title: Lung cancer signatures in plasma based on proteome profiling of mouse tumor models

city: Bethesda

middle: Wallace

last: Lockwood

address: 50 South Drive

institute: National Human Genome Research Institute

summary: Mouse models of cancer recapitulate many of the molecular and biological features of the human disease.  We sought to exploit these experimental merits in a systematic comparative proteomics search for circulating proteins associated with lung tumor development. In-depth quantitative proteomics was applied to plasmas from three mouse models of lung adenocarcinoma driven by mutant EGFR or Kras or induced by urethane exposure and a mouse model of small cell lung cancer driven by loss of Trp53 and Rb. To further refine our lung cancer-specific and broad carcinoma signatures, we intersected these lung cancer proteome profiles with those from other well-established mouse models of pancreatic, ovarian, colon, prostate and breast cancer, as well as two mouse models of inflammation. A set of proteins regulated by Titf1/Nkx2-1, a master transcription factor in cells from the peripheral airways and a known lineage-survival oncogene in lung cancer was identified in plasmas of mouse models of lung adenocarcinoma. An EGFR network of proteins was discerned in the plasma of mice with lung tumors driven by a mutant human EGFR.  Levels of these proteins returned toward baseline upon treatment with a tyrosine kinase inhibitor. Moreover, a distinct plasma signature was uncovered in the Trp53/Rb mutant small cell lung cancer model that included a set of proteins associated with neuroendocrine development. Our studies have identified novel plasma protein signatures among molecularly or histopathologically defined lung cancer subtypes.

overall_design: siRNA transfection experiments were performed in NCI-H3255 and HCC4019 lung adenocarcinoma cell lines using ON-TARGETplus SMARTpool small interfering RNAs (siRNAs) targeting TITF1 (L-019105-01-0005) along with a negative control (ON-TARGETplus siCONTROL nontargeting siRNA pool; D-001810-10-05) obtained from Dharmacon. 400000 cells were seeded in antibiotic-free RPMI-1640 media supplemented with 10% FBS, in 6-well culture plates.  The next day, cells were transfected at a final concentration of 100nM siRNA using 6ul DharmaFECT 1 (Dharmacon) according to the manufacturer's instructions.  72-hours post-transfection, RNA was harvested using Trizol (Invitrogen) and protein using RIPA buffer for microarray expression and western blotting, respectively. RNA from TITF1 knockdown and control experiments was profiled by the MSKCC Genomics Core using the Illumina Human HT-12 v3.0 array platform according to manufacturer's instructions.   Two biological replicates were profiled for each condition.  Resulting data files were exported using GenomeStudio software, log2 transformed, quantile-normalized and analyzed using Partek Genomics Suite (v6.5).  Average values of replicates for each gene were then compared between the TITF1 knockdown and non-targeting treatments for each cell line to identify candidate TITF1 regulated genes.

middle: W


title: Comparison of the gene expression profiles of a recombinant protein producing Hek 293 cell line and its non-producing parental cell line.

status: Public on Dec 20 2012

city: Brisbane

first: Stefanie

last: Dietmair

state: QLD

address: Bldg 75

department: Australian Institute for Bioengineering and Nanotechnology

country: Australia

institute: The University of Queensland

summary: Comparison of the gene expression profiles of a recombinant protein producing Hek 293 cell line (referred to as producer) and its non-producing parental cell line Hek293F (referred to as non-producer). The parental cell line was obtained from Invitrogen, Carlsbad, CA. The producer was transfected with a heavy chain variable region fused to the Fc region of a human IgG (dAb-Fc). The aim of this study was to gain a better understanding of the process of recombinant protein production in Hek293 cells and to identify targets for the engineering of an improved host cell line.

overall_design: Duplicate samples for RNA extraction were taken at four time points (approximately 30, 43, 51 and 67 hours after inoculation of the bioreactor) during the exponential phase of batch bioreactor cultures. Only one of these technical duplicates was analysed. Three bioreactor cultures were performed for each cell line representing three biological replicates resulting in 12 (3 x 4)  samples per cell line.

first: Nicholas

middle: E

last: Timmins

first: Lars

middle: K

last: Nielsen


title: Expression data from ES cells

status: Public on Dec 11 2012

city: Ann arbor

first: qiang

last: chen

state: Michigan

address: 1150 W. medical school road

country: USA

institute: umich

summary:
TET2 directly interacts with OGT, which is important for the chromatin association of OGT in vivo. Although this specific interaction does not regulate the enzymatic activity of TET2, it facilitates OGT-dependent histone O-GlcNAcylation. Moreover, OGT associates with TET2 at transcription starting sites (TSS). Down-regulation of TET2 reduces the amount of H2B S112 GlcNAc marks in vivo, which are associated with gene transcription regulation.
We used microarray to test the function of TET2 on gene expression.

overall_design: Mouse ES cells infected with control knockdown(KD) or TET2 KD virus were treated with puromycin. ES cells were extracted for RNA and hybridization on Affymetrix microarrays.

first: Qiang

last: Chen

first: Xiaochun

last: Yu

first: Yibin

first: Chunjing

last: Bian


title: GATA3 acts upstream of FOXA1 in mediating ER binding by shaping enhancer accessibility

status: Public on Nov 26 2012

city: Cambridge

first: Suraj

last: Menon

address: Li Ka Shing Center, Robinson Way

country: United Kingdom

institute: Cambridge Research Institute, Cancer Research UK

summary: Estrogen Receptor (ESR1) drives growth in the majority of human breast cancers by binding to regulatory elements and inducing transcription events that promote tumor growth. Differences in enhancer occupancy by ESR1, contribute to the diverse expression profiles and clinical outcome observed in breast cancer patients. GATA3 is an ESR1 co-operating transcription factor mutated in breast tumors, however its genomic properties are not fully defined. In order to investigate the composition of enhancers involved in estrogen-induced transcription and the potential role of GATA3, we performed extensive ChIP-sequencing in unstimulated breast cancer cells and following estrogen treatment. We find that GATA3 is pivotal in mediating enhancer accessibility at regulatory regions involved in ESR1-mediated transcription. GATA3 silencing resulted in a global redistribution of co-factors and active histone marks prior to estrogen stimulation. These global genomic changes altered the ESR1 binding profile that subsequently occurred following estrogen, with events exhibiting both loss and gain in binding affinity, implying a GATA3 mediated re-distribution of ESR1 binding. The GATA3-mediated re-distributed ESR1 profile correlated with changes in gene expression, suggestive of its functionality. Chromatin loops at the TFF locus involving ESR1 bound enhancers occurred independently of ESR1 when GATA3 was silenced, indicating that GATA3, when present on the chromatin, may serve as a licensing factor for estrogen- ESR1 mediated interactions between cis-regulatory elements. Together these experiments suggest that GATA3 directly impacts ESR1 enhancer accessibility and may potentially explain the contribution of mutant-GATA3 in the heterogeneity of ESR1+ breast cancer.

overall_design: MCF7 cells were transfected with siRNA and cultured in hormone deprived conditions for a further 3 days. Cells were subsequently treated with 100nM estrogen (E2) or control (Veh) for 6 hrs. We performed two independent biological experiments each using three different siRNAs against GATA3 individually (six siGATA3 replicates in total). For siControl we used RNA from five biological replicates.

first: Vasiliki

last: Theodorou

first: Jason

last: Carroll


title: Quiescent innate response to infective filariae by human Langerhans’ cells suggests a strategy of immune evasion

status: Public on Dec 04 2012

first: Roshanak

middle: T

last: Semnani

state: MD

address: Center Drive

department: LPD

institute: NIAID

summary: Filarial infection is initiated by mosquito-derived, third-stage larvae (L3) deposited on the skin that transits through the epidermis containing Langerhans' cells (LC) and keratinocytes (KC), among other cells. This earliest interaction between L3 and the LC likely conditions the priming of the immune system to the parasite. To determine the nature of this interaction, human LC (Langerin+, E-cadherin+, CD1a+) were generated in vitro and exposed to live L3. LC exposed to live L3 for 48 h showed no alterations in cell surface markers CD14, CD86, CD83, CD207, E-cadherin, CD80, CD40, and HLA-DR or in mRNA expression of inflammation-associated genes such as IL-18, IL-18BP, and caspase 1. In contrast to L3, live tachyzoites of Toxoplasma gondii, an intracellular parasite, induced production of CXCL9, IP 10, and IL-6 in LC. Furthermore, pre-exposure of LC to L3 did not alter TLR3- or TLR4-mediated expression of pro-inflammatory cytokines IL-1β, IFN-γ, IL-6, or IL-10. Interestingly, co-cultures of KC and LC produced significantly more IL-18, IL-1α, and IL-8 than did cultures of LC alone, although exposure of the co-cultures to live L3 did not result in altered cytokine production. Microarray examination of ex vivo LC from skin blisters that were exposed to live L3 also showed few significant changes in gene expression compared with unexposed blisters, further underscoring the relatively muted response of LC to L3. Our data suggest that failure by LC to initiate an inflammatory response to the invasive stage of filarial parasites may be a strategy for immune evasion by the filarial parasite.

overall_design: Skin blisters from 6 healthy volunteers are either cultured in culture media alone as control samples or being exposed to 5 L3s in a transwell in a 24 well tissue culture plates for 48 hours .  12 samples were analyzed in total

first: Alexis

last: Boyd

first: Sasisekhar

last: Bennuru

first: Yuanyuan

last: Wang

first: Vivornpun

last: Sanprasert

first: Melissa

last: Law

first: Damien

last: Chaussabel

first: Thomas

middle: B

last: Nutman


title: Comparison of microarray platforms for measuring differential microRNA expression (Gene Expression data)

city: Milan

first: Loris

last: De Cecco

address: via Venezian 1

country: Italy

institute: IRCSS Istituto Nazionale Tumori

summary:
Microarray technology applied to miRNA profiling is a promising tool in many research fields. At present, only few studies have addressed intra- and inter-platform reproducibility by using tissues/cell-lines of different origin to maximize differences in miRNA content. Although the approach might provide an useful system to address technical issues since, for sure, a huge modulation can be evaluated, it  does not reflect the common experimental practice in laboratory. As a matter of fact, from all these studies it is not know how concordant can be expected the results obtained by different platforms starting from biological meaningful specimens.  We investigated the issue of inter-platform reproducibility using four miRNA microarray platforms and nine paired tumor/normal colon tissues.
The tumor and the normal counter-part samples were prospectively collected from 9 patients who underwent surgical resection at the INT-MI. Neoplastic samples were obtained from the central area of the neoplasia, avoiding to select necrotic material or transition zones with healthy mucosa. Samples of colonic healthy mucosa were resected at least 20 centimeters far from the neoplasia and distant from the surgical resection margins. Tissue samples were stored in liquid nitrogen until RNA extraction. Total RNA was extracted from 10–20 mg of tumor samples and from 30–40 mg of normal samples.

