title: Profiling and Functional Analyses of MicroRNAs and Their Target Gene Products in Human Uterine Leiomyomas

status: Public on Jul 24 2010

city: LYON

first: Jiri

last: ZAVADIL

state: Other

address: 150 COURS ALBERT THOMAS

institute: IARC WHO

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

summary:
Human uterine leiomyomas (ULM) are characterized by dysregulation of a large number of genes and non-coding regulatory microRNAs. In order to identify microRNA::mRNA associations relevant to ULM pathogenesis, we examined global correlation patterns between the altered microRNA expression and the predicted target genes in leiomyomas and matched myometria.
We found that some but not all of the predicted and inversely correlated target genes in ULMs can be directly regulated by microRNAs in vitro. Our findings provide a broad overview of molecular events underlying the tumorigenesis of uterine leiomyoma and identify select genetic and regulatory events that alter microRNA expression and may play important roles in ULM pathobiology by positively regulating tumor growth while maintaining the non-invasive character of ULMs

Keywords: Differential gene expression

overall_design: Paired normal (myometrium) and tumor (ULM) samples derived from 5 patients were used

last: Zavadil

first: Huihui

last: Ye

first: Zhaojian

last: Liu

first: Jingjing

last: Wu

first: Peng

last: Lee

first: Eva

last: Hernando

first: Patricia

last: Soteropoulos

first: Gokce

middle: A

last: Toruner

first: Jian-Jun

last: Wei


title: Expression profile for Drosophila Sox14 at onset of metamorphosis

status: Public on Jul 31 2010

city: Athens

first: Robert

middle: B

last: Beckstead

state: GA

address: 119 Poultry Science Building

department: Poultry Science

country: USA

institute: The University of Georgia

summary: We used microarray analysis of RNA obtained from w1118 and w1118;sox14L1/sox14L1 animals staged at pupariation to identify genes regulated by Drosophila Sox14 at the onset of metamorphosis.

overall_design: RNA isolated from whole Drosophila w1118 and w1118; sox14L1/sox14L1 animals selected immediately after pupariation was hybridized on Affymetrix Drosophila Genome 2.0 Arrays. Each genotype was assayed independently three times with samples obtained from 10 prepupae.

first: Amanda

last: Ritter


title: Letrozole (Femara) early and late responses to treatment

status: Public on Jul 28 2010

city: San Diego

first: John

middle: R

last: Walker

state: CA

address: 10675 John Jay Hopkins

institute: Genomics Institute of the Novartis Research Foundation

summary:
In the present investigation, we have exploited the opportunity provided by neoadjuvant treatment of a group of postmenopausal women with large operable or locally advanced breast cancer (in which therapy is given with the primary tumour remaining within the breast) to take sequential biopsies of the same cancers before and after 10-14 days or 90 days treatment with letrozole.  RNA extracted from the biopsies has been subjected to Affymetrix microarray analysis and the data from paired biopsies interrogated to discover genes whose expression is most influenced by oestrogen deprivation.

Keywords: Timecourse between subjects

overall_design: Biopsies were taken from the same subjects at three timepoints: pretreatment, after 10-14 days Letrozol (2.5 mg/day, oral), and after 90 days Letrozol (2.5 mg/day, oral).

first: William

last: Miller

first: Alexey

last: Larionov

first: Lorna

last: Renshaw

first: Thomas

middle: J

last: Anderson

first: Sharon

last: White

first: Garret

last: Hampton

first: Steven

last: Ho

first: Andreas

last: Krause

first: Dean

last: Evans

first: J

middle: M

last: Dixon


title: Expression data from Arabidopsis thaliana

status: Public on Aug 25 2010

city: Capital Federal

first: Mariana

last: Obertello

address: Vuelta de Obligado 2490

department: Department of Biology

country: Argentina

institute: INGEBI-CONICET

summary:
Nitrogen and light are two major regulators of plant metabolism and development.  While genes involved in the control of each of these signals have begun to be identified, regulators that integrate gene responses to nitrogen and light signals have yet to be determined.
Here, we evaluate the role of bZIP1, a transcription factor involved in light and nitrogen sensing, by exposing wild-type (WT) and bZIP1 T-DNA null mutant plants to a combinatorial space of N and L treatment conditions.  We use ANOVA analysis combined with clustering and Boolean modeling, to evaluate the role of bZIP1 in mediating L and N signaling genome-wide.

overall_design: Arabidopsis thaliana were growth on basal MS salts (custom-made; GIBCO) with 0.5 mM KNO3, 3 mM sucrose and 0.8% BactoAgar at pH 5.7.  After 14 days under long-day (16 h light: 8 h dark) conditions with light intensity of 50 μE.m-2.s-1 and at 22°C, plants were transferred to new plates containing 20 mM KNO3 and 20 mM NH4NO3 (referred here as 1xN: concentrations in MS media) in the absence or presence of light for 2 h at the start of their light cycle.

first: Gabriel

last: Krouk

first: Manpreet

last: Katari

first: Suzan

last: Runko

first: Gloria

last: Coruzzi


title: Comparison of Fusobacterium Nucleatum stimulated and unstimulated neutrophils

status: Public on Jul 20 2010

city: Birmingham

first: Helen

middle: Joan

last: Wright

state: West Midlands

address: St Chads Queensway

department: Oral Biology

country: United Kingdom

institute: University of Birmingham

summary: Neutrophils are known to be stimulated by different periodontal bacteria to produce reactive oxygen species and cytokines. It is inportant to investigate the gene changes made by bacteria of importance, of which, for periodontal disease, fusobaterium nucleatum is one. we used microarrays to investigate gene experssion changes in peripheral blood neutrophils werwhich e stimulated with or with out Fusobacterium Nucleatum (10953).

overall_design: Neutrophils from periodonatlly healthy individuals (n=4) were isolated and stimulated for 3hrs with or without fusobaterium nucleatum (10953). RNA was then extracted from these and pooled before hybridization on Affymetrix microarrays

first: Paul

last: Cooper


title: Circadian expression profiling of purified clock neurons in adult Drosophila

status: Public on Jul 15 2010

city: Evanston

first: Elzbieta

last: Kula-Eversole

state: IL

address: 2205 Tech Drive

department: NBP

institute: Northwestern University

summary: To compare circadian gene expression within highly  discrete neuronal populations, we separately purified and characterized two adjacent but distinct groups of Drosophila adult circadian neurons: the 8 small and 10 large PDF (pigment-dispersing factor)-expressing ventral lateral neurons (s-LNvs and l-LNvs, respectively).  The s-LNvs are the principal circadian pacemaker cells, whereas recent evidence indicates that the l-LNvs are involved in sleep and light-mediated arousal. Although half of the l-LNv-enriched mRNA population including core clock mRNAs is shared between the l-LNvs and s-LNvs, the other half is l-LNv- and s-LNv specific. The distribution of four specific mRNAs is consistent with prior characterization of the four encoded proteins and therefore indicates successful purification of the two neuronal types. Moreover, an octopamine receptor mRNA is selectively enriched in l-LNvs, and only these neurons respond to in vitro application of octopamine. Dissection and purification of l-LNvs from flies collected at different times indicate that these neurons contain cycling clock mRNAs with higher circadian amplitudes as well as at least a 10-fold higher fraction of oscillating mRNAs than all previous analyses of head RNA. Many of these cycling l-LNv mRNAs are well-expressed but do not cycle or cycle much less well elsewhere in heads. The results suggest that RNA cycling is much more prominent in circadian neurons than elsewhere in heads and may be particularly important for the functioning of these neurons.

overall_design:
Gene expression was profiled in purified large PDF neurons across 4 time-points and small PDF neurons at two time-points under an LD cycle.
Circadian neurons (PDF large and small cells), general neurons (ELAV) and per01:large PDF cells were labeled by GFP using specfic drivers. Expression of these cells types were profiled after manual cell sorting of GFP-positive cells at different time-points under a light/dark (LD) cycle. The time-points included ZT0, ZT6, ZT12, and ZT18 in the case of large PDF cells, and ZT0 and ZT12 in the case of small PDF cells, ELAV cells and per01:large PDF cells. 3 biological replicates were collected for the large PDF cells and ELAV cells at ZT0 and ZT12. 2 replicates were collected for large PDF cells at ZT6 and ZT18, small PDF cells, and per01:large PDF cells.

first: Emi

last: Nagoshi


title: MYB silencing in CD34+ progenitor cells

status: Public on Jul 14 2010

city: Modena

first: Rossella

last: Manfredini

address: Via Gottardi 100

department: Life Sciences

country: Italy

institute: Centre for Regenerative Medicine

summary: The c-Myb transcription factor is highly expressed in immature hematopoietic cells and down-regulated during differentiation. To define the role of c-Myb in human hematopoietic lineage commitment, we studied the effects of its silencing during the commitment of human CD34+ Hematopoietic stem/progenitor cells. In CD34+ cells c-Myb silencing determined a cell cycle arrest in G0/G1 phase which strongly decreased the clonogenic efficiency, togheter with a reduction of erythroid colonies coupled with an increase of the macrophage and megakaryocyte ones. Moreover, morphological and flow cytometry data supported the preferential macrophage and megakaryocyte differentiation of c-Myb-silenced CD34+ cells. Taken together our data indicate that c-Myb is essential for the commitment along the erythroid and granulocyte lineages but not for the macrophage and megakaryocyte differentiation. Gene expression profiling of c-Myb-silenced CD34+ cells identified some potential c-Myb targets which can account for these effects, to study by Chromatin Immunoprecipitation and Luciferase Reporter Assay.

overall_design: To maximize siRNA transfection efficiency, we utilized the NucleofectorTM technology (Amaxa). CD34+ cells were transfected with a mixture of 3 siRNAs targeting c-Myb mRNA and with a non-targeting siRNA as a negative control. The expression level of c-Myb protein on control cells (MOCK and negative control treated cells) and MYBsiRNA treated cells was assessed by Western Blot at 24 and 48h post-nucleofection.

first: Elisa

last: Bianchi

first: Roberta

last: Zini

first: Simona

last: Salati

first: Elena

last: Tenedini

first: Ruggiero

last: Norfo

first: Enrico

last: Tagliafico

first: Sergio

last: Ferrari


title: Effects of chronic hypoxia on Duchenne Muscular Dystrophy Drosophila melanogaster model

city: Heidelberg

first: Matias

last: Mosqueira

state: Baden-Wuttenberg

address: Im Neuenheimer Feld, 326 R414

department: Institute of Physiology and Pathop

country: Germany

institute: Heidelberg University Hospital

overall_design:
In order to understand the chronic hypoxia (CH) effect upon the absence of dystrophin, Drosophila melanogaster  wild type and the model for DMD (dmDys), in which all dystrophins expression was knocked out by iRNA, were exposed to high altitude hypoxia (hypobaric hypoxia) during a 16-day climbing period reaching the summit of Mount McKinley (6194 meters above sea level). Furthermore, dmDys and Drosophila wild type were exposed to normobaric hypoxia (hypoxic chamber) following the same oxygen levels observed during the climbing expedition and to normoxic conditions for comparison. Affymetrix GeneChip® profiling was performed for individual flies from each experimental group. CH-dmDys differentially expressed 1281 genes, whereas control group differentially expressed 57 genes. Eight heat shock protein genes detected in the CH-dmDys microarray study were down-regulated, instead of up-regulated as seen in wild type hypoxic flies. This result suggests a differential gene expression response to CH, which could affect muscle performance.These results suggest that dmDys is more sensitive to CH due to reduced muscle function and hypoxic stress response.
Overall design:
Adults wild type and dystrophic flies (3-5 days old) were exposed to hypobaric hypoxia for two weeks during the summer expedition to Mount McKinley, Alaska (6194 MASL). Another set of wild types and dystrophic flies were exposed to normobaric hypoxia according to the table I obtained during the climbing expedition. During the expedition, the flies were maintained in vials with regular molasses and covered by thermo isolation to avoid low temperature, keeping the temperature at 25C. The experiment performed in the laboratory also used vials with regular molasses and at 25C.
Table I. Expedition log book for mount McKinley ascent. Information obtained during the ascent and summit of Mount McKinley, June 1st to June 16th of 2007. The oxygen pressure (PO2) was calculated from the barometric pressure. GNB means go and back from the mentioned point.

