title: Do Airway Epithelium Air-liquid Cultures Represent the In Vivo Airway Epithelium Transcriptome?

city: New York

first: Yael

last: Strulovici-Barel

state: NY

address: 1300 York Avenue

department: Department of Genetic Medicine

institute: Weill Cornell Medical College

summary: Human airway epithelial cells cultured in vitro at air-liquid interface (ALI) form a pseudostratified epithelium that forms tight junctions and cilia, and produces mucin, and are widely used as a model of differentiation, injury, and repair. To assess how closely the transcriptome of ALI epithelium matches that of in vivo airway epithelial cells, we used microarrays to compare the transcriptome of human large airway epithelial cells cultured at ALI with the transcriptome of large airway epithelium obtained via bronchoscopy and brushing. Gene expression profiling showed global gene expression correlated well between ALI cells and brushed cells, but there were some differences. Gene expression patterns mirrored differences in proportions of cell types (ALI have higher percentages of basal cells, brushed cells have higher percentages of ciliated cells), with ALI cells expressing higher levels of basal cell-related genes and brushed cells expressing higher levels of cilia-related genes. Pathway analysis showed ALI cells had increased expression of cell cycle and proliferation genes, while brushed cells had increased expression of cytoskeletal organization and humoral immune response genes. Overall, ALI cells are a good representation of the in vivo airway epithelial transcriptome, but for some biologic questions, the differences in the in vitro vs in vivo environments need to be considered.

overall_design:
Affymetrix arrays were used to assess the gene expression of large airway cells cultured in vitro at air-liquid interface (12 samples) and large airway epithelial cells obtained by fiberoptic bronchoscopy of 20 healthy nonsmokers.

*** Air-liquid interface Samples not provided in this Series. ***

first: Anna

last: Dvorak

first: Ann

middle: E

last: Tilley

first: Renat

last: Shaykhiev

first: Rui

first: Ronald

last: Crystal


title: LNCaP cells in response to DHT stimulation and inhibition/knockdown of TOPO2B

status: Public on Jul 04 2010

city: Charlestown

first: Martin

last: Aryee

state: MA

address: 149 13th Street

department: Pathology

country: USA

institute: Massachusetts General Hospital

summary: Microarray experiments were carried out to ascertain whether TOP2β is required for DHT induced androgen receptor target gene expression. We investigated the effect of pharmacological inhibition or RNA interference-mediated depletion of TOP2β on gene expression in androgen-dependent LNCaP prostate cancer cells.

overall_design: Analysis of gene expression in LNCaP cells under various conditions including serum starvation, DHT treatment, and DHT treatment combined with TOPO2B pharmacological inhibitors (Merbarone and Etoposide) and TOPO2B-shRNA knockdown.

first: Michael

last: Haffner

first: Srinivasan

last: Yegnasubramanian


title: Skin gamma delta T cells in Obesity

status: Public on Jul 01 2010

city: La Jolla

first: Steven

last: Head

state: CA

address: 10550 N Torrey Pines Rd

institute: The Scripps Research Institute

summary: Epithelial cells provide an initial line of defense against damage and pathogens in barrier tissues such as the skin; however this balance is disrupted in obesity and metabolic disease.  Skin gamma delta T cells recognize epithelial damage and release cytokines and growth factors that facilitate wound repair.  To determine the impact of obesity and metabolic disease on skin gamma delta T cells, we isolated skin gamma delta T cells from 10-week old C57BLKS/J lean db/+ and obese db/db animals for further study.  Due to a deficiency in the leptin receptor (db), homozygous db/db animals do not process satiety signals, continually eat and develop severe obesity and metabolic disease.  Skin gamma delta T cells isolated from these animals were compared for changes in mRNA expression using microarray.  We have determined that obesity and metabolic disease negatively impacts homeostasis and functionality of skin gamma delta T cells, rendering host defense mechanisms vulnerable to injury and infection.

overall_design: The goal of this experiment was to compare skin gamma delta T cells in a control mouse to skin gamma delta T cells isolated from an obese mouse to see what homeostatic changes occur in obesity and metabolic disease.  gamma delta T cells were isolated from two 10-week old lean db/+ control and two 10-week old obese db/db animals for comparison.  We wanted to determine which growth factors and signaling pathways were altered in skin gamma delta T cells residing in the obese environment.

first: Julie

middle: M

last: Jameson

first: Kristen

middle: R

last: Taylor


title: Aberrant DNA methylation in hepatitis B and C virus-related hepatocellular carcinoma

status: Public on Jul 06 2010

city: Meguro-ku

first: Atsushi

last: Kaneda

state: Tokyo

address: 4-6-1 Komaba

department: RCAST

country: Japan

institute: The University of Tokyo

summary: Chronic infections by hepatitis B virus (HBV) and hepatitis C virus (HCV) appear to be the most significant causes of hepatocellular carcinoma (HCC). Aberrant promoter methylation is known to be deeply involved in cancer, including HCC. In this study, we analyzed aberrant promoter methylation on genome-wide scale in 6 HCCs including 3 HBV-related and 3 HCV-related HCCs, 6 matched noncancerous liver tissues and 3 normal liver tissues by methylated DNA immunoprecipitation-on-chip analysis. Candidate genes with promoter methylation were detected more frequently in HCV-related HCC. Candidate genes methylated preferentially to HBV-related or HCV-related HCCs were detected and selected, and methylation levels of the selected genes were validated using 125 liver tissue samples, including 61 HCCs (28 HBV-related HCCs and 33 HCV-related HCCs) and matched 59 matched noncancerous livers, and 5 normal livers, by quantitative methylation analysis using MALDI-TOF mass spectrometry. Among analyzed genes, preferential methylation in HBV-related HCC was validated in 1 gene only. However, 15 genes were found methylated preferentially in HCV-related HCC, which was independent from age. Hierarchical clustering of HCC using these 15 genes stratified HCV-related HCC as a cluster of frequently methylated samples. The 15 genes included genes inhibitory to cancer-related signaling such as RAS/RAF/ERK and Wnt/b-catenin pathways. It was indicated that genes methylated preferentially in HCV-related HCC exist, and it was suggested that DNA methylation might play an important role in HCV-related HCC by silencing cancer-related pathway inhibitors.

overall_design:
we analyzed aberrant promoter methylation in 6 HCC clinical samples (including 3 HBV-related HCCs and 3 HCV-related HCCs) and their matched noncancerous tissues on genome-wide scale by the method. Candidate regions of promoter methylation preferentially to HBV-related HCC and HCV-related HCC were selected, and the methylation levels of these genes were measured quantitatively using MALDI-TOF mass spectrometry.
Expression levels of these 6 pairs of HCC and 4 more pairs of HCCs and surrounding noncancerous tissues were analyzed by expression array and are reported in this Series.

first: Genta

last: Nagae

first: Ying-Bing

last: Deng

first: Hiroyuki

last: Aburatani


title: CDK inhibitor PHA-793887 profiling on A2780

status: Public on Jul 14 2010

city: Nerviano

first: Roberta

last: Bosotti

state: MI

address: viale Pasteur,10

department: Biotechnology

country: Italy

institute: Nerviano Medical Sciences srl

summary: The effects of the CDK inhibitor PHA-793887 on the A2780 human adenocarcinoma ovary cell line were analysed by gene expression profiling.

overall_design: The A2780 cell line was treated with PHA-793887 (CDK-887) for 6 hours at a dose equal to 5 time the IC50. Untreated A2780 cells were used as a control. Two replicates per treatment.

first: Emanuela

last: Scacheri

first: Antonella

last: Isacchi

first: Giorgio

middle: G

last: Galli


title: Expression data from Caco-2 cells co-cultivated with B. animalis subsp. lactis BB-12

city: Horsholm

first: Ondrej

last: Valina

address: Boge alle 10-12

department: H&N Divison

country: Denmark

institute: Chr. Hansen A/S

summary:
Although intestinal microbiota play a pivotal role in the development of host immune system this biological issue was not so far studied in great detail. In this study we examined immune response of Caco-2 enterocytes after incubation with common probiotic Bifidobacterium animalis subsp. lactis BB-12 for 4 hours.
We used microarrays to inspect the global gene expression of Caco-2 cells upon co-culturing with B. animalis subsp. lactis BB-12 and several distinct immune-related genes up-regulated during this process.

overall_design: One time point (T4) and two controls (T0) were analysed. T0 represent differentiated Caco-2 cells cultivated for 3 weeks. T4 represents differentiated Caco-2 cells cultivated for 3 weeks plus consequent 4 hours of co-cultivation with B. animalis subsp. lactis BB-12. 3 technical replicates for T0-1, T0-2 or T4 were pooled to a single sample, RNA extracted and further used in gene expression experiments.

first: Karsten

last: Kristiansen

first: Thomas

middle: D

last: Leser


title: CDK inhibitors PHA-848125 and PHA-690509 profiling on A2780

summary: The effects of the CDK inhibitors PHA-848125 and PHA-690509 on the A2780 cell line were analysed by gene expression profiling.

overall_design: The A2780 cell line was treated with PHA-848125 (CDk-125) or PHA-690509 (CDk-509) for 6 hours at a dose equal to 5 times the IC50. Untreated A2780 cells were used as a control. Three replicates per treatment.

first: Sandra

last: Healy

first: Giuseppe

last: Locatelli


title: Expression data for cultured NCI-H1299 parental and spheroid cells as well as their derived xenograft models

city: San Diego

first: Douglas Fang

last: Fang

address: 10777 Science Center Drive, CB5

department: Oncology Research Unit

institute: Pfizer Inc.

summary:
Current approaches to the preclinical investigation for novel cancer therapies rely heavily on the use of traditional cancer cell lines maintained in serum-containing conditions. The discrepancy between promising preclinical efficacy and clinical outcome of most novel anticancer agents emphasizes a need for developing predictive preclinical models that preserve the integrity of original patient tumors, including cancer stem cell (CSC) compartment.
In this study, we isolate and characterize CSCs from a non-small cell lung cancer cell line, NCI-H1299, by selectively propagating the cells in a stem-cell culture condition. Isolated CSCs proliferated as nonadherent spheroids, displayed capacity to differentiate and self-renew and exhibited higher tumorigenic potential compared to the parental cells.

overall_design: The gene expression profiles of NCI-H1299 parental cells (serum-containing medium), CSCs (stem-cell medium), and xenograft tumor derived from both cell types were studied by Affymetrix array analysis

first: Douglas


title: Expression data of two human cancer cell lines cultivated in 2-dimensional (2D) vs. 3-dimensional (3D) cell culture

city: Hamburg

last: Streichert

address: Martinistr. 52, Campus Forschung N27, 2. OG

department: Institute For Clinical Chemistry / Central Laboratories

country: Germany

institute: University Medical Center Hamburg-Eppendorf

summary:
3D cultivation of cells lead to changes in morphology of the cells. This is likely to explain the higher radioresistance of cells growing in 3D compared to cells growing in 2D cell culture.
Whole genome gene expression is performed to determine genes involved in changes of cell moroholgy and radioresistance.

