title: Transgenerational gene expression down the male line in pig

status: Public on Sep 29 2011

city: Berne

first: Martin

last: Braunschweig

state: Berne

address: Bremgartenstrasse 109A

department: Vetsuisse Faculty

country: Switzerland

institute: University of Bern

summary: We investigated the nutritional effects on gene expression in a three generation Large White pig feeding experiment. A group of experimental (E) F0 boars were fed a standard diet supplemented with high amounts of methylating micronutrients whereas a control (C) group of F0 boars received a standard diet. These differentially fed F0 boars sired F1 boars which then sired 60 F2 pigs. Gene expression profiles showed significant twofold differences in mRNA level between 8 C F2 offspring and 8 E F2 offspring for 79, 64 and 53 probes for muscle, liver and kidney RNA, respectively. We found that in liver and muscle respective pathways of lipid metabolism and metabolic pathway were over-represented for the differentially expressed genes.

overall_design: Gene expression in three tissue types of F2 offspring from differentially fed F0 boars were measured. F0 boars received either a standard diet or a standard diet supplemented with methylating micronutrients. These boars produced the F1 males that received exclusively the standard diet. The F2 generation was then produced with these F1 boars. Gene expression was measured in liver, skeletal muscle and kidney of 8 F2 pigs derived from F0 boars that received the standard diet and of 8 F2 pigs derived from those F0 boars that received the standard diet supplemented with methylating micronutrients.

first: Vidhya

last: Jagannathan

first: Andreas

last: Gutzwiller

first: Giuseppe

last: Bee


title: Genome-wide analysis of vitamin D receptor (VDR) target genes in THP-1 monocytic leucemia cells

status: Public on Aug 17 2011

city: Kuopio

first: Sami

last: Heikkinen

address: Yliopistonranta 1E

department: Institute of Biomedicine

country: Finland

institute: University of Eastern Finland

summary: Identification of primary target genes of vitamin D receptor (VDR) in an immune-related cellular model (THP-1 cells) to study, in conjunction with VDR binding data from ChIP-seq, the genome-wide mechanisms of transcriptional regulation by VDR.

overall_design: THP-1 cells were treated 4 h either with 0.1% ethanol (vehicle, control) or 1α,25(OH)2D3 (1,25D)

first: Sabine

last: Seuter

first: Merja

last: Heinäniemi

last: Väisänen

first: Petri

last: Pehkonen

first: Carsten

last: Carlberg


title: Cross species hybridization of human cancer cells xenografted into different mouse organ sites

status: Public on Sep 24 2011

city: Houston

first: Sangbae

last: Kim

state: TX

address: 1 Baylor plaza

department: HGSC

country: USA

institute: Baylor Colleage of Medicine

summary: To test gene expression changes of human cancer cells and mouse surrounding tissue cells during tumor progression, 4 different types of cancer cells (MDA-MB231Br3, PC14Br4, KM12M, A375SM) were injected into mouse brain, skin and orthotopic sites. RNAs containing human cancer cells and mouse surrounding tissue cells were extracted and hybridized into human and mouse arrays at the same times and it revealed the brain microenvironment induced complete reprogramming of metasized cancer cells, resulting in a gain of neuronal cell characteristic , mimicking neurogenesis during development.

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus

overall_design:
Human in vivo: 4 KB, 4 KS, 3 KC, 5 MB, 5 MF, 4 MS, 3 PB, 3 PL, 4 PS, 5 AB, 5 AS , 1 BR_N_PC
Mouse in vivo: 4 KB, 4 KS, 3 KC, 5 MB, 5 MF, 4 MS, 3 PB, 3 PL, 4 PS, 5 AB, 5 AS , 3 BR, 3 PC_BRM, 1 BR_PCM

first: Eun-Sung

last: Park

first: Ju-seog

last: Lee

first: Isaiah

middle: J

last: Fidler


title: Genome-wide analysis of the effect of long-term cryopreservation on peripheral blood mononuclear cells

status: Public on Jul 22 2011

city: Bonn

first: Joachim

middle: L

last: Schultze

address: Carl-Troll-Str. 31

department: LIMES Institute

country: Germany

institute: University of Bonn

summary: Analysis of effect of long-term cryopreservation on peripheral blood mononuclear cells at gene expression level. The hypothesis tested in the present study was that long-term cryopreservation has an influence on the transcriptome profile of peripheral blood mononuclear cells. Results indicated remarkable changes in expression patterns upon cryopreservation of PBMCs, with decreasing signal intensities over time.

overall_design: Total RNA obtained from isolated peripheral blood mononuclear cells of melanoma patients cryopreserved in liqiud nitrogen from 20 to 60 months.

first: Gerold

last: Schuler

first: Beatrice

last: Schuler-Thurner


title: Genome-wide analysis of the effect of long-term freezing of PAXgene Blood RNA tubes

summary: Analysis of long-term freezing on the stability of transcriptome profiles in PAXgene stabilized whole blood samples.  In the present study it was tested if  long-term freezing of PAXgene RNA tubes (up to one year) has an influence on the transcriptome profile of peripheral whole blood samples. Results indicated that gene expression profiles of whole blood samples stabilized with PAXgene RNA tubes remain stable for at least 1 year.

overall_design: Total RNA was obtained from peripheral whole blood samples collected in PAXgene RNA tubes of healthy human subjects. RNA was either isolated after 24h storage at room temperature or after freezing of PAXgene RNA tubes for up to 1 year (6 weeks, 6 months and 12 months).

first: Svenja

last: Debey-Pascher

first: Andrea

last: Staratschek-Jox


title: Abcb4 liver expression profiling

status: Public on Aug 01 2011

city: Neuherberg

first: Martin

last: Irmler

state: Bayern

address: Ingolstaedter Landstrasse 1

department: Institute of Experimental Genetics

institute: Helmholtz Zentrum München GmbH

summary: The multidrug resistance gene 2 (Mdr2 or Abcb4) encodes a P-glycoprotein (Pgp) - a phospholipid flippase - that is the murine orthologue of the MDR3 gene in humans. The MDR2 protein is principally expressed in the bile canalicular membrane of the liver. A homozygous disruption of Abcb4 causes absence of phospholipids from bile. This phospholipid deficiency results in liver injury. The Balb-Abcb4-/- mouse strain has been generated by introgressing the Abcb4 knockout from the fibrosis-resistant FVB/NJ (FVB.129P2-Abcb4tm1Bor/J) strain into the susceptible BALB/cJ background, by backcrossing FVB- Abcb4-/- mice in to fibrosis-susceptible BALB/cJ mice for 10 generations.

overall_design: cDNA expression profiling of mRNA from liver of four single male mutant mice against a pool of RNA from four wild type controls (n=8). For each mutant animal two technical replicates were performed including a dye swap experiment.


title: Cryopreservation effects on peripheral blood

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

overall_design: Refer to individual Series


title: Gene expression profiles of endometriosis

status: Public on May 09 2011

first: Chad

last: Creighton

address: One Baylor Plaza, Mail Stop: BCM305

department: Biostatistics, Ducan Cancer Center

institute: Baylor College of Medicine

summary:
Endometriosis is a common disease seen by gynecologists. Clinical features involve pelvic pain and unexplained infertility. Although endometriosis is pathologically characterized by endometrial tissue outside the normal uterine location, endometriosis is otherwise not easily explained. Endometriomas, endometriotic cysts of the ovary, typically cause pain and distortion of pelvic anatomy. To begin to understand the pathogenesis of endometriomas, we carried out transcriptome:microRNAome analysis of endometriomas and eutopic endometrium, using gene expression arrays and next generation small RNA sequencing technology.
Keywords: two group comparison

overall_design:
Patients undergoing surgery for endometriomas, suspected endometriosis, pelvic pain, abnormal uterine bleeding, pelvic organ prolapse, or uterine leiomyomas were approached for participation.  After informed consent, the patients underwent scheduled surgical procedure. Tissues were collected either as cyst wall of endometrioma or endometrial curettage of hysterectomy specimen and placed directly into RNALater (Ambion, Austin, TX) and eventually frozen at -80˚C. Samples were designated as endometriomas or non-endometriosis control endometrium based on surgical pathology reports. Total RNA was isolated from frozen tissue. High quality RNA was subjected to Illumina’s Human WG-6 version 2.0 BeadChips (Illumina).
.
*** This Series represents the transcriptome component of the study. ***

last: Matzuk

first: Shannon

last: Hawkins


title: Hosts responses in critical disease caused by pandemic H1N1

status: Public on May 05 2011

city: Toronto

first: Longsi

last: Ran

state: ON

address: 101 College Street

department: Division of Experimental Therapeutics

country: Canada

institute: Toronto General Research Institute

summary: Critical disease caused by the new 2009 pandemic influenza virus (nvH1N1) is a challenge for physicians and scientist. As evidenced in SARS and H5N1, the development of an effective immune response plays a key role to overcome viral diseases.  We studied host`s gene expression signatures, cytokine and antibody responses along the first week of hospitalization in 19 critically ill patients with primary nvH1N1 pneumonia and two degrees of respiratory involvement. Presence of comorbidities and absence of immunosuppresory conditions were the common antecedents in both groups. The most severe patients (n=12) showed persistant respiratory viral secretion, increased levels of pro-inflammatory cytokines and chemokines in serum, and elevated systemic levels of two immunosuppresory cytokines (IL-10 and IL-1ra). Both groups were able to produce specific antibodies against the virus. The average day for antibody production was day 9 in the course of the disease, defining an early period of innate immunity and a late period of adaptive immunity. The most severe group evidenced a poor expression of a set of MHC class II and T cell receptor (TCR) related genes participating in antigen presentation and cell mediated immune responses in the late phase. 7 patients of this group finally died. This findings evidence that, as observed in sepsis, severe H1N1 disease course with immunoparalysis, which could explain the poor control of the virus along with the increased incidence of bacterial superinfection observed in these patients.

overall_design: 19 patients attending to the participants ICUs with primary viral pneumonia during the acute phase of influenza virus illness with acute respiratory distress and unequivocal alveolar opacification involving two or more lobes with negative respiratory and blood bacterial cultures at admission were recruited from November the 1st to December the 31st 2009. Serial blood samples for plasma, serum and RNA were collected by using Serum, EDTA and PaxGene (BD®) venous blood vacuum collection following manufacturer instructions at day 1, 3/5 and 7 according to an unified protocol for all the participant ICUs. A pharyngeal sample was collected in paralel. RNA from blood was processed for gene expression analysis by using Sentrix Human-6 v2 Expression BeadChips (Illumina, San Diego, CA). RNA from blood obtained from 4 healthy controls was used for comparison purposes. Samples were distributed in four groups depending on whether or not the patients nedeed of mechanical ventilation, and on the early/late phase of the disease (before or after day 9 respectively).

first: David

last: Kelvin


title: Genome-wide analysis of the effect of cryopreservation on peripheral blood mononuclear cells

summary: Analysis of cryopreservation effects on peripheral blood mononuclear cells at gene expression level. The hypothesis tested in the present study was that cryopreservation has an influence on the transcriptome profile of peripheral blood mononuclear cells. Results indicated remarkable changes in expression patterns upon cryopreservation of PBMCs, with a strong loss of signal intensities to background levels for several transcripts.

overall_design: Total RNA obtained from isolated peripheral blood mononuclear cells of healthy human subjects eihter cryopreserved in liqiud nitrogen (frozen) or direclty lysed  in Trizol after isolation (fresh).


