title: Expression data of SAGM-grown cells derived thyroid follicular cells

city: Nagasaki

first: Norisato

last: Mitsutake

address: 1-12-4 Sakamoto

institute: Nagasaki University

summary: We developed a novel culture system to obtain multilineage undifferentiated stem/progenitor cells from normal human thyroid tissues. This seems to be achieved by direct reprogramming of thyroid follicular cells. The objective of the study was to reveal gene expression profile of the obtained cells compared to primary thyrocytes. After enzymatic digestion, primary thyrocytes, expressing thyroglobulin and cytokeratin-18, were cultured in a serum-free medium called SAGM containing insulin and EGF. Although the vast majority of cells died, a small proportion (~0.5%) survived and proliferated. During initial cell expansion, thyroglobulin/cytokeratin-18 expression was gradually declined, suggesting that those cells are derived from thyroid follicular cells or at least thyroid-committed cells. The SAGM-grown cells did not express any thyroid-specific genes. However, after four-week incubation with FBS and TSH, cytokeratin-18, thyroglobulin, TSH receptor, PAX8 and TTF1 expressions re-emerged. Moreover, surprisingly, the cells were capable of differentiating into neuronal or adipogenic lineage depending on differentiating conditions.

overall_design: Total RNAs were extracted from PT from three different samples (PT0808, PT0811 and PT0812) and corresponding SAGM-grown lines and subjected to Affymetrix GeneChip Human Genome U133 Plus 2.0 microarray analysis


title: Integrated transcript and genome analyses reveal NKX2-1 and MEF2C as potential oncogenes in T-ALL

status: Public on Apr 11 2011

city: Utrecht

first: Jules

last: Meijerink

address: Uppsalalaan 8

country: Netherlands

institute: Princess Máxima Center for Pediatric Oncology

summary: To identify novel oncogenic pathways in T-cell acute lymphoblastic leukemia (T-ALL), we combined expression profiling of 117 pediatric patient samples and detailed molecular cytogenetic analyses including the Chromosome Conformation Capture on Chip (4C) method. Two T-ALL subtypes were identified that lacked rearrangements of known oncogenes. One subtype associated with cortical arrest, expression of cell cycle genes and ectopic NKX2-1 or NKX2-2 expression for which rearrangements were identified. The second subtype associated with immature T-cell development and high expression of the MEF2C transcription factor as consequence of rearrangements of MEF2C, transcription factors that target MEF2C or MEF2C-associated cofactors. We propose NKX2-1, NKX2-2 and MEF2C as T-ALL oncogenes that are activated by various rearrangements.

overall_design: This study includes 117 pediatric T-ALL samples of which 92 samples are available at GSE10609. In addition, this study includes 7 normal bone marrow control samples

middle: P

first: Rob

last: Pieters


title: Ewing Sarcoma cell lines treated with mithramycin

status: Public on Apr 18 2011

city: Bethesda

first: Sean

last: Davis

state: MD

address: 37 Convent Drive, Room 6138

country: USA

institute: National Cancer Institute

summary: The study aims to define gene expression changes associated with mithramycin treatment of Ewing Sarcoma cell lines.

overall_design: The data consist of 12 arrays. Two cell lines, TC71 and TC32, were treated with solvent control or with mithramycin, and RNA was extracted at 6 hours. Three biological replicates per cell line/treatment.

middle: R


title: Expression data from control and LRF-deficient mouse germinal center B cells

status: Public on Apr 08 2011

city: Duarte

first: Takahiro

last: Maeda

state: CA

address: 1500E Duarte Rd

department: Hematopoietic Stem Cell and Leukemia Research

institute: Beckman Research Institute of the City of Hope

summary:
B cells are indispensable for humoral immunity, as they ultimately give rise to antibody-secreting plasma cells. During T cell-dependent antibody responses, naive B cells form germinal centers (GCs), a distinct histologic structure found in secondary lymphoid organs. Naive B cells become activated upon interaction with T cells and antigen presenting cells, and begin to rapidly proliferate and form the characteristic GC structure.
To elucidate the overall effect of LRF loss in the GCB cell transcriptome, gene expression microarray analysis of FACS-sorted GCB cells was performed. LRF Flox/+ mb-1 Cre+ mice were used as a control to normalize the potential effects of Cre recombinase, and four RNA samples for each genotype were used for the analysis.

overall_design: B cell-specific LRF knockout (LRF Flox/Flox mb-1 Cre+) and control (LRF Flox/+ mb-1 Cre+) mice (4 each) were immunized with sheep red blood cells, and GCB cells were FACS-sorted 7 days later.

first: Nagisa

last: Sakurai

first: Min

last: Li

first: Maeda

last: Takahiro


title: Expression data from LNCap cell line treated with COP1 (RFWD2), ETV1, and JUN siRNAs

city: South San Francisco

first: Jinfeng

last: Liu

address: 1 DNA Way, MS93

department: Bioinformatics and Computational Biology

institute: Genentech Inc.

summary: The proto-oncogenes ETV1, ETV4, and ETV5 encode members of the E26 transformation-specific (ETS) transcription factor family, which includes the most frequently rearranged and overexpressed genes in prostate cancer.  Despite being critical regulators of development, little is known about their post-translational regulation.  Here we identify the ubiquitin ligase COnstitutive Photomorphogenic-1 (COP1, also called RFWD2) as a tumor suppressor that negatively regulates ETV1, ETV4, and ETV5.  ETV1, which is the member mutated more frequently in prostate cancer, was degraded after being ubiquitinated by COP1.  Truncated ETV1 encoded by prostate cancer translocation TMPRSS2:ETV1 lacks the critical COP1 binding motifs (degrons) and was 50-fold more stable than wild-type ETV1.  Almost all patient translocations eliminate these ETV1 degrons, implying that translocations rendering ETV1 insensitive to COP1 confer a significant selective advantage to prostate epithelial cells.  Indeed, COP1 deficiency in mouse prostate elevated ETV1 levels and produced increased cell proliferation, hyperplasia, and early prostate intraepithelial neoplasia.  The combined loss of COP1 and PTEN enhanced the invasiveness of mouse prostate adenocarcinomas.  Finally, relatively rare human prostate cancer samples showed hemizygous loss of the COP1 gene, loss of COP1 protein expression, and abnormally elevated ETV1 protein while lacking a translocation event.  These findings identify COP1 as a bona fide tumor suppressor whose down-regulation promotes prostatic epithelial cell proliferation and tumorigenesis.

overall_design: LNCap prostate cancer cell line were treated with 5 different sets of siRNAs: (1) control siRNA; (2) COP1 (RFWD2) siRNA; (3) COP1 siRNA + ETV1 siRNA; (4) COP1 siRNA + c-JUN siRNA; (5) COP1 siRNA + ETV1 siRNA + c-JUN siRNA. The experiments were conducted in two batches; each batch has its own control siRNA group, so that the batch effect can be properly modelled. Each group has 4-6 replicates; there are 31 samples in total.

first: Zora

last: Modrusan

first: Alberto

last: Vitari

first: Connie

last: Ha


title: Characterization of differential gene expression in adrenocortical tumors harbouring β-catenin  (CTNNB1) mutations.

status: Public on Apr 09 2011

city: Montreal

first: julien

last: durand

state: QC

address: 3840 Rue Saint-Urbain

department: Biomedicale Science

country: Canada

institute: CRCHUM

summary:
Mutations of β-catenin gene (CTNNB1) are frequent in adrenocortical adenomas (AA) and carcinomas (ACC). However, the target genes of CTNNB1 have not yet been identified in adrenocortical tumors.
Our objective was to identify genes de-regulated in adrenocortical tumors harbouring CTNNB1 genetic alterations.

overall_design: We compared gene expression profiles of AA with (n: 3) and without (n: 4) CTNNB1 mutations using Affymetrix arrays.

first: Julien

last: Durand

first: Isabelle

last: Bourdeau


title: Hypothalamic expression differences between hypertensive BPH/2J and normotensive BPN/3J mouse strains

city: Sydney

middle: J

last: Morris

state: NSW

address: Anderson Stuart Building, room N452, University of Sydney

department: Physiology

country: Australia

institute: University of Sydney

summary: Identification of hypothalamic genes whose expression differs between high blood pressure (BPH/2J) and normal blood pressure (BPN/3J) Schlager mouse strains at age 6 weeks (young) and 26 weeks (mature) using Affymetrix GeneChip® Mouse Gene 1.0 ST Arrays.

overall_design: The whole hypothalamus was removed from young (6-week-old) and adult (26-week-old) BPH/2J hypertensive mice and age-matched normotensive BPN/2J mice (n=6/group) at peak of 24 h blood pressure. No pooling was performed. After extraction of RNA, cRNA was prepared and arrays performed using Affymetrix GeneChip® Mouse Gene 1.0 ST Arrays at the Ramaciotti Gene Function Analysis facility, University of New South Wales in Sydney, Australia.

first: Francine

middle: Z

last: Marques

first: Anna

middle: E

last: Campain

first: Pamela

last: Davern

first: Yee

middle: H

last: Yang

first: Geoffrey

middle: A

last: Head

first: Brian


title: Melanoma cell culture phenotypes I

status: Public on Apr 05 2011

city: Zürich

first: Daniel

middle: Simon

last: Widmer

address: Gloriastrasse 31

department: Dermatology

country: Switzerland

institute: University Hospital Zürich

summary: Recent trials with MAPK inhibitors have shown promising results in many patients with metastatic melanoma; however, nearly all responding patients experience disease relapse. We describe here how melanoma cells respond to MAPK inhibition in a phenotype-specific manner, suggesting that slow cycling invasive phenotype cells provide a treatment-resistant pool from which disease relapse may be derived. The implication is that while MAPK inhibition may successfully treat proliferating cells, another cell population needs to be addressed at the same time.

overall_design: 12 samples

middle: S


title: Analyzing the metabolic stress response of recombinant Escherichia coli cultures expressing human interferon beta in high cell density fed batch cultures using time course transcriptomic data

status: Public on Apr 07 2011

city: New Delhi

first: Krishna

middle: Jyoti

last: Mukherjee

email: anuradha.bharara@gmail.com, ashishji101@gmail.com, shubhashreemahalik@gmail.com, kjmukherjee@mail.jnu.ac.in

state: delhi

address: New Mehrauli Road

department: School Of Biotechnology

country: India

institute: Jawaharlal Nehru University

summary: Over expression of recombinant proteins is known to cause a metabolic burden to the host cells which leads to down regulation of both growth rates and protein expression. Most studies in this regard have been conducted in low density shake flask cultures which does not capture the essential features of an industrial scale bioprocess. In the present work we studied the transcriptomic profiling at different specific growth rates while expressing the recombinant human interferon beta in fed batch cultures with complex media. These conditions mimicked the industrial fermentations for recombinant proteins.

overall_design: To determine the transcriptomic response of E.coli BL21(DE3) to recombinant protein production at three different specific growth rates, samples were collected for four time points (0h, 2h, 4h, 6h) post induction for the fed batch cultivations at specific growth rates 0.2h-1, 0.3h-1, 0.4h-1 respectively and induced at an optical density of 30. 0h (uninduced) sample was taken as control conditions for every run.

first: Anuradha

middle: B

last: Singh

first: Ashish

middle: K

last: Sharma


title: Aryl hydrocarbon receptor antagonists promote the expansion of human hematopoietic stem cells

status: Public on Apr 04 2011

city: San Diego

first: John

last: Walker

address: 10675 John Jay Hopkins

institute: Genomics Institute of the Novartis Research Foundation

summary:
Although practiced clinically for more than 40 years, the use of hematopoietic stem cell (HSC) transplants remains limited by the ability to expand these cells ex vivo. An unbiased screen with primary human HSCs identified a purine derivative, StemRegenin 1 (SR1), that promotes the ex vivo expansion of CD34+ cells. Culture of HSCs with SR1 led to a 50-fold increase in cells expressing CD34 and a 17-fold increase in cells that retain the ability to engraft immunodeficient mice. Mechanistic studies show that SR1 acts by antagonizing the aryl hydrocarbon receptor (AHR). The identification of SR1 and AHR modulation as a means to induce ex vivo HSC expansion should facilitate the clinical use of HSC therapy.
LGC006, a less potent SR1 analog, was also examined.

