title: Searching for target genes of miR-429 in HCCLM3 cells

first: Liang

state: Shanghai

address: 225 Changhai Road

institute: Eastern Hepatobiliary Surgery Hospital

summary:
miRNAs are an class of small noncoding RNAs and about 21-25 nucleotides in length. miRNAs inhibit the translation or induce mRNA degradation by binding to the 3’ UTR of target mRNAs and have been identified as the tumor promoters or suppressors regulating the progression of cancers. miR-429, which is a member of an evolutionarily conserved family of miRNAs that includes miR-200b, miR-200a, miR-200c and miR-141, is expressed in various epithelial tissues. Our goal is to search the possible target genes of miR-429 in human liver cancer cell line HCCLM3.
We analyzed possible target genes of miR-429 by identifying the shared genes among the down-regulated genes in epithelial cell adhesion molecule (EpCAM) negative HCCLM3 cells which treated with miR-429 mimics and the up-regulated genes in EpCAM positive HCCLM3 cells which treated with Antagomir-429.

overall_design: Magnetic sorted EpCAM negative HCCLM3 cells were treated with 100nM miR-429 mimics or NC mimics for 4 days; Magnetic sorted EpCAM positive HCCLM3 cells were treated with 40μM Antagomir-429 or Antagomir-NC for 4 days. The gene expression profiles were determined by Affymetrix Human U133 plus2.0 array according to the manufacturers’ instructions.

first: Hongyang

last: Wang


title: Granulocyte-monocyte progenitor cell cycle regulation occurs through calcium flux and calcineurin-NFAT signaling via Flt3-L

status: Public on Dec 31 2014

first: Bernett

last: Lee

address: 8A Biomedical Grove #03-06 Immunos

country: Singapore

institute: Singapore Immunology Network

summary:
Complex regulatory mechanisms control continuous maintenance of myeloid progenitors and renewal of differentiated cells. Transcription factors play a important role in these processes. Here we report that the activation the calcineurin-NFAT signaling pathway inhibit the proliferation of myeloid granulocyte-monocyte progenitor (GMP). Myeloid progenitor subtypes possessed different susceptibilities to Ca2+ flux induction and consequently differential engagement of the calcineurin-NFAT pathway. This study show that inhibition of the calcineurin-NFAT pathway enhanced proliferation of GMPs both in vivo and in vitro. The calcineurin-NFAT signaling in GMPs is initiated through Flt3-L. The inhibition of the calcineurin-NFAT pathway altered the expression of the cell cycle regulation genes CDK4, CDK6, and CDKN1A, thus enabling faster cell cycle progression. The extensive use of NFAT inhibitors in the clinic should take into account that, in addition to the immunosuppression role in lymphoid cells, these NFAT inhibitors also affect the maintenance of the myeloid compartment.
Microarray technology was used to understand the effects of NFAT inhibitors on C-kit enriched lineage negative cells.

overall_design: Bone marrow from C57BL/6 mouse depleted for lineage positive differentiated cells (lin-, CD3e-, B220-, CD19- CD11b-, CD11c-, Gr-1-, TER-119-, NK1.1- with addition of CD127-) and enriched for c-kit. lineage negative, cKIT positive progenitors were cultured in  IMDM (containing 200ng/ml mrFLT3-L (Stem cells), 10% heat-inactivated FCS (Life Technologies), streptomycin 100mg/ml and penicillin 100 U/ml) at 3x106 cells/ml. For culture of sorted progenitors, stem cell factor (SCF; 50ng/ml), IL-6 (20ng/ml) and IL-3 (10ng/ml; all R&D Systems) were added (referred to as HSC medium). 2µg/ml CsA or 0.2µg/ml FK506 (Cell signalling Technology) were added to the cell culture for 30 mins preceding the addition of Flt3-L were maintained throughout the culture.

first: Jan

last: Fric

first: Clarice

last: Lim

first: Alexandra

last: Mertes

first: Teresa

last: Zelante

first: Paola

last: Ricciardi-Castagnoli


title: The regulatory landscape of osteogenic differentiation

city: Oslo

first: Leonardo

middle: A.

last: Meza-Zepeda

address: Ullernchausseen 70

department: Department of Tumor Biology

country: Norway

institute: Oslo University Hospital

summary: During embryogenesis, body growth and repair the bone substance is formed by osteoblasts, which are derived from mesenchymal stem cells. Bone marrow-derived mesenchymal stroma cells (MSCs) have many of the properties of multipotent stem cells, and can be differentiated towards osteoblasts in vitro, making these cells a convenient tool for investigation of osteogenesis. We here describe the pattern of gene expression, histone modification and DNA binding of the bone master regulator RUNX2 during osteogenic differentiation of an immortalized human bone marrow-derived MSC cell line. By sequencing of immuno¬precipi¬tated chromatin we generated high resolution maps of enrichment of five histone H3 modifications associated with different functional states of chromatin, and identified differentiation-induced epigenetic changes. By the same approach, several thousand binding sites for the transcription factor RUNX2 was mapped to around 1900 target genes in differentiated osteoblasts. RUNX2 target genes were associated with cellular growth, movement, apoptosis and PDGF BB and p53 signaling. Surprisingly, RUNX2 was found to bind both at the 5’ and 3’ ends of genes, and also at distal regulatory elements, and was co-localized with activating histone modifications at approximately half of bound sites. This is to our knowledge the first genome-wide description of RUNX2 targets in bone biology. Further, we identified GTF2I and TEAD2 as regulators of differentiation by computational prediction of over-represented transcription factor motifs in regions with differential histone modification enrichment. The predictions were confirmed by siRNA knockdown of the transcription factors which lead to inhibition of differentiation.

overall_design: Comparison of DNA methylation patterns of iMSC#3 before (Undiff) and after (Day 28) osteogenic differentiation

first: Anne-Mari

last: Håkelien

middle: C

last: Bryne

first: Kristine

middle: G

last: Harstad

first: Susanne

last: Lorenz

first: Jonas

last: Paulsen

first: Jinchang

last: Sun

first: Tarjei

middle: S

last: Mikkelsen

first: Ola

last: Myklebost

middle: A


title: A Phase I/II Clinical Trial of PXD101 in Combination with Idarubicin in Patients with AML Not Suitable for Standard Intensive Therapy

city: Berlin

first: Lars

last: Bullinger

address: Augustenburger Platz 1

department: Hematology, Oncology and Tumorimmunology

country: Germany

institute: Charité

summary:
The pharmacodynamics investigations in PXD101-CLN-15 included correlation of response with gene expression (n=13).
Gene expression profiling based on 13 patients (4 responders and 9 non- responders) revealed a strong gene expression pattern associated with the response to belinostat. 1905 genes were significant at the p<0.05 level of the univariate test. MLL(p=0.0000769), a gene well known to play a crucial role in leukemogenesis via epigenetic deregulation, was among the top 20 candidates. Of these, differential expression of TP53(p=0.0001817) is also of special interest as histone deacetylase have been shown to modulate p53 transcriptional activity through regulation of p53-DNA binding activity. An additional interesting candidate was CCT5(p=0.000135), chaperonin containing TCP1, subunit 5 (epsilon), a known interactor of HDAC3 and HDAC5 (see http://www.ncbi.nlm.nih.gov/gene/22948) that encodes for a molecular chaperone that is a member of the chaperonin containing TCP1 complex (CCT). GO (gene ontology) class comparison analysis shows a significant enrichment of gene ontologies including categories associated with epigenetic regulation such as the GO category “histone methyltransferase activity” (comprising e.g. MLL, ASH2L, MEN1, and SUZ12) and “histone deacetylase activity” (comprising e.g. HDAC7, HDAC2, SIRT5, and HDAC2). The gene signature provides insights into the molecular deregulation prone to restoration of epigenetic deregulation, and the respective gene expression pattern also harbors predictive information as demonstrated by the blinded belinostat response prediction based on an in vitro cell line derived predictor.

overall_design: All samples were obtained from untreated patients at the time of diagnosis. Cells used for microarray analysis were collected from the purified fraction of mononuclear cells after Ficoll density centrifugation. Routine diagnostic algorithms, including the characterization of molecular markers are performed.


title: DNA methylation profiles of primary ovarian cancers

city: Durham

first: Susan

middle: K.

last: Murphy

state: NC

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

department: Obstetrics and Gynecology

country: USA

institute: Duke University Medical Center

type: Methylation profiling by genome tiling array

summary: Targeted approaches have revealed frequent epigenetic alterations in ovarian cancer, but the scope and relation of these changes to histologic subtype of disease is unclear. Genome-wide methylation and expression data for 14 clear cell carcinoma (CCC), 32 non-CCC, and 4 corresponding normal cell lines were generated to determine how methylation profiles differ between cells of different histological derivations of ovarian cancer. Consensus clustering showed that CCC is epigenetically distinct. Inverse relationships between expression and methylation in CCC were identified, suggesting functional regulation by methylation, and included 22 hypomethylated (UM) genes and 276 hypermethylated (HM) genes. Categorical and pathway analyses indicated that the CCC-specific UM genes were involved in response to stress and many contain hepatocyte nuclear factor (HNF) 1 binding sites, while the CCC-specific HM genes included members of the estrogen receptor alpha (ERalpha) network and genes involved in tumor development. We independently validated the methylation status of 17 of these pathway-specific genes, and confirmed increased expression of HNF1 network genes and repression of ERalpha pathway genes in CCC cell lines and primary cancer tissues relative to non-CCC specimens. Treatment of three CCC cell lines with the demethylating agent Decitabine significantly induced expression for all five genes analyzed. Coordinate changes in pathway expression were confirmed using two primary ovarian cancer datasets (p<0.0001 for both). Our results suggest that methylation regulates specific pathways and biological functions in CCC, with hypomethylation influencing the characteristic biology of the disease while hypermethylation contributes to the carcinogenic process.

overall_design: This study included 96 total samples, including 53 serous ovarian cancers, 11 endometrioid ovarian cancers, 13 clear cell ovarian cancers, 8 mucinous ovarian cancers, 4 fallopian tube epithelium specimens, 4 ovarian surface epithelium specimens, 1 universally methylated DNA sample, 1 normal human lymphocyte sample, and 1 50:50 mixture of the normal human lymphocyte DNA and universally methylated DNA samples.

middle: K

first: Berchuck

last: Andrew

first: Ken

last: Yamaguchi

first: Zhiqing

last: Huang


title: Microarray of pancreatic cancer and healthy tissue

city: Atlanta

first: Nathan

middle: J.

last: Bowen

state: GA

address: 223 James P Brawley Drive

department: Center for Cancer Research and Therapeutic Development

institute: Clark Atlanta University

summary:
Gene expression analyses of pancreatic adenocarcinoma and adjacent ductal epithelia from the same patient using bulk vs LCM dissected samples.
Our results indicate that laser capture microdissection (LCM) is necessary to identify differentially expressed genes that discriminate between PDAC and healthy pancreatic ductal tissue.

overall_design: Pancreatic tissues were collected at time of surgery and snap frozen in liquid nitrogen for RNA extraction and Affymetrix GeneChip Expression analyses.

middle: J


title: Expression of FRY-targeting shRNA in MCF10A cells

city: Piscataway

first: Jessica

middle: Corban Wos

last: Graham

state: NJ

address: 170 Frelinghuysen Road

department: Toxicology

institute: The University of Medicine and Dentistry of New Jersey

summary:
We identified the predicted FRY gene as a candidate mammary carcinoma susceptibility gene. This gene has not been characterized in mammals, so for part of our analysis we conducted microarray experiments to look at the changes in gene expression which occur when FRY-targeting shRNA is expressed in the nontumorigenic MCF10A mammary epithelial cell line (a cell line which we identified as having higher FRY mRNA expression than breast cancer cell lines).
We used microarrays to identify the FRY interactome and identified that FRY affects the expression of gene networks that maintain normal cellular and tissue architecture, organization, differentiation of epithelial cells.

