title: The nucleosome remodeler SNF2L modulates WNT signaling for cellular homeostasis

status: Public on May 11 2012

city: Martinsried

first: Tobias

last: Straub

address: Großhadener Str. 9

department: Biomedical Center, Bioinformatics

institute: LMU Munich

summary: ISWI is an evolutionary conserved ATPase that catalyzes nucleosome remodeling in several different complexes. Two mammalian ISWI orthologs, SNF2H and SNF2L, have specialized functions despite their high similarity. Due to the lack of reagents the functions of SN2L in human cells had not been established. Newly established specific monoclonal antibodies and selective RNA interference protocols now enabled a comprehensive characterization of loss-of-function phenotypes in human cells.  Contrasting earlier results obtained in the mouse model, we found SNF2L broadly expressed in primary human tissues. Depletion of SNF2L in HeLa cells led to enhanced proliferation, morphological alterations and increased migration. These phenomena were explained by transcriptome profiling, which identified SNF2L as a modulator of the Wnt signaling network. The cumulative effects of SNF2L depletion on gene expression portray the cell in a state of activated Wnt signaling characterized by increased proliferation and chemotactic locomotion. High levels of SNF2L expression in normal melanocytes contrast to undetectable expression in malignant melanoma. In summary, our data document an anti-correlation between SNF2L expression and several features characteristic of malignant cells.

overall_design: Total RNA samples from human HeLa cells. Transcript levels were analyzed after luciferase, SNF2H and SNF2L RNAi.

first: Maren

last: Eckey

first: Silke

last: Kuphal

first: Lothar

last: Schermelleh

first: Elisabeth

last: Kremmer

first: Heinrich

last: Leonhardt

first: Anja

middle: K

last: Bosserhoff

first: Peter

middle: B

last: Becker


title: Expression data from normal human epidermal keratinocytes undergoing density-induced differentiation and treated with EGF

status: Public on May 03 2012

city: Memphis

first: Thomas

middle: R

last: Sutter

state: TN

address: 3774 Walker Ave.

department: Biology

country: USA

institute: University of Memphis

summary:
Combining genome-wide microarray and functional analyses, we found that EGFR activation abrogates barrier function, increasing transepidermal water loss (TEWL) and transepithelial permeability of water-soluble ions and higher molecular weight dextrans, in part by disrupting the expression of tight junction proteins.  EGF decreases certain lipid matrix free fatty acids and ceramides by its actions to repress the expression of specific biosynthetic enzymes.
Activation of EGFR inhibits cornified envelope formation by regulating the expression of 59 percent of the known contributing genes.  EGF-responsiveness enriches more than 100 genes known to be associated with skin diseases. These data are used to obtain 2,676 density-dependent genes that are differentially expressed in response to EGF treatment.

overall_design: The 16 microarrays were preprocessed using the 5th percentile of region method in dChip. Genes with at least a 1.5 fold difference between the untrated samples at 50% and 100% confluent cell density were exported for further analysis. Two-way ANOVA was used to identify differentially expressed genes by either density or treatment factors using JMP Genomics 4.1 (SAS). Multiple hypothesis testing was corrected by Benjamini-Hochberg false discovery rate control at the 0.05 level. Pair-wise comparisons were performed using the Tukey’s Honestly Significant Difference test.

first: Quynh

middle: T

last: Tran


title: VEGF189 overexpression in breast cancer cells delays metastasis

status: Public on May 10 2012

city: paris

first: toullec

last: aurore

address: 41 boulevard de la chapelle

country: France

institute: Inserm U965

summary: Vascular endothelial growth factor is a multifunctional cytokine playing important roles in angiogenesis, tumor progression and metastasis. Alternative splicing results in the production of several different isoforms of VEGF. We have previously generated human breast cancer cells overexpressing VEGF165 or VEGF189 isoforms (referred to as the V165 and V189 clones, respectively) and showed that VEGF189-transfected cells were less tumorigenic. In this study, we used bioluminescence imaging to analyze the metastasis capacity of breast cancer cell lines (MDA-MB-321) overexpressing VEGF isoforms in nude mice. V165, V189 and control cV clones were transfected with a luciferase plasmid to generate bioluminescent clones (the V165-B, V189-B and cV clones, respectively). These clones were then injected into the left heart ventricle of nude mice.

overall_design:
Human MDA-MB-231 breast cancer cells were used to generate stable transfected clones overexpressing VEGF165 isoform, VEGF189 isoform, or control vector (referred to as 42ctl8, 13ctl3 and PCIctl3, respectively).
Analysis of the metastasis capacity of these clones in nude mice. Lung metastasis overexpressing VEGF165 isoform, VEGF189 isoform, or control vector (referred to as 42B45, 13B31 and PCIB9, respectively)were also analysed.