KEYWORDS: two compounds, multiple doses, one time point

first: Anthony

last: Boitano

first: Jian

last: Wang

first: Russell

last: Romeo

first: Laure

middle: C

last: Bouchez

first: Albert

last: Parker

first: Sue

last: Sutton

first: Colin

last: Flaveny

first: Gary

last: Perdew

first: Michael

last: Denison

first: Peter

middle: G

last: Schultz

last: Cooke


title: Polydextrose fermentation metabolite effect on Caco-2 colon cancer cells

status: Public on Apr 22 2011

city: Turku

first: Esa

last: Alhoniemi

address: Itäinen Pitkäkatu 4 C

country: Finland

institute: Pharmatest Services Ltd

summary:
Analysis of  non-differentiated Caco-2 intestinal epithelial cell line  treated with polydextrose fermentation metabolites fermented for 48 hours in 4-stage in vitro colon simulator, in which the conditions mimic the human proximal, ascending, transverse and distal colon in sequence , as well as with medium, 100 mM NaCl and 5 mM butyrate. Polydextrose, a soluble fiber fermented in colon, was fermented with the in vitro colon simulator in three amounts of 0%, 1% and 2%. Results provide insight into the mechanisms underlying  colon cancer cells and a comparison of a complex fiber metabolome to 5 mM butyrate and 100 mM NaCl. Furthermore, the results give insight of dosage effect of increasing the concentration of fiber.
High level of dietary fiber has been epidemiologically linked to protection against the risk for developing colon cancer. The mechanisms of this protection are not clear. Fermentation of dietary fiber in the colon results in production of for example butyrate that has drawn attention as a chemopreventive agent. Polydextrose, a soluble fiber that is only partially fermented in colon, was fermented in an in vitro colon simulator, in which the conditions mimic the human proximal, ascending, transverse and distal colon in sequence. The subsequent fermentation metabolome were applied on colon cancer cells, and the gene expression changes studied. Polydextrose fermentation down-regulated classes linked with cell cycle, and affected number of metabolically active cells. Further, up-regulated effects on classes linked with apoptosis implicate that polydextrose fermentation plays a role in induction of apoptosis in colon cancer cells. The up-regulated genes involved also key regulators of lipid metabolism, such as PPARg and PGC-1α. These results offer hypotheses for the mechanisms of two health benefits linked with consumption of dietary fiber, reducing risk of development of colon cancer, and dyslipidemia.

overall_design: Non-differentiated Caco-2 cells were treated with polydextrose fermentation metabolites from the vessels representing different parts of the colon, or with 100 mM NaCl or with 5 mM butyrate for 24 hours. For polydextrose fermentation three  concentrations of polydextrose were used: 0%, 1% and 2% for a simulation that lasted for 48 hours. Polydextrose fermentation samples from total of 12 vessels, as well as from medium sample, 5 mM butyrate and 100 mM NaCl were analysed as single replica.

first: Heli

last: Putaala

first: Harri

last: Mäkivuokko

first: Kirsti

last: Tiihonen

first: Nina

last: Rautonen


title: Real-time Monitoring of Cisplatin Toxicity on Cancer Cells

city: Heidelberg

first: Stefan

last: Wolfl

address: Im Neuenheimer Feld 364

department: Institute of Pharmacy and Molecular Biotechnology

country: Germany

institute: Heidelberg University, Heidelberg, Germany

summary: Treatment of MCF7 breast cancer cells by cisplatin leads to a very specific metabolic response and an onset of cell death about 10-11 h after beginning of treatment. For more detailed understanding of the molecular processes underlying the specific metabolic response, mRNA was isolated from MCF7 cells when the specific changes, (i) induction of glycolysis and (ii) onset of cell death, were detected during online measurement in the cell biosensor system.

overall_design: MCF7 breast cancer cells were treated with cisplatin in the BIONAS 2500 cell biosensor chip system, and samples were collected from the biosensor chip module at time points when glycolysis was induced (change of ph; 8-9h) and at the beginning of cell death (change of impedance; 10-11h).

first: Hamed

last: Alborzinia

first: Catharina

last: Scholl


title: Genome-wide maps of REST and its cofactors in mouse E14 cells

status: Public on Apr 01 2011

city: Singapore

first: hongbing

last: yu

address: 60 biopolis street, #02-01, genome

department: stem cell and development

country: Singapore

institute: genome institute of singapore

type: Genome binding/occupancy profiling by high throughput sequencing

summary: We report the application of single-molecule-based sequencing technology for REST and its cofactors genome wide binding sites in E14 cells.We then combine these binding sirtes with REST regulating gene profiling, to understand REST binding and regulation in E14 cells.

overall_design: Examination of REST and 5 cofactors(RCOR1, RCOR2,RCOR3,SIN3A,SIN3B) in E14 cells, REST and SIN3A endogenous antibody were used for ChIP experiment. The stable E14 cells expressing low level exogenous RCOR1, RCOR2, RCOR3,and SIN3B with V5 tag were used for ChIP experiment with V5 antibody to obtain individual ChIP DNA.

first: Hong-Bing

last: Yu

first: Rory

last: Johnson

first: Galih

last: Kunarso

first: Lawrence

last: Stanton


title: REST ChIP-chip and knockdown expression profiling

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

overall_design: Refer to individual Series


title: Integrated genomic profiling in mantle cell lymphoma

first: Louis

middle: M.

last: Staudt

address: 9000 Rockville Pike, Bldg 10, Rm 4N114

department: Lymphoid Malignancies Branch

summary: The genome of mantle cell lymphoma (MCL) is, in addition to the translocation t(11;14), characterized by a high number of secondary chromosomal gains and losses that likely account for the varying survival times of MCL patients. We investigated 77 primary MCL tumors with available clinical information using high resolution RNA expression and genomic profiling and applied our recently developed gene expression and dosage integrator (GEDI) algorithm to identify novel genes and pathways that may be of relevance for the pathobiology of MCL. We show that copy number neutral loss of heterozygosity (CNN-LOH) is common in MCL and targets regions that are frequently affected by deletions. The molecular consequences of genomic copy number changes appear complex, even in genomic loci with identified tumor suppressors, such as the region 9p21 containing the CDKN2A locus. Moreover, the deregulation of novel genes such as CUL4A, ING1 and MCPH1 may affect the two crucial pathogenetic mechanisms in MCL, the disturbance of the proliferation and DNA damage response pathways. Deregulation of the Hippo pathway may have a pathogenetic role in MCL, since decreased expression of its members MOBKL2A, MOBKL2B and LATS2 was associated with inferior outcome also in an independent validation series of 32 MCL.

overall_design: Sixty-four primary MCL specimens from previously untreated patients were investigated with Affymetrix HG U133 plus 2.0 gene expression arrays.


title: Hypothalamic expression differences between hypertensive BPH/2J during circadian variations of blood pressure

last: Morris

summary: Identification of hypothalamic genes whose expression differs between active (peak of blood pressure) and inactive periods in the high blood pressure (BPH/2J) Schlager mouse, adjusted by their age- and activity-matched normal blood pressure (BPN/3J) controls using Affymetrix GeneChip® Mouse Gene 1.0 ST Arrays.

overall_design: The whole hypothalamus was removed from BPH/2J and age-matched BPN/2J (n=3/group, 19 week old, ‘trough’ blood pressure) in the inactive period, when the blood pressure levels of the BPH/2J and BPN/3J models are similar. Hypothalamus of BPH/2J and age-matched BPN/2J (n=6/group, 26 week old, ‘peak’ blood pressure) were collected on the same way at the peak of the circadian variation, when there blood pressure difference between the strains was maximal. No pooling was performed. After extraction of RNA, cRNA was prepared and arrays performed using Affymetrix GeneChip® Mouse Gene 1.0 ST Arrays performed at the Ramaciotti Gene Function Analysis facility, University of New South Wales in Sydney, Australia.

first: Francine

last: Marques

first: Anna

last: Campain

first: Pamela

last: Davern

first: Yee

last: Yang

first: Geoffrey

last: Head

first: Brian


title: Genome-wide profiling of tumor cells in multiple myeloma

status: Public on Apr 02 2011

city: Brooklyn

first: Olcay

last: Batuman

state: NY

address: 450 Clarkson Ave, Box 20

institute: SUNY Downstate Medical Center

summary: In multiple myeloma (MM), endothelial progenitor cells (EPCs) regulate tumor angiogenesis and disease progression. They share a common bone marrow microenvironment with myeloma tumor cells. CD138+ tumor plasma cells from 12 newly diagnosed patients with advanced MM were examined for genomic instability by RNA microarrays to assess changes in gene expression.

overall_design: Tumor cells were derived from single-cell suspensions of bone marrow (BM) aspirates from newly diagnosed MM patients, and RNA was extracted for microarray hybridization.

first: Marc

last: Braunstein


title: Pervasive subtypes of pancreatic ductal adenocarcinoma (PDA) and their differing response to therapy.

city: Sutton

first: Anguraj

last: Sadanandam

state: Surrey

address: 15 Cotswold Road

department: Molecular Pathology

country: United Kingdom

institute: Institute of Cancer Research (ICR), London

summary: Pancreatic ductal adenocarcinoma (PDA) carries a dismal prognosis and current treatments are only modestly effective. We present evidence that this variation is caused in part by recurrent, pervasive molecular differences between tumors. mRNA expression profiles measured using microdissected PDA clinical samples reveal three dominant subtypes of disease; epithelial, mesenchymal and acinar-like. The classical and quasi-mesenchymal subtypes are observed in human and mouse PDA cell lines. Importantly, responses to cytotoxics and KRAS depletion in human PDA cell lines differ substantially between subtypes, and in opposing directions. Integrated genomics implicate and functional studies support overexpression of the trancription factor GATA6 as a driver of the epithelial subtype. These results provide a molecular framework for evaluating the prospects of personalized treatment in PDA.

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus

overall_design:
RNA was extracted from archival patient FFPE PDA samples and hybridized on Affymetrix U133 plus 2.0 microarrays. The CEL files were processed using R based Bioconductor and normalized values were obtained using RMA.
Note: These patient sample microarrays were done in different batches and were batch corrected prior to further analysis as described in our original paper and Nature Protocols  Community Contributed Protocol Exchange 04/04/2011 - doi:10.1038/protex.2011.231.