overall_design: Three RNA samples were utilized for each of the two types of cell transfection.  These samples varied in passage number.

first: Helmut

last: Zarbl


title: Expression data of miR-95 transfection in MCF-7 cells compared with scramble control

status: Public on Dec 30 2014

city: CANBERRA

first: Jiayu

last: Wen

state: ACT

address: 133 Garran Rd

department: Department of Genome Science

country: Australia

institute: John Curtin School of Medical Research, The Australian National University

summary:
We identified miR-95 in a screen for miRNAs which functionally affect
autophagic flux in MCF-7 cells. We over expressed miR-95 or a scramble
control and isolated total RNA for microarray analysis. We identified several
biological pathways and targets regulated by miR-95 including genes related
to endocytosis, ubiquitin mediated proteolysis and lysosomal function.

overall_design: MCF-7 cells were seeded in 6-cm plates and independent triplicate transfections were performed the following day with 50 nM miR-95 or scramble control. Total RNA was harvested 24 h after transfection using Trizol reagent. There are a total of six arrays included in this experiment, including three biological replicates of mRNA expression after miR-95 over-expression and three scramble controls in MCF-7 cells.

first: Lisa

middle: B

last: Frankel

first: Anders

middle: H

last: Lund


title: Expression data from Human primary colon cancer cells

city: Taipei

first: chia-chi

last: chang

address: No.201, Sec 2, Shih-Pai Road

country: Taiwan

institute: Medical research & education of VGHT

summary: Transcriptional profiling of Human primary colon cancer cells under spheroid culture. Goal was to determine the effects of spheroid culture on global primary colon cancer cells gene expression.

overall_design: Three-condition experiment: normal culture , spheroid culture at days of 5, and spheroid culture at days of 15.

first: Chia-Chi

last: Chang

first: Shih-Chieh

last: Hung


title: Expression data from Dnmt3a-deficient and control mouse MYC induced T-cell lymphomas

city: Omaha

first: Rene

last: Opavsky

state: NE

address: 985040 Nebraska Medical Center

institute: University of Nebraska Medical Center

summary: Dnmt3a catalyzes DNA methylation of gDNA, which contributes to the transriptional regulations of genes and genomic stability.

overall_design: Dnmt3a was deleted in the hematopoietic compartment in the presence of MYC. Mice developed T-cell lymphomas which were analyzed by expression arrays.

first: R

last: Hlady

first: J

last: Opavska


title: Ectopic expression of wild-type Cop Fry in MDA-MB-231 cells

summary:
We identified the wt Cop allele of the predicted Fry gene as a mammary carcinoma susceptibility gene. This gene has not been characterized in mammals, so for part of our analysis we conducted microarray experiments to look at the changes in gene expression which occur when the wt Cop Fry allele is ectopically expressed in the MDA-MB-231 breast cancer cell line (a cell line which we identified as having low FRY mRNA expression).
We used microarrays to identify the Fry interactome and identified that Fry affects the expression of gene networks that maintain normal cellular and tissue architecture, organization, differentiation of epithelial cells.

overall_design: Three RNA samples were utilized for each of the two cell lines.  These samples varied in passage number.


title: DNA METHYLATION DURING αβ T CELL DEVELOPMENT IN THE HUMAN THYMUS [methylation]

city: Derio

first: Ana

middle: Maria

last: Aransay

state: BIZKAIA

address: Parque tecnologico de Bizkaia, Building 801-A

department: Genome Analysis Platform

country: Spain

institute: CIC bioGUNE

summary: Thymocyte differentiation is a complex process which involves well-defined sequential developmental stages that finally result in the generation of mature αβ and γδ T cells. Here, we analyzed DNA methylation and gene expression profiles at successive human thymus developmental stages from early T-cell progenitors to single positive (SP) CD4+ and CD8+ subpopulations

overall_design: Methylation data sets were generated from two biological replicates per cell type (except CD34+/CD1a+) and each biological replicate was obtained from a pool of  3 individuals each


title: Transcriptional analysis of left-sided colitis, pancolitis and ulcerative colitis-associated dysplasia

city: Herlev

first: Jacob

middle: Tveiten

last: Bjerrum

address: Herlev Ringvej 75

department: Department of Gastroenterology, Medical Section

country: Denmark

institute: Herlev Hospital

summary: This study characterizes the inflammatory processes in left-sided colitis, pancolitis, and UC-associated dysplasia at the transcriptional level in colonics biopsies in order to identify potential biomarkers and transcripts of importance for the carcinogenic behaviour of chronic inflammation

overall_design: Colonic biopsies were obtained from forty-five patients with UC (20 left-sided colitis, 19 pancolitis, and 6 UC-associated dysplasia) and 15 controls. The Affymetrix GeneChip Human Genome U133 Plus 2.0 was used

middle: T

first: Ole

last: Nielsen

first: Lene

last: Riis

first: Valerie

last: Pittet

first: Christoph

last: Mueller

first: Gerhard

last: Rogler

first: Jørgen

last: Olsen


title: DNA METHYLATION DURING αβ T CELL DEVELOPMENT IN THE HUMAN THYMUS

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

overall_design: Refer to individual Series


title: Gene expression profile of malignant mesothelioma

city: Nishinomiya

first: Yoshie

last: Yoshikawa

state: Hyogo

address: 1-1 Mukogawa-cho

department: Genetics

country: Japan

institute: Hyogo College of Medicine

summary: Malignant mesothelioma (MM) is an asbestos-related malignancy and largely unresponsive to conventional chemotherapy or radiotherapy. Novel, more effective therapeutic strategies are needed for this fatal disease. We performed microarray analysis of MM using Affymetrix Human U133 Plus 2.0 array. Aberrant expression of the genes participating in semaphorin signaling were detected in malignant mesothelioma cells. All MM cells downregulated the expression of more than one gene for SEMA3B, 3F, and 3G when compared with Met5a, a normal pleura-derived cell line. In 12 of 14 epithelioid MM cells, the expression level of SEMA3A was lower than that in Met5a. An augmented expression of VEGFA was detected in half of the MM cells. The expression ratio of VEGFA/SEMA3A was significantly higher in the epithelioid MMs than in Met5a and the non-epithelioid MMs. Next, gene expression profiling for the polycomb and trithorax group genes revealed that expression of BAP1, the catalytic subunit of the polycomb repressive deubiquitinase complex, and many trithorax group genes was downregulated in MMs compared with the expression of the same genes in Met5a cells. Perturbation of the polycomb–trithorax balance plays a significant role in the pathogenesis of malignant mesothelioma.

overall_design: Array analysis was performed with 19 malignant mesothelioma (MM) cell samples, including 14 primary cell cultures from Japanese patients at the Hospital of Hyogo College of Medicine, and with two primary cell cultures of reactive mesothelial hyperplasia (RM) and human normal pleura transformant Met5a as reference cells.

first: Ayuko

last: Sato


title: Asymmetric Reprogramming Capacity of Parental Pronuclei in Mouse Zygote

city: beijing

first: wenqiang

last: liu

address: 7 Science Park Rd., ZGC life science park, Beijing

country: China

institute: National Institute of Biological Sciences

summary: It has been demonstrated previously that the reprogramming factors are sequestered in the pronuclei of zygote after fertilization, as the enucleated zygotes at interphase cannot support the development of cloned embryos whereas the enucleated zygotes at M-phase can reprogram somatic cells to full pluripotency. However, it remains unknown whether the parental pronucleus, derived either from the sperm or oocyte, possesses the similar reprogramming ability. Here, we provide evidence demonstrating that the parental pronuclei are asymmetric in reprogramming and the reprogramming factors reside mainly in the male pronucleus. As a result, only the female pronucleus-depleted mouse zygotes enucleated at M-phase of mitosis can support the somatic cell reprogramming, the derivation of chromosome transfer embryonic stem (ctES) cells with full pluripotency and the full term development of cloned embryos. In striking contrast, the male pronucleus-depleted zygotes enucleated at M-phase of mitosis fail to support the pre-implantation development of somatic cell cloned embryos. Furthermore, we demonstrated that the distinct epigenetic reprogramming ability of the parental pronucleus might contribute directly to the developmental difference of somatic cloned embryos. Our study highlights the developmental asymmetry of parental pronuclei in reprogramming.

overall_design: We compared the gene expression profile of ctES cells. Two biological repeats were included.

first: Wenqiang

last: Liu

first: Jiqing

last: Yin

first: Xiaochen

last: Kou

first: Yonghua

last: Jian

first: Haibo

last: Gao

first: Yanhong

last: Zhao

first: Bo

last: Huang

first: Wenteng

last: He

first: Zhiming

last: Han

first: Shaorong


title: Gene expression in Mouse thrombomoudlin+ and thrombomodulin- dendritic cell

city: Stanford

first: John

last: Morser

address: 269 Campus Drive

department: Hematology

institute: Stanford University

summary:
Previously we had shown in a mouse model of bronchial asthma that thrombomodulin (TM; CD141; BDCA3) can convert immunogenic conventional dendritic cells into tolerogenic dendritic cells while inducing its own expression on the cell surface. Thrombomodulin+ dendritic cells are tolerogenic while thrombomodulin- dendritic cells are pro-inflammatory and immunogenic. Here we hypothesized that thrombomodulin treatment of dendritic cells would modulate inflammatory gene expression. Murine bone marrow derived dendritic cells were treated with soluble thrombomodulin and expression of surface markers was determined. Treatment with thrombomodulin reduces the expression of maturation markers and increases the expression of TM on the DC surface. Thrombomodulin treated and control dendritic cells were sorted into thrombomodulin+ and thrombomodulin- dendritic cells before their mRNA was analyzed by microarray. mRNAs encoding pro-inflammatory genes and dendritic cells maturation markers were reduced while cell cycle genes were increased in thrombomodulin-treated and thrombomodulin+ dendritic cells compared to control dendritic cells and thrombomodulin- dendritic cells.
We compared the effects on global gene expression of treating dendritic cells with soulble thrombomodulin to no treatment, and dendritic cells separated into thrombomodulin+ and thrombomodulin- dendritic cell subsets.

overall_design: In 4 independent experiments, RNA from mouse bone marrow derived dendritic cells were analyzed on Affymaetrix arrays to determine differences between thrombomodulin+ and thrombomodulin- dendritic cells and if treatment with soluble thrombomodulin altered gene expression.


title: Treatment of human monocytes with TLR7 or TLR8 agonists

status: Public on Dec 24 2014

city: Columbus

first: Jonathan

middle: P

last: Butchar

state: OH

address: 400 W. 12th Avenue

department: Internal Medicine

institute: The Ohio State University

summary: Goal was to detect differences in response to TLR7 versus TLR8 agonists in human monocytes from healthy donors

overall_design: 3 deidentified donors from the Red Cross, monocytes from each donor incubated overnight with either vehicle, TLR7 agonist or TLR8 agonist


title: The role of the Janus-faced transcription factor PAX5-JAK2 in acute lymphoblastic leukemia

status: Public on Dec 29 2014

city: Vienna

first: Sabine

last: Strehl

address: Zimmermannplatz 10

department: CCRI, CHILDREN'S CANCER RESEARCH INSTITUTE

country: Austria

institute: St. Anna Kinderkrebsforschung e.V.