first: Aurore

last: Toullec

first: Hélène

last: Buteau-Lozano

first: Martine

last: Perrot-Applanat

first: Jean-Philippe

last: Jais


title: Gene expression profile of U373MG exposed to novel anti-cancer 1,2,3,4-tetrahydroisoquinoline alkaloids

status: Public on May 20 2012

city: Tokyo

first: Jun-ichi

last: Satoh

address: 2-522-1 Noshio, Kiyose

department: Bioinformatics

country: Japan

institute: Meiji Pharmaceutical University

summary: Background: Glioblastoma is the most aggressive form of brain tumors showing resistance to treatment with various chemotherapeutic agents. The most effective way to eradicate glioblastoma requires the concurrent inhibition of multiple signaling pathways and target molecules involved in the progression of glioblastoma. Recently, we obtained a series of 1,2,3,4-tetrahydroisoquinoline alkaloids with potent anti-cancer activities, including ecteinascidin-770 (ET-770; the compound 1a) and renieramycin M (RM; the compound 2a) from Thai marine invertebrates, together with a 2’-N-4”-pyridinecarbonyl derivative of ET-770 (ET-770-DR; the compound 3). We attempted to characterize the molecular pathways responsible for cytotoxic effects of these compounds on a human glioblastoma cell line U373MG. Methods: We studied the genome-wide gene expression profile on microarrays and molecular networks by using pathway analysis tools of bioinformatics. Results: All of these compounds dissolved in dimethyl sulfoxide (DMSO) as a vehicle induced apoptosis of U373MG cells at nanomolar concentrations. The compound 3 reduced the expression of 417 genes and elevated the levels of 84 genes, while ET-770 downregulated 426 genes and upregulated 45 genes. RM decreased the expression of 274 genes and increased the expression of 9 genes. The set of 196 downregulated genes and 6 upregulated genes showed an overlap among all the compounds, suggesting an existence of the common pathways involved in induction of apoptosis. We identified the ErbB (EGFR) signaling pathway as one of the common pathways enriched in the set of downregulated genes, composed of PTK2, AKT3, and GSK3B serving as key molecules that regulate cell movement and the nervous system development. Furthermore, a GSK3B-specific inhibitor induced apoptosis of U373MG cells, supporting an anti-apoptotic role of GSK3B. Conclusion: Molecular network analysis is a useful approach not only to characterize the glioma-relevant pathways but also to identify the network-based effective drug targets.

overall_design: To determine the 50% inhibitory concentration (IC50), U373MG human glioblastoma cells, incubated in Dulbecco’s Modified Eagle’s medium (DMEM) supplemented with 10% fetal bovine serum (FBS), 100 U/ml penicillin and 100 μg/ml streptomycin (feeding medium), were exposed to the chemical compounds for varying periods at variable concentrations. Then, we assessed the cell viability by morphological observations and by using the 3-[4,5-dimethylthiazol-2-yl]-2,5-diphenyl tetrazolium bromide (MTT) cell growth kit (Millipore). The cells were incubated for 4 to 72 hours in the feeding medium with inclusion of the chemical compounds at the IC50 concentration or the vehicle (DMSO) at an equivalent concentration (v/v), and then were processed for microarray analysis at 24 hours after exposure and western blot analysis of the cleavage of poly-ADP-ribose-polymerase (PARP) and caspase-3 at 4 to 72 hours after exposure.

first: Hiroko

last: Tabunoki

first: Naoki

last: Saito

first: Khanit

last: Suwanborirux

first: Kornvika

last: Charupant


title: Expression analysis in parthenogenetic cells through different potency stages

status: Public on May 04 2012

city: Barcelona

first: Rita

last: Vassena

address: Av. Dr. Aiguader 88

department: Stem Cell Bank

country: Spain

institute: CMRB

summary:
Parthenogenetic stem cells were derived from parthenotes, then differentiated to mesenchymal stem cells. These were further reprogrammed to induced pluripotent stem cells, which were finally differentiated to secondary mesenchymal stem cells.
Transcriptional analysis was performed at all 4 states of potency to indetify changes in expression stability of partehnogenetic cells.

overall_design: 4 samples for each stage of potency were analyzed, controls were biparental embryonic stem cells and their mesenchymal derivate, as well as biparental induced pluripotent stem cells

first: Nuria

last: Montserrat

first: Beatriz

last: Carrasco Canal

first: Begoña

last: Aran

first: Lorena

last: De Oñate

first: Anna

last: Veiga

first: Juan

last: Izpisua Belmonte


title: KGF effects on cutaneous SCC cells

status: Public on May 02 2012

city: Turku

first: Veli-Matti

last: Kähäri

address: Tykistökatu 6A, 4. floor

country: Finland

institute: University of Turku, Turku University Hospital

summary:
Keratinocyte growth factor (KGF, fibroblast growth factor-7) is a fibroblast-derived mitogen, which stimulates proliferation of epithelial cells. The expression of KGF by dermal fibroblasts is induced following injury and it promotes wound repair. However, the role of KGF in cutaneous carcinogenesis and cancer progression is not known. We have examined the role of KGF in progression of squamous cell carcinoma (SCC) of the skin.
Gene expression profiling was performed of three cutaneous SCC cell lines treated with KGF (10 ng/ml) for 24 h, comparable untreated cells and of normal unterated epidermal keratinocytes to explore KGF-responce in SCC cells.

overall_design: Three cutanous SCC cell lines (established from two primary and one metastatic tumors) were cultured to 70% confluency, serum starved (0% FCS) for 16 h and treated with rKGF (10 ng/ml) for 24 h. Comparable cell cultures were left untreated with rKGF. Normal epidermal keratinocytes from two individuals were cultured in specified keratinocyte culture medium to 70% confluency. All cell cultures were processed for RNA extraction and Affymetrix whole transcript microarray gene expression analysis. Thus, the samples included three untreated cutaeous SCC cell lines (n=3), the same three cell lines treated with rKGF (n=3) and untreated epidermal keratinocytes from two  individuals (n=2). Normal keratinocytes served as reference samples to untreated skin SCC cells.

