title: Effect of low-Tw treatment before panicle initiation on the chilling response of spikelets at the booting stage in rice.

status: Public on Dec 22 2014

city: Morioka

first: Kensaku

last: Suzuki

address: 4 Akahira, Shimo-Kuriyagawa

institute: NARO Tohoku Agricultural Research Center

summary: In rice (Oryza sativa L.), chilling-induced male sterility increased when plants experienced low water temperature (Tw, 18 °C for 14 days) before panicle initiation. The number of mature pollen grains after chilling at the booting stage (12 °C for 5 days) was only approximately 45% of total pollen grains in low-Tw plants, whereas it was approximately 71% in normal-Tw plants (Tw not controlled; approximately 23 °C under air temperature of 26 °C/21 °C, day/night). Microarray and quantitative PCR analyses showed that many stress-responsive genes (including OsFKBP65 and genes encoding a large heat shock protein OsHSP90.1, heat-stress transcription factors, and many small heat shock proteins) were strongly up-regulated by chilling in normal-Tw spikelets, but were not or rather down-regulated by chilling in low Tw spikelets. OsAPX2 and genes encoding some other antioxidative enzymes were also significantly down-regulated by low Tw in the chilled spikelets. In low-Tw plants, lipid peroxidation products (malondialdehyde equivalents) were significantly increased in the spikelets after chilling, and ascorbate peroxidase activity in the chilled spikelets was significantly lower than that in normal-Tw plants. Our data suggest that an OsFKBP65-related chilling response, which protects proteins from oxidative damage, is indispensable for chilling tolerance but is lost in low-Tw spikelets.

overall_design: Four conditions used: low Tw and chilled, low Tw and not chilled, normal Tw and chilled, normal Tw and not chilled, before panicle initiation and at the booting stage, respectively. Biological replicates: 4 for each treatment.

first: Naohiro

last: Aoki

first: Hisakaza

last: Matsumura

first: Masaki

last: Okamura

first: Ryu

last: Ohsugi

first: Hiroyuki

last: Shimono


title: Urban waterways microbial communities (Affymetrix)

city: Singapore

first: Gourvendu

last: Saxena

state: Singapore (General)

address: #05-02, 28 Medical Drive

department: The Singapore Centre on Environmental Life Sciences Engineering

country: Singapore

institute: National University of Singapore

summary: The increased urban pressures are often associated with specialization of microbial communities. Microbial communities being a critical player in the geochemical processes, makes it important to identify key environmental parameters that influence the community structure and its function.In this proect we study the influence of land use type and environmental parameters on the structure and function of microbial communities. The present study was conducted in an urban catchment, where the metal and pollutants levels are under allowable limits. The overall goal of this study is to understand the role of engineered physicochemical environment on the structure and function of microbial communities in urban storm-water canals. Microbial community structure was determined using PhyoChio (G3)

overall_design: Water and sediment samples were collected after a rain event from Sungei Ulu Pandan watershed of >25km2, which has two major land use types: Residential and industrial.  Samples were analyzed for physicochemical variables and microbial community structure and composition. Microbial community structure was determined using PhyoChio (G3)

first: Ezequiel

middle: M

last: Marzinelli

first: Nyi

middle: N

last: Naing

first: Zhili

last: He

first: Yuting

last: Liang

first: Lauren

last: Tom

first: Suparna

last: Mitra

first: Han

last: Ping

first: Umid

last: Joshi

first: Sheela

last: Reuben

first: Kalyan

middle: C

last: Mynampati

first: Shailendra

last: Mishra

first: Shivshankar

last: Umashankar

first: Jizhong

last: Zhou

first: Gary

last: Andersen

first: Staffan

last: Kjelleberg

first: Sanjay

last: Swarup


title: Urban waterways microbial communities (GeoChip)

first: Gourvendu

last: Saxena

summary: The increased urban pressures are often associated with specialization of microbial communities. Microbial communities being a critical player in the geochemical processes, makes it important to identify key environmental parameters that influence the community structure and its function.In this proect we study the influence of land use type and environmental parameters on the structure and function of microbial communities. The present study was conducted in an urban catchment, where the metal and pollutants levels are under allowable limits. The overall goal of this study is to understand the role of engineered physicochemical environment on the structure and function of microbial communities in urban storm-water canals.

sample_organism:
environmental samples
environmental samples
environmental samples

overall_design: Water and sediment samples were collected after a rain event from Sungei Ulu Pandan watershed of >25km2, which has two major land use types: Residential and industrial.  Samples were analyzed for physicochemical variables and microbial community structure and composition. Functional gene abundance was determined using GeoChip.


title: Uracil Repair - A Source of DNA Glycosylase Dependent Genome Instability

status: Public on Dec 31 2014

city: Basel

first: Primo

last: Schar

address: Mattenstrasse 28

department: Department of Biomedicine

country: Switzerland

institute: University of Basel

type: Expression profiling by genome tiling array

summary: Uracil DNA glycosylases (UDGs) excise uracil from DNA arising from dUMP misincorporation during replication or from cytosine deamination. Besides functioning in canonical uracil repair, UDGs cooperate with DNA base modifying enzymes to effect mutagenesis or DNA demethylation. Mammalian cells express four UDGs, the functional dissection of which represents a challenge. Here, we used Schizosaccharomyces pombe with only two UDGs, Ung1 and Thp1, as a simpler model to study functional interactions in uracil repair. We show that despite a predominance of Ung1 activity in cell extracts, both UDGs act redundantly against genomic uracil accumulation and mutations from cytosine deamination in cells. Notably, Thp1 but not Ung1-dependent repair is cytotoxic under genomic uracil stress induced by 5-fluorouracil exposure or AID expression. Also, Thp1- but not Ung1-mediated base excision is recombinogenic, accounting for more than 60% of spontaneous mitotic recombination events in a recombination assay. Hence, the qualitative outcome of uracil repair depends on the initiating UDG; while Ung1 shows expected features of a bona-fide DNA repair enzyme, Thp1-initiated repair appears slow and non-productive, implicating a function beyond canonical DNA repair. Given the epigenetic role of mammalian TDGs, we performed transcriptome analyses and identified a possible function of Thp1 in stabilizing gene expression.

overall_design: A cross was performed between an h+ wild-type (WT) and an h- Thp1-deficient (thp1Δ) S. pombe strain. Nine WT (h+) and nine thp1Δ (h+) strains were isolated from the cross and grown on YEL medium. Cells were not frozen prior to RNA extraction. RNA was extracted from all 18 strains. RNA of three strains of each genotype were pooled after RNA extraction and prior to the tiling array. Three of these RNA pools were analyzed on tiling arrays for each genotype (six samples in total). Single probes were attributed to genomic elements. Relative expression was received by normalizing the thp1Δ mean expression value to that of the WT. To check the variability of gene expression, the expression values of all six samples were compared without normalizing to the WT.

first: Claudia

last: Krawczyk

first: Marc

last: Bentele

first: Vitaly

last: Latypov

first: Katrina

middle: J

last: Woolcock

first: Faiza

last: Noreen

first: Olivier

last: Fritsch

last: Schär


title: A comparative transcriptome analysis of hybrid necrosis-showing plants in diploid and hexaploid wheat

status: Public on Dec 19 2014

city: Kobe

first: Shigeo

last: Takumi

state: Hyogo

address: Rokkodai 1-1, Nada

department: Graduate School of Agricultural Science

country: Japan

institute: Kobe University

summary:
We have employed whole genome microarray expression profiling as a discovery platform to identify genes to alter the transcript accumulation levels in two types of hybrid necrosis-showing plants; one was derived from interspecific crosses of two diploid wheat species Triticum monococcum ssp. aegilopoides and Triticum urartu, and another from intraspecific hybrids of common wheat. Of the up-regulated genes, defense-related and carbohyfrate metabosim-related genes were frequently found, whereas photosythesis-related genes down-regulated in the hybrid necrosis-showing plants.
These observations strongly suggests that autoimmune responses might be triggered by Ne1-Ne2 interaction in common wheat and by Ned1-Ned2 interaction in the wild diploid wheat, and that genetically programmed cell death could be regarded as a hypersensitive response-like cell death similar to that observed in other wheat hybrid necrosis such as type III necrosis in the ABD wheat triploids crossed between tetraploid wheat and Aegilops tauschii.

sample_organism: Triticum monococcum subsp. aegilopoides x Triticum urartu

overall_design: Expression patterns were compared between a wild-type wheat hybrid plant (as a reference) and a hybrid necrosis-showing hybrid plant in each of common and wild diploid wheat. Total RNA samples were isolated from leaf tissues. Two independent experiments were conducted in each expriment.

first: Kiyofumi

last: Takamatsu


title: DNA methylation profiles of ovarian cancer cell lines

city: Durham

first: Susan

middle: K.

last: Murphy

state: NC

address: B226 LSRC B Wing, Research Drive, Box 91012

department: Obstetrics and Gynecology

country: USA

institute: Duke University Medical Center

summary: Genome wide DNA methylation profiling of ovarian cancer cell lines and normal cells. The Illumina Infinium 27k Human DNA methylation Beadchip was used to obtain DNA methylation profiles for approximately 27,000 CpGs. Samples included 46 ovarian cancer cell lines, 4 normal counterparts and 8 controls.

overall_design: Bisulfite converted DNA from the 58 samples were hybridised to the Illumina Infinium 27k Human Methylation Beadchip

middle: K

first: Andrew

last: Berchuck


title: Urban waterways microbial communities

status: Public on Dec 21 2014

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

sample_organism:
mixed sample
environmental samples
environmental samples
environmental samples

overall_design: Refer to individual Series


title: Methylation profile of Hepatocellular Carcinoma

status: Public on Dec 10 2014

first: Lee

middle: Guat Lay

last: Caroline

address: 11 Hospital Drive

department: Department of Biochemistry, National University of Singapore

institute: National Cancer Centre Singapore

summary: DNA methylation profiling of tumor and adjacent non-tumorous tissues of Hepatocellular Carcinoma (HCC) patients. The Illumina Infinium 27k Human DNA methylation Beadchip v1.2 was used to obtain DNA methylation profiles across approximately 27,000 CpGs. Samples included 59 tumors and 59 adjacent non-tumorous samples.

overall_design: Bisulphite converted DNA from the 59 tumors and 59 adjacent non-tumorous samples were hybridised to the Illumina Infinium 27k Human Methylation Beadchip.

first: Way-Champ

last: Mah

first: Thomas

last: Thurnherr

first: Caroline

middle: G

last: Lee

first: Pierce

last: Chow

first: Alexander

middle: Y

last: Chung

first: London

middle: L

last: Ooi

first: Han

last: Toh

first: Bin

middle: T

last: Teh

first: Yogen

last: Saunthararajah


title: Epigenome analysis of lung adenocarcinoma cell lines

status: Public on Dec 08 2014

city: Houston

first: Amin

middle: A

last: mOMIN

state: TX

address: 6767 Bertner Ave

department: Clinical cancer prevention

institute: MD anderson cancer center

summary: An integrated approach combining genomics, proteomics and DNA methylation with functional profiling to define molecular features associated with epithelial to mesenchymal transition (EMT) states.

overall_design: Genomic DNA from 36 lung adenocarcinoma cell lines was bisulfite treated and analyzed on the Illumina Infinium HumanMethylation27K BeadChip


title: Molecular portraits of epithelial, mesenchymal and hybrid states in lung adenocarcinoma and their relevance to survival

status: Public on Dec 09 2014

type:
Expression profiling by RT-PCR
Methylation profiling by array

overall_design: Refer to individual Series.


