title: Characterization of an Oxaliplatin Sensitivity Predictor in a preclinical Murine Model of Colorectal Cancer

status: Public on Feb 17 2012

first: David

last: Hsu

address: Rm 2167 CIEMAS Bldg, 101 Science Dr.

department: Institute for Genome Sciences and Policy

institute: Duke University

summary: Despite advances in contemporary chemotherapeutic strategies, long term survival still remains elusive for patients with metastatic colorectal cancer. A better understanding of the molecular markers of drug sensitivity to match therapy with patient is needed to improve clinical outcomes. In this study, we used in vitro drug sensitivity data from the NCI-60 cell lines together with their Affymetrix microarray data to develop a gene expression signature to predict sensitivity to oxaliplatin. In order to validate our oxaliplatin sensitivity signature, Patient-Derived Colorectal Cancer Explants (PDCCEs) were developed in NOD-SCID mice from resected human colorectal tumors. Analysis of gene expression profiles found similarities between the PDCCEs and their parental human tumors, suggesting their utility to study drug sensitivity in vivo. The oxaliplatin sensitivity signature was then validated in vivo with response data from 14 PDCCEs treated with oxaliplatin and was found to have an accuracy of 92.9% (Sensitivity=87.5%; Specificity=100%). Our findings suggest that PDCCEs can be a novel source to study drug sensitivity in colorectal cancer. Furthermore, genomic-based analysis has the potential to be incorporated into future strategies to optimize individual therapy for patients with metastatic colorectal cancer.

overall_design: Fourty-two human tumors and murine explants of colorectal origin, both primary colon and of various metastatic sites, were processed for total RNA. The samples included RNA from 14 patient samples in addition to RNA from Patient-Derived Colorectal Cancer Explant (PDCCEs) generated from these 14 patient samples. The PDCCEs were processed as fresh frozen whole tumor in addition to formalin-fixed paraffin-embedded (FFPE) tumors.

first: Mickey

last: Kim

first: Takuya

last: Osada

first: William

last: Barry

first: Xiao

middle: Y

last: Yang

first: Jennifer

last: Freedman

first: Katherine

last: Tsamis

first: Michael

last: Datto

first: Bryan

middle: M

last: Clary

last: Morse

first: Philip

last: Febbo

first: H

last: Lyerly


title: Targeted gene correction of LMNA mutations in patient-specific iPSCs

status: Public on Mar 30 2012

city: San Diego

first: Sachin

last: Kumar

state: California

address: 10010 N.Torrey Pines Road

department: Gene Expression Laboratory

country: USA

institute: Salk Institute for Biological Studies

summary: Gene expression from iPSCs before and after gene correction

overall_design: Comparing gene expression of patient-specific fibroblasts, iPSC and gene corrected iPSC cultures (2 biological replicates)

first: Juan

middle: C

last: Izpisua-Belmonte

first: Guanghui

last: Liu

first: Jing

last: Qu

first: Fei

last: Yi

first: Keiichiro

last: Suzuki

first: Ignacio

last: Sancho-Martinez

first: Emmanuel

last: Nivet

first: Louise

last: Laurent

first: Jessica

first: Rupa

middle: D

last: Soligalla

first: Ilir

last: Dubova

first: April

last: Goebl

first: Jeanne

middle: F

last: Loring


title: miRNA expression, mRNA expression upon miRNA reconstitution, and direct mRNA target identification in prostate cancer cell lines

status: Public on Mar 07 2012

city: Leipzig

first: Kristin

last: Reiche

address: Perlickstr. 1

department: Diagnostics

country: Germany

institute: Fraunhofer Institute for Cell Therapy and Immunology

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

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

overall_design: Refer to individual Series

first: Kerstin

last: Boll

first: Nora

last: Mörbt

first: Antje

middle: K

last: Kretzschmar

first: Katharina

last: Kasack

first: Janina

last: Tomm

first: Gerald

last: Verhaegh

first: Jack

last: Schalken

first: Martin

last: von Bergen

first: Friedemann

last: Horn

first: Jörg

last: Hackermüller


title: Gene expression changes upon Dot1L knockdown and Dot1L inhibitor treatment during reprogramming

status: Public on Mar 01 2012

city: Boston

first: Tamer

middle: T

last: Onder

state: MA

address: One Blackfan Circle

institute: Children's Hospital Boston

summary: Through a loss-of-function approach, we identified that inhibition of the histone methyltransferase, Dot1L, accelerated somatic cell reprogramming, significantly increased the yield of induced pluripotent stem (iPS) cell colonies, and substituted for Klf4 and c-Myc in the reprogramming cocktail. To understand the mechanism by which Dot1L inhibition results in these phenotypes, we carried out gene expression profiling using Affymetrix microarrays.

overall_design:
GSM723207-GSM723224: Embryonic stem cell-derived fibroblasts (dH1fs) were retrovirally transduced in culture with vectors expressing either a control shRNA or an shRNA targeting Dot1L. These cells were then superinfected with either Oct4, Sox2, Klf4 and c-Myc (OSKM) retroviruses or Oct4, Sox2 and c-Myc (OSM) retroviruses. Total RNA was harvested 6 days later. There were three biologic replicates for each condition.

GSM880675-GSM880682: dH1fs were treated with 10uM Dot1L inhibitor (EPZ004777) and then superinfected with Oct4, Sox2, Klf4 and c-Myc (OSKM) retroviruses. Total RNA was harvested 6 days later. There were two biologic replicates for each condition.

first: George

middle: Q

last: Daley


title: The genomic analysis of the interaction between the lactic acidosis and hypoxia response

status: Public on Feb 27 2012

city: Durham

first: Xiaohu

last: Tang

state: NC

address: CIEMAS Rm 2133, 101 Science Dr.

department: Department of Molecular Genetics and Microbiology

summary: Lactic acidosis and hypoxia are two prominent tumor microenvironmental stresses that are both known to exert important influences on gene expression and phenotypes of cancer cells. But very little is known about the cross-talk and interaction between these two stresses. We performed gene expression analysis of MCF7 cells exposed to lactic acidosis, hypoxia and combined lactic acidosis and hypoxia. We found the hypoxia response elicited under hypoxia was mostly abolished upon simultaneous exposure to lactic acidosis. The repression effects are due to loss of HIF-1α protein synthesis under lactic acidosis. In addition, we showed lactic acidosis strongly synergizes with hypoxia to activate the unfold protein response (UPR) and inflammation response which are highly similar to amino acid deprivation responses (AAR). The statistical factor analysis of hypoxia and lactic acidosis responses indicated that ATF4 locus, an important activator in the UPR/AAR pathway, is amplified in subsets of breast tumors and cancer cell lines. Varying ATF4 levels dramatically affect the ability to survive the post-stress recovery from hypoxia and lactic acidosis and may suggest its selection of ATF4 amplification in human cancers. These data suggest that lactic acidosis interacts with hypoxia by both inhibiting the canonical hypoxia response and while activating the UPR and inflammation response. Gain of ATF4 locus may offer survival advantages to allow successful adaptation to frequent fluctuations of oxygen and acidity in tumor microenvironment. Collectively, our studies have provided linkage between the short-term transcriptional responses to the long term selection of the DNA copy number alterations (CNAs) under tumor microenvironmental stresses.

overall_design: RNAs from MCF7 cells exposed to control condition (ambient air ~21% O2, no lactate and neutral pH), lactic acidosis (ambient air, 10 mM Lactate and pH 6.7), hypoxia (1% pO2, no lactate and neutral pH) and the combined lactic acidosis and hypoxia (1% pO2, 10 mM Lactate and pH 6.7) condition for 24 hours were extracted by miRVana kits (Ambion) and hybridized to Affymetrix Human genome 133A 2.0 arrays with standard protocol.

first: Jen-Tsan

last: Chi


title: mRNA expression upon reconstitution of miR-130a, miR-203 and miR-205 in prostate cancer cell line LNCaP

status: Public on Mar 08 2012

summary: Micro RNAs (miRNAs) miR-130a, miR-203 and miR-205 are jointly downregulated in prostate cancer and act as repressors of AR-signaling.  MiRNAs are small non-coding RNAs that regulate the expression of specific mRNA targets mainly by translational repression, mRNA deadenylation or cleavage. Reconstitution of these lost miRNAs in the LNCaP PCa cell line cause morphology changes, growth arrest, and apoptosis, increasing when the miRNAs were co-expressed. Bioinformatic target prediction, mRNA expression and protein expression analysis upon overexpression of these miRNAs congruently identified targets known to be overexpressed in PCa and to be involved in AR trans-activation. This series profiles loss in mRNA expression in LNCaP cells transfected with one of the three miRNAs miR-130a, miR-203 and miR-205 compared to LNCaP cells transfected with a scramble miRNA.

overall_design: We analyzed three arrays each for miR-130a, miR-203, miR-205, and a scramble miRNA.

last: Schutt


title: Proliferation of mouse thyroid cells after partial thyroidectomy

status: Public on Apr 02 2012

city: Bethesda

first: Tsutomu

last: Matsubara

state: MD

address: 9000 Rockville Pike

institute: NCI

summary: While the thyroid has the capacity to grow in response to a stimulus that perturbs the pituitary-thyroid axis, cells involved in this process have not been well characterized.  In this study, partial thyroidectomy was used to produce regeneration.  Histological and gene profiling analyses were carried out using normal mouse thyroid as well as those after partial thyroidectomy.  In the central area of the right or left normal thyroid lobe, a proliferative center was found with the occasional presence of micro-follicles, where BrdU-positive and/or C cells were mainly localized. Two weeks after partial thyroidectomy, the number of BrdU-positive cells and cells with clear or faintly eosionphilic cytoplasm, markedly increased in the central area of the thyroid lobe and the overlapping area close to the cutting edge.  Clear-looking cells had scant cytoplasmic components as determined by electron microscopy; some retained characteristic features of C cells such as the presence of neuroendocrine granules while others retained follicular cell specific features such as those directly facing a lumen with microvilli at the apical side of the cell.  Some of the clear-looking cells were BrdU-positive and expressed FOXA2, the definitive endoderm lineage marker.  Microarray analysis further revealed that partial thyroidectomy affected the expression pattern of genes involved in cellular and/or metabolic process and their regulation categorized as Endocrine System Disorders and Embryonic Development, by Pathway analysis.  These results suggest that cells previously C cells and/or follicular cells may be altered after partial thyroidectomy to become immature cells that participate in the repair and/or regeneration of the thyroid, a process similar to embryonic thyroid development.

overall_design: Total RNAs used for microarray analysis were prepared from laser capture microdissected mouse thyroids of the central (C) and peripheral (P) areas before (N: normal) and after (D: dissected) partial thyroidectomy.   The RNAs obtained were first amplified, which were then subjected to hybridization using 5 NC (central area of the right or left lobe of normal thyroid), 3 NP (peripheral area of the right or left lobe of normal thyroid), 5DC (central area of the right or left lobe of dissected thyroid), 5 DP (peripheral area of the right or left lobe of dissected thyroid), and universal mouse RNAs as a reference.   The 4-way analysis was carried out: NC vs NP vs DC vs DP.