RNA was extracted from human PDA cell line samples and hybridized on Affymetrix U133 plus 2.0 microarrays. The CEL files were processed using R based Bioconductor and normalized values were obtained using RMA.
Note: Cell line microarrays were done separately. Our preprocessed and normalized data provided here represent analyses performed separately for patient samples and cell lines.

RNA was extracted from mouse PDA cell lines and hybridized on Affymetrix Mouse 430a 2.0 microarrays. The CEL files were processed using R based Bioconductor and normalized values were obtained using RMA.

first: Eric

last: Collisson

first: Peter

last: Olson

first: Margaret

last: Tempero

first: Douglas

last: Hanahan

first: Joe

middle: W

last: Gray


title: Stromal molecular signatures of breast and prostate cancer

status: Public on Mar 31 2011

city: Torino

first: Paolo

last: Provero

address: Via Nizza 52

department: Molecular Biotechnology and Health Sciences

country: Italy

institute: University of Turin

summary: Primary tumor growth induces host tissue responses that are believed to support and promote tumor progression. Identification of the molecular characteristics of the tumor microenvironment and elucidation of its crosstalk with tumor cells may therefore be crucial for improving our understanding of the processes implicated in cancer progression, identifying potential therapeutic targets, and uncovering stromal gene expression signatures that may predict clinical outcome. A key issue to resolve, therefore, is whether the stromal response to tumor growth is largely a generic phenomenon, irrespective of the tumor type, or whether the response reflects tumor-specific properties. To address similarity or distinction of stromal gene expression changes during cancer progression, oligonucleotide-based Affymetrix microarray technology was used to compare the transcriptomes of laser-microdissected stromal cells derived from invasive human breast and prostate carcinoma. Invasive breast and prostate cancer-associated stroma was observed to display distinct transcriptomes, with a limited number of shared genes. Interestingly, both breast and prostate tumor-specific dysregulated stromal genes were observed to cluster breast and prostate cancer patients, respectively, into two distinct groups with statistically different clinical outcomes. By contrast, a gene signature that was common to the reactive stroma of both tumor types did not have survival predictive value. Univariate Cox analysis identified genes whose expression level was most strongly associated with patient survival. Taken together, these observations suggest that the tumor microenvironment displays distinct features according to the tumor type that provides survival-predictive value.

overall_design: 6 samples of stroma surrounding invasive breast primary tumors; 6 matched samples of normal stroma. 6 samples of stroma surrounding invasive prostate primary tumors; 6 matched samples of normal stroma.

first: Anne

last: Planche

first: Marina

last: Bacac

first: Carlo

last: Fusco

first: Mauro

last: Delorenzi

first: Jean-Christophe

last: Stehle

first: Ivan

last: Stamenkovic


title: Expression data from human SGBS adipocytes under hypoxic conditions

status: Public on Apr 14 2011

city: Feldkirch

first: Heinz

last: Drexel

address: Carinagasse 47

country: Austria

institute: VIVIT

summary: Hypoxia in adipose tissue is suggested to be involved in the development of a chronic mild inflammation, which in obesity can further lead to insulin-resistance. The effect of hypoxia on gene expression in adipocytes seems to play a central role in this inflammatory response observed in obesity. However, the global impact of hypoxia on transcriptional changes in human adipocytes is unclear. Therefore, we compared gene expression profiles of human Simpson-Golabi-Behmel syndrome (SGBS) adipocytes under normoxic or hypoxic conditions to detect hypoxia-responsive genes in adipocytes by using whole human genome microarrays.

overall_design: Human SGBS adipocytes were cultured in a hypoxic environment (1% O2) for 3, 6 and 16 hours and the control group was cultured under normoxic conditions (21% O2). Total RNA was prepared from control and treated SGBS cells, in triplicate experiments, and probes were hybridized on ‘Human Genome U133 2.0’ arrays (Affymetrix).

first: Kathrin

last: Geiger


title: Genome-wide profiling of endothelial progenitor cells in multiple myeloma: disease-relevant pathways and genomic markers

first: Olcay

last: Batuman

type: Genome variation profiling by genome tiling array


title: MicroRNAs are Transported in Plasma and Delivered to Recipient Cells by High-Density Lipoproteins

status: Public on Apr 03 2011

first: Kasey

last: Vickers

address: 10 Center Dr. Bldg. 10 8N222

department: National Heart, Lung and Blood Institute

institute: National Institutes of Health

type:
Other
Expression profiling by array


title: Correlation of molecular profiles and clinical outcome of stage UICC II colon cancer patients

status: Public on Apr 10 2011

city: Berlin

first: Dido

last: Lenze

address: Hindenburgdamm 30

department: Pathologie, Campus Benjamin Franklin

institute: Charité-Universitätsmedizin Berlin

summary: Background  Published multi-gene classifiers suggested outcome prediction for patients with stage UICC II colon cancer based on different gene expression signatures. However, there is currently no translation of these classifiers for application in routine diagnostic. Therefore, we aimed at validating own and published gene expression signatures employing methods which enable RNA and protein detection in routine diagnostic specimens.    Results  Immunohistochemistry was applied to 68 stage UICC II colon cancers to determine the protein expression of five selected previously published classifier genes (CDH17, LAT, CA2, EMR3, and TNFRSF11A). Correlation of protein expression data with clinical outcome within a 5-year post-surgery course failed to separate patients with a disease-free follow-up [Group DF] and relapse [Group R]). In addition, RNA from macrodissected tumor samples from 53 of these 68 patients was profiled on Affymetrix GeneChips (HG-U133 Plus 2.0). Prognostic signatures were generated by Nearest Shrunken Centroids with cross-validation. Although gene expression profiling allowed the identification of differentially expressed genes between the groups DF and R, a stable classification and prognosis signature was not discernable in our data. Furthermore, the application of previously published gene signatures consisting of 22 and 19 genes, respectively, to our gene expression data set using ‘global tests’ and leave-one-out cross-validation was unable to predict clinical outcome (prediction rate 75.5% and 64.2%; n.s.). T-stage was the only independent prognostic factor for relapse in multivariate analysis with established clinical and pathological parameters including microsatellite status.  Conclusions  Our protein and gene expression analyses currently do not support application of molecular classifiers for prediction of clinical outcome in routine diagnostic as a basis for patient-orientated therapy in stage UICC II colon cancer. Further studies are needed to develop prognosis signatures applicable in patient care.

overall_design: 53 patients with primary stage UICC II colon cancer treated by elective standard oncological resection were selected. None of the patients received adjuvant chemotherapy. Patients with susceptibility for hereditary colorectal cancer or inflammatory bowel disease were excluded from this study. Routine histopathologic staging of resected specimen was performed by experienced pathologists.

first: Jörn

last: Gröne

first: Vindi

last: Jurinovic

first: Manuela

last: Hummel

first: Henrik

last: Seidel

first: Gabriele

last: Leder

first: Georg

last: Beckmann

first: Anette

last: Sommer

first: Robert

last: Grützmann

first: Christian

last: Pilarsky

first: Ulrich

last: Mansmann

first: Heinz-Johannes

last: Buhr

first: Harald

last: Stein

first: Michael


title: Chromosome wide analysis of parental allele specific chromatin and DNA methylation

first: Xiwei

last: Wu

address: 1500 E. Duarte Rd.

department: Computational and Quantitative Medicine

institute: City of Hope National Medical Center

summary:
Imprinted genes are monoallelically expressed according to parental inheritance. The maternally and paternally expressed alleles are distinguished epigenetically by DNA methylation and histone modifications.
RNA was extracted from MatDup.dist7 and PatDup.dist7 MEFs for hybridization to Affymetrix microarrays

overall_design: Comparsion of gene expression in MatDup.dist7 and PatDup.dist7 MEFs

first: Purnima

last: Singh

first: Piroska

last: Szabo


title: Gene expression data from temporal cortex of young adult, old and AD-like Microcebus murinus

city: Montpellier

first: Gina

last: DEVAU

address: Place Eugene Bataillon

department: Universite de Montpellier CC105

country: France

institute: Inserm U1198-UM-EPHE

summary: Aging is the primary risk factor of neurodegenerative disorders such as Alzheimer's disease (AD). However, the molecular events occurring during brain aging are extremely complex and still largely unknown. For a better understanding of these age-associated modifications, animal models as close as possible to humans are needed. We thus analyzed the transcriptome of the temporal cortex of the primate Microcebus murinus using human oligonucleotide microarrays (Affymetrix). Gene expression profiles were assessed in the temporal cortex of 6 young adults, 10 healthy old animals and 2 old, "AD-like" animals that presented b-amyloid plaques and cortical atrophy, which are pathognomonic signs of AD in humans. Gene expression data of the 14,911 genes that were detected in at least 3 samples were analyzed. By SAM (significance analysis of microarrays), we identified 47 genes that discriminated young from healthy old and "AD-like" animals. These findings were confirmed by principal component analysis (PCA). ANOVA of the expression data from the three groups identified 695 genes (including the 47 genes previously identified by SAM and PCA) with significant changes of expression in old and "AD-like" in comparison to young animals. About one third of these genes showed similar changes of expression in healthy aging and in “AD-like” animals, whereas more than two thirds showed opposite changes in these two groups in comparison to young animals. Hierarchical clustering analysis of the 695 markers indicated that each group had distinct expression profiles which characterized each group, especially the "AD-like" group.  Functional categorization showed that most of the genes that were up-regulated in healthy old and down-regulated in "AD-like" animals belonged to metabolic pathways, particularly protein synthesis. These data suggest the existence of compensatory mechanisms during physiological brain aging that disappear in “AD-like” animals. These results open the way to new exploration of physiological and “AD-like” aging in primates.

overall_design: Microcebus murinus were divided in 3 groups: the first group included 6 young adults (4 females and 2 males), the second included 10 healthy old animals (7 females and 3 males) and the third one was composed by 2 "AD-like" old females. Since Microcebus murinus microarrays do not exist, we decided to use Affymetrix human genome chips (HG U133 plus 2), since studies have illustrated the feasibility of detecting non-human primate brain transcripts using human genome chips.

first: Ronza

last: ABDEL RASSOUL

first: Sabine

last: ALVES

first: Véronique

last: PANTESCO

first: John

last: DE VOS

first: Bernard

last: MICHEL

first: Martine

last: PERRET

first: Nadine

last: MESTRE-FRANCES

first: Jean-Michel

last: VERDIER


title: Calactin - a small molecule induces DNA damage and histione modification in leukemia cells

city: Hsin-Chu

first: Sophia

last: Chan

address: 75 Bo-Ai Street

department: Institute of Bioniformatics and Systems Biology

country: Taiwan

institute: National Chiao Tung University

summary: Calactin is a small molecule isolated from the Chinese herb Asclepias curassavica. We found that calactin induced DNA damage, G2/M arrest of cell cycle, and apoptosis. The calactin also increased the H2AX and Chk2 phosphorylation, which resulted in the decrease of Cdc25C and cdk1 expressions, indicating that calactin-induced G2/M arrest. Moreover, we observed that calactin-induced DNA fragmentation (DNA ladder), PARP cleavage, increase in Bad and Bax levels, and decrease in Bcl-2 and Bcl-xl expressions, which results in apoptosis. Furthermore, calactin modulates the histone modification enzymes Aurora B, SET8, MSK1, PCAF, and Gcn5, which result in H3K9, H3K18, and H3K23 acetylation, H3S10 and H3S28 phosphorylation, and H4K20 methylation. Docking results showed that calactin has a tendency to bind the active site of TOP1.