DAY	LOCATION	ALTITUDE
m	PO2
mmHg (%)
1 	Base Camp	2200	123.6  (16.3%)
2	Base Camp	2200	123.6  (16.3%)
3	Base Camp	2200	123.6  (16.3%)
4 	Ski Hill	2400	120.7  (15.9%)
5	Kahiltna Pass	2950	113.0  (14.9%)
6	Motorcycle Hill	3350	107.7  (14.2%)
7	Motorcycle Hill	3350	107.7  (14.2%)
8	GNB from Motorcycle	4150 (5 hours)	97.7  (12.9%)
9	Medical Camp	4350	95.3  (12.5%)
10	GNB from Medical Camp	4150 (5 hours)	97.7  (12.9%)
11	Medical Camp	4350	95.3  (12.5%)
12	GNB from Medical Camp	4900	89.0  (11.7%)
13	Medical Camp	4350	95.3  (12.5%)
14	High Camp	5250	85.1  (11.2%)
15 	Summit	6194 (0.3 hours)	75.4  (9.9%)
16	High Camp	5250	85.1  (11.2%)


title: Effects of global system for mobile communications 1800 MHz radiofrequency electromagnetic fields on gene expression in MCF-7 cells

city: Hangzhou

first: Guangdi

last: Chen

state: Zhejiang

address: 388 Yuhangtang

department: School of Medicine

country: China

institute: Zhejiang University

summary: Despite many studies over a decade, it still remains ambiguous as to the real biological effects induced by radiofrequency electromagnetic fields (RF EMF). Epidemiological studies indicates that long-term exposure to EMF could increase the risk of breast cancer. Some reports have showed that in vitro EMF exposures change cellular gene expression. In this study, we investigated global gene expression responses to RF EMF simulating the Global System for Mobile Communications (GSM) 1800 MHz signal in human breast cancer cell line MCF-7 using transcriptomic approaches.

overall_design: MCF-7 cells were intermittently (5 min fields on/10 min fields off) exposed to RF EMF at an average specific absorption rate (SAR) of 2.0 W/kg (2 W/kg exposure group) or sham-exposed (2 W/kg control group) for 24 h, or exposed  to RF EMF at a higher level of 3.5 W/kg (3.5 W/kg exposure group) or sham-exposed (3.5 W/kg control group).

first: Qunli

last: Zeng

first: Zhengping

last: Xu


title: Genome-wide analysis of gene expression perturbed by reptin shRNA in MCF7 subjected to normoxic and hypoxic conditions

status: Public on Jul 13 2010

city: Los Angeles

first: Minhyung

last: Kim

address: 8700 Beverly Blvd

department: Urology

institute: Cedars-Sinai Medical Center

summary: In order to investigate the role of reptin methylation on the expression of hypoxia-responsive genes across the whole genome, we performed a microarray analysis from RNAs isolated from MCF7 cells expressing either control shRNA (shRNA) or reptin shRNA (shreptin) in normoxic and hypoxic conditions.

overall_design: MCF7 cells were transiently transfected with either non-specific shRNA or reptin shRNA in replicates. Cells were grown for 24 hours before being exposed to either normoxic (21% oxygen) or hypoxic (1% oxygen) conditions for 18 hours. Cells were then lysed and RNA was isolated.

first: Sung

middle: H

last: Baek

first: Daehee

last: Hwang

first: Jason

middle: S

last: Lee

first: Yunho

first: Ik

first: Sang

middle: C

last: Noh


title: MYB silencing in CD14-myeloblasts

first: Rossella

last: Manfredini

summary: The c-Myb transcription factor is highly expressed in immature hematopoietic cells and down-regulated during differentiation. To define the role of c-Myb during the terminal differentiation of hematopoietic precursors, we studied the effects of its silencing in human primary CD14-myeloblasts, which maintain a granulo-monocyte differentiation bipotentiality. c-Myb-silenced myeloblasts were blocked in the G1 phase of the cell cycle at 24 hours post-nucleofection and subsequently were forced towards macrophage differentiation, as demonstrated by immunophenotypic and morphological analysis. Indeed, c-Myb-silenced CD14- cells differentiate to macrophage even after the treatment with ATRA 10-6 M,  demonstrating that the c-Myb knockdown strongly impairs the ability of myeloblasts to differentiate to granulocytes. Gene expression profiling of c-Myb-silenced CD14- cells identified some potential c-Myb targets that can account for these effects.

overall_design: To maximize siRNA transfection efficiency, we utilized the NucleofectorTM technology (Amaxa). CD14- cells were transfected with a mixture of 3 siRNAs targeting c-Myb mRNA, with a non-targeting siRNA as a negative control (NegCTR) and without siRNA (MOCK). c-Myb siRNAs were transfected at days 1 to 3 after the CD14- myeloblasts purification based on the observation that this timing represented a phase of phisiological increase in c-Myb expression in myeloblasts. Western Blot analysis at 24 hours post-nucleofection demonstrated the c-Myb protein knockdown in MYBsiRNA CD14- cells as compared with control samples (MOCK, NegCTR).

first: Elisa

first: Roberta


title: Systematic analysis of a human renal transcript dataset

status: Public on Jul 19 2010

city: Ann Arbor

first: Felix

last: Eichinger

state: MI

address: 1150 W Med Center Drive

department: Internal Medicine/Nephrology

institute: University of Michigan

summary:
Glomerular diseases account for the majority of cases with chronic renal failure. Several genes have been identified with key relevance for glomerular function. Quite a few of these genes show a specific or preferential mRNA expression in the renal glomerulus. To identify additional candidate genes involved in glomerular function in humans we generated a human renal glomerulus-specific transcript dataset (GTD) by comparing gene expression profiles from human glomeruli and tubulointerstitium obtained from six transplant living donors using Affymetrix HG-U133A arrays. This analysis resulted in 677 genes with prominent overrepresentation in the glomerulus. Genes with ‘a prior’i established known prominent glomerular expression served for validation and were all found in the novel expression library (e.g. CDKN1, DAG1, DDN, EHD3, MYH9, NES, NPHS1, NPHS2, PDPN, PLA2R1, PLCE1, PODXL, PTPRO, SYNPO, TCF21, TJP1, WT1). The mRNA expression for several novel glomerulus-enriched genes identified in REGGEL was validated by qRT-PCR. Gene ontology and pathway analysis identified biological processes previously not reported to be of relevance in glomeruli including among others axon guidance. This finding was further validated by assessing the expression of the axon guidance molecules neuritin (NRN1) and roundabout receptor ROBO1 and -2. Glomerular disease associated differential mRNA regulation of ROBO2 was found in diabetic nephropathy.

In summary, using a comparative strategy on microdissected nephrons novel transcripts with predominant expression in the human glomerulus could be identified.  A systematic analysis of this glomerulus-specifc gene expression library allows the detection of target molecules and biological processes involved in glomerular biology and renal disease.

overall_design:
Sample from kidney biopsies of 6 transplant Living Donors (LD) were microdissected into tubular and glomerular compartment and separately hybridized an Affymetrix HG-U133A microarrays. Background correction and quantile normalization was ferformed using RMAexpress Version 0.3 as part of a dataset of 88 samples for glomeruli and 84 samples for tubuli. All data are reported in log2 scale. A background filter cut-off was defined to lower the count of false positive calls using the highest signal value obtained from non-human Affymetrix control oligonucleotides multiplied by a factor of 1.2, following previous studies:

Schmid H, Boucherot A, Yasuda Y, et al.: Modular activation of nuclear factor-kappaB transcriptional programs in human diabetic nephropathy. Diabetes 55:2993-3003, 2006

A linear model was fit to compensate differences in expression due to separate sample processing of the compartments. Subsequently, genes were selected based on foldchange.

first: Maja

middle: T

last: Lindenmeyer

first: Kontheari

last: Sen

first: Hans-Joachim

last: Anders

first: Ilka

last: Edenhofer

first: Deborah

last: Mattinzoli

first: Matthias

last: Kretzler

first: Maria

middle: P

last: Rastaldi

first: Clemens

last: Cohen


title: Meningioma initiating cells (MICs) derived from primary tumors

status: Public on Jul 09 2010

city: Augusta

first: Huidong

last: Shi

department: Georgia Cancer Center

institute: Augusta University

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

summary: The majority of meningiomas are benign tumors associated with favorable outcomes; however, the less common aggressive variants with unfavorable outcomes often recur and may be due to sub-populations of less-differentiated cells residing within the tumor.  These sub-populations of tumor cells, termed tumor-initiating cells, may be isolated from heterogeneous tumors when sorted or cultured in defined medium designed for enrichment of the tumor-initiating cells.  We report the isolation and characterization of a population of tumor-initiating cells derived from an atypical meningioma.  These meningioma-initiating cells (MICs) self-renew, differentiate, and can recapitulate the histological characteristics of the parental tumor when transplanted into athymic nude mice.  Immunohistochemistry reveals protein expression patterns similar to neural stem and progenitor cells while genomic profiling verified the isolation of cancer cells (with defined meningioma chromosomal aberrations) from the bulk tumor.  Furthermore, microarray analysis of gene expression reveals that many epithelial to mesenchymal transition genes are upregulated in the MICs, consistent with the presence of both neural stem cell and mature neural cell molecular markers seen in the derived cultures.  Pathway analysis identifies biochemical processes and gene networks related to aberrant cell cycle progression, particularly the loss of heterozygosity of tumor suppressor genes CDKN2A (p16INK4A), p14ARF, and CDKN2B (p15INK4B).  Flow cytometric analysis revealed the expression of CD44 and activated leukocyte adhesion molecule (ALCAM/CD166); these may prove to be markers able to identify this cell type.  In conclusion, we identify a tumor-initiating population from an atypical meningioma that displays a unique phenotype and these results provide increased understanding of atypical meningioma progression.

overall_design:
Part 1 of 2: Affymetrix SNP arrays were performed according to the manufacturer's directions on DNA extracted from primary tissue and their counterpart cell lines

Part 2 of 2: Illumina gene expression array analysis was performed according to the manufacturer's directions on RNA extracted from cultured primary Meningioma and neural stem cell lines

first: Prakash

last: Rath

first: Alan

last: Free


title: The SHR/SCR pathway directly activates genes involved in asymmetric cell division in the Arabidopsis root

city: Durham

first: Rosangela

last: Sozzani

state: NC

address: 124 Science Dr

department: Biology

institute: Duke University

summary:
Asymmetric division of cortex/endodermal initials (CEI) in the Arabidopsis root generates two layers of ground tissue and is controlled by a finely orchestrated interplay between the transcription factors, SHORT ROOT (SHR) and SCARECROW (SCR).  To understand the dynamics of the SHR/SCR regulatory network we performed microarray time course experiments using inducible versions of SHR and SCR and examined their transcriptional effects specifically in the ground tissue.