first: Takashi

last: Ozaki

first: Daekwan

last: Seo

first: Shioko

last: Kimura


title: Combined Use of Laser Capture Microdissection and Microarray Analysis Identifies Locally Expressed Disease-Related Genes in Focal Regions of Psoriasis Vulgaris Skin Lesions

status: Public on Jan 30 2012

city: New York

first: Mayte

last: Suarez-Farinas

state: NY

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

institute: Mount SinaiSchool of Medicine

summary: In this study, we sought to establish the usefulness of LCM on cDNA microarray analysis. We reported that LCM samples improved the sensitivity of detection of differentially expressed genes over conventional bulk tissue analysis. We also provided the new information of chemokine and its receptor interaction within psoriatic lesional skin.

overall_design:
For the comparison of gene expression patterns between single and double amplification techniques, total RNA was extracted from blocks of paired lesional and non-lesional psoriatic skin biopsies from four patients.
For LCM experiment, total RNA was extracted from sliced tissue sections of paired lesional and non-lesional psoriatic skin biopsies from three patients.

first: Hiroshi

last: Mitsui

last: Suárez-Fariñas

first: James

middle: G

last: Krueger


title: Identification of genes responsive to change in apical polarity in the breast epithelium

status: Public on Feb 29 2012

city: West Lafayette

first: Sophie

last: Lelievre

state: IN

address: 625 Harrison St

department: Basic Medical Sciences

institute: Purdue University

summary: Differentiation of monolayered epithelia is characterized by the formation of a basoapical polarity axis, except during the early stages of cancer development. Using mammary glandular structures (acini) produced in a three-dimensional cell culture system we have demonstrated that, in order for mammary epithelial cells to exit quiescence and enter the cell cycle, acini have to lose apical polarity. In order to identify the genes dependent on apical polarity that could control cell quiescence, and possibly other aspects of tissue homeostasis, we have used Affymetrix technology microarray analysis of the 22,277 features/genes of the Human Genome U133A 2.0 array Chip in apically polarized and non-polarized breast epithelial acinar cells in three-dimensional culture. Genes commonly down-regulated in two treatments that altered apical polarity compared to control were considered to be dependent on apical polarity status for their transcription.

overall_design: Apically polarized (Control) and two different populations of non-polarized human mammary epithelial cells (18-alpha-glycyrrhetinic acid =AGA, and 5-aza-2'-deoxycytidine =Aza) were used for microarray analysis containing four biological replicates (1-4) for each treatment.  The two treatments that cause loss of apical polarity were compared to reference apically polarized control samples using two different statistical analysis methods (FDR and Holm’s).

first: Jun

last: Cardenas-Mora

first: Cedric

last: Plachot

first: Rebecca

last: Doerge

last: Lelièvre

first: An

last: Lingling


title: STK38 is a Key Regulator of MYC Transcriptional Activity in Human B lymphoma cells

status: Public on Jan 06 2012

first: Mariano

middle: Javier

last: Alvarez

address: 1130 St. Nicholas ave.

department: Systems Biology

institute: Columbia University

summary: Post-translational regulation of the MYC Transcription Factor (TF), including its phosphorylation and ubiquitination, plays an important role in determining cell proliferation and apoptosis and has been implicated in tumorigenesis. Using a computational systems biology approach, followed by biochemical and functional validation, we have characterized the role of the STK38 kinase, an NDR family serine-threonine kinase, as a key modulator of MYC transcriptional activity in human B cells, affecting MYC protein stability in a signal-dependent fashion. Specifically, we show that in human B lymphoma ST486 cells STK38 is a key mediator of BCR pathway signaling, affecting MYC protein turnover and its phosphorylation at Ser62 in kinase-activity-dependent manner. STK38 inactivation abrogates apoptosis following BCR activation while its silencing mediates MYC protein degradation via canonical proteolytic pathways. This suggests that STK38 could provide an effective therapeutic target in MYC-dependent malignancies.

overall_design: ST486 human Burkitt's lymphoma cells were transduced with STK38 shRNA lentiviral vectors.


title: Host response and dysfunction in the CNS during chronic simian immunodeficiency virus infection

status: Public on Jan 29 2012

city: Omaha

first: Jessica

last: Winkler

address: 985800 Nebraska Medical Center- DRC I

department: Pharmacology and Experimental Neuroscience

institute: University of Nebraska Medical Center

summary:
Molecular basis for CNS dysfunction in simian immunodeficiency virus-infected rhesus monkeys.
We used microarrays to identify differentially expressed genes in chronic simian immunodeficiency virus-infected rhesus monkeys.

overall_design: Frontal lobe samples were obtained from control and SIV infected animals for RNA extraction and hybridization on Affymetrix microarrays. We sought to better understand the gene that changes in gene expression with SIV infection in the frontal lobe.

first: Eleanor

middle: S

last: Roberts

first: Howard

last: Fox


title: Post-therapeutic relapse of psoriasis associated with CD11a blockade is associated with T cells and inflammatory myeloid DCs

summary: To understand the development of new psoriasis lesions, we studied a group of moderate-to-severe psoriasis patients who experienced a relapse after ceasing efalizumab (anti-CD11a, Raptiva, Genentech). There were increased CD3+ T cells, neutrophils, CD11c+ and CD83+ myeloid DCs, but no increase in CD1c+ resident myeloid DCs. In relapsed lesions, there were many CD11c+CD1c-, inflammatory myeloid DCs identified by TNFSF10/TRAIL, TNF, and iNOS. CD11c+ cells in relapsed lesions co-expressed CD14 and CD16 in situ. Efalizumab induced an improvement in many psoriasis genes, and during relapse, the majority of these genes reversed back to a lesional state. Gene Set Enrichment Analysis (GSEA) of the transcriptome of relapsed tissue showed that many of the gene sets known to be present in psoriasis were also highly enriched in relapse. Hence, on ceasing efalizumab, T cells and myeloid cells rapidly enter the skin to cause classic psoriasis.

overall_design: To determine the transcsriptome of skin samples in 4 responding patients who relapsed after receiving efalizumab for treatment of psoriasis, using paired baseline non-lesional (=NL, n=2); lesional (LS, n=4);week 12 post-treatment (week 12, n=4), and relapse (n=4).

first: Michelle

middle: A

last: Lowes


title: Expression data from TOP-GFP sorted colon cancer cells

status: Public on Feb 16 2012

city: Munich

first: David

last: Horst

address: Thalkirchner Str. 36

institute: Pathologisches Institut der LMU

summary:
Colon cancers typically contain tumor cell populations with differential WNT signaling activity. Colon cancer cells with high WNT-activity have been attributed increase tumorigenic potential and stem cell characteristics.
We extracted tumor cells with differential WNT activity using fluorescent reporters from xenografted human colon cancer cell line tumors and primary human colon cancer xenografts and analysed their gene expression profiles.

overall_design: Colon cancer cell lines and primary colon cancer xenografts were transduced with lentiviral TOP-GFP reporters, and grown as xenografts in NOD-SCID mice. We disaggregated these tumors, flow sorted for GFPhigh and GFPlow tumor cells and subjected these populations to gene expression profiling.

first: Ramesh

last: Shivdasani


title: The gene expression response of MCF7 and MDAMB231 to glutamine deprivation

status: Public on Jan 01 2012

city: durham

first: Hsiu-Ni

last: Kung

address: CIEMAS 2141, 101 Science Drive

institute: Duke

summary:
There are two major subtype of cells in breast cancer. These cancer cells response differently to glutamine deprivation, here we use one luminal type of breast cancer cell (MCF7) and one basal type of breast cancer cell (MDAMB231) to compare the gene expression differences of these two types of cancer cells in glutamine deprivation.
Many cancer cells depend on glutamine for survival and oncogenic transformation. Although targeting glutamine metabolism is proposed as novel therapies, their heterogeneity among different tumors is unknown. Here, we found only basal-type, but not luminal-type breast cancer cells, exhibited phenotypes of glutamine dependency and may benefit from glutamine-targeting therapeutics. The glutamine independence of luminal-type cells is caused by the specific expression of glutamine synthetase (GS), a pattern recapitulated in luminal breast cancers. The co-culture of luminal cells partially rescued the basal cells under glutamine deprivation, suggesting glutamine symbiosis. The luminal-specific expression of GS is directly induced GATA3 and down-regulates glutaminase expression to maintain subtype-specific glutamine metabolism. Collectively, these data indicate the distinct glutamine phenotypes among breast cells and enable the rational design of glutamine targeted therapies.

overall_design: Gene expression analysis in MCF7 and MDAMB231 cultured with or without glutamine for 24h

first: Jeff

last: Marks

first: Jen-Tsan

last: Chi


title: Genes that mediate colorectal cancer liver metastasis

status: Public on Dec 31 2011

city: Houston

first: Mien-chie

last: Hung

state: Texas

address: 1515 Holcomb Blvd

department: Molecular and Cellular Oncology

institute: M.D. Anderson Cancer Center

summary: The study identifies a set of genes through functional selection in an orthotopic colorectal cancer mouse model that play an important role in mediating colorectal cancer liver metastasis. We look at the gene profiling of metastatic colorectal cancer cells (L1 and L2) and non-mestastatic colorectal cancer cells (sw620 and sw480) using Affymetrix U133A oligonucleotide arrays.

overall_design: 4 samples (each with triplicates) were analyzed. Genes with a fold-change ≥2 (P<0.05) were selected.

first: Ding

last: Qingqing

first: Hung

last: Mien-Chie


title: Expression data from Triticum aestivum L. roots

city: Zhengzhou

first: Yongchun

last: Li

state: Henan

address: Nongye Road No. 62

department: National Engineering Research Center for Wheat

country: China

institute: Henan Agricultural University

summary:
To better understand the regulatory mechanisms of water stress response in wheat, the transcript profiles in roots of two wheat genotypes, namely, drought tolerant 'Luohan No.2' (LH) and drought susceptible 'Chinese Spring' (CS) under water-stress were comparatively analyzed by using the Affymetrix wheat GeneChip®.
A total of 3831 transcripts displayed 2-fold or more expression changes, 1593 transcripts were induced compared with 2238 transcripts were repressed, in LH under water-stress; Relatively fewer transcripts were drought responsive in CS, 1404 transcripts were induced and 1493 were repressed. Comparatively, 569 transcripts were commonly induced and 424 transcripts commonly repressed in LH and CS under water-stress. 689 transcripts (757 probe sets) identified from LH and 537 transcripts (575 probe sets) from CS were annotated and classified into 10 functional categories, and 74 transcripts derived from 80 probe sets displayed the change ratios no less than 16 in LH or CS. Several kinds of candidate genes were differentially expressed between the LH and CS, which could be responsible for the difference in drought tolerance of the two genotypes.

overall_design: Two common wheat (Triticum aestivum L.) cultivars, Luohan No.2 (LH) and Chinese Spring (CS), were used for this study. Seedlings at the two leaf stage were stressed by cultured in PEG solutions for 6h, and some other seedlings were cultured in tap water as control. Root samples of LH and CS at 6h after the stress treatment and untreated control were prepared for microarray analysis.