overall_design: This project includes 6 human leukemia K562 cells, 3 for treated 0.15mM calactin for 12hr and the others for control (untreated) samples.

first: Chien-Chih

last: Lee

first: Yi-Hsiung

last: Lin

first: Wen-Hsin

last: Chang

first: Ying-Ting

first: Wen-Ling

first: Yang-Chang

first: Jan-Gowth


title: Mouse embryonic and induced pluripotent stem cells can form definitive endoderm despite differences in imprinted genes

city: New York

first: steve

last: shen

address: 545 First Ave

department: Biochemistry

institute: New York University

summary: The directed differentiation of induced pluripotent stem (iPS) and embryonic stem (ES) cells into definitive endoderm (DE) would allow the derivation of otherwise inaccessible progenitors for endodermal tissues. However, a global comparison of the relative equivalency of DE derived from iPS and ES populations has not been performed. Recent reports of molecular differences between iPS and ES cells have raised uncertainty as to whether iPS cells could generate autologous endodermal lineages in vitro. Here, we have shown that both mouse iPS and parental ES cells exhibited highly similar in vitro capacity to undergo directed differentiation into DE progenitors. With few exceptions, both cell types displayed similar surges in gene expression of specific master transcriptional regulators and global transcriptomes that define the developmental milestones of DE differentiation. Microarray analysis showed considerable overlap between the genetic programs of DE derived from ES/iPS cells in vitro and authentic DE from mouse embryos in vivo. Intriguingly, iPS cells exhibited aberrant silencing of imprinted genes known to participate in endoderm differentiation, yet retained a robust ability to differentiate into DE. Our results show that, despite some molecular differences, iPS cells can be efficiently differentiated into DE precursors, reinforcing their potential for development of cell-based therapies for diseased endodermal-derived tissues.

overall_design:
Comparison of mouse ES cells, mouse iPS cells, and E8.25 Mouse embryos; in the undifferentiated state and definitive endoderm differentiated state.
ckit+/Sox2dim =definitive endoderm (day 5 of differentiation in vitro); Sox2bright =undifferentiated ES or iPS cells (day 0 of differentiation); ENDM1+/Epcam+/SSlo=foregut endoderm sorted from mouse E8.25 embryos; Epcam+/ENDM1 negative =sorted comparison population from mouse E8.25 embryos.

first: Constantina

last: Christodoulou

first: Tyler

last: Longmire

first: Steven

last: Shen

first: Alice

last: Bourdon

first: Cesar

last: Sommer

first: Paul

last: Gadue

first: Avrum

last: Spira

first: Valerie

last: Gouon-Evans

first: George

last: Murphy

first: Gustavo

last: Mostoslavsky

first: Darrell

middle: N

last: Kotton


title: Genome-wide profiling of endothelial progenitor cells in multiple myeloma

first: Olcay

last: Batuman

summary: In multiple myeloma (MM), endothelial progenitor cells (EPCs) regulate tumor angiogenesis and disease progression. EPCs from 20 newly diagnosed patients with advanced MM were examined for genomic instability by RNA microarrays to assess changes in gene expression.

overall_design: EPCs were derived from single-cell suspensions of bone marrow (BM) aspirates from newly diagnosed MM patients, and RNA was extracted for microarray hybridization.

first: Marc

last: Braunstein


title: Chromosome wide analysis of parental allele specific chromatin and DNA methylation in mouse

city: Duarte

first: Xiwei

last: Wu

type: Methylation profiling by genome tiling array

type: Genome binding/occupancy profiling by genome tiling array


title: MicroRNAs are Transported in Plasma and Delivered to Recipient Cells by High-Density Lipoproteins (HG-U133 2.0)

status: Public on Mar 24 2011

city: Bethesda

first: Kasey

last: Vickers

summary:
Circulating microRNAs (miRNA) are relatively stable in plasma and are a new class of disease biomarkers. Here we present evidence that human high-density lipoprotein (HDL) transports endogenous miRNAs and delivers them to recipient cells with functional targeting capabilities. Highly-purified fractions of human HDL contain small RNAs, and the HDL-miRNA profile from normal subjects is significantly different than familial hypercholesterolemia subjects. miRNAs were demonstrated to associate with both native and reconstituted HDL particles, and reconstituted HDL injected into mice retrieved distinct miRNA profiles from normal and atherogenic models. Cellular export of miRNAs to HDL was demonstrated to be regulated by neutral sphingomyelinase. HDL-mediated delivery of miRNAs to recipient cells was demonstrated to be scavenger receptor BI-dependent. Furthermore, HDL delivery of both exogenous and endogenous miRNAs resulted in the direct targeting of mRNA reporters. Notably, HDL-miRNA from atherosclerotic subjects induced differential gene expression, with significant loss of conserved mRNA targets in cultured hepatocytes. Collectively, these observations suggest that HDL participates in a novel mechanism of intercellular communication involving the transport and delivery of miRNAs.
Gene expression changes in human Huh7 cells with familial hypercholesterolemia HDL treatment.

overall_design: Gene expression (mRNA) profiles in human Huh7 cells treated with normal HDL (n=3) or FH HDL (n=3) in lipoprotein-depleted serum (48h).

first: Brian

middle: T

last: Palmisano

first: Bassem

middle: M

last: Shoucri

first: Robert

middle: D

last: Shamburek

first: Alan

last: Remaley


title: Topography-dependent gene expression in migratory glioma cells

status: Public on Mar 25 2011

city: Columbus

first: Mariano

middle: Sebastian

last: Viapiano

state: OH

address: 1060 Carmack Rd

department: Neurological Surgery

institute: The Ohio State University

summary:
The goal of this experiment was to compare the gene expression of glioma cells migrating on substrates of different topographies and to determine a migration-associated gene profile.
Human malignant glioma U251MG cells were cultured on highly-aligned versus randomly-oriented electrospun nanofibers of poly-caprolactone. Cells migrated actively on aligned
nanofibers but motility was very restricted on randomly-oriented fibers. Results of gene expression profiling indicated upregulation of a JAK/STAT signature in actively migrating glioma cells.

overall_design:
Total RNA was extracted from 3 independent cultures of U251 glioma cells cultured on aligned versus random nanofibers and applied to Affymetrix HG-U133 plus 2 chips.
Analysis of gene expression was used to determine a gene-signature correlated with different substrate topography

first: Sean

last: Lawler

first: Sandya

last: Liyanarachchi


title: Expression data from CH/LE Mice

status: Public on Mar 23 2011

city: Irvine

first: Jacob

last: Biesinger

address: 4058 Donald Bren Hall, University of California Irvine

department: Computer Science

institute: University of California, Irvine

summary:
We are using genome-wide ChIP-seq with isoform-specific antibodies and chromatin from select tissues of mice challenged with different dietary conditions that enrich for specific SREBPs.
We show  that hepatic SREBP-2 binds preferentially to two different gene-proximal motifs  as well as SREBP-2 directly activates autophagy genes during cell sterol depletion, conditions known to induce both autophagy and nuclear SREBP-2 levels.

overall_design: Gene expression profiling was carried out using the Mouse Gene 1.0 OST (Affymetrix) by hybridizing RNA from LE and Ch livers in triplicate at the Sanford-Burnham Genomics Core facility in Lake Nona Fl. Differential expression was then assessed using the Partek Genomics Suite (Partek Inc.) and cyberT.

first: Young-Kyo

last: Seo

first: Tae-Il

last: Jeon

first: Hansook-Kim

last: Chong

first: Xiaohui

last: Xie

first: Timothy

middle: F

last: Osborne


title: Gene expression data from WT and SREBP-1a deficient macrophages

status: Public on Mar 22 2011

city: Orlando

first: Seung-Soon

last: Im

state: FL

address: 6400 Sanger Rd.

institute: Sanford-Burnham Medical Research Institute

summary: Gene expression from bone-marrow drived macrophages of WT and SREBP-1a deficient mice

overall_design: RNAs were collected 6 different macropahges and pooled RNA for microarray

first: Leyla

last: Yousef

first: Christoph

last: Blaschitz

first: Janet

middle: Z

last: Liu

last: Edwards

first: Stephen

last: Young

first: Manuela

last: Raffatellu


title: Identification of the vascular lineage specific transcriptome using two platforms

city: Zurich

first: Jay

middle: Woo

last: Shin

state: Zurich

address: Wolfgang-Paulistrasse 10; HCI H394

department: Institute of Pharmaceutical Sciences

institute: ETH Zurich

summary:
Angiogenesis and lymphangiogenesis have important roles in cancer progression and inflammatory diseases, but it has been a challenge to evaluate theses processes quantitatively. Using two different microarray platforms, we first identified the comprehensive lineage specific transcriptomes of human lymphatic (LEC) and blood vascular (BVEC) endothelial cells. We identified 226 lymphatic signature genes and 342 signature genes for blood vascular endothelium. In silico analyses of the biologic pathways associated with these genes revealed lineage specific functions for each cell type. Using a selection of 85 identified lineage specific genes, we developed a TaqMan RT PCR based, microfluidic card formatted low density microvascular differentiation array (LD MDA) that can be used to reliably identify and quantify endothelial cells based on their lineage specific differentiation. Furthermore, using LD MDA, we were able to quantify levels of angiogenesis and lymphangiogenesis in tissue samples from patients with chronic inflammatory skin disease, indicating that this assay might be developed as a novel tool for the rapid and quantitative evaluation of pathological (lymph)angiogenesis in clinical and pre clinical studies.
Keywords: cross-platform study

overall_design: For cross comparison of the results obtained with both microarray technologies, the probes were annotated with locus link IDs and genes that were present on both platforms were aligned using the Spotfire software (Spotfire; Somerville, MA). Present calls were set by a p value cutoff of 0.05 and identified by the Affymetrix Microarray Suite Software 5.0, or by a signal to noise ratio (S/N) > 3 and quality flag < 5,000 determined by the AB1700 microarray software tool.

first: Kentaro

last: Kajiya

first: Weiniu

last: Gan

first: Peter

last: Li

first: Rainer

last: Kunstfeld

first: Michael

last: Detmar


first: Jacob

last: Biesinger

summary: Sterol regulatory element binding proteins (SREBPs) are key transcriptional regulators of lipid metabolism. To define functional differences between the three mammalian SREBPs we are using genome-wide ChIP-seq with isoform-specific antibodies and chromatin from select tissues of mice challenged with different dietary conditions that enrich for specific SREBPs. We show hepatic SREBP-2 binds preferentially to two different gene-proximal motifs. Gene ontology analyses suggests SREBP-2 targets lipid metabolic processes as expected but apoptosis and autophagy gene categories were also enriched. We show SREBP-2 directly activates autophagy genes during cell sterol depletion, conditions known to induce both autophagy and nuclear SREBP-2 levels. Additionally, SREBP-2 knockdown during nutrient depletion decreased autophagosome formation and lipid droplet association of the autophagosome targeting protein LC3. Thus, the lipid droplet could be viewed as a third source of cellular cholesterol, which along with sterol synthesis and uptake, is also regulated by SREBP-2.

overall_design: Examination of hepatic SREBP-2 binding using ChIP-Seq. One ChIP-Seq dataset and one IgG control.

first: Young-Kyo

last: Seo

last: Jeon


title: Gene Expression Profiles from PBMC are Sensitive to Short Processing Delays

city: Cincinnati

last: Barnes

address: 3333 Burnet Ave

department: Rheumatology

institute: Cincinnati Childrens Hospital Medical Center

summary:
In the analysis of peripheral blood gene expression, timely processing of samples is essential to ensure that measurements reflect in vivo biology, rather than ex vivo sample processing variables.  The effect of processing delays on global gene expression patterns in peripheral blood mononuclear cells (PBMC) was assessed by isolating and stabilizing PBMC-derived RNA from three individuals either immediately after phlebotomy or following a 4 hour delay.  RNA was labeled using NuGEN Ovation labeling and probed using the Affymetrix HG U133plus 2.0 GeneChip®.  Comparison of gene expression levels (p<0.05 and ≥ 2-fold expression change) identified 327 probe sets representing genes with increased expression and 46 indicating decreased expression after 4 hours.  The trends in expression patterns associated with delayed processing were also apparent in an independent set of 276 arrays of RNA from human PBMC samples with varying processing times.  These data indicate that the time between sample acquisition, initiation of processing, and when the RNA is stabilized should be a prime consideration when designing protocols for translational studies involving PBMC gene expression analysis.

