title: Transcriptional profiling of a novel pro-angiogenic small molecule phthalimide neovascular factor 1 (PNF1)

city: Charlottesville

first: Erwin

last: Gianchandani

state: VA

department: Office of the Vice President for Research

institute: University of Virginia

summary: We generated the transcriptional regulatory footprint of phthalimide neovascular factor 1 (PNF1)—a novel synthetic small molecule that exhibits significant in vitro endothelial potency and significant in vivo microvascular network expansion—by performing comparative microarray analysis on PNF1-stimulated (versus control) human microvascular endothelial cells (HMVEC) spanning 1-48 h post-supplementation.  We subsequently applied network analysis tools (including substantial libraries of information regarding known associations among network components) to elucidate key signaling components and pathways involved in the PNF1 mechanism-of-action.  We identified that PNF1 first induces function of the tumor necrosis factor-alpha (TNF-α) signaling pathway, which in turn affects transforming growth factor-beta (TGF-β) signaling.

overall_design: HMVEC (Cambrex, Walkersville, MD, USA) were cultured in endothelial growth medium 2-microvascular (bulletkit, BioWhittaker, Walkersville, MD, USA) supplemented as directed with 5% fetal bovine serum. The cells (passage 9) were plated at 2.5 x 104 cells/cm2 at 37 degrees Celsius in a humidified chamber with 5% carbon dioxide. They were grown to confluence. After confluence, medium was refreshed, and 30 µM PNF1 or 0.6% dimethyl sulfoxide (DMSO) vehicle control was added to the sample. Total RNA from the PNF1 (n=1 at each timepoint) and control (n=1 at each timepoint) samples was isolated 1, 2, 4, 8, 16, 24 and 48 h post-supplementation using an RNeasy kit (Qiagen, Inc., Valencia, CA, USA) according to the manufacturer's protocol.

first: Kristen

last: Wieghaus

first: Mikell

last: Paige

first: Milton

last: Brown

first: Jason

last: Papin

first: Edward

last: Botchwey


title: Gene expression profiling of 35 AML FAB-M0 samples

status: Public on Jul 14 2009

city: Rotterdam

first: Peter

last: Valk

address: Postbus 2040

department: Hematology

country: Netherlands

institute: ErasmusMC

summary: Ficolled AML-M0 sample gene expression profiles on Affymetrix HGU133Plus2.0 GeneChips. Acute myeloid leukemia (AML) classified as FAB-M0 is defined as a subtype with minimally differentiated morphology. Here we investigated by gene expression (GEP) profiling whether AML-M0 cases should be considered as one or more unique molecular subgroups that discriminates them from other AML patients. By applying GEP and subsequent unsupervised analysis of 35 AML-M0 samples and 253 previously reported AML cases, we demonstrate that AML-M0 cases express a unique signature. Hematological transcription regulators such as CEBPA, CEBPD, PU.1 and ETV6 and the differentiation associated gene MPO appeared strongly down-regulated, in line with the very primitive state of this type of leukemia. Moreover, AML M0 cases appeared to have a strong positive correlation with a previously defined immature AML subgroup with adverse prognosis.  AML-M0 leukemias frequently carry loss-of-function RUNX-1 mutation and unsupervised analyses revealed a striking distinction between cases with and without mutations. RUNX1 mutant AML-M0 samples showed a distinct up-regulation of B-cell-related genes, e.g. members of the B-cell receptor complex, transcriptions regulators RUNX3, ETS2, IRF8 or PRDM1 and major histocompatibility complex class II genes. Importantly, expression of one single gene, i.e. BLNK, enabled prediction of RUNX1 mutations in AML-M0 with high accuracy. We propose that RUNX1 mutations in this subgroup of AML cause lineage infidelity, leading to aberrant co-expression of myeloid and B-lymphoid genes in the same cells.

overall_design: 35 samples

first: Micheline

last: Giphart-Gassler

middle: J


title: Expression data from relapsing-remitting MS samples

status: Public on Aug 01 2009

city: Cambridge

first: Philip

last: De Jager

state: MA

address: 7 Cambridge Center

country: USA

institute: The Broad Institute of MIT and Harvard

summary:
One of our new major finding among the genes that contributes to MS susceptibility is ICSBP1. The so called disease modifying therapies like interferon-beta (IFN-β), possibly acting on the peripheral T-cells, reduce the disease activity and the clinical progression, with a MRI-detectable effect in preventing lesion burden and cerebral atrophy development in RR-MS. It suggests a critical role of peripheral blood mononuclear cells (PBMCs) immune response and modulation in developing inflammation in the brain. We tested the hypothesis that the genetic effect of the susceptible allele ICSBP1 can impact the gene expression profile of molecules belonging to the interferon pathway. We therefore interrogated the PBMC for changes in gene expression profile. We correlate those changes with the minor allele frequency for ICSBP1, performing independent quantitative trait analysis  for each treatment category. Expression Quantitative Trait Loci Association with a p value < 0.05 have been used in follow up analysis. The regression coefficient of the Quantitative trait association represents  the degree of correlation between the gene expression for each interrogated target gene and the minor allele frequency of the SNP for our gene of interest. This coefficient has been used as input in the subsequent Gene Set Enrichment Analysis performed in a pre-ranked approach. The resulting GSEA-SNP method rests on the assumption that SNPs underlying a disease phenotype might affect genes constituting a signaling pathway or genes with a common regulation. Therefore, GSEA-SNP can facilitate the identification of  pathways or of underlying biological mechanisms.
We used microarrays to capture gene expression profile of untreated subjects and of subjects under disease modyfing treatment (Interferon Beta and Glatiramer Acetate), in order to correlate gene expression and genotype data and in order to identify sets of genes specifically regulated in the different treatment categories.

overall_design: Between July 2002 and October 2007, PBMC samples were collected from relapsing-remitting MS subjects and CIS subjects as part of the Comprehensive Longitudinal Investigation of MS at the Brigham & Women’s Hospital (CLIMB study).  We then selected the first time point for each subject with multiple measurements based on an at least three months of treatment criteria. We thereafter analyzed the data  for each treament category.

first: P

middle: L

first: L

last: Ottoboni

first: X

last: Hu


title: Human induced pluripotent stem cells (hiPSCs): gene expression and miRNA expression data

status: Public on Jul 10 2009

city: Los Angeles

first: Mark

middle: H.

last: Chin

state: CA

address: 650 Charles E. Young Dr

department: Human Genetics

institute: UCLA

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

summary:
Induced pluripotent stem cells (iPSCs) outwardly appear to be indistinguishable from embryonic stem cells (ESCs). A study of gene expression profiles of mouse and human ESCs and iPSCs suggests that, while iPSCs are quite similar to their embryonic counterparts, a recurrent gene expression signature appears in iPSCs regardless of their origin or the method by which they were generated. Upon extended culture, hiPSCs adopt a gene expression profile more similar to hESCs; however, they still retain a gene expression signature unique from hESCs that extends to miRNA expression. Genome-wide data suggested that the iPSC signature gene expression differences are due to differential promoter binding by the reprogramming factors. High-resolution array profiling demonstrated that there is no common specific subkaryotypic alteration that is required for reprogramming and that reprogramming does not lead to genomic instability. Together, these data suggest that iPSCs should be considered a unique subtype of pluripotent cell.

Detailed analysis comparing induced pluripotent stem cells revealed functional gene expression differences to hESCs that are changed with long term passaging.
We used microarrays to detail the changes that are made throughout passaging to hiPSC lines.

overall_design:
Gene expression analysis: hiPSC lines were harvested at long term passages (p50-60) for RNA extraction and hybridization on Affymetrix arrays.
miRNA expression analysis: Used a chip which comes with over 600 mature human miRNAs in quadruplicate. Two 40 mer oligo probes, one for the mature miRNA and the other for precursor oligo, are generally present, when possible from the sense strand of both arms of the hairpin structure of the microRNA precursor sequence collected from the Sanger Database.

middle: H

first: Bill

last: Lowry


title: Inducible iPS Cells Support Full-term Development of Tetraploid Blastocyst–Complemented Embryos

status: Public on Jul 09 2009

city: Dalian

first: Lan

last: Kang

address: 9 West Section, Lvshun South Road

department: Institute of Cancer Stem Cell

country: China

institute: Dalian Medical University

summary: Differentiated somatic cells can be reprogrammed into induced pluripotent stem (iPS) cells by forced expression of four transcription factors—Oct4, Sox2, Klf4, and c-Myc. However, it remains undetermined whether the reprogrammed iPS cells are fully pluripotent, resembling normal embryonic stem (ES) cells, given that no iPS cell lines have been shown to possess the capability to autonomously generate full-term mice after injection into tetraploid blastocysts. Here, we provide evidence demonstrating that iPS cells induced by the four transcription factors can be fully pluripotent and that full-term mice can be produced from complemented tetraploid blastocysts. This work serves as a proof of principle that iPS cells can generate full term embryos by tetraploid complementation.

overall_design: We compared the gene expression profile of iPS cell, ES cell and MEF. ES cell and MEF served as control for iPS cell. Three biological repeats were included for each line.

first: Jianle

last: Wang

first: Yu

last: Zhang

first: Zhaohui

last: Kou

first: Shaorong

last: Gao


title: Gene expression profile of normal and calcified stenotic human aortic valves

city: Quebec

first: Yohan

last: Bossé

state: Quebec

address: 2725, chemin Sainte-Foy

country: Canada

institute: Laval University

summary:
We explored gene expression profile of human aortic valves in patients with or without aortic stenosis. The dataset that we generated constitutes a large-scale quantitative measurements of gene expression in normal and stenotic human valves. The goal was to compare gene expression levels between the two groups and identified a list of genes that are up- or down-regulated in aortic stenosis.

Keywords: disease state analysis

overall_design: Gene expression was performed on ten normal and ten aortic stenosis valves

last: Bosse

first: Philippe

last: Pibarot

first: Patrick

last: Mathieu


title: Transwell-cultured and miRNAs-transfected T84 cells

city: Kumamoto

first: Soken

last: Tsuchiya

address: 5-1 Oe-honmachi, Chuo-ku

country: Japan

institute: Kumamoto University

summary: MicroRNAs are small non-coding RNA species, some of which are playing important roles in cell differentiation. However, the level of participations of microRNAs in epithelial cell differentiation is largely unknown. Here, we found that expression levels of four microRNAs (miR-210, miR-338-3p, miR-33a and miR-451) were significantly increased in differentiated stage of T84 cells, compared with undifferentiated stage. Additionally, we demonstrate that miR-338-3p and miR-451 contribute to the formation of epithelial basolateral polarity by facilitating translocalization of beta1 integrin to the basolateral membrane. However, candidate target mRNAs of miR-338-3p and miR-451 and the mechanism behind observed phenomena is uncertain. Then, we performed comprehensive gene expression analysis to identify candidate target mRNAs and understand their mechanisms.

overall_design: T84 cells were seeded in transwell chambers and were transfected with microRNAs. Total RNA was extracted by the acid guanidinium thiocyanate-phenol-chloroform method, and was labeled and prepared for hybridization to GeneChip Human Genome U133 Plus 2.0 arrays (Affymetrix) according to the manufacture’s instructions (standard protocol).


title: Study of human immune and memory T cells using microarray

status: Public on Jul 07 2009

city: South San Francisco

first: Alex

last: Abbas

address: 1 DNA Way

department: Bioinformatics

institute: Genentech, Inc.

