title: Synergistic interaction of gamma-secretase inhibitor therapy and glucocorticoids in T-ALL

first: Adolfo

last: Ferrando

summary:
Glucocorticoids are an essential component of the treatment of lymphoid malignancies and resistance to glucocorticoid therapy constitutes a prominent clinical problem in relapsed and refractory lymphoblastic leukemias. Constitutively active NOTCH signaling is involved in the pathogenesis of over 50% of T-cell lymphoblastic leukemia (T-ALL) which harbor activating mutations in the NOTCH1 gene. Aberrant NOTCH1 signaling has been shown to protect normal thymocytes from glucocorticoid induced cell death. Here we analyzed the interaction of glucocorticoid therapy with inhibition of NOTCH signaling in the treatment of T-ALL.  Gamma-secretase inhibitors (GSI), which block the activation of NOTCH receptors, amplified the transcriptional changes induced by glucocorticoid treatment, including glucocorticoid receptor autoinduction and restored sensitivity to dexamethasone in glucocorticoid-resistant T-ALL cells.  Apoptosis induction upon inhibition of NOTCH signaling and activation of the glucocorticoid receptor was dependent on transcriptional upregulation of BIM and subsequent activation of the mitochondrial/intrinsic cell death pathway. Finally, we used a mouse xenograft model of T-ALL to demonstrate that combined treatment with dexamethasone and a GSI results in improved antileukemic effects in vivo. These studies provide insight in the mechanisms of glucocorticoid resistance and serve as rationale for the use of glucocorticoid and GSIs in combination in the treatment of T-ALL.
Keywords: Drug response

overall_design: Duplicate samples (biologic replicas) from CUTLL1 cells were treated for 24 hours with vehicle only (DMSO), dexamethasone (1microM),  a gamma-secretase inhibitor (CompE 100nM) and a combination of dexamethasome plus gamma secretase inhibitor at the same concentrations indicated before. Gene expression profiling was analyzed to identify gene expression signatures assocuated with glucocorticoid treatment (dexamethasone), inhibition of NOTCH1 by gamma secretase inhibitor (CompE) or the combination of both treatments.

first: Predro

last: Real


title: ERAD inhibitors integrate ER stress with an epigenetic mechanism to activate BH3 only protein NOXA in cancer cells

status: Public on Feb 20 2009

city: Bethesda

first: WeiPing

last: Chen

state: MD

address: Bldg 8, Room 1A11, NIDDK/NIH

department: GCL

country: USA

institute: NIDDK/NIH

summary: The ubiquitin-proteasome system (UPS) has recently emerged as a major target for drug development in cancer therapy. The proteasome inhibitor bortezomib has clinical activity in multiple myeloma and mantle cell lymphoma. Here we report that Eeyarestatin I (EerI), a chemical inhibitor that blocks ER-associated protein degradation (ERAD), has anti-tumor and biologic activities similar to bortezomib, and can synergize with bortezomib. Like bortezomib, EerI-induced cytotoxicity requires the upregulation of the BH3 only pro-apoptotic protein NOXA.  We further demonstrate that both EerI and bortezomib activate NOXA via an unanticipated mechanism that requires cooperation between two processes: First, these agents elicit an integrated stress response program at the ER to activate the CREB/ATF transcription factors ATF3 and ATF4. We show that ATF3 and ATF4 form a complex capable of binding to the NOXA promoter, which is required for NOXA activation. Second, EerI and bortezomib also block ubiquitination of histone H2A to relieve its inhibition on NOXA transcription. Our results identify a class of anti-cancer agents that integrate ER stress response with an epigenetic mechanism to induce cell death.

overall_design:
1. EerI 10 vs 0
2. EerI 10 vs 0
3. Bzm 10 vs 0
4. Bzm 10 vs 0

first: Qiuyan

last: Wang

first: Helena

last: Mora-Jensen

first: Marc

middle: A

last: Weniger

first: Patricia

last: Perez-Galan

first: Chris

last: Wolford

first: Tsonwin

last: Hai

first: David

last: Ron

first: Weiping

first: William

last: Trenkle

first: Adrian

last: Wiestner

first: Yihong

last: Ye


title: Expression data from postmortem human brain samples with and without FTLD-U

status: Public on Oct 11 2008

city: Philadelphia

first: Alice

last: Chen-Plotkin

state: PA

address: 3600 Spruce Street 3rd Floor Maloney

department: Pathology and Neurology

institute: University of Pennsylvania

summary:
FTLD-U is the most common pathological correlate of the neurodegenerative dementia frontotemporal dementia
We used microarrays to perform global expression profiling of FTLD-U brain samples

Keywords: disease

overall_design: Postmortem brain samples were isolated from normal controls, FTLD-U patients with progranulin gene mutations (progranulin) and FTLD-U patients without progranulin gene mutations (sporadic).  Regional dissections were carried out from frontal cortex, hippocampus, and cerebellum.


title: Induction of TRAIL and TNF-alpha-dependent Apoptosis in Human mDCs by Microfilariae of Brugia Malayi

status: Public on Sep 17 2008

city: Dallas

first: Damien

last: Chaussabel

state: TX

address: 3434 Live Oak

institute: Baylor Institute for Immunology Research

summary:
Dysregulation of professional APC has been postulated as a major mechanism underlying Ag-specific T cell hyporesponsiveness in patients with patent filarial infection. To address the nature of this dysregulation, dendritic cells (DC) and macrophages  generated from elutriated monocytes were exposed to live microfilariae (mf), the parasite stage that circulates in blood and is responsible for most immune dysregulation in filarial infections. DC exposed to mf for 24–96 h showed a marked increase in cell death and caspase-positive cells compared with unexposed DC, while mf exposure did not induce apoptosis in macrophages. Interestingly, 48 h exposure of DC to mf induced mRNA expression of the pro-apoptotic gene TRAIL and both mRNA and protein expression of TNF-alpha. mAb to TRAIL-R2, TNF-R1, or TNF-alpha partially reversed mf-induced cell death in DC, as did knocking down the receptor for TRAIL-R2 using small interfering RNA. Mf also induced gene expression of BH3-interacting domain death agonist (Bid) and protein expression of cytochrome c in DC; mf-induced cleavage of Bid could be shown to induce release of cytochrome c, leading to activation of caspase 9. Our data suggest that mf induce DC apoptosis in a TRAIL- and TNF-alpha-dependent fashion.

Keywords: Dendritic Cell, Parasite, Human, Microfilariae

overall_design: Microfilariae and human monocyte derived-DCs were cultuted at a multiplicity of infection of 1:1  for 24hrs for four independent donors.  Matching samples exposed to  media alone were used for controls  The four experimental and 4 control samples were then pooled to create one experoimental and one healthy pool used for microarray analysis.


title: Expression data from human glioma samples

status: Public on Sep 09 2008

city: London

first: Linda

middle: B

last: Moran

address: Fulham Palace Road

department: Neuropathology

country: United Kingdom

institute: Imperial College London

summary:
We used microarrays to determine the gene expression profile of different types of glioma

Keywords: Disease state analysis

overall_design: Histologically identified glioma-subtypes were selected for RNA extraction and hybridization on Affymetrix microarrays (HG-U95A)

first: Manuel

last: Graeber


title: Gene expression from human prefrontal cortex (BA10)

status: Public on Sep 04 2008

city: Wako

first: Kazuya

last: Iwamoto

address: 2-1 Hirosawa

department: Brain Science Institute

country: Japan

institute: RIKEN

summary:
We performed the oligonucleotide microarray analysis in bipolar disorder, major depression, schizophrenia, and control subjects using postmortem prefrontal cortices provided by the Stanley Foundation Brain Collection. By comparing the gene expression profiles of similar but distinctive mental disorders, we explored the uniqueness of bipolar disorder and its similarity to other mental disorders at the molecular level. Notably, most of the altered gene expressions in each disease were not shared by one another, suggesting the molecular distinctiveness of these mental disorders. We found a tendency of downregulation of the genes encoding receptor, channels or transporters, and upregulation of the genes encoding stress response proteins or molecular chaperons in bipolar disorder. Altered expressions in bipolar disorder shared by other mental disorders mainly consisted of upregulation of the genes encoding proteins for transcription or translation. The genes identified in this study would be useful for the understanding of the pathophysiology of bipolar disorder, as well as the common pathophysiological background in major mental disorders at the molecular level.
Keywords: disease state analysis

overall_design: A total of 50 postmortem brains obtained from the Stanley Medical Research Institute were used for DNA microarray analysis. Fresh frozen samples were used for RNA extraction.

first: Chihiro

last: Kakiuchi

first: Miki

last: Bundo

first: Kazuhiko

last: Ikeda

first: Tadafumi

last: Kato


title: Expression data from monocytes of individuals with different collateral flow index CFI

status: Public on Aug 31 2008

city: Bern

first: Pascal

last: Meier

address: Freiburgstrasse

department: Cardîology

country: Switzerland

institute: University Hospital

summary:
using peripheral blood monocytes  to identify marker genes for an extensively grown coronary collateral circulation.
We used microarrays to detail the global programme of gene expression underlying collateralization and identified distinct classes of  differently regulated genes during this process.
Keywords: observational study

overall_design: Collateral flow index (CFI) was obtained invasively by angioplasty pressure sensor guidewire, a group of patients with coronary artery disease CAD and a group without CAD were selected for peripheral monocyte isolation, RNA extraction and hybridization on Affymetrix microarrays.

first: Janine

last: Antonov

first: Rainer

last: Zbinden

first: Alexandre

last: Kuhn

first: Steffen

last: Gloekler

first: Stephan

first: Rolf

last: Jaggi

first: Mauro

last: Delorenzi

first: Christian

last: Seiler


status: Public on Oct 16 2008

city: Brisbane

first: Gang-Ping

last: Xue

state: Qld

address: 306 Carmody Rd., St Lucia

department: Plant Industry

country: Australia

institute: CSIRO

summary:
Water soluble carbohydrates (WSC, composed of mainly fructans, sucrose, glucose and fructose) deposited in wheat stems are important carbon sources for grain filling. Variation in stem WSC concentrations among wheat genotypes is one of the genetic factors influencing grain weight and yield under water-limited environments. Here, we describe the molecular dissection of carbohydrate metabolism in stems, at the WSC accumulation phase, of recombinant inbred SB (Seri/Babax) lines of Triticum aestivum differing in stem WSC concentrations. Affymetrix GeneChip analysis of carbohydrate metabolic enzymes revealed that the mRNA levels of two fructan synthetic enzyme families (sucrose:sucrose 1-fructosyltransferase and sucrose:fructan 6-fructosyltransferase) in the stem were positively correlated with stem WSC and fructan concentrations, while the mRNA levels of enzyme families involved in sucrose hydrolysis (sucrose synthase and soluble acid invertase) were inversely correlated with WSC concentrations. Differential regulation of the mRNA levels of these sucrose hydrolytic enzymes in SB lines resulted in genotypic differences in these enzyme activities. Down-regulation of  sucrose synthase and soluble acid invertase in high WSC lines was accompanied by significant decreases in the mRNA levels of enzyme families related to sugar catabolic pathways (fructokinase and mitochondrion pyruvate dehydrogenase complex) and enzyme families involved in diverting UDP-glucose to cell wall synthesis (UDP-glucose 6-dehydrogenase, UDP-glucuronate decarboxylase and cellulose synthase), resulting in a reduction in cell wall polysaccharide contents (mainly hemicellulose) in the stem of high WSC lines. These data suggest that differential carbon partitioning in the wheat stem is one mechanism that contributes to genotypic variation in WSC accumulation.
We used Affymetrix GeneChip to dissect genotypic variation in carbohydrate metabolism related to water soluble carbohydrate accumulation in stems of wheat.
Keywords: Genotypic differences in water soluble carbohydrate metabolism in stem

overall_design: 8 genotypes of recombinant inbred lines Seri M82 x Babax  with 2 biological replicates per genotype. Grown in the field under rain-fed conditions

first: C

middle: L

last: McIntyre

first: Ray

last: Shorter

first: Anthony

middle: F

last: van Herwaarden


title: Expression data from cold treated wheat cultivars

status: Public on Oct 01 2008

city: Bristol

first: Mark

middle: Owen

last: Winfield

address: Woodland Road

department: Biological Sciences

institute: Bristol University

summary:
Different wheat cultivars may be classified as either winter or spring varieties depending on whether they require exposure to an extended period of cold in order to become competent to flower.  Using a growth regime that mimics the conditions that occur during a typical winter in Britain, we wished to survey the genes that are involved in phase transition as well as those involved in cold-acclimation.

