title: Bidirectional manipulation of SF-1 (NR5A1) in NCI-H295R cells

status: Public on Jan 11 2011

first: Bruno

last: Ferraz-de-Souza

address: 30 Guilford St

department: Clinical & Molecular Genetics Unit

institute: UCL Institute of Child Health

summary:
SF-1 (NR5A1) was overexpressed (Over) or knocked down with shRNA (shRNA) in NCI-H295R human adrenocortical tumor cells and differential global gene expression analysed 48 hours later using Affymetrix GeneChip Human Gene 1.0ST arrays. Over: 5 million cells were transfected (Amaxa Nucleofection) with 10 ug of a pIRES2-AcGPF1-Nuc construct co-expressing SF-1 cDNA and GFP. For experimental control, a mutagenized pIRES2 construct, bearing the G35E mutation in SF-1 that impairs its transactivation function in vivo and in vitro was used. shRNA: 5 million cells were transfected (Amaxa Nucleofection) with 10 ug of the SureSilencing shRNA Plasmid for Human NR5A1 with GFP marker kit (SABioscience). For experimental control, mismatch constructs provided in the kit were used. In both experiments (Over and shRNA), cells were harvested, prepared, and submitted to fluorescence-activated cell sorting (FACS) in a MoFlo XDP sorter 48 hours after transfection. Viable GFP-expressing cells were pooled and resuspended in TRIzol reagent for RNA extraction. Total RNA was extracted, and RNA quality control performed using a 2100 Bioanalyzer.
RNA samples were processed using the Affymetrix GeneChip WT Sense Target Labeling kit, starting with 200 ng total RNA. Four independent Over experiments and five independent shRNA experiments were performed and samples of labeled fragmented cDNA were hybridized to Affymetrix GeneChip Human Gene 1.0 ST Arrays. Based on  quality control of array data (R/Bioconductor and Partek Genomics Suite), two Over arrays (one SF-1 wild type and one mutant control) and one shRNA array (mismatch control) were  excluded and are not deposited here. Differential gene expression analysis was performed using the limma package in R/Bioconductor. A Benjamini-Hochberg-corrected P value cut-off of 0.05 was used to select significant differentially expressed genes in each setting (Over and shRNA). Finally, results from both analyses were combined to identify a subset of positively-regulated SF-1 target genes in these cells, ie transcripts up-regulated by SF-1 overexpression (Over) and down-regulated by SF-1 knockdown (shRNA).

overall_design: Four SF-1 overexpression experiments (Over; intervention = overexpression of wild type SF-1; control = overexpression of functionally-impaired mutant G35E SF-1) and five SF-1 knockdown experiments (shRNA; intervention = SF-1-specific small hairpin RNA; control = shRNA mismatch control) were performed in NCI-H295R cells. Differential gene expression in each setting was analysed using GeneChip Human Gene 1.0ST arrays. Data for arrays that met quality control are presented here: Over, 3 intervention and 3 control arrays; shRNA, 5 intervention and 4 control arrays. Total of 15 arrays.

first: Rebecca

last: Hudson-Davies

first: Lin

last: Lin

first: Rahul

last: Parnaik

first: Mike

last: Hubank

first: Mehul

middle: T

last: Dattani

last: Achermann


title: p73 activity and rapamycin treatment: ChIP-on-Chip and gene expression profiling studies

status: Public on Jan 05 2011

city: Nashville

first: Jennifer

last: Pietenpol

state: TN

address: 23rd Ave South at Pierce

department: Biochemistry

country: USA

institute: Vanderbilt University Medical Center

type: Genome binding/occupancy profiling by genome tiling array

summary:
p73 is a p53 family transcription factor that plays critical roles during development and tumor suppression. We analyzed p73 activity using a combination of ChIP-on-Chip and gene expression profiling, both at baseline and after treatment with the mTOR inhibitor rapamycin.

This SuperSeries is composed of the SubSeries listed below.

overall_design: Refer to individual Series

middle: M

last: Rosenbluth

middle: A


title: Expression data from rapamycin treatment and/or p73 knock-down in Rh30 cells

summary:
p73 is a p53 family transcription factor that plays critical roles during development and tumor suppression.  We analyzed p73 activity using a combination of ChIP-on-Chip and gene expression profiling, both at baseline and after treatment with the mTOR inhibitor rapamycin.
We generated an mTOR-p73 gene signature that predicts rhabdomyosarcoma tumor subtype and patient outcome, and is enriched for p73 target genes involved in mesenchymal stem cell differentiation and tumorigenesis.

overall_design: Rh30 rhabdomyosarcoma cells were infected with lentivirus (either control or expressing one of two RNAi constructs targeting p73) for 3 d, and treated with vehicle or 40 nM rapamycin for 24 h, and then total RNA was harvested.  Experiments were performed in duplicate for a total of 8 samples.  For p73 RNAi, a different targeting construct was used for each replicate.


title: Effects of IKAP/hELP1 deficiency on gene expression in differentiating neuroblastoma cells, implications for Familial dysautonomia

status: Public on Jan 06 2011

city: Tel Aviv

first: Metsada

last: Pasmanik-Chor

address: Ramat Aviv

department: Biology

country: Israel

institute: Tel Aviv University

summary: Investigate IKAP importance in the development of neuronal cells, in order to understand Familial dysautonomia  phenotype.

overall_design: Stable SHSY5Y cell lines, and control cells, in differentiated and un-differentiated conditions.


title: Effect of JMJD2B depletion on the ER signaling pathway

status: Public on Dec 31 2010

city: Toronto

first: Hitoshi

last: OKADA

state: Ontario

address: 620 University Ave Suite 7-706

department: Campbell Family Institute for Breast Cancer Research

country: Canada

institute: Ontario Cancer Institute

summary: JMJD2B is expressed in a high proportion of human breast tumors, and the expression levels significantly correlate with estrogen receptor (ER) positivity. To assess the effect of JMJD2B depletion on the ER signaling pathway, we performed genome-wide gene expression analysis using the Affymetrix Human Gene 1.0 ST array.

overall_design: RNA was extracted from steroid-depleted control MCF-7 cells (control E2(-)), control MCF-7 cells treated with E2 (control E2(+)), steroid-depleted JMJD2B-depleted MCF-7 cells (siJ2B E2(-)), and JMJD2B-depleted MCF-7 cells treated with E2 (siJ2B E2(+)).

first: Masahito

last: Kawazu

first: Kayoko

last: Saso

first: Kit

middle: I

last: Tong

first: Tracy

last: MxQuire

first: Kouichiro

last: Goto

first: Dong-Ok

last: Son

first: Andrew

last: Wakeham

first: Makoto

last: Miyagashi

first: Tak

middle: W

last: Mak

last: Okada


title: Targeting of mitochondrial Hsp90 with Gamitrinib, G-TPP, in U251 glioblastoma cells

status: Public on Dec 28 2010

city: Weehawken

first: Markus

middle: D

last: Siegelin

state: NJ

address: 963 Boulevard E

institute: Markus Siegelin

summary: U251 gliolbastoma cells were treated with vehicle (DMSO) or G-TPP, a mitochondrial targeted version of 17-AAG. 6 hours after treatment RNA was harvested and subjected to microarray analysis on Human Gene 1.0 ST Array.

overall_design: We sought to determine a mitochdondrial gene response after targeting inhibition of mitochondrial chaperones, Hsp90.


title: Expression data from LoVo colon cancer lines +/- constitutive LIN28B expression

status: Public on Dec 29 2010

city: Philadelphia

first: Catrina

last: King

state: PA

address: 415 Curie Blvd

department: Gastroenterology

institute: University of Pennsylvania

summary:
We sought to elucidate the molecular mechanisms whereby LIN28B functions by comparing the gene expression profile of cells constitutively expressing LIN28B to empty vector controls.
Accordingly, we performed microarray analysis on total RNA isolated from empty vector LoVo and LIN28B-expressing LoVo colon cancer cell lines.

overall_design: Constitutive LIN28B expression was achieved in the LoVo (ATCC #CCL-229) colon cancer cell line via retroviral transduction of MSCV-PIG-LIN28B. Contol = empty vector MSCV-PIG.

first: Anil

last: Rustgi


title: Expression data from xenograft tumors derived from LoVo colon cancer lines +/- constitutive LIN28B expression

summary: We sought to elucidate functions of LIN28B and potential mechanisms whereby it may promote metastasis by comparing the gene expression profile of LIN28B metastases to primary tumors. Accordingly, we performed microarray analysis on total RNA isolated from empty vector tumors, LIN28B-LoVo tumors, and LIN28B-LoVo metastases

overall_design:
Constitutive LIN28B expression was achieved in the LoVo (ATCC #CCL-229) colon cancer cell line via retroviral transduction of MSCV-PIG-LIN28B.
xenografts were produced via injection of 1x106 cells subcutaneously into the rear flanks of nude mice. Microarrays were conducted on primary tumors from empty vector
and LIN28B-expressing cells, as well as metastases derived from primary tumors constitutively expressing LIN28B. (Note: metastases did not occur with empty vector tumors)


title: LIN28B and colon cancer

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


title: MC70 potentiates doxorubicin efficacy in colon and breast cancer in vitro treatment

status: Public on Dec 22 2010

city: Bari

first: Pina

last: Iannelli

address: viale Orazio Flacco, 65

country: Italy

institute: National Cancer Centre "Giovanni Paolo II"

summary: A major limitation in the cancer treatment is the ability of cancer cells to become resistant to chemotherapeutic drugs, by multidrug establishment. Here, we evaluate the possibility to utilize MC70, either as ABC transporters inhibitor or as anticancer agent, in monotherapy or in combination with doxorubicin for cancer treatment.  The study was carried out in MCF7/ADR and Caco-2, breast and colon cancer cells, respectively. Cell growth and apoptosis were measured by MTT assay and DNA laddering Elisa kit, respectively. Cell cycle perturbation and cellular targets modulation were analyzed by flowcytometry and western blotting, respectively. MC70 was analyzed for its interaction with ABC transporters, MDR-1, BCRP and MRP-1, and for its anticancer activity.  In MCF7/ADR, MC70 slight inhibited cell proliferation and strongly enhanced doxorubicin effectiveness; conversely in Caco-2, it inhibited cell growth without affecting doxorubicin efficacy. In addition, it induced apoptosis, canceled in favor of necrosis when it was given in combination with high doses of the anthracycline. Moreover, MC70 inhibited cell migration probably through its residual activity as sigma-1 ligand. Among the hypothesized molecular and cellular mechanisms responsible for all these effects, modulations of cell cycle, of pAkt and of the three MAPKs phosphorylation were evidenced while activity at transcription level was excluded. MC70 can be considered as a potential new anticancer agent with the capability to enhance doxorubicin effectiveness and an interesting role in the treatment of chemotherapy resistant tumors.