title: NF-κB-direct activation of microRNAs with repressive effects on monocyte-specific genes is critical for osteoclast differentiation

status: Public on Dec 03 2014

city: Badalona, Barcelona

first: Esteban

last: Ballestar

state: N/A = Not Applicable

address: Ctra de Can Ruti, Camí de les Escoles s/n

country: Spain

institute: Josep Carreras Research Institute (IJC)

summary: In this study, analysis of miRNA expression changes in osteoclast differentiation from human primary monocytes revealed the rapid upregulation of two miRNA clusters, miR-212/132 and miR-99b/let-7e/125a. We demonstrate that they negatively target monocyte-specific and immunomodulatory genes like TNFAIP3, IGF1R and IL15. Depletion of these miRNAs inhibits osteoclast differentiation and upregulates their targets. These miRNAs are also upregulated in other inflammatory monocytic differentiation processes. Most importantly, we demonstrate for the first time the direct involvement of Nuclear Factor kappa B (NF-κB) in the regulation of these miRNAs, as well as with their targets, whereby NF-κB p65 binds the promoters of these two miRNA clusters and NF-κB inhibition or depletion results in impaired upregulation of their expression.

overall_design: Human primary CD14+ cells isolated from three different donors, and differentiated into osteoclast with MCSF and RANKL for 21 days. miRNA expression analyzed in paired samples at day 0, 2 and 21

first: Lorenzo

last: de la Rica

first: Antonio

last: García-Gómez

first: Natalia

middle: R

last: Comet

first: Javier

last: Rodríguez-Ubreva

first: Laura

last: Ciudad

first: Roser

last: Vento-Tormo

first: Carlos

last: Company

first: Damiana

last: Álvarez-Errico

first: Mireia

last: García

first: Carmen

last: Gómez-Vaquero


title: Persistence of furan-induced epigenetic aberrations in the livers of Fisher 344 rats

status: Public on Dec 02 2014

city: Jefferson

first: Volodymyr

last: Tryndyak

address: 3900 NCTR Rd

department: Division of Biochemical Toxicology

institute: US-FDA National Center for Toxicological Research

summary: Furan is a heterocyclic organic compound produced in the chemical manufacturing industry and also found in a broad range of food products, including infant formulas and baby foods.  Previous reports have indicated that the adverse biological effects of furan, including its liver tumorigenicity, may be associated with epigenetic abnormalities.  In the present study we investigated the persistence of epigenetic alterations in rat liver.  Male Fisher 344 (F344) rats were treated by gavage 5 days per week with 8 mg furan/kg body weight (bw)/day for 90 days.  After the last treatment, rats were divided randomly into four groups; one group of rats was sacrificed 24 hours after the last treatment, while other groups were maintained without further furan treatment for an additional 90, 180, or 360 days.  Treatment with furan for 90 days resulted in alterations in histone lysine methylation and acetylation, oxidative damage to DNA, and changes in the gene expression in the livers.  A majority of these furan-induced molecular changes was transient and disappeared after the cessation of furan treatment.  In contrast, histone H3 lysine 9, H3 lysine 27, and H3 lysine 56 showed a sustained and time-depended decrease in acetylation, which was associated with formation of heterochromatin and altered gene expression.  These results indicate that furan-induced adverse effects may be mechanistically related to sustained changes in histone lysine acetylation that compromise the ability of cells to maintain and control properly the expression of genetic information.

overall_design: Male Fisher 344 (F344) rats were treated by gavage 5 days per week with 8 mg furan/kg body weight (bw)/day for 90 days and gene expression profiles in the livers from four control and four Furan-treated rats were investigated.

first: Aline

last: de Conti

first: Tao

last: Han

first: James

last: Fuscoe

first: Frederick

last: Beland

first: Daniel

last: Doerge

first: Igor

middle: P

last: Pogribny


title: Gene Expression Analyses of Homo sapiens Inflammatory Skin Diseases

city: Bonn

first: Joerg

last: Wenzel

address: Sigmund Freud Str 25

department: Dermatology

country: Germany

institute: University of Bonn

summary:
Transcriptional profiling of Homo sapiens inflammatory skin diseases (whole skin biospies): Psoriasis (Pso), vs Atopic Dermatitis  (AD) vs Lichen planus (Li), vs Contact Eczema (KE), vs Healthy control (KO)
In recent years, different genes and proteins have been highlighted as potential biomarkers for psoriasis, one of the most common inflammatory skin diseases worldwide. However, most of these markers are not psoriasis-specific but also found in other inflammatory disorders.  We performed an unsupervised cluster analysis of gene expression profiles in 150 psoriasis patients and other inflammatory skin diseases (atopic dermatitis, lichen planus, contact eczema, and healthy controls). We identified a cluster of IL-17/TNFα-associated genes specifically expressed in psoriasis, among which IL-36γ was the most outstanding marker. In subsequent immunohistological analyses IL-36γ was confirmed to be expressed in psoriasis lesions only. IL-36γ peripheral blood serum levels were found to be closely associated with disease activity, and they decreased after anti-TNFα-treatment. Furthermore, IL-36γ immunohistochemistry was found to be a helpful marker in the histological differential diagnosis between psoriasis and eczema in diagnostically challenging cases.   These features highlight IL-36γ as a valuable biomarker in psoriasis patients, both for diagnostic purposes and measurement of disease activity during the clinical course. Furthermore, IL-36γ might also provide a future drug target, due to its potential amplifier role in TNFα- and IL-17 pathways in psoriatic skin inflammation.   In recent years, different genes and proteins have been highlighted as potential biomarkers for psoriasis, one of the most common inflammatory skin diseases worldwide. However, most of these markers are not psoriasis-specific but also found in other inflammatory disorders.  We performed an unsupervised cluster analysis of gene expression profiles in 150 psoriasis patients and other inflammatory skin diseases (atopic dermatitis, lichen planus, contact eczema, and healthy controls). We identified a cluster of IL-17/TNFα-associated genes specifically expressed in psoriasis, among which IL-36γ was the most outstanding marker. In subsequent immunohistological analyses IL-36γ was confirmed to be expressed in psoriasis lesions only. IL-36γ peripheral blood serum levels were found to be closely associated with disease activity, and they decreased after anti-TNFα-treatment. Furthermore, IL-36γ immunohistochemistry was found to be a helpful marker in the histological differential diagnosis between psoriasis and eczema in diagnostically challenging cases.   These features highlight IL-36γ as a valuable biomarker in psoriasis patients, both for diagnostic purposes and measurement of disease activity during the clinical course. Furthermore, IL-36γ might also provide a future drug target, due to its potential amplifier role in TNFα- and IL-17 pathways in psoriatic skin inflammation.

overall_design: Ex vivo analyses: gene expression analyses (total RNA) of lesional skin versus common skin reference (two channel)


title: Spontaneous development of hepatocellular carcinoma with cancer stem cell properties in PR-SET7 deficient livers.

status: Public on Dec 01 2014

city: Vassilika Vouton, Herakleion

first: Iannis

last: Talianidis

state: Crete

address: 100 N. Plastira Str

department: Institute of Molecular Biology and Biotechnology

country: Greece

institute: Foundation for Research and Technology - Hellas

summary: PR-SET7-mediated histone-4 lysine-20 methylation has been implicated in mitotic condensation, DNA damage response and replication licencing. Here we show that PR-SET7 function in the liver is pivotal for maintaining genome integrity. Hepatocyte-specific deletion of PR-SET7 in mouse embryos resulted in G2 arrest followed by massive cell death and defect in liver organogenesis. Inactivation at postnatal stages caused cell duplication-dependent hepatocyte necrosis. Necrotic death was accompanied by inflammation, fibrosis and compensatory growth induction of neighboring hepatocytes and resident ductal progenitor cells. Prolonged necrotic-regenerative cycles coupled with oncogenic STAT3 activation replaced pre-existing hepatocytes with hepatocellular carcinoma derived entirely from cells with cancer stem cell characteristics. Hepatocellular carcinoma in these mice displays a cancer stem cell gene signature specified by the co-expression of ductal progenitor markers and oncofetal genes.

overall_design: Mice carrying hepatocyte specific inactivation of PR-SET7 were generated in order to investigate the function of PR-SET7 histone methyl transferase in liver organogenesis, hepatocyte proliferation and liver regeneration.

first: Kostas

last: Nikolaou

first: Panagiotis

last: Moulos

first: George

last: Chalepakis

first: Pantelis

last: Hatzis

first: Hisanobu

last: Oda

first: Danny

last: Reinberg


title: Global DNA Methylation Levels in Lung Fibroblasts from Patients with Idiopathic Pulmonary Fibrosis Compared to Nonfibrotic Controls

city: Ann Arbor

first: Richard

last: McEachin

state: United States

address: 2800 Plymouth Road

department: DCM&B

institute: University of Michigan

summary: Fibroblasts are the key effector cells in idiopathic pulmonary fibrosis (IPF), a chronic, progressive scarring disorder that results in impaired gas exchange and respiratory failure.  Fibroblasts from IPF patients exhibit aberrant expression of multiple genes, but the DNA methylome of IPF fibroblasts has never been characterized. We utilized the HumanMethylation27 array, which assays the DNA methylation level of 27,568 CpG sites to compare the DNA methylation patterns of IPF fibroblasts (n=6) with those of nonfibrotic patient controls (n=3) and commercially available normal lung fibroblast cell lines (CCL190, CCL204, and CCL210). Multiple CpG sites across the genome were differentially methylated (as defined by P value less than 0.05 and fold change greater than 2) in IPF fibroblasts compared to fibroblasts from nonfibrotic controls.  These methylation changes occurred in both genes recognized to be important in fibroproliferation and extracellular matrix generation, as well as in genes not previously recognized to participate in those processes (including organ morphogenesis and potassium ion channels). We used bisulfite sequencing to independently verify DNA methylation changes in 3 genes (CDKN2B, CARD10, and MGMT); these methylation changes corresponded with changes in gene expression at the mRNA and protein level. These changes in DNA methylation were stable throughout multiple cell passages. DNA methylation changes may thus help to explain a proportion of the differences in gene expression previously observed in studies of IPF fibroblasts. Moreover, significant variability in DNA methylation was observed among individual IPF cell lines, suggesting that differences in DNA methylation may contribute to fibroblast heterogeneity among patients with IPF. These results demonstrate that IPF fibroblasts exhibit global differences in DNA methylation that may contribute to the excessive fibroproliferation associated with this disease.