Keywords: SHR and SCR time course and CEI cell-type analyses

overall_design: We performed a time course analysis (TC data set) of the ground tissue (sorted J0571 enancher trap) after transfer either SHR or SCR inducible plants to Dex containing plates 0, 1, 3, 6 and 12 hours. We sorted for CEI cells using the pCYCD6::GFP marker line.  Seedlings were grown for 5 days. SHR and SCR inducible plants were transfer to 1microM Dex MS plates. J0571 and CYCD6 sorted fluorecent cells were harvested for RNA extraction.

first: Philip

middle: N

last: Benfey


title: Whole-transcript expression data for soft-tissue sarcoma tumors and control normal fat specimens

status: Public on Jul 06 2010

city: New York

first: Barry

middle: Stephen

last: Taylor

state: NY

address: 1275 York Avenue, Box #460

institute: Memorial Sloan-Kettering Cancer Center

summary: Soft tissue sarcomas are aggressive mesenchymal cancers that affect more than 10,600 new patients per year in the US, about 40% of whom will die of their disease. Soft tissue sarcomas exhibit remarkable histologic diversity, with more than 50 recognized subtypes, but our knowledge of their genomic alterations is limited. Here we describe the results of an integrative analysis of DNA sequence, copy number, and mRNA expression in 207 samples encompassing seven major subtypes. Genes mutated in more than 5% of samples within a subtype were KIT (in gastrointestinal stromal cell tumors, or GISTs), TP53 (pleomorphic liposarcomas), PIK3CA (myxoid/round-cell liposarcoma), and NF1 (both myxofibrosarcoma and pleomorphic liposarcoma). We show evidence that PIK3CA mutations, found in 18% of myxoid/round-cell liposarcomas, activate AKT in vivo and are associated with poor outcomes. Point mutations in the tumor suppressor gene NF1 were discovered in both myxofibrosarcomas and pleomorphic liposarcomas, while genomic deletions were observed in all subtypes at varying frequencies. Finally, we found that short hairpin RNA-based knockdown of a subset of genes that are amplified in dedifferentiated liposarcoma, including CDK4 and YEATS4, decreased cell proliferation. Our study yields the most detailed map of molecular alterations across diverse sarcoma subtypes to date and provides potential subtype-specific targets for therapy.

overall_design: Human soft-tissue sarcoma specimens were profiled on Affymetrix U133A arrays per manufacturer's instructions.

first: Jordi

last: Barretina

first: Matthew

last: Meyerson

first: Samuel

last: Singer


title: Differential endothelial cell gene expression by African Americans versus Caucasian Americans: A possible contribution to health disparity in vascular disease and cancer

status: Public on Jul 03 2010

city: Minneapolis

first: Robert

last: Hebbel

email: hebbe001@umn.edu, weixx035@umn.edu

state: MN

address: 516 Delaware St SE

department: Medicine

institute: University of Minnesota

summary:
Background: African Americans (AA) have increased burdens of cardiovascular disease and cancer compared to Caucasian Americans (CA). This study addresses the possibility that genetic differences affecting the biology of the vascular endothelium could be a factor contributing to this health disparity.
Methods: From self-identified, healthy, 20-29 year old AA (n=21) and CA (n=17), we established cultures of blood outgrowth endothelial cells (BOEC) and applied microarray profiling. BOEC have never been exposed to in vivo influences, and their gene expression reflects culture conditions (meticulously controlled) and donor genetics. Analysis used two distinct approaches. Significance Analysis of Microarray, a FDR-based test, identified significant differential expression of single genes. Gene Set Enrichment Analysis examined expression of pre-determined gene sets that survey each of nine biological systems relevant to endothelial cell biology.
Results: At the highly stringent threshold of FDR=0, we identified 31 single genes that were differentially expressed, 4 higher and 27 lower in AA. “PSPH” exhibited the greatest fold-change (AA>CA), but this was entirely accounted for by a homolog (PSPHL) hidden within the PSPH probe set. Among other significantly different genes were: for AA>CA, SOS1, AMFR, FGFR3; and for AA<CA, ARVCF, BIN3, EIF4B. Many more (221 transcripts for 204 genes) were differentially expressed at the more customary, less stringent threshold of FDR<.05. Using the biological systems approach, we identified shear response biology as being significantly altered for AA versus CA. It detected an apparent tonic increase of expression (AA>CA) for 46/157 genes within that system.
Conclusions: The most significant single gene changes detected for AA involved genes having substantial, known roles in endothelial biology. Biological systems analysis suggested that shear stress response, a critical regulator of endothelial function and vascular homeostasis, may be different between AA and CA. These results potentially have direct implications for the role of endothelial cells in both vascular disease (e.g., hypertension and stroke) and cancer (via angiogenesis). The present findings are consistent with our overarching hypothesis that genetic influences stemming from ancestral continent-of-origin could impact upon endothelial cell biology and thereby contribute to disparity of vascular-related disease burden amongst AA.

first: Peng

last: Wei

first: Liming

last: Milbauer

first: Judy

last: Enenstein

first: Julia

last: Nguyen

first: Wei

last: Pan


title: Subtype-specific genomic alterations define new targets for soft tissue sarcoma therapy

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

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

overall_design: Refer to individual Series


title: Friedreich’s Ataxia Induced Pluripotent Stem Cells Recapitulate GAA•TTC Triplet-Repeat Instability

status: Public on Jul 02 2010

city: SAN DIEGO

first: JOEL GOTTESFELD ; JEANNE LORING ;

last: GULSAH ALTUN

email: joelg@scripps.edu, skusen@home2.scripps.edu, jloring@scripps.edu, gulsah@scripps.edu, gulsahaltun@gmail.com

address: 3030 Science Park Rd. 3rd floor, room 3020

department: CHEMICAL PHYSIOLOGY

institute: THE SCRIPPS RESEARCH INSTITUTE

summary: The inherited neurodegenerative disease Friedreich’s ataxia (FRDA) is caused by hyperexpansion of GAA•TTC trinucleotide repeats within the first intron of the FXN gene, encoding the mitochondrial protein frataxin. Long GAA•TTC repeats causes heterochromatin-mediated silencing and loss of frataxin in affected individuals. We report the derivation of induced pluripotent stem cells (iPSCs) from FRDA patient fibroblasts through retroviral transduction of transcription factors. FXN gene repression is maintained in the iPSCs, as are the mRNA and miRNA global expression signatures reflecting the human disease. GAA•TTC repeats uniquely in FXN in the iPSCs exhibit repeat instability similar to patient families, where they expand and/or contract with discrete changes in length between generations. The mismatch repair enzyme Msh2, implicated in repeat instability in other triplet repeat diseases, is highly expressed in the iPSCs, occupies FXN intron 1, and shRNA silencing of Msh2 impedes repeat expansion, providing a possible molecular explanation for repeat expansion in FRDA.

overall_design: 65 samples from various number of tissue, primary cell lines undifferenatiated human embryonic stem cell lines, induces pluripotent stem cell lines have been run on Illumina HT12 v3 chips.

first: Sherman

last: Ku

first: Elisabetta

last: Soragni

first: Erica

last: Campau

first: Elizabeth

last: Thomas

first: Gulsah

last: Altun

first: Louise

last: Laurent

first: Jeanne

middle: F

last: Loring

first: Marek

last: Napierala

first: Joel

last: Gottesfeld


title: Expression profiles from a variety of resting and activated human immune cells

city: South San Francisco

first: Alex

last: Abbas

address: 1 DNA Way

department: Bioinformatics

institute: Genentech, Inc.

summary:
Immune cell-specific expression is one indication of the importance of a gene's role in the immune response.
In order to identify such patterns, we set out to broadly profile gene expression in a variety of immune cells.

overall_design:
We isolated twelve different types of human leukocytes from peripheral blood and bone marrow, treated them to induce activation and/or differentiation, and profiled their gene expression before and after treatment.

The twelve cell types are:
B cells, CD14+ cells, CD4+ CD45RO+ CD45RA- T cells, CD4+ T cells, CD8+ T cells, IgG/IgA memory B cells, IgM memory B cells, Monocytes, NK cells, Neutrophils, Plasma cells from bone marrow, and Plasma cells from PBMC.

first: Alexander

first: Daryl

last: Baldwin

first: Yan

last: Ma

first: Wenjun

last: Ouyang

first: Austin

last: Gurney

first: Flavius

last: Martin

last: Fong

first: Menno

last: van Lookeren Campagne

first: Paul

last: Godowski

first: P

last: Williams

first: Andrew

last: Chan

first: Hilary

last: Clark


title: Expression data from conventional osteosarcoma compared to primary non-neoplastic osteoblast cells

status: Public on Jun 30 2010

city: Berlin

first: Raphaela

last: Fritsche

address: Chariteplatz 1

department: Institute of Pathology

institute: Charitè Universitätsklinikum Charite

summary: In osteosarcoma patients, the development of metastases, often to the lungs, is the most frequent cause of death. To improve this situation, a deeper understanding of the molecular mechanisms governing osteosarcoma development and dissemination and the identification of novel drug targets for an improved treatment are needed. Towards this aim, we characterized osteosarcoma tissue samples compared to primary osteoblast cells using Affymetrix HG U133A microarrays.

overall_design: mRNA from 5 frozen conventional osteosarcoma and 4 osteosarcoma lung metastases tumor samples and mRNA from fresh primary osteoblast cells were extracted and hybridized to HG U133A microarrays.

last: Guenther


title: Analysis of the Infrared-A radiation induced transcriptom of human skin fibroblasts.

status: Public on Jul 10 2010

city: Düsseldorf

first: Christian

last: Calles

address: Auf'm Hennekamp 50

department: Molecular Ageing Research/Cellbiology

institute: Institut fuer umweltmedizinische Forschung (IUF)

summary:
Background:

Infrared A radiation (IRA 760-1440 nm) is a major component of solar radiation and, similar to ultraviolet (UV) radiation, causes photoaging of human skin by increasing the expression of matrixmetalloproteinase-1 (MMP-1) expression in human skin fibroblasts. This gene-regulatory effect resulted from the IRA induced activation of the pleiotropic MAPKinase ERK1/2 signaling pathway, indicating that the IRA response extends beyond MMP-1. In the present study we have therefore assessed the IRA-induced transcriptom in primary human skin fibroblasts.

Results:

Microarray analysis revealed 599 transcripts to be regulated by physiologically relevant doses of IRA in primary human skin fibroblasts. The IRA induced transcriptom differed from changes known to be induced by UVB or UVA radiation in the same cell type. IRA responsive genes include four categories: extracellular matrix, calcium homeostasis, stress signaling, and apoptosis. These results were confirmed by realtime PCR experiments analyzing thirteen of these genes representing these four categories. By means of chemical inhibitors of known signaling pathways we next show that besides ERK1/2, the p38-, JNK-, PI3K/AKT-, STAT3-, and IL-6 as well as calcium mediated signaling pathways are functionally involved in the IRA gene response and that a major part of it is triggered by mitochondrial, and to a lesser extent non-mitochondrial production of reactive oxygen species.