overall_design: The study included the basic characterization of MC70 efficacy as inhibitor of MDR transporters, the investigation of its anticancer behavior and the exploration of the molecular and cellular mechanisms responsible for it

first: Amalia

last: Azzariti

first: Anna

middle: E

last: Quatrale

first: Letizia

last: Porcelli

first: Nicola

last: Colabufo

first: Mariangela

last: Cantore

first: Giuseppe

last: Cassano

last: Gasparre

first: Giuseppina

first: Stefania

last: Tommasi

first: Maria

last: Panaro

first: Angelo

last: Paradiso


title: Expression data from MTDH knockdown in the Hec50co endometrial cancer cell line

status: Public on Dec 17 2010

city: Iowa City

first: xiangbing

last: meng

state: IA

address: 375 Newton Road

institute: University of Iowa

summary: Understanding the molecular underpinnings of chemoresistance is vital to design therapies to restore chemosensitivity. In particular, metadherin (MTDH) has been demonstrated to have a critical role in chemoresistance. Over-expression of MTDH has recently been implicated in poor clinical outcome in breast cancer, neroblastoma, hepatocellular carcinoma and prostate cancer. In this present study, we focused on the therapeutic benefit of MTDH depletion to restore sensitivity to cell death mediated by a combinatorial therapy of tumor necrosis factor-alpha-related apoptosis-inducing ligand (TRAIL), which promotes death of cancerous cells of the human reproductive tract, and histone deacetylase (HDAC) inhibitors, which have been shown to increase sensitivity of cancer cells to TRAIL-induced apoptosis. Our data indicate that depletion of MTDH in endometrial cancer cells results in sensitization of cells that were previously resistant to cell death mediated by combinatorial treatment with TRAIL and HDAC inhibitor LBH589. MTDH was found to be involved in G2/M checkpoint regulation in response to LBH589 alone or LBH589 in combination with TRAIL, suggesting that MTDH functions at the cell cycle checkpoint to accomplish resistance.Using microarray technology, we identified 57 downstream target genes of MTDH, including Calbindin 1 and Galectin 1, which may contribute to MTDH-mediated resistance to combinatorial TRAIL and HDAC inhibitor targeted therapy. Inhibition of PDK1,AKT phosphorylation and increase Bim expression and XIAP degradation may result in sensitivity to cell death induction in MTDH depleted Hec50co cells by TRAIL and LBH 589 combination treatment. These findings indicate that depletion of MTDH is a potentially novel avenue for effective cancer therapy.

overall_design: The microarray was performed on three biological triplicates as well as three experimental triplictes of stable knockdown and control cells.  MTDH was knocked down using a shRNA.

first: Xiangbing

last: Meng

first: Pavla

last: Brachova

first: Kimberly

last: Leslie


title: TAL1 knock down in human erythroid progenitors

status: Public on Dec 14 2010

city: Ottawa

first: Theodore

last: Perkins

state: ON

address: 501 Smyth Rd.

department: Cellular and Molecular Medicine

institute: Ottawa Hospital Research Institute

summary: We used microarray profiling in erythroid cells to uncover TAL1 dependent genes in a hematopoietic differentiation context.

overall_design: Differentiated ex vivo hematopoietic multipotential progenitors isolated from adult peripheral blood. The knockdown of TAL1 (KD) was induced in pro-erythroblasts (Days 8 and 9 of differentiation) using lentivirus-delivered shRNA. A scramble (scr) shRNA sequence was used as a negative control.

first: Marjorie

last: Brand


title: TAL1 knock down


title: TAL1 knock down in Jurkat cells

summary: We used microarray profiling in Jurkat cells to uncover TAL1 dependent genes in a leukemic context.

overall_design: Clonal Jurkat lines expressing a Doxycycline (Dox) -inducible shRNA against TAL1 coding sequence were generated. A clone in which Dox treatment led to 80% decrease of TAL1 mRNA was chosen. Reps 1 and 4 (2 and 5 / 3 and 6)  are technical replicates.

first: Carol

last: Perez-Iratxeta


title: IL13_0-12h_RAIA_et_al

status: Public on Dec 09 2010

city: Munich

first: Andreas

last: Roller

address: Max-Lebsche-Platz 31

country: Germany

institute: Munich Leukemia Laboratory

summary: Primary mediastinal B-cell lymphoma (PMBL) and classical Hodgkin lymphoma (cHL) share a frequent constitutive activation of Janus-activated kinase (JAK) / signal transducer and activator of transcription (STAT) signaling pathway. Due to complex non-linear relations within the pathway, key dynamic properties remained to be identified to predict possible strategies for intervention. To untangle these features, we used dynamic pathway modeling that employs model development and calibration based on extensive quantitative data generation. Quantitative data were collected on JAK/STAT pathway signaling components in two lymphoma-derived cell lines, MedB-1 and L1236, representative of PMBL and cHL, respectively. We showed that the amounts of STAT5 and STAT6 are higher whereas the amount of SHP1 is lower in the two lymphoma cell lines compared to B cells from healthy donors. Distinctively, L1236 cells harbor more JAK2 and less SHP1 molecules per cell than MedB-1 or control cells. In our experimental setting interleukin-13 (IL13) stimulation levels remained constant over time. In MedB-1 cells surface IL13 receptor alpha 2 had a strong IL13-sequestering/decoy function. In both lymphoma cell lines we observed IL13-induced activation of interleukin-4 receptor alpha, JAK2 and STAT5, but not of STAT6, which was highly phosphorylated even without stimulus. Furthermore, the known STAT-inducible negative regulators CISH and SOCS3 were up-regulated within 2 hours in MedB-1 but not in L1236 cells. Global transcription profiling revealed 11 early and 16 sustained common genes up-regulated by IL13 in both lymphoma cell lines. Based on this detailed information we established two individual mathematical models, MedB-1 and L1236 model, which were able to describe the respective experimental data. Sensitivity analysis of the model identified six possible therapeutic targets able to reduce gene expression levels in L1236 cells and three in MedB-1 cells. By inhibition of STAT5 phosphorylation we successfully validated one of the predicted targets demonstrating the potential of the approach in guiding target identification for highly deregulated signaling networks in cancer cells.  We established mathematical models of the JAK/STAT pathway in two lymphoma cell types (PMBL and cHL), able to reproduce experimental data and to predict possible therapeutic targets.

overall_design: Cells from two lymphoma-derived cell lines, MedB-1 and L1236, were used for a time-course microarray analysis comprising stimulations with IL13 for 0, 0.5, 1, 1.5, 2, 3, 4, 6, 8, 12 h and unstimulated controls (0, 0.5, 1, 1.5, 2, 3, 4, 6, 8, 12 h), for a total of 20 microarrays per cell line.

first: Valentina

last: Raia

first: Marcel

last: Schilling

first: Martin

last: Böhm

first: Mettina

last: Hahn

last: Kowarsch

first: Stefan

last: Jansen

last: Raue

first: Carsten

last: Sticht

first: Sebastian

last: Bohl

last: Saile

first: Peter

last: Möller

first: Nobert

last: Gretz

first: Jens

last: Timmer

first: Fabian

last: Theis

first: Wolf-Dieter

last: Lehmann

last: Lichter

first: Ursula

last: Klingmüller


title: Characterization of Definitive Endoderm formation from HESC and iPSC lines by Microarray analysis

status: Public on Dec 25 2010

city: Cincinnati

first: James

last: Wells

state: OH

address: 3333 Burnet Ave.

department: Developmental Biology

institute: Cincinnati Children's Hospital Medical Center

summary: HESC-H9 and iPSC lines 3.5, 3.6 and 3.12 were analyzed using Affymetrix microarray before and after Definitive Endoderm (DE) formation. DE was induced using the ActivinA differentiation protocol described by D'Amour et al., 2006 (PMID: 16258519)  Clustering analysis of transcripts that were differentially regulated during DE formation indicated that iPSC lines 3.5 and 3.12 differentiate in manner that is highly similar to HESC-H9 cells iPSC line 3.6 had a more divergent transcriptional profile.

overall_design: Three induced pluripotent stem cell lines (iPSC) and one human embryonic stem cell line (hESC - H9) were  collected as undifferentiated (UD) cells, and flash frozen.  These cell lines were also subjected to definitive endoderm (DE) induction, collected and flash frozen.  RNA was harvested from the frozen cell pellets and hybridized to the Affymetrix microarray chip. The three iPSC cell lines are iPSC 3.5, iPSC 3.6. and iPSC 3.12.  In the UD state, iPSC 3.5 was analyzed in duplicate, while iPSCs 3.6 and 3.12  and H9s were analyzed in biological triplicate.  All four cell lines were analyzed as biological triplicates for DE induction.

first: Jason

middle: R

last: Spence

first: Christopher

middle: N

last: Mayhew

first: Scott

last: Rankin

first: Matthew

middle: F

last: Kuhar

first: Kathryn

last: Tolle

first: Jefferson

last: Vallance

first: Elizabeth

last: Hoskins

first: Susanne

first: Vladimir

middle: V

last: Kalinichenko

first: Aaron

last: Zorn

first: Noah

last: Shroyer


title: Desmoglein 2 is a crucial receptor for adenovirus infection of epithelial cells

status: Public on Dec 08 2010

city: Seattle

middle: William

last: MacDonald

state: WA

address: 4225 Roosevelt Way NE

department: Environmental and Occupational Health Sciences

institute: University of Washington

summary: We have identified desmoglein 2 (DSG2) as the primary high-affinity receptor used by adenovirus (Ad) serotypes Ad3, Ad7, and Ad14. These serotypes represent important human pathogens causing respiratory tract infections. In epithelial cells, adenovirus binding to DSG2 triggers events reminiscent of epithelial-to-mesenchymal transition, leading to transient opening of intercellular junctions. This improves access to receptors, e.g. CD46 and Her2/neu, that are trapped in intercellular junctions. In addition to complete virions, dodecahedral particles (PtDd) formed by viral penton and fiber in excess during viral replication, can trigger DSG2-mediated opening of intercellular junctions as shown by studies with recombinant Ad3 PtDd. Our findings shed light on adenovirus biology and pathogenesis and have implications for cancer therapy.

overall_design: 3 arrays, 3 experimental groups, 1 replicate in each group.

first: Richard

middle: P

last: Beyer

first: André

last: Lieber

first: Thomas

last: Möller


title: Expression data from discodermolide sensitive and resistant cell lines

city: Bronx

first: Susan

middle: K

last: Chao

state: NY

address: 1300 Morris Park Ave

department: Molecular Pharmacology

institute: Albert Einstein College of Medicine

summary: Discodermolide treatment of A549 results in senescence. We compared cells resistant to disco-induced senescence to those that are sensitive to senescence induction. We also examined the gene expression of resistant (AD32) cells overexpressing 4E-BP1, a protein known to restore sensitivity to discodermolide in these cells.

overall_design: Total RNA was collected from A549, A549 disco, AD32, and AD32 4E-BP1 cells and gene expression profiles were examined.

first: Suzan

middle: B

last: Horwitz


title: Effects of redox modulation by inhibition of Thioredoxin reductase on radiosensitivity and gene expression

status: Public on Dec 03 2010

city: Stockholm

first: Markus

last: Selenius

address: Karolinska University Hospital, Huddinge F46

department: Laboratory Medicine

country: Sweden

institute: Karolinska Institutet

summary: The involvement the thioredoxin system in radiation resistance was investigated in human lung cancer cells by a combination of ionizing radiation and specific thioredoxin reductase-inhibition by a phosphine gold compound.

overall_design: Gene expression profiles (Human Gene 1.0 ST) of lung cancer cells subjected to ionizing radiation and/or inhibition of thioredoxin reductase were studied. Data analyses were performed using the Affymetrix GeneChip Operating Software (GCOS) Version 1.4.

first: David

last: Brodin


title: An Integrated Approach to Uncover Drivers of Cancer

status: Public on Dec 01 2010

city: New York

first: Dana

last: Pe'er

address: 1212 Amsterdam Ave.

department: Biological Sciences

institute: Columbia University

summary: We developed a computational framework that integrates chromosomal copy number and gene expression data for detecting aberrations that promote cancer progression. We demonstrate the utility of this framework using a melanoma dataset. Our analysis correctly identified known drivers of melanoma and predicted multiple novel tumor dependencies. Two dependencies, TBC1D16 and RAB27A, confirmed empirically, suggest that abnormal regulation of protein trafficking contributes to proliferation in melanoma. Together, these results demonstrate the ability of integrative Bayesian approaches to identify novel candidate drivers with biological, and possibly therapeutic, importance in cancer.

