title: Targeting PBK/TOPK decreases growth and survival of glioblastoma stem cells in vitro and attenuates tumor growth in vivo

status: Public on Jun 16 2015

city: Oslo

first: Biljana

last: Stangeland

address: Sognsvannsveien 20

department: Institute of Surgical Research

institute: Oslo University Hospital

summary: Gene knockdown of PBK led to decreased proliferation and sphere formation in the GSC cultures. Treatment of cells with different concentrations  of HI-TOPK-032 almost completely abolished growth and proliferation and elicited a large increase in apoptosis

overall_design: Total RNA isolated from GSC cultures featuring PBK gene knock-down (shRNA) was compared to that from non-silencing control GSC cultures (NS-shRNA). Total RNA isolated from GSC cultures treated with PBK-inhibitor was compared to that from untreated GSC cultures.


title: RAI2 overexpression in MDA-MB231

status: Public on Jun 15 2015

city: Heidelberg

first: Benedikt

last: Brors

address: Im Neuenheimer Feld 280

department: Div. Applied Bioinformatics

country: Germany

institute: German Cancer Research Center (DKFZ)

summary: MDA-MB231 cells were transfected with control vector, RAI2-overexpression vector, or vector with RAI2-4A, which has a mutated interaction domain w.r.t. CtBP/CtBP2

overall_design: Three replicates each of control condition, RAI2 overexpression or RAI2-4A overexpression.

first: Stefan

last: Werner

first: Harriet

last: Wikman


title: Characterization of novel ovarian tumor cell lines that retain the phenotype of primary tumors

city: Miami

first: Tan

middle: A

last: Ince

state: FL

address: 1501 NW 10th Avenue, Rm 926

department: Sylvester Cancer Center

country: USA

institute: University of Miami - Miller School of Medicine

type:
Expression profiling by array
Genome variation profiling by SNP array
SNP genotyping by SNP array

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

overall_design: Refer to individual Series


title: Genetic analysis reveals a longevity associated protein modulating endothelial function and angiogenesis

status: Public on Jun 12 2015

city: Segrate

first: Francesco

last: Villa

state: MI

address: Via Fratelli Cervi, 93

department: Istituto di Tecnologie Biomediche

country: Italy

institute: Consiglio Nazionale delle Ricerche

summary: Transcriptome analysis in HEK293T transfected with plasmid carrying different isoforms of BPIFB4 gene. This gene was previously associated with exceptional longevity in a GWAS study performed on three different populations. Results indicate an up-regulation of stress response genes and proteostasis genes in HEK293T transfected with plasmid carrying the longevity-associated variant (LAV) of BPIFB4.

overall_design: Total RNA obtained from HEK293T over-expressing wild-type or mutated form of BPIFB4.

first: Albino

last: Carrizzo

first: Chiara

middle: C

last: Spinelli

first: Anna

last: Ferrario

first: Alberto

last: Malovini

last: Maciag

first: Antonio

last: Damato

last: Auricchio

first: Gaia

last: Spinetti

first: Elena

last: Sangalli

first: Zexu

last: Dang

first: Leopoldo

last: Sitia

first: Paolo

last: Bigini

first: Gaetano

last: Calì

last: Schreiber

first: Thomas

last: Perls

first: Sergio

last: Fucile

first: Francesca

last: Mulas

first: Almut

last: Nebel

first: Riccardo

last: Bellazzi

last: Madeddu

first: Carmine

last: Vecchione

first: Annibale

last: Puca


title: Genome wide expression profiling of mesenchymal stem cells of fetal and adult origin and dermal fibroblasts

city: Pavia

first: Patrizia

last: Danieli

address: viale Golgi, 19

institute: Fondazione IRCCS Policlinico San Matteo

summary: In animal models and human trials, intramyocardial injection of adult bone-marrow derived mesenchymal stem cells (BM-MSC) provides beneficial effects in failing hearts. These effects are mainly mediated through paracrine mechanisms. Mesenchymal stem cells of fetal origin (hAMC) can be isolated from the amniotic membrane of human placenta. Our results provide evidence that hAMC exert remarkable cardioprotective effects through paracrine mechanisms. However, the complete nature and scope of the paracrine mediators of cardioprotection have not been investigated yet. We compared the gene expression profiling of hAMC (n=8), BM-MSC (n=10) and dermal fibroblasts (n=6) to shed light onto the identity of putative cardioprotective factors secreted by fetal MSC.

overall_design: Total RNA was extracted from cultured hAMC (n=8), BM-MSC (n=10) and dermal fibroblasts (n=6) and analyzed with HumanHT-12 v3 Expression BeadChips

first: Massimiliano

last: Gnecchi

first: Rudolf

last: de Boer

first: Lennaert

last: Kleijn


title: Human brown and white preadipocyes clonal dynamics predict themorgenic potential and function

city: Boston

first: Jonathan

middle: M

last: Dreyfuss

state: MA

address: 1 Joslin Pl

department: Bioinformatics & Biostatistics Core

institute: Joslin Diabetes Center

summary: Brown adipose tissue (BAT) holds therapeutic potential for obesity and metabolic syndrome via increasing energy expenditure. Both inter- and intra-individual differences contribute to heterogeneity in human BAT and potentially to differential thermogenic capacity in human populations. Here, we demonstrated the generation of brown and white preadipocyte clones from human neck fat and characterized their adipogenic differentiation and thermogenic function. Combining a UCP1 reporter system and gene expression profiling, we defined novel sets of gene signatures in human preadipocytes that could predict the thermogenic potential of mature adipocytes. Knocking out the positive UCP1 regulators, PREX1 and EDNRB, in brown preadipocytes by CRISPRs markedly abolished the high level of UCP1 in mature brown adipocytes. Finally, we showed the ability to prospectively isolate adipose progenitors with great thermogenic potential.  These data provide new insights into the cellular heterogeneity in human fat and offer clinically relevant gene targets that mark thermogenically competent preadipocytes.

overall_design: Highly adipogenic clonal white and brown cell lines

first: Ruidan

last: Xue

first: Matthew

middle: D

last: Lynes

first: Farnaz

last: Shamsi

first: Tim

middle: J

last: Schulz

first: Hongbin

last: Zhang

first: Tian

middle: L

last: Huang

first: Kristy

last: Townsend

first: Yiming

last: Li

first: Hirokazu

last: Takahashi

first: Lauren

middle: S

last: Weiner

first: Andrew

middle: P

last: White

first: Maureen

first: Lee

last: Rubin

first: Laurie

last: Goodyear

first: Aaron

last: Cypess

first: Yu-Hua

last: Tseng


title: The antidepressant fluoxetine elicits anticancer effects by impairing aerobic glycolysis in colon cancer cells and xenografts.

status: Public on Jun 09 2015

city: Würzburg

first: Claus

middle: Juergen

last: Scholz

address: Josef-Schneider-Str. 2

department: Core Unit SysMed

institute: University Hospital Würzburg

summary:
Colon cancer is one of the most common tumors worldwide. Recent reports showed that patients treated with the antidepressant fluoxetine had reduced colon cancer risk, with effects similar to the chemotherapeutic 5-fluoro-uracil.
Here, we examined the effects of fluoxetine and 5-fluoro-uracil on gene expression of HT29 colon cancer cell xenografts.

overall_design: HT29 xenografts in NOD/SCID mice were treated with vehicle (physiological solution), fluoxetine (30mg/kg/day), or 5-Fluoro-uracil (50 mg/kg/day).

first: Vinicius

last: Kannen

first: Sergio

middle: B

last: Garcia

first: Ana

last: Waaga-Gasser

first: Helga

last: Stopper


title: Expression data from shROR HT29 and AGS cell

status: Public on Jun 05 2015

city: shanghai

first: jiayan

last: fan

address: No 639 zhi zao ju road

country: China

institute: Ninth People’s Hospital, Shanghai JiaoTong

summary:
Genome-wide cDNA array from HT29,HT29-shROR,HT29-Mock, AGS, AGS-shROR, AGS-Mock cells
We used microarrays to detail the global programme of gene expression and  identified significantly changed genes after ROR depletion.

overall_design: HT29,HT29-shROR, HT29-Mock, AGS, AGS-shROR, AGS-Mock cells were selected for RNA extraction and hybridization on Affymetrix microarrays.

first: Jiayan

last: Fan

first: Xianqun


title: MYC and CHK1 Dependent Cell Death in T-cell Lymphoma and Hodgkin Lymphoma Cell Lines and Human Xenograft Models Via Anti-Proteasomal Therapy (Illumina)

status: Public on Jun 08 2015

city: Mountain View

first: Afshin

last: Beheshti

state: CA

address: Moffett Blvd

institute: NASA Ames Research Center

summary: We examined the biological effects of a potent second-generation proteasome inhibitor, ixazomib, in T-cell lymphoma and Hodgkin lymphoma cell lines and human xenograft models. Ixazomib resulted in time- and dose-dependent cytotoxicity and apoptosis in all cell lines (IC50’s <75nM). In vivo studies via SCID tumor xenografts showed significant inhibition of tumor growth (P<0.001) with significantly improved survival (P<0.001) in Jurkat and L540 models with ixazomib-treated mice versus controls. Through global transcriptome and network analyses, ixazomib-treated Jurkat and L540 cells showed significant overlap in biological functions involved in regulation of cell cycle, chromatin modification, and DNA repair processes with a lack of conservation observed in a relatively ixazomib-resistant cell line, L428. Moreover, the predicted activation and inhibition status of tumor suppressors and oncogenes strongly favored ixazomib inhibition of tumor progression. Most notably, ixazomib down-regulated protein levels of MYC and its target genes. Additionally, chromatin immunoprecipitation showed that histone H3 acetylation affected MYC levels and cell death response to ixazomib. Furthermore, inhibition of MYC with JQ1 resulted in synergistic cell death in L428, which was confirmed utilizing MYC knockout. Collectively, ixazomib down-regulated MYC and downstream substrates in TCL and HL, while resistance appeared mediated through MYC- and CHK1-dependent mechanisms.

overall_design: L428 cells were treated with 25nM ixazomib for 24 hours, RNA was isolated using RNeasy Minikit (Qiagen), following instructions recommended supplied by the manufacturer. Purity and the yield of isolated RNA was determined using Bioanalyzer. These experiments were performed in biological triplicates. Microarray experiment with L428 was performed using Human HT 12 Genechip Illumina. Data for the L428 cell line was corrected through normalization of the housekeeping genes, quantile normalized, and then statistically relevant genes were determined with one-way ANOVA analysis with FDR <0.05.