title: Resolution of Type 2 Diabetes Following Bariatric Surgery is Associated with Changes in Whole Blood Gene Expression

status: Public on Jan 06 2011

city: Cleveland

first: Jonathan

middle: David

last: Smith

state: OH

address: 9500 Euclid Avenue

department: Cell Biology

institute: Cleveland Clinic

summary:
To investigate the effects of bariatric surgery on gene expression profile changes in whole blood in obese subjects with type 2 diabetes in a pilot study setting.  Whole blood from eleven obese subjects with type 2 diabetes was collected in PAXgene tubes prior to and 6-12 months after bariatric surgery. Total RNA was isolated, amplified, labeled and hybridized to Illumina gene expression microarrays.  Clinical and expression data were analyzed using a paired t-test, and correlations between changes in clinical trait and transcript levels were calculated.  Pathways were identified using Ingenuity Pathway Analysis and DAVID gene ontology software.  Bariatric surgery resulted in significant reduction of BMI, fasting plasma glucose and normalization of HbA1c levels.  The expression levels of 204 transcripts, representing 200 unique genes, were significantly altered after bariatric surgery.  Among the significantly regulated genes were GGT1, CAMP, DEFA1, LCN2, TP53, ZNF684, GPR50, PDSS1, OLR1, CNTNAP5, DHCR24, HHAT and SARDH, which have been previously implicated in lipid metabolism, obesity and/or type 2 diabetes.  The changes in expression of seven transcripts, WDR35, FLF45244, DHCR24, TIGD7, TOPBP1, TSHZ1, and FAM8A1 were strongly correlated with the changes in body weight, fasting plasma glucose and HbA1c content.
These preliminary data suggest that whole blood expression levels of specific transcripts may identify biomarkers associated with susceptibility for type 2 diabetes and/or therapeutic response.

overall_design: Trasncriptome profiling was performed on eleven obese subjects with type 2 diabetes, (5 females and 6 males) to compare expression changes before and 6 to 12 months after the subjects underwent bariatric surgery.

middle: D

first: Sangeeta

middle: R

last: Kashyap

first: Stela

middle: Z

last: Berisha

last: Serre

first: Philip

last: Schauer


title: Response of swine lung to H1N1 swine influenza virus infection revealed by transcription analysis

status: Public on Apr 27 2011

city: wuhan

first: yongtao

last: Li

state: Hubei

address: shizisan street,number 1

country: China

institute: Unit of Animal Infectious Diseases, National Key Laboratory of Agricultural

summary: As a mild, highly contagious, respiratory disease, swine influenza always damages the innate immune systems, and increases susceptibility to secondary infections which results in considerable morbidity and mortality in pigs. Nevertheless, the systematical host response of pigs to swine influenza virus infection remains largely unknown. To explore these, a time-course gene expression profiling was performed to detect comprehensive analysis of the global host response induced by H1N1 swine influenza virus in pigs.

overall_design: At the age of day 35, 15 pigs were randomly allocated to the non-infected group and 15 to the infected group. Each piglet of the infected group was intranasaly challenged with A/swine/Hubei/101/2009(H1N1) strain and Each piglet of the non-infected group was treated similarly with an identical volume of PBS as control.

first: Yongtao

first: Hongbo

last: Zhou


title: Gene expression profiles upon a microarray-based NSD3L-directed siRNA knockdown in human breast cancer cell line MDA-MB-231.

status: Public on Jun 15 2010

city: Aarhus

first: Zhangle

address: Wilhelm Meyers Allé 4

department: Human Genetics

country: Denmark

institute: Aarhus University

summary:
No genes have been described to be regulated by NSD3L. To identify genes regulated by NSD3L we inverstigated the effect of NSD3L depletion on gene regulation in the human breast cancel cell line MDA-MB-231 by a Illumina expression microarray (Human WG-6 v3.0) screening.
We identified 113 different potential target genes out of 25.400 probe sets which have a more than 2-fold changed expression. Of these genes 44 were up-regulated and 69 down-regulated.

overall_design: To deplete NSD3L we used siRNA directed specifically against this isoform. RNA isolated from NSD3L siRNA transfected cells was together with RNA from control siRNA transfected cells used to screen an Illumina expression microarray (HumanWG-6 v3.0). We identified 113 different potential target genes out of 25.400 probe sets which have a more than 2-fold changed expression. Of these genes 44 were up-regulated and 69 down-regulated.

first: Anders

last: Nielsen


title: PHF8 mediates histone demethylation events in cell cycle progression [expression]

status: Public on Sep 01 2010

city: La Jolla

first: Michael

last: Rosenfeld

state: CA

address: 9500 Gilman Drive

department: School of Medicine

institute: HHMI/UCSD

summary:
While reversible histone modifications are linked to an ever-expanding range of biological functions, the demethylases for histone H4 lysine 20 and their potential regulatory roles remain unknown.  Here, we report that the PHD and Jumonji C (JmjC) domain-containing protein, PHF8, while utilizing multiple substrates, including H3K9me1/2 and H3K27me2, also functions as an H4K20me1 demethylase. PHF8 is recruited to promoters by its PHD domain based on interaction with H3K4me2/3 and controls G1/S transition in conjunction with E2F1, HCF-1 and Set1A, at least in part, by removing the repressive H4K20me1 mark from a subset of E2F1-regulated gene promoters. Phosphorylation-dependent PHF8 dismissal from chromatin in prophase is apparently required for the accumulation of H4K20me1 during early mitosis, which might represent a component of the Condensin II loading process. Accordingly, the HEAT repeat clusters in two non-SMC Condensin II subunits, N-CAPD3 and N-CAPG2, are capable of recognizing H4K20me1, and ChIP-seq. analysis demonstrate a significant overlap of Condensin II and H4K20me1 sites in mitotic HeLa cells. Thus, the identification and characterization of an H4K20me1 demethylase, PHF8, has revealed an intimate link between this enzyme and two distinct events in cell cycle progression.

Keywords: Expression profiling by array

overall_design: HeLa cells were transfected with either control or PHF8 siRNAs. Experiments were performed in biological duplicates. RNA were extracted and sujected to microarray analysis.


title: Orientsia tsutsugamushi stimulates an original gene expression program in monocytes: relationship with gene expression in patients with scrub typhus

status: Public on Mar 26 2011

city: BKK

first: Thanavadee

last: Prachason

address: Division of Molecular Genetics, 10th floor Adulyadejvikrom Bld., Siriraj Hospital, Bangkoknoi

country: Thailand

institute: Mahidol University

summary: Comparative analysis of Genome wide expression was performed to demonstrate diagnostic potential of expression profiling and to identify host response genes in scrub typhus. The results showed that there is a unique expression pattern in peripheral blood leukocytes of scrub typhus infected patients that could discriminate scrub typhus from the other infections and also provided insight into host transcriptional responses to this paticular infection.

overall_design: Genome-wide expression in peripheral blood mononuclear cells (PBMCs) from patients with scrub typhus were compared to those from healthy control and from patients with dengue fever, murine typhus or malaria.


title: Differential expression of genes after over expression of miR-23a~27a~24-2 cluster in human embryonic kidney cells

status: Public on Jul 02 2010

city: Delhi

first: Neeru

last: Saini

address: Mall Road

department: FGU

country: India

institute: IGIB

summary: The experiment was deigned to identify the genes which get altered after the over expression of miR-23a~27a~24-2 cluster in HEK293T cells. The HEK293T cells plated in 6-well plate were transfected with two different concentrations of cloned miRNA cluster i.e 2micrograms and 4micrograms per well.

overall_design: Biological duplicates of 3 samples were used viz. control HEK293T cells, HEK293T cells transfected with 2micrograms of the cloned cluster and HEK293T cells transfected with 4micrograms of the cloned cluster.

first: Ravindresh

last: Chhabra

first: Richa

last: Dubey


title: Artemisinin resistance in Plasmodium falciparum is associated with an altered temporal pattern of transcription (CGH)

status: Public on Dec 07 2010

city: Singapore

first: Sachel

last: Mok

address: 60 Nanyang Drive

country: Singapore

institute: Nanyang Technological University

summary: Artemisinin resistance in Plasmodium falciparum malaria has emerged in western Cambodia.  This is a major threat to global plans to control and eliminate malaria as the artemisinins are a key component of antimalarial treatment throughout the world.  Using DNA microarrays we identify key features of a transcriptional profile that are associated with the delayed parasite clearance phenotype.  These include reduced expression of several basic metabolic and cellular pathways in the early stages, and increased expression of essentially all functionalities associated with protein metabolism in the later stages of P. falciparum intraerythrocytic development.  This is consistent with the reduced ring stage susceptibility that characterizes artemisinin resistant P. falciparum.  This modulation of the P. falciparum intraerythrocytic transcriptome may result from differential expression of several regulatory proteins such as transcription factors of chromatin remodeling associated factors.  In addition, the artemisinin resistant phenotype is strongly associated with a specific pattern of copy number variations, some of which are linked with differential expression of several regulatory proteins such as histone 4 and zinc permease.  This study reports the first global transcriptional survey of artemisinin resistant parasites and provides a set of candidate genes for further investigation.

overall_design: 6 P. falciparum parasites (field isolates) which are either Artemsinin resistant or sensitive from 3 study sites (Pailin in Cambodia, Xepon in Laos, Mae Sot in Thailand) were sampled and harvested for genomic DNA. gDNA from a total of 6 samples were extracted by phenol chloroform. Synthesis of labelled target DNA was carried out as previously described: Mackinnon, M.J. et al. Comparative transcriptional and genomic analysis of Plasmodium falciparum field isolates. PLoS Pathog 5, e1000644 (2009), and used in comparative genomic microarray hybridizations (CGH).

first: Zbynek

last: Bozdech


title: Expression profile of lungs from two fatal H5N1 influenza cases

status: Public on Jun 09 2010

city: Bangkoknoi

first: Alita

last: Kongchanagul

state: Bangkok

address: 2 Prannok Road

department: Microbiology

institute: Faculty of Medicine Siriraj Hospital

summary: The pathogenesis of avian influenza A H5N1 virus in human has not been clearly elucidated. There have been increasing evidence suggesting a role for virus-induced cytokine dysregulation in contributing to the pathogenesis of human H5N1 disease. However, the role of aberrant innate immune response in human lungs infected by avian influenza H5N1 virus has not been explored and direct evidence for inappropriate innate responses in lungs of avian influenza H5N1 virus infected patients is lacking.

overall_design: In order to obtain evidences for the proposed role of aberrant innate immune response in avian influenza H5N1 virus pathogenesis in human, we analyzed expression profile of lung tissues from two fatal cases of avian influenza H5N1 virus infected patients in comparison to normal human lung using an expression microarray.

first: Ornpreya

last: Suptawiwat

first: Chompunuch

last: Boonarkart

first: Rungrueng

last: Kitphati

first: Pilaipan

last: Puthavathana

first: Mongkol

last: Uiprasertkul

first: Prasert

last: Auewarakul


title: Differentially expressed genes and transcript isoforms in mouse NSCs expressing miR-128

status: Public on Apr 28 2011

first: Rachid

last: Karam

department: Reproductive Medicine

institute: UCSD

summary: We identify a brain-specific microRNA—miR-128—that represses Nonsense Mediated mRNA Decay (NMD) and thereby controls batteries of transcripts in neural cells. miR-128 represses NMD by targeting the RNA helicase UPF1 and the exon-junction complex core component MLN51. We employed exon arrays for this analysis, as this platform detects expression levels of individual exons and thus allows detection of not only differentially expressed transcripts (DETs), but also alternative isoform transcripts (AITs). The latter is particularly relevant to our study because alternative RNA processing events (e.g., RNA splicing, alternative promoter usage, and alternative polyadenylation-site usage) often place a translation termination codon in a premature context and thereby trigger NMD.