Conclusion:

This study identifies IRA radiation as a potent modulator of gene expression in human skin cells. The IRA response is specific and involves genes which are of critical importance for the homeostasis of human skin. Our data confirm the previous notion that IRA contributes to premature skin aging and indicate that further biological effects may result from IRA exposure of human skin.

overall_design: To identify genes differentially regulated after IRA irradiation we analyzed a set of nine independent samples pairs (IRA irradiated vs. sham irradiated), using human primary human dermal fibroblasts from three different donors (termed F1 to F3). Cells between passage number five to ten were exposed in vitro to a dose of 860 J/cm2 IRA. IRA irradiation lasted 40 min leading to a total dose of 860 J/cm2. The culture dishes were placed on a cooled plate connected to thermostated bath (Thermo Haake GmbH, Karlsruhe, Germany) to maintain temperatures below 37°C during IRA irradiation. For irradiation, medium was replaced by phosphate-buffered saline (37°C, Gibco). Control cells (sham) were held on a 37°C thermostated plate under similar conditions without irradiation. Following the treatment cells were cultivated for 24 hours with serum free MEM culture medium at 37°C.

first: Maren

last: Schneider

first: Filippina

last: Macaluso

first: Tereza

last: Benesova

first: Jean

last: Krutmann

first: Peter

last: Schroeder


title: Atonal and Senseless perturbations in Drosophila melanogaster eye-antennal imaginal discs.

status: Public on Jun 28 2010

city: Leuven

first: Rekin's

last: Janky

address: Herestraat 49 Box 816

department: Nucleomics Core

country: Belgium

institute: VIB

summary: The goal of this study is to identify co-expressed genes downstream of Atonal and Senseless. These gene lists are used as candidate target genes (technically: as foreground sets) in computational predictions of cis-regulatory elements using the cisTargetX method (http://med.kuleuven.be/cme-mg/lng/cisTargetX). Together, the gene expression results and cis-regulatory predictions, yield a gene regulatory network underlying the early events in retinal differentiation. Predicted cis-regulatory interactions have been validated extensively in vivo using enhancer reporter assays and genetic perturbations.

overall_design: Six samples were analyzed for Atonal gain-of-function (GOF) in the eye-antennal imaginal discs of third instar larvae of Drosophila melanogaster, namely three biological repeats for two different Gal4 drivers (Gal4/7 and AtoGal), crossed with UASato. Three samples were analyzed for Atonal loss-of-function (LOF) in the eye-antennal imaginal discs, namely three biological repeats of ato-/- larvae. Three samples were analyzed for Senseless GOF, namely three biological repeats of atoGal4 crossed with UASsens. Finally, eight control samples were analyzed, namely two biological repeats of four different lines (atoGal4, Gal4/7, UASato, and cantonS wild type).

first: Stein

last: Aerts

first: Annelies

last: Claeys

first: Iris

last: Leenaerts

first: Bassem

last: Hassan


title: WT and DBDmut Breast Cancer Cells

city: La Jolla

first: Joshua

middle: D

last: Stender

address: 9500 Gillman

institute: University of California at San Diego

summary: Estradiol Timecourse of MDA-MB-231ER+ cells containing a WT-ER and DBDmut-ER

overall_design: Cells were treated with 10 nM estradiol in a timecouse ranging from 1 hour to 24 hour treatments.


title: Primary human erythroid progenitor cells NK57 treatment samples

city: Boston

first: Benjamin

middle: L

last: Ebert

state: MA

address: Harvard Medical School

institute: Dana-Farber Cancer Institute

summary:
Gene expression profiling was performed on primary human erythroid progenitor cells left untreated or treated with 2uM NK57 for 3 days.
The worldwide burden of sickle cell disease is enormous, with over 200,000 infants born with the disease each year in Africa alone. Induction of fetal hemoglobin is a validated strategy to improve symptoms and complications of this disease. The development of targeted therapies has been limited by the absence of discrete druggable targets. We developed a novel bead-based strategy for the identification of inducers of fetal hemoglobin transcripts in primary human erythroid cells. A small-molecule screen of bioactive compounds identified remarkable class-associated activity among histone deacetylase (HDAC) inhibitors. Using a chemical genetic strategy combining focused libraries of biased chemical probes and reverse genetics by RNA interference, we have identified HDAC1 and HDAC2 as molecular targets mediating fetal hemoglobin induction. Our findings suggest the potential of isoform-selective inhibitors of HDAC1 and HDAC2 for the treatment of sickle cell disease.

overall_design: Gene expression profiling was performed on primary human erythroid progenitor cells left untreated (n=7) or treated with 2uM NK57 for 3 days (n=2).

first: James

middle: E

last: Bradner

first: Kenneth

last: Ross


title: The activation potential of MOF is constrained for dosage compensation, MBD-R2 transcriptome analysis

status: Public on Jun 26 2010

city: Munich

last: Feller

address: Schillerstraße 44

department: Molecular Biology

institute: Adolf-Butenandt Institute at the LMU University Munich

summary:
The H4K16 acetyltransferase MOF plays a crucial role in dosage compensation in Drosophila, but has additional, global functions in gene control. We compared the molecular context and effect of MOF activity in male and female flies combining chromosome-wide mapping and transcriptome studies with analyses of defined reporter loci in transgenic flies. MOF distributes dynamically between two types of complexes, the Dosage Compensation Complex (DCC) and complexes containing MBD-R2, a global facilitator of transcription. These different targeting principles define the distribution of MOF between the X chromosome and autosomes and at transcription units with 5’ or 3’ enrichment.
The male X chromosome differs from all other chromosomes in that H4K16 acetylation levels do not correlate with transcription output. The reconstitution of this phenomenon at a model locus revealed that the activation potential of MOF is constrained in male cells in the context of the DCC to arrive at the two-fold activation of transcription characteristic of dosage compensation.

overall_design: Drosophila SL2 cells were treated with RNAi against two different constructs targeting the MBD-R2 transcript (M1 and M2, "rep" represents "biological replicate", GST RNAi and one no dsRNA sample ("control").

last: Becker


title: HDAC1 and HDAC2 in fetal hemoglobin induction


title: Gene expression profile in root and flower mediated by GLUCOSE-INHIBITED ROOT ELONGATION1 (GIR1)

status: Public on Jul 01 2010

city: Taipei

first: Wan-Hsing

last: Cheng

address: 128, Section 2, Academia Road, Nankang

department: Institute of Plant and Microbial Biology

country: Taiwan

institute: Academia Sinica

summary: We isolated the glucose-inhibited root elongation1 (gir1) mutant from a genetic screen of activation T-DNA tagged seeds grown on 6% glucose agar plates. The gir1 mutant showed short swollen root phenotype at the presence of glucose and had a sever sterility when grown in soil. To better understand the molecular basis of GIR1-mediated gene expression, the Affymetrix ATH1 GeneChip was used to analyze the gene expression profiling in the gir1 mutant. The results showed that cell wall, carbohydrate, and lipid metabolic or transporter-related genes were altered expression pattern. These data suggest that GIR1 regulates root and flower growth and development through cell wall modification and, perhaps, membrane trafficking.

overall_design:
For root microarray assay [Samples GSM402178-GSM402183], wild type and the gir1 mutant plants were vertically grown on 0% glucose agar plates for 11 days, then transferred to 4% glucose plates for another ten days. Subsequently, the root tissues were excised for GeneChip analysis.
In the case of inflorescence microarray assay [Samples GSM402184-GSM402191], plants were grown in soil for 33 days. The opened and opening flowers were discarded and the remaining inflorescence was harvested for GeneChip analysis.

first: Ya-Huei

last: Chen

first: Ming-Hau

last: Chiang

first: Yu-wen

last: Huang

first: San-Gwang

last: Hwang

first: Pei-Rung

last: Shiu

first: Wann-Neng

last: Jane

first: Jen

last: Sheen


title: Time of day shapes the Arabidopsis drought transcriptomes

city: Toronto

first: Malcolm

middle: M.

last: Campbell

state: ON

address: 25 Willcocks Street

department: Cell & Systems Biology

country: Canada

institute: University of Toronto

summary: Under natural conditions, plants experience episodes of drought for periods of days or longer. Plants respond to drought stress by reconfiguring their transcriptome activity. Transcriptome changes in response to drought are dynamic, and are likely to be shaped by mitigating factors such as diel signals. To gain insights into the dynamics of transcriptome reconfiguration in response to gradual soil drying, the drought-induced transcriptomes of Arabidopsis thaliana were examined at four time points over a single diel period – midday, late day, midnight, and pre-dawn. A core set of genes was identified that was responsive to drought, independent of the time of day at which they were measured. Strikingly, the magnitude of the drought-induced changes for these genes varied in a time-of-day-dependent manner.  An additional set of time-of-day-specific drought-responsive genes were also identified. The diurnal patterns of transcript accumulation for these genes was strongly influenced by drought stress. This study indicates that analysis of a single time point would miss suites of drought-responsive genes that are revealed through assessment of the dynamics of diurnal changes, emphasizing the value of characterizing multiple time-of-day-specific drought transcriptomes.

overall_design: 24 arrays total. 4 time points (midday, late day, midnight, pre-dawn). 2 water regimes (well-watered, water-limited). 3 biological replicates per treatment.

first: Olivia

last: Wilkins

first: Katharina

last: Braeutigam


title: Gene expression profile of the SV40-immortalized human corneal epithelial cells

status: Public on Jun 24 2010

city: Helsinki

first: Kati-Sisko

last: Vellonen

address: Viikinkaari 5 E (P.O.Box 56)

department: Centre for Drug Research

country: Finland

institute: University of Helsinki, Faculty of Pharmacy

summary: Microarray was used to study global gene expression of a cell culture model based on SV40-immortalized human corneal epithelial (iHCE) cells. The gene expression profile of the cell line was compared to the normal human corneal epithelium. Affymetrix HG-U133A GeneChips® were used for microarray experiments and results were validated by performing RT-qPCR for selected genes. iHCE was found to over- and under-express 22 % and 14 % of the annotated genes, respectively. The results of this study suggest that differences between iHCE cells and normal corneal epithelium are substantial and therefore the use of these cells in corneal research should be considered with caution.

overall_design: SV40-immortalized human corneal epithelial (iHCE) cells were cultured on collagen coated permeable supports for one week using standard culture conditions. Subsequently the apical medium was removed and culturing was continued at the air-liquid interface which allows cells to stratify. Trans-epithelial electrical resistance was followed and total RNA was extracted from cultures with resistance > 300 Ω x cm2. RNA was amplified, labeled with biotin, fragmented and hybridized to the HG-U133A GeneChips® (Affymetrix) according to the protocol of the manufacturer. Three separate experiments with samples from three independent culture batches (iHCE1, iHCE2, iHCE3) were performed. The Global gene expression profile of iHCE was compared to previously published human corneal epithelial tissue (GSE5543) data.

first: Dario

last: Greco

first: Helen

last: Turner

first: Marika

last: Häkli

first: Timo

last: Tervo

first: Petri

last: Auvinen

first: J

last: Wolosin

first: Arto

last: Urtti


title: Genome-wide analysis of adrenocortical cells gene expression after 48 h ACTH treatment

status: Public on Jun 16 2010

first: yewei

last: xing

address: 1120 15th street

department: Physiology

institute: Medical College of Georgia


title: A revised map of the human progenitor hierarchy reveals origin of macrophages and dendritic cells in early lymphoid development

status: Public on Jun 13 2010

first: Kolja

last: Eppert

state: Ontario

address: 101 College St., rm 8-301

institute: University Health Network

summary: The classical model of hematopoiesis posits the segregation of lymphoid and myeloid lineages as the earliest fate decision. The validity of this model has recently been questioned in the mouse, however little is known concerning lineage potential of human progenitors. Here we provide a comprehensive analysis of the human hematopoietic hierarchy by clonally mapping the developmental potential of 7 progenitor classes from neonatal cord blood and adult bone marrow. Human multi-lymphoid progenitors, identified as a distinct population of Thy1-/loCD45RA+ cells within the CD34+CD38- stem cell compartment, gave rise to all lymphoid cell types, as well as monocytes, macrophages, and dendritic cells, indicating that these myeloid lineages arise in early lymphoid lineage specification. Thus, as in the mouse, human hematopoiesis does not follow a rigid model of myeloid-lymphoid segregation.