first: Ravi

last: Dashnamoorthy

first: Nasséra

last: Abermail

first: Jaya

last: Sharma

first: Michael

last: Coyle

first: Athena

last: Kritharis

first: Irawati

last: Kandela

first: Lynn

last: Hlatky

last: Mazar

first: Ronald

last: Gartenhaus

last: Evens


title: Dissecting the Genetics of the Human Transcriptome identifies novel trait-related trans-eQTLs and corroborates the regulatory relevance of non-protein coding loci

status: Public on Jun 29 2015

city: Leipzig

first: Holger

last: Kirsten

state: Saxony

address: Haertelstr. 16-18

department: IMISE

institute: University of Leipzig

summary: Genetics of gene expression (eQTLs or expression QTLs) has proved an indispensable tool for understanding biological pathways and pathomechanisms of trait associated SNPs. However, power of most genome-wide eQTL studies is still limited. We performed a large eQTL study in peripheral blood mononuclear cells of 2,112 individuals increasing the power to detect trans-effects genome-wide. Going beyond univariate SNP-transcript associations, we analyse relations of eQTLs to biological pathways, polygenetic effects of expression regulation, trans-clusters, and enrichment of co-localised functional elements.   We found eQTLs for about 85% of analysed genes, 18% of genes were trans-regulated. Local eSNPs were enriched up to a distance of 5 MB to the transcript challenging typically implemented ranges of cis-regulations. Pathway enrichment within regulated genes of GWAS-related eSNPs supported functional relevance of identified eQTLs. We demonstrate that nearest genes of GWAS-SNPs might often be misleading functional candidates. We identified novel trans-clusters of potential functional relevance for GWAS-SNPs of several phenotypes including obesity-related traits, HDL-cholesterol levels, and haematological phenotypes. We used chromatin immunoprecipitation data for demonstrating biological effects. We show for strongly heritable transcripts that a considerable gap still exists between total heritability resulting from all trans-chromosomes and explained variance of all identified trans-eSNPs. In contrast, the vast majority of most cis-heritability of these genes is already explained. Dissection of co-localised functional elements indicated a prominent role of SNPs in loci of pseudogenes and non-coding RNAs for the regulation of coding genes.   In summary, our study substantially increases the catalogue of human eQTLs and improves our understanding of the complex genetic regulation of gene-expression, pathways and disease related processes.

overall_design: Gene expression from human blood mononuclear cells from individuals of the Leipzig LIFE Heart Study was analyzed applying Illumina HT-12 v4 Expression BeadChips. After preprocessing, 28,295 expression probes for 2,112 individuals remained for analysis. In a population-based analysis, we identified associations between DNA variants and RNA expression levels and characterized these findings.

first: Frank

last: Beutner

first: Knut

last: Krohn

first: Daniel

last: Teupser

first: Joachim

last: Thiery

first: Markus

last: Scholz


title: Aurora kinase inhibition triggers senescence in human melanoma cells

city: Philadelphia

first: Gao

last: Zhang

state: PA

address: 3601 SPRUCE ST

department: Molecular and Cellular Oncogenesis Program

institute: Wistar Institute

summary: Phenotypically, there is a heterogeneous response of cancer cells to chemotherapy or targeted therapy. While therapeutically much attention is focused on cell death, there is growing evidence suggesting that a subpopulation of cancer cells undergo therapy-induced senescence. Depending on the therapy, dose and timing, senescence may be a dominant phenotype over cell death. An integrated FACS approach identified two types of therapy-induced senescence in human melanoma cells, irreversible senescence induced by Aurora kinase inhibition vs. transient senescence induced by B-RAF kinase inhibition. Autophagy and ER stress response precede and are required for therapy-induced senescence in cancer cells, mirroring their functions in normal cells undergoing oncogene-induced senescence. Importantly, autophagy serves a survival pathway for senescent cancer cells. Antagonizing autophagy converts therapy-induced senescence into cell death but paradoxically promotes cell proliferation or quiescence. Our work calls for a rationale-based design of combination therapy for cancer treatment that should lead to a greater synergy.

overall_design: There are three or four replicates per treatment per time point.

first: Wei

last: Zhi


title: In vivo effects of localization and/or CXCR4 inhibition on gene expression profiles of OCI-AML3 cells

status: Public on Jun 03 2015

city: Houston

first: Wencai

last: Ma

address: 7455 Fannin st

institute: MD Anderson Cancer Center

summary: OCI-AML3, a human acute myeloid leukemia cell line, was inoculated into NOD/SCID/IL-2rγnull (NSG) mice. After engraftment and leukemic expansion were documented, mice were divided into 3 groups: control, or treatment for 24 or 72 hours with daily injections of LY2510294, a CXCR4-inhibitory peptide. OCI-AML3 cells were isolated from peripheral blood (PB), bone marrow (BM), or spleen (SP) for gene expression profiling (GEP).

overall_design: The OCI-AML3 cells used had been engineered to express luciferase and GFP, to facilitate imaging of tumor burden and cell sorting, respectively. 1×10e6 cells/mouse were used for inoculation.  Adequate tumor burden and involvement of PB were established on Day 40 after inoculation by bioluminescence and flow cytometry (FACS), respectively, and LY2510924 was started in the treated groups. Three 24-hr mice were sacrificed on Day 41 for collection of PB, femoral BM, and SP, from which OCI-AML3 cells were isolated by FACS, on the basis of GEP and human CD45 expression, and fixed in RNAlater. Similar harvests were performed on 3 control mice on Day 42, and 2 72-hr mice on Day 43. Total RNA was isolated and underwent 2 rounds of amplification and biotin-labeling for hybridization to Illumina HT12v4.0 human gene expression arrays.

first: Byoung-Sik

last: Cho

first: Zhiqiang

last: Wang

first: R

middle: E

last: Davis

first: Marina

last: Konopleva

last: Andreeff


title: Distinct classes of genes behave as either drivers or dependents of replication timing switches.

city: La Jolla

first: Kristopher

middle: L.

last: Nazor

address: 10550 North Torrey Pines Road

department: Regenerative Medicine

institute: The Scripps Research Institute

summary: Duplication of the genome in mammalian cells occurs in a defined temporal order referred as its replication-timing program (RT). RT is regulated in units of 400-800 Kb referred as replication domains (RDs) and changes dynamically during development. Changes in RT are generally coordinated with transcriptional competence and changes in sub-nuclear position. We generated genome-wide RT profiles for 29 distinct human cell types including embryonic stem cell (hESC)-derived, primary cells and established cell lines representing intermediate stages of endoderm, mesoderm, ectoderm and neural crest (NC) development. We identified clusters of RDs that replicate at unique times in each stage (RT signatures). Surprisingly, transcriptome data revealed that, despite an overall correlation between early replication and transcriptional activity, most genes that switched RT during differentiation can be expressed when late replicating. Intriguingly, this class of genes was nonetheless induced to high expression levels prior to a late to early RT switch and down-regulated after the switch back to late replication. These results clarify the complex relationship between transcription and RT and identify classes of genes that behave as potential drivers of the RT switch vs. those that may depend upon an RT switch for transcriptional induction.

overall_design: To analyze the dynamic regulation of gene expression and replication timing during differentiation we obtained the transcriptome of 64 samples including distinct cell types and key intermediate stages across the differentiation pathways towards the three main germ layers and neural crest. Gene expression profiles were obtained using the Illumina HT12v4 Gene Expression BeadArray.

first: Juan

last: Rivera-Mulia

first: Quinton

last: Buckley

first: Takayo

last: Sasaki

first: Jared

last: Zimmerman

first: Ruth

last: Didier

first: Jeanne

middle: F

last: Loring

first: Zheng

last: Lian

first: Sherman

last: Weissman

first: Allan

last: Robins

first: Thomas

last: Schulz

first: Laura

last: Menendez

first: Michael

last: Kulik

first: Stephen

last: Dalton

first: Haitham

last: Gabr

first: Tamer

last: Kahveci

first: David

last: Gilbert


title: Stem cells respond to triiodothytonine (T3) treatment

status: Public on Jun 01 2015

first: Paul

last: Webb

address: 6670 Bertner Ave

department: Genomic Medicine

institute: Houston Methodist Research Institute

summary: Analysis of T3 response in KCL034, iKCL004 and BJ cells at gene expression level. Results provide information of the T3 response in different lines.

overall_design: Total RNA was obtained from KCL034, iKCL004 and BJ cells treated with T3 for 0 and 6 h. T3 response in each cell line was analyzed.

first: Aleksandra

last: Cvoro


title: Association between alpha-synuclein blood transcripts and early Parkinson's disease

city: Cambridge

first: Bin

last: Zheng

address: 65 Landsdowne Street

department: Center for Neurologic Diseases

institute: Brigham and Women's hospital

summary: Importance. Biological markers of Parkinson’s disease are essential for achieving disease modification. Objective. To determine the association of SNCA blood transcript levels with prevalence of Parkinson’s disease. Background. The SNCA locus is preferentially transcribed in neurons and blood cells. Non-coding genetic variants and neuronal aggregates of α-synuclein protein associate this locus with sporadic Parkinson’s disease and suggest a potential role for abnormal SNCA transcription in the disease mechanism. Here we investigated variation in intracellular SNCA gene expression and SNCA transcript isoform abundance in circulating blood cells of cases with PD and controls in a network of biobanks that represent regional, national, and international populations. Design, Setting, Participants. Three cross-sectional, case-control studies nested in observational biomarker studies. 222 cases with early-stage clinical PD and 183 controls were enrolled from 2005 to 2010 in the Harvard Biomarker Study (HBS) at two Harvard-affiliated tertiary care centers. 76 cases with dopamine transporter imaging (DAT)-confirmed PD and 42 controls were enrolled between August 2007 and December 2008 in the Blood α-Synuclein, Gene Expression and Smell Testing as Diagnostic and Prognostic Biomarkers in Parkinson’s Disease Study (PROBE) study from 22 US tertiary care centers. 202 DAT-confirmed cases with de novo PD and 138 controls were enrolled in the Parkinson’s Progression Markers Initiative (PPMI) between July 2010 and November 2012 from 22 US and international tertiary care centers. Main Outcome Measures. Association of intracellular SNCA transcript abundance with PD estimated on analog and digital expression platforms. Results. Reduced levels of SNCA transcripts were associated with early-stage clinical PD, neuroimaging-confirmed PD, and untreated, neuroimaging-confirmed PD in accessible, peripheral blood cells from a total of 863 individuals. SNCA expression was reduced by 17%, 22%, and 16% in cases compared to controls in the HBS, PROBE, and PPMI study with P values of 0.004, 0.025, and 0.018, respectively, after adjusting for clinical, hematological, and processing covariates. Specific SNCA transcripts with long 3’ untranslated regions (UTR) and those skipping exon 5 are implicated in the accumulation and mitochondrial targeting of α-synuclein protein in Parkinson’s pathology. These transcript isoforms were linked to PD through digital expression analysis. Individuals in the lowest quartile of SNCA expression values had covariate-adjusted odds ratios for PD of 2.14 (95% C. I. 1.1-4.1), 4.5 (95% C. I. 1.3-15), and 2.1 (1.1-4.0) compared to individuals in the highest quartile of expression values in the HBS, PROBE, and PPMI study, respectively. Conclusions and Relevance. Reduced levels of SNCA expression, particularly of disease-relevant transcripts with extended 3’ UTR or exon 5 skipping, are associated with early-stage PD. These findings support a potential role for SNCA as a transcriptional marker of PD and may have implications for patient stratification and risk assessment.

overall_design: 93 cases with Dopamine Transporter Imaging (DAT)-confirmed PD and 49 controls were enrolled between August 2007 and December 2008 in the Blood a-Synuclein, Gene Expression and Smell Testing as Diagnostic and Prognostic Biomarkers in Parkinson's Disease Study (PROBE) study from 22 US tertiary care centers.

first: Clemens

middle: R

last: Scherzer


title: Gene expression analysis in human focal cortical dysplasia and tuberous sclerosis

city: Washington

first: Svetlana

last: Ghimbovschi

state: DC

address: 111 Michigan Ave., NW

department: Research Center for Genetic Medicine

institute: Children's National Medical Center

summary: Focal cortical dysplasia (FCD), a focal brain malformation, is the most common cause of intractable epilepsy. One of the related disorders is tuberous sclerosis (TS). The dysplasia appears to result from a defect in cortical development, however, this disorder is heterogeneous, and FCD seizure therapy is non-specific and failure-prone.  As a final recourse, patients may undergo multiple surgical resections to control seizures. Thus, there is a clinical need to characterize this disorder with respect to structural, molecular, and electrophysiological profiles, which will lead to development of animal models and pilot therapies that we will then apply to humans.

