title: The novel antisense Bcl-2 inhibitor SPC2996 causes rapid leukemic cell clearance and immune activation in chronic lymphocytic leukemia

status: Public on May 30 2011

city: Essen

first: Ludger

last: Klein-Hitpass

address: Virchowstr. 173

department: Universitaetsklinikum

institute: Institut fuer Zellbiologie

summary:
SPC2996 is a novel locked nucleic acid (LNA) phosphorothioate antisense molecule targeting the mRNA of the Bcl-2 oncoprotein. We investigated the mechanism of action of SPC2996 and the basis for its clinically observed immunostimulatory effects in chronic lymphocytic leukemia (CLL). Patients with relapsed CLL were treated with a maximum of six doses of SPC2996 (0.2-6mg/ kg) in a multicenter phase I trial. Microarray-based transcriptional profiling of circulating CLL cells was carried out before and after the first infusion of SPC2996 in eighteen patients.
We used microarrays to characterize global  gene expression changes  of circulating CLL cells in response to SPC2996 infusion in 18 patients
Key word : Response to therapeutic agent

overall_design: We performed microarray-based gene expression profiling in serial peripheral blood samples from 18 individual CLL patients before and after treatment with SPC2996

first: J

last: Dürig

first: U

last: Dührsen

first: L

last: Worm

last: Rode Hansen

first: H

last: Ørum

first: M

last: Wissenbach


title: Combination of ABT-869 with SAHA on AML with FLT3-ITD

status: Public on May 31 2011

city: Singapore

first: Jianbiao

last: Zhou

address: 28 Medical Drive

country: Singapore

institute: Cancer Science Institute Singapore

summary: For the microarray experiments, MV4-11 and MOLM-14 cells were treated with DMSO control, ABT-869 3 nM, SAHA 6 uM and combination therapy for 24 hours. Cells were then washed in PBS and high-quality total RNA was extracted RNeasy Midi Kit, according to the manufacturer’s instruction (Qiagen, Valencia, USA). RNA quantity, quality, and purity were assessed with the use of the RNA 6000 Nano assay on the Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara CA, USA). Gene expression profiling was performed using Affymetric U133plus2.0 gene chip (Affymetrix, Santa Clara, CA, USA) according to the manufacturer’s protocol.

overall_design: MV4-11 and MOLM-14 cells were treated with DMSO control, ABT-869, SAHA or combination therapy for 24 hours.

first: Chien-Shing

last: Chen

first: Wee-Joo

last: Chng


title: E. coli K-12 mutant yjgI biofilm vs. wild type biofilm

status: Public on May 29 2011

city: State College

first: Thomas

middle: K.

last: Wood

state: PA

address: Room 161 Fenske Laboratory, University Park

department: Chemical Engineering & Biochemistry and Molecular Biology

country: USA

institute: Pennsylvania State University

summary: The gene expression of glasswool biofilm cells in E. coli yjgI mutant vs. E. coli wild type strain in LB.

overall_design:
Strains: E. coli K12 BW25113 wild type, yjgI mutant
Medium: LB
Biofilm grown on glass wool
Time: 15 h
Cell type: biofilm

middle: K

first: Qun

last: Ma


title: Expression analysis of miR-499 transgenic heart

city: San Francisco

first: Joseph

last: Shieh

state: CA

address: 533 Parnassus Ave

institute: University of California San Francisco

summary: microRNAs are small non-coding RNAs that can affect gene expression.  We used microarrays to analyze gene expression in miR-499 transgenic mouse hearts.

overall_design: Cardiac ventricles were collected at postnatal day 17 from wild type and miR-499 transgenics.


title: Relative expression profiling of ycdC knockout strain secreting HlyA protein

status: Public on May 25 2011

city: Newark

first: Kelvin

middle: H.

last: Lee

state: DE

address: 15 Innovation Way

department: Biotechnology Institute

institute: University of Delaware

summary: The most important approach to the development of platform organisms for recombinant protein production relies on random mutagenesis and phenotypic selection. Complex phenotypes, including those associated with significant elevated expression and secretion of heterologous proteins, are the result of multiple genomic mutations. Using next generation sequencing, a parent and derivative hypersecreter strain (B41) of Escherichia coli were sequenced with an average coverage of 52.8X and 55X, respectively. A new base-pair calling program, revealed a single nucleotide polymorphism in the B41 genome at position 1,074,787, resulting in translation termination near the N-terminus of a transcriptional regulator protein, RutR, coded by the ycdC gene. We verified the hypersecretion phenotype in a ycdC::Tn5 mutant and observed a 3.4-fold increase in active hemolysin secretion, consistent with the increase observed in B41. mRNA expression profiling showed decreased expression of tRNA-synthetases and some amino acid transporters in the ycdC::Tn5 mutant. This study demonstrates that power of next generation sequencing to characterize mutants leading to successful metabolic engineering strategies for strain improvement.

overall_design: 6 samples were analyzed with three biological replicates for each strain. Hly-ycdC+ is the control strain.

first: Prateek

last: Gupta

middle: H


title: Antagonistic regulation of EMT by TIF1γ and Smad4 in mammary epithelial cells

status: Public on May 26 2011

city: Lyon

first: Cedric

last: Hesling

address: 24 rue Laënnec

country: France

institute: CRCL

summary: TGFβ is known to be a potent inducer of EMT, a process involved in tumor invasion. TIF1γ has been reported to participate to TGFβ signaling. In order to understand the role of TIF1γ in TGFβ signaling and its requirement for EMT, we analyzed the TGFβ1 response of human mammary epithelial cell lines. A strong EMT increase was observed in TIF1γ-silenced cells after TGFβ1 treatment, whereas Smad4 inactivation completely blocked this process. In support of these observations, microarray data show that the functions of several TIF1γ target genes can be linked to EMT. As a negative regulator of Smad4, TIF1γ could be critical for the regulation of TGFβ signaling. This work highlights the molecular relationship between TIF1γ and Smad4 in TGFβ1 signaling and EMT.

overall_design: Total mRNA extractions were performed for 11 samples from transfected HMEC-TR. Replicates are rimo1, 6; rimo3, 9; rimo2, 7; rimo 4, 10 and rimo 5, 11. Rimo 8 is a single experiment. All RNA extractions were obtained from two independent cell cultures excepted for rimo8. Rimo 1, 6 are replicate for ctrl-; Rimo 3, 9 are replicate for ctrl+; Rimo 2, 7 are replicate for SiTIF-; Rimo 4, 10 are replicate for SiTIF+;  Rimo8 is SiSmad4-;  and Rimo5, 11 are replicate for SiSmad4+. ctrl means that HMEC-TR were transfected with an SiRNA scramble. "siSmad4" means  that HMEC-TR were transfected with an SiRNA anti Smad4.  "siTIF" means  that HMEC-TR were transfected with an SiRNA anti TIF1γ.   "-" means that cells were grown without TGFβ. "+" means that cells were treated with 5 ng/ml TGFβ1 for 24h.

first: Séverine

last: CROZE

first: Joel

last: LACHUER

first: Anne

last: WIRINCKX


title: Expression data from human CD34+ HPC subpopulations transduced with nuclear-trapped AF1q/MLLT11 (A2M)

city: Paris

first: Marc

last: Delord

address: Hopital Saint-Louis, 1 avenue Claude Vellefaux

department: Recherche clinique

institute: Centre hospitalier de Versailles

summary:
We used microarrays to examine the impact of AF1q/MLLT11 on the gene expression profile of CD34+CD45RA-Lin- and CD34+CD45RA+Lin- HPCs isolated from umbilical cord blood
CD34+CD45RA-Lin- and CD34+CD45RA+Lin- HPCs correspond respectively to early multipotent and lympho-granulo-macrophagic precursors. A2M is a nuclear mutant-derivative of AF1q/MLLT11

overall_design: CD34+CD45RA-Lin- and CD34+CD45RA+Lin- HPCs were FACS-sorted, exposed to A2M or control vectors, sorted based on GFP expression, and subjected to global gene expression analysis 72 hrs later.

first: Bruno

last: CANQUE


title: Gene Expression Analysis of Fezf1 Mutant Main Olfactory Epithelium

status: Public on May 27 2011

city: Santa Cruz

first: Matthew

middle: Joseph

last: Eckler

address: 434 Sinsheimer Labs, UCSC

department: MCDB

institute: UCSC

summary: Mice lacking the transcription factor Fezf1 exhibit defects in the structural and molecular organiztion of their olfactory system. To invetigate this at the level of gene expression, we isolated Fezf1 expressing cells by FACS from the MOE of Fezf1+/- or Fezf1-/- animals and compared their gene expression profiles.

overall_design: The targeted Fezf1 allele contains an EGFP coding sequence under control of the endogenous Fezf1 promoter. We utilized this to isolate Fezf1+/- or Fezf1 -/- cells from the microdissected MOE tissue of E18.5 mouse embryos. Total RNA was isolated from these cells and gene expression examined by Affymetrix 1.0 ST array.

middle: J

first: Bin


title: Expression data from miR-223KO and miR-223WT bone marrow cells

status: Public on May 24 2011

city: Ulm

first: Florian

last: Kuchenbauer

address: Albert-Einstein Allee 23

department: Department of Internal Medicine III

country: Germany

institute: University of Ulm

summary:
Total bone marrow (BM) from miR-223 knockout (mir-223-/-) and wildtype (miR-223+/+) mice 21 was extracted, prestimulated for 2 days. Then, the BM cells were simultaneously cotransduced with MSCV-Hoxa9-pgk-neomycin and a MSCV-Meis1-IRES-YFP by co-cultivation with irradiated (4,000 cGy) viral producers. HoxA9-Meis1 transduced cells were sorted for YFP expression and continuously selected with neomycin (1.4 mg/ml).
Processing of the pre-miRNA through Dicer1 generates a miRNA duplex, consisting of a miRNA and miRNA* strand. Despite the general view that miRNA*s have no functional role, we further investigated miRNA* species in 10 deep sequencing libraries from mouse and human tissue. Comparing miRNA/miRNA* ratios across the miRNA sequence libraries revealed that 50% of the investigated miRNA duplexes exhibit a highly dominant strand. Conversely, 10% of miRNA duplexes show a comparable expression of both strands, while the remaining 40% exhibit variable ratios across the examined libraries as exemplified by miR-223/miR-223* in murine and human cell lines. Functional analyses revealed a regulatory role for miR-223* in myeloid progenitor cells, implying an active role for both arms of the miR-223 duplex. This was further underscored by the demonstration that miR-223 and miR-223* target the IGF1R/PIK3 axis and that high miR-223* levels associate with increased overall survival in acute myeloid leukemia (AML) patients. Thus, we found a supporting role for miR-223* in differentiating myeloid cells in normal as well as the leukemic cell state. The fact that the miR-223 duplex acts through both arms extends the complexity of miRNA-directed gene regulation of this myeloid key miRNA.

overall_design: 2 biological replicates


title: Expression data from Notch-activated CD34+CD45RA-Lin- hematopoietic progenitor cells (HPCs) transduced with nuclear-trapped AF1q/MLLT11 (A2M)

summary:
We used microarrays to examine the impact of AF1q/MLLT11 on the gene expression profile of Notch-activated CD34+CD45RA-Lin- HPCs isolated from umbilical cord blood
CD34+CD45RA-Lin-  HPCs correspond to early multipotent progenitors. A2M is a nuclear mutant derivative of AF1q/MLLT11

overall_design: CD34+CD45RA-Lin- HPCs were FACS-sorted, exposed to A2M or control vectors, sorted again based on GFP expression, and cultured for 72 hrs with graded doses of plastic-immobilized Notch ligand Delta1ext-IgG


title: Functional evidence that Drosha over-expression in cervical squamous cell carcinoma affects cell phenotype and microRNA profiles [mRNA]

city: Cambridge

middle: Jonathan

last: Murray

address: Box 197, Hills Road

department: MRC/Hutchison Research Centre

country: United Kingdom

institute: MRC Cancer Cell Unit

summary:
Comparison of mRNA expression profiles in W12 Series 1 cervical ectokeratinocytes at passage number 22 versus 19 (during which time the cells gain an invasive phenotype)
As these cells demonstrate gain of chromosome 5p during this time, mRNA expression profiling data interrogated for over-expressed genes on 5p that may be important in cervical neoplastic progression.