overall_design: Bisulfite converted DNA from the 12 samples were hybridized to the Illumina Infinium 27k Human Methylation Beadchip v1.2

first: Steven

last: Huang


title: MWi001: Identification of Srp9 as a febrile seizure susceptibility gene

city: Utrecht

first: Marian

last: Groot Koerkamp

state: Utrecht

address: Heidelberglaan 25

department: Research

country: Netherlands

institute: Princess Maxima Center for Pediatric Oncology

summary: Febrile seizures (FS) are the most common type of seizures in young children. Complex FS are a risk factor for mesial temporal lobe epilepsy (mTLE). Twin studies and mutations in families with complex epilepsy syndromes including FS, indicate a genetic contribution to FS susceptibility. By employing a phenotype driven genetic strategy using consomics we mapped a quantitative trait locus (QTL) for hyperthermia-induced FS susceptibility on mouse chromosome 1. Signal Recognition Particle 9 (Srp9) in the QTL was differentially expressed between parental strains, and its binding partner Srp14 was co-identified as a strong candidate gene in another FS susceptibility QTL. The SRP complex plays a key role in the synthesis of membrane proteins, such as glutamate receptors. In vivo knock-down of brain Srp9 or inhibition of protein synthesis reduced FS susceptibility. The mouse strain (CSS1) with reduced Srp9 expression and FS susceptibility, exhibited reduced hippocampal AMPA and NMDA currents. Down-regulation of Srp9 in hippocampal neurons reduced surface expression of AMPA receptor subunit GluA1. Consistent with a role of SRP9 in human FS, we detected increased hippocampal SRP9 expression in mTLE patients with antecedent FS. Comparing mTLE patients and healthy controls we found an association of a SRP9 promoter SNP (rs12403575 G/A) with FS and mTLE, which was replicated in FS patients. Our findings identify SRP9 as a novel FS susceptibility gene and implicate ER-dependent protein synthesis and glutamate receptor expression in the mechanism.

overall_design: Dual channel mouse microarrays were analyzed. RNA samples were isolated from 4 individual mouse P14 brains per strain, for strains Bl6, CSS1 and CSS2. Bl6 RNA was also used to make a reference pool used against all individual samples. Of each 4 samples analysed per group, 2 were labeled in dyeswap.

first: Ellen

middle: V

last: Hessel

first: Marina

last: de Wit

first: Inge

last: Wolterink-Donselaar

first: Henk

last: Karst

first: Esther

last: de Graaff

first: Hein

last: van Lith

first: Ewart

last: de Bruijn

first: Sophietje

last: de Sonnaville

first: Nienke

middle: E

last: Verbeek

first: Dick

last: Lindhout

first: Carolien

last: de Kovel

first: Bobby

last: Koeleman

first: Marjan

last: van Kempen

first: Eva

last: Brilstra

first: Edwin

last: Cuppen

first: Maarten

last: Loos

first: Sabine

middle: S

last: Spijker

first: Anne

last: Kan

first: Susanne

last: Baars

first: Peter

last: van Rijen

middle: H

last: Gosselaar

first: Frank

last: Holstege

first: Cornelia

last: van Duijn

first: Jeanette

last: Vergeer

first: Henriette

last: Moll

first: Erik

last: Taubøll

first: Kjell

last: Heuser

first: Geert

last: Ramakers

first: Jeroen

last: Pasterkamp

first: Onno

last: van Nieuwenhuizen

first: Casper

last: Hoogenraad

first: Martien

last: Kas

first: Pierre

last: de Graan


title: Widespread monoallelic methylation of colorectal cancer associated tumour suppressor genes, including multiple Wnt pathway inhibitors, in Hyperplastic Polyposis Syndrome.

city: Parkville

first: Richard

last: Saffery

state: Victoria

address: Flemington Rd

department: Cancer, Disease and Developmental Epigenetics

country: Australia

institute: Murdoch Children's Research Institute

summary: Hyperplastic Polyposis Syndrome (HPS) is a condition associated with multiple serrated polyps, and an increased risk of colorectal cancer (CRC). The majority of CRCs arising in HPS show a CpG island methylator phenotype (CIMP) that encompasses several common tumor suppressor genes, including regulators of DNA mismatch repair, and negative regulators of Wnt signaling. However, little is currently known about the CIMP status of premalignant polyp tissue in HPS or the temporal changes in CIMP profile associated with transition to malignancy. Using genomescale DNA methylation analysis of HPS polyp and disease-free tissue, we identified widespread coordinated DNA methylation changes, common to all HPS polyps examined. The majority of consistent changes involve low-intermediate (10-50%) methylation and include several tumour suppressor genes, including multiple negative regulators of Wnt signalling (SFRP-1, -2, -4, -5) and cell cycle regulation (eg. RASSF1). We also confirmed selective methylation of the RUNX1, CHFR, CDKN2A, and MLH-1 promoters previously described in HPS, but found no evidence for methylation of DNA mismatch repair genes MGMT or MSH-2 in premalignant polyps. Consistent and widespread methylation of the WT-1 tumour suppressor gene also appears to be a common feature of HPS. Interestingly, where tested the majority of methylation identified was localised to a single allele within the polyp tissue. These findings reveal that premalignant HPS is associated with coordinated, widespread intermediate levels of gene promoter methylation in several TS genes implicated in CRC, primarily restricted to one of two alleles. Transition to malignancy appears to be associated with widespread elevation of methylation at these sites. These findings warrant a further investigation of the potential for future development of novel methylation-based molecular assays for the prediction of HPS cases likely to transition to malignancy.

overall_design: DNA was extracted from eleven HPS and four control colon samples.

first: Musa

last: Drini

first: Nicholas

last: Wong

first: Lavinia

last: Gordon

first: Katrinia

last: Bell

first: Boris

last: Novakovic

first: Joanne

last: Young

first: Finlay

last: MacRae


title: Expression profiles of synthetic wheat lines and their parents during amphidiploidization

status: Public on Nov 30 2014

city: Yokohama

first: Yeonju

last: Jung

state: Kanagawa

address: Maioka-cho 641-12

department: Yokohama City University

institute: Kihara Institute for Biological Research

summary: Gene expression levels of newly synthetic triploid wheat (ABD), its chromosome-doubled hexaploid (AABBDD), stable synthetic hexaploid (AABBDD), and their parents, Triticum turgidum (accession KU124, AABB) and Aegilops tauschii (accession KU2074, DD) were compared to understand genome-wide change of gene expressions during the course of amphidiploidization and genome stabilization. Stable synthetic hexaploid which were maintained through self-pollinations for 13 generations using the same combinations of the parents for production of synthetic common wheat.

sample_organism: Triticum dicoccon x Aegilops tauschii subsp. strangulata

overall_design: Amphidiploidization event between T. turgidum ssp. dicoccum (AABB) and Ae. tauschii ssp. strangulata (DD) was recreated. Gene expression levels of newly synthetic triploid wheat (ABD), its chromosome-doubled hexaploid (AABBDD), stable synthetic hexaploid (AABBDD), and their parents, Triticum turgidum (AABB) and Aegilops tauschii (DD) were compared. Total RNA of each line was extracted from three biological replicates of two leaves seedlings.

first: Y

first: K

last: Kawaura


title: Search for microRNAs under the control of Grainyhead like-2

status: Public on Oct 31 2014

city: Sapporo

first: Naoki

last: Tanimizu

address: S1, W17, Chuou-ku

institute: Sapporo Medical University

summary: Compare microRNA expression profile of HPPL (bipotential liver progenitor cell line) overexpressing Grhl2 with that of the control

platform_organism:
Homo sapiens
Mus musculus
Rattus norvegicus

overall_design: Grhl2 was introduced to HPPL by retrovirus vector and infected cells were selected by G418. Total RNA including microRNA was extracted from cells by using Qiagen miRNeasy kit.


title: ETV5 transcription program links BDNF and promotion of EMT at invasive front of endometrial carcinomas.

status: Public on Nov 05 2014

city: Santiago de Compostela

first: Miguel

last: Abal

state: A Coruña

address: Trav Choupana s/n

department: Medical Oncology

institute: University Clinical Hospital

type: Genome binding/occupancy profiling by genome tiling array

summary: We have characterized the transcriptional program regulated by ETV5 at the invasive front of endometrial carcinomas, by comparing it with non-invasive areas of the same tumor samples.

overall_design: In total 12 samples; 6 superficial (non-invasive) tumor areas and the corresponding invasive tumor zones.

first: Lorena

last: Alonso-Alconada

first: Nuria

last: Eritja

first: Laura

last: Muinelo-Romay

first: Jorge

last: Barbazan

first: Rafael

last: Lopez-Lopez

first: Xavier

last: Matias-Guiu

first: Antonio

last: Gil-Moreno

last: Dolcet


title: Interspecific Introgressive Origin of Genomic Diversity in the House Mouse

status: Public on Nov 01 2014

city: East Lansing

first: Kevin

middle: Jensen

last: Liu

state: MI

address: 428 S. Shaw Lane

department: Computer Science and Engineering

institute: Michigan State University

summary: We report on a genome-wide scan for introgression in the house mouse (Mus musculus domesticus) involving the Algerian mouse (Mus spretus), using 20 samples from the ranges of sympatry and allopatry. Our analysis reveals significant variability in introgression signatures along the genomes, as well as across the samples. We find that fewer than half of the chromosomes in each genome harbor all detectable introgression. Further, a surprising result is that European mice carry more M. spretus alleles than the sympatric African ones. Using the length distribution and sharing patterns of introgressed genomic tracts across the samples, we propose three hypotheses. First, at least three distinct hybridization events involving M. spretus have occurred, one of which is ancient, and the other two are recent. Second, several of the inferred introgressed tracts contain genes that are likely to confer adaptive advantage. Third, introgressed tracts might contain driver genes that determine the evolutionary fate of those tracts. Further, our analysis revealed introgressed genes of functional importance, including the Vkorc1 gene, which is implicated in rodenticide resistance, and olfactory receptor genes. Our findings highlight the extent and role of introgression in nature, and call for careful analysis and interpretation of house mouse data in evolutionary and genetic studies.

overall_design: Six wild M. m. domesticus samples were genotyped using the Affymetrix Mouse Diversity Genotyping Array.

first: Ethan

last: Steinberg

first: Alexander

last: Yozzo

first: Ying

last: Song

first: Michael

last: Kohn

first: Luay

last: Nakhleh


title: A screening for differentially expressed genes between peripheral NK cells of HBV-associated hepatocellular carcinoma patients and healthy donors

status: Public on Nov 13 2014

city: Beijing

first: Jun

last: Chen

address: No.15 Datun Road

country: China

institute: Institute of Biophysics, Chinese Academy of Sciences

summary: We used 3 pairs of HBV-associated hepatocellular carcinoma patients and healthy donors as samples. We tested the DNA expression profiles with DNA microarray including about 30967 probes. Through these raw data, we analyzed out several hundreds of differentially expressed genes.

overall_design: In this study, we choose 3 pairs of HBV-associated hepatocellular carcinoma patients and healthy donors. We analyzed about 30967 probes with DNA microarray, leading to the successful profiling of interesting genes.

first: Yi

last: Li

first: Chong


title: Molecular and cellular effects of in vitro shockwave treatment on lymphatic endothelial cells

status: Public on Oct 28 2014

city: Vienna

first: Matthias

last: Hackl

state: Austria

address: Leberstrasse 20

country: Austria

institute: TAmiRNA GmbH

summary: Extracorporeal shockwave treatment was shown to improve orthopaedic diseases, wound healing and to stimulate lymphangiogenesis in vivo. The aim of this study was to investigate in vitro shockwave treatment (IVSWT) effects on lymphatic endothelial cell (LEC) behavior and lymphangiogenesis. We analyzed migration, proliferation, vascular tube forming capability and marker expression changes of LECs after IVSWT compared with HUVECs. Finally, transcriptome- and miRNA analyses were conducted to gain deeper insight into the IVSWT-induced molecular mechanisms in LECs. The results indicate that IVSWT-mediated proliferation changes of LECs are highly energy flux density-dependent and LEC 2D as well as 3D migration was enhanced through IVSWT. IVSWT suppressed HUVEC 3D migration but enhanced vasculogenesis. Furthermore, we identified podoplaninhigh and podoplaninlow cell subpopulations, whose ratios changed upon IVSWT treatment. Transcriptome- and miRNA analyses on these populations showed differences in genes specific for signaling and vascular tissue. Our findings help to understand the cellular and molecular mechanisms underlying shockwave-induced lymphangiogenesis in vivo.