overall_design: Effects of knockdown of two genes -TBC1D16 and RAB27A - were tested on four cell lines each, each of them with two different hairpins. As a control, we used a hairping targeting GFP. shGFP experiments were done in biological duplicates or more. The second WM1976-shGFP sample was identified as an outlier by a PCA analysis and was excluded from our analysis.

first: Uri-David

last: Akavia

first: Oren

last: Litvin

first: Jessica

last: Kim

first: Felix

last: Sanchez-Garcia

first: Dylan

last: Kotliar

first: Helen

middle: C

last: Causton

first: Panisa

last: Pochanard

first: Eyal

last: Mozes

first: Levi

last: Garraway


title: DNA microarrays of Wilson's disease patient-specific induced pluripotent stem cells

city: Guangzhou

first: shiqiang

last: zhang

address: 190 Kai Yuan Avenue, Science Park

country: China

institute: Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences

summary: Wilson’s disease (WD) is a relevant human genetic disease caused by mutations in the ATP7B gene, whose product is a liver enzyme responsible for copper export into bile and blood. Interestingly, the spectrum of ATP7B mutations is vast and can influence clinical presentation (a variable spectrum of hepatic and neural manifestations), though the reason for this is not well understood. Here we describe the successful generation of iPSCs from a Chinese patient with Wilson’s disease that bears the R778L Chinese hotspot mutation in the ATP7B gene.

overall_design: Global gene expression profiling with DNA microarrays showed that WD iPSCs cluster together with human ESCs (H9) compared to donor fibroblasts. WD patient fibroblasts were isolated and expanded from a dermal biopsy of a middle age Chinese Han male, WD iPSCs were generated by overexpression of human Oct4/Sox2/Klf4/c-Myc in WD fibroblasts and expanded on Matrigel with mTESR1 culture medium. For DNA microarray analysis, WD fibroblasts (passage 5), 3 cell lines of WD iPSCs growing on Matrigel (passage 8) and human ES H9 growing on Matrigel (passage 40) were treated with Trizol, followed by RNA extraction and hybridization.

first: Shiqiang

last: Zhang

first: Wen

last: Li

first: Wenzhi

last: He

first: Duanqing

last: Pei

first: Miguel

last: Esteban


title: The genes regulated by SOX11 in mantle cell lymphoma

status: Public on Nov 29 2010

first: Birgitta

last: Sander

address: F56 Pathology, Karolinska University Huddinge hospital

summary: The genes regulated by SOX11 in MCL was investigated in MCL cell line Granta 519 by siRNA knock down system. Cells were transfected using the LONZA electroporation system. Results represent cells harvested after 20 hours. Details of the experiment is published in PMID 21124928.

overall_design: Gene expression profiles (Human Gene 1.0 ST) of mantle cell lymphoma (MCL) cell line Granta 519 treated with SOX11 siRNA. Data analyses were performed using the Affymetrix Expression Console (v. 1.1)

first: Xiao

last: Wang

first: David

last: Brodin


title: Gene expression profiling of ATRA-differentiated wild-type and TG2 knockout NB4 cells

city: Debrecen

first: Krisztian

last: Csomos

address: Egyetem ter 1.

country: Hungary

institute: University of Debrecen

summary: Treatment of acute promyelocytic leukemia (APL) with all-trans-retinoic acid (ATRA) results in terminal differentiation of leukemic cells toward neutrophil granulocytes. Administration of ATRA leads to massive changes in gene expression, including down-regulation of cell proliferation-related genes and induction of genes involved in immune function. One of the most induced genes in APL NB4 cells is transglutaminase 2 (TG2). RNAi-mediated stable silencing of TG2 in NB4 cells (TG2-KD NB4) coupled with whole genome microarray analysis revealed that TG2 is involved in the expression of a large number of ATRA-regulated genes. The affected genes participate in granulocyte functions and their silencing lead to reduced adhesive, migratory and phagocytic capacity of neutrophils and less superoxide production. The expression of genes related to cell cycle control also changed, suggesting that TG2 regulates myeloid cell differentiation. CC chemokines CCL2, 3, 22, 24 and cytokines IL1B and IL8 involved in the development of differentiation syndrome (DS) are expressed at significantly lower levels in TG2-KD NB4  cells than in wild-type NB4 cells upon ATRA treatment. Based on our results, we propose that reduced expression of TG2 in differentiating APL cells may suppress effector functions of neutrophil granulocytes and attenuate the ATRA-induced inflammatory phenotype of DS.

overall_design:
We used microarrays to detail the global program of gene expression underlying ATRA-induced differentiation of TG2 knockout NB4 cells.
TG2 knockout NB4 cells were differentiated for 48 and 72 hours in the presence of ATRA and their gene expression profiles were compared to the wild-type cells at the same time points. Undifferentiated wild-type and TG2 knockout NB4 cells were used as untreated controls. Three biological replicates each.

first: Zoltan

last: Balajthy

first: Istvan

last: Nagy

first: Laszlo

last: Fesus


title: Expression data from melanoma cell lines

status: Public on Nov 26 2010

city: Los Angeles

first: Mikyung

last: Lee

state: CA

address: UCLA Med-Derm BOX 951781, 13-942 Factor, 13-952 Factor Los Angeles, CA 90095-1781

institute: UCLA

summary:
Differential gene expression analysis of parental and resistant sub-lines of melanoma cell lines treated or untreated with PLX4032
Using microarray we sought to obtain a genome-wide profile of differentially expressed genes in parental melanoma cell lines and resistant sub-lines in response to PLX4032 vs DMSO control treatment.

overall_design: Representative parental melanoma cell lines and resistant sub-lines were treated with PLX4032 at 1 uM or DMSO control for 6h. Total RNA was extracted and cDNAs were generated and hybridized onto GeneChip Human Gene 1.0 ST Arrays (Affymetrix).

first: Roger

last: Lo


title: Analysis of vitamin D response element binding protein target genes reveals a role for vitamin D in osteoblast mTOR signaling

status: Public on Nov 19 2010

city: Neuherberg

first: Johannes

last: Beckers

address: Ingolstaedter Landstr. 1

department: Institute of Experimental Genetics

institute: Helmholtz Zentrum Muenchen

summary:
Heterogeneous nuclear ribonucleoprotein (hnRNP) C1/C2 plays a pivotal role in vitamin D receptor (VDR) signaling by acting as a vitamin D response element (VDRE)-binding protein (VDRE-BP). Transcriptional regulation by active 1,25-dihydroxyvitamin D3 (1,25(OH)2D3) involves occupancy of VDRE by VDRE-BP or 1,25(OH)2D3 bound-VDR.  This relationship is disrupted by over-expression of VDRE-BP and can cause a form of human hereditary vitamin D-resistant rickets (HVDRR). DNA array analyses using B-cells from an HVDRR patient and matched control defined a sub-cluster of genes where 1,25(OH)2D3-regulated transcription was abrogated by over-expression of VDRE-BP. Amongst these, the DNA-damage-inducible transcript 4 (DDIT4), an inhibitor of mammalian target of rapamycin (mTOR) signaling, was also induced by 1,25(OH)2D3 in human osteoblasts.
Chromatin immunoprecipitation using 1,25(OH)2D3-treated osteoblasts confirmed that liganded VDR and VDRE-BP compete for binding to the proximal promoter of the DDIT4 gene in a similar fashion to other known 1,25(OH)2D3-target genes. Treatment of osteoblasts with 1,25(OH)2D3 induced DDIT4 expression and suppressed phosphorylated S6K1T389 protein (a downstream target of mTOR).  The functional importance of this for 1,25(OH)2D3 responses in osteoblasts was underlined by the fact that siRNA knockdown of DDIT4 expression suppressed antiproliferative and cell growth responses to 1,25(OH)2D3. These data confirm that VDRE-BP is required for normal 1,25(OH)2D3-mediated transcription and cell function in osteoblasts. Conversely over-expression of VDRE-BP exerts a dominant-negative effect on transcription of 1,25(OH)2D3-target genes. Characterization of VDRE-BP action in 1,25(OH)2D3-treated osteoblasts highlights an entirely novel role for vitamin D as a regulator of mTOR – a known ‘master regulator’ of cell function.

overall_design: We performed gene expression microarray analysis in HVDRR EBV-transformed B-cells and control cells in the presence or absence of vitamin D.

first: Thomas

middle: S

last: Lisse

first: Ting

last: Liu

first: Martin

last: Irmler

first: Hong

last: Chen

first: John

last: Adams

last: Hewison


title: Reconstituted human epidermis cultures treated with IL-1 family cytokines for 24 hours.

status: Public on Nov 17 2010

city: Ann Arbor

first: Andrew

last: Johnston

state: Michigan

address: 1301 East Catherine Street

department: Dermatology

institute: University of Michigan

summary: Analysis of stratified epidermal cultures treated with IL-1a, IL-1F5, IL-1F6, IL-1F8 and IL-1F9 to determine the effects of these cytokines at 24h. Results provide insight into the role of IL-1 family cytokines in the pathogenesis of psoriasis.

overall_design: 16 samples. 2 untreated controls, 14 cytokine treated

first: Johann

last: Gudjonsson


title: Transcriptome analysis of the Nasu-Hakola disease brain

status: Public on Nov 20 2010

city: Tokyo

first: Jun-ichi

last: Satoh

address: 2-522-1 Noshio, Kiyose

department: Bioinformatics

country: Japan

institute: Meiji Pharmaceutical University

summary: Nasu-Hakola disease (NHD), also designated polycystic lipomembranous osteodysplasia with sclerosing leukoencephalopathy (PLOSL; OMIM 221770), is a rare autosomal recessive disorder, characterized by progressive presenile dementia and formation of multifocal bone cysts, caused by genetic mutations of DAP12 and TREM2, which constitute a receptor/adapter signaling complex expressed on osteoclasts, dendritic cells, macrophages, and microglia. No Japanese patients with TREM2 mutations have been reported previously. We reported three siblings affected with NHD in a Japanese family. Among them, two died of NHD during the fourth decade of life. The transcriptome was studied in the autopsized brain of one patient. We found a homozygous conversion of a single nucleotide T to C at the second position of intron 3 in the splice-donor consensus site (c.482+2T>C) of the TREM2 gene, resulting in exon 3 skipping. We identified 136 upregulated genes involved in inflammatory response and immune cell trafficking and 188 downregulated genes including a battery of GABA receptor subunits and synaptic proteins in the patient’s brain.

overall_design: Total RNA was isolated from a small piece of autopsized frozen frontal lobe tissues of the patient. In parallel, the normal human frontal lobe RNA (636563; Clontech) was processed for serving as a control. Microarray analysis was performed on Human Gene 1.0 ST Array (Affymetrix). The CEL file data were normalized by the robust multiarray average (RMA) method.

first: Yoshiyuki

last: Numasawa

first: Chiharu

last: Yamaura

first: Shoichiro

last: Ishihara

first: Shuzo

last: Shintani

first: Mineo

last: Yamazaki

first: Hiroko

last: Tabunoki


title: L1 retrotransposition in neurons is mediated by MeCP2

status: Public on Nov 11 2010

city: La Jolla

first: Alysson

last: Muotri

address: 9500 Gilman Drive

department: Pediatrics/CMM

institute: University of California San Diego

summary: L1 retrotransposons are active elements in the genome, capable of mobilization in neuronal progenitor cells. Previously, we showed that chromatin remodeling during neuronal differentiation allows for a transient stimulation of L1 transcription. The activity of L1 retrotransposons during brain development can impact gene expression and neuronal function. Here we show that L1 neuronal retrotransposition in rodents is increased in the absence of MeCP2, a protein involved in global methylation and human neurodevelopmental diseases. Using neuronal progenitor cells derived from human induced pluripotent stem cells and human tissues, we revealed that Rett syndrome patients, with MeCP2 mutations, have increased susceptibility for L1 retrotransposition. Our data demonstrate that disease-related genetic mutations can influence the frequency of neuronal L1 retrotransposition, thereby increasing brain-specific genetic mosaicism.