summary: PAX5-JAK2 has recently been identified as a novel recurrent fusion gene in B-cell precursor acute lymphoblastic leukemia (BCP-ALL) but the function of the encoded chimeric protein has not yet been characterized in detail. Herein we show that the PAX5-JAK2 chimera, which consists of the DNA-binding paired domain of PAX5 and the active kinase domain of JAK2, is a nuclear protein that has the ability to bind to wild-type PAX5 target loci. Moreover, our data provide compelling evidence that PAX5-JAK2 functions as nuclear catalytically active kinase that autophosphorylates and in turn phosphorylates and activates downstream STATs in an apparently non-canonical mode. The chimeric protein also enables cytokine-independent growth of Ba/F3 cells and, therefore, possessing transforming potential. Importantly, the kinase activity of PAX5-JAK2 can be efficiently blocked by JAK2 inhibitors rendering it a potential target for therapeutic intervention. Together, our data show that PAX5-JAK2 simultaneously deregulates the PAX5 downstream transcriptional program and activates the JAK-STAT signaling cascade, and thus, by interfering with these two important pathways, may promote leukemogenesis.

overall_design: Bone marrow samples were collected at diagnosis and frozen. After thawing, RNA was extracted, labelled and hybridized to Affymetrix U133 Plus 2.0 arrays.

first: Dagmar

last: Schinnerl

first: Klaus

last: Fortschegger

first: Maximilian

last: Kauer

first: João

middle: R

last: Marchante

first: Reinhard

last: Kofler

first: Monique

middle: L

last: Den Boer


title: Influence of olive pollen stimuli on the gene- expression profile in healthy controls and allergic patients

city: Madrid

first: DAVID

last: CALZADA

address: Avenida Reyes Católicos n2

department: Allergy and Immunology

institute: IIS-Fundación Jiménez Díaz

summary: Analysis of gene-expression profiles with microarrays can be very useful to dissect specific responses and to characterize with a global view, new elements for improving the diagnosis, treatment and understanding of allergic diseases. We have used this approach for studying the olive pollen response, taking advantage our previous results of T-cell epitope mapping on Ole e 1 molecule (the major allergen from olive pollen) in order to analyze the stimuli influence on the gene-expression of olive pollen allergic patients.     Peripheral blood mononuclear cells (PBMCs) from 6 healthy controls and 6 allergic subjects were stimulated 24 hours with olive pollen stimuli: Ole e 1 molecule and two Ole e 1 peptides previously defined as P2+3 (aa10-31), mainly recognized by non-allergic subjects (possible immunoregulatory epitope) and P10+12+13 (aa90-130), immunodominant T-cell epitope.     RNA extracted from basal and stimulated PBMCs was analyzed by HuGeU133 plus 2.0 GeneChip, Affymetrix (38.500genes). After assessment of data quality by standard quality checks and principal components analysis (PCA), differential gene-expression by experimental conditions was performed by multiple testing, using microarrays specific software. Differences in functional analysis were performed by KEGG, for pathways and Gene-Ontology for biological process.    The results of gene-expression by PCA showed differential clusters that correlated with the experimental conditions from samples of allergic patients. Analysis of differential gene-expression by multiple testing, and functional analysis by KEGG and Gene-Ontology revealed differential genes and pathways among the 4 experimental conditions.

overall_design: The study population comprised a total of 12 subjects (6 healthy controls and 6 Olive pollen–allergic patients), selected from a previous immunological study (Aguerri et al. Eur. J. Inflammation 2012, ), from Andalusia, who were recruited in 2 olive pollen exposure situations: during (April-June) and outside the pollen season (October-December). The subjects were unrelated and recruited at the Allergy Service of 4 hospitals in Andalusia (Granada, Jaén, Sevilla, and Málaga). These subjects fulfilled the following criteria: seasonal rhinitis and/or asthma from April to June, a positive skin prick test result for O. europaea pollen extract (ALK Abelló, Madrid, Spain), and no previous immunotherapy. Informed consent was obtained from each subject. Ethical approval for the study was obtained from the Ethical and Research Committee of the participating hospitals. PBMCs were isolated from heparin-containing peripheral blood samples taken during and outside pollen season, by gradient centrifugation on Lymphoprep (Comercial Rafer, Zaragoza, Spain) following the manufacturer’s instructions. These PBMCs (1,000,000 cls) were cultured with and without olive pollen stimuli [complete olive pollen extract (Olea, 25 µg/ ml)] peptide 2+3 (5 µg/ ml) and peptide 10+12+13 (5 µg/ ml) during 24 hours. After cell culture, total RNA was extracted using Trizol method (Invitrogen, Carlsbad, CA, USA).  A total of 96 RNAs samples were studied (12 subjects x 2 exposure moments x 4 experimental conditions).

first: Blanca

last: Cárdaba

first: David

last: Calzada

first: Miriam

last: Aguerri

first: Selene

last: Baos

first: Carlos

last: Lahoz


title: Data expression of  young and senescent human mesenchymal stem cells (hMSC).

city: Natal

first: Joana

middle: Cristina Medeiros

last: Tavares

state: Rio Grande do Norte

address: Rua Trairi, S/N Centro

department: Faculty of Health Sciences Trairi

country: Brazil

institute: Federal university of  Rio Grande do Norte

summary: The transcriptome of hMSC in late passages was compared to hMSC in early passages. Both hMSC were obtained from the umbilical vein of three donors, two of hMSC have a normal karyotype (MSC/n) and another has a constitutional paracentric chromosomal inversion (hMSC/inv).

overall_design: Total RNA was extracted using the RNeasy mini kit (Qiagen) and marked with the GeneChip ® 3 'IVT Express Kit (Affymetrix Inc.). Subsequently, the fragmented aRNA was hybridized on the microarranjo Affymetrix Human Genome U133 Plus 2.0 arrays (Affymetrix Inc.). The statistical analysis of differential gene expression was performed to each groups hMSC senescent vs young by the Partek Genomic Suite software, version 6.4 (Partek Inc.). Was considered statistically significant differences in expression to p-value Bonferroni correction  ˂.01. Only signals with fold change ˃ 3.0 were included in the list of differentially expressed. Differences in gene expression data obtained from microarrays were confirmed by Real Time RT-PCR.

middle: C

first: Deborah

last: Cornélio

first: Isabella

last: Job e Meira

first: Vivian

middle: N

last: Silbiger

first: André

middle: D

last: Luchessi

first: Silvia

last: Batistuzzo de Medeiros


title: Gene expression data from Min6 cells grown in serum containing and serum free condtions following Hes3 knock down

status: Public on Dec 23 2014

city: Dresden

first: Andreas

last: Androutsellis-Theotokis

address: Fetscherstr. 74

department: Department of Internal Medicine III

institute: University Hospital Carl Gustav Carus at the Technische Universität Dresden

summary: The basic helix-loop-helix (bHLH) transcription factor hairy and enhancer of split (Hes3) is a member of the Hes/Hey gene family that regulates developmental processes in progenitor cells from various tissues. We demonstrated the Hes3 expression in mouse pancreatic tissue, suggesting it may have a role in modulating beta-cell function. We employed a transfection approach to address specific functions of Hes3. Hes3 RNA interference opposed the growth of the mouse insulinoma cell line Min6. Western blotting and PCR approaches specifically showed that Hes3 RNA interference opposes the expression of Pdx1 and insulin. Likewise, Hes3 knock down reduced evoked insulin release from Min6 cells.

overall_design: We used microarray analysis to examine differences in gene expression when Hes3 expression was knocked down in cells grown under different culture condtions.

first: Jimmy

last: Masjkur

first: Ramu

last: Chena

first: Julia

last: Jarrells

first: Steven

last: Poser


title: Characterization of osteogenic differentiation and gene expression profile of multiple miliary osteoma cutis

city: Oulu

first: Riina

middle: M

last: Myllylä

address: Aapistie 7 A

country: Finland

institute: University of Oulu

summary: Multiple miliary osteoma cutis (MMOC) is a rare skin disorder characterized by heterotopic ossification in dermis and subcutis. The etiology and disease mechanism is unknown, but earlier data indicates that it seems to be different from other diseases containing heterotopic intramembranous ossification. The purpose of this study was to further investigate the pathogenesis of MMOC by comparing patients’ osteoma affected skin area to their unaffected healthy skin area, as well as to skin from controls. This comparison was made by using osteogenic differentiation studies in cell cultures and by gene expression experiments. Both patient and control dermal fibroblast-like cells were able to differentiate into osteoblast-like matrix mineralizing cells. The differentiation seems to diminish with bone morphogenetic protein (BMP) 4 and 2/7 exposures and seems to correlate with proportion of stem cell associated cell surface marker CD105 positive cells. Microarray analysis revealed altered gene expression patterns between skin samples of patients and controls, as well as between samples taken from different skin areas. BMP receptor II and G-protein α-stimulatory subunit genes were among downregulated and β-catenin among upregulated genes in patient compared to control samples. Genes for homeobox proteins were among downregulated and gene for secreted frizzled related protein 2 among upregulated genes when compared patients’ osteoma area to their unaffected area. Differences in unaffected skin area in patients and controls suggest that the nature of MMOC may be more systemic than previously thought.  Detected differences in separate skin areas may, in turn, provide new information for understanding the localized characteristics of MMOC. BMPs’ inhibitory effect to osteogenic differentiation of human dermal fibroblast-like cells may provide a new perspective to the clinical use of BMPs.

overall_design: Skin biopsies were taken from three patients and two controls for RNA extraction and hybridization on Affymetrix microarrays.

first: Kirsi-Maria

last: Haapasaari

first: Riitta

last: Palatsi

first: Jussi

last: Vuoristo

first: Päivi

last: Hägg

first: Tiina

last: Hurskainen

first: Petri

last: Lehenkari

first: Juha

last: Tuukkanen


title: Trancriptome analysis in mice deficient for chaperone-mediated autophagy in liver

city: New York

first: Bin

last: Ye

state: NY

address: 1301 Morris Park Ave

institute: Albert Einstein College of Medicine

summary: The activity of chaperone-mediated autophagy (CMA), a catabolic pathway for selective degradation of cytosolic proteins in lysosomes, decreases with age, but the consequences of this functional decline in vivo remain unknown. In this work, we have generated a conditional knockout mouse to selectively block CMA in liver. We have found that blockage of CMA causes hepatic glycogen depletion and hepatosteatosis. The liver phenotype is accompanied by reduced peripheral adiposity, increased energy expenditure, and altered glucose homeostasis. Comparative lysosomal proteomics revealed that key enzymes in carbohydrate and lipid metabolism are normally degraded by CMA and that impairment of this regulated degradation contributes to the metabolic abnormalities observed in CMA-defective animals. These findings highlight the involvement of CMA in regulating hepatic metabolism and suggest that the age-related decline in CMA may have a negative impact on the energetic balance of old organisms.

overall_design: Total of 12 arrays included in this study. Wildtype fed mouse (N= 3); Wildtype starved mouse (N= 3)); Knock-out fed mouse (N= 3); Knock-out starved mouse (N= 3).

first: Jaime

last: Schneider

first: Yousin

last: Suh

first: Ana-Maria

last: Cuervo


title: Microarray gene expression analysis of FFPE tissue permits molecular classification in diffuse large B-cell lymphoma.

