title: Combinatorial analysis of miRNA and mRNA expression in pancreatic ductal adenocarcinoma (PDAC)_mRNA

status: Public on Dec 30 2013

city: Rome

first: Teresa

last: Colombo

address: p.le A. Moro 7

department: Institute of Molecular Biology and Pathology (IBPM)

institute: Consiglio Nazionale delle Ricerche (CNR)

summary:
miRNAs are known to be involved in PDAC tumorigenesis, but only a few biologically relevant gene targets have been identified.
Here we show that three miRNAs (miR-21, miR-23a and miR-27a) act in concert for the cooperative suppression of several tumor suppressor genes of which we experimentally validated PDCD4, BTG2 and NEDD4L.
The synergistic inhibition of this triple miRNA combination is capable of reducing PDAC growth in a mouse model greater than inhibition of oncomiR-21 alone.

overall_design: Patients samples of normal pancreas (n=6) or pancreatic ductal adenocarcinoma (PDAC; n=6) were retrieved during surgery and placed in RNA Later stabilization fluid and then kept at minus 80 until required.

first: Adam

last: Frampton


title: MicroRNAs Cooperatively Inhibit a Network of Tumor Suppressor Genes to Promote Pancreatic Tumor Growth and Progression

country: Italy

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

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

overall_design: Refer to individual Series


title: Gene expression analysis of recurrent metastatic melanoma lesions

status: Public on Dec 31 2013

city: Budapest

first: Zoltan

last: Pos

address: 4 Nagyvarad ter

department: Dept. of Genetics, Cell- and Immunobiology

country: Hungary

institute: Semmelweis University

summary:
In this study, we sought to indentify stable individual traits in developing metastatic melanoma, assess their stability in time, and analyze typical dynamics and common trends of genomic changes in individual cases of late stage metastatic cancer.
To this end, we compared consecutive recurrent metastases developed by a special group of eight individuals with advanced metastatic melanoma, all developing several recurrent metastases over several months to years of natural disease evolution.

overall_design: Twenty-six recurrent melanoma metastases were surgically isolated from 8 patients experiencing relapse after one or more successful treatment intervention(s) with no signs of residual disease. Patients experiencing recurrent metastases were labeled with capital letters; “A”, “B”, “C”, etc., their subsequent metastases as “A/1”, “A/2”, “B/1”, “B/2”, etc., while synchronous metastases in a given patient  were labeled as “A/1a”, “A/1b” etc. Another 22 melanoma cell lines isolated and maintained as above were expanded from melanoma patients with rapid disease curse, for whom only one metastasis was available. As no extended follow up was possible in these cases, the cell lines are considered representative of random time points in the natural course of metastatic melanoma. These cell lines were labeled with Arabic numbers, as “1”, “2”, ”3”, etc

first: Tara

middle: L

last: Spivey

first: Hui

last: Liu

first: Jinguo

last: Chen

first: Michele

last: Maio

first: Paul

middle: F

last: Robbins

first: Ena

last: Wang

first: Francesco

middle: M

last: Marincola


title: Gene expression profiling in cumulus cells (CC) derived from a modified natural and stimulated in vitro fertilization (IVF) procedures

status: Public on Jan 10 2014

city: Ljubljana

first: Peter

last: Juvan

address: Zaloska 4

department: Institute of Biochemistry

country: Slovenia

institute: Faculty of Medicine, University of Ljubljana

summary: Cumulus cells surrounding mature oocytes that developed to moruale/blastocyst stage on day 5 of IVF cycle were collected and used for gene expression profiling using Affymetrix Human Gene 1.0 ST Arrays in order to determine differences in gene expression between the modified natural and stimulated in vitro fertilization (IVF) procedures.

overall_design: Microarray analysis was made on 8 individual CC samples, derived from 5 patients that first underwent MNIVF, followed by a controlled ovarian hyperstimulation (COH) cycle. As the quality of the isolated RNA derived from 2 of the MNIVF CC samples was not good, these samples were not included in the analysis. Altogether, 3 CC samples from MNIVF and 5 CC samples from COH cycles were included in microarray analysis.

first: Tanja

last: Burnik Papler

first: Klementina

last: Fon Tacer

first: Rok

last: Devjak

first: Irma

last: Virant Klun

first: Eda

last: Vrtačnik Bokal


title: Coexpression of CD49b and LAG-3 identifies human and mouse T regulatory type 1 cells

status: Public on Dec 20 2013

city: Pula

first: Mauro

last: Pala

state: Cagliari

address: Parco Scientifico Polaris Loc. Pixinamanna

summary: CD4(+) type 1 T regulatory (Tr1) cells are induced in the periphery and have a pivotal role in promoting and maintaining tolerance. The absence of surface markers that uniquely identify Tr1 cells has limited their study and clinical applications. By gene expression profiling of human Tr1 cell clones, we identified the surface markers CD49b and lymphocyte activation gene 3 (LAG-3) as being stably and selectively coexpressed on mouse and human Tr1 cells. We showed the specificity of these markers in mouse models of intestinal inflammation and helminth infection and in the peripheral blood of healthy volunteers. The coexpression of CD49b and LAG-3 enables the isolation of highly suppressive human Tr1 cells from in vitro anergized cultures and allows the tracking of Tr1 cells in the peripheral blood of subjects who developed tolerance after allogeneic hematopoietic stem cell transplantation. The use of these markers makes it feasible to track Tr1 cells in vivo and purify Tr1 cells for cell therapy to induce or restore tolerance in subjects with immune-mediated diseases.

overall_design: The transcriptome of human Tr1 cell clones to that of TH0 cell clones either unstimulated or stimulated for 6 and 16 h. Tr1 and TH0 cell clones were isolated from peripheral blood of 2 Healthy Donors (HDs). mRNA from T cell clones unstimulated (t0, n=4 Tr1 cell clones and n=10 TH0 cell clones) or stimulated with immobilized anti-CD3 and soluble anti-CD28 mAbs (6h and 16h, n=4 Tr1 cell clones and n=5 TH0 cell clones) was isolated. Differential expression of 28869 genes was investigated by whole transcript Affymetric chips.

first: Nicola

last: Gagliani

first: Chiara

last: Magnani

first: Samuel

last: Huber

first: Monica

middle: E

last: Gianolini

first: Paula

last: Licona-Limon

first: Bingege

last: Guo

first: Herbert

middle: R

last: De’Broski

first: Alessandro

last: Bulfone

first: Filippo

last: Trentini

first: Clelia

last: Di Serio

first: Rosa

last: Bacchetta

first: Marco

last: Andreani

first: Leonie

last: Brockmann

first: Silvia

last: Gregori

first: Richard

middle: A

last: Flavell

first: Maria

middle: G

last: Roncarolo


title: Differentiation of human amniotic fluid kidney progenitor cells into podocytes and comparison with human conditionally immortalized podocytes

status: Public on Dec 19 2013

city: Los Angeles

first: Stefano

last: Da Sacco

state: CA

address: 4650 Sunset Blvd MS#35

country: USA

institute: Children's Hospital Los Angeles

summary:
In this work, we isolated and characterized a novel cell population derived from human amniotic fluid cells (hAKPC-P), and we differentiated them into podocytes.
We used microarrays to study global changes in gene expression before and after differentiation in hAKPC-P and human immortalized podocytes (hIPod, positive control) and performed a detailed comparison between the different populations

overall_design: hAKPC-P were isolated by FACS sorting from the total human amniotic fluid cell population and differentiated into podocytes using VRADD media. Morphological, phenotypical and functional analysis were performed to assess their differentiation. To confirm the results, cells were compared with human conditionally immortalized podocytes.

first: Laura

last: Perin


title: COLO829 treatment with PLX4032 and/or MITF knockdown

status: Public on Jan 14 2014

city: Stanford

first: Paul

last: Khavari

address: 269 Campus Drive

institute: Stanford University

summary: Thousands of enhancers are characterized in the human genome, yet few have been shown important in cancer. Inhibiting oncokinases, such as EGFR, ALK, HER2, and BRAF, is a mainstay of current cancer therapy but is hindered by innate drug resistance mediated by upregulation of the HGF receptor, MET. The mechanisms mediating such genomic responses to targeted therapy are unknown. Here, we identify lineage-specific MET enhancers for multiple common tumor types, including a melanoma lineage-specific MET enhancer that displays inducible chromatin looping and MET gene induction upon BRAF inhibition. Epigenomic analysis demonstrated that the melanocyte-specific transcription factor, MITF, mediates this enhancer function. Targeted genomic deletion (<7bp) of the MITF motif within the MET enhancer suppressed inducible chromatin looping and innate drug resistance, while maintaining MITF-dependent, inhibitor-induced melanoma cell differentiation. Epigenomic analysis can thus guide functional disruption of regulatory DNA to decouple pro- and anti-oncogenic functions of tumor lineage-enriched transcription factors mediating innate resistance to oncokinase therapy.

overall_design: COLO829 human melanoma cell line harboring the BRAFV600E mutation was treated with BRAF inhibtior PLX4032 (Vemurafenib) and/or a hairpin against MITF

first: Dan

last: Webster


title: Gene expression and copy number analysis of recurrent metastatic melanoma lesions

first: Zoltan

last: Pos

type: Genome variation profiling by genome tiling array


title: Expression data from H358

status: Public on Jan 01 2014

city: San Francisco

first: Megan

last: Salt

state: California

department: Helen Diller Family Comprehensive Cancer Center

institute: UCSF

summary:
Tumors that show evidence of epithelial to mesenchymal transition (EMT) have been associated with metastasis, drug resistance, and poor prognosis.  EMT may alter the molecular requirements for growth and survival in different contexts, but the underlying mechanisms remain incomplete.  Given the heterogeneity along the EMT spectrum between and within tumors it is important to define the requirements for growth and survival in cells with an epithelial or mesenchymal phenotype to maximize therapeutic efficacy.
We have established an inducible cell line model in which a tamoxifen regulatable Twist-ER fusion protein is stably expressed in the H358 non-small cell lung cancer cell line.  Upon tamoxifen addition, cells undergo EMT and provide a system in which we can compare the growth and survival requirements directly related to EMT, removing confounding factors present when comparing different cell lines.

overall_design: H358 cells stably expressing either GFP or TwistER were treated for 12 days in culture with 100nM 4-hydroxytamoxifen followed by RNA isolation. Three biological replicates of each condition were collected.

middle: B

first: Sourav

last: Bandyopadhyay

first: Frank

last: McCormick


title: Expression data from spatially separated samples of different ccRCC patients

status: Public on Jan 06 2014

city: Lyon cedex 08

first: Pierre

last: Martinez

address: 28 rue Laennec

country: France

institute: Cancer Research Centre of Lyon

summary: We have sampled several tumour regions from nine clear cell renal cell carcinoma (ccRCC)  patients to investigate intra-tumour heterogeneity.

overall_design: We selected 56 tumour samples and 6 normal samples from the 9 patients for expression analysis using microarray data. All samples were fresh frozen upon extraction.

