title: Expression data from human amnion mesenchymal cells treated with interleukin-1-beta for 1hr and 8hr

status: Public on Jun 02 2011

city: Columbus

first: Douglas

middle: A.

last: Kniss

state: OH

address: 395 W. 12th Avenue

department: OB/GYN

institute: The Ohio State University

summary:
Premature birth continues to be a challenging pregnancy complication, and a body of literature indicates that inflammation can contribute to premature delivery by converting a receptive uterine environment to a hostile one.  Cytokines have been demonstrated to provoke up-regulation of inflammatory genes (e.g. interleukin-1, 6, and 8, tumor necrosis factor-alpha, cyclooxygenase-2, and microsomal prostaglandin E synthase-1).
Using monolayer cultures of human amnion mesenchymal cells (AMCs) as a model, we aimed to detail the global programme of gene expression that occurs in response to cytokine challenge.

overall_design: Human amnion mesenchymal cells were challenged with 10 ng/ml of interleukin-1-beta for 1 hour (1h) or 8 hours (8h) in serum-free media, while control cells were treated with serum free medium only (veh).  The cells (veh, 1h and 8h) were subjected to RNA extraction, quantification, and evaluation, followed by hybridization on Affymetrix GeneChip® Human Genome U133A 2.0 Arrays (Platform GPL571).  Experiments were repeated three times for a total of nine samples used for microarray analysis.  Three biological replicates were used to ensure that any results were not biased by day-to-day variation in RNA extraction.

first: Ruth

last: Li

first: William

last: Ackerman IV

first: Taryn

middle: L

last: Summerfield

first: Lianbo

last: Yu

first: Parul

last: Galati

first: Jie

last: Zhang

first: Kun

last: Huang

first: Roberto

last: Romero


title: Expression data from human endoscopic biopsy samples

status: Public on Jun 01 2011

city: Bethesda

first: Jeffrey

middle: E

last: Green

state: MD

address: Rm 4054, 37 Convent Drive

country: USA

institute: NCI

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

overall_design: Refer to individual Series


title: Dysregulated genes associated with acquired resistance

summary: This study was conducted to identify dysregulated genes associated with acquired resistance to chemotherapy.

overall_design: Endoscopic biopsy samples were collected from CF-treated metastatic gastric cancer patients prior to therapy and following the development of resistance to therapy.

first: Hark

middle: K

last: Kim


title: HNF4A-binding sites in HepG2 hepatoblastoma cells treated with TGF-beta

status: Public on Jun 08 2011

city: Tokyo

first: Daizo

last: Koinuma

address: Hongo 7-3-1, Bunkyo-ku

department: Pathology

country: Japan

institute: University of Tokyo

type: Genome binding/occupancy profiling by high throughput sequencing

summary: Specific regulation of target genes by transforming growth factor-β (TGF-β) in a given cellular context is determined in part by transcription factors and cofactors that interact with the Smad complex. In the present study, we determined Smad2 and Smad3 (Smad2/3) binding regions in the promoters of known genes in HepG2 hepatoblastoma cells, and compared them to those in HaCaT epidermal keratinocytes to elucidate the mechanisms of cell type- and context-dependent regulation of transcription induced by TGF-β. Our results show that 81% of the Smad2/3 binding regions in HepG2 cells were not shared with those found in HaCaT cells. Hepatocyte nuclear factor 4α (HNF4α) is expressed in HepG2 cells, but not in HaCaT cells, and the HNF4α binding motif was identified as an enriched motif in the HepG2-specific Smad2/3 binding regions. ChIP-sequencing analysis of HNF4A binding regions under TGF-β stimulation revealed that 32.5% of the Smad2/3 binding regions overlapped HNF4A bindings. MIXL1 was identified as a new combinatorial target of HNF4A and Smad2/3, and both the HNF4A protein and its binding motif were required for the induction of MIXL1 by TGF-β in HepG2 cells. These findings generalize the importance of binding of HNF4A on Smad2/3 binding genomic regions for HepG2-specific regulation of transcription by TGF-β, and suggest that certain transcription factors expressed in a cell-type-specific manner play important roles in the transcription regulated by the TGF-β-Smad signaling pathway.

overall_design: HepG2 cells were treated with TGF-beta for 1.5 h or left untreated. anti-HNF4A ChIP-seq was performed. One lane was used for each sample.

first: Anna

last: Mizutani

first: Shuichi

last: Tsutsumi

first: Naoko

last: Kamimura

first: Masato

last: Morikawa

first: HiroshiI

last: Suzuki

first: Kohei

last: Miyazono

first: Hiroyuki

last: Aburatani


title: Clinical response of metastatic gastric cancer patients to cisplatin and fluorouracil (CF) combination chemotherapy

summary: This study was conducted to identify transcriptional profiles predictive of a clinical response of metastatic gastric cancer patients to cisplatin and fluorouracil (CF) combination chemotherapy.


title: Expression data from MCF-7 cells stimulated by Estrogen or IGF-I

status: Public on May 09 2011

city: Houston

first: Chad

last: Creighton

state: TX

address: One Baylor Plaza, Mail Stop: BCM305

department: Biostatistics, Ducan Cancer Center

institute: Baylor College of Medicine

summary:
Although estrogen receptor (ER) and insulin-like growth factor (IGF) signaling are important for normal mammary development and breast cancer, cross-talk between these pathways, particularly at the level of gene transcription, remains poorly understood.  We performed microarray analysis on MCF-7 breast cancer cells treated with estradiol (E2) or IGF-I for 3hr or 24hr.  IGF-I regulated mRNA of 5-10-fold more genes than estradiol, and many genes were co-regulated by both ligands.  Importantly, expression of these co-regulated genes correlated with poor prognosis of human breast cancer.  Closer examination revealed enrichment of repressed transcripts.  Interestingly, a number of potential tumor suppressors were down-regulated by IGF-I and estradiol.  In fact, BLNK, one of the top repressed genes, is a potential growth suppressor in breast cancer cells.  Analysis of three down-regulated genes showed that E2-mediated repression occurred independently of IGF-IR, and IGF-I-mediated repression occurred independently of ER.  However, repression by IGF-I or estradiol required common downstream kinases.  In conclusion, E2 and IGF-I co-regulate a set of genes that affect breast cancer outcome.  There is enrichment of repressed transcripts, and the down-regulation is independent at the receptor level.  This may be important clinically, as tumors with active ER and IGF-IR signaling may require co-targeting of both pathways.
KEYWORDS: multiple group comparison

overall_design: Microarray analysis on MCF-7 breast cancer cells treated with estradiol (E2) or IGF-I for 3hr or 24hr.

last: Tsimelzon

first: Angelo

last: Casa

first: Adrian

last: Lee


title: Extensive characterization of NF-kappaB binding uncovers non-canonical motifs and advances the interpretation of genetic functional traits

status: Public on May 24 2011

city: Oxford

first: Jiannis

last: Ragoussis

address: Roosevelt Drive

department: Wellcome Trust Centre for Human Genetics

country: United Kingdom

institute: University of Oxford

summary: We report the DNA binding preferences  of 4 NF-kappaB dimers (p52p52, RELARELA, RELAp50, RELAp52)

overall_design: Proteins of the Nf-kappab family  were bound to DNA oligonucleotides containing a degenerate region. The protein-DNA complexes were selected after one or multiple rounds of SELEX and the DNA molecules were deep sequenced.

first: Daniel

last: Wong

first: Ana

last: Teixeira

first: Spyros

last: Oikonomopoulos

first: Peter

last: Humburg

first: Imtiaz

middle: N

last: Lone

first: David

last: Saliba

first: Trevor

last: Siggers

first: Martha

last: Bulyk

first: Dimitar

last: Angelov

first: Stefan

last: Dimitrov

first: Irina

last: Udalova


title: Pin1/mutant-p53 jointly controlled genes

status: Public on May 30 2011

city: Trieste

first: Silvano

last: Piazza

address: localita' Padriciano 99

country: Italy

institute: ICGEB

summary: To investigate the specific gene expression program by which mutant-p53 and Pin1 control invasion and metastasis in breast cancer cells, we compared the transcriptomic profile of control,  mutant-p53 depleted or Pin1 depleted MDA-MB-231 cells.

overall_design: MDA-MB-231 cells were transfected twice with siRNA against Pin1, p53 or LacZ as a control. Transfections were performed by using Lifofectamine 2000 (Invitrogen) according to manufacture's procedure. Forty-eight hours after second transfection, samples were then processed for total RNA extraction and hybridization on Affymetrix microarrays. Three biological replicas (A, B, C) were used for each of the three conditions, for a total of 9 samples

first: Javier

last: Girardini

first: Marco

last: Napoli

first: Alessandra

last: Rustighi

first: Carolina

last: Marotta

first: Enrico

last: Radaelli

first: Valeria

last: Capaci

first: Lee

last: Jordan

first: Phil

last: Quinlan

first: Alastair

last: Thompson

first: Miguel

last: Mano

first: Antonio

last: Rosato

first: Tim

last: Crook

first: Eugenio

last: Scanziani

first: Anthony

middle: R

last: Means

first: Guillermina

last: Lozano

first: Claudio

last: Schneider

first: Giannino

last: DelSal


title: Gene expression signatures and molecular markers associated with clinical outcome in locally advanced head and neck carcinoma

status: Public on May 31 2011

city: Barcelona

first: MIGUEL ANGEL

last: PAVON

state: Barcelona

address: Sant Antoni Maria Claret, 167

department: INSTITUT INVESTIGACIÓ BIOMÉDICA SANT PAU

country: Spain

institute: HOSPITAL DE LA SANTA CREU I SANT PAU

summary:
The purpose of our study was to identify expression signatures and molecular markers associated with tumor recurrence and survival in patients with locally advanced head and neck squamous cell carcinoma (HNSCC).
We studied the expression profile of 63 pre-treatment tumor biopsies obtained from locally advanced HNSCCs treated with standard treatments. Cluster analysis identified three tumor subtypes associated with significant differences in local recurrence-free survival (LRFS), progression free-survival (PFS) and overall survival (OS). Tumor subtype 1, associated with short LRFS, PFS and OS, showed features of epithelial-mesenchymal transition and undifferentiation. It also overexpressed genes involved in cell adhesion, NF-κB and integrin signalling. Tumor subtype 3, associated with longer LRFS, PFS and OS, showed a high degree of differentiation and overexpressed genes located in chromosomal regions 19q13 and 1q21. Tumor subtype 2, which had a clinical outcome intermediate between subtype 1 and subtype 3, overexpressed genes involved in branching morphogenesis. Receiver Operating Characteristic (ROC) analysis identified a subset of genes associated with local recurrence and survival. We validated the association between gene cluster classification and patient survival using two HNSCC data sets obtained from two independent patient cohorts. Finally, using the gene expression profile of the pre-treatment tumor biopsy, we generated a gene expression signature that could predict survival in locally advanced patients.

overall_design: Sixty three pretreatment HNSCC biopsies and five normal mucosas were assayed using the Affymetrix HG-U133A2.0 array.

