title: Global gene expression in patient keratinocytes and patient-specific iPS-derived keratinocytes

status: Public on Nov 26 2014

city: Stanford

first: Anthony

last: Oro

address: 269 Campus Drive, CCSR 2145c

department: Dermatology

institute: Stanford University

summary: Patients with recessive dystrophic epidermolysis bullosa (RDEB) lack functional Type VII collagen and suffer severe blistering and chronic wounds that ultimately lead to infection and development of lethal squamous cell carcinoma (SCC). The discovery of induced pluripotent stem cells (iPSCs) and the ability to edit the genome bring the possibility to provide definitive genetic therapy through corrected autologous tissues. We have formed a multidisciplinary team with the ultimate goal to develop an iPSC-based therapy for RDEB. Here, we present a clinical protocol that generates autologous, corrected epithelial keratinocyte sheets with the COL7A1 gene mutation corrected for grafting on to patients. We demonstrate the utility of sequential reprogramming and novel adenovirus-associated viral genome editing to generate corrected iPSC banks. iPSC-derived keratinocytes were produced with minimal heterogeneity and secreted wild-type collagen VII, resulting in stratified epidermis in vitro and in vivo in mice. Sequencing of corrected cell lines prior to tissue formation revealed heterogeneity of SCC-predisposing mutations, allowing us to select COL7A1 corrected banks with minimal mutational burden for downstream epidermis production. Our results provide a first clinical platform to use iPSCs in the treatment of debilitating genodermatoses.

overall_design: Microarray analysis of iPS-derived keratinocytes from two RDEB patients (iPS-K1 and iPS-K3), corresponding patient keratinocytes (AHK1 and AHK2), normal human keratinocytes (NHK), as well as H9 human embryonic stem cells (hESC - H9). All samples were analyzed in duplicate and differential gene expression was measured relative to H9.

first: Vittorio

last: Sebastiano

first: Hanson

last: Zhen

first: Bahareh

last: Derafshi

first: Lisa

last: Bashkirova

first: Sandra

last: Melo

first: Pei

last: Wang

first: Thomas

last: Leung

first: Zurab

last: Siprashvili

first: Andrea

last: Tichy

first: Jiang

last: Li

first: Mohammed

last: Ameen

first: John

last: Hawkins

first: Susie

last: Lee

first: Lingjie

first: Aaron

last: Schwertschkow

first: Gerhard

last: Bauer

first: Leszek

last: Lisowski

first: Mark

last: Kay

first: Seung

middle: K

last: Kim

first: Alfred

last: Lane

first: Marius

last: Wernig

middle: E


title: Analysis of gene expression to find the effect of aspirin on oral cancer cell line

status: Public on Nov 22 2014

city: Waurnponds

first: sivapriya

last: pavuluri

state: VIC

address: 75, Pigdons Road

department: School of Medicine

country: Australia

institute: Deakin University

summary: Aspirin is a non-steroidal anti-inflammatory drug. Till date there is no information on the molecular mechanism of aspirin on oral cancer cells. In this study, treated oral cancer cells were compared with untreated ones for gene expression for finding the effect of aspirin on biological process and significant pathways involved. Aspirin plays an important role in inducing apoptotic effect by activating regulators and further inhibits cell cycle progression.

overall_design: Total RNA was obtained from oral cancer cell line, SCC25, treated with 2.0mM of aspirin and untreated compared as a control

first: Sivapriya

last: Pavuluri

first: Christophe

last: Lefevre

first: Julie

middle: A

last: Sharp

first: Kevin

middle: R

last: Nicholas


title: ChIP-chip data of Rrm3-Flag in wild-type and rpb1-1 cells

status: Public on Dec 04 2014

city: Seville

first: Andrés

last: Aguilera

address: Av. Américo Vespucio 24

department: Genome BIology

country: Spain

institute: CABIMER, Universidad de Sevilla

type: Genome binding/occupancy profiling by genome tiling array

summary:
Transcription is a major contributor to genome instability.A main cause of transcription-associated instability relies on the capacity of transcription to stall replication. Such genome instability is increased in RNAPII mutants.
ChIP-chips performed in asynchronous cultures showed an increase of the Rrm3 binding signal all over the genome in rpb1-1 compared to wild-type.

overall_design: ChIP-chip studies were perfomed with antibody against Flag-tagged Rrm3 protein in both wild-type and rpb1-1 cells.

first: Irene

last: Felipe-Abrio

first: Juan

last: Lafuente-Barquero

first: María

middle: L

last: García-Rubio

first: Antonio

last: Marín


title: BCL11A is a triple-negative breast cancer gene with critical functions in stem and progenitor cells

status: Public on Nov 18 2014

city: Frederick

first: Jack

last: Chen

state: MD

address: SAIC-Frederick Miller Dr

country: USA

institute: NIH

summary: Triple negative breast cancer (TNBC) has poor prognostic outcome compared to other types  of breast cancer1. At present the molecular and cellular mechanisms underlying TNBC  pathology are not well understood1. Here we report that the transcription factor BCL11A is  overexpressed in TNBC including basal-like breast cancer (BLBC) and that its genomic locus  is amplified in up to 38% of BLBC tumours. BCL11A overexpression in immortalised human  breast epithelial cells promotes tumour formation in xenograft models, whereas knockdown  of BCL11A in TNBC cell lines suppresses their tumourigenic potential. In the DMBA-induced  mouse mammary tumour model, Bcl11a is found to be essential for tumourigenesis since  deletion of Bcl11a before DMBA treatment substantially decreases tumour formation, even in  p53-null cells, and inactivation of Bcl11a in established tumours causes their regression. At  the cellular level, BCL11A overexpression enhances clonogenicity in vitro whereas its deletion  in the mouse causes a reduction in the number of mammary epithelial stem and progenitor  cells. Thus, BCL11A has an important role in the genesis of TNBC and in normal mammary  epithelial cells. This study highlights the importance of further investigation of BCL11A in  breast cancer diagnosis and targeted therapies.

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus

overall_design:
[Mouse] KO is bcl11a deleted mammary stem cells. WT are mammary stem cells with intact Bcl11a.
[Human] HMLE tumors overexpressing BCL11A.

first: Walid

middle: T

last: Khaled

first: Song

middle: C

last: Lee

first: John

last: Stingl

first: Xiongfeng

first: H

last: Ali

first: Oscar

middle: M

last: Rueda

first: Fazal

last: Hadi

first: Juexuan

last: Wang

first: Yong

last: Yu

first: Suet-Feung

last: Chin

first: Mike

last: Stratton

first: Andy

last: Futreal

first: Nancy

last: Jenkins

first: Sam

last: Aparicio

first: Neal

middle: G

last: Copeland

first: Christine

middle: J

last: Watson

first: Carlos

last: Caldas

first: Pentao

last: Liu


title: Gene expression in malignant peripheral nerve sheat tumours and benign neurofibromas

status: Public on Mar 11 2015

city: Oslo

first: Maren

last: Høland

address: Ullernchausséen 70

department: Institute for Cancer Research

country: Norway

institute: Oslo University Hospital

summary: No consensus treatment regime exists beyond surgery for malignant peripheral nerve sheath tumours (MPNST), and the purpose of the present study was to find new approaches to stratify patients with good and poor prognosis and to better guide therapeutic intervention for this aggressive soft tissue cancer.

overall_design: Genome-wide RNA expression was analysed for 30 MPNSTs and eight neurofibromas from Scandinavian patients, and the overall gene expression in these two groups were compared in order to identify prognostic markers.

first: Matthias

last: Kolberg

first: Guro

last: Lind

first: Trude

middle: H

last: Ågesen

first: Rolf

middle: I

last: Skotheim

first: Kirsten

middle: S

last: Hall

first: Nils

last: Mandahl

first: Sigbjørn

last: Smeland

first: Fredrik

last: Mertens

first: Ben

last: Davidson

first: Ragnhild

last: Lothe


title: Radiation effects on a 3D cell culture of primary human keratinocytes and the protective effect of N-acetyl-cysteine (NAC) and the Traditional Chinese Medicine Qingre-Liyan decoction (QYD)

status: Public on Oct 16 2014

city: Pomona

first: Maria

middle: P

last: Lambros

state: CA

address: 309 E Second Street

department: Pharmaceutical Sciences

institute: Western Univ of Health Sci

summary: We studied the radiation effect on cell culture model of oral mucositis. The musositis model  (tissues) used is an organotypic model which consisted of 3-dimensional (3-D) cell cultures of primary human oral keratinocytes.  The tissues were purchased from MatTek corporation (Ashland, MA) and were grown on top of microporous membrane and supplemented with MatTek serum free media.  These tissues were irradiated with 12 Gy. Six hours after the irradiation the tissues were cut in half. Half of the tissue was used to extract total RNA (RNeasy Plus Mini kit, Qiagen, Germantown, MD) and the other half was used to evaluate the histology and the apoptosis. We had the following groups: Non-Irradiated Tissue, Irradiated Tissue with 12 Gy; Irradiated Tissue with 12 Gy pretreated with N-acetylcysteine (NAC); Irradiated Tissue with 12 Gy pretreated with the Traditional Chinese Medicine Qingre-Liyan decoction (QYD); and Irradiated Tissue with 12 Gy pretreated with 50:50 w/w NAC-QYD.

overall_design: Group 1: Human Prirmary 3-D Cultures of Human Keratinocytes were irradiated with 12 Gy; Group 2: Human Prirmary 3-D Cultures of Human Keratinocytes were pretereated with N-acetylcysteine (NAC) and then irradiated with 12 Gy; Human Prirmary 3-D Cultures of Human Keratinocytes were pretreated with the Qingre-Liyan Decoction (QYD) and then irradiated with 12 Gy; Human Prirmary 3-D Cultures of Human Keratinocytes were pretreated with  a 50:50 w/w mixture of NAC-QYD and then irradiated with 12 Gy.  Each sample was done in triplicate.

first: Hari

last: Reddy

first: Lavanya

last: Kondapali

first: Michael

last: DeSalvo


title: The influence of WWOX tumor supressor gene on endometrial cancerogenesis

status: Public on Sep 03 2014

city: Lodz

first: Magdalena

last: Nowakowska

address: Zeligowskiego 7/9

department: Department of Molecular Cancerogenesis

country: Poland

institute: Medical University of Lodz

summary: The WWOX gene is a tumor suppressor probably involved in variety of cellular processes including  and is ferquently downregulated in variety of cancer types. However, its role in endometrial cancerogenesis is not well described. The aim of this study was to characterize how WWOX  may be involved in endometrial cancerogenesis, how it influences the basic cancer cell features and modifies cell expression profile.Our observations suggest that in ECC1 endometrial cancer cell line increased expression of WWOX may  be involved in the initiation of EMT, leading to changes in cell adhesion and motility but also indicate its suppressive role in the process of mesenchymal phenotype acquisition, resulting in reduction of aggressiveness cell features

overall_design: Well differentiated ECC1 endometrial cancer cells were stably transfected with WWOX cDNA.ECC1 cells transfected with an empty vector served as a control. Total mRNA was isolated to look for gene-expression differences induced by the WWOX overexpression.