overall_design: Analyzed global mRNA expresion profiles from W12 Series 1 cells (3 replicates at passage 22 versus 3 replicates at passage 19)

first: Balaji

last: Muralidhar

first: David

middle: M

last: Winder

first: Roger

middle: D

last: Palmer

first: Nuno

last: Barbosa-Morais

first: Harpreet

last: Saini

first: Ian

last: Roberts

first: Mark

middle: R

last: Pett

first: Nicholas

last: Coleman


title: The mRNA and microRNA expression profile of the RNA-induced silencing complex in human U-87 astrocytoma cells and primary human astrocytes

city: Calgary

first: Joanna

last: Moser

state: AB

address: 3330 Hospital Drive N.W.

department: Biochemistry and Molecular Biology

country: Canada

institute: University of Calgary

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

summary: mRNA and microRNA expression was examined in global cellular fractions and in RNA-induced silencing complex (RISC)-immunoprecipitated cell fractions in cultured primary human astrocytes (ScienCell) and in cultured human U-87 MG astrocytoma cells (ATCC). ABSTRACT: Background: GW/P bodies are cytoplasmic ribonucleoprotein-rich foci that are involved in microRNA (miRNA)-mediated messenger RNA (mRNA) silencing and degradation. These mRNA regulatory functions within GW/P bodies are mediated by GW182 and its binding partner hAgo2 when bound to miRNA within the RNA-induced silencing complex (RISC). Although miRNAs and mRNAs are known to be localized to RISC in a variety of cells, to date no published study has examined the profile of specific miRNA and mRNA targeted to the RISC. Methodology/Principle Findings: In this study, RISC mRNA and miRNA components were profiled by microarray analysis of human U-87 astrocytoma cells and primary human astrocytes with total RNA extracted from the RISC as well as the global cellular fractions. The novel findings of this study were fourfold: (1) miRNAs are highly enriched in primary astrocyte RISC compared to U-87 astrocytoma RISC, (2) astrocytoma cells and primary astrocytes each contain unique RISC miRNA profiles as compared to their respective cellular miRNA profiles, (3) miR-195, 10b, 29b, 19b, 34a and 455-3p were upregulated and miR-181b was downregulated in U-87 astrocytoma RISC as compared to primary astrocyte RISC, and (4) RISC contain mostly downregulated mRNAs in primary astrocytes and U-87 astrocytoma cells. Conclusions/Significance: We show that in U-87 astrocytoma cells, miR-34a and miR-195 were upregulated in RISC suggesting an oncogenic role for these miRNAs. Three miR34a-targeted mRNAs and two miR-195-targeted mRNAs were downregulated. One miR-195-targeted mRNA was upregulated. Biological pathway analysis of RISC mRNA components suggests that the RISC plays a pivotal role in cancer, inflammatory disease, immunological disease, the cell cycle, cellular movement and numerous cell signaling pathways. This study points to the importance of the RISC and ultimately GW/P body composition and function and in miRNA and mRNA deregulation in astrocytoma cells and possibly for other brain tumors.

overall_design:
Experiments outsourced to LC Sciences who are partnered with an Affymetrix® Authorized Service Provider, SeqWright DNA Technology Services (Houston, TX).  Using Affymetrix Human Genome U133A 2.0 Array, they analyzed 14,500 well-characterized human genes across 4 replicates in each of the 4 sample groups: (1) global cellular U-87 astrocytoma, (2) global cellular primary astrocyte, (3) RISC-IP U-87 astrocytoma, and (4) RISC-IP primary astrocyte.
Experiments outsourced to LC Sciences (Houston, TX).  Using µParaflo microfluidic chips, they analyzed 6211 target human miRNAs (Sanger miRBase version 11, http://microrna.sanger.ac.uk/sequences/) or control RNAs (array hybridization controls and single-base mismatch targets) and a polyethylene glycol spacer segment to extend the coding segment away from the substrate across 4 replicates in each of the 4 sample groups: (1) global cellular U-87 astrocytoma, (2) global cellular primary astrocyte, (3) RISC-IP U-87 astrocytoma, and (4) RISC-IP primary astrocyte.

first: Marvin

last: Fritzler


title: Identification of Novel Therapeutic Targets in Microdissected Clear Cell Ovarian Cancers

city: Boston

first: Michael

last: Birrer

state: MA

address: 70 Blossom Street

department: Medicine

institute: MGH

summary:
To identify the gene signature accounting for the distinct clinical outcomes in ovarian clear cell cancer patients
Clear cell ovarian cancer is an epithelial ovarian cancer histotype that is less responsive to chemotherapy and carries poorer prognosis than serous and endometrioid histotypes. Despite this, patients with these tumors are treated in a similar fashion as all other ovarian cancers. Previous genomic analysis has suggested that clear cell cancers represent a unique tumor subtype. Here we generated the first whole genomic expression profiling using epithelial component of clear cell ovarian cancers and normal ovarian surface specimens isolated by laser capture microdissection. Arrays analyzed using BRB ArrayTools and PathwayStudio software was used to identify the signaling pathways.

overall_design: Gene expression profiling was completed for 10 clear cell ovarian cancer specimens and 10 normal ovarian surface epithelium using the Affymetrix human U133 Plus 2.0 Arrays


title: Global transcriptome response of recombinant protein xylanase producing E. coli in high cell density fed batch culture

city: New Delhi

first: Krishna

middle: Jyoti

last: Mukherjee

email: kjmukherjee@mail.jnu.ac.in, kumarsujeet@gmal.com, ashishji101@gmail.com, sudheer@imtech.res.in

state: delhi

address: New Mehrauli Road

department: School Of Biotechnology

country: India

institute: Jawaharlal Nehru University

summary: Strong production of recombinant proteins interfere with cellular processes in many ways. The extent of the bacterial stress response is determined by the specific properties of the recombinant protein, and by the rates of transcription and translation. The consideration of bacterial stress and starvation responses is of crucial importance for the successful establishment of an industrial large scale bioprocess. Stress genes can be used as marker genes in order to monitor the fitness of industrial bacterial hosts during fermentation processes. For this purpose, here in our study we have applied transcriptome analysis for the description of general and specific stress and starvation responses of Escherichia coli. Producing recombinant protein (Xylanase) in high cell density fed batch culture.

overall_design: Cells were grown in batch mode in TB media till an OD600 of 15. The specific growth rate of 0.3 h-1 was maintained by fed batch started at OD600 of 15. Cells were induced at an OD600 of 30 using 1 mM IPTG and the growth and product profile was monitored. Samples at different time points (2hrs, 4hrs, and 6hrs) were taken and frozen in liquid nitrogen quickly for transcriptome analysis.

first: Sudheer

last: Gupta

first: Ashish

last: Sharma


title: Functional evidence that Drosha over-expression in cervical squamous cell carcinoma affects cell phenotype and microRNA profiles

first: Matthew

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

summary:
Although gain of chromosome-5p is one of the most frequent DNA copy number imbalances in cervical squamous cell carcinoma (SCC), the genes that drive its selection remain poorly understood. In a previous cross-sectional clinical study we showed that the microRNA processor Drosha (located on chromosome-5p) demonstrates frequent copy-number gain and over-expression in cervical SCC, associated with altered microRNA profiles. Here, we have conducted gene depletion/over-expression experiments to demonstrate the functional significance of up-regulated Drosha in cervical SCC cells. Drosha depletion by RNA-interference (RNAi) produced significant, specific reductions in cell motility/invasiveness in vitro, with a silent RNAi-resistant Drosha mutation providing phenotype rescue. Unsupervised hierarchical clustering following global profiling of 319 microRNAs in eighteen cervical SCC cell line specimens generated two groups according to Drosha expression levels. Altering Drosha levels in individual SCC lines changed the group into which the cells clustered, with gene depletion effects being rescued by the RNAi-resistant mutation. Forty-five microRNAs showed significant differential expression between the groups, including four of fourteen that were differentially-expressed in association with Drosha levels in clinical samples. miR-31 up-regulation in Drosha over-expressing samples/cell lines was the highest-ranked change (by adjusted p-value) in both analyses, an observation validated by Northern blotting. These functional data support the role of Drosha as an oncogene in cervical SCC, by affecting expression of cancer-associated microRNAs that have the potential to regulate numerous protein-coding genes.

This SuperSeries is composed of the SubSeries listed below.

platform_organism:
Homo sapiens
Human alphaherpesvirus 1
Human alphaherpesvirus 2
Human betaherpesvirus 5
Lymphocryptovirus
Rhadinovirus
JC polyomavirus
Human immunodeficiency virus 1
Merkel cell polyomavirus
Betapolyomavirus hominis
Betapolyomavirus macacae

overall_design: Refer to individual Series.


title: Gene Expression Profiles in Stage II and III Colon Cancer. Application of a 128-gene signature

status: Public on Sep 01 2011

city: Roskilde

first: Morten

last: Thorsteinsson

address: Koegevej 7-13

department: Department of Surgery

country: Denmark

institute: Roskilde Hospital, University of Copenhagen

type:
Expression profiling by array
Third-party reanalysis

summary: Purpose: A 128-gene signature has been proposed to predict poor outcomes in patients with stage II and III colorectal cancer. In the present study we aimed to validate this previously published 128-gene signature on external and independent data from patients with stage II and III colon cancer.

overall_design: Tumor samples were obtained from 37 patients with stage II and III colon cancer, who underwent colon resection at the Department of Surgery, Roskilde Hospital, Denmark and the Department of Surgery, Bispebjerg Hospital, Denmark between 2001 and 2008. Purified tumor RNA was reverse-transcribed, labelled and hybridized to Affymetrix Human Genome U133 Plus 2.0 GeneChip Array (Affymetrix, Santa Clara, USA) according to the manufacturers instructions and scanned at the RH Microarray Center, Rigshospitalet, University of Copenhagen.

first: Lene

middle: T

last: Kirkeby

first: Leif

last: Lund

first: Lars

last: Sørensen

first: Thomas

middle: A

last: Gerds

first: Per

last: Jess

first: Jørgen

last: Olsen


title: Time-course effect of APRIL on gene expression in HepG2 cells

status: Public on May 20 2011

city: Heraklion

first: George

last: Notas

address: PO BOX 2208

country: Greece

institute: University of Crete

summary: APRIL (TNFSF13) is a ligand of the TNF superfamily which binds to two receptors, BCMA and TACI. We have found that APRIL and its receptor BCMA are specifically enhanced in hepatocellular carcinoma, as compared to non-cancerous liver tissue. We further identified that HepG2 cells present the same ligand/receptor pattern as human hepatocellular carcinomas. We investigated the role of APRIL in HepG2 gene expression in a time course study.

overall_design: 24 hour serum starved HepG2 cells were treated with 200ng/ml of APRIL and RNA was collected at 0, 2, 6, and 12h. The collected RNA was used for hybridization on commercially available Affymetrix Human Genome U133 Plus 2.0 Arrays

first: Elias

last: Castanas


title: HoxB4 in hematopoietic stem cells

status: Public on May 23 2011

city: Yokohama

first: Takaho

middle: A.