overall_design: Total RNA obtained from brain epilepsy surgical isolate from 5 patients with Focal Cortical Dysplasia (FCD) and 3 patients with Tuberous Sclerosis (TS) compared to 3 normal brain tissue controls. Gene expression profiling was performed using Illumina bead array technology and HumanHT-12_v.4 chips.

first: Judy

last: Liu


title: Evaluation of sub-culturing on whole genome expression of skeletal muscle-derived cells

status: Public on May 31 2015

city: Tehran

first: Seyed Ahmad

last: Mousavi

state: Tehran

address: Bani Hashem sq. - Resalat Hw.

country: Iran

institute: Royan Institute

summary: Today, cell therapy is considered as one of the most promising alternates to cure end-stage diseases. Using human cells for transplantation needs in vitro culture and passages which arises the concern of malignant transformation of cells. To evaluate the effect of sub-culturing on whole genome transcriptome of skeletal muscle-derived cells (SMDCs), microarray analysis was performed on passages 3, 6, 9 and 12 of SMDCs in three replicates.

overall_design: There were 4 different passage samples (3, 6, 9, and 12) each stage with three replicates. Replicates for passage 3 were determined as control group and the data was analyzed compared to this passage.

first: Sadaf

last: Vahdat

first: Seyed

first: Reza

last: Moghadasali

first: Javad

last: Gharechahi

first: Nasser

last: Aghdami

first: Ghasem

middle: H

last: Salekdeh

first: Hossein

last: Baharvand


title: Microarray analysis of IFN-response

city: Newcastle upon Tyne

first: Andrew

middle: James

last: Skelton

state: Tyne and Wear

address: Framlington Place

department: Bioinformatics

country: United Kingdom

institute: Newcastle University

summary: Type I interferon (IFN-α/β) is the first line of defense against viral infection. Mouse models have been pivotal to our understanding of IFN-α/β in immunity, although validation of these findings in humans has not been possible. We investigated a previously healthy child with fatal susceptibility to the live-attenuated measles, mumps and rubella (MMR) vaccine. By targeted resequencing we identified a homozygous mutation in the high-affinity interferon-α/β receptor (IFNAR2), which rendered cells unresponsive to IFN-α/β and led to unrestricted replication of IFN-attenuated viruses. Reconstitution of patient cells with wild-type IFNAR2 restored IFN-α/β responsiveness and viral resistance. Despite the failure to control vaccine viruses, the patient showed no evidence of susceptibility to conventional viral pathogens in vivo and adaptive immunity appeared normal. Human IFNAR2 deficiency therefore reveals an essential role for IFN-α/β in resistance to attenuated viruses, but significant and unexpected redundancy overall in antiviral immunity.

overall_design: Total RNA isolated from IFNAR2-deficient patient (in triplicate) and control (three independent control lines) fibroblasts treated with IFNalpha, IFNbeta or IFNgamma (1000 IU/mL) for 10h

first: Siti

last: Mohammad

first: Christopher

last: Duncan


title: Thermomirs a novel class of temperature-responsive microRNAs

status: Public on May 29 2015

city: Camperdown

first: william

last: ritchie

state: NSW

address: Building 93

country: Australia

institute: centenary institute

summary: Analysis of microRNA expression at 37 and 40 degrees shows a novel class of microRNAs that regulate fever. Arrays of gene expression at 37 and 40 of THP-1 derived macrophages as well as a thermomiR knockdown experiment.

overall_design: THP-1at 37 degrees VS THP-1 at 40 degrees & WT vs thermoMIR siRNA


title: A Gain-of-Function Genomic Screen Identifies the Orphan Nuclear Receptor TLX as an Enhancer of STAT1-mediated Transcription and Immunity to Toxoplasma gondii: TLX overexpression

first: daniel

last: beiting

address: 380 S. University Ave

department: Pathobiology

institute: University of Pennsylvania

summary: The protozoan parasite Toxoplasma gondii is a highly successful intracellular pathogen, owing in part to its ability to subvert the host immune system.  In particular, parasite infection suppresses STAT1 signaling in a variety of cell types, including IFN-γ activated macrophages, via a block within the nucleus.  A high-throughput screen to identify genes able to overcome parasite-mediated suppression of STAT1 activity identified 9 transcription factors as enhancers of STAT1 signaling in T. gondii infected cells, including the orphan nuclear hormone receptor TLX.  Expression profiling revealed that TLX is a transcriptional regulator that drives the steady-state expression of STAT1-independent genes involved brain function and development, while enhancing the output of a subset of IFN-γ-dependent target genes.  Infection of TLX deficient mice with Toxoplasma results in impaired production of interleukin-12 by dendritic cells and increased parasite burden in the brain during chronic infection.  These results demonstrate a previously unrecognized function for this orphan nuclear hormone receptor in regulating STAT1 signaling and host defense, and reveal that STAT1 activity can be modulated in a context-specific manner by such ‘modifiers’.

overall_design: The human osteosarcoma cell line, U2OS, was transiently transfected with human TLX under the control of the CMV promoter.  24 hours after transfection with CMV-TLX or an 'empty' control CMV vector, cells were stimulated for 8 hours with 10ng/ml of recombinant IFN-gamma.  RNA was isolated from duplicate or triplicate wells for analysis by Illumina microarray.

first: Daniel

last: Beiting

first: Sara

last: Cherry

first: David

last: Roos


title: Transcriptome data from induced Pluripotent Stem cells

status: Public on May 28 2015

city: Oxford

first: Sally

last: Cowley

address: South Parks Road

department: Sir William Dunn School of Pathology

institute: University of Oxford

summary:
We have generated human induced Pluripotent Stem cells (hiPSc) using Sendai virus-mediated delivery of reprogramming factors. hiPSc lines have been screened using SNP array to assess chromosomal stability (alongside the fibroblast lines from which they derived), and validation of the pluripotency of the hiPSc lines is provided by Pluritest assessment of transcriptome datasets, prior to differentiation and downstream assays.
Single cell RT-qPCR analysis of induced pluripotent stem cell-derived cortical neurons reveals frequent dual layer identity. Handel AE, Chintawar S, Lalic T, Whiteley E, Giustacchini A, Argoud K, Sopp P, Bowden R, Cowley SA, Newey S, Ackerman C, Ponting CP and Cader ZM. Submitted

overall_design: human iPSc lines were derived from human dermal fibroblasts from control donors. SNP and gene expression datasets from control lines. Note that iPS NHDF-1, also used in the current study, has been published previously [Van Wilgenburg B., Browne C., Vowles J. & Cowley S. A. Efficient, long term production of monocyte-derived macrophages from human pluripotent stem cells under partly-defined and fully-defined conditions. PLoS One 8, e71098 (2013);  Physiological characterisation of human iPS-derived dopaminergic neurons.  Hartfield EM, Yamasaki-Mann M, Ribeiro Fernandes HJ, Vowles J, James WS, Cowley SA, Wade-Martins R.  PLoS One. 2014 9(2):e87388]

first: A

last: Handel

first: S

last: Chintawar

first: T

last: Lalic

first: E

last: Whiteley

last: Giustacchini

first: K

last: Argoud

first: P

last: Sopp

first: R

last: Bowden

last: Newey

first: C

last: Ackerman

last: Ponting

first: Z

last: Cader


title: Orphan Nuclear Receptors ERRα/γ are competence factors for somatic cell reprogramming

status: Public on May 27 2015

first: Ruth

middle: T

last: Yu

address: 10010 N Torrey Pines Rd

department: Gene Expression Lab

institute: Salk Institute

summary: We report the expression profiles of the nuclear receptor family of transcription factors, known regulators of metabolism, during iPSC generation. Unique but overlapping expression patterns were found in iPSCs derived from adipose derived stem cells (ADSCs) and embryonic fibroblasts (human and mouse) that correlate with developmental transitions in the cell.

overall_design: Total RNA was obtained from human embryonic fibroblast IMR90 cells (IMR90s) untreated, transduced with GFP or with the four reprogramming factors (Oct4, Sox2, Klf4, c-Myc; OSKM) at day 5 of reprogramming.

first: Yasuyuki

last: Kida

first: Ronald

last: Evans


title: A Gain-of-Function Genomic Screen Identifies the Orphan Nuclear Receptor TLX as an Enhancer of STAT1-mediated Transcription and Immunity to Toxoplasma gondii

first: daniel

last: beiting

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

overall_design: Refer to individual Series


title: Gene expression profiles regulated by PLD1-E2F1 axis in two Wnt-relevant colon cancer cells

city: Busan

first: Do Sik

last: Min

address: 30 Jangjeon-dong, Geumjeong-gu

department: Molecular Biology

country: South Korea

institute: Pusan National University

summary:
1. To identify potential effectors responsible for anti-tumorigenesis by targeting PLD1, we performed microarray in two Wnt-relevant colon cancer cells and analyzed transcriptional profile of genes that were differently expressed by inhibition and knockdown of PLD1
2. We also investigated potential downstream effectors of PLD1-E2F1 axis using microarray analysis in PLD1 and E2F1-depleted CRC cells.

overall_design: Total RNA obtained from isolated DLD1 and HCT116 cells in shCTRL (Vehicle), shCTRL-PLD1-Inh, shPLD1, or shPLD1/shE2F1 groups under 1% serum condition for 36 hours, respectively.

first: Do

first: Dong

middle: W

last: Kang


title: Transcriptome of human osteosarcoma (HOS) cells induced by bisphenol A, S and AF

city: Ljubljana

first: Peter

last: Juvan

address: Zaloska 4

department: Institute of Biochemistry

country: Slovenia

institute: Faculty of Medicine, University of Ljubljana

summary: Whole genome expression data on transcriptome of human osteosarcoma (HOS) cells induced by bisfenol A (BPA), S (BPAS) and AF (BPAF) after short- (8 hours) and long-term (3 months) exposure at human-relevant (10 nM) concentrations.

overall_design: 8 experimental conditions, 4x2 design: 3 compounds (bisphenol A, S and AF) and a control, 2 exposure times (8 hours and 3 months). 3 replicates for each condition, 24 arrays in total.

first: Anja

last: Fic

first: Simona

last: Jurkovic Mlakar

first: Vid

last: Mlakar

first: Karin

last: Broberg Palmgren

first: Lucija

last: Peterlin Masic


title: Whole genome expression analysis of a skin biopsy from an individual with multi-organ epithelial inflammation associated with an inherited loss-of-function mutation in EGFR

status: Public on May 26 2015

city: London

first: Venu

middle: Madhav

last: Pullabhatla

address: Great Maze Pond

department: Guy's Hospital

institute: Biomedical Research Centre

summary: Whole-genome expression microarray analysis was performed using RNA extracted from skin biopsies sampled from the affected child as well as 4 pooled, healthy controls. The hypothesis was that the downstream effects of the inherited EGFR loss-of-function mutation in the infant would be evident by enriched pathways and processess linked to the cutaneous roles of the epidemermal growth factor receptor (EGFR). Functional analysis of the results identified a multitude of enriched gene ontology (GO) processes, pathways, networks and disease-associated transcripts germane to EGFR signaling in the infant's sample compared to controls. The top 3 up-regulated GO processes were linked to known EGFR functionality: keratinocyte differentiation, keratinization and epidermis development. Innate inflammatory response gene components were among the most significantly up-regulated GO networks. Additionally, regulation of epithelial-to-mesenchymal transition and angiogenesis, processes known to be controlled by EGFR activation, were identified as significantly down-regulated GO pathways and processes, respectively. There was also down-regulation of transcripts that are normally increased in tumors which show gain-of-function mutations in EGFR (e.g. non-small cell lung cancer, colorectal cancer, and glioblastoma).