first: Miguel-Angel

last: Pavón

first: Matilde

last: Parreño

first: Marta

last: Tellez

first: Francesc

middle: J

last: Sancho

first: Montserrat

last: López

first: Maria-Virtudes

last: Céspedes

first: Isolda

last: Casanova

last: López-Pousa

first: Maria-Antonia

last: Mangues

first: Miquel

last: Quer

first: Agustí

last: Barnadas

first: Xavier

last: León

first: Ramón


title: Expression data comparing azacitidine and decitabine in non-small cell lung cancer lines

status: Public on May 05 2011

city: San Diego

first: Helen

last: Brady

state: CA

address: 4550 Towne Centre Ct

institute: Celgene

summary: Azacitidine (AZA) and decitabine (DAC) are cytidine azanucleoside analogs with clinical activity in myelodysplastic syndromes (MDS) and potential activity in solid tumors. To better understand the mechanism of action of these drugs, we examined the effects of AZA and DAC in a panel of non-small cell lung cancer (NSCLC) cell lines. Of 5 NSCLC lines tested in a cell viability assay, all were sensitive to AZA (EC50 of 1.8–10.5 µM), while only H1299 cells were equally sensitive to DAC (EC50 of 5.1 µM). In the relatively DAC-insensitive cell line A549, both AZA and DAC caused DNA methyltransferase I depletion and DNA hypomethylation; however, only AZA significantly induced markers of DNA damage and apoptosis, suggesting that mechanisms in addition to, or other than, DNA hypomethylation are important for AZA-induced cell death. Cell cycle analysis indicated that AZA induced an accumulation of cells in sub-G1 phase, whereas DAC mainly caused an increase of cells in G2/M. Gene expression analysis of AZA- and DAC-treated cells revealed strikingly different profiles, with many genes distinctly regulated by each drug. In summary, while both AZA and DAC caused DNA hypomethylation, distinct effects were demonstrated on regulation of gene expression, cell cycle, DNA damage, and apoptosis.

overall_design: A549 and H1299 cells were treated with a dose range (0.3–3.0 μM) of AZA or DAC for 48 hours, and effects on gene expression were assessed by microarray analysis.

first: Aaron

last: Nguyen

first: Normand

last: Richard


title: Expression data from ovarian cancer cell lines

status: Public on May 16 2011

city: Kyoto

first: Ken

last: Yamaguchi

address: 54 Kawahara-cho, Shogoin, Sakyo-ku

department: Gynecology and Obstetrics

institute: Kyoto University Graduate School of Medicine

summary: Ovarian clear cell carcinoma (OCCC) shows unique clinical features including an association with endometriosis and poor prognosis. We previously reported that the contents of endometriotic cysts, especially high concentrations of free iron, are a possible cause of OCCC carcinogenesis through iron-induced persistent oxidative stress. In this study, we conducted gene expression microarray analysis using 38 ovarian cancer cell lines and identified genes commonly expressed in both OCCC cell lines and clinical samples, which comprise an OCCC gene signature. The OCCC signature reproducibly predicts OCCC specimens in other microarray data sets, suggesting that this gene profile reflects the inherent biological characteristics of OCCC. The OCCC signature contains known markers of OCCC, such as hepatocyte nuclear factor-1b (HNF-1b) and versican (VCAN), and other genes that reflect oxidative stress. Expression of OCCC signature genes was induced by treatment of immortalized ovarian surface epithelial cells with the contents of endometriotic cysts, indicating that the OCCC signature is largely dependent on the tumor microenvironment. Induction of OCCC signature genes is at least in part epigenetically regulated, as we found hypomethylation of HNF-1b and VCAN in OCCC cell lines. This genomewide study indicates that the tumor microenvironment induces specific gene expression profiles that contribute to the development of distinct cancer subtypes.

overall_design: Affymetrix Human Genome U133A 2.0 Array was conducted for 38 ovarian cancer cell lines (13 OCCC cell lines and 25 non-OCCC cell lines). All specimens were arrayed in parallel and used for RMA normalization.

first: Masaki

last: Mandai

first: Tomonori

last: Oura

first: Noriomi

last: Matsumura

first: Junzo

last: Hamanishi

first: Tsukasa

last: Baba

first: Shigeyuki

last: Matsui

first: Susan

last: Murphy

first: Ikuo

last: Konishi


title: Identification of Unique Therapeutic Targets in Esophageal Squamous Cell Carcinoma

status: Public on May 03 2011

city: Gaithersburg

first: Wusheng

last: Yan

address: 8717 Grovemont Circle

summary: We utilized tissue microdissection and expression microarrays to measure ex vivo gene expression profiles in twelve cases of patient-matched normal basal epithelial cells, normal differentiated squamous epithelium, and cancer.

overall_design: The data set from the precisely-dissected, dividing basal cell layer was used as a ‘biological filter’ to identify genes that were specifically dysregulated in tumors, and not simply increased as a consequence of normal growth.

first: Joanna

last: Shih

first: Jaime

last: Rodriguez-Canales

first: Jason

last: Hipp

first: Audrey

last: Player

last: Hu

first: Alisa

middle: M

last: Goldstein

first: Philip

last: Taylor

first: Michael

last: Emmert-Buck

first: Heidi

middle: S

last: Erickson


title: Genetic variation in radiation-induced cell death

status: Public on Aug 04 2011

city: Philadelphia

middle: Patrick

last: Morley

state: PA

address: 3400 Civic Center Blvd, Bldg 421

department: Penn Cardiovascular Institute

institute: Perelman School of Medicine at the University of Pennsylvania

summary: We used microarrays to measure the expression levels of genes in irradiated immortalized B cells, lymphoblastoid cells, from members of Centre d'Etude du Polymorphisme Humain (CEPH) Utah pedigrees. Data were collected for cells at baseline and 2 hours and 6 hours after exposure to 10 Gy of ionizing radiation (IR).

overall_design: We measured the expression levels of genes in irradiated immortalized B cells, lymphoblastoid cells, from members of 30 Centre d'Etude du Polymorphisme Humain (CEPH) Utah pedigrees (CEPH 1331, 1332, 1333, 1341, 1344, 1346, 1347, 1349, 1354, 1356, 1357, 1358, 1362, 1408, 1413, 1416, 1418, 1420, 1421, 1423, 1424, 1444, 1447, 1451, 1454, 1456, 1458, 1463, 1477, 1582). Cells were irradiated at 10 Gy in a 137Cs irradiator. Cells were harvested prior to radiation and at 2 and 6 hours following exposure to IR.

first: Denis

middle: A

last: Smirnov

middle: P

first: Sonia

last: Solomon

first: Lauren

last: Brady

first: Kris

last: Halasa

first: Vivian

middle: G

last: Cheung


title: Genome-wide analysis of ERalpha binding sites in U2OS-ERalpha cells

city: Los Angeles

first: susan

middle: a

last: krum

state: cA

address: 615 Charles E Young Dr. South; OHRC 410

institute: UCLA

summary: ChIP followed by deep sequencing was performed with antibodies to ERalpha in U2OS-ERalpha cells treated with 17beta-estradiol.

overall_design: Examination of Eralpha binding sites in U2OS-Eralpha cells.  Sequenced input was used as a control

first: Gustavo

last: Miranda-Carboni

first: Miriam

last: Guemes

first: Shannon

last: Bailey

first: Edgar

last: Anaya

first: Mirko

last: Corselli

first: Bruno

last: Peault

last: Krum


title: TGFß1-driven epithelial to mesenchymal transition in human kidney cell line

city: Belfast

first: Derek

last: Brazil

address: Grosvenor Road

institute: Queen's University

summary:
TGFbeta is the major cytokine driver of fibrosis in the kidney and other tissue. Epithelial-mesenchymal transition has been postulated to contibrute to renal fibrosis in diseases such as diabetic nephropathy.
We wished to identify novel genes that were upregulated in human kidney epithelial cells in response to TGFb1.The transcriptional responses for human proximal tubule epithelial cells to 10 ng/ml TGFbeta1 was examined over 24 and 48 hr

overall_design: There were three treatment groups: vehicle, 24hr TGFb1, 48 hr TGFb1. Each treatment was carried out in triplicate 10 cm plates and the experiment was carried out in triplicate using consecutive passages of cells.

first: Sarah

last: Roxburgh


title: Expression data from HeLa cells transiently transfected with control siRNA or SON siRNA

status: Public on Apr 01 2011

city: La Jolla

first: Dong-Er

last: Zhang

address: 3855 Health Sciences Drive, Mail Stop 0815

department: Cancer Center

institute: University of California San Diego

summary: SON is a large Ser/Arg (SR)-related protein localized in nuclear speckles. SON siRNA causes defects in mitotic progression and genome instability. We used microarrays to detail the pattern of gene expression after SON knockdown.

overall_design: HeLa cells were grown in 100 mm dishes and transfected with negative control siRNA or SON siRNA (400 pmol). Then, cells were harvested after 66 hours and RNAs were isolated. Microarrays were performed using GeneChip Human Genome U133A 2.0 (Affymetrix).

first: Eun-Young

last: Ahn

first: Russell

middle: C

last: DeKelver

first: Miao-Chia

last: Lo

first: Tuyet

last: Nguyen

first: Shinobu

last: Matsuura

first: Anita

last: Boyapati

first: Shatakshi

last: Pandit

first: Xiang-Dong

last: Fu


title: Breast Cancer Methylomes Establish an Epigenomic Foundation for Metastasis

status: Public on Mar 31 2011

city: New York

first: FANG

last: FANG

state: NY

address: 1275 York Avenue

department: The Human Oncology and Pathogenesis Program

institute: Memorial Sloan-Kettering Cancer Center

type:
Expression profiling by array
Methylation profiling by array

summary: Cancer-specific changes in DNA methylation can alter genetic stability, genomic structure, and gene expression.  Promoter CpG island methylation can result in transcriptional silencing and plays an important role in the oncogenic process. We used genome-wide analysis to characterize the methylomes of breast cancers with diverse metastatic behavior.   Here, we describe the identification of novel groups of breast tumors characterized by the presence or absence of coordinate hypermethylation at a large number of genes, demonstrating the existence of a breast-CpG island methylator phenotype (B-CIMP).  B-CIMP imparts a distinct epigenomic profile and is a strong determinant of metastatic potential.

overall_design:
Gene Expression Samples (GSM647057-GSM647077): Twenty-one breast cancer primary samples were analyzed. There are 10 CIMP positive and 11 CIMP negative samples.

Methylation Profiling Samples (GSM651372-GSM651410): Thirty-nine breast cancer primary samples were analyzed. There are 17 CIMP positive and 22 CIMP negative samples.

first: Fang

last: Fang

first: Timothy

last: Chan


title: The non-steroidal anti-inflammatory drugs Sulindac sulfide and Diclofenac induce apoptosis and differentiation in human acute myeloid leukemia cells through an AP-1 dependent pathway

status: Public on Mar 26 2011

city: Düsseldorf

first: Ingmar

last: Bruns

state: NRW

address: Moorenstr. 5

department: Hematology, Oncology and Clinical Immunology

country: Germany

institute: University of Düsseldorf

summary: Acute myeloid leukemia is a heterogeneous disease with regard to the underlying genetic and molecular pathophysiology. Non-steroidal anti-inflammatory drugs (NSAIDs) exert significant anti-proliferative effects in various malignant cells in vitro and in vivo. Hence, these agents can be utilized to study potential disease specific anti-proliferative pathways. In this study, a total number of 42 bone marrow derived CD34+ cells from de novo AML patients and the AML cell lines THP-1 and HL-60 were treated with the NSAIDs Sulindac sulfide and Diclofenac. We examined viability, apoptosis, differentiation and addressed the molecular mechanisms involved. We found a consistent induction of apoptosis and to some extent myeloid differentiation in NSAID treated AML cells. Comprehensive protein and gene expression profiling of Diclofenac treated AML cells revealed transcriptional activation of GADD45α and its downstream MAPK/JNK pathway as well as increased protein levels of the Caspase-3 precursor. This points towards a role of the c-Jun NH2-terminal kinase (JNK) in NSAID mediated apoptosis. This was dependent on JNK activity as addition of a specific JNK-inhibitor abrogated apoptosis. Furthermore, the AP-1 transcription factor family members’ c-Jun, JunB and Fra-2 were transcriptionally activated in NSAID treated AML cells. Re-expression of these transcription factors led to activation of GADD45α with induction of apoptosis. Mechanistically, we demonstrate that NSAIDs induce apoptosis in AML through a novel pathway involving increased expression of AP-1 heterodimers, which by itself is sufficient to induce GADD45α expression with consecutive activation of JNK and induction of apoptosis.