last: Endo

state: Kanagawa

address: 1-7-22 Suehiro, Tsurumi

department: IMS

country: Japan

institute: RIKEN

type: Genome binding/occupancy profiling by array

summary: Ectopic expression of homeodomain transcription factor HoxB4 in mouse ES cells enhances in vitro development of hematopoietic stem cells (HSCs).

overall_design: Mouse ES cells were differentiated for 6 days in EBs, then c-Kit+CD41+ hematopoietic precursor cells were isolated, plated onto OP9 cells, and transduced with the GFP control or 3×FLAG-tagged HoxB4 retrovirus.  At day 12 of the co-culture with OP9 cells, c-Kit+ progenitor cells overexpressing HoxB4 were collected by magnetic-activated cell sorting (MACS) and subjected to a ChIP-chip and microarray analysis. The purity of the recovered c-Kit+ cells was more than 95% as judged by flow cytometry.

first: Motohiko

last: Oshima

first: Atsushi

last: Iwama

first: Mitsujiro

last: Osawa


title: Expression data from human squamous cell lung cancer line HARA and highly bone metastatic subline HARA-B4.

status: Public on May 19 2011

city: Fukuoka

first: Soichi

last: Takiguchi

address: 3-1-1 Notame, Minami-ku

institute: National Kyushu Cancer Center

summary: We investigated the molecular mechanisms for osteolytic bone metastasis by selecting human lung cancer cell line subpopulations with elevated metastatic activity and validating genes that are overexpressed in these cells. A bone-seeking squamous lung cancer cell line (HARA-B4) was established by sequentially injecting parental HARA cells into the left ventricle of male 5-week-old nude mice 4 times.

overall_design: The parental line HARA and highly bone-metastatic line HARA-B4 were analized. Total of two samples. No replicates.

first: Haruo

last: Iguchi


title: Gene expression profiles of MCF-7 cells treated with Si-Wu-Tang, estradiol and ferulic acid

status: Public on May 18 2011

city: Shanghai

first: Leming

last: Shi

address: 2005 Songhu Road

department: School of Life Sciences

country: China

institute: Fudan University

summary:
Traditional Chinese medicines (TCM), usually composed of a mixture of components, may simultaneously target multiple genes/pathways and thus achieve superior efficacy for complex diseases such as cancer. To identify novel mechanisms of action and potential health benefits for a TCM formula Si-Wu-Tang (SWT) widely used for women’s health, we obtained the DNA microarray expression profiles for SWT, its active component ferulic acid, and estradiol in human breast cancer cell line MCF-7 and analyzed the gene expression signatures associated with each treatment using the “Connectivity Map” (cMAP).
This study indicates that DNA microarray profiling analysis and cMAP data mining provide a powerful approach to discover unknown mechanisms of actions and identify potential new health benefits for TCM.

overall_design: We profiled the gene expression of MCF-7 cell lines to SWT, its active component FA, as well as estradiol using Affymetrix human genome U133 plus 2.0 arrays. The data set includes profiles for 24 samples, divided into eight groups of treatment: 0.001% DMSO used as the vehicle control (C), 0.1 µM estradiol (EM), FA at three concentrations (0.1, 1, and 10 µM) (FL, FM and FH) and SWT at three concentrations (0.0256, 0.256, and 2.56 mg/ml) (SL, SM and SH).  For each treatment group, 3 biological replicates were included, resulting in 24 (8 groups × 3 replicates/group) RNA samples.

first: Zhining

last: Wen

first: Zhijun

last: Wang

first: Steven

first: Ranadheer

last: Ravula

first: Lun

last: Yang

first: Jun

last: Xu

first: Charles

first: Moses

last: Chow

first: Ying

last: Huang


title: Gene expression profiling in BCR/ABL expressing LSCs and BCR/ABL expressing Alox5-/-LSCs

status: Public on May 17 2011

city: Worcester

first: shaoguang

last: Li

address: 364 Plantation street

institute: Worcester

summary:
We previously demonstrated that Alox5 deficiency impairs the function of LSCs and prevents the initiation of BCR-ABL-induced CML. To identify the pathways in which Alox5 gene regulates function of LSCs, we performed a comparative DNA microarray analysis using total RNA isolated from non-BCR-ABL-expressing Lin-Sca-1+c-Kit+, BCR-ABL-expressing wild type LSCs and BCR-ABL-expressing Alox5-/- LSCs. The result was validated by quantitative real-time PCR analysis of non-BCR-ABL-expressing Lin-Sca-1+c-Kit+, BCR-ABL-expressing wild type LSCs and BCR-ABL-expressing Alox5-/- LSCs.
We have shown that Alox5 is a critical regulator of leukemia stem cells (LSCs) in a BCR-ABL-induced chronic myeloid leukemia (CML) mouse model, and we hypothesize that the Alox5 pathway represents a major molecular network that regulates LSC function. Therefore, we sought to further dissect this pathway by comparing the gene expression profiles of wild type and Alox5-/- LSCs derived from our mouse model for BCR-ABL-induced CML. DNA microarray analysis revealed a small group of candidate genes that exhibited changes in the levels of transcription in the absence of Alox5 expression.  In particular, we noted that the expression of the Msr1 gene was up-regulated in Alox5-/- LSCs, suggesting that Msr1 might suppress the proliferation of LSCs.  Using our CML mouse model, we show that Msr1 is down-regulated by BCR-ABL and this down-regulation is partially restored by Alox5 deletion, and that Msr1 deletion causes acceleration of CML development. Moreover, Msr1 deletion markedly increases LSC function through its effects on cell cycle progression and apoptosis. We also show that Msr1 affects CML development by regulating the PI3K-AKT pathway and β-Catenin. Together, these results demonstrate that Msr1 suppresses LSCs and CML development. The enhancement of Msr1 function may be of significance in the development of novel therapeutic strategies targeting CML.

overall_design: To identify genes that are regulated by BCR-ABL in LSCs and LSCs without Alox5 gene, we compared the gene profile between wild type(WT) LSCs or Alox5-/- LSCs.

first: Shaoguang

first: Yaoyu

last: Chen

first: Yiguo

last: Hu


title: Isolation and characterization of a metastatic hybrid cell line generated by ER negative and ER positive breast cancer cells in mouse bone marrow

city: BETHESDA

first: abdel

middle: G

last: Elkahloun

address: 50, SOUTH DRIVE

institute: NHGRI-NIH

summary: The origin and the contribution of breast tumor heterogeneity to its progression are not clear. We investigated the effect of a growing orthotopic tumor formed by an aggressive estrogen receptor (ER)-negative breast cancer cell line on the metastatic potential of a less aggressive ER-positive breast cancer cell line for the elucidation of how the presence of heterogeneous cancer cells might affect each other’s metastatic behavior.

overall_design: ER positive ZR-75-1/GFP/puro cells, resistant to puromycin and non-tumorigenic/non-metastatic without exogenous estrogen supplementation, were injected intracardiacally into mice bearing growing orthotopic tumors, formed by ER negative MDA-MB-231/GFP/Neo cells resistant to G418. A variant cell line B6, containing both estrogen-dependent and -independent cells, were isolated from GFP expressing cells in the bone marrow and re-inoculated in nude mice to generate an estrogen-independent cell line B6TC.

first: A

first: Keya

last: De Mukhopadhyay

first: Abhik

last: Bandyopadhyay

first: LuZhe

last: Sun

first: Weiwei

last: Wu


title: Bone morphogenetic protein-7 is a MYC target with pro-survival functions in childhood medulloblastoma

status: Public on May 16 2011

city: Zurich

first: Stefan

last: Zoller

address: Universitatstrasse 16

department: Genetic Diversity Centre

country: Switzerland

institute: ETH Zurich

summary: Medulloblastoma (MB) is the most common malignant brain tumor in children, among whom overexpression or amplification of MYC oncogenes has been associated with poor clinical outcome. Although the MYC functions during normal development and oncogenesis in various systems have been extensively investigated, the transcriptional targets mediating MYC effects in MB are still elusive. Their identification and roles during MB onset and progression are important and will ultimately suggest novel potential therapeutic targets. cDNA microarray analysis was used to compare the effects of overexpressing and silencing MYC on the transcriptome of a MB-derived cell line. We identified 209 genes with potential relevance to MYC-dependent cellular responses in MB. Among the MYC-responsive genes, we found members of the bone morphogenetic protein (BMP) signaling pathway, which plays a crucial role during the development of the cerebellum. In particular, the cytokine gene BMP7 was identified as a direct target of MYC in MB cells. Similar to the effect induced by BMP7 silencing by siRNA, the use of a small-molecule inhibitor of the BMP/SMAD signaling pathway reduced cell viability in a panel of MB cells. Altogether, our findings indicate that high MYC levels drive BMP7 expression in MB to induce pro-survival and pro-proliferative cellular pathways. This observation suggests that targeting the BMP/SMAD pathway may be a new therapeutic concept for the treatment of childhood MB.

overall_design: 6 samples (3 replicates for each sample): wild-type MB cell line, empty vector-transfected control cell line, 2 c-MYC-overexpressing clones, 1 clone upon c-MYC silencing, 1 silencing control cell line.

first: Fiaschetti

last: Giulio

first: Deborah

last: Castelletti

first: Alexandre

last: Arcaro

first: Michael

last: Grotzer

first: Martin

last: Pruschy

first: Alexander

last: Schramm

first: Christina

last: Schroeder

first: Duncan

last: Stearns

first: Angelika

last: Eggert

first: Frank

last: Westermann

first: Tarek

last: Shalaby


title: Exon-Level Expression Data from Primary Human B Cells and Lymphoblastoid Cell Lines (LCLs) on HuEx and U133 2.0 plus Platforms

city: Durham

first: Luftig

last: Laboratory

state: NC

address: 220 CARL Bldg Duke U Med Center

department: MGM

institute: Duke University

summary: Eptstein-Barr Virus, an oncogenic herpesvirus, infects and immortalizes human B cells in culture into indefinitely-prolerifating LCLs.  We examined the gene expression of primary B cells during the process of infection and growth transformation at the exon level to analyze virus-induced changes in expression and exon usage.

overall_design: 4 samples each of total RNA were extracted from purified resting B Cells and monoclonal LCLs, for a total of 8. These samples were subjected to either Human Exon Array 1.0 or Affymetrix U133 2.0 plus. Data was then RMA normalized and analyzed using SplicerEx

first: Eleonora

last: Forte

first: Timothy

last: Robinson

first: Micah

last: Luftig


title: Design of an improved host platform for the over expression of recombinant proteins in Escherichia coli

first: Krishna

last: Mukherjee

institute: New Delhi

summary: The objective of this work was to design an improved host platform for recombinant protein expression in E. coli. The approach involves first to create a library of the E. coli genomic DNA in different expression vectors and screen for probable transcripts which may lead to slow growing colonies and also simultaneously over-expression of recombinant proteins.  To observe its effect on host performance, these genes were knocked out from the E. coli genome. A CG2 strain has been created by knocking in vhb gene gene downstream of the acetate promoter and knocking down ribB gene in DH5α and transformed with Recombinant GFP cloned in pBAD33.

overall_design: E. coli DH5α (control strain), and strain CG2 were transformed with pBAD33-GFP and cultured in well controlled fed batch fermentations. The effect of three parameters was sought to be studied. The first was the effect of time post induction and thus samples were collected 0, 2, 4 and 6 hours post induction. The second parameter was the effect of host modification and hence both the control and the modified host (CG2) were studied at μ = 0.3 h-1. The third parameter was the effect of specific growth rate and thus the host (CG2) was run at μ = 0.3 h-1 and 0.6 h-1.

first: Chaitali

last: Ghosh

first: Ashish

last: Sharma


title: Canonical NF-kB Activation is Essential for Epstein-Barr Virus Latent Membrane Protein 1 TES2/CTAR2 Gene Regulation.