overall_design: Compare different expressed genes and transcript isoforms in mouse NSCs miR-128 positive vs miR-128 negative (Control). Mouse NSCs, that do not normally express miR-128, were nucleofected with either miR-128 (biological triplicates were analysed) or miR-Control (biological triplicates). RNA was extracted 72hrs later, and Exon Array was performed to identify target genes.

first: Ivone

last: Bruno

first: Miles

last: Wilkinson

first: Christopher

last: Cowing-Zitron


title: Robust prognostic biomarkers for EAC identified by systems-level characterization of tumor transcriptome

status: Public on Jan 04 2011

first: Sangbae

last: Kim

summary: Despite continual efforts to rationalize a prognostic stratification of patients with esophageal adenocarcinoma (EAC) before treatment, current staging system only shows limited success owing to the lack of molecular and genetic markers that reflect prognostic features of the tumor. To develop molecular predictors of prognosis, we used systems-level characterization of tumor transcriptome. Using DNA microarray, genome-wide gene expression profiling was performed on 75 biopsy samples from patients with untreated EAC.  Various statistical and informatical methods were applied to gene expression data to identify potential biomarkers associated with prognosis. Potential marker genes were validated in an independent cohort using quantitiative RT-PCR to measure gene expression. Distinct subgroups of EAC were uncovered by systems-level characterization of tumor transcriptome. We also identified a six-gene expression signature that could be used to predict overall survival (OS) of EAC patients. In particular, expression of SPARC and SPP1 was a strong independent predictor of OS, and a combined gene expression signature with these two genes was associated with prognosis (P < 0.024), even when all relevant pathological variables were considered together in multivariate Cox hazard regression analysis. Our findings suggest that molecular features reflected in gene expression signatures may dictate the prognosis of EAC patients, and these gene expression signatures can be used to predict the likelihood of prognosis at the time of diagnosis and before treatment.

overall_design:
64 primary esophageal adenocarcinoma,  15 Barrett's esophagus and 28 surrounding normal fresh frozen tissues were used for microarray. All the tissues were obtained after curative resection after pathologic confirm at UT M.D. Anderson Cancer Center (MDACC).  Microarray experiment and data analysis were done in the Dept. of systems biology at MDACC
DNA microarray (Illumina human V2)

first: SooMi

first: Jaffer

last: Ajani

first: Ju-seog

last: Lee


title: Reprogramming Transcriptional Responses through Functionally-Distinct Classes of Enhancers in Prostate Cancer Cells [gene expression]

status: Public on May 15 2011

last: Benner

state: California

address: 9500 Gilman Dr. MC 0640

department: Medicine

institute: University of California, San Diego (UCSD)

summary: Mammalian genomes are populated with thousands of transcriptional enhancers that orchestrate cell type-specific gene expression programs; however, the potential that there are pre-established enhancers in different functional classes that permit alternative signal-dependent transcriptional responses has remained unexplored. Here we present evidence that cell lineage-specific factors, such as FoxA1, can simultaneously facilitate and restrict key regulated transcription factors, exemplified by the androgen receptor (AR), acting at structurally- and functionally-distinct classes of pre-established enhancers, thus licensing specific signal-activated responses while restricting others. Consequently, FoxA1 down-regulation, an unfavorable prognostic sign in advanced prostate tumors, causes a massive switch in AR binding from one functional class of enhancers to another, with a parallel switch in levels of enhancer-templated non-coding RNAs (eRNAs) revealed by the global run-on assay (GRO-seq), which documents the dramatic reprogramming of the hormonal response.  The molecular basis for this switch lies in the release of FoxA1-mediated restriction of AR binding to the new enhancer class with no apparent nucleosome remodeling, which is required for stimulating their eRNA transcription and/or enhancing enhancer:promoter looping and gene activation. Together, these findings reveal a large repository of pre-determined enhancers in the human genome that can be dynamically tuned to induce their transcription and activation of alternative gene expression programs, which may underlie many sequential gene expression events in development or during disease progression.

overall_design:
ChIP-Seq, Gro-Seq, and gene expression profiling was performed in LNCaP cells with hormone treatment and siRNA against FoxA1.

Gene expression profiling data presented here.

first: Dong

last: Wang

first: Ivan

last: Garcia-Bassets

first: Wenbo

last: Li

first: Minna

middle: U

last: Kaikkonen

first: Xue

last: Su

first: Yiming

last: Zhou

first: Jinsong

last: Qiu

first: Wen

last: Liu

first: Kenny

middle: H

last: Ohgi

middle: K

last: Glass

first: Michael

middle: G

last: Rosenfeld

first: Xiang-Dong

last: Fu


title: Gene expression profiling of the classical (CD14++CD16-), intermediate (CD14++CD16+) and nonclassical (CD14+CD16+) human monocyte subsets

status: Public on May 01 2011

first: Kok Loon

last: Wong

address: 8A Biomedical Grove, Biopolis

institute: A*STAR

summary: The new official nomenclature subdivides human monocytes into three subsets, classical (CD14++CD16-), intermediate (CD14++CD16+) and nonclassical (CD14+CD16+). Here, we comprehensively define relationships and unique characteristics of the three human monocyte subsets using microarray and flow cytometry analysis. Our analysis revealed that the intermediate and nonclassical monocyte subsets were most closely related. For the intermediate subset, majority of genes and surface markers were expressed at an intermediary level between the classical and nonclassical subset. There features therefore indicate a close and direct lineage relationship between the intermediate and nonclassical subset. From gene expression profiles, we define unique characteristics for each monocyte subset. Classical monocytes were functionally versatile, due to the expression of a wide range of sensing receptors and several members of the AP-1 transcription factor family. The intermediate subset was distinguished by high expression of MHC class II associated genes. The nonclassical subset were most highly differentiated and defined by genes involved in cytoskeleton rearrangement that explains their highly motile patrolling behavior in vivo. Additionally, we identify unique surface markers, CLEC4D, IL-13RA1 for classical, GFRA2, CLEC10A for intermediate and GPR44 for nonclassical. Our study hence defines the fundamental features of monocyte subsets necessary for future research on monocyte heterogeneity.

overall_design: Three human monocyte subsets, the CD14++CD16- classical, the CD14++CD16+ intermediate and CD14+CD16+ nonclassical subsets were purified using fluorescence activated cell sorting from peripheral blood mononuclear cells. RNA was processed from the three monocyte subsets from 4 individual donors in duplicates, giving a total of 24 samples.

first: Kok

first: Jing

middle: Y

last: Tai

first: Wei

last: Yeap

first: Wing

middle: C

first: Hao

last: Han

first: Philippe

last: Kourilsky

first: Siew


title: Factors from human embryonic stem cell-derived fibroblast-like cells promote topology-dependent hepatic differentiation in primate embryonic stem cells and human induced pluripotent stem cells

status: Public on Aug 20 2010

city: Taipei

first: Chun

middle: Ying

last: Yu

address: 128 Academia Road, Section 2

department: Genomic Research center

country: Taiwan

institute: Academia sinica

summary: The future clinical use of embryonic stem cell (ESC)-based hepatocyte replacement therapy depends on the development of an efficient procedure for differentiation of hepatocyes from ESCs. Here we report that a high density of human embryonic stem cell (ESC)-derived fibroblast-like cells (hESdFs) supported the efficient generation of hepatocyte-like cells (HLCs) with functional and mature hepatic phenotypes from primate ESCs and human induced pluripotent stem cells (iPSCs). Molecular and immunocytochemistry analyses revealed that hESdFs caused a rapid loss of pluripotency and induced a sequential endoderm-to-hepatocyte differentiation in the central area of ESC colonies. Knockdown experiments demonstrated that pluripotent stem cells were directed toward endodermal and hepatic lineages by FGF2 and Activin A secreted from hESdFs. Furthermore, we found that the central region of ESC colonies was essential for the hepatic endoderm-specific differentiation, as its removal caused a complete disruption of endodermal differentiation. In conclusion, we describe a novel in vitro differentiation model, and show that hESdF-secreted factors act in concert with regional features of ESC colonies to induce robust hepatic endoderm differentiation in primate pluripotent stem cells.

overall_design: Total RNA were isolated from ORMES6 ESC, differentiated cells at IVDS2 and 3, and cells in the central foci (IVDS2-C) and peripheral (IVDS2-P) area of ESC colonies at IVDS2. Each condition was repeated twice and used ORMES6 ESC as control.

first: Hsiang-Po

last: Huang

first: Chun-Ying

first: Hsin-Fu

last: Chen

first: Pin-Hsun

first: Ching-Yu

last: Chuang

first: Sung-Jan

last: Lin

first: Shih-Tsung

first: Wei-Hung

last: Chan

first: Tzuu-Huei

last: Ueng

first: Hong-Nerng

last: Ho

first: Hung-Chih

last: Kuo


title: Isolation and Characterisation of Renal Precursor Cells Derived from Human Embryonic Stem Cells

status: Public on Mar 16 2010

city: St Lucia

first: Sean

last: Grimmond

state: Q

address: Services Rd

department: Institute for Molecular Bioscience

country: Australia

institute: University of Queensland

summary:
HES4 hESC were cultured in serum media and maintained on a layer of mouse embryonic fibroblast feeder cells at a density of 6 x 104 cells/cm2. For differentiation: hESC were differentiated for a total of 14 days. Differentiation was induced by passaging 4 human ES cell pieces onto 12 well plates seeded with 0.67 x 10E4 cells/cm2. Cells were maintained in media containing 20% FCS for 2 days before media containing 5% FCS was used. Reduced serum media was changed every second day for the remaining 12 days
ESC cells were taken at time zero and RNA was isolated (hESC_undiff).  Cells differentiated by the above procedure  at day 14 were isolated and RNA extracted (Diff).  The remaining cells were FACs sorted with antibodies to Podocalyxin, CD24 and GCTM-2.  Two populations were isolated, 1: Positive for podocalyxin and CD24 and low level of expression of GCTM-2 (POD+CD24+GCTM2Low) and 2: Positive for podocalyxin and CD24 and negative for GCTM-2 (POD+CD24+GCTM2Neg).  The experiment was repeated in triplicate.  The final aim was to determine the gene expression enrichment in cells with the marker profile (Podocalyxin+, CD24+, GCTM-2-neg) which is predicted to be enriched for kidney precursors.