overall_design: Two types of cell populations were analyzed: podoplanin high and low expressing lymphatic endothelial cells. From each population two biological replicates were hybridized onto the arrays

first: Sabrina

last: Rohringer

first: Wolfgang

last: Holnthoner

first: Anna

middle: M

last: Weihs

first: Dominik

last: Rünzler

first: Susanna

last: Skalicky

first: Johannes

last: Pröll

first: Christian

last: Gabriel

first: Bernhard

last: Schweighöfer

first: Marion

last: Gröger

first: Andreas

last: Spittler

last: Grillari

first: Heinz

last: Redl


title: Differential Roles of ERα and ERβ in Normal and Neoplastic Development in the Mouse Mammary Gland

status: Public on Oct 18 2014

city: Northbrook

first: Michael

last: Falduto

state: IL

address: 1808 Janke, Unit M

institute: GenUs BioSystems, Inc.

summary: The present experiments were performed to determine the roles of estrogen receptors α and β (ERα and ERβ) in normal and neoplastic development in the mouse mammary gland. In wild-type mice, in vivo administration of estradiol (E) + progesterone (P) stimulated mammary ductal growth and alveolar differentiation. Mammary glands from mice in which the ERβ gene has been deleted (βERKO mice) demonstrated normal ductal growth and differentiation in response to E + P. By contrast, mammary glands from mice in which the ERα gene has been deleted (αERKO mice) demonstrated only rudimentary ductal structures that did not differentiate in response to E + P. EGF demonstrates estrogen-like activity in the mammary glands of αERKO mice: treatment of αERKO mice with EGF + P (without E) supported normal mammary gland development, induced expression of progesterone receptor (PR), and increased levels of G- protein-coupled receptor (GPR30) protein. Mammary gland development in βERKO mice treated with EGF + P was comparable to that of wild-type mice receiving EGF + P; EGF had no statistically significant effects on the induction of PR or expression of GPR30 in mammary glands harvested from either wild-type mice or βERKO mice. In vitro exposure of mammary glands to 7,12-dimethylbenz[a]anthracene (DMBA) induced preneoplastic mammary alveolar lesions (MAL) in glands from wild-type mice and βERKO mice, but failed to induce MAL in mammary glands from αERKO mice. Microarray analysis of DMBA-treated mammary glands identified 28 functional pathways whose expression was significantly different in αERKO mice versus both βERKO and wild-type mice; key functions that were differentially expressed in αERKO mice included cell division, cell proliferation, and apoptosis. The data demonstrate distinct roles for ERα and ERβ in normal and neoplastic development in the mouse mammary gland, and suggest that EGF can mimic the ERα-mediated effects of E in this organ.

overall_design: Gene expression of mammary gland organ culture and DMBA-induced lesions from 4 mouse strains.

first: Rajendra

last: Mehta

last: Hawthorne

first: Rajeshwari

first: Karen

last: Torres

first: Xinjian

last: Peng

first: David

last: McCormick

first: Levy

last: Kopelovich


title: Gene expression profiling to recognize specific features of non-genotoxic carcinogens

status: Public on Oct 23 2014

city: Bilthoven

first: Mirjam

last: Schaap

address: Antonie van Leeuwenhoeklaan 9

institute: RIVM

summary: The current test strategy for carcinogenicity is generally based on in vitro and in vivo genotoxicity assays. Non-genotoxic carcinogens (NGTXC) are negative for genotoxicity and go undetected. Therefore, alternative tests to detect these chemicals are urgently needed. NGTXC act through different modes of action, which complicates the development of such assays. We have demonstrated recently in primary mouse hepatocytes that some, but certainly not all, NGTXC can be categorized according to their mode of action based on feature detection at a gene expression level (Schaap et al. 2012 (PMID 22710402)). Identification of a wider range of chemicals probably requires multiple in vitro systems. In the current study, we describe the added value of using mouse embryonic stem cells. In this study, the focus is on NGTXC, but we also included genotoxic carcinogens and non-carcinogens. This approach enables us to assess the robustness of this method and to evaluate the system for recognizing features of chemicals in general, which is important for application in future risk assessment.

overall_design:
Primary mouse hepatocytes and mouse embryonic stem cells were exposed to 26 chemicals (non-genotoxic carcinogens and non-carcinogens) representing diverse modes of action. Upon profiling, an unsupervised comparison approach was applied to recognize similar features at the transcriptomic level.

This Series consists of the gene expression data of the primary mouse hepatocytes. The expression data of the mouse embryonic stem cells is submitted separately under another accession number.
In this study we tested 26 chemicals of which 16 non-genotoxic carcinogens, 4 genotoxic carcinogens, 2 genotoxic non-carcinogens and 4 non-carcinogens. Specification of the chemicals can be found in the readme file.

first: Paul

middle: F

last: Wackers

first: Ilse

last: Huijskens

first: Martijs

middle: J

last: Jonker

first: Giel

last: Hendriks

first: Harry

last: van Steeg

first: Bob

last: van de Water

last: Luijten


title: Comparison of L-carnitine treated day 6 in vivo bovine embryos to controls, in both the Jersey and Holstein breeds.

city: Quebec

first: Eric

last: Fournier

state: Quebec

address: 2325 Rue de l'Universite

department: Departement des sciences animales

country: Canada

institute: Universite Laval

summary: The decreased rate of pregnancy obtained in cattle using frozen in vitro embryos compared to in vivo embryos has been associated with over-accumulation of intracellular lipid, which causes cell damage during cryopreservation. It is believed that the higher lipid content of blastomeres of bovine embryos produced in vitro results in darker coloured cytoplasm which could be a consequence of impaired mitochondrial function. In this study, L-carnitine was used as a treatment to reduce embryonic lipid content by increasing metabolism in cultured bovine embryos. We have observed previously that in vivo embryos of different dairy breed collected from cows housed and fed under the same conditions differed in lipid content and metabolism. As such, breed effects between Holstein and Jersey were also accounted for general appearance, lipid composition, mitochondrial activity and gene expression. Adding L-carnitine to the embryo culture medium reduced the lipid content in both breeds due to increased mitochondrial activity.

overall_design: L-carnitine vs controls, in 4 replicates for each breed, with dye-swaps.

first: Luis

last: Baldoceda

first: Dominic

last: Gagné

first: Christian

last: Vigneault

first: Patrick

last: Blondin

first: Christina

last: Ramires Ferreira

first: Claude

last: Robert


title: Renal cells Carcinoma (RCC) Genome variation profiling by genome tiling array with Nimblegen CGX6 platform

status: Public on Nov 06 2014

city: NICE

first: Thibault

last: FABAS

address: 28 av Valombrose

country: France

institute: CHU Nice

summary: Papillary renal cell carcinoma (pRCC) is the second most frequent renal cell carcinomas (RCC) after clear cell RCC. In contrast to clear cell RCC, there is no consensual protocol using targeted therapy for metastatic pRCC. Moreover, diagnosis of some pRCC, especially pRCC of type 2 (pRCC2) may be challenging. Our aim was to identify molecular biomarkers that could be helpful for the diagnosis and treatment of pRCC.

overall_design:
19 samples was analysed by arrayCGH method using Nimblegen recommendations. Sample was labeled in Cy3 and co-hybridized with control DNA cy5 labeled.

Please note that normalized data matrix contains logRatio Cy3/Cy5 values with non-unique 'PROBE_ID' identifiers (mostly duplicated), and thus included as a Series supplementary file.


title: Molecular characterization of Plasmodium falciparum Bruno/CELF RNA binding proteins

city: Pathumthani

first: Philip

middle: James

last: Shaw

state: Pathumthani

address: 113 Phahonyothin Road

department: National Center for Genetic Engineering and Biotechnology

country: Thailand

institute: National Science and Technology Development Agency

type:
Expression profiling by array
Other

summary: The human malaria parasite Plasmodium falciparum employs intricate post-transcriptional regulatory mechanisms in different stages of its life cycle. Despite the importance of post-transcriptional regulation, key elements of these processes, namely RNA binding proteins (RBPs), are poorly characterized. In this study, the RNA binding properties of P. falciparum proteins were characterized including two putative members of the Bruno/CELF family of RBPs (PfCELF1 and PfCELF2), dihydrofolate reductase-thymidylate synthase (PfDHFR-TS), and adenosine deaminase (PfAda).The mRNA targets of these P. falciparum proteins were investigated by ribonomics using DNA microarrays.

overall_design: Two-condition ribonomic experiment, RBP vs. Mock enrichment of mRNAs. Ribonomic experimental replicates: 4-7 for each RBP, 5 for Mock. One replicate per array.

first: Chayaphat

last: Wongsombat

first: Sumalee

last: Kamchonwongpaisan

first: Hugh

last: Morgan

first: Malcolm

middle: D

last: Walkinshaw

first: Yongyuth

last: Yuthavong

first: Aiyada

last: Aroonsri


title: Gene expression of Leuconostoc gasicomitatum LMG18811T during growth on glucose, ribose or inosine

status: Public on Nov 11 2014

city: Helsinki

first: Elina

last: Jääskeläinen

address: P.O. Box 66 (Agnes Sjöbergin katu 2)

department: Food Hygiene and Environmental Health

country: Finland

institute: University of helsinki

summary: Comparing of transcriptonal profiling of Leuconostoc gasicomitatum LMG18811T grown in semi-defined medium with different carbon sources (20 mM glucose, ribose, inosine).

overall_design: two-condition expreiments 1) LMG18811T wild glucose vs LMG18811T with ribose,  2) LMG18811T wild glucose vs LMG18811T with inosine


title: Chromosome constitution in embryos generated after in vitro maturation in a culture system supplemented with cAMP modulators

status: Public on Nov 12 2014

city: Brussels

first: Kurt

last: Jacobs

address: Laarbeeklaan 103

department: Faculty of Medicine and Pharmacy

country: Belgium

institute: Vrije Universiteit Brussel (VUB)

type: Genome variation profiling by genome tiling array

summary: Ten volunteers underwent 13 research IVM cycles.  Immature oocytes were retrieved after mild ovarian stimulation with gonadotropins but no hCG ovulation trigger, in vitro matured and fertilized using ICSI. Oocyte maturation rate in vitro was 47% (94/199), the mean fertilization rate was 71% (67/94) and 37% (25/67) of mature oocytes developed into a morphologically good quality embryo on day 3 after ICSI, after which the blastomeres were analysed by single-cell aCGH. Sixty-seven of the 111 blastomeres analysed showed at least one chromosomal abnormality.  Two out of seventeen embryos had only normal cells while one embryo carried a meiotic abnormality, 11 were mosaic and three were chaotic.  Although the number of embryos tested as well as the data available in the literature are too small to allow any statistical analysis, these data are comparable to the few data available on the total chromosome complement of day 3 ICSI embryos.  This would indicate that other mechanisms than chromosomal abnormalities explain the low efficiency and high miscarriage rate in IVM cycles.

overall_design: Between July 2012 and December 2012, 13 research IVM cycles were performed in 10 healthy egg donors.  Eighteen embryos developed to the eight-cell stage and their blastomeres were analysed using array comparative genomic hybridization (aCGH).