overall_design: Total RNA was extracted from 5 - 10,000 sorted cord blood progenitor cells to compare gene expression

first: S

last: Doulatov

first: F

last: Notta

first: K

first: L

last: Nguyen

first: P

last: Ohashi

last: Dick


title: Genome-wide analysis of adult adrenocortical cells gene expression after 48 h ACTH treatment

summary: Analysis of ACTH-regulation on adrenocortical cells at gene expression level. The hypothesis tested in the present study was that ACTH increases chronic cell growth and steroidogenesis in adrenal glands by changing the gene expression profile. Results provide important information of the response of adrenocortical cells gene expression to chronic ACTH treatment.

overall_design: Total RNA obtained from primary cultured adult adrenal cells subjected to 48 hours in vitro treatment of ACTH compared to untreated control cell.

first: Yewei

last: Xing

first: William

last: Rainey

first: Micheal

last: Edwards


title: Clinical implications of gene dosage and gene expression patterns in diploid breast carcinoma

status: Public on Jun 10 2010

city: Gothenburg

first: Toshima

middle: Z.

last: Parris

address: Medicinaregatan 1G, 6th floor

department: Department of Oncology

country: Sweden

institute: University of Gothenburg

type:
Expression profiling by array
Genome variation profiling by array

summary:
Genomic and expression profiling using 38K BAC array-CGH and Illumina HT-12 beadchips were performed on 97 diploid invasive breast tumors to assess the impact of gene dosage on gene expression patterns and the effect of other mechanisms on transcriptional levels. Patient stratification was performed according to axillary lymph node status (node-negative, pN0; node-positive, pN1) and overall survival (>8-year survivors; breast cancer-specific mortality within 8 years of diagnosis). Array-CGH results was validated by FISH using tumors showing HER2/neu gene amplification and expression profiling was confirmed using qPCR for 16 transcripts.

This SuperSeries is composed of the SubSeries listed below.


title: Gene Experssion Profiling-Based Identification of Molecular Subtypes in Stage IV Melanoma with Different Clinical Outcome (validation set)

status: Public on Jun 08 2010

city: Lund

first: Johan

last: Staaf

address: Medicon Village

institute: SCIBLU - Swegene Centre for Integrative Biology at Lund University

summary: Purpose: The incidence of malignant melanoma is increasing worldwide in fair-skinned populations.  Melanomas respond poorly to systemic therapy, and metastatic melanomas inevitably become fatal. Although  spontaneous regression, likely due to immune defense activation, rarely occurs, we lack a biological  rationale and predictive markers in selecting patients for immune therapy.  Experimental Design: We performed unsupervised hierarchical clustering of global gene expression  data from stage IV melanomas in 57 patients. For further characterization, we used immunohistochemistry  of selected markers, genome-wide DNA copy number analysis, genetic and epigenetic analysis of the  Q3 CDKN2A locus, and NRAS/BRAF mutation screening.  Results: The analysis revealed four distinct subtypes with gene signatures characterized by expression  of immune response, pigmentation differentiation, proliferation, or stromal composition genes. Although  all subtypes harbored NRAS and BRAF mutations, there was a significant difference between subtypes  (P < 0.01), with no BRAF/NRAS wild-type samples in the proliferative subtype. Additionally, the proliferative  subtype was characterized by a high frequency of CDKN2A homozygous deletions (P < 0.01). We  observed a different prognosis between the subtypes (P = 0.01), with a particularly poor survival for patients  harboring tumors of the proliferative subtype compared with the others (P = 0.003). Importantly,  the clinical relevance of the subtypes was validated in an independent cohort of 44 stage III and IV melanomas.  Moreover, low expression of an a priori defined gene set associated with immune response signaling  was significantly associated with poor outcome (P = 0.001).  Conclusions: Our data reveal a biologically based taxonomy of malignant melanomas with prognostic  effect and support an influence of the antitumoral immune response on outcome.

overall_design: Expression profiles of 20 liver and lymphnode metastases. MM76 and MM23 were made in duplicate. Used as validationset in Jönsson et al. Clin Can Res 2010.

first: Göran

last: Jönsson

first: Christian

last: Busch

first: Stian

last: Knappskog

first: Jürgen

last: Geisler

first: Hrvoje

last: Miletic

first: Markus

last: Ringnér

last: Lillehaug

first: Ake

last: Borg

first: Per

last: Lønning


title: Clinical implications of gene dosage and gene expression patterns in diploid breast carcinoma (transcriptomic profiling)

summary: Genomic and expression profiling using 38K BAC array-CGH and Illumina HT-12 beadchips were performed on 97 diploid invasive breast tumors to assess the impact of gene dosage on gene expression patterns and the effect of other mechanisms on transcriptional levels. Patient stratification was performed according to axillary lymph node status (node-negative, pN0; node-positive, pN1) and overall survival (>8-year survivors; breast cancer-specific mortality within 8 years of diagnosis). Array-CGH results was validated by FISH using tumors showing HER2/neu gene amplification and expression profiling was confirmed using qPCR for 16 transcripts.

overall_design: Total RNA was isolated from fresh-frozen tissue samples

middle: Z

first: Anna

last: Danielsson

first: Szilard

last: Nemes

first: Anikó

last: Kovács

first: Ulla

last: Delle

first: Ghita

last: Fallenius

first: Elin

last: Möllerström

last: Karlsson

first: Khalil

last: Helou


title: Gene expression profiles in CLL

status: Public on Jun 25 2010

city: Rochester

first: Brian

last: Bot

address: 200 1st Street SW

institute: Mayo Clinic

summary: Evaluation of differential expression between CLL patients in a chemoimmunotherapy trial with age-matched controls

overall_design: 41 CLL tumor samples and 11 age matched controls run on both Affy U133A and U133B chips

first: Diane

last: Jelinek

first: Neil

last: Kay


title: Gene Expression Profiling-Based Identification of Molecular Subtypes in Stage IV Melanoma with Different Clinical Outcome

first: Johan

last: Staaf

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

overall_design: Refer to individual Series


title: Toxicogenomic Effect of Burkholderia pseudomallei in a Human Macrophage Cell (THP-1) Model of Acute Melioidosis Using Whole-genome Microarray

status: Public on May 31 2010

city: Augusta

first: Pachiappan

last: Arjunan

state: Georgia

address: 1120 15th ST, Laney walker Blvd,

department: Anatomy, Unit on Retinal Vascular Neurobiology, BMB

institute: NUS, NIH, GRU

summary:
Gene expression profiles of human cell (THP-1) lines exposed to a novel Daboiatoxin (DbTx) isolated from Daboia russelli russelli, and specific cytokines and inflammatory pathways involved in acute infection caused by Burkholderia pseudomallei.
Keywords: Melioidosis, Burkholderia pseudomallei, Daboiatoxin, Cytokines, Inflammation.

sample_organism:
Homo sapiens
Burkholderia pseudomallei

overall_design:
1.	Group I:- Human monocytic macrophage (THP-1) cell lines grown in the culture medium without any bacterial infection served as untreated control group (Three Biological Replicates).
2.	Group II:- THP-1 cells were infected with Burkholderia pseudomallei (A600 nm = OD 0.6, ~5 x 107 cfu/ml) for 24h served as a disease control group (Three Biological Replicates).
3.	Group III:- THP-1 cells were infected with B. pseudomallei and treated with Daboiatoxin (0.5 mM) isolated from Daboia russelli russelli venom served as a treatment group (Three Biological Replicates).
4.	Group IV:- THP-1 cells were infected with B. pseudomallei (A600 nm = OD 0.6, ~5 x 107 cfu/ml) treated with standard antimicrobial drug ceftazidime (10mg/ml) served as a drug control (Three Biological Replicates).
5.	Group V:- THP-1 cells were exposed to Daboiatoxin (0.5 mM) without bacterial infection (Three Biological Replicates).

first: Perumal

last: Ramar

first: Gopalakrishnakone

last: Ponnampalam

first: Tin

middle: A

last: Lay

first: Eong

last: Ooi


title: Human colorectal cancer cell lines treated with several inhibitors of PI3Kinase – AKT signaling pathway

status: Public on Jun 14 2010

first: Karsten

last: Jürchott

address: Luisenstraße

department: Rahel Hirsch Center

institute: BIH at Charité

summary:
Signal transduction processes mediated by phosphatidyl inositol phosphates affect a broad range of cellular processes such as cell cycle progression, migration and cell survival. The protein kinase AKT is one of the major effectors in this signaling network. Chronic AKT activation contributes to oncogenic transformation and tumor development. Therefore, new small drugs were designed to block AKT activity for cancer treatment.
Here we characterize the biological effects of the phosphatidyl inositol phosphate analogs SH-5 and SH-6 in colorectal cancer cell lines. We demonstrate that the two compounds did not reduce AKT phosphorylation significantly in the presence of growth factors, but induce a broad range of morphological and transcriptional alterations. Transcriptomic profiling in inhibitor-treated SW480 cells revealed a cluster of down- regulated genes associated with mitosis. Moreover, the treatment of SW480 cells with either SH-5 or SH-6 caused the formation of binucleated cells as a result of a specific abscission defect.

overall_design: The cells were treated with certain inhibitors for 48 hours. We used one sample per cell line treated with DMSO as a control, and one sample for each of the treatments.

first: Till

last: Krech

first: Reinhold

last: Schäfer


title: T-cell development

city: Wageningen

first: Dick

middle: de

last: de Ridder

address: Droevendaalsesteeg 1

department: Plant Sciences

country: Netherlands

institute: Wageningen University

summary: T cells develop from progenitors that migrate from the bone marrow into the thymus. Thymocytes are subdivided roughly as being double negative (DN), double positive (DP), or single positive (SP), based on the expression of the CD4 and CD8 coreceptors. The DN stage is heterogeneous and can be subdivided into four distinct subsets in mice based on the expression of CD44 and CD25. In human, three distinct DN stages can be recognized: a CD34+CD38−CD1a− stage that represents the most immature thymic subset and the consecutive CD34+CD38+CD1a− and CD34+CD38+CD1a+ stages. Human DN thymocytes mature via an immature single positive (ISP CD4+) and a DP stage into CD4+ or CD8+ SP T cells that express functional T cell receptors (TCR) and that exit the thymus. In this study, gene expression  was measured in each of these nine stages.