first: Fanrong

last: Meng


title: Variation in chromatin accessibility is a key determinant of heritable variation in gene expression

status: Public on Jan 26 2012

city: Chicago

first: Jacob

last: Degner

state: IL

department: Human Genetics

institute: University of Chicago

type: Genome variation profiling by high throughput sequencing

summary: While it is well established that variation in gene expression levels can be influenced by single nucleotide polymorphisms (SNPs), little is known about the regulatory mechanisms by which this occurs. To address this gap, we used DNaseI sequencing to measure genome-wide chromatin accessibility in 70 Yoruba lymphoblastoid cell lines (LCLs), for which genome-wide genotypes and estimates of gene expression levels based on RNA-sequencing are also available. We obtained a total of 2.8 billion uniquely mapped DNase-seq reads, which allowed us to produce genome-wide maps of chromatin accessibility for each individual. We identified 7,759 locations at which DNase-seq read depth correlates significantly with variation at a nearby SNP or indel (FDR=10%). We call such variants 'chromatin accessibility Quantitative Trait Loci' (or caQTLs). Most caQTLs lie within or very near the target DNaseI hypersensitive sites, and they are strongly enriched within inferred transcription factor binding sites. We find that a substantial fraction (14%) of caQTLs are also significantly associated with variation in the expression levels of nearby genes (namely, these loci are also classified as eQTLs), suggesting that changes in chromatin accessibility or transcription factor binding frequently lead to gene expression changes. Conversely, 12% of eQTL SNPs are also classified as caQTLs and, accounting for incomplete power, we estimate that the true fraction may be as high as 41%. Our observations indicate that caQTLs are abundant in the human genome, and are likely to be significant contributors to phenotypic variation.

overall_design: DNaseI-Seq on 70 YRI Hapmap cell lines. Each individual sequenced on several lanes of a flow cell on the Illumina Genome Analyzer II

first: Athma

last: Pai

first: Roger

last: Pique-Regi

first: Jean-Baptiste

last: Veyrieras

first: Daniel

last: Gaffney

first: Joseph

last: Pickrell

first: Sherryl

last: De Leon

first: Katelyn

last: Michelini

first: Noah

last: Lewellen

first: Gregory

middle: E

last: Crawford

first: Matthew

last: Stephens

first: Yoav

last: Gilad

first: Jonathan

last: Pritchard


title: Inhibition of MYCN by a PNA anti-gene in alveolar rhabdomyosarcoma

city: Bologna

first: Andrea

last: Pession

state: BO

address: Massarenti 11

department: Pediatrics

country: Italy

institute: University of Bologna

summary:
The objective was to identify the molecular mechanisms responsible for in vitro and in vivo efficacy of an anti-MYCN peptide nucleic acid on a preclinical model of alveolar rhabdomyosarcoma. Cells treated with a anti-MYCN PNA exhibit growth arrest and apoptosis, and in vivo tumor growth is blocked.
Keywords: oncogene inhibition

overall_design: RH30 alveolar rhabdomyosarcoma cell line was treated with a 10uM concentration of anti-MYCN PNA or a mutated PNA devoid of any activity. After 12 hours RNA was extracted from untreated and treated cells and gene expression was analyzed by Affymetrix Gene Chips.

first: Roberto

last: Tonelli

first: Annalisa

last: Astolfi

first: Serena

last: Formica


title: IRE1-dependent transcriptome remodelling upon ER stress in human glioma cells

city: Bordeaux

first: eric

last: chevet

address: 146 rue Leo Saignat

country: France

institute: inserm

summary: We investigate the contribution of IRE1 signaling to the modulation of U87 glioma cells transcriptome upon various stresses. To this end, IRE1 control and IRE1 dominant negative expressing U87 glioma cells were subjected to environmental or chemical challenges and their transcriptome monitored using Affymetrix microarrays.

overall_design: Stress-induced transcriptome modulation in function of IRE1 proficiency/deficiency

first: Eric

last: Chevet


title: Expression data on APM effect in vitro

status: Public on Dec 02 2011

city: Davis

first: Hnin

middle: H

last: Aung

state: CA

address: 451 E Health Science Dr., GBSF 5404

department: Internal Medicine

institute: University of California, Davis

summary:
To seek whether seasonal variation in environmental particulate matter composition affected the global gene response patterns in cultured human cells representing pulmonary and systemic vascular targets.
We used microarrays to detail the global program of gene expression affected on different cells type by different seasonal collections of Ambient Particulate Matter.

overall_design: After treatment with 10 ug/mL either summer2006 or winter2007APM, endothelial or bronchail epithelial cells were isolated by RNA extraction and hybridization on Affymetrix microarrays. We sought to obtain the genes responses correlated with current concepts of systemic inflammation in cardiovascular effects of particulate air pollution.


title: Gene expression profiling in arterial tissue from type 2 diabetic patients

status: Public on Dec 08 2011

city: Roskilde

first: Vibe

last: Skov

address: Koegevej 7-13

department: Hematology

country: Denmark

institute: Roskilde Hospital

overall_design: 10 patients with type 2 diabetes and 11 control subjects participated in the study

first: Lars

last: Melholt Rasmussen

first: Jonas

last: Armstrup Funder


title: In vitro models of glioblastoma (GBM)

status: Public on Dec 01 2011

first: Jason

middle: W

last: Reeves

state: North Carolina

address: 101 Science Dr

institute: Duke University

summary:
Characterization of gene expression for a panel of 50 in vitro and in vivo models of glioblastoma (GBM).  Models include subcutaneously established xenograft lines, orthotopically grown subcutaneously established
xenograft lines, serum derived cell lines and stem cell media derived cell lines.  Multiple replicates of each line were run on different dates to determine the effect of batch and processing date on reproducibility of
gene expression profiles

overall_design: 117 samples analyzed from 50 distinct GBM xenografts or cell lines.  Biological replicates from the same passage number were included for many, but not all, of the lines.

first: Joseph

last: Lucas

first: Micheal

last: Gatza

first: Stephen

last: Keir

first: Oscar

middle: B

last: Persson

first: David

last: Reardon

first: Charles

last: Kanaly

middle: R

last: Nevins


title: Human cancer cells express Slug-based epithelial-mesenchymal transition gene expression signature obtained in vivo

status: Public on Dec 29 2011

first: Dimitris

last: Anastassiou

address: 1328 S. W. Mudd Building, MC 4712

summary:
Background: The biological mechanisms underlying cancer cell motility and invasiveness remain unclear, although it has been hypothesized that they involve some type of epithelial-mesenchymal transition (EMT).

Methods: We used xenograft models of human cancer cells in immunocompromised mice, profiling the harvested tumors separately with species-specific probes and computationally analyzing the results.

Results: Here we show that human cancer cells express in vivo a precise multi-cancer invasion-associated gene expression signature that prominently includes many EMT markers, among them the transcription factor Slug, fibronectin, and α-SMA. We found that human, but not mouse, cells express the signature and Slug is the only upregulated EMT-inducing transcription factor. The signature is also present in samples from many publicly available cancer gene expression datasets, suggesting that it is produced by the cancer cells themselves in multiple cancer types, including nonepithelial cancers such as neuroblastoma. Furthermore, we found that the presence of the signature in human xenografted cells was associated with a downregulation of adipocyte markers in the mouse tissue adjacent to the invasive tumor, suggesting that the signature is triggered by contextual microenvironmental interactions when the cancer cells encounter adipocytes, as previously reported.

Conclusions: The known, precise and consistent gene composition of this cancer mesenchymal transition signature, particularly when combined with simultaneous analysis of the adjacent microenvironment, provides unique opportunities for shedding light on the underlying mechanisms of cancer invasiveness as well as identifying potential diagnostic markers and targets for metastasis-inhibiting therapeutics.

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus

overall_design: 18 neuroblastoma tumor samples were profiled for gene expression twice by human U133A 2.0 and mouse 430A 2.0 arrays.

first: D

first: V

last: Rumjantseva

first: W

last: Cheng

first: J

last: Huang

first: P

last: Canoll

middle: J

last: Yamashiro

last: Kandel


title: Gene expression of LNCaP human prostate cells by cholesterol diet

city: Pohang

first: Taek-Kyun

last: Kim

state: Gyeongbuk

address: San 31, Hyoja-dong, Nam-gu

department: Interdisciplinary Bioscience and Bioengineering

country: South Korea

institute: POSTECH

summary: Understanding the systemic regulation of normal prostate gene expression by cholesterol diet is critical for deciphering the mechanisms responsible for the transition from healthy to pathogenic prostate conditions. To understand mechanism under cholesterol effect on prostate, we performed microarray analysis using LNCaP human prostate cells cultured in low cholesterol medium.

overall_design: The RNA is obtained from LNCaP human prostate cells serum-starved for 0h, 3h, 16h followed by CLM medium.

first: Daehee

last: Hwang

first: Jayoung


title: The Response of the Prostate to Changes in Circulating Cholesterol: Activating Transcription Factor 3 (ATF3) as a Cholesterol Sensor

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

overall_design: Refer to individual Series


title: A single intradermal injection of IFN-γ induces a psoriasis-like state in both non-lesional psoriatic and healthy skin

status: Public on Nov 30 2011

first: Mayte

last: Suarez-Farinas

summary: Psoriasis is a chronic, debilitating, immune-mediated inflammatory skin disease. As IFN-γ is involved in many cellular processes, including activation of T cells and dendritic cells (DCs), antigen processing and presentation, cell adhesion and trafficking, and cytokine and chemokine production, IFN-γ-producing Th1 cells were proposed to be integral to the pathogenesis of psoriasis. Recently, IFN-γ was shown to enhance IL-23 and IL-1 production by DCs and subsequently induce Th17 cells, important contributors to the inflammatory cascade in psoriasis lesions.  To determine if IFN-γ indeed induces the pathways leading to the development of psoriasis lesions, a single intradermal injection of IFN-γ was administered to an area of clinically normal, non-lesional skin of psoriasis patients and biopsies were collected 24 hours later. Although there were no visible changes in the skin, IFN-γ induced molecular and histological features characteristic of psoriasis lesions.  IFN-γ increased a number of differentially expressed genes in the skin, including many chemokines concomitant with an influx of T cells and inflammatory DCs. Furthermore, inflammatory DC products TNF, iNOS, IL-23, and TRAIL were present in IFN-γ-treated skin. Thus, IFN-γ, which is significantly elevated in non-lesional skin compared to healthy skin, appears to be a key pathogenic cytokine that can induce the inflammatory cascade in psoriasis.

overall_design: RNA was isolated from whole skin punch biopsies of either healthy or non-lesional psoraisis patients at baseline or 24 hours after placebo or IFN-g injection.

last: Suárez-Fariñas

first: Leanne

middle: M

last: Johnson-Huang

first: Michelle

last: Lowes


title: Comparison of TEX and M9-ENL1 cell lines to HL60 and THP1 cell lines

status: Public on Nov 24 2011

city: Toronto

first: Kolja

last: Eppert

state: Ontario

address: 101 College St., rm 8-301

country: Canada

institute: University Health Network

type:
Third-party reanalysis
Expression profiling by array

summary:
Gene regulatory networks that govern hematopoietic stem cells (HSC) and leukemia–initiating cells (L-IC) are deeply entangled. Thus, the discovery of compounds that target L-IC while sparing HSC is an attractive but difficult endeavor. Presently, most drug discovery approaches fail to counter-screen compounds against normal hematopoietic stem/progenitor cells (HSPC) to assess therapeutic index. Here, we present a combined in vitro and in vivo strategy to identify compounds specific to L-IC in acute myeloid leukemia (AML). A high-throughput screen of 4000 compounds on novel leukemia cell lines derived from human experimental leukemogenesis models yielded 80 hits, of which most were toxic to normal HSPC. Of the 10 compounds that passed this initial filter, we chose to characterize a single compound, kinetic riboside (KR), on AML L-IC and HSPC. KR demonstrated comparable efficacy to standard therapies against 63 primary AMLs. In vitro, KR effectively targeted the L-IC-enriched CD34+CD38- AML fraction, while sparing normal HSPC enriched fractions, although these effects were mitigated on HSC assayed in vivo, and highlights the importance of in vivo L-IC and HSC assays to measure function. Overall, we provide a novel approach to screen large drug libraries for the discovery of anti-L-IC compounds for human leukemias.