overall_design: Nine paired tumor/normal colon tissues on Illumina HT12_v3 gene expression Beadchips

first: Maurizio

last: Callari


title: Attenuation of miR-126 activity expands HSC in vivo without exhaustion

status: Public on Nov 30 2012

city: Toronto

first: John

last: Dick

address: 101 College St. Toronto

country: Canada

institute: Ontario Cancer Institute

summary: Life-long blood cell production is governed through the poorly understood integration of cell-intrinsic and -extrinsic control of hematopoietic stem cell (HSC) quiescence and activation. MicroRNAs (miRNAs) coordinately regulate multiple targets within signaling networks making them attractive candidate HSC regulators. We report that miR-126, a miRNA expressed in HSC and early progenitors, plays a pivotal role in restraining cell cycle progression of HSC in vitro and in vivo. miR-126 knockdown using lentiviral sponges increased HSC proliferation without inducing exhaustion, resulting in expansion of mouse and human long-term repopulating HSC. Conversely, enforced miR-126 expression impaired cell cycle entry leading to progressively reduced hematopoietic contribution. In HSC/early progenitors, miR-126 regulates multiple targets within the PI3K/AKT/GSK3β pathway thus attenuating signal transduction in response to extrinsic signals. These data establish that miR-126 sets a threshold for HSC activation and thus governs HSC pool size, demonstrating the importance of miRNA in the control of HSC function.

overall_design: Total RNA was extracted from cord blood Lin- cells and treated with mir126 shRNA or mir126 containing viral particles (and corresponding controls)

first: Eric

middle: R

last: Lechman

first: Peter

last: van Galen

first: Veronique

last: Voisin

first: Gary

middle: D

last: Bader


title: Global Gene Expression Profiles of  Visceral Adipose in Females with Type 2 Diabetes.

status: Public on Nov 15 2012

city: Delhi

first: Abhay

last: Sharma

state: Delhi

address: Delhi University campus, Mall Road

department: Functional Genomics Unit

country: India

institute: CSIR-Institute of Genomics and Integrative Biology (IGIB)

summary: Gene expression profiles of biopsy samples of visceral adipose of three female patients of type 2 diabetes and three non-diabetic female patients were generated using Illumina HumanHT-12 v3 Expression BeadChip arrays. The primary indications of surgery were non-infective and non-malignant conditions, namely, cholelethiasis, hernia and trauma.

overall_design: Three biological replicates with four technical replicates each were used to generate expression profiles. Total cellular RNA from biopsy samples was isolated using mirVana™ miRNA Isolation Kit (Ambion, Austin, TX). The quantity and the quality of RNA samples were determined using Nanodrop-1000 (Thermo Fischer Scientific, Wilmington, USA) and Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA), in that order. RNA samples with a RIN (RNA Integrity Number) value between 5-8 were used for expression profiling. Starting with 500 ng of total RNA, Illumina TotalPrepTM RNA Amplification Kit was used for preparing first and second strand cDNA, purification of cDNA, in vitro transcription to synthesize biotin labeled cRNA, and purification of the labeled cRNA, in that sequence. The quantitation of cRNA was performed using Nanodrop-1000. Illumina HumanHT-12 v3 Expression BeadChip arrays were hybridized with 750 ng of labeled cRNA samples. Hybridization and washing were perforemd according to the manufacturer's protocol. The arrays were scanned and read using Illumina iScan System, and the data extraction, average normalization and downstream analysis performed using Illumina GenomeStudio V2010.1.

first: Priyanka

last: Jain

first: Saurabh

last: Vig

first: D

last: Bharadwaj

first: Malabika

last: Dutta

first: Sandeep

last: Mathur


title: Gene expression profile of KM-H2 cells conditional expressing PU.1

status: Public on Nov 22 2012

city: Kumamoto

first: Yutaka

last: Okuno

state: Kumamoto

address: 1-1-1 Honko, Chuo Ku

department: Department of Hematology

country: Japan

institute: Kumamoto university of Medicine

summary: PU.1 is an Ets family transcription factor that is essential for the differentiation of both myeloid and lymphoid cells. PU.1 is down-regulated in classical Hodgkin lymphoma cells via methylation of the PU.1 promoter. To evaluate whether down-regulation of PU.1 is essential for the growth of cHL cells, we generated KM-H2 derived  cell lines conditionally express PU.1 by tet-off system (designated KM-H2tetPU.1). Conditonally expressed PU.1 by tetracycline removal induced complete growth arrest and apoptosis in KM-H2 cells. To elucidate the mechanisms underlying cell cycle arrest and apoptosis induced by PU.1, we compared gene expression profiles of KM-H2tetPU.1 cells 0, 1 and 3 days after PU.1 induction, by DNA microarray.

overall_design: We extracted total RNA from KM-H2tetPU.1 cells 0, 1 and 3 days after PU.1 induction by tetracycline removal. We compared gene expression profiles of KM-H2tetPU.1 cells 0, 1 and 3 days after PU.1 induction using DNA microarray analysis. 4 independent experiments were performed with each RNA samples.

first: Hiromichi

last: Yuki

first: Shikiko

last: Ueno

first: Hiro

last: Tatetsu

first: Hiroaki

last: Niiro

first: Tadafumi

last: Iino

first: Shinya

last: Endo

first: Yawara

last: Kawano

first: Yoshihiro

last: Komohara

first: Motohiro

last: Takeya

first: Hiroyuki

last: Hata

first: Seiji

last: Okada

first: Toshiki

last: Watanabe

first: Koichi

last: Akashi

last: Mitsuya


title: Vastus lateralis muscle aging

status: Public on Dec 03 2012

city: Leiden

first: Marius

last: Gheorghe

address: Einthovenweg 20

department: Human Genetics

country: Netherlands

institute: LUMC

summary: Development of a method to identify age-regulated expression trends in skeletql muscles and study the underlying molecular processes of the age_associated progressive changes in skeletal muscles. See abstract from associated manuscript below :  Aging is characterized by progressive tissue degeneration and it is associated with genome-wide changes of mRNA expression profiles. Therefore, it is expected that age-regulated changes in expression profiles could describe the process of aging. We have developed a robust and unbiased methodology to identify age-regulated expression trends in cross-sectional data sets from healthy donors. Our analysis in four different tissues reveals that in brain cortex and Vastus lateralis muscles, two major age-associated expression inclinations were found, one during midlife and one in elderly. In kidney medulla and cortex, however, transcriptional changes were found only in elderly. In concurrence with increased degeneration in aged tissue, the elderly-associated expression changes are predominantly downwards. Our results suggest that a non-linear trend describes the aging process, and can be the result of inclinations of gene expression at two distinct age-positions affecting different molecular and cellular processes.

overall_design: RNA was extracted from vastus lateralis muscles. cDNA synthesis and labeling were preformed with the Illumina cDNA labeling kit.

first: Vered

last: Raz

first: Andrea

last: Venema


title: Involvement of ERK, Wnt and BMP2 signaling in human articular chondrocyte dedifferentiation in monolayer culture

status: Public on Nov 14 2012

city: Enschede

first: Jeroen

last: Leijten

address: Drienerlolaan 5

institute: University of Twente

summary: Objective: When primary chondrocytes are cultured in monolayer, they undergo dedifferentiation during which they lose their phenotype and their capacity to form cartilage.  Dedifferentiation is an obstacle for cell therapy for cartilage degeneration. In this study, we aimed to systemically evaluate the changes in gene expression during dedifferentiation of human articular chondrocytes to identify underlying mechanisms.  Methods: RNA was isolated from monolayer-cultured primary human articular chondrocytes at serial passages. Gene expression was analyzed by microarray. Based on the microarray analysis, relevant genes and pathways were identified. Their functions in chondrocyte dedifferentiation were further investigated in detail.   Results: In vitro expanded human chondrocytes showed progressive changes in gene expression during dedifferentiation. Strikingly, an overall decrease in total gene expression was detected. Genes in the Wnt and BMP pathways exhibited significant changes in expression. The non-canonical rather than the canonical Wnt pathway was found to be involved in the loss of collagen II synthesis. BMP2 was able to decelerate the dedifferentiation and reinforce the maintenance of chondrocyte phenotype in monolayer culture. DNA methylation was in part responsible for the expression downregulation of a set of genes.   Conclusion: Our study revealed the roles of ERK, Wnt and BMP pathways as well as DNA methylation in chondrocyte dedifferentiation in monolayer culture.

overall_design: RNA human chondrocytes were allowed to dedifferentiate for 8 passages. RNA was isolated at week 0, 2 ,4, 6 and 8, which was subjected to whole genome gene expression analysis.

first: Bin

last: Ma

middle: C

first: Ling

last: Wu

first: Janine

last: Post

first: Marcel

last: Karperien


title: Global Gene Expression Profiles of  Skeletal Muscle in Males with Type 2 Diabetes.

first: Abhay

last: Sharma

summary: Gene expression profiles of biopsy samples of skeletal muscle of three male patients of type 2 diabetes and three non-diabetic male patients were generated using Illumina HumanHT-12 v3 Expression BeadChip arrays. The primary indications of surgery were non-infective and non-malignant conditions, namely, cholelethiasis, hernia and trauma.

first: Priyanka

last: Jain

first: Saurabh

last: Vig

first: D

last: Bharadwaj

first: Malabika

last: Dutta

first: Sandeep

last: Mathur


title: Global Gene Expression Profiles of Subcutaneous Adipose in Females with Type 2 Diabetes.

summary: Gene expression profiles of biopsy samples of subcutaneous adipose of three female patients of type 2 diabetes and three non-diabetic female patients were generated using Illumina HumanHT-12 v3 Expression BeadChip arrays.  The primary indications of surgery were non-infective and non-malignant conditions, namely, cholelethiasis, hernia and trauma.


title: Gene expression in benign and prostate cancer tissue

status: Public on Dec 01 2012

first: Naomi

middle: Laura

address: Robinson Way

institute: Cambridge Research Institute

summary: Benign prostate tissue and prostate cancer tissue (untreated, androgen deprivation therapy responding, or castrate-resistant) was collected from patients at the time of transurethral resection of the prostate surgery.

overall_design: 24 samples, technical replicates.

middle: L

first: Charlie

last: Massie

first: Antonio

last: Ramos-Montoya

first: Helen

last: Scott

first: Alastair

last: Lamb

first: Stewart

last: MacArthur

first: Rory

last: Stark

first: Anne

middle: Y

last: Warren

first: Ian

middle: G

last: Mills

first: David

last: Neal


title: Boswellic acid induced changes in gene expression and methylation in colorectal cancer cells

city: Dallas

first: Masanobu

last: Takahashi

address: 3500 Gaston Avenue, suite H-250

institute: Baylor University Medical Center

type:
Expression profiling by array
Methylation profiling by array

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

overall_design: Refer to individual Series

first: Yan

last: Shen

first: Ajay

last: Goel


title: Disease-specific sequence change DSC3 in TAF1/DYT3 affects genes in vesicular transport and dopamine metabolism

status: Public on Nov 27 2012

city: Bonn

first: Joachim

last: Schultze

state: NRW

address: Carl-Troll-Strasse 31

department: Genomics and Immunoregulation

country: Germany

institute: LIMES (Life and Medical Sciences Center Genomics and Immunoregulation)

summary: The X-chromosomal dystonia parkinsonism syndrome (XDP) is associated with sequence changes within the TAF1/DYT3 multiple transcript system. While most sequence changes are intronic, one, DSC3, is located within an exon (d4). Transcribed exon d4 occurs as part of multiple splice variants. These variants include exons d3 and d4 spliced to exons of TAF1, and an independent transcript composed of exons d2-d4. Location of DSC3 in an exon (d4) and utilization of this exon in multiple splice variants suggests an important role of DSC3 in the pathogenesis of XDP. To test this hypothesis we transfected neuroblastoma cells with four expression constructs, including exons d2-d4 (d2-d4/wild-type (wt) and d2-d4/DSC3) and d3-d4 (d3-d4/wt and d3-d4/DSC3). Expression profiling revealed a dramatic effect of DSC3 on overall gene expression. 362 genes differ between cells containing d2-d4/wt and d2-d4/DSC3. Annotation clustering revealed high enrichment of genes related to dopamine metabolism, vesicular transport, synapse function, Ca++ metabolism, and oxidative stress. 211 genes were differentially expressed in d3-d4/wt vs. d3-d4/DSC3. Annotation clustering highlighted genes in signal transduction and cell-cell interaction. The data shows an important role of physiologically occurring transcript d2-d4 in normal brain function. Interference with this role by DSC3 is a likely pathological mechanism in XDP. Disturbance of dopamine function and of Ca++ metabolism can explain abnormal movement; loss of protection against reactive oxygen species may account for the neurodegenerative changes in XDP. Although d3-d4 also affect genes potentially related to neurodegenerative processes their physiologic role as splice variants of TAF1 awaits further exploration.