overall_design:
Genetic reprogramming of somatic cells to a pluripotent state (induced pluripotent stem cells, or iPSCs) by over-expression of specific genes has been accomplished for fibroblasts derived from controls and Rett syndrome patients. Different clones from each were compared to respective original fibroblasts and a human embryonic stem cell line.
Gene expression profiles measured using human genome Affymetrix Gene Chip arrays were grouped by hierarchical clustering, and correlation coefficients were computed for all pair-wise comparisons.

first: Maria

last: Marchetto

first: Gene

last: Yeo

first: Fred

last: Gage


title: Gene expression profile associated with p53R2 in human cancer cells

status: Public on Nov 10 2010

city: Duarte

first: keqiang

last: zhang

address: 1500 East Duarte Road

institute: City of Hope National Medical Center

summary:
Deregulation of the expression of p53R2, a p53-inducible homologue of the R2 subunit of ribonucleotide reductase, has been found in various human cancer tissues; however, the roles p53R2 plays in cancer progression and malignancy remain controversial. In present design, we aimed to identify changes in gene expression profiles associated with p53R2 in cancer cells. We compared gene expression file of control KB cells with that of p53R2-attenuated KB cells by its specific siRNA by using cDNA microarray technology.
We used microarrays to display the global gene expression profile change, after knockdown of p53R2 expression in human oropharyngeal carcinoma KB cells, to find the gene set regulated by p53R2.

overall_design: To compare changes in gene expression profile in human oropharyngea carcinoma KB cells, KB cells were transfected with control siRNA or p53R2 siRNA, 48h later, total RNA and protein were subjected to Q-PCR and Western blot to confirm a significantly decreased p53R2 mRNA and protein, and then these total RNA samples were for microarray analysis. The cDNA microarray data was analyzed to explore gene sets/pathways, which were significantly impacted by knockdown of p53R2.

first: Keqiang

last: Zhang

first: Xiwei

last: Wu

first: Yun

last: Yen


title: Effect of cellular and viral miRNAs on target RNA half-life in three human B-cell lines

status: Public on Nov 04 2010

city: Cambridge

first: Lars

last: Dölken

state: Cambridgeshire

address: Addenbrookes Hospital, Hills Road

department: Medicine

country: United Kingdom

institute: University of Cambridge

summary: Total, nascent and unlabeled RNA were prepared following 1h of labeling with 100 µM 4-thiouridine and 3 replicates analyzed by Affymetrix Gene ST 1.0 arrays

overall_design: Transcript half-lives were determined in DG75-eGFP, DG75-10/12 and BCBL-1 based on nascent/total RNA ratios; unlabeled RNA was analyzed in addition

first: Georg

last: Malterer

first: Reinhard

last: Hoffmann

first: Ralf

last: Zimmer

first: Ulrich

middle: H

last: Koszinowski

first: Jürgen

last: Haas


title: Gene expression data by the Artemisia iwayomogi (Ai) on the LPS-stimulated human gingival fibroblast

status: Public on Oct 23 2010

city: Seoul

first: Sabina

last: Lim

address: #1 Hoegi-dong Dongdaemoon-gu

country: South Korea

institute: East-West Medical Research Institute, Kyung Hee University

summary:
The Artemisia iwayomogi (Ai) has been known to inhibit the inflammatory cytokine production and the allergic reactions, and has been used to treat liver diseases.
This study investigated the gene expression changes by lipopolysaccharide (LPS) stimulation in the cultured human gingival fibroblast and the gene expression changes by the Ai when challenged with LPS using a microarray chip.

overall_design: Human gingival fibroblast were divided into four experimental groups; ① C: Control, ② LPS: LPS-treatment only, ③ Ai20: LPS- and Ai20-treatments, ④ Ai40: LPS- and Ai40-treatments. Total RNA was isolated from each experimental fibroblast (4 experimental group × 1 sample of each experimental group = total 4 samples).

first: Yeong-Gon

last: Choi


title: Response of A549 cells treated with Aspergillus fumigatus [WT-CF_vs_PrtT-CF]

status: Public on Oct 29 2010

city: Tel-Aviv

first: Nir

last: Osherov

address: Ramat Aviv Campus

department: Medical Microbiology and Immunology

institute: Tel-Aviv University

summary:
Response of A549 cells treated with Aspergillus fumigatus wild type culture filtrate (WT-CF) or PrtT protease deficient mutant culture filtrate (PrtT-CF) for 8h
Aspergillus fumigatus is the most commonly encountered mold pathogen of humans, predominantly infecting the respiratory system. Colonization and penetration of the lung alveolar epithelium is a key but poorly understood step in the infection process. This study focused on identifying the transcriptional and cell-signaling responses activated in A549 alveolar carcinoma cells incubated in the presence of A. fumigatus wild-type and ΔPrtT protease-deficient germinating conidia and culture filtrates (CF). Microarray analysis of exposed A549 cells identified distinct classes of genes whose expression is altered in the presence of germinating conidia and CF and suggested the involvement of both NFkB and MAPK signaling pathways in mediating the cellular response. Phosphoprotein analysis of A549 cells confirmed that JNK and ERK1/2 are phosphorylated in response to CF treatment in a protease-dependent manner. Inhibition of JNK or ERK1/2 kinase activity substantially decreased CF-induced cell damage, including cell peeling, actin-cytoskeleton damage, and reduction in metabolic activity and necrotic death. These results suggest that inhibition of MAPK-mediated host responses to treatment with A. fumigatus CF decreases cellular damage, a finding with possible clinical implications.

overall_design: 3 independent controls (uninfected A549 cells) as ctrl2_1-3, 3 independent treatments of A549 cells with wild-type A. fumigatus culture filtrates (WT-CF1_1-3) and 2 independent treatments of A549 cells with A. fumigatus prtT mutant culture filtrates (PrtT-CF_1-2).

first: Haim

last: Sharon

first: David

last: Amar

first: Ron

last: Shamir


title: Expression data of cHL cell lines after KLF4 activation

status: Public on Oct 22 2010

city: Ulm

first: Alexey

last: Ushmorov

address: Albert-Einstein-Allee 11

department: Institute of Physiological Chemistry

institute: Ulm University

summary:
Characteristic extinguishing of B-cell phenotype in cHL is believed to be a result of transcription factor network deregulation due to the overexpression of repressor proteins ID2 and ABF-1. KLF4 is a versatile transcription factor, participating in regulation of differentiation processes in various tissues. Epigenetic silencing of KLF4 in cHL hints that KLF4 is involved in the complex mechanism of extinguishing of B-cell phenotype in cHL.
To clarify this issue we investigated transcriptome changes, induced by KLF4 activation in two cHL cell lines KM-H2 and L428.

overall_design: KM-H2-KLF-ER and L428-KLF-ER cells were incubated with 200 µM 4-OHT or vehicle (ethanol). The experiment was done twice. After 24 h, total RNA was isolated with RNeasy mini kit (QIAGEN). Microarray analyses were performed using 200 ng total RNA as starting material and 5.5 µg ssDNA per hybridization (GeneChip Fluidics Station 450; Affymetrix, Santa Clara, CA). The total RNAs were amplified and labeled following the Whole Transcript (WT) Sense Target Labeling Assay (http://www.affymetrix.com). Labeled ssDNA was hybridized to Human Gene 1.0 ST Affymetrix GeneChip arrays (Affymetrix, Santa Clara, CA). The  chips were scanned with a Affymetrix GeneChip Scanner 3000 and subsequent images analyzed using Affymetrix® Expression Console Software (Affymetrix). Probe level data were obtained using the robust multichip average (RMA) normalization algorithm.

first: Thomas

last: Wirth

first: Hanfeng

last: Guan


title: Effects of dietary obesity in fathers on gene expression of islets in the female offspring

status: Public on Oct 21 2010

city: Wallace Wurth Building, Sydney

first: Margaret

middle: J

last: Morris

state: NSW

address: University of New South Wales

department: School of Medical Sciences

country: Australia

institute: University of New South Wales

summary: The global prevalence of obesity is increasing across age and gender. The rising burden of obesity in young people contributes to the early emergence of type 2 diabetes. Having one parent obese is an independent risk factor for childhood obesity. While the detrimental impact of diet-induced maternal obesity on offspring is well established, the extent of the contribution of obese fathers is unclear, as is the role of non-genetic factors in the casual pathway. Here we show that paternal high fat diet exposure programmed β-cell ‘dysfunction’ in their F1 female offspring. Chronic high fat diet consumption in Sprague Dawley fathers led to increased body weight, adiposity, impaired glucose tolerance and insulin sensitivity. Relative to controls, their female offspring had lower body weight at day-1, increased pubertal growth rate, impaired insulin secretion and glucose tolerance, in the absence of obesity or increased adiposity.  Paternal high fat diet was observed to alter gene expression of pancreatic islet genes in adult female offspring (P < 0.001); affected functional clusters includes calcium ion binding, insulin, apoptosis, Wnt and cell cycle organ/system development. This is the first reported study in mammals describing non-genetic, intergenerational transmission of metabolic sequelae of high fat diet from father to offspring. These findings support a role of fathers in metabolic programming of offspring and form a framework for further studies.

overall_design: F0 founders were male Sprague Dawley rats, divided into two groups, high fat (HF) and control. The HF fathers were given commercially prepared high-fat pellets (43% as fat); while the controls ate standard laboratory chow (9% as fat). The two groups of fathers had distinct phenotype; the HF fathers were significantly heavier with increased adiposity, they were also glucose intolerant and insulin resistant. At 15 weeks of age, fathers were mated with normal females consuming chow, to generate the F1 offspring. Only female offspring were studied. Female offspring were weaned unto standard laboratory chow at 3 weeks. At 6 and 12 weeks, intraperitoneal glucose tolerance test (IpGTT) was performed to measure blood glucose and insulin profile; at 11 weeks, intraperitoneal insulin tolerance test was done. The body weight and adiposity of these offspring were not different between the two groups. The HF offspring had glucose intolerance and impaired glucose-induced insulin response, mainly at the acute phase, observed since 6 weeks. The IpITT was not different between groups. At 13 weeks, islets were harvested from the two groups of offspring.

first: Sheau-Fang

last: Ng

first: Ruby

last: Lin


title: Expression data of human perirenal adipose tissue-derived mesenchymal stem cells cultured under various conditions

status: Public on Oct 01 2010

city: rotterdam

first: Mario

last: Pescatori

address: Westplein 11

country: Netherlands

institute: Health e-genomics

summary:
Human mesenchymal stem cells (MSC) derived from perirenal adipose tissue (PV) of living kidney donors were cultured under various conditions, namely (1) control (medium+foetal bovine serum(FBS)) or (2) control (medium+heat-inactivated FBS); (3) with mixed-lympohocyte reactions (MLR) in transwell culture systems for 4 days; (4) with mixed-lympohocyte reactions (MLR) in transwell culture systems for 7 days; or (5)with pro-inflammatory cytokines(IFNgamma, TNFalpha and interleukin 6).
We used microarrays to detail the effect of the various culture conditions on MSC.