Keywords: Time course

overall_design: We wished to study the profiles of expression of genes involved in both phase transition (vegetative to reproductive growth transition) and cold-acclimation.  To that end we we exposed plants to a gradual, stepped decline in both temperature and light.  We sampled plants at three time points (3 weeks post-germination, 5 weeks post germination and 9 weeks post germination).  We took samples from two separate tissues (crown and leaf) to se whether responses were different.  We used two biological reps for each time point and tissue.  Control plants were exposed to a delined in day-length and light intensity, but not in temperature.

middle: O

first: Chungui

last: Lui

first: Ian

middle: D

last: Wilson

first: Jane

last: Coghill

first: Keith

middle: J

last: Edwards


title: Transcript profiling of Lr1- and Lr34-mediated leaf rust resistance in wheat

status: Public on Nov 01 2008

city: St. Paul

first: David

last: Garvin

state: MN

address: 411 Borlaug Hall, 1991 Upper Buford Circle

department: Plant Science Research Unit

institute: USDA

summary:
The wheat gene Lr34 confers partial resistance to all races of Puccinia triticina, the causal agent of wheat leaf rust.  However, the biological basis for the exceptional durability of Lr34 is unclear.  The Affymetrix wheat genome array was used to identify wheat genes differentially expressed in a compatible interaction (Tc), an R-gene mediated incompatible interaction (Tc-Lr1), and a race non-specific resistance interaction (Tc-Lr34) in response to infection challenge by P. triticina race 1 at anthesis.  Transcriptome interrogation was conducted by comparing mock- and P. triticina-inoculated leaves harvested at 3 and 7 days post inoculation (dpi).
Keywords: Time course

overall_design: The Affymetrix wheat genome array was used to identify wheat genes differentially expressed in a compatible interaction (Tc), an R-gene mediated incompatible interaction (Tc-Lr1), and a race non-specific resistance interaction (Tc-Lr34) in response to infection challenge by P. triticina race 1 at anthesis.  Transcriptome interrogation was conducted on leaves harvested at 3 and 7 days post inoculation (dpi).  The study utilized a randomized complete block design with three replicates for each genotype, and employed univariate analysis (t-tests) between mock- and P. triticina-inoculated plants within each genotype at each timepoint, for a total of six comparisons across the entire experiment, utilizing a total 36 Affymetrix Wheat Genome Array GeneChips.

first: Melvin

last: Bolton

first: James

last: Kolmer

first: Wayne

middle: W

last: Xu


title: SAOS-2 cells, RBP2 knockdown or pRB overexpression

status: Public on Aug 29 2008

city: Chicago

first: Elizaveta

middle: V

last: Benevolenskaya

state: IL

address: 900 S. Ashland Ave.

department: Biochemistry and Molecular Genetics

institute: University of Illinois at Chicago

summary:
RBP2 is downstream of pRB pathway
We used gene expression profiling experiments to investigate if gene expression changes in cells with RBP2 knockdown significantly overlap with gene expression changes in cells overexpressing pRB, consistent with the data that knockdown of RBP2 phenocopies reintroduction of pRB in SAOS-2 (RB-/-) cells
Keywords: epistatic experiment

overall_design: Knockdown of RBP2 by siRNA to RBP2 (RBP2siRNA) in SAOS-2 (RB-/-) cells in comparison to overexpression of pRB in the SOAS-2 (RB-/-) cells and scrambled version of the RBP2 siRNA (RBP2scsiRNA)

first: William

middle: G

last: Kaelin


title: Nude mouse model of endometriosis

status: Public on Dec 22 2008

city: Cambridge

first: D. Stephen

last: Charnock-Jones

address: The Rosie Hospital

department: Obstetrics and Gynaecology

institute: University of Cambridge

summary:
The pathophysiology of endometriotic lesion development remains unclear but involves a complex interaction between ectopic endometrium and host peritoneal tissues. We hypothesised that disruption of this interaction was likely to suppress endometriotic lesion formation. We hoped to delineate the molecular and cellular dialogue between ectopic human endometrium and peritoneal tissues in nude mice, as a first step towards testing this hypothesis. Human endometrium was xenografted into nude mice and the resulting lesions were analysed using microarrays. A novel technique was developed that unambiguously determined whether RNA transcripts identified by the microarray analyses originated from human cells (endometrium) or mouse cells (stroma).  Four key pathways (ubiquitin/proteosome, inflammation, tissue remodelling/repair and ras-mediated oncogenesis) were revealed, that demonstrated communication between host stromal cells and ectopic endometrium.

Morphometric analysis of nude mouse lesions confirmed that necrosis, inflammation, healing and repair and cell proliferation occurred during xenograft development. These processes were entirely consistent with the molecular networks revealed by the microarray data.  The transcripts detected in the xenografts overlapped with transcripts differentially expressed in a comparison between paired eutopic and ectopic endometrium from human endometriotic patients.

For the first time components of the interaction between ectopic endometrium and peritoneal stromal tissues have been revealed in ectopic endometrial lesions. Targeted disruption of this dialogue is likely to disrupt endometriotic tissue formation and may prove to be an effective therapeutic strategy for endometriosis.

Keywords: time course, disease state analysis.

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus

overall_design: Xenografts of human endometrium in nude mice hybridised to both human and mouse specific genechips.   2 biological replicates, at 3 time points.  Control human endometrium and mouse pertioneum were hybridised to both human and mouse genechips

first: D

middle: S


title: Ebp1's effect in prostate cancer

status: Public on Oct 31 2008

city: Baltimore

first: Anne

last: Hamburger

address: 655 W. Baltimore St

department: Cancer Center

institute: University of Maryland Baltimore

summary: Therapies targeting the androgen receptor are critical for treatment of hormone refractory prostate cancer. We have previously demonstrated that Ebp1, a protein isolated by its ability to bind ErbB3, is a downstream effector of heregulin activated pathways and an AR corepressor. As Ebp1 is decreased in preclinical models of hormone refractory prostate cancer, we studied the ability of Ebp1 to mitigate the hormone refractory phenotype. As we previously found that Ebp1 affected the expression of some androgen receptor target genes, we sought to determine a full spectrum of genes changed using an unbiased appraoch by microarry analysis.

overall_design: A hormone independent cell line C81 was derived from LNCaP cells by long term passage and was a kind gift of Dr. Lin (University of Nebraska). C81 cell were transfected with a vector control or EBP1 expression plasmids and mass cultures selected. RNA was collected from logaritmically growing cultures.

first: Yuexing

last: Zhang

first: Douglas

last: Linn


title: Gene expression profiling of N-CoR2 overexpression in response to death induction

status: Public on Sep 01 2008

city: San Francisco

first: Kelvin

middle: Kun-Chih

last: Tsai

state: CA

address: 513 Parnassus Avenue, Rm S1364

department: Surgery

institute: University of California, San Francisco

summary:
The series represent gene expression profiles of T4-2 neoplastic breast epithelial cells that overexpressed N-CoR2 and were treated with the death ligand TRAIL in three-dimensional reconstituted basement membrane culture.
Keywords: Genetic modification; response to death induction

overall_design: Four replicate cultures were established for each of the 4 experiment groups, including those using T4-2 cells that stably expressed N-CoR2 (T4-2_NCOR2), T4-2 cells expressing the empty vector (T4-2_vector), TRAIL-treated T4-2 N-CoR2 cells (T4-2_NCOR2_TRAIL), and TRAIL-treated T4-2 vector cells (T4-2_vector_TRAIL). Cells were grown on top of reconstituted basement membrane for 6 days and then treated with TRAIL (1 μg/mL) or vehicles for 4 hours before the collection of RNA samples.

middle: K

first: Valerie

middle: M

last: Weaver

first: Chandrima

last: Chatterjee

first: Jonathan

middle: N

last: Lakins

first: Manunya

last: Nuth

first: John

last: Tobias

first: I.

last: Mian


title: Transcription profiling of myotubes from patients with type 2 diabetes

status: Public on Sep 03 2008

city: Odense

first: Casper

last: Frederiksen

address: Kloevervaenget 6

country: Denmark

institute: Odense University Hospital

summary:
Microarray-based studies of skeletal muscle from patients with type 2 diabetes and high-risk individuals have demonstrated that insulin resistance and reduced mitochondrial biogenesis co-exist early in the pathogenesis of type 2 diabetes independent of hyperglycaemia and obesity. It is unknown whether reduced mitochondrial biogenesis or other transcriptional alterations co-exist with impaired insulin-responsiveness in primary human muscle cells from patients with type 2 diabetes.
Results: No single gene was differently expressed after correction for multiple testing, and no biological pathway was differently expressed using both approaches for global pathway analysis. In particular, we found no evidence for differential expression of genes involved in mitochondrial oxidative metabolism. Consistently, there was no difference in mRNA levels of genes known to mediate the transcriptional control of mitochondrial biogenesis, PPARGC1A and NRF-1, or in mitochondrial mass between diabetic and control myotubes.

Keywords: Cell culture, genetic, oxidative phosphorylation, microarray, skeletal muscle, type 2 diabetes

overall_design: Human Genome U95Av2 GeneChips (Affymetrix) was used for ten obese patients with type 2 diabetes and ten healthy control subjects.With global pathway analysis with Gene Map Annotator and Pathway Profiler (GenMapp 2.1) and Gene Set Enrichment Analysis (GSEA 2.0.1), we examined transcript levels in myotubes established from obese patients with type 2 diabetes and matched obese healthy subjects, who have been extensively metabolically characterized both in vivo and in vitro.

first: K

last: Højlund

first: L

last: Hansen

first: E

last: Oakeley

first: B

last: Hemmings

last: Abdallah

last: Brusgaard

first: H

last: Beck-NielsenH

first: M

last: Gaster


title: Th17 cytokines interleukin (IL)-17 and IL-22 modulate distinct inflammatory and keratinocyte-response pathways

status: Public on Jul 15 2008

city: New York

first: Mayte

last: Suarez-Farinas

state: NY

address: 1425 Madison Ave, L2-70C, Box 1077,

institute: Mount SinaiSchool of Medicine

summary:
In this study, we shought to identify the cytokines produced by skin-resident T cells in normal skin, localize the receptors for these cytokines, and examine how these cytokines alter gene expression profiles of the cells bearing cognate receptors.