first: Claudia

last: Spits

last: Guzman

first: Afroditi

last: Mertzanidou

first: Carolina

last: Ortega-Hrepich

first: Michel

last: De Vos

first: Karen

last: Sermon

first: Johan

last: Smitz


title: Spatial encoding of cyclic AMP signaling specificity by GPCR endocytosis

city: San Francisco

first: Nikoleta

last: Tsvetanova

state: CA

address: 600 16th street

institute: University of California, San Francisco

summary: G protein-coupled receptors (GPCRs) are well known to signal via cyclic AMP (cAMP) production at the plasma membrane, but it is now clear that various GPCRs also signal after internalization. Apart from its temporal impact through prolonging the cellular response, we wondered if the endosome-initiated signal encodes any discrete spatial information. Using the beta2-adrenoceptor (β2-AR) as a model, we show that endocytosis is required for the full repertoire of downstream cAMP-dependent transcriptional control. Next, we describe an orthogonal optogenetic approach to definitively establish that the location of cAMP production is indeed the critical variable determining the transcriptional response. Finally, our results suggest that this spatial encoding scheme helps cells functionally discriminate chemically distinct β2-AR ligands according to differences in their ability to promote receptor endocytosis. These findings reveal a discrete principle for achieving cellular signalling specificity, based on endosome-mediated spatial encoding of intracellular second messenger production and 'location aware' downstream transcriptional control.

overall_design: This study includes a total of 8 microarray experiments with 4 different conditions, each condition is done in duplicate.

middle: G

first: Mark

last: von Zastrow


title: Expression data from regenerating prostates of wild-type or Gli1-/- mutant mice

city: Stanford

first: Agnes

last: Lim

address: 265 Campus Drive

department: Developmental Biology

institute: Stanford University

summary:
Attenuation of Hedgehog (Hh) pathway activity leads to increased prostate branching during adult prostate regeneration.
In order to identify genes regulated by the Hh pathway that might be involved in adult prostate branching, we performed transcriptional profiling of regenerating prostates from wild-type or Gli1-/- mutant mice, which have attenuated Hh pathway activity.

overall_design: 6 total samples were analyzed. 3 wild-type prostates and 3 Gli-/- mutant prostates were analyzed.

first: Philip

last: Beachy


title: Renal cells Carcinoma (RCC) Genome variation profiling by genome tiling array

first: Thibault

last: FABAS

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

overall_design: Refer to individual Series


title: FOXP1 inhibits cell growth and attenuates tumorigenicity of neuroblastoma

status: Public on Oct 17 2014

city: Cologne

first: Sandra

last: Ackermann

address: Kerpener Str. 62, Geb. 26, UG

department: Pediatric Oncology and Hematology

institute: University Hospital of Cologne

summary: Single-color gene expression profiles from 3 neuroblastoma cell lines were generated using 44K oligonucleotide microarrays. To gain insights into the molecular processes occurring upon FOXP1 re-expression, we performed series of time-resolved gene expression measurements in FOXP1 and GFP transgenic neuroblastoma cell lines.

overall_design: Single-color gene expression profiles from 3 neuroblastoma cell lines were generated using 44K oligonucleotide microarrays. Total RNA of FOXP1- and GFP-expressing IMR-32, CHP-212 and SK-N-BE(2) cells was isolated at 0, 12, 24 and 72 h using Trizol. To determine global differences in the expression profiles of FOXP1- and GFP-induced  IMR-32, CHP-212 and SK-N-BE(2)  cells, mean expression levels of each gene between FOXP1-induced and control (GFP) cells were compared.

first: Matthias

last: Fischer

first: Frederik

last: Roels


title: Gene expression profiling to recognize specific features of (non-) genotoxic carcinogens

status: Public on Oct 27 2014

first: Mirjam

last: Schaap

summary:
The current test strategy for carcinogenicity is generally based on in vitro and in vivo genotoxicity assays. Non-genotoxic carcinogens (NGTXC) are negative for genotoxicity and go undetected. Therefore, alternative tests to detect these chemicals are urgently needed. NGTXC act through different modes of action, which complicates the development of such assays. We have demonstrated recently in primary mouse hepatocytes that some, but certainly not all, NGTXC can be categorized according to their mode of action based on feature detection at a gene expression level (Schaap et al. 2012, PMID22710402). Identification of a wider range of chemicals probably requires multiple in vitro systems. In the current study we describe the added value of using mouse embryonic stem cells. In this study the focus is on NGTXC, but we also included genotoxic carcinogens and non-carcinogens. This approach enables us to assess the robustness of this method and to evaluate the system for recognizing features of chemicals in general, which is important for application in future risk assessment.
This serie consists of the gene expression data of the mouse embryonic stem cells. The expression data of the primary mouse hepatocytes cells is submitted separately under accession number GSE44088.

overall_design: Primary mouse hepatocytes and mouse embryonic stem cells were exposed to 26 chemicals ((non-) genotoxic carcinogens and non-carcinogens) representing diverse modes of action. Upon profiling, an unsupervised comparison approach was applied to recognize similar features at the transcriptomic level.

first: Paul

last: Wackers

first: Ilse

last: Huijskens

first: Martijs

last: Jonker

first: Giel

last: Hendriks

first: Harry

last: van Steeg

first: Bob

last: van de Water

last: Luijten


title: The RSC Complex localizes to coding sequences to regulate Pol II and histone occupancy (Agilent)

status: Public on Nov 24 2014

city: Rochester

first: Chhabi

last: Govind

state: mi

address: 333 Science and Engineering Building

department: Biological Sciences

institute: Oakland University

summary:
ATP-dependent chromatin remodelers regulate chromatin structure during multiple stages of transcription. We report that RSC, an essential chromatin remodeler, is recruited to the open reading frames (ORFs) of actively transcribed genes genome-wide, suggesting a role for RSC in regulating transcription elongation. Consistent with such a role, Pol II occupancy in the ORFs of weakly transcribed genes is drastically reduced upon depletion of the RSC catalytic subunit Sth1. RSC inactivation also reduced histone H3 occupancy across transcribed regions. Remarkably, the strongest effects on Pol II and H3 occupancy were confined to the genes displaying the greatest RSC ORF enrichment. Additionally, RSC recruitment to the ORF requires the activities of the SAGA and NuA4 HAT complexes and is aided by the activities of the Pol II CTD Ser2 kinases Bur1 and Ctk1. Overall, our findings strongly implicate ORF-associated RSC in governing Pol II function and in maintaining chromatin structure over transcribed regions.
ChIP-chip experiments to measure Sth1, Rpb3 and H3 occupancy in WT and various mutants (histone acetyltransferase and  Pol II CTD kinase mutants). The histone H3 and Rpb3 occupancy were also measured in cells upon Sth1 depletion.

overall_design: The WT and mutant strains were grown in Synthetic complete or YPD media to an O.D. 600 of 0.6-0.8.  For inducing Gcn4, the cells grown in SC were treated with Sulfometuron methyl for 20-25 minutes and process for chromatin immunoprecipitation using antibodies again Myc, Rpb3 or histone H3.

middle: K

first: Randall

last: Morse


title: Profiling of serum microRNAs in children with atopic dermatitis

city: Shenyang

first: Xinghua

last: Gao

state: Liaoning

address: No.155  Nanjing  North  Street

department: Department  of  Dermatology

institute: No.1  Hospital  of  China  Medical  University

summary: Atopic dermatitis (AD) is the most prevalent chronic inflammatory skin disease in children characterized by dermatitis and pruritus. MicroRNAs (miRNAs) have been shown as great potential biomarkers for disease fingerprints to predict prognostics. We aimed to identify miRNA signature from serum and urine for the prognosis of AD patient by genome-wide miRNA profiling analysis.

overall_design: Serum from 8 children with AD and 8 healthy children were collected

first: Yani

last: Lv

first: Ruiqun

last: Qi

first: Jing

last: Xu

first: Zhenghong

last: Di

first: Heng

last: Zheng

first: Wei

last: Huo

first: Li

last: Zhang

first: Hongduo

last: Chen


title: Profiling of serum and urinary microRNAs in children with atopic dermatitis


title: HAC1 mapping in Arabidopsis

status: Public on Oct 15 2014

city: Shanghai

first: Daiyin

last: Chao

address: 300 Fenglin Road

department: Shanghai Institute of Plant Physiology and Ecology

institute: Shanghai Institutes for Biological Sciences

summary: ABSTRACT: Inorganic arsenic is a carcinogen and its ingestion in foods such as rice presents a significant risk to human health. Plants chemically reduce arsenate to arsenite. Using genome-wide association (GWA) mapping of loci controlling natural variation in arsenic accumulation in Arabidopsis thaliana allowed us to identify the arsenate reductase required for this reduction, which we named High Arsenic Content1 (HAC1). Complementation verified the identity of HAC1, and expression in Escherichia coli lacking a functional arsenate reductase confirmed the arsenate reductase activity of HAC1. The HAC1 protein accumulates in the epidermis, the outer cell layer of the root, and also in the pericycle cells surrounding the central vascular tissue. Plants lacking HAC1 lose their ability to efflux arsenite from roots, leading to both increased transport of arsenic into the central vascular tissue and on into the shoot. HAC1 therefore functions to reduce arsenate to arsenite in the outer cell layer of the root, facilitating efflux of arsenic as arsenite back into the soil to limit its accumulation in the root and transport to the shoot. Arsenate reduction by HAC1 in the pericycle may play a role in limiting arsenic loading into the xylem. Loss of HAC1 encoded arsenic reduction leads to a significant increase in arsenic accumulation in shoots causing an increased sensitivity to arsenate toxicity. We also confirmed the previous observation that the ACR2 arsenate reductase in A. thaliana plays no detectable role in arsenic metabolism. Further, ACR2 does not interact epistatically with HAC1, since arsenic metabolism in the acr2 hac1 double mutant is disrupted in an identical manner to that described for the hac1 single mutant. Our identification of HAC1 and its associated natural variation provides an important new resource for the development of low arsenic containing food stuffs such as rice.

overall_design: Hybridizations from a set of Bulk Segregant analysis. We measured the elemental profile of 315 F2 plants from a cross between the high arsenic Arabidopsis thaliana accession Kr-0 and the the low arsenic accession Col-0, data available at www.ionomicshub.org <http://www.ionomicshub.org>. Leaves from the 59 highest and 61 lowest arsenic accumulating plants (calculated as a percentage of the Col-0 accumulation in the same growth tray) were pooled and the genomic DNA was extracted using Qiagen kits.


title: High miR-449b expression in prostate cancer is associated with biochemical recurrence after radical prostatectomy

city: Aarhus N

first: Lars

last: Dyrskjot

address: Brendstrupgaardsvej

department: Department of Molecular Medicine

country: Denmark

institute: Aarhus University Hospital, Skejby

summary: MicroRNA profiling was performed using multiplex qPCR on laser micro dissected material from 36 PC patients to identify microRNAs associated with recurrence after radical prostatectomy

overall_design: Biopsies from prostatectomy specimens were analyzed for tumor tissue and normal prostate glandular epithelium. Respective areas were laser micro dissected and the microRNA fraction was extracted. The microRNA was profilled using Taq-man Low Density Array Human microRNA A+B Cards v3.0.