first: Andrew

last: Rowan

first: Charles

last: Swanton


title: Hypermethylation of GABRE~miR-452~miR-224 in prostate cancer predicts biochemical recurrence after radical prostatectomy

status: Public on Dec 11 2013

city: Aarhus

first: Kasper

last: Thorsen

address: Brendstrupgaardsvej

country: Denmark

institute: Aarhus University Hospital

summary:
Purpose: Available tools for prostate cancer (PC) diagnosis and prognosis are suboptimal and novel biomarkers are urgently needed. Here, we investigated the regulation and biomarker potential of the GABRE~miR-452~miR-224 genomic locus.
Experimental design: GABRE/miR-452/miR-224 transcriptional expression was quantified in 80 non-malignant and 281 PC tissue samples. GABRE promoter methylation was determined by methylation-specific qPCR (MethyLight) in 35 non-malignant, 293 PC (radical prostatectomy (RP) cohort 1) and 198 PC tissue samples (RP cohort 2). Diagnostic/prognostic biomarker potential of GABRE methylation was evaluated by ROC, Kaplan-Meier, uni- and multivariate Cox regression analyses. Functional roles of miR-224 and miR-452 were investigated in PC3 and DU145 cells by viability, migration, and invasion assays and gene-set enrichment analysis (GSEA) of post-transfection transcriptional profiling data.
Results: GABRE~miR-452~miR-224 was significantly downregulated in PC compared to non-malignant prostate tissue and had highly cancer-specific aberrant promoter hypermethylation (AUC=0.98). Functional studies and GSEA suggested that miR-224 and miR-452 inhibit proliferation, migration, and invasion of PC3 and DU145 cells by direct/indirect regulation of pathways related to the cell cycle and cellular motility. Finally, in uni- and multivariate analyses, high GABRE promoter methylation was significantly associated with biochemical recurrence in RP cohort 1, which was successfully validated in RP cohort 2.
Conclusion: The GABRE~miR-452~miR-224 locus is downregulated and hypermethylated in PC and is a new promising epigenetic candidate biomarker for PC diagnosis and prognosis. Tumor suppressive functions of the intronic miR-224 and miR-452 were demonstrated in two PC cell lines, suggesting that epigenetic silencing of GABRE~miR-452~miR-224 may be selected for in PC.

overall_design: Affymetrix GeneChip Human Gene 1.0 ST Arrays were used for whole-genome transcriptional profiling of DU145 and PC3 cells at 48 hours post-transfection with either miR-224, miR-452, or scrambled miRNA mimics, or untransfected. All experiments were performed in duplicate. Transcript expression levels were determined after RMA16 normalization in GeneSpringGX 11.0 software (Agilent). PC3 and DU145 arrays were normalized separately. DU145 48 t Scr2a were excluded from the study because of bad performance of this microarray.

first: Karina

middle: D

last: Sørensen

first: Helle

last: Kristensen


title: Differential gene expression between WT MARC-145 cells and MARC-145 cells stably expressing Non-Structural Protein 11 of Porcine Respiratory and Reproductive Syndrome Virus

status: Public on Dec 16 2013

city: Philidelphia

first: Yan

last: Sun

address: 380 South University Ave

department: Pathobiology

institute: University of Pennsylvania

summary:
Porcine respiratory and reproductive syndrome virus (PRRSV) is a virus infecting swine and causes swine abortion. Previously, non-structural protein 11 (Nsp11) from PRRSV was shown to have inhibitory function to type I IFN signaling.
In this project, we want to see in addition to type I IFN, whether other cellular pathways are influenced by Nsp11 systemtically. A cell line stably expressing PRRSV Nsp11 was established, designated as MARC-Nsp11 cells, and an RNA microarray was conducted using these cells and WT MARC-145 cells

overall_design: MARC-145 and MARC-Nsp11 cells were seeded one day prior to experiments and total cellular RNAs were extracted using Trizol (Invitrogen) and purified by RNeasy mini kit (Qiagen). The quantity and quality of RNA were determined using an Align 2100 bioanalyzer (Agilent Technologies, Palo, Alto, CA, USA), and the RNA integrity was determined above 7. The RNA samples were then subjected to microarray using Human Gene 1.0 ST arrays (Affymetrix UK Ltd, High Wycombe, UK) at the Keck Biotechnology Center, University of Illinois, Urbana, IL). The microarray was repeated twice in duplicates each.

first: Dong

last: Li

first: Dongwan

last: Yoo


title: Expression profile of E. coli in response to exogenous addition of isopentenol

status: Public on Dec 10 2013

city: Emeryville

first: Robert

last: Dahl

address: 5885 Hollis St, JBEI

department: Chemical Engineering

institute: University of California-Berkeley

summary:
Exogenous isopentenol was added to a culture of E. coli and the RNA expression response was measured using Nimblegen arrays.  Genes highly upregulated were then subsequently overexpressed to improve the tolerance to isopentenol toxicity.  In addition a subset of genes that improved the tolerance were also overexpressed in a producing strain, leading to improved production over the empty vector control.
This work is described in Foo et al, Improving microbial bio-gasoline production in E. coli using tolerance engineering (in preparation)

overall_design: Six independent biological replicates were grown in M9 medium.  0.2% v/v isopentenol was added to 3 cultures while 3 cultures received no treatment, and 2.5 hr later total RNA was extracted.  One sample from each culture was hybridized.

first: Jee

last: Foo

first: Heather

last: Jensen

middle: H

first: Kevin

last: George

first: Jay

last: Keasling

first: Taek

middle: S

last: Lee

first: Susanna

last: Leong

first: Aindrila

last: Mukhopadhyay


title: Identification of miR-205 targets using an RIP-Chip assay with AGO2 antibody

city: Lund

first: Yvonne

last: Ceder

address: Medicon Village

department: Laboratory Medicine

country: Sweden

institute: Lund University

type:
Expression profiling by array
Other

summary: In this study, the prognostic properties of miR-205 expression levels are investigated in a well-documented prostate cancer cohort. We show that miR-205 is correlated to shortened overall survival, significantly dividing the PCa patients into high and low risk groups. Furthermore, miR-205 is shown to inversely correlate to occurrence of metastases. In situ hybridization is also performed, demonstrating high miR-205 expression in the basal cells of benign prostate tissue glands. A RIP-Chip assay using an AGO2 antibody was implemented and the miR-205 targets identified were found to be enriched in MAPK/ERK, Toll-like receptor and IL-6 signaling pathways. We also found individual targets involved in cancer and androgen receptor signaling. Ectopic levels of miR-205 are shown to decrease the level of androgen receptor both at the mRNA and protein levels in prostate cancer cell lines. This is further corroborated in the prostate cancer cohort were miR-205 expression levels in the prostatic tissues are found to inversely correlate to assessment of androgen receptor (AR) immunostaining and to serum levels of PSA, a protein regulated by AR signaling. The level of miR-205 is also found to be significantly lower in castration resistant prostate cancer patients than in hormone naïve patients. Our data indicates that miR-205 is regulated by androgens and act by different mechanisms in androgen depleted settings, e.g. giving opposite effects on adhesion. Taken together these findings imply that miR-205 might have therapeutic potential especially for the castration resistant and currently untreatable form of prostate cancer.

overall_design: Experiment done with biological triplicates. Three with miR-205 ectopic expression and three with negative control mimic ectopic expression. Followed by a RIP-Chip, ending with mRNA extraction and gene expression array.

first: Zandra

last: Hagman


title: Gene expression profilling of anaplastic thyroid carcinomas (ATC) and normal thyroid tissues

status: Public on Dec 07 2013

city: Lisboa

first: Branca

middle: Maria

last: Cavaco

address: Rua Prof. Lima Basto

department: Unidade de Investigação de Patobiologia Molecular (UIPM)

country: Portugal

institute: Instituto Português de Oncologia de Lisboa Francisco Gentil (IPOLFG)

summary:
ATC are among the most lethal malignancies, for which there is no effective treatment.
ATC global gene expression was profiled and compared to normal thyroid tissues, in order to elucidate the molecular alterations contributing to ATC development, and to identify novel therapeutic targets.

overall_design: RNA were extracted from 5 ATC samples. 3 samples were obtained at time of surgery, and were immediately frozen in liquid nitrogen. The RNA from the remaining samples were collected during fine-needle aspiration biopsies, being conserved in RLT buffer (RNeasy Mini Kit, Quiagen) and maintained at -70ºC. RNA were also extracted from 3 normal thyroid samples, which were collected during surgery, taken from the opposite lobe of thyroid tumors. We also hybridized a commercial pool of human thyroid total RNA (BD Bioscience).

first: Jaime

last: Pita

first: Valeriano

last: Leite


title: Annotating the secretome of mature primary human muscle cells

status: Public on Dec 03 2013

city: Neuherberg

first: Johannes

last: Beckers

address: Ingolstaedter Landstr. 1

department: Institute of Experimental Genetics

country: Germany

institute: Helmholtz Zentrum Muenchen

summary:
The Skeletal muscle is a metabolic active tissue that secretes various proteins. These so called myokines act auto-, para- and endocrine affecting muscle physiology and exert systemic effects on other tissues and organs. Myokines are also described to play a crucial role in the pathophysiology of metabolic diseases.
Combining three different mass spectrometry based non-targeted and one antibody based targeted approach we investigated the secretome of differentiated primary human skeletal muscle cells derived from adult donors. A total of 548 non-redundant proteins were detected by combined proteomic profiling. Expression was confirmed on mRNA level for 501. Stringent consecutive filtering recruiting several database, i.e. SignalP, SecretomeP and ER_retention signals, the computational analysis assigned 306 as secretory proteins including 33 potentially novel myokines.
This comprehensive profiling study of the human skeletal muscle secretome expands our knowledge of the composition of the human myokinome and further highlights the pivotal role of myokines in the regulation of multiple biological processes.

overall_design: We performed gene expression microarray analysis of primary human myotubes derived from twelve healthy individuals

first: Mika

last: Scheler

first: Martin

last: Irmler

first: Stefan

last: Lehr

first: Sonja

last: Hartwig

first: Harald

last: Staiger

first: Hadi

last: Al-Hasani

last: de Angelis

first: Hans

middle: U

last: Häring

first: Cora

last: Weigert


title: Expression data from THP-1 cells and THP-1 cells stimulated with PMA

status: Public on Dec 28 2013

city: Omaha

first: Jessica

last: Winkler

address: 985800 Nebraska Medical Center- DRC I

department: Pharmacology and Experimental Neuroscience

institute: University of Nebraska Medical Center

summary: Macrophages play a key role in both innate and adaptive immunity, but our knowledge on the changes in transcription regulation that occurs during their differentiation from monocytes is still limited. In this study, we used a meta-analysis followed by a systems biology approach for the identification of differentially expressed genes between monocytes and macrophages and possible regulators of these changes in transcription. Based on the pattern of gene expression change, transcription regulator analysis predicted a decrease in Enhancer of Zeste homolog 2 (EZH2), a histone 3 lysine 27 methyl transferase, activity after differentiation of monocytes into macrophages. This inhibition was validated by a significant decrease in trimethylated H3K27 during differentiation of both human primary monocytes into macrophages and the THP-1 cell line into macrophage-like cells. Overexpressing EZH2 during differentiation of monocytes and THP-1 cells obstructs cellular adhesion, thus preventing the first step in differentiation. Another facet of macrophage differentiation is the cessation of proliferation, and inhibition of EZH2 by the small molecule inhibitor GSK126 in THP-1 cells indeed impedes proliferation. This study shows an important part for epigenetic changes during monocyte differentiation. It highlights the role of EZH2 activity behind the changes needed in adhesion and proliferation mechanisms for macrophage formation.

overall_design: THP-1s were differentiated into macrophage like cells by PMA stimulation.

first: Howard

last: Fox


title: Gene expression profiling in true interval breast cancer reveals overactivation of mTOR signalling pathway

status: Public on Dec 23 2013

city: Barcelona

first: Ana

last: Rovira

address: Dr. Aiguader 88

country: Spain

institute: IMIM-Hospital del Mar

summary:
Background: Interval breast cancers can occur through failure to detect an abnormality at the time of screening (missed interval cancer), or as a new event after a negative screen (true interval cancer). The development and progression of true interval tumors (TIBC) is known to be different than screen-detected tumors (SDBC). However, much work still needs to be done to understand the biological characteristics and clinical behaviour of these TIBC.  Objectives: To characterize the gene expression profile in TIBC and SDBC aimed to identify biological markers that may be associated with the emergence of symptomatic breast cancer in the screening interval.   Material and Methods: An unsupervised exploratory gene expression profile analysis was performed among 10 samples (discovery set, TIBC=5 and SDBC=5) using Affymetrix Human Gene 1.0 ST arrays and interpreted by Ingenuity Pathway Analysis. Differential expression of selected genes was confirmed in validation series of 91 patients (TIBC=12 and SDBC=79) by immunohistochemistry and 24 patients (TIBC=8 and SDBC=16) by RT-qPCR, expanding the analysis to other genes in same pathway (mTOR, 4E-BP1, eIF-4G and S6).