city: Manchester

first: Kim

last: Linton

address: Department of Haemato-oncology, The Christie NHS Foundation Trust, Wilmslow Road

department: Faculty of Medical and Human Sciences

country: United Kingdom

institute: The University of Manchester

summary:
Refractory/relapsed diffuse large B-cell lymphoma (DLBCL) has a poor prognosis. Novel drugs targeting the constitutively activated NF- B pathway characteristic of ABC-DLBCL are promising, but  evaluation depends on accurate activated B cell-like (ABC)/germinal center B cell-like (GCB) molecular classification. This is traditionally performed on gene microarray expression profiles of fresh biopsies, which are not routinely collected, or by immunohistochemistry on formalin-fixed, paraffin-embedded (FFPE) tissue, which lacks reproducibility and classification accuracy. We explored the possibility of using routine archival FFPE tissue for gene microarray applications.
We examined Affymetrix HG U133 Plus 2.0 gene expression profiles from paired archival FFPE and fresh-frozen tissues of 40 ABC/GCB-classified DLBCL cases to compare classification accuracy and test the potential for this approach to aid the discovery of therapeutic targets and disease classifiers in DLBCL. Unsupervised hierarchical clustering of unselected present probe sets distinguished ABC/GCB in FFPE with remarkable accuracy, and a Bayesian classifier correctly assigned 32 of 36 cases with >90% probability. Enrichment for NF- B genes was appropriately seen in ABC-DLBCL FFPE tissues. The top discriminatory genes expressed in FFPE separated cases with high statistical significance and contained novel biology with potential therapeutic insights, warranting further investigation. These results support a growing understanding that archival FFPE tissues can be used in microarray experiments aimed at molecular classification, prognostic biomarker discovery, and molecular exploration of rare diseases.

overall_design: Forty DLBCL cases were selected from the University of Nebraska pathology archives, including 20 cases each of ABC and GCB DLBCL previously classified in the Leukemia/ Lymphoma Molecular Profiling Project using Affymetrix HG U133 Plus 2.0 gene expression profiles of fresh-frozen tissue (FT). In the current study, routinely processed, diagnostic FFPE tissue blocks were identified for the same 40 cases, profiled on Affymetrix Plus 2.0 microarrays, and then re-classified using published FT gene classifiers.

first: Christopher

last: Howarth

first: Mark

last: Wappett

first: Gillian

last: Newton

first: Cynthia

last: Lachel

first: Javeed

last: Iqbal

first: Stuart

last: Pepper

first: Richard

last: Byers

first: Wing

last: Chan

first: John

last: Radford


title: Hypoxic MDA-MB-231 U133 Plus 2.0 array

city: Jupiter

first: Donald

middle: G.

last: Phinney

state: Florida

address: 130 Scripps Way Bldg A215

department: Molecular Medicine

institute: The Scripps Research Institute

summary:
MiR-544 was inhibited by either a miR-544 antagomir or compound 1 under hypoxic conditions in MDA-MB-231 cells
U133 Plus 2.0 microarray was utilized to examine the specificity of 1 for miR-544.

overall_design: 3 MDA-MB-231 samples treated with a miR-544 antagomir or compound 1 were subjected to hypoxia for a period of 5 days.  After 5 days, samples were pooled and subjected to gene level microarray analysis.

last: Haga


title: Profiling gene and microRNA expression in hypoxic MDA-MB-231 cells

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

platform_organism:
Homo sapiens
synthetic construct


title: Human Prostate Cancer Illumina Infinium Human Methylation450 (HM450K bead array) BeadChip samples (benign vs tumor)

city: Melbourne

first: Haroon

last: Naeem

state: Clayton, VIC

address: 15 Innovation Walk (Room G98), Wellington Road

department: Monash Bioinformatics Platform

institute: Monash University

summary: In order to examine the impact our probe filtering efforts might have on the analysis of real-world primary data, we analyzed clinical prostate cancer specimens. This included profiling of four prostate tumour tissue samples and four benign prostate tissues using the Illumina Infinium Human Methylation450 (HM450K bead array) BeadChip. These samples were used to explore the effects on analysis with and without a probe filtering.

overall_design: Four tumour samples containing Gleason 6 cancer and four benign samples from other prostate glands containing Gleason 6 cancer were selected for study. Tissue samples were cryosectioned for histopathological assessment. Genomic DNA was extracted from the homogenized samples using the Allprep Micro Kit (Qiagen, CA, USA) following manufacturer’s instructions and bisulfite converted using the Zymo EZ DNA Methylation kit (Zymo Research Corporation, CA, USA). The resulting libraries were hybridized onto the Illumina HumanMethylation450 (HM450K bead array) BeadChip. Raw intensity data was generated using an iScan microarray reader (Illumina).

last: Hovens

first: Matthew

middle: K

last: Hong

middle: S

last: Pedersen


title: Expression data from  Min6 cells maintained under different culture conditons that affect Hes3 expression and localization

first: Andreas

last: Androutsellis-Theotokis

summary: The basic helix-loop-helix (bHLH) transcription factor hairy and enhancer of split (Hes3) is a member of the Hes/Hey gene family that regulates developmental processes in progenitor cells from various tissues. We demonstrated the Hes3 expression in mouse pancreatic tissue, suggesting it may have a role in modulating beta-cell function. We employed the mouse insulinoma cell line MIN6 to perform gene expression profiles in conditions known to modulate Hes3 based upon our previous work using neural stem cell cultures.  In these conditions, cells showed elevated Hes3 expression and nuclear localization, grew efficiently and showed higher evoked insulin release responses, compared to serum-containing conditions. They also exhibited higher expression of the transcription factor Pdx1 and insulin.

overall_design: Microarrays of RNA isolated from quadruplicate samples of Min6 cells grown under three different culture conditions.

first: Jimmy

last: Masjkur

first: Ramu

last: Chena

first: Julia

last: Jarrells

first: Steven

last: Poser


title: Extremely low frequency electromagnetic fields enhance neuronal differentiation of human mesenchymal stem cells on graphene-based substrate

city: Seoul

first: YooJung

last: Lee

address: Department of Life Science, Dongguk University-Seoul, 3–26 Phil-dong, Chung-gu

department: Life science

country: South Korea

institute: Dongguk University

summary:
Graphene-based substrate has efficient neuronal differentiation of hMSCs. Stimulatory effects of graphene on hMSCs neurogenesis can be enhanced by ELF-EMF exposure and it is mediated by enhancement of cell adhesion accompanied by intracellular signal pathway.
We used microarrays to assess up-regulated genes in human gene expression profiles during neurogenesis induced by ELF-EMF exposure on graphene.

overall_design: 3 groups (HMSCs grown in neuronal medium on glass, graphene, graphene under ELF-EMF exposure) were selected for RNA extraction and hybridization on Affymetrix microarrays. We sought to obtain total human gene expression. To that end, we hand-selected up-regulated gene involved in neurogenesis, extracellular matrix, and cell migration.

first: Yoojung


title: Viral Expression and Molecular Profiling in Liver Tissue versus Microdissected Hepatocytes in Hepatitis B Virus - Associated Hepatocellular Carcinoma

status: Public on Dec 22 2014

city: Bethesda

first: Patrizia

last: Farci

state: MD

address: 50 South Drive

department: National Institute of Allergy and Infectious Diseases

institute: National Institutes of Health

summary: The molecular mechanisms whereby hepatitis B virus (HBV) induces hepatocellular carcinoma (HCC) remain elusive. We used genomic and molecular techniques to investigate host-virus interactions by mapping the entire liver of patients with HCC. We compared the gene signature of whole liver tissue (WLT) versus laser capture-microdissected (LCM) hepatocytes with intrahepatic expression of HBV. Gene expression profiling was performed on up to 17 WLT specimens obtained at various distances from the tumor center in individual livers of 11 patients with HCC and on selected LCM samples. HBV biomarkers were determined by real-time PCR and confocal immunofluorescence. Analysis of 5 areas of the liver showed a sharp change in gene expression between the immediate perilesional area and tumor periphery that correlated with a significant decrease in the intrahepatic expression of HBsAg. The tumor was characterized by a large preponderance of down-regulated genes, mostly involved in the metabolism of lipid and fatty acid, glucose, amino acids and drugs, with down-regulation of pathways involved in the activation of PXR/RXR and PPARa/RXRa nuclear receptors, comprising PGC1 and FOXO1, two key regulators of the hepatic metabolic functions and HBV transcription. These findings were confirmed by gene expression of microdissected hepatocytes. However, LCM of malignant hepatocytes also revealed up-regulation of unique genes associated with cancer and signaling pathways, including two novel HCC-associated cancer testis antigen (CTA) genes, NUF2 and TTK. HCC-associated with HBV is characterized by a metabolism switch-off and by a significant reduction in HBsAg. LCM proved to be a critical tool to validate gene signatures associated with HCC and to identify genes that may play a role in hepatocarcinogenesis opening new perspectives for the discovery of novel diagnostic markers and therapeutic targets.

overall_design: Samples were obtained at various distances from the tumor center in individual livers of 11 patients with HBV-associated HCC. Whole liver tissue samples were compared to LCM samples of malignant and non-malignant hepatocytes obtained from the same livers.

first: Marta

last: Melis

first: Giacomo

last: Diaz

first: David

middle: E

last: Kleiner

first: Fausto

last: Zamboni

first: Juraj

last: Kabat

first: Jinping

last: Lai

first: Giulia

last: Mogavero

first: Ashley

last: Tice

first: Ronald

last: Engle

last: Becker

first: Charles

last: Brown

first: Jeffrey

last: Hanson

first: Jaime

last: Rodriguez-Canales

first: Michael

last: Emmert-Buck

first: Sugantha

last: Govindarajan

last: Kew


title: TOX2 regulates human natural killer cell development by controlling T-BET expression

city: Memphis

last: Finkelstein

state: TN

address: 332 N. Lauderdale St.

department: Computational Biology

institute: St Jude Children's Research Hospital

summary: Thymocyte selection-associated high mobility group box protein family member 2 (TOX2) is a transcription factor belonging to the TOX family that shares a highly conserved high mobility group DNA binding domain with the other TOX members. While TOX1 has been shown to be an essential regulator of T-cell and natural killer (NK) cell differentiation in mice, little is known about the roles of the other TOX family members in lymphocyte development, particularly in humans. In this study, we found that TOX2 was preferentially expressed in mature human NK cells and was upregulated during in vitro differentiation of NK cells from human umbilical cord blood (UCB)–derived CD34+ cells. Gene silencing of TOX2 intrinsically hindered the transition between early developmental stages of NK cells, while overexpression of TOX2 enhanced the development of mature NK cells from UCB CD34+ cells. We subsequently found that TOX2 was independent of ETS-1 but could directly upregulate the transcription of TBX21 (encoding T-BET). Overexpression of T-BET rescued the TOX2 knockdown phenotypes. Given the essential function of T-BET in NK cell differentiation, TOX2 therefore plays a crucial role in controlling normal NK cell development by acting upstream of TBX21 transcriptional regulation.

overall_design: survey of NK cells over time

first: Queenie

last: Vong

first: Wai-Hang

last: Leung

first: Jim

last: Houston

first: Barbara

last: Rooney

first: Martha

last: Holladay

first: Wing


title: human aggressive fibromatosis tumors

city: toronto

first: benjamin

last: alman

state: ontario

address: 555 university avenue

department: Developmental and stem cell biology

country: Canada

institute: Hospital for Sick Children

summary: This study examines the expression profile of cells from human aggressive fibromatosis tumors.

overall_design: Cells from human aggressive fibromatosis tumors were manually minced, and visible clumps were removed. Enzymatic digestion using 10 mg/mL of collagenase IV, 2.4 units/mL Dispase, 0.05% trypsin, was used for 45 min at 37°C.  Cells were then centrifuged at 1400 rpm for 5 min and washed thrice in PBS. RNA was extracted using RNA was extracted using Trisol as per the manufacturer's instructions, and used for gene profiling studies.