Keywords: cell type comparison

overall_design: Three consecutive passages of HES4 cells were grown in standard conditions, RNA derived or differentiated for 14 days subject to FACs sorting, collection and RNA isolated.   Microarray was performed on a total of 12 samples, (3 replicates of 4 populations).

first: Gabriel

last: Kolle


title: Gene Experssion Profiling-Based Identification of Molecular Subtypes in Stage IV Melanoma with Different Clinical Outcome (test set)

status: Public on Jun 08 2010

city: Lund

first: Johan

last: Staaf

address: Medicon Village

country: Sweden

institute: SCIBLU - Swegene Centre for Integrative Biology at Lund University

summary: Purpose: The incidence of malignant melanoma is increasing worldwide in fair-skinned populations.  Melanomas respond poorly to systemic therapy, and metastatic melanomas inevitably become fatal. Although  spontaneous regression, likely due to immune defense activation, rarely occurs, we lack a biological  rationale and predictive markers in selecting patients for immune therapy.  Experimental Design: We performed unsupervised hierarchical clustering of global gene expression  data from stage IV melanomas in 57 patients. For further characterization, we used immunohistochemistry  of selected markers, genome-wide DNA copy number analysis, genetic and epigenetic analysis of the  Q3 CDKN2A locus, and NRAS/BRAF mutation screening.  Results: The analysis revealed four distinct subtypes with gene signatures characterized by expression  of immune response, pigmentation differentiation, proliferation, or stromal composition genes. Although  all subtypes harbored NRAS and BRAF mutations, there was a significant difference between subtypes  (P < 0.01), with no BRAF/NRAS wild-type samples in the proliferative subtype. Additionally, the proliferative  subtype was characterized by a high frequency of CDKN2A homozygous deletions (P < 0.01). We  observed a different prognosis between the subtypes (P = 0.01), with a particularly poor survival for patients  harboring tumors of the proliferative subtype compared with the others (P = 0.003). Importantly,  the clinical relevance of the subtypes was validated in an independent cohort of 44 stage III and IV melanomas.  Moreover, low expression of an a priori defined gene set associated with immune response signaling  was significantly associated with poor outcome (P = 0.001).  Conclusions: Our data reveal a biologically based taxonomy of malignant melanomas with prognostic  effect and support an influence of the antitumoral immune response on outcome.

overall_design: Expression profiles of 57 lymphnode and subcutaneous melanoma metastases

first: Göran

last: Jönsson

first: Christian

last: Busch

first: Stian

last: Knappskog

first: Jürgen

last: Geisler

first: Hrvoje

last: Miletic

first: Markus

last: Ringnér

last: Lillehaug

first: Ake

last: Borg

first: Per

middle: E

last: Lønning


title: Predictive Gene Signatures as Strong Prognostic Indicators of the Effectiveness of BCG Immunotherapy

status: Public on Mar 26 2010

city: Daejeon

first: Seon-Kyu

last: Kim

address: 125 Gwahak-ro, Yuseong-gu, Daejeon 305-806, Korea

department: Personalized Genomic Medicine Research Center

country: South Korea

institute: Korea Research Institutue of Bioscience & Biotechnology

summary:
Full title: Predictive Gene Signatures as Strong Prognostic Indicators of the Effectiveness of Bacillus Calmette–Guérin (BCG) Immunotherapy in Primary pT1 Bladder Cancers
Intravesical BCG immunotherapy is effective in prevention of recurrence and progression in many cases of non-muscle invasive bladder cancer, but many patients fail to respond. This study identified predictive gene signatures in primary pT1 bladder cancer with BCG immunotherapy. Fourty-Eight patients with primary pT1 bladder cancer treated with BCG immunotherapy were used. Microarray gene expression analysis of the 48 primary bladder cancers was carried out. Predictive gene signatures were individually selected based on the recurrence and progression status. Among 43,148 unique genes, 424 and 287 candidate predictive genes that could predict recurrence and progression, respectively, were selected. Time to recurrence or progression was shorter for patients with poor-predictive gene signatures than good-predictive gene signatures (log-rank test, p <0.001, respectively). Validation of predictive gene signatures with RT-PCR was nearly identical to those of microarray (log-rank test, p <0.05, respectively). In multivariate regression analysis, predictive gene signatures were the only independent predictors of recurrence (HR 3.38, p = 0.048) or progression (HR 10.49, p = 0.048) in validation cohorts. Predictive gene signatures have strong diagnostic value for determining the response to intravesical BCG immunotherapy in primary pT1 bladder cancer.
Keywords: Gene expression, Bladder cancer, BCG

overall_design: Total RNA, extracted from the fresh frozen tissues of 48 pT1 bladder cancers, was isolated by TRIzol reagent (Life Technologies, NY, USA), according to the manufacturer's protocol. The quality and integrity of the RNA were confirmed by agarose gel electrophoresis and ethidium bromide staining, followed by visual examination under ultraviolet light. Five-hundred nanograms of total RNA were used for labeling hybridization according to the manufacturer’s protocol (Illumina HumanWG-6 BeadChip, version 2, Illumina, Inc., San Diego, CA, USA). Arrays were scanned with an Illumina Bead Array Reader confocal scanner (BeadStation 500GXDW; Illumina, Inc.) according to the manufacturer's instructions. Initial microarray gene expression data were obtained using Bead Studio software with gene expression analysis module (version 3.1.3, Illumina, Inc.).

first: Sun-Hee

last: Leem

first: Yong-June

first: Wun-Jae


title: Specification of functional floor plate tissue from human embryonic stem cells occurs at the expense of anterior neurectoderm

status: Public on Apr 12 2010

city: New York

first: Stuart

middle: M

last: Chambers

state: NY

address: 1270 York Ave

institute: Sloan-Kettering Institute

summary: Here we report the derivation of human embryonic stem cells (hESC-) derived FP tissue capable of secreting Netrin-1 and SHH and patterning primary and hESC derived tissues.

overall_design: Three replicate plates of human embryonic stem cells (A-C) were differentiated to various days (D#) using Noggin+SB431542 with or without SHH (C25II)


title: In utero and lactational exposure to TCDD induces disruption of prostate glands and fibrosis in rhesus monkeys

status: Public on Jan 28 2010

city: Kagoshima

first: Akihiro

last: Arima

address: 2438 Miyanoura

country: Japan

institute: Shin Nippon Biomedical Laboratories, Ltd.

summary:
[Original title] In utero and lactational exposure to 2,3,7,8-tetrachlorodibenzo-p-dioxin (TCDD) induces disruption of the prostate glands and fibrosis in rhesus monkeys.

We investigated the effects of 2,3,7,8-tetrachlorodibenzo-p-dioxin (TCDD) exposure on the prostate in rhesus monkey offspring.  Dams received 0, 30 or 300 ng/kg TCDD subcutaneously on Day 20 of gestation, and then 5% of the initial dose was injected every 30 days until Day 90 after delivery.  The offspring were maintained until reaching sexual maturity, and examined histopathologically.  Dose-dependent decreases in the prostate glands and widespread fibrosis were observed in offspring.  It is noteworthy that 7 years from the final lactational TCDD exposure, inflammatory cell infiltration and disruption of the prostate glands were also observed.  Differential mRNA expression associated with fibrosis, inflammatory response and disruption of cell components were demonstrated by microarray analysis, and up-regulation of TGM4, TGFB1, COL1A1 and MMP2 was confirmed with Real-time PCR.  In conclusion, in utero and lactational exposure to TCDD induced dose-proportional prostatic fibrosis, indicating prostatic dysfunction and inducible semen quality reduction in second-generation rhesus monkeys.

overall_design:
Dam received 0, 30 or 300 ng/kg TCDD subcutaneously on Day 20 of gestation, and then 5% of the initial dose was injected every 30 days until Day 90 after delivery.  The offspring were maintained until reaching sexual maturity, and the prostates from 3 offspring in each group were evalutated by histopathological examination, microarray analysis and Real-time quantitative PCR.

Supplementary file: Fold_change comparison results of 'control group vs 30 ng/kg group' and 'control group vs 300 ng/kg group'.


title: Genome-wide analysis of SATB1 target genes in human T helper cells

status: Public on Jan 07 2010

city: Turku

first: Helena

last: Ahlfors

address: Tykistökatu 6A

institute: Turku Centre for Biotechnology

summary: Special AT-rich binding protein 1 (SATB1) is a global chromatin organizer and a transcription factor induced by interleukin-4 (IL-4) during the early T helper 2 (Th2) cell differentiation. In this study, we investigated the role of SATB1 in T helper cell differentiation by performing gene expression profiling of human differentiating Th cells in which expression of SATB1 was downregulated by RNA interference (RNAi). Our results indicate that SATB1 is involved in the regulation of more than three hundred genes in primary human CD4+ T cells, including several IL-12 and/or IL-4 regulated factors, suggesting a role in the development or function of Th subtypes.

overall_design:
Set 1: Total RNA obtained from human CD4+ T cells isolated from peripheral blood transfected with SATB1-shRNA or scramble control plasmids and cultured in Th1 and Th2 conditions for 0, 24 and 48 h (Thp - non antigen exposed precursor).

Set 2: Total RNA obtained from human CD4+ T cells isolated from peripheral blood transfected with SATB1-shRNA or scramble control plasmids and cultured in Th1 and Th2 conditions for 0, 24 and 48 h (Thp - non antigen exposed precursor).

Set 3: Total RNA obtained from human CD4+ T cells isolated from umbilical cord blood transfected with SATB1-siRNA or scramble control siRNAs and cultured in Th0, Th1 and Th2 conditions for 0, 12, 24 and 48 h (Thp - non antigen exposed precursor).

Set 4: Total RNA obtained from human CD4+ T cells isolated from umbilical cord blood transfected with SATB1-siRNA or scramble control siRNAs and cultured in Th0, Th1 and Th2 conditions for 0, 12, 24 and 48 h (Thp - non antigen exposed precursor).

Set 5: Total RNA obtained from human CD4+ T cells isolated from umbilical cord blood transfected with SATB1-siRNA or scramble control siRNAs and cultured in Th0, Th1 and Th2 conditions for 24 h.

first: Riitta

last: Lahesmaa


title: Biocompatibility and Discovery of the Potential Applications of Magnetite (Fe3O4) Nanoparticles

status: Public on Mar 13 2010

first: Jameel

middle: Ahmad

last: Khan

state: Delhi

institute: Institute Of Genomics and Integrative Biology (CSIR)

summary:
A Transcriptomics Approach to Study the Biocompatibility and Finding out the Potential Applications of Magnetite (Fe3O4) Nanoparticles
Here in this study, we examine the molecular effects of uptake of Fe3O4 nanoparticles using a whole genome microarray study in human epithelial cancer cell line. 38 genes (55%) out of 69 downregulated genes were found to be associated with TGF-beta or BMP signaling including six genes, Id1, Id2, Id3, Caspase-9, Smad6 and SMAD7, important negative regulators of these signaling pathways involved in development and tumorigenesis.

overall_design: Total RNA isolated from MNP treated HeLa cells compared to untreated controls.

middle: A

first: Tarun

last: Mandal

first: Taposh

last: Das

first: Yogendra

last: Singh

first: Souvik

last: Maiti

first: Beena

last: Pillai


title: Expression profiling of primitive neuroectodermal tumours

status: Public on Dec 22 2009

first: David

middle: J. H.

last: Shih

address: 686 Bay St

department: Developmental and Stem Cell Biology

institute: Hospital for Sick Children

summary:
Primitive neuro-ectodermal tumours (PNET) of the supratentorial region are rare, highly malignant embryonal brain tumours affecting young children. Although supratentorial PNET (sPNET) are histologically similar to infratentorial PNET/medulloblastoma, sPNET have more aggressive clinical phenotypes, which suggest sPNET represents distinct biological entities. In contrast to considerable progress in understanding the signalling pathways involved in medulloblastoma, little is known about sPNET pathogenesis. We utilized the Illumina Human-6 v2 Expression BeadChip platform to define pathways dysregulated in sPNET pathogenesis.
Copy number analysis was also performed on an overlapping set of PNET tumours, also available on GEO with accession code GSE14087.