Results: Exploratory gene expression analysis identified 1060 transcripts with a p value <0.05 and 132 transcripts with an adjusted p value <0.01 difference between TIBC and SDBC samples. Based on biological implications in breast cancer, four genes were selected for further validation: CP (ceruloplasmin) and RPS6KB2 (ribosomal protein S6 kinase, 70kDa, polypeptide 2) both up-regulated in TIBC vs SDBC and PTEN (phosphatase and tensin homolog) and TGFBR3 (transforming growth factor beta receptor III), down-regulated in TIBC vs SDBC. Their differential expression was confirmed by RT-qPCR and immunohistochemistry, suggesting mTOR pathway overexpression in TIBC at both mRNA and protein level. Further expanded analysis by immunohistochemistry for mTOR pathway activation, including expression of phosphorylated forms of mTOR, 4E-BP1, eIF-4G, RPS6KB2 and S6, confirmed the upregulation of this pathway in TIBC.

Conclusions: TIBC and SDBC shows differential expression profile both at the gene and protein levels. The mTOR signaling is significantly upregulated in TIBC compared with SDBC, suggesting an enhanced aggressiveness of TIBC. Besides, CP may also represent novel immunohistochemical marker helpful in distinguishing between TIBC and SDBC. Further studies with larger sets of patients are guaranteed to verify these findings associated with TIBC.

overall_design: 5 TIBC samples where compared with 5 SDBC

first: Laia

last: Domingo

first: Federico

last: Rojo


title: Changes in global gene expression in lung cancer cell lines A549 (A) and HTB56 (H) [Affymetrix microarrays]

status: Public on Dec 18 2013

city: Heidelberg

first: Christian

last: Rohde

address: Im Neuenheimer Feld 410

institute: Heidelberg University

summary: Here, we analyzed global gene expression changes that were associated with pro-metastatic phenotypes in non-small cell lung cancer using the Affymetrix microarray platform.

overall_design: Changes in global gene expression were determined with Affymetrix microarrays in lung cancer cell lines A549 (A) and HTB56 (H). We generated NSCLC lines with highly increased propensity to form tumor nodules in murine lungs after intravenous injections. In addition to the normal cell lines (0R) we analyzed gene expression of the the cell lines after three rounds of in vivo selection towards a highly metastatic phenotype (3R).

first: Dominik

last: Jungen

first: Carsten

last: Müller-Tidow


title: Expression data from inflammatory myopathies

status: Public on Dec 01 2013

first: Xavier

last: Suárez-Calvet

address: Sant Antoni Maria Claret, 167

department: Neurology

institute: Institut de Recerca Sant Pau

summary: MHC-I overexpression in muscle biopsies is a hallmark of inflammatory myopathies.However the mechanisms of MHC-I overexpression in each disease is not well understood. Microarray analysis from MHC-I-microdissected myofibers showed a differential expression signature in each inflammatory myopathy. Innate immunity and IFN-I pathways are upregulated vs healthy controls, specifically in dermatomyositis (DM).

overall_design: RNA from MHC-I-positive myofibers were obtained from muscle biopsies of 5 patients with dermatomyositis, 5 with polymyositis, 4 with inclusion body myositis and normal looking fibers from healthy controls.

first: Isabel

last: Illa


title: Direct reprogramming of human astrocytes into neural stem cells and neurons

city: Milan

first: Stefania

last: Corti

address: via F. Sforza 35

department: Neurological Sciences

institute: University of Milan

summary: Ectopic expression of the reprogramming factors OCT4, SOX2, or NANOG into human astrocytes in specific cytokine/culture conditions activated the neural stem gene program and induced generation of cells expressing neural stem/precursor markers.

overall_design: Here we compare the whole gene expression profile of primary human astrocytes (Astro) with neural stem cells (HNSC) derived from astrocytes reprogramming


title: Expression profiling of MDR1+ and MDR1- human memory T cells from the blood and clinically-inflamed gut tissue

status: Public on Dec 17 2013

city: Cambridge

first: Scott

last: Davis

state: MA

address: 200 Technology Square, Suite 602

department: Tempero DPU

institute: GSK

summary: The aim of this study was to characterize the transcriptional signature of MDR1+ human memory T cells isolated from clinically inflamed gut tissue, and compare it to local MDR1- memory T cells

overall_design:
Human mononuclear cells were isolated from the peripheral blood of a healthy adult donor (Ficol density centrifugation) or from resected lesioned gut tissue of a patient with active Crohn's disease. For cell isolation from gut tissue, tissue was rinsed with PBS, treated with 0.15% DTT to remove mucous, then with 1 mM EDTA to remove epithelial cells and intra-epithelial lymphocytes. Remaining tissue was digested using Liberase-TL (Roche) plus 10 U/mL DNase I. Mononuclear cells were then filtered through 70 mM nylon filters and isolated via a 30%/ 70% Percol gradient. Mononuclear cells from blood or gut tissue were FACS-sorted into CD3+ CD4+ CD45RO+ MDR1+ or MDR1- memory T cells, using Rhodamine 123 (Rh123) efflux as a surrogate for MDR1 expression/ activity. Sorted cells were harvested directly ex vivo (without further in vitro culture or manipulation) prior to RNA extraction.
MDR1- memory CD4+ T cells vs. MDR1+ memory CD4+ T cells from healthy donor peripheral blood or from active Crohn's disease lesioned tissue; MDR1- or MDR1+ memory CD4+ T cells from blood vs. inflamed gut tissue

first: Mark

last: Sundrud

first: Radha

last: Ramesh


title: Transcriptional profiles of CCR7lo effector memory human T cell subsets

summary: The aim of this study was to identify differentially-expressed genes in CCR4hi/CXCR3- and CCR4lo CXCR3+ CCR6+ human Th17 cell subsets

overall_design:
Human CD45RO+ memory T cells isolated from the peripheral blood of healthy adult donors were sorted into 4 predominant CCR7lo CD25- effector memory subsets: (1) Th1 - CCR6- CCR4lo CXCR3+; (2) Th2 - CCR6- CCR4hi CXCR3+; (3) Th17 - CCR6+ CCR4hi CXCR3-; (4) Th17.1 - CCR6+ CCR4lo CXCR3-. Sorted cells were cultured in media and activated via anti-CD3/anti-CD28 beads for 36 hours. All subsets were then harvested and used for RNA extraction and microarray experiments.
Th1 vs Th2; Th1 vs Th17; Th1 vs Th17.1; Th2 vs Th17; Th2 vs Th17.1; Th17 vs Th17.1

first: Ivana

last: Djuretic


title: System-Wide Analysis Reveals a Complex Network of Tumor-Fibroblast Interactions Involved in Tumorigenicity

status: Public on Nov 21 2013

city: Stony Brook

first: Jinyu

last: Li

state: NY

address: 101 Nicolls Rd

department: Cancer Center

institute: Stony Brook University

summary: We’ve undertaken a genome-wide approach to identify and test genes in fibroblasts that are both induced upon interaction with basal breast cancer cells in culture and upregulated in stromal cells from primary human breast cancers.  Several of the upregulated genes encode secreted growth factors or cytokines.  Using RNAi and a co-injection tumorigenicity assay, we determined that the majority of secreted factors selected for functional validation played significant, yet functionally diverse, roles in promoting tumorigenicity.  Rather than a single major mediator, these results indicate multiple points of intervention to prevent fibroblasts from supporting basal breast cancer.  Additionally, we show that breast cancer subtypes differ markedly in the expression of these and other stromally secreted proteins using data from microdissected stromal samples.

overall_design: Induction of genes in four different fibroblast strains (HFFF2, HFF1, CCD1112Sk and Wi38) upon coculture with Cal51 and MDAMB231 human basal breast cancer cell lines. Monocultures of each group are used as the experimental control with each group having 3-4 independent biological replicates.

first: Megha

last: Rajaram

first: Mikala

last: Egeblad

last: Powers


title: Gene expression data from MGHU3 bladder cancer cells (FGFR3-Y375C) treated with TAK1 siRNA and/or PD173074

status: Public on Nov 19 2013

city: Irvine

first: Leslie

last: Thompson

address: Biological Sciences III

institute: University of California, Irvine

summary:
The NFκB transcription factor is constitutively active in a number of hematologic and solid tumors, and many signaling pathways implicated in cancer are likely connected to NFκB activation.  A critical mediator of NFκB activity is TGFβ-activated kinase 1 (TAK1).  Here, we identify TAK1 as a novel interacting protein and direct target of fibroblast growth factor receptor 3 (FGFR3) tyrosine kinase activity.
We further demonstrate that activating mutations in FGFR3 associated with both multiple myeloma and bladder cancer can modulate expression of genes which regulate NFκB signaling, and promote both NFκB transcriptional activity and cell adhesion in a manner dependent on TAK1 expression in both cancer cell types.  Our findings suggest TAK1 as a potential therapeutic target for FGFR3-associated cancers, and other malignancies in which TAK1 contributes to constitutive NFκB activation.

overall_design: A total of 12 samples of MGHU3 (Y375C) mutant FGFR3 bladder cancer cells (a kind gift from Dr. Margaret Knowles (University of Leeds, Leeds, UK)) were used for array-based gene expression analysis.  3 replicates of each condition: Control siRNA, Control siRNA + PD173074, TAK1 siRNA, and TAK1 siRNA + PD173074.

first: L


title: Expression data from LPS-treated HBVP (human brain vascular pericytes)

status: Public on Dec 04 2013

city: Majadahonda

first: Laura

last: Sanz

state: Madrid

address: Joaquín Rodrigo 2

department: Molecular Immunology

institute: Hospital Puerta de Hierro

summary: Identification of TLR4 as one of the most abundant RNA species in pericytes with respect to MSC, and corroboration of TLR4 expression on the cell surface, led us to obtain a comprehensive overview of the expression program of lipopolysaccharide (LPS) stimulated pericytes. Microarray analyisis demonstrated the significant upregulation of 76 annotated genes including transcripts for adhesion molecules, inflammation mediators, pro-angiogenic factors, transcription factors and anti-apoptotic proteins.

overall_design: Cells were cultured in 24-w plates in complete medium for 24h before stimulation with 1 microgram/ml LPS for 4h. Samples are biological triplicates.