Keywords: repeated measures experiment

overall_design: In this study,  primary keratinocytes were treated with either IL-17, IL-22 or IFNg for 24 hours then harvested for RNA extraction and subsequent gene array analysis

first: Kristine

middle: E

last: Nograles

last: Suárez-Fariñas

first: James

last: Krueger


title: Gene Expression Changes in Myeloma Cells Following Short Term In-vivo Drug Exposure

status: Public on Aug 04 2008

city: Little Rock

first: Yiming

last: Zhou

state: AR

address: 4301 West Markham St., Slot 776

institute: Myeloma Institute for Research and Therapy

summary:
In vivo changes of gene expression profiles (GEP) of tumor cells 48hr after single agent therapy may vary by treatment and provide added predictive power over baseline GEP information. In newly diagnosed patients with multiple myeloma (MM), GEP data were obtained on tumor cells prior to and 48hr after dexamethasone (n=45) or thalidomide treatment (n=42); in case of relapsed MM, GEP data were obtained prior to (n=36) and after (n=19) lenalidomide administration. Dexamethasone and thalidomide induced both common and unique GEP changes. Combined baseline and 48hr changes of GEP in a subset of genes that were discovered in newly diagnosed MM also predicted event-free and overall survival in relapsed patients receiving lenalidomide. Combined with baseline molecular features, changes in GEP following short-term single agent treatment may help guide treatment decisions for patients with MM. The genes whose altered expression is related to eventual survival may also point to mechanisms of action and resistance to different classes of drugs.
Keywords: drug response

overall_design: See above (Series_summary)

last: Shaughnessy Jr


title: Immune Dysregulation/Tumor-Associated Gene Changes in Recurrent Respiratory Papillomatosis: A Paired Microarray Analysis

status: Public on Jul 16 2008

city: Manhasset

middle: Allen

last: DeVoti

address: 350 Community Drive, Rm 140

department: Immunology and Inflammation

institute: Feinstein Institute for Medical Research

summary:
The goal of this study was to determine the differential expression of specific genes within the papilloma tissues themselves and to characterize the array of host genes that might be important in the pathophysiology of recurrent respiratory papillomatosis.
Keywords: papilloma vs normal adjacent autologous larynx

overall_design: Total RNAs from papillomas (n=12) and adjacent tissues (n=12) were analyzed by Affymetrix microarray, and the matched sets of tissues compared by Genesifter paired t-test to identify differentially expressed genes in papilloma tissues while minimizing variations that are intrinsic to individual patients.

middle: A

last: Devoti

first: David

last: Rosenthal

first: Rong

last: Wu

first: Allan

last: Abramson

first: Bettie

last: Steinberg

first: Vincent

middle: R

last: Bonargua


title: Expression data from buccal and nasal epithelium of current and never smokers

status: Public on Jul 03 2008

city: Gaithersburg

first: Sriram

last: Sridhar

address: 1 MedImmune Way

department: Translational Medicine

institute: MedImmune

summary:
Smoking is the leading cause of lung cancer death, although only a small percentage of smokers develop the disease. Cigarette smoke exposure is known to cause a field of injury in cells throughout the respiratory tract, and while these airway epithelial cells are morphologically normal, they can undergo genetic alterations in response to cigarette smoke exposure.
We used microarrays to analyze the gene expression of epithelial cells in the extrathoracic epithelium, specifically nasal and buccal epithelium, to see if these cells underwent similar genetic alterations in response to tobacco exposure as seen in bronchial epithelial cells as has been previously reported.
Keywords: cross sectional

overall_design: Buccal and nasal epithelial cell samples were collected from healthy current and never smokers. RNA was isolated from these samples and hybridized to Affymetrix microarrays. Gene expression from never smokers was compared to never smoker gene expression from bronchial epithelium as well as expression data from other tissues to determine commonalities in expression patterns in normal extra- and intra-thoracic samples. In addition, gene expression from smokers and nonsmokers was compared in bronchial, nasal, and buccal epithelium to determine similarities in gene expression in these tissues in response to cigarette smoker exposure.

first: Avrum

last: Spira


title: O-glycan inhibitors generate aryl-glycans, induce apoptosis, and inhibit growth in colorectal cancer cell lines

status: Public on Aug 18 2008

city: Berlin

first: Andreas

last: Klein

address: Charitéplatz 1

department: Institute of Biochemistry

country: Germany

institute: Charité (CCO)

summary:
Our studies provide direct evidence that O-glycosylation pathways play a role in the regulation of cell growth through apoptosis and proliferation pathways. Eight small molecular weight analogues of the GalNAc-alpha-1-O-serine/threonine structure based on 1-benzyl-2-acetamido-2- deoxy-alpha-O-D-galactopyranoside have been synthesised and tested in 5 human colorectal cancer cell lines. Three inhibitors, 1-benzyl-2-acetamido-2-deoxy-alpha-O-D-galactopyranoside and the corresponding 2-azido- and C-glycoside analogues, were screened in two colorectal cancer cell lines at 0.5mM and showed induction of apoptosis. Proliferation was down regulated in the same two cell lines with all three inhibitors, as detected by Ki67 staining and gene array. Treatment both cell lines with inhibitors led to changes in glycosylation detected with peanut lectin. The competitive action of the inhibitors resulted in the intracellular formation of 28 aryl-glycan products which were identified by MALDI and electrospray mass spectroscopy. The structures found map onto known O-glycosylation biosynthetic pathways and showed a differential pattern for each of the inhibitors in both cell lines. Gene array analysis of the glycogenes illustrated a pattern of glycosytransferases that matched the glycan structures found in glycoproteins and aryl-glycans formed in the PC/AA/C1/SB10C cells, however there was no action of the three inhibitors on glycogene transcript levels. The inhibitors act at both intermediary metabolic and genomic levels, resulting in altered protein glycosylation and arylglycan formation. These events may play a part in growth arrest.

Keywords: Response to inhibitors, Apoptosis, Aryl-glycans, Benzyl-O-GalNAc, Growth Inhibition, O-Glycans

overall_design:
The effects of the O-glycan inhibitors Benzyl 2-azido-2-deoxy-alpha-D-galactopyranoside (alpha-OBn GalN3), Benzyl 2-acetamido-2-deoxy-alpha-D-galactopyranoside (alpha-OBn GalNAc), and 2-(2-acetamido-2-deoxy-alpha-D-galactopyranosyl)-1-phenylethane (alpha-CBn GalNAc) on the colorectal cancer cell line PC/AA/C1/SB10C were examined.
The PC/AA/C1/SB10C cells were treated with with 0.5 mM of the inhibitors for four days. In control experiments cells were cultivated without inhibitor. All experiments were performed twice. Total RNA was extracted with RNAzol reagent in accordance to the manufacturer instructions (PeQLab, Biotechnology Fareham, UK), treated with RNase-free DNase (DNA-free, Ambion,Warrington, UK) and integrity verified using the Agilent Bioanalyzer (Agilent Technologies, West Lothian, UK), by the presence of the 28S and 18S rRNA on agarose gels and an A260/280 ratio in the range of 1.9–2.1. A sample (5 μg) of total RNA was used for production of biotinylated cRNA as described in the Affymetrix GeneChip analysis instruction manual (Affymetrix UK, High Wycombe, UK). The human genome 133A 2.0 array was then hybridized with the biotin-labeled cRNA fragments for 16 h at 45°C. Washing steps for the chip, staining with streptavidin-phycoerythrin, signal amplification and scanning were performed according to the manufacturer’s instructions (Affymetrix UK, High Wycombe, UK). Signal values were exported with the GeneChip operating software (GCOS, Affymetrix). Further analyses were performed with the software “CorrXpression”, which is described in detail elsewhere (Klein et al. 2005, J Mol Med. 83:362-376; Wessel et al. 2006, In Silico Biol.6:61-70).

first: Georgios

last: Patsos

first: Anthony

last: Corfield


title: Celecoxib pre-treatment in human colorectal adenocarcinoma patients.

status: Public on Aug 21 2008

city: Chapel Hill

middle: Todd

last: Auman

state: NC

address: 3304 Kerr Hall, Campus Box 7360

department: Institute for Pharmacogenomics and Individualized Therapy

institute: University of North Carolina at Chapel Hill

summary:
Pharmacological inhibition of cyclooxygenase-2 (COX-2) is being explored as a chemotherapeutic option because COX-2 protein expression is often elevated in many cancers.  Cancer cells treated with COX-2 inhibitors, such as the selective COX-2 inhibitor celecoxib, show growth inhibition and the induction of apoptosis, through alterations in inflammatory processes, angiogenesis, cell adhesion and transforming growth factor-β signaling.  This study was conducted to determine if the same processes are relevant to celecoxib’s effects on human colorectal adenocarcinomas treated in vivo.  A cohort of 23 patients with primary colorectal adenocarcinomas was randomized to receive a 7-day course of celecoxib (400 mg b.i.d.) or no drug prior to surgical resection.  Gene expression profiling was performed on resected adenocarcinomas from patients with and without celecoxib pre-treatment.  Using fold change (>1.5) and p-value (<0.05) cut-offs, 190 genes were differentially expressed between adenocarcinomas from patients receiving celecoxib and those that did not.  Of the differentially expressed genes, multiple genes involved in cellular lipid and glutathione metabolism showed decreased expression levels in celecoxib pre-treated samples; changes associated with diminished cellular proliferation.  Other observed gene expression changes consistent with reduced proliferation include: altered expression of genes involved in cell adhesion (including collagen, laminin, von Willebrand factor and tenascin C), increased expression of inflammatory modulators (including inerleukin-6, S100 calcium binding protein A8, and several chemokines) and decreased expression of the pro-angiogenic gene, angiogenin.  Celecoxib pre-treatment for 7 days in vivo is associated with alterations in colorectal adenocarcinoma gene expression which are suggestive of diminished cellular proliferation.
Keywords: treatment outcome

overall_design:
Patients undergoing surgical resection of histologically proven primary colorectal adenocarcinomas were consented for participation in the study.  The patients enrolled in this study were randomized to receive either 400 mg celecoxib two times per day (n=11) or no COX-2 inhibitor (n=12) for 7 days prior to surgical resection. Total RNA (5 ug) from each sample was converted to double stranded cDNA using a dT-T7 promoter primer.  The double stranded cDNA was then used as a template to synthesize biotinylated RNA, which was fragmented and hybridized to the Affymetrix HG_U95av2 microarray chip using Affymetrix’s labeling and hybridization protocol.
The array data was imported into GeneSpring GX 7.3 using the GC-RMA file preprocessor.  The data was normalized by: (1) setting all expression measurements <0.01 to 0.01, (2) a per chip normalization to the 50th percentile, and (3) a per gene normalization to the median value across all chips.

middle: T


title: Gene expression of CML CD34+ cells during Imatinib therapy

status: Public on Jul 30 2008

city: Duesseldorf

first: Daniela

last: Bruennert

address: Universitaetsstr. 1

department: Clinic for Hematology, Oncology and clin. Immunology

institute: University Clinic Duesseldorf

summary: Imatinib has become the current standard therapy for patients with chronic myelogenous leukaemia (CML). For a better understanding of the Imatinib-related molecular effects in vivo, we assessed gene expression profiles of Philadelphia Chromosome positive (Ph+) CD34+ cells from peripheral blood of 6 patients with de novo CML in chronic phase. After 7 days of treatment with Imatinib the Ph+ CD34+ cells were reassessed to look for changes in the transcriptome. The expression level of 303 genes was significantly different comparing the transcriptome of the Ph+ CD34+ cells before and after 7 days of Imatinib therapy (183 down-regulated, 120 up-regulated, lower bound ≥1.2-fold). For a substantial number of genes governing cell cycle and DNA replication, the level of expression significantly decreased (CDC2, RRM2, PCNA, MCM4). On the other hand, therapy with Imatinib was associated with an increase of genes related to adhesive interactions, such as L-selectin or CD44. A group of 8 genes with differential expression levels were confirmed using a gene specific quantitative real-time PCR. Thus, during the first week of treatment, Imatinib is preferentially counteracting the bcr-abl induced effects related to a disturbed cell cycle and defective adhesion of leukemic Ph+ CD34+ cells.