last: Dyrskjøt

first: Martin

last: Mortensen


title: CGH + SNP microarray analysis in consanguineous family with ovarian dysgenesis

status: Public on Oct 16 2014

city: Pittsburgh

first: Svetlana

last: Yatsenko

state: PA

address: 300 Halket St

institute: University of Pittsburgh

summary: homozygosity mapping in a family with ovarian failure

overall_design: Two affected and four unafected  siblings from consanguineous family were studied to identify shared regions of homozygosity in affected females with gonadal dysgenesis

first: Aleksandar

last: Rajkovic


title: Expression analyses of protein secretion and dithiothreitol-induced stress in recombinant Ashbya gossypii

city: Braga

first: Tatiana

middle: Quinta

last: Aguiar

address: Campus de Gualtar

country: Portugal

institute: Centre of Biological Engineering of the Universisty of Minho

summary:
Investigation of whole genome gene expression level changes in Ashbya gossypii VTT D-101398 secreting recombinant endoglucanase I (EGI) from Trichoderma ressei (Ribeiro et al. 2010 - PMID: 20422178), compared to the its corresponding empty vector control strain and to conditions where VTT D-101398 EGI secreting cultures were treated with dithiothreitol (DTT).
Background: Ashbya gossypii is a filamentous Saccharomycete used for the industrial production of riboflavin that has been recently explored as a host system for recombinant protein production. To gain insight into the protein secretory pathway of this biotechnologically relevant fungus, we undertook genome-wide analyses to explore its secretome and its transcriptional responses to protein secretion stress.
Results: A computational pipeline was used to predict the inventory of proteins putatively secreted by A. gossypii via the general secretory pathway. The proteins actually secreted by this fungus into the supernatants of submerged cultures in minimal and rich medium were mapped by two-dimensional gel electrophoresis, revealing that most of the A. gossypii secreted proteins have an isoelectric point between 4 and 6, and a molecular mass above 25 kDa. These analyses together indicated that 1-4% of A. gossypii proteins are likely to be secreted, of which less than 33% are putative hydrolases. Furthermore, transcriptomic analyses carried out in A. gossypii cells under recombinant protein secretion conditions and dithiothreitol-induced secretion stress unexpectedly revealed that a conventional unfolded protein response (UPR) was not activated in any of the conditions, as the expression levels of several well-known UPR target genes (e.g. IRE1, KAR2, HAC1 and PDI1 homologs) remained unaffected. However, several other genes involved in protein unfolding, endoplasmatic reticulum-associated degradation, proteolysis, vesicle trafficking, vacuolar protein sorting, secretion and mRNA degradation were up-regulated by dithiothreitol-induced secretion stress. Conversely, the transcription of several genes encoding secretory proteins, such as components of the glycosylation pathway, was severely repressed by dithiothreitol
Conclusions: This study provides the first insights into the secretion stress response of A. gossypii, as well as a basic understanding of its protein secretion potential, which is more similar to that of yeast than to that of other filamentous fungi. Contrary to what has been widely described for yeast and fungi, a conventional UPR was not observed in A. gossypii, but alternative protein quality control mechanisms enabled it to cope with secretion stress. These data will help provide strategies for improving heterologous protein secretion in A. gossypii.

overall_design: A twenty four chip study using total RNA recovered from: two separate bioreactor cultures of A. gossypii VTT D-101398 secreting recombinant EGI at 4h, 7h, 10h and 13.5h of culture; two separate bioreactor cultures of A. gossypii containing the empty vector at 4h, 7h, 10h and 14h of culture; and two separate bioreactor cultures of A. gossypii VTT D-101398 secreting recombinant EGI treated with DTT (added at 9.5h of culture) for 0h, 0.5h, 1h and 4h.

middle: Q

first: Orquídea

last: Ribeiro

first: Mikko

last: Arvas

first: Marilyn

last: Wiebe

first: Merja

last: Penttilä

first: Lucília

last: Domingues


title: Profiling of urinary microRNAs in children with atopic dermatitis

first: Xinghua

last: Gao

overall_design: Urine from 3 children with AD and 3 healthy children were collected

first: Yani

last: Lv

first: Ruiqun

last: Qi

first: Jing

last: Xu

last: Di


title: Dynamics of intercellular and exosomal miRNAs in hypoxia-resistant U266 cells

city: Shinjyuku

first: Tomohiro

last: Umezu

state: Tokyo

address: 6-1-1 Shinjyuku

department: Department of Molecular Pathology

institute: Tokyo Medical University

summary: In multiple myeloma (MM), abnormal plasma cells interact with bone marrow (BM) stromal cells and vascular cells among others. A part of the BM milieu is considered highly hypoxic, and myeloma cells in situ may be influenced by circumstances other than normoxia in vitro. Hence, we attempted to confirm the role of hypoxic MM-derived exosomes in the BM milieu. We established a novel hypoxia-resistant cell line, U266HR, derived from U266 cells cultured for >4 months under hypoxia (1% O2), as a model of MM cells localizing in an extensively hypoxic milieu. We used U266 cells and U266HR cells, as donor cells, and HUVECs as recipient cells. Exosomes derived from U266 cells (normoxia or hypoxia) and exosomes derived from U266HR cells (hypoxia-resistant sub-line) were used for validation of angiogeneic activity, such as tube formation assay. Exosomes derived from the U266HR cells significantly increased tube formation of HUVECs than those from U266 cells. To identify intercellular and exosomal miRNAs specifically expressed in hypoxia-resistant cells, we assess the expression profiles of intercellular and extracellular miRNAs in U266 cells and U266HR cells using Taqman MicroRNA Array v2.0 (Applied Biosystems, Bedford, MA).

overall_design: U266 cells were cultured for 24 hours under hypoxic conditions (1% O2) or normoxic conditions (20% O2). The exosome fraction was obtained from culture medium using Exoquick Exosome Precipitation Solution (System Biosciences, Mountain View, CA, USA). Isolation of cellular and exosomal miRNAs was performed using the miRNsasy kit (Qiagen). The expression profile of miRNAs was determined using the Human Taqman miRNA Arrays A (Applied Biosystems). RNU6B and a spike control (ath-miR159) were used as an invariant control for the cell and exosome, respectively. QRT-PCR was carried out on an Applied Biosystems 7900HT thermal cycler using the manufacturer’s recommended program. Finally, all the raw data from each array was run on Data Assist Software ver.3.1 (Applied Biosystems).


title: Dynamics of intercellular and exosomal miRNAs in hypoxia-resistant cells


title: Dynamics of intercellular and exosomal miRNAs in hypoxia-resistant RPMI8226 cells

summary: In multiple myeloma (MM), abnormal plasma cells interact with bone marrow (BM) stromal cells and vascular cells among others. A part of the BM milieu is considered highly hypoxic, and myeloma cells in situ may be influenced by circumstances other than normoxia in vitro. Hence, we attempted to confirm the role of hypoxic MM-derived exosomes in the BM milieu. We established a novel hypoxia-resistant cell line, RPMI8226HR, derived from RPMI8226 cells cultured for >4 months under hypoxia (1% O2), as a model of MM cells localizing in an extensively hypoxic milieu. We used RPMI8226 cells and RPMI8226HR cells, as donor cells, and HUVECs as recipient cells. Exosomes derived from RPMI8226 cells (normoxia or hypoxia) and exosomes derived from RPMI8226HR cells (hypoxia-resistant sub-line) were used for validation of angiogeneic activity, such as tube formation assay. Exosomes derived from the RPMI8226HR cells significantly increased tube formation of HUVECs than those from RPMI8226 cells. To identify intercellular and exosomal miRNAs specifically expressed in hypoxia-resistant cells, we assess the expression profiles of intercellular and extracellular miRNAs in RPMI8226 cells and RPMI8226HR cells using Taqman MicroRNA Array v2.0 (Applied Biosystems, Bedford, MA).

overall_design: RPMI8226 cells were cultured for 24 hours under hypoxic conditions (1% O2) or normoxic conditions (20% O2). The exosome fraction was obtained from culture medium using Exoquick Exosome Precipitation Solution (System Biosciences, Mountain View, CA, USA). Isolation of cellular and exosomal miRNAs was performed using the miRNsasy kit (Qiagen). The expression profile of miRNAs was determined using the Human Taqman miRNA Arrays A (Applied Biosystems). RNU6B and a spike control (ath-miR159) were used as an invariant control for the cell and exosome, respectively. QRT-PCR was carried out on an Applied Biosystems 7900HT thermal cycler using the manufacturer’s recommended program. Finally, all the raw data from each array was run on Data Assist Software ver.3.1 (Applied Biosystems).


title: CTCF binding profiles in Drosophila melanogaster 3rd instar larva T1 and T3 leg discs

status: Public on Oct 11 2014

city: Cambridge

first: Robert

last: White

address: Downing Street

department: Physiology, Development and Neuroscience

country: United Kingdom

institute: University of Cambridge

summary:
Although the majority of genomic binding sites for the insulator protein CTCF are constitutively occupied, a subset show variable occupancy. Such variable sites provide an opportunity to assess context-specific CTCF functions in gene regulation.
Here we have identified a variably occupied CTCF site in the Ultrabithorax (Ubx) gene in Drosophila. This site is occupied in tissues where Ubx is active (third thoracic imaginal leg disc) but is not bound in tissues where the Ubx gene is repressed (first thoracic imaginal leg disc).

overall_design: Comparison of CTCF binding in T1 leg disc vs T3 leg disc in from 3rd instar larva

first: JosePaolo

last: Magbanua

first: Steven

last: Russell

middle: A


title: Dynamics of intercellular and exosomal miRNAs in hypoxia-resistant KMS-11 cells

country: Japan

summary: In multiple myeloma (MM), abnormal plasma cells interact with bone marrow (BM) stromal cells and vascular cells among others. A part of the BM milieu is considered highly hypoxic, and myeloma cells in situ may be influenced by circumstances other than normoxia in vitro. Hence, we attempted to confirm the role of hypoxic MM-derived exosomes in the BM milieu. We established a novel hypoxia-resistant cell line, KMS-11-HR, derived from KMS-11 cells cultured for >4 months under hypoxia (1% O2), as a model of MM cells localizing in an extensively hypoxic milieu. We used KMS-11 cells and KMS-11-HR cells, as donor cells, and HUVECs as recipient cells. Exosomes derived from KMS-11 cells (normoxia or hypoxia) and exosomes derived from KMS-11-HR cells (hypoxia-resistant sub-line) were used for validation of angiogeneic activity, such as tube formation assay. Exosomes derived from the KMS-11-HR cells significantly increased tube formation of HUVECs than those from KMS-11 cells. To identify intercellular and exosomal miRNAs specifically expressed in hypoxia-resistant cells, we assess the expression profiles of intercellular and extracellular miRNAs in KMS-11 cells and KMS-11-HR cells using Taqman MicroRNA Array v2.0 (Applied Biosystems, Bedford, MA).

overall_design: KMS-11 cells and KMS-11-HR cells were cultured for 24 hours under hypoxic conditions (1% O2). The exosome fraction was obtained from culture medium using Exoquick Exosome Precipitation Solution (System Biosciences, Mountain View, CA, USA). Isolation of cellular and exosomal miRNAs was performed using the miRNsasy kit (Qiagen). The expression profile of miRNAs was determined using the Human Taqman miRNA Arrays A (Applied Biosystems). RNU6B and a spike control (ath-miR159) were used as an invariant control for the cell and exosome, respectively. QRT-PCR was carried out on an Applied Biosystems 7900HT thermal cycler using the manufacturer’s recommended program. Finally, all the raw data from each array was run on Data Assist Software ver.3.1 (Applied Biosystems).