overall_design: CD34+ lineage negative “stem cell-like” cells were obtained from umbilical cord blood (UCB) and CD34+CD38− CD1a−, CD34+CD38+CD1a−, CD34+CD38+CD1a+, ISP CD4+, DP CD3−, DP CD3+, SP CD4+, and SP CD8+ subpopulations were obtained from thymi which represented consecutive stages of T cell development. Thymi were obtained as surgical tissue discards from children aged 7 wk to 3 yr (median of 6 mo) undergoing cardiac surgery at the Erasmus MC Rotterdam, with informed consent from the parents. The children did not have immunological abnormalities. Thymocytes were isolated by cutting the thymic lobes into small pieces and squeezing them through a metal mesh, and stored at +-80C until further analyses. Mononuclear cells (MNCs) were isolated by Ficoll-Paque (Amersham Biosciences) density centrifugation from human umbilical cord blood (UCB) obtained from full-term normal deliveries and from peripheral blood of healthy volunteers. All samples were obtained according to the guidelines of the Medical Ethical Committee of the Erasmus MC that also approved the human studies. For the isolation of CD34+ lineage (lin)- UCB cells and thymocyte subsets, total MNCs or thymocytes from five donors were pooled to reduce intrasample variation. After thawing, pooling, and Ficoll density separation, thymocytes were labeled with fluorochromeconjugated monoclonal antibodies. To isolate the CD34+ lin- UCB cells, CD34+CD38-CD1a-, CD34+CD38+CD1a-, and CD34+CD38+CD1a+ thymocytes, magnetic beads were used to enrich for CD34+ cells. For isolation of the ISP population, thymocytes were depleted of CD3-expressing cells using magnetic beads. All magnetic beads were used according to the manufacturer’s protocol. After MACS sorting, the enriched cells were labeled with fluorochrome-conjugated monoclonal antibodies for further purification by high speed cell sorting. All cell sorting was performed on a FACS DiVa cell sorter (BD Biosciences). Monoclonal antibodies used, with the clone in brackets: CD4-FITC (SK3), CD38-FITC (HB7), TCRGD- FITC (WT31), CD1a-RDI (T6), CD3-PE (SK7), CD16-PE (B73.1), CD19-PE (4G7), CD56-PE (M431), TCRGD-PE (11F2), CD3-PerCP (SK7), CD8- PerCP (SK1), CD19-PerCP (SJ25C1), CD3-APC (SK7), CD8-APC (SK1) and CD34-APC (8G12) (all obtained from BD Biosciences), CD13- RDI (MY7), and CD33-RDI (906) (obtained from Beckman Coulter). Purity of sorted population was determined on the FACS Calibur (BD Biosciences) and shown to be >95% for all populations. All populations were sorted twice using different donors for each sort.

first: Wim

last: Dik

first: Karin

last: Pike-Overzet

first: Floor

last: Weerkamp

first: Edwin

last: de Haas

first: Miranda

middle: R

last: Baert

first: Peter

last: van der Spek

first: Esther

last: Koster

first: Marcel

middle: J

last: Reinders

first: Jacques

last: van Dongen

first: Anton

middle: W

last: Langerak

first: Frank

last: Staal


title: Analysis of genes in HNSCC cells regulated following exposure to cisplatin and involved in tumourigenesis

city: Woolloongabba

first: Kim

last: Poth

state: Qld

address: Ipswich Rd

country: Australia

institute: Diamantina Institute

summary: Analysis of genes regulated by cisplatin exposure, using non-tumourigenic keratinocytes to filter out genes regulated following cisplatin exposure that are unlikely to be involved in tumourigenesis. Results identify genes that may be important in mediating an increase in tumourigenic potential in cisplatin-resistant HNSCC cells.

overall_design:
Where indicated, cisplatin (CDDP)-treated cells were incubated after treatment to allow susceptible cells to undergo cell death. Two time points were used to investigate earlier and later gene expression changes following cisplatin treatment. The FaDu and Detroit-562 cell lines were sorted at the indicated times to obtain the smallest 10-20% of cells as these had been previously found to be the cells with the highest viability following treatment.
Total RNA was obtained from head and neck squamous cell carcinoma (HNSCC) cells (FaDu, Detroit-562) at 2 timepoints subsequent to cisplatin treatment, and compared to untreated control cells. Genes differentially expressed in the same direction in non-tumourigenic human epidermal keratinocytes (HEKs) were excluded from subsequent analyses as these were deemed unlikely to be involved in mediating tumourigenic potential.
There were a total of 9 conditions analysed, with 3 biological replicates for each, for a total of 27 samples.

The supplementary file 'GSE20185_non-normalized.txt' contains non-normalized data for Samples GSM506367-GSM506393.

first: Nicholas

last: Saunders


status: Public on May 25 2010

city: Trondheim

first: Per

last: Winge

address: Høgskoleringen 5e

department: Department of Biology

country: Norway

institute: Norwegian University of Science and Technology

summary:
Transcriptional profiling of an Fd-GOGAT1/GLU1 mutant in Arabidopsis thaliana reveals a multiple stress response and extensive reprogramming of the transcriptome
Glutamate plays a central position in the synthesis of a variety of organic molecules in plants and is synthesised from nitrate through a series of enzymatic reactions. Glutamate synthases catalyse the last step in this pathway and two types are present in plants: NADH- or ferredoxin-dependent. Here we report a genome wide microarray analysis of the transcriptional reprogramming that occurs in leaves and roots of the A. thaliana mutant glu1-2 knocked-down in the expression of Fd-GOGAT1 (GLU1; At5g04140), one of the two genes of A. thaliana encoding ferredoxin-dependent glutamate synthase.

overall_design: Rosette leaves and roots from the glu1-2 mutant, which is a T-DNA knockout of a ferredoxin dependent glutamate synthase in Arabidopsis (locus ID: At5g04140), were analyzed on Affymetrix microarrays. As a reference control, leaves and roots from Col(0) plants were used. The glu1-2 mutant is derived from a Col(0) accession. Four independent biological replicas from leaves and roots were used in the analysis (from both glu1-2 and Col(0) reference). In total 16 hybridizations were done.

first: Ralph

last: Kissen

first: Diem

middle: H

last: Tran

first: Tommy

middle: S

last: Jørstad

first: Torfinn

last: Sparstad

first: Tone

last: Christensen

first: Atle

middle: M

last: Bones


title: Gene expression pattern of alveolar macrophages of allergic asthmatics in comparison with control subjects

city: Chicoutimi

first: Catherine

last: Laprise

state: Qc

address: 555 Boul. Université

institute: Université du Québec à Chicoutimi

summary: The implication of alveolar macrophages (AM) in asthma, a Th2 disease, has not been well characterized. Thus, the goal of this study is to better characterize AM phenotype of allergic asthmatic compared with normal subjects using genomic expression analyses. Microarray analyses were performed with AM isolated from bronchoalveolar lavage. Robust multiarray analysis (RMA) normalization and Smyth’s moderated t test were used to select differentially expressed genes. Fifty differentially expressed genes were identified. Nineteen have been classified in categories linked to stress or immune responses and among them; nine are part of the heat shock protein (HSP) family. Difference of expression for three (HSPD1, PRNP, SERPINH1) of the five selected genes were validated using real-time reverse transcription–polymerase chain reaction. Enzyme linked immunosorbent assay was used to measure the protein level of heat shock protein 60 (HSP60), the protein encoded by HSPD1, and showed difference in AM protein level between allergic asthmatic and control subjects. In summary, this study suggests that HSP gene family, particularly HSP60, is involved in AM functions in a context of allergic asthma. These results also support the involvement of AM immune functions in the development of an allergic asthmatic response.

overall_design: Ten alveolar macrophage samples from bronchoalveolar lavages have been studied. Five of them are from allergic asthmatic subjects and five from control subjects (without allergy and asthma).

first: Anne-Marie

last: Madore

first: Alyse

middle: Y

last: Bissonnette

first: Michel

last: Laviolette

first: Stephanie

last: Perron

first: Véronique

last: Turmel


title: Expression data from testes and abdomen in fertile and sterile introgression males

status: Public on May 19 2010

city: Beijing

first: Jin

last: Xu

address: Beijing Institute of Genomics, Chinese Academy of Sciences No.7 Beitucheng West Road, Chaoyang District, Beijing 100029, PR China

institute: BIG,CAS

summary:
Postmating reproductive isolation is often manifested as hybrid male sterility, for which X-linked genes are over-represented. In contrast, X-linked gene are significantly under-represented among testis-expressing gene.This seeming contradiction may be germane to the X:autosome imbalance hypothesis on hybrid sterility ,in which the X-linked effect is mediated mainly through the misexpression of autosomal genes.
We compared gene expression in fertile and sterile males in the hybrids between two Drosophila species. These hybrid males differ only in a small region of the X chromosome containing the OdsH locus of hybrid sterility. Of genes expressed in the testis, autosomal genes were indeed more likely to be misexpressed than X-linked genes under the steriizing action of OdsH.

overall_design: We compared gene expression between D. simulans males that carried either a fertile or sterile introgression (referred to as F or S males, respectively) from D. mauritiana. The introgressions span approximately 1/10 of the X chromosome, but the difference between the two introgressions is only about 3 Kb which contains exons 3 – 4 of OdsH. In short, F and S males have the same genetic background with respect to species origin, except the source of a portion of the OdsH gene. Three separate extractions and hybridizations were carried out for the RNA samples derived from testes and abdomens in each of two introgression lines.

first: Xuemei

last: Lu

first: Chung-I

last: Wu


title: Interaction between the light environment and the Arabidopsis wound response

status: Public on Apr 22 2010

first: Rekin's

last: Janky

address: Herestraat 49 Box 816

institute: VIB

summary:
We have previously identified a significant increase in chloroplast reactive oxygen species in wounded leaves of Arabidopsis and other plants, which is light-dependent (Flor-Henry et al. (2004) BMC Plant Biology 4:19). The aims of this study were to (i) examine the early response to mechanical wounding in Arabidopsis leaves, (ii) test the hypothesis that light-dependent chloroplast ROS may play a role in signalling for changes in gene expression in wounded leaves, and (iii) examine the broader impact of the light environment on the wound response in Arabidopsis.

Keywords: Stress response

overall_design: The experiment was a two-by-two factorial design, with wounding and light as the two variables. In each replicate, there are 4 treatments: unwounded/light, unwounded/dark, wounded/light, wounded/dark. Three independent biological replicate experiments were performed, with one array hybridisation performed per treatment.

first: Michael

last: Roberts

first: Krishna

last: Morker

first: Dawn

last: Worrall


title: Microarray analysis of cross-talks between Jasmonate acid and ethylene signaling in Arabidopsis seedlings

status: Public on May 11 2010

city: Peking

first: Hongwei

last: Guo

address: No.5 Yiheyuan Road

department: College of life sciences

institute: Peking University

summary: Jasmonate and ethylene are two important plant hormones contributing plant resistance to biotic stresses synergistically. Our experimental results showed that two ethylene activated transcription factors (EIN3/EIL1) integrated both jasmonate and ethylene signaling in multiple developmental and defense events. To understand the importance of EIN3/EIL1 in jasmonate signaling, we utilized microarray analysis to identify how much the jasmonate regulated genes are governed by EIN3/EIL1. Our results indicated that EIN3/EIL1 act sequentially in a cascade of transcriptional regulation initiated by jasmonate.

overall_design: Compare the JA regulated genes in Col-0, coi1-2 and ein3 eil1 to identify how much transcripts are dependent on COI1 or EIN3/EIL1

first: Ziqiang

last: Zhu

first: Zhiqiang

last: Jiang


title: Involvement of the Chromatin Modifier ATX1 and of the Arabidopsis Myotubularin Homolog (MYO1) in the Response to Drought

status: Public on Apr 21 2010

city: Lincoln

first: Jean-Jack

last: Riethoven

state: NE

address: 1901 Vine Street

department: Beadle Center for Biotechnology

institute: University of Nebraska-Lincoln

summary:
Plants respond to environmental stresses by altering transcription of genes involved in the response. The chromatin modifier ATX1 influences gene expression and factors that modulate ATX1 activity would affect indirectly the expression of ATX1-regulated genes.  Here, we demonstrate that dehydration is such a factor indicating that ATX1 is involved in the plant’s response to drought. In addition, we show that a hitherto unknown Arabidopsis gene, At3g10550, encodes MYO1, a phosphoinositide 3’-phosphatase related to the animal myotubularins. By a functional genomics approach, we show that ATX1 and MYO1 participate in overlapping drought-response pathways. The shared set of genes, representing the ultimate targets of an ATX1-MYO1 signaling mechanism responding to drought, provided insights into the relationship of the epigenetic factor and the lipid phosphatase from the other end of the response pathway.