overall_design: In total 6 patients with new diagnosis CML (Chronic Myelogenous Leukemia) in chronic phase are inculded in the study. The gene expression profiles of the CD34+ hematopoietic stem and progenitor cells from the patients before first treatment with Glivec (Imatinib) are compared to the gene expression profiles of the CD34+ hematopoietic stem and progenitor cells of the same patients after 7 days of treatment with 400 mg Glivec / day.

middle: C

first: Akos

last: Czibere

first: Ingmar

last: Bruns

first: Ralf

last: Kronenwett

first: Norbert

last: Gattermann

first: Rainer

last: Haas

first: Frank

last: Neumann


title: GAR22: A novel target gene of thyroid hormone receptor causes growth inhibition in human erythroid cells

status: Public on Jul 31 2008

city: Aachen

first: Martin

last: Zenke

state: NRW

address: Universitatsklinikum Aachen, RWTH

department: Cell Biology

institute: Institute for Biomedical Engineering

summary:
Objective: Thyroid hormone receptors (TRs) are ligand-dependent transcription factors with a major impact on erythroid cell development. Here we investigated TR activity on red cell gene expression and identified TR target genes. The impact of the TR target gene GAR22 (growth arrest specific 2 [GAS2]-related gene on chromosome 22) on red cell differentiation was determined.
Methods: SCF/Epo dependent red cell progenitors were differentiated in vitro in the presence or absence of thyroid hormone. Hormone-induced changes in gene expression were measured by a genome-wide approach with DNA microarrays. Ectopic expression of the TR target gene GAR22 was used to determine its impact on red cell differentiation.
Results: Ligand-activated TR effectively accelerated red cell progenitor differentiation in-vitro concomitantly with inducing growth arrest. We demonstrate that activated TR induced specific gene expression patterns of up- or down-regulated genes, including distinct clusters associated with accelerated differentiation in response to treatment. Mining for T3 induced genes identified BTEB1 (basic transcription element binding protein 1/Krüppel-like factor 9) and GAR22 as TR target genes. BTEB1/KLF9 is a known TR target gene while GAR22, initially identified as a putative tumor suppressor, represents a novel TR target gene. We demonstrate that ectopic GAR22 expression in red cell progenitors lengthens the cell cycle and causes growth inhibition, but leaves red cell gene expression unaffected.
Conclusion: This study identifies GAR22 as a novel and direct TR target gene. Our results suggest that hormone-induced GAR22 might represent an important trigger of growth inhibition induced by thyroid hormone in red cell progenitors.

overall_design:
13 hybridizations in two individual experiments.
Experiment 1:
1_SCF/Epo, 1_Epo/insulin(8h), 1_Epo/insulin(24h), 1_Epo/insulin(48h)
Experiment 2:
2_SCF/Epo, 2_Epo/insulin(8h), 2_Epo/insulin(24h), 2_Epo/insulin(48h)
2_Epo/insulin+T3(8h), 2_Epo/insulin+9cRA(8h)
2_Epo/insulin+T3+9cRA(8h), ,  2_Epo/insulin+T3+9cRA(24h), 2_Epo/insulin+T3+9cRA(48h)

first: Ivonne

last: Gamper

first: Ki-Ryang

last: Koh

first: David

last: Ruau

first: Katrin

last: Ullrich

first: Jana

last: Bartunkova

first: Christine

last: Hacker

first: Petr

last: Bartunek


title: Gene expression profiling of fibroblasts and lymphoblastoid cells derived from four individuals

status: Public on Jun 13 2008

city: Philadelphia

first: Maja

last: Bucan

address: 415 Curie Blvd

institute: UPENN

summary:
Fibroblasts and lymphoblastoid cells (LCLs) are the most widely used cells in genetic, genomic, and transcriptomic studies in relation to human diseases. Examining the gene expression patterns in these two cell types will provide valuable information regarding the validity of using them to study gene expression related to various human diseases.
Fibroblasts and LCLs from four members of the Old Order Amish family 884 were purchased from Coriell cell repositories (Coriell Institute for Medical Research, Camden, NJ). We used microarrays to profile the patterns of gene expression in these eight cell lines. By employing the PennCNV algorithm to the Illumina HumanHap550 SNP genotyping data, we detected 13 Copy Number Variants (CNV) that exist in these four individuals. CNV-expression association analysis revealed that seven of these 13 CNVs were associated with the expression of genes within or near (<2Mb sweep) these CNVs at a nominal regression P value of 0.05.

overall_design: Fibroblast GM05930 and LCL GM05931 were from individual GM05930/5931, fibroblast GM05932 and LCL GM05933 were from individual GM05932/5933, fibroblast GM05934 and LCL GM05935 were from individual GM05934/5935, fibroblast GM05936 and LCL GM05937 were from individual GM05936/5937. These four individuals are siblings within a large sibship; two of them (GM05932/5933 and GM05934/5935) have bipolar type I disorder (BPI). Five μg of total RNA from each cell line was subjected to microarray experiments using HG U133A 2.0 Array (Affymetrix, Santa Clara, CA). Affymetrix Microarray Suite 5.0 was used to quantitate expression levels and assign Calls (Flags of present, marginal, and absent) for each probe set. The CEL files were used to generate normalized expression data that were corrected by the GCRMA algorithm in GeneSpring7.2.

first: Shuzhang

last: Yang


title: HOCL induced airway epithelial gene expression

status: Public on Jun 03 2008

city: Research Triangle Park

first: Yin

last: Chen

address: 6 Davis Dr.

department: Division of Translational Biology

institute: Hamner Institutes for Health Sciences

summary: In inflammatory diseases of the airway, a high level (estimated to be as high as 8 mM) of HOCl can be generated through a reaction catalyzed by the leukocyte granule enzyme myeloperoxidase (MPO). HOCl, a potent oxidative agent, causes extensive tissue injury through its reaction with various cellular substances, including thiols, nucleotides, and amines. In addition to its physiological source, HOCl can also be generated by chlorine gas inhalation from an accident or a potential terrorist attack. Despite the important role of HOCl-induced airway epithelial injury, the underlying molecular mechanism is largely unknown. In the present study, we found that HOCl induced dose-dependent toxicity in airway epithelial cells. By transcription profiling using GeneChip, we identified a battery of HOCl-inducible antioxidant genes, all of which have been reported previously to be regulated by nuclear factor erythroid-related factor 2 (Nrf2), a transcription factor that is critical to the lung antioxidant response. Consistent with this finding, Nrf2 was found to be activated time and dose dependently by HOCl. Although the epidermal growth factor receptor-MAPK pathway was also highly activated by HOCl, it was not involved in Nrf2 activation and Nrf2-dependent gene expression. Instead, HOCl-induced cellular oxidative stress appeared to lead directly to Nrf2 activation. To further understand the functional significance of Nrf2 activation, small interference RNA was used to knock down Nrf2 level by targeting Nrf2 or enhance nuclear accumulation of Nrf2 by targeting its endogenous inhibitor Keap1. By both methods, we conclude that Nrf2 directly protects airway epithelial cells from HOCl-induced toxicity.

overall_design: This is genechip study. Detailed study design is described in: Am J Physiol Lung Cell Mol Physiol. 2008 Mar;294(3):L469-77. Epub 2007 Dec 21.

first: Lingxiang

last: Zhu

first: Jingbo

last: Pi

first: Shinichiro

last: Wachi

first: Melvin

last: Zndersen

first: Reen

last: Wu


title: Monocyte gene expression profiling in familial combined hyperlipidemia and its modification by atorvastatin treatment

city: Barcelona

first: Marta

last: Alegret

address: Diagonal 643

country: Spain

institute: University of Barcelona

summary:
Introduction: The genetic origin of familial combined hyperlipidemia (FCH) is not well understood. We used microarray profiling of peripheral blood monocytes to search  novel genes and pathways involved in FCH. Methods: Fasting plasma for determination of lipid profiles, inflammatory molecules, and adipokines was obtained and peripheral blood monocytes were isolated from male FCH patients basally and after 4 weeks of atorvastatin treatment. Sex-, age- and adiposity-matched controls were also studied. Gene expression profile was analyzed using Affymetrix Human Genome U133A 2.0 GeneChip arrays. Results: Analysis of gene expression by cDNA microarrays showed that 82 genes were differentially expressed in FCH monocytes compared to controls. Atorvastatin treatment modified the expression of 87 genes. Changes in the expression of some genes, confirmed by real time RT-PCR, (CD36, leucine-rich repeats and immunoglobulin-like domains-1, tissue factor pathway inhibitor 2, myeloid cell nuclear differentiation antigen tumor necrosis factor receptor superfamily, member 25 and CD96) may be related to a proinflammatory environment in FCH monocytes, which is partially reversed by atorvastatin. Higher plasma levels of triglycerides and free fatty acids and lower levels of adiponectin in FCH patients could also trigger changes in gene expression that atorvastatin cannot modify. Conclusions: Our results demonstrate clear differences in gene expression in FCH monocytes compared with those of matched healthy controls, some of which are influenced by atorvastatin treatment.
Keywords: comparative study differential gene expression

overall_design: Peripheral blood monocytes were isolated from male FCH patients basally and after 4 weeks of atorvastatin treatment. Sex-, age- and adiposity-matched controls were also studied. Gene expression profile was analyzed using Affymetrix Human Genome U133A 2.0 GeneChip arrays (3 replicates for each condition)

first: Gemma

last: Llaverias

first: Jordi

last: Pou

first: Emilio

last: Ros

first: Daniel

last: Zambón

first: Montserrat

last: Cofán

first: Alex

last: Sánchez

first: Manuel

last: Vázquez-Carrera

first: Rosa

first: Juan

last: Laguna


title: Bioadhesive black rasberry gel effect on gene expression and proinflammatory proteins in human premalignant oral lesions

status: Public on Jun 01 2008

city: Columbus

first: Ping

last: Pei

state: OH

address: 305 West 12th Ave

department: Oral Pathology

institute: OSU

summary:
This portion of the study evaluated the effects of topical 10% black raspberry gel application on gene expression profiles of premalignant oral lesions. Topical application of the bioadhesive black rasberry gel was observed to modulate gene expression and reduce proinflammatory proteins in human premalignant oral lesions.
Keywords: Human oral tissues treated with 10% berry gfel

overall_design: Each patient served as their own internal control.  A pretreatment specimen of the premalignant lesion was obtained for baseline parameters.  Following six weeks of treatment, the treated lesional tissue was removed.  All tissue samples were immediately placed in RNA later and placed in a -80 degree freezer until sample preparation.

first: Susan

last: Mallery

first: Jared

last: Zwick

first: Meng

last: Tong

first: Peter

last: Larsen

first: Brian

last: Shumway

first: Bo

last: Lu

first: Henry

last: Fields

first: Russell

last: Mumper

first: Gary

middle: D

last: Stoner


title: Expression Data From HCMV-Infected Human Monocytes Study 2

status: Public on May 13 2008

city: Shreveport

first: Andrew

middle: D.