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

overall_design: Refer to individual Series


title: Time course profile of umbilical cord blood cells in culture

status: Public on Jul 01 2009

city: Toronto

first: Daniel

last: Kirouac

state: Ontario

department: Biomaterials and Biomedical Engineering

institute: University of Toronto

summary: Despite the importance of inter-cellular communication networks in regulating stem cell fate decisions, very little is known about the topology, dynamics, or functional significance.  Using human blood stem cell cultures as an experimental paradigm, we present a novel bioinformatic approach to integrate genome-scale molecular profiles (transcriptome and secretome) and publicly available databases to reconstruct soluble factor-mediated inter-cellular signalling networks regulating blood stem cell fate decisions.

overall_design: Umbilical cord blood UCB cells were lineage depleted via immuno-magnetic column and placed in serum free media, supplemented with SCF, FL, and TPO. At culture day 4, cells were either subject to Lin- cell re-selection + media exchange (S/E) or not (NS/NE) and cultured for an additional 4 days. At day-8, S/E cell sample was subject to another S/E procedure and cultured for an additional 4 days. At day-0, 4, 8, and 12, cells were separated into Lin- and Lin+ for independent profiling using Affymetrix HU133 v2.0 arrays.

middle: C

first: Caryn

last: Ito

first: Mei

last: Yu

first: Peter

middle: W

last: Zandstra


title: Epigenetic signature of breast cancer and its association with gene expression and copy number

status: Public on Jul 03 2009

city: London

first: Ann

last: Chambers

address: 790 Commissioner's Road E

department: Victoria research labs

institute: London Regional Cancer program

type: Methylation profiling by genome tiling array

summary:
Recent advances in multiple whole genome technologies provide unprecedented opportunities to profile epigenomic signatures in cancer cells. Previously we used a human gene promoter tiling microarray platform to identify genome-wide DNA methylation changes in a cell line model of breast cancer metastasis. Interestingly, the clustered nature of epigenetic targets that we identified, along with our concurrent karyotype analyses, have now led us to hypothesize that complex genomic alterations in cancer cells (deletions, translocations and ploidy) may be superimposed over promoter-specific methylation events that are responsible for gene-specific expression changes.

This SuperSeries is composed of the SubSeries listed below.

overall_design:
Refer to individual Series.
In the present study, we have refined our previous epigenetic profiling study by crossreferencing data sets generated from multiple whole-genome platforms. We undertook simultaneous highresolution, whole-genome analyses using Affymetrix gene expression (U133), promoter (1.0R) and SNP/CNV (SNP 6.0) microarray platforms to correlate epigenetic (DNA methylation), gene expression and combination single nucleotide polymorphism / copy number variant (SNP 6.0) microarrays in an isogenic paired cell line model of breast cancer metastasis.


title: Memory T Cell Subsets

summary:
Microarray deconvolution is a technique for quantifying the relative abundance of constituent cells in a mixture based on that mixture's microarray signature and the signatures of the purified constituents.  It has been applied to yeast and other systems but not to blood samples.
Here we test the ability of this technique to determine the fractions of subsets of memory T cells in peripheral blood mononuclear cell (PBMC) samples.
Keywords: cell type comparison

overall_design: PBMC samples from several donors were split. One portion of each PBMC sample was set aside, while the remainder of each was sorted into naive, central memory, and effector memory T cell subsets.

first: Alexander

middle: R

first: Dhaya

last: Seshasayee

first: Zora

last: Modrusan

first: Hilary

middle: F

last: Clark


title: Immune Cell Line Mixtures

summary:
Microarray deconvolution is a technique for quantifying the relative abundance of constituent cells in a mixture based on that mixture's microarray signature and the signatures of the purified constituents.  Its ability to discriminate related human cells is unknown.
Here we test the ability of this technique to determine the fractions of transformed cells of immune origin in mixed samples.
Keywords: cell type comparison

overall_design:
Four immune cell lines were grown and run on microarrays either by themselves or in mixtures of various relative proportions.  Mixtures of cells were performed in triplicate.
MixA (Jurkat: 2.5, IM-9: 1.25, Raji: 2.5, THP-1: 3.75)
MixB (Jurkat: 0.5, IM-9: 3.17, Raji: 4.75, THP-1: 1.58)
MixC (Jurkat: 0.1, IM-9: 4.95, Raji: 1.65, THP-1: 3.3)
MixD (Jurkat: 0.02, IM-9: 3.33, Raji: 3.33, THP-1: 3.33)

first: Kristin

last: Wolslegel


title: Integrated pathways for neutrophil recruitment and inflammation in leprosy

status: Public on Jun 30 2009

first: Delphine

last: Lee

address: 10833 Le Conte Ave.

summary: Neutrophil recruitment is pivotal to host defense against microbial infection, but also contributes to the immunopathology of disease.  We investigated the mechanism of neutrophil recruitment in human infectious disease by bioinformatic pathways analysis of the gene expression profiles in the skin lesions of leprosy.  In erythema nodosum leprosum (ENL), which occurs in patients with lepromatous leprosy (L-lep), and is characterized by neutrophil infiltration in lesions, the most overrepresented biologic functional group was 'cell movement' including E-selectin, which was coordinately regulated with IL-1beta.  In vitro activation of TLR2, upregulated in ENL lesions, triggered induction of IL-1beta, which together with IFN-gamma, induced E-selectin expression on, and neutrophil adhesion to endothelial cells.  Thalidomide, an effective treatment for ENL, inhibited this neutrophil recruitment pathway.  The gene expression profile of ENL lesions comprised an integrated pathway of TLR2/FcR activation, neutrophil migration and inflammation, providing insight into mechanisms of neutrophil recruitment in human infectious disease.

overall_design: 6 ENL skin lesions and 7 Lepromatous leprosy skin lesions

first: Huiying

last: Li

first: Maria

middle: T

last: Ochoa

first: Motoyuki

last: Tanaka

first: Ryan

last: Carbone

first: Robert

last: Damoiseaux

first: Anne

last: Burdick

first: Euzenir

middle: N

last: Sarno

first: Thomas

last: Rea

last: Modlin


title: Dysregulated gene expression networks in human acute myelogenous leukemia stem cells

city: Seattle

first: Qiang

last: Tian

state: WA

institute: Institute for Systems Biology

summary: We performed the first genome-wide expression analysis directly comparing the expression profile of highly enriched normal human hematopoietic stem cells (HSC) and leukemic stem cells (LSC) from patients with acute myeloid leukemia (AML). Comparing the expression signature of normal HSC to that of LSC, we identified 3,005 differentially expressed genes. Using 2 independent analyses, we identified multiple pathways that are aberrantly regulated in leukemic stem cells compared with normal HSC. Several pathways, including Wnt signaling, MAP Kinase signaling, and Adherens Junction, are well known for their role in cancer development and stem cell biology. Other pathways have not been previously implicated in the regulation of cancer stem cell functions, including Ribosome and T Cell Receptor Signaling pathway. This study demonstrates that combining global gene expression analysis with detailed annotated pathway resources applied to highly enriched normal and malignant stem cell populations, can yield an understanding of the critical pathways regulating cancer stem cells.

overall_design: Total RNAs were isolated from both AML stem cells (9 patients) and normal bone marrow hematopoietic stem cells (HSCs) (4 control subjects).

first: Ravindra

last: Majeti

first: Michael

last: Becker

first: Tsung-Lu

middle: M

first: Xiaowei

last: Yan

first: Rui

last: Liu

first: Jung-Hsien

last: Chiang

first: Leroy

last: Hood

last: Clarke

first: Irving

last: Weissman


title: Many Human Large Intergenic Non-coding RNAs Associate with Chromatin Modifying Complexes and Affect Gene Expression

first: Mitchell

last: Guttman

institute: Broad Institute

type: Non-coding RNA profiling by genome tiling array

summary: We recently showed that the mammalian genome encodes more than a thousand large intergenic non-coding RNAs (lincRNAs) that are clearly conserved across mammals and thus functional.  Gene expression patterns have implicated these lincRNAs in diverse biological processes including cell cycle regulation, immune surveillance, and embryonic stem cell pluripotency.  However, the mechanism by which these lincRNAs function is unknown.  Here, we expand the catalog of human lincRNAs to ~3300 by analyzing chromatin-state maps of various human cell types.  Inspired by the observation that the well-characterized lincRNA HOTAIR bind the Polycomb Repressive Complex 2 (PRC2), we tested whether many lincRNAs are physically associated with PRC2.  Remarkably, we observe that ~20% of lincRNAs expressed in various cell types are bound by PRC2, and that additional lincRNAs are bound by other chromatin-modifying complexes.  Moreover, we show that siRNA-mediated depletion of certain lincRNAs associated with PRC2 leads to changes in gene expression and that the upregulated genes are enriched for those normally silenced by PRC2.  We propose a model in which some lincRNAs guide chromatin–modifying complexes to specific genomic loci to regulate gene expression.

overall_design:
siRNA-mediated lincRNA knockdown
siRNAs targeting specific lincRNAs were transected into human fibroblasts. Non-targeting siRNAs were used as controls. Both of these experiment types were hybridized to Affymetrix gene expression arrays.

PRC2 RIP-Chip
The PRC2 complex was immunoprecipitated using antibodies targetting Suz12 and the associated RNA was hybridized to Nimblegen tiling arrays representing lincRNAs.
In parallel an IgG IP was performed and hybridized to the same NG arrays.
RIP was performed for PRC2 and hybridized using a Cy3 label. In parallel, RIP was performed using IGG and labelled with Cy5

PRC2 RIP-Chip (dye swap)
The PRC2 complex was immunoprecipitated using antibodies targetting Suz12 and the associated RNA was hybridized to Nimblegen tiling arrays representing lincRNAs.
In parallel an IgG IP was performed and hybridized to the same NG arrays.
RIP was performed for PRC2 and hybridized using a Cy5 label. In parallel, RIP was performed using IGG and labelled with Cy3

PRC2 RIP-Chip (no proteins)
The PRC2 complex was immunoprecipitated using antibodies targetting Suz12 and the associated RNA was hybridized to Nimblegen tiling arrays representing lincRNAs.
In parallel an IgG IP was performed and hybridized to the same NG arrays.
RIP was performed for PRC2 and hybridized using a Cy3 label. In parallel, RIP was performed using IGG and labelled with Cy5

COREST RIP-Chip
The COREST complex was immunoprecipitated using antibodies targetting COREST and the associated RNA was hybridized to Nimblegen tiling arrays representing lincRNAs.
In parallel an IgG IP was performed and hybridized to the same NG arrays.
RIP was performed for COREST and hybridized using a Cy3 label. In parallel, RIP was performed using IGG and labelled with Cy5

H3K27me3 and H3K4me2 modified histones RIP-Chip
The H3K27me3 and H3K4me2 modified histones were immunoprecipitated using antibodies targetting COREST and the associated RNA was hybridized to Nimbelgen tiling arrays representing lincRNAs.
In parallel an IgG IP was performed and hybridized to the same NG arrays.
RIP was performed for COREST and hybridized using a Cy3 label. In parallel, RIP was performed using IGG and labelled with Cy5

Human lincRNA expression
Human lincRNAs were profiled in HeLa, Lung FB, and Foot FB. In addition, nuclear and cytoplasmic fractions were taken in HeLa cells
Total RNA was extracted from HeLa, Foot, and Lung cells and hybridized to NG tiling array. In addition, the nucleus was fractionated and RNA was hybridized to an array.

