title: Expression data from Fog1+/+ and Fog1 ki/ki mouse megakaryocyte-erythroid progenitors (MEP).

status: Public on Apr 11 2010

city: Philadelphia

first: Gregory

middle: D

last: Gregory

address: 3615 Civic Center Blvd, ARC 315

department: Pediatrics/Hematology

institute: Children's Hospital of Philadelphia

summary:
The transcription co-factor FOG1 interacts with the chromatin remodeling complex NuRD to mediate gene activation and gene repression during hematopoiesis. We have generated mice with a targeted mutation in the endogenous Fog1 locus that results in an N-ternimal mutation in FOG1 that disrupts the interaction with NuRD.
We used gene expression microarrays to explore the global transcriptional programs regulated by FOG1 and NuRD in megakaryocyte-erythroid progenitors (MEP) to aid in understanding its role during hematopoiesis.

overall_design: Flow cytometry was used to isolate Megakaryocyte-Erythroid progenitors (MEP) from murine bone marrow. MEP were identified as Lineage neg, kit pos, Sca1 neg, CD34 neg, FcgrII/III low cells.

first: Zhe

last: Zhang

first: Gerd

last: Blobel


title: Analysis of differences in gene expression due to small adaptive mutations in RNA polymerase B' subunit (rpoC)

status: Public on Apr 01 2010

city: La Jolla

first: Bernhard

last: Palsson

state: CA

address: 9500 Gilman Dr.

department: Bioengineering

country: USA

institute: UCSD

summary: Studies of the RNA polymerase-binding molecule ppGpp in bacteria and plants have shown that changes to the kinetics of the RNA polymerase can have dramatic biological effects in the short-term as a stress response.  Here we describe the reprogramming of the kinetic parameters of the RNAP through mutations arising during laboratory adaptive evolution of Escherichia coli in minimal media.  The mutations cause a 10- to 30-fold decrease in open complex stability at a ribosomal promoter and approximately a 10-fold decrease in transcriptional pausing in the his operon.  The kinetic changes coincide with large scale transcriptional changes, including strong downregulation of motility, acid-resistance, fimbria, and curlin genes which are observed in site-directed mutants containing the RNA polymerase mutations as well as the evolved strains harboring the mutations.  Site-directed mutants also grow 60% faster than the parent strain and convert the carbon-source 15% to 35% more efficiently to biomass.  The results show that long-term adjustment of the kinetic parameters of RNA polymerase through mutation can be important for adaptation to a condition.

overall_design: Mutations in the RNA polymerase beta prime subunit (rpoC) were discovered in E. coli following adaptation to continual logarithmic growth (OD <= 0.3) in glycerol M9 minimal media at 30 C.  We used site-directed mutagenesis to make strains of E. coli isogenic to wild-type except for single adaptive rpoC mutations.  We found they increase growth rate in this condition by 60%.  In order to understand how the mutations affect gene expression in this condition, we extracted total mRNA from the strains, which had been growing in the adaptive evolution condition, at OD=0.3.  There were three RNAP mutants and the wild-type (E. coli K-12 MG1655).  Each strain had three flasks from which RNA was extracted (three biological replicates).  There were no technical replicates.  The mRNA was synthesized into cDNA, labeled, and hybridized to an Affymetrix E. coli 2.0 GeneChip.

first: Tom

middle: M

last: Conrad

first: Michael

last: Frazier

first: Andrew

middle: R

last: Joyce

first: Robert

last: Landick

middle: O


title: Basal Gene Expression Measurements in HEK293T Cells

status: Public on Mar 31 2010

city: Research Triangle Park

first: Russell

middle: Scott

last: Thomas

state: NC

address: 6 Davis Drive

institute: The Hamner Institutes for Health Sciences

summary: Gene expression microarray profile for human embryonic kidney cells (HEK293T, CRL-11268) under untreated conditions.

overall_design: Gene expression microarray profile for human embryonic kidney cells (HEK293T, CRL-11268) under untreated conditions (DMEM, 10% FBS).

middle: S

first: Frank

last: Boellmann


title: Human B cell subsets

city: Sydney

first: Santi

last: Suryani

state: NSW

address: 384 Victoria Street, Darlinghurst

department: Immunology and Inflammation

country: Australia

institute: Garvan Institute of Medical Research

summary: Goals/objectives: to identify various gene expression in B cell subsets derived from human PBMC and cord blood

overall_design:
Sample: human PBMC and human cord blood

Cell subsets: memory B cell (CD20+CD10-CD27+), naive B cell (CD20+CD10-CD27-), CD21lo transitional B cell (CD20+CD10+CD27-CD21lo), CD21hi transitional B cell (CD20+CD10+CD27-CD21hi)

Number of sample: PBMC (pooled from 2 donors), cord blood (pooled from 2-3 donors)

Number of repeats: 2

Microarray: Affymetrix HU133Plus2

RNA extraction: Trizol (Invitrogen)

RNA preparation/hybridization: All according to affymetrix protocol

first: Stuart

middle: G

last: Tangye


title: Gene expression profiles regulated by Stat5a/b vs. Stat3 in human prostate cancer cells.

status: Public on Apr 30 2010

first: Marja

last: Nevalainen

state: PA

department: Cancer Biology

institute: Thomas Jefferson University

summary:
Identification of the molecular changes that promote viability and metastatic behavior of prostate cancer cells is critical for the development of improved therapeutic interventions for prostate cancer. Stat5a/b and Stat3 are both constitutively active in locally-confined and advanced prostate cancer, and both transcription factors have been reported to be critical for the viability and growth of prostate cancer cells.
We used microarrays to compare gene expression profiles regulated by Stat5a/b vs. Stat3 in human prostate cancer cells.

overall_design: DU145 and CWR22Rv1 human prostate cancer cells were transfected with Stat3 siRNA, Stat5a/b siRNA or scramble siRNA as control. After 48 h, the cells were harvested and total RNA was prepared for Affymetrix microarrays.

first: Lei

last: Gu

first: Ayush

last: Dagvadorj

first: Jacqueline

last: Lutz

first: Benjamin

last: Leiby

first: Gloria

last: Bonucelli

middle: P

last: Lisanti

first: Sankar

last: Addya

first: Paolo

last: Fortina

first: Abhijit

last: Dasgupta

first: Terry

last: Hyslop

first: Johng

last: Rhimm

first: Lukas

last: Bubendorf

middle: T


title: Gene array data for Fas knock-out human cancer cell line and mouse liver tissue

status: Public on Apr 02 2010

city: Chicago

first: Marcus

last: Peter

state: IL

address: 303 East Superior Street, Lurie 6-123

institute: Northwestern University Feinberg School of Medicine

summary:
CD95 (also called FAS and APO-1) is a prototypical death receptor that
regulates tissue homeostasis mainly in the immune system through induction of apoptosis. During cancer progression CD95 is frequently downregulated or cells are rendered apoptosis resistant raising the possibility that loss of CD95 is part of a mechanism for tumour evasion. However, complete loss of CD95 is rarely seen in human cancers and many cancer cells express large quantities of CD95 and are highly sensitive to CD95 mediated apoptosis in vitro. Furthermore, cancer patients frequently have elevated levels of the physiological ligand for CD95, CD95L. These data raise the intriguing possibility that CD95 could actually promote the growth of tumours through its nonapoptotic activities. Here we show that cancer cells in general, regardless of their CD95 apoptosis sensitivity, depend on constitutive activity of CD95, stimulated by cancer-produced CD95L, for optimal growth. Consistently, loss of CD95 in mouse models of ovarian cancer and liver cancer reduces cancer incidence as well as the size of the tumours. The tumorigenic activity of CD95 is mediated by a pathway involving JNK and c-Jun. These results demonstrate that CD95 plays a major growth promoting role during tumorigenesis and suggest that efforts to inhibit its activity rather than to enhance its activation should be considered during cancer therapy.

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus

overall_design: There are 3 arrays for human ovarian cancer cell line, 2 arrays for human liver cancer cell line, and 2 arrays for mouse liver tissue. All the arrays are paired arrays with or without Fas knock-out.

first: Lina

last: Chen

first: Sun-Mi

last: Park

first: Alexei

middle: V

last: Tumanov

first: Annika

last: Hau

first: Kenjiro

last: Sawada

first: Christine

last: Feig

first: Jerrold

last: Turner

first: Yang-Xin

last: Fu

first: Iris

last: Romero

first: Ernst

last: Lengyel

middle: E


title: Global transcriptional response of macrophage-like THP-1 cells

city: Galveston

first: Ashok

middle: K

last: Chopra

state: TX

address: 301 University Blvd.

department: Microbiology & Immunology

institute: University of Texas Medical Branch

summary: Shiga toxins (Stxs) are bacterial cytotoxins produced by the enteric pathogens Shigella dysenteriae serotype 1 and some serotypes of Escherichia coli that cause bacillary dysentery and hemorrhagic colitis, respectively. To date, approaches to studying the capacity of Stxs to alter gene expression in intoxicated cells have been limited to individual genes. However, it is known that many of the signaling pathways activated by Stxs regulate the expression of multiple genes in mammalian cells. To expand the scope of analysis of gene expression and to better understand the underlying mechanisms for the various effects of Stxs on cell functions, we carried out comparative microarray analyses to characterize the global transcriptional response of human macrophage-like THP-1 cells to Shiga toxin type 1 (Stx1) and LPS. Data were analyzed using a rigorous combinatorial approach with three separate statistical algorithms. Thirty-six genes met the criteria of up-regulated expression in response to Stx1 treatment with 14 genes uniquely up-regulated by Stx1. Microarray data were validated by real time RT-PCR for genes encoding Egr-1 (transcriptional regulator), COX-2 (inflammation), and DUSP1, 5 and 10 (regulation of MAPK signaling). Stx1-mediated signaling through ERK1/2 and Egr-1 appears to be involved in the increased expression of the proinflammatory mediator TNF-α. Activation of COX-2 expression is associated with the increased production of proinflammatory and vasoactive eicosanoids. However, the capacity of Stx1 to increase the expression of genes encoding phosphatases suggests that mechanisms to dampen the macrophage proinflammatory response may be built into host response to the toxins.

overall_design: Three separate experiments were performed for each of three treatment types: 3 untreated controls, 3 Stx-1 treated cell (400 ng/ml for 6h), 3 LPS-stimulated cells (200 ng/ml for 6h). Total RNA was isolated, processexc, and hybridized to a total of 9 Affymetrix human HG U133 arrays.