last: Yurochko

state: LA

address: 1501 Kings Highway

department: Microbiology & Immunology

institute: LSUHSC-S

summary:
Human cytomegalovirus induces a pro-inflammatory monocyte following infection.  To begin to address how HCMV induces these rapid changes in infected monocytes, we examined the transcriptome of infected monocytes.  Global transcriptional profiling using cDNA microarrays revealed a significant number of pro-inflammatory genes were upregulated within 4 hours post infection.
Keywords: Disease State

overall_design: To begin to globally define the HCMV-induced changes in monocyte function, we performed a transcriptome analysis.  Specifically, a cDNA microarray containing 12,626 unique probe sets was utilized to assess the modulation of the monocyte transcriptome at 4 hours post infection.  A total of 6 replicates from mock-infected and 6 replicates from HCMV-infected monocytes were analyzed in this study.

last: Chan

first: Elizabeth

last: Bivins-Smith

first: M

last: Smith


title: Gene expression profiling of human decidual macrophages

status: Public on May 12 2008

city: Braunschweig

first: Robert

last: Geffers

address: Inhoffenstr. 7

department: Dep. Molecular Bacteriology

institute: HCI - Helmholtz Centre for Infection Research

summary:
Uterine macrophages are thought to play an important regulatory role at the maternal-fetal interface. We report here a unique gene expression pattern intrinsic of first trimester decidual monocytes/macrophages, but not of their blood counterparts. The micro-array data comprises approximately 14,000 genes. Some of the key findings were confirmed by real time PCR or secreted protein measurements. A large number of regulated genes were found to be functionally related to immunomodulation and tissue remodelling, corroborating polarization patterns of differentiated macrophages of M2 phenotype. These include M2 markers such as CCL-18, CD209, insulin-like growth factor (IGF)-1, mannose receptor c type (MRC)-1 and fibronectin-1. Further, the selective up-regulation of triggering receptor expressed on myeloid cells (TREM)-2, alpha-2-macroglobulin (A2M) and prostaglandin D2 synthase (PGDS) provides new insights into the regulatory function of decidual macrophages in pregnancy. In addition, a large number of regulated genes in the micro-array analysis were related to cell cycle regulation. Taken together, molecular characterization of decidual macrophages presents a unique transcriptional profile replete with important components for fetal immunoprotection.
Keywords: disease state analysis, comparative gene expression

overall_design: Comparative expression analyis of CD14+ cells isolated either from blood or decidua. Decidual tissue and blood was obtained from eleven women between 18 and 41 years of age

first: R

first: C

last: Gustafsson

first: J

middle: H

last: Ernerudh


title: SCLC cell line profiling on HG-U133A arrays set 2

status: Public on May 01 2008

city: Abbott Park

first: Mark

last: Anderson

address: 100 Abbott Park Road

institute: Abbott Laboratories

summary:
RNA expression analysis was performed to compare patterns to sensitivity to BCL2 inhibitors (ABT-263).
Overexpression of the prosurvival Bcl-2 family members (Bcl-2, Bcl-xL and Mcl-1) is commonly associated with tumor maintenance, progression and chemoresistance.  We previously reported the discovery of ABT-737, a potent, small molecule Bcl-2 family protein inhibitor.  A major limitation of ABT-737 is that it is not orally bioavailable.  This may limit its use for chronic single agent treatment and the flexibility to dose in combination with parenteral chemotherapy.  Here we report the discovery and biological properties of ABT-263, a potent, orally bioavailable Bad-like BH3 mimetic (Kiâ??s of < 1 nM for Bcl-2, Bcl-xL and Bcl-w).  The oral bioavailability of ABT-263 in preclinical animal models is 20% - 50%, depending on formulation.  ABT-263 disrupts Bcl-2/Bcl-xL interactions with pro-death proteins (e.g., Bim) in cells leading to the initiation of apoptosis within 2 hr post-treatment.  In human tumor cells, ABT-263 rapidly induces Bax translocation, cytochrome c release and subsequent programmed cell death.  Oral administration of ABT-263 alone induces complete tumor regressions in xenograft models of small cell lung cancer and acute lymphoblastic leukemia.  In xenograft models of aggressive B-cell lymphoma and multiple myeloma where ABT-263 exhibits modest or no single agent activity, it significantly enhances the efficacy of clinically relevant therapeutic regimens. These data provide the rationale for clinical trials evaluating ABT-263 in SCLC and B-cell malignancies. The oral efficacy of ABT-263 should provide dosing flexibility to maximize clinical utility as both a single agent and in combination with standard chemotherapeutic regimens.
Keywords: cell line comparison

overall_design: Naive cell lines were isolated in duplicate or triplicate (only a single for H69AR) to determine RNA expression pattern.

first: Stephen

last: Tahir


title: Non-invasive electric magnetic fields: Effects on keratinocyte migration and proliferation

status: Public on Apr 22 2008

city: Miami

first: Jie

last: Li

state: FL

address: 1600 NW 10th Avenue, RMSB2049A

department: Department of Dermatology and Cutaneous Surgery

institute: University of Miami Miller School of Medicine

summary:
Although evidence has shown that very small electric currents produce a beneficial therapeutic result for wounds, non-invasive EMF therapy has consisted mostly of anecdotal clinical reports with very few well controlled laboratory mechanistic studies. In this study, we evaluated the effects and potential mechanisms of a non-invasive EMF device on skin wound repair. In vitro analyses with human skin keratinocyte cultures demonstrated that the non-invasive EMF has a very strong effect on accelerating keratinocyte migration and a relatively weaker effect on promoting keratinocyte proliferation. The positive effects of the non-invasive EMF on cell migration and proliferation seem keratinocyte specific without such effects seen on dermal fibroblasts. cDNA microarray and RT-PCR performed revealed increased expression of CRK7 and HOXC8 genes in treated keratinocytes. This study suggests that a non-invasive electric magnetic field accelerates wound reepithelialization through a mechanism of promoting keratinocyte migration and proliferation, possibly due to upregulation of CRK7 and HOXC8 genes.
Keywords: Comparative Genomic Hybridization

overall_design:
Non-invasive EMF:
In this study, we used the Field Therapy Accelerator (FTA; Advatech, Miami, Florida) device to produce a magnetic field which in turn induces a non-invasive electric current in the target’s surroundings. All human and animal studies have been approved by the authors' Institutional Review Board. The FTA device generates a continuous series of direct current (DC)-like pulses of voltage followed for a very short time interval by a negative voltage spike. The induced EMF comprises of a series of concentric circles centered on the axis of the coil. The EMF vectors are at each point perpendicular to the surface of the circle and in the plane of that circle, that plane being parallel to the face of the coil.

In vitro Studies with Cell Cultures:
Cells and Cell Cultures: Normal human keratinocytes were maintained in growth medium of EpiLife (Cascade Biologics, Portland, Oregon) with human keratinocyte growth supplement at concentration of 0.2% v/v of bovine pituitary extract, 5 ug/ml bovine insulin, 0.18 ug/ml hydrocortisone, 5 ug/ml bovine transferrin, 0.2 ng/ml human epidermal growth factor (Cascade Biologics, Portland, Oregon), plus antibiotics of 100 U/ml penicillin G and 100 ug/ml streptomycin at 37ºC and 5% CO2. Media were changed every 24 hours.

cDNA Microarray and RT-PCR Analysis:
Cell cultures and migration assay: Normal human epidermal keratinocytes were maintained in 35-mm cell culture dishes and in EpiLife at 37ºC and 5% CO2. Keratinocytes were maintained in growth media and grown to confluency. At time 0, a cross-shaped wound gap or cell-free zone was made among confluent monolayer cells in the center of the culture dish, and detached cells were washed off with PBS and then replaced with growth medium. Non-invasive EMF treatment: Group 1 was treated for 1 hour immediately after wounding, at a frequency of 2080 cycles/second, electric field strength of 20mV/cm, and duty cycle of 90%. Group 2 was the control group, and received no treatment but was placed in the same hood at temperatures of 31±2ºC for the same period of time as their treatment counterparts. Each group was performed in triplicates.

cDNA Microarray: RNA was isolated from cells using an RNeasy Mini RNA Isolation Kit (Qiagen Sciences, Germantown, Maryland), and converted to double stranded cDNA using a cDNA RT Kit (Applied Biosystems, Foster City, California). An in vitro transcription reaction was subsequently performed to produce biotin-labeled complementary RNA (cRNA) from the cDNA. Gene expression profiles were assessed using the Affymetrix Human Genome HU133A 2.0 GeneChip array, containing 22,277 sequenced human genes. GeneChip arrays were scanned using a GeneArray Scanner (Hewlett-Packard, Santa Clara, Calif). Hybridization data were analyzed using MAS 5.

first: Ran

last: Huo


title: Transcriptomes of breast epithelium and stroma in normal reduction mammoplasty and invasive breast cancer patients.

status: Public on Apr 03 2008

city: Burlington

first: Jeffrey

middle: P

last: Bond

state: VT

address: 95 Carrigan Dri e

department: Microbiology and Molecular Genetics

institute: University of Vermont

summary:
The molecular basis of breast cancer invasion and metastasis is not well understood.  Our objective was to analyze transcriptome differences between stromal and epithelial cells in normal breast tissue and invasive breast cancer to define the role stroma plays in invasion.  Total RNA was isolated from epithelial and stromal cells that were laser captured from normal breast tissue (n=5) and invasive breast cancer (n=28).  Gene expression was measured using Affymetrix U133A 2.0 GeneChips.  Differential gene expression was evaluated and compared within a model that accounted for cell type (epithelial [E] versus stromal [S]), diagnosis (cancer [C] versus normal [N]) as well as cell type-diagnosis interactions. Compared to NE, the CE transcriptome was highly enriched with genes in proliferative, motility and ECM ontologies.  Differences in CS and NS transcriptomes suggested that the ECM was being remodeled in invasive breast cancer, as genes were over-represented in ECM and proteolysis ontologies.   Genes more highly expressed in CS compared to CE were primarily ECM components or were involved in the remodeling of ECM, suggesting that ECM biosynthesis and remodeling were initiated in the tumor stromal compartment.
Keywords: cell type comparison, disease state analysis

overall_design: Breast tissue was collected at surgery from patients undergoing surgical resection for  invasive breast cancer (n=28) and reduction mammoplasty (n=5).  Tissue was cryopreserved in OCT and serial sections were cut using a cryostat.  Sections were stained and epithelial and stromal cells were isolated by laser capture microdissection.  Total RNA was isolated and target was prepared using NuGen Ribo-SPIA Ovation Technology.  Gene expression was measured using Affymetrix U133A 2.0 GeneChips. Gene expression differences were evaluated using a linear model of the Robust Multichip Average gene expression statistic, a model that accounted for cell type (E and S), patient diagnosis (C and N), as well as cell type-diagnosis interactions. Data were examined to determine false discovery rate and were filtered for fold changes in gene expression and p-value.