overall_design: MSC were cultured under control conditions (n=4 in FBS and n=3 in heat-inactivated FBS), with MLR in transwell culture systems for 4 days (n=3) and 7 days (n=4), and with pro-inflammatory cytokines(IFNgamma, TNFalpha and interleukin 6)(n=4) and collected for gene analysis

first: Meindert

last: Crop

first: Carla

last: Baan

first: Sander

last: Korevaar

first: Jan

last: Ijzermans

first: Andrew

last: Stubbs

first: Wilfred

last: van Ijken

first: Marc

last: Dahlke

first: Elke

last: Eggenhofer

first: Willem

last: Weimar

first: Martin

last: Hoogduijn


title: Demethyl fructiculin A (SCO-1) induces apoptosis by inducing reactive oxygen species in mitochondria

status: Public on Oct 15 2010

city: Genova (GE)

first: Massimiliano

last: Monticone

address: Largo R. Benzi, 10

institute: IRCCS AOU San Martino – IST, Genova

summary:
Demethyl fructiculin A is a diterpenoid quinone component of the exudates from Salvia corrugata (SCO-1) leafes. SCO-1 was recently reported to induce anoikis in mammalian cell lines via a molecular mechanism involving the presence of the membrane scavenging receptor CD36. However, experiments performed with cells lacking CD36, showed that SCO-1 was able to induce apoptosis also via alternate pathways. To contribute to a better characterization of the molecular mechanisms underlining the cytotoxic activity of SCO-1, we decided to pursue an unbiased pharmacogenomic approach by generating the gene expression profile of GBM TICs subjected to the administration of SCO-1 and comparing it with that of control cells exposed to the solvent. With this strategy we hypothesized to highlight those pathways and biological processes unlashed by SCO-1.
Using this approach we unveiled that the main mechanism responsible for the SCO-1 pro-apoptotic effect is superoxide generation in mitochondria and that this molecule has potential chemotherapeutic properties that should be further investigated in GBM xenotransplant models.

overall_design:
To get an insight on the biological processes and pathways elicited by Demethyl fructiculin A (SCO-1), we undertake an unbiased genomic approach in order to identify genes deregulated by SCO-1.
Cells were treated with 9.3 μg/ml concentration (IC50 at 48h) or vehicle alone (DMSO) and kept in a humidified 5% CO2 atmosphere at 37°C for the indicated time period (24 or 48 hours).
After 24 hours of exposure of glioblastoma tumor initiating cells (GBM TICs) to SCO-1, we found the deregulation of genes belonging to the Glutathione metabolism pathway and of those belonging to the biological processes related to the response to stress and chemical stimulus.

first: Angela

last: Bisio

first: Antonio

last: Daga

first: Paolo

last: Giannoni

first: Massimo

last: Maffei

first: Ullrich

last: Pfeffer

first: Francesco

last: Romeo

first: Rodolfo

last: Quarto

first: Giorgio

last: Corte

first: Patrizio

last: Castagnola


title: Gene expression profiling for placentas from pre-eclamptic, unexplained FGR and normal pregnancies.

status: Public on Sep 15 2010

city: Toyoake

first: Haruki

last: Nishizawa

state: Aichi

address: 1-98 Dengakugakubo, Kutsukake

department: Obstetrics and Gynecology

institute: Fujita Health University

summary:
It has been well documented that pre-eclampsia and unexplained fetal growth restriction (FGR) has a common etiological background, but little is known about the linkage al the molecular level.
we have performed global gene expression profiling by oligonucleotide microarrays for placentas from pre-eclamptic, unexplained FGR and normal pregnancies to further elucidate the mechanisms underlying the development of these two disorders.

overall_design: The total number of samples used was 8 from pre-eclampsia, 8 from normotensive pregnancies with FGR and 8 from those without FGR.

first: Hiroki

last: Kurahashi


title: Comparison of gene expression profiles in chromate transformed BEAS-2B cells

status: Public on Sep 14 2010

city: New York

first: Hong

last: Sun

address: 341 East 25 Street

institute: NYU School of Medicine

summary:
We established chromate transformed cell lines by chronic exposure of normal human bronchial epithelial BEAS-2B cells to low doses of hexavalent chromium followed by anchorage-independent growth. The gene expression profiles were analyzed in the established cell lines.
The gene expression profiles from six chromate transformed cell lines were remarkably similar to each other yet differed significantly from that of either control cell line or normal Beas-2B cells. A total of 409 differentially expressed genes were identified in chromate transformed cells compared to control cells.

overall_design: We analyzed gene expression profiles from 10 cell lines ( six chromated transformed cells lines, three control cell lines, and parental BEAS-2B cells) using Affymetrix Human Gene 1.0 ST array. No techinical replicates were performed.

first: Harriet

middle: A

last: Clancy

first: Thomas

last: Kluz

first: Jiri

last: Zavadil

first: Max

last: Costa


title: Whole gene expression profiling: A study for analysing the gene expression of the retinal stem cells and the differentiated cells

status: Public on Jul 31 2010

city: Bangalore

first: Genotypic

last: technology

state: Karnataka

address: 259, Apoorva 4th cross,80 feet Road,RMV 2ND STAGE

country: India

institute: Genotypic Technology

summary:
Comparitive analysis of the retinal stem/progentior cells derived from the ciliary and iris pigment epithelial cells and the subsequent differentiated cells derived from the stem/progenitor cells.
Gene expression profiling has shown great promise in analysing the reprogramming pattern of the cells under various culture conditions, in this context we analysed the various differential gene expression pattern of the neurospheres derived from the ciliary and iris pigment epithelial cells, and their differentiated cells. This provide an insite for the stem cell transplantation studies.

overall_design: We analysed 3 biological cultures derived from each catogory like the primary cells of both ciliary and iris pigment epithelial cells, the stem/progenitor cells (Neurospheres), neurosphere derived differentiated cells. No technical replicates were performed.

first: Srilatha

last: Jasty

first: S

last: Krishnakumar


title: Response of A549 cells treated with Aspergillus fumigatus [WT-GC_vs_PrtT-GC]

first: Nir

last: Osherov

summary:
Response of A549 cells treated with Aspergillus fumigatus wild type germinating conidia (WT_GC) or PrtT protease deficient mutant conidia (PrtT-GC) or inert acrylic 2-4 micron beads (Beads) for 8h
Aspergillus fumigatus is the most commonly encountered mold pathogen of humans, predominantly infecting the respiratory system. Colonization and penetration of the lung alveolar epithelium is a key but poorly understood step in the infection process. This study focused on identifying the transcriptional and cell-signaling responses activated in A549 alveolar carcinoma cells incubated in the presence of A. fumigatus wild-type and ΔPrtT protease-deficient germinating conidia and culture filtrates (CF). Microarray analysis of exposed A549 cells identified distinct classes of genes whose expression is altered in the presence of germinating conidia and CF and suggested the involvement of both NFkB and MAPK signaling pathways in mediating the cellular response. Phosphoprotein analysis of A549 cells confirmed that JNK and ERK1/2 are phosphorylated in response to CF treatment in a protease-dependent manner. Inhibition of JNK or ERK1/2 kinase activity substantially decreased CF-induced cell damage, including cell peeling, actin-cytoskeleton damage, and reduction in metabolic activity and necrotic death. These results suggest that inhibition of MAPK-mediated host responses to treatment with A. fumigatus CF decreases cellular damage, a finding with possible clinical implications.

overall_design: 2 independent controls (uninfected A549 cells) as ctrl3_1-2, 2 independent treatments of A549 cells with wild-type A. fumigatus germinating conidia (WT_GC_1-2 ) , 2 independent treatments of A549 cells with inert acrylic beads (Beads 1-2), 3 independent treatments of A549 cells with A. fumigatus prtT mutant germinating conidia (PrtT-GC_1-3).

first: Haim

last: Sharon

first: David

last: Amar

first: Ron

last: Shamir


title: Expression data from Gambian children with and without the clinical signs of active trachoma: HG-focus array

status: Public on Sep 03 2010

city: London

first: Martin

middle: James

last: Holland

address: Keppel Street

department: Infectious and Tropical Diseases

institute: London School of Hygiene and Tropical Medicine

summary: Results from 29 samples tested on the Affymetrix HG-focused target array identified transcriptional changes characteristic of ocular disease and ocular Chlamydia trachomatis infection phenotypes. Large numbers of differentially regulated genes were demonstrated. These were characteristic of the host defence response and typical of innate responses at epithelial surfaces and infiltrating leukocytes. These results provide an insight into the complexity of the acute response in trachoma.

overall_design: Samples from 29 participants were tested on the HG-Focus target arrays (17 participants with clinical signs of active trachoma and 12 study participants with normal conjunctivas from the same trachoma endemic population as controls). Conjunctival samples from an additional 60 participants were tested on U133 plus 2.0 arrays and are reported elsewhere.  This second set of independent samples was used to assess different gene classifier selection methods and validation tests using >8500 common probe-sets shared between HG-focus target and U133 plus 2.0 arrays. Potential biomarkers of disease and infection are identified.

first: Angels

last: Natividad

last: Jeffries

first: Matthew

last: Burton

last: Mabey

first: Robin

middle: L

last: Bailey


title: PARE analysis of six mouse tissues to investigate cleavage products and degradome

city: Adelaide

first: Jan

middle: Marek

last: Szubert

state: South Australia

address: Frome Rd

institute: Centre for Cancer Biology

summary: A Parallel Analysis of six mouse tissues to investigate cleavage products and degradome

overall_design: Survey of polyA transcripts having 5' monophosphates (a characteristic of RNA cleavage events) in six mouse tissues.

first: Cameron

last: Bracken

first: Gregory

last: Goodall

middle: M


title: Expression data from Hodgkin lymphoma cell lines UHO-1 and L-1236 transduced with shRNAs against GATA-3 or non-functional control shRNAs

status: Public on Jul 24 2010

city: Frankfurt

first: Claudia

last: Döring

address: Theodor Stern Kai 7

department: Medical School, Institite of Pathology

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

summary:
The transcription factor network in Hodgkin lymphoma (HL) represents a unique composition of proteins found in no other hematopoietic cell. Among these factors, an aberrant expression of the T cell transcription factor GATA-3 is observed in the B cell-derived Hodgkin and Reed/Sternberg (HRS) tumor cells. Herein, we elucidated the regulation and function of this factor in HL
To obtain a more comprehensive overview of GATA-3 regulated genes in cHL cell lines, we performed a gene chip analysis comparing gene expression in GATA-3-specific shRNA-transduced L-1236 and U-HO1 cells compared to samples transduced with vectors encoding scrambled shRNAs.

overall_design: 12 Total samples were analyzed. Three independent samples were analyzed per condition and cell line.We generated the following pairwise comparisons using Bioconductor: shRNA Gata-3 UHO-1 < control shRNA UHO-1; shRNA Gata-3 L1236 < control shRNA L-1236. Genes with an FDR≤ 25% and a fold-change ≥ 1.5 and ≤ -1.5 were selected.

first: Jens

last: Stanelle


title: Gene expression data by the leaves of Eriobotrya japonica (Ej) on the LPS-stimulated human gingival fibroblast

first: Sabina

last: Lim

summary:
The leaf of Eriobotrya japonica (Ej) has been used for a long time as an oriental medicine to treat pulmonary inflammatory diseases.
This study investigated the gene expression changes by lipopolysaccharide (LPS) stimulation in the cultured human gingival fibroblast and the gene expression changes by the leaves of Ej when challenged with LPS using a microarray chip.

overall_design: Human gingival fibroblast were divided into four experimental groups; ① C: Control, ② LPS: LPS-treatment only, ③ Ej20: LPS- and Ej20-treatments ④ Ej40: LPS- and Ej40-treatments.  Total RNA was isolated from each experimental fibroblast (4 experimental group × 1 sample of each experimental group = total 4 samples).