Keywords: gene expression, pediatric brain tumour

Raw BeadStudio output files (GSE14295_normalization-none*) linked below as Supplementary files.
Supplementary File GSE14295_Array2SampleTitle_associations.txt maps Array IDs (e.g., 1814647101_B) to GEO Sample Titles (e.g., PNET2).

overall_design: A total of 56 primary sPNET samples were collected for this study from The Hospital for Sick Children, John Hopkins University, St. Jude Research Hospital, University of Cambridge, Children’s Hospital Boston, Virginia Commonwealth University, Instituto nazionale per lo studio e la cura dei tumori, and Texas Children’s Hospital, with local Institutional Research Ethics Board approval. Pineoblastoma and rhaboid tumours were specifically excluded, leaving 52 samples, 33 of which had good quality RNA available. These samples, in addition to normal fetal and adult brain reference samples (Clontech, Palo Alto, CA), were analyzed on Illumina Human-6 V2 Expression BeadChips.

first: Mei

last: Li

first: Kyle

middle: F

last: Lee

first: Yun

middle: T

last: Lu

middle: J

first: Charles

last: Eberhart

first: Ching

last: Lau

first: Scott

last: Pomeroy

first: Peter

last: Collins

first: Piergiorgio

last: Modena

first: Amar

last: Gajjar

first: Michael

last: Taylor

first: Eric

last: Bouffet

first: Cynthia

last: Hawkins

first: Annie

last: Huang


title: Direct comparison of HES2 ESC overexpressing CD30 variant with HES2 overexpressing GFP

status: Public on Oct 10 2009

first: Sean

last: Grimmond

summary:
HES2 ESC were infected with a lentivirus construct containing either CD30 (TNFRSF8) extracellular deficient variant or GFP, using the ViraPower™ Promoterless Lentiviral Gateway® Kits (Invitrogen).  HES2 cells were recovered and grown for 19 passages.  HES2 were commonly grown on Mouse Embryonic Feeder cells in the presence of KSOR media.
Before collection of RNA, ES cells were FACs sorted with antibodies to GCMT-2 and CD9 to separate ES cells from differentiated cells and mouse feeders.  The experiment was repeated in triplicate.  The final aim was to deduce the effect of overexpressing the variant form of CD30 on gene expression in HES2 cells.

overall_design: Three consecutive passages of HES2 cells over-expressing either CD30V or GFP were grown and subject to FACs sorting, collection and microarray.  A total of 6 samples, (3 replicates of these 2 populations) were used in the experiment.

first: Gabriel

last: Kolle


title: Characterization of whole blood gene expression profiles of healthy miniature pigs with increasing age

status: Public on Apr 14 2011

city: Tsukuba

first: Junko

last: Takahashi

state: Ibaraki

address: 1-1-1 Umezono

institute: National Institute of Advanced Industrial Science and Technology　(AIST)

summary: Studying the causes and correlations of individual or age variation in gene expression is necessary for securing  the reliability of the experimental animal. Feature of the blood gene expression of miniature pigs of fetus, 12, 20 and 30 weeks of age was examined.

overall_design: Gene expression in male and female miniature pigs was measured at fetus, 12, 20 and 30 weeks of age.

first: Hitoshi

last: Iwahashi


title: Expression profiling in Neuroblastoma Primary tumors and Cell lines

status: Public on Dec 03 2009

city: Philadelphia

first: Jayanti

last: Jagannathan

state: PA

address: 34th & Civic center blvd

department: Oncology

institute: Childrens Hospital of Philadelphia

overall_design: We studied the expression profiles of Neuroblastoma Primary tumors and Cell lines using Illumina Human 6 version 2 expression l bead chip.

first: Eddie

last: Attiyeh


title: A Global Genomic View of MIF Knockdown Cell

status: Public on Nov 03 2009

city: Shanghai

first: Lingfeng

last: Liu

address: Handan Road 220#

department: Life Science

institute: Fudan University

summary:
siRNA-mediated knockdown of MIF expression in HEK293 cells resulted in  inhibition of cell proliferation and cell cycle progress.   The microarray study of MIF KD cells reveald knockdown of MIF would lead to extensive changes in gene expression profiles which may elucidate the molecular mechanism of MIF siRNA-mediated inhibition of cell cycle and cell proliferation.
Keywords: The whole-genome expression analysis in MIF knockdown cells and the control cells

overall_design: HEK293 cells were transfected  MIF siRNA (50pmol/ml & 100pmol/ml) or control RNA using LipofectamineTM 2000 reagent and re-incubated for 24 hours.At the designed time point, totol RNA was isolated from the different treated cells.The normal cells were used as control.


title: Networks and miRNAs implicated in aggressive prostate cancer

status: Public on Feb 04 2010

city: Rochester

first: LIANG

last: WANG

state: MN

address: 200 FIRST ST SW

department: LAB MED PATH

institute: MAYO CLINIC

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

summary:
Background: Prostate cancer (PC), a complex disease, can be relatively harmless or extremely aggressive. To identify candidate genes involved in causal pathways of aggressive PC, we implemented a systems biology approach by combining differential expression analysis and co-expression network analysis to evaluate transcriptional profiles using lymphoblastoid cell lines from 62 PC patients with aggressive phenotype (Gleason grade > 8) and 63 PC patients with nonaggressive phenotype (Gleason grade < 5). From 13935 mRNA genes and 273 microRNAs tested, we identified significant differences in 1100 mRNAs and 7 microRNAs with false discovery rate < 0.01. We also identified a co-expression module demonstrating significant association with the aggressive phenotype of PC (p=3.67x10-11). The module of interest was characterized by over-representation of cell cycle-related genes (false discovery rate = 3.50x10-50). From this module, we further defined 20 hub genes that were highly connected to other genes. Interestingly, five of the 7 differentially expressed microRNAs have been implicated in cell cycle regulation and two (miR-145 and miR-331-3p) are predicted to target three of the 20 hub genes. Ectopic expression of these two microRNAs reduced expression of target hub genes and subsequently resulted in cell growth inhibition and apoptosis. These results suggest that cell cycle is likely to be a molecular pathway causing aggressive phenotype of PC. Further characterization of cell cycle-related genes (particularly, the hub genes) and miRNAs that regulate these hub genes could facilitate identification of candidate genes responsible for the aggressive phenotype and lead to a better understanding of PC etiology and progression [Cancer Res 2009;69(24):9490–7].

Keywords: weighted gene coexpression analysis, network analysis, microRNA regulation

overall_design: Apply weighted gene coexpression network analysis to identify gene expression module responsible for aggressive prostate cancer.

first: Liang

last: Wang


title: Membrane-polysome associated fractionation of HES2 embryonic stem cells

status: Public on Oct 01 2009

summary:
The membrane fraction and the cytosolic fraction of HES2 cells were collected and subjected to microarray.  The experiment was performed in triplicate

Keywords: membrane-polysome fractionation of RNA

overall_design: Three consecutive passages of HES2 cells were grown and subject to membrane-polysome fractionation.  A total of 6 samples, (3 replicates of 2 fractions) were included in the experiment


title: IL-23 100ng/ml Treatment of CD3 CD28 Stimulated PBMCs

city: London

first: Graham

last: Heap

address: 4 Newark Street

country: United Kingdom

institute: QMUL

summary:
Cryopreserved human PBMCs from six donors were stimulated with anti-CD3/CD28 beads in the presence or absence of 100ng/ml IL-23 for 22 hours. RNA samples were assessed for consistency with a Bioanalyzer (Agilent) and quantified by a Nanodrop® ND 1000 Spectrophotometer (Nanodrop Technologies, USA). Expression array data was quantile normalised, detection above background statistical testing performed, comparison between activated un-stimulated versus activated IL-23 stimulated conditions performed as a paired test using the Illumina Custom differential expression algorithm (all implemented in Illumina BeadStudio GeneExpression Module v3.2).

Two sample groups were compared, each with 6 biological replicates. Group 1 was stimulated with CD3CD28 antibody coated beads as a control group for 22hours. Group 2 was stimulated as the control group and treated with IL-23 100ng/ml for the same time period.
Keywords: Cytokine Treatment

overall_design: Genome wide association studies have recently identified common risk variants in IL23R, encoding a subunit of the heterodimeric interleukin-23 receptor, associated with Crohn’s disease, psoriasis and ankylosing spondylitis. IL-23 is a critical cytokine for the development of pathogenic TH17 cells, and drives intestinal and dermal inflammation in animal models. The influence of IL23R genetic variation on human immune responses is not known. Here, we have correlated disease associated IL23R genotypes (for nine markers reaching genome wide significance in the initial Crohn’s disease report) with responses to IL-23 in anti-CD3/CD28 activated human peripheral blood mononuclear cells from 40 genotyped healthy donors. IL-23 stimulation induced leucocyte IL-10 secretion and IL17F mRNA expression. Leucocytes of IL23R rs11209032 AG genotype had higher IL-23 stimulated IL-10 secretion (P=0.00030) and IL17F mRNA expression (P=0.026) than those of GG genotype. Lower IL23R mRNA expression (P=0.046) was observed by quantitative PCR assay in leucocytes of GG genotype. Disease associated IL23R variants lead to gain of function in human cells, by a mechanism involving increased IL23R expression, suggesting novel therapeutic strategies should aim to block IL-23 receptor signalling.

first: G

first: K

last: Hunt

first: N

last: Makwana

first: R

last: Playford

first: D

last: van Heel


title: ESC (HES2, MEL1 or H9) grown in various conditions and FACs sorted for GCTM-2 and CD9

summary:
In the following experiment, three different hESC cell lines (HES2, MEL1 and H9) were grown in the presence of KOSR, KOSR or mTESR containing media respectively. KOSR (Knockout serum replacement medium) is a standard media allowing the growth of hESC without the need for manual passaging - Enzymatic passaging is used instread.  mTESR (Ludwig et al., 2007) is a media allowing the growth of hESC on matrigel with enzymatic passaging.   At day 7 after passaging, these cells were FACs sorted for the presence of GCTM-2 and CD9 into 4 distinct fractions (p4: GCTM-2-neg, CD9-neg; p5: GCTM-2-low, CD9-low; p6: GCTM-2-medium, CD9-medium and p7: GCTM-2-high, CD9-high).   For each cell line-subfraction combination, RNA was harvested and subject to microarray.