Keywords: comparison of 2D vs. 3D cell culture

overall_design: RNA of cells was isolated four days after growing in the two different cell culture systems

first: Oliver

last: Zschenker

first: Nils

last: Cordes


title: Expression profile of IL-1beta stimulated and non-stimulated endothelial cells

city: Berlin

first: Matthias

last: Futschik

address: Invalidenstrasse 41

institute: Charite

summary:
Complete identification of the bone marrow niche remains one of the most progressing fields. Attempts to identify soluble factors involved in stem cell renewal have been less successful. We have previously shown that endothelial cells (EC) can induce the long-term proliferation of hematopoietic progenitor cells (HPC), especially when they had been subjected to an inflammatory stimulus like interleukins (IL) 1.
To identify yet unknown growth factors, we compared the expression profile of IL-1 stimulated and non-stimulated endothelial cells.

overall_design: Human endothelial cells were subjected to IL-1 for 4, 8, and 16 hours. Isolated mRNA was analyzed by oligonucleotide microarray chips covering over 46,000 human genes.

first: Anja

last: Moldenhauer


title: Multilineage dysplasia and AML with mutated nucleophosmin

first: Hans-Ulrich

last: Klein

department: Neurology

institute: Columbia University Medical Center

summary:
Multilineage dysplasia (MLD) has no impact on biological, clinico-pathological and prognostic features of AML with mutated nucleophosmin (NPM1)
NPM1-mutated AML is a provisional entity in the WHO-2008 classification of myeloid neoplasms. The significance of concomitant multilineage dysplasia (MLD) in NPM1-mutated AML is unclear. Thus, in the WHO-2008 classification, NPM1-mutated AML with MLD is classified as AML with myelodysplasia(MD)-related changes. We evaluated the MLD impact in 378 NPM1-mutated AML patients. MLD was found in about 25% cases. Except for a lower WBC and FLT3-ITD incidence in MLD+ group, no significant differences were observed in age, sex, cytogenetics and FLT3-TKD between NPM1-mutated AML with and without MLD. Notably, NPM1-mutated AML with/without MLD showed overlapping immunophenotype (CD34-negativity) and GEP (CD34 downregulation and HOX genes upregulation).
Moreover, OS and EFS did not differ among NPM1-mutated AML patients, independently of whether they carried or not MLD, the NPM1-mutated/FLT3-ITD negative cases showing the better prognosis. Lack of MLD impact on survival was confirmed by multivariate analysis that highlighted FLT3-ITD as the most significant prognostic parameter in NPM1-mutated AML. Our findings indicate that NPM1 mutations rather than MLD dictate the distinctive features of NPM1-mutated AML. Thus, irrespective of MLD, NPM1-mutated AML should be considered as one disease entity clearly distinct from AML with MD-related changes. These findings have important diagnostic and prognostic implications in AML.

overall_design: All bone marrow samples were obtained from untreated patients at the time of diagnosis. Cells used for microarray analysis were collected from the purified fraction of mononuclear cells after Ficoll density centrifugation.  48 samples

first: Brunangelo

last: Falini

first: Katja

last: Macijewski

first: Tamara

last: Weiss

first: Ulrike

last: Bacher

first: Susanne

last: Schnittger

first: Wolfgang

last: Kern

first: Alexander

last: Kohlmann

first: Marco

last: Vignetti

first: Alfonso

last: Piciocchi

first: Paola

last: Fazi

first: Maria

middle: P

last: Martelli

first: Stefano

last: Pileri

first: Miriam

last: Miesner

first: Teresa

last: Marafioti

last: Santucci

first: Claudia

last: Haferlach

first: Franco

last: Mandelli

first: Torsten


title: Expression data from TKI258 treated 4T1 cells and 4T1 tumors

status: Public on Jul 07 2010

city: Basel

first: Julien

middle: Herve

last: Dey

address: Maulbeerstrasse

department: growth control

country: Switzerland

institute: FMI

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

overall_design: Refer to individual Series


title: Diabetic Microangiopathy in the Bone Marrow Causes Hypoperfusion and Depletion of the Stem Cell Niche.

city: Amsterdam

first: Anton

middle: J

last: Horrevoets

address: van der Boechorststraat 7

department: Molecular Cell Biology

country: Netherlands

institute: VU University Medical Center

summary: Diabetes mellitus [DM], with its burden of premature morbidity and mortality, represents one of the major threats to human health in the 21st century (Zimmet 2001). Accelerated atherosclerosis affecting arteries that supply the heart, brain and lower extremities is responsible for an increased risk of acute ischemic events. DM is also associated with microvascular disease, which is a leading cause of blindness, renal failure and debilitating neuropathies. Endothelial dysfunction, increased vascular permeability and microvascular cell loss by apoptosis are all hallmarks of diabetic microangiopathy. Diabetic patients not only incur cardiovascular complications more frequently, but also experience worse outcomes due to attenuation of vascular repair mechanisms. This impairment includes quantitative and qualitative abnormalities of bone marrow [BM]-derived progenitor cells (Emanueli 2002&2004; Loomans 2004; Krankel 2005; Fadini 2006). The mechanisms underlying BM dysfunction remain however enigmatic, especially when considering the privileged location that protects stem cells [SC] and progenitor cells [PC] of the marrow from external insults (Kopp 2008 and Kiel 2008). BM endothelial cells [EC] are instead an obvious target of DM, because they are directly exposed to blood glucose and incapable to regulate glucose influx. Strangely enough, little is known about the impact of diabetes on BM microvasculature. We hypothesize that damage induced by DM might start at the microvascular level, in a similar fashion to microangiopathy, which occurs in kidney, retina, heart and brain. We also propose that enduring microvascular cell loss might result in marrow hypo-perfusion and destabilization of SC homeostasis.

overall_design: In order to test this hypothesis, we studied streptozotocin-induced (STZ) type-1 DM and age-matched non-DM mice (n=6 to 10 per group in each experiment). Histological examination of femurs, collected from STZ-mice at 28-30 weeks from induction of DM or controls, showed remarkable differences in bone density and marrow composition. Bone marrow cells from healthy and diabetic animals were next selected for endothelial progenitors and cultured for 10 days under endothelial cell growth conditions. Next RNA was isolated and analysed by Illumina Sentrix Beadarrays.

first: Paolo

last: Madeddu


title: Gene expression in circulating mononuclear cells after exposure to ultrafine carbon particles

status: Public on Jun 30 2010

city: Durham

first: Yuh-Chin

middle: Tony

last: Huang

state: NC

address: Erwin Rd

department: Medicine

institute: Duke University Medical Center

summary:
Peripheral blood samples were collected before (0 hour) and at 24 hours after exposure from healthy subjects who participated in previous controlled exposures to ultrafine carbon particles (UFP, 50 microg/m3) or filtered air (FA)(n = 3 each). The exposure time was 2 hours. RNA from mononuclear cell fraction (>85% lymphocytes) was extracted, amplified and hybridized to Affymetrix HU133 plus 2 microarrays.
We used microarray to explore significantly altered genes after ultrafine carbon particle exposure.

overall_design: Each subject was exposed to filtered air or ultrafine carbon particles. Two peripheral blood samples (pre- and post-exposure) were taken. Mononuclear cells were isolated for gene expression analysis.

middle: T


title: Gene expression profile of normal human mammary epithelial stem/progenitor and myoepithelial cells

status: Public on Jun 26 2010

city: Omaha

first: Gautam

last: Malhotra

state: NE

address: 985805 Nebraska Medical Center

institute: UNMC

summary: There is increasing evidence that breast and other cancers originate from and are maintained by a small fraction of stem/progenitor cells with self-renewal properties. Whether such cancer stem/progenitor cells originate from normal stem cells based on initiation of a de novo stem cell program, by reprogramming of a more differentiated cell type by oncogenic insults or both remains unresolved.  A major hurdle in addressing these issues is lack of immortal human stem/progenitor cells that can be deliberately manipulated in vitro.  We present evidence that normal and human telomerase reverse transcriptase (hTERT)-immortalized human mammary epithelial cells (hMECs) isolated and maintained in DFCI-1 medium retain a fraction with progenitor cell properties.  These cells co-express basal, luminal and stem/progenitor cell markers.  Clonal derivatives of progenitors co-expressing these markers fall into two distinct types: K5+/K19- (Type I) and K5+/K19+ (Type II).  We show that both types of progenitor cells have self-renewal and differentiation ability. Through microarray analysis, we want to identify genes and pathways linked to human mammary epithelial stem/progenitor cell self-renewal and differentiation.

overall_design: Normal human mammary epithelial cells (hMECs) were isolated from Reduction Mammoplasty and immortalized by hTERT.  Type I K5+/K19-  and Type II K5+/K19+  cell colonies were isolated from hTERT-immortalized hMECs and cultured in MEGM medium for self-renewal and differentiation. Total RNA isolated from Type I, Type II, and differentiated Myoepithelial (Myo) cells were used on Affymetrix microarrays.

first: Vimla

last: Band


title: Human adult germline stem cells in question

status: Public on Jun 29 2010

city: Aachen

first: Martin

last: Zenke

state: NRW

address: Universitatsklinikum Aachen, RWTH

department: Cell Biology

institute: Institute for Biomedical Engineering

summary: Conrad et al. Nature 456, 344–349 (2008) have generated human adult germline stem cells (haGSCs) from human testicular tissue, which they claim have similar pluripotent properties to human embryonic stem cells (hESCs). Here we investigate the pluripotency of haGSCs by using global gene-expression analysis based on their gene array data and comparing the expression of pluripotency marker genes in haGSCs and hESCs, and in haGSCs and human fibroblast samples derived from different laboratories, including our own. We find that haGSCs and fibroblasts have a similar gene-expression profile, but that haGSCs and hESCs do not. The pluripotency of Conrad and colleagues’ haGSCs is therefore called into question.

overall_design: RNA samples from human testicular fibroblast cells (hTFCs) were obtained and applied to global gene expression analysis using gene arrays.

first: Kinarm

last: Ko

first: Marcos

last: Araúzo-Bravo

first: Natalia

last: Tapia

first: Julee

last: Kim

first: Qiong

last: Lin

first: Christof

last: Bernemann

first: Dong

middle: W

last: Han

first: Luca

last: Gentile

first: Peter

last: Reinhardt

first: Boris

last: Greber

first: Rebekka

middle: K

last: Schneider

first: Sabine

last: Kliesch

first: Hans

last: Schöler


title: Comparison of the expression data between vacant vector and SPRR2a expressing cell of cholagiocarcinoma cell lines SG231 and HuCCT1

city: Pittsburgh

first: Yoshiaki

last: Mizuguchi

state: PA

address: 200 Lothrop st

institute: UPMC

summary:
Small proline rich protein (SPRR) 2a is one of the 14 SPRR family member genes which are coded in the region of the epidermal differentiation complex (EDC).  SPRR2 genes are  coordinately expressed with other EDC genes and function primarily as cross-linking proteins which confer structural integrity to the cornified cell envelope.  More recently, SPRR2a was associated with functions independent of the EDC.  Non-coordinate up-regulation of SPRR2a is seen  during  stress/injury induced remodeling of barrier epithelia and during  epithelial-mesenchymal transition (EMT).
Forced SPRR2a expression in a cholangiocarcinoma cell line (SG231) down-regulates the epithelial cell adherens molecule E-cadherin and upregulates mesenchymal components, such as vimentin and fibronectin. Thus, we sought to identify which genes were commonly involved in SPRR2a induced EMT by cDNA microarray analysis using SG231 and HuCCT-1 SPRR2a stable transfectants.

overall_design: SPRR2a expressing stable cell lines of SG231 and HuCCT1 and their control cell lines were selected  for  Affymetrix microarrays.