status: Public on May 15 2011

first: Benjamin

last: Gewurz

address: 181 Longwood Ave

department: Medicine, Infectious Disease

institute: Brigham and Women's Hospital

summary: Epstein-Barr Virus (EBV) Latent Membrane Protein 1 (LMP1) transforms rodent fibroblasts and is expressed in most EBV-associated malignancies. LMP1 Transformation Effector Site 2 (TES2)/C-Terminal Activation Region 2 (CTAR2) activates NF-kappaB, p38, JNK, ERK and IRF7 pathways. We have investigated LMP1 TES2 genome-wide RNA effects at 4 time points after LMP1 TES2 expression in HEK 293 cells. Using a False Discovery Rate (FDR) of < 0.001 after correction for multiple hypotheses, LMP1 TES2 caused > 2-fold changes in 1916 mRNAs; 1479 RNAs were up-regulated and 437 down-regulated.  In contrast to TNFalpha stimulation, which transiently up-regulates many target genes, LMP1 TES2 maintained most RNA effects through the time course, despite robust and sustained induction of negative feedback regulators, such as IkappaBalpha and A20. LMP1 TES2 regulated RNAs encode many NF-kappaB signaling proteins and secondary interacting proteins. Consequently, many LMP1 TES2-regulated RNAs encode proteins that form an extensive interactome. Gene Set Enrichment Analyses found LMP1 TES2 up-regulated genes to be significantly enriched for Pathways in Cancer, B-and T-cell receptor signaling, and Toll-like receptor signaling.  Surprisingly, LMP1 TES2 and IkappaBalpha super-repressor co-expression decreased LMP1 TES2 RNA effects to only 5 RNAs with FDR<0.001 and >2 fold change. Thus, canonical NF-kappaB activation is critical for almost all LMP1 TES2 RNA effects in HEK-293 cells and a more significant therapeutic target than previously appreciated.

overall_design: An LMP1 double point mutant (P204A, Q206A) was used to construct a HEK-293 TET-On LMP1 TES2 cell line.  Stable cell clones were selected that carry an inducible system for LMP1 TES2 expression.  The Tet-system is composed of three parts: 1) the LMP1 TES2 cDNA cloned into the tetracycline-regulated pJEF vector; 2) a tetracycline suppressor (tTS) that binds Tet-operator sites in the absence of tetracyclines and silences expression; 3) a reverse-tetracycline transactivator fused to the 4-hydroxy tamoxifen (4HT) ligand binding domain (rTTA M2).  LMP1 expression was induced by addition of doxycycline (1 ug/ml) and 4HT (100 nM).  For simultaneous inducible expression of LMP1 TES2 and an IkBa super-repressor, a stable cell line was derived.  A pJEF vector encoding IkBa residues 37-317 was introduced into the inducible LMP1 TES2 cell line.  Cell lines were cultured with DMEM (GIBCO) supplemented with 10% tetracycline-free serum (Clontech). LMP1 expression was induced by addition of tetracycline (1 ug/ml).  RNA samples were collected from triplicate samples using RNABee (Qiagen) according to the manufacturer’s instructions from 293 cells induced for LMP1 TES2 (and IkBa super-repressor, where indicated) expression at 0, 6, 9, 12 and 24 hours of induction.  Cells were in the log-phase of growth.  Gene expression profiles were assayed using the Affymetrix HU-133 plus2 GeneChip according to the manufacturer's instructions. Real-time RT-PCR was performed with the Power SYBR Green RNA-to-CT™ 1-Step Kit (Applied Biosystems, Foster City, CA). Fold changes were determined using delta delta Ct method and normalized by GAPDH expression levels.  RNA expression data were normalized using RMA and array quality assessed by NUSE and RLE scores. The data was collected according to methods that fall under the MIAME standards.

first: Jessica

middle: C

last: Mar

first: Megha

last: Padi

first: Bo

last: Zhao

first: Nicholas

middle: P

last: Shinners

first: Kaoru

last: Takasaki

first: E

last: Bedoya

first: James

middle: Y

last: Zou

first: Ellen

last: Cahir-McFarland

first: John

last: Quackenbush

first: Elliott

last: Kieff


title: RAP1A signaling in Leishmania donovani infected macrophages

status: Public on May 13 2011

city: Lucknow

first: Neeloo

last: Singh

state: Uttar Pradesh

address: Jankipuram Extension Sitapur Road

department: Biochemistry

institute: Central Drug Research Institute

summary: Monastrol treatment of Leishmania donovani infected macrophages

overall_design: Macrophages were infected with Leishmania donovani and treated with monastrol to look for signalling molecules

first: Jaspreet

last: Kaur


city: Toledo

first: Robert

last: Trumbly

state: OH

address: 3000 Arlington Avenue

department: Biochemistry and Cancer Biology

institute: University of Toledo

summary:
Under conditions of hormonal adjuvant treatment the estrogen receptor apoprotein supports breast cancer cell cycling through the retinoic acid receptor α1 apoprotein.
Basal proliferation persisted in estrogen-sensitive breast cancer cells grown in hormone depleted conditioned media without or with 4-hydroxytamoxifen (OH-Tam). Downregulating ER using siRNA  inhibited basal proliferation by promoting cell cycle arrest. The basal expression of RARα1, the only RARα isoform that was expressed in breast cancer cell lines and in most breast tumors, was supported by apo-ER but was unaffected by OH-Tam. The overlapping tamoxifen-insensitive gene regulation by apo-ER and apo-RARα1 comprised activation of mainly genes promoting cell cycle and mitosis and suppression of genes involved in growth inhibition.

overall_design: Cells were plated at 20% confluence in low glucose phenol red free medium supplemented with 5% charcoal stripped FBS and glutamine 24h-48h prior to transfection. Treatment with vehicle, OH-Tam (100nM), or OH-Tam (500nM) was begun an additional 24h later. Cells were transfected with control siRNA, ERα siRNA or RARα siRNA.

first: Marcela

last: d’Alincourt Salazara

first: Ratnam

last: Maya

first: Patki

last: Mugdha

first: Kisovic

last: Ivana

first: Mohamed

last: Iman

first: Manohar

last: Ratnam


title: Role of BACH1 in HEK 293T cells

city: Berlin

first: Hans-Jörg

last: Warnatz

address: Ihnestrasse 63-73

department: Vertebrate Genomics

institute: Max Planck Institute for Molecular Genetics

type: Genome binding/occupancy profiling by high throughput sequencing

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

overall_design: Refer to individual Series


title: Transcriptional and post-transcriptional regulation of VEGF by the unfolded protein response

city: Memphis

first: Geoffrey

last: Neale

state: TN

address: 262 Danny Thomas Place

department: Hartwell Center

institute: St Jude Childrens Research Hospital

summary: Inadequate extracellular conditions can adversely affect the environment of the ER and impinge on the maturation of nascent proteins.  The resultant accumulation of unfolded proteins activates a signal transduction pathway, known as the unfolded protein response, which serves primarily to protect the cell during stress and helps restore homeostasis to the ER. Microarray analysis of the unfolded protein response in a human medulloblastoma cell line treated with thapsigargin revealed that, in addition to known targets, a large number of proangiogenic factors were up-regulated.  Real-time PCR analyses confirmed that four of these factors, VEGF, FGF2, angiogenin and IL-8, were transcriptionally up-regulated in multiple cell lines by various ER stress inducers.  Our studies on VEGF regulation revealed that XBP-1(S), a UPR-inducible transcription factor, bound to two regions on the VEGF promoter, and analysis of XBP-1 null mouse embryonic fibroblasts revealed that it contributes to VEGF expression in response to ER stress.  ATF4, another UPR-inducible transcription factor, also binds to the VEGF gene, although its contribution to VEGF transcription appeared to be fairly modest.  We also found that VEGF mRNA stability is increased in response to UPR activation, via activation of the AMP and p38MAP kinases, demonstrating that increased mRNA levels occur at two regulatory points.  In keeping with the mRNA levels, we found that VEGF protein is secreted at levels as high as or higher than that achieved in response to hypoxia. Our results indicate that the UPR plays a significant role in inducing positive regulators of angiogenesis.  It also regulates VEGF expression at multiple levels and is likely to have widespread implications for promoting angiogenesis in response to normal physiological cues as well as in pathological conditions like cancer.

overall_design: We used microarrays to perform genome wide expression analysis in Daoy medulloblastoma cells to identify gene profiles that change in response to thapsigargin treatment which causes induction of the unfolded protein response.

first: Ethel

last: Pereira

last: Liao

first: Linda

last: Hendershot


title: Expression data from colon fibroblasts treated with Sonic hedgehog homolog (SHH)

city: SSF

first: Weiwei

last: Chen

address: 1st DNA Way

institute: Genentech

summary:
Canonical Hedgehog (Hh) signaling regulates the expression of genes that are critical to the patterning and development of a variety of organ systems. In adult, both ligand-dependent and ligand-independent Hh pathway activation are known to promote tumorigenesis. Recent studies have shown that in tumors promoted by Hh ligand, activation occurs within the stromal microenvironment (Yauch et al., 2009). In situ hybridization of the pathway target gene, Ptch1, shows that signaling is located at stromal perivascular fibroblast-like cells in xenograft tumor sections derived from Hh-expressing colorectal cancer cell lines.
To study the downstream genes regulated by Hh signaling, we treated a primary human colon myofibroblast, CCD-18Co, with SHH (1 ug/ml) or no treatment (control) in serum-free medium supplemented with 0.1% BSA for 72 hrs and performed microarray analysis (Affymetrix U133P) on these samples.

overall_design: Three biological replicates of SHH stimulated and three replicates of unstimulated primary colon myofibroblast cells CCD-18Co were used in the experiment to analyze their gene expression.

last: Yauch

first: Zora

last: Modrusan


title: Tissue Specific Pathways for Estrogen Regulation of Ovarian Cancer Growth and Metastasis

city: Aurora

first: Monique

last: Spillman

state: CO

address: Mail Stop B198-4, PO Box 6511

institute: University of Colorado Denver

summary: Menopausal estrogen (E2) replacement therapy increases the risk of estrogen receptor (ER)-positive epithelial ovarian cancers (EOC). Whether E2 is tumorigenic or promotes expansion of undiagnosed pre-existing disease is unknown. To determine E2 effects on tumor promotion, we developed an intraperitoneal mouse xenograft model using ZsGreen fluorescent ER- 2008 and ER+ PEO4 human EOC cells. Tumor growth was quantified by in vivo fluorescent imaging. In ER+ tumors, E2 significantly increased size, induced progesterone receptors, and promoted lymph node metastasis, confirming that ER are functional and foster aggressiveness. Laser captured human EOC cells from ER- and ER+ xenografted tumors were profiled for expression of E2-regulated genes. Three classes of E-regulated EOC genes were defined, but less than 10% were shared with E-regulated breast cancer genes. Since breast cancer selective ER modulators (SERM) are therapeutically ineffective in EOC, we suggest that our EOC-specific E-regulated genes can assist pharmacologic discovery of ovarian targeted SERM.

overall_design: 15 samples were included in this experiment with a 2x2 factorial design with 2 different cell lines (2008 and PEO4) and 2 different hormone treatments (E for Estrogen and C for Placebo Control) and 4 replicates per treatment. 1 sample was excluded (a replicate of PEO4 with C treatment) because of poor quality.

first: Nicole

last: Manning

first: Wendy

middle: W

last: Dye

first: Carol

last: Sartorius

first: Miriam

last: Post

first: Chuck

last: Harrell

first: Britta

last: Jacobsen

first: Kathryn

middle: B

last: Horwitz


title: R1 ESC

status: Public on May 07 2011

first: jiayu

last: chen

address: No1239, Siping Road

institute: Tongji University

overall_design: Gene expression profile of R1 ESC was generated by Affymetrix Mouse Gene 1.0 ST Array.  Three biological repeats were included.