title: Transcriptomic analysis of Staphylococcus xylosus in the presence of nitrate and nitrite in meat reveals its response to nitrosative stress

status: Public on Oct 08 2014

city: Saint-Genès Champanelle

first: Sabine

last: Leroy

address: Clermont-Ferrand Theix Research Center

department: MICA

institute: INRA

summary: Staphylococcus xylosus is one of the major starter cultures used for meat fermentation because of its crucial role in the reduction of nitrate to nitrite, which contributes to color and flavor development. Despite the long use of these additives, their impact on the physiology of S. xylosus has not yet been explored. We present the first in situ global gene expression profile of S. xylosus in meat supplemented with nitrate and nitrite. More than 600 genes of S. xylosus were differentially expressed at 24 or 72 hours of incubation. They represent more than 20% of the total genes and led us to suppose that addition of nitrate and nitrite to meat leads to a global change in gene expression. This profile revealed that S. xylosus is subject to nitrosative stress caused by reactive nitrogen species generated from nitrate and nitrite. To overcome this stress, S. xylosus has developed several oxidative stress resistance mechanisms, such as modulation of the expression of several genes involved in iron homeostasis and in antioxidant defense. Most of these genes belong to the Fur and PerR regulons respectively. S. xylosus has also counteracted this stress by developing DNA and protein repair. Furthermore, it has adapted its metabolic response—carbon and nitrogen metabolism, energy production and cell wall biogenesis—to the alterations produced by nitrosative stress.

overall_design: Microarray was used to evaluate modification in the transcriptome of S. xylosus C2a strain in the presence (N) or absence (V) of nitroso compounds. Three biological replicates collected on separate days for each meat matrix and labelled following a dye-switch design; for each condition one labeling in Cy3 and one in Cy5.

first: Aurore

last: Vermassen

first: Anne

last: de La Foye

first: Valentin

last: Loux

first: Régine

last: Talon


title: Genome wide analysis of bivalent domains in two HUES cell lines

status: Public on Oct 06 2014

city: Marseille

first: michel

last: PUCEAT

address: 27 bd Jean moulin

department: University aix marseille

institute: INSERM

type: Genome binding/occupancy profiling by array

summary: Human embryonic stem (HUES) cells are derived from early individual embryos with unique genetic properties. However, how their epigenetic status might affect their potential to differentiate toward specific lineages remains a puzzling question.   Using ChIP-on-chip, the status of bivalent domains on gene promoters (i.e. H3K4 and H3K27 trimethylation) was monitored for both undifferentiated and BMP2 induced cardiac committed cells. A marked difference in the epigenetic profile of HUES cell lines was observed and this was correlated to the pattern of gene expression induced by BMP2 as well as to their potential to generate cardiac progenitors and differentiated myocytes. Thus, the epigenetic H3trimeK4 and H3trimeK27 prints generating bivalent domains on promoters, could be used to predict a preference in their differentiation toward a specific lineage.

first: Julia

last: Leschik

first: Michel

last: Puceat


title: Gene expression profiles during long-term low-temperature treatment and cold acclimation in synthetic wheat hexaploids

status: Public on Oct 10 2014

city: Kobe

first: Shigeo

last: Takumi

state: Hyogo

address: Rokkodai 1-1, Nada

department: Graduate School of Agricultural Science

institute: Kobe University

summary:
We conducted microarray analysis to study comprehensive changes of gene expression profile under long-term low-temperature (LT) treatment and to identify other LT-responsive genes related with cold acclimation in seedling leaves and crown tissues (shoots containing apical meristems) of a synthetic hexaploid wheat line. The microarray analysis revealed marked up-regulation of a number of Cor/Lea genes and fructan biosynthesis-related genes under the long-term LT treatment. For validation of the microarray data, we selected four synthetic wheat lines, which contained the A and B genomes from a tetraploid wheat cultivar Langdon and the diverse D genomes originating from the different Ae. tauschii accessions, with distinct levels of freezing tolerance after cold acclimation. Quantitative RT-PCR analyses showed that the transcription accumulated levels of the Cor/Lea, CBF, and fructan biosynthesis-related genes were higher in more freezing-tolerant lines than those in the sensitive lines.
The fructan biosynthesis pathway would be associated with cold acclimation to develop wheat freezing tolerance and related with diversity of the freezing tolerance level in addition to the CBF-mediated Cor/Lea expression pathway.

overall_design: Expression patterns were compared between a synthetic wheat line which treated 24℃ and 4℃. Total RNA samples were respectively isolated from leaves and crown tissues of the synthetic line grown at normal temperature for 3 weeks and then at 4°C for 12 and 6 weeks. Two independent experiments were conducted in each exprement.

first: Julio

middle: C

last: Iehisa


title: Molecular profiling of blastic plasmacytoid dendritic cell neoplasm reveals a unique pattern and suggests selective sensitivity to nf-kb pathway inhibition

status: Public on Oct 03 2014

city: Bologna

first: Fabio

last: Fuligni

address: Via Massarenti 9

department: Department of Experimental, Diagnostic, and Specialty Medicine Bologna University Medical School

country: Italy

institute: University of Bologna

overall_design:
To better understand the pathobiology of BPDCN and discover new targets for effective therapies, the gene expression profile (GEP) of 25 BPDCN samples was analyzed and compared with that of pDCs, their postulated normal counterpart
Raw matrix per probe not available. Raw matrix collapsed by gene available as suppplementary file (GSE62014_non-normalized.txt).

first: Maria

last: Sapienza

first: Claudio

last: Agostinelli

last: Tripodo

first: Simona

last: Righi

last: Laginestra

first: Alessandro

last: Pileri jr

first: Maura

last: Rossi

first: Francesca

last: Ricci

first: Anna

last: Gazzola

first: Claudia

last: Mannu

last: Ulbar

first: Mario

last: Arpinati

first: Marco

last: Paulli

first: Takahiro

last: Maeda

first: Davide

last: Gibellini

first: Livio

last: Pagano

first: Nicola

last: Pimpinelli

last: Santucci

first: Lorenzo

last: Cerroni

first: Carlo

last: Croce

last: Facchetti

first: Stefano

last: Pileri

first: Pier

last: Piccaluga


title: Anaerobic Degradation of Phenylacetate By the Hyperthermophilic Archaeon, Ferroglobus placidus

status: Public on Oct 01 2014

city: Amherst

first: Dawn

last: Holmes

state: Massachusetts

address: 639 N Pleasant St Morrill IVN 422C

department: Microbiology

country: USA

institute: University of Massachusetts Amherst

summary: Comparison of acetate- to phenylacetate-grown F. placidus cells to identify genes that are potentially involved in anaerobic phenylacetate degradation by this unique hypertherophilic archaeon.

overall_design: A four chip study using total RNA recovered from two separate cultures of Ferroglobus placidus DSM 10642 grown with 1 mM phenylacetate (experimental condition) and two separate cultures of Ferroglobus placidus DSM 10642 grown on 10 mM acetate (control condition).  Each chip measures the expression level of 2613 genes from Ferroglobus placidus DSM 10642 with nine 45-60-mer probe pairs (PM/MM) per gene, with three-fold technical redundancy.

first: Carla

last: Risso

first: Jessica

last: Smith

first: Derek

last: Lovley


title: Expression of miRNAs in human colorectal carcinoma cells upon autophagy induction

status: Public on Oct 02 2014

city: Xi'an

first: Ni

last: Hou

state: Shaanxi Province

address: 76 Western Yanta Road

department: Department of Genetics and Molecular Biology

institute: Xi'an Jiaotong University

summary: The expression profile of miRNAs during the response of human colon cancer cells (HT29s) to 5-FU treatment and nutrient starvation was examined using miRNA microarray analysis. Combining with the following real time PCR and bioinformatics analysis, the physiological importance of the miRNA-autophagy interconnection is far more likely to be elucidated.

platform_organism:
Homo sapiens
Human alphaherpesvirus 1
Human alphaherpesvirus 2
Cytomegalovirus
Lymphocryptovirus
Rhadinovirus
JC polyomavirus
Human immunodeficiency virus 1
Merkel cell polyomavirus
Betapolyomavirus hominis
Betapolyomavirus macacae

overall_design: In the study presented here, autophagy induction was confirmed in both 5-FU-treated HT29 cells and nutrient-starved HT29 cells. These cells were used to acquire expression profiles of all human miRNAs annotated in miRBase 18.0

first: Chen

last: Huang


title: Gene expression analysis of Hammondia hammondi and Toxoplasma gondii sporulated oocysts

first: Jon

middle: P

last: Boyle

address: 4249 Fifth Avenue

summary: To date little is known about the transcriptome of Hammondia hammondi, the nearest extant relative of Toxoplasma gondii.  In this study we used an existing microarray to query Toxoplasma gondii and Hammondia hammondi transcript abundance in sporulated oocysts.

sample_organism:
Toxoplasma gondii
Hammondia hammondi

overall_design: Oocysts of the VEG strain of Toxoplasma gondii, and the HhCatGer041 strain of Hammondia hammondi, were isolated from cat feces by sucrose flotation, and sporulated for ~3-6 months in 2% sulfuric acid.  RNA was isolated from Bleach-treated oocyst preparations using the Trizol reagent.  RNA was biotinylated for hybridization to Toxo 169 Affymetrix chips using the Illumina Total Prep RNA labeling kit (Ambion).  For each species 3 separate RNA isolations were performed on the same batch of oocysts and hybridized to individual microarrays.


title: Regulation of Coagulation Factor XI expression by MicroRNAs in the Human Liver

city: Murcia

first: Salam

last: Salloum-Asfar

state: Murcia

address: Ronda Garay, s/n

country: Spain

institute: Centro Regional de Hemodonación, Universidad de Murcia

summary: High levels of factor XI (FXI) increase the risk of thromboembolic disease. However, the genetic and environmental factors regulating FXI expression are still largely unknown. The aim of our study was to evaluate the regulation of FXI by microRNAs (miRNAs) in the human liver. In silico prediction yielded four miRNA candidates that might regulate FXI expression. HepG2 cells were transfected with miR-181a-5p, miR-  23a-3p, miR-16-5p and miR-195-5p. We used mir-494, which was not predicted to bind to F11, as a negative control. Only miR-181a-5p caused a significant decrease both in FXI protein and F11 mRNA levels. In addition, transfection with a miR-181a-5p inhibitor in PLC/PRF/5 hepatic cells increased both the levels of F11 mRNA and extracellular FXI. Luciferase assays in human colon cancer cells deficient for Dicer (HCT-DK) demonstrated a direct interaction between miR-181a-5p and 3'untranslated region of F11. Additionally, F11 mRNA levels were inversely and significantly correlated with miR-181a-5p levels in 114 healthy livers, but not with miR-494. This study demonstrates that FXI expression is directly regulated by a specific miRNA, miR-181a-5p, in the human liver. Future studies are necessary to further investigate the potential consequences of miRNA dysregulation in pathologies involving FXI.