first: colleen

last: wu

first: Saied

last: Amini Nik


title: Whole transcriptome analysis of FACS purified somatosensory neuron subtypes and whole dorsal root ganglia tissue

city: Boston

first: Isaac

last: Chiu

state: MA

address: 3 Blackfan Circle

department: Neurology

institute: Boston Children's Hospital

summary: The goal of this study was to analyze global gene expression in specific populations of somatosensory neurons in the periphery, including major, non-overlapping populations that include nociceptors, pruriceptors, and prorioceptors. The mammalian somatosensory nervous system encodes the perception of specific environmental stimuli. The dorsal root ganglion (DRG) contains distinct somatosensory neuron subtypes that innervate diverse peripheral tissues, mediating the detection of thermal, mechanical, proprioceptive, pruriceptive, and nociceptive stimuli. We purified discrete subtypes of mouse DRG somatosensory neurons by flow cytometry using fluorescently labeled mouse lines (SNS-Cre/TdTomato, Parv-Cre/TdTomato) in combination with Isolectin B4-FITC surface staining (IB4). This allowed identification of transcriptional differences between these major populations, revealing enrichment of voltage-gated ion channels, TRP channels, G-protein coupled receptors, transcription factors, and other functionally important classes of genes within specific somatosensory neuron subsets.

overall_design: SNS-Cre mice were bred with Rosa26-TdTomato mice to generate SNS-Cre/TdTomato reporter mice. Parv-Cre mice were bred with Rosa26-TdTomato mice to generate Parv-Cre/TdTomato mice. Isolectin B4-FITC was used to stain the surface of SNS-Cre/TdTomato reporter mice. We used these strategies of fluorescent labeling to purify distinct murine sensory neuron subsets from the dorsal root ganglia (DRG) by fluorescence activated cell sorting (FACS). Neurons were sorted directly in Qiazol for total RNA extraction and microarray analysis. Whole DRG tissue was also included for transcriptome analysis to compare with purified neuronal populations.

first: Clifford

middle: J

last: Woolf


title: Histone deacetylase 7 role in B cell acute lymphoblastic leukemia and B cell lymphoma

status: Public on Dec 18 2014

city: L'Hospitalet de Llobregat

first: Manel

last: Esteller

state: Barcelona

address: Hospital Duran i Reynals Av. Gran Via s/n km, 2.7

department: PEBC

institute: IDIBELL

summary: The generation of B cells is a complex process requiring several cellular transitions, including cell commitment and differentiation, that are tightly controlled by the action of linage-specific transcription factors. Proper transcriptional control to establish the genetic programs characteristic of each cellular stage is essential for the correct development of B lymphocytes. In fact, deregulation of these particular transcriptional programs may result in a block in B cell maturation, contributing to the development of hematological malignancies such as leukemia and lymphoma. In this experiments, We study  the HDAC7 expression levels in pro-B-ALL and Burkitt lymphoma.

overall_design: SD-1 Tet-On-Tight-HDAC7 or SD-1 cells were treated or not for 24 hours with doxycycline. We compare the effects in gene expression between the different situations (in presence or in absence of doxycycline)

first: Bruna

last: Barneda-Zahonero

first: Maribel

last: Parra


title: Transmitted/founder hepatitis C viruses induce cell type- and genotype-specific differences in innate signaling within the liver

status: Public on Dec 20 2014

city: Aurora

last: Edwards

state: CO

address: 12700 East 19th Avenue, Box C272

department: Pulmonary

institute: UC Denver

summary:
Primary human hepatocytes (PHHs) are a liver-specific cell subtype, and we have shown that these cells respond in a unique manner to the introduction of hepatitis C viral RNA (HCV vRNA) derived from different genotypes of the virus.
We used microarray to analyze the transcriptional differences between the PHHs exposed to the different genotypes of HCV to further shed light on their differential effects on HCV innate immune responses in vitro

overall_design: HCV vRNA from either genotype 3a HCV or genotype 1a HCV was introduced into the PHH cells for 8 hours. Total RNA was then harvested to determine transcriptional differences.

first: Angela

last: Mitchell

first: Amy

last: Stone

first: Linling

last: Cheng

first: Kimberly

last: Ballinger

middle: G

first: Mark

last: Stoddard

first: Hui

last: Li

first: Lucy

last: Golden-Mason

first: George

last: Shaw

first: Salman

last: Khetani

first: Hugo

last: Rosen


title: Expression data from BM-CD138+, obtained from newly diagnosed Multiple Myeloma patients

city: Bologna

first: Carolina

last: Terragna

address: Via Massarenti, 9

department: Department of Experimental, Diagnostic and Specialty Medicine - DIMES

country: Italy

institute: Institute of Hematology "L.A.Seràgnoli"

summary: A subanalysis of the GIMEMA-MMY-3006 trial was performed to characterize treatment-emergent peripheral neuropathy (PN) in patients randomized to thalidomide-dexamethasone (TD) or bortezomib-TD (VTD) before and after double autologous transplantation (ASCT) for multiple myeloma (MM). 236 patients randomized to VTD and 238 to TD were stratified according to the emergence of grade ≥2 PN. Gene expression profiles (GEP) of CD138+ plasma cells were analyzed from 122 VTD-treated patients. The incidence of grade ≥2 PN was 35% in the VTD arm and 10% in the TD arm (p<0.001). PN resolved in 88% and 95% of patients in VTD and TD groups, respectively. Rates of complete/near complete response, progression-free and overall survival were not adversely affected by emergence of grade ≥2 PN. Baseline characteristics were not risk factors for PN, while GEP analysis revealed the deregulated expression of genes implicated in cytoskeleton rearrangement, neurogenesis and axonal guidance. In conclusion, in comparison with TD, incorporation of VTD into ASCT was associated with a higher incidence of PN which, however, was reversible in most of the patients and did not adversely affect their outcomes nor their ability to subsequently receive ASCT. GEP analysis suggests an interaction between myeloma genetic profiles and development of VTD-induced PN.

overall_design: 120 samples have been analyzed; the homogeneity of samples has been ensured by the immunomagnetic enrichment procedure: only >90% pure CD138+ cells have been employed.

first: Marina

last: Martello

first: Flores

last: Dico

first: Sandra

last: Durante


title: Expanding epigenomics to archived FFPE tissues: An evaluation of DNA repair methodologies

status: Public on Dec 17 2014

city: Tampa

first: Steven

last: Eschrich

state: FL

address: 12902 Magnolia Drive

department: Biostatistics & Bioinformatics

institute: Moffitt Cancer Center

summary: A study to evaluate techniques for repairing DNA from formalin-fixed paraffin-embedded (FFPE) tissue samples by direct comparison of FFPE DNA repair methods prior to analysis on genome-wide methylation array to matched fresh frozen (FF) tissues.

overall_design: Formalin-fixed paraffin-embedded tissue from three colon adenocarcinoma samples were subjected to different FFPE-oriented DNA repair approaches and sequences, then compared with corresponding fresh frozen tissues. All samples were hybridized to the Illumina Infinium 450k Human Methylation BeadChip.

first: Erin

last: Siegel


title: Anti-BRAF mutation drug resistance enhances EGFR expression in melanomas [methylation profiling]

city: Santa Monica

first: Dave

last: Hoon

state: CA

address: 2200 Santa Monica Boulevard

department: Translational Molecular Medicine

institute: Saint John's Cancer Institute

summary: We treated melanoma cells with BRAF mutation with BRAF inhibitor and screened for BRAF inhibitor resistant cells. We extracted DNA from parental cells and resistant cell lines.  We compared the DNA methylation via Illumina 450K Methylation Array

overall_design: Bisulphite converted DNA from the 4 specimens was hybridised to the Illumina Infinium 450k Human Methylation Beadchip

first: Jinhua

last: Wang


title: Adult mouse stage synchronized testis array

city: Pullman

first: Cathryn

last: Hogarth

state: Washington

address: 1770 NE Stadium Way

institute: Washington State University

summary: WIN 18,446/RA treatment of neonatal male mice was used to synchronize spermatogenesis to 2-3 different stages of the cycle of the seminiferous epithelium in the adult testis

overall_design: 6 different groups of synchronized adult mouse testis samples (N = 2 per group), each representing only 2-3 stages of the cycle, were collected and analyzed using  GeneChip Mouse Gene ST 1.0 Arrays

first: Michael

last: Griswold


title: Gene expression changes induced by BRD9876 in MM1S cells

status: Public on Dec 16 2014

city: Cambridge

first: Shrikanta

last: Chattopadhyay

address: 415 Main Street

department: Center for the Science of Therapeutics

institute: Broad Institute

summary: The goal of this study was to identify transcriptional changes induced by a novel compound BRD9876 as a starting point to identify the compound's mechanism of action.

overall_design: Compound-treated cells are compared in duplicate with cells treated vehicle control (DMSO).


title: Dendritic cells are contained within melanocytic nevus nests in vivo and can alter gene expression of epidermal melanocytes in vitro

status: Public on Dec 15 2014

first: Mayte

last: Suarez-Farinas

address: 1425 Madison Ave, L2-70C, Box 1077,

institute: Mount SinaiSchool of Medicine

summary: We sought to determine what if any changes dendritic cells induce in melanocytes when they are grown together (co-cultured)

overall_design: Comparison of transcriptomes among melanocytes alone, dendritic cells alone, and melanocytes after co-culture with dendritic cells

first: Nicholas

last: Gulati

last: Suárez-Fariñas

first: James

last: Krueger


title: Anti-BRAF mutation drug resistance enhances EGFR expression in melanomas

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

overall_design: Refer to individual Series


title: Methylomic trajectories across human fetal brain development

status: Public on Dec 19 2014

city: London

first: Jon

last: Mill

address: De Crespigny Park

department: Institute of Psychiatry

institute: King's College London

summary: Dynamic changes to the epigenome mediate key neurobiological and cognitive processes in the central nervous system, and also play a role in transcriptional regulation during brain development. Although the importance of DNA methylation in brain development is highlighted by the neurodevelopmental deficits associated with mutations in genes including methyl-CpG binding protein 2 (MECP2), our knowledge about the specific methylomic trajectories associated with human neurodevelopment is extremely limited. Here we report an analysis of genome-wide patterns of DNA methylation in 179 human fetal brain samples.

overall_design: Bisulphite converted DNA from 179 human brain samples was hybridized to the Illumina 450K Human Methylation Beadchip.

first: Helen

last: Spiers

first: Eilis

last: Hannon

first: Leonard

last: Schalkwyk

first: Chloe

last: Wong

first: Rebecca

last: Smith

first: Mick

last: O'Donovan

first: Nick

last: Bray

first: Jonathan


title: Genome-wide expression analysis demonstrates a dominant role of TLR4 for activation of human phagocytes by the alarmin MRP8

status: Public on Dec 12 2014

city: Bonn

first: Joachim

last: Schultze

state: NRW

address: Carl-Troll-Strasse 31

department: Genomics and Immunoregulation

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

summary:
The alarmins myeloid-related protein (MRP) 8 and MRP14 are the dominant cytoplasmic proteins in phagocytes. After release by activated phagocytes extracellular MRP8/MRP14 complexes promote inflammation in many diseases, including infections, allergies, autoimmune diseases, rheumatoid arthritis or inflammatory bowel disease. As receptors for the pro-inflammatory effects of human MRP8, the active component of the MRP8/MRP14-complex, Toll-like receptor (TLR) 4 and the multi-ligand receptor of advanced glycation end products (RAGE) are controversial discussed. Using a comparative bioinformatics analysis between genome-wide response patterns of monocytes to MRP8, endotoxin and different cytokines we demonstrated a dominant role of TLR4 during MRP8-mediated phagocyte activation. The relevance of this signaling pathway could be confirmed in independent cell models for TLR4 and RAGE dependent signaling in mouse and man. In addition to well-known proinflammatory functions of MRP8 our systems biology approach unraveled a novel anti-apoptotic effect of MRP8 on monocytes which was confirmed in independent functional experiments. Our data define the dominance of the TLR4-MRP8 axis in activation of human phagocytes which represents a novel attractive target for modulation of overwhelming innate immune responses.
We used microarrays to detail the global programme of gene expression underlying cellularisation and identified distinct classes of up-regulated genes during this process.