overall_design: We transfected neuroblastoma cells with four expression constructs, including exons d2-d4 (d2-d4/wild-type (wt) and d2-d4/DSC3) and d3-d4 (d3-d4/wt and d3-d4/DSC3).

first: Thilo

last: Herzfeld

first: Dagmar

last: Nolte

first: Maria

last: Grznarova

first: Andrea

last: Hofmann

first: Ulrich

last: Müller


title: Rescue Of Dysfunctional Autophagy By Peptide IDR-1018 Attenuates Hyperinflammatory Phenotype Of Cystic Fibrosis Cells

status: Public on Nov 05 2012

city: Vancouver

first: Christopher

last: Fjell

state: BC

address: Room 166 - 1081 Burrard Street

department: Medicine

institute: University of British Columbia

summary: Genome-wide gene expression was measured in two cell lines: CF bronchial epithelial cell line IB3-1 (compound heterozygote for the ΔF508 and W1282X CFTR mutations) and the isogenic, CFTR-corrected C38 cell line, after treatment with the flagellin protein FliC, and/or synthetic peptide IDR-1018.

overall_design: Total RNA was obtained from cell lines representing CF and normal epithelial cells after treatment with the fliC protein (that is known to play a role in CF lung inflammation), and/or the peptide IDR-1018 that has anti-inflammatory properties. Comparison of genes and pathways affected by these treatments indicated the role of autophagy process in CF disease.

first: Matt

last: Mayer

first: Christoph

middle: J

last: Blohmke

first: Reza

last: Falsafi

first: Laurence

last: Madera

first: Stuart

last: Turvey

first: Robert

last: Hancock


title: Genome-wide analysis of Human Upf1, SMG5, SMG7 and PNRC2 downregulated substrates in HeLa cell

status: Public on Nov 01 2012

city: Seoul

first: Hana

last: Cho

address: Anam 5ga, Sungbukku

department: School of Life Sciences and Biotechnology

country: South Korea

institute: Korea University

summary: Analysis of cellular NMD (Nonsense-mediated mRNA decay) substrates that regulated by Upf1, SMG5, SMG7 and/or PNRC2 in HeLa cell. The hypothesis tested in the present study was that endogenous NMD substrates may co-regulated by Upf1, SMG5, SMG7 and PNRC2.

overall_design: Total RNA obtained from HeLa cells with downregulation of Upf1, SMG5, PNRC2 or SMG7 by siRNA. The up- or down-regulated transcripts were compare to control siRNA treated HeLa cell RNA extract. Significant transcripts were confirmed by replication

first: Sisu

last: Han

first: Junho

last: Choe


title: IL-17 downregulates filaggrin and affects epidermal barrier function gene expression; potential role in the pathogenesis of atopic eczema

city: Oxford

first: Stephen

last: Taylor

address: Headington

institute: CBRG

summary: Genome-wide analysis of gene expression after stimulation with cytokines to assess the main processes, molecular functions and cellular components affected as well as genes related to skin barrier function.

overall_design: HaCaT cells were exposed to IL-17A (200ng/ml) for 12h. The cells were lysed, total RNA was extracted and microarray study was performed on Illumina HT12 platform.

first: Graham

middle: S

last: Ogg

first: Danuta

last: Gutowska-Owsiak


title: Sucrose modulation of the Arabidopsis thaliana guard-cell transcriptome

city: Tallahassee

first: George

middle: W.

last: Bates

state: FL

address: 89 Cheiftain Way

department: Department of Biological Science

institute: Florida State University

summary: Microarrays were used to evaluate the effect of sucrose on gene expression in guard cells.  Strips of Arabidopsis leaves were incubated with sucrose or mannitol or no sugars, then the leaves were freeze dried and guard cells were dissected from the leaf strips and analyzed.

overall_design: RNA was extracted from guard cells dissected from leaf strips that had been treated with sucrose or with mannitol or no sugars as controls.  Triplicate biological replicates were prepared for the treatments and controls.  The RNA was amplified twice with T7 RNA polymerase and hybridized to Affymetrix ATH1 arrays.


title: Allele-specific FKBP5 DNA demethylation: a molecular mediator of gene-childhood trauma interactions

status: Public on Nov 03 2012

city: Munich

first: Divya

last: Mehta

institute: MPI

summary:
While the paradigm that genetic predisposition and environmental exposures interact to shape development and function of the human brain and ultimately the risk of psychiatric disorders has drawn wide interest, the corresponding molecular mechanisms have not been elucidated yet. Here we show that a functional polymorphism altering chromatin interaction between the transcription start site and long range enhancers in the FK506 binding protein 5 (FKBP5) gene, an important regulator of the stress hormone system, increases the risk of developing stress-related psychiatric disorders in adulthood by allele-specific, childhood trauma-dependent DNA demethylation in functional glucocorticoid response elements (GREs) of FKBP5. This demethylation is linked to increased stress-dependent gene transcription followed by a long-term dysregulation of the stress hormone system and a global impact on the function of immune cells and brain areas associated with stress regulation. This first identification of molecular mechanisms of genotype-directed long-term environmental reactivity will also critically contribute to designing more effective treatment strategies for stress-related disorders.
Effects of FKBP5 rs1360780 genotype x environment interaction on peripheral blood mRNA expression of GR responsive genes, as measured by gene expression arrays, were explored in 129 individuals (child abuse/risk allele carrier N = 40, child abuse/protective allele carrier N = 15; and no child abuse/risk allele carrier N = 60, no child abuse/protective allele carrier N = 14).

overall_design: In all 129 individuals, 1627 transcripts showed a significant correlation with plasma cortisol concentrations, suggesting their GR responsiveness. The correlation of 76 of these transcripts with cortisol plasma levels showed significant differences when stratifying by FKBP5 genotype in individuals with child abuse (Fisher z score ≥ 1.96) For these 76 transcripts, the mean absolute correlation coefficient with plasma cortisol was R = 0.23 in the risk allele carriers with child abuse, that is those exhibiting a demethylation of FKBP5 intron 7 as compared to R = 0.74 in the carriers of the protective genotype with child abuse where intron 7 methylation remains largely stable. This indicates a relative GR-resistance in the trauma exposed FKBP5 risk allele vs. protective genotype carriers. These 76 transcripts did not show a genotype-dependent difference in correlation coefficients in non-trauma exposed individuals suggesting that exposure to early trauma enhances FKBP5 genotype-dependent effect of GR sensitivity, most likely by epigenetic mechanisms. These findings suggest that the combination of FKBP5 risk allele carrier status and early trauma exposure alters the stress hormone-dependent regulation of several genes in peripheral blood cells, and might thereby enhance the reported association of early trauma with immune and inflammatory dysregulation, further promoting system-wide symptoms of stress-related disorders.

first: Torsten

last: Klengel

last: Anacker

first: Monika

last: Rex-Haffner

first: Jens

last: Pruessner

first: Carmine

middle: M

last: Pariante

first: Thaddeus

last: Pace

first: Kristina

last: Mercer

first: Helen

last: Mayberg

first: Bekh

last: Bradley

first: Charles

last: Nemeroff

first: Florian

last: Holsboer

first: Christine

last: Heim

first: Kerry

last: Ressler

first: Theo

last: Rein

first: Elisabeth

last: Binder


title: NO-deficient vs wild type Col-0 Arabidopsis seedlings

city: Valencia

first: Jose

last: Leon

address: CPI Edificio 8E, Ingeniero Fausto Elio s/n

country: Spain

institute: IBMCP (CSIC-UPV)

summary: Nitric oxide regulates plant development and responses to stress. However, the mechanisms underlying its regulatory role are still poorly known, and the impact of endogenous NO on the genome-wide transcriptome of plants has not been studied. For that purpose, we compared the transcriptomes of NO-deficient nia1nia2, noa1-2 and nia1nia2noa1-2 mutant versus wild type Arabidopsis thaliana plants. A core comprising 66 NO-responsive genes with similar expression in all NO-deficient genotypes was identified. Among them, 46 were down- and 20 up-regulated in NO-deficient plants, and thus positively and negatively regulated by endogenous NO, respectively. Accordingly with changes in its transcriptome, the NO-deficient nia1nia2noa1-2 mutant accumulated anthocyanins and indolic glucosinolates, displayed abnormal iron homeostasis in shoots and roots, and also showed altered root sensitivity to hormones such as ABA, ET, CYK and IAA. Together the presented data suggest NO functions essentially as a modulator of hormone action.

overall_design: Compared analysis of the transcriptomes of 15-day old seedlings from 3 different nitric oxide (NO)-deficient mutant genotypes versus wild type background Col-0 (3 independent biological replicates per genotype). NO-deficient mutant seedlings in Col-0 background were the double nia1nia2 mutant in nitrate reductases (NR/NIA) 1 and 2 (abbreviated as nia); the noa1-2 mutant allele in Nitric Oxide Associated 1 (AtNOA1) (abbreviated as noa); and, the triple nia1nia2noa1-2 (abreviated as nino).

first: José

last: León


title: Transcriptomics of Axillary Bud Outgrowth Regulation by Shade Signals in Arabidopsis

status: Public on Nov 21 2012

city: Loughborough

first: nasc

last: nasc

address: Sutton bonington Campus

department: Plant&Crop Sciences

institute: NASC

summary:
Aims: To determine the changes in the Arabidopsis axillary bud transcriptome in response to changes in the red light (R) to far red light (FR) ratio (R:FR).
Background: The branching habit of plants is a key determinant of overall plant form and function with great relevance to modern agriculture. Shade signals transduced by phytochromes are major regulators of axillary bud outgrowth, and in turn control branching in both natural and agricultural environments. To continue our investigations into the regulation of branching by R:FR, we have developed a system using supplemental FR LEDs to tightly control the outgrowth of Arabidopsis axillary buds. Depending on the position of the bud in the rosette, outgrowth is either repressed (uppermost bud) or rapidly promoted (bud in the axil of the third leaf down) by the transition from low to high R:FR.
Treatment: Two separate experiments were conducted to evaluate the effects of R:FR on transcriptome changes in the uppermost rosette bud (bud n) and the axillary bud in the axil of the third leaf from the top (bud n-2). WT Col-60000 was used as the experimental material. Plants were grown individually in 25 by 50 mm tubes and watered and fertilized optimally. Plants were grown in a split growth chamber (providing uniform temperature and PPFD but allowing for differential R:FR) with 18 h photoperiods (185 Moles m-2 s-1 PPFD provided by T12 VHO CW fluorescent lamps) and 24oC/18oC day/night temperatures. One day after sowing, the R:FR was reduced on both sides of the chamber from 3.5 to 0.08 using FR LEDs fixed in clear overhead arrays. Prior to anthesis, the plants were matched and split into two treatment groups. In experiment 1, the FR source for one of the groups was switched off at 12:00 pm on the day of anthesis, causing the R:FR to increase to 3.5. Unelongated axillary buds in the axil of the uppermost leaves (approx. 2.5 mm long) were harvested for RNA preparation from both groups (low and transiently increased R:FR) 3 h after changing the R:FR. Each treatment was composed of three biological replicates, each containing buds from about 15-18 plants. Experiment 2 was conducted exactly the same as experiment 1, except the R:FR was altered 3 days after anthesis and the unelongated axillary buds in the axils of the third leaves down (approx. 1 mm long) were harvested for RNA preparation.