first: Dinorah

last: Leyva-Illades

first: Rama

last: Cherla

first: Cristi

middle: L

last: Galindo

first: Vernon

last: Tesh


title: Pseudopod Experiment

status: Public on Mar 30 2010

city: Vancouver

first: Ivan

middle: Robert

last: Nabi

state: British columbia

address: LSI, 2350 health sciences Mall

department: CPS

country: Canada

institute: University of British Columbia

summary:
Cell body and pseudopod RNA are differentially regulated during the migration of the metastatic cancer cells.We wanted to identify the RNA which are upregulated in the pseudopodial (PS) fraction as compared to cell body fraction (CB).
We used microarray to see which are the RNAs upregulated in the PS fraction as compared to CB fraction

overall_design: PS and CB fractions were isolated from six different metatstatic cell lines


title: Regulation of gene expression in murine liver by IL-6

status: Public on Mar 25 2010

city: Vienna

first: Martin

last: Bilban

country: Austria

institute: Medical University of Vienna

summary: STEAP4 is a plasma membrane metallo-reductase involved in the transport of iron and copper. Recently, STEAP4 was implicated in promoting insulin sensitivity by acting in white adipose tissue (WAT) to control the production of inflammatory cytokines such as IL-6. Indeed, the loss of STEAP4 expression in mice leads to increased production of inflammatory cytokines in visceral WAT and systemic insulin resistance. In this report, we demonstrate that in mouse liver STEAP4 is produced at significant levels and that STEAP4 transcription is induced by IL-6. We further demonstrate that the STEAP4 gene is a direct target of phosphorylated STAT3 in mouse liver. In addition, hepatic STEAP4 expression is regulated by feeding and fasting, and obesity leads to the induction of STEAP4 expression in the liver. Interestingly, the regulation of STEAP4 in both feeding and fasting and the obese state appears to require the transcription factor C/EBPalpha that may act in concert with STAT3 as they both bind to the proximal STEAP4 promoter in vivo. Taken together these data suggest the transcriptional regulation of hepatic STEAP4 may play a critical role in the response to nutritional and inflammatory stress and contribute to the protective effect of STEAP4 in vivo.

overall_design: 10-week old male C57BL6 mice were fasted for 16 h overnight and then given either saline or IL-6 (100 ng/mouse) injections intraperitoneally for 1 h. Mice were euthanized using CO2, and the livers were collected and snap-frozen in liquid nitrogen and stored at -800C until further use.

first: Preeti

last: Ramadoss

first: Anthony

middle: N

last: Hollenberg


title: Plasma cells from 52 patients with multiple myeloma: mRNA and miRNA expression profiling

status: Public on Mar 26 2010

city: Little Rock

first: Yiming

last: Zhou

state: AR

address: 4301 West Markham St., Slot 776

institute: Myeloma Institute for Research and Therapy

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

summary: We used microarray analyses of patient myeloma cells (n=52) to correlate individual miRNA expression profiles with GEP-based risk defined by mRNA expression profilesx as well as clinical features of the disease. Unlike for mRNAs, genome-wide elevation of miRNA expression patterns were significantly positively associated with a mRNA-based GEP-risk score (P <.01) and proliferation index (P <.05). Consistent with our observation of global deregulation of miRNA expression profiles, silencing EIF2C2/AGO2, a gene component of the mRNA-based high-risk signature and a master regulator of the genesis and functionality of all miRNAs, dramatically decreased viability in myeloma cell lines.

overall_design:
mRNA expression profiling: We performed protein-coding gene expression profiles of myeloma cells from newly diagnosed patients with different molecularly defined disease types.

miRNA expression profiling: We used microarray analyses of patient myeloma cells (n=52) to correlate individual miRNA expression profiles with GEP-based risk defined by mRNA expression profiles as well as clinical features of the disease.

first: John

last: Shaughnessy

first: Owen

last: Stephens

first: Lijuan

last: Chen

first: Xiaosong

last: Wu

first: Bart

last: Barlogie


title: Gene expression profiles of E15.5 endothelial cells isolated from TIE2-GFP transgenic mice using FACS. (GUDMAP Series ID:38)

status: Public on Mar 23 2010

city: Edinburgh

first: GUDMAP

last: Developers

address: Crewe Road

country: United Kingdom

institute: IGMM MRC Human Genetics Unit

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

overall_design: Tie2-GFP transgenic mice were utilized to isolate the endothelial cell population from  E15.5 embryonic  kidneys.  The endothelial cells were isolated from embryos using trypsin treatment and FACS.   The RNA was isolated from purified endothelial cells and the gene expression profiles were determined by microarrays.

first: Steve

last: Potter

first: Eric

last: Brunskill


title: Altered levels of MOF and decreased levels of H4K16ac correlate with a defective DNA damage response (DDR).

status: Public on Mar 15 2010

city: St Louis

first: Rekha

last: Meyer

state: MO

address: 4320 Forest Park Av

institute: Washington University School of Medicine

summary:
Full title: Altered levels of MOF (member of MYST family histone acetyl transferase) and decreased levels of H4K16ac correlate with a defective DNA damage response (DDR).
The human MOF gene encodes a protein that specifically acetylates histone H4 at lysine 16 (H4K16ac). Here we show that altered levels of H4K16ac correlate with a defective DNA damage response (DDR) to ionizing radiation (IR). The defect however is not due to altered expression of proteins involved in DDR. Specific inhibition of H4K16ac deacetylation in MOF-depleted cells rescued IR-induced abrogation of DDR. MOF was found associated with DNA-dependent protein kinase catalytic subunit (DNAPKcs), a protein involved in non-homologous end joining (NHEJ) repair, whose ATMdependent IR-induced phosphorylation was abrogated in MOF-depleted cells. Our data indicate that MOF depletion greatly decreased the repair of DNA double-strand breaks (DSBs) by NHEJ and homologous recombination (HR). In addition, the MOF protein activity associates with chromatin upon DNA damage and colocalizes with the synaptonemal complex in male meiocytes. We propose that MOF, through H4K16ac, plays a critical role in the cellular DNA damage response.

Keywords: Cell type comparison

overall_design: HEK293 cells were transfected with plasmids encoding hMOF for over-expression of the histone acetyl transferase that leads to elevated levels of acetylation of Lysine 16 of histone H4. siRNA mediated knock-down of hMOF was performed to deplete the H4K16ac levels. Total RNA samples for expression profiling was obtained from wild type (293 cells without any treatment), hMOF over-expressed and hMOF knock-down 293 cell lines. Each sample was analyzed in triplicates using EGPF dsRNA treated samples as control.

first: Girdhar

last: Sharma

first: Tej

last: Pandita


title: Molecular signatures in natural-killer (NK) cell lymphoma

status: Public on Mar 18 2010

city: omaha

first: Javeed

last: Iqbal

state: NE

address: 40th street

department: Pathology and Microbiology

institute: University of Nebraska Medical Center

summary: NK-cell lymphoma shares strikingly similar molecular features with a distinct subset of gamma-delta T-cell lymphoma. Gene expression profiling of NK-cell lymphoma patient samples was performed to investigate whether molecular signatures can be used to identify entities of peripheral T-cell lymphoma (PTCL) with NK-cell-like features.

overall_design: Gene expression profiling was performed on NK-cell maligancies to examine extranodal NK/T-cell lymphoma (ENKTL) and aggressive NK-cell leukemia (ANKL) and well-characterized cell lines of NK- and T-cell lineages to define molecular classifiers that can distinguish ENKTL from other lymphomas.


title: Expression levels in immortalized B cells from unrelated individuals and twins undergoing ER stress

first: Renuka

last: Nayak

address: 3516 Civic Center Blvd

institute: HHMI, University of Pennsylvania

summary:
The accumulation of unfolded or misfolded proteins in the endoplasmic reticulum (ER) results in the condition called “ER stress” which induces the unfolded protein response (UPR) which is a complex cellular process that includes changes in expression of many genes. Failure to restore homeostasis in the ER is associated with human diseases. To identify the underlying changes in gene expression in response to ER stress, we induced ER stress in human B-cells and then measured gene expression at 10 time-points. We followed up those results by studying cells from 60 unrelated people. We rediscovered genes that were known to play a role in ER stress response and uncovered several thousand genes that are not known to be involved. Two of these are VLDLR and INHBE which showed significant increase in expression following ER stress in B-cells and
in primary fibroblasts. To study the links between unfolded protein response and disease susceptibility, we identified ER stress responsive genes that are associated with human diseases and assessed individual differences in ER stress response. Many of the UPR genes are associated with Mendelian disorders such as Wolfram syndrome and complex
human diseases including amyotrophic lateral sclerosis and diabetes. Data from two independent samples showed extensive individual variability in ER stress response. Additional analyses with monozygotic twins revealed significant correlations within twin pairs in their responses to ER stress thus showing evidence for heritable variation among individuals. These results have implications for basic understanding of ER function and its role in disease susceptibility.

Keywords: array-based gene expression

overall_design:
We measured gene expression levels in immortalized B cells from members of 60 unrelated CEPH-Utah grandparents. Each individual was treated for 8 hours with either DMSO or with 4 ug/ml of tunicamycin. Gene expression was measured to identify tunicamycin-responsive genes.
To assess whether there is a genetic component to the individual variation in gene expression response to ER stress, we  used microarrays to measure expression of genes in 26 monozygotic twin pairs treated with either DMSO or 500 nM thapsigargin for 4 hours.

first: Beth

middle: A

last: Dombroski

first: Kathryn

last: Ewens

first: Wendy

last: Ankener

first: Vivian

last: Cheung

first: Richard

last: Spielman


title: Cell-Specific Gene Expression in Langerhans Cell Histiocytosis

city: Houston

first: Carl

last: Allen

address: 6621 Fannin St

department: Pediatrics

institute: Texas Children's Cancer Center/Baylor College of Medicine

summary: Langerhans-cell histiocytosis (LCH) is characterized by heterogeneous lesions containing CD207+ Langerhans cells (LCs) and lymphocytes.   In this study, we isolated CD207+ cells and CD3+ T cells from LCH lesions to determine cell-specific gene expression.  Compared to control epidermal CD207+ cells, the LCH CD207+ cells yielded 2113 differentially-expressed genes (FDR<0.01).  Surprisingly, expression of many genes previously associated with LCH, including cell-cycle regulators, pro-inflammatory cytokines and chemokines were not significantly different from control LCs in our study.  However, several novel genes whose products activate and recruit T cells to sites of inflammation, including SPP1 (osteopontin), were highly over-expressed in LCH CD207+ cells.  Furthermore, several genes associated with immature myeloid dendritic cells were over-expressed in LCH CD207+ cells.  Compared to the peripheral CD3+ cells from LCH patients, the LCH lesion CD3+ cells yielded only 162 differentially-regulated genes (FDR<0.01), and the expression profile of the LCH lesion CD3+ cells was consistent with an activated regulatory T cell phenotype with increased expression of FOXP3, CTLA4 as well as SPP1.  Based on these results, we propose a new model of LCH pathogenesis in which lesions do not arise from epidermal Langerhans cells, but from accumulation of bone-marrow derived immature myeloid dendritic cells that recruit activated lymphocytes.

overall_design: Cell-specific gene expression from LCH biopsy specimens was evaluated by comparing hybridization signal from amplified cDNA on Affymetrix gene chips (U133A Plus 2.0) (Table1).  Three sets of comparisons were performed: 1) Thirteen LCH CD207+ samples were compared to 12 control skin LCH CD207+ samples. 2) Seven LCH lesion CD3+ samples were compared to 7 peripheral blood CD3+ samples from the same patients.  3) Twelve LCH lesion CD3+ samples were compared to 4 pooled control tonsil CD3+ samples (5 individual tonsil CD3+ samples/pool).

