining their potential as both disease markers and therapeutic targets.

overall_design: 6-8 sequential passages of 4 HPV-transformed human foreskin primary keratinocyte cell lines were treated with the demethylating agent 5-aza-2’-deoxycytidine (DAC). Genome-wide microRNA (miRNA) expression was measured by Agilent 8x60K miRNA microarrays for all 6-8 passages of all 4 cell lines with and without DAC treatment.

first: Viktorian

last: Miok

first: Annelieke

last: Jaspers

first: Debby

last: Boon

first: Hanne

last: Sørgård

first: Malin

last: Lando

first: Barbara

middle: C

last: Snoek

first: Wessel

last: van Wieringen

first: Chris

last: Meijer

first: Heidi

last: Lyng

first: Peter

last: Snijders

first: Renske

last: Steenbergen


title: Epigenome-wide assoication analysis of HIV infection

city: New Haven

first: Ke

last: Xu

address: 300 George St.

department: department of psychiatry

institute: Yale University

summary:
Genome wide DNA methylation profiling of HIV-infected and uninfected individuals for DNA samples extracted from peripheral blood. The Illumina Infinium  Human DNA methylation 450 Beadchip was used to obtain DNA methylation profiles across approximately 480,000 CpGs. Samples included 261 HIV-infected and 117 HIV-uninfected individuals. The goal was to identify genome-wide differentially methylated CpG sites between HIV-infected and uninfected samples.
Bisulfite converted DNA from the 378 DNA samples were hybridized to the Illumina Infinium 450K Human Methylation Beadchip. The samples were extracted from whole blood. The subjects including 261 HIV-infected and 117 HIV-uninfected were recruited from the Veteran Aging Cohort Study. All subjects were inform consented and the study protocol was approved by Connecticut Veteran Affair Healthcare System IRB and Yale Human Research Protection Program at Yale University.

overall_design: Ke, Xu

first: Xinyu

first: Amy

last: Justice


title: Transcriptomic changes in maize roots triggered by urease inhibitor NBPT

city: Verona

first: Anita

last: Zamboni

address: Strada Le Grazie, 15

department: Biotechnology

country: Italy

institute: University of Verona

summary: In the soil the stability of urea is affected by the presence of urease, a ubiquitous enzyme released in the rhizosphere by microbial population and by decomposition of organic matter. To reduce the impact on farmer economies and environmental pollution, a common agronomical practice consists of applying urease inhibitors which delays the hydrolysis of urea and, in turn, ammonia is slowly release in the soil. General aim of the present work was the description of changes in maize root transcriptome occurring in response to treatment with the urease inhibitor NBPT.

overall_design:
5-d-old maize plants were treated for 8 hours with nutrient solution containing nitrogen in form of urea (0.5 mM) and 0.897 µM NBPT (N(n-butyl)thiophosphoric-triamide), urease inhibitor.
Three different biological replicates were used for each sample repeating the experiment three times. All samples were obtained pooling roots of six plants.

first: Laura

last: Zanin

first: Silvia

last: Venuti

first: Nicola

last: Tomasi

first: Zeno

last: Varanini

first: Roberto

last: Pinton


title: The dynamic transcriptome of natural competence in Streptococcus suis

city: Wageningen

last: van Baarlen

address: De Elst 1

department: Animal Sciences

institute: Wageningen University

summary: Streptococcus suis is a major pig pathogen as well as an emerging zoonotic pathogen. In a previous study (Zaccaria et al. Plos One DOI: 10.1371/journal.pone.0099394) we identified the natural pheromone-induced competence system of S. suis. To identify the mechanisms enabling competence, gene expression analysis of bacteria induced or not for competence, and in presence or absence of exogenous DNA, was assessed at 5, 15 and 45 minutes after pheromone addition. The transcriptomes showed how competence was induced and eventually shut down, and which metabolic pathways were repressed or induced when competence was active or shut down.