overall_design: HL-60 and THP-1 AML cells were treated with 100 µM Diclofenac or DMSO as control for 48 hours. Each experiment was performed in duplicate. After this treatment total RNA of the cells was harvested and analysed by means of gene expression profiling with the Affymetrix HU-133A array.

first: Raminder

last: Singh

first: Annemarie

last: Koch


title: Transcriptional targets of EphB2 and Ephrin-A4 signaling in epidermal keratinocytes

status: Public on Mar 01 2011

first: Miroslav

last: Blumenberg

address: 455 First Ave #874

department: Dermatology

institute: NYU School of Medicine

summary: Human epidermal keratinocytes were treated with 25 ng.ml EphB2 or EFNA4, both as-Fc conjugates (Sigma).

overall_design: Human epidermal keratinocytes are treated with 25 ng/ml EphB2 or EFNA4 Fc conjugates in a 48hr time course.

first: Rebecca

last: Walsh


title: Expression data of MCF-7 cells treated with gamma tocotrienol (g-T3)

city: Washington

first: Habtom

last: Ressom

state: DC

address: 4000 Reservoir Rd.

institute: Georgetown University

summary:
Gamma tocotrienol induces apoptosis in breast cancer cells however, the molecular mechanisms are not completely understood.
We used microarrays to detail the global programme of gene expression underlying the effects of gamma tocotrienols on MCF-7 cells and identified distinct classes of up-regulated genes during this process.

overall_design: MCF-7 cells were grown in DMEM medium with 5% FBS. The cells were treated with vehicle control (DMSO) or 40 uM of gamma tocotrienol for 24 h for RNA extraction and hybridization on Affymetrix microarrays. Four independent experiments were performed.

first: Dorrelyn

last: Patacsil

first: Anh-Thu

last: Tran

first: Youn-Sook

last: Cho

first: Simeng

last: Suy

first: Francisco

last: Saenz

first: Irina

last: Malyukova

first: Robert

last: Clarke

first: Deepak

last: Kumar


title: Analysis of gene expression in esophageal squamous cell carcinoma (ESCC)

status: Public on Mar 15 2011

city: Rockville

last: Clifford

address: 2115 E Jefferson

department: CCR

summary: To characterize gene expression in esophageal squamous cell carcinoma, we examined gene expression in tumor and matched normal adjacent tissue from 17 ESCC patients from a high-risk region of China.

overall_design:
RNA was extracted from 17 micro-dissected tumor and matched normal tissue pairs using the PureLink Micro-to-Midi Total RNA Purification System (Invitrogen, Carlsbad, CA)
Affymetrix HG-U133A 2.0 gene expression arrays were performed according to the manufacturer's directions.
The Robust Multiarray Average (RMA) algorithm implemented in Bioconductor in R was used for background correction and normalization across all samples.

last: Hu

first: Maxwell

last: Lee

first: Philip

last: Taylor


title: Genomic Collaboration of Estrogen Receptor-α and ERK2 in Regulating Gene and Proliferation Programs

status: Public on Jan 10 2011

city: Urbana

first: Zeynep

last: Madak Erdogan

state: IL

address: 1201 S Goodwin Ave

department: FSHN

institute: UIUC

summary:
The nuclear hormone receptor, estrogen receptor-alpha (ERα), and MAP kinases both play key roles in hormone-dependent cancers, yet their interplay and the integration of their signaling inputs remain poorly understood. In these studies, we document that estrogen-occupied ERα activates and interacts with ERK2, a downstream effector in the MAPK pathway, resulting in ERK2 and ERα colocalization at chromatin binding sites across the genome of breast cancer cells.
KEYWORDS: siRNA knock-down, ligand treatment

overall_design: MCF-7 human breast adenocarcinoma cells were tranfected with control, ERK1 and ERK2 siRNA for 60 hours and treated with 0.1% EtOH (Vehicle) or 10 nM E2 for 4 hours or 24 hours, and cDNA microarray analyses were carried out using Affymetrix [HG-U133A_2] Affymetrix Human Genome U133A 2.0 Array.

last: Erdogan

first: Benita

last: Katzenellenbogen


title: Targets of Ephrin-A signaling in epidermal keratinocytes

last: Blumenberg

summary: Both ephrins and their receptors are membrane bound, restricting their interactions to the sites of direct cell-to-cell interfaces. They are widely expressed, often co-expressed and regulate developmental processes, cell adhesion, motility, survival, proliferation, and differentiation. Both tumor suppressor and oncogene activities are ascribed to EFNs and Ephs in various contexts. A major conundrum regarding the EFN/Eph system concerns their large number and functional redundancy, given the promiscuous cross-activation of ligands and receptors and the overlapping intracellular signaling pathways. To address this issue, we treated human epidermal keratinocytes with 5 EFNAs individually and defined the transcriptional responses in the cells. We found that a large set of genes is coregulated by all EFNAs. However, while the responses to EFNA3, EFNA 4 and EFNA 5 are identical, the responses to EFNA1 and EFNA2 are characteristic and distinctive. All EFNAs induce epidermal differentiation markers and suppress cell adhesion genes, especially integrins. Ontological analysis shows that all EFNAs induce cornification and keratin genes, while suppressing wound-healing associated, signaling, receptor and ECM associated genes. Transcriptional targets of AP1 are selectively suppressed by EFNAs. EFNA1 and EFNA2, but not the EFNA3, EFNA4, EFNA5 cluster, regulate the members of the ubiquitin-associated proteolysis genes. EFNA1 specifically induces collagen production. Our results demonstrate that the EFN-Eph interactions in the epidermis, while promiscuous, are not redundant but specific. This suggests that different members of the EFN/Eph system have specific, clearly demarcated functions.

overall_design: Human epidermal keratinocytes are treated with 25 ng/ml EFNA1; EFNA2; EFNA3; EFNA4 or EFNA5 (all as Fc conjugates) for 24h.

last: Walsh


title: Mutational screening of linkage assay-identified candidate regions in familial breast cancer

status: Public on Feb 18 2011

city: Madrid

first: Javier

last: Benitez

address: Melchor Fernandez Almagro 3

department: Human Cancer Genetics Program

institute: National Cancer Research Centre CNIO

type: Genome variation profiling by high throughput sequencing

summary:
Background: The classical candidate-gene approach has failed to identify novel breast cancer susceptibility genes. Nowadays, massive parallel sequencing technology allows the development of studies unaffordable a few years ago. However, analysis protocols are not yet sufficiently developed to extract all information from the huge amount of data obtained.
Methodology/Principal Findings: In this study, we performed high throughput sequencing in two regions located on chromosomes 3 and 6, recently identified by linkage studies by our group as candidate regions for harbouring breast cancer susceptibility genes. In order to enrich for the coding regions of all described genes located in both candidate regions, a hybrid-selection method on tiling microarrays was performed.
Conclusions/Significance: We developed an analysis pipeline based on SOAP aligner to identify candidate variants with a high real positive confirmation rate (0.89), with which we identified eight variants considered candidates for functional studies. The results suggest that the present strategy is a valid second step for identifying high penetrance genes.

overall_design: 20 Samples / 4 Pooled Controls

first: Juan

last: Rosa-Rosa

last: Gracia-Aznárez

first: Emily

last: Hodges

first: Guillermo

last: Pita

first: Michelle

last: Rooks

first: Zhenyu

last: Xuan

first: Arindam

last: Bhattacharjee

first: Leonardo

last: Brizuela

first: José

last: Silva

first: Greg

last: Hannon


title: Expression data from Human foreskin fibroblasts (HFFs) infected with Toxoplasma gondii.

city: Cambridge

last: Rosowski

state: MA

address: 77 Massachusetts Ave, 68-258d

department: Biology

institute: MIT

summary:
Toxoplasma strains have been shown to modulate host cell transcription.  We have found a type II Toxoplasma gene, GRA15, which activates the nuclear translocation of the NF-kappaB p65 transcription factor.
We used microarrays to determine how GRA15II modulates host cell transcription.

overall_design: HFFs were infected with type I (RH), type I GRA15II (RH GRA15II), type II (Pru), type II GRA15KO (Pru GRA15KO), type III (cep), or type III GRA15II (cep GRA15II) parasites for 18-24 hours.  Some samples were also stimulated with TNF-alpha.  Total RNA was isolated and hybridized to Affymetrix GeneChip Human Genome U133A 2.0 arrays.

first: Jeroen

last: Saeij

first: Lindsay

last: Julien


title: Malignant Fibrous Histiocytoma - Pleomorphic Sarcoma, NOS -Gene expression, Histology and clinical course -A pilot study

status: Public on Jan 03 2011

city: Essen

first: Ludger

last: Klein-Hitpass

address: Virchowstr. 173

department: Universitaetsklinikum

institute: Institut fuer Zellbiologie

summary:
This study was performed to identify gene expression differences in not otherwise specified soft tissue sarcomas (NOS, malignant fibrous histiocytomas) and correlate them to histological findings and the clinical course. RNA was isolated and differential gene expression was analysed by the microarray technique.
We used microarrays to detail the global gene expression differences between primary soft tissue sarcoma samples, harvested intraoperatively.

Keywords: response to chemotherapeutic agent

overall_design: We compared the gene expression of ten different tumor samples of MFH/NOS sarcoma to determine global gene expression differences by microarray analysis.

first: L

first: A

last: Daigeler


title: [E-MTAB-345] ChIP-Seq of human MCF-7 cells with anti-ERalpha following estrogen treatment

status: Public on Feb 05 2011

city: Hinxton

first: ArrayExpress

last: EBI

state: Cambridgeshire

address: Wellcome Trust Genome Campus

institute: European Bioinformatics Institute

summary:
We performed chromatin immunoprecipitation (ChIP) with overnight with antibodies against the C-terminus (HC-20, from Santa Cruz Biotechnology, Europe) or the N-terminus (anti-Estrogen Receptor 18-32, from SigmaAldrich, Italy) of human ER-alpha with or without estrogen treatment for 45 minutes on TAP-ER-beta cells, and the immunoprecipitated DNA was sequenced with the Illumina/Solexa Genome Analyzer. (Note: Raw data files not provided by submitter)

Publication Title: Global analysis of ERbeta binding to human breast cancer cell genome
Publication Author List: Grober OMV, Mutarelli M, Paris O, Giurato G, De Filippo MR, Cicatiello L, Ravo M, Ferraro L, Nassa G, Tarallo R, Papa MF, Benes V, Alessandro Weisz.