first: Mervi

last: Toriseva


title: Cartilage zone arrays

status: Public on Aug 01 2012

city: La Jolla

first: Shawn

middle: Patrick

last: Grogan

state: CA

address: 10550 N. Torrey Pines Road, MEM161

department: MEM

institute: TSRI

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

sample_organism:
Homo sapiens
Bos taurus

platform_organism:
Homo sapiens
Bos taurus

overall_design: Refer to individual Series


title: Circadian Clock Activity in Mouse and Human CD4+ T Cells

status: Public on May 01 2012

city: Goettingen

first: Gabriela

last: Salinas

state: Lower-Saxony

address: Kreuzbergring 57

department: Department of Pathology

country: Germany

institute: Universitaetsmedizin Goettingen

summary: Though it is well established that immunological functions of CD4+ T cells are time of day-dependent, the underlying molecular mechanisms remain largely obscure. To address the question whether T cells themselves harbor a functional clock driving circadian rhythms of immune function, we analyzed clock gene expression and immune responses of CD4+ T cells purified from blood of healthy subjects at different time points throughout the day. Circadian clock function as well as immune function was further analyzed in cultivated T cells and circadian clock reporter systems. We found robust rhythms of clock gene expression as well as, after stimulation, of IFN-g production and CD40L expression in both freshly isolated and in cultured CD4+ T cells. Moreover, circadian luciferase reporter activities in CD4+ T cells and in thymic sections from PER2::LUCIFERASE reporter mice suggest that endogenous T cell clock rhythms are self-sustained under constant culture conditions. Microarray analysis of stimulated CD4+ T cell cultures revealed a rhythmic regulation of the NF-kB pathway as a candidate mechanism regulating circadian immune responses. Collectively, these data demonstrate for the first time that CD4+ T cell responses are regulated by an intrinsic cellular circadian oscillator capable of driving rhythmic adaptive immune responses in vitro and in vivo.

overall_design: The study is designed with 3 biological replicates from three different time points.

first: Thomas

last: Bollinger

first: Anton

last: Leutz

first: Alexei

last: Leliavski

first: Ludmila

last: Skrum

first: Judit

last: Kovac

first: Luigi

last: Bonacina

first: Christian

last: Benedict

first: Tanja

last: Lange

first: Juergen

last: Westermann

first: Henrik

last: Oster

first: Werner

last: Solbach


title: Gene expression data from human lymphocytes

status: Public on Jun 01 2012

city: Duarte

first: Nancy

last: Chen

address: 1500 Duarte Road

department: Diabetes

institute: City of Hope

summary: Both genetic and environmental factors are implicated in Type 1 Diabetes (T1D). Since environmental factors can trigger epigenetic changes, we hypothesized that variations in  histone posttranslational modifications (PTMs) at the promoter/enhancer regions of T1D susceptible genes may be associated with T1D. We therefore evaluated histone PTM variations at known T1D susceptible genes in blood cells from T1D patients versus healthy non-diabetic controls, and explored their connections to T1D. We used the chromatin-immunoprecipitation-linked-to-microarray approach to profile key histone PTMs, including H3-lysine-4 trimethylation (H3K4me3), H3K27me3, H3K9me3, H3K9 acetylation (H3K9Ac) and H4K16Ac at genes within the T1D susceptible loci in lymphocytes, and H3K4me3, H3K9me2, H3K9Ac and H4K16Ac at the IDDM1 region in monocytes of T1D patients and healthy controls separately. We screened for potential variations in histone PTMs using computational methods to compare datasets from T1D and controls. Interestingly, we observed marked variations in H3K9Ac levels at the upstream regions of HLA-DRB1 and HLA-DQB1 within the IDDM1 locus in T1D monocytes relative to controls. Additional experiments with THP-1 monocytes demonstrated increased expression of HLA-DRB1 and HLA-DQB1 in response to interferon- and TNF-treatment that were accompanied by changes in H3K9Ac at the same promoter regions as that seen in the patient monocytes. These results suggest that the H3K9Ac status of HLA-DRB1 and HLA-DQB1, two genes highly associated with T1D, may be relevant to their regulation and transcriptional response towards external stimuli. Thus, the promoter/enhancer architecture and chromatin status of key susceptible loci could be important determinants in their functional association to T1D susceptibility.

overall_design: We used microarrays to obtain global gene expression data in human lymphocytes. Human lymphocytes were prepared from four healthy non-diabetic volunteers. Total RNAs were extracted using Qiagen RNeasy mini kits following the manufacturer's instructions. Biotinylated single-strand cDNA was generated and subjected to expression profiling with Affymetrix Human Gene 1.0 ST arrays, followed by data analyses and conversion into expression measurements using Affymetrix's Expression Console v1.1.1. The data set is used for integration with ChIP array data.

first: Rama

last: Natarajan

first: Feng

last: Miao

first: Zhuo


title: Expression data of rhabdoid tumor cell line A204 treated with HDAC-inhibitor SAHA

status: Public on Apr 20 2012

city: Muenster

first: Kornelius

last: Kerl

address: Robert-Koch-Strasse 43

institute: Institute of molecular tumorbiology

summary:
Rhabdoid tumors are a highly aggressive pediatric tumor entity affecting infants and very young children. These tumors do not respond to conventional type chemotherapy. In recent approaches epigenetic compounds has been effective to inhibit cell growth of these tumors.
Using microarray analysis we detect mechanism which are responsible for cell death induced by histone deacetylase inhibitors.