first: Yeong-Gon

last: Choi

first: Yeong-Hwan

last: Seok

first: Mi

middle: Y

last: Jeong


title: Comparison of Expression profile between CD3-CD56dimCD16+ CD57+ and CD57neg NK cells

status: Public on Aug 18 2010

city: San Francisco

first: Sandra

middle: Laurence

last: Lopez-Verges

address: 513 Parnassus Ave, Room HSE 1001G

department: Microbiology and Immunology

institute: University of California San Francisco

summary:
Thirty to 60% of CD56dimCD16bright NK cells in healthy adults express CD57, which is not expressed on immature CD56bright NK cells or fetal and newborn NK cells. We hypothesized that CD57+ NK cells within the CD56dim mature NK cell subset are highly mature and might be terminally differentiated.
We used microarrays to assess the transcriptional differences between CD57+ and CD57neg NK cells within the CD56dim mature NK subset.

overall_design:
PBMC were obtained from leukocyte reduction Pall filters (Blood Centers of the Pacific) after density gradient centrifugation over Ficoll-Paque (GE Healthcare). CD57+CD3negCD56dimCD16+ and CD57negCD3negCD56dimCD16+ NK cells from three healthy adult donors were sorted into Lysis Solution (100 ml per 10,000 cells) (RNAqueous-Micro kit, Ambion).  RNA was analyzed by BioAnalyzer (Agilent) before amplification with the NuGEN WT-Ovation kit (Roche) and analyzing transcripts using Affymetrix Human Gene 1.0 ST arrays.  Moderated paired t-tests were used to identify differentially expressed genes (>1.7-fold different) between CD57+ and CD57neg NK cells.  The P values were set at <0.001 and <0.005.

Supplementary table below reports Fold difference and M data.

first: Lewis

last: Lanier


title: Feedback amplification of fibrosis through matrix stiffening and COX-2 suppression

status: Public on Jul 15 2010

city: Boston

first: Alvin

middle: T.

last: Kho

state: MA

address: 320 Longwood Avenue

department: Informatics Program

institute: Boston Children's Hospital

summary:
We tested the hypothesis that increasing matrix stiffness on which normal human lung fibroblasts are grown promotes the expression of a fibrogenic cellular transcriptomic program.

Keywords: Human lung fibroblast, matrix stiffness, PTGS2, COX-2, Prostaglandin E2

overall_design: Total RNA extracted from normal human lung fibroblasts from 3 human subjects and separately grown on 5 discrete matrix stiffness conditions: 100, 400, 1600, 6400, 25600 Pascals.

middle: T

first: Fei

last: Liu

first: Justin

middle: D

last: Mih

first: Daniel

last: Tschumperlin


title: edelfosine and wortmannin effect at 22°c and 4°c-PI4-kinase and phospholipase C signaling in cold response

status: Public on Aug 01 2010

city: Evry

first: Delphine

last: Gey

address: 2 rue Gaston Crémieux

department: URGV

country: France

institute: INRA

summary:
rs09-04_plc_2 - edelfosine and wortmannin effect at 22°c and 4°c - Is there an overlap between PI4-kinase and phospholipase C signaling in cold response ? - Experiments were carried out with Columbia suspension cells. Cells were treated or not with edelfosine (PLC inhibitor) or wortmannin (PI4-kinase inhibitor). These agents were added 15 min before cold stress. ARN were extracted 4h after stress. Controls were made at 22°C.

Keywords: treated vs untreated comparison

overall_design: 11 dye-swap - CATMA arrays

first: Jean-Pierre

middle: P

last: Renou

first: Eric

last: Ruelland

first: Marie-Laure

last: Martin-Magniette


title: Pico profiling from 10 cells

city: Barcelona

first: Victoria

last: Core

address: Baldiri Reixac, 10

department: Functional Genomics Core

country: Spain

institute: Institute for Research in Biomedicine

summary: Current expression profiling methods use RNA from hundreds of thousands or thousands cells. Many fields of biology can not use microarrays due to the nature of the biological systems used that are formed by hundreds or dozens of cells. Here we present a method that can handle RNA amount limitation and gives gene expression profiles from as little as 10 cells. We first validate the method hybridizing amplified RNA from MAQC samples A and B. To do that, 25 ng or 100 pg were used and expression profiles obtained as good as when compared to Affymetrix's chemistry for amplification and labeling. The same experiment was done but using sorted cells from two comercial cell lines (SW620 and SW480) obtaining the same differential expression profiling from 2000 cells or 10 cells. The central step of the method is Whole Transcriptome Amplification (WTA) from Sigma that allows the amplification of very small amounts of RNA as starting material.

overall_design: MAQC samples A and B where amplified using Whole Transcriptome Amplification (WTA) kit from Sigma starting from 25 ng (standard conditions) or 100 pg in triplicates. Amplified cDNA was the fragmented and labeled using the 10kv2 SNP chemistry from Affymetrix and hybridized onto Affymetrix GeneST arrays. The same method was used for RNA isolated from 2000 and 10 cells from cell lines SW620 and SW480. RNA was isolated by magnetic bead purification after treating sorted cells with high DTT concentration and 65ºC to inactivate RNAses.

first: Herbert

last: Auer

first: Eva

last: Gonzalez

first: Silvia

last: Rodriguez-Mulero


title: NLRC5 is a transcriptional regulator of MHC class I genes

status: Public on Jun 30 2010

first: Amy

last: Li

address: 44 Binney Street

department: Cancer Immunology and AIDS

institute: Dana Farber Cancer Institute

summary:
NLRC5 is a member of the NLR family of proteins. The observation that NLRC5 is found in the nucleus prompted us to perform a gene array to identify putative target genes of NLRC5. We generated Jurkat T cell lines that stably express either the wild-type or mutant forms of NLRC5 harboring mutations in the nucleotide binding domain (NBD): Walker  A (deficient in nucleotide binding), Walker B (deficient in nucleotide hydrolysis), and the combined Walker AB, carrying both mutations.
Site-directed mutagenesis was used to create the NLRC5 NBD mutants: Walker A (K234A), Walker B (E311Q), and Walker AB (both mutations).

overall_design: We compared the expression profiles of Jurkat T cells expressing GFP, or the GFP-tagged wild-type, Walker A, Walker B, or Walker AB forms of NLRC5. GFP and the Walker  A and Walker  AB forms of NLRC5 were considered functionally inactive, while the wild-type and Walker B forms of NLRC5 were considered functionally active.  These groups were used as biological replicates to assess the effect of NLRC5 activity on gene expression.

first: Koichi

last: Kobayashi

first: Torsten

last: Meissner


title: Expression data of influenza A-infected human type I-like alveolar epithelial cells

status: Public on Oct 06 2010

city: Hong Kong

first: SMY

last: Lee

address: 21 Sassoon Road

country: Hong Kong

institute: The University of Hong Kong

summary: Pandemic influenza H1N1 (pdmH1N1) virus causes mild disease in humans but occasionally leads to severe complications and even death, especially in those who are pregnant or have underlying disease. Cytokine responses induced by pdmH1N1 viruses in vitro are comparable to other seasonal influenza viruses, suggesting the cytokine dysregulation as seen in H5N1 infection is not a feature of the pdmH1N1 virus. However, a comprehensive gene expression profile of pdmH1N1 in relevant primary human cells in vitro has not been reported. Type I alveolar epithelial cells are a key target cell in pdmH1N1 pneumonia. We carried out a comprehensive gene expression profiling using the Affymetrix microarray platform to compare the transcriptomes of primary human alveolar type I-like alveolar epithelial cells infected with pdmH1N1 or seasonal H1N1 virus.

overall_design: Primary type II alveolar epithelial cells were isolated from human non-malignant lung tissue of three patients who underwent lung resection, and cells were differentiated to type I-like before use. Type I-like alveolar epithelial cells were mock infected, or infected with pdmH1N1 or seasonal H1N1 viruses at a multiplicity of infection (MOI) of two. Total RNA was extracted from cells after 8h post-infection, and gene expression profiling was performed using an Affymetrix Human Gene 1.0 ST microarray platform.

first: Suki

first: Renee

middle: W

last: Chan

first: Jennifer

last: Gardy

first: Cheuk

middle: K

last: Lo

first: Alan

last: Sihoe

first: Sara

last: Kang

first: Timothy

last: Cheung

first: Yi

last: Guan

first: Michael

first: Robert

middle: E

last: Hancock

first: J

last: Peiris


title: Identification and characterization of two novel primate-specific histone H3 variants H3.X and H3.Y

status: Public on Sep 17 2010

city: Martinsried

first: Tobias

last: Straub

address: Großhadener Str. 9

department: Biomedical Center, Bioinformatics

institute: LMU Munich

summary: Nucleosomal incorporation of specialized histone variants is an important mechanism to generate different functional chromatin states. Here we report the identification and characterization of two novel primate-specific histone H3 variants, H3.X and H3.Y. Their mRNAs are found in certain human cell lines, in addition to several normal and malignant human tissues. In keeping with their primate-specificity, H3.X and H3.Y are detected in different brain regions. Transgenic H3.X and H3.Y proteins are stably incorporated into chromatin in a similar fashion to the known H3 variants. Importantly, we demonstrate biochemically and by mass spectrometry that endogenous posttranslationally modified H3.Y protein exists in vivo, and that stress-stimuli, such as starvation and cellular density, increase the abundance of H3.Y-expressing cells. Global transcriptome analysis revealed that knock-down of H3.Y affects cell growth and leads to changes in the expression of many genes involved in cell cycle control. Thus, H3.Y is a novel histone variant involved in the regulation of cellular responses to outside stimuli.

overall_design: Total RNA samples from human U2OS cells. Transcript levels after luciferase, H3.X and/or H3.Y RNAi was analyzed.

first: Sonja

last: Wiedemann

first: Silke

middle: N

last: Mildner

first: Clemens

last: Bönisch

first: Lars

last: Israel

first: Andreas

last: Maiser

first: Sarah

last: Matheisl

first: Rainer

last: Merkl

first: Heinrich

last: Leonhardt

first: Elisabeth

last: Kremmer

first: Lothar

last: Schermelleh

first: Sandra

middle: B

last: Hake


title: Effect of FGF19 and TNFalpha on human DU145 prostate cancer cells

status: Public on Jul 09 2010

city: La Jolla

first: Nick

last: Webster

address: 9500 Gilman Drive

country: USA

institute: UCSD

summary: DU145 prostate cancer cells were treated with 50 ng/ml FGF19 and 50 ug/ml heparin, or 10 ng/ml TNFalpha, or both

overall_design: drug treatment groups

first: Dan

last: Donoghue


title: The anti-proliferative effects of progestins in T47D breast cancer cells are tempered by progestin-induction of the ETS transcription factor Elf5.

status: Public on Jun 17 2010

city: Darlinghurst

first: Mark

last: Cowley

address: 384 Victoria St.

department: Genome Informatics & Clinical Genomics

institute: Garvan Institute of Medical Research

summary: Prolactin and progesterone act together to regulate mammary alveolar development, and both hormones have been implicated in breast cancer initiation and progression. Here we show that Elf5, a prolactin-induced ETS transcription factor that specifies the mammary secretory cell lineage, is also induced by progestins in breast cancer cells via a direct mechanism. To define the transcriptional response to progestin elicited via Elf5 we made an inducible Elf5 sh-RNA knock down model in T47D breast cancer cells and used it to prevent the progestin-induction of Elf5. Functional analysis of Affymetrix gene expression data using Gene Ontologies and Gene Set Enrichment Analysis showed enhancement of the progestin effects on cell cycle gene expression. Cell proliferation assays showed a more efficacious progestin-induced growth arrest when Elf5 was kept at baseline levels. These results showed that progestin-induction of Elf5 expression tempered the anti-proliferative effects of progestins in T47D cells, providing a further mechanistic link between prolactin and progestin in the regulation of mammary cell phenotype.