ArrayExpress Release Date: 2010-10-05

Person Roles: submitter
Person Last Name: Weisz
Person First Name: Alessandro
Person Mid Initials:
Person Email: alessandro.weisz@unina2.it
Person Phone:
Person Address:
Person Affiliation: Second University of Naples

overall_design:
Experimental Design: compound_treatment_design
Experimental Design: in_vivo_design
Experimental Design: binding_site_identification_design
Experimental Design: high_throughput_sequencing_design
Experimental Factor Name: COMPOUND
Experimental Factor Name: IMMUNOPRECIPITATE
Experimental Factor Name: GENOTYPE
Experimental Factor Name: DOSE
Experimental Factor Type: compound
Experimental Factor Type: immunoprecipitate
Experimental Factor Type: genotype
Experimental Factor Type: dose
Quality Control Type: real_time_PCR_quality_control
Quality Control Type: technical_replicate


title: Effects of Glucocorticoids in Epidermal Keratinocytes

status: Public on Jan 07 2011

first: Miroslav

last: Blumenberg

summary: Glucocorticoids (GCs) have a long history of use as therapeutic agents for numerous skin diseases. Surprisingly, their specific molecular effects are largely unknown. To characterize GC action in epidermis, we compared the transcriptional profiles of primary human keratinocytes untreated and treated with dexamethasone (DEX) for 1, 4, 24, 48 and 72 hours using large-scale microarray analyses. The majority of genes were found regulated only after 24 hours and remained regulated throughout the treatment. In addition to expected anti-inflammatory genes, we found that GCs regulate cell fate, tissue remodeling, cell motility, differentiation and metabolism. GCs not only effectively block signaling by TNF-alpha and IL-1 but also by IFN-gamma, which was not previously known. Specifically, GCs suppress the expression of essentially all IFN-gamma-regulated genes, including IFN-gamma receptor and STAT-1.  GCs also block STAT-1 activation and nuclear translocation. Unexpectedly, GCs have anti-apoptotic effects in keratinocytes by inducing the expression of anti-apoptotic and repressing pro-apoptotic genes. Consequently, GCs treatment blocked UV-induced apoptosis of keratinocytes. GCs have a profound effect on wound healing by inhibiting cell motility and the expression of pro-angiogenic factor VEGF. They play an important role in tissue remodeling and scar formation by suppressing the expression of TGF-beta-1 and -2, MMP1, 2, 9 and 10 and inducing TIMP-2. Finally, GCs promote terminal stages of epidermal differentiation while simultaneously inhibiting the early stages. These results provide new insights into the beneficial and adverse effects of GCs in epidermis, defining the participating genes and mechanisms that coordinate the cellular responses important for GC-based therapies.

overall_design: Human epidermal keratinocytes are grown in delipidized, phenolphtalein-free medium and left as controls or treated with 0.1μM dexamethasone. Time course of treated and parallel control samples over a 72 hr period was performed twice with independent batches of cells.

first: Olivera

last: Stojadinovic

first: Brian

last: Lee

first: Constantinos

last: Vouthounis

first: Sasa

last: Vukelic

first: Irena

last: Pastar

first: Harold

last: Brem

first: Marjana

last: Tomic-Canic


title: Expression data from host cells infected with different strains of Toxoplasma gondii

first: Emily

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

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus

overall_design: Refer to individual Series


title: A Transcriptomic Analysis of NET1 (a RhoA GEF Exchange Factor) in AGS Gastric Cancer Cells

status: Public on Jan 02 2011

city: Dublin

first: David

last: MURRAY

address: 123 St Stephens Green

country: Ireland

institute: RCSI

summary:
Stable knockdown of NET1, a RhoGEF, was achieved in AGS Gastric Cancer cells.  This gene is known to be overexpressed in the disease.
Knockdown was achieved using lentiviral shRNA particles.  Gene expression was compared between knockdown and scrambled shRNA treated control cells.
Cells were treated with and without LPA, a known activator of RhoA.

overall_design: Three distinct cell lines were used in this study (all AGS cells); (i) Non Target cell (NT) stably expressing non targetting shRNA (ii) 63 and (iii) 65; the latter two are stable NET1 knockdown cells and are seperatly transduced with separate NET1 targetting shRNA particles.  Cells were treated with and without 10microM LPA for 4 hr.  Experimental replicates were performed for each treatment (A & B), RNA was prepared from each and seperatly hybridised to U133A arrays.

last: Murray


title: Epidermal differentiation: basal vs. suprabasal keratinocytes

status: Public on Dec 15 2010

summary: In epidermal differentiation basal keratinocytes detach from the basement membrane, stop proliferating, and express a new set of structural proteins and enzymes, which results in an impermeable protein/lipid barrier that protects us. To define the transcriptional changes essential for this process, we purified large quantities of basal and suprabasal cells from human epidermis, using the expression of b4 integrin as the discriminating factor. The expected expression differences in cytoskeletal, cell cycle and adhesion genes confirmed the effective separation of the cell populations. Using DNA microarray chips, we comprehensively identify the differences in genes expressed in basal and differentiating layers of the epidermis, including the ECM components produced by the basal cells, the proteases in both the basal and suprabasal cells, and the lipid and steroid metabolism enzymes in suprabasal cells responsible for the permeability barrier. We identified the signaling pathways specific for the two populations, and found two previously unknown paracrine and one juxtacrine signaling pathway operating between the basal and suprabasal cells. Furthermore, using specific expression signatures, we identified a new set of late differentiation markers and mapped their chromosomal loci, as well as a new set of melanocyte-specific markers. The data represent a quantum jump in understanding the mechanisms of epidermal differentiation. Basal keratinocytes are defined as integrin b4-positive. Suprabasal sample contains all melanocytes as well.

overall_design: Basal (integrin b4+), suprabasal (b4-) and total epidermal keratinocytes. In duplicate, from 2 independent donors, breast reduction surgery.

first: Alix

last: Gazel

first: Nada

last: Radoja

first: Tomohiro

last: Banno

first: Shoichiro

last: Yano


title: Complementary patterns of gene expression by human oligodendrocyte progenitors and their environment predict determinants of progenitor maintenance and differentiation.

status: Public on Feb 01 2011

city: Buffalo

first: Fraser

middle: James

last: Sim

address: 3435 Main Street

department: Pharmacology

institute: University at Buffalo

summary:
OBJECTIVE: Glial progenitor cells are abundant in adult human white matter. This study was designed to identify signaling pathways regulating their self-renewal and fate.

METHODS: We compared the transcriptional profiles of freshly sorted adult human white matter progenitor cells (WMPCs), purified by A2B5-based immunomagnetic sorting, with those of the white matter from which they derived.

RESULTS: We identified 132 genes differentially expressed by WMPCs; these included principal components of five receptor-defined signaling pathways, represented by platelet derived growth factor receptor alpha (PDGFRA) and type 3 fibroblast growth factor receptor (FGFR3), receptor tyrosine phosphatase-beta/zeta (RTPZ), notch, and syndecan3. WMPCs also differentially expressed the bone morphogenetic protein 4 (BMP4) inhibitors neuralin and BAMBI (BMP and activin membrane-bound inhibitor), suggesting tonic defense against BMP signaling. Differential overexpression of RTPZ was accompanied by that of its modulators pleiotrophin, NrCAM, tenascin, and the chondroitin sulfate proteoglycans, suggesting the importance of RTPZ signaling to WMPCs. When exposed to the RTPZ inhibitor bpV(phen), or lentiviral-shRNAi against RTPZ, WMPCs differentiated as oligodendrocytes. Conversely, when neuralin and BAMBI were antagonized by BMP4, astrocytic differentiation was induced, which was reversible by noggin.

INTERPRETATION: The RTPZ and BMP pathways regulate the self-maintenance of adult human WMPCs, and can be modulated to induce their oligodendrocytic or astrocytic differentiation. As such, they provide targets by which to productively mobilize resident progenitor cells of the adult human brain.

overall_design: 6 samples, three biological replicates (individual patients), 2 groups (A2B5+ and unsorted cells).

first: Jennifer

last: Lang

first: Ben

last: Waldau

first: Theodore

last: Schwartz

first: Webster

middle: H

last: Pilcher

first: Karen

last: Chandross

first: Sridaran

last: Natesan

first: Jean

last: Merrill

first: Steven

last: Goldman


title: Expression data from DU145 cells treated with STAT3 siRNA

status: Public on Dec 07 2010

first: Olga

last: Timofeeva

address: 3900 Reservoir Rd NW

department: Oncology

institute: Georgetown University Medical Center

summary:
Activation of Signal Transducer and Activator of Transcription 3 (STAT3) is common in prostate cancers. STAT3 may induce cell proliferation and resistance to apoptosis, as well as promote tumor angiogenesis, invasion, and migration by activating gene expression. Many STAT3-dependent transcriptional responses are mediated through protein-protein interactions that involve the amino-terminal domain (N-domain).
In this study, we found that inhibition of the STAT3 N-domain using novel inhibitor ST3-Hel2A-2 induces apoptotic death in prostate cancer cells. The cell death was accomponied by robust activation of pro-apoptotic gene. Using chromatin immunoprecipitation and tiling human promoter arrays (ChIP-chip), we have defined genome-wide targets of STAT3 in DU145 prostate cancer cells. We found that upregulated pro-apoptotic genes were bound by STAT3 in prostate cancer cells, and that STAT3 binding was decreased following inhibition of the STAT3 N-domain. STAT3 siRNA knockdow confirmed specificity of STAT3 binding and changes in gene expression.

overall_design: DU145 cells were treated with STAT3 siRNA or scrambled siRNA for 48hr. Total RNA has been extracted and prepared for hybridization on Affymetrix HG-U133A 2.0 arrays.

first: O


title: Genome-wide empirical binding sites co-occupied by p53 and NF-kB in human cardiomyopathy

status: Public on Jan 01 2011

first: Mun-Kit

last: Choy

address: Box 110, Level 6, ACCI Building, Addenbrooke’s Hospital, Hills Road

department: Division of Cardiovascular Medicine

institute: University of Cambridge

summary:
p53 and NF-kB are important transcription factors involved in the pathogenesis of cardiac hypertrophy and the progression to heart failure/dilatation. We report the genome-wide empirical binding sites co-occupied by the transcription factors in human dilated hearts. p53-NF-kB sequential chromatin immunoprecipitation and high-throughput sequencing were performed using tissues from control and diseased hearts. These data may facilitate the discovery of mechanisms by which transcription factors cooperate in close proximity or a multi-molecular complex at a cis-regulatory element to control gene expression.

Raw data (qseq format) files are available on the following FTP site:
ftp://ftp.ncbi.nlm.nih.gov/pub/geosup/Series/GSE21356

overall_design: Examination of p53 and NF-kB transcription factor binding sites in 4 control and 4 diseased hearts (pooled) using ChIP-Seq.

first: Roger

last: Foo


title: Role of STAT3 in DU145 prostate cancer cell line

status: Public on Dec 10 2010

type: Genome binding/occupancy profiling by genome tiling array


title: Normal prostate cells were immortalized and cultured for 650 days till several transformation hallmarks were observed

status: Public on Dec 01 2010

city: Raanana

first: Yuval

last: Tabach

address: Hativat Givaty 30

department: Molecular Cell Biology

country: Israel

institute: Weizmann Institute of Science

summary: Duplication of chromosomal arm 20q occurs in prostate, cervical, colon, gastric, bladder, melanoma, pancreas and breast cancer, suggesting that 20q amplification may play a key causal role in tumorigenesis. According to an alternative view, chromosomal instabilities are mainly a common side effect of cancer progression. To test whether a specific genomic aberration might serve as a cancer initiating event, we established an in vitro system that models the evolutionary process of early stages of prostate tumor formation; normal prostate cells were immortalized and cultured for 650 days till several transformation hallmarks were observed. Gene expression patterns were measured and chromosomal aberrations were monitored by spectral karyotype analysis at different times. Several chromosomal aberrations, in particular duplication of chromosomal arm 20q, occurred early in the process and were fixed in the cell populations, while other aberrations became extinct shortly after their appearance. A wide range of bioinformatic tools, applied to our data and to data from several cancer databases, revealed that spontaneous 20q amplification can promote cancer initiation. Our computational model suggests that deregulation of some key pathways, such as  MAPK, p53, cell cycle regulation and Polycomb group factors, in addition to activation of several genes like Myc, AML, B-Catenin and the ETS family  transcription factors, are key steps in cancer development driven by 20q amplification. Finally we identified 13 cancer initiating genes, located on 20q13, which were significantly overexpressed in many tumors, with expression levels correlated with tumor grade and outcome; these probably play  key roles  in inducing malignancy via20q amplification.