first: Anthony

last: Demetris


title: Human umbilical cord blood-derived endothelial colony forming cells under serum-free conditions

city: Zurich

first: Stefan

last: Zoller

address: Universitatstrasse 16

department: Genetic Diversity Centre

institute: ETH Zurich

summary:
Derivation and expansion of human umbilical cord blood-derived endothelial colony forming cells under serum-free conditions - a transcriptome analysis.
Endothelial colony forming cells (ECFCs) were isolated from term umbilical cord blood units. ECFCs were expanded under standard, fetal bovine serum (FBS) containing endothelial medium, or transferred to chemically defined endothelial media without FBS. Microarray expression profiling was applied to compare the transcriptome profiles in FBS-containing versus FBS-free culture.

overall_design: Comparison of the expression patterns of ECFCs that were either cultured in FBS-containing medium or in serum-free medium (five replicates each).

first: Steffen

last: Zeisberger

first: Mariluce

last: Riegel

first: Shuhua

last: Chen

first: Guido

last: Krenning

middle: C

last: Harmsen

first: Agapios

last: Sachinidis

first: Andreas

middle: H

last: Zisch


title: Transcriptome analysis of human Wharton’s jelly stem cells: meta-analysis

status: Public on Jul 19 2010

city: Singapore

first: Woon-Khiong

last: Chan

email: dbscwk@nus.edu.sg, g0500139@nus.edu.sg

address: S2-05-19, 14 Science Drive 4

department: Biological Sciences

country: Singapore

institute: National University of Singapore

type:
Third-party reanalysis
Expression profiling by array

summary: Human Wharton’s jelly stem cells (hWJSCs) are derived ethically in large amounts from the umbilical cord matrix. Besides their differentiation capabilities, WJSCs also display a notable lack of ability to form teratoma. hWJSCs have been shown to exert immunomodulatory effects and have recently been reported to kill or diminish cancer cell growth. These characteristics are important considerations for their use in cell therapy. In this transcriptome analysis, hWJSCs were profiled using Affymetrix DNA microarrays and compared to a panel of human stem cells and stromal cells. Although hWJSCs are multipotent, they expressed very low levels of the majority of stem cell markers, including POU5F1, NANOG, SOX2 and LIN28. BIRC5 has recently been shown to be required for teratoma formation in SCID mice. The lower levels of BIRC5 expression in hWJSCs compared to hESCs and the very low levels of stem cell markers might account for hWJSCs inability to form teratomas. IL12A which is known to be associated with the induction of apoptosis, was amongst the several cytokines identified to be significantly upregulated in hWJSCs. The ability of hWJSCs to compliment the host immune responses was further highlighted with the GO Biological Process analysis showing high association with immune system, chemotaxis and cell death. The ability to modulate immune responses confers hWJSCs an additional advantage in stem cell therapy and potentially allows hWJSCs as a form of treatment for cancer and immune disorders. In summary, the transcriptome profile of hWJSCs has provided indications on the genetic basis for their biological characteristics in immunomodulatory response, anti-cancer effects, and the lack of teratoma formation.

overall_design: This 'meta-analysis' dataset contains hWJSCs and hFC that were generated by our group, and selected samples available from the public GEO database (human mesenchymal stem cells, umbilical vein endothelial cells, normal stroma, tumour stroma, fibroblast).

first: Chui-Yee

last: Fong

first: Li-Ling

last: Chak

first: Arijit

last: Biswas

first: Jee-Hian

last: Tan

first: Kalamegam

last: Gauthaman

first: Ariff

last: Bongso


title: Expression data from pulmonary metastases and primary tumors of clear-cell renal cell carcinoma (ccRCC) with different disease-free survivals

status: Public on Jun 25 2010

city: Dresden

first: Wuttig

last: Daniela

address: Fetscherstr. 74

department: Department of Urology

institute: Dresden, University of Technology

summary:
The understanding of metastatic spread is limited and molecular mechanisms causing particular characteristics of metastasis are largely unknown. This comprises the extremely varying dormancy periods of tumor cells in the secondary organ after metastatic spread, represented by the disease-free survival (DFS) of the patients, or differing numbers of metastases in different patients. Knowing the molecular fundamentals of these phenomena would support the individual prediction of patients´ outcome and facilitate the decision for an appropriate monitoring and therapy regime.
In a first study (PMID 19391132) we analyzed the transcriptome-wide expression profiles of 20 pulmonary metastases of renal cell carcinoma (Met1-9, Met11-18, Met20, Met23, Met25) to identify expression patterns associated with the dormancy period and the number of metastases per patient. Pre-processed and analyzed data for this study are available in GEO Series GSE14378.
In this second study, we validated the DFS-associated expression pattern from the first study on four further metastases and also included primary ccRCC with different DFS. For this, the microarray data of all metastases and primary tumors were pre-processed together. The aim of this second study was to identify those genes, which are differentially expressed in metastases developed after different dormancy periods and which are already deregulated in primary tumors. Genes differentially expressed in synchronously vs. metachronously metastases might contribute functionally to the dormancy period. Genes already deregulated in primary ccRCC might be suitable for prognostic purposes.

overall_design:
metastases manifested synchronously or metachronously (DFS less than or equal to 9 months compared with DFS greater than or equal to 60 months);
primary ccRCC which developed synchronous or metachronous metastases (DFS less than or equal to 6 months compared with DFS greater than or equal to 45 months)

first: Daniela

last: Wuttig

first: Susanne

last: Fuessel

first: Marieta

middle: I

last: Toma

first: Matthias

last: Meinhardt

last: Zastrow

first: Jimsgene

last: Sanjmyatav

first: Kerstin

last: Junker

first: Barbara

last: Baier

first: Axel

last: Rolle

first: Alexander

last: Herr

last: Meye

first: Marc-Oliver

last: Grimm

first: Manfred

last: Wirth


title: Induction of pluripotent stem cells from human third molar   mesenchymal stromal cells

city: Amagasaki

first: Hajime

last: Ohgushi

state: Hyogo

address: 3-11-46 Nakouji

department: Research Institute for Cell Engineering

institute: National Institute of Advanced Industrial Science and Technology

summary: The expression of four transcription factors (OCT3/4, SOX2, KLF4, and c-MYC) can reprogram mouse as well as human somatic cells to induced pluripotent stem (iPS) cells.  Expression of the c-MYC, also known as an oncogene, might induce carcinogenesis and thus, iPS cells produced with the use of c-MYC transduction cannot be used for human therapeutic applications. Furthermore, reprogramming efficiency was significantly reduced in the absence of c-MYC transduction. Here, we generated iPS cells from mesenchymal stromal cells (MSCs) derived from human third molars (wisdom teeth) by retroviral transduction of OCT3/4, SOX2, and KLF4 without c-MYC. Interestingly, clonally expanded MSCs, named 10F-15, could be used for iPS cell generation with 100-fold higher efficiency compared to that of other clonally expanded MSCs and human dermal fibroblasts. These iPS cells resembled human embryonic stem (ES) cells in many aspects, including morphology, ES markers expression, global gene expression, epigenetic states, and the ability to differentiate into the three germ layers in vitro and in vivo. Because human third molars are discarded as clinical waste, our data indicate that MSCs isolated from human third molars are a valuable cell source for the generation of iPS cells.

overall_design: Three types of cells were used for 1-channel expression analysis:  (a) human dermal fibroblasts (1 array)  (b) human third molar cells (2 different cell lines, 1 array each)  (c) virus-carrying human induced pluripotent stem cells (4 different cell lines, 1 array each)

first: Yasuaki

last: Oda

first: Yasuhide

last: Yoshimura

first: Hiroe

last: Ohnishi

first: Mika

last: Tadokoro

first: Mari

last: Sasao

first: Yoko

last: Kubo

first: Yoshihiro

last: Katsube

first: Koji

last: Hattori


title: Expression data from ejaculated spermatozoa of normozoospermic and asthenozoospermic men

city: Shenzhen

first: Jing

last: Chen

state: Guangdong

address: NO.1120 Lianhua Rd

department: Laboratory of Male Reproductive Medicine and Genetics

country: China

institute: Peking University Shenzhen Hospital

summary:
Analysis of ejaculated spermatozoav from normozoospermic men and asthenozoospermic men. Some of genes were up-regulated or down-regulated in asthenozoospermia, and their abnormal expression were the causes of the impaired sperm motility. Results provide insight into the mechanisms by which asthenozoospermia is controlled.
We used microarrays to detail the global programme of gene expression of ejaculated spermatozoa between normozoospermic and asthenozoospermic men and identified distinct classes of genes expressed differentially in two groups.

overall_design: The liquefied semen samples from normozoospermic and asthenozoospermic men were purified by Percoll on a discontinuous density gradients for RNA extraction and hybridization on Affymetrix microarrays. 30 sperm samples of each group were pooled to abtain enough total RNA.

first: J

first: T

middle: Y

last: Gui


title: Transcriptional profile of Escherichia coli K12 strain JM109 harboring pMG1 and pMG1-IrrE under 1M NaCl shock

status: Public on Jul 29 2010

city: Beijing

first: Ming

address: Zhongguancun Nandajie 12th,Haidian Zone

institute: Biotechnology Research Institute, Chinese academy of Agricultural Sciences

summary:
IrrE is a unique gene in Deinococcus, which is the switch of DNA repair and celluar surival network. Expressing IrrE enhanced the salt tolence in E. coli. To understand the effect of IrrE to E. coli during salt shock, we constructed the IrrE-expressing plasmid pMG1-IrrE. And pMG1 is the empty vector used as a control.
The GroESL promoter was amplified from D. radiodurans R1 genomic DNA by PCR with proper primers. The PCR product was ligated into the T-cloning site of T-vector pMD18T, generating the plasmid pMG1.

overall_design: RNA extracted from cells of E. coli K-12 JM109 cells with pMG1 after 4 h of growth to OD 600 achieve 0.4, or  cells with pMG1 after 1mol/L NaCl shock for 10 min (and 60 min) when their OD600 achieved 0.4. RNA extracted from cells of E. coli K-12 JM109 cells with pMG1-IrrE after 4 h of growth to OD 600 achieve 0.4, or  cells with pMG1-IrrE after 1mol/L NaCl shock for 10 min (and 60 min)when their OD600 achieved 0.4. pMG1 and pMG1-IrrE datasets normalized separately.

first: Min

last: Lin

first: Jie

last: Pan

first: Yongliang

last: Yan


title: Impact of NRSF variant over-expression in SK-N-AS human neuroblastoma cells

city: Liverpool

first: Stuart

last: Gillies

address: Crown Street

department: Physiology

country: United Kingdom

institute: University Of Liverpool

summary:
Neuron-restrictive silencer factor (NRSF) and its isoforms are differentially regulated in  rodent models of self-sustaining status epilepticus (SSSE). NRSF isoforms regulate genes  associated with SSSE, including the proconvulsant tachykinins, brain-derived neurotrophic  factor and multiple ion channels. NRSF isoforms may direct distinct gene expression  patterns during SSSE and the ratio of each isoform may be a causative factor in traumatic  damage to the CNS. Here we analysed global gene expression changes by microarray in  human SK-N-AS neuroblastoma cells following the over expression of NRSF and a truncated  isoform, HZ4.
We used bioinformatics software to analyse the microarray dataset and  correlated these data with epilepsy candidate gene pathways. Findings were validated by  RT-PCR. We demonstrated that NRSF and HZ4 direct overlapping as well as distinct gene  expression patterns and that they differentially modulated gene expression patterns  associated with epilepsy. Finally we revealed that NRSF gene expression may be modulated  by the anticonvulsant, phenytoin. This study provides fundamental information on networks  of genes that may be altered during SSSE, following altered NRSF expression, which may be  important in future therapeutic research and clinical analysis of genetic variation  predisposing to epilepsy.