first: Ahmad

last: Khalil

first: Eric

middle: S

last: Lander

first: John

last: Rinn


title: Subtype-specific peripheral blood gene expression profiles in recent onset JIA

city: Cincinnati

last: Barnes

state: OH

address: 3333 Burnet Ave

department: Rheumatology

institute: Cincinnati Childrens Hospital Medical Center

summary:
Objective:  A multi-center study of recent onset juvenile idiopathic arthritis (JIA) subjects prior to treatment with DMARDS or biologics was undertaken to identify peripheral blood gene expression differences between JIA subclasses and controls.  Methods:  PBMC from 59 healthy children and 136 JIA subjects (28 enthesitis-related arthritis[ERA], 42 persistent oligoarthritis, 45 RF- polyarthritis, and 21 systemic) were isolated on Ficoll.  Poly-A RNA was labeled using NuGEN Ovation and gene expression profiles were obtained using Affymetrix HG-U133 plus 2.0 Arrays.  Results:  9,501 differentially expressed probe sets were identified among JIA subtypes and controls (ANOVA, FDR 5%).  Specifically, 193, 1036, 873 and 7595 probe sets were different between controls and ERA, persistent oligoarthritis, RF- polyarthritis and systemic JIA samples respectively.  In persistent oligoarthritis, RF- polyarthritis and systemic JIA subtypes, up-regulation of gene associated with IL-10 signaling was prominent.  A hemoglobin cluster was identified that was under-expressed in ERA patients but over-expressed in systemic JIA. The influence of JAK/STAT, ERK/MAPK, IL-2 and B cell receptor signaling pathways was evident in persistent oligoarthritis. In systemic JIA, up regulation of innate immune pathways, including IL-6, TLR/IL1R, and PPAR signaling were noted, along with down regulation of gene networks related to NK and T cells.  Complement and coagulation pathways were up-regulated in systemic JIA with a subset of these components differentially-expressed in the other three subtypes.  Conclusions:  Expression analysis identified differentially expressed genes in PBMCs between subclasses of JIA early in disease and controls, thus providing evidence for immunobiologic differences between these forms of childhood arthritis.

Keywords: Gene expression.  PBMC.  Patients compared with controls.

first: M

middle: G

first: A

middle: A

last: Grom

first: S

middle: D

last: Thompson

first: T

last: Griffin

first: P

last: Pavlidis

first: L

last: Itert

first: N

last: Fall

first: D

middle: P

last: Sowders

first: C

last: Hinze

first: B

last: Aronow

middle: K

last: Luyrink

last: Srivastava

last: Ilowite

last: Gottlieb

first: J

last: Olson

last: Sherry

last: Couri

last: Getz

last: Glass

first: R

last: Colbert


title: Expression Signatures in Polyarticular JIA Show Heterogeneity and Offer a Molecular Classification of Disease Subsets

first: Michael

last: Barnes

summary:
Objective. Microarray analysis was used to determine whether children with recent onset polyarticular juvenile idiopathic arthritis (JIA) exhibit biologically or clinically informative gene expression signatures in peripheral blood mononuclear cells (PBMC).   Methods. Peripheral blood samples were obtained from 59 healthy children and 61 children with polyarticular JIA prior to treatment with second-line medications, such as methotrexate or biological agents.  RNA was purified from Ficoll-isolated mononuclear cells, fluorescently labeled and then hybridized to Affymetrix U133 Plus 2.0 GeneChips.  Data were analyzed using ANOVA at a 5% false discovery rate threshold after Robust Multi-Array Average pre-processing and Distance Weighted Discrimination normalization.   Results. Initial analysis revealed 873 probe sets for genes that were differentially expressed between polyarticular JIA and controls.  Hierarchical clustering of these probe sets distinguished three subgroups within polyarticular JIA.  Prototypical subjects within each subgroup were identified and used to define subgroup-specific gene expression signatures.  One of these signatures was associated with monocyte markers, another with transforming growth factor-beta-inducible genes, and a third with immediate-early genes.  Correlation of these gene expression signatures with clinical and biological features of JIA subgroups suggests direct relevance to aspects of disease activity and supports the division of polyarticular JIA into distinct subsets.  Conclusions.  PBMC gene expression signatures in recent onset polyarticular JIA reflect discrete disease processes and offer a molecular classification of disease.

Keywords: Patient vs. control, reassessment of phenotype

overall_design: PBMC samples were obtained from 59 healthy children and 61 children with polyarticular JIA prior to treatment with second-line medications, such as methotrexate or biological agents.  RNA was purified from Ficoll-isolated mononuclear cells, fluorescently labeled and then hybridized to Affymetrix U133 Plus 2.0 GeneChips.  Data were analyzed using ANOVA at a 5% false discovery rate threshold after Robust Multi-Array Average pre-processing and Distance Weighted Discrimination normalization.

first: Thomas

last: Griffin

first: Norman

first: Judyann

first: David

first: Beth

first: Bruce

middle: J

first: Paul

first: Claas

first: Sherry

last: Thornton

first: Susan

last: Thompson

first: Alexei

last: Grom

first: Robert


title: Gene expression signatures in breast cancer distinguish phenotype charact., histological subtypes, and tumor invasivness

city: Granada

first: Mª Esther

last: Farez-Vidal

address: Avda Dr. Oloriz s/n

country: Spain

institute: Hospital Universitario San Cecilio

summary:
Background. The development of reliable gene expression profiling  technology is having an increasing impact on our understanding of breast cancer biology.
Methods. In this study, microarray analysis was performed in order to establish gene signatures for different breast cancer phenotypes, determine differentially expressed gene sequences at different stages of the disease, and identify sequences with biological significance for tumor progression. Samples were taken from patients before their treatment. After microarray analysis, the expression level of 153 selected genes was studied by qPCR.
Results. A number of gene sequences were differentially expressed in tumor versus control samples and were also associated with different breast cancer phenotypes, ER status, tumor histology, and grade of tumor differentiation. In N0 tumors were found a set of genes related to tumor differentiation grade.
Conclusion. A number of differentially expressed gene sequences were found at different stages of the breast cancer disease.

Key Words: Breast cancer, gene expression signature, tumor invasiveness, microarrays, qPCR

overall_design: In total, 58 samples were studied, 31 tumors and 27 controls. Some of the samples are paired

first: Vicente

last: Pedraza

first: Georgia

last: Escaramis

first: Jose

last: Gomez-Capilla

first: Carolina

last: Gomez-Llorente

first: Pablo

last: Torne

last: Rivera

first: Angel

last: Gil

first: Patricia

last: Araque

first: Nicolas

last: Olea

first: Xavier

last: Estivill

first: Maria-Esther


title: Expression data from OCUBM cells trasfected with IGF1R

city: Nishigo

first: Mayumi

last: Sugimoto

institute: National Livstock Breeding Center

summary:
To investigate genes that might influence resistance to infection through IGF1R, we screened human breast cancer-derived OCUB-M cells transfected with expression vector encoding IGF1R using microarray analysis.
Keywords: overexpression comparison

overall_design: OCUBM cells were transfected with/without IGF1R for RNA extraction and hybridization on Affymetrix microarrays.


title: Gingival Epithelial Cell Responses to a Complex Microbiome Comprising Commensal and Opportunistic Oral Microbial Species

city: Gainesville

first: Martin

last: Handfield

state: FL

address: 1600 SW Archer Road, BOX 100424

department: Oral Biology

institute: University of Florida

summary:
Transcriptional profiling was utilized to define the biological pathways of gingival epithelial cells modulated by mono- and complex co-culture with oral commensal S. gordonii and pathogenic P. gingivalis.
We used microarrays to detail the global programme of gene expression underlying infection and identified distinct classes of up- and down-regulated genes during this process.

Keywords: infection state

overall_design: Gingival epithelial HIGK cells were sham infected (CTRL) and infected with either the oral commensal S. gordonii (Sg) or the pathogenic P. gingivalis (Pg) as well as co-cultured in mixed cultures of Sg and Pg (Sg+Pg). These samples were hybridized to Affymetrix microarrays. Understanding how host cells have adapted to commensals, and how barrier cells respond to limit their impact, provides a mechanistic biological basis of health in the mixed bacterial-human ecosystem of the oral cavity and provides insight on how the degree of complexity of a microbiome influences this balance.

first: Kate

last: von Lackum

first: Jeffrey

last: Mans

first: Cassandra

last: Dorsey

first: Shaun

last: Willis

first: Shannon

last: Wallet

first: Henry

middle: V

last: Baker

first: Richard

last: Lamont


title: IGF1R Mediates Mammalian Immune Function in Response to FEZL


title: Identifying mutant genes in the LNCaP and 22Rv1 prostate cancer cell lines

city: Buffalo

first: Yurij

last: Ionov

state: NY

address: Elm and Carlton streets

department: Cancer Genetics

institute: Roswell Park Cancer Institute

summary:
We used a modification of GINI analysis to identify genes containing premature translation termination codons (PTC) generated by nonsense or frameshift mutations in prostate cancer cell lines. The analysis was performed in two steps. In the first step nonsense mediated mRNA decay (NMD) was inhibited in prostate cancer cell lines using incubation with medium containing caffeine for 4 hours. Gene expression analysis of caffeine treated or untreated cells after  this step detects mRNA accumulation  that takes place for genes containing PTC and as well as for genes that show induction of transciption due to stress caused by NMD inhibition. In the second step either both  transcription and NMD or transcription only are blocked  by incubating cell in a medium containing either both actinomycin D and caffeine or actinomacin D only for 4 hours. Gene expression analysis after this second step detects mRNA degradation for genes containing PTC as well as for genes that show induction of transciption due to stress caused by NMD inhibition. The efficiency of mRNA degradation for genes containing PTC during this step depends on whether NMD is inhibited or not. The efficiency of mRNA degradation for stress response genes does not depend on whether NMD is inhibited or not.
Our modified GINI protocol allows efficient separation of genes containing PTC from the genes that show mRNA increases due to stress response to NMD inhibition.

overall_design: The LNCaP and 22Rv1 cells were seeded into four  60 mm tissue culture plates each.  Caffeine (10 mM) was added to three plates and one plate was incubated without caffeine as a control. Following four hours? incubation, the medium was removed from one plate (with caffeine) and from the control plate and total RNA was prepared using TRIZOL reagent, according to manufacturer?s instructions, and used for an Affymetrix U133Plus2.0 oligonucleotide array hybridization. The caffeine-containing medium of the two remaining plates was removed, the cells were washed twice with phosphate-buffered saline and the medium with actinomycin D (2  mkg/ml) together with caffeine (10 mM) was added to one plate.  Actinomycin D alone was added to the other plate. Following another four hours? incubation, the total RNA from both plates was prepared and used for an Affymetrix U133Plus2.0 oligonucleotide array analysis.

first: Yuri


title: Jag1-dependent gene expression in human endometrial stromal cells

city: Stony Brook

first: Anatoly

last: Mikhailik

address: HSC-T8, Rm 053

department: OB/GYN/Pathology

institute: SUNY at Stony Brook

summary: The goal is to investigate gene regulation in endometrial stromal cells expressing the Notch ligand Jag1.

overall_design: This study compares gene expression in Jag1 retrovirus-infected and control (empty virus-infected) stromal cells.

first: James

last: Mazella

first: Sharon

last: Liang

first: Linda

last: Tseng


title: MSCs Exposed to Keratinocyte Condition Medium

city: New Brunswick

first: Pravin

last: Mishra

state: NJ

address: 195 Little Albany St.