first: Theresa

last: Casey

first: Scott

last: Tighe

first: Timothy

last: Hunter

first: Laura

last: Lintault

first: Osman

last: Patel

first: Jonathan

last: Eneman

first: Abigail

last: Crocker

last: White

first: Joseph

last: Tessitore

first: Mary

last: Stanley

first: Seth

last: Harlow

first: Donald

last: Weaver

first: Hyman

last: Muss

first: Karen

last: Plaut


title: Gene Expression in Acute Appendicitis

city: Boston

first: Bruce

last: Horwitz

state: MA

address: 77 Avenue Louis Pasteur

institute: Brigham and Women's Hospital

summary:
Gene expression was evaluated in 9 appendix samples removed from patients who went to the operating room with the diagnosis of acute appendicitis and 4 samples removed for non-inflammatory reasons.
A circumferential piece of tissue was obtained at the distal aspect of each specimen.  The tissue was flash frozen at -80 degrees for later processing.  Frozen specimens were homogenized into TriReagent  and RNA was isolated according to the manufacturer's instruction.  RNA was processed and hybridized to Affymetrix microarray.
Keywords: Disease state analysis

overall_design: 9 patients and 4 controls


title: p73 inhibits malignant transformation

status: Public on Apr 01 2008

city: Wuerzburg

first: Christof

last: Burek

address: Josef-schneider-Str. 2

department: Pathologie

institute: Universitaet Wuerzburg

summary:
sh RNA of p73 in Fibroblasts compared to non-silencing control
Keywords: cell growth, shRNA, p73

overall_design: 2 different confluent stages of the BJ-TE cells were analyzed

first: Thorsten

last: Stiewe

middle: J


title: NatB N-terminal acetyltransferase (hNAT5) inhibition

status: Public on Mar 12 2008

city: Pamplona

first: Rafael

last: Aldabe

state: Navarra

address: Av Pio XII 55

department: Hepatology and Gene Therapy

institute: FIMA

summary:
Search for genes differently expressed when we inhibit NatB N-terminal acetyltransferase.
We compare gene expression after inhibiting hNAT5 expression in Hela cells with specific siRNAs expressed with adenoviruses.
Keywords: gene expression comparison

overall_design:
We analyzed duplicate samples and we used as controls Hela cells and Hela cells that express a siRNA that doesn't inhibit any gene expression.
The N-terminal acetyltransferase NatB, composed in Saccharomyces cerevisiae by the Nat3p and Mdm20p subunits, is an important factor for yeast growth and resistance to several stress agents. However, the expression and functional role of the mammalian counterpart has not yet been analysed. Here, we report the identification of Nat3p human homologue (hNAT5/hNAT3) and the characterization of its biological function. We found that hNAT5/hNAT3 silencing in HeLa cells results in inhibition of cell proliferation and increased sensitivity to the proapoptotic agent MG132. Moreover, inhibition of hNAT5/hNAT3 expression induces p53 activation and upregulation of the antiproliferative protein p21(WAF1/CIP1). The changes of the cellular transcriptome after hNAT5/hNAT3 knockdown confirmed the involvement of this protein in cell growth and survival processes. Among the genes differentially expressed we observed upregulation of several p53-dependent antiproliferative and proapoptotic genes. In the c-myc transgenic mice which is a model of inducible hepatocarcinoma we found that hNAT5/hNAT3 was upregulated when the tumor was induced. In accordance with this observation we noticed increased hNAT5/hNAT3 protein level in neoplastic versus non-neoplastic tissue in a high proportion of patients with hepatocellular carcinoma. Consequently, our results suggest that the expression of the protein hNAT5/hNAT3 is required for cellular proliferation and tumor growth.

first: Amagoia

last: Ametzazurra


title: eIF4GI Links Nutrient Sensing by mTOR to Cell Proliferation and  Inhibition of Autophagy

city: New York

first: Robert

last: Schneider

address: 550 First Ave, MSB 238

department: Microbiology

institute: NYU School of Medicine

summary:
Translation initiation factors have complex functions in cells which are not yet understood. We show that depletion of initiation factor eIF4GI only modestly reduces overall protein synthesis in cells, but phenocopies nutrient-starvation or inhibition of protein kinase mTOR, a key nutrient sensor. eIF4GI depletion impairs cell proliferation, bioenergetics and mitochondrial activity, thereby promoting autophagy. Translation of mRNAs involved in cell growth, proliferation and bioenergetics were selectively inhibited by reduction of eIF4GI, whereas mRNAs encoding proliferation inhibitors and catabolic pathway factors were increased. Depletion or over-expression of other eIF4G family members did not recapitulate these results. The majority of mRNAs that were translationally impaired with eIF4GI depletion were excluded from polyribosomes due to  the presence of multiple upstream open reading frames and low mRNA abundance. These results suggest that the high levels of eIF4GI observed in many breast cancers might act to specifically increase proliferation, prevent autophagy and release tumor cells from control by nutrient sensing.
Global regulation of transcription and polysomal association in eIF4GI-silenced cells.
Keywords: Gene Silencing

overall_design: Two sets of experiments are presented. First, overall transcriptome changes were determined for control or eIF4GI silenced cells.  Next, mRNAs associated with polysomes were compared between control and eIF4GI silenced cells.

first: Francisco

last: Ramirez-Valle

first: Steve

last: Braunstein

first: Jiri

last: Zavadil

first: Silvia

last: Fermenti


title: Retinoic acid effect on sebocytes and the skin

status: Public on Mar 04 2008

city: Hershey

first: Diane

last: Thiboutot

address: 500 University Drive

department: Department of Dermatology; Jake Gittlen Res. Fnd.

institute: The Pennsylvannia State University College of Medicine

summary:
The pathogenesis of acne has been linked to multiple factors such as increased sebum production, inflammation, follicular hyperkeratinization, and the action of Propionibacterium acnes within the follicle. 13-cis Retinoic Acid (13-cis RA, isotretinoin) is the most potent agent in acne treatment.  Surprisingly, its mechanism of action in acne is still unknown.  Gene expression profiling of cultured human immortalized sebocytes (SEB-1)  treated with 13-cis RA  was performed to gain insights into its sebocyte-specific mechanism of action. SEB-1 sebocytes were cultured with 0.1 uM 13-cis RA for 72 hours or vehicle control. Gene array expression profiling was conducted using Affymetrix HG-U95Av2 arrays in order to examine changes in gene expression as a result of treatment. A total of 85 genes (78 different genes) were significantly influenced by 13-cis RA:  58 were upregulated and 27 were down-regulated.  There were changes in several genes involved in apoptosis and innate immunity.  These studies are the first describing the sebocyte- specific response in gene expression associated with isotretinoin therapy and are valuable in identifying potential therapeutic targets in acne.

The pathogenesis of acne has been linked to multiple factors such as increased sebum production, inflammation, follicular hyperkeratinization, and the action of Propionibacterium acnes within the follicle. 13-cis Retinoic Acid (13-cis RA, isotretinoin) is the most potent agent in acne treatment.  Surprisingly, its mechanism of action in acne is still unknown.  Gene expression profiling of skin from 6 patients treated with isotretinoin was performed to gain insights into its mechanism of action. Skin biopsies were obtained from the patients at baseline and at one-week isotretinoin treatment. Gene array expression profiling was conducted using Affymetrix HG-U133A 2.0 arrays in order to examine changes in gene expression as a result of treatment. After treatment, 43 genes were significantly changed: 38 up-regulated and 5 down-regulated. A significant proportion of these genes are involved in pathways that regulate differentiation, tumor suppression, serine proteases, serine protease inhibitors and solute transfer. These studies are the first describing the initial changes in gene expression associated with isotretinoin therapy and are valuable in identifying potential therapeutic targets in acne.

This SuperSeries is composed of the SubSeries listed below.

overall_design: Refer to individual Series


title: Human Skin: Before and 1 week after Isotretinoin Treatment

summary:
The pathogenesis of acne has been linked to multiple factors such as increased sebum production, inflammation, follicular hyperkeratinization, and the action of Propionibacterium acnes within the follicle. 13-cis Retinoic Acid (13-cis RA, isotretinoin) is the most potent agent in acne treatment.  Surprisingly, its mechanism of action in acne is still unknown.  Gene expression profiling of skin from 6 patients treated with isotretinoin was performed to gain insights into its mechanism of action. Skin biopsies were obtained from the patients at baseline and at one-week isotretinoin treatment. Gene array expression profiling was conducted using Affymetrix HG-U133A 2.0 arrays in order to examine changes in gene expression as a result of treatment. After treatment, 43 genes were significantly changed: 38 up-regulated and 5 down-regulated. A significant proportion of these genes are involved in pathways that regulate differentiation, tumor suppression, serine proteases, serine protease inhibitors and solute transfer. These studies are the first describing the initial changes in gene expression associated with isotretinoin therapy and are valuable in identifying potential therapeutic targets in acne.
Keywords: drug treatment effects

overall_design: Total 12 chips:  6 baseline/before isotretinoin and 6 after 1-week isotretinoin treatment.


title: Microarray Analysis of Acute Lung Injury

status: Public on Feb 15 2008

first: Judie

middle: Ann

last: Howrylak

address: 75 Francis Street

department: Pulmonary and Critical Care Medicine

summary:
The Acute Respiratory Distress Syndrome (ARDS)/Acute Lung Injury (ALI) was described 30 years ago, yet the interaction between specific sets of genes involved in this syndrome remains incompletely understood.
Keywords: disease state analysis

overall_design: 13 patients with ALI + sepsis and 21 patients with sepsis alone were recruited from the Medical Intensive Care Unit of the University of Pittsburgh Medical Center between February 2005 and June 2007.  Whole blood was obtained from each patient within 48 hours of admission, and RNA was extracted for gene expression profiling, and comparison analysis.


title: siRNA-mediated knockdown of Sp3 induces a pro-inflammatory pattern of cytokine production: relevance to MS

status: Public on Feb 21 2008

city: Bethesda

first: Azik

last: Schwechter

state: MD

address: NIH/NIMH 10 Center Drive Room 4D/14

department: NIMH

institute: NIH

summary:
Multiple sclerosis (MS) is an inflammatory disease of the central nervous system and is generally considered to be autoimmune in nature. We previously demonstrated that the transcription factor Sp3 is significantly down-regulated in immune cells from MS patients. The potential role of Sp3 down-regulation in MS pathogenesis is not well understood. The function of endogenous Sp3 was assessed in vitro after siRNA-mediated knockdown of its transcript in Jurkat cells. Sp3 protein levels were reduced an average of 70%. ELISA studies demonstrated decreased endogenous production of IL-10 and TGFβ1 and increased endogenous production of TNFα (p<0.05 in all assays).  Subsequent microarray analysis demonstrated significantly altered expression of 36 genes (p<0.001 for each gene) compared with control samples. Analysis showed differential expression (p<0.005) of 8 gene pathways.  Many of the genes and pathways that were regulated by Sp3 are involved in immune function, specifically with regard to apoptosis, cell-to-cell adhesion, integrin signaling, T-cell differentiation, and cytokine production. This study identifies mechanisms by which Sp3 may regulate immune function and suggests a basis for its potential contribution to MS disease pathogenesis.
Keywords: siRNA knockdown; Jurkat T-cells; Multiple Sclerosis

overall_design: Two Sp3 siRNA knockdown groups (siRNA Sp3 #2: n=3, and #6: n=3) were clustered together into the Treated condition, and the two control groups (siRNA for GAPDH: n=3, and Non-transfected cells: n=3)were assembled to constitute the Control condition.  Thus a total of 12 arrays (6 Controls and 6 treated) were used in this experiment.