overall_design: Human SK-N-AS cells were treated with expression constructs over-expressing either the full length human transcription factor, NRSF, (via the RE-EX1 construct) or a truncated variant (via the HZ4 construct). Cells were treated for either 0hrs (base line controls), 24hrs or 48hrs, before being immediately processed for RNA extraction. An affymetrix microarray was employed to investigate gene expression patterns, comparing each time point (24hrs or 48hrs) againsts its baseline ()hrs) control. This experiment was performed in triplicate samples per batch, and over three batches.

first: S

first: K

last: Haddley

last: Vasiliou

first: G

last: Jacobson

first: B

last: Von Mentzer

first: V

last: Bubb

last: Quinn


title: Integration of transcript expression, copy number and LOH analysis of infiltrating ductal carcinoma of the breast: expression analysis

status: Public on Jun 24 2010

city: Augusta

first: Lesleyann

last: Hawthorn

state: GA

department: Molecular Oncology

institute: Medical College of Georgia Cancer Center

summary:
Introduction: A major challenge in the interpretation of genomic profiling data generated from breast cancer samples is the identification of driver genes as distinct from bystander genes which do not impact tumorigenesis. One way to assess the relative importance of alterations in the transcriptome profile is to combine complementary analyses that assess changes in the copy number alterations (CNAs). This integrated  analysis  permits the identification of genes with altered expression that map within specific chromosomal regions that demonstrate copy number alterations, providing a mechanistic approach to  identify the 'driver genes’.

Methods:  We have performed whole genome analysis of CNAs using the Affymetrix 250K Mapping array on 22 infiltrating ductal carcinoma samples (IDCs). Analysis of transcript expression alterations was performed using the Affymetrix U133 Plus2.0 array on 16 IDC samples. Twelve IDC samples were analyzed using both platforms and the data integrated. We also incorporated data from LOH analysis to identify genes showing loss of expression in LOH regions.

Results:  Copy number analysis results demarcated smaller boundaries for many previously reported CNAs, and in some cases, the CNAs were defined as more than a single contiguous event. Additionally, we were able to assign driver genes to these commonly reported regions using a rigorous methodology. For example, RAB25 showed a large increased expression in the tumors and mapped to the commonly reported amplification at 1q22. We also identified 5 genes in the 8q24 amplicon and TSEN4 in the 17q25 amplified region. LOH analysis confirmed some previously reported regions, and integration with copy number data determined that the detected LOH were copy neutral events. Finally, we have identified several RXR pathways that demonstrated down-regulation in IDC whose members may represent further targets of therapeutic intervention.

Conclusion: We have demonstrated the utility of the application of integrated analysis using high-resolution CGH and whole genome transcript analysis for detecting driver genes in IDC. The high resolution platform allowed a refined demarcation of CNAs, and gene expression profiling provided a mechanism to detect genes directly impacted by the CNA. This is the first report of LOH in IDC using a high resolution platform.

overall_design: 16 IDC samples analyzed with the U133 Plus 2.0 array compared to 4 normal control samples.


title: Identification of TSGs Frequently Methylated in Renal Cell carcinoma (expression profiles of Renal cell lines following  de-methylation)

city: Birmingham

first: Mark

middle: Richard

last: Morris

address: Medical School

department: Medical and Molecular Genetics

institute: Univeristy of Birmingham

summary: Promoter region hypermethylation and transcriptional silencing is a frequent cause of tumour suppressor gene (TSG) inactivation in many types of human cancers. Functional epigenetic studies, in which gene expression is induced by treatment with demethylating agents, may identify novel genes with tumour-specific methylation. We used high-density gene expression microarrays in a functional epigenetic study of 11 renal cell carcinoma (RCC) cell lines. Twenty eight genes were then selected for analysis of promoter methylation status in cell lines and primary RCC. Eight genes (BNC1, PDLIM4/RIL, REPRIMORPRM, CST6, SFRP1, GREM1, COL14A1 and COL15A1) demonstrated frequent (>30% of RCC tested) tumour-specific promoter region methylation.  Hypermethylation was associated with transcriptional silencing. Re-expression of BNC1, CST6, RPRM, and SFRP1 suppressed the growth of RCC cell lines. Whereas, RNAi-knock-down of BNC1, SFRP1 and COL14A1 increased the growth potential of RCC cell lines. Methylation of BNC1 or COL14A1 was associated with a poorer prognosis independent of tumour size, stage or grade. The identification of these epigenetically inactivated candidate RCC tumour suppressor genes can provide insights into renal tumourigenesis and a basis for developing novel therapies and biomarkers for prognosis and detection.

overall_design: We used expression microarrays to identified genes that were frequently methylated and silenced in RCC by determining the globlal expression patterns of RCC-derived cell lines following de-methylation by treatment with 5-Aza-2'-deoxycytidine.

first: Chris

last: Ricketts

first: Dean

last: Gentle

first: Mahera

last: Abdulrahman

first: Noel

last: Clarke

first: Michale

last: Brown

first: Takeshi

last: Kishida

first: Masahiro

last: Yao

first: Farida

last: Latif

first: Eamonn

last: Maher


title: Immature cell populations and an erythropoiesis gene expression signature in systemic juvenile idiopathic arthritis: Implications for pathogenesis

city: Cincinnati

first: Michael

last: Barnes

state: OH

address: 3333 Burnet Ave

department: Rheumatology

institute: Cincinnati Childrens Hospital Medical Center

summary:
Objective. Previous observations suggest that active systemic juvenile idiopathic arthritis (sJIA) is associated with a prominent erythropoiesis gene expression signature. The aim of this study was to determine the association of this signature with peripheral blood mononuclear cell (PBMC) subpopulations and its specificity for sJIA as compared to related conditions.

125 patients with JIA (18 sJIA and 107 non-sJIA) and 29 controls were studied. PBMC were isolated and analyzed for multiple surface antigens by flow cytometry and for gene expression profiles. The proportions of different PBMC subpopulations were compared among sJIA, non-sJIA patients and controls and subsequently correlated with the strength of the erythropoiesis signature. Additional gene expression data from patients with familial hemophagocytic lymphohistiocytosis (FHLH) and from a published sJIA cohort were analyzed to determine if the erythropoiesis signature was present.

Keywords: Patient Vs Control, reassassment of phenotype

overall_design: Peripheral blood samples were obtained from 29 healthy children and 125 children with JIA .  RNA was purified from Ficoll-isolated mononuclear cells, fluorescently labeled and then hybridized to Affymetrix U133 Plus 2.0 GeneChips.  Data were analyzed using ANOVA at a 5% false discovery rate threshold after Robust Multi-Array Average pre-processing and Distance Weighted Discrimination normalization.

first: Claas

last: Hinze

first: Ndate

last: Fall

first: Thomas

middle: A

last: Griffin

first: Susan

last: Thompson

first: David

middle: N

last: Glass

first: Robert

last: Colbert

first: Alexei

last: Grom


title: Gene expression profiles of adult renal cortical endothelial cells isolated from TIE2-GFP transgenic mice using FACS. (GUDMAP Series ID: 41)

status: Public on Jun 23 2010

city: Edinburgh

first: GUDMAP

last: Developers

address: Crewe Road

institute: IGMM MRC Human Genetics Unit

summary: The long term objective is to create an encyclopedia of the expression levels of all genes in multiple components of the developing kidney.  The central thesis is straightforward. The combination of fluorescent activated cell sorting (FACS) plus microarray analysis offers a powerful, efficient and effective method for the creation of a global gene expression atlas of the developing kidney. Microarrays with essentially complete genome coverage can be used to quantitate expression levels of every gene in FACS isolated components of the developing kidney. The ensuing rapid read-out provides an expression atlas that is more sensitive, more economical and more complete than would be possible by in situ hybridizations alone.

overall_design: Tie2-GFP transgenic mice were utilized to isolate the endothelial cell population from  the cortical region of adult  kidneys.  The cortical endothelial cells were isolated from kidneys using a combination of collagenase treatment, differential seiving, trypsin treatment and FACS.   The RNA was isolated from purified endothelial cells and the gene expression profiles were determined by microarrays.

first: Steve

last: Potter

first: Eric

last: Brunskill


title: miR-155 role in osteoclast differentiation

city: Rehovot

first: Omer

last: Barad

address: Herzel

country: Israel

institute: Weizmann Institute of Science

summary: We used microarrays to understand the effect miR-155 has on osteoclast differentiation.

overall_design: RAW264.7 cells were grown in a-MEM supplemented with 10% FBS and antibiotics. mRNA extracted from wild-type RAW264.7 cells and miR-155 mis-expressing cells either before or after 72 hr of stimulation with 20ng/ml RANKL and M-CSF to induce osteoclast differentiation.

first: Mati

last: Mann

first: Reuven

last: Agami

first: Benjamin

last: Geiger

first: Eran

last: Hornstein


title: Over-expression and knockdown of KLF5

first: H. Leighton

last: Grimes

address: 3333 Burnet Ave. MLC 7038

department: Immunobiology

summary:
Activation of the Ras/Erk pathway upregulates expression of the Kruppel-like Factor 5 (KLF5) transcription factor, and KLF5 is a downstream mediator of Ras oncogenic signaling.  Specifically, in bladder and colon cancer cell lines KLF5 upregulates the Ras-pathway target gene cyclin D1, and facilitates entry into the S phase of the cell cycle.  Ras mutations are common in lung cancer, but a role for KLF5 in lung tumorigenesis has not been defined.  To this end, we manipulated KLF5 expression in four Ras-mutant human lung adenocarcinoma cell lines to find that KLF5 significantly modulates anchorage-independent growth, a mutant Ras phenotype.  However, in a mouse model of human lung adenocarcinoma, K-RasG12D does not critically require Klf5 to mediate oncogenesis or induce cyclin D1 expression.
Patients with lung tumors expressing high levels of KLF5 have significantly better prognosis than those with low or no KLF5 expression (opposite of mutant Ras prognosis).  The latter may be explained by KLF5 transcriptional repression of the ATP-binding cassette, sub-family G (WHITE), member 2 (ABCG2), an anthracycline transporter.  In agreement with this, KLF5 knockdown cells display significantly more Hoechst “side population” and resistance to doxorubicin. In summary, while KLF5 is not an obligate partner in Ras oncogenic signaling, KLF5 control of ABCG2 expression is significant to patient survival.

overall_design: Total RNA was extracted from H441 cells transduced with KLF5-specific shRNA (KD), KLF5 over expression (OE) and MSCV empty vertor (NT) respectively. The cRNAs was then hybridized to Human Genome U133 Plus 2.0 Arrays (Affymetrix) according to manufacturer’s protocol.