The gene expression profile of TEX and M9-ENL1 cells were compared to HL-60 (Series GSE16160, GSE28185) and THP1 (Series GSE28185), to determine if TEX and M9-ENL1 cells were more enriched in stem cell (embryonic, adult, leukemia, and cancer) gene sets using Gene Set Enrichment Analysis (GSEA).

overall_design: TEX and M9-ENL1 cells were treated with DMSO in triplicate. Total RNA was harvested and analyzed with the Affymetrix Human Genome U133A 2.0 Array. Raw data was background corrected with RMA, normalized using quantiles method, corrected using only PM values, and median polished to generate log2 values. Published HL-60 and THP-1 raw data using the same Affymetrix array were processed identically. To account for batch variation, the log2 values were adjusted using ComBat in GenePattern with a parametric Empirical Bayes priors distribution estimation method and without covariate analysis.

first: Sean

middle: P

last: McDermott

first: John

last: Dick


title: Identical gene regulation patterns of triiodothyronine (T3) and selective thyroid hormone receptor modulator GC-1 [Affymetrix]

status: Public on Oct 31 2011

first: Paul

last: Webb

department: Diabetes Research Center

institute: Methodist Hospital Reseach Institute

summary: Synthetic selective thyroid hormone (TH) receptor (TR) modulators (STRMs) exhibit beneficial effects on dyslipidemias in animals and humans and reduce obesity, fatty liver and insulin resistance in preclinical animal models. STRMs differ from native THs in preferential binding to the TRβ subtype versus TRα, increased uptake into liver and reduced uptake into other tissues. However, selective modulators of other nuclear receptors (NRs) exhibit important gene-selective actions which have been attributed to differential effects on receptor conformation and dynamics and these effects can have profound influences in animals and humans. While there are suggestions that STRMs could exhibit such gene-specific actions, the extent to which these effects are actually observed in vivo has not been explored. Here, we show that saturating concentrations of the main active form of TH, triiodothyronine (T3), and the prototype STRM GC-1 induce identical gene-sets in livers of euthyroid and hypothyroid mice and a human cultured hepatoma cell line that only expresses TRβ, HepG2.  We find one case in which GC-1 exhibits a modest gene-specific reduction in potency versus T3, at angiopoietin-like factor 4 (ANGPTL4) in HepG2. Investigation of the latter effect confirms that GC-1 acts through TRβ to directly induce this gene. However, this gene-selective GC-1 activity is not related to unusual T3 response element (TRE) sequence, unlike previously documented promoter-selective STRM actions. Together, our data suggest that T3 and GC-1 exhibit almost identical gene regulation properties and that gene-selective actions of GC-1 and similar STRMs will be subtle and rare.

overall_design: We treated HepG2 with vehicle or 10nM ligand (T3 or GC1; n=3 / treatment), analyzing mRNA 24h post treatment [Affymetrix]. We also treated 9-week old euthyroid male C57/Bl6 mice with vehicle or ligand (T3 or GC-1) by a single oral gavage (n=5 per treatment) and also performed a similar study in which mice were first made hypothyroid by two week feeding on iodine deficient diet (n=3-4 per treatment), analyzing mRNA 24h post treatment [Illumina].

last: Sieglaff

last: WEbb


title: Impact of G protein versus beta-arrestin-dependent signal transduction at the FSH receptor (affy_fsh_human)

status: Public on Nov 25 2011

city: Beaucouze

first: sandrine

last: balzergue

address: Rue G. Morel

institute: INRA

summary:
affy_fsh_human - affy_fsh_human - - G protein-coupled receptors (GPCR) are centrally involved in most physiological processes and are a major drug targets. They transduce extracellular signals inside the cells through at least two different mechanisms: i) the classical coupling to heterotrimeric G proteins and ii) a newly discovered beta-arrestin-dependent pathway. The fundamental issue of the respective impacts that these two transduction mechanisms exert on gene regulation has not been clearly addressed to date. To tackle this question, we have developed two mutants of the follicle stimulating hormone (FSH) receptors which do not couple to G proteins upon FSH activation but continue to recruit beta-arrestins and signal through them.-In the present study, we compare the wild-type FSH receptor to either the R466A or the T469F mutants. These two mutations are localized in the second intra cellular loop of the FSH receptor and prevent G protein coupling to the active FSH receptor. Each receptor was permanently expressed in HEK-293 cells at comparable levels. Cells were treated or not for 6 hours with 3 nM FSH.

Keywords: treated vs untreated comparison,wt vs mutant comparison

overall_design: 18 arrays - Human GenomeU133A 2.0

first: Sandrine

last: Balzergue

first: Eric

last: Reiter

first: Marie-Laure

last: Martin-Magniette


title: Whole Blood Gene Expression Profiles Distinguish Patients with Single versus Recurrent Venous Thromboembolism

status: Public on Nov 10 2011

city: Durham

first: Thomas

middle: L.

last: Ortel

address: Box 3422 DUMC

institute: Duke University Medical Center

summary: Venous thromboembolism (VTE) is a major cause of morbidity and mortality. Pulmonary embolism is a life threatening manifestation of VTE that occurs in at least half the patients on presentation.  In addition, VTE recurs in up to 30% of patients after a standard course of anticoagulation, and there is not a reliable way of predicting recurrence.  We investigated whether gene expression profiles of whole blood could distinguish patients with VTE from healthy controls, single VTE from those with recurrence, and DVT alone from those with PE. 70 adults with VTE on warfarin and 63 healthy controls were studied.  Patients with antiphospholipid syndrome or cancer were excluded.  Blood was collected in PAXgene tubes, RNA isolated, and gene expression profiles obtained using Affymetrix arrays.  We developed a 50 gene model that distinguished healthy controls from subjects with VTE with excellent receiver operating characteristics (AUC 0.94; P < 0.0001).  We also discovered a separate 50 gene model that distinguished subjects with a single VTE from those with recurrent VTE with good receiver operating characteristics (AUC 0.75; P=0.008).  In contrast, we were unable to distinguish subjects with DVT from those with PE using gene expression profiles.  Gene expression profiles of whole blood can distinguish subjects with VTE from healthy controls and subjects with a single VTE from those with recurrence.  Additional studies should be performed to validate these results and develop diagnostic tests.  Gene expression profiling is likely translatable to other thrombotic disorders(e.g., patients with cancer and VTE).

overall_design: 70 adults with one or more prior VTE on warfarin and 63 healthy controls were studied.  Patients with antiphospholipid syndrome or cancer were excluded.  Blood was collected in PAXgene tubes, RNA isolated, and gene expression profiles obtained using Affymetrix arrays.

first: Deborah

last: Lewis

first: Gregg

last: Stashenko

first: Olga

last: Akay

first: Lulit

last: Price

first: Kouros

last: Owzar

first: Geoffrey

last: Ginsburg

first: Jen-Tsan

last: Chi

middle: L


title: Overall aiEMT in surgical samples of esophageal cancer patients

status: Public on Oct 20 2011

city: Chuo-ku

first: Hiroki

last: Sasaki

state: Tokyo

country: Japan

institute: National Cancer Center Reseach Institute

summary:
Surgical samples have long been used as important subjects for cancer research. In accordance with an increase of neoadjuvant therapy, biopsy samples have recently become imperative for cancer transcriptome. On the other hand, both biopsy and surgical samples are available for expression profiling for predicting clinical outcome by adjuvant therapy; however, it is still unclear whether surgical sample expression profiles are useful for the prediction by the use of biopsy samples because little has been done about comparative gene expression profiling between the two kinds of samples.

When gene expression profiles were compared between biopsy and surgical samples, artificially induced epithelial-mesenchymal transition (aiEMT) was found in the surgical samples. This study will evoke the fundamental misinterpretation including underestimation of the prognostic evaluation power of markers by overestimation of EMT in past cancer research, and will furnish some advice for the near future as follows: 1) Understanding how long the tissues were under an ischemic condition; 2) Prevalence of biopsy samples for in vivo expression profiling with low biases on basic and clinical research; and 3) Checking cancer cell contents and normal- or necrotic-tissue contamination in biopsy samples for prevalence.

overall_design: We used microarrays to compare gene expression profiles between 31 biopsy (A, D) and 65 surgical (O) samples derived from the cancerous portion of the esophagus of different esophageal cancer patients.

first: Keiko

last: Minashi


title: A gene expression signature from peripheral whole blood for stage I lung adenocarcinoma

status: Public on Sep 23 2011

city: Rockville

first: Melissa

last: Rotunno

address: 6120 Executive Blvd

department: DCEG

institute: NIH/NCI

summary: Affordable early screening in subjects with high risk of lung cancer has great potential to improve survival from this deadly disease. We measured gene expression from lung tissue and peripheral whole blood (PWB) from adenocarcinoma cases and controls to identify dysregulated lung cancer genes that could be tested in blood to improve identification of at-risk patients in the future. Genome-wide mRNA expression analysis was conducted in 153 subjects (73 adenocarcinoma cases, 80 controls) from the Environment And Genetics in Lung cancer Etiology (EAGLE) study using PWB and paired snap-frozen tumor and non-involved lung tissue samples. Analyses were conducted using unpaired t-tests, linear mixed effects and ANOVA models. The area under the receiver operating characteristic curve (AUC) was computed to assess the predictive accuracy of the identified biomarkers. We identified 50 dysregulated genes in stage I adenocarcinoma versus control PWB samples (False Discovery Rate ≤0.1, fold change ≥1.5 or ≤0.66). Among them, eight (TGFBR3, RUNX3, TRGC2, TRGV9, TARP, ACP1, VCAN, and TSTA3) differentiated paired tumor versus non-involved lung tissue samples in stage I cases, suggesting a similar pattern of lung cancer-related changes in PWB and lung tissue. These results were confirmed in two independent gene expression analyses in a blood-based case-control study (n=212) and a tumor-non tumor paired tissue study (n=54). The eight genes discriminated patients with lung cancer from healthy controls with high accuracy (AUC=0.81, 95% CI=0.74-0.87). Our finding suggests the use of gene expression from PWB for the identification of early detection markers of lung cancer in the future.

overall_design: Samples from 164 subjects were initially included in the study. Two samples with poor quality profile based on quality assessment (described in Supplemental Material 2) were excluded before normalization. The remaining 162 samples were processed and normalized with the Robust Multichip Average (RMA) method. Nine additional subjects were excluded after data normalization because of reclassification to non-adenocarcinoma morphology during histologic review. The final analyses were based on 73 adenocarcinoma cases and 80 controls. All 22,277 probe sets based on RMA summary measures were used in the analyses.

last: Hu

first: Hua

last: Su

first: Chaoyu

last: Wang

first: Alisa

last: Goldstein

first: Andrew

last: Bergen

first: Dario

last: Consonni

first: Angela

middle: C

last: Pesatori

first: Pier-Alberto

last: Bertazzi

first: Sholom

last: Wacholder

first: Joanna

last: Shih

first: Neil

last: Caporaso

first: Phil

last: Taylor

first: Maria-Teresa

last: Landi


title: Overall aiEMT in non-cancerous samples of esophageal cancer patients

status: Public on Oct 07 2011

overall_design: We used microarrays to compare gene expression profiles between 5 biopsy (BPY) and 5 surgical (OPE) samples derived from the non-cancerous portion of the esophagus of different esophageal cancer patients.