first: Irene

last: Guijarro-Muñoz


title: Knockdown of EI24 in ZR-75-1 cells

status: Public on Nov 20 2013

city: Seoul

first: Han-Woong

last: Lee

address: Yonsei university, Yonseiro 50

department: Biochemistry

country: South Korea

institute: Yonsei University

summary:
Analysis of ZR-75-1 cells folowing knockdown of EI24 (P53-Induced Gene 8) and control vector. As a p53 response gene, EI24 is known to controlling cell growth, apoptosis, and autophagy.
Results provide insight into the role of EI24 in epithelial-to-mesenchymal

overall_design: Parental ZR-75-1 cells, ZR-75-1 cells with shGFP knockdown (control), Two independent clone of knockdown of EI24 in ZR-75-1. All samples are perfomed in duplicate. Total 8 samples exist.

first: J

last: Choi


title: The effects of chronic cadmium exposure on gene expression in MCF7 breast cancer cells

status: Public on Nov 16 2013

city: Skövde

first: Zelmina

last: Lubovac Pilav

address: Box 408

institute: University of Skövde

summary: Cadmium is a metalloestrogen known to activate the estrogen receptor and promote breast cancer cell growth. Previous studies have implicated cadmium in the development of more malignant tumors; however the molecular mechanisms behind this cadmium-induced malignancy remain elusive. Using clonal cell lines derived by exposing breast cancer cells to cadmium for over 6 month (MCF7-Cd4, -Cd6, -Cd7, -Cd8 and -Cd12), this study aims to identify gene expression signatures associated with chronic cadmium exposure. Our results demonstrate that prolonged exposure does not merely result in the deregulation of genes but actually leads to a distinctive expression profile. The genes deregulated in cadmium-exposed cells are involved in multiple biological processes (i.e cell growth, apoptosis, etc.) and molecular functions (i.e. cadmium/metal ion binding, transcription factor activity, etc). Hierarchical clustering demonstrates that the five clonal cadmium cell lines share a common gene expression signature of breast cancer associated genes, clearly differentiating control from cadmium exposed cells. The results presented in this study offer insights into the cellular and molecular impacts of cadmium on breast cancer carcinogenesis and emphasize the importance of studying chronic cadmium exposure as one possible mechanism of promoting breast cancer progression.

overall_design: To understand the effects of chronic cadmium exposure on gene expression in breast cancer, two control MCF7 parental cell lines and five different clonal cadmium-adapted cell lines (MCF7-Cd4, -Cd6, -Cd7, -Cd8, and -Cd12) - previously derived from cells chronically exposed to cadmium - were used for microarray analysis.

first: Maggie

middle: C

last: Louie


title: Comparative expression data from HBVP (human brain vascular pericytes) and human MSC (mesenchymal stem cells)

summary: Pericytes and mesenchymal stem cells (MSC) are ontogenically related, and in fact no phenotypic differences were observed by flow cytometry using a panel of surface antigen markers. Global gene expression profiles of human pericytes and MSC revealed that 43 genes were expressed more than 10 fold in pericytes as compared to MSC.

overall_design: Cells were cultured in 24-w plates in complete medium for 24h in biological triplicates


title: Aire co-opts the repressive ATF7ip/MBD1 protein complex for the induction of immune tolerance

city: San Francisco

middle: Stuart

last: Anderson

address: 513 Parnassus Avenue, HSW Room  1102, Box 0540

department: Diabetes Center

institute: UCSF

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

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus

overall_design: Refer to individual Series


title: Expression data from skeletal muscle biopsies of healthy adults

status: Public on Nov 15 2013

first: Brian

middle: Yee Hong

last: Lam

address: Box 289 Addenbookes Hospital, Hills Road

department: Metabolic Research Laboratories

country: United Kingdom

institute: University of Cambridge

summary:
Healthy adults with serum insulin like growth factor -1 (IGF-I) levels at the lowest quartile of normal ranges have increased fat metabolism and reduced glucose utlisation compared with those in the highest quartile during fasting
We used gene expression in skeletal muscle to explore metabolism during fasting

overall_design: We selected healthy males from a bioresource based on extremes of circulating IGF-I levels on stored sera and evaluated during a 24 hour fasting

first: David

last: Dunger

first: Giles

last: Yeo

first: Ajay

last: Thankamony


title: Nodular lymphocyte predominant hodgkin lymphoma and T cell/histiocyte rich large B cell lymphoma - endpoints of a spectrum of one disease?

city: Frankfurt

first: Claudia

last: Döring

address: Theodor Stern Kai 7

department: Medical School, Institite of Pathology

institute: Johann Wolfgang-Goethe University Frankfurt a.M.

summary: Tumor cells were microdissected from frozen sections of NLPHL and THRLBCL. RNA was amplified using the NUGEN WT-Ovation-One-direct-Kit. Samples were compared to tonsilar germinal center CD77 B cells.

overall_design: 30 microdissected tumour samples were compared with 5 sorted CD77 samples.

first: Sylvia

last: Hartmann


title: Gene expression profiling of MYC-amplified medulloblastoma cell lines treated by JQ1, a BET bromodomain inhibitor

status: Public on Dec 02 2013

city: Boston

first: Rameen

last: Beroukhim

address: 450 Brookline Av

department: Cancer Biology

institute: DANA-FARBER CANCER INSTITUTE

summary: MYC-amplified medulloblastomas are highly lethal tumors. BET bromodomain inhibition was recently described to downregulate MYC-associated transcriptional activity in various cancer subtypes. To investigate whether JQ1, a BET bromodomain inhibitor is downregulation MYC and MYC-associated transcriptional activity, we performed global gene expression profiling of five medulloblastomas MYC-amplified patient-derived cell lines treated by JQ1 and the inactive form of JQ1.

overall_design: Five medulloblastomas patient-derived MYC-amplified cell lines were treated with the active and the inactive form of the drug (JQ1S or JQ1R, respectively, 1μM for 24 hours) followed by RNA extraction and hybridization on Affymetrix microarrays

first: Beroukhim

last: Rameen

first: Cho

last: Yoon-Jae


title: In vitro Expansion of Hematopoietic Stem Induces Gene Expression Changes

city: Aachen

first: Wolfgang

last: Wagner

address: Pauwelsstrasse 20

department: Helmholtz Institute for Biomedical Engineering

institute: RWTH Aachen University

summary: Hematopoietic stem and progenitor cells (HPCs) can be maintained in vitro, but the vast majority of their progeny loses “stemness” during culture. We have analyzed DNA methylation (DNAm) profiles of freshly isolated CD34+ cells and upon expansion on either tissue culture plastic (TCP) or mesenchymal stromal cells (MSCs). Cultured HPCs acquired significant DNA-hypermethylation, particularly in up-stream promoter regions and shore-regions of CpG islands (CGIs). To analyze if these DNAm changes are relevant for differential gene expression we analyzed gene expression profiles of additional samples. As expected highly expressed genes (10% with highest signal intensity in gene expression arrays) were hardly methylated at promoter regions, CGIs and shore-regions.

overall_design: 9 samples were hybridized GeneChip Human Gene 1.0 ST Arrays (Affymetrix)

first: Carola

middle: I

last: Weidner

first: Thomas

last: Walenda

first: Qiong

last: Lin

first: Monika

last: Wölfler

first: Bernd

last: Denecke

first: Martin

last: Zenke


title: Identification of miR-34c targets

city: Lund

first: Yvonne

last: Ceder

address: Medicon Village

institute: Lund University

summary:
In this study we set out to characterize the mechanisms by which miR-34c deregulation contribute to PCa progression. The genes regulated by miR-34c in the prostate cancer cell line PC3 were identified by microarray analyses, and the top biofunctional pathways enriched for identified genes were found to be cell death, cell cycle, cellular growth, and cellular movement. One of the identified targets was MET, a receptor protein tyrosine kinase activated by hepatocyte growth factor, that is crucial for metastatic progression.
see above

overall_design: A total of 6 samples. Where 3 are ectopic expression of miR-205 and 3 are ectopic expression of a scramble mimic.

first: Zandra

last: Hagman


title: Expression data from monocytes and monocyte derived macrophages

status: Public on Nov 22 2013

first: Jessica

last: Winkler

address: 985800 Nebraska Medical Center- DRC I

institute: University of Nebraska Medical Center

summary: Macrophages play a key role in both innate and adaptive immunity, but our knowledge on the changes in transcription regulation that occurs during their differentiation from monocytes is still limited. In this study, we used a meta-analysis followed by a systems biology approach for the identification of differentially expressed genes between monocytes and macrophages and possible regulators of these changes in transcription. Based on the pattern of gene expression change, transcription regulator analysis predicted a decrease in Enhancer of Zeste homolog 2 (EZH2), a histone 3 lysine 27 methyl transferase, activity after differentiation of monocytes into macrophages. This inhibition was validated by a significant decrease in trimethylated H3K27 during differentiation of both human primary monocytes into macrophages and the THP-1 cell line into macrophage-like cells. Overexpressing EZH2 during differentiation of monocytes and THP-1 cells obstructs cellular adhesion, thus preventing the first step in differentiation. Another facet of macrophage differentiation is the cessation of proliferation, and inhibition of EZH2 by the small molecule inhibitor GSK126 in THP-1 cells indeed impedes proliferation. This study shows an important part for epigenetic changes during monocyte differentiation. It highlights the role of EZH2 activity behind the changes needed in adhesion and proliferation mechanisms for macrophage formation.

overall_design: Monocytes isolated from human peripherial mononuclear cells were differentiated in monocyte derived macrophages by M-CSF stimulation

first: Howard

last: Fox


title: Ewing sarcoma compared to a normal body map

status: Public on Nov 01 2013

city: Berlin

first: Guenther

middle: HS

last: Richter

address: Augustenburger Platz 1

department: Department of Pediatrics, Division of Oncology and Hematology

institute: Charité - Universitätsmedizin Berlin

summary: Primary pediatric Ewing sarcoma (ES), one uncharacterized sarcoma as well as primary and well established ES cell lines were compared to probes of different normal tissues

overall_design: 8 Ewing sarcoma patient samples (MuET-x), 6 Ewing sarcoma patient samples (TUMK00XX), 3 primary ES cell lines (SB-KMS-y), 3 well established ES cell lines (A673, SK-N-MC, RD-ES) and 22 normal tissues (PBMC, spleen, thymus, stomach, ...., uterus, fetal brain, fetal liver) were analyzed.

first: Günther

first: Olivia

middle: P

last: da Costa

first: Kristiana

last: Hauer

first: Thorsten

last: Buch

first: Stefan

last: Burdach


title: HOXC9-induced neuronal differentiation in human neuroblastoma BE(2)-C cells [Gene expression profiling]

status: Public on Nov 03 2013

city: Augusta

first: Justin

last: Choi

state: GA

address: 1410 Laney Walker Blvd.

institute: Georgia Regents University

summary: Cell differentiation is an essential process of normal development by which a stem cell or progenitor cell becomes a post-mitotic, specialized cell with unique morphology and function. Also, it has long been recognized that differentiation is associated with a marked reduction in DNA damage response at the global level. The molecular basis for the coordination between cell cycle exit, acquirement of specialized structure and function, and attenuation of DNA damage response during differentiation is not well understood. We have conducted a genome-wide analysis of the HOXC9-induced neuronal differentiation program in human neuroblastoma cells. Gene expression profiling reveals that HOXC9-induced differentiation is associated with transcriptional regulation of 2,395 genes, which is characterized by global upregulation of neuronal genes and downregulation of cell cycle and DNA repair genes. Remarkably, genome-wide mapping demonstrates that HOXC9 occupies 40% of these genes, including a large number of genes involved in neuronal differentiation, cell cycle progression and DNA damage response. These findings suggest that HOXC9 directly activates and represses the transcription of distinct sets of genes to coordinate the cellular events characteristic of neuronal differentiation.