first: Kenneth

last: McClain

first: Eastwood

last: Leung

first: Tsz-Kwong

last: Man

first: Alexander

last: Yu

first: Sivashankarappa

last: Gurusiddappa

first: Trishia

last: Peters

first: Michelle

last: Phillips

first: Miriam

last: Merad

first: M

middle: J

last: Hicks

first: Liunan

last: Li


title: Expression data from total knee arthroplasty patients

city: Dublin

first: Kevin

last: Mulhall

address: Belfield

country: Ireland

institute: University College Dublin

summary:
Ischaemic preconditioning is a method of protecting tissue against ischaemia-reperfusion injury. It is an innate protective mechanism that increases a tissue's tolerance to prolonged ischaemia when it is first subjected to short burst of ischaemia and reperfusion.  It is thought to provide this protection by increasing the tissue's tolerance to ischaemia, therby reducing oxidative stress, inflammation and apoptosis in the preconditioned tissue.
We used microarrays to investigate the genomic response induced by ischaemic preconditioning in muscle biopsies taken from the operative leg of total knee arthroplasty patients in order to gain insight into the ischaemic preconditioning mechanism.

overall_design: Patients undergoing primary knee arthroplasty were randomised to control and treatment (ischaemic preconditioning) groups. Patients in the treatment group received a preconditioning stimulus immediately prior to surgery. The ischaemic preconditioning stimulus consisted of three five-minute periods of tourniquet insufflation on the lower operative limb, interrupted by five minute periods of reperfusion. All patients had a tourniquet applied to the lower limb after the administration of spinal anaesthesia, as per normal protocol for knee arthroplasty surgery. Muscle biopsies were taken from the quadriceps muscle of the operative knee at the immediate onset of surgery (T0) and at 1 hour into surgery (T1). Total RNA was extracted from biospies of four control and four treatment patients and hybridised to the Affymetrix Human U133 2.0 chip.

first: Pauline

last: Walsh

first: Terence

last: Murphy


title: Gene expression profiles of myeloma cells interacting with bone marrow stromal cells in vitro

status: Public on Mar 14 2010

city: Boston

first: Constantine

middle: S.

last: Mitsiades

state: MA

address: 44 Binney Street

department: Medical Oncology

institute: Dana-Farber Cancer Institute

summary: Conventional anti-cancer drug screening is typically performed in the absence of accessory cells (e.g. stromal cells) of the tumor microenvironment, which can profoundly alter anti-tumor drug activity. To address this major limitation, we have developed assays (e.g. the tumor cell-specific in vitro bioluminescence imaging (CS-BLI) assay) to selectively quantify tumor cell viability, in presence vs. absence of non-malignant stromal cells or drug treatment. These assays have allowed us to identify that neoplastic cells from diverse malignancies exhibit stroma-induced resistance to different anti-tumor agents. In this analysis, we evaluated the molecular changes triggered in myeloma cells by their in vitro interaction with stromal cells. The transcriptional profile of 3 human multiple myeloma (MM) cell lines (MM.1S, MM.1R, INA-6) co-cultured with stromal cells vs. when cultured alone was characterized by oligonucleotide microarray analysis, using the human U133 plus 2.0 Affymetrix GeneChip.

overall_design: Three human multiple myeloma (MM) cell lines (MM.1S, MM.1R, INA-6) stably expressing green fluorescent protein (GFP) were cultured in vitro for 24hrs either alone or in the presence of the human bone marrow stromal cell line HS-5. Fluorescence activated cell sorting was used to separate the GFP+ MM cells from GFP- stromal cells. The gene expression profiles of MM cells after their co-culture with stromal cells were compared with the profiles of MM cells cultured alone, according to previously described protocols for total RNA extraction and purification; cDNA synthesis; production of biotin-labeled cRNA; hybridization of cRNA with U133plus2.0 Affymetrix gene chips; and scanning of image output files. Scanned image output files were analyzed using DNA-Chip Analyzer (dChip) (www.dchip.org), including conversion to DCP files, normalization and modeling, and averaging of duplicate chips according to standard parameters recommended by the software. For each cell line, the gene expression profile in the presence of stomal cells was compared to the profile of the same cell line cultured in the absence of stromal cells. Technical replicates for each condition were analyzed (total of 12 gene expression profiles).

first: Douglas

middle: W

last: McMillin


title: Gene expression profiles of adult mesangial cells isolated from Meis1-EGFP transgenic mice using FACS. (GUDMAP Series ID: 37)

status: Public on Mar 13 2010

first: GUDMAP

last: Developers

overall_design: Meis1-GFP BAC transgenic mice were utilized to isolate the mesangial cells from adult  kidneys.  The mesangial cells were isolated from the glomerulus using collagenase digestion, differential sieving, trypsin treatment and FACS.   The RNA was isolated from purified mesangial cells and the gene expression profiles were determined by microarrays.

first: Steve

last: Potter

first: Eric

last: Brunskill


title: Members of the microRNA-17-92 cluster exhibit a cell intrinsic anti-angiogenic function in endothelial cells

city: Frankfurt am Main

first: Carmen

last: Doebele

address: Theodor-Stern-Kai 7

country: Germany

institute: Goethe University

summary: MicroRNAs are endogenously expressed small non-coding RNAs that regulate gene expression on the posttranscriptional level. The miR-17-92 cluster (encoding miR-17, -18a, -19a/b, -20a and miR-92a) is highly expressed in tumor cells and is up-regulated by ischemia. Whereas miR-92a was recently identified as negative regulator of angiogenesis, the specific functions of the other members of the cluster are less clear. Here we demonstrate that overexpression of miR-17, -18a, -19a and -20a significantly inhibited 3D spheroid sprouting in vitro, whereas inhibition of miR-17, -18a and -20a augmented endothelial cell (EC) sprout formation. Inhibition of miR-17 and miR-20a in vivo using antagomirs significantly increased the number of perfused vessels in matrigel plugs, whereas antagomirs, that specifically target miR-18a and miR-19a were less effective. However, systemic inhibition of miR-17/20 did not affect tumor angiogenesis. Further mechanistic studies showed that miR-17/20 targets several pro-angiogenic genes. Specifically, Janus kinase 1 (Jak1) was shown to be a direct target of miR-17. In summary, we show that miR-17/20 exhibit a cell intrinsic anti-angiogenic activity in ECs. Inhibition of miR-17/20 specifically augmented neovascularization of matrigel plugs, but did not affect tumor angiogenesis indicating a context-dependent regulation of angiogenesis by miR-17/20 in vivo.

overall_design: 6 samples of 3 independent experiments (n=3): per experiment Pre-miR-Co (10 nM, Ambion) and Pre-miR-17 (10 nM, Ambion) transfected HUVEC 24h after transfection

first: Angelika

last: Bonauer

first: Ariane

last: Fischer

last: Scholz

first: Yvonne

last: Reiss

last: Urbich

first: Wolf-Karsten

last: Hofmann

first: Andreas

middle: M

last: Zeiher

first: Stefanie

last: Dimmeler


status: Public on Mar 10 2010

city: Tucson

first: Ty

last: Lebsack

state: AZ

address: 1656 E Mabel

department: Immunobiology

institute: University of Arizona

summary: Microarray Analysis of Space-flown Murine Thymus Tissue Reveals Changes in Gene Expression Regulating Stress and Glucocorticoid Receptors. We used microarrays to detail the gene expression of space-flown thymic tissue and identified distinct classes of up-regulated genes during this process. We report here microarray gene expression analysis in young adult C57BL/6NTac mice at 8 weeks of age after exposure to spaceflight aboard the space shuttle (STS-118) for a period of 13 days. Upon conclusion of the mission, thymus lobes were extracted from space flown mice (FLT) as well as age- and sex-matched ground control mice similarly housed in animal enclosure modules (AEM). mRNA was extracted and an automated array analysis for gene expression was performed. Examination of the microarray data revealed 970 individual probes that had a 1.5 fold or greater change. When these data were averaged (n=4), we identified 12 genes that were significantly up- or down-regulated by at least 1.5 fold after spaceflight (p≤0.05). Together, these data demonstrate that spaceflight induces significant changes in the thymic mRNA expression of genes that regulate stress, glucocorticoid receptor metabolism, and T cell signaling activity. These data explain, in part, the reported systemic compromise of the immune system after exposure to the microgravity of space.

overall_design: Young adult C57BL/6NTac mice at 8 weeks of age (n=4) were subjected to spaceflight aboard the space shuttle (STS-118) for a period of 13 days. Upon conclusion of the mission, thymus lobes were extracted from space-flown mice (Mouse_Space) as well as age- and sex-matched ground-control mice (Mouse_Control) similarly housed in animal enclosure modules (n=4). mRNA was extracted and an automated array analysis for gene expression was performed.

first: Ann

last: Manziello

first: Vuna

last: Fa

first: Raphael

last: Gruener

first: Dominick

last: DeLuca

first: Chris

middle: C

last: Woods


title: Gene profiles induced by overexpression of wild-type and mutant Notch1 variants in MCF10A mammary epithelial cell line

status: Public on Mar 12 2010

first: Joan

last: Brugge

address: 240 Longwood Avenue

department: Department of Cell Biology

institute: Harvard Medical School

summary: Expression of a constitutively active Notch-1 intracellular domain (NICD) in MCF-10A cells was found to induce two distinct types of 3D structures: large, hyperproliferative structures and small, growth-arrested structures with reduced cell-to-matrix adhesion.  These heterogeneous phenotypes reflect differences in Notch pathway activation levels.  High Notch activity caused loss of cell adhesion and inhibition of proliferation, whereas low Notch activity maintained matrix adhesion and provoked a strong hyperproliferative response. In order to gain insight into the dosage-dependent transcriptional events triggered by Notch1 activation, gene expression profiles induced 48 hours after infection of MCF-10A cells with retroviral vectors expressing full-length Notch-1, L1601P+∆P, or NICD were compared.  Full-length Notch-1 induced the weakest effect,  L1601P+∆P induced an intermediate effect and NICD induced the strongest effect.  Results provide insight into the dichotomous activites of Notch during development and tumorigenesis.

overall_design: Twelve samples were harvested 48 h after retroviral infection with either vector control, full-length Notch1, Notch1 L1601P+∆P, or NICD.  Each condition was performed in triplicate.

first: Marco

last: Mazzone

first: Laura

last: Selfors

first: John

last: Albeck

first: Michael

last: Overholtzer

first: Sanja

last: Sale

first: Danielle

last: Carroll

first: Darshan

last: Pandya

first: Yiling

last: Lu

first: Gordon

middle: B

last: Mills

first: Jon

last: Aster

first: Spyros

last: Artavanis-Tsakonas


title: Mitochondrial and nuclear genomic response to loss of LRPPRC expression

first: Vishal

last: Gohil

address: 185 Cambridge Street

department: Center for Human Genetic Research

institute: Massachusetts General Hospital

summary:
Rapid advances in genotyping and sequencing technology have dramatically accelerated the discovery of genes underlying human disease.  Elucidating the function of such genes and understanding their role in pathogenesis, however, remains challenging.  Here, we introduce a genomic strategy to functionally characterize such genes, and apply it to LRPPRC (leucine-rich PPR-motif containing), a poorly studied gene that is mutated in Leigh Syndrome, French Canadian type (LSFC).
We utilize RNAi to engineer an allelic series of cellular models in which LRPPRC has been stably silenced to different levels of knockdown efficiency.  Using expression profiling, we discovered a specific role for LRPPRC in the expression of all mitochondrial DNA (mtDNA)-encoded mRNAs, but not the rRNAs, without affecting nuclear genes encoding mitochondrial proteins.