title: Alterations in Gene Expression in Human Mesothelial Cells Correlate with Mineral Pathogenicity

status: Public on Sep 19 2011

city: Burlington

first: Jeffrey

last: Bond

state: VT

address: 95 Carrigan Dri e

department: Microbiology and Molecular Genetics

institute: University of Vermont

summary: Human mesothelial cells (LP9/TERT-1) were exposed to low and high (15 and 75 μm2/cm2 dish) equal surface area concentrations of crocidolite asbestos, nonfibrous talc, fine titanium dioxide (TiO2), or glass beads for 8 or 24 h. RNA was then isolated for Affymetrix microarrays, GeneSifter analysis and QRT-PCR. Gene changes by asbestos were concentration- and time-dependent. At low nontoxic concentrations, asbestos caused significant changes in mRNA expression of 29 genes at 8 h and 205 genes at 24 h, whereas changes in mRNA levels of 236 genes occurred in cells exposed to high concentrations of asbestos for 8 h. Human primary pleural mesothelial cells also showed the same patterns of increased gene expression by asbestos. Nonfibrous talc at low concentrations in LP9/TERT-1 mesothelial cells caused increased expression of 1 gene Activating Transcription Factor 3 (ATF3) at 8 h and no changes at 24 h, whereas expression levels of 30 genes were elevated at 8 h at high talc concentrations. Fine TiO2 or glass beads caused no changes in gene expression. In human ovarian epithelial (IOSE) cells, asbestos at high concentrations elevated expression of 2 genes (NR4A2, MIP2) at 8 h and 16 genes at 24 h that were distinct from those elevated in mesothelial cells. Since ATF3 was the most highly expressed gene by asbestos, its functional importance in cytokine production by LP9/TERT-1 cells was assessed using siRNA approaches. Results reveal that ATF3 modulates production of inflammatory cytokines (IL-1β, IL-13, G-CSF) and growth factors (VEGF and PDGF-BB) in human mesothelial cells.

overall_design: Microarrays were performed on samples from 3 independent experiments. All cell types, time points, and mineral types and concentrations were included in all 3 experiments. For each experiment, n=3 dishes were pooled into one sample per treatment group. Each of the pooled samples was analyzed on a separate array, i.e., n=3 arrays per condition (3 independent biological replicates). We tested the hypothesis that alteration in gene expression in human cells correlate with mineral pathogenicity. We used GeneSifter program to analyze our data and pairwise analysis showed that number of gene changes correlate with toxicity of pathogenic  minerals. While non-pathogenic minerals glass beads and fine TiO2 treatment to cell resulted in no gene change, crocidolite asbestos caused maximum number of gene changes followed by talc.

first: Arti

last: Shukla

first: Maximillian

last: MacPherson

first: Jedd

last: Hillegass

first: Maria

last: Ramos-Nino

first: Vlada

last: Alexeeva

first: Pamela

last: Vacek

first: Harvey

last: Pass

first: Chad

last: Steele

first: Brooke

last: Mossman


title: The pioneer factor PBX1 guides a distinct ERa signaling in breast cancer [ChIP-seq]

status: Public on Sep 30 2011

city: Lebanon

first: luca

last: magnani

state: NH

address: NCCC one medical drive

department: Genetics

institute: Dartmouth College

type: Genome binding/occupancy profiling by high throughput sequencing

summary: We profiled global PBX1 binding in MCF7 cells. The hypothesis tested was that PBX1 binds regions that recruit ERa following estradiol stimulation.

overall_design: Profiling of PBX1 cistrome in MCF7 breast cancer cells

first: Luca

last: Magnani

first: Mathieu

last: Lupien


title: The pioneer factor PBX1 guides a distinct ERa signaling in breast cancer


title: Prolonged Drug Selection of Breast Cancer Cells and Enrichment of Cancer Stem Cell Characteristics.

status: Public on Sep 26 2011

city: Bethesda

first: Suresh

middle: V.

last: Ambudkar

address: 37 Convent Dr., Room 2120

institute: National Cancer Institute, NIH

summary:
Background: Cancer stem cells are presumed to have virtually unlimited proliferative and self-renewal abilities and to be highly resistant to chemotherapy, a feature that is associated with overexpression of ATP-binding cassette transporters. We investigated whether prolonged continuous selection of cells for drug resistance enriches cultures for cancer stem-like cells.
Methods: Cancer stem cells were defined as CD44+/CD24– cells that could self-renew (ie, generate cells with the tumorigenic CD44+/CD24– phenotype), differentiate, invade, and form tumors in vivo. We used doxorubicin-selected MCF-7/ADR cells, weakly tumorigenic parental MCF-7 cells, and MCF-7/MDR, an MCF-7 subline with forced expression of ABCB1 protein. Cells were examined for cell surface markers and side-population fractions by microarray and flow cytometry, with in vitro invasion assays, and for ability to form mammospheres. Xenograft tumors were generated in mice to examine tumorigenicity (n = 52). The mRNA expression of multidrug resistance genes was examined in putative cancer stem cells and pathway analysis of statistically significantly differentially expressed genes was performed. All statistical tests were two-sided.
Results: Pathway analysis showed that MCF-7/ADR cells express mRNAs from ABCB1 and other genes also found in breast cancer stem cells (eg, CD44, TGFB1, and SNAI1). MCF-7/ADR cells were highly invasive, formed mammospheres, and were tumorigenic in mice. In contrast to parental MCF-7 cells, more than 30% of MCF-7/ADR cells had a CD44+/CD24– phenotype, could self-renew, and differentiate (ie, produce CD44+/CD24– and CD44+/CD24+ cells), and overexpressed various multidrug resistance-linked genes (including ABCB1, CCNE1, and MMP9). MCF-7/ADR cells were statistically significantly more invasive in Matrigel than parental MCF-7 cells (MCF-7 cells = 0.82 cell per field and MCF-7/ADR = 7.51 cells per field, difference = 6.69 cells per field, 95% confidence interval = 4.82 to 8.55 cells per field, P<.001). No enrichment in the CD44+/CD24– or CD133+ population was detected in MCF-7/MDR.
Conclusion: The cell population with cancer stem cell characteristics increased after prolonged continuous selection for doxorubicin resistance.

overall_design:
PARALLEL study design with 4 samples Parental MCF-7 cell line versus Doxorubicin Resistant MCF-7 cell sublines Biological replicates: 2 parental controls, 2 drug resistant, independently grown and harvested.
agent:Selection agent is multi-step doxorubicin selection: MCF7226ng, MCF7262ng
biological replicate: MCF71, MCF72
biological replicate: MCF226ng, MCF7262ng

first: Anna

last: Calcagno

first: Crystal

middle: D

last: Salcido

first: Jean-Pierre

last: Guillet

first: Chung-Pu

last: Wu

first: Jennifer

last: Fostel

first: Melanie

last: Mumau

first: Michael

last: Gottesman

first: Lyuba

last: Varticovski

middle: V


title: PI3K-targeted therapy can be evaded by gene amplification along the MYC-eukaryotic translation initiation factor 4E (eIF4E) axis

status: Public on Sep 14 2011

city: Boston

first: Nina

last: Ilic

address: 44 Binney Street

department: Cancer Biology

institute: Dana-Farber Cancer Institute

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


title: An integrative multi-platform analysis for biomarker discovery of osteosarcoma

status: Public on Sep 16 2011

city: Xiamen

first: Long

middle: Ji

last: Liu

address: 59# Daxue Road

institute: NEAU

summary: Three osteosarcoma (OS) cell lines (MG-63, Saos-2 and U-2 OS) and 1 osteoblastic cell line (hFOB1.19) were collected for this work. MG-63 was kindly provided by Dr. Agi Grigoriadis from University College London. Saos-2, U-2 OS and hFOB1.19 were purchased from ATCC. All cells used were kept in exponential phase of growth. Total RNA was extracted using the RNeasy Total RNA Isolation kit (QIAGEN). The quality and purity of the products were controlled by Agilent 2100. The final synthesized biotinylated cDNAs were hybridized to Affymetrix GeneChip® U133A 2.0 arrays following the protocol strictly. Arrays were scanned with the Affymetrix scanner 3000. Data analysis was performed by Microarray Suite 5.0 after pre-standard procedure.

overall_design: Link-test on datasets from both SELDI-TOF-MS and microarray high-throughput analysis platforms can accelerate the identification of tumor biomarkers. The results confirmed that CYC-1 with important biomedical function was an effective candidate biomarker for osteosarcoma early diagnosis.

first: Dong

middle: G

last: Li

first: Juan

last: Zhang

first: zong

last: Zeng


title: Transcription profiling of wheat interacting with incompatible and compatible yellow rust in a Yr1-containing genotype

status: Public on Aug 31 2011

city: Ames

first: PLEXdb Curator

middle: Sudhansu

state: IA

address: 1023  Crop Genomes Informatics Lab (Iowa State University)

department: Virtual Reality Application Center

institute: Iowa State University

summary: Transcriptional changes were monitored in the wheat cultivar Avocet*6/Yr1 following inoculation with avirulent and virulent wheat yellow rust (Puccinia striiformis f.sp. tritici) isolates using the Affymetrix wheat genome array GeneChip®.  Seedlings of Avocet*6/Yr1 were grown to growth stage 12-13 (Zadoks et al., 1974) before inoculating with either the P.s. f.sp. tritici isolate 169E136 (Yr1-virulent) or 232E137 (Yr1-avirulent) or with talc for the Mock inoculation (Boyd and Minchin 2001).  Plants were grown under a 16/8 hour photoperiod cycle, supplemented with sodium lighting (240 μmol m-2 s-1) at day/night temperatures of 20°C/15°C and a relative humidity of 60%, both before and after inoculation, in a spore-free, containment level 2 greenhouse.  Leaf samples from six seedlings were collected 6, 12, 24, 48 and 72 hpi for RNA extraction and transcriptomics analysis from three independent biological experiments.  Leaf tissue was ground under liquid nitrogen and total RNA extracted using the TRIzol reagent method, following the manufacturer’s instructions (Invitrogen, Carlsbad, CA).  RNA from each time point (16 μg) were pooled to obtain 80 μg of total RNA for each treatment (mock inoculated control; avirulent isolate inoculated; virulent isolate inoculated).  Pooled RNA samples were further purified using the Qiagen RNeasy mini-kit according to the manufacturer instructions (Qiagen) and RNA integrity was confirmed using the Agilent 2100 Bioanalyzer (Agilent).  Affymetrix GeneChip processing, including RNA quality control, microarray hybridisation and data acquisition was performed through contract research services by the John Innes Genome Laboratory, John Innes Centre, Norwich, U.K.  A total of nine hybridisations were performed.   ****[PLEXdb(http://www.plexdb.org) has submitted this series at GEO on behalf of the original contributor,  Osman Bozkurt.  The equivalent experiment is TA25 at PLEXdb.]