department: Pharmacology

institute: UMDNJ

summary: In the present study, we demonstrate that hMSCs migrate toward human keratinocytes as well as toward conditioned medium from cultured human keratinocytes (KCM) indicating that the hMSCs can respond to signals from keratinocytes. Incubation of hMSCs with KCM induced dermal myofibroblast like differentiation characterized by expression of cytoskeletal markers vinculin and F-actin filaments with increased expression of alpha smooth muscle actin. We then examined the therapeutic efficacy of hMSCs in wound healing in two animal models representing normal and chronic wound healing. Accelerated wound healing, as determined by quantitative measurements of wound area, was observed when hMSCs and KCM exposed hMSCs (KCMSCs) were injected near the site of incisional/excisional wounds in nondiabetic athymic and NOD/SCID mice as compared with normal human fetal lung fibroblast WI38 cells or saline control induced wound healing.

overall_design:
Keratinocyte conditioned media exposed MSCs(KCMSCs)  were used in the experiment in triplicates as follows;
KCM_1
KCM_2
KCM_3
Where as MSCs were exposed to Keratinocyte growth media for 30 days were used as a controls as follow;
KGM_1
KGM_2
KGM_3
All the samples were analyzed.

first: Prasun

first: Shridhar

last: Ganeshan

first: Gabriela

last: Alexe

first: John

middle: w

last: Glod

first: Debabrata

last: Banerjee


title: Expression data from OCUBM cells trasfected with 12G FEZL

first: Mayumi

last: Sugimoto

summary:
To identify genes that influence resistance to mastitis, we scanned
a whole genome of 181 susceptible and 297 resistant cows and revealed
significant linkage to Bos taurus autosomal chromosome (BTA) 21 with a
likelihood of odds (LOD) score of 28. Because FEZL is a transcription factor that influences resistance to mastitis, we compared LOD scores of BTA21 among cows carrying 12G/12G, 12G/13G, and 12G/13GFEZL to evaluate whether FEZL affects linkage in this chromosome. Cows carrying 13G/13GFEZL had the most significant linkage with a LOD score of 35, despite a decrease in the number of samples from 478 to 224. This finding suggested that the gene influencing resistance to mastitis on BTA21 might be controlled by FEZL.
To investigate genes that might influence resistance to mastitis through FEZL, we screened human breast cancer-derived OCUB-M cells transfected with expression vector encoding 12GFEZL using microarray analysis.
Keywords: overexpression comparison

overall_design: OCUBM cells were transfected with/without 12G FEZL for RNA extraction and hybridization on Affymetrix microarrays.


title: 5-azacytidine and entinostat treatment of patients with MDS, chronic myelomonocytic leukemia (CMMoL), and high risk AML

status: Public on Jun 20 2009

city: New York

first: Weijia

last: Zhang

address: 1425 Madison Avenue

department: Department of Medicine

institute: Mount Sinai School of Medicine

summary: Early epigenetic changes and DNA damage do not predict clinical response in an overlapping schedule of 5-azacytidine and entinostat in patients with myeloid malignancies. The patients with MDS, chronic myelomonocytic leukemia (CMMoL), and high risk AML were treated with sequential administration of methylation inhibitor drugs (5AC and entinostat). To study gene expresion regulation in treated patients, microarray analysis was done on RNA samples extracted from CD34+ cells from 18 patients before and 15 days after treatment using Affymetrix U133Plus2.0.

overall_design: 18 enrolled patients were treated with sequential administration of 5AC and entinostat and microarray analysis were done on RNA samples from CD34+ cells before and 15 days after treatment using Affymetrix U133Plus2.0. One chip was used for one sample and there was no technical replicates. Twelve pairs of day 0 and day 15 specimens passed quality control for hybridization and RNA integrity. A list of differentially regulated genes was created after GC-RMA normalization by t-test paired using a 1.5 fold cut-off with p<0.005.

first: Tamer

middle: E

last: Fandy

last: Herman

first: Patrick

last: Kerns

first: Anchalee

last: Jiemjit

first: Elizabeth

last: Sugar

first: Si-Ho

last: Choi

first: Allen

last: Yang

first: Timothy

last: Aucott

first: Tianna

last: Dauses

first: Rosalie

last: Odchimar-Reissig

first: Jonathan

last: Licht

first: Melanie

last: McConnell

first: Chris

last: Nasrallah

first: Marianne

last: Kim

first: Yezou

last: Sun

first: Anthony

last: Murgo

first: Igor

last: Espinoza-Delgado

first: Katharine

last: Oteiza

first: Ibitayo

last: Owoeye

first: Lewis

last: Silverman

first: Steven

last: Gore

first: Hetty

last: Carraway


title: Characterization of whole blood gene expression profiles in sickle-cell disease patients using globin mRNA reduction

city: Bethesda

first: Xiuli

last: Xu

state: MD

address: Building 10-CRC, Room 5-5140

department: VMB,

institute: NHLBI, NIH

summary:
Room temperature whole blood mRNA stabilization procedures, such as the PAX gene system, are critical for the application of transcriptional analysis to population-based clinical studies. Global transcriptome analysis of whole blood RNA using microarrays has proven to be challenging due to the high abundance of globin transcripts that constitute 70% of whole blood mRNA in the blood. This is a particular problem in patients with sickle-cell disease, secondary to the high abundance of globin-expressing nucleated red blood cells and reticulocytes in the circulation .  In order to more accurately measure the steady state whole blood transcriptome in sickle-cell patients, we evaluated the efficacy of reducing globin transcripts in PAXgene stabilized RNA samples for genome-wide transcriptome analyses using oligonucleotide arrays. We demonstrate here by both microarrays and Q-PCR that the globin mRNA depletion method resulted in 55-65 fold reduction in globin transcripts in whole blood collected from healthy volunteers and sickle-cell disease patients. This led to an improvement in microarray data quality with increased detection rate of expressed genes and improved overlap with the expression signatures of isolated peripheral blood mononuclear (PBMC) preparations. The differentially modulated genes from the globin depleted samples had a higher correlation coefficient to the 112 genes identified to be significantly altered in our previous study on sickle-cell disease using PBMC preparations.  Additionally, the analysis of differences between the whole blood transcriptome and PBMC transcriptome reveals important erythrocyte genes that participate in sickle-cell pathogenesis and compensation. The combination of globin mRNA reduction after whole-blood RNA stabilization represents a robust clinical research methodology for the discovery of biomarkers for hematologic diseases and in multicenter clinical trials investigating a wide range of nonhematologic disorders where fractionation of cell types is impracticable.

Keywords: Microarrays, PAXgene, globin reduction, whole blood, PBMC

overall_design: There are 10 samples for each of PBMC, PAX and PAX globin-reduced, where 5 samples come from sickle-cell patients and 5 from healthy controls.

first: Nalini

last: Raghavachari

first: Ronald

last: Cooper

first: Peter

last: Munson

first: Mark

last: Gladwin


title: The genomic response of a human uterine endometrial adenocarcinoma cell line to 17alpha-ethynyl estradiol.

status: Public on Jun 24 2009

city: MASON

first: Jay

middle: Patrick

last: Tiesman

address: PO BOX 8006

department: Global Biotechnology

institute: Procter & Gamble

summary: We have determined the gene expression profile induced by 17 alpha-ethynyl estradiol (EE) in Ishikawa cells, a human uterine-derived estrogen-sensitive cell line, at various doses (1 pM, 100 pM, 10 nM, and 1 microM) and time points (8, 24, and 48 h). The transcript profiles were compared between treatment groups and controls (vehicle-treated) using high-density oligonucleotide arrays to determine the expression level of approximately 38,500 human genes. By trend analysis, we determined that the expression of 2560 genes was modified by exposure to EE in a dose- and time-dependent manner (p </= 0.0001). The annotation available for the genes affected indicates that EE exposure results in changes in multiple molecular pathways affecting various biological processes, particularly associated with development, morphogenesis, organogenesis, cell proliferation, cell organization, and biogenesis. All of these processes are also affected by estrogen exposure in the uterus of the rat. Comparison of the response to EE in both the rat uterus and the Ishikawa cells showed that 71 genes are regulated in a similar manner in vivo as well as in vitro. Further, some of the genes that show a robust response to estrogen exposure in Ishikawa cells are well known to be estrogen responsive, in various in vivo studies, such as PGR, MMP7, IGFBP3, IGFBP5, SOX4, MYC, EGR1, FOS, CKB, and CCND2, among others. These results indicate that transcript profiling can serve as a viable tool to select reliable in vitro systems to evaluate potential estrogenic activities of target chemicals and to identify genes that are relevant for the estrogen response.

overall_design: 75 total samples:  5 Doses [Vehicle Control, Very Low (1 pM), Low (100 pM), High (1 nM), Very High (1 uM)]; 3 Timepoints [8 hour, 24 hour, 48 hour]; 5 Replicates each

first: Jorge

last: Naciff

first: Zubin

last: Khambatta

first: Ryan

last: Thomason

first: Gregory

last: Carr

first: David

last: Singleton

first: Sohaib

last: Khan

first: George

last: Daston


title: Expression data from  human chondrosarcoma cells resistance to ET-743 and PM00104

city: Boston

first: Zhenfeng

last: Duan

address: 100 Fruit St

institute: Massachusetts General Hospital

summary: ET-743 (trabectedin, Yondelis®) and PM00104 (Zalypsis®) are marine derived compounds that have antitumor activity.  ET-743 and PM00104 exposure over sustained periods of treatment will result in the development of drug resistance, but the mechanisms which lead to resistance are not yet understood.    Human chondrosarcoma cell lines resistant to ET-743 (CS-1/ER) or PM00104 (CS-1/PR) were established in this study.  The CS-1/ER and CS-1/PR exhibited cross resistance to cisplatin and methotrexate but not to doxorubicin.  Human Affymetrix Gene Chip arrays were used to examine relative gene expression in these cell lines.

overall_design: Three samples CS-1/ER, CS-1/PR and CS-1 were compared.

first: Francis

last: Hornicek


title: A Brief Bout of Exercise Alters Gene Expression and Distinct Gene Pathways in PBMC of Early- and Late-Pubertal Females

status: Public on Jun 17 2009

city: Irvine

first: Shlomit

last: Radom-Aizik

address: 101 Academy

department: Pediatrics

institute: University of California, Irvine

summary:
We compared PBMC genomic response to exercise in both early (EG) and late-pubertal girls (LG)

Keywords: stress response

overall_design: Twenty healthy females (age range 8-17 y/o) participated in this study. A blood sample was taken before the onset of exercise and immediately after 30-min exercise bout. PBMCs were isolated using OptiPrep® Density Gradient Medium (SIGMA). Total RNA was extracted using TRIzol®.  cRNA was hybridized onto Affymetrix U133+2 arrays (total of 40 chips).

first: Szu-Yun

last: Leu

first: Frank

last: Zaldivar

first: Dan


title: Comparison of mouse placental labyrinth and human villus tree

status: Public on Jun 16 2009

first: Brian

middle: Joseph

last: Cox

address: 1 King's College Circle, Rm 3360

department: Physiology

summary:
An important question for the use of the mouse as a model  for studying human disease is the degree of functional conservation of genetic control pathways from human to mouse. The human placenta and mouse placenta show structural similarities but there has been no systematic attempt to assess their molecular similarities or differences. We built a comprehensive database of protein and microarray data for the highly vascular exchange region micro-dissected from the human and mouse placenta near-term.  Abnormalities in this region are associated with two of the most common and serious complications of human pregnancy, maternal preeclampsia (PE) and fetal intrauterine growth restriction (IUGR), each disorder affecting ~5% of all pregnancies.
To compare the gene expression patterns in the vascular exchange regions of the human (villus tree) and mouse (labyrinth) placenta.