overall_design: 12 samples (3 bud n and low R:FR, 3 bud n and high R:FR, 3 bud n-2 and low R:FR, 3 bud n-2 and high R:FR) were used in this experiment.

first: Scott

last: Finlayson


title: Dynamic regulation of miRNA and mRNA signatures during in vitro pancreatic differentiation (mRNA)

status: Public on Nov 07 2012

city: La Jolla

first: Xiaoyan

last: Liao

state: CA

address: 200 W Arbor Street

department: Reproductive Medicine

institute: University of California, San Diego

summary: The remarkable differentiation capacity of pluripotent stem cells into any adult cell types have enabled researchers to model human embryonic development and disease process in dishes, as well as deriving specialized cells for replacing damaged tissues. Type 1 diabetes is a degenerative disease characterized by autoimmune destruction of the insulin-producing beta islet cells in the pancreas. Recent advances have led to the establishment of different methods to direct differentiation of human or mouse pluripotent stem cells toward beta cell lineages. However, existing strategies have not yet succeeded in generating fully functional beta cells in vitro. Thus, it remains a major challenge to identify novel regulators of beta cell differentiation and maturation, and the islet-specific genetic and epigenetic regulatory networks are logical targets.

overall_design: To obtain a comprehensive view of the mRNA expression pattern during in vitro directed differentiation of hPSC into pancreatic beta islet cells, we collected 16 samples of 6 stages of differentiated derivatives, 2 samples of human fetal pancreas and 5 samples of purified human beta islet cells for analysis. With these samples, we performed genome-wide mRNA expression profiling using the Illumina Infinium HT-12 v4 Gene Expression BeadArray.

first: Haipeng

last: Xue

first: Yu

last: Wang

first: Kristopher

last: Nazor

first: Neha

last: Trivedi

first: Suzanne

last: Peterson

first: Ying

last: Liu

first: Jeanne

middle: F

last: Loring

first: Louise

last: Laurent


title: PU.1 is a potent tumor suppressor in classical Hodgkin lymphoma cells

first: Yutaka

last: Okuno


title: A Novel Orthotopic Mouse Model of Head and Neck Cancer and Lymph Node Metastasis

status: Public on Oct 29 2012

city: Los Angeles

first: Masood

last: Rizwan

department: Otolaryngology-Head and Neck Surgery

institute: University of Southern California

summary: Analysis of the genes involved in the metastasis of head and neck squamous cell carcinoma (HNSCC). We hypothesized that there would be overexpression of certain genes in the highly metastatic USC-HN1-GFP-G1 and USC-HN1-GFP-G2 cell lines compared to the parental USC-HN1-GFP cell line.

overall_design: We used the USC-HN1 cell line stably transfected with H2B-GFP and developed an immortal cell line (USC-HN1-GFP), which was injected into the tongues of SCID/nude mice. The metastatic cells were collected at the LN, separated and cultured, forming an immortal USC-HN1-GFP-G1 cell line. These cells were reinjected into the tongues of mice and the USC-HN1-GFP-G2 cell line was formed by the same LN collection method. The gene expression in these three cell lines were compared using Illumina microarray chips.

first: Rizwan

last: Masood


title: p53-dependent regulation of gene expression following DNA damage

status: Public on Nov 20 2012

city: Stanford

first: Adam

last: Schmitt

address: 269 Campus Drive

department: Department of Dermatology

institute: Stanford University

summary: Long noncoding RNAs (lncRNAs) are prevalent genes with frequently exquisite regulation but mostly unknown functions. Here we demonstrate a role of lncRNAs in guiding signal transduction. DNA damage activates transcription of DINO (Damage Induced NOncoding) via p53. DINO knockdown blocks DNA damage-induced gene expression and cell cycle arrest. Conversely, enforced expression of DINO activates damage signaling without DNA damage. DINO binds p53 and selectively promotes SET7 methylation of p53 at lysine 372 over other substrates, which stabilizes p53 in an auto-amplification loop. Our results suggest that inducible lncRNA can achieve catalysis-like effects to rewire cellular signaling networks.

overall_design: RNA was isolated from human fetal lung fibroblasts, HCT116 p53+/+, or HCT116 p53-/- cells  treated with doxorubicin or sham for 26 hours. Human fetal lung fibroblasts were transfected with siRNAs targeting DINO or non-targeting control and subsequently treated with doxorubicin for 26 hours.

first: Tiffany

last: Hung

first: Howard

last: Chang


title: Transcriptional analysis of whole blood in patients with auto-inflammatory disorders

status: Public on Oct 28 2012

city: Memphis

first: Zhaohui

last: Xu

state: TN

address: 262 Danny Thomas Place

department: Infectious Diseases

institute: St. Jude Children's Research Hospital

summary: HOIL1 deficient disease is a new early onset fatal autosomal recessive human disorder charaterized by chronic auto-inflammation, recurrent invasive bacterial infections and progressive muscular amylopectinosis. We studied the transcriptional profiles of whole blood from one HOIL dificient patient and other auto-inflammatory patients, including CINCA, Muckle-Wells syndrome and MVK deficiency.

overall_design: Whole blood was collected in Tempus tubes from 41 healthy children and patients with CINCA (2), MWS (5),  MVK deficiency (2) and  HOIL deficiency (1) diseases. RNA was extracted and globin reduced. Labeled cRNA was hybridized to Illumina Human HT-12 Beadchips.


title: Transcriptome analysis in peripheral blood mononuclear cells (PBMC) from HOIL-1-deficient patients upon TNF-α or IL-1β stimulation

summary: HOIL-1 deficient disease is a new early onset fatal autosomal recessive human disorder charaterized by chronic auto-inflammation, recurrent invasive bacterial infections and progressive muscular amylopectinosis. We studied the effect of TNF-α and IL-1β on transcriptional changes of PBMCs from HOIL-1- and MYD88-deficient patients.

overall_design: PBMCs were obtained from HOIL-1 and MYD88-deficient patients and healthy donors and stimulated with TNF-α or IL-1β for 2 and 6 hours. RNA were extracted. Labeled cRNA were hybridized to Illumina Human HT-12 V4 Beadchips.


title: Gene expression analysis after selective expression of tissue factor isoforms

status: Public on Oct 27 2012

first: Henri

middle: H

last: Versteeg

address: Albinusdreef 2

department: Einthoven Lab for Experimental Vascular Medicine

institute: Leiden University Medical Center

summary: Analysis of TF isoform-induced breast cancer cell transformation at gene expression level. The hypothesis tested in the present study was that expression of TF isoforms upregulate genes involved in proliferation and transformation, while downregulating genes involved in cell cycle arrest and apoptosis. Results provide important information on the cellular response to TF expression with respect to pro-oncogenic programs .

overall_design: Total RNA obtained from an MCF-7-based cell model (2A3-3) expressing full length tissue factor (2A3-3-flTF) or alternatvively spliced tissue factor (2A3-3-asTF) compared to cells expressing an empty vector control (2A3-3-pcDNA).

first: Begüm

last: Kocatürk


title: Transcriptome analysis  in primary fibroblasts from HOIL-1-deficient patients upon TNF-α or IL-1β stimulation

summary: HOIL-1 deficient disease is a new early onset fatal autosomal recessive human disorder charaterized by chronic auto-inflammation, recurrent invasive bacterial infections and progressive muscular amylopectinosis. We studied the effect of TNF-α  and IL-1β on transcriptional changes of primary fibroblasts from HOIL-1-, MYD88- and NEMO-deficient patients.

overall_design: Primary fibroblasts were obtained from HOIL-1, MYD88- and NEMO-deficient patients and healthy donors and stimulated with TNF-α  or IL-1β for 2 and 6 hours. RNA were extracted and globin reduced. Labeled cRNA were hybridized to Illumina Human HT-12 Beadchips.


title: Transcriptional analysis of whole blood, primary fibroblasts, and PBMCs upon TNF-alpha or IL-1beta stimulation from HOIL-1-deficient patients


title: Induced pluripotent stem cell models of progranulin-deficient frontotemporal dementia uncover specific reversible neuronal defects.

status: Public on Oct 25 2012

first: Giovanni

last: Coppola

address: 1524 Gonda, 695 Charles Young Drive South

department: Psychiatry and Neurology

institute: UCLA

summary:
Multiple FTD patient-specific iPSC lines were generated for the first time, Human neurons of progranulin haploinsufficiency have been established.
PGRN S116X neurons are more sensitive to kinase inhibitors-induced cell stress, which can be rescued by ectopic progranulin expression, revealing progranulin-dependent cellular defects in FTD. Microarray analysis reveals that the serine/threonine kinase S6K2 (RPS6KB2) and other genes involved in MAPK signaling are dysregulated specifically in neurons with progranulin deficiency.

overall_design: 32 independent human neuronal cultures were analyzed in this study

first: Sandra

last: Almeida

first: Zhijun

last: Zhang

first: Wenjie

last: Mao

first: Kensuke

last: Futai

first: Anna

last: Karydas

first: Michael

last: Geschwind

first: M

last: Tartaglia

first: Fuying

last: Gao

first: Davide

last: Gianni

first: Miguel

last: Sena-Esteves

first: Daniel

first: Bruce

last: Miller

first: Robert

middle: V

last: Farese Jr

first: Fen-Biao


title: Response prediction to neoadjuvant chemotherapy

status: Public on Oct 26 2012

city: Vienna

first: Florian

middle: Leopold

last: Klinglmueller

address: Spitalgasse 23

department: Medizinische Statistik und Informatik

country: Austria

institute: Medizinische Universitaet Wien

summary: We investigated whether we could identify gene expression profiles in initial core biopsies of breast cancer samples that would permit to a) predict a clinically meaningful response to Epi/Doc in terms of tumor size reduction, b) predict a profound reduction in intratumoral Ki67 protein expression, and c) predict an in vitro response to Epi/Doc in the ATP-TCA.

overall_design: 22 Samples from breast cancer patients with corresponding treatment response indicators

first: Christian

last: Singer

first: Martin

last: Bilban


title: Microarray analysis of human monocytic THP-1 cell treated with 1α,25-dihydroxyvitamin D3 or Trichostatin A and the combination of both

city: Kuopio

first: Sami

last: Heikkinen

address: Yliopistonranta 1E

department: Institute of Biomedicine

country: Finland

institute: University of Eastern Finland

summary: The nuclear hormone 1α,25-dihydroxyvitamin D3 (1α,25(OH)2D3) regulates its target genes via activation of the transcription factor vitamin D receptor (VDR) far more specifically than the chromatin modifier trichostatin A (TsA) via its inhibitory action on histone deacetylases. We selected the thrombomodulin gene locus with its complex pattern of three 1α,25(OH)2D3 target genes, five VDR binding sites and multiple histone acetylation and open chromatin regions as an example to investigate together with a number of reference genes, the primary transcriptional responses to 1α,25(OH)2D3 and TsA. Transcriptome-wide, 18.4% of all expressed genes are either up- or down-regulated already after a 90 min TsA treatment; their response pattern to 1α,25(OH)2D3 and TsA sorts them into at least six classes. TsA stimulates a far higher number of genes than 1α,25(OH)2D3 and dominates the outcome of combined treatments. However, 200 TsA target genes can be modulated by 1α,25(OH)2D3 and more than 1000 genes respond only when treated with both compounds. The genomic view on the genes suggests that the degree of acetylation at transcription start sites and VDR binding regions may determine the effect of TsA on mRNA expression and its interference with 1α,25(OH)2D3. Our findings may have implications on dual therapies using chromatin modifiers and nuclear receptor ligands.