overall_design: Total RNA extracted from a skin biopsy of the infant was compared to skin biopsies from 4 pooled, healthy controls.

first: John

middle: A

last: McGrath


title: VEPH1 expression in ovarian cancer cell lines and its relationship to TGF-B signaling

status: Public on May 25 2015

city: Toronto

first: carl

last: virtanen

state: Ontario

address: 101 College St

department: Princess Margaret Genomics Centre

country: Canada

institute: University Health Network

summary: The current study examines the functional role of VEPH1, a PH domain containing protein and the human ortholog of Drosophila melted, in ovarian cancer cell lines. Elevated VEPH1 is associated with FOXO and Hippo signaling and was found to suppress TGF-ß induced target genes.

overall_design: SKOV3 cell lines were established as either CdCl2 inducible Flag-tagged VEPH1 expression or mock-transfected. Gene expression profiles were then generated both with and without the presence of TGF-ß to induce TGF-ß signaling.  3 replicates per treatment group were used.

first: Premalatha

last: Shathasivam

first: Alexandra

last: Kollara

first: Maurice

last: Ringuette

first: Carl

last: Virtanen

first: Jeffrey

last: Wrana

first: Theodore

last: Brown


title: Functional cortical neurons and astrocytes from human pluripotent stem cells in 3D culture

city: Los Angeles

first: Daniel

middle: H.

last: Geschwind

state: California

address: 2309 Gonda Bldg, 695 Charles E. Young Dr. South

department: Neurology

institute: UCLA

summary: Expression profiles of human cortical spheroids (hCSs) derived from pluripotent stem cells using Illumina cDNA microarrays. The goal of the study is to assess the developmental maturity and the regional identity of those hCSs at two distinct time points with expression profiles and compare the expression pattern with in vivo data. Results show that those hCSs can map transcriptionally to in vivo fetal development.

overall_design: Use transcriptional profiling to assess the developmental maturity and the regional identity of hCSs at two distinct time points.

first: Anca

middle: M

last: Pasca

first: Steven

last: Sloan

first: Laura

last: Clarke

first: Yuan

last: Tian

first: Christopher

middle: D

last: Makinson

first: Nina

last: Huber

first: Chul

last: Kim

first: Jin-Young

last: Park

first: Nancy

last: O'Rourke

first: Khoa

last: Nguyen

first: Stephen

last: Smith

last: Huguenard

first: Ben

last: Barres

first: Sergiu


title: Different Preference of Degradome in Invasion versus Angiogenesis

status: Public on May 20 2015

city: Graz

first: Silvija

last: Tokic

address: Auenbruggerplatz 14

country: Austria

institute: Medical University of Graz

summary:
We hypothesized altered expression of Proteases in calls capable of physiological invasion vs angiogenesis. We analyzed trophoblasts isolated from first trimester placenta that are invasive, and placental endothelial cells, that gave a high angiogenic potential. We found different expression levels of most proteases.
We found that the expression of proteases differes in cells performing invasion vs cells performing angiogenesis.

overall_design: Trophoblasts were isolated from first trimester placenta, endothelial cells were isolated from third trimester placenta. A pool of 5 preparations from different cell types was used for each microarray.

first: Ursula

last: Hiden

last: Cvitic

first: Martin

last: Bilban

first: Alejandro

last: Majali-Martinez

first: Karin

last: Schramke

first: Gernot

last: Desoye

first: Nassim

last: Ghaffari Tabrizi-Wiszy


title: Whole Blood Transcriptional Response to Early Acute HIV

status: Public on May 18 2015

city: Dallas

first: Damien

last: Chaussabel

state: TX

address: 3434 Live Oak

institute: Baylor Institute for Immunology Research

summary: The objective of this study is to: 1) Characterize the transcriptional signature of early acute HIV infection.  2)  Eucidate the evolution of the signature in both anti-retroviral treated and untreated populations over a 24 week time course. 3) Correlate clinical and disease related parameters to heterogenaity in the transcriptional signature to identify pathways explaining clinical heterogeneity 4) Compare the acute signature of HIV infection to other acute viral signatures.

overall_design: 58 acute HIV patients were recruited from locations in Africa (n=43) and the United States (n=15).  These patients were  allocated into training (n=18), test (n=10) and validation sets (n=30).  Patient samples were collected at study enrollment (confirmed acute) for all patients and at  weeks 1,2,4,12,and 24 for training and test set constituents.  13 of 15 US patients initiated anti-retroviral therapy after after enollment and before the week 1 visit.  The remining 2 US patients and 43 African patients were not placed on therapy through the 24 week time course.  Matched uninfected controls patients were also recuited from each site (n= 55).  In total 232 samples were collectd.


title: Genome-wide analysis of CPC populations

status: Public on May 30 2015

city: Leiden

first: Matthew

last: Birket

address: Einthovenweg 20

department: Anatomy and Embryology

country: Netherlands

institute: Leiden University Medical Center

summary: Gene expression data from hESC-derived cardiac progenitor populations expanded with a MYC transgene

overall_design: Two biological replicates for each population.

middle: J

first: Christine

middle: L

last: Mummery


title: A Gain-of-Function Genomic Screen Identifies the Orphan Nuclear Receptor TLX as an Enhancer of STAT1-mediated Transcription and Immunity to Toxoplasma gondii: TLX siRNA

city: Philadelphia

first: daniel

last: beiting

overall_design: The human astroglioma cell line, U251, was transiently transfected with siRNA targeting human TLX.  72 hours after transfection with siRNA to TLX or a negative control siRNA, cells were stimulated for 8 hours with 10ng/ml of recombinant IFN-gamma.  RNA was isolated from duplicate or triplicate wells for analysis by Illumina microarray.

first: Daniel

last: Beiting

first: Sara

last: Cherry

first: David

last: Roos


title: Identification of KDM3A regulated genes in the ER positive breast cancer cell line MCF-7

status: Public on May 16 2015

city: Newcastle Upon Tyne

first: Mark

last: Wade

address: Paul O'Gorman Building, Framlington Place

department: Northern Institute for Cancer Research

summary: Using a siRNA screen we identified the histone demethylase enzyme KDM3A as a potential positive regulator of ER signalling in breast cancer. To interrogate the full extent of KDM3A regulation on ER signalling we assessed basal and estrogen (E2)- stimulated global gene expression changes in KDM3A-depleted MCF-7 cells by microarray analysis using the Illumina Human HT12 Version 4 BeadChip array. We identified ER regulated genes affected by KDM3A knockdown and determined that KDM3A is required for ER recruitment to estrogen response elements in the promotors of ER regulated genes. We also identified that KDM3A regulates expression of a number of genes involved in proliferation and that knockdown of KDM3A inhibits ER positive breast cancer cell growth.

overall_design: MCF-7 cells were transfected with either a non-silencing scrambled control siRNA (siSCR) or a KDM3A targeting siRNA (siKDM3A-B) using Lipfectamine RNAiMAX (Invitrogen) to a final concentration of 25 nM in steroid depleted conditions. Cells were grown for 48 hours prior to treatment with vehicle or 10 nM E2 for 4 hours before RNA extraction using TRIzol (Ambion, Life Technologies) and hybridization of triplicate samples to an Illumine HT-12 v4 BeadChip array. One sample failed due to low amounts of cRNA and was therefore not included in the analysis (siKDM3A + E2 Replicate 3). The array for replicates 1 and 2 was performed in August 2013 (Array 1) and replicate 3 in August 2014 (Array 2). When processing the data Array 2 was normalized to Array 1.

first: Dominic

last: Jones

first: Laura

last: Wilson

first: Jacqueline

last: Stockley

first: Kelly

last: Coffey

first: Craig

middle: N

last: Robson

first: Luke

last: Gaughan


title: Cells with features of totipotency derived from human ESC and iPSC by transient BMP4 exposure

status: Public on Jun 11 2015

city: Columbia

first: Ying

last: Yang

state: MO

address: 1201 East Rollins Street

department: Division of Animal Sciences

institute: University of Missouri-Columbia

summary: Human pluripotent stem cells (hPSC) exposed to BMP4 (B) and inhibitors of ACTIVIN signaling (A83-01; A) and FGF2 (PD173074; P) in absence of FGF2 (BAP conditions) differentiate into colonies primarily comprised of trophoblast. In an attempt to isolate trophoblast stem cells, colonies of hESC were exposed to BAP for 24 h at which time they had begun to transition into a CDX2-positive state. Cultures were then dissociated into single cells by trypsin and grown on a gelatin substratum. Under these conditions, organized CDX2+/KRT7- colonies began to emerge within a few days. The self-renewing cell lines were not TBSC, but met standard criteria for pluripotency. They were named H1BP cells. They differed from the progenitor hPSC in morphology, ability to be clonally propagated from single cells onto gelatin, requirements for FGF2, and transcriptome profile.

overall_design: RNA was isolated from control human embryonic stem cells H1 cells, H1 cells exposed to BAP conditions for 24 and 48 h, H1BP colonies picked individually at two different passage numbers (p7 and p18), and H1BP cells that had been allowed to differentiate spontaneously in standard non-conditioned hESC medium in absence of FGF2. In order to collect RNA from cells, medium was removed and RNA STAT60  (I ml; Tel-Test, Friendswood, TX) was immediately added to culture dish and RNA extracted by following the manufacturer’s instructions. The samples of RNA were submitted to University Texas Southwestern Medical Center Microarray Core Facility (https://microarray.swmed.edu/) and microarray analysis performed with Illumina HumanHT-12 v4 expression BeadChips. Raw intensity data were background subtracted by using BeadStudio software and analyzed further by GeneSpring 12.6 software (Agilent Technologies Inc., Santa Clara CA), according to the advanced workflow protocol: percentile shift and filter by flags (detected).

first: Yang

last: Ying

first: Adachi

last: Katsuyuki

first: Ezashi

last: Toshihiko

first: Roberts

last: Michael


title: caArray_geral-00143: An estrogen receptor-negative breast cancer subset characterized by a hormonally regulated transcriptional program and response to androgen

status: Public on May 15 2015

city: Rockville

first: Mervi

last: Heiskanen

state: MD

address: 9609 Medical Center Drive, 1W378

department: CBIIT

institute: NCI

summary: Clinical heterogeneity of esrtrogen receptor-negative, progesterone receptor-negative [ER(-)/PR(-)] breast cancer (BC) suggests biological heterogeneity.  We performed gene expression analysis of primary BCs and BC cell lines to identify the underlying biology of ER(-)/PR(-) disease, define subsets, and identify potential therapeutic targets.