first: Elzbieta

last: Pluciennik

first: Karolina

last: Pospiech

first: Anna

last: Stepien

first: Mateusz

last: Wolkowicz

first: Malgorzata

last: Galdyszynska

first: Marta

last: Popeda

first: Katarzyna

last: Wojcik-Krowiranda

first: Andrzej

last: Bienkiewicz

last: Bednarek


title: ChIP-chip data of Thp1-Flag and Sac3-Flag in wild-type cells, and Rrm3-Flag in sac3∆ and thp1∆ cells

status: Public on Oct 08 2014

first: Andrés

last: Aguilera

type: Genome binding/occupancy profiling by high throughput sequencing

summary:
Transcription is a major obstacle for replication fork progression and a cause of genome instability. Such instability increases in mutants with a suboptimal assembly of the nascent messenger ribonucleo-protein particle (mRNP), as THO/TREX and the NPC-associated THSC/TREX-2 complex.
Here we show that yeast sac3∆ and thp1∆ cells accumulate genome-wide replication obstacles as determined by the distribution of the Rrm3 helicase. Such obstacles preferentially occur at long and highly expressed genes, to which Sac3 and its interacting partner Thp1 are preferentially bound in wild-type cells.

overall_design: ChIP-chip studies were perfomed with antibodies against Flag-tagged Thp1 and Sac3 proteins in wild-type cells of the yeast S. Cerevisiae, as well as Flag-tagged Rrm3 protein in sac3∆ and thp1∆ cells that were compared with Rrm3 in wild-type cells from Santos-Pereira et al., 2013 (accession number GSE50185).

first: José

last: Santos-Pereira

first: María

last: García-Rubio

first: Cristina

last: González-Aguilera

first: Rosa

last: Luna


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

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.
In these experiments, we have analyzed Sth1 (catalytic subunit of the RSC chromatin remodeling complex) enrichment to the transcribing genes.

overall_design: The cells (WT and gcn4Δ) harboring STH1-MYC allele were treated by SM for 20 minutes to induce Gcn4 regulated genes. The chromatin extracts were prepared and subjected to chromatin immunoprecipitation using anti-Myc antibodies. The ChIP DNA as well the corresponding input DNA were biotinylated and hybridized to the Affymetrix tiling Arrays. Chromatin samples from two different cultures were used in this analysis.

first: Randal

last: Morse


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

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

overall_design: Refer to individual Series


title: Molecular targets affected in the human whole-genome expression by Coriandrum sativum L. essential oil

status: Public on Apr 03 2014

city: Piracicaba

first: Irlan

middle: de Almeida

last: Freires

state: Sao Paulo

address: 901 Limeira Ave.

department: Physiological Sciences

country: Brazil

institute: University of Campinas

summary: Analysis of the effect of C. sativum (coriander) essential oil on the human genome with toxicological purposes.

overall_design: Total RNA was obtained from Hela Cells (CCL-2) treated with the essential oil at IC30 (inhibition concentration).

first: Ramiro

last: Murata

first: Pedro

last: Rosalen


title: Indole-3-Carbinol Preferentially Target ERα-Positive Breast Cancer Cells.

status: Public on Aug 12 2014

city: Houston

first: Khandan

last: Keyomarsi

state: Tx

address: 1515 Holcombe Blvd. Unit 66

department: Experimental Radiation Oncology

institute: MD Anderson Cancer Center

summary:
Indole-3-carbinol (I3C) is a natural anti-carcinogenic compound found at high concentrations in Brassica vegetables. ER-positive cell lines demonstrated the greatest sensitivity to the anti-tumor effects of I3C compared to ER-negative breast cancer cell lines. Gene expression analysis was performed to identify genes and pathways that accounted for sensitivity to I3C.
Microarray analysis performed using Illumina HT-12 v4 expression arrays

overall_design: A total of 36 samples were analyzed with six breast cancer cell lines treated with either the vehicle control or the drug Indole-3-carbinol in triplicate. The cell lines were: MCF-7, T47D, ZR751(sensitive to the drug, apoptosis/growth arrest) and MDA-MB-231, MDA-MB-157, and MDA-MB-436 (insensitive to the drug). Sensitive cell lines are of the luminal subtype and insensitive cell lines are of the basal subtype.

first: Joseph

last: Caruso


title: Differentiated human stem cells resemble fetal, not adult, β cells

status: Public on Mar 25 2014

city: Boston

first: Sinisa

last: Hrvatin

state: MA

address: 220 Longwood ave, GB405

department: Neurobiology

institute: Harvard Medical School

summary: Human pluripotent stem cells (hPSCs) have the potential to generate any human cell type, and one widely recognized goal is to make pancreatic β cells. To this end, comparisons between differentiated cell types produced in vitro and their in vivo counterparts are essential to validate hPSC-derived cells. Genome-wide transcriptional analysis of sorted insulin-expressing (INS(+)) cells derived from three independent hPSC lines, human fetal pancreata, and adult human islets points to two major conclusions: (i) Different hPSC lines produce highly similar INS(+) cells and (ii) hPSC-derived INS(+) (hPSC-INS(+)) cells more closely resemble human fetal β cells than adult β cells. This study provides a direct comparison of transcriptional programs between pure hPSC-INS(+) cells and true β cells and provides a catalog of genes whose manipulation may convert hPSC-INS(+) cells into functional β cells

overall_design: RNA is isolated and processed using MARIS from the following samples: H1 human embryonic stem cells (hESCs) in duplicate, HUES8 hESCs in duplicate, human induced pluripotent stem cells (hiPSCs) in duplicate, H1 cells differentiated to a stage in which insulin-expressing cells are present (stage 6) in duplicate, HUES8 cells differentiated to stage 6 in duplicate, hiPSCs differentiated to stage 6, insulin-expressing cells sorted from H1 cells differentiated to stage 6 in duplicate, insulin-expressing cells sorted from HUES8 cells differentiated to stage 6 in duplicate, insulin-expressing cells sorted from hiPSCs differentiated to stage 6 in duplicate, human week 16 fetal pancreata in duplicate, insulin-expressing cells sorted from human week 16 fetal pancreata in triplicate, adult human pancreatic islets in triplicate, and insulin-expressing cells sorted from adult human pancreatic islets in triplicate.

first: Siniša

first: Charles

middle: W

last: O'Donnell

first: Francis

last: Deng

first: Jeffrey

last: Millman

first: Felicia

last: Pagliuca

first: Philip

last: DiIorio

first: Alireza

last: Rezania

first: David

last: Gifford

first: Douglas

last: Melton


title: Analysis of the DNA methylome and transcriptome in granulopoiesis reveal timed changes and dynamic enhancer methylation [expression]

status: Public on Apr 29 2014

city: Stockholm

first: Karl

last: Ekwall

address: Alfred Nobels Alle 7

country: Sweden

institute: Karolinska Inst

summary: The study investigated the changes in DNA-methylation and gene expression during granulopoiesis. To this end CMP, GMP, PMC and PMN cell populations were isolated by FACS from bonemarrow from healty donors and analysed by CAGE as well as expression and DNA microarrays

overall_design: total RNA was isolated from CMP, GMP, PMC and PMN cells from human bonemarrow from 5 healty donors.

first: Michelle

last: Rönnerblad

first: Tor

last: Olofsson

first: Robin

last: Andersson

first: Iyadh

last: Douagi

first: Mohsen

last: Karimi

first: Sören

last: Lehmann

first: Hoof

last: Ilka

first: Albin

last: Sandelin

first: Itoh

last: Masayohi

first: Sayaka

last: Nago-Sato

first: Hideya

last: Kawaji

first: Timo

last: Lassmann

first: Piero

last: Carninici

first: Yoshihide

last: Hayashizaki

first: R

last: Forrest

first: Erik

last: Arner

first: Andreas

last: Lennartsson


title: Progesterone Receptor–Cyclin D1 Complexes Induce Cell Cycle–Dependent Transcriptional Programs in Breast Cancer Cells

status: Public on Feb 27 2014

city: Minneapolis

first: Todd

last: Knutson

state: MN

address: 117 Pleasant St SE

department: Minnesota Supercomputing Institute

institute: University of Minnesota

summary: The progesterone receptor (PR) and its coactivators are direct targets of activated cyclin-dependent kinases (CDKs) in response to peptide growth factors, progesterone, and deregulation of cell cycle inhibitors. Herein, using the T47D breast cancer model, we probed mechanisms of cell cycle-dependent PR action. In the absence of exogenous progestin, the PR is specifically phosphorylated during the G2/M phase. Accordingly, numerous PR target genes are cell cycle regulated, including HSPB8, a heat-shock protein whose high expression is associated with tamoxifen resistance. Progestin-induced HSPB8 expression required cyclin D1 and was insensitive to antiestrogens but blocked by antiprogestins or inhibition of specificity factor 1 (SP1). HSPB8 expression increased with or without ligand when cells were G2/M synchronized or contained high levels of cyclin D1. Knockdown of PRs abrogated ligand-independent HSPB8 expression in synchronized cells. Notably, PRs and cyclin D1 copurified in whole-cell lysates of transiently transfected COS-1 cells and in PR-positive T47D breast cancer cells expressing endogenous cyclin D1. PRs, cyclin D1, and SP1 were recruited to the HSPB8 promoter in progestin-treated T47D breast cancer cells. Mutation of PR Ser345 to Ala (S345A) or inhibition of CDK2 activity using roscovitine disrupted PR/cyclin D1 interactions with DNA and blocked HSPB8 mRNA expression. Interaction of phosphorylated PRs with SP1 and cyclin D1 provides a mechanism for targeting transcriptionally active PRs to selected gene promoters relevant to breast cancer progression. Understanding the functional linkage between PRs and cell cycle regulatory proteins will provide keys to targeting novel PR/cyclin D1 cross talk in both hormone-responsive disease and HSPB8-high refractory disease with high HSPB8 expression.

overall_design: The study contains 4 different sample groups measured in triplicate, for a total of 12 individual samples (12 arrays). In T47D human breast cancer cell lines stably expressing PR-B, cells were synchronized (or not synchronized) before G2/M phase using nocodazole. These cell lines (synchronized or not synchronized) were treated with either (1) vehicle control (ethanol) or (2) PR ligand R5020 10e-8 M for 6 hours before total RNA harvest. Thus, the experiment contains two cell lines, and two treatments (4 sample groups) treated and analyzed in triplicate (12 microarrays). Standard Illumina HT-12v4 chip controls were used during hybridization.

first: Gwen

last: Dressing

first: Carol

last: Lange


title: miRNA profiling in mouse peritoneal macrophages treated without or with LPS

status: Public on Feb 28 2014

city: Birmingham

first: Gang

last: Liu

state: Alabama

address: 901 19TH ST S

department: Medicine

institute: University of Alabama at Birmingham

summary: We have identified a number of miRNAs that are differentially expressed in LPS treated mouse peritoneal macrophages, as compared to untreated cells

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

overall_design: Peritoneal macrophages treated with LPS for 0, 4, 12, 24h. RNA was isolated and miRNA array assays were performed by Exiqon (miRCURY™ LNA Array version 10.0)


title: Klinefelter Syndrome testicular gene expression profile by a whole genome microarray approach.