overall_design: pathogen isolates: Mock inoculated (Control)(3-replications);  pathogen isolates: Yr1-avirulent wheat yellow rust isolate 232E137(3-replications);  pathogen isolates: Yr1-virulent wheat yellow rust isolate 169E136(3-replications)

first: Osman

last: Bozkurt

first: Mahinur

last: Akkaya


title: Transcription profiling wheat responses to adapted and non-adapted isolates of the blast fungus, Magnaporthe

summary: Transcriptional changes were monitored in the wheat cultivar Renan 24 hours post i noculation with adapted and non-adapted Magnaporthe isolates using the Affymetrix wheat genome array GeneChip®.  Wheat plants cv. Renan were grown in a peat and sand (1:1) mix at 23 C in a Sanyo Fitotron growth cabinet (Sanyo Gallenkamp PLC, Loughborough, U.K.) with a 16/8 h, light/dark cycle.  Three Magnaporthe isolates were used in this expt, two wheat-adapted isolates (BR32, BR37) and one wheat non-adapted isolate (BR29). Magnaporthe isolates were grown for eleven days on Complete Media Agar at 25 C under a 16/8h, light/dark cycle.  Conidia were harvested by flooding the plates with 5 mL of sterile inoculation solution [0.25% (w/v) gelatine and 0.01% (v/v) Tween 20] and scraping the conidia from the surface using a sterile glass rod.  Conidia were filtered through sterile miracloth and the density adjusted to 1 x 10 5 conidia mL-1 with inoculation solution.   Fourteen day old wheat seedlings mist inoculated with 4 mL of a Magnaporthe conidia suspension and plants were sealed in plastic propagators to maintain relative humidity c.100% and kept at 25 C in the dark for the first 24 hours post inoculation (hpi).  Inoculation solution without Magnaporthe conidia was used as a mock-inoculation control.  Leaf samples were collected 24 hpi for transcriptomics analysis from three independent biological experiments.  Leaf tissue was ground under liquid nitrogen and total RNA extracted using a QIAquick RNeasy Plant Extraction Kit (Qiagen, Hilden, Germany), followed by TURBO DNaseTM (Ambion, Texas, U.S.A.) treatment.  RNeasy Mini Spin column purification (Qiagen) was used to further purify RNA samples for array hybridisation.  RNA quality checks, cRNA conversion and Affymetrix genome array hybridisation was carried out by the Nottingham Arabidopsis Stock Centre (NASC) array hybridisation service (http://affymetrix.arabidopsis.info/).   ****[PLEXdb(http://www.plexdb.org) has submitted this series at GEO on behalf of the original contributor,  Graham McGrann.  The equivalent experiment is TA24 at PLEXdb.]

overall_design: pathogen isolates: Mock-inoculated (Control)(3-replications);  pathogen isolates: Wheat non-adapted Magnaporthe isolate BR29(3-replications);  pathogen isolates: Wheat adapted Magnaporthe isolate BR32(3-replications);  pathogen isolates: Wheat adapted Magnaporthe isolate BR37(3-replications)

first: Graham

last: McGrann

first: Lesley

last: Boyd


title: Genomic distribution and inter-sample variation of non-CG methylation across human cell types

status: Public on Sep 01 2011

city: Munich

middle: Johannes

last: Ziller

address: Kraepelinstrasse 2-10

department: Translational Psychiatry

institute: Max Planck Institute of Psychiatry

type: Methylation profiling by high throughput sequencing

summary: DNA methylation plays an important role in development and disease. The primary sites of DNA methylation in vertebrates are cytosines in the CpG dinucleotide context, which account for roughly three quarters of the total DNA methylation content in human and mouse cells. While the genomic distribution, inter-individual stability and functional role of CpG methylation are reasonably well understood, little is known about DNA methylation targeting CpA, CpC and CpT dinucleotides. Here we report a comprehensive analysis of non-CG methylation in 72 genome-scale DNA methylation maps across human pluripotent and differentiated cell types. We confirm non-CG methylation to be predominant in pluripotent cell types and observe an expected decrease upon differentiation and near complete absence in various differentiated cells. Our data highlight that non-CG methylation is highly variable and shows little conservation between different pluripotent cell lines. While we show a strong correlation of non-CG methylation and DNMT3 expression levels we find a statistical independence of non-CG methylation from pluripotency associated gene expression. Finally, non-CG methylation appears to be spatially correlated with CpG methylation. In summary these results contribute further to our understanding of DNA methylation in human cells and help clarify previous observations using a large representative sample set.

overall_design: Examination of nonCG DNA methylation patterns in pluripotent and differentiated cells

first: Alexander

last: Meissner


title: Differential transcriptome analyses of three wheat genotypes in their response to Fusarium Head Blight and trichothecenes

city: Lethbridge

first: Nora

last: Foroud

state: Alberta

address: 5403 1st Ave South

institute: Agriculture and Agri-Foods Canada

summary: Fusarium Head Blight (FHB) is a disease of wheat and other cereal crops, where Fusarium graminearum and related species infects the wheat inflorescence during and post-anthesis.  The fungus produces trichothecene toxins that accumulate in the grain of infected head, and are required for disease spread. Microarrays were used to observe differential gene expression in the uninoculated spikelets of FHB-challenged wheat spikes in three wheat genotypes. A summary of our findings will be published in Plant Pathology.

overall_design: Three wheat genotypes were used: (1) 'Superb', an FHB-susceptible Canadian wheat cultivar; (2) GS-1-EM0040 (CIMMYT11x'Superb'*2), a double haploid line with good resistance to initial infection (Type 1 resistance), and moderate resistance to disease spread (Type 2 resistance); and (3) GS-1-EM0168 (CM82036x'Superb'*2), a double haploid line with moderate Type 1 resistance, and good Type 2 resistance.  Five inocula were used: (A) water, (B) FgTri5+ (GZ3639, a trichothecene-producing F. graminearum strain); (C) FgTri5- (GZT40, a trichothecene-non-producing mutant of the F. graminearum strain GZ3639); (D) FgTri5 supplemented with deoxynivalenol (DON), which is the main trichothecene produced by FgTri5+; and (E) DON.  The inocula were injected into two spikelets near the center of the spike during early stages of anthesis, and spikelets above and below the inoculation point were collected at 3, 8, and 24 h after inoculation.  A zero-hour un-inoculated control was also collected from each line.  Total RNA was extracted from collected spikelets, and microarray analysis was perfomed using the Affymetrix Wheat GeneChip.

middle: A

first: Thérèse

last: Ouellet

first: André

last: Laroche

first: Brenda

last: Oosterveen

first: Mark

last: Jordan

first: Brian

middle: E

last: Ellis

first: François

last: Eudes


title: Drought stress in Wheat at grain filling stage

summary: To provide a global study of transcriptome changes under drought stress, the gene expression levels of a durum wheat genotype (Triticum durum Desf. cultivar Creso) and two bread wheat genotypes (Triticum aestivum L. cultivar Chinese Spring -CS- and its deletion line CS_5AL-10) were investigated. The 5A chromosome deletion line (5AL-10)  lacks the distal part (43%) of the long arm of chromosome 5A.  Each genotype was subjected to two different levels of water stress at the grain filling stage. After anthesis, three different levels of soil water content (SWC) were induced as described below: control (CTRL; SWC=28%), moderate stress (MS; SWC=18%), and severe stress (SS; SWC=12.5%). For each sample, three biological replicates were performed, for a total of 27 hybridizations.   ****[PLEXdb(http://www.plexdb.org) has submitted this series at GEO on behalf of the original contributor,  Alessio Aprile.  The equivalent experiment is TA23 at PLEXdb.]

sample_organism:
Triticum aestivum
Triticum turgidum subsp. durum

overall_design: genotype: Creso - stress condition: Control(3-replications);  genotype: Creso - stress condition: Mild stress(3-replications);  genotype: Creso - stress condition: Severe stress(3-replications);  genotype: CS - stress condition: Control(3-replications);  genotype: CS - stress condition: Mild stress(3-replications);  genotype: CS - stress condition: Severe stress(3-replications);  genotype: CS-5AL - stress condition: Control(3-replications);  genotype: CS-5AL - stress condition: Mild stress(3-replications);  genotype: CS-5AL - stress condition: Severe stress(3-replications)

first: Alessio

last: Aprile

first: Luigi

last: Cattivelli


title: Wild emmer wheat comparison of drought resistant vs. susceptible genotypes under terminal drought

summary: Six months old seed grown under well-watered greenhouse conditions were used in the current study. The seedlings of the two wild emmer wheat genotypes were vernalized on a moist germination paper (Hofman Manufacturing, Inc, Jefferson, OR, USA) for three weeks in the dark at 4oC, followed by three days acclimation at 24oC. Seedlings were then transplanted into 5L pots containing a mixture of pure quartz sand and peat (4:1 v/v), supplemented with a slow release fertilizer (2 g/L, Osmocote® Standard 14-14-14, Scotts-Sierra Horticulture, Marysville, OH, USA) and by a weekly application of 100 ml/pot of 0.5X Murashigi and Skoog growth solution (Sigma Chemical Co., St Louis, MO, USA). Pots were placed in a screen-house under natural winter conditions (December to February; 5-18°C) in Haifa, Israel (Mt. Carmel; 35o01′ E, 32o45′ N; 480 m above sea level) for 10 weeks and irrigated daily by a drip irrigation system. Three weeks prior to application of terminal drought stress, the pots were transferred to a controlled environment greenhouse (22/18 oC; 12 h day/12 h night) in order to prevent rainfall during the drought experiment. Five pots per genotype served as biological replicates, plants of three pots of each genotype/treatment were used for transcriptome study whereas two additional pots were used for quantitative PCR analysis (altogether five biological replicated of were used for quantitative real time PCR). Three individual plants were grown in each pot, one plant was used for measurements of leaf relative water content (RWC) (Barrs and Weatherley 1968), whereas the other two plants were used for sampling of flag leaf tissue for RNA extraction. Terminal drought stress (D) was applied at inflorescence emergence stage (Zadoks 50-60), (Zadoks et al. 1974), after emergence of 1-2 spikes in all biological replicates of both genotypes. The time from transplanting to inflorescence emergence stage was not significantly different between genotypes (70 days in the S genotype and 72 days in the R genotype). Drought stress application initiated after irrigation with excess amount of water in order to assure that all pots start the experiment at the same soil water capacity. Drought stress was imposed by withholding water for eight days until stress symptoms (i.e. leaf rolling and wilting symptoms) were visible in plants of both genotypes. Stress symptoms were more visible in the S genotype, however, leaf relative water content (RWC), measured after eight days of drought stress was low but was not significantly different between the two genotypes (49.68%±1.48 in the R genotype and 53.34%±1.83 in the S genotype). The well-watered control (C) plants were irrigated daily by ample amount of water. Flag leaf tissues of drought-stressed plants and well-watered control plants were harvested, immediately frozen in liquid nitrogen, and stored at -80ºC for RNA extraction.   ****[PLEXdb(http://www.plexdb.org) has submitted this series at GEO on behalf of the original contributor,  Krugman Tamar.  The equivalent experiment is TA33 at PLEXdb.]

overall_design: genotype: Drought resistant (R) Y12-3 - treated or untreated: Well-watered(3-replications);  genotype: Drought resistant (R) Y12-3 - treated or untreated: terminal drought(3-replications);  genotype: Drought susceptible (S) A24-39 - treated or untreated: Well-watered(3-replications);  genotype: Drought susceptible (S) A24-39 - treated or untreated: terminal drought(3-replications)

first: Krugman

last: Tamar

first: Fahima

last: Tzion


title: Transcriptome analysis of a wheat NIL pair carrying FHB resistant and susceptible alleles

first: PLEXdb Curator

summary: In this study, we used the Affymetrix wheat GeneChip to examine the transcript accumulation in a near-isogenic line pair carrying resistant and susceptible alleles at the wheat Fhb1 locus. The objectives of this study were: (1) to identify the overall response in wheat to F. graminearum infection; (2) to identify key genes involved in FHB resistance/susceptibility pathways in wheat; (3) to compare the transcript profiles of wheat and barley during F. graminearum infection; and (4) to examine the relationship between transcript accumulation, disease severity, fungal biomass and trichothecene accumulation in wheat.   ****[PLEXdb(http://www.plexdb.org) has submitted this series at GEO on behalf of the original contributor,  Seungho Cho.  The equivalent experiment is TA20 at PLEXdb.]