first: Jiayu

first: Yawei

last: Gao

first: Shaorong


title: The Notch/Hes1 pathway sustains NF-κB activation through CYLD repression in T cell leukemia

city: New York

first: Iannis

last: Aifantis

state: NY

address: 550 First Ave

department: Pathology

institute: NYU Sch of Medicine

summary:
The NF-κB pathway is a critical regulator of the immune system and has been implicated in cellular transformation and tumorigenesis. NF-κB response is regulated by the activation state of the IκB kinase (IKK) complex and triggered by a wide spectrum of stimuli. We previously reported that NF-κB is downstream of Notch1 in T cell acute lymphoblastic leukaemia (T-ALL), however both the mechanisms involving Notch1-induced NF-κB activation and the potential importance of NF-κB in the maintenance of the disease are unknown. Here we visualize Notch-induced NF-κB activation using both human T-ALL cell lines and animal models of this type of leukemia. We show that it is not Notch1 itself but Hes1, a canonical Notch target, the responsible for sustaining IKK activation in T-ALL. Hes1 exerts its effects by a direct transcriptional repression of the deubiquitinating enzyme CYLD, a well-characterized IKK inhibitor. Consistently, CYLD expression is significantly reduced in primary T-ALL leukemias. Finally, we demonstrate that IKK complex inhibition is a promising option for the targeted therapy of T-ALL as suppression of IKK function affected both the survival of human T-ALL cells in vitro and the maintenance of the disease in vivo.
Transcriptional consequences of NF-kB inactivation in human T-ALL1 cell line

overall_design: Twenty samples were analyzed: human T-ALL, CEM, KOPT-K, DND41, HPB-ALL cells lines have been treated at 100uM for 16 hours with control peptide or IKKγ Nemo binding domain (NBD) inhibitory peptide, that specifically block the canonical NF-κB activity by disrupting the interaction of IKKγ to IKKβ and IKKα

first: Lluis

last: Espinosa

first: Severine

last: Cathelin

first: Teresa

last: D’Altri

first: Thomas

last: Trimarchi

first: Jordi

last: Guiu

first: Veronica

last: Rodilla

first: Julia

last: Inglés-Esteve

first: Josep

last: Nomdedeu

first: Beatriz

last: Bellosillo

first: Carles

last: Besses

first: Klaus

last: Rajewsky

first: Anna

last: Bigas


title: A Pathobiological Role of the Insulin Receptor in CLL.

status: Public on May 06 2011

city: Ann Arbor

first: Sami

middle: N

last: Malek

state: MI

address: 4410 Cancer Center; 1500 E Medical Center Dr

department: Internal Medicine, Hematology-Oncology

institute: University of Michigan

summary:
Purpose: The chromosomal deletion 11q affects biology and clinical outcome in CLL but del11q-deregulated genes remain incompletely characterized.
Results:  We have identified differential expression of the insulin receptor (INSR) in CLL, including high-level INSR expression in the majority of CLL with del11q.  High INSR mRNA expression in 11q CLL (~10-fold higher mean levels than other genomic categories) was confirmed by Q-PCR in 247 CLL cases. INSR protein measurements in 257 CLL cases through FACS, compared with measurements in normal CD19+ B-cells and monocytes, confirmed that a subset of CLL aberrantly expresses high INSR levels.

overall_design:
We have employed integrated genomic profiling approaches upon CLL cases with and without del11q to identify 11q-relevant genes.
Included are 10 primary human cases with del11q and 9 cases without del11q

first: Kamlai

last: Saiya-Cork

first: Roxane

middle: L

last: Collins

first: Brian

last: Parkin

first: Peter

last: Ouillette

first: Erlene

last: Kuizon

first: Lisa

last: Kujawski

first: Harry

last: Erba

first: Erica

last: Campagnaro

first: Kerby

last: Shedden

first: Mark

middle: S

last: Kaminski


title: Expression data from knockdown of BACH1 in HEK 293T cells

first: Hans-Jörg

last: Warnatz

summary: BTB and CNC homology 1 (BACH1) is a heme-binding transcription factor repressing the transcription from a subset of MAF recognition elements (MAREs) at low intracellular heme levels. Upon heme binding, BACH1 is released from the MAREs, resulting in increased expression of antioxidant response genes. To systematically address the gene regulatory networks involving BACH1, we performed knock-down of BACH1 in HEK 293T cells using three independent types of small interfering RNAs followed by transcriptome profiling using microarrays.

overall_design:
Knockdown of BACH1 in HEK 293T cells was carried out with three different types of siRNA molecules (esiRNA = e, siRNA1 SI00309876 from Qiagen = q and Stealth siRNA2 HSS100910 from Invitrogen = s), followed by RNA extraction after 24h and 72h of knockdown and hybridization on Affymetrix microarrays. For each siRNA type, we performed the experiments in triplicates, with four control replicates (mock transfections without siRNA) at 24h and three control replicates at 72h, resulting in nine samples and four controls at 24h and nine samples and three controls at 72h.
Samples at 24h of knockdown: e_1_24, e_2_24, e_3_24, q_1_24, q_2_24, q_3_24, s_1_24, s_2_24, s_3_24.
Controls at 24h: m_1_24, m_2_24, m_3_24, m_4_72.
Samples at 72h of knockdown: e_1_72, e_2_72, e_3_72, q_1_72, q_2_72, q_3_72, s_1_72, s_2_72, s_3_72.
Controls at 72h: m_1_72, m_2_72, m_3_72.

REPEATS:
biological replicate: BACH1_e_1_24, BACH1_e_2_24, BACH1_e_3_24
biological replicate: BACH1_q_1_24, BACH1_q_2_24, BACH1_q_3_24
biological replicate: BACH1_s_1_24, BACH1_s_2_24, BACH1_s_3_24
biological replicate: BACH1_m_1_24, BACH1_m_2_24, BACH1_m_3_24, BACH1_m_4_24
biological replicate: BACH1_e_1_72, BACH1_e_2_72, BACH1_e_3_72
biological replicate: BACH1_q_1_72, BACH1_q_2_72, BACH1_q_3_72
biological replicate: BACH1_s_1_72, BACH1_s_2_72, BACH1_s_3_72
biological replicate: BACH1_m_1_72, BACH1_m_2_72, BACH1_m_3_72

first: Ilaria

last: Piccini

first: Wasco

last: Wruck

first: Marie-Laure

last: Yaspo


title: Expression Data from HNF4a RNAi Knockdown in HepG2 cells

status: Public on May 05 2011

city: Riverside

first: Eugene

last: Bolotin

address: 900 university ave

department: Cell Biology and Neuroscience

institute: UC Riverside

summary: HNF4a is an important liver transcription factor that regulates at least a thousand genes in the liver. Here we used expression profiling in HepG2 cells, a hepatocellular carcinoma cell line, in which HNF4a was knocked down by RNAi to identify some of those target genes. This dataset accompanies the article in Hepatology 2010 Feb;51(2):642-53. Integrated approach for the identification of human hepatocyte nuclear factor 4alpha target genes using protein binding microarrays by Bolotin E, Liao H, Ta TC, Yang C, Hwang-Verslues W, Evans JR, Jiang T, Sladek FM.

overall_design: RNA interference (RNAi) against HNF4a2 was performed in HepG2 cells using small, interfering RNAs (siRNAs) corresponding to nucleotides +179 to +197 of human HNF4A (NM_178849, sense siRNA: 5'-UGUGCAGGUGUUGACGAUGdTdT-3', antisense siRNA 5'-CAUCGUCAACACCUGCACAdTdT-3') (Dharmacon, Lafayette, CO). Total RNA was extracted with Trizol (Life Technologies, Carlsbad, CA) and reverse transcribed with the Reverse Transcription System (Promega, Madison, WI). Polymerase chain reaction (PCR) amplification was performed in the linear range (see Supporting Table 3B for a list of PCR primers). Expression profiling analysis was performed with Affymetrix oligonucleotide arrays (HGU133 Plus 2.0) using RNA from control (PGL3 siRNA) or treated (HNF4a siRNA) HepG2 cells

first: Frances

last: Sladek


title: Neurofibromin (Nf1) is required for skeletal muscle development

first: Mateusz

last: Kolanczyk

address: Ihnestr 73

institute: Max Planck Institute

summary: Neurofibromatosis type 1 (NF1) is a multi-system disease caused by mutations in the NF1 gene encoding a Ras-GAP protein, neurofibromin, which negatively regulates Ras signalling. Besides neuroectodermal malformations and tumours, the skeletal system is often affected (e.g. scoliosis and long bone dysplasia), demonstrating the importance of neurofibromin for development and maintenance of the musculoskeletal system. Here we focus on the role of neurofibromin in skeletal muscle development. Nf1 gene inactivation in the early limb bud mesenchyme using Prx1-cre (Nf1Prx1) resulted in muscle dystrophy characterised by fibrosis, reduced number of muscle fibres, and reduced muscle force. To gain insight into the molecular changes of the observed muscle dystrophy and fibrosis and to compare these with other known muscle dystrophies, we performed transcriptional profiling of the entire triceps muscles of threemonth-old wild type (wt) and mutant animals using Affymetrix high-density microrrays.

overall_design: We analyzed triceps muscles from 4 three-month-old wt controls and 4 three-month-old Nf1Prx1 mice using the Affymetrix Mouse Gene 1.0 ST platform. Array data was processed by the Affymetrix Exon Array Computational Tool. RNA isolated from each animal was hybridized to a separate microarray.

first: Nadine

last: Kossler

first: Sigmar

last: Stricker

first: Christian

last: Rödelsperger

last: Robinson

first: Johnny

last: Kim

first: Carola

last: Dietrich

first: Monika

last: Osswald

first: Jirko

last: Kühnisch

first: David

last: Stevenson

first: Thomas

last: Braun

first: Stefan

last: Mundlos


title: Numb variant specific transcriptome analysis

status: Public on May 09 2011

city: Bethesda

first: Robert

last: Cheng

state: MD

address: 10 Center Drive

department: CCR

institute: NCI

summary:
Numb has 4 known variants and we are reporting two novel Numb variants, Numb5 and Numb6 in this study.
The metastaticability variations between the numb variants were evaulated through the transcriptome.

overall_design: breast cancer cells were transfected with GFP-Numb4, GFP-Numb5, GFP-Numb6 or GFP-only vectors and their transcriptome were assessed on Affymetrix platform

first: Aldona

last: Karaczyn

first: Joseph

last: Verdi


title: Mechanisms of urokinase plasminogen activator (uPA)-mediated atherosclerosis

status: Public on May 03 2011

city: Seattle

first: Jie Hong

last: Hu

state: WA

address: 1959 NE Pacific St, HSB K-127

institute: University of Washington

summary: Data from clinical studies, cell culture, and animal models implicate the urokinase (uPA)/Plasminogen (Plg) system in the development of atherosclerosis and aneurysms.  However, the mechanisms through which uPA/Plg stimulate these diseases are not yet defined.  We used genetically modified, atherosclerosis-prone mice, including mice with macrophage-specific uPA overexpression to clarify mechanisms of uPA/Plg-accelerated atherosclerosis and aneurysm formation.   Microarray studies were performed to identify potential mediators of uPA-accelerated atherosclerosis.  These studies identified S100A8 and S100A9 mRNA as the most highly upregulated transcripts in uPA-overexpressing macrophages; upregulation of S100A9 protein in uPA-overexpressing macrophages was confirmed by Western blotting.  S100A8/A9, which are atherogenic in mice and are expressed in human atherosclerotic plaques, are also upregulated in aortae of mice with uPA-overexpressing macrophages, and macrophage S100A9 mRNA is upregulated by exposure of wild-type macrophages to medium from uPA-overexpressing macrophages.  Bioinformatics analysis of the microarray data suggest significant effects of uPA overexpression on cell migration and cell-matrix interactions.  Our results confirm—in a second animal model—that macrophage-expressed uPA stimulates atherosclerosis and aortic dilation.  They also implicate specific pathways in uPA/Plg-accelerated atherosclerosis and aneurysmal disease.