first: Maria

last: Grekova

first: Habtom

middle: W

last: Ressom

first: Vicente

last: Notario

first: John

last: Richert


title: Myeloid differentiated cells vs hemopoietic progenitors

status: Public on Feb 05 2008

city: Modena

first: Rossella

last: Manfredini

address: Via Gottardi 100

department: Life Sciences

country: Italy

institute: Centre for Regenerative Medicine

summary:
Differential gene expression profiling of human hemopoietic progenitors and myeloid differentiated cells
Keywords: parallel sample

overall_design: We assessed the gene expression in Lin+CD34+, CD14+, CD16+ and CD16- cells.


title: Bcl2-induced vascular maturation

status: Public on Mar 05 2008

city: Auckland

first: Cris

last: Print

address: Grafton Campus, Park Rd

country: New Zealand

institute: Auckland University

summary:
Overexpression of a caspase-resistant form of Bcl-2 (D34A) in human umbilical vein endothelial cells (EC) implanted into immunodeficient mice promotes the maturation of human EC-lined microvessels invested by vascular smooth muscle cells (VSMC) of mouse origin. In contrast, EC implants  not overexpressing Bcl-2 form only simple, uncoated EC tubes. Here we compare the phenotypes of vessels formed in vivo and the transcriptomes in vitro of EC expressing different forms of Bcl-2. Wild type Bcl-2, like the caspase resistant D34A Bcl-2 mutant, is anti-apoptotic in vitro and promotes VSMC recruitment in vivo, whereas a G145E mutant that has diminished anti-apoptotic activity in vitro does not promote vessel maturation in vivo. The D34A and wild type forms of Bcl-2, but not the G145E mutant form of Bcl-2 significantly regulate RNA transcripts previously associated with EC-VSMC interactions and VSMC biology, including matrix Gla protein, insulin like growth factor binding protein (IGFBP)-2, matrix metaloproteinase-14 (MMP14), ADAM17 and Stanniocalcin-1. These effects of Bcl-2 on the transcriptome are detected in EC cultured as angiogenic 3-D tubes but are attenuated in EC cultured as 2-D monolayers. Bcl-2-regulated transcription in EC may contribute to vascular maturation, and support design of tissue engineering strategies using EC.
Keywords: genetic modification, growth condition modification.

overall_design: This study consists of the analysis of human umbilical vein endothelial cells (HUVEC) cultured under several conditions, including retroviral transduction, as well as on different culture substrates and in different geometries. For a full description please see our paper in the journal Endothelium, 2008. For

middle: G


title: 13-cis retinoic acid treatment of human sebocytes (SEB-1)

middle: M

state: PA

summary:
The pathogenesis of acne has been linked to multiple factors such as increased sebum production, inflammation, follicular hyperkeratinization, and the action of Propionibacterium acnes within the follicle. 13-cis Retinoic Acid (13-cis RA, isotretinoin) is the most potent agent in acne treatment.  Surprisingly, its mechanism of action in acne is still unknown.  Gene expression profiling of cultured human immortalized sebocytes (SEB-1)  treated with 13-cis RA  was performed to gain insights into its sebocyte-specific mechanism of action. SEB-1 sebocytes were cultured with 0.1 uM 13-cis RA for 72 hours or vehicle control. Gene array expression profiling was conducted using Affymetrix HG-U95Av2 arrays in order to examine changes in gene expression as a result of treatment. A total of 85 genes (78 different genes) were significantly influenced by 13-cis RA:  58 were upregulated and 27 were down-regulated.  There were changes in several genes involved in apoptosis and innate immunity.  These studies are the first describing the sebocyte- specific response in gene expression associated with isotretinoin therapy and are valuable in identifying potential therapeutic targets in acne.
Keywords: effects of 72 hour 13-cis RA treatment on cultured human sebocyte cells (SEB-1)

overall_design: Total of 6 chips: 3 vehicle (DMSO) control and 3 13-cis RA (0.1 uM) treatment.


title: A novel lung cancer gene signature mediates metastatic bone colonization by a dual mechanism

city: Salamanca

first: Javier

last: De Las Rivas

address: Campus Miguel de Unamuno

department: CSIC and University of Salamanca

institute: Cancer Research Center (CiC-IBMCC)

summary:
Bone is a frequent target of lung cancer metastasis, which is associated with significant morbidity and a dismal prognosis. To identify and functionally characterize genes involved in the mechanisms of osseous metastasis we developed a murine lung cancer model. Comparative transcriptomic analysis identified genes encoding signaling molecules (such as TCF4 and PRKD3), and cell anchorage related proteins (MCAM, and SUSD5), some of which were basally modulated by TGFbeta in tumor cells and in conditions mimicking tumor-stroma interactions. Triple gene combinations induced not only high osteoclastogenic activity but also a marked enhancement of global metalloproteolytic activities in vitro. These effects were strongly associated with robust bone colonization in vivo, whereas this gene subset was ineffective in promoting local tumor growth and cell homing activity to bone. Interestingly, global inhibition of metalloproteolytic activities and simultaneous TGFbeta blockade in vivo led to increased survival and a remarkable attenuation of bone tumor burden and osteolytic metastasis. Thus, this metastatic gene signature mediates bone-matrix degradation by a dual mechanism of induction of TGFbeta-dependent osteoclastogenic bone resorption and enhancement of stroma-dependent metalloproteolytic activities. Our findings suggest the cooperative contribution of host-derived and cell-autonomous effects directed by a small subset of genes in mediating aggressive osseous colonization.
Keywords: disease state analysis of human metastatic cell lines

overall_design:
Human highly metastatic cell lines derived from Non-Small Cell Lung Carcinoma (NSCLC) with specific bone tropism. Cell lines were selected by induction of prominent bone metastases lesions. The metastatic lines were systematically and accurately discriminate using 3 complementary parameters: survival curves of newly injected mice; computerized image analysis of bone metastatic areas; conspicuous SCCs derived from each animal (10 mice/group).
Genome-wide expression analysis was done using 13 microarrays, corresponding to 4 samples of control non-metastatic cell lines and 9 samples of 3 different highly metastatic cell lines (M1, M4, M5) each with 3 biological replicates. Moreover, in each microarray pools of 3 groups of the corresponding cells were used.

first: Fernando

last: Lecanda

last: Dotor

last: Borras-Cuesta

first: Ignacio

last: Garcia-Tuñon

first: Iker

last: Anton

first: Diego

last: Luis-Ravelo

first: Silvestre

last: Vicent


title: Gene expression data on human optic nerve head astrocytes in normal Caucasian and African americans

status: Public on Jan 31 2008

city: Chicago

first: Pan

last: Du

address: 676 N ST Clair St, 1200#

institute: Northwestern University

summary:
To determine whether optic nerve head astrocytes, a key cellular component of glaucomatous neuropathy, exhibit differential gene expression in primary culture of astrocytes from normal African American donors, compared to astrocytes from normal Caucasian American donors. All donors have no histories of eye disease, diabetes, or chronic CNS disease.
Keywords: Gene expression profile

overall_design: We divided samples into two groups: normal Caucasian American and normal African American. We analyzed data from Affymetrix Human Genome Human Genome U133A and U133A 2.0 chips.

first: M

last: Hernandez

first: Haixi

last: Miao


title: Phase II exploratory pharmacogenomics study of cetuximab monotherapy in patients with advanced metastatic CRC

city: Pennington

first: Shirin

middle: Khambata

last: Ford

state: NJ

address: 311 Pennington-Rocky Hill Road, 3B-2.06

institute: Bristol-Myers Squibb Pharmaceutical Research Institute

summary:
Patients with metastatic colorectal cancer were enrolled for treatment with cetuximab monotherapy.  Transcriptional profiling was conducted on RNA from pre-treatment metastatic site biopsies to identify genes whose expression correlates with best clinical responses.
Keywords: comparison of disease control group versus non-responder group of patients

overall_design: single pre-treatment metastatic biopsy from each patient analyzed

first: S

last: Khambata-Ford

first: C

last: Garrett

first: X

last: Huang

first: D

last: Mauro


title: Gene expression data on human optic nerve head astrocytes

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


title: Tumor Immunobiological Differences in Prostate Cancer between African-American and European-American Men

status: Public on Jan 01 2008

first: Robert

middle: Scott

last: Hudson

address: National Cancer Institute Room Blgd.37/3044

department: NCI

summary:
The incidence and mortality rates of prostate cancer are significantly higher in African-American men when compared to European-American men. We tested the hypothesis that differences in tumor biology contribute to this survival health disparity. Using microarray technology, we obtained gene expression profiles of primary prostate tumors resected from 33 African-American and 36 European-American patients. These tumors were matched on clinical parameters. We also evaluated 18 non-tumor prostate tissues from 7 African-American and 11 European-American patients. The resulting datasets were analyzed for expression differences on the gene and pathway level comparing African-American with European-American patients. Our analysis revealed a significant number of genes, e.g., 162 transcripts at a false-discovery rate less than 5%, to be differently expressed between African-American and European-American patients. Using a disease association analysis, we identified a common relationship of these transcripts with autoimmunity and inflammation. These findings were corroborated on the pathway level with numerous differently expressed genes clustering in immune response, stress response, cytokine signaling, and chemotaxis pathways. Furthermore, a two-gene tumor signature was identified that accurately differentiated between African-American and European-American patients. This finding was confirmed in a blinded analysis of a second sample set. In conclusion, the gene expression profiles of prostate tumors indicate prominent differences in tumor immunobiology between African-American and European-American men. The profiles portray the existence of a distinct tumor microenvironment in these two patient groups.
Keywords: Microdissected tissue analysis

overall_design: A total of 69 fresh-frozen prostate tumors were obtained from the NCI Cooperative Prostate Cancer Tissue Resource (CPCTR) and the Department of Pathology at the University of Maryland (UMD). All tumors were resected adenocarcinomas that had not received any therapy prior to prostatectomy. The macro-dissected CPCTR tumor specimens (n = 59) were reviewed by a CPCTR-associated pathologist, who confirmed the presence of tumor in the specimens. These tissues were collected between 2002 and 2004 at four different sites, with each site providing tissues from both African-American and European-American patients. Information on race/ethnicity (33 African-Americans and 36 European-Americans) was either extracted from medical records (CPCTR) or obtained through an epidemiological questionnaire in which race/ethnicity was self-reported (UMD). Only one patient, a European-American, was also Hispanic.  Surrounding non-tumor prostate tissue was collected from 18 of the recruited patients in this study. Of those, 7 were African-American men and 11 were European-American men. We also isolated total RNA from 10 needle biopsy specimens collected from patients at the National Naval Medical Center (one African-American and 9 European-Americans) that did not have prostate cancer. From those, we prepared two RNA pools, each representing 5 patients.  Clinicopathological characteristics of the patients, including age at prostatectomy, histology, Gleason score, pathological stage, PSA at diagnosis, tumor size, extraprostatic extension, margin involvement, and seminal vesicle invasion were obtained from CPCTR.  For UMD cases, this information was extracted from the medical and pathology records, if available. Written informed consent was obtained from all donors. Tissue collection and study design were approved by the institutional review boards of the participating institutions.

first: Stefan

last: Ambs

first: Ming

last: Yi


title: Gene expression data on human optic nerve head astrocytes in Caucasian and African americans with or without glaucoma

summary:
To determine whether optic nerve head astrocytes, a key cellular component of glaucomatous neuropathy, exhibit differential gene expression in primary culture of astrocytes from African American donors with or without glaucoma, compared to astrocytes from Caucasian American donors with or without glaucoma.
Keywords: Gene expression profile

overall_design: We divided samples into four group: Caucasian American normal, Caucasian American with glaucoma, African American normal and African American with glaucoma. We analyzed data from Affymetrix Human Genome U133A 2.0 and U95 chips.