Keywords: Technical comparison

overall_design: 3 subjects, 3 samples each.  First sample is prepared immediately, 2nd after 2 hour delay and last after a 4 hour delay.

first: M

first: A

middle: A

last: Grom

first: T

last: Griffin

first: R

last: Colbert

first: S

last: Thompson


title: Genome-wide Localization of SREBP-2 in Hepatic Chromatin Predicts a Novel Role in Autophagy

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

overall_design: Refer to individual Series


title: Hierarchical synergy of Pten, p53 and Rb pathways in high-grade astrocytoma induced in adult brain

city: Memphis

first: Chunxu

last: Qu

state: TN

address: 262 Danny Thomas Pl

department: Pathology

institute: St Jude Children's Research Institute

summary: Mutations in the PTEN, TP53 and RB1 pathways are obligate events in the pathogenesis of human glioblastomas, the highest grade of astrocytoma. To investigate synergy between these tumor suppressors in mice, we induced various combinations of compound deletions conditionally in astrocytes and neural precursors in the mature brain.  The resulting highly penetrant astrocytomas showed a spectrum of histopathological variation reminiscent of human tumors, and ranged from grade III to grade IV (glioblastoma). Secondary somatic mutations varied depending on the combination of initiating deletions and were relevant to human disease. Receptor tyrosine kinase amplifications were frequent in tumors initiated by combined conditional deletion of Pten and Tp53, but not when Rb, Pten and Tp53 were simultaneously deleted. Multiple mutations within PI3K and Rb pathways were acquired, however, Mapk activation was not consistently detected in astrocytomas.  Gene expression profiling revealed striking similarities to previously described human astrocytoma subclasses.  A subset of astrocytomas initiated outside of proliferative niches in the adult brain.

overall_design: Gene expression of 8 human brain samples including 2 normal brainstem and 6 brainstem low-grade gliomas were profiled using HG-U133 plus 2 arrays.  Gene expression of 38 mouse tumor samples, including 24 Pten;p53 double knockout and 14 Pten;p53;Rb1 triple knockout, were profiled using Affymetrix Mouse Genome 430 v2 arrays.  Copy number changes of 51 double knockout tumor samples were analysed using Roswell Park Cancer Institute 6.5k BAC arrays.  Copy number changes of 21 triple knockout tumor samples were analysed using Agilent mouse genome CGH mocirarray 244A.

first: Lionel

last: Chow

first: Raelene

last: Endersby

first: Xiaoyan

last: Zhu

first: Sherri

last: Rankin

first: Junyuan

last: Zhang

first: David

last: Ellison

first: Suzanne

middle: J

last: Baker


title: Mapping and analysis of chromatin state dynamics in nine human cell types (gene expression)

city: Los Angeles

first: Jason

last: Ernst

address: 615 Charles E Young Dr South

department: Biological Chemistry

institute: UCLA

summary: Chromatin profiling has emerged as a powerful means for annotating genomic elements and detecting regulatory activity. Here we generate and analyze a compendium of epigenomic maps for nine chromatin marks across nine cell types, in order to systematically characterize cis-regulatory elements, their cell type-specificities, and their functional interactions. We first identify recurrent combinations of histone modifications and use them to annotate diverse regulatory elements including promoters, enhancers, transcripts and insulators in each cell type. We next characterize the dynamics of these elements, revealing meaningful patterns of activity for promoter states and exquisite cell type-selectivity for enhancer states. We define multi-cell activity profiles that reflect the patterns of enhancer state activity across cell types, as well as analogous profiles for gene expression, regulatory motif enrichments, and expression of the corresponding regulators. We use correlations between these profiles to link enhancers to putative target genes, to infer cell type-specific activators and repressors, and to predict and validate functional regulator binding motifs in specific chromatin states. These functional annotations and regulatory predictions enable us to revisit intergenic single-nucleotide polymorphisms (SNPs) associated with human disease in genome-wide association studies (GWAS). We find that for several diseases, top-scoring SNPs are precisely positioned within enhancer elements specifically active in relevant cell types. In several cases a disease variant affects a motif instance for one of the predicted causal regulators, thus providing a potential mechanistic explanation for the disease association. Our study presents a general framework for applying multi-cell chromatin state analysis to decipher cis-regulatory connections and their role in health and disease.

overall_design: 9 human cell types were cultured in duplicate and subject to Affymetrix profiling

first: Pouya

last: Kheradpour

first: Tarjei

middle: S

last: Mikkelsen

first: Noam

last: Shoresh

first: Lucas

last: Ward

first: Charles

last: Epstein

first: Xiaolan

first: Li

last: Wang

first: Robbyn

last: Issner

last: Coyne

first: Manching

last: Ku

first: Timothy

last: Durham

first: Manolis

last: Kellis

first: Bradley

middle: E

last: Bernstein


title: Expression data from HAART interruption in HIV patients

status: Public on Mar 26 2011

city: Davis

first: Michael

last: George

address: 451 Health Sciences Drive

department: Medical Microbiology and Immunology

institute: University of California, Davis

summary: We evaluated longitudinal changes in viral replication and emergence of viral variants in the context of T cell homeostasis and gene expression in GALT of three HIV-positive patients who initiated HAART during primary HIV infection but opted to interrupt therapy thereafter. Longitudinal viral sequence analysis revealed that a stable proviral reservoir was established in GALT during primary HIV infection that persisted through early HAART and post-therapy interruption. Proviral variants in GALT and peripheral blood mononuclear cells (PBMCs) displayed low levels of genomic diversity at all times. A rapid increase in viral loads with a modest decline of CD4  T cells in peripheral blood was observed, while gut mucosal CD4 T cell loss was severe following HAART interruption. This was accompanied by increased mucosal gene expression regulating interferon (IFN)-mediated antiviral responses and immune activation, a profile similar to those found in HAART-naive HIV-infected patients.

overall_design: Gut mucosal responses to HAART interruption were evaluated with Affymetrix arrays


title: Gene expression profiles of interstitial lung disease (ILD) patients

city: Seattle

first: Ji-Hoon

last: Cho

state: WA

address: 401 Terry Avenue North

institute: Institute for Systems Biology

summary:
The mechanisms and molecular pathways underlying interstitial lung diseases (ILDs) are poorly understood. Systems biology approaches were used to identify perturbed networks in these disease states to gain a better understanding of the underlying mechanisms of disease. Through profiling genes and miRNAs, we found subsets of genes and miRNAs that distinguish different disease stages, ILDs from controls, and idiopathic pulmonary fibrosis (IPF) from non-specific interstitial pneumonitis (NSIP).  Traditional pathway analysis revealed several disease-associated modules involving genes from the TGF-beta, Wnt, focal adhesion and smooth muscle actin pathways that may be involved in advancing fibrosis.
A comprehensively integrative approach was used to construct a global gene regulatory network based on the perturbation of key regulatory elements, transcriptional factors and miRNAs.  The data also demonstrated that several subnetworks were significantly associated with key molecules involved in the diseases.  We present a broad overview of the disease at a molecular level and discuss several possibly key regulatory molecular circuits that could play central roles in facilitating the progression of ILDs.

overall_design: Lung tissue samples from 23 patients with IPF or related disorders were obtained from the Lung Tissue Research Consortium (www.ltrcpublic.org). 11 samples came from patients who had been diagnosed with usual interstitial pneumonia/ idiopathic pulmonary fibrosis (UIP/IPF), 5 samples came from patients with non-specific interstitial pneumonia (NSIP),  the remaining from patients with uncharacterized fibrosis and from patients with other ILD variants. B. Biopsies from uninvolved lung tissue from lung cancer patients (5 samples) and from one lung transplant patient were used as controls for comparison with the ILD samples.

first: Richard

last: Gelinas

first: Kai

first: Alton

last: Etheridge

first: Melissa

last: Piper

first: Kara

last: Batte

first: Riscili

last: Brent

first: Jennifer

last: Price

first: Dan

last: Bornman

first: Shile

last: Zhang

first: Clay

last: Marsh

last: Galas


title: PU.1 and C/EBPalpha synergistically program distinct response to NF-kappaB activation through establishing monocyte specific enhancers (expression data)

status: Public on Mar 15 2011

city: Cleveland

first: Fulai

last: Jin

state: OH - OHIO

address: 10900 Euclid Avenue

institute: Case Western Reserve University

summary: Unraveling the complexity of transcriptional programs coded by different cell types has been one of the central goals of cell biology. Using genome-wide location analysis, we examined how two different cell types generate different responses to the NF-kappaB signaling pathway. We showed that, after tumor necrosis factor-alpha (TNF-alpha) treatment, NF-kappaB p65 subunit binds to distinct genome locations and subsequently induces different subsets of genes in human monocytic THP-1 cells versus HeLa cells . Interestingly, the differential p65 binding in two cell types correlates with pre-existing cell-type specific enhancers prior to TNF-alpha stimulation, marked by histone modifications. We also found that two transcription factors, PU.1 and C/EBPalpha, appear to synergistically mediate enhancer creation and affect NF-kappaB target selection in THP-1 cells. In HeLa cells, co-expression of PU.1 and C/EBPalpha conferred TNF-alpha responsiveness to a subset of THP-1 specific NF-kappaB target genes. These results suggest that the diversity of transcriptional programs in mammalian cells arises, at least in part, from pre-existing enhancers that are established by cell specific transcription factors.

overall_design: We used Affymetrix microarray (GPL570) to obtain gene expression data for THP1 and HeLa cells before and after TNF-alpha treatment.

first: Yan

last: Li

first: Rama

last: Natarajan

first: Bing

last: Ren


title: Expression data of human eGFP-SOX17+ endoderm cells

city: Stanford

first: Pei

last: Wang

address: 279 Campus Dr.

department: Dev. Bio.

institute: Stanford University

summary:
Using homologous recombination in human ESC, we inserted an enhanced green fluorescent protein (eGFP) transgene into a locus encoding a postulated marker of human endoderm, SOX17 in H9 human embryonic stem cells.
This allowed purification of SOX17+ hESC endodermal progeny by fluorescence activated cell sorting (FACS) to generate microarray gene expression profile.