overall_design: We used Affymetrix expression arrays to determine to what extent Elf5 mediated the transcriptional effects of progestins in T47D cells. We transcript profiled our inducible Elf5 hold-down model using triplicate independent experiments under three conditions: (1) treatment with ethanol vehicle only (Baseline), (2) ORG2058 treatment for 4 days (Pg), and (3) Dox and ORG2058 treatment for 4 days, (Pg-Elf5) designed to prevent the progestin-induction of Elf5 expression.

first: Heidi

last: Hilton

first: Maria

last: Kalyuga

middle: J

first: Marie

middle: C

last: Alles

first: Heather

last: Lee

first: Catherine

last: Caldon

first: Katrina

last: Blazek

first: Warren

last: Kaplan

first: Elizabeth

last: Musgrove

first: Roger

last: Daly

first: Matt

last: Naylor

first: Justine

last: Graham

first: Christine

last: Clarke

first: Christopher

last: Ormandy


title: Expression data in HeLa S3 cells transfected with control-, UAP56- or URH49-siRNA

status: Public on Aug 15 2010

city: Kyoto

first: Seiji

last: Masuda

state: Kyoto

address: Kitashirakara oiwaketyo

department: Graduate School of Biostudies

institute: Kyoto university

summary: Nuclear export of mRNA is an essential process for eukaryotic gene expression. TREX complex couples the gene expression from transcription and splicing to mRNA export. Sub2, a core component of TREX complex in yeast is diversified to two closely related RNA helicases, UAP56 and URH49 in human.UAP56 and URH49 are required for bulk poly (A)+ RNA export but their target genes are quite different. In conclusion, UAP56 and URH49 have a different function in vivo despite the highly similarity.

overall_design: Cytoplasmic RNA was prepared in HeLa cells transfected with control-, UAP56- and URH49-siRNA and analyzed by gene expression array.

first: Tomohiro

last: Yamazaki

first: Hiroko

last: Yukinaga

first: Miki

last: Ebisuya

first: Eisuke

last: Nishida


title: Direct conversion of human fibroblasts to multilineage blood progenitors

status: Public on Oct 20 2010

city: Hamilton

first: Mickie

last: Bhatia

state: Ontario

address: 1200 Main Street West

institute: McMaster Stem Cell and Cancer Research Institute (SCC-RI)

summary:
Similar to embryo-derived stem cells, application of human induced pluripotent stem cells (iPSCs) is limited by our understanding of lineage specification. Here, we demonstrate the ability to generate progenitors and mature cells of the hematopoietic fate directly from human dermal fibroblasts without establishing pluripotency. POU domain activation of hematopoietic transcription factors by ectopic expression of Oct-4, together with specific cytokine treatment, allowed generation of cells expressing the pan-leukocyte marker CD45. These unique fibroblast-derived cells gave rise to granulocytic, monocytic, megakaryocytic, and
erythroid lineages, and demonstrated in vivo engraftment capacity. Distinct from PSC-derived hematopoietic cells, adult and not embryonic hematopoietic programs are activated, consistent with bypassing pluripotent state to generate blood fate. These findings suggest an alternative approach to cellular reprogramming for autologous cell-replacement therapies that avoids complications associated with the use of human PSCs.

overall_design:
Molecular analysis was done on purified untransduced Fibs, Oct-4 transduced Fibs at day 4, CD45+ve Fibs at day 21 and hematopoietic cytokine treated CD45+ve Fibs at day 37. The day 4 Oct-4 transduced Fibs were isolated by puromycin selection overnight (Oct-4 vector contains puromycin resistance cassette), purity of sample was validated by staining for Oct-4 followed by Oct-4 expression analysis using flow cytometry; samples used for molecular analysis exhibited 99% Oct-4 levels. The day 21 and day 37 CD45+veFibsOct-4 were isolated based on their CD45 expression. D21 and D37 cells were stained with CD45-APC antibody (BD Biosciences) and sorted using FACSAria II (Becton-
Dickinson); samples used for molecular analysis exhibited 99% CD45 levels. Analysis was performed on two biological replicates per sample.

first: Eva

last: Szabo

first: Shravanti

last: Rampalli

first: Ruth

last: Risueño

first: Angelique

last: Schnerch

first: Ryan

last: Mitchell

first: Aline

last: Fiebig

first: Marilyne

last: Levadoux-Martin


title: Vitamin D and Gene Expression [A589]

status: Public on Jun 19 2010

city: Aarhus N

first: Thomas

last: Thykjaer

address: IncubaSciencePark Skejby

country: Denmark

institute: AROS Applied Biotechnology

overall_design: Genome-wide expression analysis of hapmap lymphoblastoid and ENCODE project cell lines stimulated with calcitriol and/or estrogen for 36 hours as compared to untreated.

first: Sreeram

last: Ramagopalan


title: Vitamin D and Gene Expression

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

overall_design: Refer to individual Series


title: Gene expression changes associated with resistance to intravenous corticosteroid therapy in children with severe ulcerative colitis

status: Public on Aug 31 2010

city: Toronto

first: Boyko

last: Kabakchiev

address: 60 Murray Street, Room L3-004

department: Samuel Lunenfeld Research Institute

country: Canada

institute: Mount Sinai Hospital

summary:
Although corticosteroids remain a mainstay of therapy for UC, a meta-regression of cohort studies in acute severe ulcerative colitis (UC) showed that 29% of patients fail corticosteroid therapy and require escalation of medical management or colectomy.
We aimed to determine whether genes expressed in whole blood early following initiation of intravenous corticosteroid treatment can be associated with response.

overall_design: 20 corticosteroid responsive (PUCAI < 35 by day 5) and 20 corticosteroid resistant patients (PUCAI ≥ 35 by day 5 and need for 2nd line medical therapy or colectomy by hospital discharge) were selected from a prospectively accrued cohort of patients hospitalized for intravenous corticosteroid treatment of severe UC. Total RNA was extracted from blood samples collected on day 3 of intravenous corticosteroid therapy. The eluted transcriptomes were quantified on Affymetrix Human Gene 1.0 ST arrays. The data was analysed by the local-pooled error method for discovery of differential gene expression and false discovery rate correction was applied to adjust for multiple comparisons. P-values less than 0.05 after correction were considered significant.

first: Dan

last: Turner

first: Anne

last: Griffiths

first: Mark

middle: S

last: Silverberg


title: Efficacy of bortezomib in a direct xenograft model of primary effusion lymphoma

status: Public on Jul 20 2010

city: Miami

first: Kristopher

middle: A

last: Sarosiek

state: FL

address: 1580 NW 10th Ave

institute: University of Miami

summary: Primary effusion lymphoma is an aggressive B-cell lymphoma most commonly diagnosed in HIV-positive patients and universally associated with Kaposi’s sarcoma-associated herpesvirus (KSHV). Chemotherapy treatment of PEL yields only short-term remissions in the vast majority of patients yet efforts to develop superior therapeutic approaches have been impeded by lack of animal models that more accurately mimic human disease. To address this issue we developed a direct xenograft model, UM-PEL-1, by transferring freshly-isolated human PEL cells into the peritoneal cavities of NOD/SCID mice without in vitro cell growth. We utilized this model to show that bortezomib induces PEL remission and extends overall survival of mice bearing lymphomatous effusions.  Transcriptome analysis by genomic arrays revealed that bortezomib downregulated cell cycle progression, DNA replication, and Myc-target genes.

overall_design: The microarray analysis was conducted on mice bearing UM-PEL-1 xenografts after treatment for 24 hours with PBS or bortezomib.  Both arms of the experiment had three mice and the RNA was pooled from the three treated mice for gene expression analysis.

first: Lucas

last: Cavallin

first: Shruti

last: Bhatt

first: Ngoc

last: Toomey

first: Yasodha

last: Natkunam

first: Wilfredo

last: Blasini

first: Andrew

last: Gentles

first: Juan

last: Ramos

first: Enrique

last: Mesri

first: Izidore

last: Lossos


title: Affymetrix microarray for gene expression patterns influenced by syndecan-1 overexpression in malignant mesothelioma STAV-AB cells

city: Stockholm

first: Fang

last: Zong

address: F46, Huddinge university hospital

department: LabMed

institute: Karolinska

summary:
We aimed to investigate the function of syndecan-1 in tumor cell adhesion and migration, with special focus on the importance of its distinct protein domains, to better understand the structure-function relationship of syndecan-1 in tumor progression. We utilized two mesenchymal tumor cell lines which were transfected to stably overexpress full-length syndecan-1 or truncated variants: the 78 which lacks the extracellular domain except the DRKE sequence proposed to be essential for oligomerization, the 77 which lacks the whole extracellular domain, and the RMKKK which serves as a nuclear localization signal. Various bioassays for cell adhesion, chemotaxis, random movement and wound healing were studied. Furthermore we performed gene microarray to analyze the global gene expression pattern influenced by syndecan-1.

We found that full-length syndecan-1 enhanced cell adhesion in a dose-dependent manner. The truncated constructs only affected adhesion marginally, or not at all. Both full-length syndecan-1 and all its distinct domains inhibited serum-induced cell migration and wound closure. The full-length syndecan-1 and the 78 constructs specifically reduced cell motility/migration in random movement assay. Cell adhesion depends on the extracellular domain and also associates with the DRKE motif. Effects of syndecan-1 on migration are more complex; the pro-adhesive effect of the extracellular domain is one factor hampering migration, but the transmembrane/cytoplasmic portion seems to have additional impact. Gene microarray analysis showed that a number of genes involved in cell adhesion and migration were differentially expressed in syndecan-1 overexpressing cells.