status: Public on Jun 15 2014

city: Chieti

first: Valentina

last: Gatta

state: Abruzzo

address: Via Colle Dell'Ara

department: Department of Psychological SciencesDepartment of Psychological Sciences

country: Italy

institute: University G.d'Annunzio

summary:
Objective: Klinefelter Syndrome (KS) is the most common sexual chromosome abnormality (47,XXY) and represents the first genetic cause of male infertility. The mechanisms leading to KS testis degeneration are still unclear and no therapy is so far available for affected patients.
The present study is aimed to unravel information about molecules playing a key role in the disruption of the spermatogenesis.
Design: Gene expression profiles analysis of KS azoospermic testis versus normal testis, could provide useful information about the molecular basis of the alteration of the spermatogenesis.
Materials and Methods: Transcriptome analysis was performed carrying out gene expression profile by a whole genome microarray approach on testis biopsies obtained from 6 azoospermic non-mosaic KS men and from 3 controls, for a total of 12 experiments. T-test and False Discovery Rate were used to evaluate differentially expressed genes. Identified transcripts were analysed by Ingenuity Pathways Analysis software to disclose genes biological functions.
Results: Data analysis revealed the differentially up- and down-expression, in KS testis versus the control ones, of 656 and 247 genes related to Endocrine system development and function, Lipid metabolism, Reproductive disease, Free radical scavenging, and Cell death.
Conclusions: Take together these data show the presence of several genes involved in testis microenvironment deregulation leading to the spermatogenesis failure.
This information, associated with an early diagnosis could help to unravel possible therapeutic targets for testis failure prevention and limitation.

overall_design: Gene expression profile of 6 azoospermic KS testicular biopsies versus 3 pooled control testicular biposies form patients with normal spermatogenesis. A total of 12 experiments was carried out including biological and technical replicates.


title: Chronic low-dose-irradiation of Drosophila melanogaster larvae induces gene expression changes and enhances locomotive behavior

status: Public on Sep 26 2014

city: Daejeon

first: Lee

last: Sunwoo

address: #211, Next2Vill, 278-2, Jangdae-dong, Yuseong-gu

country: South Korea

institute: GenomicWorks

summary: Although radiation effects have been extensively studied, the biological effects of low-dose radiation (LDR) are controversial. This study investigates LDR-induced alterations in locomotive behavior and gene expression profiles of Drosophila melanogaster. We measured locomotive behavior using larval pupation height and rapid iterative negative geotaxis (RING) assay after exposure to 0.1 Gy gamma-radiation (dose rate of 16.7 mGy/h). We also observed chronic LDR effects on development (pupation and eclosion rates) and longevity (life span). To identify chronic LDR effects on gene expression, we performed whole-genome expression analysis using gene-expression microarrays, and confirmed the results using quantitative real-time PCR. Pupation height was significantly higher after LDR treatment at the first larval instar. Locomotive behavior of male flies was significantly greater approximately 35 weeks after LDR, but pupation and eclosion rates and life spans were not significantly different. Genome-wide expression analysis identified 344 genes that were differentially expressed in irradiated larvae compared with those of controls. We identified several genes belonging to larval behavior functional groups such as locomotive behavior and oxidation reduction, and genes involved in conventional functional groups modulated by irradiation such as defense response, sensory and perception. Four candidate genes were confirmed as differentially expressed genes in irradiated larvae using qRT-PCR. These data suggest that LDR stimulates locomotion-related genes, and these genes can be used as potential markers for LDR.

overall_design: Eggs were collected from 5-day-old female flies and cultivated for 24 h on standard medium. Then, twenty larvae were manually selected and seeded on fresh standard medium in a new vial. After transfer, the experimental group of first-instar larvae was immediately irradiated with chronic gamma-radiation at a dose rate of 16.7 mGy/h. After treatment, gamma-irradiated flies and non-irradiated control flies were maintained in the same incubator at 25degC.

first: Cha

last: Kim

first: Ki

last: Seong

first: Byung

last: Lee

first: In

first: Kwang

last: Yang

first: Ji-Young


title: The yeast and human FACT complexes resolve R-loop-mediated transcription-replication conflicts

status: Public on Mar 17 2014

first: Andrés

last: Aguilera

summary:
Transcription is a major obstacle for replication fork progression and transcription-replication collisions constitute a main cause of genome instability. At a genome-wide scale these obstacles can be detected by the accumulation of the replicative Rrm3 helicase required for RF progression through protein obstacles.
Here we show that FACT, a chromatin-reorganizing complex that swaps nucleosomes around the RNA polymerase during transcription elongation and that also has a role in replication, is needed to resolve transcription-replication conflicts in Saccharomyces cerevisiae. Importantly, ChIP-chip analyses of Rrm3 reveal that replication progression impairment in FACT mutants occur genome-wide, but preferentially at highly transcribed regions.

overall_design: ChIP-chip studies were perfomed with antibodies against Rrm3-FLAG in the yeast S. cerevisiae.

first: Emilia

last: Herrera-Moyano

first: Xénia

last: Mergui

first: María

last: García-Rubio

first: Sonia

last: Barroso


title: H2B mono-ubiquitylation facilitates fork stalling and recovery during replication stress by coordinating Rad53 activation and chromatin assembly

status: Public on Sep 12 2014

city: Taipei

first: Cheng-Fu

last: Kao

address: 128, Academia Rd., Sec. 2, Nankang

department: Institute of Cellular and Organismic Biology

country: Taiwan

institute: Academia Sinica

summary: The influence of mono-ubiquitylation of histone H2B (H2Bub) on transcription via nucleosome reassembly has been widely documented. Recently, it has also been shown that H2Bub promotes recovery from replication stress; however, the underling molecular mechanism remains unclear. Here, we show that H2B ubiquitylation coordinates activation of the intra-S replication checkpoint and chromatin re-assembly, in order to limit fork progression and DNA damage in the presence of replication stress. In particular, we show that the absence of H2Bub affects replication dynamics (enhanced fork progression and reduced origin firing), leading to γH2A accumulation and increased hydroxyurea sensitivity. Further genetic analysis indicates a role for H2Bub in transducing Rad53 phosphorylation. Concomitantly, we found that a change in replication dynamics is not due to a change in dNTP level, but is mediated by reduced Rad53 activation and destabilization of the RecQ helicase Sgs1 at the fork. Furthermore, we demonstrate that H2Bub facilitates the dissociation of the histone chaperone Asf1 from Rad53, and nucleosome reassembly behind the fork is compromised in cells lacking H2Bub. Taken together, these results indicate that the regulation of H2B ubiquitylation is a key event in the maintenance of genome stability, through coordination of intra-S checkpoint activation, chromatin assembly and replication fork progression.

overall_design: S.cerevisiae oligonucleotide microarrays were provided by Affymetrix (S.cerevisiae Tiling 1.0R, P/N 900645). BrdU and proteins ChIP-chip analyses were carried out as described (Fachinetti et al., M Cell, 2010).

first: CY

last: Lin

first: MY

last: Wu

first: S

last: Gay

first: L

last: Marjavaara

first: MS

last: Lai

first: WC

last: Hsiao

first: SH

last: Hung

first: HY

last: Tseng

first: D

last: Wright

last: Wang

first: GS

last: Hsu

last: Devys

first: A

last: Chabes

first: CF


title: Lung adenocarcinoma subtypes definable by lung development-related miRNA expression profiles in association with clinicopathologic features [miRNA analysis - miRNA Microarray, pre-commercial version 6.0]

status: Public on Jun 19 2014

city: Nagoya

first: Takashi

last: Takahashi

state: Aichi

address: 1-1 Kanokoden, Chikusa-ku

country: Japan

institute: Aichi Cancer Center

summary: Accumulation of genetic and epigenetic changes alters regulation of a web of interconnected genes including miRNAs, which confer hallmark capabilities and characteristic cancer features. In this study, the miRNA and mRNA expression profiles of 126 non-small cell lung cancer specimens were analyzed, with special attention given to the diversity of lung adenocarcinomas. Of those, 76 adenocarcinomas were classified into two major subtypes, developing lung-like and adult lung-like, based on their distinctive miRNA expression profiles resembling those of either developing or adult lungs, respectively. A systems biology-based approach using a Bayesian network and nonparametric regression was employed to estimate the gene regulatory circuitry functioning in patient tumors in order to identify subnetworks enriched for genes with differential expression between the two major subtypes. miR-30d and miR-195, identified as hub genes in such subnetworks, had lower levels of expression in the developing lung-like subtype, while introduction of miR-30d or miR-195 into the lung cancer cell lines evoked shifts of mRNA expression profiles towards the adult lung-like subtype. Conversely, the influence of miR-30d and miR-195 was significantly different between the developing lung- and adult lung-like subtypes in our analysis of the patient dataset. In addition, RRM2, a child gene of the miR-30d-centered subnetwork, was found to be a direct target of miR-30d. Together, our findings reveal the existence of two miRNA expression profile-defined lung adenocarcinoma subtypes with distinctive clinicopathologic features and also suggest the usefulness of a systems biology-based approach to gain insight into the altered regulatory circuitry involved in cancer development.

overall_design: Microarray analysis was conducted to examine miRNA expression profiles using a Human miRNA Microarray, pre-commercial version 6.0 (Agilent) with 470 miRNA probes, according to the manufacturer’s instructions

first: Chinatsu

last: Arima

first: Taisuke

last: Kajino

first: Yoshinori

last: Tamada

first: Seiya

last: Imoto

first: Yukako

last: Shimada

first: Masahiro

last: Nakatochi

first: Motoshi

last: Suzuki

first: Hisanori

last: Isomura

first: Yasushi

last: Yatabe

first: Tomoya

last: Yamaguchi

first: Kiyoshi

last: Yanagisawa

first: Satoru

last: Miyano


title: HDACs act on ribosomal DNA to control the yeast replication program and the competition between origins for limiting initiation factors [BrdU-IP-chip]

status: Public on Mar 26 2014

city: Montpellier

first: Philippe

last: Pasero

address: 141 rue de la Cardonille

country: France

institute: Institute of Human Genetics - CNRS

summary: In S. cerevisiae, replication timing is controlled by epigenetic mechanisms restricting the accessibility of origins to limiting initiation factors. About 30% of these origins are located within repetitive DNA sequences such as the ribosomal DNA (rDNA) array, but their regulation is poorly understood. Here, we have investigated how histone deacetylases (HDACs) control the replication program in budding yeast. This analysis revealed that two HDACs, Rpd3 and Sir2, control replication timing in an opposite manner. Whereas Rpd3 delays initiation at late origins, Sir2 is required for the timely activation of early origins. Moreover, Sir2 represses initiation at rDNA origins whereas Rpd3 counteracts this effect. Remarkably, deletion of SIR2 restored normal replication in rpd3 cells by reactivating rDNA origins. Together, these data indicate that HDACs control the replication timing program in budding yeast by modulating the ability of repeated origins to compete with single-copy origins for limiting initiation factors.

overall_design: BrdU-IP-chip analysis of origin usage in different yeast HDAC mutants

first: Kazumasa

last: Yoshida

first: Armelle

last: Lengronne

first: Philipe


title: DNA bending facilitates the error-free DNA damage tolerance pathway and upholds genome integrity

status: Public on Jan 28 2014

city: Milan

first: Federica

last: Castellucci

address: via Adamello 16

institute: IFOM-IEO Campus

summary: DNA replication is sensitive to damage in the template. To bypass lesions and complete replication, cells activate recombination-mediated (error-free) and translesion synthesis-mediated (error-prone) DNA damage tolerance pathways. Crucial for error-free DNA damage tolerance is template switching, which depends on the formation and resolution of damage-bypass intermediates consisting of sister chromatid junctions. Here we show that a chromatin architectural pathway involving the high mobility group box protein Hmo1 channels replication-associated lesions into the error-free DNA damage tolerance pathway mediated by Rad5 and PCNA polyubiquitylation, while preventing mutagenic bypass and toxic recombination. In the process of template switching, Hmo1 also promotes sister chromatid junction formation predominantly during replication. Its C-terminal tail, implicated in chromatin bending, facilitates the formation of catenations/hemicatenations and mediates the roles of Hmo1 in DNA damage tolerance pathway choice and sister chromatid junction formation. Together, the results suggest that replication-associated topological changes involving the molecular DNA bender, Hmo1, set the stage for dedicated repair reactions that limit errors during replication and impact on genome stability.