overall_design: We designed seven shRNAs targeting the LRPPRC cDNA sequence to silence its expression in MCH58 immortalized human fibroblasts. The LRPPRC expression level in these cells ranged from 9% to 100%. We demonstrated that knockdown cells carried stable silencing of the target gene and associated biochemical phenotypes. Our goal was to engineer stable knockdown cells which recapitulate the LSFC disease phenotype and subject them to expression profiling using Affymetric microarrays to identify genesets and biochemical pathways that are altered.

first: Vamsi

last: Mootha


title: TGF or TNF Time series in ARPE19

status: Public on Mar 11 2010

city: Kisarazu

first: Rui

last: Ose

state: Chiba

address: 2-6-7 Kazusa-Kamatari

department: Department of Human Genome Research

country: Japan

institute: Kazusa DNA Research Institute

summary: Aberrant epithelial-mesenchymal transition (EMT) is involved in　pathological processes including fibrotic disorders and cancer invasion and metastasis. Alterations of the cell-extracellular matrix　(ECM) interaction also contribute to those pathological settings.　However, the functional interplay between EMT and cell-ECM　interaction is poorly understood. Here, we show that tumor necrosis factor (TNF)-α, a potent mediator of inflammation, induces　EMT-associated fibrosis in retinal pigment epithelial cells, and that this is regulated by hyaluronan (HA)-CD44-Moesin interaction. TNF-α elicits both HA synthesis and Moesin phosphorylation through protein kinase C activation, promoting binding of CD44 to the newly synthesized HA. The HA-CD44-Moesin interaction leads to cell-cell dissociation through actin remodeling and increased cellular motility associated with mesenchymal phenotype. Furthermore, we　established an in vivo model of TNF-α-induced fibrosis in the mouse eye, and the ocular fibrosis was completely suppressed in CD44-null mice. Therefore, HA production and its interaction with CD44 plays essential role in TNF-α-induced-EMT, and the interference of the complex formation can be a new strategy for the fibrotic disorders.

overall_design:
ARPE19 cell lines were treated with TGF and TNF for 6 and 42 hour. Each experiment were repeated three times. But 1hour experiment was repeated two times.
For this submission, total RNA was extracted from TGF- or TNF-treated ARPE-19 cells and differential gene expression between each time point (6 and 42 hours) was determined using genechip arrays (Affymetrix, Human Genome U133).


title: Gene Expression in Gold Nanoparticle Oligonucleotide Complexes treated Primary Immune Cells

status: Public on Mar 09 2010

first: Eun-Young

last: Kim

address: 303 E Superior Street

department: Feinberg School of Medicine

institute: Northwestern University

summary:
A transcriptome-wide functional analysis of gene expression implicated multiple signaling pathways specific for Au-NP oligonucleotide complexes.
Exposure to Au-NP oligonucleotide complexes is also accompanied by marked activation of immune cells.

overall_design: We investigated the effect of Au-NP antisense EGFP oligonucleotide complexes on the transcriptome by expression profiling of 293T cells under four conditions and PBMCs under six conditions with the Affymetrix U133 Plus 2.0 microarray

first: Steven

last: Wolinsky

first: Schulz

last: Reiner


title: Diagnosis-relapse in ALL

city: Wageningen

first: Dick

middle: de

last: de Ridder

address: Droevendaalsesteeg 1

department: Plant Sciences

country: Netherlands

institute: Wageningen University

summary: Almost a quarter of pediatric patients with Acute Lymphoblastic Leukemia (ALL) suffer from relapses. The biological mechanisms underlying therapy response and development of relapses have remained unclear.  In an attempt to better understand this phenomenon, we have analyzed 41 matched diagnosis relapse pairs of ALL patients using genome–wide expression arrays (82 arrays) on purified leukemic cells.  In roughly half of the patients very few differences between diagnosis and relapse samples were found (“stable group”), suggesting that mostly extra-leukemic factors (e.g., drug distribution, drug metabolism, compliance) contributed to the relapse. Therefore, we focused our further analysis on 20 samples with clear differences in gene expression (“skewed group”), reasoning that these would allow us to better study the biological mechanisms underlying relapsed ALL.  After finding the differences between diagnosis and relapse pairs in this group, we identified four major gene clusters corresponding to several pathways associated with changes in cell cycle, DNA replication, recombination and repair, as well as B cell developmental genes.  We also identified cancer genes commonly associated with colon carcinomas and ubiquitination to be upregulated in relapsed ALL. Thus, about half of relapses are due to selection or emergence of a clone with deregulated expression of a genes involved in pathways that regulate B cell signaling, development, cell cycle, cellular division and replication.

overall_design: The study contains 41 pairs of samples taken from patients at diagnosis and relapse (a total of 82 arrays).

first: Frank

last: Staal

last: deRidder

first: Tomasz

last: Szczepanski

first: Tom

last: Schonewille

first: Els

last: vanderLinden

first: Elizabeth

middle: R

last: vanWering

first: Vincent

middle: H

last: vanderVelden

first: Jacques

last: vanDongen


title: Expression analysis of AOM-induced tumors and serrated tumors in mice

status: Public on Mar 06 2010

city: Muenchen

first: Moritz

last: Bennecke

address: Ismaninger Str. 22

department: II. Med Klinik

institute: Klinikum r.d.Isar

summary: Abstract: Colonic cancers with a serrated morphology have been proposed to comprise a molecularly distinct tumor entity following an alternative pathway of genetic alterations independently of APC mutations. Here we demonstrate that intestinal cell specific expression of oncogenic K-rasG12D in mice induces serrated hyperplasia, which is characterized by p16ink4a overexpression and induction of senescence. Deletion of Ink4a/Arf in K-rasG12D expressing mice prevents senescence and leads to invasive, metastasizing carcinomas with morphological and molecular alterations comparable to human KRAS mutated serrated tumors. Thus, we suggest that oncogenic K-ras is sufficient to initiate an alternative, serrated pathway to colorectal cancer and hence propose RAS-RAF-MEK signaling apart from APC as an additional gatekeeper in colorectal tumor development.

overall_design: 2 to 3 tissue samples for each genotype were analyzed

first: Florian

last: Greten


title: Whole blood gene expression analysis of stable and acute rejection pediatric kidney transplant patients

status: Public on Mar 08 2010

city: Stanford

first: Shai

last: Shen-Orr

address: 251 Campus Dr. Rm.X-251

institute: Stanford University

summary:
Full title: Expression data from whole blood gene expression analysis of stable and acute rejection pediatric kidney transplant patients

Tissues are often made up of multiple cell-types. Blood, for example, contains many different cell-types, each with its own functional attributes and molecular signature. In humans, because of its accessibility and immune functionality, blood cells have been used as a source for RNA-based biomarkers for many diseases.  Yet, the proportions of any given cell-type in the blood can vary markedly, even between normal individuals. This results in a significant loss of sensitivity in gene expression studies of blood cells and great difficulty in identifying the cellular source of any perturbations.  Ideally, one would like to perform differential expression analysis between patient groups for each of the cell-types within a tissue but this is impractical and prohibitively expensive.   This dataset is the validation dataset used to test the csSAM gene expression deconvolution algorithm as reported in the accompanying paper.

overall_design: Whole blood gene expression measurements for 24 pediatric renal transplant patients were analyzed on human specific HGU133V2.0 (+) whole genome expression arrays. Blood drawn using PaxGene Blood RNA Tubes (PreAnalytiX, Qiagen).

first: Minnie

last: Sarwal

middle: S


title: Gene expression profiles of adult renal capsule isolated from kidneys using micro-dissection. (GUDMAP Series ID: 36)

first: GUDMAP

last: Developers

overall_design: CD-1 mice were utilized to isolate the capsule cells from the adult  kidneys.  The capsule cells were isolated from the kidney using microdissection treatment.   RNA was isolated and the gene expression profiles were determined by microarrays.

first: Steve

last: Potter

first: Eric

last: Brunskill


title: 21T series cell lines show distinct stage-specific gene expression alterations

city: London

first: Ann

last: Chambers

state: Ontario

address: 790 Commissioner's Road E

department: Victoria research labs

institute: London Regional Cancer program

summary:
Pathologic and epidemiologic evidence has led to a histologic model of breast cancer progression that involves advancement through specific morphologic stages including atypical ductal hyperplasia (ADH), ductal carcinoma in situ (DCIS) and invasive mammary carcinoma (IMC), although not necessarily always in a linear fashion.  Numerous observational studies have examined genetic, epigenetic and gene expression differences in breast tissues representing these different stages of progression, but model systems which would allow for experimental testing of specific factors influencing transition through these stages are scarce.  The 21T series cell lines, all originally derived from the same patient with metastatic breast cancer, have been proposed to represent a mammary tumor progression series.  We report here that three of the 21T cell lines indeed mimic specific stages of human breast cancer progression (21PT-derived cells, ADH; 21NT-derived cells, DCIS; 21MT-1 cells, IMC) when grown in the mammary fat pad of nude mice, albeit after up to a year post-injection.  In order to develop a more rapid, readily manipulatable in vitro assay for examining the biologic differences between these cell lines, we have made use of a 3D Matrigel system.  When grown in 3D Matrigel, we have found characteristic morphologies of the three cell lines in which quantifiable aspects of the stage-specific in vivo behaviors (i.e. differences in acinar structure formation, cell polarization, cell cohesiveness, cell proliferation, cell invasion) are re-capitulated in a reproducible fashion.  Gene expression profiling has revealed a characteristic pattern for each of the three cell lines. Interestingly, WNT pathway alterations are particularly predominant in the early transition from 21PTci (ADH) to 21NTci (DCIS), whereas alterations in expression of genes associated with control of cell motility and invasiveness phenomena are more prominent in the later transition of 21NTci (DCIS) to 21MT-1 (IMC).  This system thus reveals potential therapeutic targets and will provide a means of testing the influences of identified genes on transitions between these stages of pre-malignant to malignant growth.