Keywords: comparison

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus

overall_design: Mouse labyrinth tissue was micro-dissected form naturally mated crosses of C57Bl/6J mice. Placentas were individually dissected on embryonic day 17.5. From each litter ¼ of the tissue were set aside for RNA extraction and microarray analysis and ¾ for cellular fractionation and proteomic analysis, as recently described (Kislinger et al., 2006).  Human villous trees were dissected from term normal placenta delivered by cesarean section from a term pregnancy (~ 38 weeks). Tissue was divided for organellar fractionation and RNA extraction.

first: Thomas

last: Kisslinger

first: Janet

last: Rossant

first: Lee

last: Adamson


title: Expression data from human 293 cells

status: Public on Jun 15 2009

city: Niigata

first: Masayuki

last: Nashimoto

address: Higashijima 265-1

institute: Niigata University of Pharmacy and Applied Life Sciences

summary: A long form (tRNase ZL) of tRNA 3' processing endoribonuclease (tRNase Z, or 3' tRNase) can cleave any target RNA at any desired site under the direction of artificial small guide RNA (sgRNA). We discovered in human kidney 293 cell extracts various new small noncoding RNAs (ncRNAs) including 5'-half-tRNAs and 28S rRNA fragments, co-immunoprecipitated with tRNase ZL, and demonstrated that two of these ncRNAs work as sgRNAs for tRNase ZL in vivo as well as in vitro. In order to find genuine mRNA targets of tRNase ZL guided by ncRNAs, we performed DNA microarray analysis for mRNAs from the 293 cells transfected with the tRNase ZL expression plasmid, and found that PPM1F and DYNC1H1 mRNAs are its genuine targets.

overall_design: In order to find genuine mRNA targets of tRNase ZL guided by ncRNAs, we performed DNA microarray analysis for mRNAs from the 293 cells transfected with the tRNase ZL expression plasmid.

first: Reyad

last: Elbarbary


title: Hematopoietic Progenitor Cells of Different Donor Age

status: Public on Jun 12 2009

city: Aachen

first: Wolfgang

last: Wagner

address: Pauwelsstrasse 20

department: Helmholtz Institute for Biomedical Engineering

country: Germany

institute: RWTH Aachen University

summary: In this series we have analyzed the effect of donor age on the gene expression profile of human hematopoietic stem and progenitor cells (HPC). Cells were taken from umbilical cord blood (CB) or from G-CSF mobilized blood of healthy donors for allogeneic blood stem cell transplantation.

overall_design: Hematopoietic progenitor cells (HPC) were isolated within the CD34+ cell fraction from fresh human cord blood (CB) or from G-CSF mobilized peripheral blood (PB) as described in detail before (Wagner et al., Blood, 2004, 104:675-684; Wagner et al., Stem cells, 2005, 23:1180-1191; Wagner et al., 2007, 10:2638-2657). Differential gene expression was subsequently compared in the CD34+ samples of different donor age.

first: Simone

last: Bork

first: Patrick

last: Horn

first: Anthony

last: Ho


title: Unique early gene expression patterns in adult to adult living donor liver grafts compared to deceased donor grafts

status: Public on Jun 11 2009

city: La Jolla

first: Sunil

last: Kurian

address: 10550 N Torrey Pines Road

department: Molecular and Experimental Medicine

institute: The Scripps Research Institute

summary:
Because of inherent differences between deceased donor (DD) and living donor (LD) liver grafts, we hypothesize that the molecular signatures will be unique, correlating with specific biologic pathways and clinical patterns.    Following reperfusion, 579 genes in DD grafts and 1324 genes in LDs were differentially expressed (p<0.005). Many up-regulated LD genes were related to regeneration, biosynthesis and cell cycle, and a large number of down-regulated genes were linked to hepatic metabolism and energy pathways correlating with post-transplant clinical laboratory findings.  There was significant up-regulation of inflammatory/immune genes in both DD and LD, each with a distinct pattern. Gene expression patterns of select genes associated with inflammation and regeneration in LD and DD grafts correlated with protein expression.
Unique patterns of early gene expression are seen in LD and DD liver grafts, correlating with protein expression and clinical results, demonstrating distinct inflammatory profiles and significant down-regulation of metabolic pathways in LD grafts.

Keywords: liver transplantation, live donor transplantation, liver regeneration, microarrays, mRNA expression, reperfusion injury

overall_design: Microarray profiles of 63 biopsies in 13 DD and 8 LD liver grafts done at serial time points (procurement - No Manipulation, backbench - Cold Preservation, and 1-hour post-reperfusion - Post reperfusion) were compared between groups using class comparisons, network and biological function analyses. Specific genes were validated by quantitative PCR and immunopathology. Clinical findings were also compared.


title: Genome-wide gene expression profile analysis in pulmonary sarcoidosis

city: columbus

first: Elliott

middle: David

last: Crouser

address: 473 West 12th Ave.

institute: The Ohio State University

summary:
We hypothesized that tissue genome-wide gene expression analysis, coupled with gene network analyses of differentially expressed genes, would provide novel insights into the pathogenesis of pulmonary sarcoidosis.

Keywords: Disease state analysis

overall_design: Genome-wide gene expression profiles were compared in tissues derived from subjects with active pulmonary sarcoidosis (n=6) and those with normal lung anatomy (n=6).  Differentially expressed genes were analyzed by gene network analysis

first: Daniel

last: Culver

first: Kenneth

last: Knox

first: Mark

middle: W

last: Julian

first: Guohong

last: Shao

first: Susamma

last: Abraham

first: Sandya

last: Liyanarachchi

first: Jennifer

last: Macre

last: Wewers

first: Mikhail

last: Gavrilin

last: Ross

first: Abbas

last: Abbas

first: Charis

last: Eng


title: Expression data from skin fibroblasts derived from Setleis Syndrome patients and normal controls

city: San Juan

first: Carmen

middle: Lydia

last: Cadilla

state: PR

address: University of Puerto Rico Medical Sciences Campus, Area of Medical Center

department: Biochemistry

country: Puerto Rico

institute: University of Puerto Rico School of Medicine

summary:
Setleis Syndrome is a rare type of facial ectodermal dysplasia characterized by an aged leonine appearance with puckered skin about the eyes, absent eyelashes on both lids or multiple rows on the upper lids and none on the lower lids, eyebrows that slant sharply upward laterally, and a rubbery feel of the nose and chin. Some of the patients showed bilateral temporal marks superficially like forceps marks and like the lesions seen in focal facial dermal dysplasia. We have evidence that Setleis Syndrome is caused by nonsense mutations in the gene coding for the small bHLH transcription factor known as TWIST2  in Puerto Rican and Omani patients.

We performed expression microarray analysis of RNA samples derived from skin fibroblasts grown from skin biopsies of Setleis Syndrome patients and normal controls in order to identify genes potentially involved in facial development and the pathogenesis of Setleis Syndrome.

overall_design: A total of 4 control and 4 Setleis Syndrome RNA samples were hybridized to U133 plus 2 Affymetrix 3'IVT arrays in the Mount Sinai School of Medicine Microarray Core Facility.

first: Robert

last: Desnick

middle: L


title: Effect of genomic imbalances on gene expression in rhabdomyosarcoma

status: Public on Jun 04 2009

city: Amsterdam

first: Richard

last: Volckmann

state: Noord-Holland

address: van der Boechorststraat 6a

department: Laboratory of Experimental Oncology and Radiobiology

institute: msterdam UMC and University of Amsterdam

summary:
Rhabdomyosarcoma (RMS) is the most common paediatric soft-tissue
sarcoma and resembles developing skeletal muscle. Specific genomic
alterations including translocations, deletions and amplification events
have been associated with the alveolar and embryonal subtypes of RMS.
Characterizing these changes has led to increased understanding of the
underlying molecular biology.  However, further aberrations and their
significance remain to be defined. Genomic copy number variations have
been shown to affect the level of transcription in several tumor types. In
this study, we have combined array comparative genomic hybridization analysis of 13 RMS cell lines, supported by confirmatory PCR analyses, with their corresponding expression profiles. This identified sets of genes that are altered in their level of expression by genomic imbalances. We also show that the effect on gene expression was proportional to the level of genomic gain or loss.
Keywords: Rhabdomyosarcoma cell lines

overall_design: will be added later on

first: Marcel

last: Kool


title: Microarray Analysis of Lymphatic Tissue Reveals Stage-Specific, Gene-Expression Signatures in HIV-1 Infection

status: Public on Jun 02 2009

city: minneapolis

first: qingsheng

last: li

state: MN

address: Box 196, 420 Delaware ST SE

department: Microbiology

institute: University of Minnesota

summary: Untreated HIV-1 infection progresses through acute and asymptomatic stages to AIDS. While each of the three stages has well-known clinical, virologic and immunological characteristics, much less is known of the molecular mechanisms underlying each stage. Here we report lymphatic tissue microarray analyses revealing for the first time stage-specific patterns of gene expression during HIV-1 infection. We show that while there is a common set of key genes with altered expression throughout all stages, each stage has a unique gene-expression signature. The acute stage is most notably characterized by increased expression of hundreds of genes involved in immune activation, innate immune defenses (e.g.MDA-5, TLR-7 and -8, PKR, APOBEC3B, 3F, 3G), adaptive immunity, and in the pro-apoptotic Fas-Fas-L pathway. Yet, quite strikingly, the expression of nearly all acute-stage genes return to baseline levels in the asymptomatic stage, accompanying partial control of infection. In the AIDS stage, decreased expression of numerous genes involved in T cell signaling identifies genes contributing to T cell dysfunction. These common and stage-specific, gene-expression signatures provide new insights into the molecular mechanisms underlying the host response and the slow, natural course of HIV-1 infection.

overall_design: A total of 52 patients were analyzed: 10 patients unaffected, 18 patients with asymptomatic stages of AIDs, 16 patients with acute stages of AIDs, and 8 patients with AIDs.

first: Qingsheng

last: Li

first: Anthony

last: Smith

first: Timothy

last: Schacker

first: John

last: Carlis

first: Lijie

last: Duan

first: Cavan

last: Reilly

first: Ashley

middle: T

last: Haase


title: Expression data from human primary fibroblasts, endothelial and smooth muscle cells infected with Trypanosoma cruzi

city: Quito

first: Jaime

middle: Alfredo

last: Costales

address: 12 de Octubre y Patria

department: Biological Sciences

country: Ecuador

institute: Pontificia Universidad Catolica del Ecuador

summary: Trypanosoma cruzi is an obligate intracellular protozoan parasite that causes human Chagas’ disease, a leading cause of heart failure in Latin America. Using Affymetrix oligonucleotide arrays we screened phenotypically diverse human cells  (foreskin fibroblasts, microvascular endothelial cells and vascular smooth muscle cells) for a common transcriptional response signature to T. cruzi. A common feature was a prominent type I interferon response, indicative of a secondary response to secreted cytokines. Using transwell plates to distinguish cytokine-dependent and -independent gene expression profiles in T. cruzi-infected cells, a core cytokine-independent response was identified in fibroblasts and endothelial cells that featured metabolic and signaling pathways involved in cell proliferation, amino acid catabolism and response to wounding. Significant downregulation of genes involved in mitotic cell cycle and cell division predicted that T. cruzi infection impedes cell cycle progression in the host cell.