overall_design: Affymetrix microarray assays were performed according to the manufacturer's directions on total RNA isolated from three independent samples of BE(2)-C/Tet-Off/Myc-HOXC9 cells cultured in the presence or absence of doxycycline for 6 days.

first: Han-Fei

last: Ding

first: Jane


title: Vitamin D treatment of M.tb. infected macrophages

status: Public on Nov 28 2013

city: Montreal

first: John

last: White

state: QC

address: 3655 Prom. Sir William Osler

department: Physiology

country: Canada

institute: McGill University

summary:
As macrophages are the primary site of Mtb infection and are sites of vitamin D signaling, we have used these cells to understand the molecular mechanisms underlying modulation of the immune response by the hormonal form of vitamin D, 1,25-dihydroxyvitamin D (1,25D).
Microarrays were used to measure the changes in gene expression induced by 1,25D treatment of H37Rv-infected THP-1 cells

overall_design: Cells were infected at an MOI of 5 or left uninfected, and treated with 10^-7 M 1,25D for 24 hours

first: Mark

last: Verway


title: Expression data from a reversible dasatinib-resistant state in long-term dasatinib-treated c-KIT-mutated Kasumi-1 cell line

status: Public on Nov 27 2013

city: Ulm

first: Karlheinz

last: Holzmann

address: Helmholtzstreet 8/1

department: Medical Faculty

institute: Ulm University

summary:
Long-term treatment of Kasumi-1 cells at clinically attained doses of dasatinib led to decreased drug-sensitivity by means of IC50 values (relative to treatment-naive cells). Changes were paralled by profound alterations in c-KIT expression and cell signaling signatures. Upon brief discontinuation of dasatinib treatment, these alterations reversed and drug sensitivity was restored.
We used gene expression profiling to examine reversal of dasatinib-resistance at the molecular/expression level.

overall_design: Kasumi-1 cells were either treated with dasatinib for 12 weeks (R48) or left untreated (K). Subsequently, dasatinib was withdrawn from R48 cells for 1 week (PR48). RNA was extracted from R48 and K cells and hybridized on Affymetrix microarrays after 12 weeks and PR48 after a total time span of 13 weeks.

first: Markus

last: Herrmann


title: Transcriptional and functional profiling of human intestinal dendritic cells

city: Palo Alto

first: Katharina

last: Lahl

address: 3801 Miranda Avenue

institute: Stanford University

summary: This file contains gene microarray data from subsets of human intestinal dendritic cells, as defined by their expression of CD103 and Sirpa. This will allow for better understanding of human intestinal DC subsets in general and will facilitate translation from findings in the mouse.

overall_design: We analyzed transcript expression data from small intestine DC subsets isolated from de-identified human subject undergoing bariatric surgery.

first: Eugene

last: Butcher

first: Payal

last: Watchmaker

first: Mike

last: Lee

last: Morton


title: Expression data from pheochromocytoma (PHEO) and paraganglioma (PGL) tumor samples

status: Public on Nov 12 2013

city: Bethesda

first: Uma

middle: T

last: Shankavaram

state: MD

address: 9000 Rockville Pike

department: NCI

institute: NIH

summary:
Genotype specific differences in expression profiles have been evaluated using human HuGene1.0-ST Gene Chips. In this dataset we include expression data obtained from 8 normal adrenal medulla and 45 PHEOs/PGLs patient samples.
Viable appearing tissue from the center of the lesions was collected and snap frozen for RNA extraction. Each of the 45 PHEO/PGL samples was examined by pathologist upon resection. Patients PKh_27 and PKh_28 with SDHB mutation were from the same patient with samples taken from two different locations at different times. Diagnosis of PHEO/PGL has been confired in all cases histopathologically. The tissues were grouped according to genetic/syndromic background and tumor location into SDHB (n = 18), SDHD-A/T (n = 6), SDHD-HN (n= 8), and VHL (n = 13).

overall_design: Microarray analysis was performed on normal and tumor samples. We used PAM model to identify minimum subset of genes selective for each mutation class. Heirarchical cluster analysis was used to identify samples with similar expression patterns. Data was validated using qRT-PCR analysis.

first: Stephanie

last: Fliender

first: Karel

last: Pacak


title: Gene expression of HEK 293 cells transfected with Vector (PCMV), Aire, or MBD-VP16

last: Anderson

summary:
HEK 293 cells were transiently transfected with plasmids expressing Vector only(PCMV), Aire, or MBD-VP16 with the goal of comparing the global gene expression profiles in the Aire and MBD-VP16 groups
We used microarrays to detail the global gene expression profile.

overall_design: HEK 293 cells were transiently transfected with plasmids expressing Vector only(PCMV), Aire, or MBD-VP16 and 72 hrs post transfection total RNA was collected for microarray analysis.

first: Michael

last: Waterfield


title: Gene expression data from non-infected and M. hyorhinis-infected gastric cancer cell lines using Affymetrix genechip (HuGene-1_0-st)

city: Beijing

first: Chengchao

last: Shou

address: 52 Fucheng Road

department: Biochemistry and Molecular Biology

country: China

institute: Peking University Cancer Hospital & Institute

summary:
Chronic infection of M. hyorhinis is postulated to be associated with cancer cell migration and invasion. To explore the mechanisms of M. hyorhinis-promoted invasiveness, we performed Affymetrix genechip (HuGene-1_0-st) analysis to examine differential gene expression profiles between non-infected and infected gastric cancer cells.
We used microarrays to detail global programme of gene expression and identified distinct classes of upregulated genes after M. hyorhinis infection of gastric cancer cell lines.

overall_design: noninfected or M. hyorhinis-infected gastric cancer cells were utilized for RNA extraction and  hybridization on Affymetrix microarrays.

first: Hongying

last: Duan


title: Gene expression data from 1833 cells and 1833 cells depleted of BACH1 mRNA expression

status: Public on Oct 31 2013

city: Chicago

first: Marsha

last: Rosner

state: IL

address: 929 East 57th Street

department: Ben May Department for Cancer Research

institute: University of Chicago

summary: The transcription factor BACH1 is a master regulator of human breast  cancer metastasis.  Here we use gene expression array analysis to identify and compare the genes regulated by BACH1 depletion in a metastatic human breast cancer cell line.

overall_design: Total RNAs were extracted from vector control 1833 cells or 1833 cells with shBACH mRNA BACH1 depletion. Affymetrix GeneChip Human Gene 1.0 ST Arrays were performed to detail the gene expression and identify the genes regulated by BACH1in metastatic human breast cancer cells.

first: Casey

last: Frankenberger


title: Derivation of novel human ground state naïve pluripotent stem cells [gene expression array]

status: Public on Oct 29 2013

city: Rehovot

first: Yair

last: Manor

address: 234 Hertzel st.

country: Israel

institute: Weizmann Institute of Science

summary: Mouse embryonic stem (ES) cells are isolated from the inner cell mass of blastocysts, and can be preserved in vitro in a naive inner-cell-mass-like configuration by providing exogenous stimulation with leukaemia inhibitory factor (LIF) and small molecule inhibition of ERK1/ERK2 and GSK3b signalling (termed 2i/LIF conditions). Hallmarks of naive pluripotency include driving Oct4 (also known as Pou5f1) transcription by its distal enhancer, retaining a pre-inactivation X chromosome state, global reduction in DNA methylation and in H3K27me3 repressive chromatin mark deposition on developmental regulatory gene promoters.Upon withdrawal of 2i/LIF, naïve mouse ES cells can drift towards a primed pluripotent state resembling that of the post-implantation epiblast. Although human ES cells share several molecular features with naive mouse ES cells, they also share a variety of epigenetic properties with primed murine epiblast stem cells (EpiSCs). These include use of the proximal enhancer element to maintain OCT4 expression, pronounced tendency for X chromosome inactivation in most female human ES cells, increase in DNA methylation and prominent deposition of H3K27me3 and bivalency acquisition on lineage regulatory genes. The feasibility for establishing human ground state naive pluripotency in vitro with equivalent molecular and functional features to those characterized in rodent ES cells remains to be defined. Here we establish defined conditions that facilitate the derivation of genetically unmodified human naive pluripotent stem cells from already established primed human ES cells, from somatic cells through induced pluripotent stem (iPS) cell reprogramming or directly from blastocysts. The novel naive pluripotent cells validated herein retain molecular characteristics and functional properties that are highly similar to mouse naive ES cells, and distinct from conventional primed human pluripotent cells. This includes competence in the generation of cross-species chimaeric embryos that underwent organogenesis following microinjection of human naive iPS cells into mouse morulas. Collectively, our findings establish new avenues for regenerative medicine, patient-specific iPS cell disease modelling and the study of early human development in vitro and in vivo.

overall_design: Total of 12 samples of naïve and primed human ESC lines were analyzed for gene expression. Many of the lines analyzed are genetically matched (H9, WIBR3).

first: Noa

last: Novershtern

first: Jacob

last: Hanna


title: CBC-ARS2 stimulates 3'-end maturation of multiple RNA families and favors cap-proximal processing

status: Public on Nov 08 2013

city: Montpellier

first: Edouard

last: BERTRAND

address: 1919 Route de Mendes

institute: CNRS

type: Expression profiling by genome tiling array

summary: The nuclear cap-binding complex (CBC) stimulates multiple steps in several RNA maturation pathways, but how it functions in humans is incompletely understood. For small capped RNAs like pre-snRNAs, the CBC recruits PHAX. Here, we identify the CBCAP complex, composed of CBC, Ars2 and PHAX, and show that both CBCAP and CBC-Ars2 complexes can be reconstituted from recombinant proteins. Ars2 stimulates PHAX binding to the CBC as well as snRNAs 3'-end processing, hereby coupling maturation with export. In vivo, CBC and Ars2 bind similar capped non-coding and coding RNAs, and stimulate their 3’-end processing. Strongest effects are displayed for cap-proximal polyadenylation sites, thereby favoring premature transcription termination. Ars2 functions in part through the mRNA 3’-end cleavage factor CLP1, which binds RNA Polymerase II through PCF11. Ars2 is thus a major CBC effector that stimulates functional and cryptic 3'-end processing sites.

overall_design: In total 12 samples; 4 control IP, 2 Flag- Ars2 IP and 2 Flag-CBP20 IP; 2 control FFL siRNA and 2 siRNA Ars2

first: Marie

last: Hallais

first: Frederic

last: Pontvianne

first: Peter

last: Andersen

first: marcello

last: Clerici

first: daniela

last: Lener

first: Nour

middle: E

last: Benbahouche

first: Thierry

last: Gostan

first: Franck

last: Vandermoere

first: Marie-Cécile

last: Robert

first: Stephen

last: Cusack

first: Céline

last: Verheggen

first: Torben

last: Jensen

last: Bertrand


title: Expression data in the presence of miR-29a inhibition in human dermal fibroblast cells

status: Public on Oct 28 2013

city: New Haven

first: Pei

last: Zhang

address: 10 Amistad

institute: Yale University

summary: miR-29 can target many gene transcripts encoding extracellular matrix proteins. To unravel novel targets, we used microarray analysis to detect global gene expression changes when inhibiting endogenous miR-29.

overall_design: Total RNA from human dermal fibroblast cells after 48 h treatment with miR-29a inhibitor or control inhibitor were isolated and subjected to whole gene expression microarray analysis.