overall_design: Human blood monocyte stimulated with various stimuli (control, MRP8, LPS, TNF, IL1) were selected for RNA extraction and hybridization on Affymetrix microarrays.

first: Selina

last: Fassl

first: Judith

last: Austermann

first: Olympia

last: Papantonopoulou

first: Mona

last: Riemenschneider

first: Jia

last: Xue

first: Christoph

last: Spiekermann

first: Anika

last: Witten

first: Dorothee

last: Viemann

first: Monika

last: Stoll

first: Johannes

last: Roth

first: Thomas

last: Vogl


title: Application of a low cost array-based technique - TAB-Array - for quantifying and mapping both 5mC and 5hmC at single base resolution.

city: La Jolla

first: Kristopher

middle: L.

last: Nazor

address: 10550 North Torrey Pines Road

department: Regenerative Medicine

institute: The Scripps Research Institute

summary: 5-hydroxymethylcytosine (5hmC), an oxidized derivative of 5-methylcytosine (5mC), has been implicated as an important epigenetic regulator of mammalian development.  Current procedures use cost-prohibitive DNA sequencing methods to discriminate 5hmC from 5mC, limiting their accessibility to the scientific community.  Here we report a method that combines TET-assisted bisulfite conversion with Illumina 450K DNA methylation arrays for a low-cost high-throughput approach that distinguishes 5hmC and 5mC signals. Implementing this approach, termed TAB-array, we assessed DNA methylation dynamics in the differentiation of human pluripotent stem cells into cardiovascular and neural progenitors. With the ability to discriminate 5mC and 5hmC, we found a much larger number of dynamically methylated genomic regions implicated in the development of these lineages than we could detect by 5mC analysis alone. The increased resolution and accuracy afforded by this approach provides a powerful means to investigate the distinct contributions of 5mC and 5hmC in human development and disease.

overall_design: We generated illumina 450k DNA methylation data for a total of 9 sample groups with two biological replicates for each group.   Data for 4/9 groups were generated from glucosylated and bisulfite converted DNA, from human induced plurupotent stem cells (hIPSCs), differentiated cardiovascular progenitors (CVPs), differentiated neural progenitors (NPCs), and fibroblasts. Data for the next 4/9 groups were generated from glucosylated, TET-oxidized and bisulfite converted DNA, from and included replicates of hIPSCs, CVPs, NPCs, and fibroblasts.  Data for the last group was generated  from standard bisulfite converted DNA (not glucosylated) from fibroblasts.

first: Suzanne

last: Peterson

first: Michael

last: Boland

first: Marina

last: Bibikova

first: Brandy

last: Klotzle

first: Miao

last: Yu

first: Victoria

last: Glenn-Pratola

first: John

last: Schell

first: Ronald

last: Coleman

first: Mauricio

last: Cabral-da-Silva

first: Ulrich

last: Schmidt

first: Chuan

last: He

first: Jeanne

middle: F

last: Loring

first: Jian-Bing

last: Fan


title: MYC-negative BL frequent in posttransplant patients

city: Leuven

first: Julio

last: Finalet

address: Herestraat 49

country: Belgium

institute: KULeuven

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


title: Expression data (U133 Plus 2.0) from fibroblast like synoviocytes from patients with rheumatoid arthritis (RA-FLS) stimulated by TL1A

status: Public on Dec 10 2014

city: Kobe

first: Toshihisa

last: Maeda

address: 7-5-1, Kusunokicho, Chuo-ku

department: Department of Orthopaedic Surgery

institute: Kobe University Graduate School of Medicine

summary:
TNF-like ligand 1A (TL1A) is a member of TNF receptor superfamily and involved in the pathogenesis of autoimmune diseases by inducing apoptosis via intracellular death domain or promoting inflammation through the activation of NFκB by binding to its specific receptor death receptor 3 (DR3). Meanwhile, decoy receptor 3 (DcR3) competitively binds soluble TL1A in addition to Fas-ligand (FasL) and LIGHT and inhibits the signaling of TL1A via DR3. DcR3 overexpressed in rheumatoid synovial fibroblasts (RA-FLS) stimulated with inflammatory cytokines such as TNFα or IL-1β inhibits Fas-induced apoptosis. In contrast, DcR3 inhibited cell proliferation induced by inflammatory cytokines via membrane-bound TL1A expressed on RA-FLS. Therefore, TL1A-DcR3/DR3 signaling may be involved in the pathogenesis of RA by modulating apoptosis and proliferation of RA-FLS.
We hypothesized that TL1A regulates the gene expression in RA-FLS. We used to search for genes in which expression in RA-FLS is regulated by the ligation of TL1A.

overall_design: RA-FLS were obtained from 4 RA patients (sample1-4). Each sample was incubated with either 1.0 μg/ml recombinant human TL1A protein or phosphate buffered saline (PBS) diluted with serum-free Opti-MEM medium as non-stimulated control for 12 hours at 37°C with 5% CO2. Gene expression in RA-FLS stimulated by TL1A was compared with that of their respective non-stimulated controls.

first: Yasushi

last: Miura

first: Koji

last: Fukuda

first: Shinya

last: Hayashi

first: Masahiro

last: Kurosaka


title: Braf inhibitors reverse the unique molecular signature and phenotype of hairy cell leukemia, and exert anti-leukemic activity

city: Perugia

first: Enrico

last: Tiacci

address: Santa M. della Misericordia Hospital, San Sisto

department: Department of Medicine

institute: Institute of Hematology

summary: Hairy cell leukemia (HCL) shows unique clinico-pathological and biological features. HCL responds well to purine analogues but relapses are frequent and novel therapies are required. BRAF-V600E is the key driver mutation in HCL and distinguishes it from other B-cell lymphomas, including HCL-like leukemias/lymphomas (HCL-variant and splenic marginal zone lymphoma). The kinase-activating BRAF-V600E mutation also represents an ideal therapeutic target in HCL. Here, we investigated the biological and therapeutic importance of the activated BRAF-MEK-ERK pathway in HCL by exposing in vitro primary leukemic cells purified from  26 patients to clinically available BRAF (Vemurafenib; Dabrafenib) or MEK (Trametinib) inhibitors. Results were  validated in vivo in samples from Vemurafenib-treated HCL patients within a phase-2 clinical trial. BRAF and MEK inhibitors caused, specifically in HCL (but not HCL-like) cells, marked MEK/ERK dephosphorylation, silencing of the BRAF-MEK-ERK pathway transcriptional output, loss of the HCL-specific gene expression signature, downregulation of the HCL markers CD25, TRAP and cyclin-D1, smoothening of leukemic cells' hairy surface, and, eventually, apoptosis. Apoptosis was partially blunted by co-culture with bone marrow stromal cells antagonizing MEK-ERK dephosphorylation. This protective effect could be counteracted by combined BRAF and MEK inhibition. Our results strongly support and inform the clinical use of BRAF and MEK inhibitors in HCL.

overall_design: Analysis of  differential gene expression in primary leukemic cells purified from peripheral blood of 6 HCL patients (from A to F), treated with Vemurafenib 1000 nM, in comparison  with vehicle-treated (DMSO) HCL cells, for 48 hours or/and 72 hours. 24 gene expression profiles were analysed.

first: E

first: L

last: Klein-Hitpass


title: Differentially expressed genes between osteochondroprogenitor sub-populations

city: Rockville

first: Anju

last: Aingh

address: 9800 Medical Center DRive

department: DPI

institute: NIH

summary: Cell based bone regeneration strategies offer promise for traumatic bone injuries, congenital defects, non-union fractures and other skeletal pathologies. Postnatal bone remodeling and fracture healing provide evidence that an osteochondroprogenitor cell is present in adult life which can differentiate to remodel or repair the fractured bone. However, cell based skeletal repair in the clinic is still in its infancy mostly due to poor characterization of progenitor cells and lack of knowledge about their in vivo behavior. Here we took a combined approach of high throughput screening, flow based cell sorting and in vivo transplantation to identify markers that identify osteochondroprogenitor cells. We show that the presence of tetraspanin CD9 enriches for osteochondroprogenitors within CD105+vemesenchymal cells and these cells readily form bone upon transplantation. In addition we have used Thy1.2 (CD90) and the ectonucleotidase CD73 to identify subsets within the CD9+ve population that lead to endochondral or intramembranous-like bone formation. Utilization of this unique cell surface phenotype to enrich for osteochondroprogenitor cells will allow for further characterization of the molecular mechanisms that regulate their osteogenic properties.

overall_design: Osteochondroprogenitor sub-populations were arrayed for differentially expressed genes. Osteochondroprogenitor cells were FACS sorted from E16.5 mouse embryonic limb suspension after staining with Flurochrome conjuigated antibodies

last: Singh

first: Laurie

last: Glimcher

first: Dallas

last: Jones


title: Expression data from healthy human PB B cell subsets

status: Public on Dec 11 2014

city: Essen

first: Marc

last: Seifert

address: Virchowstrasse 173

department: Institute of Cell Biology (Cancer Research)

institute: University of Duisburg Essen

summary:
Human PB B cell subsets are functionally distinct and may derive from different developmental pathways, reflected by their differential gene expression profiles.
We used microarrays to detail the global programme of gene expression underlying germinal center transition and functional propensities of individual subsets according to surface receptor and cell adhesion molecule expression.

overall_design: Human PB B cell subsets were sort-purified, RNA was extracted and processed. Data were vsn-normalized, corrected for batch-effects (ComBat) and analysed with GeneSpring GX7.

first: Ralf

last: Küppers


title: Knockdown of TERC with siRNA in normal bone marrow stromal cells (BMSCs) recapitulates the defective BMSC phenotype in patients with telomere biology disorders

status: Public on Dec 09 2014

city: Bethesda

first: Prasun

middle: J.

last: Mishra

address: 37 Convent Drive

department: United States Department of Health and Human Services

institute: National Cancer Institute, National Institutes of Health

summary:
Dyskeratosis congenita (DC) is an inherited multi-system disorder, characterized by oral leukoplakia, nail dystrophy, and abnormal skin pigmentation, as well as high rates of bone marrow failure, solid tumors, and other medical problems such as osteopenia.  DC and telomere biology disorders (collectively referred to as TBD here) are caused by germline mutations in telomere biology genes leading to very short telomeres and limited proliferative potential of hematopoietic stem cells.  We found that skeletal stem cells (SSCs) within the bone marrow stromal cell population (BMSCs, also known as bone marrow-derived mesenchymal stem cells), may contribute to the hematological phenotype.
TBD-BMSCs exhibited reduced clonogenicity, reduced telomerase activity, spontaneous differentiation into adipocytes and fibrotic cells, and increased senescence in vitro.  Upon in vivo transplantation into mice, TBD-BMSCs failed to form bone or support hematopoiesis, unlike normal BMSCs. TERC reduction (a TBD-associated gene) in normal BMSCs by siTERC-RNA recapitulated the TBD-BMSC phenotype by reducing proliferation and secondary colony forming efficiency, and by accelerating senescence in vitro.  Microarray profiles of control and siTERC-BMSCs showed decreased hematopoietic factors at the mRNA level, and decreased secretion of factors at the protein level.  These findings are consistent with defects in SSCs/BMSCs contributing to bone marrow failure in TBD.