overall_design:
In this experiment, S. suis bacteria were grown in THB, exposed to three different conditions and RNA was extracted at three different timepoints: 5, 15 and 45 minutes after the zer timepoint which was essentially the induction of competence. The three conditions were: bacteria were (i) either growing in THB with no other additions, or (ii) grown in THB in the presence of competence-inducing pheromone but without exogenously added DNA, or (iii) grown in presence of pheromone and exogenous DNA. RNA samples extracted from the bacteria were hybridised once per array.
-----------------------------
The samples above refer to the raw array data shown in the Matrix worksheet. The corresponding biological comparisons and their statistics are shown in the separate worksheet, Array Results.
The samples are as follows:
Sample 1: suis WT O.D. 0.04 + 15 minutes of incubation with competence peptide and DNA VS suis WT O.D. 0.04 + 5 minutes of incubation with competence peptide and DNA
Sample 2: suis WT O.D. 0.04 + DNA 15’ (No peptide) VS suis WT O.D. 0.04 + 15 minutes of incubation with competence peptide (No DNA)
Sample 3: suis WT O.D. 0.04 + DNA 45’ (No peptide) VS suis WT O.D. 0.04 + 45 minutes of incubation with the competence peptide and DNA
Sample 4: suis WT O.D. 0.04 + 15 minutes of incubation with competence peptide and DNA VS suis WT O.D. 0.04 + DNA 15’ (No peptide)
Sample 5: suis WT O.D. 0.04 + Pep 15’ (no DNA) VS suis WT O.D. 0.04 + 15 minutes of incubation with competence peptide and DNA
Sample 6: suis WT O.D. 0.04 + DNA 15’ (No peptide) VS suis WT O.D. 0.04 + DNA 45’ (No peptide)
Sample 7: suis WT O.D. 0.04 + 45 minutes of incubation with the competence peptide and DNA VS suis WT O.D. 0.04 + 15 minutes of incubation with competence peptide and DNA
Sample 8: suis WT O.D. 0.04 + 5 minutes of incubation with competence peptide and DNA VS suis WT O.D. 0.04 + 45 minutes of incubation with the competence peptide and DNA

first: Edoardo

last: Zaccaria

first: Michiel

last: Wels


title: Fusarium oxysporum f.sp. radicis-lycopersici induces distinct transcriptome reprogramming in resistant and susceptible isogenic tomato lines

first: Alberto

last: Ferrarini

state: Veneto

address: Strada le Grazie, 15

department: Scientific and Technological Department

summary: Background: Fusarium oxysporum f.sp. radicis-lycopersici (FORL) is one of the most destructive necrotrophic pathogen of tomato, causing important field and greenhouse yield losses.  Despite the relevant economic impact, little is known about the molecular mechanisms regulating the Fusarium oxysporum f.sp. radicis-lycopersici resistance in tomato.   Results: A transcriptomic experiment was carried out in order to  investigate major mechanisms of FORL response in resistant and susceptible isogenic tomato lines. The microarray analysis at 15 DPI reveals a distinct gene expression pattern between the two genotypes in the inoculated vs not inoculated conditions, furthermore confirmed by a q-PCR experiment. A model of plant response for both compatible and incompatible reaction was proposed. In particular,  in the incompatible interaction an activation of defense genes related to secondary metabolites production and tryptophan metabolism was observed. Moreover, the cell osmotic potential maintenance after the FORL roots challenging was mediated by a dehydration induced protein. As for the compatible interaction the activation of an oxidative burst mediated by Peroxidases and a Cytochrome monooxigenase,  conducedthe cells to degeneration and  necrosis.   Conclusions: Our work allowed a comprehensive understanding of the molecular basis of the tomato-FORL interaction. Result obtained emphasizes a different transcriptional reaction between the resistant and the susceptible genotype to FORL challenging. Our findings could lead to the improvement of strategies of this disease control.

overall_design: Transcriptional profiles obtained by roots inoculated with Fusarium oxysporum f.sp. radicis-lycopersici (FORL) and by healthy control roots from tomato varieties resistant (Momor) or susceptible (Monalbo) to FORL were compared. Two different biological replicates were used for each sample.