overall_design: BrdU and proteins ChIP-chip analyses analysis were carried out as described (Bermejo et al., 2009). Labelled probes were hybridized to Affymetrix S.cerevisiae Tiling 1.0 (P/N 900645) arrays and processed with TAS software.

first: Victor

last: Gonzalez-Huici

first: Barnabas

last: Szakal

first: Madhusoodanan

last: Urulangodi

first: Ivan

last: Psakhye

first: Demis

last: Menolfi

first: Eerappa

last: Rajakumara

first: Marco

last: Fumasoni

first: Rodrigo

last: Bermejo

first: Stefan

last: Jentsch

first: Dana

last: Branzei


title: Diverse effect of WWOX overexpression in HT29 colon cancer cell line.

status: Public on Jan 23 2014

first: Magdalena

last: Nowakowska

summary: The WWOX gene is a tumor suppressor probably involved in regulation of cell cycle and apoptosis and downregulated in variety of cancer types.However, its role in colon cancerogenesis is unknown. The aim of this study was to characterize how WWOX  may be involved in colon cancerogenesis or cancer progression, how it influences the basic cancer cell features and modifies cell expression profile.Our observations suggest that in HT29 colon cancer cell line increased expression of WWOX may result in transition of cancer cells into more normal- like colon epithelium phenotype, on the other hand in SW480 WWOX revealed the well-known tumour suppressor properties. However, as the colon cancer is very heterogeneous disease, obtained discrepancies may reflect the known differences between cell lines and cancerogenesis pathway, which they undergone.

overall_design: HT29 colon cancer cells were stably transfected with WWOX cDNA. HT29 cells transfected with an empty vector served as a control. Total mRNA was isolated to look for gene-expression differences induced by the WWOX overexpression.

first: Karolina

last: Pospiech

first: Urszula

last: Lewandowska

first: Agnieszka

last: Piastowska-Ciesielska

first: Andrzej

last: Bednarek


title: Diverse effect of WWOX overexpression in HT29 and SW480 colon cancer cell lines.


title: miR-634 restores drug sensitivity in resistant ovarian cancer cells by targeting the Ras-MAPK pathway

status: Public on Feb 04 2014

city: Rotterdam

first: Erik

last: Wiemer

address: Wytemaweg 80

department: Medical Oncology

country: Netherlands

institute: Erasmus University Medical Center

summary:
The development of drug resistance is still a major impediment for the successful treatment of cancer, such as advanced stage ovarian cancer, which has a 5-year survival rate of only 30%. The molecular processes that contribute to resistance have been extensively studied, however, not much is known about the role of microRNAs. We compared microRNA expression profiles of three isogenic cisplatin sensitive and resistant cell line pairs. The only microRNA that was consistently downregulated (FDR = 0.000) in all resistant cell lines was miR-634. We investigated the effects of miR-634 modulation in ovarian cancer cell lines and patient derived tumor cells. Overexpression of miR-634 gave rise to a modest G1 phase block and enhanced apoptosis. Furthermore, miR-634 resensitized resistant ovarian cancer cell lines and patient derived tumor cells to cisplatin chemotherapy. Similarly, miR-634 enhanced the response of tumor cells to carboplatin and doxorubicin, but not to paclitaxel.
We showed that miR-634 regulates cyclin D1 (CCND1), which is required for the G1-S phase transition, explaining the effects on the cell cycle. In addition, miR-634 repressed expression of GRB2, ERK2, RSK1 and RSK2, components of the Ras-MAPK pathway. Altogether, our findings suggest that miR-634 modulates several cancer relevant targets and therefore miR-634 is an attractive therapeutic candidate to resensitize chemotherapy resistant ovarian tumors.

overall_design: The miRNA expression profile was determined of three cisplatin sensitive/resistant cell line pairs (ovarian cancer cell line pair A2780/A2780 DDP; colon cancer cell line pair HCT8/HCT8 DDP; bladder cancer cell line pairT24/T24 DDP10).

first: Marijn

last: van Jaarsveld

first: Patricia

middle: F

last: van Kuijk

first: Antonius

last: Boersma

first: Jozien

last: Helleman

first: Wilfred

last: van IJcken

first: Ron

last: Mathijssen

first: Joris

last: Pothof

first: Els

last: Berns

first: Jaap

last: Verweij


title: Diverse effect of WWOX overexpression in SW480 colon cancer cell line.

overall_design: SW480 colon cancer cells were stably transfected with WWOX cDNA. SW480 cells transfected with an empty vector served as a control. Total mRNA was isolated to look for gene-expression differences induced by the WWOX overexpression.

middle: K


title: Genome-wide profiling of human gene in HPV16E2 protein expressing human keratinocyte

status: Public on Jan 14 2014

city: Khantharawichai

first: Nuchsupha

last: Sunthamala

state: Mahasarakham

address: Department of Biology, Faculty of Science, Mahasarakham University

department: Biology

country: Thailand

summary: In the early stage of human papillomavirus (HPV) infection, E2 and E6 proteins are expressed and elicit specific immune response to clear cervical lesion. HPV E6 protein can reduce type I interferon (IFN) including IFN-? that involves in immune evasion and HPV persistence. To evaluate the role of E2 protein in modulation of the expression of cellular genes as well as innate immune associated genes in HPV associated cervical cancer, genome-wide expression profiling of human primary keratinocytes (HPK) harbouring HPV16 E2 and HPV18 E2 was investigated using microarray assay and innate immune associated genes were analyzed. These results indicated that HPV E2s altered cellular gene expression including immune associated genes. Altered cellular signaling pathways in HPK expressing HPV E2s based on KEGG database. The top 10 canonical pathways include metabolic pathway, cytokine-cytokine receptor interaction, pathway in cancer, viral carcinogenesis, protein processing in endoplasmic reticulum, PI3K-AKT signaling pathway, MAPK signaling pathway, leukocyte transendothelial migration, chemokine signaling, and focal adhesion.

overall_design: The human primary neonatal foreskin keratinocytes (HPK) (Lonza, Basel, Switzerland) were cultured in supplemented CnT-57 medium (CELLnTEC, Bern, Switzerland). All cells used were tested and found free of mycoplasma.  HPK was transduced 4 replicates of either recombinant adenoviruses containing GFP, GFP-HPV16E2, and GFP-HPV18E2 at MOI 50 and collected cells for RNA extraction after 48 h. Total RNA were isolated and analyzed on an RNA 6000 Nano Lab-on-a-Chip in the 2100 Bioanalyzer (Agilent Technology, ON, CA), showing RIN score above 9.4 and then Illumina microarray was performed using platform Human HT-12 v4.0 BeadChip. Gene expression data were imported into Partek Genomics Suite 6.5 (Partek, St Louis, Mo). Raw data were preprocessed, in steps of background correction, normalization, and summarization using robust multiarray average analysis, and the expression data were transformed to log2. Principal-component analysis (PCA) was performed to identify outliers of sample group. Differential expression analysis for the samples was performed using one way analysis of variance (ANOVA). Gene lists were created using a cut-off of P<0.05, 1.5-fold change (ANOVA_results.txt).

first: Sebastien

last: Teissier

first: Francoise

last: Thierry


title: Gene expression profile of A549 cells from tissue of 4D model predicts poor prognosis in lung cancer patients

status: Public on Sep 16 2013

first: Chad

last: Creighton

state: TX

address: One Baylor Plaza, Mail Stop: BCM305

department: Biostatistics, Ducan Cancer Center

institute: Baylor College of Medicine

summary: Tumor microenvironment plays an important role in regulating cell growth and metastasis.  Recently we developed an ex vivo lung cancer model (4D) that forms perfusable tumor nodules on a lung matrix that mimics human lung cancer histopathology and protease secretion pattern.  We compared the gene expression profile (Human OneArray v5 chip) of A549 cells, a human lung cancer cell line, grown on petri dish (2D), and of the same cells grown in the matrix of our ex vivo model (4D).  Furthermore, we obtained gene expression data of A549 cells grown on petri dish (2D) and matrigel (3D) from a previous study and compared the 3D expression profile with that of 4D.  Expression array analysis showed 2954 genes differentially expressed between 2D and 4D. Gene Ontology (GO) analysis showed up-regulation of several genes associated with extracellular matrix, polarity, and cell fate and development.  Moreover, expression array analysis of 2D versus 3D showed 269 genes that were most differentially expressed, with only 35 genes (13%) having similar expression patterns as observed between 2D and 4D.  Finally, the differential gene expression signature of 4D cells (versus 2D) correlated significantly with poor survival in patients with lung cancer (n=1492), while the expression signature of 3D versus 2D correlated with better survival in lung cancer patients.  Since patients with larger tumors tend to have worse survival, the ex vivo 4D model may offer additional features over the 3D model, to better mimic of natural progression of tumor growth in lung cancer patients.

overall_design: We compared the gene expression profile (Human OneArray v5 chip) of A549 cells, human lung cancer cell line, grown on petri dish (2D) and same cells grown in the matrix of our ex vivo model (4D).

first: Min

last: Kim

first: Dhruva

last: Mishra


title: ArrayCGH from human neural progenitor cells (NHNP) and NHNP cells after differentiation induction

status: Public on Jan 01 2014

city: Homburg

first: Andreas

last: Keller

address: Building 60

country: Germany

institute: Saarland University

summary: NHNP cells (Lonza, Belgium) were grown in Maintenance medium for 24 h. Differentiation was induced by withdrawal of EGFand FGF and addition of BDNF. ArrayCGH experiments were done before differentiation, 24h, 2d and 5d after differentiation induction.

overall_design: ArrayCGH from undifferentiated NHNP cells, 24h differentiated NHNP cells, 2d differentiated NHNP cells and 5d differentiated NHNP cells

first: Ulrike

last: Fischer

first: Eckart

middle: U

last: Meese


title: R-loops are marks for histone H3 Ser10 phosphorylation and chromatin compaction

status: Public on Nov 13 2013

city: Seville

first: Andrés

last: Aguilera

address: Av. Américo Vespucio 24

institute: CABIMER, Universidad de Sevilla

summary:
R-loops are transcription by-products that may constitute a threat to genome integrity. In addition to specific enzymes to remove them, eukaryotes rely on a number of mRNP biogenesis factors such as the THO complex, to prevent co-transcriptional R-loop formation. We show in Saccharomyces cerevisiae that R-loops are tightly and specifically linked with histone H3-Ser10 phosphorylation (H3S10P), a mark of chromatin condensation.
Importantly, ChIP-chip analyses reveal a clear H3S10P accumulation at the pericentromeric chromatin during the G1-phase of the cell cycle only in R loop-accumulating yeast strains but not in those non-accumulating R-loops, and a significantly higher accumulation during S-phase. Such a difference can also be detected in a number of genes along the genome.

overall_design: ChIP-chip studies were perfomed with antibodies against Histone H3 and the phosphorylated Histone H3 at Serine10 in the yeast S. cerevisiae.