first: Jason

middle: R

last: Hasenstein

first: Avinash

last: Baktula

first: Chinavenmani

middle: S

last: Velu

first: Yan

last: Xu

first: Huajing

last: Wan

first: Jeffrey

last: Whitsett

first: C

middle: B

last: Gilks

first: H

middle: L


title: Changes in cardiac transcription profiles following off-pump coronary revascularization surgery

status: Public on Jun 22 2010

city: Bristol

first: Mohamed

middle: T.

last: Ghorbel

address: Level 7, BRI, Marlborough street

department: Bristol Heart Institute

institute: University of Bristol

summary:
To investigate changes in cardiac transcription profiles caused by off-pump cardiac surgery, we collected myocardial samples, prior and after grafting, from patients undergoing off-pump coronary revascularization surgery. The transcriptional profile of the mRNA in these samples was measured with gene array technology. Changes in transcriptional profiles can be correlated with the stress response of heart to off-pump surgery.
Keywords: human, cardiac, OPCAB coronary surgery, gene expression.

overall_design: Myocardial samples were collected, prior and after grafting, from patients undergoing off-pump coronary artery bypass grafting.

first: Myriam

last: Cherif

first: Amir

last: Mokhtari

first: Gianni

middle: D

last: Angelini

first: Massimo

last: Caputo


title: Changes in cardiac transcription profiles following on-pump coronary artery bypass grafting

summary:
To investigate changes in cardiac transcription profiles caused by on-pump cardiac surgery, we collected myocardial samples, prior and after grafting, from patients undergoing on-pump coronary artery bypass grafting with cardiopulmonary bypass and cardiac arrest. The transcriptional profile of the mRNA in these samples was measured with gene array technology. Changes in transcriptional profiles can be correlated with the stress response of heart to surgery, cardiopulmonary bypass and cardiac arrest.
Keywords: human, cardiac, CABG coronary surgery, gene expression, cardiopulmonary bypass.

overall_design: Myocardial samples were collected, prior and after grafting, from patients undergoing on-pump coronary artery bypass grafting with cardiopulmonary bypass and cardiac arrest.


title: mRNA immunoprecipitated with CUGBP1 in C2C12

status: Public on Jun 21 2010

city: Newark

first: Ju Youn

last: Lee

state: NJ

address: 185 South Orange Ave. MSB-E501

department: Biochemistry

institute: UMDNJ-New Jersey Medical School

summary: Dramatic changes in gene expression occur in response to extracellular stimuli and during differentiation.  Although transcriptional effects are important, alterations in mRNA decay also play a major role in achieving rapid and massive changes in mRNA abundance.  Moreover, just as transcription factor activity varies between different cell types, the factors influencing mRNA decay are also cell-type specific.GREs are recognized by CUGBP1, an RNA-binding protein and instability factor whose function is affected in several neuromuscular diseases. To dectect the mRNA associated with CUGBP1, we utilized RNA immunoprecipitation followed by microarray (RIP-Chip) to identify CUGBP1-associated transcripts.

overall_design: To identify the mRNA associated with CUGBP1, we performed the immunoprecipitation followed by microarray (RIP-Chip)

first: Jerome

middle: E

first: Ju

last: Wilusz

first: Bin

last: Tian

first: Carol

middle: J


title: Hearts after off-pump coronary revascularization surgery and on-pump coronary artery bypass grafting

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

overall_design: Refer to individual Series


title: Gene expression profiles of adult glomerular endothelial cells isolated from TIE2-GFP transgenic mice using FACS. (GUDMAP Series ID: 42)

first: GUDMAP

last: Developers

overall_design: Tie2-GFP transgenic mice were utilized to isolate the endothelial cell population from  the glomerulus of adult  kidneys.  The glomerular endothelial cells were isolated from kidneys using a combination of collagenase treatment, differential seiving, trypsin treatment and FACS.   The RNA was isolated from purified endothelial cells and the gene expression profiles were determined by microarrays.

first: Steve

last: Potter

first: Eric

last: Brunskill


title: Systematic analysis of cis-elements in unstable mRNAs demonstrates that CUGBP1 is a key regulator of mRNA decay in muscle cells


title: Expression data from C2C12 mouse myoblast with treatment actinomycin D

summary: Dramatic changes in gene expression occur in response to extracellular stimuli and during differentiation.  Although transcriptional effects are important, alterations in mRNA decay also play a major role in achieving rapid and massive changes in mRNA abundance.  Moreover, just as transcription factor activity varies between different cell types, the factors influencing mRNA decay are also cell-type specific. We have established the rates of decay for over 7000 transcripts expressed in mouse C2C12 myoblasts.

overall_design: To estimate mRNA decay rate in mouse muscle cells, we treated C2C12 mouse myoblasts with actinomycin D to inhibit transcription and collected samples at 0, 10, 50, 110 and 230 min.


title: Expression data from Adam17 knock out mice and wild type

status: Public on Jun 18 2010

city: Kiel

first: Robert

last: Haesler

address: Schittenhelmstr. 12

department: IKMB / 1st Dept. of Medicine

institute: University Clinic of Schleswig Holstein

summary: Adam17, a shedding protease, is strongly upregtulated during inflammation and cancer. Here we investigate the genome wide effects of Adam17 knock out on the transcriptome.

overall_design: Mouse tissue samples from n=3 wildtype colon, n=3 Adam17 knockout colon, n=3 wildtype skin and n=3 Adam17 knockout skin were used in the study.

last: Häsler

first: Athena

last: Chalaris

first: Stefan

last: Rose-John


title: Periostin, a cell adhesion molecule, facilitates invasion in the tumor microenvironment and annotates a novel tumor invasive signature in esophageal cancer

city: Houston

first: Sangbae

last: Kim

state: TX

address: 1 Baylor plaza

department: HGSC

institute: Baylor Colleage of Medicine

summary: Human squamous cell cancers are the most common epithelially derived malignancies. One example is esophageal squamous cell carcinoma (ESCC), which is associated with a high mortality rate that is related to a propensity for invasion and metastasis. We report that periostin, a highly expressed cell adhesion molecule, is a key component of a novel tumor invasive signature obtained from an organotypic culture model of engineered ESCC. This tumor invasive signature classifies with human ESCC microarrays, underscoring its utility in human cancer. Genetic modulation of periostin promotes tumor cell migration and invasion as revealed in gain of and loss of function experiments. Inhibition of EGFR signaling and restoration of wild-type p53 function were each found to attenuate periostin, suggesting interdependence of two common genetic alterations with periostin function. Our studies reveal periostin as an important mediator of ESCC tumor invasion and they indicate that organotypic (3D) culture can offer an important tool to discover novel biologic effectors in cancer.

overall_design: Invading and non-invading genetically engineered human esophageal cells with hTERT and EGFR overexpression and p53 mutations were grown in organotypic culture. These invading and non-invading cells were excised using laser-capture microdissection. RNA was isolated and amplified for Affymetrix U133 microarrays. Subsequent microarray analysis & comparison with 2 independent cohorts of primary ESCC tumors revealed upregulation of periostin as gene with highest upregulation found in novel tumor invasive signature in esophageal cancer.

first: Carmen

middle: Z

last: Michaylira

first: Gabrielle

last: Wong

first: Charles

middle: G

last: Miller

first: Christie

last: Gutierrez

first: Hiroshi

last: Nakagawa

first: Rachel

last: Hammond

first: Andres

last: Klein-Szanto

first: Ju-Seog

first: Meenhard

last: Herlyn

first: J

last: Diehl

first: Phyllis

last: Gimotty

first: Anil

last: Rustgi


title: Gene expression discriminates chromophobe renal cell carcinoma and oncocytoma

city: Grand Rapids

first: Min-Han

last: Tan

address: 333 Bostwick Ave NE

institute: Van Andel Research Institute

summary:
[original title] Genomic expression and single-nucleotide polymorphism profiling discriminates chromophobe renal cell carcinoma and oncocytoma.

Background : Chromophobe renal cell carcinoma (chRCC) and renal oncocytoma are two distinct but closely related entities with strong morphologic and genetic similarities.  While chRCC is a malignant tumor, oncocytoma is usually regarded as a benign entity.  The overlapping characteristics are best explained by a common cellular origin, and the biologic differences between chRCC and oncocytoma are therefore of considerable interest in terms of carcinogenesis, diagnosis and clinical management. Previous studies have been relatively limited in terms of examining the differences between oncocytoma and chromophobe RCC.
Methods : Gene expression profiling using the Affymetrix HGU133Plus2 platform was applied on chRCC (n=15) and oncocytoma specimens (n=15).  Supervised analysis was applied to identify a discriminatory gene signature, as well as differentially expressed genes.  Immunohistochemical validation was performed in an independent set of tumors.
Results : A novel 14 probe-set signature was developed to classify the tumors internally with 93% accuracy, and this was successfully validated on an external data-set with 94% accuracy. Parafibromin, aquaporin 6, and synaptogyrin 3 were novel immunohistochemical markers effectively discriminating the two pathologic entities.
Conclusion : Gene expression profiles and pathway analysis effectively distinguish chRCC from oncocytoma. We have generated a novel transcript predictor that is able to discriminate between the two entities accurately, and which has been validated both in an internal and an independent data-set, implying generalizability. We have identified a series of immunohistochemical markers that are clinically useful in discriminating chRCC and oncocytoma.

overall_design: 30 mRNA profiling samples (15 chromophobe RCC, 15 oncocytoma)

first: Min

first: Bin

middle: T

last: Teh


title: Monocyte vs Macrophage Study

city: Davis

first: William

last: Hu

address: 451 Health Science Dr.

department: Medical Microbiology & Immunology

institute: UC Davis

summary: Human intestinal macrophages contribute to tissue homeostasis in noninflamed mucosa through profound down-regulation of pro-inflammatory cytokine release. Here, we show that this down-regulation extends to Toll-like receptor (TLR)-induced cytokine release, as intestinal macrophages expressed TLR3-TLR9 but did not release cytokines in response to TLR-specific ligands. Likely contributing to this unique functional profile, intestinal macrophages expressed markedly down-regulated adapter proteins MyD88 and Toll interleukin receptor 1 domain-containing adapter-inducing interferon beta, which together mediate all TLR MyD88-dependent and -independent NF-kappaB signaling, did not phosphorylate NF-kappaB p65 or Smad-induced IkappaBalpha, and did not translocate NF-kappaB into the nucleus. Importantly, transforming growth factor-beta released from intestinal extracellular matrix (stroma) induced identical down-regulation in the NF-kappaB signaling and function of blood monocytes, the exclusive source of intestinal macrophages. Our findings implicate stromal transforming growth factor-beta-induced dysregulation of NF-kappaB proteins and Smad signaling in the differentiation of pro-inflammatory blood monocytes into noninflammatory intestinal macrophages.

overall_design: Comparison of unstimulated monocytes and macrophages, and flagellin stimulated monocytes and macrophages.