overall_design: All conditions are performed in triplicate: one time point with TsA treatment and vehicle control and one time point with TsA, 1α,25-dihydroxyvitamin D3, the combination of both and vehicle

first: Sabine

last: Seuter

first: Carsten

last: Carlberg


title: Genome-wide comparison of trisomy 21 iPSCs and derived isogenic disomy 21 iPSCs.

status: Public on Oct 23 2012

city: Seattle

first: LI

last: LI

state: WA

address: 1905 NE pacific st

institute: University of Washington

summary: Human trisomies can alter cellular phenotypes and produce congenital abnormalities such as Down Syndrome (DS).  Here we have generated induced pluripotent stem cells (iPSCs) from DS fibroblasts, and introduced a TKNEO transgene into one copy of chromosome 21 by gene targeting.  When selecting against TKNEO, spontaneous chromosome loss was the most common cause for survival, with a frequency of ~10-4, while point mutations, epigenetic silencing, and TKNEO deletions occurred at lower frequencies in this unbiased comparison of inactivating mutations.  Mitotic recombination events resulting in extended loss of heterozygosity were not observed in DS iPSCs.  The disomic cells that we derived proliferated faster and produced more endothelia in vivo than their otherwise isogenic trisomic counterparts, but hematopoietic differentiation, pluripotency and survival were statistically unchanged.  Our study describes the first targeted removal of a human trisomy, which could prove useful in both clinical and research applications.

overall_design: RNA samples were from  two trisomic iPSC clone (C2-4, C3-5) and four derived disomic subclones (C2-4-3, C2-4-4 and C3-5-11, C3-5-13). Duplicate RNA samples from human embyonic stem cells (H1) were included as control.

first: Li

last: Li

first: Kai-Hsin

last: Chang

first: Pei-Rong

last: Wang

first: Roli

middle: K

last: Hirata

first: Thalia

last: Papayannopoulou

first: David

middle: W

last: Russell


title: The blood transcriptional signature of chronic HCV

status: Public on Oct 22 2012

city: New Haven

first: Christopher

last: Bolen

state: CT

address: 300 George Street, Suite 505

department: Pathology

institute: Yale University

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

overall_design: Refer to individual Series


title: The blood transcriptional signature of chronic HCV [Illumina data]

summary:
This study characterizes the effects of chronic Hepatitis C virus (HCV) infection on gene expression by analyzing blood samples from 10 treatment-naive HCV patients and 6 healthy volunteers.
Differential expression analysis of microarray data from peripheral blood mononuclear cells (PBMCs) identified a 136 gene signature, including 66 genes elevated in infected individuals. Most of the up-regulated genes were associated with interferon (IFN) activity (including members of the OAS and MX families, ISG15 and IRF7), suggesting an ongoing immune response. This HCV signature was also found to be consistently enriched in many other viral infection and vaccination datasets. Validation of these genes was carried out using a second cohort composed of 5 HCV patients and 5 healthy volunteers, confirming the up-regulation of the IFN signature. In summary, this is the first study to directly compare blood transcriptional profiles from HCV patients with healthy controls. The results show that chronic HCV infection has a pronounced effect on gene expression in PBMCs of infected individuals, and significantly elevates the expression of a subset of interferon-stimulated genes.

overall_design: Treatment-naïve HCV patients were recruited by hepatologists in the outpatient hepatitis clinic within the Yale Liver Center. Healthy volunteers were recruited from Yale’s PhenoGenetic Cohort of Healthy controls. PBMCs were isolated from whole blood by density gradient centrifugation using Ficoll-Paque (GE Healthcare) centrifugation. Total RNA was isolated from PBMCs using an RNeasy kit (Qiagen, Valencia, CA), and the quality of total RNA was evaluated by A260/A280 ratio and by electrophoresis on an Agilent Bioanalyzer.  All subsequent processing, hybridization to the Illumina HumanHT-12 microarray, and quality control analyses were carried out by the Yale Center for Genome Analysis using standard protocols.

middle: R

first: Michael

last: Robek

first: Leonid

last: Brodsky

first: Vincent

last: Schulz

first: Joseph

last: Lim

first: Milton

last: Taylor

first: Steven

last: Kleinstein


title: Gene expression in a three-dimensionally cultivated human hepatocellular carcinoma (HCC) model

city: Ilmenau

first: Uta

last: Fernekorn

department: Nano-Biosystem Technology

institute: Ilmenau Technical University

summary: The development of more complex but reliable systems for compound testing in a pharmaceutical context is a challenging task to date. Three-dimensional (3D), organ mimetic cell culture is aiming to become an alternative to common two-dimensional (2D) cell culture or animal testing in that field. We developed a biocompatible 3D cell culture environment for a hepatocellular carcinoma (HCC) model that enables cellular maintenance in a polycarbonate scaffold structure. Albumin, regarded as a differentiation marker, was elevated in statically 3D cultivated HepG2 cells. Expression of HCC tumor marker alpha-fetoprotein (AFP) was reduced compared to immunofluorescence stainings of 2D cultivated cells. Remarkably, expression of cytokeratin and pathophysiologically relevant beta-1 integrin (ITGB1) was found enhanced in nonperfused 3D cell culture. Changes in gene expression induced by the 3D cultivation environment were investigated using Ingenuity Pathway Analysis (IPA). Our findings revealed involvement of the insulin growth factor (IGF) signaling pathway in upregulation of matrix metalloproteinases (MMP) and ITGB1. The experimental data indicate a more differentiated state in 3D cultivated HepG2 cells than in the respective 2D experiments. Hence, scaffold-supported 3D cultivation of HepG2 cells may lead to a gain of information valuable for both drug testing and cancer research.

overall_design: HepG2 cells were cultivated for five days under 2D and 3D statical and perfused conditions. Cultivation was started with 0.25x10^6 cells in 2D and with 1x10^6 vital cells for the 3D experiments. The day of seeding was defined as d0. The groups were classified as follows: 2D, i.e., monolayer cultures, 3D, i.e., statical 3D cultures and BR, which denotes perfused 3D culture of HepG2 cells. The perfusable bioreactor system was operated using a peristaltic pump. It houses the MatriGrid, a polycarbonate-based microporous cellular support. For 3D static cultivation, cell-inoculated MatriGrids were placed in wells of a 24-well plate. Microarray experiments of three 2D (i.e., control), three 3D statically and three actively perfused 3D cultivations were performed at SIRS-Lab GmbH (SIRS-Lab GmbH, Jena, Germany) according to the manufacturer's instructions (Illumina, San Diego, CA). Altogether, 9 RNA samples of hepatocyte cultures and an internal control RNA were hybridized on two HumanHT-12 v4 Expression BeadChips.

first: Jörg

last: Hampl

first: Caroline

last: Augspurger

first: Christian

last: Hildmann

first: Frank

last: Weise

first: Maren

last: Klett

first: Annette

last: Läffert

first: Karin

last: Friedel

last: Gebinoga

first: Andreas

last: Schober


title: The blood transcriptional signature of chronic HCV [Affymetrix data]

last: Bolen

overall_design: Whole blood was collected from a group of 10 patients who were infected with genotype 1 hepatitis C, before initiation of treatment at the Indiana University School of Medicine. Control blood samples were harvested from healthy student volunteers. Peripheral blood mononuclear cells (PBMCs) were isolated from the whole blood samples of the cohort using centrifugation through a 10-ml Ficoll-Hypaque gradient (Amersham/Pharmacia, Piscataway, NJ), and RNA was isolated within a few hours. RNA was then processed according to the protocols recommended by Affymetrix (Santa Clara, CA), and run on an Affymextrix Human Genome U133 array.

middle: D


title: Modeling Human Cortical Development in vitro using induced Pluripotent Stem Cells

status: Public on Oct 19 2012

first: Flora

last: Vaccarino

address: 230 South Frontage Road

department: Child Study Center

summary: Human iPSCs grown in suspension in the presence of rostral neuralizing factors generated three-dimensional structures containing polarized radial glia, intermediate progenitors and a spectrum of layer-specific cortical neurons reminiscent of their organization in vivo. The hiPSC-derived multilayered structures express a gene expression profile typical of the embryonic telencephalon, but not that of other CNS regions.

overall_design: Total RNA obtained from iPSC lines and H1 line was submitted for microarray analysis using HumanHT-12 v4 BEADCHIP (Illumina).

first: Jessica

last: Mariani


title: Siomycin A treatment in prostate cancer cell lines PC3 and LNCaP

city: Heidelberg

first: Ruprecht

last: Kuner

address: Im Neuenheimer Feld 460

department: Molecular Genetics

institute: German Cancer Research Center and National Center of Tumor Diseases

summary: Siomycin A treatment in prostate cancer cell lines resulted in a concurrent inhibition of specific cell cycle genes and strongly impaired cell viability.

overall_design: Illumina microarray experiments were done using PC3 and LNCaP cell lines treated with 0.5 microM Siomaycin A either 24h or 48h in triplicates.

first: Holger

last: Sültmann

first: Maria

last: Fälth


title: Somatic copy-number mosaicism in human skin revealed by induced pluripotent stem cells

summary: Reprogramming human somatic cells into induced pluripotent stem cells (iPSC) has been suspected of causing de novo copy number variations (CNVs). To explore this issue, we performed a whole-genome and transcriptome analysis of 20 human iPSC lines derived from primary skin fibroblasts of 7 individuals using next-generation sequencing. Prior to this CNV study, the human iPSC lines and one hES (H1) were characterized by a set of quality control criteria, including gene expression analyses by microarray.  This analysis demonstrated uniform up-regulation of hESC-specific genes in all our hiPSC lines, while fibroblast specific genes were downregulated

first: Alexej

last: Abyzov


title: MELK and UBE2C gene knockdown in prostate cancer cell line PC3

summary: In order to address the putative role of MELK and UBE2C in prostate cancer development and progression, we performed functional analysis upon siRNA-based knockdown, and searched for downstream genes and processes by microarray experiments. RNAi-based inhibition of MELK and UBE2C was efficient in PC3 prostate cancer cells and decreased transcriptional level down to about 30% remaining expression level.

overall_design: Illumina microarray experiments were done upon siRNA based knockdown 48h after transfection of PC3 cells in triplicates.

first: Nicole

last: Chui-Pressinotti

first: Helmut

last: Klocker


title: In vitro generation of long-lived human Plasma Cells

status: Public on Oct 18 2012

city: York

first: Matthew

middle: Anthony

last: Care

state: North Yorkshire

address: Wentworth Way

department: Department of Biology

institute: The University of York

summary: Gene expression profiling of B-cells from a model differentiation series: from Naïve B-cells, through a proliferative plasmablast stage to long-lived antibody secreting plasma cells.

overall_design: B-cells were isolated from the peripheral blood of three adult donors and differentiated in vitro (see individual samples for culture conditions)

middle: A

first: Mario

last: Cocco


title: Gene signatures in prostate cancer linked to the Gleason score

summary: The identification of novel oncogenic and druggable targets in patient subgroups with poor prognosis may help to develop corresponding targeted therapy approaches. Microarray data analyses of 59 prostate cancer and 39 benign tissue samples revealed major transcriptional differences. More than 5.000 genes were identified to be differentially expressed between matched tumor and benign samples. In the prostate cancer samples we identified 144 differentially expressed associated with Gleason pattern.