first: Maikel

last: Castellano-Pozo

first: Jose

last: Santos-Pereira

first: Ana

last: Rondón

first: Eloisa

last: Andújar

first: Mónica

last: Pérez-Alegre

first: Tatiana

last: García-Muse


title: Propagation of Human corneal Endothelial Cells – A Novel Dual Media Approach

status: Public on Aug 28 2013

city: Singapore

first: Jodhbir

last: Mehta

address: 11 Third Hospital Ave

department: Stem Cell and Tissue Engineering

country: Singapore

institute: Singapore Eye Research Institute

summary:
Human corneal endothelial cells (CECs) are not able to proliferate or regenerate within the eye. However, limited in vitro expansion of primary human CECs has been demonstrated by several laboratories, including ours. Due to the nature of these primary cells, various culture conditions supporting the active proliferation of these cells also drives them towards an endothelial-to-mesenchymal transformation (EMT) into fibroblastic-like cells. The occurrence of such a phenomenon has been observed as early as after the first round of passage. However, it should be noted that the degree of such transformation is highly heterogeneous, due likely to donor variability. In the current study, propagation of primary human CECs was carried out using a novel dual media approach, where M4 (F99: Ham’s F12/M199, 5% FBS, 20 μg/ml ascorbic acid, 1% ITS, 1% antibiotic/antimycotic and 10 ng/ml bFGF) was used to promote the proliferation of the CECs, and M5 (Endo: Human Endothelial-SFM, 5% FBS and 1% antibiotic/antimycotic), was used to stabilized these primary CECs when they reached 80% to 90% confluence.Primary cultures exposed to M5 were able to maintain the unique cellular structure of the human corneal endothelial cells and do not undergo EMT.
In order to better understand the observed morphological changes at the molecular level following the switch from the proliferative M4 medium to the maintainance M5 medium, high throughput microarray analysis was performed on human CECs isolated from two donors and cultivated to the third passage. Subsequently, the global gene expression profile of the confluent human CECs expanded in M4 for the first (D17p) and second donor (D18p), were compared to the same set of the confluent human CECs maintained in M5 medium (D17m and D18m) for a further seven days.

overall_design: Primary human CECs were expanded using the dual media approach to the third passage. Total RNA obtained from confluent P3 human CECs samples grown in the proliferative M4 medium (D17p and D18p) were compared to the same set of primary cultures that were exposed to M5 for a further 7 days (D17m and D18m).

first: Gary

last: Peh

first: Zhenzhi

last: Chng

first: HengPei

last: Ang

first: Terence

middle: Y

last: Cheng

first: Khadijah

last: Adnan

first: Benjamin

last: George

first: XinYi

last: Seah

first: KahPeng

last: Toh

last: Yam

first: Donald

last: Tan

first: Alan

last: Colman


title: Effect of neurotrophin receptor p75 (p75NTR) over-expression on the miRNAome of human umbilical vein endothelial cells

status: Public on Jan 11 2014

city: EDINBURGH

first: Andrea

last: Caporali

address: 47 Litlte France Crescent

country: United Kingdom

institute: University of Edinburgh

summary: MicroRNAs (miRNAs) are small non-protein-coding RNAs that are incorporated into the RNA-induced silencing complex (RISC) and inhibit gene expression by regulating the stability and/or the translational efficiency of target mRNAs. p75NTR, which is scarcely present in healthy endothelial cells (ECs), becomes strongly expressed by capillary ECs after induction of peripheral ischemia in type-1 diabetic mice. p75NTR expression promotes endothelial cells apoptosis and inhibits angiogenesis. In order to identify miRNAs sub-sequentely modulated by p75NTR, miRNA expression profiles of human umbilical vein endothelial cells (HUVEC) over-expressing p75NTR were generated, allowing the identification of miRNAs modulated upon p75NTR up-regulation.

overall_design: HUVEC over-expressing p75NTR or Null (empty vector) were generated by adenoviral infection. miRNA expression profiles were then measured and miRNAs modulated upon p75NTR up-regulation were identified.

first: C

last: Emanueli

first: A

last: Voellenkle

first: F

last: Martelli


title: Effects of FGF2 and cell culture surface on the transcriptome of adult human dermal fibroblasts

status: Public on Oct 15 2013

city: Worcester

first: Tanja

last: Dominko

address: 100 Institute Rd

department: Biology and Biotechnology

institute: Worcester Polytechnic Institute

summary: The current study set to determine the effects of Fibroblast Growth Factor 2 and cell culture surface (tissue culture plastic and glass) on the transcriptome of adult human dermal fibroblasts. Transcriptional profiles of adult human dermal fibroblasts grown in four experimental conditions (glass, glass and addition of FGF2, plastic, plastic and addition of FGF2) were compared. Comparison of the transcriptomes will allow to identify significantly differentially expressed genes due to FGF2 and surface treatment, which in turn will allow for identification of the pathways affected by these factors in the human adult fibroblasts.

overall_design: Transcriptome analysis of adult human dermal fibroblasts grown on tissue culture plastic and glass, with and without 4ng/ml FGF2, was performed in two biological replicates and three technical replicates for each treatment condition.

first: Olga

last: Kashpur


title: Global gene expression analysis of vascular progenitors differentiated from human embryonic stem cells or induced pluripotent stem cells, corresponding donor starting cells, and mature human endothelial cells

status: Public on Oct 17 2013

city: Baltimore

first: Elias

middle: Thomas

last: Zambidis

address: 733 N. Broadway

department: Oncology

institute: Johns Hopkins School of Medicine

summary: Global gene expression analysis of FACS-purified CD31+CD146+ vascular progenitors (VP) derived from (a) human embryonic stem cells (VP-hESC), (b) adult fibroblast derived induced pluripotent stem cells (VP-AdF-iPSC), (c) stromal primed cord blood CD34+ myeloid progenitor derived iPSC (VP-sp-CB-iPSC), (d) corresponding starting fibroblasts and myeloid progenitors, (e) human umbilical vein endothelial cells, and (f) human dermal microvascular endothelial cells.

overall_design: Total RNA was harvested from (a) adult fibroblasts, (b) human myeloid progenitors: Non-nucloefected CD34+ CB cells that were expanded with growth factors from Day -3 until Day 0 and harvested, (c) FACS-purified CD31+CD146+ vascular progenitors (VP) that were differentiated from human embryonic stem cells (hESC), (d) VP differentiated from low passage stromal-primed episomal iPSC derived from growth-factor activated cord blood myeloid progenitors, (e) VP differentiated from iPSC derived from adult fibroblasts, (f) human umbilical vein endothelial cells, and (g) human dermal microvascular endothelial cells.. Illumina HumanHT-12 V4.0 expression beadchips were used for all analyses in this series. Three or independent samples of each sample type were each run on individual microarrays.

first: Tea

last: Park

first: Ludovic

last: Zimmerlin

first: Jeffrey

last: Huo

last: Talbot

first: Jack

last: Aguilar

first: Wayne

last: Yu


title: Validating the Impact of a Molecular Subtype in Epithelial Ovarian Cancer (EOC) on Progression Free and Overall Survival

city: Vienna

first: Dietmar

last: Pils

address: Waehringer Guertel 18-20

department: Dept. of Surgery

country: Austria

institute: Medical University of Vienna

summary:
Purpose: The majority of patients with epithelial ovarian cancer (EOC) is diagnosed at advanced stage and has a poor prognosis. A proportion of these patients though will fare well, with a prognosis similar to patients with early stage disease while others die very quickly. Clinicopathological prognostic factors do not allow precise identification of these subgroups. Thus we have validated a molecular subclassification as prognostic factor in EOC.   Experimental Design: One hundred ninety-four patients with EOC stage II to IV were characterized by whole-genome expression profiling of tumor tissues and classified using a published 112 gene-set, derived from a FIGO stage directed supervised classification approach.  Results: The 194 tumor samples were classified into two subclasses of 95 (subclass 1) and 99 (subclass 2) tumors, grouping all 9 FIGO II tumors in subclass 1 (p=0.001). Subclass 2 (54% of advanced stage tumors) correlated significantly with peritoneal carcinomatosis and non-optimal debulking. Patients with subclass 2 tumors had a worse progression free survival (HR 1.67, p=0.005) by univariate analysis, but it was not an independent factor in multiple analysis. However, overall survival was impaired both, univariate (HR 3.68, p<0.001) and in models corrected for relevant clinicopathologic parameters (HR 3.13, p<0.001). Significance analysis of microarrays revealed 2,115 genes differentially expressed in both subclasses (FDR 5%).  Conclusion: In this validation study we showed that in advanced-stage epithelial ovarian cancer two approximately equally large molecular subtypes exist, independent from classical clinocopathological parameters presenting with highly different whole genome expression profiles and an impressively different overall survival.  Purpose: The majority of patients with epithelial ovarian cancer (EOC) is diagnosed at advanced stage and has a poor prognosis. A proportion of these patients though will fare well, with a prognosis similar to patients with early stage disease while others die very quickly. Clinicopathological prognostic factors do not allow precise identification of these subgroups. Thus we have validated a molecular subclassification as prognostic factor in EOC.   Experimental Design: One hundred ninety-four patients with EOC stage II to IV were characterized by whole-genome expression profiling of tumor tissues and classified using a published 112 gene-set, derived from a FIGO stage directed supervised classification approach.  Results: The 194 tumor samples were classified into two subclasses of 95 (subclass 1) and 99 (subclass 2) tumors, grouping all 9 FIGO II tumors in subclass 1 (p=0.001). Subclass 2 (54% of advanced stage tumors) correlated significantly with peritoneal carcinomatosis and non-optimal debulking. Patients with subclass 2 tumors had a worse progression free survival (HR 1.67, p=0.005) by univariate analysis, but it was not an independent factor in multiple analysis. However, overall survival was impaired both, univariate (HR 3.68, p<0.001) and in models corrected for relevant clinicopathologic parameters (HR 3.13, p<0.001). Significance analysis of microarrays revealed 2,115 genes differentially expressed in both subclasses (FDR 5%).  Conclusion: In this validation study we showed that in advanced-stage epithelial ovarian cancer two approximately equally large molecular subtypes exist, independent from classical clinocopathological parameters presenting with highly different whole genome expression profiles and an impressively different overall survival.
Targeted therapies in second line treatment gain more and more importance in managing recurrent or progressive carcinomas, particularly in ovarian cancer, a cancer entity characterized by a very high recurrence rate. One step ahead, it is necessary to define new therapeutic targets and to select patients who might benefit from these therapies already in first line settings. A robust molecular subclassification could provide both, an adequate patient selection and potential new targets. Notably, the validation of such a subclassification is of outstanding importance to obtain a reliable basis for a specific clinical decision and a rational for the expensive development of new targeted therapies. This work provides a comprehensive basis for both.

overall_design: The expression values of 204 epithelial ovarian cancer tissues are determined and used for the validation of a subclassification approach (Cancer Sci. 2009 Aug;100(8):1421-8.)

first: Dan

last: Castillo-Tong

first: Robert

last: Zeillinger


title: Over-expression of the transcription factor ARID3A (Bright)

status: Public on Nov 15 2013

city: Oklahoma City

first: Bart

last: Frank

state: OK

institute: OMRF

summary: Retroviral contructs containing the full-length murine ARID3A (aka Bright) gene and a GFP gene or the GFP gene alone were used to electroporate the human RAJI B cell line. GFP positive cells were sorted and expanded in vitro. Differences in gene expression between the constructs were identified.

overall_design: Total RNA was isolated from 4 independent cell culture replicates of each retroviral construct.