first: Daniele

last: Manzo

first: Francesca

last: Ferriello

first: Gerardo

last: Puopolo

first: Astolfo

last: Zoina

first: Daniela

last: D'Esposito

first: Luca

last: Tardella

first: Luigi

last: Frusciante

first: Maria

last: Ercolano


title: Transcriptome response of avocado roots subjected to flooding and infection by the oomycete Phytophthora cinnamomi

city: Pretoria

first: Bianca

last: Reeksting

address: 117 Lunnon Road

department: Department of Genetics

country: South Africa

institute: University of Pretoria

summary: Transcriptome response of avocado roots subjected to flooding, infection by the oomycete Phytophthora cinnamomi or a combination of both. Analysis was carried out at two time-points. Aim was to identify important genes in response to these stresses.

overall_design: Four-condition experiment: Flooded,Infected, Control, Flooded and Infected. Reference design. Biological Replicates: Three replicates for each treatment at each time-point.

first: Noelani

last: van den Berg


title: Modular Transcriptional Repertoire and microRNA target Analyses Characterize Genomic Dysregulation in the Thymus of Down Syndrome Infants

city: Sao Paulo

first: Carlos

middle: Alberto

last: Moreira-Filho

state: SP

address: Av. Dr. Eneas Carvalho de Aguiar 647

department: Departments of Pediatrics

country: Brazil

institute: Faculdade de Medicina da Universidade de Sao Paulo

summary: Trisomy 21- driven transcriptional alterations in human thymus were characterized through gene coexpression network (GCN) and microRNA-target analyses. We used whole thymic tissue (corticomedullar sections) - obtained at heart surgery from Down syndrome (DS) and karyotipically normal individuals (CT) - and a network-based approach for GCN analysis that allows the identification of modular transcriptional repertoires and the interactions between all the system’s constituents through community detection. Changes in the degree of connections observed for hierarchically important hubs/genes in CT and DS gene networks corresponded to sub-network changes, i.e. module (communities) changes. Distinct communities of highly interconnected gene sets were topologically identified for DS and CT networks. The role of microRNAs in modulating the expression of highly connected genes in CT and DS was revealed through microRNA-target analysis. Trisomy 21 gene dysregulation in thymus may well be depicted as the breakdown and altered reorganization of transcriptional modules.

overall_design: Thymus miRNA transcriptomic profiles of patients with and without Down Syndrome were compared in order to identify differentially expressed transcripts.

first: Silvia

middle: Y

last: Bando

first: Fernanda

last: Bertonha

first: Filipi

last: Silva

first: Luciano

middle: d

last: Costa

first: Leandro

last: Ferreira

first: Glaucio

last: Furlanetto

first: Paulo

last: Chacur

first: Madga

last: Carneiro-Sampaio


title: Comparisons of toxicogenomic responses in zebrafish (Danio rerio) exposed to ZnO nanoparticles and ZnSO4: The impact of sublethal concentration (LC25) on global gene expression profiles

city: Jinju

first: June-Woo

last: Park

address: 17, Jegok-gil, Munsan-eup

department: Environmental Risk Research

institute: Korea Institute of Toxicology

summary: To investigate the patterns of global gene expression profiles modulated by the ZnO nanoparticles and ZnSO4, and to differentiate their modes of toxicity, zebrafish (Danio rerio) will be exposed to the ZnO nanoparticles and ZnSO4 (LC25), and used for microarray analysis by Agilent Zebrafish Oligo Microarray system. 244 genes overlaped between ZnO nanopartices and ZnSO4 treatments in a total of 1,586 differential expressed genes.G-protein coupled receptor protein (GPCR)-signaling pathways, cell-surface receptor-linked signal transduction and immune response are most significant GO terms enriched in genes up regulated by two treatments. Cytokine-cytokine receptor interactions pathway and intestinal immune network for IgA production pathway were enriched among ZnO nanoparticles activated genes, and specifically induced by ZnSO4 include cell adhesion molecules (CAMs) pathway.

overall_design: The zebrafish embryos were exposed to ZnO nanoparticles and ZnSO4 for 96hr. And then after total RNA extration from the each samples, the ZnO nanoparticles and ZnSO4 related gene expression profiles identified using Agilent Zebrafish Oligo Microarray. Significant alterations in gene expression were found for all treatments and many of the gene pathways connected.

first: Jin

middle: S

last: Choi

first: Woo-Keun

last: Kim

first: Jinjong

last: Bong