overall_design: Six independent biological replicate RNA samples were prepared from thioglycollate-elicited peritoneal macrophages from mice of two different genotypes: SR-uPA+/0 transgenic (overexpress uPA in macrophages) and nontransgenic, respectively), for a total of 12 independent RNA samples.  Both transgenic and nontransgenic mice were Apoe-/- and were fed Western diet from 5-15 weeks before peritoneal macrophages were elicited.  In addition, from the six samples of each genotype, a pooled sample was prepared by combining the six genotype-specific samples.  Each of the two pooled samples was assayed on the BeadChip in two technical replicates, for a total of 16 hybridizations performed using two Illumina Mouse Ref-8 v1.1 chips.

first: Stephen

last: Farris

first: Jie

middle: H

first: Ranjini

last: Krishnan

first: Isaac

last: Emery

first: Talyn

last: Chu

first: Liang

last: Du

first: Michael

last: Kremen

first: Helén

last: Dichek

first: Elizabeth

last: Gold

last: Ramsey

first: Lynn

last: Amon


title: Characterisation of Myocardial Infarction and Unstable Angina with mRNA Profiles from Whole Blood of individual patients

city: Sheffield

first: Marta

last: Milo

state: South Yorkshire

address: Western Bank

department: Biomedical Science

institute: University of Sheffield

summary:
Coronary artery disease (CAD) remains a leading cause of death worldwide. Acute coronary syndromes (ACS) are the spectrum of diseases arising from coronary atherosclerotic plaque rupture, ranging from unstable angina (UA; clinical symptoms of cardiac ischemia without myocardial necrosis) to myocardial infarction (MI; clinical symptoms of cardiac ischemia with myocardial necrosis).
We use microrray to identify changes in pathways following MI.This study examines mRNA expression levels in human whole blood at 7 and 30 days post ACS. Patients with MI are compared to those with UA (not healthy controls), thus focusing on differences in mRNA expression due to the acute clinical events rather than underlying atherosclerosis and its treatment.

overall_design:
We recruited 26 patients presenting with acute coronary syndromes (ACS); 8 with unstable angina (UA) and 18 with MI.

Supplementary files:
The files contain the combined values (for each group) of the single patients' expression levels, the fold changes and the significance levels associated. Gene expression levels were estimated using probabilistic models implemented in puma (Propagating Uncertainty in Microarray Analysis, bioconductor.org), which provide estimates for the variance and credibility interval for probe level errors of each transcript. FCs were calculated after combining gene expression values within groups using Bayesian hierarchical model, incorporating probe level errors into the variance estimate. Significance levels for differentially expressed genes were detected by calculating the probability of positive log ratio (PPLR). The higher is the probability the more confident is the estimate of that positive FC, conversely the lower is the probability the more confident is the estimate of that FC to be negative. This model was implemented in the pumaComb and pumaDE modules within puma.
file1 = mRNA_MI_combday30_exprs
file2 = mRNA_MI_combDay7_exprs

first: Alex

middle: M

last: Rothman


title: Expression data from MCF7 cell line after silencing of Estrogen receptor

status: Public on May 01 2011

city: Kuwait

first: fahd

last: Al-Mulla

address: Faculty of medicine

country: Kuwait

institute: Kuwait University

summary:
We propose the hypothesis that loss of estrogen receptor function which leads to endocrine resistance in breast cancer, also results in de-differentiation from an epithelial to a mesenchymal phenotype that is responsible for increased aggressiveness and metastatic propensity. siRNA mediated silencing of the estrogen receptor in MCF7 breast cancer cells resulted in estrogen/tamoxifen resistant cells (pII) with altered morphology, increased motility with rearrangement and switch from an actin to a vimentin based cytoskeleton, and ability to invade simulated components of the extracellular matrix. Phenotypic profiling using an Affymetrix Human Genome U133 plus 2.0 GeneChip indicated fold changes ≥ 3 in approximately 2500 identifiable unique sequences, with about 1270 of these being up-regulated in pII cells. Changes were associated with genes whose products are involved in cell motility, loss of cellular adhesion and interaction with the extracellular matrix. Selective analysis of the data also showed a shift from luminal to basal cell markers and increased expression of a wide spectrum of genes normally associated with mesenchymal characteristics, with consequent loss of epithelial specific markers. Over-expression of several peptide growth factors and their receptors are indicative of an increased contribution to the higher proliferative rates of pII cells as well as aiding their potential for metastatic activity. Signalling molecules that have been identified as key transcriptional drivers of epithelial to mesenchymal transition were also found to be elevated in pII cells. We suggest that these data support our hypothesis that induced loss of estrogen receptor in previously antiestrogen sensitive cells is a trigger for the concomitant loss of endocrine dependence and onset of a series of possibly parallel events that changes the cell from an epithelial to a mesenchymal type. Inhibition of this transition through targeting of specific mediators may be a useful supplementary strategy to circumvent the effects of loss of endocrine sensitivity.
We used microarrays to detail the global programme of gene expression underlying Epithelial to mesenchymal transition and identified distinct classes of regulated genes during this process.

overall_design: MCF7 cell line was selected before and after (PII) silencing of Estrogen receptor for RNA extraction and hybridization on Affymetrix expression microarrays.

first: Fahd

first: Yunus

last: Lugmani


title: Liver gene expression in animals with hepatocyte-specific deletion of JAK2

city: San Francisco

first: Ethan

middle: J

last: Weiss

address: 555 Mission Bay Blvd South, Rm 382

department: CVRI

institute: UCSF

summary: Growth hormone signaling in hepatocytes is fundamentally important. Disruptions in this pathway have led to fatty liver and other metabolic abnormalities. Growth hormone signals through the JAK2/STAT5 pathway. Mice with hepatocyte specific deletion of STAT5 were previously shown to develop fatty liver. Our aim in this study was to determine the effect of deleting JAK2 in hepatocytes on liver gene expression. To do so, we generated animals with hepatocyte specific deletion of JAK2.

overall_design: Hepatocyte-specific JAK2-deficient mice (JAK2L) were generated by mating floxed JAK2 mice (in a mixed (C57Bl/6:129Sv) background) to mice carrying an Alb promoter-regulated Cre transgene on a 100% C57Bl/6 background purchased from the Jackson Labs. Livers were harvested from 8 week old animals for RNA extraction and hybridization.


title: IL-4 mediated gene expression profiles in vascular endothelial cells

city: Tokyo

first: Yasuharu

last: Kanki

address: 4-6-1 Komaba, Meguro-ku

institute: The University of Tokyo

summary: Endothelial cell activation and dysfunction underlie many vascular disorders, including atherosclerosis and inflammation. Here, we show that interleukin (IL)-4 markedly induced vascular cell adhesion molecule (VCAM)-1, both in cultured endothelial cells and in the intact endothelium in mice. Combined treatment with IL-4 and tumor necrosis factor (TNF)- alpha resulted in further, sustained induction of VCAM-1 expression. IL-4-mediated induction of VCAM-1 and secondary monocyte adhesion was predominantly regulated by the transcription factor, STAT6. Genome-wide survey of IL-4-mediated STAT6 binding from sequential chromatin-immunoprecipitation with deep-sequencing (ChIP-seq) in endothelial cells revealed regions of transient and sustained transcription factor binding. By combining DNA microarrays and ChIP-seq at the same time points, the majority of IL-4-responsive genes were shown to be STAT6-dependent and associated with direct STAT6 binding to their promoter. IL-4-mediated stable binding of STAT6 led to sustained target gene expression. Moreover, our strategy led to the identification of a novel functionally important STAT6 binding site within -16 kb upstream of the VCAM-1 gene. Taken together, these findings support a critical role for STAT6 in mediating IL-4 signal transduction in endothelial cells. Identification of a novel IL-4-mediated VCAM-1 enhancer may provide a foundation for targeted therapy in vascular disease (ChIP-seq data not submitted to GEO).

overall_design: Total 13 samples were derived from [1] HUVEC treated in the absence (0h) or presence of IL-4 (1,2,4,8, and 16h) to determine IL-4 regulated gene in endotherial cells, [2] control-siRNA or si-STAT6 transfected HUVEC cells treated in the absence or presenceof IL-4 [3] Ad-control or Ad-CA-STAT6 transfected HUVEC cells for the identification of STAT-6 dependent genes in endothelial cells.

first: Hideto

last: Tozawa

first: Jun-ichi

last: Suehiro

first: Shuichi

last: Tsutsumi

first: Takahide

last: Kohro

first: Hiroyuki

last: Aburatani

first: Tatsuhiko

last: Kodama

first: Takashi

last: Minami


title: Expression data from CD11cHI and CD11cLO decidual macrophage populations.

city: Cambridge

first: Brandy

middle: Lynn

last: Houser

address: 52 Oxford St.

department: Stem Cell and Regenerative Biology

institute: Harvard University

summary:
Decidual macrophage populations, CD11cHI and CD11cLO cells were analyzed for expression profiles and unique characteristics.
We used microarrays to detail the global program of gene expression and to determine differences between these two unique decidual macrophage populations.

overall_design: First trimester decidual tissue was digested in order to release immune cells.  Cells were stained for CD14 and CD11c and purified by MoFlo sorting.  Cells were immediately lysed for RNA extraction and hybridization on Affymetrix microarrays. We utilized 8 patient paired samples (total of 16 microarrays).

first: Jonathan

last: Hill

first: Tamara

last: Tilburgs

first: Matthew

last: Nicotra

first: Jack

last: Strominger


title: CREB3L1 Target Genes in Response to Hepatitis C Replicon Infection

city: Dallas

first: Bray

last: Denard

state: TX

address: 5323 Harry Hines Blvd. L5.226

department: Molecular Genetics

institute: University of Texas Southwestern Medical Center

summary:
Membrane-bound transcription factor CREB3L1 undergoes Regulated Intramembrane Proteolysis (RIP) in response to Hepatitis C infection.  RIP activates CREB3L1 so that it can prevent the growth of HCV infected cells through the action of downstream genes.  We over-expressed a truncated form of CREB3L1 that does not require RIP to enter the nucleus.  Cells over-expressing this truncated form were isolated by Fluorescence Activated Cell Sorting (FACS).
We used microarray to determine the downstream genes of CREB3L1 in comparison to a flow sorted empty vector control.

overall_design: HCV Replicon-containing cells were transfected with a CREB3L1Δ381-519 to determine the downstream genes.

first: Jin

last: Ye


title: Host Factors with Reduced Expression in Two HCV Permissive Cell Lines as Compared to the Non-Permissive Parent Cell Line Huh7

summary:
Drugs directly targeting Hepatitis C (HCV) are often rendered useless by the high mutation rate of the virus. Thus, we deduce that targeting of host factor that affect HCV replication may provide enhanced therapy fort HCV infection. Hepatocyte cell line Huh7 is known to be non-permissive for Hepatits C (HCV) replication.  Through a method developed by the Rice laboratory (Blight, K.J.,  et al., J Virol, 2002), selection of a small subset of permissive hepatocytes is possible. The Rice laboratory generated the first permissive cell line, Huh7.5, using this method. We generated another permissive cell line, HRP1, using the same method.
With microarray, we compared the expression of host mRNAs in non-permissive Huh7 to both Huh7.5 and HRP1 searching for host factors lost in the cell lines permisive for HCV replication.