overall_design: Illumina microarray experiments were done from of 59 prostate cancer and 39 matched benign tissue samples. We analyzed for differentially expressed genes between tumor and benign tissues, and between tumors with  higher Gleason patter (4+3 and higher) against lower Gleason patter (3+4 and lower).


title: Expression data from IRE1a or XBP1 deficient mouse liver

status: Public on Oct 17 2012

city: Boston

first: Ann-Hwee

last: Lee

state: MA

address: 651 Huntington Ave, FXB/205

institute: Harvard School of public health

summary: IRE1a and XBP1 are key regulators of the unfolded protein response (UPR). XBP1 ablation causes profound hypolipidemia in mice, and triggers feedback activation of its upstream enzyme IRE1a, instigating regulated IRE1-dependent decay (RIDD), an mRNA degradation mechanism dependent on IRE1a's endoribonuclease activity. Comprehensive microarray analysis of XBP1 and/or IRE1a deficient liver identified genes involved in lipogenesis and lipoprotein metabolism as RIDD substrates, which might contribute to the suppression of plasma lipid levels by activated IRE1a.

overall_design: To identify RIDD substrate mRNAs and direct XBP1 targets in the liver, we performed a comprehensive comparative microarray analysis of three groups of RNA samples: WT and XBP1 deficient mice, WT and IRE1a deficient mice untreated or injected with tunicamycin, and XBP1 deficient mice injected with luciferase or IRE1a siRNA.

first: Jae-Seon

last: So

first: Kevin

last: Fitzgerald

first: Takao

last: Iwawaki

first: Laurie

last: Glimcher


title: Genome-wide analysis of the SNAPc complex [Illumina array]

status: Public on Oct 12 2012

city: Miami

first: Alessandro

last: Gardini

address: 1501 NW 10 Avenue

department: Sylvester Comprehensive Cancer Center

institute: University of Miami

summary: The small nuclear RNA (snRNA)-activating protein complex (SNAPc) is a basal transcription factor that mediates the transcriptional activation of snRNAs. Here, we describe the genome-wide occupancy of the SNAPC1_and SNAPC4 subunits of SNAPc. While the SNAPC4 occupancy was in accord with the role for SNAPc in snRNA transcription, SNAPC1_displayed a broader genomic profile mirroring that of RNA polymerase II at highly active protein-coding genes. Our functional analysis revealed a role for SNAPC1_in regulation of both basal and activator-induced transcription of protein-coding genes. These studies expand the role for SNAPC1_beyond its regulation of snRNA transcription.

overall_design: EGF stimulation of Hela cells, transfected with a control sh (scr) or a SNAPC1_sh

first: Ramin

last: Shiekhattar


title: Defective ribosomal protein gene expression alters transcription, translation, apoptosis, and oncogenic pathways in Diamond-Blackfan anemia.

status: Public on Oct 16 2012

first: Alvin

middle: T.

last: Kho

address: 320 Longwood Avenue

department: Informatics Program

institute: Boston Children's Hospital

summary: Transcriptome profile of highly purified multipotential (P), erythroid (E), and myeloid (M) bone marrow progenitors from three RPS19 mutated Diamond-Blackfan anemia and six control human subjects.

overall_design:
Two group comparison of sex and age matched subjects.
Bone marrow progenitors, gene expression profiling, Diamond-Blackfan anemia, RPS19

middle: T

first: Hanna

last: Gazda


title: Deep sequencing of gastric carcinoma reveals somatic mutations relevant to personalized medicine [Illumina mRNA expression array data]

city: Singapore

first: Joanna

middle: Dawn

last: Holbrook

address: 30 Medical Drive

country: Singapore

institute: Singapore Institute of Clinical Sciences

summary:
Background: Globally, gastric cancer is the second most common cause of cancer-related death, with the majority of the health burden borne by economically less-developed countries.
Methods: Here, we report a genetic characterization of 50 gastric adenocarcinoma samples, using affymetrix SNP arrays and Illumina mRNA expression arrays as well as Illumina sequencing of the coding regions of 384 genes belonging to various pathways known to be altered in other cancers.
Results: Genetic alterations were observed in the WNT, Hedgehog, cell cycle, DNA damage and epithelial-to-mesenchymal-transition pathways.
Conclusions: The data suggests targeted therapies approved or in clinical development for gastric carcinoma would be of benefit to ~22% of the patients studied. In addition, the novel mutations detected here, are likely to influence clinical response and suggest new targets for drug discovery.

overall_design: DNA and RNA samples were obtained from hospitals in Russia and Vietnam according to IRB approved Protocols and with IRB approved consent forms from which informed consents were given for molecular and genetic analysis. The medical centres themselves also have internal ethical committees with reviewed the protocol and ICFs. The samples were sourced through Tissue Solutions Ltd (http://www.tissue-solutions.com/). Gene expression profiles were generated using Illumina mRNA expression arrays.


title: Defining precision probes which differentiate between the activity of type I and type II interferons.

status: Public on Oct 08 2012

city: Baltimore

first: John

last: Hall

address: 5200 Eastern Ave, MFL Center Twr STE 5300

department: Medicine

institute: Johns Hopkins School of Medicine

summary:
To define probes which differentiate between the activity of type I or type II IFN, a human submandibular gland (HSG) cell line was cultured for 48 hours in the absence or presence of IFNa or
IFNg. Gene expression was assayed at 4, 12, 24 or 48 hours and was compared to gene expression in untreated cells at each time point to define genes which are induced by type I or type
II IFN.

overall_design:
HSG cells were cultured for 2 days in the absence or presence of IFNa [1000U/ml] or IFNg [50ng/ml], and total RNA was isolated at 4, 12, 24, and 48 hours of culture.
Details are in the Analytical Methods section of the manuscript: John C. Hall, Livia Casciola-Rosen, Alan E. Berger, Efstathia Kapsogeorgou, Chris Cheadle,
Athanasios G. Tzioufas, Alan N. Baer, Antony Rosen,Precise probes of type II interferon activity define the origin of interferon signatures in
target tissues in rheumatic diseases accepted for publication in PNAS (this GEO dataset will be released immediately upon electronic publication).

middle: C

first: Livia

last: Casciola-Rosen

first: Alan

middle: E

last: Berger

first: Efstathia

last: Kapsogeorgou

first: Chris

last: Cheadle

first: Athanasios

middle: G

last: Tzioufas

middle: N

last: Baer

first: Antony

last: Rosen


title: H1N1 influenza A/New Caledonia/20/1999 time series in monocyte-derived dendritic cells

status: Public on Oct 01 2012

first: Juilee

last: Thakar

address: 300 George street

institute: Yale medical school

summary: Genome-wide gene expression patterns were measured in human monocyte-derived dendritic cells (DCs)  infected in vitro with seasonal H1N1 influenza A/New Caledonia/20/1999. To provide a mechanistic  explanation for the timing of gene expression changes over the first 12 hours post-infection, we developed a  statistically rigorous enrichment approach integrating genome-wide expression kinetics and time-dependent  promoter analysis. Our approach, TI me-Dependent Activity Linker (TIDAL), generates a regulatory network  that connects transcription factors associated with each temporal phase of the response into a coherent linked  cascade. TIDAL infers 12 transcription factors and 32 regulatory connections that drive the antiviral response to  influenza. To demonstrate the generality of this approach, TIDAL was also used to generate a network for the  DC response to measles infection.

overall_design: Monocyte-derived DCs were obtained from healthy human blood donors following a standard protocol. The recent seasonal H1N1 influenza virus A/New  Caledonia/20/1999 (NC) virus was titrated by immunofluorescence 18 hours after infection of MDCK cell plates using monoclonal antibodies specific for Influenza-NP protein generated by the Mount Sinai Hybridoma Core Facility followed by addition of anti-mouse IgG-FITC and  visualization using fluorescent microscopy. For infection of naive DCs, NC stocks were appropriately  diluted in Dulbecco’s Modified Eagle Medium (DMEM) and added directly into pelleted DCs at a  multiplicity of infection (MOI) of 1 After incubation for 40 minutes at 37 ◦C, fresh DC growth  medium (without GMCSF and IL-4) was added back to the infected cells (1 106 cells/ml) for the  remainder of the infection. The reaction was stopped at 1, 2, 4, 6, 8, 10, and 12 hours after infection by  fixing the cells with RNAprotect Cell Reagent (Qiagen, Duesseldorf Germany). Naive non-infected DCs  underwent the same experimental procedure as infected DCs in the absence of virus to ensure that  mechanical manipulations could not be responsible for differences in experimental readouts. All time  points and controls were performed in triplicates. Cells were homogenized by using QIAshredder microcentrifuge spin-columns (Qiagen,  Duesseldorf Germany) and RNA was isolated from cells using Qiagen Micro RNeasy plus kit following the  manufactures protocol (Qiagen, Duesseldorf Germany). RNA quality was assayed by determination of the  RNA integrity number using the 2100 Bioanalyzer (Agilent). RNA samples were processed and hybridized to HumanHT-12 v4 Expression  BeadChip Kit (Illumina San Diego, CA) by the Mount Sinai Genomics Institute following the  manufacturer’s instructions, and raw expression data were output by the Illumina GenomeStudio software.

first: Elena

last: Zaslavsky

first: German

last: Nudelman

first: Susanna

last: Marquez

first: Uri

last: Hershberg

first: Boris

middle: M

last: Hartmann

first: Stuart

last: Sealfon

first: Steven

last: Kleinstein


title: Molecular profiling of primary lung carcinomas

status: Public on Oct 09 2012

city: Lund

first: Johan

last: Staaf

address: Medicon Village

country: Sweden

institute: SCIBLU - Swegene Centre for Integrative Biology at Lund University

type: Genome variation profiling by genome tiling array

first: Göran

last: Jönsson

first: Mats

first: Anna

last: Karlsson

first: Sofi

last: Isaksson

first: Annette

last: Salomonsson

first: Helen

last: Pettersson

first: Maria

last: Soller

first: Sven-Börje

last: Ewers

first: Leif

last: Johansson

first: Per

last: Planck


title: Effects of PD-0332991 on gene expression of human pancreatic ductal adenocarcinoma (PDAC) cell lines

status: Public on Oct 10 2012

city: Indianapolis

first: Fang

last: Liu

state: IN

address: Walnut street

department: Endocrinology

institute: Indiana University

summary: PD-0332991 is a small molecule inhibitor for Cdk4 and Cdk6. It exerted growth inhibitory effects on PDAC cell lines (AsPC-1 and COLO-357). Microarray analysis was used to characterize the changes in gene expression profiles of AsPC-1 and COLO-357 upon PD-0332991 incubation

overall_design: AsPC-1 and COLO-357 cells were treated in the absence or presence of 5 µM PD-0332991 for 24 h and 72 h. Each expreimental condition had biological triplicates. Twenty-four samples were analyzed in total.

first: Murray

last: Korc


title: The contribution of RNA decay quantitative trait loci to inter-individual variation in steady-state gene expression levels

city: Chicago

first: Athma

last: Pai

state: IL

address: 920 E. 58th Street

institute: University of Chicago

summary: Analysis of the extent to which inter-individual variation in mRNA decay contributes to inter-individual variation in gene expression levels in humans. The study examines properties of genome-wide decay rates and the relationship between mRNA decay and gene expression across genes, across individuals, and finally across genotype classes.