Keywords: DCIS or IDC vs ADH

overall_design: RNA derived from three biological replicates of a cell line representing atypical ductal hyperplasia (ADH), Ductal carcinoma in situ (DCIS), and Invasive ductal carcinoma (IDC)

first: Lesley

last: Souter

first: Joseph

last: Andrews

first: Guihua

last: Zhang

first: Amy

last: Cook

first: Carl

last: Postenka

first: Waleed

last: Al-Katib

first: David

last: Rodenhiser

first: Alan

last: Tuck


title: Caco-2 cocultured with THP-1, time course

city: Aomori

first: Yuji

last: Nakai

state: Aomori

address: 2-1-1, Yanagawa

department: Institute of Regional Innovation

institute: Hirosaki University

summary: Previously, we constructed a coculture model to analyze the effect of macrophages on intestinal epithelial cells, and found that TNF-a secreted from human macrophage-like THP-1 cells induced cell damage to intestinal epithelial Caco-2 cells (Exp.Cell.Res. 2006, 312(19):3909-19). In this study, we present activation of NF-kB in Caco-2 cells within 15 min after coculturing. To reveal how TNF-a secreted from THP-1 cells affects Caco-2 cells in an early stage of coculture, we exhaustively analyzed the changes of gene expression in Caco-2 cells cocultured with THP-1 cells over the time periods of 0, 1, 3, 6, 24, and 48 h by using a DNA microarray. Differentially expressed genes extracted with maSigPro demonstrated that IEX-1 was the lowest p-value gene, that is, the most significantly changed gene among the up-regulated genes. The genes expressed in a similar pattern to IEX-1 involved immunity, apoptosis, and protein kinase cascade. These findings suggest that the stimuli of TNF-a from THP-1 cells activates NF-kB, leading induction of various gene expression. This pattern of gene expression indicates that not only early defense response but also cell death occurs at the same time, causing inflammatory condition.

overall_design: Caco-2 cells were cultured for 14 days on a semi-permeable support, and THP-1 cells were differentiated with phorbol myristate acetate (PMA) for 4 days in 12-well plates. Then, the semi-permeable support membrane in which Caco-2 cells had been cultured was placed on the 12-well plates on which THP-1 has been cultured.

first: Yoko

last: Ishimoto

first: Hideo

last: Satsu

first: Mamoru

last: Totsuka

first: Makoto

last: Shimizu


title: Primary NKcells vs. NKAES-derived NK cells vs. NKcells stimulated by low/high dose IL2 after 7days of culture

city: Memphis

first: Noriko

last: Shimasaki

state: TN

address: 262 Danny Thomas Place

department: Oncology

institute: St. Jude Children's Research Hospital

summary: Transcriptional profiling of NKAES-derived NK cells after 7 days of culture compared to primary human NK cells and NK cells stimulated by low or high dose IL2 after 7 days of culture.

overall_design: Four-condition experiment, primary NK cells vs. NKAES-derived NK cells after 7 days of culture vs. NK cells stimulated by low/high dose IL2 after 7 days of culture. Biological replicates: 5 control, 5 NKAES-derived NK cells, 3 NK cells stimulated by low dose IL2, 3 NK cells stimulated by high dose IL2 independently grown and harvested. One replicate per array.


title: Gene expression analysis of human monocytic cells (THP-1) exposure to Streptococcus suis serotype 2

city: Wuhan

first: Liu

middle: Man

last: li

address: Shizishan Road Number 1, Hongshan Area, Wuhan , Hubei Provience, China

department: College of Veterinary Medicine

country: China

institute: Huazhong Agricultural University

summary:
Streptococcus suis is an important zoonosis pathogen that causes significant economic losses worldwide characterized by meningitis, septicaemia, arthritis, bronchopneumonia endocarditis. Streptcoccus suis 2 strain SC19 was isolated in Sichuan province in China, during the outbreak in 2005. Septicemia is most popular symptoms for SC19 infection, and mortality is high.
We used human acute monocytic leukemia cell line (THP-1) infected SC19 to analysis the pathomechanism of septicemia in SS2 infection.

overall_design: Human acute monocytic leukemia cell line (THP-1) cells were stimulated with Streptcoccus suis 2 (SS2) strain SC19. We added SS2 to THP-1 cells at a MOI of 1:1 (bacteria/cells). Uninfected control cells were incubated with PBS only. After 3 hours incubation, cells were collected for RNA extraction and hybridization on Affymetrix microarrays. A total of 4 samples were challenged, and 4 samples were used as controls. 4 microarrays were used in this experiment.

last: Manli

first: Tan

last: Chen

first: Fang

last: Liurong

first: Chen

last: Huanchun

first: Xiao

last: Shaobo


title: EGFR Isoforms and Gene Regulation in Human Endometrial Cancer Cells

city: Albuquerque

first: Gavin

last: Pickett

state: NM

address: 2325 Camino de Salud NE

department: Genomics

institute: UNM

summary:
Microarrays were used to analyze differential gene expression and to help determine the efficacy of Iressa (gefitinib), a tyrosine kinase inhibitor, on endometrial cancer cells.
Type I Ishikawa H and type II Hec50co endometrial carcinoma cells both express EGFR and sEGFR, but differ markedly in their responsiveness to the EGFR inhibitor gefitinib.  This difference is paralleled by differences in the expression of sEGFR and EGFR, as well as in their transcriptional response following treatment with either EGFor gefitinib.  The small cluster of differently regulated genes reported here in these type I vs. type II endometrial cancer-derived cell lines may identify candidate biomarkers useful for predicting sensitivity to EGFR blockade.

overall_design: Type I (Ishikawa H cells) and type II (Hec50co) derived endometrial carcinomas, were dosed with either EGF(epidermal growth factor) or Iressa (gefitinib) for 12 or 24 hours and gene expression was examined.

first: Lina

last: Albitar

first: Marilee

last: Morgan

first: Jason

last: Wilken

first: Nita

last: Maihle

first: Kimberly

last: Leslie


title: The Effect of Translocation-Induced Nuclear Re-organization on Gene Expression

status: Public on Mar 05 2010

city: Lausanne

first: Frédéric

last: Schütz

address: Batiment Amphipole

country: Switzerland

institute: Swiss Institute of Bioinformatics

summary:
To study the effect of balanced chromosomal rearrangements on gene expression, we compared the transcriptomes of cell lines from control and t(11;22)(q23;q11) individuals. This translocation between chromosomes 11 and 22 is the only recurrent constitutional non-Robertsonian translocation in humans. The number of differentially expressed transcripts between the translocated and control cohort is significantly higher than that observed between control samples alone, suggesting that balanced rearrangements have a greater effect on gene expression than normal variation. Altered expression is not limited to genes close to the translocation breakpoint suggesting that a long-range effect is operating. Indeed we show that the nuclear position of the derivative chromosome is altered compared to the normal chromosomes. Our results are consistent with recent studies that indicate a functional role for nuclear position in regulating the expression of some genes in mammalian cells. They may also have implications on reproductive separation, as we show that reciprocal translocations not only provide partial isolation for speciation but also significant changes in transcriptional regulation through alteration of nuclear chromosomes territories.

Keywords: Genetic modification

overall_design: Comparison of the transcriptomes of cell lines from control, t(11;22)(q23;q11) and Emanuel syndrome individuals.

first: Louise

last: Harewood

first: Shelagh

last: Boyle

first: Paul

last: Perry

first: Mauro

last: Delorenzi

first: Wendy

last: Bickmore

first: Alexandre

last: Reymond


title: Indolent MCL identified by genomic and gene expression profiling

status: Public on Mar 04 2010

city: Barcelona

first: Pedro

last: Jares

state: Barcelona

address: c/ Villarroel 170

department: Genomics Unit

country: Spain

institute: IDIBAPS

summary: Mantle cell lymphoma (MCL) is an aggressive neoplasm with poor outcome. However, some patients have an indolent disease (iMCL) and may not require intensive treatment at initial diagnosis. Diagnostic criteria to recognize these patients are not available. We hypothesized that the analysis of the genetic and expression features of the tumors may help to identify patients with an indolent clinical evolution and provide biomarkers that could be used in the clinical setting.

overall_design: Seven patients with an iMCL that did not require chemotherapy for more than 2 years were compared to 15 conventional MCL (cMCL) that needed systemic therapy at diagnosis. MCL were compared with other leukemic lymphoid neoplasms including 17 CLL, 7FL, HCL and 2HCLv.

first: V

last: Fernandez

first: P

first: E

last: Campo


title: Transcriptome profiling of control and TNFalpha treated HepG2 cells

city: Delhi

first: Malabika

last: Datta

address: Mall Road

country: India

institute: Institute of Genomics and Integrative Biology

summary: The proinflammatory cytokine, TNFalpha is critical in maintaining liver homeostasis since it is a major determiner of hepatocyte life and death. Considering this, gene transcription profiling was examined in control and TNFalpha treated HepG2 cells. Results indicated that TNFalpha could significantly alter the expression of a significant number of genes; most of them were functionally distributed among molecular functions like catalytic activity, binding, molecular transducer activity, transporter activity, translation and transcription regulator activities or enzyme regulator activity. Also, within genes up-regulated by TNFalpha, several GO terms related to lipid and fat metabolism were significantly overrepresented indicating global dysregulation of fat metabolism within the hepatocyte and those within the down-regulated dataset included genes involved in immunoglobulin receptor activity and IgE binding thereby indicating a compromise in immune defense mechanism(s) apart from those involved the DNA binding and protein binding categories.  The interacting network of “lipid metabolism, small molecule biochemistry” was derived to be significantly affected that correlated well with the top canonical pathway of “biosynthesis of steroids” and molecular and cellular function of “lipid metabolism”. All these indicate TNFalpha to be significantly altering the transcriptome profiling within HepG2 cells with genes involved in lipid and steroid metabolism being the most favoured. This study suitably addresses the genes that determine TNFalpha mediated alterations within the hepatocyte mainly the phenotypes of hepatic steatosis and fatty liver that are associated with several hepatic pathological states.

overall_design: HepG2 cells were maintained in DMEM supplemented with 10% fetal calf serum with 1% antibiotic-antimycotic. On attaining confluency, cells were serum starved overnight and incubated in the absence (control) and presence of TNFalpha (0.5nM, 12h). On termination of incubation, total RNA was isolated, reverse transcribed to cDNA and subjected to in vitro transcription to produce biotinylated cRNA that was hybridized to the human array chip (Human Genome U133 Plus 2.0, Affymetrix) according to the manufacturer's instructions. Images were scanned using the GeneChip 3000 7G scanner (Affymetrix) and analysed. The experiment was performed with triplicates of each set (Control and TNF alpha treated).

first: Neha

last: Munjal

first: Amit

last: Pandey


title: Extraction of high-quality epidermal RNA after NH4SCN induced dermo-epidermal separation of 4 mm human skin biopsies

status: Public on Mar 03 2010

city: Odense

first: Mads

last: Thomassen

address: Soender Boulevard 9

department: Clinical Genetics (KKA)

country: Denmark

institute: Odense University Hospital

summary: To obtain a separation of the epidermal and dermal compartments in order to examine compartment specific biological mechanisms in the skin we incubated 4 mm human skin punch biopsies in ammonium thiocyanate (NH4SCN). We wanted to test 1) the histological quality of the dermo-epidermal separation obtained by different incubation times 2) the amount and quality of extractable epidermal RNA, and 3) its impact on sample RNA expression profiles assessed by large-scale gene expression microarray analysis in both normal and inflamed skin. At 30 minutes incubation, the split between dermis and epidermis was not always histologically well-defined (i.e. occurred partly intra-epidermally) but varied between subjects. Consequently, curettage along the dermal surface of the biopsy was added to the procedure. This modified method resulted in an almost perfect separation of the epidermal and dermal compartments and satisfactory amounts of high-quality RNA were obtained. Hybridization to Affymetrix HG_U133A 2.0 GeneChips showed that ammonium thiocyanate incubation had a minute effect on gene expression resulting in only one significantly downregulated gene (cystatin E/M). We conclude that epidermis can be reproducibly and almost completely separated from the dermis of 4 mm skin biopsies by 30 min incubation in 3.8% ammonium thiocyanate combined with curettage of the dermal surface, producing high-quality RNA suitable for transcriptional analysis. Our refined method of dermo-epidermal separation will undoubtedly prove valuable in the many different settings, where the epidermal and dermal compartments need to be evaluated separately.