overall_design: 33 samples were analysised, 12 were in replicate

first: Ira

last: Kogan-Sakin

first: Yossi

last: Buganim

first: Naomi

last: Goldfinger

first: Eytan

last: Domany

first: Varda

last: Rotter


title: Expression data from DU145 cells treated with ST3-Hel2A-2 STAT3 N-domain inhibitor coupled to analysis of genome-wide STAT3 binding sites

summary:
Activation of Signal Transducer and Activator of Transcription 3 (STAT3) is common in prostate cancers. STAT3 may induce cell proliferation and resistance to apoptosis, as well as promote tumor angiogenesis, invasion, and migration by activating gene expression. Many STAT3-dependent transcriptional responses are mediated through protein-protein interactions that involve the amino-terminal domain (N-domain).
In this study, we found that inhibition of the STAT3 N-domain using novel inhibitor ST3-Hel2A-2 induces apoptotic death in prostate cancer cells. The cell death was accomponied by robust activation of pro-apoptotic gene. Using chromatin immunoprecipitation and tiling human promoter arrays (ChIP-chip), we have defined genome-wide targets of STAT3 in DU145 prostate cancer cells. We found that upregulated pro-apoptotic genes were bound by STAT3 in prostate cancer cells, and that STAT3 binding was decreased following inhibition of the STAT3 N-domain.

overall_design: DU145 cells were treated with ST3-Hel2A-2 or DMSO as a control for 3 hr. Total RNA has been extracted and prepared for hybridization on Affymetrix HG-U133A 2.0 arrays.


title: The role of integrins in human cytomegalovirus (HCMV)-infected monocytes.

status: Public on Oct 31 2010

city: Shreveport

first: Andrew

middle: D.

last: Yurochko

state: LA

address: 1501 Kings Highway

department: Microbiology & Immunology

institute: LSUHSC-S

summary: We have established that human cytomegalovirus (HCMV) infection modulates the biology of target primary blood monocytes, allowing HCMV to use monocytes as “vehicles” for its systemic spread.  HCMV infection of monocytes results in rapid induction of PI(3)K and NF-κB activity.  Integrins, which are upstream of the PI(3)K and NF-κB pathways, were shown to be involved in HCMV binding to and entry into fibroblasts, suggesting that receptor-ligand-mediated signaling following viral binding to integrins on monocytes could trigger the functional changes seen in infected monocytes.  We now show that integrin engagement and the activation of the integrin/Src-signaling pathway is essential for the induction of HCMV-infected monocyte motility.  To investigate how integrin engagement by HCMV triggers monocyte motility, we examined the infected monocyte transcriptome and found that the integrin/Src-signaling pathway regulates the expression of paxillin, which is an important signal transducer in the regulation of actin rearrangement during cell adhesion and movement.  Functionally, we observed that paxillin is activated via the integrin/Src-signaling pathway and is required for monocyte motility.  Because motility is intimately connected to cellular cytoskeletal organization, a process that is also important in viral entry, we investigated the role paxillin regulation plays in the process of viral entry of monocytes. New results confirmed that HCMV`s ability to enter target monocytes is significantly inhibited in cells deficient in paxillin expression or that had their integrin/Src/paxillin signaling pathway blocked. From our data, HCMV-cell interactions emerge as an essential trigger for the cellular changes that allow for HCMV entry and hematogenous dissemination.

overall_design:
Monocytes were mock-infected, HCMV-infected, or pretreated with PP2 inhibitor prior to HCMV infection. There were three samples analyzed per individual replicate. Three replicates are included.
comparative studies with a use of the specific Src kinase activity inhibitor

first: Maciej

middle: T

last: Nogalski

first: Gary

last: Chan

middle: D


title: Integrative genomics identifies molecular alterations that differentiate superficial spreading and nodular melanoma

first: Iman

last: Osman

address: 522 First Avenue, SML405

department: Urology

institute: New York University School of Medicine

type: Genome binding/occupancy profiling by SNP array


title: Glucocoritcoid regulated genes in omental and subcutaneous human adipose tissues

status: Public on Dec 17 2010

city: Boston

first: Mi-Jeong

last: Lee

address: 650 Albany St 810

department: Medicine

institute: Boston University

summary:
To provide a comprehensive understanding of how GC affect adipose tissue and adipocyte function, we analyzed patterns of gene expression after culture of abdominal subcutaneous (sc) and omental (Om))
Adipose tissue of severely obese subjects (3F, 1M) in the presence of insulin or insulin (7 nM) plus dexamethasone (dex, 25 nM) for 7d.

overall_design: 14 chips total (8x HG_U95Av2, 6x HG_U95A)

first: Dawei

last: Gong

first: Brian

last: Burkey

first: Susan

middle: K

last: Fried


title: Gene expression data from melanoma cell lines and melanocyte controls

summary: The two most common melanoma histopathologic subtypes, superficial spreading (SSM) and nodular melanoma (NM), are believed to represent sequential phases of linear progression from radial to vertical growth. Studies suggest, however, that SSM and NM are biologically distinct. We utilized an integrative genomic approach to examine the possibility that SSM and NM are the result of independent pathways characterized by unique molecular alterations. Cell lines including SSM, NM, metastatic melanoma, and melanocyte controls were evaluated for copy number changes and differential mRNA expression using single nucleotide polymorphism array (SNP 6.0, Affymetrix) and gene array (U133A 2.0, Affymetrix). Data sets were integrated to identify copy number alterations that correlated with gene expression, and array results were validated using immunohistochemistry on human tissue microarrays (TMAs) and an external data set.  The functional effect of genomic deletion was assessed by lentiviral overexpression. Integrative genomics revealed 8 genes in which NM/SSM-specific copy number alterations were correlated with NM/SSM differential gene expression (P<0.05, Spearman’s rank). Pathways analysis of differentially expressed genes (N=114) showed enrichment for metabolic-related processes. SSM-specific genomic deletions (DIS3, MTAP, G3BP2, SEC23IP, USO1) were verified in an expanded panel of cell lines, and forced overexpression of MTAP in SSM resulted in reduced cell growth. Metabolism-related gene ALDH7A1 was verified as overexpressed in NM using human TMAs.The identification of recurrent genomic deletions in SSM not present in NM challenges the linear model of melanoma progression and supports the unique molecular classification of SSM and NM.

overall_design: Gene expression profiling using Affymetrix U133A 2.0 arrays was performed on 18 melanoma cell lines including 2 primary superficial spreading melanoma, 2 primary nodular melanoma, 2 metastatic nodular melanoma, and 12 metastatic cell lines. Four melanocyte control lines were also evaluated including 2 immortalized melanocyte cell lines (Hermes 1 and 2B) and 2 normal melanocyte lines cultured from neonatal foreskin (HEM-N and HEM-LP).


title: Response of A549 cells treated with Aspergillus fumigatus [WT-CF_vs_WT-GC]

status: Public on Oct 29 2010

city: Tel-Aviv

first: Nir

last: Osherov

address: Ramat Aviv Campus

department: Medical Microbiology and Immunology

institute: Tel-Aviv University

summary:
Response of A549 cells treated with Aspergillus fumigatus germinating conidia (WT-GC) or culture filtrate (WT-CF) for 8h
Aspergillus fumigatus is the most commonly encountered mold pathogen of humans, predominantly infecting the respiratory system. Colonization and penetration of the lung alveolar epithelium is a key but poorly understood step in the infection process. This study focused on identifying the transcriptional and cell-signaling responses activated in A549 alveolar carcinoma cells incubated in the presence of A. fumigatus wild-type and ΔPrtT protease-deficient germinating conidia and culture filtrates (CF). Microarray analysis of exposed A549 cells identified distinct classes of genes whose expression is altered in the presence of germinating conidia and CF and suggested the involvement of both NFkB and MAPK signaling pathways in mediating the cellular response. Phosphoprotein analysis of A549 cells confirmed that JNK and ERK1/2 are phosphorylated in response to CF treatment in a protease-dependent manner. Inhibition of JNK or ERK1/2 kinase activity substantially decreased CF-induced cell damage, including cell peeling, actin-cytoskeleton damage, and reduction in metabolic activity and necrotic death. These results suggest that inhibition of MAPK-mediated host responses to treatment with A. fumigatus CF decreases cellular damage, a finding with possible clinical implications.

overall_design: 3 independent controls (uninfected A549 cells) as ctrl2_1-3, 2 independent treatments of A549 cells with wild-type A. fumigatus culture filtrates (WT-CF2_1-2) and 2 independent treatments of A549 cells with wild-type A. fumigatus germinating conidia (WT-GC_2-3).

first: Haim

last: Sharon

first: David

last: Amar

first: Ron

last: Shamir


title: Using a Stem Cell-Based Signature to Guide Therapeutic Selection in Cancer

status: Public on Oct 16 2010

city: Durham

first: Igor

last: Shats

state: NC

address: 101 Science Drive

institute: Duke University

summary:
Given the very substantial heterogeneity of most human cancers, it is likely that most cancer therapeutics will be active in only a small fraction of any population of patients. As such, the development of new therapeutics, coupled with methods to match a therapy with the individual patient, will be critical to achieving significant gains in disease outcome. One such opportunity is the use of expression signatures to identify key oncogenic phenotypes that can serve not only as biomarkers but also as a means of identifying therapeutic compounds that might specifically target these phenotypes. Given the potential importance of targeting tumors exhibiting a stem-like phenotype, we have developed an expression signature that reflects common biological aspects of various stem-like characteristics.  The Consensus Stemness Ranking (CSR) signature is upregulated in cancer stem cell enriched samples, at advanced tumor stages and is associated with poor prognosis in multiple cancer types. Using two independent computational approaches we utilized the CSR signature to identify clinically useful compounds that could target the CSR phenotype. In vitro assays confirmed selectivity of several predicted compounds including topoisomerase inhibitors and resveratrol towards breast cancer cell lines that exhibit a high-CSR phenotype. Importantly, the CSR signature could predict clinical response of breast cancer patients to a neoadjuvant regimen that included a CSR-specific agent.  Collectively, these results suggest therapeutic opportunities to target the CSR phenotype in a relevant cohort of cancer patients.