first: Michael

last: George

middle: K


title: Clinical score and gene profiling patterns identify Kawasaki disease patients who may benefit from methylprednisolone

status: Public on Jun 17 2010

city: Sagamihara

first: Shohei

last: Ogata

state: Kanagawa

address: 1-15-1, Kitasato

department: Pediatrics

institute: Kitasato University, School of Medicine

summary:
Clinical score and transcript abundance patterns identify Kawasaki disease patients who may benefit from addition of methylprednisolone.
Intravenous immunoglobulin (IVIG) treatment-resistant patients are high risk of developing coronary artery lesions (CALs) with Kawasaki disease (KD). The IVIG-responsive (Group A; n = 6) and -resistant patients (Group B) were predicted before starting the initial treatment using the Egami scoring system, and randomly allocated a single-IVIG treatment group (Group B1; n = 6) or a IVIG-plus-methylprednisolone (IVMP) combined therapy group (Group B2; n = 5). We investigated transcript abundance in the leukocytes of those patients using microarray analysis.
Results: five patients in Group A and 1 patient in Group B1 responded to initial IVIG treatment. All Group B2 patients responded to IVIP-plus-IVMP combined therapy. Prior to performing these treatments, those transcripts related to IVIG-resistance and to the development of CALs, such as IL1R, IL18R, oncostatin M, suppressor of cytokine signaling-3, S100A12 protein, carcinoembryonic antigen-related cell adhesion molecule-1, matrix metallopeptidase-9 and polycythemia rubra vera-1 were more abundant in Group B patients in comparison to Group A patients. Moreover, those transcripts in Group B2 patients were more profoundly and broadly suppressed than Group B1 patients after treatment.                                                        Conclusion: this study elucidated the molecular mechanism of the effectiveness of IVIG-plus-IVMP combined therapy.

overall_design: 34 samples of pre- and post-treatment in three groups consisting of predicted as  IVIG-responsive patients,  given single-IVIG treatment patients and IVIG-plus-IVMP combined therapy group in predicted as IVIG-resistant patients. Samples were analyzed without replicates.

first: Yoshihito

last: Ogihara

first: Keiko

last: Nomoto

first: Kazumasa

last: Akiyama

first: Yayoi

last: Nakahata

first: Kayoko

last: Sato

first: Kastunori

last: Minoura

first: Kenichi

last: Kokubo

first: Hirosuke

last: Kobayashi

first: Masahiro

last: Ishii


title: Brain metastasis from lung adenocarcinoma patients

city: New York

first: Don

middle: X

last: Nguyen

address: 1275 York Box 116

department: Cancer Biology and Genetics

institute: MSKCC

summary: Microarray analysis of 28 brain metastasis samples from lung adenocarcinoma patients.

overall_design:
28 brain metastasis samples:
19 from Marc Ladanyi
9 from William L. Gerald

first: Marc

last: Ladanyi

last: Gerald

first: Xiang

middle: F

last: Zhang


title: Hyperactivation of PI3K promotes escape from hormone dependence in estrogen receptor-positive breast cancer

status: Public on Jun 15 2010

city: Nashville

first: Todd

middle: W

last: Miller

state: TN

address: 2220 Pierce Ave, 777 PRB

department: Medicine

institute: Vanderbilt Univ

summary:
Hyperactivation of phosphatidylinositol-3 kinase (PI3K) promotes escape from hormone dependence in estrogen receptor-positive breast cancer.

A significant fraction of breast cancers exhibit de novo or acquired resistance to estrogen deprivation. We used gene expression microarrays to identify genes and pathways that are commonly dysregulated in ER+ cell lines with acquired hormone-independent growth. MCF-7, ZR75-1, MDA-361, and HCC-1428 ER+, estrogen-responsive breast cancer cells were cultured under hormone-depleted conditions (10% DCC-FBS) for several months until sustainable hormone-independent cell populations emerged.

overall_design: Parental and long-term estrogen-deprived (LTED) cells were treated with 10% dextran-coated charcoal-treated fetal bovine serum (DCC-FBS) x 24 hrs prior to RNA harvest for array analysis.

first: Carlos

last: Arteaga


title: Expression data from cones in degenerated retinas from C3H/HeNCrl (Pde6brd1) mice

city: Basel

first: Erik

last: Cabuy

address: Maulbeerstrasse 66

department: Single Cell Genomics

institute: Friedrich Miescher Institute

summary:
We used FACS isolated RD cone photoreceptors from C3H mice (we refer this mouse model as f-RD) that were transfected by AAVs to express fluorescent reporters to genomic analyses. We tested three different ages.
Many cone photoreceptor markers are highly enriched, identifying the isolated RD cones as cones.

overall_design:
Two different treatments: mCAR-EGFP or mCAR-eNpHR-EYFP, where mCAR-EGFP served as a control condition and mCAR-eNpHR-EYFP was the light sensor.
Mouse cone arrestin-3 promoter (mCAR) was used to drive EGFP/eNpHR-EYFP in RD photoreceptors. Cones are brightly labeled by these constructs, indicating that the intrinsic promoter is active and intrinsic cone markers are expressed.

first: Volker

last: Busskamp


title: Markers of Taxane Sensitivity in Breast Cancer

first: Jennifer

last: Pietenpol

address: 652 Preston Research Building, 23rd Avenue South at Pierce

institute: Vanderbilt University Medical Center

summary: The purpose of this study was to identify molecular markers of pathologic response to neoadjuvant paclitaxel/radiation treatment, protein and gene expression profiling were done on pretreatment biopsies.  Patients with high-risk, operable breast cancer were treated with three cycles of paclitaxel followed by concurrent paclitaxel/radiation. Tumor tissue from pretreatment biopsies was obtained from 19 of the 38 patients enrolled in the study. Protein and gene expression profiling were done on serial sections of the biopsies from patients that achieved a pathologic complete response (pCR) and compared to those with residual disease, non-pCR (NR).  Proteomic and validation immunohistochemical analyses revealed that α-defensins (DEFA) were overexpressed in tumors from patients with a pCR. Gene expression analysis revealed that MAP2, a microtubule-associated protein, had significantly higher levels of expression in patients achieving a pCR. Elevation of MAP2 in breast cancer cell lines led to increased paclitaxel sensitivity. Furthermore, expression of genes that are associated with the basal-like, triple-negative phenotype were enriched in tumors from patients with a pCR. Analysis of a larger panel of tumors from patients receiving presurgical taxane-based treatment showed that DEFA and MAP2 expression as well as histologic features of inflammation were all statistically associated with response to therapy at the time of surgery.  We show the utility of molecular profiling of pretreatment biopsies to discover markers of response. Our results suggest the potential use of immune signaling molecules such as DEFA as well as MAP2, a microtubule-associated protein, as tumor markers that associate with response to neoadjuvant taxane–based therapy.

overall_design: Tumor tissues from pretreatment needle biopsies from patients enrolled on a paclitaxel/radiation clinical trial were laser capture microdissected for RNA extraction and hybridization to Affymetrix microarrays. We analyzed one array (sample A) from duplicate samples from each patient. 14 subject, 2 replicates each.

first: Joshua

middle: A

last: Bauer


title: Gene expression in mouse neonatal cardiomyocytes, cardiac fibroblasts, reprogramming failed GFP- cells, and GFP+ iCMs

status: Public on Jun 12 2010

city: San Francisco

first: Masaki

last: Ieda

address: 1650 Owens street,

institute: Gladstone Institute

summary: The reprogramming of fibroblast cells to induced pluripotent stem (iPS) cells raises the possibility that a somatic cell could be reprogrammed to an alternative differentiated fate without first becoming a stem/progenitor cell. A large pool of fibroblast cells exists in the post-natal heart, yet no single “master regulator” of direct cardiac reprogramming has been identified. Here, we report that a combination of three developmental transcription factors (i.e., Gata4, Mef2c and Tbx5) rapidly and efficiently reprogrammed post-natal cardiac or tail-tip fibroblasts directly into differentiated cardiomyocyte-like cells. Induced cardiomyocytes expressed cardiac-specific markers, had a global gene expression profile similar to cardiomyocytes, and contracted spontaneously. Fibroblast cells transplanted into mouse hearts one day after transduction of the three factors also differentiated into cardiomyocyte-like cells. These findings demonstrate that functional cardiomyocytes can be directly reprogrammed from differentiated somatic cells by defined factors. Reprogramming of endogenous or explanted fibroblast cells might provide a source of cardiomyocytes for regenerative approaches.

overall_design: To compare the progressive global gene expression pattern of iCMs, cardiomyocytes and cardiac fibroblasts, we isolated RNA from mouse neonatal cardiomyocytes, cardiac fibroblasts, reprogramming failed GFP- cells and GFP+ iCMs, and profiled mRNA expressions by microarray analyses. Arrays were performed using Affymetrix mouse Gene 1.0 ST arrays. Analysis was performed on three biological replicates for each group.

first: MASAKI

last: IEDA

first: DEEPAK

last: SRIVASTAVA


title: Reprogramming of T Cells from Human Peripheral Blood

status: Public on Jun 10 2010

city: Boston

first: Hu

last: Li

address: 3 Blackfan Circle

institute: Wyss Institute

summary: Human induced pluripotent stem (iPS) cells derived from somatic cells of patients hold great promise for modelling human diseases. Dermal fibroblasts are frequently used for reprogramming, but require an invasive skin biopsy and a prolonged period of expansion in cell culture prior to use. Here, we report the derivation of iPS cells from multiple human blood sources including peripheral blood mononuclear cells (PBMCs) harvested by routine venipuncture. Peripheral blood-derived human iPS lines are comparable to human embryonic stem (ES) cells with respect to morphology, expression of surface antigens, activation of endogenous pluripotency genes, DNA methylation and differentiation potential. Analysis of Immunoglobulin and T-cell receptor gene rearrangement revealed that some of the PBMC iPS cells were derived from T-cells, documenting derivation of iPS cells from terminally differentiated cell types. Importantly, peripheral blood cells can be isolated with minimal risk to the donor and can be obtained in sufficient numbers to enable reprogramming without the need for prolonged expansion in culture. Reprogramming from blood cells thus represents a fast, safe and efficient way of generating patient-specific iPS cells.

overall_design: We isolated RNA from multiple human blood sources including peripheral blood mononuclear iPS cells, multiple somatic cells and iPS cells and human embryonic cells and hybridized them to Affymetrix gene expression microarrays.

first: Yuin-Han

last: Loh

first: James

last: Collins

first: George

middle: Q

last: Daley


title: BRCA1 depletion effect on HeLa cells

status: Public on Jun 09 2010

city: Columbus

first: Ekaterina

last: Lamber

address: 904 BRT, 460 W. 12th Avenue

department: Biomedical Informatics

institute: Ohio State University

summary: Analysis of HeLa cells following depletion of BRCA1 tumor supressor using RNAi against BRCA1. Results provide insight into the molecular mechanisms underlying loss of the BRCA1 function.

overall_design: Six samples (three control samples and three BRCA1 depleted samples) have been analysed. For the control, the samples derived from the HeLa cells treated with RNAi against GFP were used.

middle: P

first: Andrew

last: Horwitz

first: Jeffrey

last: Parvin


title: Oxidoreductase transcript data from human umbilical vein endothelial cells

status: Public on Jun 05 2010

city: London

first: Yiannis

last: Ioannou

address: Centre For Rheumatology, Rm 331, Windeyer Building 46 Cleveland Street

institute: University College London

summary: Oxidoreductase enzymes are critical to redox regulation of intracellular proteins within human cells. We used microarrays to identify which oxidreducatse genes are expressed in unstimulated human umbilical vein endothelial cells.

overall_design: Human umbilical vein endothelial cells were grown under optimal conditions and then RNA extracted and hybridized on Affymetrix microarrays.

first: Steven

last: Krilis

first: Pei

last: Yu


title: Expression profiling of small intestine lamina propria dendritic cells

city: SÃO PAULO

first: Helder

middle: I.