overall_design: A204 rhaboid tumor cell lines were treated for 12h with the HDAC inhibitor SAHA

first: Michael

last: Frühwald


title: Targeting the MTOR-AKT pathway in DLBCL

status: Public on Apr 30 2012

city: Bronx

first: Samir

last: Parekh

state: NY

address: 1300 Morris Park Ave

department: cancer Center

institute: Albert Einstein College of Medicine

summary: The mTOR (mammalian Target of Rapamycin) pathway is constitutively activated in Diffuse Large B-Cell Lymphoma (DLBCL).  mTOR inhibition has been shown to have clinical activity in patients with DLBCL, although overall response rates remain low. We therefore evaluated differences in the transcriptome between DLBCL cell lines with differential sensitivity to the mTOR inhibitor Rapamycin, to (A) identify gene-expression patterns(GEP) capable of identifying sensitivity to Rapamycin, (B) understand the underlying mechanisms of resistance to Rapamycin in DLBCL and (C) identify bioactive molecules likely to synergize with mTOR inhibitors.  Using Affymetrix HuGene ST 1.0 microarrays, we were able to identify a gene expression signature capable of accurately predicting sensitivity and resistance to Rapamycin in DLBCL cell lines.  Pathway analysis identified the serine/threonine kinase Akt as central to the differentially-expressed gene network.  Connectivity mapping of our datasets identified compounds targeting the AKT pathway with a high likelihood of reversing the GEP associated with resistance to Rapamycin.  Specifically, we evaluated the HIV protease inhibitor (PI) Nelfinavir, which is known to have anti-cancer and Akt-inhibitory properties, as well as the small molecule Akt inhibitor MK-2206, for their potential to synergize with to Rapamycin in DLBCL.  Nelfinavir and MK-2206 caused profound inhibition of cell viability in combination with Rapamycin in DLBCL cell lines. Low nanomolar concentrations of Rapamycin inhibited phosphorylation of Akt and also downstream targets of activated mTOR when used in combination with these Akt inhibitors.  These findings have the potential to significantly improve patient selection for mTOR inhibitor therapy, and to improve rates and depths of response.  More broadly, they support the use of global RNA expression and connectivity mapping to improve patient selection and identify synergistic drug combinations for cancer therapy.

overall_design: DLBCL cell lines were tested for Rapamycin sensitivity and classified as "sensitive" or "resistant."  Genome-wide analysis of all cell lines were performed using the Affymetrix HuGene ST 1.0 Array Platform.  Genes with differential expression between sensitive and resistant cell lines were analyzed using Statistical Analysis of Microarrays (SAM) software, and a signature of genes determnined.  This signature was found to accurately predict sensitivity or resistance of other DLBCL cell lines, and to identify the protein kinase Akt as central to resistance.

first: Adam

last: Petrich

first: Violetta

last: Leshchenko

first: Pei-Yu

last: Kuo

first: Bing

last: Xia

first: Netha

last: Ulahannan

first: Shanisha

last: Gordon

first: B

middle: H

last: Ye

first: Joseph

last: Sparano


title: Time-varying expression data from WI38 cell lines that were exposed to a challenge dose with or without a priming dose

city: Berkeley

first: Bahram

last: Parvin

state: Ca

institute: Lawrence Berkeley National Laboratory

summary: The purpose of this experiment is to elucidate temporal activities and biological processes that can be inferred in response to a 200cGy challenging dose with or without a 10 cGy priming dose in embryonic human fibroblasts

overall_design:
The experiment is designed around the human diploid embryonic lung fibroblast cell line WI38 (TP53 proficient), which was grown as a monolayer (2D) under physiological cell culture conditions (3% O2; 10% CO2). Cells are exposed to 2Gy (e.g., the challenge dose) of ionizing radiation (160 kV X-rays) with or without a priming dose of 10cGy (e.g., the adaptive dose)  4 hours prior to the challenge dose. Three biological replicates for each treatment group (e.g., with and without the priming dose) were collected 1, 2, 4 and 8 hours after the challenge dose. The time course was selected on the basis of our prior research on early response to ionizing radiation [1,2]. Purified total cellular RNA was extracted using an RNeasy Mini Kit (Qiagen) and quantified for Affymetrix microarray analysis using Human Gene 1.0 ST Array. Robust multi-array analysis (RMA) was performed to normalize data collected from the different samples. Samples were examined for quality control using the NUSE protocol.
Reference [1] Groesser T. et al., Int J of Radiation Research, 2011. 87(7): p. 696-710.
Reference [2] Han J. et al., Microscopy, 2010. 241(3): p. 315-326

first: Torsten

last: Groesser

first: Lakshmi

last: Jakkula

first: Ju

last: Han


title: The HDAC inhibitor panobinostat (LBH589) inhibits Acute Lymphoblastic leukemia (ALL) in vitro and in vivo in a new characterized human ALL mice model (ALL-B and ALL-T)