This SuperSeries is composed of the SubSeries listed below.

overall_design: Refer to individual Series.

first: Joseph

last: Nevins


title: Organotpyic Human Epithelial Neoplasia

status: Public on Oct 15 2010

city: Stanford

first: Todd

middle: W.

last: Ridky

address: 269 Campus Drive

institute: Stanford University

summary: Refined cancer models are required to assess the burgeoning number of potential targets for cancer therapeutics within a rapid and clinically relevant context.  Here we utilize tumor-associated genetic pathways to transform primary human epithelial cells from epidermis, oropharynx, esophagus, and cervix into genetically defined tumors within an entirely human 3-dimensional (3-D) tissue environment incorporating cell-populated stroma and intact basement membrane (BM). These engineered organotypic tissues recapitulated natural features of tumor progression, including epithelial invasion through the BM, a complex process critically required for biologic malignancy in 90% of human cancers. Invasion was rapid, and potentiated by stromal cells.  Oncogenic signals in 3-D tissue, but not 2-D culture, resembled gene expression profiles from spontaneous human cancers. Screening well-characterized signaling pathway inhibitors in 3-D organotypic neoplasia helped distil a clinically faithful cancer gene signature. Multi-tissue 3-D human tissue cancer models may provide an efficient and relevant complement to current approaches to characterize cancer progression.

overall_design: Organotypic human epidermal epithium expressing LacZ, cdk4 and Hras, or cdk and Ras with U0126 mediated MEK inhibition were harvested for RNA extraction and hybridization on Affymetrix microarrays. There are 8 biologic replicates for the LacZ, and cdk4 Ras groups, and 2 biologic replicates for the U0126 treated samples.

middle: W

first: Paul

last: Khavari


title: Gene expression profiling of CD34+ subsets in Multiple Myeloma and healthy individuals

status: Public on Oct 27 2010

first: Ingmar

last: Bruns

address: Moorenstr. 5

institute: University of Düsseldorf

summary: Multiple myeloma (MM) is a clonal plasma cell disorder frequently accompanied by hematopoietic impairment. Genomic profiling of distinct HSPC subsets revealed a consistent deregulation of signaling cascades, including TGF beta signaling, p38MAPK signaling and pathways involved in cytoskeletal organization, migration, adhesion and cell cycle regulation in MM patients.

overall_design: CD34+ subsets of 7 patients with Multiple Myeloma and 5 healthy volunteers were analysed by means of gene expression profiling with the Affymetrix HU-133A 2.0 array


title: Basal gene expression of breast cancer cell lines

status: Public on Oct 08 2010

summary: Given the very substantial heterogeneity of most human cancers, it is likely that most cancer therapeutics will be active in only a small fraction of any population of patients. As such, the development of new therapeutics, coupled with methods to match a therapy with the individual patient, will be critical to achieving significant gains in disease outcome. One such opportunity is the use of expression signatures to identify key oncogenic phenotypes that can serve not only as biomarkers but also as a means of identifying therapeutic compounds that might specifically target these phenotypes. Given the potential importance of targeting tumors exhibiting a stem-like phenotype, we have developed an expression signature that reflects common biological aspects of various stem-like characteristics.  The Consensus Stemness Ranking (CSR) signature is upregulated in cancer stem cell enriched samples, at advanced tumor stages and is associated with poor prognosis in multiple cancer types. Using two independent computational approaches we utilized the CSR signature to identify clinically useful compounds that could target the CSR phenotype. In vitro assays confirmed selectivity of several predicted compounds including topoisomerase inhibitors and resveratrol towards breast cancer cell lines that exhibit a high-CSR phenotype. Importantly, the CSR signature could predict clinical response of breast cancer patients to a neoadjuvant regimen that included a CSR-specific agent.  Collectively, these results suggest therapeutic opportunities to target the CSR phenotype in a relevant cohort of cancer patients.

overall_design: Untreated breast cancer cell lines

middle: R


title: Response of A549 cells treated with Aspergillus fumigatus


title: Expression data from CD133+ and CD133- glioma cells

overall_design: CD133+ and CD133- cells were separated from two glioma xenograft tumors. Both CD133+ and CD133- glioma cells were cultured in serum-free media for 48 hours in the presence of absence of laminin.


title: Expression data from PonA stimulated transfected U373 Cells

status: Public on Oct 01 2010

city: St. Peter

first: Sanjive

last: Qazi

state: MN

address: 800 west College Av

institute: Gustavus Adolphus College

summary:
Induction of proximal components of the PI3-K/AKT pathway stimulates the expression of several genes, including several genes in the JAK/STAT pathway, documenting a crosstalk between these two important pathways.
These changes were accompnied by nuclear translocation of certain transcription factors as well.

overall_design: we measured levels of RNA transcripts using the Human Genome U95 Av2 geneChip microarrays.  We used an ecdysone-inducible mammalian expression system.

first: F

middle: M

last: Uckun

first: S


title: Gene expression of bone marrow fibroblasts from monoclonal gammopathy of undetermined significance and active multiple myeloma

status: Public on Oct 30 2010

city: Bari

first: angelina

last: boccarelli

state: Bari

address: P.zza G. Cesare, 11

institute: University of Bari

summary:
Fibroblasts are a key cellular component of tumour microenvironment, along with other stromal cells playing a critical role in disease initiation and progression (1). In this study, bone marrow fibroblasts deriving from patients with monoclonal gammopathy of undetermined significance (MGUS) or active multiple myeloma (MM) were subjected to global gene expression analysis, in order to identify  progression-associated alterations of gene expression.  Through immunoselection procedures, primary cultures of bone marrow fibroblasts were established  from bone marrow aspirate of 18 patients fullfilling the International Myeloma Working Group diagnostic criteria for MM (n=10) and MGUS (n=8). Differentially expressed genes were investigated through cDNA microarray (21,329 70-mer oligonucleotides; dual-label competitive hybridization), using the reference design as experimental protocol and t-test statistics for identifying differentially expressed genes.   A number of genes functionally involved in survival, proliferation, motility, inflammation   and angiogenesis  were found to be up-regulated in bone marrow fibroblasts from MM patients with respect to MGUS patients. In parallel, several genes were down-regulated in MM fibroblasts.  Overall, bone marrow fibroblasts from MM patients show a distinct gene expression pattern that differentiates them from bone marrow fibroblasts of MGUS. The observation of differentially expressed genes indicates an activation state of  fibroblasts in MM, which very likely concur to determine a microenvironment supporting disease progression.
1. Kalluri R, Zeisberg M:  Fibroblasts in cancer. Nat Rev Cancer 2006; 6: 392:401.

overall_design: Bone marrow fibroblasts deriving from patients with monoclonal gammopathy of undetermined significance (MGUS) and active multiple myeloma (MM), were provided by A.Vacca, (Department of Biomedical Sciences and Human Oncology, Università degli Studi di Bari Aldo Moro, Italy). Briefly, primary coltures of bone marrow fibroblasts were established through immunoselection procedures on aspirates of 18 patients fullfilling the IMWG diagnostic criteria for active MM (n=10) and MGUS (n=8). Total RNA was extracted from each primary culture (test samples), and 1 μg-aliquots of RNA from MGUS samples were pooled to obtain the reference RNA. Linear amplification of mRNA and fluorescent labelling of cDNA targets  (Cy5, MM and MGUS test samples; Cy3, reference RNA) were performed by using the Amino Allyl MessageAmp II aRNA Amplification Kit (Ambion), and examined on  Micro-CRIBI Human Oligo Array (Operon V2.0) microarrays. Array scanning was carried out using a VersArray ChipReader® 5μm dual confocal laser scanner with VersArray ChipReader v3.1 analysis software , while row scanner images were analyzed with VersArray Analyzer Software v4.5 (Bio-Rad Laboratories) using media pixel intensities for each spot. Global background was subtracted by biquadratic polynomial approximation,  and cross-channel normalization was performed by local regression (LOESS);  logarithmic transformation was then performed for each expression level.


title: BI Human Reference Epigenome Mapping Project: Characterization of chromatin modification by ChIP-Seq in human subject

status: Public on Nov 12 2010

first: BROAD

last: INSTITUTE

institute: Broad Institute

summary:
Genome scale characterization of chromatin modification, RNA expression, and cytosine methylation in a diverse panel of primary human cells and tissues, stem cells, and iPS cells derived from deidentified human subjects

****************
For data usage terms and conditions, please refer to:
http://www.drugabuse.gov/funding/funding-opportunities/nih-common-fund/epigenomics-data-access-policies
****************

overall_design:
BI Human Reference Epigenome Mapping Project - samples and experiments will continue to be added to this study over the course of the project.

EDACC Genboree Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FSTUDY%2FEDACC.3212

first: Bradley

middle: E

last: Bernstein

first: Alex

last: Meissner


title: Profiling of novel p53-inducing compounds

city: Baltimore

first: hester

last: liu

address: 1550 Orleans st

department: Radiation Oncology

institute: Johns Hopkins University

summary:
We describe six novel lead compounds activating the p53 tumor suppressor pathway.  Transcriptional profiling indicated that they invoked highly similar responses involving p53 and cell cycle pathways and DNA damage response signaling.

Keywords: Stress response

overall_design: Six compounds and one vehicle control, with four biological replicates each, for a total of 28 samples.

first: Hester

last: Liu

first: Marikki

last: Laiho


title: Organotypic Human Epithelial Neoplasia

status: Public on Sep 15 2010

overall_design: Organotypic human cervical epithium expressing LacZ, cdk4 and Ras, or cdk and Ras with U0126 mediated MEK inhibition were harvested for RNA extraction and hybridization on Affymetrix microarrays. There are 2 biologic replicates for each group.


title: Cyclin D1 in AL Amyloidosis Baseline Plasma Cells

first: Lakshmanan

last: Iyer

address: 136 Harrison Ave

department: Neuroscience

institute: Tufts University

summary:
CD138-selected marrow plasma cells from newly diagnosed AL patients were studied for cyclin D1 expression.
We identified patients whose plasma cells overexpressed cyclin D1 and compared them to those whose cells did not.

overall_design: We compared two groups of AL patients based cyclin D1 expression being high or low.

first: Raymond

middle: L

last: Comenzo


title: Effect of imatinib on philadelphia chromosome positive acute lymphoblastic leukemia

status: Public on Sep 10 2010

city: Los Angeles

first: Markus

last: Müschen

address: 4650 Sunset Blvd

department: Childrens Hospital Los Angeles

institute: University of Southern California

summary: The Philadelphia chromosome (Ph) encodes the oncogenic BCR-ABL1 tyrosine kinase, which defines a subset of acute lymphoblastic leukemia (ALL) with a particularly unfavorable prognosis. In this study, the tyrosine kinase inhibitor imatinib was used for pharmacological inhibition of BCR-ABL1. Gene expression profiles of Ph+ ALL cell lines were analyzed in response to imatinib treatment.

overall_design: Four Ph+ ALL cell lines (BV-173, NALM-1, SUP-B15, and TOM1) were either treated with 10µM STI571 (Imatinib) for 16 hours or cultured in absence of STI571.

first: Cihangir

last: Duy

first: Christian

last: Hurtz

first: Leandro

last: Cerchietti

first: Lars

last: Klemm

first: Srividya

last: Swaminathan

first: Seyedmehdi

last: Shojaee

first: Weimin

last: Ci

first: Huimin

last: Geng

first: Melanie

last: Braig

first: Wolf-Karsten

last: Hofmann

first: Phillip

last: Koeffler

first: Jessica

middle: J

last: Yu

first: Rahul

last: Nahar

first: Soo-mi

last: Kweon

first: Lothar

last: Hennighausen

first: Sebastian

last: Herzog

first: Hassan

last: Jumaa

first: Eugene

last: Park

first: Yong-mi

last: Kim

first: John

last: Groffen

first: Nora

last: Heisterkamp

first: Hilda

middle: B

last: Ye

first: Ari

last: Melnick


title: Expression data from human colon cancer cell line HCT116 with NFX1-91 knockdown and control cells

status: Public on Aug 18 2010

city: Seattle

first: Mei

last: Xu

state: WA

address: 1100 Fairview Ave N

department: MCB

institute: Fred Hutchinson Cancer Research Center

summary: NFX1-91, a novel E6 cellular downstream target, functions as a transcriptional regulator and is involved in repressing hTERT expression.  Other functions and downstream targets regulated by NFX1-91 were not well understood. We used microarrays to determine gene expression deregulated when NFX1-91 was knocked down.

overall_design: HCT116 cells was infected with lentivirus carrying NFX1-91 shRNA or control β-Galactosidase shRNA to stably knock down target gene expression. Total RNAs were extracted and hybridized on Affymetrix microarrays.