overall_design: Using Wnt3 and Activin to differentiate hSOX17-2 to stage 1 cells, and subsequently FGF10 and cyclopamine to stage 2 cells,  we isolated eGFP+ cells by FACS at each stage, performed microarray analysis.

first: Kim

last: Seung


title: PU.1 and C/EBPalpha synergistically program distinct response to NF-kappaB activation through establishing monocyte-specific enhancers


title: Gene expression in mouse liver depleted of HDAC3

status: Public on Mar 11 2011

city: Buffalo

first: Tao

last: Liu

address: Elm and Carlton St

department: Biostatistics and Bioinformatics

institute: Roswell Park Comprehensive Cancer Institute

summary:
Liver-specific depletion of HDAC3 leads to liver steatosis (fatty liver), suggesting disregulation of lipid metabolism. This is correlated with changes in lipid metabolic gene expression.
Livers depleted of HDAC3 were removed from 12 week old male HDAC3 fl/fl mice (loxP sites flanking exon 4 to 7 of the HDAC3 gene encoding the catalytic domain of HDAC3) one week after the injection of AAV2/8-Tbg-Cre virus. Livers from the HDAC3 fl/fl mice injected with AAV2/8-Tbg-GFP were used as normal controls.

overall_design: mRNA was extracted from 100mg mouse liver samples and hybridized to Affymetrix microarrays. For each group (HDAC3 depleted liver and normal liver), we have 5 samples from different mice.

first: Zheng

last: Sun

last: Feng

first: Mitchell

last: Lazar


title: Gene expression profiling of human gliomas and human glioblastoma cell lines

status: Public on Mar 18 2011

city: Basel

first: Michal

last: Grzmil

address: Maulbeerstrasse 66

department: Growth control

institute: Friedrich Miescher Institute for Biomedical Research

summary:
To identify signaling pathways that are differentially regulated in human gliomas, a microarray analysis on 30 brain tumor samples (12 primary glioblastomas (GBM), 3 secondary glioblastomas (GBM-2), 8 astrocytomas (Astro) and 7 oligodendrogliomas (Oligo)) and on  5 glioblastoma cell lines (LN018, LN215, LN229, LN319 and BS149) was performed. Normal brain tissue (NB) and normal human astrocytes (NHA) were used as a control. Kinase expression in each tumor was compared to expression in normal brain and expression values from normal human astrocytes were used as an additional control.

Keywords: Kinase expression in each tumor was compared to expression in normal brain and expression values from normal human astrocytes were used as an additional control.

overall_design: Frozen tissue samples of human gliomas and normal brain obtained from the operating room were processed according to the guidelines of the Ethical Committee of the University Hospitals of Basel. Human brain tumor cell lines were derived from human patients. The BS149 cell line was generated at the University of Basel, Switzerland while the “LN” series were a kind gift of Erwin van Meir in Lausanne, Switzerland. Normal human astrocytes (NHAs) were purchased by Cambrex (Walkersville, MD) and cultured according to manufacturer’s recommendations.

first: Pier

last: Morin

first: Edward

last: Oakeley

first: Brian

last: Hemmings

first: Adrian

last: Merlo

first: Maria

last: Lino


title: Epiphyseal cartilage

city: Setagaya-ku

first: Akihiro

last: Umezawa

state: Tokyo

department: Center for Regenerative Medicine

country: Japan

institute: National Center for Child Health and Development

summary:
Chondrocytes from extra fingers exhibited a high proliferative capacity: the cells reached to population doublings (PD) 30-35 within 4 weeks before replicative senescence. The propagated cells formed hyaline cartilage at 2 weeks after subcutaneous implantation of NOD/Scid/IL-2 receptor gamma knock out (NOG) mice, and the generated cartilage showed enchondral ossification at 8 to 12 weeks. The cartilage formation with osteogenesis depends on the number of cell division in vitro.

Keywords: NCCH BioResource

overall_design: Affymetrix human U133 plus 2.0 array was used to transcriptionally profile to determine the expression changes in epiphyseal cartilage.

first: A

first: M

last: Nasu


title: An RNAi Screen Identifies TRRAP as a Regulator of Brain Tumor-Initiating Cell Differentiation

status: Public on Mar 14 2011

city: San Diego

first: John

middle: R

last: Walker

address: 10675 John Jay Hopkins

institute: Genomics Institute of the Novartis Research Foundation

summary:
Glioblastoma multiforme is the most common and most aggressive type of primary brain tumor. The brain-infiltrative character of glioblastoma makes complete surgical removal of the tumor impossible and neither radiation nor current chemotherapy provide cure. Recent evidence shows that glioblastoma multiforme consists of heterogeneous cell populations which differ in tumor-forming potential. Enriched tumor-initiating capacity has been linked to poorly differentiated glioblastoma cells sharing features with neural stem cells. Thus, these cells are important targets for new therapeutic strategies.
We aim to identify novel targets controlling maintenance and differentiation in glioblastoma-initiating cells through high throughput screening. To this end, we utilized libraries of small chemical compounds and small interference RNAs in combination with automated imaging and data analysis. Patient-derived glioblastoma cells were expanded and characterized using neural stem cell conditions. In culture, the cells showed low differentiation but expression of neural stem cell markers such as Nestin and Sox2. Upon intracranial injection into SCID mice these cells gave rise to tumors displaying the hallmarks of the human disease.
Differentiation of glioblastoma-initiating cells (for example elicited through bone morphogenetic protein, BMP) was associated with strong morphological changes. Hence, cellular morphology, as well as markers specific for differentiation or death were used as screen readout. Lentiviral RNA interference-based screening yielded several gene knockdowns leading to ‘forced’ differentiation of glioblastoma-initiating cells. For example, knockdown of TRRAP (transformation/transcription domain associated protein) led to strongly increased differentiation and loss of proliferative and self-renewing capacity in these cells. TRRAP is an adapter protein implicated in oncogenic transformation through c-MYC transcription activation, also participating in chromatin remodeling and DNA repair. Glioblastoma-initiating cells with reduced TRRAP displayed increased apoptosis upon treatment with the genotoxic agent temozolomide. In vivo, Trapp knockdown cells were not able to give rise to glioblastoma upon transplantation into the brain of SCID mice. Together, these findings support a crucial role for TRRAP in maintenance and tumorigenicity of glioblastoma-initiating cells and might offer future therapeutic options.

overall_design: Two treatments compared to control: two different shRNA sequences for TRRAP were compared to a control shRNA sequence in their effects on global transcription in brain tumor initiating cells

first: Heiko

last: Wurdak

first: Angelica

last: Romero

first: Shoutian

last: Zhu

first: Mihaela

last: Lorger

first: James

last: Watson

first: Chih-yuan

last: Chiang

first: Jay

last: Zhang

first: Vanita

last: Natu

first: Buu

middle: P

last: Tu

first: Griffith

last: Harsh

first: Hannes

last: Vogel

first: Brunhilde

last: Felding-Habermann

first: Anthony

last: Orth

first: Loren

last: Miraglia

first: Daniel

last: Rines

first: Stephen

middle: L

last: Skirboll

first: Peter

last: Schultz


title: Gene expression analysis of HepG2 cells by NOTUM RNAi

city: Kyoto

first: Akira

last: Watanabe

state: Kyoto

address: Rm504, Miyako Bldg, 233, Isa-cho, kamigyo-ku

institute: CyberomiX Inc

summary:
We identified human NOTUM, a new member of beta-catenin target gene. The aim of this analysis is to examine downstream genes of NOTUM.
Keywords: Gene expression analysis in response to RNA interference

overall_design: HepG2 cells with RNAi duplexed were used. One control (control-low GC) and 2 RNAi duplexes (NOTUM RNAi#1 and #2) for NOTUM silencing were added to HepG2 cells, and total RNAs were isolated at 72 hours after transfection.

first: Saori

last: Kawanabe

first: Hiroko

last: Meguro

first: Hiroyuki

last: Aburatani


title: MiR-30b/30d regulation of GalNAc transferases enhances invasion and immunosuppression during metastasis

status: Public on Mar 08 2011

city: LYON

first: Jiri

last: ZAVADIL

state: Other

address: 150 COURS ALBERT THOMAS

institute: IARC WHO

summary:
To metastasize, a tumor cell must acquire abilities such as the capacity to colonize new tissue and evade immune surveillance. Recent evidence suggests that microRNAs can promote the evolution of malignant behaviors by regulating multiple targets simultaneously. We performed a microRNA analysis of human melanoma, an aggressively invasive cancer, and found that miR-30b/30d upregulation correlates with stage, metastatic potential of primary tumors, shorter time to recurrence and reduced overall survival. Ectopic expression of miR-30b/30d promoted the metastatic behavior of melanoma cells by directly targeting the GalNAc transferase GALNT7, resulted in increased synthesis of the immunosuppressive cytokine IL-10, and reduced immune cell activation and recruitment. These data point to a key role of miR-30b/30d and GalNAc transferases in metastasis, by simultaneously promoting cellular invasion and immune suppression.
MicroRNAs are emerging as key contributors to tumor metastasis because of their ability to regulate multiple targets, and thereby alter several functions, simultaneously. We found a miRNA cluster that promotes metastasis by concurrently enhancing invasive capabilities of melanoma cells and suppressing immune surveillance mechanisms, allowing the tumor cells to migrate and invade foreign tissue. Both these effects of miR-30b/30d are mediated by direct suppression of GalNAc transferases. Aberrant glycosylation has previously been connected to tumor progression, but the underlying molecular mechanisms and their impact on specific cellular pathways are poorly understood. Our work places the control of glycosylation as a novel molecular link between tumor cell migration and immune evasion, two processes that act synergistically during metastasis.

overall_design:
2 different melanoma cell line, 2 biological duplicates for each cell line
Differentially expressed genes (mRNAs) in response to miRNA over-expression

first: Avital

last: Gaziel-Sovran

first: Miguel

last: Segura

first: Raffaella

last: Di Micco

first: Mary

middle: K

last: Collins

first: Douglas

last: Hanniford

first: Eleazar

last: Vega-Saenz de Miera

first: John

last: Rakus

last: Dankert

first: Shulian

last: Shang

first: Robert

last: Kerbel

first: Nina

last: Bhardwaj

first: Yongzhao

last: Shao

first: Farbod

last: Darvishian

last: Zavadil

first: Adrian

last: Erlebacher

first: Lara

last: Mahal

first: Iman

last: Osman

first: Eva

last: Hernando


title: Gene expression of expanded and non-expanded natural killer cells from healthy donor and myeloma patients

city: Little Rock

first: Tarun

middle: Kumar

last: Garg

state: AR

address: 4301 W Markham St

department: Myeloma Institute for Research and Therapy

institute: University of Arkansas for Medical Sciences

summary:
Natural Killer cells (NK), a major constituent of innate immune system, have the ability to kill the transformed and infected cells without prior sensitization; can be put to immunotherapeutic use against various malignancies. NK cells discriminate between normal cells and transformed cells via a balance of inhibitory and activating signals induced by interactions between NK cell receptors and target cell ligands. Present study investigates whether expansion of NK cells could augment their anti-myeloma (MM) activity.  For NK cell expansion, peripheral blood mononuclear cells from healthy donors and myeloma patients were co-cultured with irradiated K562 cells transfected with 4-1BBL and membrane-bound IL15 (K562-mb15-41BBL). A genome-wide profiling approach was performed to identify gene expression signature in expanded NK (ENK) cells and non-expanded NK cells isolated from healthy donors and myeloma patients. A specific set of genes involved in proliferation, migration, adhesion, cytotoxicity, and activation were up regulated post expansion, also confirmed by flow cytometry. Exp-NK cells killed both allogeneic and autologous primary MM cells more avidly than non-exp-NK cells in vitro. Multiple receptors, particularly NKG2D, natural cytotoxicity receptors, and DNAM-1 contributed to target lysis, via a perforin mediated mechanism. In summary, vigorous expansion and high anti-MM activity both in vitro and in vivo provide the rationale for testing exp-NK cells in a clinical trial for high risk MM.
Differential gene expression profile in expanded natural killer (ENK) cells and non-expanded natural killer (NK) cells from healthy donors and myeloma patients

overall_design: Eight healthy donor and eight myeloma patients were used in the study. Non-expanded natural killer (NK) cells were isolated from PBMCs of healthy donors and myeloma patients. Expanded natural killer (ENK) cells were generated from same set of samples as mentioned in expansion protocol. All ENK and NK cells were used for gene expression profiling.