overall_design: Primary human foreskin fibroblasts and human microvascular endothelial cells were grown in transwell dishes to reach 80% confluency. The cells in the bottom of the transwell were infected with T. cruzi for 24 hours, while the cells on the top of the transwel were not infected but exposed to the same culture medium bathing the infected cells. Transwells containing uninfected cells in both levels were also included as controls.  Vascular smooth muscle cells were omitted from the transwell experiments due to difficulties obtaining adequate RNA from cells plated on the top chamber. Instead they were cultred in Petri dishes and mock/infected with T. cruzi for 24 or 48 hours.Total RNA was extracted and gene expression levels analyzed with Affymetrix microarrays. Two independent biological replicates were included for each type of treatment.

first: Johanna

last: Daily

first: Reddy

last: Gali

first: Barbara

last: Burleigh


title: Expression data from CXCR4pos (centroblast) and CXCR4neg (centrocyte) Human Germinal Center B cells

city: RENNES

first: Thierry

last: FEST

address: 2 avenue du Pr. Léon Bernard

country: France

institute: Unité INSERM

summary:
Functional discrimination between normal centroblast and centrocyte obtained from human inflamed tonsils after cell sorting.
We used microarrays to detail the segregation between these two B cell subsets

overall_design: Flow cytometry analysis was done on human germinal center B cells and cell subsets, i.e. CXCR4pos and CXCR4neg, sorted before RNA extraction and hybridization on Affymetrix microarrays. Both B-cell subsets where obtained from an identical tonsil allowing paired statistical analysis.

first: Simon

last: Le Gallou

last: Fest

first: Gersende

last: Caron


title: 8 hours BMP6 treated vs untreated human mesenchymal stem cells (hMSC)

status: Public on Jun 01 2009

city: Cold Spring Harbor

first: Weijun

last: Luo

address: 1 Bungtown Rd

institute: Cold Spring Harbor Lab

summary:
We have established that BMP6 is an important endogenous regulator of human osteoblast differentiation. Our preliminary experiment showed that 8 hour BMP6 treatment induced early osteoblast markers in hMSC.
In this study, we used microarrays to profile the global gene expression program in hMSC induced by BMP6 treatment and further identify the early osteogenic responses to BMP6 stimulation.

Keywords: Stress response

overall_design: The dataset contains a total of 4 gene chip measurements from duplicate experiments each with paired measurements of human MSC with or without 8 hours BMP6 treatment.

first: Michael

middle: S

last: Friedman

first: Peter

last: Woolf

first: Kurt

last: Hankenson


title: Evaluation of methods for amplification of picogram amounts of total RNA for whole genome expression profiling

city: Paris

first: charles

last: decraene

address: 26 rue d'ULM

institute: Institut Curie

summary: For more than a decade, microarrays have been a powerful and widely used tool to explore the transcriptome of biological systems. However, the amount of biological material from cell sorting or laser capture microdissection is much too small to perform microarray studies. To address this issue, RNA amplification methods have been developed to generate sufficient targets from picogram amounts of total RNA to perform microarray hybridisation. In this study, four commercial protocols for amplification of picograms amounts of input RNA for microarray expression profiling were evaluated and compared. The quantitative and qualitative performances of the methods were assessed. Microarrays were hybridised with the amplified targets and the amplification protocols were compared with respect to the quality of expression profiles, reproducibility within a concentration range of input RNA, and sensitivity.

overall_design:
Four commercial protocols for amplification of picograms amounts of input RNA for microarray expression profiling were evaluated and compared. For each protocol, one RNA amplification was performed from 250 pg, and one from 500 pg of human universal RNA by two operators in two independent laboratories and compared to the amplified aRNA obtained from 2 µg and 100 ng RNA inputs following the standard protocol proposed by Affymetrix. A negative control (amplification without total RNA) and a positive control (if available) were included in each experimental batch.
Samples indicating 50, 100, and 1000 pg RNA inputs correspond to 3 additional quantities of total RNA used to synthesise the cDNA target using the nugen protocol for comparison (250, 500 pg + 50, 100, 1000 pg).

first: Mathieu

last: Clément-Ziza

first: David

last: Gentien

first: Stanislas

last: Lyonnet

first: Jean-Paul

last: Thiery

first: Claude

last: Besmond

first: Charles

last: DECRAENE


title: GBM and microglia fraction of same glioblastoma multiforme (GBM)

status: Public on May 30 2009

city: Lausanne

first: Monika

middle: E.

last: Hegi

state: Vaud

address: Bugnon 46

department: Neurosurgery

country: Switzerland

institute: CHUV

summary: Little is known about the immune performance and interactions of CNS microglia/macrophages in glioma patients. Microglia/macrophages were found to be the predominant immune cell infiltrating gliomas (approximately 1% of total cells); others identified are myeloid dendritic cells (DCs), plasmacytoid DCs, and T cells. Using a procedure enriching for CD11b/c+CD45+ glioma-infiltrating microglia/macrophages (GIMs) from postoperative tissue specimens of glioma patients (Hussain et al. Neuro Oncol. 2006 J;8(3):261-79) gene expression profiles were obtained form paired samples. The expression profiles are used to identify expression signatures contributed by GIMs in glioblastoma data sets (Murat et al, submitted).

overall_design: Gene expression profiles of a set of paired samples consisting of glioblastoma and the respective GIM fraction from the same male patient.

first: Anastasia

last: Murat

first: Eugenia

last: Migliavacca

first: Mauro

last: Delorenzi

first: Amy

last: Heimberger


title: Differential gene expression in GBS6 cells after EWS-POU5F1 knockdown

status: Public on May 31 2009

city: Koto ward

first: Takashi

last: Fujino

state: Tokyo

address: 3-10-6 Ariake

department: Carcinogenesis

institute: The Cancer Institute of Japanese Foundation of Cancer Research

summary:
Our objective is to clarify the function of EWS-POU5F1 chimera.
Specifially, GBS6 cells were established from an undifferentiated bone sarcoma carrying translocation t(6;22)(p21;q12). The translocation resulted in a gene fusion between EWS and POU5F1. Gene expression analysis of t(6;22) undifferentiated sarcoma cell line GBS6 transfected with POU5F1 specific siRNA to investigate the function of EWS-POU5F1.

overall_design: Knockdown of EWS-POU5F1 using POU5F1 specific siRNAs. 3 control and 6 experimental replicates representing the same experiment repeated 3 times (1st, 2nd, 3rd).

first: Kimie

last: Nomura

first: Yuichi

last: Ishikawa

first: Hiroyuki

last: Aburatani

first: Takuro

last: Nakamura


title: Gene expression in macrophages treated with IFNalpha

status: Public on Jun 29 2009

city: Bethesda

first: Teresa

last: Wild

address: 30 Convent Drive

department: NIDCR

institute: NIH

summary: To study effects of IFNalpha treatment on monocyte-derived macrophages which may influence susceptibility or resistance to HIV.

overall_design: Human monocyte-derived macrophages were stimulated with IFNalpha and analyzed for global gene expression.

first: Sal

last: Nares

first: Zoila

last: Rangel

first: Peter

last: Munson

first: Sharon

last: Wahl


title: Synthetic Lethal Interaction Between Oncogenic KRAS Dependency and Suppression of STK33 in Human Cancer Cells

city: Berlin

first: Lars

last: Bullinger

address: Augustenburger Platz 1

department: Hematology, Oncology and Tumorimmunology

institute: Charité

summary: Many human oncogenes are challenging therapeutic targets. An alternative to direct targeting of oncogenes is to perform “synthetic lethality” screens for genes that are essential only in the context of specific cancer-causing mutations. We used high-throughput RNA interference (RNAi) to identify synthetic lethal interactions in cancer cells harboring mutant KRAS, the most commonly mutated human oncogene. We find that cells that are dependent on mutant KRAS exhibit sensitivity to suppression of the serine/threonine kinase STK33 irrespective of tissue origin, whereas STK33 is not required by KRAS-independent cells. STK33 promotes cancer cell viability in a kinase activity-dependent manner by regulating the suppression of mitochondrial apoptosis mediated through S6K1-induced inactivation of the death agonist BAD selectively in mutant KRAS-dependent cells. These observations identify STK33 as a target for treatment of the broad spectrum of mutant KRAS-driven cancers, and demonstrate the potential of RNAi screens for discovering critical functional dependencies created by oncogenic mutations that may enable therapeutic intervention for cancers associated with “undruggable” genetic alterations.

overall_design: NOMO-1 and SKM-1 acute myeloid leukemia (AML) cells were stably transduced with different pLKO.1puro lentiviral shRNA vectors targeting STK33 or a nontargeting control shRNA. VSV-G-pseudotyped lentiviral particles were produced by cotransfection of 293T cells with pLKO.1 constructs and the compatible packaging plasmids pMD.G and pCMVR8.91. Virus was harvested 48 and 72 hours after transfection, cells were incubated with lentiviral supernatants for 30 hours, and infected cells were selected with 2 µg/ml puromycin. RNA was isolated after 2 days of puromycin selection and isolation of viable cells by density gradient centrifugation, and gene expression was profiled using GeneChip Human Genome U133 Plus 2.0 microarrays (Affymetrix). Fluorescence ratios were normalized according to the RMA algorithm, and data were filtered as previously described (Bullinger et al. Blood 110:1291-300, 2007) using the BRB-ArrayTools software package. For subsequent analyses, only probe sets with a p-value for the log intensity variation of less than 0.01 were included. Average linkage clustering was used for hierarchical clustering (distance measure, correlation uncentered), and results were visualized using TreeView (Eisen et al. Proc Natl Acad Sci USA 95:14863-14868, 1998). Differentially expressed genes (p < 0.005) were identified by “class comparison analysis” for paired samples (cell line transduced with an shRNA targeting STK33 versus cell line transduced with a control shRNA) using the BRB-ArrayTools software package (Version 3.3.0 Beta_3; http://linus.nci.nih.gov/BRB-ArrayTools.html) and R (Version 2.2.1; http://www.r-project.org). Screening for an enrichment of genes belonging to distinct BioCarta pathways in the different gene sets was performed with the BRB Pathway Comparison tool computing several statistics, including the Fisher (LS) statistic and the Kolmogorov-Smirnov (KS) statistic. A pathway was considered differentially regulated if the significance level was less than 0.005.

first: Claudia

last: Scholl

first: Stefan

last: Fröhling

first: Gary

last: Gilliland


title: Defining the chromatin signature of inducible genes in T cells

city: Bruce

first: Kristine

last: Hardy

state: ACT

address: University of Canberra

country: Australia

institute: University of Canberra

type: Genome binding/occupancy profiling by genome tiling array

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

overall_design: Refer to individual Series


title: PAX2: A Potential Biomarker for Low Malignant Potential Ovarian Tumors and Low-Grade Serous Ovarian Carcinomas

city: Houston

first: Kwong-Kwok

last: Wong

state: TX

address: T4-3900, 1515 Holcombe Boulevard

department: Gynecologic Oncology and Reproductive Medicine

institute: UT M. D. Anderson Cancer Center

summary:
Objective: Ovarian tumors of low-malignant potential (LMP) and low-grade serous ovarian carcinomas are thought to represent different stages on a tumorigenic continuum and to develop along pathways distinct from that of high-grade serous ovarian carcinoma.  Past studies have utilized gene expression profiles to support this theory.  The objective of the current study was to identify new genes whose expression profiles in LMP ovarian tumors and low-grade ovarian carcinomas differ from that in high-grade ovarian carcinomas.