overall_design: Upper buttock skin in 4 healthy subjects was exposed to sodium lauryl sulphate, or sampled directly. For each subject, 4 biopsies were obtained: Two from inflamed skin, and two from adjacent normal skin. One irritated and one normal skin sample was placed directly in RNAlater. The remaining two samples were incubated in ammonium thiocyanate for 30 minutes at RT and then placed in RNAlater without performing any separation of the dermal and epidermal layers. This was done to investigate the effect of 30 minutes treatment with ammonium thiocyanate on both inflamed and non-inflamed skin. Data was normalized with quantile method (matrix 1)  Forearm biopsies from 13 volunteers were separated to epidermis and dermis by use of ammonium thiocyanate. For comparison of full skin and epidermis without irritation, data from identical probe sets from HG_U133A 2.0 and HG_U133 plus 2.0 was extracted and normalised as one data set using quantile method (matrix 2).

first: Anders

last: Clemmensen


title: Expression data from NS398-treated and control HT29 colon adenocarcinoma cell line samples

city: Budapest

first: Wichmann

last: Barna

address: Szentkirály

country: Hungary

institute: SOTE

summary: The whole-genome oligonucleotide microarray analysis of  NS398-treated HT29 colon adenocarcinoma cells samples can give an insight into global molecular background of selective COX2 inhibitor administration in order to find other target molecules and pathways influenced by NS398 selective COX2 inhibitor treatment in the epithelial cells.

overall_design: Total RNA was extracted from NS398-treated and control HT29 colon adenocarcinoma cells and hybridized on Affymetrix HGU133 Plus 2.0 microarrays

first: Orsolya

last: Galamb

first: Bela

last: Molnar

first: Sandor

last: Spisak

first: Ferenc

last: Sipos


title: Gene expression profiling of three paired parental and cisplatin-resistant TGCT cell lines

city: LONDON

first: YONG-JIE

last: LU

address: Charterhouse Square

department: Barts Cancer Institute

institute: BLSMD, Queen Mary University of London

summary:
The development of chemo-resistance has dramatically limited the clinical efficiency of platinum-based therapy. Although many resistant mechanisms have been demonstrated, genetic/molecular alterations responsible for drug resistance in the majority of clinical cases has not been identified.

We analyzed three pairs of testicular germ cell tumor (TGCT) cell lines using Affymetrix expression microarrays to identify differential expressed genes. Then the expression of CCND1/CyclinD1, selected from the microarray analysis, was determined in cisplatin sensitive and resistance cancer samples including TGCTs, ovarian and prostate cancers by quantitative reverse transcription PCR analysis (qRT-PCR). Finally, we determined the gene knocked-down effect of CyclinD1.

Expression microarray study revealed a limited number of differentially expressed genes across all three cell lines when comparing the parental and resistant cells. Among them, CyclinD1 was the most significantly differentially expressed gene. Importantly, we found that, in clinical TGCT samples, the overall expression level of cyclinD1 is higher in resistant cases compared to those sensitive samples (9/12 in the resistant group and only 3/8 in the sensitive group). We also found that cyclinD1 expressed dozens of fold higher in the resistant than in the sensitive ovarian cancer cell lines and dramatically overexpressed in prostate cancer. We re-sensitized the resistant cells by knocking-down cyclinD1.

We demonstrated that deregulation of cyclinD1 is the major cause of TGCT cisplatin resistance and it may also be commonly involved in other human cancers. Combined cyclinD1 inhibition and cisplatin chemotherapy may be used clinically to treat the large number of cyclinD1 deregulated resistant tumors.

overall_design: RNA from three paired parental and cisplatin-resistant TGCT cell lines was extracted and analysed by Affymetrix gene expression microarray profiling (Human Genome U133 plus 2.0 arrays). Expression changes associated with the resistant phenotype were identified by comparing the three cisplatin-resistant derivatives to their parental counterparts.

first: ELODIE

middle: E

last: NOEL


title: Differentially expressed gene profiles in CA 9-transfected C33-A, human cervix carcinoma cell line

status: Public on Mar 02 2010

city: Goyang-si

first: Hye-Jin

last: Shin

state: Gyeonggi-do

address: 323 Ilsan-ro, Ilsandong-gu

department: Research Institute and Hospital

country: South Korea

institute: National Cancer Center

summary:
Carbonic anhydrase IX (CA 9) is a transmembrane isoform of carbonic anhydrase (CA) that contributes to an acidification of tumor microenvironment. The expression of CA 9 in cervical tumors was shown to be strongly involved in high incidence of metastasis and poor prognosis.
To search for the key regulators of metastasis related to ectopic expression of CA 9, we investigated differentially expressed gene profiles in CA 9- transfected cervix carcinoma cell line C33-A (CF) compared with mock-transfected (CP) cell line, using Affymetrix Human Genome U133 Plus 2.0 Array.

overall_design: CF and CP stable cell-lines trasfected respectively with full-length human CA 9 cDNA cloned into the vector pcDNA3.0 and empty vector control were used for RNA extraction and hybridization on affymetrix microarrays.

first: Jooyoung

last: Kim

first: Hyejin


title: Gene expression signature reflects differentiation differences rather than telomere maintenance mechanism

city: Philadelphia

first: Jay

last: Johnson

address: 422 Curie Blvd

department: Pathology and Laboratory Medicine

institute: University of Pennsylvania

summary: A gene expression signature purporting to distinguish between telomerase and ALT immortalization has recently been described (Lafferty-Whyte et al., 2009).  This was obtained as the intersection of two independent signatures, one obtained from cell lines and the other from a panel of liposarcomas, which utilize different telomere maintenance mechanisms (TMMs).   To assess the utility of this signature we used Affymetrix U133plus2.0 arrays to undertake a similar analysis of an independent collection of liposarcomas of defined TMM.  In our dataset, the 297 gene signature causes the liposarcomas to cluster not on the basis of TMM, but rather on the basis of tumor histological subtype [Figure 1], consistent with the signatures reported by others (Matushansky et al., 2008).

overall_design: Expression analyses were performed on 38 liposarcoma tumors using Affymetrix U133plus2.0 arrays.  Using cosine distance as a distance metric, hierarchical clustering of these samples was performed according to the expression levels of the 297 genes identified in the study by Lafferty-Whyte et al.

first: Marcy

last: Mitchell

first: David

last: Kipling

first: Margaret

last: von Mehren

first: Yan

last: Zhou

first: Catherine

last: Doyle

first: Chad

last: Roberts

first: Dominique

last: Broccoli


title: C/EBPbeta-2 regulation of gene expression in MCF10A cells

city: Nashville

first: Linda

last: Sealy

address: 2202 Pierce Ave

department: Cancer Biology

institute: Vanderbilt University Medical Center

summary:
C/EBPbeta-2 results in EMT and ErbB indpendence this project investigated the gene changes in related genes upon C/EBPbeta-2 overexpression in MCF10A cells.
We used microarray analysis  to detail the global gene expression mediated by C/EBPbeta-2 and identified changes in known EMT genes, however, known ErbB related genes were not altered.

overall_design: MCF10A with or without C/EBPbeta-2 were compared.

first: Alisha

last: Russell

first: Braden

last: Boone

first: Aixiang

last: Jiang


title: Expression data from human colonic epithelial cells normal (N), adenoma (AD) or colorectal cancer (CRC) tissues

first: Wichmann

last: Barna

summary:
The whole-genome oligonucleotide microarray analysis of  laser microdissected human colonic epithelial cells can contribute to determination of disease-specific expression alterations in colonic epithelial cells and to localize the origin the expression changes measured in whole biopsy samples.

Keywords: whole genomic expression

overall_design: Total RNA was extracted from laser microdissected human colon epithelial cells and hybridized on Affymetrix HGU133 Plus 2.0 microarrays

first: Orsolya

last: Galamb

first: Bela

last: Molnar

first: Sandor

last: Spisak

first: Ferenc

last: Sipos


title: EHEC and K-12 E. coli QseD mutant analysis

status: Public on Mar 01 2010

city: Dallas

first: Vanessa

last: Sperandio

address: 5323 Harry Hines Blvd.

institute: UT Southwestern Medical Center

summary: We used arrays to examine the overall transcriptional differences between WT K-12 E. coli, and EHEC 86-24 and their corresponding QseD (yjiE) mutants.

sample_organism:
Escherichia coli
Escherichia coli K-12

overall_design: Strains were grown to OD600 ~1.0, RNA was harvested, cDNA synthesized, fragmented, labeled and hybridized to the chips.  Expression of the QseD mutants was compared to the corresponding WT.

first: Benjamin

last: Habdas


title: CXCL4 induces a unique transcriptome in monocyte-derived macrophages

city: Eggenfelden

first: Christian

middle: Albert

last: Gleissner

address: Simonsöder Allee 20

department: Cardiology

institute: Rottal-Inn Kliniken KU

summary:
Human blood monocytes were differentiated over six days with either 100 ng/ml M-CSF or 1 umol/l CXCL4
In atherosclerotic arteries, blood monocytes differentiate to macrophages in the presence of growth factors like macrophage colony-stimulation factor (MCSF) and chemokines like platelet factor 4 (CXCL4). To compare the gene expression signature of CXCL4-induced macrophages with MCSF-induced macrophages or macrophages polarized with IFN-γ/LPS (M1) or IL-4 (M2), we cultured primary human peripheral blood monocytes for six days. mRNA expression was measured by Affymetrix gene chips and differences were analyzed by Local Pooled Error test, Profile of Complex Functionality and Gene Set Enrichment Analysis. 375 genes were differentially expressed between MCSF- and CXCL4-induced macrophages, 206 of them overexpressed in CXCL4 macrophages coding for genes implicated in the inflammatory/immune response, antigen processing/presentation, and lipid metabolism. CXCL4-induced macrophages overexpressed some M1 and M2 genes and the corresponding cytokines at the protein level, however, their transcriptome clustered with neither M1 nor M2 transcriptomes. They almost completely lost the ability to phagocytose zymosan beads. Genes linked to atherosclerosis were not consistently up- or downregulated. Scavenger receptors showed lower and cholesterol efflux transporters higher expression in CXCL4- than MCSF-induced macrophages, resulting in lower LDL content. We conclude that CXCL4 induces a unique macrophage transcriptome distinct from known macrophage types, defining a new macrophage differentiation that we propose to call M4.

overall_design: two MCSF samples and two CXCL4 samples

first: Klaus

last: Ley


title: Mutations in CHMP2B in lower motor neuron predominant amyotrophic lateral sclerosis (ALS)

city: Sheffield

first: Paul

middle: Roy

last: Heath

state: S. Yorks

address: SITraN, 385a Glossop Road

department: Academic Neurology Unit

institute: University of Sheffield

summary: Gene expression profiling has been performed on motor cortex and spinal cord homogenates and of sporadic ALS cases and controls, to identify genes and pathways differentially expressed in ALS. More recent studies have combined the use of laser capture microdissection (LCM) with gene expression profiling to isolate the motor neurons from the surrounding cells, such as microglia and astrocytes, in order to determine those genes differentially expressed in the vulnerable cell population – i.e. motor neuron.