overall_design:
geral-00143
Assay Type: Gene Expression
Provider: Affymetrix
Array Designs: HG-U133A
Organism: Homo sapiens (ncbitax)
Material Types: cRNA, cell, OrganismPart, whole_organism, total_RNA
Disease States: breast carcinomas


title: SNP data from AH017 human fibroblasts and induced Pluripotent Stem cells

first: Sally

last: Cowley

type:
Expression profiling by array
SNP genotyping by SNP array


title: Knockdown of CUL3 and PTEN in A549 lung adenocarcinoma cells

city: Minneapolis

first: Casey

last: Dorr

state: MN

address: 701 Park Avenue

institute: Minneapolis Medical Research Foundation

summary:
Non-small cell lung cancers (NSCLCs) harbor thousands of passenger events that hide genetic drivers. Even highly recurrent events in NSCLC, such as mutations in PTEN, EGFR, KRAS, and ALK,   are only detected in, at most, 30% of patients. Thus, many unidentified low-penetrant events are causing   a significant portion of lung cancers. To detect low-penetrance drivers of NSCLC a forward genetic   screen was performed in mice using the Sleeping Beauty (SB) DNA transposon as a random mutagen to   generate lung tumors in a Pten deficient background. SB mutations coupled with Pten deficiency were   sufficient to produce lung tumors in 29% of mice. Pten deficiency alone, without SB mutations, resulted   in lung tumors in 11% of mice, while the rate in control mice was ~3%. In addition, thyroid cancer and   other carcinomas as well as the presence of bronchiolar and alveolar epithelialization in mice deficient   for Pten were also identified. Analysis of common transposon insertion sites identified 76 candidate  cancer driver genes. These genes are frequently dysregulated in human lung cancers and implicate   several signaling pathways. Cullin3 (Cul3), a member of an ubiquitin ligase complex that plays a role in   the oxidative stress response pathway, was identified in the screen and evidence demonstrates that Cul3   functions as a tumor suppressor
HumanHT-12 v4 Expression BeadChip Kit for human A549 lung adenocarcinoma cells with CUL3, PTEN, CUL3 and PTEN or no knockdown.

overall_design: A549 cells were stably transfected under Puromycin or Hygromycin selection to knockdown PTEN (SA Biosystems) or CUL3 (Open Biosystems) shRNAs.  RNA was extracted in triplicate from each condition and used for microarray

first: Tim

middle: K

last: Starr


title: The UBC-40 Urothelial Bladder Cancer Cell Line Index

status: Public on Jun 19 2015

city: Madrid

first: Enrique

last: Carrillo de Santa Pau

address: C/ Melchor Fernández Almagro, 3

department: Cancer Cell Biology Programme

country: Spain

institute: Spanish National Cancer Research Centre (CNIO)


title: Gene expression profiling of T47D breast cancer cells following progestin administration in presence or absence of Telapristone

city: PHILADELPHIA

first: Chirayu

middle: Pankaj

last: Goswami

address: 110 S 11TH STREET

department: MOLECULAR DIAGNOSTIC LABORATORY

institute: THOMAS JEFFERSON UNIVERSITY HOSPITAL

summary: Analysis of the effect of progesterone blockade at the gene expression level.  The hypothesis tested in the present study is that elapristone (CDB4124), an antiprogestin, will downregulate genes that are stimulated by R5020, a synthetic progestin, in the T47D breast cancer cell line.

overall_design: Total RNA obtained from T47 breast cancer cells grown for 24 hours in the presence of:  1.  The sythetic progestin R5020 compared to vehicle control; 2.  The antiprogestin Telapristone (CDB4124) compared to vehicle control; and 3.  R5020 compared to R5020 ± Telapristone.

first: Susan

middle: E

last: Clare


title: Divergent genome wide transcriptional profiles from immune cell subsets isolated from SLE patients with different ancestral backgrounds

city: Rochester

first: Timothy

last: Niewold

address: 1216 2nd St SW

department: Rheumatology

institute: Mayo Clinic Rochester MN

summary:
Background/Purpose:  Systemic lupus erythematosus (SLE) is a complex multi-system autoimmune disease of uncertain etiology. Patients from different ancestral backgrounds demonstrate differences in clinical manifestations and autoantibody profiles.  In this study we examined genome-wide transcriptional patterns in major immune cell subsets across different ancestral backgrounds.

Methods:  Peripheral blood was collected from 21 African-American (AA) and 21 European-American (EA) SLE patients, 5 AA controls, and 5 EA controls. CD4+ T-cells, CD8+ T-cells, monocytes and B cells were purified by flow sorting. Each cell subset from each subject was run on an Illumina HumanHT-12 V4 expression BeadChip array (n=208 arrays). Differentially expressed genes (DEGs) were determined by comparing cases and controls of the same ancestral background.

Results: The overlap in DEG lists between different cell types from the same ancestral background was very modest (<1%).  Typically between 5-10% of DEGs were shared when comparing the same cell type between different ancestral backgrounds (for ex. CD20 AA vs. CD20 EA).  Quantitative measurement of global IFN-stimulated gene (ISG) expression revealed that AA subjects demonstrated more concordance across all studied cell types. Two subgroups of patients were identified based on the ISG expression profiles. One subgroup showed higher ISGs expression in all cell types, and the other subgroup had higherISG expression only in T and B lymphocytes but not in monocytes.  The correlation of ISG expression with medication data revealed that only the B cells had lower ISG expression in patients taking immunosuppressants, while ISG expression in the other cell types did not differ based upon medication use.

Conclusion: We find striking differences in gene expression between different immune cell subsets and between ancestral backgrounds in SLE patients.  The IFN signature is diverse, with different transcripts represented in different cell populations, and signature-positive cell subsets differed in EA vs. AA patients. We also find that treatment with the immunosuppressive agents correlates with the down-regulation of B cell ISG expression, and this was not observed in other cell types.

first: Shruti

last: Sharma

first: Zhongbo

last: Jin

first: Elizabeth

last: Rosenzweig

first: Swapna

last: Rao

first: Kichul

last: Ko

middle: B


title: Gene expression analysis of A549 (adenocarcinomic human alveolar basal epithelial cells) exposed to obese visceral exosomes

status: Public on May 14 2015

city: Washington

first: Robert

last: Freishtat

address: 111 Michigan Avenue NW

department: Center for Genetic Medicine

institute: Children's National Medical Center

summary: Analysis of A549 gene expression (mRNA) after 24 hour exposure to ten different doses of obese visceral adipocyte exosomes. The hypothesis is that obese visceral adipocyte exosomes genetically regulate genes in the TGFβ and Wnt-βcatenin pathways.

overall_design: Total RNA obtained from A549 cells after 24 hour exposure to obese visceral adipocyte exosomes (0.02-10 μg)

first: Dinesh

last: Pillai

first: Justin

last: Wang

first: Sarah

last: Ferrante

first: Humaira

last: Mubeen


title: A Systematic Approach to Identify Markers of Distinctly Activated Human Macrophages

city: Iowa City

first: Joel

last: Graff

state: IA

address: 400 EMRB

department: Internal Medicine

institute: University of Iowa

summary: Polarization has been a useful concept for describing activated macrophage phenotypes and gene expression profiles.  However, macrophage activation status within tumors and other settings are often inferred based on only a few markers.  Complicating matters for relevance to human biology, many of the best studied macrophage activation markers have been best characterized in mice and sometimes are not similarly regulated in human macrophages.  To identify novel markers of activated human macrophages, gene expression profiles for human macrophages of a single donor subjected to 33 distinct activating conditions were obtained and a set of putative activation markers were subsequently evaluated in macrophages from multiple donors using integrated fluidic circuit (IFC)-based RT-PCR.  Using unsupervised hierarchical clustering of the microarray screen, highly-altered transcripts (>4-fold change in expression) sorted the macrophage transcription profiles into two major and 13 minor clusters.  Among the 1874 highly-altered transcripts, over 100 were uniquely altered in one major or two related minor clusters.  IFC PCR-derived data confirmed the microarray results and to show the kinetics of expression of potential macrophage activation markers.  Transcripts encoding chemokines, cytokines, and cell surface were prominent in our analyses.  The activation markers identified by this study could be used to better characterize tumor-associated macrophages from biopsies as well as other macrophage populations collected from human clinical samples.

overall_design: 36 samples total from primary human monocyte-derived macrophages (3 technical replicates for untreated controls and 33 individual samples of uniquely activated macrophage types)


title: YBX1-dependent LNA-tRF-mediated modulation of gene expression under hypoxia

status: Public on May 08 2015

city: San Francisco

first: Hani

last: Goodarzi

department: Biochemistry and Biophysics

institute: UCSF

summary: In order to test whether inhibition of tRFs induced under hypoxia would counteract the YBX1-dependent reduction of target transcripts, we used transient transfection of antisense locked-nucleic acids (pooled LNAs) against tRFAsp, tRFGly, tRFGlu, and tRFTyr under hypoxia followed by microarray profiling.

overall_design: Synthetic antisense locked-nucleic acids (LNAs) targeting the YBX1 binding site on tRFAsp, tRFGly, tRFGlu, and tRFTyr  were transfected (as a pool) in control and YBX1-knockdown cells under hypoxia to assess the consequences of inhibiting tRFs induced in hypoxic MDA-parental cells.

first: H

first: X

last: Liu

first: S

last: Zhang

first: L

last: Fish

middle: F

last: Tavazoie


title: caArray_gray-00215: A collection of breast cancer cell lines for the study of functionally distinct cancer subtypes

status: Public on May 19 2015

first: Mervi

last: Heiskanen

summary:
Recent studies suggest that thousands of genes may contribute to breast cancer pathophysiologies when deregulated by genomic or epigenomic events. Here, we describe a model system to appraise the functional contributions of these genes to breast cancer subsets. In general, the recurrent genomic and transcriptional characteristics of 51 breast cancer cell lines mirror those of 145 primary breast tumors, although some significant differences are documented. The cell lines that comprise the system also exhibit the substantial genomic, transcriptional, and biological heterogeneity found in primary tumors. We show, using Trastuzumab (Herceptin) monotherapy as an example, that the system can be used to identify molecular features that predict or indicate response to targeted therapies or other physiological perturbations.
**NOTE: Migrated from caArray 1.x, identifier='gov.nih.nci.ncicb.caarray:Experiment:1015897590151581:1'

overall_design:
gray-00215
Assay Type: Gene Expression
Provider: Affymetrix
Array Designs: HG-U133A
Organism: Homo sapiens (ncbitax)


title: YBX1-dependent LNA-tRF-mediated modulation of transcript stability

summary: In order to identify YBX1-dependent targets that are modulated upon changing the levels of endogenous tRFs, we used transient transfection of antisense locked-nucleic acids (LNAs) against tRFAsp, tRFGly, tRFGlu, and tRFTyr followed by alpha-amanitine treatment, RNA extraction at time points 0 and 8hr post-treatment, and transcriptomic profiling.

overall_design: Synthetic antisense locked-nucleic acids (LNAs) targeting the YBX1 binding site on tRFAsp, tRFGly, tRFGlu, and tRFTyr  were transfected into control and YBX1-knockdown cells to identify YBX1-dependent targets whose stabilities are modulated due to tRF loss-of-function. We used alpha-amanitine mediated inhibition of RNA-polymerase to measure transcript stability across the entire transcriptome.


title: YBX1-dependent hypoxia-induced modulation of gene expression

summary: In order to identify YBX1-dependent targets that are modulated under hypoxic conditions, we used control and YBX1 knockdown cells grown under normoxia and hypoxia to profile gene expression levels.

overall_design: Control and YBX1-knockdown cells were grown and profiled under hypoxia and normoxia to identify YBX1-dependent hypoxia-induced target transcripts.


title: YBX1-dependent LNA-tRF-mediated modulation of gene expression

summary: In order to identify YBX1-dependent targets that are modulated upon changing the levels of endogenous tRFs, we used transient transfection of antisense locked-nucleic acids (LNAs) against tRFAsp, tRFGly, tRFGlu, and tRFTyr followed by microarray profiling.

overall_design: Synthetic antisense locked-nucleic acids (LNAs) targeting the YBX1 binding site on tRFAsp, tRFGly, tRFGlu, and tRFTyr  were transfected into control and YBX1-knockdown cells to identify YBX1-dependent targets that are modulated due to tRF loss-of-function.