overall_design: FHB resistant and susceptible plants 48 an 96 hours after treatment with Fusarium graminearum strain Butte 86

first: Seungho

last: Cho

first: Gary

last: Muehlbauer


title: ZEBOV-induced changes in macrophage gene expression

city: Beaverton

first: Victor

last: DeFilippis

state: OR

address: 505 NW 185th Ave.

department: Vaccine and Gene Therapy Institute

institute: Oregon Health and Science University

summary: Zaire ebolavirus (ZEBOV) infections are associated with high lethality in primates. ZEBOV primarily targets mononuclear phagocytes, which are activated upon infection and secrete mediators believed to trigger initial stages of pathogenesis. The characterization of the responses of target cells to ZEBOV infection may therefore not only further understanding of pathogenesis but also suggest possible points of therapeutic intervention. Gene expression profiles of primary human macrophages exposed to ZEBOV were determined using DNA microarrays and quantitative PCR to gain insight into the cellular response immediately after cell entry. Significant changes in mRNA concentrations encoding for 88 cellular proteins were observed. Most of these proteins have not yet been implicated in ZEBOV infection. Some, however, are inflammatory mediators known to be elevated during the acute phase of disease in the blood of ZEBOV-infected humans. Interestingly, the cellular response occurred within the first hour of Ebola virion exposure, i.e. prior to virus gene expression. This observation supports the hypothesis that virion binding or entry mediated by the spike glycoprotein (GP1,2) is the primary stimulus for an initial response. Indeed, ZEBOV virions, LPS, and virus-like particles consisting of only the ZEBOV matrix protein VP40 and GP1,2 (VLPVP40-GP) triggered comparable responses in macrophages, including pro-inflammatory and pro-apoptotic signals. In contrast, VLPVP40 (particles lacking GP1,2) caused an aberrant response. Notably, some cellular interferon-inducible genes were upregulated six hours after exposure to virions and LPS, but not after exposure to VLPVP40-GP. This suggests that GP1,2 binding to macrophages plays an important role in the immediate cellular response.

overall_design: Primary human macrophages from three donors (D1, D2, D3) were harvested at 1 h and 6 h after in vitro exposure to purified Ebola virions and compared to RNA from mock-exposed cells derived from the same donors.

first: Victoria

last: Wahl-Jensen

first: Sabine

last: Kurz

first: Friedericke

last: Feldmann

first: Lukas

middle: K

last: Buehler

first: Jason

last: Kindrachuk

first: Jean

last: da Silva

first: Klaus

last: Früh

first: Jens

middle: H

last: Kuhn

first: Dennis

last: Burton

first: Heinz


title: Mapping translocation breakpoints using a wheat microarray

type:
Expression profiling by array
Genome variation profiling by array

summary: Five RNA samples were used.  The RNA source material was from wheat cytogenetic stocks from Dr. Adam Lukaszewski, University of California, Riverside. The lines used for this study are Pavon, Pavon Dt1BL, 1RS.1BL, 1B+5 and T-1 wheat samples. whole seedling minus starchy endosperm.  Equal portions of RNA from unstressed and 48 hr drought-stressed seedling were combined to make one RNA sample. The person who produced the RNA was Prasanna R. Bhat in the TJ Close lab at University of California, Riverside. Everything downstream of RNA production was done at the UC Irvine DNA and Protein Microarray Facility  (Denis Heck, manager) by Sriti Misra. ****[PLEXdb(http://www.plexdb.org) has submitted this series at GEO on behalf of the original contributor,  Prasanna Bhat.  The equivalent experiment is TA10 at PLEXdb.]

overall_design: genetic line: Pavon(2-replications);  genetic line: Pavon Dt1BL(2-replications);  genetic line: 1RS.1BL(2-replications);  genetic line: T-1(2-replications);  genetic line: 1B+5(2-replications)

first: Prasanna

last: Bhat

first: Timothy

middle: J

last: Close


title: Secreted Factors from Staphylococcus aureus Biofilm and Planktonic Cultures Differentially Impact Human Keratinocytes, in vitro

city: Bozeman

first: Kate

last: McInnerney

state: MT

address: 109 Lewis Hall

department: Microbiology

institute: Montana State University

summary:
Interactions between human keratinocytes and secreted factors from Staphylococcus aureus biofilm and planktonic cultures were investigated using microarray analysis.
Relative to planktonic secreted factors, biofilm secreted factors up regulated cytokine and chemokine genes in keratinocytes.   Genes associated with DNA damage and oxidative stress were also induced in keratinocytes treated with secreted factors from S. aureus biofilm.
Here we show that secreted factors from S. aureus planktonic (PCM) and biofilm (BCM) cultures differentially impact several aspects of wound healing processes.

overall_design: Secreted factors from S. aureus biofilm and planktonic cultures with equivalent population sizes were placed in contact with human foreskin keratinocytes for 4 hours.  Keratinocytes were grown to ~90% confluency between passages 4-10.

first: Garth

last: James

first: Patrick

middle: R

last: Secor

first: Philip

last: Fleckman

first: John

last: Olerud

first: Scot

last: Dowd

middle: S

last: Stewart


title: FOXP3-mediated inhibition of the global gene regulator SATB1 is required for maintaining regulatory T cell commitment

status: Public on Aug 14 2011

city: Bonn

first: Joachim

last: Schultze

state: NRW

address: Carl-Troll-Strasse 31

department: Genomics and Immunoregulation

institute: LIMES (Life and Medical Sciences Center Genomics and Immunoregulation)

summary: Regulatory T (Treg) cells are involved in self tolerance, immune homeostasis, prevention of autoimmunity, and suppression of immunity to pathogens or tumours. The forkhead transcription factor FOXP3 is essential for Treg cell development and function as mutations in FOXP3 cause severe autoimmunity in mice and humans. However, the FOXP3-dependent molecular mechanisms leading to this severe phenotype are not well understood. Here we introduce the chromatin remodelling enzyme SATB1 (special AT-rich sequence-binding protein-1) as an important target gene of FOXP3. So far, SATB1 has been associated with normal thymic T-cell development, peripheral T-cell homeostasis, TH1/TH2 polarization, and reprogramming of gene expression. In natural and induced murine and human FOXP3+ Treg cells SATB1 expression is significantly reduced. While there is no differential epigenetic regulation of the SATB1 locus between Treg and Teffector cells, FOXP3 reduces SATB1 expression directly as a transcriptional repressor at the SATB1 locus and indirectly via miR-155 induction, which specifically binds to the 3’UTR of the SATB1 mRNA. Reduced SATB1 expression in FOXP3+ cells achieved either by overexpression or induction of FOXP3 is linked to significant reduction in TH1 and TH2 cytokines, while loss of FOXP3 function either by knock down or genetic mutation leads to significant upregulation of SATB1 and subsequent cytokine production. Alltogether, these findings demonstrate that reduced SATB1 expression in Treg cells is necessary for maintenance of a Treg-cell phenotype in vitro and in vivo and places SATB1-mediated T cell-specific modulation of global chromatin remodelling central during the decision process between effector and regulatory T-cell function.

overall_design:
Gene expression profiling of freshly isolated CD4+ T cells, separated into CD25 negative and positive subpopulations, from three different donors.
FOXP3 is stably and constitutively expressed at a high level in CD4+CD25+ regulatory T cells and at a low level in CD4+CD25- cells.

first: Marc

last: Beyer

first: S

last: Classen

first: J


title: Wheat Yr5 isolines treated with P.s. tritici PST-100 (06-194)

first: PLEXdb Curator

summary: Comparison of 2 P. s. tritici-inoculated and mock-inoculated isolines that differ for the putative Yr5 resistance gene over a time course (6, 12, 24, 48h)    ****[PLEXdb(http://www.plexdb.org) has submitted this series at GEO on behalf of the original contributor,  Tristan Coram.  The equivalent experiment is TA9 at PLEXdb.]

overall_design: Yr5 and yr5 isolines 6, 12, 24, and 24h after inoculation with P. s. tritici

first: Tristan

last: Coram

first: Xianming

last: Chen


title: Wheat Yr39 and yr39 (Alpowa) genotypes treated with P.s. tritici PST-78

summary: Comparison of 2 P. s. tritici-inoculated and mock-inoculated genotypes that differ for the Yr39 high-temperature adult-plant resistance phenotype over a time course (12, 24, 48h)    ****[PLEXdb(http://www.plexdb.org) has submitted this series at GEO on behalf of the original contributor,  Tristan Coram.  The equivalent experiment is TA11 at PLEXdb.]

overall_design: Yr39 and yr39 isolines 12, 24, and 48h after inoculation with P. s. tritici


title: MYC drives resistance to PI3K/mTOR targeted inhibition (gene expression)

first: Nina

last: Ilic

state: MA

summary: Gene expression signatures were measured after treatment of cells with 50nM BEZ235. Affymetrix HG-U133AV2 expression arrays were performed according to the manufacturer's directions using RNA extracted by Qiagen RNeasy from engineered human cell-lines grown for 72h in the presence of 50nM BEZ235

overall_design: Resulting expression signatures where derived based on phenotypic properties(resistance to BEZ235) of the cells (enriched vs GFP/HR).

first: Thomas

last: Roberts


title: Unique gene expression profile based upon pathologic response in epithelial ovarian cancer

status: Public on Aug 12 2011

first: Dimitrios

last: Spentzos

address: 330 Brookline Avenue

institute: Beth Israel Deaconess Medical Center

summary:
PURPOSE:
We investigated whether tumor tissue obtained at diagnosis expresses a specific gene profile that is predictive of findings at second-look surgery in patients with epithelial ovarian cancer (EOC).
PATIENTS AND METHODS:
Tumor tissue obtained at the time of diagnosis was profiled with oligonucleotide microarrays. Class prediction analysis was performed in a training set of 24 patients who had undergone a second-look procedure. The resultant predictive signature was then tested on an independent validation set comprised of 36 patients.
RESULTS:
A 93-gene signature referred to as the Chemotherapy Response Profile (CRP) was identified through its association with pathologic complete response. When applied to a separate validation set, the CRP distinguished between patients with unfavorable versus favorable overall survival (median 41 months v not yet reached, respectively, log-rank P = .007), with a median follow-up of 52 months. The signature maintained independent prognostic value in multivariate analysis, controlling for other known prognostic factors such as age, stage, grade, and debulking status. There was no genetic overlap between the CRP and our previously described Ovarian Cancer Prognostic Profile (OCPP), which demonstrated similar prognostic value. The combination of the CRP and OCPP yielded better prognostic discrimination then either profile alone. Genes present in the CRP include BAX, a proapoptotic protein previously associated with chemotherapy response in ovarian cancer.
CONCLUSION:
Identification of a gene expression profile based on pathologic response in EOC provides independent prognostic information and offers potential insights into the mechanism of drug resistance. Efforts to identify a more tailored profile using selected genes from both the CRP and OCPP are underway.
keyword(s): Correlation with outcome

overall_design: All microarray experiments were performed at the BIDMC Genomics Center. Ovarian cancer samples were collected at the time of primary debulking surgery and frozen at 80°C. Tumor samples were pulverized in liquid nitrogen and homogenized in Trizol solution, followed by RNA isolation, probe labeling, and Affymetrix GeneChip hybridization using standard manufacturer protocols. The dChip algorithm was used for data normalization and for generating gene expression signal values. Two outlier arrays as identified by the dChip software were excluded from further analysis.