first: Carol

last: Webb


title: Leukocyte gene expression variation as a function of psychological well-being

status: Public on Jul 31 2013

city: Los Angeles

first: Steve

last: Cole

address: 11-934 Factor Bldg, UCLA

institute: UCLA School of Medicine

summary: Individual differences in basal leukocyte gene expression profiles as a function of hedonic and eudaimonic well-being.

overall_design:
Gene expression profiling was carried out on peripheral blood mononuclear cell RNA samples collected from 79 healthy adults measured for hedonic and eudaimonic dimensions of well-being using the Short Flourishing Scale (Keyes, C (2014). The Mental Health Continuum-Short Form (MHC-SF) for adults). Higher values of the hedonic well-being scale indicate greater levels of positive affect, higher values of eudaimonic well-being scale indicate greater experience of purpose and meaning in life, higher values of social well-being scale indicate greater experience of social well-being in life, higher values of psychological well-being scale indicate greater experience of psychological well-being in life, greater TotalMHCSF scores indicate greater experience of all forms of well-being measured by the MHC-SF, the FlourishGroup variable indicates individuals showing flourishing mental health as defined by the MHC-SF scoring instructions referenced above, greater BrownPsychological scores indicate greater experience of psychological well-being as measured by the MHC-SF with an alternative scoring, and greater BrownSocial scores indicate greater experience of social well-being as measured by the MHC-SF with an alternative scoring.
key word: Risk prediction


title: 14-3-3ζ promotes TGF-β-induced bone metastasis program in 231 cells

status: Public on Nov 05 2013

city: Houston

first: Jia

last: Xu

address: 1515 Holcombe Blvd.

department: Molecular & Cellular Oncology

institute: UT-M.D. Anderson Cancer Center

summary:
To explore the regulatory role of 14-3-3ζ in TGF-β induced bone metastasis program in 231 cells, we generated MDA-MB-231 human breast cancer cell sublines with 14-3-3ζ shRNA knockdown (231.ZKD-4 and 231.ZKD-5) and scrambled shRNA (231.Scr)
We performed cDNA microarray analysis on these cells treated with vehicle or TGF-β (5ng/ml, 2 hours) respectively in vitro

overall_design: Total RNA were extracted from 231.scr, 231.ZKD-4, 231.ZKD-5 cells treated with vehicle or TGF-β, and subjected to illumina Human HT-12 v4 arrays analysis

first: Dihua


title: Outlier detection of biologically significant genes from combinatorial microarray data

status: Public on Sep 05 2013

city: Ames

first: Chris

last: Minion

state: IA

address: 1130 Vet Med

department: VMPM

institute: Iowa State University

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

overall_design: Refer to individual Series


title: Gene expression profiles of EZH2 knockdown

status: Public on Oct 28 2013

first: Chad

last: Creighton

summary: Enhancer of Zeste Homolog 2 (EZH2) is a histone methyltransferase that catalyzes the trimethylation of histone H3 lysine 27 (H3K27me3). EZH2 expression is significantly upregulated in MPNST. In our study, we investigated the function of EZH2 and the molecular mechanisms that are regulated by EZH2 in MPNST pathogenesis. Our findings enhance the knowledge of EZH2’s function and biology, and have the potential to provide a novel therapeutic approach for MPNST patients in the clinic.

overall_design:
An EZH2 knockdown experiment was carried out in MPNST cells. There are one control and one siEZH2 samples for two cell lines (724 and 462) and two repeats for each cell line, so in total there are 8 samples.
Two group comparison

first: Dina

last: Lev

first: Yiqun

last: Zhang

first: Pingyu


title: MARIS: Method for Analyzing RNA following Intracellular Sorting [array]

status: Public on Jan 13 2014

city: Boston

first: Sinisa

last: Hrvatin

address: 220 Longwood ave, GB405

institute: Harvard Medical School

summary: We've developed a new Method to Analyze RNA following Intracellular Sorting (MARIS) allowing us to carry out gene expression studies on cells sorted based on intracellular immunoflourescence. The purpose of this study is to determine the degree of bias that MARIS introduces on gene expression. We report Illumina microarray gene expression data from human embryonic stem cells differentiated to a stage in which insulin-expressing cells are present. Gene expression data using RNA isolated from live cells is compared to gene expression data using RNA isolated from MARIS processed cells (fixed, permeabilized, antibody stained and mock sorted) to determine the degree of correlation in gene expression between these two biologically identical samples.

overall_design: Human embryonic stem cells are differentiated to a stage in which insulin-expressing cells are present and split into two biologically identical samples. RNA is immediately isolated from one sample using the RNAeasy protocol (live sample). RNA is isolated from the second sample following MARIS (processed sample) with all cells collected after the sort in order to keep the cell type composition between the live and processed samples the same.

first: Siniša

first: Francis

last: Deng

first: Charles

last: O'Donnell

first: David

last: Gifford

first: Douglas

middle: A

last: Melton


title: Gene expression profiling of WWOX-overexpressing glioblastoma T98G cells

status: Public on Oct 22 2013

city: Lodz

first: Karolina

last: Pospiech

address: Zeligowskiego 7/9

department: Department of Molecular Carcinogenesis

institute: Medical University of Lodz

summary: The WWOX gene is known for its tumor suppressor character and seems to be one of the main cellular regulators of cell cycle and apoptosis. The aim of the study was to identify cellular pathways and biological processes influenced by WWOX in glioblastoma cells. Our experiment showed that in this type of cancer WWOX, beside cell cycle and apoptosis control, may be involved in metabolism, cytoskeleton structure and differentiation.

overall_design: T98G glioblastoma cells were stably transfected with WWOX cDNA. T98G cells transfected with an empty vector served as a control. Total mRNA was isolated to look for gene-expression differences induced by the WWOX overexpression.

first: Katarzyna

last: Kośla

first: Magdalena

last: Nowakowska

first: Andrzej

last: Bednarek


title: Comparison study of glioma stem cells and adult human neural stem cells

status: Public on Jul 27 2013

city: Oslo

first: Cecilie

middle: Jonsgar

last: Sandberg

address: Sognsvannsveien 20

department: Neurosurgery

institute: Oslo Univercity Hospital

summary: Glioblastoma, the most common and malignant brain tumor, harbors stem-like cells that self-renew and propagate upon serial transplantation. Although they share functional, morphological and developmental similarities to adult brain neural stem cells, stem cell characteristic pathways contributing to glioblastoma stem-like cells have not been consistently determined. Towards this goal we have provided an internally coherent molecular reference that compares adult neural and glioblastoma stem cells cultivated under identical conditions. Genes dysregulated between these populations are correlated with clinical outcome in glioblastoma, and are highly expressed in embryonic and induced pluripotent stem cells.  The resource yields a key role for Wnt and a core group of dysregulated pathways. We have verified the contribution to proliferation and sphere formation of Wnt- differentially activated genes through the Wnt inhibitor SFRP1. The glioblastoma and neural stem cell gene-expression and pathway comparative resource provides a powerful new tool for the identification of potential therapeutic targets.

overall_design: 14 samples was analyzed; 5 individual samples of adult neural stem cells and 9 individual samples of glioma stem cells

first: Gabriel

last: Altschuler

first: Jieun

last: Jeong

first: Kirsten

last: Strømme

first: Biljana

last: Stangeland

first: Wayne

last: Mureell

first: Unn-Hilde

last: Wendler

first: Ola

last: Myklebost

first: Eirik

last: Helseth

first: Einar

middle: O

last: Vik-Mo

first: Winston

last: Hide

first: Iver

last: Langmoen


title: Hepatocellular carcinoma (HCC)

status: Public on Oct 25 2013

city: Tokyo

first: Ken

last: Okano

address: Toyo Ekimae bldg. 2-20, Toyo 2-Chome, Koto-Ku

institute: Cosmo Bio Co., LTD.

summary: BACKGROUND & AIMS: Expression of microRNAs (miRNAs) in metastatic foci of hepatocellular carcinoma (HCC) is unknown. We identified metastasis-related miRNAs in recurrent cases after living donor liver transplantation (LDLT). Methods: We performed a comprehensive analysis of primary HCC (T), noncancerous liver (N), and resected recurrent (metastatic) HCC (M) using microarray analyses to identify metastasis-related miRNAs in in three patients with post-transplant recurrence. The RNA samples from three cases that underwent resection of recurrences after LDLT were made available for miRNA microarray analysis. The three cases included a 57-year-old man (case 1) with peritoneal recurrence and infected by hepatitis B virus (HBV), and a 48-year-old woman (case 2) and a 51-year-old man (case 3) with lung recurrences and hepatitis C virus (HCV) infection. Microarray analysis was performed for each RNA sample from the (T), (N) in the explanted liver, and (M). A sample containing equal amounts of RNAs from histologically normal livers of three living donors (NL: normal liver) was analyzed as a control.

overall_design: The RNA samples from three cases that underwent resection of recurrences after living donor liver transplantation were made available for microRNA microarray analysis. Microarray analysis was performed for each RNA sample from the primary HCC (T), noncancerous liver (N) in the explanted liver, and resected recurrent metastatic HCC (M). A sample containing equal amounts of RNAs from histologically normal livers of three living donors (NL: normal liver) was analyzed as a control.

first: Kazutoyo

last: Morita


title: DCP5, a highly conserved P-body-nucleating protein, regulates multiple small RNA-mediated silencing pathways in Arabidopsis

status: Public on Aug 16 2013

city: Wilmington

first: Qi

last: Zheng

state: DE

address: 1701 Rockland Road

institute: Nemours Children's Health

type: Expression profiling by high throughput sequencing

type: Non-coding RNA profiling by high throughput sequencing


title: hPTTG1-/- HCT116 human colorectal cancer cells: pcDNA3.1 control vs. pcDNA3.1-hPTTG1

status: Public on Jan 02 2014

city: Hualien

first: Yi Chu

last: Liao

address: Rm. D416, No.701, Sec. 3, Zhongyang Rd.

institute: Tzu Chi University

summary: Transcriptional profiling of  hPTTG1-/- HCT116 human colorectal cancer cells comparing hPTTG1-/- HCT116 cells transfected with pcDNA3.1, and with hPTTG1-/- HCT116 cells transfected with pcDNA3.1-hPTTG1 plasmid.

overall_design: Two-condition experiment, pchyg vs. 7-2 and 18-2 cells. 1 control, 2 different transfected cells.

first: Wei-Lin

last: Chen


title: Human osteosarcoma cells respond to sorafenib chemotherapy by downregulation of the tumor progression factors S100A4, CXCR4 and the oncogene FOS

status: Public on Dec 13 2013

city: Graz

first: Birgit

last: Gallé

address: Stiftingtalstr. 24

institute: ZMF

summary: Osteosarcoma is a rare but aggressive bone neoplasm in humans, which is commonly treated with surgery, classical chemotherapy and radiation. Here, we studied the antimetastatic potential of 4 μM of the multikinase inhibitor Sorafenib in a human osteosarcoma cell line using DNA microarray-based gene expression profiling.

overall_design: 3 untreated replicates of human osteosarcoma cells (ATCC CRL-1543™), 3 replicates of human osteosarcoma cells (ATCC CRL-1543™) treated with 4 µM Sorafenib

first: Ingrid

last: Walter

first: Birgitt

last: Wolfesberger

first: Ralf

last: Steinborn


title: Ectopical expression of miR-125b by lentiviral-vector in neuroblastoma cell line SKNDZ

status: Public on Dec 01 2013

city: Taipei

first: Sheng-Kai

last: Chang

address: NO.1 JEN AI ROAD SECTION 1 TAIPEI 100 TAIWAN R.O.C.