overall_design: The aim of this study was to determine the gene expression profiles from a small subset of cases which all carry mutations in the CHMP2B gene. These mutations have been found to be associated with the lower motor neuron dominant variant of ALS. Expression profiles from isolated motor neurons in CHMP2B-related ALS cases were compared to those from control motor neurons, in order to establish the pathways implicated in CHMP2B-related motor neuronal cell death.

first: Laura

last: Cox

last: Ferraiuolo

first: Emily

last: Goodall

first: Adrian

last: Higginbottom

first: Heather

last: Mortiboys

first: Hannah

last: Hollinger

first: Judith

last: Hartley

first: Alice

last: Brockington

first: Christine

last: Burness

first: Karen

last: Morrison

first: Stephen

last: Wharton

first: Andrew

last: Grierson

middle: G

last: Ince

first: Janine

last: Kirby

first: Pamela

last: Shaw


title: Doxorubicin resistance in a novel in vitro model of human pleomorphic liposarcoma associated with ALT

first: Jay

last: Johnson

state: PA

type:
Expression profiling by array
Genome variation profiling by SNP array
SNP genotyping by SNP array

summary: Soft tissue sarcomas are a diverse set of fatal human tumors where few agents have demonstrable clinical efficacy, with the standard therapeutic combination of doxorubicin and ifosfamide showing only a 25-30% response rate in large multi-institutional trials. Although liposarcomas are the most common histological form of adult soft tissue sarcomas, research in this area is severely hampered by the lack of experimentally tractable in vitro model systems.  To this end, here we describe a novel in vitro model for human pleomorphic liposarcoma.  The cell line (LS2) is derived from a pleomorphic liposarcoma that utilizes Alternative Lengthening of Telomeres (ALT) mechanism of telomere maintenance, which may be particularly important in modulating the response of this tumor type to DNA damaging agents. We present detailed baseline molecular and genomic data, including genome wide copy number and transcriptome profiles, for this model compared to its parental tumor and a panel of liposarcomas covering multiple histologies.   The model has retained essentially all of the detectable alterations in copy number that are seen in the parental tumor, and shows molecular karyotypic and expression profiles consistent with pleomorphic liposarcomas.   We also demonstrate the utility of this model, together with two additional human liposarcoma cell lines, to investigate the relationship between topoisomerase 2A expression and the sensitivity of ALT-positive liposarcomas to doxorubicin. This model, together with its associated baseline data, provide a powerful new tool to develop treatments for this clinically poorly-tractable tumor, and to investigate the contribution that ALT makes to modulating sensitivity to DNA damaging chemotherapeutic agents such as doxorubicin.

overall_design: Affymetrix U133 2.0 expression analyses were performed for 30 liposarcoma tumors, including 2 recurrences of 2 tumors. In addition, analyses were performed for three replicates of a tumor-derived cell line, LS2, as well as the tumor from which it was derived (5228). Finally, the Affymetrix Human Genome 50K DNA Mapping Array was used to determine copy number profiles for two Passages of LS2, as well as tumor 5228.

first: Marcy

last: Mitchell

first: Kara

last: Pascarelli

first: Neil

last: Beeharry

first: Maria

last: Chiourea

first: Sarantis

last: Gagos

first: Margaret

last: von Mehren

first: David

last: Kipling

first: Dominique

last: Broccoli


title: Comparison of CD4+ T cell function between HIV-1 resistant and HIV-1 susceptible individuals

city: Boston

first: Paul

last: McLaren

address: 77 Avenue Louis Pasteur, NRB150

department: Medicine

institute: Harvard Medical School

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

overall_design: Refer to individual Series


title: Comparison of CD4+ T cell function between HIV-1 resistant and HIV-1 susceptible individuals (Affymetrix)

summary:
Understanding why some indidivual resist HIV-1 infection despite continued exposure is an important goal for vaccine development.
We compared CD4+ T cell gene expression at baseline in HIV-1 resistant commercial sex-workers from Nairobi, Kenya to HIV-1 high-risk negative (non-resistant) commercial sex-workers using gene expression arrays

Keywords: Case-control, disease state analysis

overall_design: CD4+ T cells from both HIV resistant and HIV low-risk negative individuals were isolated from PBMC after 24 hours of culture by negative slelction. Total RNA was isolated and gene expression compared using Affymetrix total genome arrays.

first: T

last: Ball

first: Charles

last: Wachihi

first: Walter

last: Jaoko

last: Kelvin

first: Ali

last: Danesh

first: Michael

last: Mayne

first: Larry

middle: D

last: Greller

first: Roland

last: Somogyi

first: Joshua

last: Kimani

first: Francis

last: Plummer

first: Keith

last: Fowke


title: Effect of imatinib on FIP1L1-PDGFRA-expressing EOL1 cells

city: Brussels

first: Jean-Baptiste

last: Demoulin

address: av Hippocrate 75, B1.74.05

department: de Duve Institute

country: Belgium

institute: Université catholique de Louvain

summary:
The Eol1 cell line has been derived from a patient with chronic eosiniphilic leukemia. Eol1 cells express the FIP1L1-PDGFRalpha oncogene. Inhibition of  FIP1L1-PDGFRalpha with imatinib mesylate (Glivec) blocks proliferation and survival of the cells. We performed microarray expression analysis to identify genes specifically regulated by FIP1L1-PDGFRalpha using imatinib-treated cells as baseline. The list of regulated genes was consistent with the activation of STAT trancription factors by FIP1L1-PDGFRA.

Keywords: 4 hours treatment with Glivec

overall_design: Eol1 cells were cultured in presence or absence of Glivec for 4 hours before RNA extraction and hybridization on Affymetrix microarray.

first: Federica

last: Toffalini


title: Gene expression response to implanted drug (paclitaxel)-eluting or bare metal stents in denuded human LIMA arteries

city: Lund

first: Ann-Sofie

last: Albrekt

address: Solvegatan 19

country: Sweden

institute: Lund University

summary:
[original title] Gene expression response to the implantation of drug (paclitaxel)-eluting or bare metal stents in denuded human LIMA arteries.

Different clinical outcomes have been observed for paclitaxel-eluting and bare metal cardiovascular stents. The aim of this project was to identify genes that might be associated with the observed clinical outcomes.

overall_design: Human left internal mammary artery (LIMA) was divided into three segments and and two of the segments were fitted with either a paclitaxel-eluting stent or a bare metal stent. The experiment includes three groups: control, paclitaxel-eluting stent, and bare metal stent, respectively. Each group includes four biological replicates (patients 1, 2, 4 and 5).

first: Stefan

last: Amisten


title: Expression data from human neutrophils exposed to uropathogenic and commensal Esherichia coli.

city: St Louis

first: Rekha

last: Meyer

address: 4320 Forest Park Av

country: USA

institute: Washington University School of Medicine

summary:
The establishment of bacterial infections at epithelial surfaces is determined by the balance of virulence attributes of the pathogen with the activity of innate host defenses.  Polymorphonuclear leukocytes (PMN) are key responders in many bacterial infections, but the mechanisms by which pathogens subvert these early responses to establish infection are largely undefined.  Here, we model these early interactions between human PMN and the primary cause of urinary tract infections, namely uropathogenic Escherichia coli (UPEC).  Our objective was to define virulence phenotypes of uropathogens (as compared with laboratory and commensal E. coli strains) that permit evasion of PMN activity.  We found that UPEC strains resist phagocytic killing and dampen the production of antimicrobial reactive oxygen species by PMNs.  Analysis of the global transcriptional responses of PMN to E. coli strains revealed that UPEC exposure downregulates the expression of PMN genes involved in proinflammatory signaling and PMN chemotaxis, adhesion, and migration.  Consistent with these data, UPEC attenuated transepithelial neutrophil recruitment in an in vitro model of acute infection.  We propose that these UPEC strategies are important in the establishment of epithelial infection, and that the findings are germane to a range of bacterial infections at epithelial surfaces.
We used microarrays to detail the global program of gene expression in human neutrophils in response to a uropathogenic bacteria compared to a closely related non-pathogenic strain relative to control samples with no bacteria. Our goal was to elucidate a pathogen-specific response. We chose an early time point of 60 minutes to evaluate the accute response to infection.

overall_design: Human neutrophils were exposed to pathogenic or commensal Escherichia coli for RNA extraction and hybridization on Affymetrix microarrays

first: Jennifer

middle: A

last: Loughman

first: David

last: Hunstad


title: 3D culture of AIDS-NHL cells influences gene expression related to B-cell development, proliferation and survival

city: New Orleans

first: Laura

last: Levy

state: LA

address: 1430 Tulane Ave SL38

department: Microbiology & Immunology

institute: Tulane University

summary:
Full title: Three-dimensional culture of AIDS-NHL cells influences gene expression related to B-cell development, proliferation and survival
The AIDS-NHL-derived cell line, UMCL01-101, representing diffuse large B-cell lymphoma of immunoblastic morphology (AIDS-IBL), was grown in conventional, static suspension culture or three-dimensionally (3D) in the Rotating Wall Vessel (RWV) bioreactor.  The objective was to assess the impact on gene expression of growth as a three-dimensional tissue assembly.
Global gene expression analysis was performed on UMCL01-101 cells grown under either condition using Affymetrix microarray.

overall_design: UMCL01-101 cells were cultured in the Rotating Wall Vessel bioreactor to form 3D assemblies, or in conventional suspension culture, for 15 days.  RNA was prepared from triplicate samples under each growth condition and submitted for microarray analysis.

first: Kerstin

last: Honer zu Bentrup

first: Cheryl

last: Nickerson

first: Adriana

last: Zapata

first: Adriane

last: Puetter


title: Expression data of diagnostic biopsy samples from Hodgkin lymphoma patients

city: Vancouver

first: Christian

last: Steidl

state: BC

address: 675 West 10th Avenue

department: Pathology

country: Canada

institute: BC Cancer Agency

summary: Despite advances in Hodgkin lymphoma (HL) treatment, about 20% of patients still die due to progressive disease. Current prognostic models predict treatment outcome with imperfect accuracy, and clinically relevant biomarkers are yet to be established that improve upon the International Prognostic Scoring (IPS) system. We analyzed 130 frozen diagnostic lymph node biopsies from classical HL patients by gene expression profiling to describe cellular signatures correlated with treatment outcome.

overall_design: Diagnostic fresh-frozen lymph node specimens from 130 patients with cHL were selected for GEP from the tissue archive at the British Columbia Cancer Agency and the University of Nebraska Medical Center according to the following criteria: primary diagnosis of cHL following central review, representative lymph node tissue (at least 1 cm² area in tissue sections), HIV-negative status and first line treatment with systemic chemotherapy ABVD (doxorubicin, bleomycin, vinblastine and dacarbazine) or ABVD-like regimen with or without radiation therapy if indicated or, in the case of seven patients with limited-stage disease, wide field radiation.