first: Rachel

middle: A

last: Katzenellenbogen

first: Carla

last: Grandori

first: Denise

last: Galloway


title: Expression profile of proliferating and differentiating primary human keratinocytes in vitro

status: Public on Aug 01 2010

city: Lausanne

first: Magdalena

last: Obarzanek-Fojt

address: Beaumont 29

department: Dermatology

country: Switzerland

institute: CHUV

summary: Human epidermal keratinocytes undergo tightly controlled program of cell differentiation, leading to the formation of cornified envelope. Primary keratinocytes in vitro, under calcium stimulation mimic the differentiation program observed in vivo. Analysis of the transcription profile of two cell population, such as proliferating cells and differentiating cells helps to discover new genes implicated in that process and to understand the mechanisms of regulation of the keratinocyte differentiation.

overall_design: Primary human keratinocytes were cultured under proliferating (Day 0, sub-confluent cells) and differentiating (seven days of high calcium medium) conditions. As a source of cells, we used normal skin from different body sites: back, foreskin, palmoplantar. RNA extracted from cultured primary human keratinocytes were isolated from five different donors. We compared the expression profiles of proliferating versus differentiating keratinocytes.

first: Bertrand

last: Favre

first: Marcel

last: Huber

first: Daniel

last: Hohl

first: Keith

last: Harshmann

first: Sylvain

last: Pradervand

first: Otto

last: Hagenbüchle

first: Alexandra

last: Paillusson


title: Imaging-guided microarray: Identifies molecular markers in the pathogenesis of Parkinson’s disease

status: Public on Aug 19 2010

city: new york

first: scott

last: small

institute: Columbia University

summary: The full complement of molecular pathways contributing to Parkinson’s disease (PD) pathogenesis remains unknown.  Here, to address this issue, we began by using a high-resolution variant of functional magnetic resonance imaging (fMRI) to pinpoint brainstem regions differentially affected by, and resistant to, the disease. Then, relying on the imaging information as a guide, we profiled gene expression levels of postmortem brain samples and used a factorial statistical model to identify a disease related decrease in the expression of the polyamine enzyme spermidine/spermine N1-acetyltransferase 1 (SAT1).  Next, a series of studies were performed to confirm the pathogenic relevance of this finding. First, to test for a causal link between polyamines and α-synuclein toxicity, we investigated a yeast model expressing α-synuclein. Polyamines were found to enhance the toxicity of α-synuclein, and an unbiased genome-wide screen for modifiers of α-synuclein toxicity identified Tpo4, a member of a family of proteins responsible for polyamine transport.   Second, to test for a causal link between SAT1 activity and PD histopathology we investigated a mouse model expressing α-synuclein.  DENSPM (N1, N11-diethylnorspermine), a polyamine analog that increases SAT1 activity, was found to reduce PD histopathology, while Berenil (diminazene aceturate), a pharmacological agent that reduces SAT1 activity, worsened the histopathology.  Third, we genotyped PD patients and controls and isolated a rare but novel variant in the SAT1 gene, although the functional significance of this genetic variant was not identified.  Taken together, the results suggest that the polyamine pathway contributes to PD pathogenesis.

overall_design:
Imaging-guided microarray

In principle, gene expression profiling techniques like microarray are well suited to identify molecular pathways contributing to the pathogenesis of complex diseases.  In practice, however, microarray applied to diseases of the brain present a number of analytic challenges.  By identifying regions within the same brain structure that are differentially targeted by and resistant to a disease, imaging-guided microarray is an approach designed to address these limitations.  Specifically, guided by the spatial information generated from high resolution functional imaging, a 2x2 factorial analysis-of-variance can be designed, including both within and between group factors, and this “double subtraction” model is effective in improving signal-to-noise in a microarray experiment.

Relying on imaging findings, we harvested the DMNV from 6 postmortem brains with evidence of PD and from 5 control brains.  The postmortem PD cases were evaluated for pathological changes (Lewy body-containing neurons and Lewy neurites evidenced with antibodies directed against α-synuclein aggregates) that matched the pattern proposed by Braak.

We relied on the imaging results to identify a neighboring medullary region relatively unaffected by the disease to be used as a within-brain control. We decided on the inferior olivary nucleus (ION), because it is histologically identifiable, and harvested the ION from each of the 6 PD cases and 5 controls. Microarray techniques were used to generate gene expression profiles for each of the 22 tissue samples.

A repeated-measures 2x2 factorial ANOVA model constructed for the imaging study was applied to the expression dataset, in which expression levels from two regions of the medulla  (DMNV vs. ION) were included as the first within group factor, diagnosis (PD vs. controls) was the between group factor, and age and sex were included as covariates.  Based on current literature, one of the top hits (SAT1) was investigated further to determine if it played a role in PD pathogenesis.

first: nicole

middle: m

last: lewandowski

middle: a


title: IFNα-mediated gene expression patterns

status: Public on Jul 23 2010

city: Pamplona

first: Iranzu

last: Gonzalez

state: Navarra

address: Avda. Pio XII nº 55

department: Hepathology and Gene Therapy

institute: Center for applied medical research

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

overall_design: Refer to individual Series


title: Gene Expression Profiles in a Rabbit Model of Systemic Lupus Erythematosus

city: Frederick

first: Richard

last: Lempicki

state: MD

address: PO Box B

department: Clinical Services Program

institute: Leidos Biomedical Research, Inc.

summary: We previously reported the establishment of a rabbit (Oryctolagus cuniculus) model of Systemic Lupus Erythematosus (SLE) in which peptide immunization led to lupus-like autoantibody production including anti-Sm, -RNP, -SS-A, -SS-B and -dsDNA. Some neurological symptoms in form of seizures and nystagmus were observed.  The animals used in the previous and in the present study were from a National Institute of Allergy and Infectious Diseases colony of rabbits that were pedigreed, immunoglobulin allotype-defined but not inbred. Their genetic heterogeneity may correspond to that found among patients of a given ethnicity.  We extended the information about this rabbit model of SLE by microarray based expression profiling. We first demonstrated that human expression arrays could be used with rabbit RNA to yield information on molecular pathways. We then designed a study evaluating gene expression profiles in 8 groups of control and SLE rabbits (46 rabbits in total). Genes significantly upregulated in SLE rabbits were associated with NK cytotoxicity, antigen presentation, leukocyte migration, cytokine activity, protein kinases, RNA spliceosomal ribonucleoproteins, intracellular signaling cascades, and glutamate receptor activity. These results link increased immune activation with up-regulation of components associated with neurological and anti-RNP responses, demonstrating the utility of the rabbit SLE model to uncover biological pathways related to SLE-induced clinical symptoms, including Neuropsychiatric Lupus. Our finding of distinct gene expression patterns in rabbits that made anti-dsDNA compared to those that only made other anti-nuclear antibodies should be further investigated in subsets of SLE patients with different autoantibody profiles.

sample_organism:
Homo sapiens
Oryctolagus cuniculus

overall_design: An important goal of biomedical research is to translate basic findings into clinical applications. Models in inbred mice that spontaneously develop SLE, along with various mutant, transgenic and knockout models have documented a variety of genetic defects leading to SLE, but from the clinical perspective, the degree to which these findings using the inbred or homogeneous artificially mutated strains apply to individuals in heterogeneous outbred human populations is open to question. Given that there is still no cure available for SLE, it is important that we continue to explore possibilities using new animal models of SLE including neuropsychiatric lupus (NPSLE). The gene expression study reported here was conducted to expand our understanding of SLE and in particular NPSLE using our rabbit model.  We reported earlier that immunization of rabbits with the SM- or GR-MAP peptides led to development of anti-nuclear autoantibodies, including anti-dsDNA, as well as neurological symptoms in the form of seizures and nystagmus in some rabbits.  After establishing that it was possible to use the Affymetrix U95 human microarray for the rabbit gene expression studies, through comparative hybridization of identically prepared cRNA from human and rabbit PWBC, the human microarray was used due to lack of rabbit-specific microarrays. We describe unique gene expression changes associated with lupus like serological patterns in immunized rabbits. Our results also demonstrate that caution must be applied when choosing the structure of the carrier Multiple Antigen Peptide (MAP-peptide) for immunization. We discovered that using MAP-4 rather than MAP-8 significantly altered patterns of immune response and gene expression. Currently, microarrays specific for study of gene expression profiles are not available for rabbits. Therefore, we first conducted studies that compared identically prepared rabbit and human cRNA binding to the Affymetrix U95 microarray available for human gene expression analyses. It was determined that the human microarray could be used with rabbit cRNA to yield information on genetic pathways activated and/or suppressed in autoantibody-producing immunized rabbits. In the current report, gene expression profiles of a total of 46 rabbits, from 4 generations within a pedigreed group of control and immunized rabbits, were obtained and analyzed.

first: Geeta

last: Rai

first: Satyajit

last: Ray

first: Jacqueline

last: Milton

first: Jun

last: Yang

first: Ping

last: Ren

first: Rose

middle: G

last: Mage


title: The effect of IFNα on human CD8 T cells_with other concomitant signals

summary:
IFN alpha mediated gene expression pattern. The effect of IFN alpha on human CD8 T cells responding to antigen (signal 1) and costimulatory signals (signal 2) provided by beads coated with anti-CD3 and anti-CD28 mAbs.
This analysis examined the effects of IFN alpha on human CD8 T cells responding to antigen (signal 1) and costimulatory signals (signal 2) provided by beads coated with anti-CD3 and anti-CD28 mAbs. Magnetically sorted untouched CD8+CD45R0- T cells from three different donors were unstimulated or stimulated with IFNa2b or with anti-CD3/CD28 Beads alone or along with IFNa2b or IFNa5 for 48 hours. Individual mRNA samples were analyzed using HG-U133A 2.0 array gene chips.

Keywords: Gene expression analysis after different stimulation

overall_design: Magnetically sorted untouched CD8+CD45R0-T cells from three different donors (named A, B and C) unstimulated or stimulated with IFN alpha 2b or with anti-CD3/CD28 beads alone or along with IFN alpha 2b or IFN alpha 5 for 48 hours.

first: Sandra

last: Hervás-Stubbs

first: Jose

middle: I

last: Riezu

last: González

first: Uxua

last: Mancheño

first: Juan

last: Dubrot

first: Arantza

last: Azpilicueta

first: Izaskun

last: Gabari

first: Asis

last: Palazón

first: Pedro

last: Esquiroz

last: Ruiz

first: Jesus

last: Prieto

first: Agnes

last: Le Bon

first: Fernando

last: Corrales

first: Esther

last: Larrea

first: Ignacio

last: Melero


title: Direct effects of IFNα on human CD8 T cells_without any other concomitant signals

first: Iranzu

last: Gonzalez

summary:
IFNα-mediated gene expression pattern. Direct effects of IFNα on human CD8 T cells without any other concomitant signal.
This analysis examined the direct effects of IFNa on human CD8 T cells without any other concomitant signal. Total human CD8 T cells were magnetically sorted from peripheral blood by negative selection. In order to minimize the presence of antigen-experienced cells, total human CD8 T cells were depleted of CD45RO+ cells by labelling with anti-CD45RO magnetic bead. In both steps of cellular sorting, negative selection were preferred to positive selection to avoid direct labelling of CD8 T cell surface molecules could interfere with downstream IFNa-mediated signalling. Magnetically sorted untouched human CD8+CD45R0- T cells from three different donors were unstimulated or stimulated with IFNa2b or IFNa5 and cells were harvested 7 hours later. mRNAs from the 3 subjects were pooled and analyzed using Affymetrix human HG-U133A 2.0 array gene chips Fold-change ≥ 2 criterion was used to identify genes which expression differed between treatment and control (unstimulated cells).