first: Susann

last: Szmania

first: Junaid

last: Khan

last: Shaughnessy Jr.

first: Joshua

last: Epstein

first: Bart

last: Barlogie

first: Frits

last: vanRhee


title: Genes Express in Catalase Overexpression MAECs

city: Nashville

first: Xinghua

last: Lin

state: Tennessee

address: 1005 D. B. Todd Jr. Blvd

department: Physiology

institute: Meharry Medical College

summary: Study the global genes expression in mouse aorta endothelial cells (MAECs) overexpressing human catalase (hcatTg).

overall_design: The wild type and overexpressing human catalase (hcatTg) MAECs grown to 80% confluence in six-well plates were made quiescent in serum-free DMEM for 12 h and then cultured in 10% FBS DMEM for 12 h.  Total RNA was extracted with Trizol® reagent and purified by Rneasy Mini kit. Two independent wild type and two hcatTg total RNA samples were performed microarray with GeneChip® Mouse gene 1.0 ST array (Affymetrix, USA).


title: Transcriptome of the maturing erythroblast

status: Public on Mar 02 2011

city: Oxford

first: Alison

last: Merryweather-Clarke

address: John Radcliffe Hospital, Headley Way, Headington

institute: NHSBT Oxford

summary: Understanding the pattern of gene expression and identifying the specific genes expressed during erythropoiesis is crucial for a synthesis of erythroid developmental biology. Here we have isolated four distinct populations of erythroblasts at successive erythropoietin-dependent stages of erythropoiesis including the terminal, pyknotic stage. The transcriptome has been determined using Affymetrix arrays. First, we show that cells sorted by surface expression profile express not only significantly fewer genes than unsorted cells, but also significantly more differences in the expression levels of particular genes between stages than unsorted cells, demonstrating the importance of working with defined cell populations to identify lineage and temporally-specific patterns of gene expression. Second, using standard software and matched filtering we identify eleven differentially regulated genes and one continuously expressed gene previously undetected in erythroid expression studies with unknown roles in erythropoiesis (CA3, CALB1, CTSL2, FKBP1B, GSDMB, ITLN1, LIN7B, RRAD, RUNDC3A, UNQ1887, ZNF805, MYL12B). Finally, using transcription factor binding site analysis we identify potential transcription factors that may regulate gene expression during terminal erythropoiesis. Our stringent lists of differentially regulated and continuously expressed transcripts are a resource for functional studies of erythropoietic protein function and gene regulation.

overall_design: PBMC-derived erythroblasts grown in vitro were harvested at the CFU-E, Pro-E, Int-E and Late-E stages and FACS sorted based on expression of cell surface markers. RNA was extracted from those populations which met rigorous specifications of time cultured in the presence of erythropoietin, morphology and CD36, CD71 and CD235a expression. For each stage, 3 chips were hybridised, each representing a pool of 4 different samples. In addition to these 12 chips, one chip representing a pool of RNA extracted from unsorted cells at each stages was also hybridised.

first: Ann

last: Atzberger

first: Shamit

last: Soneji

first: Nicki

last: Gray

first: Kevin

last: Clark

first: Craig

last: Waugh

first: Simon

last: McGowan

first: Stephen

last: Taylor

first: Asoke

last: Nandi

first: William

middle: G

last: Wood

first: David

last: Roberts

first: Douglas

last: Higgs

first: Veronica

last: Buckle

first: Kathryn

last: Robson


title: Recapitulation of human premature aging by using iPSCs from Hutchinson-Gilford progeria syndrome

city: Barcelona

first: Stephanie

last: Boue

address: Dr Aiguader 88

country: Spain

institute: CMRB

summary: Hutchinson-Gilford progeria syndrome (HGPS) is a rare and fatal human premature aging disease1-5, characterized by premature atherosclerosis and degeneration of vascular smooth muscle cells (SMCs)6-8. HGPS is caused by a single-point mutation in the LMNA gene, resulting in the generation of progerin, a truncated mutant of lamin A. Accumulation of progerin leads to various aging-associated nuclear defects including disorganization of nuclear lamina and loss of heterochromatin9-12. Here, we report the generation of induced pluripotent stem cells (iPSCs) from fibroblasts obtained from patients with HGPS. HGPS-iPSCs show absence of progerin, and more importantly, lack the nuclear envelope and epigenetic alterations normally associated with premature aging. Upon differentiation of HGPS-iPSCs, progerin and its associated aging consequences are restored. In particular, directed differentiation of HGPS-iPSCs to SMCs leads to the appearance of premature senescent SMC phenotypes associated with vascular aging. Additionally, our studies identify DNA-dependent protein kinase catalytic subunit (DNAPKcs) as a component of the progerin-containing protein complex. The absence of nuclear DNAPKcs correlates with premature as well as physiological aging. Since progerin also accumulates during physiological aging6,12,13, our results provide an in vitro iPSC-based model with an acceleration progerin accumulation to study the pathogenesis of human premature and physiological vascular aging.

overall_design:
Microarray gene expression profiling was done to:
(1) Compare differences between WT fibroblasts and fibroblasts from patients suffering of the Hutchinson-Gilford progeria syndrome
(2) Check that iPSC originating from WT and patients are in fact similar to ESC

first: Guang-Hui

last: Liu

first: Basam

last: Barkho

first: Sergio

last: Ruiz

first: Dinh

last: Diep

first: Sheng-Lian

last: Yang

first: Jing

last: Qu

first: Leo

last: Kurian

first: Christopher

last: Walsh

first: Athanasia

last: Panopoulos

first: James

last: Thompson

first: Ho-Lim

last: Fung

first: Kun

last: Zhang

first: John

last: Yates III

first: Juan-Carlos

last: Izpisua-Belmonte


title: Expression data from human PBMCs from breast cancer patients and controls

status: Public on Mar 01 2011

city: Durham

first: Erich

last: Huang

state: NC

address: 101 Science Drive

department: Institute for Genome Sciences and Policy

institute: Duke University

summary: We analyzed gene expression in human peripheral blood mononuclear cells (PBMCs) from breast cancer patients, patients with benign breast abnormalities, healthy cancer-free individuals as well as patients with other types of cancer (gastrointestinal and brain cancers).

overall_design: Peripheral blood mononuclear cell (PBMC) samples were collected from women with a suspect initial mammogram prior to undergoing a diagnostic biopsy procedure to determine whether the detected abnormality was benign or malignant. In total, we collected blood from 57 women with a diagnosis of breast cancer and 37 with a benign diagnosis. We also collected blood from 31 women with normal initial mammograms as negative controls and 15 breast cancer patients following surgery. All breast cancer patient samples were collected at the Duke University Medical Center (DUMC) under an institutional review board (IRB)-approved protocol (Duke eIRB#12025) after obtaining informed consent and were provided by Dr. Jeffrey Marks. PBMC samples from patients with various gastrointestinal cancers (n=15) were colelcted and stored at DUMC under IRB-approved protocols (Duke eIRB#12010 and 12025) and were provided by Dr. Jeffrey Marks. Peripheral blood leukocyte samples from patients with brain tumors (n=7) were provided by Dr. John Sampson and were collected by leukapheresis under Duke eIRB#00003877 and #00009403.

first: Heather

last: LaBreche

first: Joseph

last: Nevins


title: Epigenetic Regulation of IL17RC in Age-related Macular Degeneration

city: Bethesda

first: Lai

last: Wei

state: MD

address: 10 Center Dr. Room 2B47

institute: NIH/NEI/NCCAM

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

overall_design: Refer to individual Series


title: Integrating Factor Analysis and a Transgenic Mouse Model to Reveal a Peripheral Blood Predictor of Breast Tumors


title: Expression data of embryonic stem (ES) cells from both control and Prmt6 overexpressed population

status: Public on Mar 04 2011

city: Singapore

first: Qiang

last: Wu

address: 8 Medical Drive

institute: National University of Singapore

summary:
ES cells are able to self-renew and remain pluripotent. These characteristics are maintained by both genetic and epigenetic regulators. Protein arginine methyltransferase (PRMT) 4 and 5 are shown to be important in early embryonic development and in ES cells. PRMT6-mediated di-methylation of histone H3 at arginine 2 (H3R2me2) can antagonize the tri-methylation of histone H3 at lysine 4, which marks active genes. However, it is unclear whether PRMT6 and PRMT6-mediated H3R2me2 play crucial roles in early embryonic development and ES cell identity. In this study, we investigate their functions using mouse ES cells as the model.
We used microarray (Affymetrix GeneChip Mouse Gene 1.0ST) to examine the global change of gene expression in mouse ES cells when Prmt6 was overexpressed and identified distinct classes of genes that are up-regulated and down-regulated during this process.

overall_design: Mouse ES cells were transfected with either pCAGIP.puro empty vector (control) or Prmt6 overexpressing plasmid (P+6 OE). After 3 days of selection by puromycin, cells from both populations were subjected to RNA extraction and hybridization on Affymetrix microarrays.

first: Yun-Hwa

last: Lee

first: Tuan-Zea

last: Tan

first: Mori

last: Seiichi


title: The Anterior Gradient Homolog 3 (AGR3) Gene Is Associated with Differentiation and Survival in Ovarian Cancer

city: Houston

first: Kwong-Kwok

last: Wong

state: TX

address: T4-3900, 1515 Holcombe Boulevard

department: Gynecologic Oncology and Reproductive Medicine

institute: UT M. D. Anderson Cancer Center

summary: Low-grade serous ovarian carcinoma is believed to arise from serous borderline ovarian tumors, yet the progression from serous borderline tumors to low-grade serous ovarian carcinoma remains poorly understood. The purpose of this study was to identify differentially expressed genes between the two groups. Expression profiles were generated from 6 human ovarian surface epithelia (HOSE), 8 serous borderline ovarian tumors (SBOT), 13 low-grade serous ovarian carcinomas (LG), and 22 high-grade serous ovarian carcinomas (HG). The anterior gradient homolog 3 (AGR3) gene was found to be highly upregulated in serous borderline ovarian tumors; this finding was validated by real-time quantitative RT-PCR, Western blotting, and immunohistochemistry. Anti-AGR3 immunohistochemistry was performed on an additional 56 LG and 103 HG tissues and the results were correlated with clinical data.  Expression profiling determined that 1254 genes were differentially expressed (P < 0.005) between SBOT, LG and HG tumors. Serous borderline ovarian tumors exhibited robust positive staining for AGR3, with a lower percentage of tumor cells stained in LG and HG. Immunofluorescence staining indicated that AGR3 expression was limited to ciliated cells. Tumor samples with a high percentage (>10%) of AGR3 positively stained tumor cells were associated with improved longer median survival in both the LG (P = 0.013) and HG (P = 0.008) serous ovarian carcinoma groups. The progression of serous borderline ovarian tumors to low-grade serous ovarian carcinoma may involve the de-differentiation of ciliated cells. AGR3 could serve as a prognostic marker for survival in patients with low-grade and high-grade serous ovarian carcinomas.