title: HIV-1 gp120 impairs B cell proliferation by inducing TGF-β1 production and FcRL4 expression via an α4β7-dependent mechanism

status: Public on Oct 17 2013

city: Frederick

first: Richard

last: Lempicki

address: 1050 Boyles Street / P.O. Box B

institute: NCI-Frederick

summary: The anti-HIV humoral immune response following acute infection is delayed and ineffective. HIV envelope protein gp120 binds to and signals through α4β7 on T cells. We show that gp120 also binds and signals through α4β7 on B cells, resulting in an abortive proliferative response. In primary B cells, gp120 signaling through α4β7 resulted in increased expression of TGF-β1 and the B cell inhibitory receptor FcRL4. Co-culture of B cells with HIV-infected autologous CD4+ T cells also resulted in increased B cell FcRL4 expression. These findings indicate that, in addition to inducing chronic immune activation, viral proteins can contribute directly to HIV-associated B cell dysfunction, thus providing a mechanism whereby the virus subverts the early HIV-specific humoral immune response.

overall_design: Forty-two samples in two batches were run with different treatments and different time points.

first: Katija

last: Jelicic

first: Fatima

last: Nawaz

first: Da

middle: W

last: Huang

first: Xin

last: Zheng

first: Jun

last: Yang

first: Massimiliano

last: Pascuccio

first: Don

last: Van Ryk

first: Catherine

last: Schwing

first: Joe

last: Hiatt

first: Danlan

last: Wei

first: Greg

last: Roby

first: Raffaello

last: Cimbro

first: Antonio

last: David

first: II

middle: Y

last: Hwang

first: John

last: Kehrl

first: James

last: Arthos

first: Claudia

last: Cicala

first: Anthony

last: Fauci


title: Metabolic syndrome exercise training

status: Public on Nov 05 2013

city: Nijmegen

first: Gerwen

last: Lammers

address: PO Box 9101

country: Netherlands

institute: Radboud University Nijmegen Medical Centre

summary: We assessed vastus lateralis muscle gene expression levels of 12 women with the metabolic syndrome before and after a 6 month exercise training program

overall_design: RNA was isolated from a vastus lateralis muscle biopsy of 6 women with the metabolic syndrome before and after a 6 month guided endurance exercise training program

first: Fleur

last: Poelkens

first: Maria

last: Hopman


title: Gene expression profiling of lung cancer cells transfected with scrambled siRNA and siRNA targeting the ETS2 gene

city: Houston

first: Humam

last: Kadara

state: TX

address: 2130 W. Holcombe Blvd

institute: University of Texas MD Anderson Cancer Center

summary:
ETS2 is a canonical transcriptional factor and member of the ETS family of genes. ETS2 binds to consensus ERE binding sites in a broad spectrum of genes thus affecting many intracellular molecular functions. However, the role of ETS2 in the biology and pathogenesis of lung cancers is still not known.
We have found that ETS2 is down-regulated in lung tumors compared to normal lung tissue and the expression of the coding protein of the gene was a significant independent predictor of favorable outcome in NSCLC patients pinpointing to a potential tumor suppressor role for this gene. To better understand its molecular function in NSCLC, we compared and contrasted the transcriptome of lung cancer cells transfected with control siRNA and siRNA targeting ETS2.

overall_design: H441 lung cancer cells were transfected with SMARTpool (Dharmacon)control/scrambled siRNA or siRNA targeting ETS2. Three independent transfections were performed cells with control siRNA and for cells with siRNA specific to ETS2 where each transfection consittutes a biological replicate. Knock-down of ETS2 in all samples was confirmed by quantitative real-time PCR. Total RNA was then profiled using the Human Gene

first: Ignacio

last: Wistuba


status: Public on Oct 25 2013

city: San Juan

first: Pablo

last: Vivas-Mejia

state: PR

address: Medical Sciences Campus

department: Cancer Medicine

country: Puerto Rico

institute: University of Puerto Rico Cancer Center

summary: Differences in gene expression in A2780C20 vs. A2780 and A2780 treated with temsirolimus at 24-hr and 48-hr. The A2780 are human ovarian carcinoma  cellls were purchased to the European Collection of Cell Cultures (ECACC). The A2780CP20 are cisplatin resisatnt cells derived of the A2780 cells. A2780CP20 cells were generated by Dr. Robert Ozols (J. Natl. Cancer Inst. 84, 264-267 (1992) by treatment of A2780 cells with incresing concentrations of cisplatin. The goal of this study is to determine whether the cisplatin and temsirolimus resistance are co-regulated. The objectives of this study are to identify additional genes differentially expressed in cisplatin sensitive and cisplatin resistant ovarain cancer cells and the changes in gene expreession upon temsirolimus treatment of A2780 cells.

overall_design: RNA was isolated from A2780, A2780CP20, A2780 plus temsirolimus 24-hr, and A2780 plus temsirolimus 48-hr. Labelled samples were hybridized to Affymetrix GeneChip Gene 1.0 ST Human Arrays.


title: A Splice Variant of HER2 Activates Key Signaling Cascades and Evokes Mammary Tumors and Metastases

status: Public on Oct 22 2013

city: Basel

first: Tim

last: Roloff

address: Maulbeerstrasse 66

department: Functional Genomics

country: Switzerland

institute: FMI

summary: The Epidermal Growth Factor Receptor 2 (ERBB2 or HER2) is amplified and overexpressed in approximately 20% of invasive breast cancers and is associated with metastasis and poor prognosis. Here we describe the role of a constitutively active splice variant of HER2 (Delta-HER2) in human mammary epithelial cells. Overexpression of Delta-HER2 in human mammary cells decreased apoptosis and increased proliferation and expression of epithelial-to-mesenchymal markers. It also induced invasion in three-dimensional cultures and promoted tumorigenicity and metastasis in vivo. In contrast, similar overexpression of wild-type HER2 failed to evoke the same effects. Unbiased protein-tyrosine phosphorylation profiling revealed a significant increase in phosphorylation of several key signaling proteins upon Delta-HER2 expression, some of which not previously shown to belong to the HER2 pathway. In addition, microarray analysis revealed the expression of a set of genes specifically associated with Delta-HER2 expression. We found those genes to be highly expressed in ER-negative, high grade and metastatic primary breast tumors. Altogether, these results provide new insights into the function of a tumorigenic splice variant of HER2 and the signaling cascade deriving from its activity

overall_design: RNA was extracted from MCF10A expressing empty vector, WT-HER2 or Delta-HER2 (n=3).

first: Abdullah

last: Alajati

first: Mohamed

last: Bentires-Alj

first: Stephan

last: Duss

first: Stephane

last: Thiry


title: A Subset of Genes Can Distinguish between Bortezomib Responsive Versus Bortezomib Resistant Myeloma

city: Be'er Yacob

first: Yossi

last: Cohen

state: Zerifin

address: Assaf Harofhe, Institute of Hematology

department: Hematology

institute: Asaf Harofhe Hospital

summary: Gene expression profile (GEP) was analyzed from cultured bone marrow (BM) samples from patients with bortezomib responsive versus bortezomib resistant myeloma after 6-8 hours incubation in vitro with bortezomib 2 µg/ml or with PBS. Case D also had a fresh BM sample taken 75 minutes after IV injection of bortezomib.

overall_design: Comparative gene expression profiling of cultured bone marrow samples from from patients with bortezomib responsive versus bortezomib resistant myeloma after 6-8 hours incubation in vitro with bortezomib 2 µg/ml or with PBS.

first: Osnat

last: Garach-Jehoshua

first: Adina

last: Bar-Chaim

first: Abraham

last: Kornberg


title: Expression analysis of Escherichia coli MG1655 K-12 WT and ∆arcA mutant

city: Madison

first: Dan

last: Park

state: WI

address: 440 Henry Mall

institute: UW Madison

summary:
Investigation of whole genome gene expression level changes in a Escherichia coli MG1655 K-12 ∆arcA mutant, compared to the wild-type strain.  The mutations engineered into this strain produce a strain lacking the ArcA protein.
The results are further described in the manuscript The response regulator ArcA uses a diverse binding site architechture to globally regulate carbon oxidation in E. coli

sample_organism: Escherichia coli str. K-12 substr. MG1655

overall_design: A six chip study using total RNA recovered from three separate cultures of Escherichia coli MG1655 K-12 WT and three separate cultures of the ∆arcA mutant strain. Each chip measures the expression level of 4,661 genes from Escherichia coli MG1655 K-12 with eight 60-mer probes per gene, with each probe represented twice on the array.

first: Sohail

last: Acktar

first: Aseem

last: Ansari

first: Robert

last: Landick

first: Patricia

last: Kiley


title: Cytokines dominate the secretome of primary human myotubes in an in vitro exercise model

status: Public on Oct 09 2013

city: Neuherberg

first: Johannes

last: Beckers

address: Ingolstaedter Landstr. 1

department: Institute of Experimental Genetics

institute: Helmholtz Zentrum Muenchen

summary:
Muscle contraction during exercise is the major stimulus for the release of peptides and proteins (myokines) that are supposed to take part in the benefical adaptation to exercise. We hypothesize that application of an in vitro exercise stimulus as electric pulse stimulation (EPS) to human myotubes enables the investigation of the human muscle secretome in a clearly defined model. We applied EPS for 24 h to primary human myotubes and studied the whole genome-wide transcriptional response and as well as the release of candidate myokines. We observed 183 differentially regulated transcripts with fold-changes > 1.3. The transcriptional response resembles several properties of the in vivo situation in the skeletal muscle after endurance exercise, namely significant enrichment of pathways associated with interleukin and chemokine signaling, lipid metabolism, and anti-oxidant defense; notably without increased release of creatin kinase.
Multiplex immunoassays verified the translation of the transcriptional response of several myokines into high secretion levels (IL6, IL8, CXCL1, LIF, CSF3, IL1B, TNF) and identified an increased secretion of additional cytokines (IL2, IL4, IL13, IL17A). Inhibitor studies and immunoblotting revealed the participation of ERK1/2 and AMPK dependent pathways in the upregulation of myokines. To conclude our data highlight the importance of skeletal muscle cells per se as endocrine cells. This in vitro exercise model is not only suitable to identify known and novel exercise-regulated myokines but it might be applied to primary human myotubes obtained from different muscle biopsy donors to study molecular mechanisms of the individual response to exercise.

overall_design: We performed gene expression microarray analysis of myotubes in vitro stimulated by EPS and control myotubes

first: Mika

last: Scheler

first: Martin

last: Irmler

first: Stefan

last: Lehr

first: Sonja

last: Hartwig

first: Harald

last: Staiger

first: Hadi

last: Al-Hasani

last: de Angelis

first: Hans

last: Häring

first: Cora

last: Weigert


title: Clonal Immortalized Human Glial Cell Lines Support Varying Levels of JC Virus Infection due to Differences in Cellular Gene Expression

first: Kory

middle: R

last: Johnson

address: 10/3B01, 9000 Rockville Pike

department: DIR IT & Bioinformatics

institute: NINDS/NIH

summary: JC virus (JCV) is a ubiquitous human polyomavirus that causes the demyelinating disease Progressive Multifocal Leukoencephalopathy (PML). JCV replicates in limited cell types in culture, predominantly in human glial cells. Thus, productive JCV infection is an indicator of the host cell transcription environment. Following introduction of a replication defective SV40 mutant that expressed large T protein into a heterogeneous culture of human fetal brain cells, multiple phenotypes became immortalized (SVG cells). A subset of SVG cells could support JCV replication. This mixed culture was called SVG cells. In the current study, clonal cell lines were selected from the original SVG cell culture. The SVG-5F4 clone showed low levels of viral growth. The SVG-10B1 clone was highly permissive for JCV DNA replication and gene expression. Microarray analysis revealed that viral infection did not significantly change gene expression in these cells. More resistant 5F4 cells expressed high levels of transcription factors known to inhibit JCV transcription. Interestingly, 5F4 cells highly expressed RNA of markers of Bergman or radial glia and 10B1 cells had high expression of markers of immature glial cells and activation of transcription regulators important for stem/progenitor cell self-renewal. These SVG-derived clonal cell lines provide a biologically relevant model to investigate cell type differences in JCV host range and pathogenesis, as well as neural development.