title: Expression data of  freshly microdissected human hair follicle dermal papilla and its comparisons

status: Public on Aug 11 2011

city: Tokyo

first: Manabu

last: Ohyama

address: 6-20-2 Shinkawa Mitaka-shi

department: Department of Dermatology

institute: Kyorin University School of Medicine

summary:
The dermal papilla (DP) of the hair follicle plays crucial roles in the hair follcie morphogenesis and cycling. Thus, the elucication of human DP molecular signature is of great interest. DP cell culture by conventional method impairs intrinsic properties of DP cells.
Isolatoion of human DP is hampered by the lack of specific cell surface markers. Thus, it still depends on manual microdissection, with which the removal of minor contamination is unfeasible. Cultured DP cells are mostly pure. Aggregation of cultured DP cells was shown to restore some intrinsic properties in cultured DP cells. Fibroblasts are distinct dermal cell population and provide baseline for DP arrays.

overall_design: Four sets of Genechip microarrays were generated from freshly-microdissected DPs (fDP), cultured DP cells (cDP), cultured fibroblasts (Fibro) collected from respective volunteers. Two sets of Genechips were additionally prepared from aggregated DP cells (agDP) and cultured DP cells which were used for the generation of agDPs (each set derived from respective volunteer). These Genechips can be compared to elucidate the genes possibly contribute to intrinsic property of intact human DPs. For instance, comparisons between cultured DP (cDP) and fibroblast (Fibro) or between aggregated DP (agDP) and cDP could sort out potential DP signature genes, as each population is predominantly consisted of DP cells. When the expression levels of those genes were compared between fDP and cDP chips, the genes up- or equally expressed in fDPs should represent DP signature genes.

first: Atsushi

last: Shimizu


title: Transcriptome Analysis of Human Diabetic Kidney Disease (DKD Glomeruli vs. Control Glomeruli)

status: Public on Aug 03 2011

city: Bronx

first: Karolina

last: Woroniecka

state: NY

address: 1300 Morris Park Ave

institute: AECOM

summary: We identified 1,700 differentially expressed probesets in DKD glomeruli and 1,831 in diabetic tubuli; 330 probesets were commonly differentially expressed in both compartments. The canonical complement signaling pathway was determined to be statistically differentially regulated in both DKD glomeruli and tubuli and was associated with increased glomerulosclerosis even in an additional set of DKD samples.

overall_design:
Affymetrix expression arrays were used to identify differentially regulated transcripts in 44 microdissected human kidney samples. Stringent statistical analysis using the Benjamini_Hochberg corrected 2-tailed t-test was used to identify differentially expressed transcripts in control and diseased glomeruli and tubuli.
This Series includes DKD and control glomeruli samples.

first: A

last: Park

first: Davoud

last: Mohtat

first: David

middle: B

last: Thomas

first: Katalin

last: Susztak


title: Transcriptome Analysis of Human Diabetic Kidney Disease (Control Glomeruli vs. Control Tubuli)

overall_design:
Affymetrix expression arrays were used to identify differentially regulated transcripts in 44 microdissected human kidney samples. Stringent statistical analysis using the Benjamini_Hochberg corrected 2-tailed t-test was used to identify differentially expressed transcripts in control and diseased glomeruli and tubuli.
This Series includes control glomeruli and tubuli samples.


title: Expression analysis of ZBP-89 deficient human primary erythroid progenitors

status: Public on Aug 02 2011

first: Andrew

middle: Jonghan

last: Woo

address: 1 Blackfan Circle, Karp Res Bldg

department: Hematology / Oncology

institute: Children's Hospital Boston / Harvard Medical School

summary:
The molecular mechanisms underlying erythroid-specific gene regulation remain incompletely understood.  Closely spaced binding sites for GATA, NF-E2/maf and CACCC interacting transcription factors play functionally important roles in globin and other erythroid-specific gene expression.  We and others recently identified the CACCC-binding transcription factor ZBP-89 as a novel GATA-1 and NF-E2/mafK interacting partner.  Here, we examined the role of ZBP-89 in human globin gene regulation and erythroid maturation using a primary CD34+ cell ex vivo differentiation system.  We show that ZBP-89 protein levels rise dramatically during human erythroid differentiation, and that ZBP-89 occupies key cis-regulatory elements within the globin and other erythroid gene loci.  ZBP-89 binding correlates strongly with RNA Pol II occupancy, active histone marks, and high-level gene expression.  ZBP-89 physically associates with the histone acetyltransferases (HATs) p300 and Gcn5/Trrap, and occupies common sites with Gcn5 within the human globin loci.  Lentiviral shRNA knockdown of ZBP-89 results in reduced Gcn5 occupancy, decreased acetylated histone 3 levels, lower globin and erythroid-specific gene expression, and impaired erythroid maturation.  Addition of the HDAC inhibitor valproic acid partially reverses the reduced globin gene expression.  These findings reveal an activating role for ZBP-89 in human globin gene regulation and erythroid differentiation.
Keywords: Human primary erythroid progenitors

overall_design: Expression data of human erythroid progenitors transduced with lentivirus expressing short hairpins against ZBP-89 and control empty vector

last: Kim

last: Xu

first: H

last: Huang

last: Cantor


title: Transcriptome Analysis of Human Diabetic Kidney Disease

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

overall_design: Refer to individual Series

first: Esther


title: A Methodology for Utilization of Predictive Genomic Signatures in FFPE Samples

status: Public on Jun 24 2011

first: Holly

middle: Kloos

last: Dressman

state: NC

address: 101 Science Drive

department: Institute for Genome Sciences and Policy

institute: Duke University Medical Center

summary: Purpose: Gene expression signatures developed to measure the activity of oncogenic signaling pathways have been used to dissect the heterogeneity of tumor samples and to predict sensitivity to various cancer drugs that target components of the relevant pathways, thus potentially identifying therapeutic options for subgroups of patients. To facilitate broad use, including in a clinical setting, the ability to generate data from formalin-fixed, paraffin-embedded (FFPE) tissues is essential.  Experimental Design: Patterns of pathway activity in matched fresh-frozen and FFPE xenograft tumor samples were generated using the MessageAmp Premier methodology in combination with assays using Affymetrix arrays. Results generated were compared with those obtained from fresh-frozen samples using a standard Affymetrix assay. In addition, gene expression data from patient matched fresh-frozen and FFPE melanomas were also utilized to evaluate the consistency of predictions of oncogenic signaling pathway status.  Results: Significant correlation of pathway activity predictions was observed between paired fresh-frozen and FFPE xenograft tumor samples. In addition, significant concordance of pathway activity predictions was also observed between patient matched fresh-frozen and FFPE melanomas.  Conclusion: Reliable and consistent predictions of oncogenic pathway activities can be obtained from FFPE tumor tissue samples. The ability to reliably utilize FFPE patient tumor tissue samples for genomic analyses will lead to a better understanding of the biology of disease progression and, in the clinical setting, will provide tools to guide the choice of therapeutics to those most likely to be effective in treating a patient’s disease.

overall_design: 8 replicates of HMECs infected with adenovirus expressing GFP, 8 replicates of HMECs infected with adenovirus expressing RAS, 6 replicates of HMECs infected with adenovirus expressing MYC, 25 fresh-frozen melanoma xenografts, 25 FFPE melanoma xenografts, 6 FFPE human melanoma

first: Jennifer

last: Freedman

first: Christina

last: Augustine

first: Douglas

last: Tyler

first: Joseph

last: Nevins


title: Whole blood gene expression data from PFAPA syndrome

status: Public on Jun 20 2011

first: Silvia

last: Stojanov

state: MD

address: 10 Center Drive

institute: NIH/NIAMS

summary:
PFAPA, the syndrome of periodic fever associated with aphthous stomatitis, pharyngitis and/or cervical adenitis, is the most common periodic fever disease in children. Cases are mostly sporadic; the etiopathogenesis is unknown.
In order to shed more insights into pathogenesis, we performed microarray expression analysis on samples from patients with PFAPA during and between flares, healthy controls and patients with hereditary autoinflammatory diseases during flares.

overall_design: RNA was extracted from whole peripheral blood from six patients with PFAPA syndrome during flares and asymptomatic intervals, six healthy controls and six patients with hereditary autoinflammatory diseases (2 familial Mediterranean fever (FMF), 1 TNF-receptor-asociated periodic fever syndrome (TRAPS) and 3 cryopyrin-associated periodic syndromes (CAPS)).


title: Wilms Tumor-1 (WT-1) and its candidate target genes in gliomagenesis

city: Richmond

first: William

middle: C

last: Broaddus

state: VA

address: 417 North 11th Street, Sixth floor

department: Neurosurgery

institute: VCU

summary:
WT-1 is a zinc-finger transcription factor with important roles during development. WT-1 is associated with the development of tumors of varied origins.
Our lab has previously demonstrated aberrant expression of WT-1 in tumor cells.  Necessity of WT-1 for tumor cell growth- in vitro & in vivo- was also shown.

overall_design: Human glioma U251 cells were treated with Oligofectamine (CTRL), Oligofectamine + non-targeting siRNA control (SCR) or Oligofectamine+ si-WT1 siRNA (Si). Biological triplicates were run on microarrays.

first: Helen

last: Fillmore

first: Catherine

middle: I

last: Dumur

first: Archana

last: Chidambaram


title: Profiling of Jurkat T cells activated with CD3, CD28 and PMA at 1 and 8 hours

status: Public on Jul 16 2011

city: Ede

first: Wynand

last: Alkema

address: Kernhemseweg 2

country: Netherlands

institute: NIZO Food Research

summary: T lymphocytes are orchestrators of adaptive immunity. Naïve T cells may differentiate into the Th1, Th2, Th17 or iTreg phenotype, depending on environmental co-stimulatory signals. In order to identify the genes and pathways involved in differentiation of Jurkat T cells towards Th1 and Th2 subtypes we performed comprehensive transcriptome analyses of Jurkat T cells stimulated with various stimuli an pathway inhibitors

overall_design: Jurkat T cells were treated with CD3/CD28 and CD3/PMA and CD28/PMA. RNA was isolated after 1 and 8 hrs stumalation.

first: Ruben

last: Smeets

first: Paul

last: Vink

first: Frank

last: Wijnands

first: Monika

last: Gorecka

first: Henri

last: Klop

first: Anja

last: Garritsen

first: Susanne

last: Bauerschmidt

first: Mieke

last: Boots


title: Transcriptome Analysis of Human Diabetic Kidney Disease (DKD Tubuli vs. Control Tubuli)

first: Karolina

last: Woroniecka

overall_design:
Affymetrix expression arrays were used to identify differentially regulated transcripts in 44 microdissected human kidney samples. Stringent statistical analysis using the Benjamini_Hochberg corrected 2-tailed t-test was used to identify differentially expressed transcripts in control and diseased glomeruli and tubuli.
This Series includes DKD and control tubuli samples.

first: A

last: Park

first: Davoud

last: Mohtat

first: David

last: Thomas

first: Katalin

last: Susztak