overall_design: RNA (5 mg) isolated from N-BMSCs, siNC-BMSCs and siTERC-BMSCs 72hrs after transfection using an RNeasy Mini kit (Qiagen), was reverse transcribed and hybridized to an Affymetrix GeneChip Human Genome U133 Plus 2.0 array (LMT, NCI-Frederick).  Three independent replicates for each experimental condition were carried out to control for intra-sample variation.  Genes that were under/over-represented by >2-fold were analyzed using GeneSpring software.  Signal intensity values were normalized using RMA (Robust Multi-array Analysis) summarization and baseline transformation to median of all samples was performed.  Entities were filtered based on their signal intensity values.  Hierarchical clustering was performed on filtered signal intensity (>20.0), non-averaged, fold change >2.  A fold change analysis (>10-fold) was performed to generate a list of top genes under/over represented between the groups.


title: Expression data from 8-10 week old WT mice maintained in room air or exposed to hyperoxia (FiO2>95%) for 48 hrs

city: Houston

first: Krithika

last: Lingappan

address: 6621 Fannin

institute: Baylor College of Medicine

summary:
To detect sex-specific differences in gene expression in a model of hyperoxic lung injury in adult C56BL/6J mice.
In this dataset, we include the expression data obtained from lungs from 8-10 week old male and female WT C57BL/6J mice exposed to hyperoxia for 48 hours amd room air controls.These data were used to determine differences in transcriptome between male and female mice after hyperoxia exposure

overall_design:
12 total samples were analyzed. We generated the following pairwise comparisons: 5 comparisons (M/F: male/female, A/O: air/oxygen): 1) M_O - M_A,
 2) F_O - F_A,
3) M_O - F_O,
4) M_A - F_A,
5) (M_O - M_A) - (F_O - F_A). Genes with an FDR≤5% and a fold-change ≥1.4 were selected.

first: Chandra

last: Srinivasan


title: Changes in gene expression caused by RhoH/TTF

city: Bern

first: Christina

last: Stoeckle

address: Friedbuehlstrasse 49

department: Institute of Pharmacology

country: Switzerland

institute: University of Bern

summary: RhoH/TTF is upregulated in eosinophils by exposure to cytokines. To find out which genes are regulated by RhoH, we investigated changes in gene expression in eosinophilic HL-60c15 cells overexpressing RhoH

overall_design: HL-60c15 transduced with 4-OHT (4-hydroxytamoxifen)-inducible llentiviral constructs coding for RhoH (HL-60-RhoH) were treated or not treated with 4-OHT. 4-OHT-treated HL-60c15 cells transduced with a GFP control construct (HL-60-GFP) were included as an additional controls. Analysis was performed on 3 biological replicates

first: Hans-Uwe

last: Simon


title: RNA-seq of autistic and control cortex

city: Los Angeles

first: Neelroop

last: Parikshak

state: California

address: 695 Charles E. Young Dr. South

institute: UCLA

type: Expression profiling by high throughput sequencing

summary:
Purpose: The goal of this study was to assess the status of splicing changes in microexons in the cortex of individuals with autism.
Methods: We performed RiboZero Gold (rRNA depleted) 50bp PE RNA-seq in a larger set of case and control samples to define 12 autism and 12 control samples showing the greatest global differential gene expression change. These samples, which show differential expression of the splicing regulator SRRM4, were used to evaluate global splicing changes.
Results: Within these samples, 126 of 504 (30%) detected alternative microexons display a mean ΔPSI > 10 between ASD and control subjects of which 113 (90%) also display neural-differential regulation. By contrast, only 825 of 15,405 (5.4%) longer (i.e. >27 nt) exons show such misregulation, of which 285 (35%) correspond to neural-regulated exons. Notably, we also observe significantly higher correlations between microexon inclusion and nSR100 mRNA expression levels across the stratified ASD samples and controls, for those microexons regulated by nSR100 relative to those microexons that are not regulated by this factor (p=1.4×10-7, Wilcoxon Sum Rank test).
Conclusions: These data suggest microexon regulation is a potentially important mechanism underlying ASD and likely other neurodevelopmental disorders

overall_design: 12 case samples representing a more extreme autism gene expression signature and 12 representative controls; raw data have been submitted to dbGaP

first: Daniel

middle: H

last: Geschwind


title: Expression data from cultured human esophageal squamous cell carcinoma cell lines and cultured human fibroblasts.

city: Shimotsuke

first: Toshiro

last: Niki

state: Tochigi

address: 3311-1 Yakushiji

department: Department of Integrative Pathology

institute: Jichi Medical University

summary:
Cancer cells express different sets of receptor type tyrosine kinases. These receptor kinases may be activated through autocrine or paracrine mechanisms. Fibroblasts may modify the biologic properties of surrounding cancer cells through paracrine mechansms.
We used microarrays to obtain the global gene expression of human esophageal squamous cell carcinoma cell lines and various esophageal fibroblasts.

overall_design: A total of 22 human esophageal squamous cell carcinoma cell lines and fibroblasts were analyzed. 4 fibroblasts were obtained from surgically resected human esophagus. Cells were cultured under standard conditions, total  RNA was extracted and hybridized on Affymetrix microarrays.

first: Shin

last: Saito

first: Kazue

last: Morishima

first: Takashi

last: Ui

first: Hiroko

last: Hoshino

first: Daisuke

last: Matsubara

first: Shumpei

last: Ishikawa

first: Hiroyuki

last: Aburatani

first: Masashi

last: Fukayama

first: Yoshinori

last: Hosoya

first: Naohiro

last: Sata

first: Alan

middle: T

last: Lefor

first: Yoshikazu

last: Yasuda


title: Blocking IL-4Rα with dupilumab (REGN668/SAR231893) rapidly suppresses major pathomechanisms in the skin of severe atopic dermatitis patients

status: Public on Dec 04 2014

city: New York

first: Mayte

last: Suarez-Farinas

summary:
Atopic dermatitis (AD) is the most common inflammatory skin disease, with high unmet need for new therapies that are safe for chronic use. Emerging data suggest that TH2-cytokines play important roles in a variety of allergic and atopic conditions, including asthma and AD.  In early phase clinical trials, dupilumab (a fully human monoclonal antibody against IL-4Rα that potently blocks IL-4 and IL-13 signaling) rapidly and markedly improved clinical measures in adults with either asthma (with elevated eosinophil counts) or moderate-to-severe AD.  The pathomechanisms that may be impacted by IL-4/13 blockade in these disease settings have not yet been characterized in detail.
Transcriptome analyses in pre- and post-treatment skin biopsies from patients with moderate-to-severe AD treated with dupilumab or placebo in two completed clinical trials

overall_design: 18 Patients with AD treated with dupilumab or placebo . 28 biopsies in LS Skin (16 pre-treatment and 12 post-treatment). 12 biopsies in NL Skin (7 pre-treatment and 5 post treatment)

first: Jennifer

last: Hamilton

last: Suárez-Fariñas

first: Emma

last: Guttman-Yasky


title: Expression profiling COUP-TFI Nex vs WT

status: Public on Dec 05 2014

city: Valbonne - Sophia-Antipolis

first: Kevin

last: Lebrigand

address: 660 route des lucioles

country: France

institute: IPMC/CNRS

summary: We aim to identify genes differentially expressed between mouse WT and COUP-TFI_Nex-Cre mutant cortices.

overall_design: 4 CKO versus 3 WT

first: M

last: Studer

first: C

last: Alfano

first: P

last: Barbry

first: K

last: Moreilhon


title: Expression data from the orthotopic tumors of MES-SA

status: Public on Dec 08 2014

city: Fukui

first: Shinya

last: Kawabe

address: 23-3 Shimoaizuki, Matsuoka, Eiheiji

department: Department of Biochemistry

institute: University of Fukui

summary:
The spontaneous pulmonary metastasis model of human uterine sarcoma was established using GFP-expressed MES-SA cells. Several sublines with different metastatic potentials were generated by in vivo passaging.
We used microarrays to identify the metastatic-related genes using the orthotopic tumors with different metastatic potentials.

overall_design: Orthotopic transplanted uterine sarcoma were observed after 3 weeks post-transplantation and the xenografted tumor reached about 2000 mm3 in additional 3 weeks. After 6 weeks post-transplantation, the animals were sacrificed under isoflurane anesthesia, and the tumors were resected. The GFP-positive regions were collected using Leica MZ10F fluorescent stereomicroscope. This study compared the gene expression profiling between the orthotopic tumors with high (H)- and low (L)-metastatic potentials.

first: Shin

last: Ishikane

first: Tetsuya

last: Mizutani

first: Kaoru

last: Miyamoto


title: CD44s transfection in HEK cells

city: Penzberg

first: Fabian

last: Birzele

address: Nonnenwald 2

department: Pharmaceutical Sciences

country: Germany

institute: Roche Diagnostics GmbH

summary: In order to understand the transcriptional effects of CD44s expression in a cell line that does not express CD44 in its native form we transfected CD44s into HEK cells and measured the transcriptional chances compared to native HEK cells

overall_design: Three biological replicates from each condition (native HEK cells and CD44s transfected cells) were measured using Affymetrix arrays

first: Konrad

last: Honold


title: MYC-negative BL frequent in posttransplant patients (expression)

first: Julio

last: Finalet

summary: We performed genomic and transcriptomic analysis of seven cases of molecular Burkitt lymphoma (mBL) developed in immunosuppressed patients who underwent solid organ transplantation. Interestingly, three cases (43%) were MYC-translocation-negative and revealed the 11q-gain/loss aberration recently identified in 3% of mBL developed in immunocompetent hosts.1 Based on array CGH data, minimal gain and loss regions of 11q (MGR/~4Mb and MLR/~13.5Mb, respectively) were defined and integrative genomic and transcriptomic analysis identified 35 differentially expressed genes, when compared with classic BL. All 16 MGR-dysregulated genes were upregulated, including cancer related USP2, CBL and PAFAH1B2. As expected, all 19 MGL-dysregulated genes were downregulated and two of them, TBRG1 and EI24, are potential tumor suppressor genes. Interestingly, the vast majority of dysregulated 11q23-q25 genes are involved in the MYC and TP53 networks. We hypothesize that the 11q-gain/loss aberration represents a “molecular variant” of t(8q24/MYC) and affects the same pathological pathways as the MYC oncogene.

overall_design: Seven cases of PTLD with BL features were selected from a cohort of 174 posttransplant patients diagnosed with PTLD between 1989 and 2012 at the University Hospitals of KU Leuven (Leuven, Belgium). In addition, five classic BL cases were selected as immunocompetent controls (IC-BL). Morphologic, immunophenotypic, clinical and cytogenetic characteristics of the selected cases were reviewed.

last: Finalet Ferreiro

first: Julie

last: Morscio

first: Daan

last: Dierickx

first: Lukas

last: Marcelis

first: Gregor

last: Verhoef

first: Peter

last: Vandenberghe

first: Thomas

last: Tousseyn

first: Iwona

last: Wlodarska


title: The DNMT1 associated lncRNA Dali is an epigenetic regulator of neural differentiation [1]

status: Public on Dec 03 2014

city: Oxford

first: Vladislava

last: Chalei

address: Sherrington building, Parks road

department: MRC FUnctional Genomics Unit, Department of Physiology, Anatomy and Genetics

institute: University of Oxford

summary: Many intergenic long noncoding RNA (lncRNA) loci regulate the expression of adjacent protein coding genes. Less clear is whether intergenic lncRNAs commonly regulate transcription by modulating chromatin at genomically distant loci. Here, we report both genomically local and distal RNA-dependent roles of Dali, a conserved central nervous system expressed intergenic lncRNA. Dali is transcribed downstream of the Pou3f3 transcription factor gene and its depletion disrupts the differentiation of neuroblastoma cells. Locally, Dali transcript regulates transcription of the Pou3f3 locus. Distally, it preferentially targets active promoters and regulates expression of neural differentiation genes, in part through physical association with the POU3F3 protein. Dali interacts with the DNMT1 DNA methyltransferase in mouse and human and regulates DNA methylation status of CpG island-associated promoters in trans. These results demonstrate, for the first time, that a single intergenic lncRNA controls the activity and methylation of genomically distal regulatory elements to modulate large-scale transcriptional programmes.