last: Nakaya

state: SÃO PAULO

address: AVENIDA PROFESSOR LINEU PRESTES, 580, Block 17

country: Brazil

institute: Universidade de São Paulo

summary:
Dendritic cells play a vital role in initiating robust immunity against pathogens as well as maintaining immunological tolerance to self antigens, food antigens and intestinal commensals. However, the intracellular signaling networks that program DCs to become tolerogenic are largely unknown. To address this, we analyzed gene expression profiles using microarray analysis of purified intestinal lamina propria DCs (CD11c+ CD11b+ DCs and CD11c+ CD11b- DCs) from mice.
Keywords: Lamina propria, DCs, cell type comparison

overall_design: We sought to determine the expression profile of small intestine lamina propria CD11c+ cells. RNA was extracted from DCs sorted from mouse small intestine (CD11c+CD11b- and CD11c+CD11b+ cells) and hybridized on Affymetrix microarrays.

first: Santhakumar

last: Manicassamy

middle: I

first: Bali

last: Pulendran


title: Gene expression associated with liver metabolism during viral hemorrhagic fever

status: Public on Jun 08 2010

city: Blacksburg

first: kommidi

middle: Reddy

last: Chaitanya

state: VA

address: Virginia Tech

institute: VBI

summary: Rhesus macaques (Macaca mulatta) infected with a lethal dose of lymphocytic choriomeningitis virus-strain WE (LCMV-WE) provide a model for Lassa fever virus infection of man.  Like Lassa fever in human beings, disease begins with flu-like symptoms but can progress to morbidity fairly rapidly.  Previously, we profiled the blood transcriptome of LCMV-infected monkeys (M. Djavani et al. J. Virol. 2007: PMID 17522210) showing distinct pre-viremic and viremic stages that discriminated between virulent and benign infections.  In the present study, changes in liver gene expression from macaques infected with virulent LCMV-WE were compared to gene expression in uninfected monkeys as well as to monkeys that were infected but not diseased.  We observed gene expression changes that occurred before the viremic stage of the disease, and could potentially serve as biomarkers that discriminate between exposure to a hemorrhagic fever virus and exposure to a benign virus.  Based on a functional pathway analysis of differentially expressed genes, virulent LCMV-WE had a much broader effect on liver cell function than non-virulent virus.  During the first few days of infection, virulent virus impacted gene expression associated with the generation of energy, such as fatty acid metabolism and glucose metabolism, with the complement and coagulation cascades, and with steroid metabolism, MAPK signaling and cell adhesion.  For example, the energy profile resembled that of an organism entering starvation: acetyl-CoA carboxylase, a key enzyme of fatty acid synthesis, was shut down and gene products involved in gluconeogenesis were up-regulated.  In conclusion, this study identifies several potential gene markers of LCMV-WE-associated liver disease and contributes to the database of gene expression changes correlated with LCMV pathogenesis in primates.

overall_design: 6 groups: uninfected controls, LCMV-WE infected (pre-viremic; day 1 to day 3), LCMV-WE infected (viremic; day 4 to day 7), LCMV-WE infected (post-viremic; day 8 to day 12), LCMV-Armstrong (LCMV-ARM; non-virulent strain) infected, and LCMV-ARM/LCMV-WE infected but not diseased. Each sample is from the liver of a different rhesus macaque.

first: Mahmoud

last: Djavani

first: Oswald

middle: R

last: Crasta

first: Yan

last: Zhang

first: Juan

middle: C

last: Zapata

first: Bruno

last: Sobral

first: Joseph

last: Bryant

first: Harry

last: Davis

first: Maria

middle: S

last: Salvato


title: Gene expression analysis of 3 node positive vs 3 node negative intestinal type gastric cancers by gene array technology.

first: Eva

last: Simon

state: Schleswig-Holstein

address: Arnold-Heller-Straße 3, Haus 14

department: Institute of Pathology

institute: Christian-Albrechts-University

summary: Gastric cancer is one of the most common causes of cancer-related deaths worldwide. The lymph node status represents the strongest prognostic factor. Due to its extremely poor prognosis, the identification of novel therapeutic targets is urgently needed. Therefore, we aimed to assess differentially expressed genes in nodal negative versus nodal positive intestinal type gastric carcinoma by GeneChip array technique. The transcriptional profile of 6 gastric cancers with and without lymphatic dissemination was analyzed. A total of 115 transcripts were found to be up- and 219 to be down-regulated in node positive compared with node negative gastric cancers. Next we searched for differentially expressed GPCRs. We identified 52 GPCRs and GPCR-related genes, which were up- or down-regulated with a fold change factor greater 1.5.

overall_design: Tissue samples of gastric cancer were obtained surgically at the Charité University Hospital Berlin. Tumours were classified by histology according to the WHO and Laurén classification. Fresh frozen tissue of 6 intestinal type gastric carcinoma cases was used for Affymetrix GeneChip analysis (nodal negative: 3 patients; nodal positive: 3 patients; female-male-ratio: 1:2). Total RNA was isolated from each sample. Subsequently to gene array analysis the transcription of candidate genes was validated by real-time RT-PCR on an independent series of 37 gastric cancers.

first: Barbara

last: Ingold

first: Ute

last: Ungethüm

first: Ralf

last: Kuban

first: Ulf

last: Neumann

first: Matthias

last: Ebert

first: Wilko

last: Weichert

first: Stefan

last: Schulz

first: Christoph

last: Röcken


title: Comparison of splenic and small intestine lamina propria dendritic cells

first: Helder

last: Nakaya

summary:
Dendritic cells play a vital role in initiating robust immunity against pathogens as well as maintaining immunological tolerance to self antigens, food antigens and intestinal commensals. However, the intracellular signaling networks that program DCs to become tolerogenic are largely unknown. To address this, we analyzed gene expression profiles using microarray analysis of purified intestinal lamina propria DCs (CD11c+ CD11b+ DCs and CD11c+ CD11b- DCs) and compared it to splenic DCs (CD11c+ DC), from mice.

This SuperSeries is composed of the SubSeries listed below.

overall_design:
We sought to determine the unique genetic profile of small intestine lamina propria CD11c+ cells compared to splenic CD11c+ cells. We performed a meta-analysis using the expression profiles of Intestinal lamina propria CD11c+ CD11b+ DCs (GSM550122), Intestinal lamina propria CD11c+ CD11b- DCs (GSM550121) and Splenic CD11c+ DCs (GSM550126). This study combined and re-normalized the microarray data from GSE22127 and GSE22128 studies.

Refer to individual Series for additional details


title: Clinical Microfluidics for Neutrophil Genomics and Proteomics

status: Public on Jun 03 2010

first: Wenzhong

last: xiao

state: MA

address: 55 Fruit Street, GRB 1302

institute: Massachusetts General Hospital

summary:
Neutrophils play critical roles in modulating the immune response. However, neutrophils have a short circulating half life, are readily stimulated in vitro, and have low levels of cellular mRNA when compared to other blood leukocyte populations. All of these factors have made it difficult to evaluate neutrophils from clinical populations for molecular and functional studies.
Here we present a robust methodology for rapidly isolating neutrophils directly from whole blood and develop ‘on- chip’ processing for mRNA and protein isolation for genomics and proteomics.  We validate this device with an ex vivo stimulation experiment and demonstrate the ability of the device to discriminate subtle differences in the genomic and proteomic response of peripheral blood neutrophils to direct and indirect stimulation. Lastly, we implement this tool as part of a near patient blood processing system within a multi-center clinical study of the immune response to severe trauma and burn injury and demonstrate that this technique is easy to use by nurses and technical staff yielding excellent quality and sufficient quantity of mRNA for sensitive genomic readout of the host response to injury

overall_design: 1. Ex vivo Stimulation Studies: We assessed whether the relatively small number of isolated neutrophils captured by the microfluidics cassettes would impact the resulting genomic sensitivity and potential discriminatory genomic capabilities in response to various stimuli. To do this, we compared the genome-wide expression profile in neutrophils from 4 independent repeated experiements under three conditions - untimulated, ex vivo activation with either Escherichia coli lipopolysaccharide (LPS), or with granulocyte-macrophage colony-simulating factor (GM-CSF) and interferon-gamma (INF-g) (referred to as GM+I). In both protocols, whole blood was stimulated ex vivo to allow leukocyte and plasma protein interactions. 2.  Inter-subject Reproducibility: To further ensure the reliability of the of the microfluidics cassette isolation method, we directly compared the gene expression of neutrophils captured in the microfluidics cassettes with neutrophils isolated using density centrifugation with Ficoll-dextran. We performed parallel neutrophil isolations using both methodologies from five different healthy volunteers and processed the cell lysates for microarray analysis using identical protocols.

first: Kenneth

last: Kotz

first: Wenzong

last: Xiao

first: Carol

last: Miller-Graziano

first: Wei-Jun

last: Qian

first: Elizabeth

last: Warner

first: Lyle

middle: L

last: Moldawer

first: Weihong

last: Xu

first: Julie

last: Wilhelmy

first: Michael

middle: N

last: Mindrinos

first: Richard

middle: D

last: Smith

first: Ronald

last: Tompkins

first: Mehmet

last: Toner


title: Gene expression of colon from control or VilCre;Ihhflox/flox mice

status: Public on Jun 04 2010

first: Xin

last: Chen

state: CA

institute: UCSF

summary:
Ihh expression is required for intestinal stem cell niche development.
Loss of Ihh leads to disruption of intestinal stem cell niche, which leads to abnormal stem cell development and epithelial cell differentiation.

overall_design:
3 paired control (C) and mutant (M) mice here harvested. Their colon tissues were analyzed using Affymetrix Mouse Gene 1.0ST array
Control and VilCre;Ihhflox/flox mice were harvested at p12
There are 3 pairs (total 6) samples:
M1 and C1 are littermates
M2 and C2 are littermates
M3 and C3 are littermates


title: Expression data from Epiderm cultured skin derived from four different donors

city: MASON

first: Jay

middle: Patrick

last: Tiesman

address: PO BOX 8006

department: Global Biotechnology

institute: Procter & Gamble

summary:
This study provides a comparison of genes expressed in reconstructed cultured epidermis derived from four different donors.
GeneChips were used to compare reconstructed human EpiDerm™ EPI-200 tissues prepared from four different neonatal foreskin donors (254, 1188, 219 and 926).  This work will assist in providing a deeper understanding of genes expressed in cultured skin equivalents.