department: Clinical Laboratory Science of Medical Biotechnology

institute: NATIONAL TAIWAN UNIVERSITY COLLEGE OF MEDICINE

summary: Differential expression of mRNA were conducted in neuroblastoma cell line SKNDZ, which successfully transduced human miR-125b

overall_design: MYCN-amplification SKNDZ neuroblastoma cell line was transduced with MIRN125B2 gene with lentiviral vector (pLKO.1-puro), and selected by puromycin for 48 hours. Then the total RNA was extracted and analyzed the differential expression of a total of 29,187 genes by Oligonucleotide DNA microarray.

first: Sheng-kai

first: Chung-Yi

last: Hu


title: DCP5, a highly conserved P-body-nucleating protein, regulates multiple small RNA-mediated silencing pathways in Arabidopsis (smRNA-seq)

summary: MicroRNAs (miRNAs) and small-interfering RNAs (siRNAs) negatively regulate their targets by 1) repressing translation, 2) endonucleolytic RNA cleavage, or 3) DNA methylation resulting in transcriptional silencing. P-body/decapping components are likely required for translational repression, but are not known to function in other posttranscriptional regulatory pathways or to affect smRNA levels. Here, we show that the P-body/decapping protein DCP5 is required for miRNA-mediated translational repression but not cleavage, and to regulate the transcription of specific miRNAs. We find that this protein also affects the abundance of tRNA-derived smRNAs. Significantly, DCP5 is required for the transcriptional silencing and DNA methylation of numerous transposable/repetitive elements and imprinted genes, indicating that it is a novel component of the RNA-directed DNA methylation pathway. Our results demonstrate that DCP5 and likely the P-body itself are required for multiple smRNA-mediated silencing pathways and provide the first evidence for the spatial separation of translational inhibition and cleavage by miRNAs.

overall_design: small RNA (smRNA) expression comparison between wildtype (Col-0) and dcp5 mutant plants in Arabidopsis

first: Matthew

last: Endres

first: Isabelle

last: Dragomir

first: Li

last: Yang

first: Ross

last: Weber

first: Ian

middle: M

last: Silverman

first: R

last: Poethig

first: Brian

middle: D

last: Gregory


title: Detection of the genes induced by the stromal cell-derived factor-1 (SDF-1)/CXCR4 system in oral cancer cells

status: Public on Dec 31 2013

city: Toon

first: Koh-ichi

last: Nakashiro

state: Ehime

address: 454 Shitsukawa

department: Oral and Maxillofacial Surgery

institute: Ehime University Graduate School of Medicine

summary: Robust genes were up-regulated in the oral cancer cells with SDF-1/CXCR4 system; however, most of the genes did not exhibit metastasis-related functions.

overall_design: Mock cells and B88-SDF-1 cells, which have an autocrine SDF-1/CXCR4 system and exhibit distant metastatic potential in vivo were used.

first: Daisuke

last: Uchida

first: Nobuyuki

last: Kuribayashi


title: TALEN-Engineered AR Gene Rearrangements Reveal Endocrine Uncoupling of Androgen Receptor in Prostate Cancer

status: Public on Sep 01 2013

city: Minneapolis

first: Michael

middle: David

last: Nyquist

address: Masonic Cancer Center, University of Minnesota, Mayo Mail Code 806 420 Delaware St SE

department: Genetics Cell Developmental Bio

institute: University of Minnesota

summary: This experiment addressed the question of whether full length Androgen receptor and Androgen Receptor variant ARv567es have similar transciptional activities.  The transcriptomes of R1-AD1, a AR full length expressing cell line, are compared in an AR on (1nM DHT) to an AR off (ethanol vehicle) state.  R1-D567 was derived from R1-AD1 and modified with TALENs in such a way as to express only AR-V567es.  The AR on and off states were induced with a control siRNA (AR on) or a siRNA targeting exon 1 (AR off).

overall_design: R-AD1 was cultured for 24 hours in either base RPMI media with 1nM DHT or ethanol vehichle and RNA extracted.  R1-D567 cells were electroporated with control siRNA or siRNA targeting exon 1 of AR and allowed to recover 48 hours and then cultured in base media with 1nM DHT or ethanol for 24 hrs.  Each conditon was done in triplicate.

first: Scott

last: Dehm


title: AI-2 quorum sensing in *Yersinia pestis*

first: Chris

last: Minion


title: Gene expression and microRNA profiles of EZH2 knockdown

first: Chad

last: Creighton

address: One Baylor Plaza, Mail Stop: BCM305

institute: Baylor College of Medicine

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


title: Genome-wide enrichment of Gcn5 and H3K18/H4K16 acetylation under physiological change of stress adaptation and stress recovery

status: Public on Jul 22 2013

city: Huddinge

first: Anthony

last: Wright

address: Blickagången 6

institute: Karolinska Institute

summary: The data provide information of Gcn5 enrichment, H3K18 and H4K16 acetylation level and Histone H3 density  for 5 different physioloigcal conditions during stress adpatation and stress recovery  (normal growth, during stress adaptation, after stress adaptation, under stress recovery, after stress recovery) in yeast. The purpose of the study is to understand how histone acetyltransferase HATs (Gcn5) apply it is function in gene regulation by changing global or local histone acetylation level under different physiological conditions.

overall_design: Gcn5 enrichment, H3K18 and H4K16 acetylation level and Histone H3 density are mearured and compared to input signal for 5 different physioloigcal conditions (normal growth, during stress adaptation, after stress adaptation, under stress recovery, after stress recovery). Replicates are used.

first: Yongtao

last: Xue-Franzén


title: Identification of CpG island methylator phenotype predicts the prognosis of small cell lung cancer

status: Public on Aug 29 2013

city: Koto

first: YUICHI

last: SAITO

state: Tokyo

address: 3-8-31 Ariake

department: Pathology

institute: The Cancer Institute of Japanese Foundation Cancer Research

summary:
We analyzed 28 fresh frozen samples from pure SCLC patients and 13 noncancerous lung tissues, using the Illumina Infinium 27k Human DNA methylation Beadchip v1.2
Background: Small cell lung cancer (SCLC) accounts for 13-15% of new lung cancer cases in worldwide and has the poor therapeutic outcomes with a median survival of just over one year. A CpG island methylate phenotype (CIMP) is well known as a methylator phenotype with characteristic promoter DNA methylation alterations, in colorectal cancers, glioblastoma and breast cancers, although there has been no report about any CIMP of SCLC. We investigated whether DNA methylation profiles can provide useful molecular subtyping of SCLC in terms of etiology and prognosis of SCLC.  Results: We selected a total of 1741 most differentially methylated CpG sites (s.d. > 0.20) across the 28 SCLC tumor tissues in each DNA methylation platform, after an elimination of the probes related with the X- and Y- chromosome. Unsupervised hierarchical clustering of methylation data from SCLC samples reveals two major subgroups with different prognosis: the 5 years disease-free interval (DFI) rate of patients in cluster 1 (11.1%) was lower than that of patients in cluster 2 (61.57%) (p = 0.001). By multivariate analysis for DFI, both postoperative chemotherapy and cluster 1 were a significant prognostic factor (p = 0.002 and 0.002; respectively). Next, among 1220 genes with methylation and expression data both available, the CpG sites were ranked on the basis of the spearman’s correlation coefficient between cluster 1 and cluster 2 into an ascending order. Finally, we identified that fifty-five CpG sites were nagetively correlated and found that apoptosis pathway was a most differentially expressed.  Conclusion: By comprehensive DNA methylation profiling, two distinct subgroups with different molecular and clinical phenotype were identified to evoke a CIMP of SCLC. We found some promoter markers in the apoptosis pathway could make a difference between the two groups, and we hope that our data can contribute to provide a useful resource for the construction of therapeutic strategy and the development of a new chemotherapeutic agent.

overall_design: After genomic DNA was treated with sodium bisulfite, bisulfite-converted genomic DNA was analyzed using Illumina’s Infinium HumanMethylation27 BeadChip.

first: Y

last: Saito

first: K

last: Nakagawa

first: G

last: Nagae

first: N

last: Motoi

first: E

last: Miyauchi

first: H

last: Ninomiya

first: M

last: Nakao

last: Uehara

last: Mun

first: S

last: Okumura

last: Nishio

last: Satoh

last: Aburatani

last: Ishikawa


title: ChIP-chip data of Npl3-Myc and Rrm3-Flag in wild-type and npl3∆ cells

status: Public on Nov 15 2013

city: Seville

first: Andrés

last: Aguilera

address: Av. Américo Vespucio 24

department: Genome BIology

country: Spain

institute: CABIMER, Universidad de Sevilla

summary:
Transcription is a major obstacle for replication fork progression and a cause of genome instability. Such instability increases in mutants with a suboptimal assembly of the nascent messenger ribonucleo-protein particle (mRNP), as THO/TREX and some heterogeneous nuclear ribonucleoproteins (hnRNPs) mutants.
Here we show that yeast npl3∆ cells show genome-wide replication obstacles as determined by accumulation of the Rrm3 helicase. Such obstacles preferentially occur at long and highly expressed genes, to which Npl3 is preferentially bound in wild-type cells.

overall_design: ChIP-chip studies were perfomed with antibodies against Myc-tagged Npl3 protein in wild-type cells of the yeast S. Cerevisiae, as well as Flag-tagged Rrm3 protein in both wild-type and npl3∆ cells.

first: José

last: Santos-Pereira

first: Ana

middle: B

last: Herrero

first: María

middle: L

last: García-Rubio

first: Antonio

last: Marín

first: Sergio

last: Moreno


title: cDNA microarray data after ATP treatment

status: Public on Mar 30 2013

city: Beijing

first: Weihua

last: Li

address: 38 Xue Yuan Road, Beijing 100191, P. R. China

country: China

institute: Peking University Health Science Center

summary: A comparative gene expression analysis was performed using cDNA microarray technology in 2B4 and 1E8 cells (subclones derived from PC-3M human prostate carcinoma cell line) to identified the differentially expressed genes between ATP treated and untreated cells

overall_design: Six samples were analyzed. RNA was extracted from 2B4 and 1E8 cells, which further divided as control, ATP treatment for 6h (ATP 6h) and ATP treatment for 12h (ATP 12h), respectively.

first: Weigang

last: Fang

first: Xinxia

last: Tian


title: Gene expression profiling of pancreatic cancer cell line BxPC-3 induced by PAR-2 AP

status: Public on Apr 30 2013

first: Che-Ming

last: Teng

address: No.1, Jen-Ai Road

department: Pharmacology

institute: National Taiwan University

summary:
Protease-activated receptor-2 (PAR-2), a G protein-coupled receptor activated by trypsin and coagulant factors, plays broad spectrum of physiological and pathological roles especially in cancer development. In this study, we used PAR-2 activating peptide to mimic the action of trypsin to trigger PAR-2 signaling pathway and effects of PAR-2 activation on gene expression in human pancreatic cancer cell line BxPC-3 investigated by microarray analysis.
Through DAVID bioinformatic resources, we observed that activated PAR-2-mediated genes are summarized to two different pathways, renal cell carcinoma and NFkB pathway. In renal cell carcinoma pathway, activated PAR-2 dysregulated hypoxia-inducible factors and its target genes, including glucose transporter 1 (GLUT1), transforming growth factor-b (TGF-b) and vascular endothelial growth factor-A (VEGF-A). In addition, activated PAR-2 induced MAPK signaling and transcriptional factors, such as JUN, MAP2K1 and ETS1. The regulation of these genes by PAR-2 assumed that PAR-2 signaling was associated with cancer progression.
On the other hand, activated PAR-2 upregulated interleukin-1b (IL-1b) and toll-like receptor 4 (TLR4) related with NFkB activation, which indicated that PAR-2 signaling may cause cancer-related inflammation. In conclusion, PAR-2 may be a factor to regulate cancer progression and inflammation.