overall_design: N2A cells transfected with a non-targeting control vector were compared to N2A cells transfected with a Dali knockdown construct. Three biological replicates of each condition were analysed on Affymetrix GeneChip Mouse Gene 1.0 ST Arrays.

first: Stephen

last: Sansom

first: Lesheng

last: Kong

first: Sheena

last: Lee

first: Juan

last: Montiel

first: Keith

middle: W

last: Vance

first: Chris

middle: P

last: Ponting


title: Distinct roles of Tet1 and Tet2 in mouse embryonic stem cells [MeDIP-Seq]

city: Heidelberg

last: Chavez

address: Im Neuenheimer Feld 280

institute: German Cancer Research Center (DKFZ)

type: Methylation profiling by high throughput sequencing

summary: The TET proteins TET1, TET2 and TET3 constitute a new family of dioxygenases that utilize molecular oxygen and the cofactors Fe(II) and 2-oxoglutarate to convert 5-methylcytosine (5mC) to 5-hydroxy-methylcytosine (5hmC) and further oxidation products in DNA1-5. Here we show that Tet1 and Tet2 have distinct roles in regulating 5hmC deposition and gene expression in mouse embryonic stem cells (mESC). Tet1 depletion in mESC primarily diminishes 5hmC levels at transcription start sites (TSS), whereas Tet2 depletion is mostly associated with decreased 5hmC in gene bodies relative to TSS. 5hmC is enriched at exon start and end sites, especially in exons that are highly expressed, and is significantly decreased upon Tet2 knockdown at the boundaries of high-expressed exons that are selectively regulated by Tet2. In differentiating murine B cells, Tet2 deficiency is associated with selective exon exclusion in the gene encoding the transmembrane phosphatase CD45. Tet2 depletion is associated with increased 5hmC and decreased 5mC at promoters/ TSS regions, possibly because of the redundant activity of Tet1. Together, these data indicate a complex interplay between Tet1 and Tet2 in mESC, and show that loss-of-function of a single TET protein does not necessarily lead to loss of 5hmC and a corresponding gain of 5mC, as generally assumed. The relation between Tet2 loss-of-function and selective changes in exon expression could potentially explain the frequent occurrence of both TET2 loss-of-function mutations and mutations in proteins involved in pre-mRNA splicing in myeloid malignancies in humans.

overall_design: Gene and exon expression analysis in mESC, Tet1 knockdown mESC, and Tet2 knockdown mESC by RNA-sequencing. Mapping of 5-hydroxymethylcytosine in mESC, Tet1 knockdown mESC, and Tet2 knockdown mESC by anti-CMS-seq. Mapping of methylcytosine in mESC, and Tet2 kd mESC by MeDIP-seq.

first: Yun

last: Huang

first: Anjana

last: Rao


title: The DNMT1 associated lncRNA Dali is an epigenetic regulator of neural differentiation [3]

overall_design: N2A cells transfected with a non-targeting control vector were compared to N2A cells transfected with a Pou3f3 knockdown construct. Three biological replicates of each condition were analysed on Affymetrix GeneChip Mouse Gene 1.0 ST Arrays.


title: Gene expression of SUM159-mir100 ALDH+ and ALDH- cells from CTRL or mir100-overexpressing group

city: Hefei

first: Suling

last: Liu

state: Anhui

address: 96 Jin Zai Road

department: School of Life Sciences and Medical Center

institute: University of Science & Technology of China

summary: Emerging evidence suggest that miRNAs play an essential role in self-renewal and differentiation of normal and malignant stem cells by regulating the expression of key stem cell regulatory genes. Here we demonstrate that mir-100 expression is related to cellular differentiation state with lowest expression in cells displaying stem cell markers. Utilizing a tetracycline inducible lentivirus driving mir-100 expression, we found that mir-100 overexpression decreased breast cancer stem cells (BCSCs) and inhibited cancer cell proliferation in vitro and in mouse xenografts by targeting SMARCA5, SMARCD1 and BMPR2.

overall_design: In order to determine the cellular targets of mir-100 in BCSCs and non-BCSCs, ALDH-positive and -negative populations of pTRIPZ-SUM159-mir-100 cells were separated and cultured in suspension for ten hours in the presence or absence of DOX. Gene expression profiles of the four populations were determined utilizing Affymetrix microarrays

first: Lu

last: Deng


title: The retinoblastoma tumor suppressor modulates DNA repair and radio responsiveness

city: PHILADELPHIA

first: Adam

last: Ertel

state: PA

address: 233 S 10TH ST

department: Cancer Biology

country: USA

institute: Thomas Jefferson University

summary: In this study, we show that RB loss promotes sensitization to genotoxic stress through mechanisms distinct from cell cycle checkpoint control, and identify RB as a potent effector of the response to radiotherapy.

overall_design: Transcriptome analysis was performed, validated, and mechanisms discerned and multiple mechanisms were interrogated including cell cycle, apoptosis, and DNA damage repair.

first: Chellappagounder

last: Thangavel

first: Ettickan

last: Boopathi

first: Steve

last: Ciment

first: Yi

first: Anku

last: Sharma

middle: B

last: McMahon

first: Hestia

last: Mellert

first: Sankar

last: Addya

first: Ruth

last: Birbe

first: Paolo

last: Fortina

last: Dicker

first: Karen

last: Knudsen

first: Robert

last: Den


title: VEGF induction of HUVEC and CEP

status: Public on Dec 06 2014

city: Wien

first: Julia

last: Testori

address: Lazarettgasse 19

department: Vascular Biology and Thrombosis Research

institute: Medical University Vienna

summary: Angiogenesis, the formation of new capillaries by sprouting from preexisting vessels, is mainly induced by VEGF-A. To identify genes which are induced by VEGF-A in endothelial cells and genes which are differently expressed or VEGF-A induced in HUVEC and CEP, HUVEC and CEP were starved and induced by VEGF-A165 for 30, 60 and 150min. RNA of induced and uninduced cells was isolated and subjected to microarray analysis using Affymetrix microarray.

overall_design: Human umbilical vein endothelial cells and circulating endothelial progenitor cells were grown in complete EGM-2 medium in dense culture for four days without change of medium and before the stimulation in EGM-2 medium without growth factors over night. The cells were stimulated with 100ng/ml VEGF-A165 for 30, 60 and 150 min. CD34 positive cells were isolated by MACS from cord blood. RNA was isolated with Trizol according to the manufacturer's instructions.

first: Martin

last: Bilban

first: Erhard

last: Hofer


title: Identification of odorant receptors activated by odorants in vivo

status: Public on Dec 02 2014

city: Lexington

first: Tim

last: McClintock

state: KY

address: 780 Rose St.

department: Physiology

institute: University of Kentucky

summary:
Odorants are thought to activate sets of odorant receptors in vivo, but capturing sets of responsive receptors in vivo has never been accomplished.
GeneChip microarrays were used to identify the odorant receptor mRNAs enriched in samples from activated olfactory neurons

overall_design: olfactory neurons, which each express only one odorant receptor allele, marked by an activity reporter after odorant stimulation were captured by FACS; these samples were hybridized to GeneChip arrays


title: MicroRNA-188 regulates age-related switch between osteoblast and adipocyte differentiation [osteoblast]

city: Changsha

first: Xianghang

last: Luo

state: Hunan

address: 139# Middle Renmin Road, Changsha, Hunan 410011, PR China

institute: Institute of Endocrinology & Metabolism, The Second Xiangya Hospital of Central South University, Changsha, Hunan, PR China.

summary:
We identified microRNA-188 differentially expressed in the BMSCs of aged and young mice and influented on BMSCs differentiation with ageing.
Then we used microarrays to detail the osteogenic gene expression during osteogenic differention of BMSCs from 188KO mice.

overall_design: BMSCs isolated from WT and 188KO mice were cultured with osteogenic induction medium for RNA extraction and hybridization on Affymetrix microarrays.

first: Changjun

last: Li

first: Peng

last: Cheng

first: Mengke

last: Liang

first: Jinyu

last: Wang

first: Yusi

last: Chen

first: Zhuying

last: Xia

first: Houde

last: Zhou

first: Eryuan

last: Liao

first: Hui

last: Xie


title: MicroRNA-188 regulates age-related switch between osteoblast and adipocyte differentiation [adipocyte]

summary:
We identified microRNA-188 differentially expressed in the BMSCs of aged and young mice and influenced on BMSCs differentiation with ageing.
Then we used microarrays to detail the adipogenic gene expression during adipogenic differention of BMSCs from 188KO mice.

overall_design: BMSCs isolated from WT and 188KO mice were cultured with adipogenic induction medium for RNA extraction and hybridization on Affymetrix microarrays.


title: MicroRNA-188 regulates age-related switch between osteoblast and adipocyte differentiation

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

overall_design: Refer to individual Series


title: Expression data from invariant natural killer T (iNKT) cells in spleen and adipose tissue

status: Public on Dec 01 2014

city: Boston

first: Lydia

last: Lynch

address: One Jimmy Fund Way

department: Medicine

institute: Harvard Medical School

summary:
Adipose tissue iNKT cells have different functions than iNKT cells in the blood and other organs.
We used microarrays to detail the global gene expression profiles that might underlie these phenotypic and functional differences in adipose iNKT cells compared to splenic iNKT cells.

overall_design: We isolated iNKT cells from adipose tissue and spleen from the same C57/B6 mice by cell sorting on a flow cytometer (Facs Aria). We pooled iNKT cells from ~50 together and sent it for Affymetrix microarray analysis through the Immune Genoa Project pipeline.

first: Michael

last: Brenner


title: Expression data comparing TMNK-1 to HMEC

city: Aurora

last: Edwards

address: 12700 East 19th Avenue, Box C272

department: Pulmonary

institute: UC Denver

summary:
Liver sinusoidal endothelial cells (LSECs) are an endothelial subtype specific to the liver with unique functions when compared to other endothelial subtypes.  We have demonstrated that supernatants from an immortalized LSEC line (TMNK-1) control HCV viral replication in vitro.  Supernatants from a human microvascular endothelial cell line (HMEC) did not control viral replication suggesting this anti-viral effect is unique to LSECs.
We used microarray to analyze the transcriptional differences between these cell lines to further shed light on their differential effects on HCV replication in vitro

overall_design: TMNK-1 cells or HMEC were cultured for 48h without stimulation; total RNA was then harvest to determine transcriptional differences.

first: Silvia

last: Giugliano

last: Kriss

first: Lucy

last: Golden-Mason

first: Evgenia

last: Dobrinskikh

first: Amy

last: Stone

first: Alejandro

last: Soto-Gutierrez

first: Angela

last: Mitchell

first: Salman

middle: R

last: Khetani

first: Daisuke

last: Yamane

first: Mark

last: Stoddard

first: George

last: Shaw

first: Stanley

last: Lemon

last: Gale Jr

first: Vijay

last: Shah

first: Hugo

last: Rosen