Methods: We used RNA from 3 normal human ovarian surface epithelia (HOSE) and from 10 low-grade and 10 high-grade serous ovarian carcinoma samples to perform gene expression profiling. Using real-time reverse-transcription polymerase chain reaction (RT-PCR), we evaluated changes in PAX2 mRNA expression in cDNA created from RNA extracted from an independent set of ovarian tissue samples (7 LMP tumors and 17 low-grade and 23 high-grade serous carcinomas).  We also examined  PAX2 expression using Western blot analysis of protein extracted from a set of ovarian LMP and low- and high-grade carcinoma tissue samples.  Additionally, we used immunohistochemistry (IHC) to validate PAX2 overexpression in a third independent set of paraffin ovarian tissue sections from 17 LMP tumors and 16 low- and 257 high-grade carcinomas.

Results:  Gene profiling revealed higher expression of PAX2 in low-grade than in high-grade ovarian carcinomas.  Real-time RT-PCR demonstrated a statistically significant difference in median PAX2 mRNA expression, expressed as fold change, among ovarian LMP tumor (1837.38), low-grade (183.12), and high-grade (3.72) carcinoma samples (p=0.015).  Western blot analysis revealed strong PAX2 expression in ovarian LMP and low-grade carcinoma samples but no PAX2 protein expression in high-grade carcinomas. On IHC, more LMP tumor and low-grade carcinoma samples expressed moderate to high levels of PAX2 than did high-grade ovarian carcinoma samples. The numbers of samples with strong nuclear staining was significantly higher for ovarian LMP tumors (10 of 17, p<0.001) and low-grade serous carcinomas (10 of 16, p<0.001) than for high-grade carcinomas (27 of 257).

Discussion:  Our identification and validation of higher PAX2 expression in ovarian LMP tumors and low-grade serous carcinomas than in high-grade carcinomas supports the two-tiered hypothesis that the first two are on a continuum and are distinct from high-grade ovarian carcinomas.  PAX2 may represent a potential biomarker and future therapeutic target for individualizing chemotherapy for ovarian LMP tumors and low-grade carcinomas in the future.

first: Celestine

last: Tung

first: Samuel

middle: C

last: Mok

first: Yvonne

last: Tsang

first: Zhifei

last: Zu

first: Jinsong

last: Liu

first: Michael

last: Deavers

first: Anais

last: Malpica

first: Judith

last: Wolf

first: Karen

middle: H

last: Lu

first: David

middle: M

last: Gershenson


title: Generation of Human Induced Pluripotent Stem Cells by Direct Delivery of Reprogramming Proteins

status: Public on May 29 2009

city: Belmont

first: Kwang-Soo

last: Kim

state: MA

address: 115 Mill st

department: Molecular neurobiology lab

institute: McLean Hospital

summary: To date, all methods to generate induced pluripotent stem (iPS) cells require the use of genetic materials and/or potentially mutagenic chemicals. Here we report the generation of stable human iPS cells from human fibroblasts by directly delivering defined reprogramming proteins. This system eliminates the potential risks associated with genetic and/or chemical manipulation, and could provide a safe and physiologically intact source of cells for regenerative medicine.

overall_design: Total RNAs were prepared from human fibroblasts, H9, and hiPS lines using TRIzol reagent (Invitrogen, Carlsbad, CA) and hybridized to Affymetrix Human Expression Array U133 Plus 2.0 analyzing over 47,000 human transcripts at the Harvard Partners Center for Genomics and Genetics. Detailed procedure is described in the website at http://www.hpcgg.org/Microarrays/overview.jsp

first: Dohoon

first: Chun-Hyung

first: Jung-Il

last: Moon

first: Young-Gie

last: Chung

first: Mi-Yoon

last: Chang

first: Baek-Soo

last: Han

first: Sanghyeok

last: Ko

first: Eungi

last: Yang

first: KwangYul

last: Cha

first: Robert

last: Lanza


title: HIV Integration analysis in quiescent CD4 T cells

city: Los Angeles

first: Jerome

middle: A

last: Zack

state: CA

address: 615 Charles Young Dr South

department: Medicine - Hem/Onc

institute: David Geffen School Of Medicine at UCLA

summary: This study examines the sites of HIV integration in quiescent CD4 T cells and compares them to activated T cells. The expression patterns of the sites hosting integration events were determined using microarray analysis data from quiescent and activated CD4 T cells.

overall_design: Integration sites were isolated by inverse PCR analysis. Quiescent and stimulated T cells from different donors were assayed in 10 µg of leukocyte total RNA using a high-density oligonucleotide array (U133a; Affymetrix, Santa Clara, Calif) at baseline and after PSD for genome-wide mRNA expression profiles. All assays were performed by the UCLA DNA Microarray Core (Affymetrix) following the manufacturer's standard protocol, with sample quality assured for RNA concentration and purity using a bioanalyzer (Agilent, Palo Alto, Calif) prior to probe synthesis. Following hybridization of fluorescent complementary RNA probes, microarrays were imaged using a scanner (Affymetrix), and low-level gene expression values were derived using GeneChip Operating Software (GCOS) (Affymetrix) and analyzed using dChip software (Harvard School of Public Health). The data submitted here have been normalized using RMAExpress.


title: Gene expression differences between TAF4b-KO, Het and WT ovaries at 3 weeks of age

city: Providence

first: Lindsay

last: Lovasco

state: RI

address: 70 Ship St.

department: MCB

institute: Brown University

summary:
The rapid decline of ovarian function in TAF4b-null mice begins in early postnatal life and follicle depletion is completed by sixteen weeks.
To uncover differences in gene expression that may underlie accelerated ovarian aging, we compared genome-wide expression profiles of three week old, pre-pubescent TAF4b-null and wild-type ovaries.

overall_design:
Total RNA from 9, 3-week-old mice (3 wild-type, 3 TAF4b-heterozygous, 3 TAF4b-null) was obtained as described as above.  RNA quality was checked using a Bioanalyzer, and concentration determined using a Nanodrop.
300 ng of each RNA sample was used in the Affymetrix Whole-transcript Sense Target Labeling Assay (Rev 3) followed by hybridization to a GeneChip® Mouse Gene 1.0 ST Array. 9 GeneChips were used to provide biological triplicates of each genotype.
The Affymetrix Expression Console (v 1.1) was used to normalize data and determine signal intensity (RMA-Sketch).

first: L


title: Functional collaboration of the meningioma 1 (MN1) oncogene with MLL-fusions in pediatric leukemia

city: Basel

first: Dragana

last: Jankovic

address: Hebelstrasse 20

department: Dept. of Research

institute: University Hospital Basel

summary: Expression of meningioma 1 (MN1) has been proposed to be a negative prognostic molecular marker in adult AML with normal cytogenetics, however its role in pediatric leukemia is unknown. We found elevated MN1 expression in 53 of 88 pediatric leukemia cases: significant amounts of MN1 were found in immature B-cell ALL and most cases of infant leukemia but no MN1 expression was detected in T-cell acute lymphoblastic leukemia (T-ALL). Interestingly 17 of 19 cases harboring MLL-X fusions showed also elevated MN1 expression. Lentiviral siRNA mediated MN1 knock-down resulted in cell cycle arrest and impaired clonogenic growth of 3 MLL-X-positive human leukemia cell lines overexpressing MN1 (THP-1, RS4;11, MOLM13). In a mouse MLL/ENL-induced leukemia MN1 overexpression resulted from retroviral provirus insertion. Strikingly co-expression of MN1 with MLL/ENL resulted in significantly reduced latency for induction of an AML phenotype in mice suggesting functional cooperation. MN1 overexpression in MLL/ENL-carrying cells resulted in expansion of the L-GMP population and facilitated disease induction in secondary recipients. Gene expression profiling allowed to define a number of potential MN1 hematopoietic targets. Up-regulation of CD34, FLT3, HLF, or DLK1 was validated in bone marrow transiently overexpressing MN1, in MN1-induced mouse leukemias, as well as in some cases of pediatric leukemias overexpressing MN1. Taken together, our work suggests that MN1 overexpression is essential for growth of leukemic cells, and that MN1 can act as a cooperating oncogene with MLL-X fusion genes most probably through modification of a distinct gene expression program that leads to expansion of a leukemia initiating cell population.

overall_design: In three independent experiments bone marrow cells were transduced with MSCV-MN1-IRES/YFP or empty vector. 72h after transduction EYFP-positive cells were FACS-sorted and RNA isolated by ion-exchange chromatography with RNAmini (Qiagen) according to the manufacturer’s protocol

first: Ting

last: Liu

first: Laurent

last: Brault

first: Sabine

last: Ehret

first: Vaia

last: Stavropoulu

first: Vincenco

last: Rossi

first: Andrea

last: Biondi

first: Juerg

last: Schwaller


title: Transcriptional profiling of bone marrow cells of MDS patients

status: Public on May 28 2009

first: Xianwen

last: Ren

address: 6565 Fannin Street

institute: The Methodist Hospital Research Institute

summary: Myelodysplastic Syndromes (MDSs) are a heterogeneous family of clonal disorders of hematopoietic stem cells characterized by ineffective hematopoiesis and frequently leukemia progression. To exlore how MDS develop into leukemia, we performed the transcriptional profiling of lesional cells and normal lymphoid cells from the MDS patients.

overall_design: Bone marrow cells from the MDS patients were sorted into blastic, myeloid, erythroid and lymphoid fractions by flow cytometry and then were profiled transcriptionally by Human Human Genome U133 Plus 2.0 arrays. Differentially expressed genes between lesional cells and lymphoid cells were identified by SAM.

first: Wanting

last: Huang

first: Xiaobo

last: Zhou

first: Chung-Che


title: Mesenchymal Stromal Cells of Different Donor Age

city: Aachen

first: Wolfgang

last: Wagner

address: Pauwelsstrasse 20

institute: RWTH Aachen University

summary: In this series we have analyzed the effect of donor age on the gene expression profile of mesenchymal stromal cells (alternatively named mesenchymal stem cells; MSC) from human bone marrow. Cells were taken from bone marrow aspirates from iliac crest (BM) of healthy donors or from the caput femoris (HIP) of elderly patients that received femoral head prosthesis.

overall_design: Mesenchymal stromal cells (MSC) were isolated from human bone marrow as described before  (Wagner et al., 2005, Exp Hematol, 33, 1402-1416; Wagner et al., 2006, Exp Hematol, 34, 536-548). Cells were always replated when grown to confluency. A sample for RNA isolation was taken at every passage until the cells finally became senescent. For this series (donor age) we have only used the samples of passage 2 to minimize effects by replicative senescence.