Our results demonstrate that syndecan-1 regulates mesenchymal tumor cell adhesion and migration, and different domains have differential effects. Our study provides new inputs into the better understanding of structure-function relationship of this PG in tumor progression.

overall_design: Gene expression profiles (Human Gene 1.0 ST) of malignant mesothelioma cells were studied in syndecan-1 overexpressing cells (N=3) and vector control cells (N=3) .

first: David

last: Brodin


title: Gene expression following CDK9 silencing

status: Public on May 09 2010

city: Nashville

first: Yan

last: Guo

state: TN

address: 639 Preston Research Bld

institute: Vanderbilt Cancer Center

summary:
To determine the expression of genes in cells following silencing of CDK9 by siRNA.
U2OS human osteosarcoma cell lines were utilized.

overall_design: The cell lines were grown in previously described culture media in biological quadruplicates. Total RNA was isolated and array experiments were performed.

last: Yu

last: Cortez


title: Estrogen Coordinates Translation and Transcription Revealing a Role for NRSF in Human Breast Cancer Cells

status: Public on Apr 21 2010

city: PROVIDENCE

first: Alexander

last: Brodsky

state: RI

address: 593 Eddy St.

department: MCB

institute: Rhode Island Hospital/Brown University

summary:
Analysis of estrogen receptor (ER)-positive MCF7 cell total RNA expression and polysome-assiciated RNA expression following treatment with estradiol (E2) and vehicle (etoh).
We used expression microarrays to measure polysome association and total RNA abundance in E2 treated MCF7.  These data, along with previously published data, show that  genes that are upregulated by estrogen treatment are biased towards association with polysomes.

overall_design: MCF7 cells were grown in hormone depleted media for three days before a 1 hour treatment with E2 or 0.1 % ethanol (vehicle).  Total RNA was collected using standard methods and polysome-association RNA from the same cells were collected using sucrose gradient fractionation.  Both RNA populations were purified, labeled, and hybridized to Affymetrix Human Genest  arrays.

first: Sara

last: Hillenmeyer


title: ADIPOSE TISSUE PATHWAYS INVOLVED IN WEIGHT LOSS OF CANCER CACHEXIA

status: Public on Apr 10 2010

city: Update

first: Ingrid

last: Dahlman

address: Update

institute: Karolinska Institute

summary: The regulatory gene pathways underlying the loss of adipose tissue in cancer cachexia are unknown and were explored using pangenomic transcriptome profiling.

overall_design: Gene expression profiles (Human Gene 1.0 ST) of abdominal subcutaneous adipose tissue were studied in gastrointestinal cancer patients with (N=13) or without (N=14) cachexia. Data analyses were performed using the Affymetrix GeneChip Operating Software (GCOS) Version 1.4.


title: Expression in lymphoblastoid cell lines following hydrogen peroxide bolus at 5 times

city: Washington

first: Kimberly

last: Chapman

state: DC

address: 111 Michigan Ave NW

department: genetics

institute: Children's National

summary: The general expression profile in human lymphoblastoid cell lines treated with 9 uM, 90 uM or 900 uM bolus of hydrogen peroxide at 0, 4,12,24, and 48 hours.  Four cell lines (GM07055, GM14569, GM14467, and 12057) were treated separately and total RNA was pooled in equal amounts prior to labeling and hybridization to Affymetrix Human Gene 1.0 ST microarray.

overall_design: Four lymphoblastoid cell lines (GM07055, GM12057, GM14569, and GM14467) were obtained from the Coriell Institute for Medical Research (Camden, NJ).  24 hours before bolus treatments, cells were cultured at a density of 1 x10^6 cells/mL to create 17 cultures for each cell line (a total of 68 samples).  At the beginning of the experiment, one culture was collected from each cell line and total RNA prepared, this was equally pooled and prepared for microarray analysis (time zero, treatment zero).  Each cell line was then treated with a 9 (4 cultures), 90 (4 cultures), or 900 uM hydrogen peroxide bolus (4 cultures) or water (4 cultures).  Four, 12, 24 or 48 hours following the hydrogen peroxide bolus, cells were collected for each cell line of each treatment and total RNA prepared.  RNA from the four cell lines were equalling pooled for each time and each hydrogen peroxide (or water) bolus amount resulting in a total of 16 additional samples which were also labeled and hybridized to Affymetrix Human Gene 1.0 ST microarrays.


title: H2O2 Treatment of Human PBMC

status: Public on Jun 20 2010

city: Singapore

first: Lim

last: Chee Seng

address: Singapore

country: Singapore

institute: National University of Singapore

summary: To mimic the effect of ROS in contributing to ageing process in immune cells of PBMC. The PBMC cells were harvested from old human subjects (>50) and induced with H2O2 during 3 hour and 6 hour. The CEL file were normalized using RMA methods. We used microarray to explore the gene expression profiling before and after ROS. Gene related to cell cycle, apoptosis, metabolism and signal transduction were differentially expressed after inducing with H2O2 in compared to baseline.

overall_design: Human PBMC cell were harvested before induce with H2O2 (T0), 3 hours (T3) and 6 hours (T6) from the older PBMC. Eight individual samples were collected and hybridized for each time point.

last: Keong


title: Expression data from undifferentiated human pluripotent stem cells

status: Public on Apr 09 2010

city: Jerusalem

first: Uri

last: Ben-David

address: Givat-Ram

department: Genetics

country: Israel

institute: Hebrew University

summary: Due to their somatic cell origin, human induced pluripotent stem cells (HiPSCs) are assumed to carry a normal diploid genome, and adaptive chromosomal aberrations have not been fully evaluated. Here, we analyzed the chromosomal integrity of 66 HiPSC and 38 human embryonic stem cell (HESC) samples from 18 different studies by global gene expression meta-analysis. We report identification of a substantial number of cell lines carrying full and partial chromosomal aberrations, half of which were validated at the DNA level. Several aberrations resulted from culture adaptation, and others are suspected to originate from the parent somatic cell. Our classification revealed a third type of aneuploidy already evident in early passage HiPSCs, suggesting considerable selective pressure during the reprogramming process. The analysis indicated high incidence of chromosome 12 duplications, resulting in significant enrichment for cell cycle related genes. Such aneuploidy may limit the differentiation capacity and increase the tumorigenicity of HiPSCs.

overall_design:
Expression data from undifferentiated human embryonic stem cells and induced pluripotent stem cells
total RNA was isolated from undifferentiated pluripotent stem cells grown in standard HESC growth conditions on mouse embryonic fibroblast feeder layer.

first: Yoav

last: Mayshar

first: Ori

last: Bar-Nur

first: Marjorie

last: Pick

first: Ofra

last: Yanuka

first: Henia

last: Darr

first: Nissim

last: Benvenisty


title: Expression in induced sputum during acute exacerbations in asthmatic children with/without chronic airflow obstruction

status: Public on Mar 29 2010

city: Subiaco

first: Anthony

last: Bosco

address: 100 Roberts Road

institute: Telethon Kids Institute

summary:
Asthma exacerbations are associated with subsequent deficits in lung function.
Here, we tested the hypothesis that a specific pattern of inflammatory responses during acute exacerbations may be associated with susceptibility to chronic airway obstruction.

overall_design: The study design consisted of 20 asthmatic children; 10 children had relatively low FEV1/FVC ratios at baseline, and 10 children had relatively high FEV1/FVC ratios at baseline.

first: Samira

last: Ehteshami

first: Debra

last: Stern

first: Fernando

last: Martinez


title: Express data from Du145 cells

status: Public on Apr 03 2010

city: chicago.

first: Wei

last: Du

address: 929 E. 57th Street

institute: University of Chicago

summary: The retinoblastoma (Rb) tumor suppressor is often inactivated in cancers. To identify genes that can be used to specifically target such cancers, we carried out a genetic screen in Drosophila. We identified gig (fly TSC2) and found that inactivation of rbf (fly Rb) and gig synergistically induced cell death. Interestingly, inactivation of TSC2 specifically kills Rb mutant cancer cells under stress conditions, which is correlated with an inhibition of tumor growth. We show that cancer cell killing induced by concomitant inactivation of Rb and TSC2 is mediated by increased cellular stress, including oxidative stress. Inactivation of TSC2 and Rb synergistically induce oxidative stress via increased protein synthesis, inhibited de novo lipid synthesis, and decreased ROS scavenger enzyme SOD2 induction.

overall_design: Du145 was treated by shTSC2 or control, and then cultured in hypoxic conditions for 24h, and finally the total RNA was collected for microarray analysis.

first: Binghui

last: Li


title: Effects of RGMc on BMP2 and BMP6-mediated Gene Expression in Hep3B Liver Cells

status: Public on Jun 15 2010

city: Portland

first: Mahta

last: Nili

state: OR

address: 3181 SW Sam Jackson Park Road

department: Biochemistry and Molecular Biology

institute: Oregon Health & Science University

summary:
Mutations in repulsive guidance molecule c (RGMc) / hemojuvelin (HJV) cause juvenile hemochromatosis, an aggravated iron overload disorder that presents early in life.  Patients with juvenile hemochromatosis, and RGMc knockout mice, have diminished expression of the key iron-regulatory peptide, hepcidin.  This suggests that RGMc plays a critical role in the regulation of iron homeostasis; however the mechanisms of RGMc actions are unknown.  Recent studies have shown that RGMc directly binds to the growth factors, bone morphogenetic protein 2 and 6 (BMP2 and BMP6), and it is possible that this interaction regulates aspects of iron metabolism.
We used microarrays to examine the effects of RGMc on BMP2- and BMP6-mediated gene expression.

overall_design: In our experimental model we treated Hep3B liver cells that had been serum starved for 16 hours as follows: (1) un-treated, (2) BMP2, (3) BMP2 + 10-fold molar excess of Noggin (a potent BMP2 inhibitor), (4) BMP2 + 20-fold molar excess of RGMc, (5) BMP6, (6) BMP6 + 10-fold molar excess of Noggin, (7) BMP6 + 20-fold molar excess of RGMc.  Binding was allowed to proceed for BMP and Noggin or RGMc for 3 hr at 20°C prior to treatment of Hep3B cells.  Treatment time was 4 hr at which cells were collected for RNA isolation.

first: Peter

last: Rotwein


title: Gene expression profiles of dental follicle cells after 7 days of differentiation in vitro with BMP2, IGF2 and dexamethasone

status: Public on Mar 20 2010

city: Regensburg

first: Christian

last: Morsczeck

address: Franz-Josef Strauss Allee 11

country: Germany

institute: University of Regensburg

summary: We analysed gene expression profiles in dental follicle cells after 7 days of osteogenic differentiation with different inducers.

overall_design: Total RNAs were isolated from dental follicle cells after 7 days of differentiation with dexamethasone, BMP2, IGF2 and for control with standard cell culture medium


title: Vitamin D and Gene Expression [A690]

first: Thomas

last: Thykjaer

overall_design: Genome-wide expression analysis of hapmap lymphoblastoid and ENCODE project cell lines stimulated with calcitriol for 8 or 36 hours as compared to untreated.

first: Sreeram

last: Ramagopalan


title: Gene expression profiling of mesenchyme-derived cell populations in the human airways

status: Public on Apr 01 2010

city: NOTTINGHAM

first: SHAILENDA

last: SINGH

address: QUEEN'S MEDICAL CENTRE, DERBY ROAD

department: DIVISION OF THERAPEUTICS AND MOLECULAR MEDICINE

institute: UNIVERSITY OF NOTTINGHAM

summary:
Mesenchyme-derived cells in the human airway wall including airway smooth muscle cells, fibroblasts and myofibroblasts are known to play important roles in airway remodeling. The lack of specific phenotypic markers makes it difficult to define these cell populations in primary cultures. The objectives of this study were to evaluate reported markers and to identify novel markers to define these cell types.
We could not identify a specific single marker to define any of these cell populations in vitro that permitted unequivocal identification. We therefore used global gene expression profiling to identify genes that were differentially expressed in human airway mesenchymal cells.

overall_design: 3 samples were analysed in total - low passage human airway smooth muscle (HASM) cells (HASM-LP), high passage HASM cells (HASM-HP), MRC5 (lung fibroblasts) were used in this study for RNA extraction. MRC5 cells were used as the control cell population and were co-hybridised with HASM-LP and HASM-HP on cDNA microarrays. Spot arrays or cDNA arrays were used as a confirmatory gene expression profiling data to affymetrix arrays.

first: Ian

last: Hall

first: Shailendra

middle: R

last: Singh

first: Charlotte

last: Billington

last: Sayers


title: DNA microarrays of 4 human iPSC cell lines and the ESC cell line H9

status: Public on Mar 16 2010

city: Guangzhou

first: Duanqing

last: Pei

state: Guangdong

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

department: Center for Molecular Medicine

country: China

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

summary: Documents of DNA expression of 4 human induced pluripotent stem cell (iPSC) lines from umbilical cord mesenchymal cells (UMCs) and amniotic mesenchymal cells (AMCs). We used microarrays to identify similarity between 4 iPSC cell lines and the human embryonic stem cell (ESC) line H9.

overall_design: 2 AMC iPSC cell lines, 2 UMC iPSC cell lines, H9 ESC cell line. TRIZOL cell lysates were prepared.

first: Jinglei

last: Cai

first: Wenzhi

last: He