title: Gene expression in fetal mesenchymal stem cells for identification of epitopes suitable for non-invasive isolation

city: Stockholm

first: Cecilia

last: Götherström

address: Karolinska University Hospital Huddinge

department: Department for Laboratory Medicine

institute: Karolinska Institutet

summary: Human mesenchymal stem cells circulate in 1st and early 2nd trimester fetal blood, but not in adults. Like other fetal cell types they cross the placenta, and can be found in maternal organs decades later. To determine potential ligands in human fetal mesenchymal stem cells not present in maternal blood, the gene expression of 1st trimester human fetal bone marrow, liver and blood derived mesenchymal stem cells will be compared to blood mononuclear cells from pregnant women using a Affymetrix human gene array system.

overall_design: Human fetal bone marrow (3 samples), liver (3 samples) and blood derived mesenchymal stem cells (3 samples) compared to blood mononuclear cells (3 samples) from pregnant women

last: Gotherstrom

first: Jerry

last: Chan

first: Keelin

last: O’Donoghue

first: Nicholas

last: Fisk


title: Iron Chelators Treatment on MCF-7 Human Breast Cancer Cell

status: Public on Feb 28 2010

city: Sydney

first: Des

middle: Raymond

last: Richardson

state: New South Wales

address: 92-94 Parramatta Rd, Sydney

department: Bosch Institute

country: Australia

institute: University of Sydney

summary: Iron-deficiency affects 500 million people, yet the molecular role of iron in gene expression remains poorly characterized. Moreover, the alterations in global gene expression after iron chelation remains unclear and are important to assess for understanding the molecular pathology of iron-deficiency and the biological effects of iron chelators. We assessed the effect on whole genome gene expression of two iron chelators (desferrioxamine and 2-hydroxy-1-napthylaldehyde isonicotinoyl hydrazone) that have markedly different permeability properties. Sixteen genes were significantly regulated by both chelators, while a further 50 genes were regulated by either ligand.  Most of the genes identified in this study have not been previously described to be iron-regulated and are important for understanding the molecular and cellular effects of iron-deficiency.

overall_design:
The MCF-7 cells were incubated with either control medium or this medium containing DFO (250 µM) or 311 (25 µM) for 24 h at 37oC. These concentrations were used since our previous studies demonstrated that under these conditions these chelators lead to up-regulation of iron-responsive genes such as the TfR1 after this incubation time.8 Moreover, the higher concentration of DFO was implemented due to its limited ability to permeate cell membranes.
Total RNA was isolated from cells in 1 mL of TRIzol® reagent (Invitrogen). Samples were then prepared and hybridized to the Human Genome U133 Plus 2.0 430 2.0. The human GeneChip® U133 Plus 2.0 consists of greater than 47,000 transcripts and variants from over 38,500 well characterized human genes. On completion of hybridization and washing, microarray chips were scanned with the Affymetrix GeneChip® Scanner 3000 (Affymetrix).

first: Dong

last: Fu

first: Yu

last: Yu

last: Saletta

first: Yohan

last: Suryo Rahmanto


title: Expression data from placenta harvested from WT and Pth-null fetuses treated 90 minutes prior with saline or PTH (1-84)

city: St. John's

first: Christopher

last: Kovacs

state: Newfoundland

address: Health Sciences Centre, 300 Prince Philip Drive

department: Faculty of Medicine - Endocrinology

institute: Memorial University of Newfoundland

summary: Parathyroid hormone (PTH) plays an essential role in regulating calcium and bone homeostasis in the adult, but whether PTH is required at all for regulating fetal-placental mineral homeostasis is uncertain. To address this we treated Pth-null mice in utero with 1 nmol PTH (1-84) or saline and examined placental calcium transfer 90 minutes later. It was found that placental calcium transfer increased in Pth-null fetuses treated with PTH as compared to Pth-null fetuses treated with saline. Subsequently, to determine the effect of PTH treatment on placental gene expression, in a separate experiment, 90 minutes after the fetal injections the placentas were removed for subsequent RNA extraction and microarray analysis.

overall_design: 12 mouse placentas were selected for RNA extraction and hybridization on the Affymetrix Mouse Gene 1.0 ST Array. Of the 12 placenta, 3 were from WT fetuses treated in utero with saline, 3 were from WT fetuses treated in utero with PTH (1-84), 3 were from Pth-null fetuses treated in utero with saline, and 3 were from Pth-null fetuses treated in utero with PTH (1-84).

first: Charlene

last: Simmonds


title: Examining smoking-induced differential gene expression changes in buccal mucosa

city: Oklahoma City

first: Dennis

last: Burian

state: OK

address: 6500 S. MacArthur Blvd., AAM610

department: Aviation Medicine

institute: Federal Aviation Administration

summary: A tissue like buccal mucosa (from cheek swabs) would be an ideal sample material for rapid, easy collection for testing of biomarkers as an alternative to blood.  A limited number of studies, primarily in the smoker/oral cancer literature, address this tissue's efficacy for quantitative PCR or microarray gene expression analysis.  In this study both qPCR and microarray analyses were used to evaluate gene expression in buccal cells.  An initial study comparing blood and buccal cells from the same individuals looked at relative amounts of four genes.  The RNA isolated from buccal cells was degraded but was of sufficient quality to be used with RT-qPCR to detect expression of specific genes. Second, buccal cell RNA was used for microarray-based differential gene expression studies by comparing gene expression between smokers and nonsmokers.  The isolation and amplification protocol allowed use of 150-fold less buccal cell RNA than had been reported previously with human microarrays.  We report here the finding of a small number of significant gene expression differences between smokers and nonsmokers, using buccal cells as target material.  Additionally, Gene Set Enrichment Analysis confirmed that these genes were changing expression in the same pattern as seen in an earlier buccal cell study performed by another group.  Our results suggest that in spite of a high degree of RNA degradation, buccal cells from cheek mucosa could be used to detect differential gene expression between smokers and nonsmokers.  However the RNA degradation, increase in sample variability and microarray failure rate show that buccal samples should be used with caution as source material in expression studies.

overall_design: Samples were collected from eight subjects, four smokers (Sm)and four nonsmokers (NS). Each cheek was sampled creating an a and b sample for each subject which is reflected in the array name. All samples were isolated separately for total RNA. Each was hybridzed to microarrays to examine for differential gene expression between smokers and nonsmokers. There are 14 total samples in the main dataset (Set 2). One cheek sample failed in microarray analysis for two individuals, 08BCNS23 a and 08BCSm27 a, and so are not included here. A sample set (Set 1) was created which contains the four samples shown in this file. They represent repeated sampling of both cheeks for two individuals to test for reproducibility. There is a separate RMA file and metadata file (this file) for these data. These included samples 08BC11Sm a and b, a smoker, and 08BC12NSa and b a nonsmoker.

first: Doris

last: Kupfer


title: Genome-wide analysis of YY2 versus YY1 target genes

first: Emmett

middle: Vance

last: Schmidt

address: 55 Fruit St. - GRJ904

department: Tumor Biology

institute: Cancer Research Center at MGH

summary: Yin Yang 1 (YY1) is a critical transcription factor controlling cell proliferation, development and DNA damage responses. Although two homologous Drosophila YY family members (pleiohomeotic (pho)) and pleiohomeotic-like (phol)) are redundant, the functional significance of a recently described mammalian YY1-like gene (YY2) is unknown. Using microarray and gene set enrichment analysis (GSEA), we found that lentiviral constructs containing short hairpin loop YY1- and YY2-specific inhibitory RNAs (shYY1 and shYY2) caused significant changes in both redundant and distinguishable expression patterns. Ribosomal protein genes were the most significant gene set up-regulated by both shYY1 and shYY2, although combined shYY1/shYY2 knockdowns were not additive. In contrast, shYY2 reversed anti-proliferative effects of shYY1 on E2F target genes, and shYY2 particularly altered UV damage response, platelet-specific genes and mitochondrial function genes. The most YY2-specific gene was the platelet glycoprotein CD36 whose ligand is thrombospondin - a key UV response gene. We found that decreases in YY1 or YY2 caused inverse changes in UV sensitivity, and that their combined loss reversed their respective individual effects. Taken together, our studies show that YY2 is not redundant to YY1, and YY2 is a significant regulator of genes previously thought to uniquely respond to YY1. Functions of thrombospondin and CD36 in inflammation, atherogenesis, innate immunity and malaria pathogenesis reveal new potential regulatory roles for YY1 and YY2.

overall_design:
Four treatment groups were used that included control vector (pLKO) virus, shYY1, shYY2 and shYY1 combined with shYY2. Three replicas were performed for all except shYY2, where we performed four replicas.
Target gene comparison of YY1 And YY2 homologous genes.

middle: V

first: Li

last: Chen


title: Antiviral response dictated by choreographed cascade of transcription factors

city: New Haven

first: Uri

last: Hershberg

state: CT

address: 300 George st

institute: Yale School of Medicine

summary: The dendritic cell (DC) is a master regulator of immune responses. Pathogenic viruses subvert normal immune function in DCs through the expression of immune antagonists. Understanding how these antagonists interact with the host immune system requires knowledge of the underlying genetic regulatory network that operates during an uninhibited antiviral response. In order to isolate and identify this network, we studied DCs infected with Newcastle Disease Virus (NDV), which is able to stimulate innate immunity and DC maturation through activation of RIG-I signaling, but lacks the ability to evade the human interferon response. To analyze this experimental model, we developed a new approach integrating genome-wide expression kinetics and time-dependent promoter analysis. We found that the genetic program underlying the antiviral cell state transition during the first 18-hours post-infection could be explained by a single regulatory network. Gene expression changes were driven by a step-wise multi-factor cascading control mechanism, where the specific transcription factors controlling expression changed over time. Within this network, most individual genes are regulated by multiple factors, indicating robustness against virus-encoded immune evasion genes. In addition to effectively recapitulating current biological knowledge, we predicted, and validated experimentally, antiviral roles for several novel transcription factors. More generally, our results show how a genetic program can be temporally controlled through a single regulatory network to achieve the large-scale genetic reprogramming characteristic of cell state transitions.

overall_design: Total RNA from Monocyte-derived conventional DCs of 2 different donors were infected with Newcastle disease virus (NDV) or as control with allantoic fluid (AF) alon. DC were then harvested at : 0, 1, 2, 6, 10 and 18 hour for control and 1, 2, 4, 6, 8, 10, 12, 14, 16 and 18 hours for NDV infection. Replicates were performed for each of the donors at all timepoints.

first: Jeremy

last: Seto


title: Expression data from breast cancer cells overexpressing NF1-C2

status: Public on Feb 27 2010

city: Gothenburg

first: Jeanette

last: Nilsson

address: Box 462

department: Cell and Molecular Biology

institute: Gothenburg University

summary: NF1-C2 suppresses tumorigenesis and epithelial-to-mesenchymal transition by repressing FoxF1. We used microarray to identify direct targets for NF1-C2.

overall_design: The human breast tumor cell line MDA-MB-436 were stably transfected with an expression plasmid including NF1-C2. RNA from these cells and wildtype cells were extracted and hybridized on Affymetrix microarrays (platform GPL570). Three replicates each.

first: Marie

middle: K

last: Janson