status: Public on Apr 18 2012

city: Pamplona

first: Xabier

last: Agirre

state: Navarra

address: Pio XII, 55

department: Oncology

institute: CIMA

summary: Histone deacetylases (HDACs) have been identified as therapeutic targets due to regulatory function in DNA structure and organization. We have analyzed the role of the LBH589, a novel pan inhibitor of class I and II HDACs, in Acute Lymphoblastic Leukemia.  In vitro, LBH589 was shown to induce a dose dependent antiproliferative and apoptotic effect which was associated with an increase in the acetylation of H3 and H4 histone acetylation which was uniformly in every genetic subgroup of ALL. In vivo administration of LBH589 in BALB/c-RAG2-/-γc-/- mice in which T and B-cell leukemic cell lines were injected induced a significant reduction in tumor growth (TOM-1, p<0.01 and MOLT-4 p<0.05). Leukemic cells from patients were employed to establish a xenograft model of human leukemia in BALB/c-RAG2-/-γc-/- mice and further transplanted in consecutive generations of mice. Treatment of these xenografts with LBH589 induced an increase in the acetylation of H3 and H4 and prolonged the survival of mice in comparison with the animals treated with Vincristine and Dexametasone (p<0.05) and this effect was significantly higher when LBH589 was combined with Vincristine and Dexametasone (p<0.001). Our results that the use of LBH589 in combination with standard chemotherapy represents an attractive option for treatment of patients with ALL.

overall_design: Two primary samples of ALL (one ALL-B and one ALL-T) and two samples of each leukemia after passages in immunodeficient mice.

first: Amaia

last: Vilas-Zornoza

first: Gloria

last: Abizanda

first: Cristina

last: Moreno

first: Victor

last: Segura

first: Alba

middle: D

last: Rodriguez

first: Edurne

last: San José-Eneriz

first: María

first: Jose

middle: A

last: García de Jalón

first: José

last: Rifón

first: Juan

middle: C

last: Cigudosa

last: Martinez-Climent

last: Román-Gómez

middle: J

last: Calasanz

first: Felipe

last: Prósper


title: The HDAC inhibitor panobinostat (LBH589) inhibits Acute Lymphoblastic leukemia (ALL) in vitro and in vivo in a new characterized human ALL mice model (TOM-1 and MOLT-4)

overall_design: Three different biological replicates of ALL derive cell lines TOM-1 and MOLT-4 after and before treatment with LBH589


title: LBH589 (Panobinostat) treatment of a gastric cancer cell line

status: Public on Apr 15 2012

city: Munich

first: Ivonne

last: Regel

address: Ismaninger Strasse 22

institute: Klinikum rechts der Isar

summary: LBH589 is a histone deacetylase (HDAC) inhibitor, treatment and changes in acetylated histones alters gene expression

overall_design: Gastric cancer cell line AGS was treated with 100nM LBH589 for 24h.

first: Matthias

last: Ebert


title: Combined hepatocellular-cholangiocarcinomas exhibit progenitor features and activation of Wnt and TGFbeta signaling pathways

status: Public on Apr 01 2012

city: 91400 Orsay

first: Florent

last: Dumont

state: Ile de France

address: 17 avenue des sciences

institute: Université Paris-Saclay

summary: Primary liver tumours include hepatocellular carcinomas (HCC), cholangiocarcinomas  (CC) and a group of rare tumours exhibiting biliary and hepatocytic differentiation called combined hepatocholangiocarcinomas (cHCC-CC). To better define this latter group, we take advantage of a series of these tumours based on their morphological characteristics and we performed transcriptional analysis allowing thereafter global comparison with published data. We show that most cHCC-CCs express progenitor cell traits, are committed to biliary lineage and are mainly associated to the activation of Wnt/beta-catenin and TGFbeta signalling pathways. Wnt/beta-catenin pathway activation in cHCC-CC is evidenced by the expression of both its direct targets such as LEF1 and EPCAM. In addition, extracellular matrix (ECM) genes and ECM-remodelling genes which are upon the control of TGF profibrotic program were found up-regulated in cHCC-CC. Interestingly, we show that CC and  most cHCC-CC share characteristics associated to a subtype of poorly differentiated HCC suggesting that these tumours could originate from a stem/progenitor cell. The plasticity of these cells may explain the phenotypical heterogeneity of these tumors with the maintenance of some hepatocellular differentiation features such as albumin expression. Interestingly, this is shared by at least one third of CC, raising the hypothesis of a potential continuum between CC, cHCC-CC and poorly differentiated HCC.

overall_design: Patients serie include 3 intra-hepatic CC, 7 typical HCC and 20 cHCC-CC that was used for microarray hybridisation. All these tumours did not show any mutation of the beta-catenin gene. The degree of hepatic fibrosis of the non-cancerous liver was graded according to the METAVIR classification. Paraffin sections were processed as described previously. Immunohistochemistry was done on standard slides for the series.

first: Catherine

last: Cavard

first: Cédric

last: Coulouarn


title: The HDAC inhibitor panobinostat (LBH589) inhibits Acute Lymphoblastic leukemia (ALL) in vitro and in vivo in a new characterized human ALL mice model

first: Xabier

last: Agirre

type:
Expression profiling by array
Methylation profiling by array
Expression profiling by SNP array
SNP genotyping by SNP array


title: Engraftment of limited numbers of pediatric leukemia into NOD/SCID/IL2Rcg-null mice enables surrogate markers for clinical outcome