overall_design: 70 human lymphoblastoid cell lines were treated with Actinomycin D to arrest transcription. Transcript abundance was measured at 5 timepoints: before transcription (0 hours) and after  transcription (0.5 hours, 1 hour, 2 hours, and 4 hours). Data was then used to estimate gene-specific decay rates genome-wide.

first: Carolyn

last: Cain

first: Orna

last: Mizrahi-Main

first: Sherryl

last: De Leon

first: Noah

last: Lewellen

first: Jean-Baptiste

last: Veyrieras

first: Jacob

middle: F

last: Degner

first: Daniel

middle: J

last: Gaffney

first: Joseph

last: Pickrell

first: Matthew

last: Stephens

first: Jonathan

last: Pritchard

first: Yoav

last: Gilad


title: Transcriptome wide analysis of  untreated, classically  and alternatively activated macrophages

city: Bonn

first: Andrea

last: Nino Castro

address: Carl Troll str. 31

institute: Life and Medical Sciences institute

summary: Analysis  of human M0-, M1-, and M2-like macrophages.

overall_design: Total RNA was isolated from untreated, classically and aternative activated human macrophages

first: Michael

last: Mallmann

first: Marc

last: Beyer

first: Joachim

middle: L

last: Schultze


title: Elucidating the gene expression profiles of human mammary subpopulations

status: Public on Oct 11 2012

city: Cambridge

first: Roslin

last: Russell

address: Robinson Way

institute: Cambridge Research Institute, Cancer Research UK

summary: The organisation of the mammary epithelial cell hierarchy and how these cells relate to the presentation of human breast tumours is poorly understood. Our results demonstrate that the luminal cell compartment of the mouse mammary gland can be resolved into terminally differentiated oestrogen receptor (ER)+ luminal cells, ER+ luminal progenitors and ER- luminal progenitors. The ER+ luminal progenitors are unique in regards to cell survival, as they are relatively insensitive to loss of oestrogen and progesterone when compared to the other types of mammary epithelial cells. Analysis of normal human breast tissue reveals a similar hierarchical organisation that is composed of terminally differentiated luminal cells and relatively differentiated (EpCAM+CD49f+ALDH-) and undifferentiated (EpCAM+CD49f+ALDH+) luminal progenitors. In addition, approximately one third of human breast samples examined contained an additional population that had a luminal progenitor phenotype, but is characterised by low expression of ERBB3 and low proliferative potential. Parent-progeny relationship experiments demonstrated that all luminal progenitor populations in both species are highly plastic and, at low frequencies, can generate progeny representing all mammary cell types. Gene expression profiling demonstrates that the ER- luminal progenitors in the mouse and the undifferentiated ALDH+ luminal progenitors in the human have gene signatures that resemble those obtained from basal-like breast tumours. Overall, our work reveals a more defined mammary cell hierarchy, which may in turn provide greater insight into the aetiology of breast cancer.

overall_design: Normal human breast tissues from reduction mammoplasties were dissociated into single cells and the epithelial cell populations were flow sorted. Total RNA was extracted for each group in 11 independent patient samples.

first: Mona

last: Shehata

first: John

last: Stingl


title: Suberoylanilide hydroxamic acid (SAHA) induces limited changes in the transcriptome of primary CD4+ T cells

city: La Jolla

first: Nadejda

middle: S.

last: Beliakova-Bethell

address: 9500 Gilman Dr.

institute: University of California, San Diego

summary: This study evaluated primary CD4+ T cell gene expression treated with pharmacologically achievable concentration (340 nM) of SAHA for 24 hours in order to evaluate potential side effects of this compound in cells relevant to HIV infection.

overall_design: Analysis of human primary CD4+ T cells taken from 9 healthy donors treated with 340 nM of SAHA for 24 hours. Results identify genes modulated by SAHA treatment in human primary CD4+ T cells.

first: Christopher

last: Woelk


title: Indentification of special gene expressions in synovial tissues of rheumatoid arthritis

city: Jinan

first: Xiaotian

last: Chang

address: Jingshi road 18877

country: China

institute: Shandong Acedemy of medicinal sciences

summary: Gene expression microarray was applied to discover novel rheumatoid arthritis (RA)-specific gene expressions by comparing the expression profiles of synovial membranes from patients with RA, osteoarthritis (OA) and ankylosing spondylitis (AS). We performed a gene expression microarray analysis of RA synovial membranes and simultaneously compared the expression profile with the profiles of AS and OA synovial membranes.

overall_design: This study was undertaken to investigate the global gene expression profiles in synovial tissues from RA (n=10), OA (n=7), and AS patients (n=5). The Illumina HumanHT-12 v4 Expression BeadChip were used for a complete genome-wide transcript profiling.


title: Expression data from Arabidopsis roots and shoots grown with or without iron

status: Public on Sep 30 2012

city: Hanover

first: Alicia

last: Sivitz

state: NH

address: 78 College St

institute: Dartmouth College

summary: Iron-deficiency repsonses in Arabidopsis are controlled by several bHLH transcription factors.  FIT, for example has been shown to direct iron-uptake responses.  However, the role of shoot and root expressed genes bHLH100 and bHLH101 has not be clarified.  We used microarray to study what genes might be miss-regulated in the double mutant bhlh100/bhlh101 background

overall_design: 10-day-old Arabidopsis plants were divided into root and shoot tissues and harvested for RNA extraction.

middle: B

first: Catherine

last: Curie

first: Gergory

last: Vert


title: Rosette iron deficiency transcript profiling in Arabidopsis thaliana ecotypes Kas-1 and Tsu-1

city: Columbia

first: Samuel

middle: Alonzo

last: McInturf

state: Missouri

address: 1201 Rollins Street

department: Plant Sciences

institute: University of Missouri - Columbia

summary: Iron (Fe) is an essential plant micronutrient, and its deficiency limits plant growth and development on alkaline soils.  Under Fe deficiency, plant responses include upregulation of genes involved in Fe uptake from the soil.  However, little is known about shoot responses to Fe deficiency.  Using microarrays to probe gene expression in Kas-1 and Tsu-1 ecotypes of Arabidopsis thaliana revealed conserved rosette gene expression responses to Fe deficiency. Fe regulated genes included known metal homeostasis-related genes, and a number of genes of unknown function.

overall_design: Kas and Tsu Arabidopsis seedlings were grown on complete media for 24 d, and then put on complete or -Fe media and collected after 24 and 48 h.

first: Brian

last: Waters

first: Ricardo

last: Stein


title: Liposome transfection of miR-145 induces immune response via RIG-I in mesenchymal stem cells

city: Oslo

first: Tommy

middle: Aleksander

last: Karlsen

address: Sognsvannsveien

department: Norwegian center for stem cell research

country: Norway

institute: Oslo University Hospital, Rikshospitalet

summary: Liposomal transfection reagents are frequenly used in gene deliverytransfer experiments. The validity of these experiments depends on the absence of changes in genes other than the target gene. Here we report that transfection of synthetic microRNA-145 using liposomes, but not electroporation, induced the upregulation of a range of immune-related genes in human mesenchymal stem cells. The immune response was dependent on the binding of microRNA-145 to retinoic acid inducible gene-I, and was independent on endosome functionality and toll-like receptors. Immune response was not observed after transfection of any of nine other small RNAs, suggesting a sequence restricted response. One of the upregulated mRNAs encode interferon β, which presumably in turn induced the upregulation of another group of immune associated genes. Interestingly, exposure of liposomes alone led to the upregulation of some immune genes, one of them retinoic acid inducible gene-I mRNA.

overall_design: Comparison of immune gene expression patterns in BM-MSC donors after transfection of synthetic miR-145.

first: Jan

last: Brinchmann


title: Transcriptome Profiling of Roots and leaves Under High Osmotic Stress in Arabidopsis

status: Public on Sep 19 2012

city: No.12 Zhongguancun South Street, Haidian

first: Jun

last: Liu

state: Beijing

address: 1230 York Avenue

department: Chinese Academy of Agricultural Sciences

institute: Institute of Crop Science

summary: The functions of miRNAs and their target mRNAs in Arabidopsis development have been widely documented, however, roles of stress responsive miRNAs and their targets are not as well understood. Using small RNA deep sequencing and ATH1 microarrays to profile mRNAs, we identified IAR3 (IAA-Ala Resistant 3) as a novel target of miR167a.

overall_design:
2 organs X 3 treatments X 3 replicates

This submission represnts ATH1 microarrays component of study.

first: Natsuko

last: Kinoshita

first: Huan

last: Wang

first: Hiroyuki

last: Kasahara

first: Cameron

last: MacPherson

first: Yasunori

last: Machida

first: Yuji

last: Kamiya

first: Matthew

last: Hannahm

first: Nam-Hai

last: Chua


title: Detectable changes in the blood transcriptome are present after two weeks of antituberculosis therapy

city: London

first: Chloe

last: Bloom

address: The Ridgeway

institute: MRC National Institute for Medical Research

summary:
Analysis of UK blood transcriptional profiles before treatment to indentify changes that occur during (2 weeks, 2 months), at the end of treatment (6 months) and after treatment (12 months)
Analysis of South African blood transcriptional profiles before treatment to indentify changes that occur during (2 weeks, 2 months), at the end of treatment (6 months) and after treatment (12 months)

overall_design: Total RNA obtained from active TB patients before, during and after treatment

first: Anne

last: O'Garra


title: Conversion of human fibroblasts into vascular cells (gene expression)

status: Public on Sep 18 2012

first: Rathi

middle: D

last: Thiagarajan

address: 2880 Torrey Pines Scenic Drive

department: Reproductive Medicine

institute: UCSD

summary: We report a novel technique to reprogram human fibroblasts into endothelial and smooth muscle cells using partial iPSC reprogramming and chemically defined media. Using appropriate media conditions for differentiation of human pluripotent cells to CD34+ vascular progenitor cells, we show that temporary expression of pluripotent transcription factors and treatment with chemically-defined media, will induce differentiation of human fibroblasts to CD34+ vascular progenitor cells. Sorted CD34+ cells can then be directed to differentiate into vascular endothelial cells expressing a variety of smooth muscle markers.

overall_design: We have assessed the global DNA methylation (Illumina Infinium HD 450K DNA methylationBeadChips) and transcriptional (Illumina HT12v3 and HT12v4 Gene Expression Bead Array) profiles of transdifferentiated endothelial cells and smooth muscle, human embryonic stem cell (hESC) and human induced pluripotent stem cell (hiPSC) differentiated CD34+ angioblasts, hESCs,  hiPSC, primary smooth muscle and primary human umbilical vein endothelial cells using microarrays.

first: Leo

last: Kurian

first: Ignacio

last: Sancho-Martinez

first: Emmanuel

last: Nivet

first: Krystal

last: Moon

first: Caroline

last: Pendaries

first: Cecile

last: Volle-Challier

first: Francoise

last: Bono

first: Jean-Marc

last: Herbert

first: Yun

last: Xia

first: Mo

last: Li

first: Julian

last: Pulecio

first: Nuria

last: Monserrat

first: Sergio

last: Ruiz

first: Aitor

last: Aguirre

first: Ilir

last: Dubova

first: Francesca

middle: S

last: Boscolo

first: Jeanne

last: Loring

first: Louise

last: Laurent

first: Juan

last: Belmonte


title: Expression data from Drosophila embryos, control vs. dMyc+

status: Public on Sep 15 2012

city: Charlotte

first: Kaveh

last: Daneshvar

state: NC

address: 9201 University City Blvd.