overall_design: 13 Human samples: 3 SVG 10B1 clones 14 days post mock-infection, 3 SVG 10B1 clones 14 days post JCV Mad-4 strain infection, 3 SVG 5F4 clones 14 days post mock-infection, 4 SVG 5F4 clones 14 days post JCV Mad-4 strain infection.

first: M

last: Ferenczy

first: K

first: S

middle: M

last: Steinberg

first: L

middle: J

last: Marshall

first: P

middle: N

last: Jensen

first: E

middle: O

last: Major


title: TET2 loss-of-function mutations associate with a DNA hypermethylation signature in diffuse large B-cell lymphoma (mRNA)

status: Public on Oct 10 2013

city: Los Angeles

first: Vasu

last: Punj

address: Biggy Street

institute: USC

summary: Global gene expression in TET2 mutant and Wild type patients. We performed an integrated analysis of global DNA methylation and gene expression data to investigate the effects of DNA hypermethylation on gene expression.

overall_design: Total RNA was isolated from 4 TET2mut and 5 TET2wt  were isolated using standard RNAeasy kit protocol (Qiagen). Their gene expression profiles were obtained using the[HuGene-1_0-st] Affymetrix.

first: Fazila

last: Asmar

first: Jesper

last: Christensen

first: Marianne

last: Pedersen

first: Anja

first: Anders

middle: B

last: Nielsen

first: Christoffer

last: Hother

first: Ulrik

last: Ralfkiaer

first: Peter

middle: D

last: Brown

first: Elisabeth

first: Kristian

last: Helin

first: Kirsten

last: Gronbaek


title: Expression data from human heart

city: Valencia

first: Maria Micaela

last: Molina Navarro

address: Avenida Campanar, 21

institute: Health Research Institute of the Hospital La Fe

summary:
Global gene expression is altered in heart failure. This syndrome can be caused by cardiovascular diseases, including dilated cardiomyopathy (DCM), ischemic cardiomyopathy (ICM), hypertrophic cardiomyopathy, viral or toxic myocarditis, hypertension, and valvular diseases.
We used microarrays to evaluate the impact of heart failure on human nucleocytoplasmic transport-related genes examining simultaneoulsly both dilated and ischemic human cardiomyopathies compared to normal hearts.

overall_design: Transmural samples were taken from near the apex of the left ventricle. 29 heart samples were used in the microarray assay (dilated cardiomypathy, n = 12; ischemic cardiomyopathy, n = 12, and control hearts n = 5).

first: Maria

last: Molina-Navarro

first: Esther

last: Roselló-Lletí

first: Estefanía

last: Tarazón

first: Ana

last: Ortega

first: Dolors

last: Sánchez-Izquierdo

first: Francisca

last: Lago

first: José

last: González-Juanatey

first: Pablo

last: García-Pavía

first: Antonio

last: Salvador

middle: A

last: Montero

first: Manuel

last: Portolés

first: Miguel

last: Rivera


title: Functional heterogeneity of cancer-associated fibroblasts from human colon tumors shows specific prognostic gene expression signature

status: Public on Oct 30 2013

city: Madrid

first: Cristina

last: Pena

address: Joaquín Rodrigo, 2. Peine 7, Planta 3 28222 Majadahonda. Madrid, SPAIN

department: Oncology Department

institute: Hospital Universitario Puerta de Hierro

summary: Tumor growth and metastasis is controlled by paracrine signaling between cells of the tumor microenvironment and malignant cells. Cancer-associated fibroblasts (CAFs), are functionally important components of the tumor microenvironment. Although some steps involved in the cross-talk between these cells are known, there is still a lot that is not clear. Thus, the addition of, the consideration of microenvironment in the development of the disease, to the clinical and pathological procedures (currently admitted as the consistent value cancer treatments) could lay the foundations for the development of new treatment strategies to control the disease.

overall_design: Primary CAF cultures from 15 primary human colon tumors were established Their purity was evaluated by the expression of various epithelial and myofibroblast specific markers Co-culture assays of primary CAFs with different colon tumor cells were performed to evaluate pro-migratory CAF-derived effects on cancer cells CAF gene expression profiles were analyzed by microarray to identify deregulated genes in different pro-migratory CAFs

last: Peña

first: Mercedes

last: Herrera

first: Abul

last: Islam


title: Comparative analysis of gene expression by human Umblical Cord (UCB)-CD34+ Hematopoietic Stem Cells (HSCs) and human induced pluripotent stem (iPS) cell-derived CD34+ Hematopoietic Progenitor Cells (HPCs)

status: Public on Oct 23 2013

city: Iowa City

first: Eunmi

last: Kim

state: IA

address: 601 HWY 6 w

institute: University of Iowa

summary:
Hematopoietic stem and progenitor cells are a rare, self-renewing bone marrow resident population capable of giving rise to all circulating hematopoietic cells. They can be used therapuetically for reconstituting defective or ablated hematopoietic systems following chemotherapy, and for inducing tolerance toward allografts of the same haplotype as the HSC donor. There are several sources for HSCs, such as the adult bone marrow, or umblical cord blood, which is more replete with such HSCs. However, HSCs obtained from such sources may be immunogenic, especially if isolated from adult bone marrow. To overcome this issue, our lab has establsihed human induced pluripotent stem cell-derived HPCs with the hope of creating a nonimmunogenic, readily available and unlimited source of HSCs to use for therapy.
The goal of this study was to compare the gene expression profiles of naturally found HSCs (UCB-CD34+ HSCs) and HPCs differentiated from 4 different human iPS cell lines (iPS-HPCs), so as to determine the variation between the four iPS-HPCs and whether there were any differences between these HPCs and naturally found HSCs.

overall_design: We utilized 4 iPS cells for this study (detailed descriptions are provided below). iPS cells were differentiated into hematopoietic progenitor cells by coculture on OP9 stromal cells, followed by enrichment of CD34+ cells through immunomagnetic bead separation. The UCB-CD34+ cells were isolated from frozen cord samples through immunomagnetic bead separation. Total RNA was isolated and human gene  Affymetrix ST 1.0 arrays performed at the University of Iowa DNA core facility. Data was analyzed, normalized and plotted on BRB Array Tools.

first: Nicholas

last: Zavazava


title: Abiraterone acetate and di-n-butyl phthalate (DBP) response in a human fetal testis xenograft bioassay

city: Providence

first: Daniel

middle: James

last: Spade

state: RI

address: Box G-E5

department: Pathology and Laboratory Medicine

institute: Brown University

summary:
The goal of this study was to determine the effects of a well-characterized anti-androgen, abiraterone acetate, and a suspected human anti-androgen, di-n-butyl phthalate (DBP) on the androgenic function of human fetal testis. Human fetal testis was xenografted into the renal subcapsular space of castrated male athymic nude mice.  Hosts were treated with hCG to stimulate testosterone production in the xenografts, and were concurrently treated with either abiraterone acetate or DBP.  While abiraterone acetate (14 d, 75 mg/kg/d p.o.) dramatically reduced testosterone and the weights of androgen-sensitive host organs, DBP (14 d, 500 mg/kg/d p.o.) had no effect on androgenic endpoints.
Three paired analyses were performed using the LIMMA package in R (commands lmfit and eBayes), with the Benjamini-Hochberg correction for multiple comparisons (Smyth 2005):  vehicle-treated xenografts vs. unimplanted testis (n=5), abiraterone-treated xenografts vs. matched control xenografts (n=3), and DBP-treated xenografts vs. matched control xenografts (n=3).  There were significant differences in gene expression between grafted and ungrafted samples, including dramatic upregulation of microRNAs.  Gene expression analysis also showed that abiraterone decreased expression of genes related to cell differentiation, while DBP induced expression of oxidative stress response genes and decreased expression of factors related to embryonic development.

overall_design: 17 xenograft samples were analyzed, including 5 unimplanted samples, 6 vehicle treated xenografts, 3 abiraterone acetate-treated xenografts, and 3 DBP-treated xenografts.  Samples were paired (derived from the same donor tissue) for each comparison:  vehicle vs. unimplanted (n=5), abiraterone vs. vehicle (n=3), and DBP vs. vehicle (n=3).

first: Susan

last: Huse

first: Christoph

last: Schorl

first: Kim

last: Boekelheide


title: mRNA microarray analysis on HepG2 cells exposed to amorphous Silica Nanoparticles (SiO2-NP)

status: Public on Oct 01 2013

city: seoul

first: jinhee

last: choi

address: 90 Jeonnong-dong, Dongdaemun-gu

department: College of Urban Science

institute: University of Seoul

summary:
In order to evaluate the identification of genes and pathways, the global gene expression profiles were assessed in response to amorphous Silica nanoparticles on Human hepatoma (HepG2) cells. We performed whole genome DNA microarray experiments using HepG2 cells exposed to  for 24h.
We used whole genome microarrays to screen for global changed in HepG2 transcription profiles and with subsequent quantitative analysis conducted on selected genes.

overall_design: 24h SiO2-NP (100 mg/L) exposed HepG2 cells were used for total RNA extraction and hybridization on Affymetrix microarrays.

first: Jinhee

last: Choi

first: Nivedita

last: Chatterjee


title: Effect of CCAR1 depletion on androgen-dependent gene expression in LNCaP cells

city: Seoul

first: Jeong

middle: Hoon

address: Irwon-dong Gangnam-gu

institute: Sungkyunkwan University

summary:
Androgen receptor (AR) plays a critical role in prostate cancer onset and progression, and cell cycle and apoptosis regulator 1 (CCAR1) functions as an AR co-activator.
We performed genome-wide gene expression analysis in control (shNS) and CCAR1-depleted (shCCAR1) LNCaP cells to assess the global effect of CCAR1 on the expression of androgen responsive genes.

overall_design: LNCaP cells expressing shNS or shCCAR1 were treated with ethanol or 10 nM DHT for 24 hr, and total RNA was isolated using the RNeasy mini kit (Qiagen). The integrity of RNA was analyzed using an Agilent 2100 Bioanalyzer. Two independent biological replicates were assayed for each sample. The microarrays were performed following the Affymetrix standard protocol.

first: Woo-Young

last: Seo

middle: H


title: Transcription analysis of photocoagulated human retinal pigment epithelial cells in culture

status: Public on Oct 03 2013

city: Malmo

first: Poya

last: Tababat-Khani

address: CRC, Jan Waldenstroms gata 35

department: Department of Clinical Sciences, Malmo

institute: Lund University

summary: ARPE-19 cells were either laser treated or not, and analyzed 2, 6 and 24 hours after laser treatment. In addition, the cells were treated with high or low glucose (T2D complications analysis). The difference in glucose levels did not make much difference in regards to gene expression.

overall_design: 52 ARPE-19 samples including controls and laser-treated samples. Separate analysis for high and low glucose levels.