From each experiment (individual cell line), 4 samples were collected (p4, p5, p6 and p7) and these were subject to microarray.  In each case the experiment was performed in triplicate

overall_design: Three independent experiments of three consecutive passages of ESC cells were grown and subject to FACs sorting, collection and microarray.  A total of 36 samples, (3 experiments of 3 replicates of 4 sorted populations of cells (p4, p5, p6, p7))


title: Orthotopic Xenograft Model of Ependymoma that Maintains Genomic Signature of the Primary Tumor

status: Public on Aug 08 2009

city: Houston

first: Hon-chiu

middle: Eastwood

last: Leung

address: 1102 Bates Street  Room C1030.09

department: Pediatrics

institute: Baylor College of Medicine

summary: The hypothesis was that the orthotopic xenograft model of ependymoma faithfully recapitulate the genomics signatures of the original tumor patient tissue

overall_design: Original tumor cells were implanted into the same location of SCID mice and check for transcriptome profiles upon subsequent passages to show that the passages preserve the overall genomics signature of the original tumor tissue.


title: Osteogenic differentiation of human mesenchymal stem cells (hMSCs) within a perfusion bioreactor system

status: Public on Sep 16 2009

first: Eijiro

last: Maeda

address: Mile End Road

department: Engineering

institute: Queen Mary, University of London

summary: hMSCs were cultured for eight days within perfused three-dimensional matrices under conditions of oscillatory, continuous or static fluid flow of osteogenic media.

overall_design: Total RNA was obtained from hMSC samples seeded within porous glass scaffolds following eight days exposure to either a high flow rate oscillatory (10L/24hrs), low flow rate oscillatory (1L/24hrs), continuous (1mL/24hrs) or a static (0mL/24hrs) flow rate condition.  3 RNA samples from each flow rate condition were analysed.

first: Jonathan

last: Campbell

first: Christina

last: Fleischmann

first: Charles

last: Mein

first: David

last: Lee


title: Comparative transcriptome analysis of weaned pigs in response to different dietary starch sources displaying metabolic changes of lipids in liver

status: Public on Mar 11 2010

city: Ya'an

first: Jun

last: He

address: Xinkang Road

institute: Sichuan Agricultural University

summary: Diets rich in carbohydrates not only lead to obesity but also contribute to the liver metabolic diseases. Starch is the major energy source of the daily diet. However, little is known about the metabolic changes due to the intake of different dietary starches. Our aim was to assess the overall metabolic changes at the transcriptome level. Animal model was used, and a total of 16 weaned pigs were randomly allotted to two experimental diets containing either of cassava starch (CS) or maize starch (MS) during 21 days. At the end of the trial, liver tissues were sampled and used for analysis of digestive enzymes, metabolites and transcriptomes. The growth performance was not affected by dietary starch sources. However, CS-feeding significantly increased the serum insulin and cholesterol concentrations (P<0.05). The liver triglyceride and cholesterol content were both elevated by CS-feeding (P<0.05). Microarray analysis led to the identification of 648 genes differentially expressed in liver (P<0.05). The CS-feeding activated the transcription of lipogenic genes such as HMGR and FASN, but decreased the expression of lipolytic genes such as ACOX1, PPARA and FBP. The microarray results correlated well with the measurements of several key enzymes involved in hepatic lipid metabolisms. These results suggested that dietary starch source alters hepatic transcriptome in weaned pigs. The slowly digestible starch (i.e. MS) seemed to be more healthful for mammals as the dietary energy supplier by transcriptional down-regulation of lipogenesis and steroidogenesis.

overall_design: Sixteen weaned pigs (Duroc×Landrace×Yorkshire) with an average initial body weight of 7.37±0.25 kg were selected and randomly allotted to two dietary treatments (either Cassava or maize starch as the energy source) for 21 d. At the end of the trial, the liver tissue were collected for transcriptome analysis using Agilent porcine microarrays.

first: Daiwen

last: Chen


title: Gene Expression Profiles in Peripheral Blood Mononuclear Cells Can Distinguish Patients with NonSmall Cell Lung Cancer.

status: Public on Dec 01 2009

first: Louise

last: Showe

address: 3601 Spruce St

institute: The Wistar Institute

summary: We report a 29-gene diagnostic signature, which distinguishes individuals with NSCLC from controls with non-malignant lung disease with 91% Sensitivity, 79% Specificity and a ROC AUC of 92%.  Accuracy on an independent set of 18 NSCLC samples from the same location was 79%. Samples from an independent location including 12 stage 1 NSCLC and 15 controls, achieved an accuracy of 74%.  A study of 18 paired samples taken pre and post surgery shows that the PBMC associated “cancer” signature is significantly reduced after tumor removal, supporting the hypothesis that the signature detected in pre-surgery samples is a response to the presence of the tumor.

overall_design: We compared microarray gene expression profiles in PBMC from patients with NSCLC and a control group with smoking-related non-malignant lung disease, a likely confounding factor.   We found a distinguishing gene signature which was validated on 2 independent sets of hold-out samples one set from a different location. Gene expression changes were also compared between pre and post surgery samples from 18 patients.

first: Michael

first: Anil

last: Vachani

first: Andrew

middle: V

last: Kossenkov

first: Malik

last: Yousef

first: Calen

last: Nichols

first: Elena

last: Nickonova

first: Linda

last: Alila

first: Ting

last: Yie

first: William

last: Rom

first: Steven

last: Albelda


title: Gene expression profiling in mouse liver infected with Clonorchis sinensis metacercariae.

status: Public on Apr 01 2009

first: Suk-Jin

last: Yang

address: 111 Gwahanggno, Yuseong-gu

department: Medical Genomics Research Center

institute: Korea Research Institute of Bioscience & Biottechnology

summary: Analysis of host response to the infected Clonorchis sinensis metacercariae and adult worm. The infected tissues evidenced altered expression of genes involved in systems such as immune response and cell cycle regulation, as compared with normal tissues.

overall_design: Total RNA obtained from isolated liver tissues subjected to 1, 2, 4, and 6 weeks post-infection compared to uninfected liver tissues.

first: Dong-Min

last: Kim

first: Jung-Won

last: Ju

first: Young-Il

last: Yeom

first: Yonggwan

last: Won

first: Syung-Sam

last: Ko

first: Shin-Hyeong

last: Cho

first: Tong-Soo

first: Il-Chul


title: GPR30-mediated estrogen signaling in Estrogen Receptor alpha and beta negative SKBR3 breast cancer cells

status: Public on Feb 19 2009

city: Geneva

first: Deo Prakash

last: Pandey

address: 30 Quai Ernest-Ansmert

department: Cell Biology

institute: University of Geneva

summary:
Gene expression analyses were carried out to identify genes regulated by 17-beta estradiol (E2) and Hydroxytamoxifen (OHT) through GPR30 in SKBR3 cells, a breast cancer cell-line which expresses GPR30 but lacks Estrogen Receptor alpha or beta.

Keywords: Gene expression analysis, Non-genomic signaling in breast cancer cells.

overall_design: Gene expression analyses were done for control transfected SKBR3 cells: 1) Uninduced, 2) Induced with 10 microM OHT,  3) Induced with 1 microM E2 and 4) GPR30-antisense transfected cells induced with 10 microM OHT. The cells were induced for 1h and all the samples were collected in triplicates.

first: Deo

middle: P

first: Rosamaria

last: Lappano

first: Lidia

last: Albanito

first: Antonio

last: Madeo

first: Marcello

last: Maggiolini

first: Didier

last: Picard


title: Lung cancer prediction

status: Public on Feb 28 2010

city: Cologne

first: Thomas

last: Zander

address: Kerpenerstr. 62

institute: University Hospital Cologne

summary: We generated a blood-derived transcriptional signature that discriminates patients with lung cancer from non-affected smokers. When applied to blood samples from one of the largest prospective population-based cancer studies (the European Prospective Investigation into Cancer and Nutrition), this signature accurately predicted the occurrence of lung cancer in smokers within two years before the onset of clinical symptoms. Such a blood test could be used as a screening tool to enable early diagnosis of lung cancer at a curable stage.

overall_design: All samples were taken from smokers. EPIC cases were taken from the EPIC trial (a large prospective epidemiological trial in Europe, and are incident cases), Cosmos and BC cases are prevalent cases from a Cologne, Germany based epidemiological trial.

first: Svenja

last: Debey-Pascher

first: Daniela

last: Eggle

first: Jürgen

last: Wolf

first: Joachim

middle: L

last: Schultze


title: Immunity and Defense Genes in Peripheral Blood Mononuclear Cells of Rheumatoid Arthritis patients

status: Public on Sep 03 2009

city: Evry

first: Robert

last: Olaso

address: 2 rue gaston cremieux

department: CNG Technology Department

country: France

institute: CEA IG

summary: Large-scale gene expression profiling of peripheral blood mononuclear cells from Rheumatoid Arthritis (RA) patients could provide a molecular description that reflects the contribution of diverse cellular responses associated with this disease. The aim of our study is to identify peripheral blood gene expression profiles for RA patients, using Illumina technology, to gain insights into RA molecular mechanisms. The Illumina Human-6v2 Expression BeadChips were used for a complete genome-wide transcript profiling of peripheral blood mononuclear cells from 18 RA patients and 15 Controls. Differential analysis per gene was performed with one-way analysis of variance (ANOVA) and P values were adjusted to control the False Discovery Rate (FDR<5%). Genes differentially expressed at significant level between patients and controls were analyzed using Gene Ontology (GO) in the PANTHER database to identify biological processes. A differentially expression of 339 Reference Sequence genes (238 down-regulated and 101 up-regulated) between the two groups was observed. We identified a remarkably elevated expression of a spectrum of genes involved in Immunity and Defense in peripheral blood mononuclear cells of RA patients compared to Controls. This result is confirmed by GO analysis, suggesting that these genes could be activated systemically in RA. No significant down-regulated ontology groups were found. Microarrays data were validated by real time PCR in a set of nine genes showing a high degree of correlation. Our study highlighted several new genes that could contribute in the identification of innovative clinical biomarkers for diagnostic procedures and therapeutic intervention. Further studies on larger scale groups of patients should be performed with the same technology to replicate these results and to allow clinical stratification.

overall_design: 33 samples analyzed corresponding to 18 Rheumatoid Arthritis Patients and 15 Controls

first: Vitor

middle: H

last: Teixeira

first: Marie-Laure

last: Martin-Magniette

first: Laurent

last: Jacq

first: Catarina

middle: R

last: Oliveira

first: Sandra

last: Lasbleiz

first: Pascal

last: Hilliquin

first: Ivo

last: Gut

first: François

last: Cornelis

first: Elisabeth

last: Petit-Teixeira


title: Activated TNFa/NFkB Signaling Via Down Regulation of Faf1 in Asbestos-Induced Mesotheliomas from Arf Knock-out Mice

status: Public on Dec 31 2008

first: JIANMING

last: PEI

address: 333 Cottman Ave.

department: Population Science

institute: Fox Chase Cancer Center

type: Genome variation profiling by genome tiling array

summary: The human CDKN2A locus encodes two distinct proteins, p16(INK4A) and p14(ARF) [mouse p19(Arf)], designated INK4A and ARF herein, that are translated from alternatively spliced mRNAs.  Human ARF is implicated as a tumor suppressor gene, mainly in association with the simultaneous deletion of INK4A.  However, questions remain as to whether loss of ARF alone is sufficient to drive tumorigenesis.  Here we report that mice deficient for Arf are susceptible to accelerated asbestos-induced malignant mesothelioma (MM).  MMs arising in Arf (+/-) mice consistently exhibit biallelic inactivation of Arf, but unexpectedly, do not acquire additional recurrent genetic alterations that we previously identified in asbestos-induced MMs arising in Nf2 (+/-) mice.  Array CGH analysis was used to detect a recurrent deletion at chromosome 4C6.  A candidate in this region, Faf1 (FAS-associated factor 1), was further explored because it encodes a protein implicated in tumor cell survival and in the pathogenesis of some human tumor types.  We confirmed hemizygous loss of Faf1 and down regulation of Faf1 protein in a series of MMs from Arf (+/-) mice, and then showed that Faf1 regulates TNFalpha-mediated NFkappaB signaling, a mechanism previously implicated in asbestos-induced oncogenesis of human mesothelial cells.  Collectively, these investigations divulge important information regarding the significance of Arf inactivation in MM pathogenesis, and implicate Faf1 as a key component in the TNFalpha/NFkappaB signaling node that has now been independently implicated in the asbestos-induced oncogenesis.