department: Biology

institute: University of North Carolina at Charlotte

summary:
dMyc is a conserved transcription factor that controls growth and proliferation by regulating its target genes.
We used Affymetrix microarray to identify and classify targets of dMyc during Drosophila embryogenesis.

overall_design: RNA was extracted from 0-24 hour old Drosophila embryos in control (Gal 4 expressing animals) and Myc+ (flies over-expressing dMyc under UAS enhancer) to identify genomic targets od dMyc during embryogenesis

first: Julie

last: Goodliffe


title: Comparison of two sets of microarray experiments to define allergic asthma expression pattern

city: Chicoutimi

first: Catherine

last: Laprise

state: Qc

address: 555 Boul. Université

institute: Université du Québec à Chicoutimi

summary: Allergic asthma is a complex trait. Several approaches have been used to identify biomarkers involved in this disease. This study aimed at demonstrating the relevance and validity of microarrays in the definition of allergic asthma expression pattern. The authors compared the transcript expressions of bronchial biopsy of 2 different microarray experiments done 2 years apart, both including nonallergic healthy and allergic asthmatic subjects (n = 4 in each experiment). U95Av2 and U133A GeneChips detected respectively 89 and 40 differentially expressed genes. Fifty-five percent of the U133A genes were previously identified with the U95Av2 arrays. The immune signaling molecules and the proteolytic enzymes were the most preserved categories between the 2 experiments, because 3/4 of the genes identified by the U133A were also significant in the U95Av2 study for both categories. These results demonstrate the relevance of microarray experiments using bronchial tissues in allergic asthma. The comparison of these GeneChip studies suggests that earlier microarray results are as relevant as actual ones to target new genes of interest, particularly in function categories linked to the studied disease. Moreover, it demonstrates that microarrays are a valuable technology to target novel allergic asthma pathways as well as biomarkers.

overall_design: 4 healthy controls without history of allergy and asthma and 4 allergic asthmatic subjects according to the American Thoracic Society (ATS) criteria were selected

first: Annie

last: Chamberland

first: Anne-Marie

last: Madore

first: Karine

last: Tremblay

first: Michel

last: Laviolette


title: Gene expression analysis of FSHD muscle with different MRI pattern

status: Public on Sep 14 2012

city: rotterdam

first: Mario

last: Pescatori

address: Westplein 11

institute: Health e-genomics

summary: Objective: to focus on the molecular mechanisms involved in the dystrophic process that leads to selective wasting of single muscles or muscle groups in Facioscapulohumeral muscular dystrophy (FSHD). By muscle MRI we observed that T2-short tau inversion recovery (T2-STIR) sequences identify two different patterns in which each muscle can be found before the irreversible dystrophic alteration, marked as T1-weighted sequence hyperintensity. We studied these conditions in order to obtain further information on the disease pathogenesis. Design: histopathology, gene expression profiling and real time PCR were performed on muscle biopsies. Subjects: muscles (n=8) with different MRI pattern (T1-weighted normal/T2-STIR normal and T1-weighted normal/T2-STIR hyperintense) from FSHD patients. Data were also compared with inflammatory myopathies (n=7), dysferlinopathies (n=4) and normal controls (n=7). Results: myopathic and inflammatory changes characterize T2-STIR hyperintense FSHD muscles, at variance with T2-STIR normal muscles. These two states can be easily distinguished from each other by their transcriptional profile. Comparison of T2-STIR hyperintense FSHD muscles with muscles of inflammatory myopathies shows peculiar changes, although many alterations are shared among these conditions. Conclusions: at the single muscle level, different stages of the disease correspond to the two MRI patterns. T2-STIR hyperintense FSHD muscles are more similar to inflammatory myopathies than to T2-STIR normal FSHD muscles or other muscular dystrophies, and share with them upregulation of genes involved in innate and adaptive immunity. Our data suggest that selective inflammation, together with perturbation in biological processes such as neoangiogenesis, lipid metabolism and adipokine production, may play a role in FSHD progression.

overall_design: 26 samples of human muscle muscle tissue were analysed using the Illumina beadchip technology.

first: Giorgio

last: Tasca

first: Tiziana

last: Cubeddu

first: Enzo

last: Ricci


title: The MET oncogene is a functional marker of a glioblastoma stem cell subtype and drives the invasive phenotype

status: Public on Oct 05 2012

city: Candiolo

last: Medico

state: TO

address: Strada Prov. 142, km 3,95

department: Oncology

institute: Candiolo Cancer Institute, University of Torino

summary:
Eighteen independent neurospheres derived from patients affected by primary glioblastoma were grouped into “classical”, “mesenchymal” or “proneural” subtypes according to analysis of genetic lesions and gene expression profiling. Here we show that expression of the MET oncogene, encoding the tyrosine kinase receptor for HGF, associates with mesenchymal and proneural neurospheres (Met-pos-NS). Met expression is almost absent from classical neurospheres (Met-neg-NS), and mutually exclusive with amplification and expression of the EGF receptor gene.
Met-pos-NS and Met-neg-NS display distinct growth factor requirements, differentiate along divergent pathways, and generate tumors with distinctive histological features. Met-pos-NS contain a variable percentage of Met positive (Methigh) and Met negative (Metneg) cells. After purification, only Methigh cells display clonogenic ability in vitro, and regenerate neurospheres containing both Methigh and Metneg cells. After in vivo transplantation, Methigh cells display highly enriched tumorigenic potential as compared with Metneg cells. At functional level, in Methigh cells, HGF concomitantly sustains proliferation, clonogenicity, expression of self-renewal markers, migration and invasion. These data show that Met is a functional marker of glioblastoma stem cells, and a candidate target for molecular diagnosis and therapy of a glioblastoma subset.

overall_design: 37 samples (17 replicate samples and 1 triplicate sample)

last: De Bacco

first: Carla

last: Boccaccio


title: Effect of paraquat and nicotine on gene expression in a Drosophila melanogaster Parkinson's disease model

status: Public on Sep 05 2012

city: Albany

first: Haydeh

last: Payami

state: NY

address: 150 New Scotland Ave.

department: Wadsworth Center

institute: NY State Department of Health

summary: Cigarette smoking is associated with reduced risk of developing Parkinson’s disease (PD). To identify genes that interact with nicotine/smoking, we performed hypothesis-free genome-wide experiments in a paraquat-induced Drosophila model and in a case-control study of PD. We demonstrated that nicotine extends life-span in paraquat-treated Drosophila (P=4E-30).  Brain tissue from flies treated with combinations of paraquat and nicotine revealed elevated expression of CG14691 with paraquat which was restored with nicotine co-treatment (P(interaction)=2E-11, P(FDR-adjusted)=4E-7).  Independently, variants in the 5’ region of SV2C, a human ortholog of CG14691, gave the strongest signal for interaction with smoking (P(interaction)=9E-8).  The effect of smoking on PD risk varied six-fold by SV2C genotype (P(heterogeneity)=4E-10).  Moreover, SV2C variants identified here were associated with SVC2 gene-expression in the HapMap data.  Present results suggest synaptic vesicle protein SV2C plays a role in PD pathogenesis, and that the SV2C genotype may be useful for clinical trials of nicotine for treating PD.

overall_design: Drosophila female heads were dissected after exposure to plain food, food with paraquat, food with nicotine, or food with both paraquat and nicotine, and genome-wide expression was quantified using Affymetrix microarrays. 20 heads were pooled per replicate, with each treatment in triplicate, and all flies were dissected at the same timepoint, after 10 days of pretreatment (with 0.1 mg/ml nicotine or no nicotine, depending on treatment group), and then a further 6 days of treatment with either 5 mM paraquat or no paraquat, continuing on the pretreatment dose of nicotine. One biological replicate in the paraquat-only group showed RNA degradation and was not included in the normalization or subsequent analyses.

first: Erin

last: Hill-Burns

first: Prabarna

last: Ganguly


title: Genome-Wide Progesterone Receptor Binding: Cell Type-Specific and Shared Mechanisms in Uterine Fibroids and Breast Cancer (Expression BeadChip)

status: Public on Sep 11 2012

city: Basel

first: Damian

last: Roqueiro

address: Mattenstrasse 26

department: Biosystems Science and Engineering

country: Switzerland

institute: ETH Zurich

summary:
Analysis of genes regulated by RU486 (an progesterone antagonist) in human breast cancer T47D cells and human uterine leiomyoma smooth muscle cells. The hypothesis is that RU486 inhibits tumor growth by inactivating the transcription of multiple genes which trigger critical signaling pathways to induce tumorigenesis in both breast caner and uterine leomyoma.  Tissue-specific and common patterns of gene regulation may determine the therapeutic effects of antiprogestins in uterine leiomyoma and breast cancer.

Keywords: Expression profiling by array

overall_design: Total RNA isolated from T47D cells subjected to RU486 treatment for 6 hours compared to vehicle (ethanol) treated cells. Total RNA isolated from uterine leiomyoma cells subjected to RU486 treatment for 6 hours compared to vehicle (ethanol) treated cells.

first: Bulun

last: Serdar

first: Frasor

last: Jonna


title: Expression analyses in Drosophila young virgin female ovary

status: Public on Sep 01 2012

city: Iowa City

first: Alexey

middle: A

last: Soshnev

state: Iowa

address: 3159C MERF 375 Newton Rd

department: Biochemistry

country: USA

institute: University of Iowa

summary: Insulators delimit independent transcriptional domains within genomes by constraining enhancer and silencer action. These transcriptional effects depend upon DNA recognition by insulator binding proteins that recruit partners that protect against inappropriate long range modulation of non-target  promoters. Insulator binding proteins are broadly expressed during development, with largely constitutive binding to thousands of genomic sites. Yet, tissue-specific transcriptional changes result from the loss of individual insulator binding proteins.  To understand the molecular basis for such effects, we are studying the classic Drosophila insulator protein Suppressor of Hairy-wing [Su(Hw)]. Genetic studies show that loss of this broadly expressed insulator protein prevents oocyte development. To determine the basis for the block in oogenesis, we coupled transcriptional analyses in su(Hw) mutant ovaries with genome-wide definition of Su(Hw) binding in this tissue. These studies identified 71 direct targets of Su(Hw) regulation, with nearly 70% of these genes showing increased RNA accumulation when Su(Hw) is lost. Surprisingly, derepressed Su(Hw) target genes correspond to genes normally highly expressed in neural tissues, suggesting that Su(Hw) has a critical role in silencing neural genes in the ovary. Support for this postulate was obtained by genetic studies. We found that oocyte production was restored in su(Hw) mutant females that carry a deletion of one allele of the elav  family RNA binding protein 9 (Rbp9) gene. These su(Hw) null oocytes can be fertilized, with evidence that embryos lacking Su(Hw) show compromised development. Our studies extend the known transcriptional activities of Su(Hw), indicating that Su(Hw) can function as an insulator, activator and repressor, the latter function being essential for oogenesis. These findings highlight that insulator proteins are versatile transcriptional regulatory proteins, suggesting that tissue specific contributions to transcription result from direct regulation of individual genes.

overall_design: Ovaries for RNA isolation were dissected from 4-6 hour old virgin females of wild type, su(Hw)f/v (fertile), su(Hw)2/v (sterile) and su(Hw)Pb/2 (sterile) Drosophila melanogaster. At this stage of development, ovaries only contain egg chamber stages 1-8. Loss of Su(Hw) causes apoptosis at stage 9. Thus, the experimental design compares transcriptionl changes in the ovary prior to induction nof apoptosis in su(Hw) mutants.

first: Pamela

middle: K

last: Geyer