Keywords: control/treatment

overall_design: Arabidopsis thaliana Col0 wild type, atx1 mutant, and MYO-OX line RNA was isolated from control (watered) and treatment (water-deficit) samples for analysis on microarrays with two biological reps.

first: Yong

last: Ding

first: Hanna

last: Lapko

first: Ivan

last: Ndamukong

first: Yuannan

last: Xia

first: Ayed

last: Al-Abdallat

first: Sreedevi

last: Lalithambika

first: Monther

last: Sadder

first: Abdelaty

last: Saleh

last: Fromm

first: Gouqing

first: Zoya

last: Avramova


title: ATF3 is a positive regulator of human IFN gene expression

status: Public on Apr 11 2010

city: Turku

first: Sanna

last: Filén

address: Tykistökatu 6

institute: Turku Centre for Biotechnology

summary: The aim of this study was to identify genes regulated by IL-12, IL-18 and IFN-alpha during early differentiation of human Th1 cells

overall_design: Human cord blood CD4+ T cells were activated via TCR and cultured in the presence of IL-12, IFN-alpha or IL-12+IL-18. Cytokine induced gene expression was compared to activation only after 2h, 6h or 48h of cell culture. 12 samples were analyzed in total.

first: Emmi

last: Ylikoski

first: Subhash

last: Tripathi

first: Anne

last: West

first: Mari

last: Björkman

first: Joel

last: Nyström

first: Helena

last: Ahlfors

first: Eleanor

last: Coffey

first: Kanury

middle: V

last: Rao

first: Omid

last: Rasool

first: Riitta

last: Lahesmaa


title: Cooperative interaction between retinoic acid receptor-alpha and estrogen receptor in breast cancer.

status: Public on Jun 09 2010

city: Cambridge

first: Roslin

last: Russell

address: Li Ka Shing Centre, Robinson Way

institute: Cambridge Research Institute, Cancer Research UK

summary: Retinoic acid receptor-alpha (RAR alpha) is a known estrogen target gene in breast cancer cells. The consequence of RAR alpha induction by estrogen was previously unknown. We now show that RAR alpha is required for efficient estrogen receptor-alpha (ER)-mediated transcription and cell proliferation. RAR alpha can interact with ER-binding sites, but this occurs in an ER-dependent manner, providing a novel role for RAR alpha that is independent of its classic role. We show, on a genome-wide scale, that RAR alpha and ER can co-occupy regulatory regions together within the chromatin. This transcriptionally active co-occupancy and dependency occurs when exposed to the predominant breast cancer hormone, estrogen--an interaction that is promoted by the estrogen-ER induction of RAR alpha. These findings implicate RAR alpha as an essential component of the ER complex, potentially by maintaining ER-cofactor interactions, and suggest that different nuclear receptors can cooperate for effective transcriptional activity in breast cancer cells.

overall_design: RAR alpha silenced breast cancer MCF-7 cell lines or control siRNA in the presence of estrogen or a vehicle. MCF-7 cells were hormone-depleted for 3 d and treated with 100 nM estrogen for 12 h. There were three biological replicates for each of the four different groups.

first: Caryn

last: Ross-Innes

first: Jason

last: Carroll


title: Transcript profiling of auxin/cytokinin crosstalk in the Arabidopsis primary root apex

status: Public on Apr 20 2010

city: Loughborough

last: Nottingham Arabidopsis Stock Centre (NASC)

address: Sutton Bonington Campus

department: School of Biosciences, University of Nottingham

summary: AtIPT8/pga22 seedlings (gain-of-function mutant in Ws background; Sun et al. 2003, Plant Physiology 131, pp167-176) were grown on vertical plates for 7 days in LD. The seedlings were then incubated directly on the plate with medium containing 5 uM 17-beta-estradiol (for induction of the IPT8 gene) or 5 uM trans-zeatin for 12 and 24 h. 5 mm primary root tips were harvested from the seedlings and pooled for microarray analysis. Total RNA was isolated from the samples with the RNeasy Plant Mini Kit from Qiagen.

overall_design: 14 samples were used in this experiment.

first: Karin

last: Ljung


title: Intergrated expression profiling and ChIP-SEQ analyses of ChREBP-mediated glucose response network (expression data only)

status: Public on Jun 04 2010

city: incheon

first: DeokHoon

last: Kim

address: 7-45 songdo-dong yeonsu-ku

country: South Korea

institute: Lee Gil Ya cancer and diabets institute

summary: We identified ChREBP-binding regions from the DNA of human hepatocellular targets as well as previously-known targets

overall_design: Total RNA from hepG2 cell line

first: Yoon-Seung

last: Jung

first: Deokhoon

first: Yong-seok

last: Lee

first: Ha-Jung

first: Jung-Youn

last: Han

first: Seung-Soon

last: Im

first: Je-Keun

last: Kwon

first: Yong-Ho

last: Ahn

first: Hee-Sook

last: Jun

first: Sung-Min

first: Ji-Young

last: Cha


title: Preferred analysis methods for Affymetrix GeneChips. II. An expanded, balanced, wholly-defined spike-in dataset

status: Public on Apr 15 2010

city: Buffalo

first: Qianqian

last: Zhu

address: 701 Ellicott St.

department: Biochemistry

institute: State University of New York at Buffalo

summary: We present a new wholly defined Affymetrix spike-in dataset consisting of 18 microarrays. Over 5700 RNAs are spiked in at relative concentrations ranging from 1- to 4-fold, and the arrays from each condition are balanced with respect to both total RNA amount and degree of positive- versus negative-fold change. We use this new “Platinum Spike” dataset to evaluate microarray analysis routes and contrast the results to those achieved using our earlier Golden Spike dataset.

overall_design: PCR products from 5725 Drosophila Gene Collection release 1.0 (DGCr1) cDNA clones were collected into 28 distinct pools, and three independent in vitro transcription and labeling reactions were performed for each pool. Labeled cRNAs from each individual pool were then added at specified amounts to samples A and B to achieve the desired fold change differences between samples. 24 cRNAs generated from DGCr2 cDNA clones were added to each sample in known concentrations before hybridization.

first: Marc

last: Halfon


title: Enhancement of metastasis by spontaneous ploidy doubling of breast cancer cell MDA-MB-231.

status: Public on Jun 01 2010

city: Princeton

first: Yibin

last: Kang

state: NJ

address: LTL 254, Washington Road

institute: Princeton University

summary:
MDA-MB-231 bone-metastatic subline 1833 and lung metastatic subline 4175 underwent spontaneous ploidy doubling in culture, i.e. the genome approximately duplicated itself gradually. The modal- and hyper-ploid subpopulations during the ploidy transition were sorted into two separate sublines, 1833-Modal and 1833-Hyper for 1833, 4175-Modal and 4175-Hyper for 4175. Their expresssion patterns were compared to each other as well as to other MDA-MB-231 sublines isolated previously by Kang et al. 2003 and Minn et al. 2005.

Keywords: Cell type comparison

overall_design: 19 cell lines were analyzed, including the parental line MDA-MB-231, modal-ploid sublines 1833-Modal and 4175-Modal, hyper-ploid sublines 1833-Hyper and 4175-Hyper, strongly bone-metastatic lines 1833 (the original subline after short culture), 2274, 2268 and 2269, weakly bone-metastatic lines 2293, 2295 and 2297, strongly lung-metastaic lines 4142, 4173, 4175 (the original subline after short culture) and 4180, and weakly lung-metastatic lines SCP6, SCP21 and SCP26. Single sample for each line.

first: Xin

last: Lu


title: Histologically normal epithelium from breast cancer patients and cancer-free prophylactic mastectomy patients

city: Boston

first: Kelly

last: Graham

address: 650 Albany Street

department: Hematology/Oncology

institute: Boston University School of Medicine

summary:
Gene expression in histologically normal epithelium from breast cancer patients and cancer-free prophylactic mastectomy patients share a similar profile
Introduction: We hypothesized that gene expression in histologically normal epithelium (NlEpi) would differ in breast cancer patients (HN) compared to usual-risk controls undergoing reduction mammoplasty (RM), and that gene expression in NlEpi from cancer-free prophylactic mastectomies from high-risk women (PM), would resemble HN gene expression. Methods: We analyzed gene expression in 73 NlEpi samples microdissected from frozen tissue. In 42 cases, we used Affymetrix HU133A microarrays to compare gene expression in 18 RM vs 18 age-matched HN (9 ER+, 9 ER-) and 6 PM. Data were validated with qPCR in 31 independent NlEpi samples (8 RM, 17 HN, 6 PM). Results: 98 probesets (86 genes) were differentially expressed between RM and HN samples. Perfoming supervised hierarchical analysis with these 98 probesets, PM and HN samples clustered together, away from RM samples. qPCR validation of independent samples was high (84%) and uniform in RM vs HN, and lower (58%), but more heterogeneous, in RM vs PM. The 86 genes were implicated in many processes including transcription and the MAPK pathway. Conclusion: Gene expression differs between NlEpi of cancer cases and controls. The cancer cases' profile can be discerned in high-risk NlEpi. This suggests that the profile is not an effect of the tumor, but may mark increased risk and reveal breast cancer's earliest genomic changes.
We determined that 98 probesets significantly differed between reduction mammoplasty and histologically normal epithelium from breast cancer patients. We also found that the histologically normal epithelium from prophylactic mastectomy patients' gene expression was more similar to histologically normal epithelium from breast cancer patients' than to reduction mammoplasty patients' gene expression. These results demonstrate that gene expression differs between NlEpi of cancer cases and controls. The cancer cases’ profile can be discerned in high-risk NlEpi. This suggests that the profile is not an effect of the tumor, but may mark increased risk and reveal breast cancer's earliest genomic changes.

overall_design: 42 total laser capture microdissected histologically normal breast tissue samples were analyzed with Affymetrix HU133A microarrays. 36 samples were age-matched between reduction mammoplasty (n=18) and histologically normal epithelial samples from breast cancer patients (n=18; 9ER+, 9ER-). 6 histologically normal epithelial samples from prophylactic mastectomy patients were then compared to data generated from the original 36 sample comparison. Sample numbers correspond to individual patient samples.

first: Carol

last: Rosenberg

first: Paola

last: Sebastiani


title: Anthracycline treatment and resistance in four human cancer cell lines (HGU133A)

city: Budapest

first: Balazs

last: Györffy

address: Bókay 53

country: Hungary

institute: Hungarian Academy of Sciences

summary:
Reliable clinical tests for predicting cancer chemotherapy response are not available and individual markers failed to correctly predict resistance against anticancer agents. We hypothesized that gene expression patterns attributable to chemotherapy-resistant cells can be used as a classification tool for chemoresistance and provide novel candidate genes involved in anthracycline resistance mechanisms. We contrasted the expression profiles of 4 different human tumor cell lines of gastric, pancreatic, colon and breast origin and of their counterparts resistant to the topoisomerase inhibitors daunorubicin or doxorubicin. We also profiled the sensitive parental cells treated with doxorubicin for 24h. We interrogated Affymetrix HGU133A and U95A arrays independently. We applied two independent methods for data normalization and used Prediction Analysis of Microarrays (PAM) for feature selection. In addition, we established data sets related to drug resistance by using a “virtual array” composed of features represented on both types of oligonucleotide arrays. We identified 71 candidate genes associated with doxorubicine/daunorubicine resistance. To validate the microarray data, we also analyzed the expression of 12 selected genes by quantitative RT-PCR or immunocytochemistry, respectively. While the comparison of drug-sensitive versus drug-resistant cells yields candidates associated with drug resistance, the 24h treatment of sensitive parental cells produced a distinct transcriptional profile related to short-term drug effects.
Keywords: cell type and treatment comparison

overall_design: See Summary. Note: this series includes Affymetrix HGU133A chips (difference between resistance and treatment response).