title: SLAMF1/CD150 regulates chemotaxis, autophagy and therapy responses in chronic lymphocytic leukemia patients

status: Public on May 23 2015

city: Turin

first: SILVIA

last: DEAGLIO

address: Via Nizza 52

department: Medical Sciences

institute: University of Torino & Human Genetics Foundation

summary: This work shows that signaling-lymphocytic-activation-molecule-1 (SLAMF1), a co-stimulatory molecule and a microbial sensor, is expressed by normal CD19+/CD5+ B-lymphocytes. Its expression is lost in a subset of patients with chronic lymphocytic leukemia (CLL) characterized by an aggressive form of the disease, with shorter time to first treatment and overall survival.   Silencing of SLAMF1 in the CLL-like Mec-1 cell line (constitutively SLAMF1+) modulated pathways connected to cell migration, cytoskeletal organization and intracellular vesicle formation/recirculation. Loss of SLAMF1 was associated to increased expression of CXCR4, CD38 and CD44, positively affecting chemotactic responses to CXCL12. Ligation of SLAMF1 with an agonistic monoclonal antibody promoted the autophagic flux, by increasing reactive oxygen species (ROS) accumulation and inducing phosphorylation of p38, JNK1/2 and bcl-2. The direct consequence was the assembly of the autophagy macro-complex that included SLAMF1, the scaffold protein Beclin1 and the enzyme Vps34. Consistently, SLAMF1-silenced cells or SLAMF1low primary CLL cells were resistant to autophagy-activating therapeutic agents, such as fludarabine or the BH3 mimetic ABT-737. These results indicate that loss of SLAMF1 expression modulates genetic pathways regulating chemotaxis and autophagy and potentially affecting drug responses, thus providing a likely explanation for the unfavorable clinical outcome experienced by this patient subset.

overall_design: Microarrays were performed comparing genetic signature of CLL-like Mec-1 cell line (constitutively SLAMF1+), transfected with a non-effective (scrambled) shRNA cassette (TR30013) used as control, and a Mec-1 variant generated silencing SLAMF1 gene using pGFP-V-RS construct for SLAMF1 shRNA (TG309422). For each cell line variants, grown in vitro in complete medium, three biological replicates were included in the chip.

first: Cinzia

last: Bologna

first: Roberta

last: Buonincontri

first: Sara

last: Serra

first: Tiziana

last: Vaisitti

first: Valentina

last: Audrito

first: Davide

last: Brusa

first: Andrea

last: Pagnani

first: Marta

last: Coscia

first: Giovanni

last: D'Arena

first: Richard

middle: R

last: Furman

last: Rossi

first: Gianluca

last: Gaidano

first: Cox

last: Terhorst

first: Silvia

last: Deaglio


title: Effect of MEL-18 knockdown on estrogen-sensitive MCF7 breast cancer cells

status: Public on May 01 2015

city: Seoul

first: Gu

last: Kong

address: 17 Haengdang-dong, Seongdong-gu

department: Department of Pathology

institute: College of Medicine, Hanyang University

summary: Gene expression analysis of MEL-18-silenced MCF7 cell lines. MEL-18 is a component of the polycomb repressive complex (PRC)-1, which is a critical epigenetic modulator of stem cell regulation and normal and cancerous development. Accumulating studies have suggested that MEL-18 might act as a tumor suppressor in several human tumors, including breast cancer. Results provide insight into the functional role of MEL-18 in estrogen-dependent breast cancer.

overall_design: MCF7 cells stably infected with lentiviruses encoding either control (shCon) or MEL-18 shRNA (shMEL) were cultured in phenol-red free DMEM supplemented with 10% FBS for 48 h. Total RNA was isolated from the cultures using Trizol reagent. For each of the 2 conditions, 2 biological replicates were included. In total, 4 microarray samples were analyzed; 2 controls and 2 shRNA MEL-18 knockdowns. All labeling, hybridization and scanning steps were performed according to the manufacturers’ instructions.

first: Jeong-Yeon

last: Lee


title: Identification of the differences between gene expression in normal human dermal fibroblasts (NHDF cell line) infected with Borrelia burgdorferi sensu lato spirochetes

status: Public on May 12 2015

city: Sosnowiec

first: Sławomir

last: Dudek

address: Jagiellonska 4

country: Poland

institute: Medical University of Silesia

summary: The similarity of Lyme borreliosis to other diseases and the complex pathogenesis cause diagnostic and therapeutic difficulties. Changes at the cellular and molecular level after Borrelia sp. infection remain still poorly understood. Therefore, the present study focused on the gene expression in human dermal fibroblasts in differentiation of infection with Borrelia garinii, Borrelia afzelii and Borrelia burgdorferi sensu stricto spirochetes.

overall_design: For microarray analysis 10 samples were used: 3 control samples - K, 2 samples of NHDF cells infected with Borrelia garinii - G, 2 samples of NHDF cells infected with Borrelia afzelii - A and 3 samples of NHDF cells infected with Borrelia burgdorferi sensu stricto - SS.

first: Urszula

last: Mazurek

first: Slawomir


title: The long noncoding RNA HOTAIR has tissue and cell type dependent effects on HOX gene expression and phenotype of cancer cells

status: Public on Jun 05 2015

city: Duesseldorf

first: Karl

last: Koehrer

address: Universitaetsstr. 1

department: BMFZ

institute: University of Duesseldorf

summary: HOTAIR was found to be overepressed in a subset of urothelial cancer tissues and cell lines compared to normal controls. Ectopic HOTAIR expression in urothelial cancer cells in vitro demonstrated cell type dependent changes in phenotype. While some cell lines showed increased proloferation activity and induction of an aggressive phenotypes (e.g. stable transfected VM-CUB1 cells), others displayed rather a reduction of proliferation and migration. Stable transfection of 5637 cells resulted in induction of an immune response. Results of  microarray analysis of stable transfected VM-CUB1 and 5637 cells concurred well with observed phenotypical cell type-specific changes.

overall_design: For differential gene expression analyses three independent high quality RNA preparations from VM-CUB1 cells, stably transfected with HOTAIR (clone 20), and 5637 cells, stably transfected with HOTAIR (clone 4), were compared to the respective vector control cells.

first: J

last: Heubach

last: Monsior

first: R

last: Deenen

first: G

last: Niegisch

first: W

last: Schulz

first: M

last: Hoffmann


title: caArray_jacob-00182: Gene expression-based survival prediction in lung adenocarcinoma: a multi-site, blinded validation study

status: Public on May 02 2015

first: Mervi

last: Heiskanen

summary: Here we report a large, training*testing, multi-site, blinded validation study to characterize the performance of several prognostic models based on gene expression for 442 lung adenocarcinomas. The hypotheses proposed examined whether microarray measurements of gene expression either alone or combined with basic clinical covariates (stage, age, sex) could be used to predict overall survival in lung cancer subjects. Several models examined produced risk scores that substantially correlated with actual subject outcome. Most methods performed better with clinical data, supporting the combined use of clinical and molecular information when building prognostic models for early-stage lung cancer. This study also provides the largest available set of microarray data with extensive pathological and clinical annotation for lung adenocarcinomas.

overall_design:
jacob-00182
Assay Type: Gene Expression
Provider: Affymetrix
Array Designs: HG-U133A
Organism: Homo sapiens (ncbitax)
Material Types: cell, synthetic_RNA, organism_part, whole_organism, total_RNA
Disease States: Lung Adenocarcinoma


title: caArray_notte-00422: Molecular Dissection of Colon Cancer

summary: RNA expression data was generated as part of a colon cancer study. Samples were obtained from patients, including primary colon cancer, polyps, metastases, and matched normal mucosa (obtained from the margins of the resection). The RNA was extracted from tissue samples obtained from resections and hybridized to Affymetrix HG-U133 arrays. RNA expression data was also obtained for a few cell lines.

overall_design:
notte-00422
Assay Type:  Gene Expression
Provider: Affymetrix
Array Designs: HG-U133A
Organism: Homo sapiens (ncbitax)
Material Types: cell, total_RNA, synthetic_RNA, organism_part, whole_organism
Disease States: colon cancer, colon polyp, Colon Carcinoma, colon adenocarcinoma, breast cancer, Normal, Prostate Adenocarcinoma


title: Syngergistic Effect of JQ1 and Rapamycin for Treatment of Human Osteosarcoma

city: Singapore

first: Henry

last: Yang

address: 28 Medical Drive

country: Singapore

institute: Cancer Science Institute of Singapore

summary: Bromodomain and extra terminal domain (BET) proteins are important epigenetic  regulators facilitating the transcription of genes in chromatin areas linked to acetylated  histones. JQ1, a BET protein inhibitor, has antiproliferative activity against many  cancers, mainly through inhibition of c-MYC and upregulation of p21. In this research,  we investigated the use of JQ1 for human osteosarcoma (OS) treatment. JQ1 significantly  inhibited the proliferation and survival of OS cells inducing G1 cell cycle arrest,  premature senescence, but little effect on apoptosis. Interestingly, c-MYC protein levels  in JQ1-treated cells remained unchanged, whereas the upregulation of p21 protein was  still observable. Although effective in vitro, JQ1 alone failed to reduce the size of the  MNNG/HOS xenografts in immunocompromised mice. To overcome the resistance of  OS cells to JQ1 treatment, we combined JQ1 with rapamycin, an mTOR inhibitor. JQ1  and rapamycin synergistically inhibited the growth and survival of OS cells in vitro and  in vivo. We also identified that RUNX2 is a direct target of BRD4 inhibition by JQ1 in OS cells. Chromatin immunoprecipitation (ChIP) showed that enrichment of BRD4 protein around RUNX2 transcription start sites diminished with JQ1 treatment in MNNG/HOS cells. Overexpression of RUNX2 protected JQ1-sensitive OS cells from the effect of JQ1, and siRNA-mediated inhibition of RUNX2 sensitized the same cells to JQ1. In conclusion, our findings suggest that JQ1, in combination with rapamycin, is an effective chemotherapeutic option for OS treatment. We also show that inhibition of RUNX2 expression by JQ1 partly explains antiproliferative activity of JQ1 in OS cells.

overall_design: MNNG/HOS cells treated with 7.5mM JQ1, 12.5nM Rapamycin or both were used for RNA extraction and hybridization on Affymetrix microarrays. We compared these microarray samples with the corresponding control (treated with DMSO).

first: Dhong

middle: H

first: Jun

last: Qi

first: James

last: Bradner

first: Jonathan

last: Said

first: Ngan

last: Doan

first: Charles

last: Forscher

first: Phillip

last: Koeffler


title: FACT and Spt6 Prevent Cryptic Transcription by Impeding H2A.Z Loading in Gene Bodies

city: Montreal

first: Francois

last: Robert

state: QC

address: 110 av des Pins Ouest

institute: IRCM

type: Genome binding/occupancy profiling by genome tiling array

summary: H2A.Z is a highly conserved histone variant involved in several key nuclear processes. It is incorporated into promoters by SWR-C-related chromatin remodeling complexes, but whether it is also actively excluded from non-promoter regions is not clear. Here, we provide genomic and biochemical evidence that RNA polymerase II (RNAPII) elongation-associated histone chaperones FACT and Spt6 both contribute to restricting H2A.Z from intragenic regions. In the absence of FACT or Spt6, the lack of H2A.Z eviction, coupled to its pervasive incorporation by mislocalized SWR-C, alters chromatin composition and contributes to cryptic initiation. Thus, chaperone-mediated H2A.Z removal is crucial for restricting the chromatin signature of gene promoters, which otherwise may license or promote cryptic transcription.