city: Tuebingen

first: Michael

last: Bonin

state: BW

address: CAlwerstr. 7

department: Medical Genetics

institute: University Tuebingen

summary: Cultured immortalized cell lines have been extensively used to study the characteristics of various malignant stem cell clones and to optimize new treatment strategies. Nonetheless, the usefulness of such in vitro systems to recapitulate primary disease proved to be limited. Therefore, the design of more meaningful pre-clinical in vivo models ideally utilizing primary patient-derived material is of critical importance. In this context, the recently described NOD.Cg-Prkdcscid IL2rgtmWjl/Sz (NSG) mouse strain has been reported to sustain superior engraftment rates of patient-derived acute lymphatic and myeloid leukemic samples. However, limited data exist whether NSG-derived blasts retain their leukemogenecity over successive mouse generations and whether characteristics of this mouse model will indeed allow correlation to clinical parameters. In the present study, we thus engrafted NSG mice with 18 different pediatric B cell precursor ALL, AML and T-ALL samples and could demonstrate that NSG-derived blasts retained their leukemogenic profile with respect to immune-phenotype, chromosomal aberrations, transcriptome, flowcytometric- and PCR-minimal residual disease (MRD) marker expression. Moreover, the extent of leukemic engraftment and the overall survival of NSG mice highly correlated with the individual prognosis of pediatric B cell precursor ALL, AML and T-ALL patients. Thus, we here report on a complex in vivo model that provides a valuable tool for studying the heterogeneity of leukemic disease and for improving patient-tailored leukemia-targeting strategies .

first: Jeanette

last: Woiterski

first: Martin

last: Ebinger

first: Udo

middle: F

last: Hartwig

first: Kai

middle: E

last: Witte

first: Barbara

last: Goecke

first: Vanessa

last: Heininger

last: Philippek

first: Andre

last: Schrauder

first: Silja

last: Röttgers

first: Wolfgang

last: Herr

first: Peter

last: Lang

first: Rupert

last: Handgretinger

first: Maya

last: André


status: Public on Apr 13 2012

first: Anna

last: Bigas

state: Barcelona

address: Dr. Aiguader 88

department: Cancer Research

institute: Institut Hospital del Mar d'Investigacions Mèdiques

summary:
Gene expression from MCF7 breast cancer cells at different times of TNFa incubation:pcs2 and 14-3-3 transduced cells

Keywords: Expression Profiling by array

overall_design: We analyzed 2 arrays from each condition:MCF7-control tnf 0, MCF7-control tnf 20min, MCF-control tnf 90min, MCF7-14-3-3 tnf 0, MCF7-14-3-3 tnf 20min, MCF7-14-3-3 tnf 90min

first: Lluis

last: Espinosa


title: Global analysis of mRNA decay in induced pluripotent stem cells

status: Public on Apr 17 2012

city: Newark

first: Ju Youn

last: Lee

state: NJ

address: 185 South Orange Ave. MSB-E501

department: Biochemistry

institute: UMDNJ-New Jersey Medical School

summary: Expression data from human induced pluripotent stem cells(iPSCs) and Human foreskin fibroblasts (HFFs) with treatment actinomycin D

overall_design: In order to estimate mRNA decay rates, HFF and iPS cells were treated with actinomycin D to inhibit transcription and total RNA was isolated from three replicates at 0, 15, 30, 60, 120 and 240 minutes.

first: Ashley

last: Neff

first: Ju-Youn

first: Jeffrey

last: Wilusz

first: Bin

last: Tian

first: Carol


title: MicroRNA Profiling in Mucosal Biopsies of Eosinophilic Esophagitis Patients Pre and Post Glucocorticoid Steroid Treatment and Relationship with mRNA Target Expression

status: Public on Mar 23 2012

city: Providence

first: Shaolei

last: Lu

state: Rhode Island

address: 593 Eddy Steet

department: Pathology

institute: Rhode Island Hospital

type:
Expression profiling by array
Expression profiling by RT-PCR

first: Kelly

last: Cleveland

first: Alexander

middle: S

last: Brodsky

first: Vincent

last: Mukkada

first: Murray

last: Resnick


title: Gene expression analysis in Panc-1 cells in response to treatment with Gli3T, a dominant-negative repressor of Gli

status: Public on Mar 29 2012

city: Worcester

first: Mihir

last: Rajurkar

state: MA

address: 364 Plantation st, 470Q LRB

department: Cancer Biology

institute: UMASS Medical School

summary:
Pancreatic Ductal Adenocarcinoma (PDAC) is one of the most aggressive human malignancies. In our studies, we find that the Gli transcription factors are required for Kras initiation of pancreatic tumorigenesis. In order to identify the downstream transcriptional targets of Gli in PDAC, we conducted gene expression analysis using Gli3T, a transcriptional repressor of Gli.
In this data set we include the expression data from 6 samples with three of them expressing a control vector and another three expressing Gli3T

overall_design: Gli3T with IRES-GFP, or an empty vector was ectopically expressed in Panc-1 cells using lipofectamine transfection. GFP positive cells were sorted 24 hours post transfection and RNA was isolated from the cells using Qiagen RNAeasy kit. Affymetrix gene expression array was conducted on the Panc-1 cells expressing the control vector and cells expressing Gli3T. Relative gene expression between the two sample sets was analyzed. Three samples were analyzed for each set.

first: Junhao

last: Mao


title: Gene expression profile in Barrett's esopahgus

status: Public on Mar 30 2012

city: Cambridge

first: Massimiliano

last: di Pietro

address: Hills Road

country: United Kingdom

institute: MRC Cancer Cell Unit

summary: Microarray was used to identify differential gene expression pattern in Barrett's esophagus (BE), compared to the normal adjacent epithelia gastric cardia (GC) and normal squamous esophagus (NE)

overall_design: RNA was extraxted from endoscopic  biopsies of BE (n=10), GC (n=10) and NE (n=10, only 8 uploaded). One NE sample was excluded since clustered with BE and all the intestinal markers were positive, indicating sampling error.