overall_design: Non-permissive cell line Huh7 and permissive cell lines Huh7.5 and HRP1 were harvested for RNA extraction and hybridization on Affymetrix microarrays.

first: Quiyue

last: Chen

first: Saada

last: Abdalla


title: Xenograft model systems of adenoid cystic carcinoma

city: Charlottesville

first: Alexander

last: Baras

state: Virginia

address: 3024 University Hospital, PO Box 800214

institute: University of Virginia

summary: Adenoid cystic carcinoma (ACC) is one of the most common malignancies that arise in the salivary glands, with an incidence of 4.5 per 1,000,000. It can also arise in glandular tissue closely related to salivary glands in the lacrimal gland, nasal passages and tracheobronchial tree, as well as in glands of the breast and vulva. At all of these sites, it is characterized by a distinctive histology of basaloid epithelial cells arranged in cribriform or tubular patterns, usually demonstrating abundant hyaline extracellular matrix secretion and some degree of myoepithelial differentiation. ACC is generally a slow-growing tumor characterized by a protracted clinical course, usually well over 5 years in duration, marked by regional recurrence, distant metastasis and/or spread along peripheral nerves. A recurrent chromosomal translocation, t(6;9)(q23;p21), has been identified in ACC, and recently it has been discovered that in a majority of ACC the MYB gene on chromosome 6 is fused to the 3’ terminus of the NFIB gene on chromosome 9, creating a fusion gene product resulting in increased MYB-related transcriptional activation.    Recently it has been determined that most cell lines with attribution of ACC derivation are either contaminants of other cell lines or do not have the characteristic MYB-NFIB translocation. Also, there are no animal models of this histologically and genetically defined tumor type. To address the paucity of experimental and pre-clinical models systems of ACC, we have for several years been establishing xenograft tumor lines from clinical samples of ACC. We describe our experience with these models and their characterization here.

overall_design: Analysis of 12 xenografts of human adenoid cystic carcinoma (ACC) along with 10 samples of ACC directly from humans. Note, that 12 of these samples are paired primary ACC & xenograft ACC  from the same individual (6 pairs in total).

first: Christopher

last: Moskaluk


title: Endogenous Muscle Atrophy F-box Regulates Pressure Overload-Induced Cardiac Hypertrophy

city: Seoul

first: Jiyeon

last: Park

address: 222, Banpo-daero

department: Catholic Center for Precision Medicine Research

country: South Korea

institute: The Catholic University of Korea

summary: Muscle atrophy F-box (MAFbx) is an E3 ubiquitin ligase which plays a critical role in mediating skeletal muscle atrophy. We investigated the effect of MAFbx KO in cardiac hypertrophy in response to pressure overload. A DNA microarray analysis was conducted using total RNA prepared from wild type and MAFbx KO mouse hearts subject to transverse aortic constriction (TAC). Results provide insight into the molecular mechanism to mediate the effect of MAFbx upon pathological hypertrophy.

overall_design: We applied TAC to wild type and MAFbx KO mice, and extracted total RNA one week after the surgery. The gene expression profiles were examined by Affymetrix Mouse Gene ST Array.

first: Soichiro

last: Usui

first: Yasuhiro

last: Maejima

first: Jayashree

last: Pain

first: Chull

last: Hong

first: Jaeyeoan

last: Cho

first: Daniela

last: Zablocki

first: Bin

last: Tian

first: David

last: Glass

first: Junichi

last: Sadoshima


title: Expression data from non-malignant fallopian tube epithelium

status: Public on Apr 28 2011

city: Toronto

first: carl

last: virtanen

state: Ontario

address: 101 College St

department: Princess Margaret Genomics Centre

institute: University Health Network

summary: Microarrays were used to examine gene expression changes that may be present in the fallopian tube epithelium of morphologically normal BRCA1 mutation positive and negative subjects. Fallopian tube epithelia has been implicated as an early point of origin for serous carcninoma. By examining the early events present in the microenvironment of this tissue between BRCA1 mutation carriers and non-carriers, we hoped to elucidate mechanisms that may lead to the development of epithelial ovarian cancer.

overall_design: Laser microcapture of samples from 12 BRCA1 mutation carriers and 12 non-mutation subjects was performed. Samples were further grouped according to menstrual cycle.

first: Carl

last: Virtanen

first: Sophia

last: George

first: Patricia

last: Shaw


title: Gene Expression in early and advanced atherosclerotic plaque from human carotid

status: Public on Apr 25 2011

city: Maastricht

first: Marco

last: Manca

state: Limburg

address: P. Debyelaan 25

department: CARIM

country: Netherlands

institute: University of Maastricht

summary: The objective of this study is to identify genes and pathways involved in the progression of atherosclerotic plaques from early to advanced stage in humans.

overall_design:
Samples from atherosclerotic carotid artery segments, from early ((pathological) intimal thickening and intimal xanthoma) and from advanced (thin or thick fibrous cap atheroma) lesions, have been retrieved from the Maastricht Pathology Tissue Collection (MPTC).
Tissue was obtained during autopsy (Dept of Pathology, Maastricht University Medical Centre). Collection, storage  in the Maastricht Pathology Tissue Collection (MPTC) and use of tissue and patient data were performed in agreement with the "Code for Proper Secondary Use of Human Tissue"

first: Erik

last: Biessen

first: Mat

last: Daemen


title: Human Skin Transcriptome during Epidermal Wound Healing

status: Public on Apr 29 2011

city: Helsinki

first: Kristo

middle: Juhana

last: Nuutila

address: Haartmaninkatu 8, Biomedicum 1

department: Institute of Biomedicine

country: Finland

institute: University of Helsinki

summary: In order to clarify the human response of re-epithelialization, we biopsied split-thickness skin graft donor site wounds immediately before and after harvesting, as well as during the healing process 3 and 7 days thereafter. Altogether 25 biopsies from 8 patients qualified for the study. All samples were analysed by genome-wide microarrays. Here we identified the genes associated with normal skin re-epithelialization on time-scale, and organized them by similarities according to their induction or suppression patterns during wound healing.

overall_design: Overall 25 samples were analyzed

first: Antti

last: Siltanen

first: Matti

last: Peura

first: Jozef

last: Bizik

first: Ilkka

last: Kaartinen

first: Hannu

last: Kuokkanen

first: Tapio

last: Nieminen

first: Ari

last: Harjula

first: Pertti

last: Aarnio

first: Jyrki

last: Vuola

first: Esko

last: Kankuri


title: mRNA expression data from human adenocarcinomas of the stomach

city: Berlin

first: Susann

last: Förster

address: R. Rössle Str 10

institute: MDC

summary:
Gastric cancer can be divided in two major histological subtypes: diffuse and intestinal-type adenocarcinomas. Since both types diverge in many clinical and molecular characteristics, is widely accepted that both represent distinct disease entities that may benefit from different therapeutic approaches. The diffuse type is explicitly more invasive and affected patients possess extremely poor prognosis. Gene expression profiling studies identified numerous genes with differences in mRNA expression between the two types. However, little overlap of published gene lists exists forcing the need for further and more comprehensive analyses.
We used microarray-based whole-transcriptome expression profiling to characterize the gene expression profile of both histologiocal types and to identify differentially expressed genes.

overall_design: Tumor tissue samples were controlled for tumor contents higher than 75% and pathologically evaluated by two independent blinded pathologist. Total RNA was extracted and controlled for high quality (Agilent Bioanalyzer RIN above 7). Messenger RNA population was labelled and hybrizied on Affymetrix microarrays. The obtained gene expression data was bioinformatically and statistically analyzed with the goal to identify differentially expressed genes.

first: Wolfgang

last: Kemmner


title: Gene expression profiles of pretreatment biopsies from dose-dense-docetaxel-treated breast cancers

status: Public on Apr 22 2011

city: Nashville

first: Jennifer

last: Pietenpol

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

institute: Vanderbilt University Medical Center

summary: The purpose of this study was to identify molecular markers of pathologic response to neoadjuvant dose-dense docetaxel treatment using gene expression profiling on pretreatment biopsies.  Patients with high-risk, operable breast cancer were treated with 75 mg/m2 IV of docetaxel on day 1 of each cycle every 2 weeks x 4 cycles . Tumor tissue from pretreatment biopsies was obtained from 12 patients enrolled in the study. Gene expression profiling were done on serial sections of the biopsies from patients that achieved a pathologic complete response (pCR) and compared to those with residual disease, non-pCR (NR).

overall_design: Tumor tissues from pretreatment needle biopsies from patients enrolled in a dose-dense docetaxel clinical trial were laser capture microdissected for RNA extraction and hybridization to Affymetrix microarrays. We analyzed one array (sample A) from duplicate samples from each patient.

first: Joshua

last: Bauer


title: Smoking-induced Wnt pathway downregulation

status: Public on Apr 20 2011

city: New York

first: Yael

last: Strulovici-Barel

address: 1300 York Avenue

department: Department of Genetic Medicine

institute: Weill Cornell Medical College

summary: The Wnt pathway plays a central role in controlling differentiation of epithelial tissues; when Wnt is on, differentiation is suppressed, but when Wnt is off, differentiation is allowed to proceed. Based on this concept, we hypothesized that expression of key genes in the Wnt pathway are suppressed in the human airway epithelium under the stress of cigarette smoking, a stress associated with dysregulation of the differentiated state of the airway epithelium. For this purpose, HG-U133 Plus 2.0 microarrays were used to assess the expression of Wnt-related genes in the small airway (10th-12th generation) epithelium (SAE) obtained via bronchoscopy and brushing of healthy nonsmokers (n=47), healthy smokers (n=58), and smokers with established COPD (n=22). With expression defined as present in >20% of samples, microarray analysis demonstrated that 35 of 57 known Wnt-related genes are expressed in the adult SAE. Wnt pathway downstream targets β-catenin (p<0.05) and the transcription factor 7-like 1 were down-regulated in healthy smokers, and smokers with COPD, as were a number of Wnt target genes, including VEGFA, CCND1, MMP7, CLDN1, SOX9, RHOU (all p<0.05 compared to healthy nonsmokers). As a mechanism to explain this broad, smoking-induced suppression of the Wnt pathway, we assessed expression of the DKK and SFRP families, extracellular regulators that suppress the Wnt pathway. Among these, secreted frizzled-related protein 2 (SFRP2), was up-regulated 4.3-fold (p<0.0001) in healthy smokers and 4.9-fold (p<0.0001) in COPD smokers, an observation confirmed by TaqMan Real-time PCR. AT the protein levels, Western analysis demonstrated SFRP2 up-regulation, and immunohistochemistry demonstrated that the smoking-induced SFRP2 upregulation occurred in differentiated ciliated cells. Finally, cigarette smoke extract mediated up-regulation of SFRP2 and downregulation of Wnt target genes in airway epithelial cells in vitro. These observations are consistent with the hypothesis that the Wnt pathway plays a role in airway epithelial cell differentiation in the adult human airway epithelium, with smoking associated with down-regulation of Wnt pathway, contributing to the dysregulation of airway epithelial differentiation observed in the smoking-related airway disorders.

overall_design: Affymetrix arrays were used to assess gene expression data of genes in the Wnt pathway in small airway epithelium obtained by fiberoptic bronchoscopy of 47 healthy non-smokers and 58 healthy smokers and 22 smokers with COPD.

first: Rui

last: Wang

first: Guoqing

first: Ibrahim

last: Hassan

first: Neil

middle: R

last: Hackett

first: Ronald

last: Crystal


title: Isolation and characterization of stem-like cells from a human ovarian cancer cell line

status: Public on Apr 23 2011

city: Atlanta

first: Roman

middle: F. N.