overall_design: We profiled H2A.Z occupancy in S. cerevisiae by ChIP-chip on tiling arrays in different mutants for chromatin remodelers and histone chaperones. In most experiments, H2A.Z ChIP samples (Cy5-labeled) were performed using a polyclonal antibody against H2A.Z and hybridized against H2B ChIP samples (Cy3-labeled), also performed using a polyclonal antibody. Temperature-sensitive mutants for the histone chaperones Spt16 and Spt6 (spt16-197 and spt6-1004 respectively) showed strong H2A.Z localization defects so the role of these factors in H2A.Z localization was further analyzed. H2A.Z ChIP-chip experiments in spt16-197 and spt6-1004 were repeated using different experimental designs [normalized against Input DNA or Mock (IgG) ChIP samples]. The contribution of Spt16 and Spt6 on H2A.Z localization was also confirmed by nuclear depletion of Spt16 and Spt6 using the anchor-away system. H2A.Z ChIP-chip experiments were also performed in sic1Δ and spt16-197/sic1Δ cells in order to rule out any G1-arrest artifact. H2A.Z ChIP-chip experiments were repeated using spike-in controls for normalization, revealing widespread H2A.Z occupancy in Spt16 and Spt6 mutants. In addition, the localization of the chromatin remodeler SWR-C was determined in wild type cells as well as in spt16-197 and spt6-1004 cells. Finally, we also profiled histone H4 occupancy by ChIP-chip in wild type, spt16-197, spt6-1004, spt16-197/htz1Δ and spt6-1004/htz1Δ cells. All ChIP-chip experiments were done in duplicates. Each microarray was normalized using the Lima Loess and replicates were combined using a weighted average method as previously described (Pokholok et al., 2005).

first: Célia

last: Jeronimo

first: Shinya

last: Watanabe

first: Craig

last: Kaplan

last: Peterson

first: François


title: High mitochondrial respiration and glycolytic capacity represent a metabolic phenotype of human tolerogenic dendritic cells

first: Kaibo

last: Duan

address: 8A Biomedical Grove, Immunos Building, Level 4

institute: Singapore Immunology Network

summary: Human monocyte-derived dendritic cells (moDCs) have been used as an in vitro model for studying tolerance and immunity. However, the underlying metabolic states of tolerogenic (dexamethasone and vitamin D3-treated), immature and immunogenic (mature, LPS-treated) moDCs have not been completely characterized. Through transcriptomic analyses, we determined that tolerogenic moDCs exhibit augmented catabolic pathways with respect to oxidative phosphorylation (OXPHOS), fatty acid oxidation (FAO) and glycolysis. Functionally, tolerogenic moDCs showed the highest mitochondrial membrane potential, production of reactive oxygen species and superoxide, and increased mitochondrial spare respiratory capacity. Tolerogenic and mature moDCs manifested differential FAO gene expression with FAO activity being significantly higher in tolerogenic and immature moDCs than in mature. In addition, tolerogenic and mature moDCs demonstrated similar levels of glycolytic rate, but not glycolytic capacity and reserve, which were more pronounced in tolerogenic and immature moDCs. Finally, tolerogenic and immature moDCs, but not mature moDCs, showed high plasticity to compensate the intracellular ATP content after inhibition of different energetic metabolic pathways. Overall, tolerogenic moDCs exhibit a metabolic signature of increased, stable OXPHOS programing and high plasticity for metabolic adaptation. These findings provide a framework for future research of metabolic properties of human DCs.

overall_design: Total RNA of sixteen samples from four moDC types (tolerogenic, LPS-tolerogenic, immature and mature) were extracted by Trizol (Invitrogen) followed by a clean-up procedure using RNeasy Micro Kit (Qiagen). All RNA samples had an integrity number ≥9.6 assessed by Agilent Bioanalyzer. Total RNA samples were amplified using TargetAmp™ and the biotinilated cRNA was prepared by Nano-g™ Biotin-aRNA Labeling Kit for the Illumina® System (Epicentre). After the hybridization to the Illumina Human HT-12 v4 Beadchips for 17 h at 58°C, the arrays were washed, stained (Illumina Wash Protocol) and then scanned using BeadArray Scanner 500GX. Array data were extracted at the probe level without background correction using Illumina GenomeStudio software. These raw data were quantile normalized and log2 transformed. Technical replicates were obtained from the hybridization in duplicate of three samples. Pearson correlation analysis showed high correlation between the technical replicates (r>0.99). Differentially expressed genes (DEGs) were identified using Limma16 with Benjamini-Hochberg multiple testing correction (p<0.05). DEGs were further clustered into different groups according to the patterns of expression change among the different moDC types using STEM software17. The analysis was performed in R v.2.12.2 (http://www.R-project.org) with Bioconductor 2.12 (http://www.bioconductor.org) and enabled by Pipeline Pilot (www.accelrys.com).

first: Frano

last: Malinarich

first: Raudhah

last: Hamid

first: Au

last: Bijin

first: Michael

last: Poidinger

first: Anna-Marie

last: Fairhurst

first: John

last: Connolly


title: Constitutively-active MAVS inhibits HIV-1 replication via type I interferon secretion and induction of HIV-1 restriction factors

status: Public on Jun 01 2015

city: Silver Spring

first: BIJU

last: ISSAC

address: 503 Robert Grant Ave, Rm 2W123

department: Military HIV Research Program

institute: Walter Reed Army Institute of Research

summary: Type I interferon plays a critical role in the control of viral infections, including HIV-1. Interferon induces a number of restriction factors that block HIV-1 entry, replication and release from the host cell. Currently, systemic treatment of HIV-1 infection with interferon has little efficacy in the clinic due to side effects including fatigue and flu-like symptoms. However, understanding the role of interferon in HIV-1 restriction, and developing molecular tools to generate type I interferons locally, provide an opportunity to inhibit HIV-1 replication while avoiding the side effects associated with systemic administration.  Here, we tested a constitutively active inducer of high levels of interferon beta (dLMP1-MAVS).  Supernatant from cell transfected with dLMP1-MAVS inhibited HIV-1 replication in both culture cells and primary human CD4+ T cells. CD4+ T cells upregulated a number of known HIV-1 restriction factors, including Viperin, Tetherin, MxB, and ISG56 in response to dLMP1-MAVS. In addition, dLMP1-MAVS activated human dendritic and acted as a molecular adjuvant in a mouse HIV-1 vaccine model. Our study generates new insights into the role of type I interferon in HIV-1 restriction, and provides a novel strategy to induce both type I interferon and anti-HIV-1 immune responses at sites of ongoing viral replication.

overall_design: T cells were  transfected with pcDNA3.1 plasmid and cultured in DMEM media plus 10% fetal bovine serum

first: Sachin

last: Gupta

first: James

last: Termini

first: Biju

last: Issac

first: Elizabeth

last: Guirado

first: Geoffrey

last: Stone


title: The human airway epithelial basal cell transcriptome in the early response to injury

status: Public on Apr 30 2015

city: Chicago

first: Shwu-Fan

last: Ma

state: IL

address: 5841 S. Maryland Ave.,

department: Medicine

institute: University of Chicago

summary: Background: Basal cells within the human airway epithelium constitute the stem/progenitor cells for other epithelial cell types. Basal cells respond to mucosal injury and damage to the airway mucosa in an ordered sequence of spreading, migration, proliferation and phenotype shifting (differentiation) to other needed cell types. However, dynamic gene transcription in the early events of injury and repair has not been examined in these cells. Methodology and findings: Airway epithelial cells were obtained from donated lungs and grown in submersion culture on pliable membranes to obtain a pure population of basal cells. Microarrays were used to assess the transcriptome of basal cells 8 and 24 hr after mechanical injury (MI), or to cyclic stretch (CS) in a Flexcell system (0.5 Hz, 20% distension), or both treatments. We identified 121 signature genes with > 2-fold higher differential expression (DE) 8 hr after MI; expression of nearly all of these genes returned to baseline at 24 hr after injury. In cells subjected to CS, little change in DE was noted at 8 hr, whereas at 24 hr a CS signature of 1430 DE genes were identified. The MI signature was characterized by genes encoding growth factor receptors related to the EGF pathway, IL-6, IL-8 and IL-33, extracellular matrix components, and NF-kB and p38-MAPK signaling pathways, whereas the CS signature was characterized by a broad range of genes that did not identify specific signaling pathways. Combined MI and CS at 8 hr elicited DE of down-regulated genes not seen with either stimulus alone, and at 24 hr elicited DE that was similar to that seen with CS alone. Conclusion and significance: The human airway basal epithelial cell transcription signature in the first hours after MI, after CS, and after both stimuli identifies unique differentially expressed genes and pathways that may be important in the early molecular response and biology to airway injury.

overall_design: Total RNA obtained from primary (AEC) and differentiated (dAEC) human airway epithelial cells subjected to 8 or 24 hours in vitro mechanical or cyclic stretch or both injuries compared to sham control as well as to type of injury. Cells were collected from four donated lungs and cultured separated in submission or air liquid interface condition prior to injury for various durations.

first: Steven

last: White

first: Bharathi

last: Laxman

first: Yong

last: Huang

first: Randi

last: Stern

first: Konstantin

last: Birukov


title: Expression data from CUTLL1 cells infected with shHES1

status: Public on May 07 2015

city: New York

first: Alberto

last: Ambesi-Impiombato

state: NY

address: 1130 St. Nicholas Avenue

department: ICG

institute: Columbia University

summary:
To formally address the biological activity of HES1 in vitro, we measured the transcriptional effect of HES1 inactivation infectiing CUTLL1 leukemia cell lines with shHES1
HES1 knockdown triggered apoptosis in human T-ALL lymphoblasts. We show that HES1 inactivation induces programmed cell death in leukemia lymphoblasts

overall_design: We performed microarray gene expression analysis of shHES1 vs shRNA LUC

first: Stephanie

last: Schnell

first: Luyao

last: Xu

first: Yue

last: Qin

first: Ryoichiro

last: Kageyama

first: Adolfo

last: Ferrando


title: Establishing and improving retroviral episome transfer of transcription factors to achieve cell fate conversion and reprogramming

status: Public on May 06 2015

city: Kiel

first: Franz-Josef

last: Müller

address: Niemannsweg 147

department: Klinik für Psychiatrie und Psychotherapie

institute: Zentrum für Integrative Psychiatrie Kiel

summary: Gene transfer of distinct cocktails of transcription factors enables the targeted modification of cell fate. Reprogramming somatic cells to induced pluripotent stem cells (iPSCs) via ectopic expression of the transcription factors Oct4, Sox2, Klf4 and c-Myc allows creation of pluripotent cells with the potential to differentiate into any cell type of the body. To achieve a high degree of biosafety for future application of converted cells, technologies are required to express the required transcription factors without affecting the target cell genome. Retroviral vectors are widely employed gene transfer vehicles and can be converted into transient gene delivery vehicles by mutation of the viral integrase, thus avoiding risks associated with retroviral integration. We improved the retroviral episome transfer system by identifying the most suitable vector architecture, by enhancing episomal expression and by tuning the activity of the transcription factor Oct4. Repeated episomal transductions allowed establishment of stable, fully reversible expression levels over time. Providing proof-of-principle in the reprogramming context, we were able to generate human iPSCs following retroviral episomal transfer of Oct4 in fibroblasts stably expressing Klf4, Sox2 and c-Myc, with a high percentage of clones not carrying residually integrated vector copies.