first: Pierre

last: Lao-Sirieix

first: Rebecca

last: Fitzgerald


title: Gene profiling in mucosal biopsies of Eosinophilic Esophagitis patients pre and post glucocorticoid steroid treatment

summary:
Eosinophlic esophagitis (EoE) is increasely recognized as an antigen-drived disorder. The goal of this study is to reveal the gene expression changes in EoE before and after a successful glucocorticoid steroid treatment.
We used microarrays to identify distinct genes involving the pathophysiology of EoE.

overall_design: Esophageal mRNA from the epithelial layers of 5 paired paraffin-embedded biopsies before and after treatment with glucocorticosteroids were harvested and profiled using  Affymetrix Human Gene 1.0 ST array to generate differentially regulated mRNA transcripts.

first: Christopher

last: Schorl


title: Exposure of an immortalized human bronchial epithelial cell line, BEAS-2B, to one of four metals (arsenic, chromium, nickel or vanadium) to determine the early changes that lead to cell transformation

status: Public on Mar 22 2012

city: Tuxedo

first: Hailey

middle: A.

last: Clancy

address: 57 Old Forge Road

department: Environmental Medicine

institute: New York University

summary: To determine early changes leading to human cell transformation (cancer) we exposed an immortalized human bronchial epithelial cell line, BEAS-2B, to one of four different metals that may cause cancer via inhalation in humans or rodents: 2.0 micro-Molar soluble sodium arsenite (NaAsO2), 0.50 micro-Molar potassium chromate (K2CrO4), 250 micro-Molar nickel (II) sulfate (NiSO4), 10 micro-Molar sodium meta-vanadate (NaVO3), or were left untreated (control).  After a 30-60 day exposure, cells were rinsed of metals and seeded in soft agar.  A small number of the cells formed colonies in the soft agar, demonstrating the potential for anchorage independent growth, a characteristic of cancer.  These colonies that originated from a single cell were extracted from the agar and grown out in monolayer for 3-4 weeks. The RNA data provided here is taken from these cells.  The significance it that the metal exposure was stopped many generations before the analysis, yet each sample demonstrates changes in gene expression based on the original metal exposure.

overall_design: A total of 39 samples were analyzed, consisting of 3 parental cell lines (BEAS-2B cells that were never seeded in agar or exposed to any metal), 11 controls cells (grouped into three sets, based on those seeded at the same time as the V-treated clones, the Cr-treated clones, or the As-treated and Ni-treated clones), and 25 metal-treated clones (7 each for Ni and As, processed in two separate batches of 3 and 4 clones each, 6 Cr clones and 5 Vanadium clones).  Because the samples were processed in different batches, the data was batch-normalized using the COMBAT package in R prior to importing into GeneSpring.  Once in GeneSpring the data was base-lined with each sample compared to its control samples (Batch 1:  Cr 1-6, P-2, Ctrls 6-8; Batch 2: As1-3, Ni 1-3, P-1 and Ctrl 1-3; Batch 3: As4-7, Ni 4-7, and Ctrl 4-5; Batch 4: V 1-5, P-3 and Ctrl 9-11).   When the same analysis was performed but with baseline of samples to all controls combined, a similar result was obtained, albeit with less tight clustering.  Arsenic clones 2 and 5 appear to be outliers as their removal nicely cleans up the PCA, but this appears to be genuine biological variation as we did not identify any significant problems with the data.

first: Hong

last: Sun

first: Lisa

last: Passantino

first: Thomas

middle: P

last: Kluz

first: Alexandra

last: Munoz

first: Jiri

last: Zavadil

first: Max

last: Costa


title: Expression data from patient iPSC

city: Stanford

first: Leng

last: Han

address: 265 Campus Dr

institute: Stanford University

summary: Baseline gene expression of patient dermal fibroblasts derived iPSCs generated by lentiviral Yamanaka 4 factors. We used microarrays to detail the global gene expression of Hypertrophic cardiomyopathy (HCM) patient specific iPSCs.

overall_design: Compare the global gene expression of iPSCs with hESCs and fibroblasts

first: Feng

last: Lan

first: Joseph

last: Wu


title: Transcriptome analysis of diabetic and non diabetic patients affected by post-ischemic heart failure

status: Public on Mar 21 2012

city: Milan

first: Fabio

last: Martelli

address: via morandi 30

country: Italy

institute: IRCCS-Policlinico San Donato

summary:
Increased morbidity and mortality associated with post-ischemic heart failure (HF) in diabetic patients underscore the need for a better understanding of the underlying molecular events. Indeed, effective HF therapy in diabetic patients requires a complex strategy encompassing the development of improved diagnostic and prognostic markers and innovative pharmacological approaches.
Whole mRNAs expression was measured in the heart of patients with heart failure (HF) with or without concomitant Type 2 diabetes mellitus (T2DM)  and compared it to control non-failing hearts.  We identified distinct genes modulated in HF patients compared to controls, as well as to T2DM HF  patients compared to  not diabetic HF patients.