last: Mezencev

state: GA

address: 310 Ferst Dr

department: School of Biology

institute: Georgia Institute of Technology

summary: Increasing evidence supports the existence of a subpopulation of cancer cells capable of self-renewal and differentiation into diverse cell lineages. These cancer stem-like or cancer-initiating cells (CICs) also demonstrate resistance to chemo- and radiotherapy and may function as a primary source of cancer recurrence. We report here on the isolation and in vitro propagation of multicellular ovarian cancer spheroids from a well-established ovarian cancer cell line (OVCAR-3). The spheroid-derived cells (SDCs) display self-renewal potential, the ability to produce differentiated progeny, and increased expression of genes previously associated with CICs. SDCs also demonstrate higher invasiveness, migration potential, and enhanced resistance to standard anticancer agents relative to parental OVCAR-3 cells. Furthermore, SDCs display up-regulation of genes associated with epithelial-to-mesenchymal transition (EMT), anticancer drug resistance and/or decreased susceptibility to apoptosis, as well as, down-regulation of genes typically associated with the epithelial cell phenotype and pro-apoptotic genes. Pathway and biological process enrichment analyses indicate significant differences between the SDCs and precursor OVCAR-3 cells in TGF-beta-dependent induction of EMT, regulation of lipid metabolism, NOTCH and Hedgehog signaling. Collectively, our results indicate that these SDCs will be a useful model for the study of ovarian CICs and for the development of novel CIC-targeted therapies.

overall_design: Dataset includes 3 replicate cultures of parental OVCAR-3 cells and 3 replicate cultures of stem cell-like spheroid-derived cells

first: Lijuan

first: Nathan

last: Bowen

first: Lilia

middle: V

last: Matyunina

first: John

middle: F

last: McDonald


title: Gene expression profiling of epithelial and mesenchymal subpopulations within immortalized human mammary epithelial cells

status: Public on Apr 19 2011

first: Christina

last: Scheel

state: MA

address: 9 Cambridge Center

institute: Whitehead Institute for Biomedical Research

summary:
For gene expression profiling, we used immortalized human mammary epithelial cells (HMLE) to isolate a pure epithelial fraction of cells by positive selection for CD24 expression using Magnetic Activated Cell Sorting (=24hi).
We independently isolated 3 mesenchymal subpopulations (msp1-3) from HMLE cells by collecting floating cells from cultured monolayer HMLE cells.

overall_design: See summary


title: Assessment of genotoxic effects and changes in gene expression in humans exposed to formaldehyde by inhalation under controlled conditions

status: Public on May 04 2011

city: Ulm

first: Karlheinz

last: Holzmann

address: Helmholtzstreet 8/1

department: Medical Faculty

institute: Ulm University

summary: 41 volunteers (male non-smokers) were exposed to formaldehyde (FA) vapors for 4 h per day over a period of 5 working days under strictly controlled conditions. For each exposure day, different exposure concentrations were used in a random order ranging from 0 up to 0.7 ppm. At concentrations of 0.3 ppm and 0.4 ppm, four peaks of 0.6 or 0.8 ppm for 15 min each were applied. During exposure, subjects had to perform bicycle exercises (about 80 W) four  times for 15 min. Blood samples, exfoliated nasal mucosa cells and nasal biopsies were taken before the first and after the last exposure. Nasal epithelial cells were additionally sampled 1, 2 and 3 weeks after the end of the exposure period. The alkaline comet assay, the sister chromatid exchange (SCE) test and the cytokinesis-block micronucleus test (CBMNT) were performed with blood samples. The micronucleus test (MNT) was also performed with exfoliated nasal mucosa cells. The expression (mRNA level) of the GSH-dependent formaldehyde dehydrogenase (FDH, identical to alcohol dehydrogenase 5; ADH5; EC 1.2.1.46) was measured in blood samples by quantitative real-time RT-PCR with TaqMan probes. DNA microarray analyses using a full-genome human microarray were performed on blood samples and nasal biopsies of selected subgroups with the highest FA exposure at different days. None of the tests performed showed a biologically significant effect related to FA exposure. Under the experimental conditions of this study, inhalation of FA did not lead to genotoxic effects in peripheral blood cells and nasal mucosa and had no effect on the expression of the FDH gene. Inhalation of FA also did not cause biologically relevant alterations in the expression of genes in a microarray analysis with nasal biopsies and peripheral blood cells.

overall_design: Gene expression analysis of nasal biopsies and blood samples before and after inhalation of 0.7ppm formaldehyde (0 h, 24 h, or 72 h before sampling), and of blood cells before and after exposure to 200µM formaldehyde for 4 hours.

first: Jasmin

last: Zeller

first: Simone

last: Neuss

first: Joerg

middle: U

last: Mueller

first: Stefanie

last: Kühner

first: Josef

last: Högel

first: Christoph

last: Klingmann

first: Thomas

last: Bruckner

first: Gerhard

last: Triebig

first: Günter

last: Speit


title: Expression data from human PBMC induced by PCB 153

city: Washington DC

first: Sisir

middle: K.

last: Dutta

state: DC

address: 415 College Street, NW

department: Biology

institute: Howard University

summary:
Exposure to Polychlorobiphenyls (PCBs) is known to cause serious health effects in human but the gene expression profiles leading to development of differnet diseases and disorders are not fully understood. The knowledge of global gene expression will help us to devlop early disease or disorder biomarkers for PCB induced health effects.
We used microarrays to detail the global gene expression profile underlying the effects of PCB 153 exposure to human PBMC leading to identification of distinct classes of up-regulated and down-regulated genes and cellular processes.

overall_design: PBMC cells are grown for 48 hours in RPMI 1640 supplemented with 10% FBS and 1X Pennicilllin-Streptromycin with 1.25 mircogram/ml PHA-M and 0.15% (v/v)pokeweed mitogen and 50 microgram Beta-mercaptoethanol.Trizol extraction of total RNA was performed according to the manufacturer's instructions. Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 6 microgram of total RNA (Expression Analysis Technical Manual, 2001, Affymetrix). Following fragmentation, 10 microgram of cRNA were hybridized for 16 hr at 45C on GeneChip Human Genome Array (HGU133 plus 2.0). GeneChips were washed and stained in the Affymetrix Fluidics Station 450 and scanned using the Affymetrix GeneArray Scanner 3000. The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings and global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 150.

middle: K

first: Eric

middle: P

last: Hoffman

first: Somiranjan

last: Ghosh

first: Partha

last: Mitra

first: Shizhu

last: Zang


title: NKT, CD1d-aGC+ Va24-, and CD4 T cell clones from human peripheral blood

city: Chicago

first: Albert

last: Bendelac

state: IL

address: 929 East 57th Street, GCIS W506

institute: The University of Chicago

summary: Microarray analysis was performed to determine the transcriptional profiles of NKT, CD1d-aGC+ Va24-, and CD4 T cells.

overall_design: Clones of NKT, CD1d-aGC+ Va24-, and CD4 T cells were generated using peripheral blood drawn from two healthy individuals.  RNA was extracted from cells that had been either rested (18 days post-stimulation) or stimulated (3 days post-stimulation).

first: Michael

middle: G

last: Constantinides

first: Damien

last: Picard


title: Laser-capture microdissected invasive micropapillary carcinomas of the breast

first: Melinda

middle: E

last: Sanders

address: 23rd Ave. S. at Pierce Ave.

institute: Vanderbilt University

summary: The purpose of this study was to identify differentially expressed genes in laser-capture microdissected (LCM) invasive mammary carcinomas (IMCs).

overall_design: Invasive mammary carcinoma of the breast surgical resection specimens were laser capture microdissected for RNA extraction and hybridization to Affymetrix microarrays.


title: Functional analysis of HOXD9 in human gliomas and glioma cancer stem cells

status: Public on Apr 16 2011

city: Shinjuku-ku

first: Masanao

last: Tabuse

state: Tokyo

address: 35 Shinanomachi

institute: Keio University School of Medicine

summary: HOX genes encode a family of homeodomain-containing transcription factors involved in the determination of cell fate and identity during embryonic development. They also behave as oncogenes in some malignancies. In this study, we found high expression of the HOXD9 gene transcript in glioma cell lines and human glioma tissues by quantitative real-time PCR. Using immunocytochemistry, we observed HOXD9 protein expression in human brain tumor tissues, including astrocytomas and glioblastomas. To investigate the role of HOXD9 in gliomas, we silenced its expression in the glioma cell line U87 using HOXD9-specific siRNA, and observed decreased cell proliferation, cell cycle arrest, and induction of apoptosis. It was suggested that HOXD9 contributes to both cell proliferation and/or cell survival. The HOXD9 gene was highly expressed in a side population (SP) of SK-MG-1 cells that was previously identified as an enriched-cell fraction of glioma cancer stem-like cells. HOXD9 siRNA treatment of SK-MG-1 SP cells resulted in reduced cell proliferation. Finally, we cultured human glioma cancer stem cells (GCSCs) from patient specimens found with high expression of HOXD9 in GCSCs compared with normal astrocyte cells and neural stem/progenitor cells (NSPCs). Our results suggest that HOXD9 may be a novel marker of GCSCs and cell proliferation and/or survival factor in gliomas and glioma cancer stem-like cells, and a potential therapeutic target.

overall_design: we analyzed the expression and function of HOXD9 in human gliomas and found high expression of HOXD9 in GCSCs. HOXD9 contributes to cell proliferation and/or survival in glioma cells and glioma cancer stem-like cells.

first: Shigeki

last: Ohta

first: Yohei

last: Ohashi

first: Raita

last: Fukaya

first: Aya

last: Misawa

first: Kazunari

last: Yoshida

first: Takeshi

last: Kawase

first: Hideyuki

last: Saya

first: Cécile

last: Thirant

first: Hérve

last: Chneiweiss

first: Yumi

last: Matsuzaki

last: Okano

first: Yutaka

last: Kawakami

first: Masahiro

last: Toda


title: Genome-wide CTCF binding maps in mouse ES and fibroblast cells

status: Public on Apr 15 2011

city: Barcelona

first: David

last: Martin

address: C/ Dr. Aiguader, 88

department: Bioinformatics and Genomics

country: Spain

institute: CRG

summary: Chromatin immunoprecipitation against CTCF followed by Illumina High-throughput sequencing.

overall_design: Examination of CTCF binding in embryonic stem cells and embryonic fibroblasts

first: Cristina

last: Pantoja

first: Manuel

last: Serrano

first: MarÃa

middle: A

last: Blasco


title: Systems biology of interstitial lung diseases

city: Seattle

first: Ji-Hoon

last: Cho

address: 401 Terry Avenue North

institute: Institute for Systems Biology

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

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

overall_design: Refer to individual Series


title: Expression data of reprogrammed miR-302/367-iPS cells

city: Philadelphia

first: Frederick

last: Anokye-Danso

state: Pa

address: 421 Curie Blvd Room 938

department: Medicine

institute: University of Pennsylvania

summary: Pluripotent marker correlation between miR-302/367-iPS, ES and fibroblast cells

overall_design: Mouse fibroblast were reprogrammed with miR-302/367 lentiviral vector, total RNA was extracted by trizol and microarray assay was performed

first: Edward

last: Morrisey


title: Expression data from human PBMC induced by PCB 138.

first: Sisir

last: Dutta

summary:
Exposure to Polychlorobiphenyls (PCBs) is known to cause serious health effects in human but the gene expression profiles leading to development of differnet diseases and disorders are not fully understood. The knowledge of global gene expression will help us to devlop early disease or disorder biomarkers for PCB induced health effects.
We used microarrays to detail the global gene expression profile underlying the effects of PCB 138 exposure to human PBMC leading to identification of distinct classes of up-regulated and down-regulated genes and cellular processes.

Keywords: PCB 138 Exposures

first: Eric

last: Hoffman

first: Somiranjan

last: Ghosh

first: Shizhu

last: Zang

first: Partha

middle: S

last: Mitra