title: gene expression in monkey aorta with aging and gender

status: Public on Dec 27 2007

city: newark

first: hongyu

last: qiu

address: 185 south orange ave

department: Cell biology and molecular medicine

institute: UMDNJ

summary:
Although increased vascular stiffness is more prominent in aging males than females, and males are more prone to vascular disease with aging, no study has investigated the genes potentially responsible for gender differences in vascular aging.  We tested the hypothesis that the transcriptional adaptation to aging differs in males and females using a monkey model, which is not only physiologically and phylogenetically closer to humans than the more commonly studied rodent models, but also is not afflicted with the most common forms of vascular disease that accompany the aging process in humans, e.g., atherosclerosis, hypertension, and diabetes. Gene expressions of monkey aorta from four groups (YF, OF, YM, OM) were detected to find out the molecular mechanism of aorta stiffness.
Keywords: aging and genders

overall_design: Four groups were used in this experiment. 6 samples per group.The transcriptional profile of the aorta was compared by high-density microarrays between young and old males or females.  About 600 genes were expressed differentially when comparing old versus young animals. Analysis of the different groups was further performed by gene ontology.We also analyzed  whether the transcriptional regulation described above might correspond to specific transcription factors

first: Hongyu

last: Qiu

first: Ijen

last: Ye

first: Bin

last: Tian

first: Christophe

last: Depre

first: Dorothy

last: Vatner

first: Stephen


title: Age-Specific Differences of Oncogenic Pathway Deregulation Seen in Human Breast Tumors

status: Public on Jan 16 2008

city: Durham

first: Carey

middle: K.

last: Anders

address: 101 Science Drive

department: Institute for Genome Sciences and Policy

institute: Duke University

summary:
Breast cancer arising in young women has a poorer prognosis, is less likely to be hormone sensitive, and represents a particularly challenging clinical entity.  The biology driving the aggressive nature of breast cancer arising in young women has yet to be defined.
Among 784 patients with early stage breast cancer, using prospectively-defined, age-specific cohorts (young <= 45 years; older >= 65 years), 411 eligible patients (n = 200 < 45 years; n = 211 >= 65 years) with clinically-annotated Affymetrix microarray data were identified. Gene set enrichment analyses, signatures of oncogenic pathway deregulation and predictors of chemotherapy sensitivity were evaluated within the two age-defined cohorts.
In comparing deregulation of oncogenic pathways between age groups, a statistically higher probability of PI3K (p = 0.006) and Myc (p = 0.03) pathway deregulation was observed in the tumors of younger women.  When evaluating unique patterns of pathway deregulation, a low probability of Src and E2F deregulation in tumors of younger women, concurrent with activation of PI3K, Myc, and beta-catenin, conferred a worse prognosis (HR = 4.15; p = 0.008).  In contrast, a higher probability of Src and E2F pathway activation in tumors of older women, concurrent low probability of PI3K, Myc and beta-catenin deregulation, was associated with a poorer outcome (HR = 2.7; p = 0.006). Similar pathway differences were identified using gene set enrichment analysis. Importantly, in multivariate analyses including clinico-pathologic variables, genomic clusters of pathway deregulation were identified to be independent predictors of disease-free survival.  Finally, a significant relationship (p = 0.02) between anthracycline sensitivity and genomic clusters was observed among women aged >= 65 years.

Submitters do not have approval to publish the .CEL files
Keywords: Retrospective analyses

middle: K

first: Chaitanya

last: Acharya

first: David

middle: S

last: Hsu

first: Gloria

last: Broadwater

first: Katherine

last: Garman

first: John

last: Foekens

first: Yi

last: Zhang

first: Yixin

last: Wang

first: P

last: Marcom

first: Jeffrey

last: Marks

first: Sayan

last: Mukherjee

first: Joseph

last: Nevins

first: Kimberly

middle: L

last: Blackwell

first: Anil

last: Potti


title: Collagen 1 Hydrogel Dynamic Loading Tests

status: Public on Jan 11 2008

city: Berkeley

first: Justyn

middle: Wayne

last: Jaworski

address: 1 Cyclotron Rd

department: Bioengineering

institute: UC Berkeley/ LBNL

summary:
Cell viability and global gene expression was anayzed from collagen 1 hydrogel scaffolds following 3 hours of cyclic mechanical loading and compared with non-loaded scaffolds.
Keywords: human dermal fibroblasts; dynamic cell culture; mechanical stress

overall_design: 6 samples are analyzed (2 sets in triplicate).  The first set is the Loaded condition in which Collagen 1 hydrogels seeded with Human dermal fibroblasts underwent cyclic loading of 0.1Hz for 180 minutes at 37 degrees Celsius.  The second set is the control Unloaded condition in which the Collagen 1 hydrogels seeded with Human dermal fibroblasts are incubated at 37 degrees Celsius with no loading.

first: Catherine

last: Klapperich

first: Cassandra

last: Noack


title: Transcriptional regulation of aldo-keto reductase 1C1 in human colon cancer cells resistant to methotrexate

status: Public on Dec 30 2007

city: Barcelona

first: Carlos

last: Ciudad

state: Barcelona

address: Av. Juan XXIII-27

department: Biochemistry and Molecular Biology

institute: University of Barcelona

summary:
The abstract of the associated publication (Selga E, Noé V, Ciudad CJ. Biochemical Pharmacology, 2008) is the following:

While studying differentially expressed genes between sensitive and 10-5 M Methotrexate (MTX) resistant HT29 human colon cancer cells, we identified some members of the aldo-keto reductase (AKR) superfamily. The study was followed with the member AKR1C1 (EC 1.1.1.213), validating its increase in mRNA and protein levels in MTX resistant cells. The genomic content for AKR1C1 remained unchanged between sensitive and resistant cells, thereby excluding a mechanism of AKR1C1 gene amplification. Thus, we cloned the AKR1C1 human promoter and performed luciferase experiments that revealed a transcriptional regulation of the gene in the resistant cells. Computational studies showed a putative binding site for the transcription factor Sp1. The co-transfection of Sp1 or Sp3 with different constructs of AKR1C1 promoter deletions, including and excluding the proximal GC-box, demonstrated a key role for these factors in regulating AKR1C1 transcriptional activity. Gel-shift assays revealed an increase in Sp1 and Sp3 binding in resistant compared to sensitive cells, without differences in Sp1 protein levels. Dephosphorylation of the extracts coincided with a decrease in Sp1 binding, which is consistent with a process of regulation of Sp1 by phosphorylation. We also investigated the possible relationship between AKR1C1 expression and MTX action. Overexpression of AKR1C1 counteracted the S-phase accumulation of cells and apoptosis caused by MTX treatment. This suggests a role of AKR1C1 in cell proliferation. Finally, overexpression of AKR1C1 in MTX sensitive HT29 cells conferred resistance to the chemotherapeutic agent and silencing of AKR1C1 by means of iRNA technology sensitized the cells to MTX.
Keywords: DHFR, Methotrexate, drug-resistance

overall_design: Two cell lines are compared in the study, which are HT29 colon cancer cells sensitive to methotrexate and HT29 cells resistant to 10e-5M methotrexate. Six samples are provided, which correspond to triplicates of each cell line. The samples provided were subsequently normalyzed and analyzed using the specific software GeneSpring GX 7.3.1

first: Elisabet

last: Selga

first: Veronique

last: Noé


title: Gene expression profiling suggests PCNSL to be derived from a late germinal center B cell.

status: Public on Dec 16 2007

city: Cologne

first: Manuel

last: Montesinos-Rongen

address: Kerpenerstr. 62

department: Institute for Neuropathology

institute: University Hospital Cologne

summary:
To characterize the molecular origin of primary lymphomas of the central nervous system (PCNSL), 21 PCNSL of immunocompetent patients were investigated by microarray-based gene expression profiling. Comparison of the transcriptional profile of PCNSL with various normal and neoplastic B cell subsets demonstrated PCNSL (i) to display gene expression patterns most closely related to late germinal center B cells, (ii) to display a gene expression profile similar to systemic diffuse large B cell lymphomas (DLBCL), and (iii) to be in part assigned to the activated B cell-like (ABC) or the germinal center B cell-like (GCB) subtype of DLBCL.
Keywords: PCNSL – DLBCL – gene expression profiling

overall_design: Total RNA was extracted from tissue blocks containing > 80% tumor cells using the TRIzol reagent (Invitrogen, Carlsbad, CA) and purified using RNeasy Kit (Qiagen, Valencia, CA). Double-stranded cDNA (ds-cDNA) was generated from 5 μg of total RNA using the SuperScript Double Stranded cDNA Synthesis Kit (Invitrogen) and a poly-dT oligonucleotide that contains T7 RNA polymerase initiation site (Sigma-Proligo, St. Louis, MO). The ds-cDNA was used as template to generate biotinylated cRNA by in vitro transcription using MEGA-script T7 High Yield Transcription Kit (Ambion, Austin, TX), biotin-11-CTP, and biotin-11-UTP (Perkin Elmer, Altham, MA). The biotinylated cRNA was purified by RNAeasy Kit (Qiagen) and fragmented according to the Affymetrix protocol. 15 μg of fragmented cRNA was hybridized to HG-U95Av2 microarrays (Affymetrix, Santa Clara, CA). Gene expression values were determined by GCOS1.2 software (Affymetrix) using the global scaling option.

first: Anna

last: Brunn

first: Stefan

last: Bentink

first: Katia

last: Basso

first: Wei

last: Lim

first: Wolfram

last: Klapper

first: Carlo

last: Schaller

first: Guido

last: Reifenberger

first: James

last: Rubenstein

first: Otmar

last: Wiestler

first: Rainer

last: Spang

first: Riccardo

last: Dalla-Favera

first: Reiner

last: Siebert

first: Martina

last: Deckert


title: Expression Data From HCMV-Infected Human Monocytes

status: Public on Nov 15 2007

city: Shreveport

first: Andrew

last: Yurochko

address: 1501 Kings Highway

department: Microbiology & Immunology

institute: LSUHSC-S

summary:
Human cytomegalovirus induces a pro-inflammatory monocyte following infection and we have evidence that NF-κB and phosphatidylinositol 3-kinase [PI(3)K] are key mediators in this early activation.  To begin to address how these signalling pathways are responsible for the rapid activation of infected monocytes, we examined the role these pathways played in the transcriptome of infected monocytes.  Global transcriptional profiling using cDNA microarrays revealed a significant number of genes, including inflammatory genes, were regulated in a NF-κB- and/or PI(3)K-dependent manner, identifying these pathways as key cellular control points in the conversion of monocytes to an activated pro-inflammatory state following HCMV infection.
Keywords: disease state analysis

overall_design: To begin to globally define how NF-κB and PI(3)K are involved in the HCMV-induced changes in monocyte function, we performed a transcriptome analysis in the presence of inhibitors to NF-κB and PI(3)K signalling pathways.  Specifically, a cDNA microarray containing 12,626 unique probe sets was utilized to assess the modulation of the monocyte transcriptome at 4 hours post infection in the presence of the pharmalogical agents Bay11-7082 (Bay11; a NF-κB inhibitor) and LY294002 (LY; a PI(3)K inhibitor).  A total of 6 replicates from HCMV-infected monocytes, 3 replicates from Bay11-pretreated infected monocytes and 3 replicates from LY-pretreated infected monocytes were analyzed in this study.

first: Gary

last: Chan

first: Elizabeth

middle: R

last: Bivins-Smith

first: M

last: Smith