title: Comparison between NuGEN's WT-Ovation Pico and One-Direct Amplification Systems

status: Public on May 26 2010

city: Gainesville

first: Lauren

last: McIntyre

state: FL

address: 2033 Mowry Rd

department: Department of Molecular Genetics and Microbiology

institute: University of Florida

summary: Differential gene expression between groups of homogenous cell types is a biological question whose time has come.  RNA can be extracted from small numbers of cells, such as those isolated by laser capture microdissection, but the small amounts obtained often require amplification to enable whole genome transcriptome profiling by technologies such as microarray analysis and RNA-seq.  Recently, advances in amplification procedures make amplification directly from whole cell lysates possible.  The aim of this study was to compare two amplification systems for variations in observed RNA abundance attributable to the amplification procedure for use with small quantities of cells isolated by laser capture microdissection.   Arabidopsis root cells undergoing giant cell formation due to nematode infestation and un-infested control root cells were laser captured and used to evaluate 2 amplification systems.  One, NuGEN's WT-Ovation Pico amplification system, uses total RNA as starting material while the other, NuGEN's WT-One-Direct Amplification system, uses lysate containing the captured cells.   The reproducibility of whole genome transcript profiling and correlations of both systems were investigated after microarray analysis.  The NuGEN WT-Ovation One-Direct system was less reproducible and more variable than the NuGEN WT-Ovation Pico system.  The NuGEN WT-Ovation Pico Amplification kit resulted in the detection of thousands of genes differentially expressed genes between giant cells and control cells.  This is in marked contrast to the relatively few genes detected after amplification with the NuGEN WT-Ovation One-Direct Amplification kit.

overall_design: Evaluation of each amplification system consisted of three biological replicates per treatment (control root cells or giant cells) with one biological replicate split into three technical replicates for a total of 10 samples per amplification procedure.  RNA samples for amplification with the NuGEN WT-Ovation Pico kit were isolated from 150 control cells or from 80 giant cells using the PicoPure RNA Isolation Kit (Arcturus, Mountain View, USA).  For amplification with the NuGEN WT-Ovation One-Direct kit, samples containing 150 control or 80 giant cells were collected directly into 2ul of the NuGEN lysis buffer.  RNA amplifications were carried out according to the respective kits’ protocols.

first: Alison

last: Morse

first: Valentina

last: Carballo

first: Donald

last: Baldwin

first: Christopher

middle: G

last: Taylor


title: OCT4 Knockdown in human embryonic stem cells

status: Public on Apr 05 2010

city: Singapore

first: Justin

middle: Jeyakani

last: Joseph Gnanakkan

state: Singapore

address: 60, Biopolis street

department: Computational and Systems Biology

country: Singapore

institute: Genome Institute of Singapore

summary: We studied the genomic locations of three key regulatory proteins (OCT4, NANOG and CTCF) in human and mouse embryonic stem (ES) cells [see Series GSE20650]. To identify the conserved and unique human OCT4 targets, we performed an OCT4 RNAi knock-down experiment. We find that species-specific transposable elements have profoundly altered the transcriptional circuitry of pluripotent stem cells.

overall_design:
To identify the mRNA targets of OCT4:
12 samples were collected in total. Each sample is done in triplicate and samples were collected at 2 different time point, 2 days and 3 days after transfection. Luciferase knockdown serves as negative control and OCT4 knockdown is the experimental sample.

first: G

last: Bourque

first: Huck-Hui

last: Ng


title: Expression data from Arabipdosis msh1 recA3 double mutant under heat stress

status: Public on Mar 31 2010

first: Jaime

last: Davila

department: Plant Science Innovation Center

country: USA

institute: University of Nebraska

summary:
In Arabidposis thaliana, the msh1 recA3 double mutant shows an extensive mitochondrial genome rearrangement and displays pronounced thermotolerance.
We use microarray analysis to characterize genes and their response in the double mutant to a heat shock experiment in which plants were exposed to a temperature of 37 C for two hours.

overall_design: Wild type and double mutant plant were exposed to a temperature of 37 C for two hours and RNA samples were collected for the wild type and the double mutant before and after the heat shock.

first: Vikas

last: Shedge


title: Multiple Sclerosis Blood Cell mRNA Transcriptome

status: Public on Apr 02 2010

city: Westmead

first: David

middle: Richmond

last: Booth

state: NSW

address: Darcy Rd

department: Immunology

institute: Westmead Millennium Institute

summary: We measured mRNA expression for all known genes in whole blood from 144 individuals, 99 with MS (43 PPMS, 36 RRMS and 20 SPMS). Analysis of gene expression and genotype in these individuals has indicated the dominant genetic association with T cell regulation is matched by the dominant pattern of dysregulation of T cell gene expression in MS and its clinical subtypes.

overall_design:
Whole blood mRNA expression was compared between different types of MS and age-matched healthy control to identify differentially expressed genes between them.

The supplementary file 'GSE17048_non-normalized_data.txt' contains non-normalized data for Samples GSM426595-GSM426738.

first: Kaushal

last: Gandhi


title: Curcumin Extends Lifespan, Improves Healthspan, and Modulates the Expression of Age-Associated Aging Genes in Drosophila melanogaster

status: Public on Apr 06 2010

city: Daejeon

first: Kyu-Sun

last: Lee

address: 111 Gwahangno Yuseong-gu

department: Aging Research Center

institute: KRIBB

summary: Curcumin, a yellow pigment extracted from the rhizome of the plant Curcuma longa (turmeric) has been widely used as a spice and herbal medicine in Asia. It has been suggested to have many biological activities such as anti-oxidative, anti-inflammatory, anti-cancer, chemopreventive, and anti-neurodegenerative properties. We evaluated the impact of curcumin on lifespan, fecundity, feeding rate, oxidative stress, locomotion and gene expression in two different wild type Drosophila melanogaster strains, Canton-S and Ives, under two different experimental conditions.  We report that curcumin extended the lifespan of two different strains of Drosophila and was accompanied by protection against oxidative stress, improvement in locomotion and chemopreventive effects. Curcumin also modulated the expression of several aging related genes (genes with age-dependent changes in gene expression) such as mth, thor, InR, and JNK.

overall_design: In order to evaluate the impact of curcumin and aging on gene expression, we first determined which genes were affected by aging alone in Canton S flies. Age-related changes in gene expression were defined as changes in expression levels that occurred between 3 and 40 days of age (median lifespan). Among the 18,880 probe sets in the Affymetrix GeneChip® Drosophila Genome 2.0 Array, 1,383 genes (Data on file, 7.3%, P < 0.05) had statistically significant changes in expression levels during this time frame. We next determined the effect of curcumin on gene expression levels in young and aged Canton S flies. Gene expression were defined as changes in expression levels that occurred between 3 and 40 days of aged flies with or without curcumin-feeding.

first: Kweon

last: Yu

first: Kyung-Jin

last: Min

first: Mahtab

last: Jafari


title: DECREASED FIBRONECTIN PRODUCTION SIGNIFICANTLY CONTRIBUTES TO DYSREGULATED REPAIR OF ASTHMATIC EPITHELIUM

city: Seattle

first: James

middle: William

last: MacDonald

state: WA

address: 4225 Roosevelt Way NE

department: Environmental and Occupational Health Sciences

institute: University of Washington

summary: Rationale: Damage to airway epithelium is followed by deposition of extracellular matrix (ECM) and migration of adjacent epithelial cells. We have shown that epithelial cells from asthmatic children fail to heal a wound in vitro. Objectives: To determine whether dysregulated ECM production by the epithelium plays a role in aberrant repair in asthma. Methods: Airway epithelial cells (AEC) from children with asthma (n=36), healthy atopic (n=23) and healthy non-atopic controls (n=53) were investigated by microarray, gene expression and silencing, transcript regulation analysis and ability to close mechanical wounds. Results: Wound repair of AEC from healthy and atopic children were not significantly different and were both faster than AEC from asthmatics. Microarray analysis revealed differential expression of multiple gene sets associated with repair and remodeling in asthmatic AEC. Fibronectin (FN) was the only ECM component whose expression was significantly lower in asthmatic AEC. Expression differences were verified by qPCR and ELISA, and reduced FN expression persisted in asthmatic cells over passage. Silencing of FN expression in non-asthmatic AEC inhibited wound repair, while addition of FN to asthmatic AEC restored reparative capacity. Asthmatic AEC failed to synthesize FN in response to wounding or cytokine/growth factor stimulation. Exposure to 5’, 2’deoxyazacytidine had no effect on FN expression and subsequent analysis of the FN promoter did not show evidence of DNA methylation. Conclusions: These data show that the reduced capacity of asthmatic epithelial cells to secrete FN is an important contributor to the dysregulated AEC repair observed in these cells.

overall_design: 16 arrays, 2 experimental groups, asthma atopic, AA, and healthy non-atopic, HN.

first: Richard

middle: P

last: Beyer

first: Anthony

last: Kicic

first: Teal

last: Hallstrand

first: Erika

middle: N

last: Sutanto

first: Paul

middle: T

last: Stevens

first: Michael

last: Kobor

last: Taplin

first: Peter

middle: D

last: Paré

first: Stephen

last: Stick

first: Darryl

last: Knight


title: Expression data identifying hypermethylated genes associated with acquired cisplatin resistance

status: Public on Apr 01 2010

city: Baltimore

first: Xiaofei

last: Chang

state: MD

address: 1550 Orleans Street, CRBII, Rm574A

department: Otolaryngology

institute: Johns Hopkins University

summary:
Treatment-related DNA hypermethylation may play a role in creating drug resistant phenotypes by inactivating genes that are required for cytotoxicity, but there have been no genome-wide studies to systematically investigate methylation of individual genes following exposure to chemotherapy.
We used microarrays and a pharmacologic unmasking protocol in isogenic cisplatin-sensitive and -resistant cell lines to identify genes that were down-regulated in cisplatin-resistant cells and could be re-activated by the DNA methyltransferase inhibitor 5-Aza-2'-deoxycytidine (5-Aza-dC). We identified several hundred genes that were down-regulated in each resistant cell line. Of these, 30 genes were common to > 2 cell lines, and/or reported to be down-regulated in previous studies. siRNA knockdown of two candidate genes increased cell viability with cisplatin treatment in sensitive parental cell lines

overall_design: Cisplatin-sensitive and -resistant SCC cells and KB and KB cisplatin-resistant clones (n=2) were split to low density and treated with freshly prepared 5 microM 5-Aza-dC dissolved in 50% acetic acid/50% PBS or were mock treated with the same volume of vehicle in the media for 5 days. Subsequently, RNA was extracted and hybridized on Affymetrix U133A microarrays.  Signal intensity and statistical significance was established for each transcript, and a 2-fold decrease in signal in each paired sensitive/resistant cell line in combination with 1.5-fold increase after 5Aza-dC treatment was used to identify candidate genes.

first: Constance

middle: L

last: Monitto

first: Semra

last: Demokan

first: Joseph

middle: A

last: Califano

last: Sidransky