Keywords: Cell type/donor comparison

overall_design: 20 total samples:  5 Replicates obtained from four different donors.


title: High VEGFC expression is associated with unique gene expression profiles and predicts adverse prognosis in pediatric and adult acute myeloid leukemia.

status: Public on Jun 02 2010

city: Rotterdam

first: Brian

last: Balgobind

address: Dr. Molewaterplein 60

department: Pediatric Oncology/Hematology

institute: Erasmus MC - Sophia Children's Hospital

summary: High VEGFC mRNA expression of AML blasts is related to increased in vitro and in vivo drug resistance. The prognostic significance of VEGFC on long-term outcome and its associated gene expression profiles remain to be defined. We studied the effect of VEGFC on treatment outcome and investigated gene expression profiles associated with VEGFC using microarray data of 525 adult and 100 pediatric AML patients. High VEGFC expression appeared strongly associated with reduced complete remission rate, reduced overall and event-free survival (OS and EFS) in adult AML. Multivariable analysis established high VEGFC as prognostic indicator independent of cytogenetic risk, FLT3-ITD, NPM1, CEBPA, age and WBC. Also in pediatric AML high VEGFC was related to reduced OS. A unique series of differentially expressed genes was identified that distinguished AML with high VEGFC from AML with low VEGFC, i.e., 331 upregulated genes (representative of proliferation, VEGF-receptor activity, signal transduction) and 44 downregulated genes (e.g. related to apoptosis) consistent with a role in enhanced chemoresistance. In conclusion, high VEGFC predicts adverse long-term prognosis and provides prognostic information in addition to well-known prognostic factors.

overall_design: 98 bone marrow and peripheral blood samples were collected at diagnosis and frozen. They were later thawed and hybridized to Affymetrix U133 Plus 2.0 arrays.

middle: V

first: Monique

last: Den Boer

first: Henk-Marijn

middle: J

last: de Jonge

first: Eveline

last: de Bont


title: DNA microarrays of three shRNA control iPS clones (Ctrl 2,3,4) and shECAD iPS clones (shECAD 4,8,9)

status: Public on Jun 01 2010

city: Guangzhou

first: Duanqing

last: Pei

address: Room 301, International Business Incubator, Guangzhou science park

department: Center for Molecular Medicine

institute: Guangzhou Institute of Biomedicine and Health, Chinese Academy of Sciences(GIBH.CAS)

summary: E-cadherin upregulation is an early event of reprogramming of fibroblasts to induce pluripotent stem cells (iPS). Knocking down of E-cadherin by shRNA impairs iPS generation, though some colonies with great morphorlogical difference to shRNA control colonies remain. To illustrate the molecular and functional difference between shECAD iPS clones and shRNA control iPS clones, three respective iPS clones (shECAD 4,8,9 and Ctrl 2,3,4) were derived and DNA microarrays were run to analyze the transcriptional profile of these clones.

overall_design: OG2 MEFs were infected with Sox2, Klf4, Oct4 and c-Myc (SKOM) plus either Luciferase shRNA (shLUC) or E-cadherin shRNA (shECAD) retrovirus. At Day 6 post infection cells were split onto feeder cells. Several colonies from SKOM+shLuc and SKOM+shECAD were picked out at Day 14 post infection respectively and three cell lines were established, namely Ctrl 2,3,4 for SKOM+shLuc iPS and shECAD 4,8,9 for SKOM+shECAD iPS. All clones were maintained on feeder cells in mESC medium. RNA were extracted from these six cell lines and DNA microarrays were run to analyze the transcriptional profile.

first: Ronghui

last: Li

first: Wenzhi

last: He


title: Molecular mechanisms underlying reprogramming of mouse fibroblasts into pluripotent stem cells

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

overall_design: Refer to individual Series

first: Jialiang

last: Liang


title: Expression data from Human seminal vesicles

city: Rennes

first: Charles

last: PINEAU

address: Campus de Beaulieu (batiment 24)

country: France

institute: INSERM

summary: The human seminal plasma is a potential source of biomarkers for male reproductive disorders. A tissue-profiling analysis of the main organs participating in the secretion of this body fluid was conducted to identify tissue-specific genes along the male reproductive tract.

overall_design: Total RNA from non pathological Human seminal vesicles were extracted and hybridized on Affymetrix microarrays. Expression signals in seminal vesicles (present dataset), prostates (GEO; GSE7307), epidydimises (GEO; GSE7808) and testicular samples (Arrayexpress; E-TABM-130) were compared to identify genes that are detected in one of these organs only.

first: Antoine

last: Rolland

last: Pineau


title: Gene expression profiling of human unstimulated regulatory T cells (Tregs) and naïve CD4+ T cells

status: Public on May 29 2010

city: Milwaukee

first: Martin

last: Hessner

state: WI

address: 8701 Watertown Plank Road

institute: Medical College of Wisconsin

summary: Human regulatory T cells (TR) cells have potential for the treatment of immune mediated diseases, such as graft versus host disease, but the anergic phenotype of these cells makes them difficult to expand in vitro.  We have examined the requirements for growth and cytokine expression from highly purified human TR cells, and correlated these findings with the signal transduction events of these cells.  We demonstrate that these cells do not proliferate or secrete IL-10 even in the presence of high doses of IL-2.  Stimulation with a superagonistic anti-CD28 antibody (clone 9D4) and IL-2 partially reversed the proliferative defect, and this correlated with reversal of the defective calcium mobilization in these cells.  Dendritic cells were effective at promoting TR cell proliferation, and under these conditions the proliferative capacity of TR cells was comparable to conventional CD4 lymphocytes.  Blocking TGF-beta activity abrogated IL-10 expression from these cells, while addition of TGF-beta resulted in IL-10 production.  These data demonstrate the ability of dendritic cells to provide proper costimulation to overcome the anergic phenotype of TR cells.  In addition, these data demonstrate for the first time that TGF-beta is critical to enable TR cells to express IL-10.

overall_design: In order to confirm that our isolation strategy resulted in cells with characteristics of TR cells, we performed gene expression profiling of highly purified TR cells from two different individuals, which were compared to the gene expression profile of naïve CD4+CD45RA+ cells.  We first performed hierarchical clustering of the gene expression profiles of unactivated naïve and TR cells from the two individuals.  We show that the gene expression patterns of TR cells were highly similar between the two samples (correlation coefficient of 0.82), as were the gene expression profiles of naïve CD4 cells between the two samples (correlation coefficient of 0.91).  After averaging the gene expression signal from these two individuals, we compared the gene expression profile of unactivated TR cells with naïve CD4 cells and show that TR cells over-express a variety of genes known to be associated with a TR phenotype (e.g.  CTLA-4, IKZF2, IL-2RA).  In addition, we also detected very high levels of expression of genes not typically associated with a TR phenotype, with the highest level of expression of IL-1 receptors in resting TR cells (Figure 2).  These data confirm that the sorting strategy was effective at isolating T cells expressing a TR phenotype.

first: Benedetta

last: Bonacci

first: Brandon

last: Edwards

first: Shuang

last: Jia

first: Calvin

last: Williams

first: Stephen

last: Gauld

first: James

last: Verbsky


title: Gene expression data from S. aureus-exposed neutrophils

city: Hamilton

first: Addie

last: Whitney

state: MT

address: 903 S 4th St

department: LHBP

institute: NIH/NIAID/RML

summary:
Neutrophil lysis after phagocytosis is a process potentially important in the pathogenesis of community-associated methicillin-resistant S. aureus (CA-MRSA) infection.  The mechanism for this process is not currently known.  Therefore, to better understand CA-MRSA virulence we used human oligonucleotide microarrays to investigate the mechanism underlying enhanced PMN lysis that occurs after phagocytosis of CA-MRSA.
In order to examine the effect of S. aureus on the neutrophil transcriptome and to elucidate any possible differences in this effect between hospital- and community-associated S. aureus, we performed microarray expression analysis on human neutrophils treated with hospital- and community-associated S. aureus.

overall_design: Polymorphonuclear leukocytes (PMNs) were isolated from the blood of healthy donors.  Control and S. aureus-exposed PMNs were incubated at 37C for 1, 2, 3 or 6 hours.

first: A

middle: M

last: Palazzolo-Ballance

first: S

last: Kobayashi

last: Kennedy

first: K

last: Braughton

first: D

middle: E

last: Sturdevant

last: Dorward

first: B

last: Kreiswirth

first: J

last: Musser

first: F

last: DeLeo


title: Identification of genes that regulated by IRF4 in human cutaneous T cell lymphoma HuT-102 cells

city: Toyama

first: Yoshiaki

last: Tabuchi

state: Toyama

address: 2630 Sugitani

department: Life Science Research Center

institute: University of Toyama

summary: The microarray analysis showed an interesting up-regulation in the set of genes controlling the development of Th1, mainly IFN-gamma, and other type 1 interferon response genes including CXCL10 in IRF4 knocked-down HuT-102 cells.

overall_design: HuT-102 cells, a human cutaneous T cell lymphoma, were transiently transfected with siRNAs against human IRF4 or firefly luciferase. Cells were incubated for 60 h at 37 centigrade. Total RNA samples were prepared from the cells. Gene expression was analyzed by an Affymetrix GeneChip® system with a Human Genome U133-plus 2.0 array for analysis of over 47,000 transcripts. Sample preparation for array hybridization was carried out as described in the manufacturer’s instructions.

first: Alaa

last: Refaat

first: Yue

last: Zhou

first: Ichiro

last: Takasaki

first: Hiroaki

last: Sakurai


title: A large-scale clinical study of gene expression response to severe burn injury

city: Palo Alto

first: Weihong

last: Xu

address: 855 California Ave

department: Department of Biochemistry

institute: Stanford Genome Technology Center

summary:
To understand the age-dependent response to burn injury, blood samples from pediatric and adult patients  were collected at different times after severe burn injury.
Gene expression was measured using Affymetrix U133 Plus 2.0 arrays for both patient samples and healthy controls. Time points were binned into two groups: early stage for <11 days and middle stage for 11-49 days.

overall_design: 114 arrays for 57 patients (2 time points per patient) and 63 arrays for 63 healthy controls.

first: Wenzhong

last: Xiao

first: Ron

last: Tompkins


title: The mutation spectrum revealed by paired genome sequences from a lung cancer patient

status: Public on May 27 2010

city: South San Francisco

first: Peter

last: Haverty

address: 1 DNA Way

department: Bioinformatics

institute: Genentech, Inc.

type: Genome variation profiling by genome tiling array


title: Expression data from WT SIRT6 and SIRT6 albumin CRE conditional mice

status: Public on May 28 2010

city: Bethesda

first: Chuxia

last: Deng

state: MD

address: 9000 Rockville Pike

institute: NIDDK, National Institutes of Health

summary: Microarray analysis of liver tissue from WT SIRT6 and conditional knockout of SIRT6 using albumin-Cre (SIRT6Co/Co ;Alb-Cre) at 2 and 8 months of age

overall_design: RNA was extracted from mouse liver tissue at 2 and 8 months of age.  RNA from three pairs of WT SIRT6 and SIRT6Co/Co ;Alb-Cre mice was combined and hybridized to Affymetrix mouse gene 1.0 ST arrays.


title: Induced Sputum Genes Associated With Spirometroc and Radiological Disease Severity in COPD Ex-smokers

city: Stevenage

first: steve

middle: matthew

last: fox

address: Gunnels Wood Road

department: Statistics

institute: GlaxoSmithKline

summary: Induced sputum is used to sample inflammatory cells, predominantly neutrophils and macrophages, from the airways of COPD patients. Our aim was to identify candidate genes associated with the degree of airflow obstruction and the extent of emphysema by expression profiling, and then to confirm these findings for selected candidates using specific PCR and protein analysis.

overall_design: Two sputum studies were performed in GOLD stage 2 -4 COPD ex-smokers from the ECLIPSE cohort. First, gene array profiling at baseline in 1480 patients was performed. At year 1, samples from a separate population of 176 patients were used for real-time PCR. The gene expression findings for IL-18R were further analysed using immunohistochemistry in lung tissue and induced sputum samples from patients outside the ECLIPSE cohort.

first: Dave

last: Singh

first: Steve

last: Fox

first: Ruth

last: Tal-Singer

first: Jonathan

last: Plumb

first: Stuart

last: Bates

last: Broad

first: John

last: Riley

first: Bartolome

last: Celli