overall_design:
In the study presented here, we report arrays including 1,898 human mature miRNAs (LCSciences, Houston, TX; Sanger mirBase Release 18.0) using total RNA extracted from a healthy human liver sample E122; a Caucasian donor that gave informed consent were provided by biobanc CIBERehd. Human liver studies were apporved by Local Ethics Committee from Hospital Universitario Morales Meseguer in Murcia.
In the study presented here, we report arrays including 2,019 human mature miRNAs (LCSciences, Houston, TX; Sanger mirBase Release 19.0) using total RNA extracted from 3 healthy human liver samples (662, 664, 771) from Caucasian donors that gave informed consent were provided by St. Jude Liver Resource at St. Distribution System and by cooperative Human Tissue Network. Human liver studies were apporved by Local Ethics Committee from Hospital Universitario Morales Meseguer in Murcia

first: Constantino

last: Martínez


title: TRIM37 is a novel H2A ubiquitin ligase and a Breast Cancer Oncogene

city: Davis

first: Sanchita

last: Bhatnagar

address: 1275 Health Sciences, Tupper Hall 3134

department: Medical Microbiology and Immunology

institute: University of California Davis

summary: The TRIM37 gene is mutatedin Mulbery nanism, a rare autosomal recessive disorder, and is in the 17q23 chromosomal region that is amplified in up to ~40% of breast cancers. Trim37 contains a RING finger domain, a hallmark of E3 ubiquitin ligases, but the protein substrate(s) of Trim37 is unknown.  Mono-ubiquitination of histone H2A is a chromatin modification associated with transcriptional repression and here we report that Trim37 is an H2A ubiquitin ligase.  Genome-wide Chip-CHIP experiments indicate that in human breast cancer cells containing amplified 17q23, Trim37 is bound to the promoters of many tumor suppressor genes.  RNA interference (RNAi)-mediated knockdown of Trim37 results in loss of ubiquitinated H2A, dissociation of PRC1 and PRC2, and transcriptional reactivation of silenced genes. Knockdown of Trim37 in human breast cancer cells containing amplified 17q23 substantially decreases tumor growth in mouse xenografts. Collectively, our results reveal Trim37 as a new H2A ubiquitin ligase that is overexpressed in a subset of breast cancers and redirects PRC2 to silence tumor suppressors and other genes resulting in oncogenesis.

overall_design: Identification of TRIM37 Binding targets in MCF7 cells from the two replicate experiments

first: Michael

middle: R

last: Green


title: Uromodulin-retention in thick ascending limb affects SCD1 in neighboring S3 proximal tubule in males: transcriptome studies in mouse models of Uromodulin-associated kidney disease

city: Neuherberg

first: Martin

last: Irmler

state: Bayern

address: Ingolstaedter Landstrasse 1

department: Institute of Experimental Genetics

country: Germany

institute: Helmholtz Zentrum München GmbH

summary: Uromodulin-associated kidney disease (UAKD) summarizes different clinical features of an autosomal dominant heritable disease syndrome in humans with a proven uromodulin (UMOD) mutation involved. It is often characterized by hyperuricemia, gout, alteration of urine concentrating ability, as well as a variable rate of disease progression inconstantly leading to renal failure and histological alterations of the kidneys. We recently established the two Umod mutant mouse lines UmodC93F and UmodA227T on the C3H inbred genetic background both showing kidney defects analogous to those found in human UAKD patients. The aim of this study was the further analysis of the phenotypic alterations by examining the kidneys as primarily affected organs. Transcriptome and quantitative PCR analyses as well as IHC analyses found significant changes related to the phenotyping changes.

overall_design: 4 male mice of each mutant cohort (Umod C93F & Umod A227T) and the corresponding wildtype controls, each mutant mouse was compared to the mean of the corresponding wildtype including a technical replicate (dye swap)

first: Johannes

last: Beckers

first: Marion

last: Horsch


title: Genomic analysis of low-grade serous ovarian carcinomas [IL610Q]

city: East Melbourne

first: Dariush

last: Etemadmoghadam

address: St Andrew's Place

institute: Peter MacCallum Cancer Centre

summary: Low-grade serous ovarian carcinomas are typically Ras-pathway mutated, TP53 wild-type, have limited chromosomal aberration, and are frequently associated with borderline tumors. By contrast, high-grade serous ovarian carcinoma lack Ras-pathway mutations, are invariably TP53 mutated, show widespread genomic change, and are commonly BRCA-pathway disrupted. We sought to identify differences in genomic copy number changes between co-existing borderline and invasive components of serous carcinoma.

overall_design: Paired co-existing borderline and invasive tumor components of ovarian serous carcinoma were sampled and profiled from tumors from 7 patients

first: Anna

last: deFazio

first: David

last: Bowtell

first: Catherine

last: Emmanuel

first: Yoke-Eng

last: Chiew

first: Joshy

last: George


title: Genomic analysis of low-grade serous ovarian carcinomas [ILOEF]

summary: Low-grade serous ovarian carcinomas are typically Ras-pathway mutated, TP53 wild-type, have limited chromosomal aberration, and are frequently associated with borderline tumors. By contrast, high-grade serous ovarian carcinoma lack Ras-pathway mutations, are invariably TP53 mutated, show widespread genomic change, and are commonly BRCA-pathway disrupted.We sought to identify differences in genomic copy number changes between co-existing borderline and invasive components of serous carcinoma.

overall_design: Paired co-existing borderline and invasive tumor components were sampled and profiled from formalin-fixed paraffin embedded tumors from 6 patients


title: Genomic analysis of low-grade serous ovarian carcinomas [ILOE]

summary: Low-grade serous ovarian carcinomas are typically Ras-pathway mutated, TP53 wild-type, have limited chromosomal aberration, and are frequently associated with borderline tumors. By contrast, high-grade serous ovarian carcinoma lack Ras-pathway mutations, are invariably TP53 mutated, show widespread genomic change, and are commonly BRCA-pathway disrupted. We sought to identify differences in genomic copy number changes in borderline and invasive components of serous carcinoma.

overall_design: Borderline and invasive tumor components were profiled from patients with LGSC


title: Large-scale identification and comparative analysis of miRNA expression profile in the respiratory tree of the sea cucumber Apostichopus japonicus during aestivation (part 1)

city: QINGDAO

first: Muyan

last: Chen

address: 5 YUSHAN ROAD

institute: Ocean University of China

summary: The sea cucumber Apostichopus japonicus withstands high water temperatures in the summer by suppressing metabolic rate and entering a state of aestivation. We hypothesized that changes in the expression of miRNAs could provide important post-transcriptional regulation of gene expression during hypometabolism via control over mRNA translation. The present study analyzed profiles of miRNA expression in the sea cucumber respiratory tree using Solexa deep sequencing technology. We identified 279 sea cucumber miRNAs, including 15 novel miRNAs specific to sea cucumber. Animals sampled during deep aestivation (DA; after at least 15 days of continuous torpor) were compared with animals from a non-aestivation (NA) state (animals that had passed through aestivation and returned to an active state). We identified 30 differentially expressed miRNAs ([RPM (reads per million) >10, |FC| (|fold change|) ≥1, FDR (false discovery rate) <0.01]) during aestivation, which were validated by two other miRNA profiling methods: miRNA microarray and real-time PCR. Among the most prominent miRNA species, miR-124, miR-124-3p, miR-79, miR-9 and miR-2010 were significantly over-expressed during deep aestivation compared with non-aestivation animals, suggesting that these miRNAs may play important roles in metabolic rate suppression during aestivation.

overall_design: In the present study, an analysis of the global profile of small RNAs was conducted using Solexa sequencing technology in non-aestivation (NA) and deep aestivation (DA) sea cucumbers. We focus on respiratory tree in the present study because it is the important site responsible for the strong metabolic rate depression seen under deep aestivating conditions and the global expression profile of mRNA from the this organ has also been constructed applying RNA-seq technology in our previous study (Zhao and Chen, unpublished data). A preliminary analysis of the functional relevance of miRNA expression in relation to hypometabolism during aestivation is presented. A miRNA microarray and RT-qPCR were both used to supplement and confirm differentially expressed miRNAs. Our findings provide important new insights into the molecular mechanisms of sea cucumber aestivation.


title: Human K562 cells overexpressing ETO2

city: Kamakura

first: Satoshi

last: Kondo

state: Kanagawa

address: Tebiro 6-10-1

department: New Projects Development Division

institute: Toray Industries,Inc.

summary: microRNA profiling of human K562 cells comparing control or ETO2-overexpressed cells

overall_design: Two-condition experiment, K562-pcDNA vs. K562-pcDNA-ETO2, Biological replicates: 1, 1 pcDNA, 1 pcDNA-ETO2, independently.

first: Tohru

last: Fujiwara


title: Initiation of DNA replication from non-canonical sites on an origin-depleted chromosome

status: Public on Sep 26 2014

city: Seattle

first: Toshio

last: Tsukiyama

state: WA

address: 1100 Fairview Ave N.

department: Basic Sciences

institute: Fred Hutchinson Cancer Research Center

summary: Eukaryotic DNA replication initiates from multiple sites on each chromosome called replication origins. In the budding yeast Saccharomyces cerevisiae, origins are defined at discrete sites. Regular spacing and diverse firing characteristics of origins are thought to be required for efficient completion of replication, especially in the presence of replication stress. However, a S. cerevisiae chromosome III harboring multiple origin deletions has been reported to replicate relatively normally, and yet how an origin-deficient chromosome could accomplish successful replication remains unkown. To address this issue, we deleted seven well-characterized origins from chromosome VI, and found that thsese deletions do not cause gross growth defects even in the presence of replication inhibitors. We demonstrated that the origin deletions do cause a strong decrease in the binding of the origin recognition complex. Unexpectedly, replication profiling of this chromosome showed that DNA replication initiates from non-canonical loci around deleted origins in yeast. These results suggest that replication initiation can be unexpectedly flexible in this organism.

overall_design: In this study, we aimed to establish an independent system to investigate how an origin-deficient chromosome is replicated. To this end, we systematically deleted seven well-characterized origins on the left arm of S. cerevisiae chromosome VI and analyzed (1) Orc2 localization during G2/M arrest and (2) BrdU incorporation during synchronous release from G1 arrest into S-phase, and compared the results to wild-type cell signals. For Orc2 ChIP-Chip experiments, Orc-bound DNA was isolated from Orc2-2Xlinker-3XFlag epitope-tagged cells arrested in G2/M using antibodies against Flag. For BrdU ChIP-Chip experiments, actively replicating DNA was isolated from cells harboring a single integrated BrdU incorporation vector released synchronously into 200mM HU using antibodies against BrdU. Immunoprecipitated and input (Orc2) or G1 (BrdU) DNA was then amplified and competitively hybridized to high-resolution strand-specific microarrays covering chromosomes III, VI, and XII.

first: Naomi

middle: L

last: Bogenschutz

first: Jairo

last: Rodriguez


title: Gene expression in response to exposure to nitric oxide

status: Public on Sep 30 2014

city: Ikoma

first: Ryo

last: Nasuno

address: 8916-5, Takayama-cho

institute: Nara Institute of Science and Technology

summary: To analyze gene expression pattern in response to nitric oxde in Saccharomyces cerevisiae, we performed microarray analysis using yeast cells treated with a nitric oxide donor S-nitroso-N-acetyl-DL-penicillamine (SNAP). S. cerevisiae S288c strain was cultured in synthetic dextrose (SD) minimal medium up to log phase (OD600 = 1), and then treated with 100 micro molar of SNAP for 10, 30, or 60 min. After treatment with SNAP, cells were disrupted adn total RNA was extracted. We commissioned following experiments to BIO MATRIX RESEARCH Inc.

overall_design: Nitric oxide-induced gene expression in S. cerevisiae was measured at 10, 30, or 60 minutes after exposure to 100 micro molar of nitric oxide donor SNAP.

first: Akira

last: Nishimura

first: Hiroshi

last: Takagi