Keywords: Gene expression pattern analysis

overall_design: Magnetically sorted untouched CD8+CD45R0-T cells mRNA pooled sample from three different donors unstimulated or stimulated with IFN alfa 2b or IFN alfa 5 for 7 hours.


title: Eicosapentaenoic acid improves metabolic switching in human myotubes

status: Public on Jun 23 2010

city: Wageningen

first: Guido

last: Hooiveld

address: HELIX, Stippeneng 4

department: Div. Human Nutrition & Health

country: Netherlands

institute: Wageningen University

summary:
Metabolically healthy skeletal muscle is characterized by the ability to switch easily between glucose and fat oxidation, whereas loss of this ability seems to be related to insulin resistance. The aim of this study was to investigate whether different fatty acids (FAs) and the LXR ligand T0901317 affected metabolic switching in human skeletal muscle cells (myotubes). Pretreatment of myotubes with eicosapentaenoic acid (EPA) increased suppressibility, the ability of glucose to suppress FA oxidation, and metabolic flexibility, the ability to increase FA oxidation when changing from “fed” to “fasted” state. Adaptability, the capacity to increase FA oxidation with increasing FA availability, was increased after pretreatment with EPA, linoleic acid (LA) and palmitic acid (PA). T0901317 counteracted the effect of EPA on suppressibility and adaptability, but did not affect these parameters alone. EPA itself accumulated less, however, EPA, LA, OA and T0901317 increased the number of lipid droplets (LDs) in myotubes, whereas LD size and mitochondria amount were independent of pretreatment. Microarray analysis showed that EPA regulated more genes than the other FAs. Some pathways involved in carbohydrate metabolism were induced only by EPA. The present study suggests a possible favorable effect of EPA on skeletal muscle metabolic switching and glucose utilization.

Keywords: Analysis of target gene regulation by using microarrays.

overall_design: Primary human myotubes, derived from 3 healthy, female donors, were preincubated with different fatty acids  (oleic acid [OA], palmitic acid [PA], eicosapentaenoic acid [EPA] or linoleic acid [LA], each at 100 µM) or bovine serum albumin [BSA] (40 µM) for 24 h.

first: Nina

middle: P

last: Hessvik

first: Siril

middle: S

last: Bakke

first: Katarina

last: Fredriksson

first: Mark

middle: V

last: Boekschoten

first: Anne

last: Fjorkenstad

first: Gerbrand

last: Koster

first: Matthijs

last: Hesselink

first: Sander

last: Kersten

first: Eili

last: Kase

first: Arild

middle: C

last: Rustan

first: Hege

last: Thoresen


title: Human epidermal keratinocytes treated with retinoic acid or thyroid hormone

status: Public on Jun 11 2010

city: New York

first: Miroslav

last: Blumenberg

address: 455 First Ave #874

institute: NYU School of Medicine

summary: Targets of Retinoic Acid (RA) were identified in primary human epidermal keratinocytes grown in the  presence or absence of all-trans retinoic acid for 1, 4, 24, 48 and 72 hours. Targets of Thyroid Hormone (T3) were identified in primary human epidermal keratinocytes grown in the  presence or absence of the hormone; same controls as for RA.

overall_design: Time course,  1, 4, 24, 48 and 72 hours

first: Marjana

last: Tomic-Canic

first: Ding-Dar

last: Lee

first: Olivera

last: Stojadinovic

first: Brian

first: Rebecca

last: Walsh


title: Expression profiling of BRAFV600E melanoma cell lines upon RAF inhibition

status: Public on Jul 18 2010

first: Christine

middle: Anne

last: Pratilas

address: 1275 York Avenue

department: Molecular Pharmacology

institute: Memorial Sloan-Kettering Cancer Center

summary:
Microarray expression analysis to identify global changes in transcription in response to RAF inhibition.
Genes under RAF control were identified in a panel of BRAFV600E tumor cells, following the short-term inhibition of RAF using a pan-RAF kinase inhibitor, PLX4032 (Plexxikon). For comparison with changes in gene expression in response to MEK inhibition using PD0325901 (Pfizer), the following array data was referenced: (http://www.ncbi.nlm.nih.gov/geo/  (accession no. GSE10086)).

overall_design: Cell lines growing in culture (n=5) were treated with the RAF inhibitor PLX4032 (250nM or 1000nM) or vehicle alone (0.1% DMSO) as control, for eight hours.

first: Eric

last: Joseph


title: Affymetrix HG-U133A 2.0 Expression data

status: Public on Jul 08 2010

city: Heidelberg

first: Andreas

last: Gast

state: BW

address: INF 580

department: Division of Molecular Genetic Epidemiology

institute: Gernman Cancer Research Center

summary: Expression .CEL files from Affymetrix HG-U133A 2.0 arrays using DNA from 14 human cell lines derived from metastasized melanoma

overall_design:
Study of global gene expression differences in malignant melanoma cell lines with or without specific abberations in BRAF NRAS or CDKN2A.
UKRV-Mel-16a was wrongly described as Ma-Mel-16a in Blöthner et al. 2005

first: Sandra

last: Bloethner

first: Bowang

last: Chen

first: Ranjit

middle: K

last: Thirumaran

first: Jan

last: Mueller-Berghaus

first: Selma

last: Ugurel

first: Kari

last: Hemminki

first: Dirk

last: Schadendorf

first: Rajiv

last: Kumar


title: Transcriptome of inflammatory myeloid DCs in psoriasis

status: Public on May 24 2010

first: Mayte

last: Suarez-Farinas

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

institute: Mount SinaiSchool of Medicine

summary: Background: Previous work has identified CD11c+CD1c- dendritic cells (DCs) as the major ”inflammatory” dermal DC population in psoriasis vulgaris and CD1c+ DCs as the “resident” cutaneous DC population. Objective:  To further define molecular differences between these two myeloid dermal DC populations. Methods: Inflammatory and resident DCs were single-cell sorted from psoriasis lesional skin biopsies, and gene array expression profiling was performed.  Results were confirmed with RT-PCR, flow cytometry, immunohistochemistry, and double label immunofluorescence.  Pooled human keratinocytes were cultured for functional studies.   Results:  TNF-related apoptosis-inducing ligand (TRAIL), Toll-like receptors (TLRs) 1 and 2, S100A12/EN-RAGE, CD32, and many other inflammatory products were selectively expressed in inflammatory DCs than in resident DCs.  Flow cytometry and immunofluorescence confirmed higher protein expression on CD1c- versus CD1c+ DCs.  TRAIL receptor, death receptor 4 (DR4), was expressed on basal keratinocytes and blood vessels, and in vitro culture of keratinocytes with rh-TRAIL induced CCL20 leukocyte chemokine.  Conclusion:  CD11c+CD1c- inflammatory DCs in  psoriatic lesional skin express a wide range of inflammatory molecules compared to skin resident CD1c+ DCs.  Some molecules made by inflammatory DCs, including TRAIL, could have direct effects on keratinocytes or other skin cell types to promote disease pathogenesis.

overall_design: Shave biopsies were cultured overnight in dispase to remove the epidermis. Dermis was cultured for 36-48 hours to  obtain dermal single cell suspensions. These cells were stained with HLA-DR, CD11c, BDCA-1 (DCs) and FACS-sorted into HLA-DR+11c+BDCA-1+,  HLA-DR+11c+BDCA-1- populations into Trizol. RNA was extracted and processed for microarray.  2 dependent groups.

last: Suárez-Fariñas

first: Lisa

last: Zaba

first: James

last: Krueger


title: Pleiotropic expression of endogenous genes upon fungus infection of wheat plants containing anti-fungal transgenes

status: Public on Jun 02 2010

city: Zurich

first: Alessandro

last: Fammartino

address: Universitaettstrasse 2

department: IPAS

institute: ETHZ

summary:
Recent attempts to increase endogenous disease resistance of plants by overexpression of anti-fungal transgenes have shown a potential of this method. However, it has also been shown that such improvements are usually small. One of the obvious reasons for this low anti-fungal effect might be the regulation of endogenous genes in parallel. In this project, we will study the effect of anti-fungal transgenes on the endogenous gene expression. Such effects might relate to substantial equivalence which is a biosafety issue of concern to the public.
The GeneChip Wheat Genome Array will be used to detect expression of defence response genes and key genes of metabolic pathways. We will use wheat plants transformed with anti-fungal gene of specific effect against a small group of seed transmitted, pathogenic fungi (KP4 against smuts and bunts). Transformed spring wheat line will be challenged by stinking smut (inhibited by KP4). The effect on the endogenous gene expression will be tested for plants grown in the field in collaboration with the USDA Department. This work will contribute to our understanding of plant defence responses in general and may allow improving strategies to strengthen these responses.

overall_design: Teliospores of pathogenic races T-1, T-5 and T-16 of T. caries provided by a collection in Aberdeen, ID, USA were used for the tests. Seeds of the genetically engineered Swiss spring wheat variety Greina (GrKP4) and the null-segregant control line (Gr0) were coated with spores and Individual plants were scored for bunt symptoms. For microarray analysis only samples inoculated with T1 and T16 were used.

first: Blair

last: Goates

first: Sylvain

last: Bischof

first: Wilhelm

last: Gruissem

first: Christof

last: Sautter


title: RNA profiling of Fusarium head blight-resistant wheat addition lines containing the Thinopyrum elongatum chromosome 7E

status: Public on Jun 15 2010

city: Ottawa

first: Thérèse

last: Ouellet

state: ON

address: 960 Carling Ave, room 2091

department: Eastern Cereal and Oilseed Research Centre

country: Canada

institute: Agriculture and Agri-Food Canada

summary:
Fusarium head blight (FHB) is a major disease of cereal crops caused by the fungus Fusarium graminearum (Fg). FHB affecting the flowering heads (or spikes). A FHB resistance locus has been identified on the chromosome 7E of the wild wheat relative Thinopyrum elongatum (Th.e.). That chromosome (7E) or a long arm fragment of it (7EL) have been transferred as additions in the wheat background 'Chinese Spring' (CS).
The two addition lines are resistant to FHB while 'Chinese Spring' is moderately susceptible to it. The mechanism of resistance is not known. The analysis of this work is published in the Canadian Journal of Plant Pathology (Wang et al, 2010).

overall_design: We used the wheat microarray to determine the global expression profil in inoculated spikelets of the addition and parental lines, after water or Fg treatment, with samplings at 2 and 4 days after inoculation (DAI).

first: Li

last: Wang


title: Altered modulation of WNT-β-catenin and PI3K/Akt pathways in IgA nephropathy

status: Public on May 26 2010

city: Valenzano-Bari

first: Sharon

middle: Natasha

last: Cox

department: Renal Lab

institute: Schena Foundation

summary:
To uncover new molecular mechanisms involved in IgAN pathogenesis, we compared the genomic profiles of 12 IgAN patients with 8 healthy subjects,
We included addiotional disease controls 3 FSGS(Focal Segmenal glomerulosclerosis) patients and 3 membrano proliferative glomerulonephritis type I (MPGN-I) controls in our study to evaluate if the  WNT-β-catenin and PI3K/Akt pathways were specfic to IgAN.

overall_design: Gene expression profile comparison between 12IgAN patients and 8 Healthy Subjects. Gene Set Enrichment Analysis (GSEA) performed on the additional disease controls determined that the a priori defined set of genes and the pathways generated were specific to the IgAN

middle: N

first: Fabio

last: Sallustio

first: Grazia

last: Serino

first: Raffaella

last: Verrienti

first: Paola

last: Pontrelli

first: Francesco

last: Schena

first: Gianluigi

last: Zaza

last: Pesce