overall_design: We performed aCGH on primary MM cells from four Arf (+/-) mice to identify recurrent genomic imbalances connected with MM in these mice.

first: Deborah

last: Altomare

first: Craig

middle: W

last: Menges

first: Jianming

last: Pei

first: Lili

last: Zhang

first: Kristine

last: Skele

first: Michele

last: Carbone

first: Agnes

middle: B

last: Kane

first: Joseph

last: Testa


title: Genome-wide Transcriptional Profiling Reveals MicroRNA-correlated Genes and Pathways in Human Lymphoblastoid Cell Lines

status: Public on Jun 25 2009

first: LIANG

last: WANG

summary:
Background: Expression level of many genes shows abundant natural variation in human populations. The variations in gene expression are believed to contribute to phenotypic differences. Emerging evidence has shown that microRNAs (miRNAs) are one of the key regulators of gene expression. However, past studies have focused on the miRNA target genes and use loss- or gain-of-function approach that may not reflect natural association between miRNA and mRNAs.   Methodology/Principal Findings: To examine miRNA regulatory effect on global gene expression under endogenous condition, we performed pair-wise correlation coefficient analysis on expression levels of 366 miRNAs and 14,174 messenger RNAs (mRNAs) in 90 immortalized lymphoblastoid cell lines, and observed significant correlations between the two species of RNA transcripts. We identified a total of 7,207 significantly correlated miRNA-mRNA pairs (false discovery rate q <0.01). Of those, 4,085 pairs showed positive correlations while 3,122 pairs showed negative correlations. Gene ontology analyses on the miRNA-correlated genes revealed significant enrichments in several biological pathways related to cell cycle, cell communication and signal transduction. Individually, each of three miRNAs (miR-331, -98 and -33b) demonstrated significant correlation with the genes in cell cycle-related biological processes, which is consistent with important role of miRNAs in cell cycle regulation. Surprisingly, most miRNA-correlated genes were not direct targets predicted by mRNA target prediction program, TargetScan, suggesting indirect endogenous relationship between miRNAs and their correlated mRNAs.  Conclusions/Significance: This study demonstrates feasibility of using naturally expressed transcript profiles to identify endogenous correlation between miRNA and miRNA. By applying this genome-wide approach, we have identified thousands of miRNA-correlated genes and revealed potential role of miRNAs in several important cellular functions. The study results along with accompanying data sets will provide a wealth of high-throughput data to further evaluate the miRNA-regulated genes and eventually in phenotypic variations of human populations.

Keywords: correlation coefficient analysis, gene ontology analysis

overall_design: to correlate miRNA expression levels with microRNA expression at genome-wide scale in 90 cell lines.

first: Liang

last: Wang


title: Effects of DZNep and 5-Aza-CdR on gene expression in MCF7 cells after 72 h treatment

status: Public on Mar 24 2009

city: Los Angeles

first: Tina

last: Miranda

address: 1441 Eastlake Ave

institute: USC

summary: DNA methylation, histone modifications, and nucleosomal occupancy collaborate to cause silencing of tumor related genes in cancer. The development of drugs that target these processes is therefore important for cancer therapy. Inhibitors of DNA methylation and histone deacetylation have already been approved by the FDA for the treatment of hematologic malignancies. However, drugs that target the other mechanisms still need to be developed. Recently, 3-deazaneplanocin A (DZNep) was reported to selectively inhibit the trimethylation of lysine 27 on histone H3 (H3K27me3) and lysine 20 on histone H4 (H4K20me3) as well as re-activate silenced genes in cancer cells. This finding opens the door to pharmacological inhibition of histone methylation and we therefore wanted to further study the mechanism of action of 3-deazaneplanocin A in cancer cells. Western blot analysis showed that two other drugs, sinefungin and adenosine-dialdehyde (Adox), have similar effects on the trimethylation H3K27 as 3-deazaneplanocin A and that DZNep is not selective, but globally inhibits histone methylation. Intriguingly, chromatin immunoprecipitation of various histone modifications and microarray analysis show DZNep acts via a different pathway to 5-aza-2´-deoxycytidine (5-azaCdR), a DNA methyltransferase inhibitor and gives us an interesting insight into how chromatin structure effects gene expression. We also determine the kinetics of gene activation in order to understand if the induced changes were somatically heritable. We have found that upon removal of DZNep, gene expression is reduced to its original state suggesting that there is a homeostatic mechanism which returns the histone modifications to their “ground state” after DZNep treatment. Not only do these studies show the strong need for further development of histone methylation inhibitors but also allow us to better understand how chromatin structure affects gene expression.

overall_design: There are two different drug treatments (DZNep and 5-Aza-CdR). Each drug treatment was harvested on two separated days (D1 and D7). There was also and untreated control sample. Each treatment has 4 technical repeats.

first: Terry

middle: K

last: Kelly

first: Connie

middle: C

last: Cortez


title: Physiological defects associated with short hairpin RNA-mediated silencing of PGC-1-related coactivator (PRC)

status: Public on Jan 16 2009

city: Chicago

first: Richard

last: Scarpulla

state: IL

address: 303 East Chicago Ave.

department: CMB

institute: Northwestern Medical School

summary: PRC, a member of the PGC-1 coactivator family, is responsive to serum growth factors and up regulated in proliferating cells. Here, we investigated its in vivo role by stably silencing PRC expression with two different short hairpin RNAs (shRNA#1 and shRNA#4) that were lentivirally introduced into U2OS cells. ShRNA#1 transductants exhibited nearly complete knockdown of PRC protein whereas shRNA#4 transductants expressed PRC protein at approximately 15 percent of the control level. Complete PRC silencing by shRNA#1 resulted in a severe inhibition of respiratory growth, reduced expression of respiratory protein subunits from complexes I, II, III and IV, markedly lower complex I and IV respiratory enzyme levels and diminished mitochondrial ATP production. Surprisingly, shRNA#1 transductants exhibited a striking proliferation of abnormal mitochondria that were devoid of organized cristae and displayed severe membrane abnormalities. Although shRNA#4 transductants had normal respiratory subunit expression and a moderately diminished respiratory growth rate, both transductants showed markedly reduced growth on glucose accompanied by inhibition of G1/S cell cycle progression. Microarray analysis revealed striking overlaps in the genes affected by PRC silencing in the two transductants and the functional identities of these overlapping genes were consistent with the observed mitochondrial and cell growth phenotypes. The consistency between phenotype and PRC expression levels in the two independent transductant lines argues that the defects result from PRC silencing and not from off target effects. These results support a role for PRC in the integration of pathways directing mitochondrial respiratory function and cell growth.

overall_design: U2OS cells were infected with lentivirus expressing either a control short hairpin RNA, or two independent short hairpin RNAs (shRNA1 and shRNA4) targeting PRC mRNA, and stable clones were isolated under blasticidin selection. Total RNA was isolated from U2OS control shRNA, shRNA1, and shRNA4 transductants using TRIzol (Invitrogen) and DNase treated with the TURBO DNA-free kit (Ambion). RNA samples were further purified using the RNeasy MinElute Cleanup kit (Qiagen). Integrity of the RNA was evaluated using the Agilent 2100 BioAnalyzer. 500 ng of RNA was used to perform in vitro transcription in the presence of biotin UTP with the Illumina TotalPrep RNA amplification kit (Ambion). The amplified, labeled RNA (1.5 μg) was then hybridized in triplicate to an Illumina Whole-Genome Sentrix Human-6 v2 Expression BeadChip, and detected according to the Illumina user manual.

first: Kristel

last: Vercauteren

first: Natalie

last: Gleyzer


title: Gene expression analysis of cancer-related fatigue in whole blood from breast cancer survivors

status: Public on Jul 01 2009

city: Oslo

first: Hege

last: Landmark-Høyvik

address: Montebello

country: Norway

institute: Radiumhospitalet

summary:
Cancer-related fatigue is one of the most frequent complaints among breast cancer survivors, with a major negative impact on general life. However, the etiology behind this syndrome is still unraveled. Gene expression analysis was performed on whole blood samples from breast cancer survivors classified as either fatigued or non-fatigued at two consecutive time points. The analysis identified several gene sets concerning plasma and B cell pathways as different between the fatigue and non-fatigue groups, suggesting that a deregulation in these pathways might underlie the fatigue syndrome. The fatigue group also showed a higher mean level of leucocytes, lymphocytes and neutrophiles compared with the non-fatigue group, thus further implicating the immune system in the biology behind the fatigue syndrome.

Keywords: Blood RNA and late side effects

overall_design: Breast cancer survivors treated with adjuvant radiotherapy at The Norwegian Radium Hospital between 1998 and 2002 were invited to participate in a study assessing late treatment effects in breast cancer survivors. In the present study, gene expression analysis was performed on whole blood samples from breast cancer survivors with and without persistent fatigue, to look for different expression patterns that might shed light on the biology behind cancer-related fatigue.

first: Kristin

last: Valborg Reinertsen

first: Jon

last: Håvard Loge

first: Sophie

middle: D

last: Fosså

first: Anne-Lise

last: Børresen-Dale

first: Vanessa

last: Dumeaux


title: Microvesicles derived from human mesenchymal stem cells protect against acute tubular injury

status: Public on Jan 20 2009

city: Torino

first: Raffaele

last: Calogero

state: To

address: Via Nizza 52

department: Molecular Biotechnology Center

country: Italy

institute: University of Torino

summary: Administration of exogenous mesenchymal stem cells (MSCs) has been shown to improve the recovery from acute kidney injury (AKI). It has been suggested that the beneficial effect of MSCs is related to the paracrine release of factors favouring proliferation of intrinsic epithelial cells survived to injury rather than to their trans-differentiation. However the factors involved remain to be determined. In the present study we demonstrated that microvesicles (MVs) derived from human bone marrow MSCs are able to stimulate in vitro proliferation and apoptosis resistance of tubular epithelial cells (TEC). In addition, MVs were found to accelerate in vivo the morphological and functional recovery of glycerol induced AKI in SCID mice by inducing TEC proliferation. The effect of MVs on the recovery of AKI was comparable to that of human MSC treatment. In vitro we found that the CD44 and beta1-integrin-dependent incorporation of MVs in TEC was required for their biological action. However, despite their internalization, RNase-treated MVs failed to induce in vitro apoptosis resistance and TEC proliferation, and in vivo recovery from AKI, suggesting an RNA-dependent biological effect. Microarray analysis and quantitative RT-PCR of MV-RNA extract indicated that MVs were shuttling a specific subset of cellular mRNA, such as mRNA associated with the mesenchymal differentiative phenotype and with several cell functions involved in the control of transcription, proliferation, apoptosis and cell immune regulation. These results suggest that MVs derived from MSCs may activate a proliferative program in TEC survived to injury in AKI by an horizontal transfer of mRNA.

overall_design: Microarrays were used not to define the amount of mRNAs in the MVs but only to define which transcripts were present. Transcripts present in the MVs were defined as those characterized by a positive linear relation between the transcript signal detected by the microarray analysis and the amount of total RNA hybridized. This analysis was done hybridizing arrays with labelled-cRNA produced using three different concentrations of total RNA extracted from two independent preparations of MVs.