first: Francesc

last: Canals

first: Hedvig

last: Bennett

first: Rafael

last: Simo

first: Christina

last: Hernandez

first: Malin

last: Fex

first: Carl

last: Agardh

first: Ola

last: Hansson

first: Elisabet


title: Gene expression profiling in cells with Ago1 knockdown (Affymetrix)

status: Public on Sep 27 2013

city: San Francisco

first: Vera

last: Huang

address: 1450 Third Street, Helen Diller Cancer Research Building, Room 302

department: Urology

institute: UCSF

summary: Argonautes, a family of highly evolutionarily conserved proteins, are the central platform for small RNA-mediated gene regulatory mechanisms which occur mainly in the cytoplasm. To understand a potential role of Argonaute 1 (Ago1) protein in the nucleus of mammalian cells in regulating gene transcription and epigenetics, we performed integrated analyses of Ago1 ChIP-sequencing (GSE40536) and gene expression profiling in cells depleted of Ago1. For gene expression profiling, we knocked down the expression of Ago1 by siRNA in PC-3 cells and compared gene expression profiles in the cells depleted of Ago1 and cells receiving control treatments. We found that Ago1 depletion resulted in more downregulated genes which were enriched in gene responsible for promoting cell cycle progression, DNA replication and repair, and response to endogenous stimuli. Integrated analyses of Ago1-chromosomal interactions and gene expression changes in response to Ago1 depletion reveal a significant correlation between Ago1-bound genes and genes altered by Ago1 depletion. These genes are significantly enriched in cancer-related pathways. Our data suggests a nuclear function of Ago1 in regulating gene transcription.

overall_design: PC-3 cells were mock transfected or transfected with an Ago1 specific siRNA or a control siRNA. Each treatment was done in duplicates.

first: Jiashun

last: Zheng

first: Long-Cheng

last: Li


title: Expression data from NSCs treated with REST inhibitor X5050

city: 91400 Orsay

first: Florent

last: Dumont

state: Ile de France

address: 17 avenue des sciences

institute: Université Paris-Saclay

summary:
REST has been initially described as a repressor of neuronal genes in non-neuronal cells by binding to its recognition sequence RE1. Over-activation of this factor has been shown in several diseases such as Huntington disease or central nervous system cancers. High-throughput screening of a library of 6,984 compounds with luciferase-assay measuring REST activity in neural derivatives of human embryonic stem cells led to the identification of one benzoimidazole-5-carboxamide derivative (X5050) that inhibited REST silencing in a RE1-dependent manner.
Differential transcriptomic analysis revealed the upregulation of neuronal genes targeted by REST.

overall_design: RNA was extracted from 6 samples, corresponding to 3 independent cultures of NSC SA-01, each one treated either with DMSO (0.1 % final) or with X5050 (100 µM final). RNA was isolated using RNeasy Mini kit with DNase I digestion and genome-wide gene expression profiling was performed by hybridization on Affymetrix microarrays

first: Jérémie

last: Charbord

first: Anselme

middle: L

last: Perrier


title: Assesing an improved protocol for plasma microRNA extraction

status: Public on Oct 18 2013

first: Dolors

last: Sanchez-Izquierdo

state: Valencia

address: Avda. Campanar 21

department: Genomics Unit

institute: IIS La Fe

summary:
The first step in biomarkers discovery is to identify the best protocols for their purification and analysis. We have identified an optimal RNA extraction method of microRNAs from human plasma samples.
We also report that the addition of low doses of carrier RNA before starting RNA extraction improves microRNA extraction and quantification.

overall_design: Human plasma and matched biopsies were obtained from healthy donors and patients attended at the Hospital Universitari i Politècnic La Fe (Valencia, Spain). RNA was extracted by different preanalytal conditions and reagents, testing the suitable of carrier addition at differnt doses. The best protocol was followed up by hybridation on Affymetrix microarrays.

last: Sánchez-Izquierdo

first: Inés

last: Moret-Tatay


title: Gene expression profile of canine mammary malignancy

city: Warsaw

first: Magdalena

last: Król

address: Nowoursynowska 159

department: Physiological Sciences

country: Poland

institute: Warsaw University of Life Sciences

summary: Molecular mechanisms of the canine mammary malignancy. RNA isolated from canine mammary tumours of the 3rd grade of malignancy was pooled and hybrydized on the same microarray as RNA isolated from canine mammary tumours of the 1st grade of malignancy. Based on the results the "malignancy portrait" was assessed.

overall_design: Dye-swap experiment, gene expression in the most malignant canine mammary tumours (the 3rd grade of malignancy) was compared to the less malignant tumours (1st grade of malignancy).

first: Karol

last: Pawłowski

first: Agata

last: Homa

first: Małgorzata

last: Bulkowska

first: Alicja

last: Majewska

first: Tomasz

last: Motyl


title: Effect of BET inhibitors (JQ1 and RVX-208) on gene expression in HepG2 cells

status: Public on Sep 24 2013

city: Oxford

first: Panagis

last: Filippakopoulos

state: Oxfordshire

address: ORCRB - Roosevelt Drive

department: Nuffield Department of Medicine

institute: Oxford University

summary: Bromodomains have emerged as attractive candidates for the development of inhibitors targeting gene transcription. Inhibitors of the bromo-and-extra-terminal (BET) family recently showed promising activity in diverse disease models. However, the pleiotropic nature of BET proteins regulating tissue specific transcription has raised safety concerns and suggested that attempts should be made for domain-specific targeting. Here we report that RVX-208, a compound currently in phase II clinical trials, is a BET bromodomain inhibitor specific for second bromodomains (BD2). Co-crystal structures revealed binding modes of RVX-208 and its synthetic precursor and fluorescent recovery after photobleaching demonstrated that RVX-208 displaces BET proteins from chromatin. However, gene expression data showed that BD2 inhibition only modestly affects BET-dependent gene transcription. Our data demonstrate the feasibility of specific targeting within the BET family resulting in different transcriptional outcomes and highlight the importance of BD1 in transcriptional regulation

overall_design:
HepG2 Cells were treated with eitther DMSO or 0.5uM JQ1 or 5uM RVX-208. Three samples per condition, total of nine samples. Inhbitor treatment was carried out for 4h before RNA was extracted.
HepG2 cells (ATCC: HB-8065) were maintained in α-MEM (Cat.#BE12-169F; BioWhittaker) supplemented with 10 % heat-inactivated foetal calf serum (PAA #A15-152), non-essential amino acids (Cat. #M7145; Sigma), glutamine (Cat.#M11-004; PAA), and vitamins (Cat.#M6895; Sigma). Cells were grown at 37 °C in a humidified cabinet at 5 % CO2 (Heraeus Function Line). For experiments, cells were seeded the day prior to treatment at 2x105/ml. Treatments were performed for 4 h so that a final concentration of 0.1 % DMSO (Cat.#D1435; Sigma) was achieved. At harvest, cells were washed once with PBS (Cat.#H15-002; PAA), and lysed in situ using RLT buffer supplemented with 10 μl/ml β-mercaptoethanol (Cat.#M7522; Sigma). Total RNA was extracted and prepared using RNeasy columns (Cat.#74106 plus; Qiagen) including a Qia shredding step (Cat.#79656; Qiagen) and an on-column DNAse digestion (Cat.#EN0521; Fermentas), according to the manufacturer’s instructions. The resulting RNA was quantified and quality controlled using a Nanodrop spectrophotometer (model ND1000; Thermo Fisher).
RNA integrity was assessed on a BioAnalyzer (model G2938C; Agilent Laboratories, USA) and all samples had a RNA Integrity Number (RIN) ≥ 9. Labelled sense ssDNA for hybridization was generated from 200 ng starting RNA with the Ambion WT expression kit (Cat.#4411973; Ambion) and the Affymetrix GeneChip WT Terminal Labelling and Controls Kit (Cat.#901525; Affymetrix) according to the manufacturer’s instructions. The distribution of fragmented sense ssDNA lengths was measured on the BioAnalyser. The fragmented ssDNA was labelled and hybridized for 17 hours at 45 °C on the Affymetrix GeneChip Human Gene 1.0 ST Array (Affymetrix). Chips were processed on an Affymetrix GeneChip Fluidics Station 450 and Scanner 3000 and the affymetrix Command Console (v.3.2.4; Affymetrix) was used to generate CEL files.

first: Deborah

last: Brotherton

first: Sheena

last: Lee


title: Genes affected by Ret activation during estrogen stimulation or inhibition in MCF7/Aro cells

status: Public on Sep 25 2013

first: Tim

last: Roloff

address: Maulbeerstrasse 66

institute: FMI

summary: Endocrine therapy is the main therapeutic option for patients with estrogen receptor alpha positive (ER+) breast cancer. Nevertheless, most of them become estrogen-independent and relapse after the treatment. Ret is a tyrosine kinase receptor that shows elevated expression levels in ER+ human breast tumors. In this study, we demonstrate that activation of the Ret receptor promotes proliferation as well as cell migration irrespective of endocrine therapy. Microarray data show that Ret activation involves changes in the expression of inflammatory- and motility-related genes. In vivo treatment with a Ret pathway inhibitor in a ER+/Ret+ mouse mammary cancer model, reduces tumor growth and lung metastasis even after endocrine therapy. Additionally, we show a connection between Ret and inflammatory pathways. The pro-inflamatory cytokine IL6 lies at the core of this regulation, which involves a positive feedback loop with IL6 and the Ret pathway reciprocally stimulating each other to further leading metastasis risk. Our findings provide insight into endocrine resistance mechanism and point at the Ret pathway as a potential target for future therapies.

overall_design: In order to model letrozole-sensitive breast cancer we use aromatase expressing MCF7 cells (MCF7/Aro). Six-day treatment (6 days) of cultures with letrozole (L) or fulvestrant (F) reversed the proliferative effects of the exposure to the estrogen (E2) precursor androstenedione (D4A). The addition of only EtOH (E) to the cells was used as control condition of deprivation. Treatment with the Ret ligand GDNF (G) partially rescues the inhibition of estrogen-dependent proliferation in these cells. To go deeper insight into the pathways involved, we decided to perform a microarray following different treatments (1-8: E, E+G, D, D+G, L, L+G, F, F+G) used in proliferation assays. Three biological replicates (rep 1-3) were used to the array.

first: Albana

last: Gattelli

first: Nancy

last: Hynes

first: Stephane

last: Thiry


title: The human placental sexome differs between trophoblast epithelium and villous vessel endothelium

city: Graz

first: Silvija

last: Tokic

address: Auenbruggerplatz 14

country: Austria

institute: Medical University of Graz

summary:
As susceptibility to many adult disorders originates in utero, we here hypothesized that fetal sex influences gene expression in placental cells and produces functional differences in human placentas. We found that fetal sex differentially affects gene expression in a cell-phenotype dependent manner among all four placental cell-phenotypes studied: cytotrophoblasts, syncytiotrophoblasts, arterial endothelial cells and venous endothelial cells. The markedly enriched pathways in males were identified to be signaling pathways for graft-versus-host disease as well as the immune and inflammatory systems, both supporting the hypothesis that there is reduced maternal-fetal compatibility for male fetuses.
Our study is the first microarray study investigating sexual dimorphism in purified and characterized somatic cells from a single human tissue, the placenta, that underlines the importance of considering fetal sex as an independent variable in any work using human placenta.

overall_design: Arterial and venous endothelial cells were isolated from eight different placentas, four of each sex. A total of ten placentas were used for isolation of cytotrophoblasts and six for syncytiotrophoblasts, with equal numbers from each sex.

last: Cvitic

first: Mark

last: Longtine

first: Hubert

last: Hackl

first: Karin

last: Wagner

first: Michael

last: Nelson

first: Gernot

last: Desoye

first: Ursula

last: Hiden