overall_design: RNA obtained from human embryonic stem cells, fibroblasts and induced pluripotent stem cell lines reprogrammed with the mentioned reprogramming protocol

first: Juliane

last: Schott


title: Combination of HDAC inhibitors and Azacytidine for Cancer Cell Selective Targeting of Esophageal Cancer Cells

status: Public on Apr 29 2015

city: Lübeck

first: Hauke

last: Busch

state: Schleswig-Holstein

address: Ratzeburger Allee 160

department: Lübeck Institute of Experimental Dermatology

institute: University of Lübeck

summary:
Esophageal cancers (ECs) are highly aggressive tumors with poor prognosis and few treatment options. This study investigated the possibility of treating esophageal squamous cell carcinoma (ESCC) and esophageal adenocarcinoma (EAC) cells by inhibitors of broad and specific histone deacetylases (HDACi; SAHA, MS-275, FK228) and/or of DNMT (Azacytidine, AZA).
Drug targets (HDAC1,2,3 and DNMT1) were present in non-neoplastic (HET-1A), ESCC (OE21) and EAC (OE33) cell lines. All cell lines responded to HDACi by reduced HDAC activity and increased histone acetylation as well as to AZA by up-regulation of p21. Expression of drug targets remained largely unaffected by HDACi and AZA treatment. Importantly, cell viability, apoptosis, cell cycle dynamics and DNA damage were only affected by HDACi and/or AZA in ESCC and EAC, but not the non-neoplastic cells. This was specifically seen for the combination of MS-275 and AZA, leading to enhanced cancer cell selectivity and drug efficiency. By transcriptome analyses of MS-275, AZA and MS-275/AZA treated cells, known (e.g. p21) as well as novel regulated genes significantly associated with the cellular effects post HDACi and/or AZA treatment in ESCC and EAC cells were identified. Finally, human EC tissue specimens frequently expressed the actionable drug targets HDAC1/2/3 and DNMT1.
In summary, a combined HDACi (MS-275)/AZA treatment is cancer cell selective and efficient in vitro. Since the majority of ECs express the drug targets in situ, this paves the way for further investigations of HDACi/AZA treatment in esophageal cancer cells and their translation into a clinico-pathological setting.

overall_design: To elucidate the transcriptome response to HDAC inhibitors of  normal esophageal cells and esophageal tumor cells, total RNA was isolated from non-neoplastic esophageal epithelial cells (Het1A cells) a well as from two esophageal tumor cell lines (OE21 and OE33), respectively. Cells were treated with either MS-275, Azacytidine (AZA) or in combination of both. DMSO treatment was used as control in each case. Total RNA was isolated from cells 24 h after treatment and experiments were performed in biological triplicates.

first: Melanie

last: Boerries

first: Silke

last: Lassmann

first: Theresa

last: Ahrens


title: Regulation of tumor associated macrophages by cooperative inflammatory signaling

status: Public on Apr 28 2015

city: Memphis

first: Geoffrey

last: Neale

state: TN

address: 262 Danny Thomas Place

department: Hartwell Center

institute: St Jude Childrens Research Hospital

summary: Tumor associated macrophages show signs of both, classical pro-inflammatory as well as alternative macrophage activation. The aim of this study was to compare TAMs across tumor types, to characterize their phenotype in detail and to identify the signaling nodules involved regulating classical and alternative activation traits.

overall_design: To identify gene expression profiles and pathways differentially activated in tumor-associated macrophages (TAMs) we isolated TAMs from in vivo animal models of EG7 thymoma (n=3), glioma (n=3) and neuroblastoma (n=3) by tumor digestion and subsequent enrichment of CD11b+ cells using Miltenyi magnetic beads. Thymomas grown in WT or Myd88-/- mice (n=5 per group) were used to identify TLR/IL1R dependent signaling in TAMs. RNA extracted from CD11b+ TAMs was analyzed using the Affymetrx HT_MG-430_PM arrays. For in-depth analysis of the role of inflammatory signaling by TNFR1 (Tnfrsf1a) and/or Myd88, EG7 TAM populations A (CD11b+, Ly6G-, Ly6C+, MHCII-) and C (CD11b+, Ly6C-, MHCII+) were isolated by flow cytometric sorting from WT, TNFR1-/-, Myd88flox/flox; Tie2-Cre and TNFR-/-; Myd88flox/flox; Tie2-cre mice and extracted RNA was analyzed by microarray using the Mouse Gene 2.0 GeneChip arrays (n=2 per genotype and population).

first: Franz

last: Kratochvill

first: Peter

last: Murray


title: Gene expression profiling of CREB knockdown in Acute Lymphoblastic Leukemia cells

city: Groningen

first: Naomi

middle: Eline

last: van der Sligte

state: Nederland

address: Hanzeplein 1

department: Pediatrics

institute: University Medical Center Groningen

summary: Gene expression profiling was performed to examine genetic consequences that resulted from shRNA mediate knockdown of CREB in the four ALL cell lines Jurkat, Nalm6, Molt4, and RS4;11 using two CREB shRNAs.

overall_design: Leukemic cells were incubated with lentiviral supernatants for one or two consecutive days after which stably transduced cells were expanded. Transduced cells were pelleted and total RNA was isolated from CREB or scrambled transduced cells. The quality control, RNA labeling, hybridization, and data extraction was profiled on Illumina Human v2 Expression BeadChips, all performed at ServiceXS B.V.

first: Kim

last: Kampen

first: Arja

last: ter Elst

first: Frank

middle: G

last: Scherpen

first: Tiny

last: Meeuwsen - de Boer

first: Victor

last: Guryev

last: van Leeuwen

first: Steven

last: Kornblau

first: Eveline

middle: S

last: de Bont


title: caArray_dobbi-00100: Interlaboratory comparability study of cancer gene expression analysis using oligonucleotide microarrays

city: Rockville

first: Mervi

last: Heiskanen

address: 9609 Medical Center Drive, 1W378

department: CBIIT

institute: NCI

summary: A key step in bringing gene expression data into clinical practice is the conduct of large studies to confirm preliminary models. The performance of such confirmatory studies and the transition to clinical practice requires that microarray data from different laboratories are comparable and reproducible. We designed a study to assess the comparability of data from four laboratories that will conduct a larger microarray profiling confirmation project in lung adenocarcinomas. To test the feasibility of combining data across laboratories, frozen tumor tissues, cell line pellets, and purified RNA samples were analyzed at each of the four laboratories. Samples of each type and several subsamples from each tumor and each cell line were blinded before being distributed. The laboratories followed a common protocol for all steps of tissue processing, RNA extraction, and microarray analysis using Affymetrix Human Genome U133A arrays. High within-laboratory and between-laboratory correlations were observed on the purified RNA samples, the cell lines, and the frozen tumor tissues. Intraclass correlation within laboratories was only slightly stronger than between laboratories, and the intraclass correlation tended to be weakest for genes expressed at low levels and showing small variation. Finally, hierarchical cluster analysis revealed that the repeated samples clustered together regardless of the laboratory in which the experiments were done. The findings indicate that under properly controlled conditions it is feasible to perform complete tumor microarray analysis, from tissue processing to hybridization and scanning, at multiple independent laboratories for a single study.

overall_design:
dobbi-00100
Assay Type: Gene Expression
Provider: Affymetrix
Array Designs: HG-U133A
Organism: Homo sapiens (ncbitax)
Tissue Sites: Kidney, Lung, Stomach, Uterus, Liver, Lymphoid tissue, Ovary, Skin, Adrenal Gland, Lymph_Node
Material Types: cell, nuclear_RNA, synthetic_RNA, organism_part, total_RNA
Disease States: Recurrent Renal Cell Carcinoma, Squamous Cell Carcinoma,Conventional_Clear_Cell_Renal_Cell_Carcinoma,Gastrointestinal_Stromal_Tumor, Lung_Adenocarcinoma, Leiomyoma, Non neoplastic liver with cirrosis, Stomach Adenocarcinoma, Large Cell Lymphoma, Ovarian Adenocarcinoma, Melanoma, Malignant G1 Stromal Tumor, Adrenal Cortical Adenoma, Metastatic Renal Cell Carcinoma, Malignant Melanoma


title: Genome-wide analysis of energy-starved fibroblasts in quiescence

status: Public on Apr 18 2015

city: Philadelphia

first: Andres

last: Kriete

state: PA

address: 3141 Chestnut St

department: School of Biomedical Engineering

institute: Drexel University

summary: This analysis investigated changes in transcripts in quiescent dermal fibroblast cell cultures in response to energy stress. A quiescent control was compared to a 24h energy starvation sample using DNP/2DG inhibitor combination.

overall_design: Two chips were used for the control sample, and two chips were used each for the treated sample and its biological replicate.

first: David

last: Alfego


title: The effect of SUZ12 knockdown on the responsivness of IFNg Stimulated Genes

city: Toronto

first: Rod

last: Bremner

state: ON

address: 600 University Ave

department: Lunenfeld-Tanenbaum Research Institute

institute: Mount Sinai Hospital

type: Expression profiling by high throughput sequencing

summary:
We studied the effect of knowking down SUZ12 +/- knowckdown of BRM on the responsivness of IFNg stimulated genes. Cells were transfected with siSZU12+/-siBRM or control siRNA+/-siBRM. Cells were then left untreated or exposed to IFNg for 6 hours.
Total RNA was collected and analyzed with Illumina arrays.

overall_design: SW13 cells were transfected with siSUZ12+/-siBRM or control siRNA+/-siBRM. Cells were left untreated or exposed to IFNg for 6 hours.

first: Mohamed

last: Abou El Hassan

first: Katherine

last: Huang


title: Telomerase subunit TERT regulates MYC stability independent of its role on telomeres (array)

status: Public on Apr 23 2015

first: Julius

last: Müller

address: 61 Biopolis Drive

department: IMCB

institute: A*Star Singapore

summary: Constitutively active MYC and reactivated telomerase often co-exist in cancers. While the reactivation of telomerase is thought to be essential for replicative immortality, MYC, in conjunction with co-factors, confers several growth advantages to cancer cells. However, it is unclear which co-factors sustain elevated MYC activity in tumors . Here, we identify TERT, the catalytic subunit of telomerase, as a novel regulator of MYC stability in cancers. Binding of TERT to MYC stabilizes its levels on chromatin, contributing to either activation or repression of its target genes. Mechanistically, TERT regulates MYC ubiquitination and stability, and this effect of TERT is independent of its role on telomeres. Genetic inhibition and knocking out of TERT phenocopied the loss of MYC, resulting in reduced disease burden of early- and late-stage MYC-driven murine lymphomas. Conversly, the ectopic expression of TERT could substitute for reduced MYC in these functions. Finally we show that TERT null mice, unlike Terc null mice, show delayed onset of MYC induced lymphomagenesis. Accordingly, inhibiting TERT function in primary human leukemia cells blocked the expression of MYC targets, while Terc depletion had no effects .  Based on our data, we conclude that the re-expression of TERT, a direct MYC target in tumors, provides a feed-forward mechanism to potentiate MYC-dependent oncogenesis.

overall_design: P493 cells were stably infected with the following viruses: pLKO shControl and pLKO shTERT.

first: Cheryl

last: Koh

first: Ekta

last: Khattar

first: Shi

middle: C

last: Leow

first: Chia

middle: Y

last: Liu

last: Muller

first: Wei

middle: X

last: Ang

first: Yinghui

last: Li

first: Guido

last: Franzoso

first: Shang

first: Ernesto

last: Guccione

first: Vinay

last: Tergaonkar


title: H9 human embryonic stem cells, Neural Precursor Cells

first: Dong-Wook

last: Kim

address: 50-1 Yonsei-ro, Seodaemun-gu

department: Dept. of Physiol.

institute: Yonsei University College of Medicine

summary: Identify gene expression patterns of different neural precursor cells derived from human embryonic stem cells.

overall_design: The total of 12 samples were analyzed which could be grouped into 4 groups

first: Dae-Sung

first: Dongjin

last: Lee