first: Stefania

last: Bruno

first: Cristina

last: Grange

first: Silvia

last: Saviozzi

first: Federica

last: Collino

first: Laura

last: Morando

first: Alessandro

last: Busca

first: Benedetta

last: Bussolati

first: Chiara

last: Deregibus

first: Ciro

last: Tetta

first: Giovanni

last: Camussi


title: Gene profile in H1299 cells treated with PTD-DRBD GAPDH siRNA or treated with Lipofection GAPDH siRNA

status: Public on May 22 2009

city: La Jolla

first: Steven

last: Dowdy

address: 9500 Gilman Drive #0686

department: CMM

country: USA

institute: UCSD

summary: Whole genome microarrays were probed with total mRNA from PTD-DRBD GAPDH siRNA treated H1299 cells at 12 h and 24 h. Using a 1.6x fold increase/decrease filter of cellular mRNAs, we detected a dramatic reduction in the target GAPDH mRNA along with a limited number of both up and down regulated genes. The up regulated genes were reduced in numbers and to nearly background 1.6x levels at 24 h, while the down regulated genes increased slightly in numbers and maintained a similar magnitude at 24 h. In contrast, lipofection treated cells showed both a dramatic increase in both the total number of genes altered and the magnitude of the increase. In addition, the numbers of genes affected increased between 12 h and 24 h, suggesting that lipofection of siRNAs into cells results in a substantial alteration to the transcriptome and may thereby confound interpretation of experimental outcomes. Moreover, the GAPDH specific knockdown was significantly smaller than PTD-DRBD mediated knockdown.

overall_design: Total RNA obtained from H1299 cells treated with PTD-DRBD GAPDH siRNA, Lipofection GAPDH siRNA or PBS (Control) after 12 or 24 hours post-treatment

first: Akiko

last: Eguchi


title: Illumina expression data from LNCaP cells overexpressing either SOX4 or GFP

status: Public on Nov 10 2008

city: Atlanta

first: Chris

last: Scharer

state: GA

address: 1510 Clifton Rd, Suite 3086A

department: Microbiology and Immunology

institute: Emory University

summary:
SOX4 is a critical developmental transcription factor in vertebrates and is required for   precise differentiation and proliferation in multiple tissues.  In addition, SOX4 is   overexpressed in many human malignancies, but the precise role of SOX4 in cancer   progression is not well understood.  Here we have performed an expression profiling experiment of LNCaP cells either overexpressing SOX4 or GFP to identify SOX4 target genes.

Keywords: Gene expression

overall_design: LNCaP prostate cancer cells were transfected with either SOX4 or GFP expression vectors and total RNA harvested 24 hours post-transfection.  Each transfection and RNA isolation was performed in triplicate and each hybridization was performed in duplicate providing 12 overall hybridizations on the Illumina platform.

first: Carlos

middle: S

last: Moreno

first: Christopher


title: Development of gene expression signatures for practical radiation biodosimetry

status: Public on Jul 01 2008

city: New York

first: Sally

last: Amundson

department: Center for Radiological Research

institute: Columbia University

summary:
To further development of our gene expression approach to biodosimetry, we have employed whole genome microarray expression profiling as a discovery platform to identify genes with the potential to distinguish radiation dose across an exposure range relevant for medical decision-making in a radiological emergency.   Human peripheral blood from healthy donors was irradiated ex vivo, and a 74-gene consensus signature was identified that distinguished between four radiation doses (0.5, 2, 5 and 8 Gy) and control samples.  The same set of genes separated samples by exposure level at both six and 24 hours after treatment, with overlap evident only at the highest two doses (5 and 8 Gy).  Expression of five genes (CDKN1A, FDXR, SESN1, BBC3 and PHPT1) from this signature was quantified in the same RNA samples by real-time PCR, confirming low variability between donors as well as the predicted radiation response pattern.
Keywords: Dose Response, stress response, radiation response, biodosimetry

overall_design: Radiation induced gene expression in human blood was measured at 6 and 24 hours after exposure to doses of 0, 0.5, 2, 5 and 8 Gy g-rays.  Five independent experiments were performed at each time (6 or 24 hours) using different donors for each experiment

middle: A

first: Sunirmal

last: Paul


title: Macs isolated E-cadherin positive Fetal liver stem progenitor cells vs adult mouse liver (pooled)

status: Public on Jun 20 2007

first: Leslie

last: Rogler

address: 1300 Morris Park Ave

department: Liver Research Center/ Department of Medicine

institute: Albert Einstein College of Medicine

summary:
The isolation of hepatic stem cells from the adult liver has not yet been achieved due to the lack of specific surface markers.  To identify new surface markers for hepatic stem cells, we analyzed differences in the gene expression profile of fetal liver epithelial cells (FLEC) and adult liver by microarray technology.  In contrast to previous microarray studies on fetal liver, we purified FLEC by immunomagnetic selection for E-cadherin to more than 90% to analyze their specific expression profile.
Keywords: cell type comparison

overall_design: Three independent biological repeats of purified FLEC were compared with adult liver and for each analysis, a dye switch was included to control for preferential dye incorporation, using a total of 6 microarrays.

first: Dirk

last: Nierhoff

first: Lauretta

last: LeVoci

first: David

last: Shafritz

middle: E


title: Atm-/-,mTerc-/-,p53-/- triple knock-out lymphoma vs normal mouse DNA (GPL2884)

status: Public on Jun 05 2007

city: boston

first: bin

last: feng

state: MA

address: 44 binney street

institute: dfci

summary:
Highly rearranged and mutated cancer genomes present major challenges in the identification of pathogenetic events driving the cancer process.  Here, we engineered lymphoma-prone mice with chromosomal instability to assess the utility of mouse models in cancer gene discovery and the extent of cross-species overlap in cancer-associated copy number aberrations.  Integrating with targeted re-sequencing, our comparative oncogenomic studies efficiently identified FBXW7 and PTEN as commonly deleted or mutated tumor suppressors in human T-cell acute lymphoblastic leukemia/lymphoma (T-ALL).  More generally, the murine cancers acquire widespread recurrent clonal amplifications and deletions targeting loci syntenic to alterations present in not only human T-ALL but also diverse tumors of hematopoietic, mesenchymal and epithelial types. These results thus support the view that murine and human tumors experience common biological processes driven by orthologous genetic events as they evolve towards a malignant phenotype.  The highly concordant nature of genomic events encourages the use of genome unstable murine cancer models in the discovery of biologically relevant driver events in human cancer.
Keywords: comparative genomic hybridization, genetic modification

overall_design: 22 lymphoma samples from Atm-/-, mTerc-/-, p53-/- triple knock-out mice were analyzed. DNA from healthy mice of the same line was used as reference. Each sample was hybridized with dye-swap replica.

first: B

last: Feng

first: R

last: Maser

first: K

last: Wong

first: A

last: Protopopov

first: E

last: Lin

first: L

last: Chin

last: Depinho


title: Whole-genome tiling array analysis in normal human bronchial/tracheal epithelial cells (NHBE)

status: Public on Nov 22 2007

first: Damon

middle: Scott

last: Perez

address: 200 Fist Street SW

department: Experimental Pathology & Lab Medicine

institute: Mayo Clinic

type: Expression profiling by genome tiling array

summary:
Identify transcriptionally-active regions (TARs) greater than 400 nt long across the entire human genome. A total of 578 were identified in NHBE cells. We then focused on those TARs originating from non-coding sequence and that displayed a moderate to high degree of sequence conservation. A subset of 15 non-coding transcripts were then further examined to determine if they are altered in cancer (deregulated expression in breast and ovarian cancer and sequenced for mutations in a panel of cancer samples).
Only transcriptionally-active regions originating from non-coding sequence, expressing at the 99.5th percentile, and longer than 400 nt were examined so far in our studies.
Keywords: whole-genome mapping, transcriptionally-active regions, tiling arrays, non-coding transcripts, bronchial/tracheal epithelial cells

overall_design: Total RNA isolated from NHBE cell cultures were labeled and hybridized to 3 sets of the GeneChip® Human Tiling 1.0R Array set of 14 (3 x 14 = 49 chips total) according to supplier's protocol. A total of 3 biological replicates were run. Each biological replicate was run on an entire set of 14 chips which covers the entire non-repetitive portion of the human genome. The first 2 sets were labeled and hybridized together and the 3rd set was hybridized at a later date.  Also, for the first 2 tiling array sets, ribosomal RNA removal was not part of the initial protocol. However, since we ran the 3rd set at a later date the protocol changed and included a ribosomal removal step.

middle: I

last: Smith


title: Tumor Liver vs Normal Liver: ChIP-chip and RNA expression

status: Public on Jun 04 2008

city: Calgary

first: Mark

last: Bieda

state: AB

address: 3330 Hospital Dr NW

department: Biochemistry and Molecular Biology

institute: University of Calgary

summary:
There is widespread interest in efficient characterization of differences between tumor and normal samples. Here, we demonstrate an effective methodology for genome-scale characterization of tumors.

Using matched normal and tumor samples from liver cancer patients, as well as non-cancer-related normal liver tissue, we first determined changes in gene expression as monitored on RNA expression arrays. We identified several hundred mRNAs that were consistently changed in the tumor samples.

To characterize the mechanisms responsible for creation of the tumor-specific transcriptome, we performed ChIP-chip experiments to assay binding of RNA polymerase II, H3me3K27, and H3me3K9 in 25,000 promoter regions. These experiments identified changes in active and silenced regions of the genome in the tumor cells.

Finally, we used a “virtual comparative genomic hybridization” (vCGH) method to identify copy number alterations in the tumor samples.

Through comparison of RNA Polymerase II binding, chromatin structure, and copy number changes, we suggest that the major contributor to creation of the liver tumor transcriptome was changes in gene copy number.
Keywords: ChIP-chip, gene expression, CGH

overall_design:
Source material: Liver samples from human liver cancer patients, normal human liver samples, liver cell lines and normal human hepatocytes.
Experiments: ChIP-chip with abs against POLII, H3me3K27, and H3me3K9, and DNA methylation using NimbleGen 5 kb promoter arrays. RNA expression from the listed sources using Illumina Bead system.
Compare normal liver to tumor liver and normal cell lines to tumor cell lines.

first: Luis

middle: G

last: Acevedo

first: Roland

last: Green

first: Peggy

middle: J

last: Farnham


title: Genomic aberrations in MMTV-cdc25a;MMTV-neu murine cell line

status: Public on Nov 13 2006

city: Newark

first: Eleftherios

middle: Terry

last: Papoutsakis

state: DE

address: 15 Innovation Way

department: Chemical Engineering

institute: University of Delaware

summary:
CDC25A is a critical target of checkpoint, and its overexpression is observed in various cancers.  Here we demonstrate that in vivo levels of Cdc25A expression determine the efficiency of transformation and tumorigenesis. Transgenic expression of CDC25A in murine mammary glands cooperates with tumorigenesis induced by expression of ras or neu.  CDC25A- overexpressing tumors display aggressiveness and genomic instability with changes in fragile chromosomal regions, including the region orthologous to human 1p32-36.
Keywords: genetic modification, aCGH

overall_design: Genomic DNA from a MMTV-cdc25a;MMTV-neu double transgenic murine cell line derived from a mammary tumor was compared to normal mammary tissue DNA from the parental strain.  A total of two hybridizations were completed.

first: Peter

last: Fuhrken

first: Hiroaki

last: Kiyokawa

middle: T

first: Dipankar

last: Ray