overall_design: Total RNA were extracted from microdissected human ovarian surface epithelia (HOSE, n=6), and microdissected serous borderline ovarian tumors (LMP, n=8), low-grade serous ovarian carcinomas (LGOSC, n=13), and 22 high-grade serous ovarian carcinomas (HGOSC, n=22). Gene Expression profiles were then generated with commercial GeneChip Human Genome U133 Plus 2.0 Array. dChip was used to identify significant differentially expressed genes between LMP/LGOSC and HGOSC


title: Increased SRF Transcriptional Activity is a Novel Signature of Insulin Resistance in Humans and Mice

city: Boston

first: Mary Elizabeth

last: Patti

state: MA

address: 1 Joslin Place

department: Research Division

institute: Joslin Diabetes Center

summary: Insulin resistance in skeletal muscle is a key phenotype associated with type 2 diabetes (T2D) and is even present in offspring of diabetic parents. However, molecular mediators of insulin resistance remain unclear. We find that the top-ranking gene set in expression analysis of muscle from humans with T2D and normoglycemic insulin resistant subjects with parental family history (FH+) of T2D is increased expression of actin cytoskeleton genes regulated by serum response factor (SRF) and its coactivator MKL1. Furthermore, the SRF activator STARS is upregulated in FH+ and T2D and inversely correlated with insulin sensitivity. These patterns are recapitulated in insulin resistant mice, and linked to alterations in two other regulators of this pathway: reduced G-actin and increased nuclear localization of MKL1. Both genetic and pharmacologic manipulation of STARS/MKL1/SRF pathway significantly alter insulin action: 1) Overexpression of MKL1 or reduction in G-actin decreased insulin-stimulated Akt phosphorylation; 2) reduced STARS expression increased insulin signalling and glucose uptake, and 3) SRF inhibition by CCG-1423 reduced nuclear MKL1, improved glucose uptake, and improved glucose tolerance in insulin resistant mice in vivo. Thus, SRF pathway alterations are a signature of insulin resistance which may also contribute to T2D pathogenesis and be a novel therapeutic target.

overall_design: Skeletal muscle samples were obtained from 10 subjects with type 2 diabetes, 25 subjects with a family history of type 2 diabetes (one or both parents), and 15 subjects with no family history of type 2 diabetes. In this analysis RNA was isolated for cRNA preparation and hybridized to Affymetrix Human Genome U133 Plus 2.0 microarrays.

first: MaryElizabeth

first: Wanzhu

last: Jin

first: Allison

last: Goldfine

first: Tanner

last: Boes

first: Robert

last: Henry

first: Theodore

last: Ciaraldi

first: Eun-Young

last: Kim

first: Merve

last: Emecan

first: Connor

last: Fitzpatrick

first: Anish

last: Sen

first: Ankit

last: Shah

first: Edward

last: Mun

first: Martha

last: Vokes

first: Joshua

last: Schroeder

first: Elizabeth

last: Tatro

first: Josep

last: Jiminez-Chillaron


title: HAV acute infection in chimpanzees

status: Public on Mar 09 2011

city: San Antonio

first: Bernadette

last: Guerra

state: Texas

department: Virology and Immunology

institute: Southwest Foundation for Biomedical Research

summary: Hepatitis A virus (HAV) is a hepatotropic human picornavirus that has been associated only with acute infection. Its pathogenesis is not well understood since there have been few recent studies in animal models using modern methodologies. We characterized HAV infections in three chimpanzees, quantifying viral RNA by qRT-PCR and examining critical aspects of the innate immune response including intrahepatic interferon-stimulated gene expression. We compared these infection profiles with similar studies of chimpanzees infected with hepatitis C virus (HCV), a hepatotropic flavivirus that frequently causes persistent infection. Surprisingly, HAV-infected animals exhibited very limited induction of type I interferon-stimulated genes in the liver compared to chimpanzees with acute resolving HCV infection, despite similar levels of viremia and 100-fold greater quantities of viral RNA in the liver. Minimal ISG15 and IFIT1 responses peaked 1-2 weeks after HAV challenge, then subsided despite continuing high hepatic viral loads. An acute inflammatory response at 3-4 weeks correlated with the appearance of virus-specific antibodies, and both apoptosis and proliferation of hepatocytes. Despite this, HAV RNA persisted in the liver for months, remaining present long after its clearance from serum and feces and revealing dramatic differences in the kinetics of clearance in the three compartments. Viral RNA was detected in the liver for significantly longer (35 to >48 weeks) than HCV RNA in animals with acute resolving HCV infection (10-20 weeks). Collectively, these findings suggest that early HAV infection is far stealthier than HCV infection and represents a distinctly different paradigm in viral-host interactions within the liver.

overall_design: Chimpanzee liver was biopsied during an acute HAV infection. Chimp 1 and 2 had two baseline samples. Chimp 3 used the baselines from chimps 1 and 2. Chimp 1 had 8 samples during the HAV acute infection. Chimp 2 had 9 samples during the HAV acute infection. Chimp 3 had 4 samples during the HAV acute infection.

last: Lanford


title: Microarray analysis of differentiation of human glioblastoma stem cells

city: Pamplona

first: Victor

last: Segura

state: Navarra

address: Avda. Pío XII, 55

department: Unit of Proteomics, Genomics and Bioinformatics

institute: FIMA

summary: Glioblastoma multiforme is one of the most devastating cancers and presents unique challenges to therapy due to its aggressive behaviour. Cancer stem cells have been described to be the only cell population with tumorogenic capacity in glioblastoma. Therefore, effective therapeutic strategies targeting these cells may be beneficial. We have established different cultures of glioblastoma stem cells (GSCs) derived from surgical specimens and found that, after induction of differentiation, NFκB was activated, which allows intermediate tumor precursor cells to remain cycling. We also showed that blockade of NFκB signaling in differentiating GSCs by different genetic strategies or treatment with small molecule inhibitors, promoted replication arrest, progression to a mature phenotype, mainly neuronal cells, and senescence. This effect was partly mediated by downregulation of the NFκB target gene cyclin D1. Furthermore, intravenous treatment of immunodeficient mice bearing human GSC-derived tumors with a novel small-molecule inhibitor of the NFκB pathway induced senescence of tumor cells but no ultraestructural alterations of the brain parenchymal cells were detected. These findings reveal that activation of NFκB may keep differentiating GSCs from acquiring a mature postmitotic phenotype, thus allowing cell proliferation, and support the rationale for therapeutic strategies aimed at promoting premature senescence in GSCs undergoing differentiation.

overall_design: Gene expression in differentiated cells relative to stem cells in three different glioblastoma cultures

first: JoseLuis

last: Fernandez-Luna

first: JoseAngel

last: Martinez-Climent


title: Human airway epithelial responses to rhinovirus infection and cigarette smoke extract alone and in combination

city: Calgary

first: David

last: Proud

state: AB

address: 3330 Hospital DRive NW

department: Physiology & Pharmacology

institute: University of Calgary

summary:
This study was performed to test the hypothesis that cigarette smoke extract would alter the responses of primary cultures of human bronchial epithelial cells to infection with purified human rhinovirus 16.
The data show marked alterations in rhinovirus-induced expression profiles of a number of genes in the presence of cigarette smoke extract (CSE).

overall_design: Cultured epithelial cells from each of 4 donors were exposed to medium alone, rhinovirus 16 (RV16) alone, CSE alone, or RV16 in the presence of CSE. After a 24 h incubation gene expression was assessed.

first: Richard

last: Leigh


title: Expression data from human peripheral blood samples

city: Budapest

first: Wichmann

last: Barna

address: Szentkirály

country: Hungary

institute: SOTE

summary:
Gene expression profile based classification of colonic diseases are suitable for identification of diagnostic mRNA expression patterns which can establish the basis of a new molecular biological diagnostic method.

Keywords: whole genomic expression

overall_design: Total RNA was extracted from peripheral blood samples Diverticulitis and Infective colitis were hybridized on Affymetrix HGU133 Plus 2.0 microarrays.

first: Ferenc

last: Sipos

first: Orsolya

last: Galamb

first: Barna

last: Wichmann

first: Bela

last: Molnar


title: Effects of IFITM1 knockdown in colorectal cancer

city: Hong Kong

first: William

middle: K. C.

last: Cheung

address: Pokfulam Road

department: Chemistry

country: China

institute: The University of Hong Kong

summary: Interferon-induced transmembrane protein 1 (IFITM1) is one of the three members of the interferon-induced transmembrane family and has recently been identified as a new molecular marker in human colorectal cancer. However, its functional roles in colorectal cancer are still elusive. In this study, we investigate the gene expression profiling of HT-29 cells with IFITM1 knockdown. We revealed that several invasive- and carcinogenesis-related genes were differentially expressed.

overall_design: We transfected siRNAs targeting firefly luciferase and human IFITM1 mRNAs into HT-29 colorectal adenocarcinoma cells. At 72 h post-transfection, total RNA was harvested for microarray hybridization. A siLuc-transfected sample was used as the baseline control.

first: Fang

last: Yu

first: Marie

last: Lin


title: Transcriptome analysis on ovarian cancer

city: Athens

first: Juan

last: Cui

address: 120 Green Street

department: Biochemistry and Molecular Biology

country: USA

institute: University of Georgia

summary: We are studying signaling pathways and growth properties of cultured human ovarian cancer cells that are expressing the G protein-coupled receptor, luteinizing hormone receptor (LHR),particularly interested in the changes that occur when the receptor is activated by its cognate ligand, gonadotropin (LH). To investigate these questions, we have employed the SKOV3 ovarian cancer cell line that has been stably transfected with LHR, and can then test the response of these cells in culture following exposure to LH.

overall_design: The parent SKOV-3 ovarian cancer cell line was chosen as a control in this study since it does not express LHR, and, following transfection, the LHR+ cells serve to determine the alterations in gene expression elicited by LH. The LHR+ cells bound human chorionic gonadotropin with a Kd of 0.3 nM (human chorionic gonadotropin and LH utilize the same G protein-coupled receptor, LHR), consistent with the binding affinity using ovarian reproductive cells, and responded to LH with increased intracellular levels of cAMP and inositol phosphates. In total, six groups of SKOV-3 cells (LHR-, LHR+, and LHR+ incubated with LH for various times: 1, 4, 8, and 20 h), each with three independent replicates, were used for examining the cell response.

first: J

last: Puett