first: Simone

last: Bork

first: Patrick

last: Horn

first: Anthony

middle: D

last: Ho


title: Lipopolysaccharide-induced Changes in Gene Expression in Human Lung Microvascular Endothelial Cells over Time

first: Anya

middle: Carmen

last: Harry

address: 10 Center Dr. MSC 1662 Bldg 10

department: CCMD

summary:
The vascular endothelium may play a role in the response to infectious agents and in the pathophysiology of disease processes resulting in capillary leak such as septic shock and acute respiratory distress syndrome.  In order to study the effect of endotoxin on endothelial cell function, human lung microvascular endothelial cells in culture were exposed to lipopolysaccharide (LPS), 10 ng, for 4, 8, or 24 hours and changes in mRNA expression were studied using Affymetrix HG U133plus2 gene arrays.  A principal components analysis revealed that LPS treatment was the primary source of variability in the data.  LPS treatment of endothelial cells for 4, 8, or 24 hours resulted in the upregulation by two-fold or greater of 275, 260 and 141 genes respectively.  LPS treatment resulted in the down regulation by 50% or greater of 176, 263 and 79 genes at 4, 8, or 24 hours respectively.  Up regulated genes at 4 or 8 hours were enriched in those encoding for cytokines, secreted proteins, cell membrane proteins and proteins controlling signal transduction and transcriptional regulation.  Down regulated genes at each of the time points included those coding for cell membrane proteins, transcriptional regulation and metabolism.  At each time point, a significant proportion of the genes identified as changed were unique to that time point.
Keywords: Time course

overall_design: In order to study the effect of endotoxin on endothelial cell function, human lung microvascular endothelial cells in culture were exposed to lipopolysaccharide (LPS), 10 ng, for 4, 8, or 24 hours and changes in mRNA expression were studied using Affymetrix HG U133plus2 gene arrays.  Controls for each time point with no LPS exposure were also run.  An N of 4 for each time point and treatment was used.

first: Douglas

last: Joubert

first: Peter

middle: J

last: Munson

first: Jennifer

last: Barb

first: Grzegorz

last: Woszczek

first: Sahrudaya

last: Nagineni

first: Carolea

last: Logun

middle: F

last: Suffredini

first: Robert

last: Danner

first: James

last: Shelhamer


title: Expression analysis upon NMNAT1 knockdown in MCF-7 cells

city: Dallas

first: W. Lee

last: Kraus

address: 5323 Harry Hines Blvd.

institute: UT Southwestern Medical Center

summary: NMNAT1 is a nuclear enzyme in the mammalian NAD+ salvage pathway. Expression microarray analysis was used to study the effect of NMNAT1 knockdown on gene expression in MCF-7 breast cancer cells.

overall_design:
NMNAT1 stable knockdown was achieved using a retroviral shRNA construct. An shRNA directed against Luciferase was used to generate the Luc control cells.  Three independent cell populations with matching Luc controls were prepared for the expression analysis.  Each cell population was treated with either vehicle control (ethanol) or estradiol (E2) for 3 hours before harvest of RNA samples.  Four samples in one replicate (LUC2 CON, LUC2 E2, NMNAT2 CON and NMNAT2 E2) were hybridized to Affymetrix U133 Plus 2.0 arrays, while the other two replicates of eight samples were hybridized to Affymetrix U133A 2.0 arrays.

All 12 samples were included for the following data normalization steps: common probe sets on both U133A 2.0 and U133 Plus 2.0 platforms were selected; within each sample group hybridized to the same microarray platform, the signal values were log2 transformed, median centered for each array, and median centered for each gene; the data sets were further adjusted using the parametric empirical Bayes method (Combat R) to eliminate batch effect caused by the different array platforms.

first: Tong

last: Zhang

first: William


title: Defective Cohesin in CdLS Mediates Gene Expression with Characteristics of Transcription Factor and Insulator Activity

city: Philadelphia

first: IAN

middle: D.

last: KRANTZ

state: PA

address: 34th and Civic Blvd.

department: Division of Human and Molecular Genetics

institute: The Children's Hospital of Philadelphia

summary:
The Cohesin apparatus has a canonical role in sister chromatid cohesion. Heterozygous mutations in Nipped B-like (NIPBL), SMC1A, and SMC3 have been found in 60% of probands with Cornelia de Lange Syndrome (CdLS), a dominant multi-system genetic disorder with variable expression. We have performed a genome-wide transcription assessment as well as cohesin binding analysis using human lymphoblastoid cell lines (LCLs) from probands with CdLS and controls. Here, we report a unique profile of genes dysregulated in CdLS that correlates with different clinical presentations. Genome-wide analysis of cohesin binding demonstrates a preference for intergenic regions suggesting a cis-regulatory function mimicking that of an insulator.  However, the binding sites are enriched within the promoter regions of the dysregulated genes and are significantly decreased in CdLS probands, indicating an alternative role of cohesin as a classic transcription factor.  Cohesin also co-localizes with CTCF at the boundary elements affecting neighboring gene expression in CdLS probands. We propose that the CdLS phenotype is the result of dysregulated gene expression rather than defective sister chromatid cohesion.  Phenotype specific expression profiles are also described.

Keywords: Disease state analysis, Genetic modification

overall_design: To identify differentially expressed genes between CdLS patients and controls, age and gender matched samples from 16 normal Caucasian controls and 17 clinical severely affected Caucasian patients with NIPBL protein truncating mutations (nonsense or frameshift) were chosen as the training set for the discriminate analysis.  To validate the expression pattern obtained from the training set, 6 samples including 1 healthy control, 1 Egyptian CdLS patient, 2 Roberts syndrome patients, and 2 Alagille patients were used as the testing set.  All the 39 cell lines were growing anonymously and the processing of these 39 cell lines were randomized by genotypes to eliminate batch effects that may contribute to genotype-specific gene expression

first: Jinglan

last: Liu

first: Zhe

first: Eric

last: Rapapport

first: Matthew

last: Deardorff

first: Maninder

last: Kaur

first: Dinah

last: Clark

first: Stepheny

last: Tandy

first: Hugo

last: Vega

first: Nancy

middle: B

last: Spinner

first: Laird

middle: G

last: Jackson

first: Ian

last: Krantz


title: Gene expression in laboratory models and primary tumors in Small Cell Lung Cancer

status: Public on May 26 2009

city: Baltimore

first: Luigi

last: Marchionni

address: 1550 Orleans St., CRB2, Room 1M52

department: Oncology

institute: Johns Hopkins University

summary: Gene expression was measured on the Affymetrix platform in primary xenografts, xenograft-derived cell lines, secondary xenografts, normal lung, and primary tumors obtained from chemotherapy naive Small Cell Lung Cancer (SCLC). The SCLC primary xenografts were serially propagated in vivo in immunodeficient mice. Cell lines were derived from each xenograft and grown for 6 months using conventional tissue culture conditions. Secondary xenografts were obtained from cell cultures by re-implantation in immunodeficient mice. Such SCLC laboratory models were analyzed along with conventional SCLC cell lines and the derivative secondary xenografts, with normal lung and primary tumors, to assess irreversible gene expression changes induced by culturing conditions.

overall_design: SCLC primary xenografts were compared to the corresponding xenograft-derived cell lines, and to the secondary xenografts established from the cell lines using the Affymetrix GeneChip Human Genome U133 Plus 2.0 Array. Gene expression from SCLC primary tumors was measured using the Affymetrix GeneChip Human Genome U133A 2.0 Array. 3 datasets: GSM380476-GSM380512, GSM380513-GSM380516, and GSM380517-GSM380520

first: Neil

last: Watkins

first: Craig

last: Peacock

first: Vincent

last: Daniel

first: Jared

last: Hierman


title: Expression analysis in a breast cancer metastasis model

city: London

first: Ann

last: Chambers

state: Ontario

address: 790 Commissioner's Road E

department: Victoria research labs

institute: London Regional Cancer program

summary: This study compares a cell line (MDA-MB-468GFP-LN) that aggressively metastasizes to lymph nodes to its parental line MDA-MB-468GFP.  Derivation of the lines is described in Vantyghem et al, Clinical & Experimental Metastasis (2005) 22: 351–361.  The goal here was to compare the gene expression profile of MDA-MB-468GFP-LN to MDA-MB-468GFP,  Compare differential expression to databases of genes known to be involved in either cancer stem cell identification or lymph node specific metastasis in large scale clinical studies, and to confirm genes by RT-PCR

overall_design: For each cell line, 3 biological replicates were grown, RNA isolated, and gene expression profiles determined using Affymetrix HGU133_Plus_2 genechips.  The MDA-MB-468GFP-LN cell line was the "experimental" group, and the MDA-MB-468GFP was the control group. Intensity values were calculated using MAS5.0, Data was then imported into Genespring 7.0, and ANOVA (nominal alpha set to 0.05) was used to determine probe sets showing significant differential expression.  A Benjamini and Hochberg algorithm was implemented in Genespring to reduce the false discovery rate.

first: David

last: Rodenhiser

first: Alan

last: Tuck

first: Joseph

last: Andrews

first: Terlika

last: Sharma

first: Wendy

last: Kennett

first: Sharon

last: Vantyghem


title: SIRT1-Dependent Gene Regulation Through Promoter-Directed Recruitment of a Nuclear NAD+ Synthase

first: W. Lee

last: Kraus

summary:
In mammals, nicotinamide phosphoribosyltransferase (NAMPT) and nicotinamide mononucleotide adenylyltransferase 1 (NMNAT-1) constitute a nuclear NAD+ salvage pathway, regulating cellular functions of the NAD+-dependent deacetylase SIRT1.  However, little is known about the molecular mechanisms by which NAD+ biosynthesis controls gene transcription in the nucleus.  In this study, we show that stable knockdown of NAMPT or NMNAT-1 in MCF-7 breast cancer cells significantly reduced total cellular NAD+ levels.  Expression microarray analyses demonstrate that both enzymes have broad and overlapping functions in gene regulation.  SIRT1 is a key mediator of NAMPT- and NMNAT-1-dependent gene regulation, and is found at promoters of many of the target genes.  Furthermore, SIRT1 deacetylase activity at these promoters is regulated by NAMPT and NMNAT-1.  Most significantly, NMNAT-1 interacts with SIRT1 and is recruited to target gene promoters by SIRT1.  Our results reveal an unexpected mechanism for the direct control of SIRT1 deacetylase activity at target gene promoters by NMNAT-1.  Interactions between NMNAT-1 and SIRT1 at gene promoters may provide a platform for integration of multiple signaling pathways that regulate transcription.

This SuperSeries is composed of the SubSeries listed below.

overall_design:
Refer to individual Series.
Each of the 3 Series has its own matching luciferase knockdown controls and the three data sets were generated independently of each other.

first: Tong

last: Zhang

first: Kristine

last: Frizzell

first: Matthew

last: Gamble

first: William


title: Differential gene expression of young and senescent HUVECs under static and laminar shear stress conditions

status: Public on May 23 2009

city: Daegu

first: Yong Chool

last: Boo

address: 101 Dongindong

department: Department of Molecular Medicine

country: South Korea

institute: Kyungpook National University School of Medicine

summary:
Laminar shear stress due to constant blood flow is known to play a critical role in maintaining vascular health. In contrast, endothelial cell senescence appears to be closely associated with the incidence of vascular disorder. In an attempt to identify functional biomarkers for age-related vascular health/disease, the present study investigated differential gene expression of young and senescent human umbilical vein endothelial cells (HUVECs) under static and laminar shear stress.

We used a cDNA microarray method to compare gene expression profiles of young and senescent HUVECs under static and laminar shear stress conditions.

Keywords: stress response, age state analysis

overall_design: Senescent cells were prepared by continuous subculture in vitro, and a cone-and-plate device was used to impose laminar shear stress onto cells. Young and senescent cells were exposed to laminar shear stress or maintained under static conditions. Total mRNA was extracted and gene expression profiles were analyzed by cDNA microarray.

first: Gyeong

middle: I

last: Mun

first: Yong