overall_design: Two-condition experiment, control cells vs PAR-2 AP-treated cells.

first: Li-Hsun

last: Chang

first: Shiow-Lin

last: Pan

first: Chin-Yu

last: Lai

first: An-Chi

last: Tsai


title: Epigenetic treatment of B-cell lymphoma cell lines

status: Public on Apr 18 2013

first: Nicole

last: Bethge

address: Montebello veien

department: Immunology

country: Norway

institute: Institute for Cancer Research

summary: We used DNA microarray technology to assess changes in gene expression after treatment of 11 lymphoma cell lines with epigenetic drugs. We identified genes with upregulated expression in treated cell lines and with downregulated expression in B-cell lymphoma patient samples when compared to normal B cells.

overall_design: Assess changes in gene expression after treatment of 11 lymphoma cell lines with epigenetic drugs (aza and TSA).


title: Functional DNA methylation is accompanied by chromatin accessibility [gene expression]

status: Public on Mar 08 2013

city: Los Angeles

first: Kurinji

last: Pandiyan

address: 1441 Eastlake Avenue NOR 7344

department: Department of Urology - Norris Comprehensive Cancer Center

country: USA

institute: University of Southern California

summary: Analysis of nucleosome positioning and chromatin state by using CpG methyltransferase M.SssI to methylate nuclei. Unmethylated regions that gain methylation (low to high beta value) are known to be accessible and nucleosome depleted. Method used to study changes after epigenetic drug treatments identified that majority of demethylation events are not accompanied by chromatin accessibility changes.

overall_design: RNA harvested from cells post epigenetic drug treatment, with 5-Aza-CdR or SAHA

first: Gangning

last: Liang


title: Budding yeast ATM/ATR contribute to meiotic double-strand-break (DSB) homeostasis by down-regulating Rec114, an essential component of the DSB-machinery

status: Public on Jun 01 2013

city: Vienna

first: Franz

last: Klein

address: Dr. Bohrg. 9

department: Chromosome Biology

institute: University of Vienna, MFPL

summary: In most organisms, meiotic recombination begins with programmed DNA double strand  break (DSB) formation by Spo11. Here, we present evidence that Tel1/Mec1, the  budding yeast ATM/ATR, regulate DSB formation by phosphorylating Rec114, an  essential Spo11-accessory protein. Analyses of a non-phosphorylatable- or phosphomimetic-  alleles of rec114 revealed that DSB-dependent phosphorylation of Rec114  limited its association with DSB-hotspots resulting in reduction in DSB formation. Also  observed were the impact of Rec114 phosphorylation on its homolog synapsis-associated  removal from chromosomes and NDT80-dependent turnover. Specifically, we found that  the synapsis- and NDT80-dependent Rec114 downregulation occurred later in the rec114  mutant with a reduced Spo11-catalysis, but earlier in the other with an enhanced  catalysis, strongly implicating the existence of a feedback mechanism coupling the extent  of Spo11-catalysis to Rec114 activity. Taken together, these observations suggest that  three different mechanisms of down regulating Rec114 contribute to meiotic DSB  homeostasis, a feedback mechanism to maintain the number of meiotic DSBs at the  developmentally programmed level.

overall_design: 6 genome wide ChIPchip sets: 3 for meiotic DSB formation (Spo11-ChIP) and 3 for protein-DNA association (Rec114-ChIP), each for wild type and two mutants during meiosis (corresponding to the main Figure 3, as well as to Figures S3, S4, S5).

first: Jesus

last: Carballo

first: Silvia

last: Panizza

first: Maria-Elisabetta

last: Serrentinoc

first: Anthony

last: L. Johnsona

first: Marco

last: Geyomat

first: Valerie

last: Borde

first: Rita

last: Cha


title: Reproductive status alters transcriptomic response to infection in female Drosophila melanogaster

status: Public on Mar 19 2013

city: Baltimore

first: George

last: Dimopoulos

state: MD

address: 615 N Wolfe St.

department: Molecular Microbiology and Immunology

institute: Johns Hopkins School of Public Health

summary: In this analysis, we used microarrays to contrast genome-wide transcript levels in virgin versus mated females before and after infection. We repeated the entire experiment using female mutants that do not form a germline. We found  that multiple genes involved in egg production show reduced expression in response to infection, and that this reduction is stronger in virgins than it is in mated females. In germline-less females, expression of egg-production genes was predictably low and not differentially affected by infection. We also identified several immune responsive genes that are differentially induced after infection in virgins versus mated females.

overall_design: Eight treatment groups were analzyed, with three replicates for each treatment group.

first: Sarah

last: Short

first: Brian

last: Lazzaro


title: Murine primary dendritic cells: Control vs. Influenza-infected vs. polyI:C stimulated.

status: Public on Dec 05 2012

city: Seattle

first: Aderem

last: Lab

state: WA

address: 307 Westlake Avenue North, Suite 500

institute: Seattle Children's Research Institute

summary: MIcroRNA expression profiling of primary murine splenic dendritic cells (Flt3L expanded) comparing untreated cells to cells infected with Influenza A or stimulated with polyI:C in vitro.

overall_design: Three-condition experiment, Influenza A/PR/8/34 virus MOI=10 vs polyI:C 30 ug/mL vs. mock treated; RNA collected after 8 hours.  3 Independent biological replicates from cells prepared on different days. One replicate per array.

first: Carrie

last: Rosenberger


title: Gene Expression analysis of PST001 in cancer cell lines

status: Public on Dec 31 2012

city: Bangalore

first: madavan

last: vasudevan

state: Karnataka

address: Kasturi Nagar

country: India

institute: Theomics International Private Limited

summary:
Analysis of expression variation of PST001 for elucidating cell death mechanism in cancer cell lines.
Analysis of expression variation of PST001 for elucidating cell death mechanism in cancer cell lines.

overall_design: Total RNA isolated from PST001 treated cancer cell lines subjected to 24 or 48 hr treatment compared to untreated samples.

first: T

middle: T

last: Sreelekha

first: S

middle: R

last: Aravind


title: Arabidopsis AGO1 and AGO10 bound sRNAs

status: Public on Aug 04 2012

first: Xiuying

last: Liu

address: No. 1 West Beichen Road, Chaoyang District

department: Bioinformatics

institute: CAS

summary: The shoot apical meristem (SAM) comprises a group of undifferentiated cells that divide to maintain the plant meristem and also give rise to all shoot organs. SAM fate is specified by class III HOMEODOMAIN-LEUCINE ZIPPER (HD-ZIP III) transcription factors, which are targets of miR166/165. In Arabidopsis, AGO10 is a critical regulator of SAM maintenance, and here we demonstrate that AGO10 specifically interacts with miR166/165. The association is determined by a distinct structure of the miR166/165 duplex. Deficient loading of miR166 into AGO10 results in a defective SAM. Notably, the miRNA-binding ability of AGO10, but not its catalytic activity, is required for SAM development, and AGO10 has a higher binding affinity for miR166 than does AGO1, a principal contributor to miRNA-mediated silencing. We propose that AGO10 functions as a decoy for miR166/165 to maintain the SAM, preventing their incorporation into AGO1 complexes and the subsequent repression of HD-ZIP III gene expression.

overall_design: Homozygous T2 progeny of complemented plants expressing ago10-3;PAGO10-HF-AGO10 and ago1;PAGO1-HF-AGO1 were used for preparation of AGO complexes. Flower samples including floral buds, open flowers, and newly set siliques (1-2 day old) were collected for protein extraction and isolation of dual-tagged AGO complexes using a two-step affinity purification. The isolated AGO complexes were divided into two parts, one aliquot was used for sRNA extraction with Trizol reagent, whereas the other part was used for monitoring protein purity by Gelcode blue staining and western blot using a monoclonal anti-Flag antibody (Sigma) as previous described.

first: Ronghui

last: Wang

first: Xin

last: Zhou

first: Sing-Hoi

last: Sze

first: Xiuren

last: Zhang


title: Differential gene expression in circulating leukocytes from breast cancer patients treated with Cognitive Behavioral Stress Management

status: Public on Jan 01 2012

first: Steve

last: Cole

state: CA

address: 11-934 Factor Bldg, UCLA

department: Medicine

institute: UCLA School of Medicine

overall_design:
Gene expression profiling was carried out on peripheral blood mononuclear cell mRNA samples collected from 53 female breast cancer patients at 6- or 12-month follow-ups in a randomized controlled trial of Cognitive Behavioral Stress Management or an active control condition.  The primary research question is whether gene expression differs in patients treated with Cogntive Behavioral Stress Management vs control conditions.
Risk prediction


title: Genome-wide analysis of gene expression response to MI-2 and z-VRPR-fmk in ABC-DLBCL cell lines

status: Public on Dec 11 2012

city: New York

first: Lorena

last: Fontan

state: NY

address: 1300 York Ave

institute: Weill Cornell Medical College

summary: MALT1 Small Molecule Inhibitors Specifically Suppress ABC-DLBCL In Vitro and In Vivo

overall_design: Total RNA was obtained from HBL-1 and TMD8 cell lines subjected to 8 hours treatment with MI-2, z-VRPR-fmk or vehicle.

first: Hao

last: Wu

first: Ari

last: Melnick


title: Senataxin associates with replication forks to protect fork integrity across RNAPII transcribed genes

status: Public on Nov 09 2012

city: Milan

first: Rodrigo

last: Bermejo

state: Lombardy

address: Via Adamello 16

institute: IFOM-IEO-Campus

summary:
Here we analysed the role of yeast Senataxin (Sen1) in coordinating replication with transcription and in protecting genome integrity. Senataxin is mutated in the two severe neurodegenerative diseases AOA2 and ALS4.
We show that a fraction of Sen1/Senataxin DNA/RNA helicase associates with replication forks and protects the integrity of those fork encountering highly expressed RNAPII genes.
sen1 mutants accumulate aberrant DNA structures and RNA-DNA hybrids while forks clash head-on with RNAPII transcription units and counteract recombinogenic events and accumulation of checkpoint signals.
Nrd1, which acts togheter with Sen1 in trascription temination, is not recruited at replication forks. nrd1 mutants does not display replication defects, high genome instability and checkpoint activation observed in sen1 mutants
The Sen1 function in replication can be therefore separable from its role in RNA processing.
We propose a role for Sen1/Senataxin during chromosome replication in facilitating replisome progression across RNAPII transcribed genes thus preventing DNA-RNA hybrids accumulation when forks encounter nascent transcripts on the lagging strand template.

overall_design:
Chip on chip analysis was carried out as described (Bermejo et al., 2011), employing anti-Flag monoclonal antibody M2 (Sigma-Aldrich)
Labelled probes were hybridized to Affymetrix S.cerevisiae Tiling 1.0 (P/N 900645) arrays and processed with TAS software.

first: Amaya

last: Alzu

first: Martina

last: Begnis

first: Chiara

last: Lucca

first: Daniele

last: Piccini

first: Walter

last: Carotenuto

first: Marco

last: Saponaro

first: Alessandra

last: Brambati

first: Andrea

last: Cocito

last: Foiani

first: Giordano

last: Liberi