overall_design: Our study included left ventricle (LV) cardiac biopsies taken from the vital, non-infarcted zone (remote zone) derived from patients affected by dilated hypokinetic post-ischemic cardiomyopathy, undergoing surgical ventricular restoration procedure.  Inclusion criteria for diabetic were: GLICEMIA: ≥126 mg/dl, previous T2DM diagnosis  or anti-diabetic therapy, while for non diabetic: GLICEMIA: <100 mg/dl and HbA1c:  n.v. 4.8-6.0%. Moreover, HF patients were matched for End Systolic Volume (ESV), Ejection fraction (LVEF), Age, Sex, Ethnic distribution, Smoke habits, Hypertension, Glomerular filtration rate (GFR), Body Mass Index (BMI). Genes expression was assessed by Affymetrix GeneChips Human Gene 1.0 ST array, using total RNA extracted from 7 T2DM HF patients, 12 non-T2DM HF patients and 5 controls.

first: Simona

last: Greco

first: Pasquale

last: Fasanaro

first: Lorenzo

last: Menicanti

first: Diego

last: Arcelli


title: Microarray analysis of Epidermolysis bullosa simplex-mottled pigmentation

status: Public on Mar 10 2012

city: Chicoutimi

first: Catherine

last: Laprise

state: Qc

address: 555 Boul. Université

country: Canada

institute: Université du Québec à Chicoutimi

summary: The goal of this study is to characterize the expression profile of Epidermolysis bullosa simplex-mottled pigmentation (EBS-MP) patient compared with normal subjects using genomic expression analyses. Microarray analyses were performed with RNA isolated from skin biopsies. Robust multiarray analysis (RMA) normalization and Smyth’s moderated t test were used to select differentially expressed genes. Expression profiling comparisons show that 52 genes are differentially expressed in EBS-MP patients compared to control subjects. Difference of expression for three genes (TYR, CCL22 , and ACVR1C )  was validated using real-time reverse transcription–polymerase chain reaction. Twelve genes were related to lipid biosynthesis process, two to keratinisation and skin pigmentation, Nineteen to cell growth and apoptosis, five to immune response and fourteen to predicted or less known function cluster.  To our knowledge, the distinctive pattern of gene expression that characterizes EBS-MP versus healthy skin tissue has never been reported.

overall_design: RNA used for the microarrays analysis was isolated from superficial 2mm punch biopsies composed of mainly epidermis with minimal dermis amounts of normal-appearing skin of one EBS-MP patient and seven healthy volunteers.

first: Mbarka

last: Bchetnia

first: Jacynthe

last: Lacroix

first: Tarik

last: Farez

first: Georgette

last: Leclerc

first: Audrey

last: Dupérée

first: Julie

last: Powell

last: McCuaig

first: Charles

last: Morin

first: Yosra

last: Bouyacoub

first: Valérie

last: Legendre-Guillemin


title: Parkin pathway activation mitigates glioma cell proliferation and predicts patient survival

status: Public on Mar 15 2012

first: Felicia

last: Ng

address: Wellcome Trust/MRC Building, Addenbrooke's Hospital, Hills Road

institute: Cambridge Institute for Medical Research

summary: Mutations in the parkin gene, which encodes a ubiquitin ligase, are a major genetic cause of parkinsonism. Interestingly, parkin also plays a role in cancer as a putative tumor suppressor, and the gene is frequently targeted by deletion and inactivation in human malignant tumors. Here, we investigated a potential tumor suppressor role for parkin in gliomas. We found that parkin expression was dramatically reduced in glioma cells. Restoration of parkin expression promoted G1 phase cell cycle arrest and mitigated the proliferation rate of glioma cells in vitro and in vivo. Notably, parkin-expressing glioma cells showed a reduction in levels of cyclin D1, but not cyclin E, and a selective downregulation of Akt serine-473 phosphorylation and VEGF receptor levels. In accordance, cells derived from a parkin null mouse model exhibited increased levels of cyclin D1, VEGF receptor and Akt phosphorylation and divided significantly faster when compared with wild type cells, with suppressionof these changes following parkin re-introduction. Clinically, analysis of parkin pathway activation was predictive for the survival outcome of glioma patients. Taken together, our study provides mechanistic insight into the tumor suppressor function of parkin in brain tumors, and suggests that measurement of parkin pathway activation may be used clinically as a prognostic tool in brain tumor patients.

overall_design: Total RNA obtained from U-87MG cells stably expressing parkin or vector alone. Replicate arrays were performed for each of the 3 vector and parkin-expressing U-87MG clones.

first: Calvin

middle: W

last: Yeo

first: Chou

last: Chai

first: Jeanne

last: Tan

first: Geraldene

last: Koh

first: Yuk-Kien

last: Chong

first: Lynette

first: Charlene

last: Foong

first: Edwin

last: Sandanaraj

first: Joanna

last: Holbrook

first: Beng-Ti

last: Ang

first: Takahashi

last: Ryosuke

first: Carol

last: Tang

first: Kah-Leong

last: Lim


title: Airway gene expression is dynamic with corticosteroid treatment and reflects disease activity

status: Public on Mar 03 2012

city: Groningen

first: Maarten

last: van den Berge

address: Hanzeplein 1

department: Pulmonary Diseases

country: Netherlands

institute: University Medical Center Groningen

summary: Introduction: In the recently completed Dutch GLUCOLD study, treatment of COPD patients with fluticasone ± salmeterol reduced the rate of decline in FEV1. These results indicate that ICS can have therapeutic efficacy in COPD. Aim: To explore the molecular mechanisms by which ICS exert their effects, we performed genome-wide gene expression profiling on bronchial biopsies from COPD patients who participated in the GLUCOLD study. Methods: An Affymetrix Human Gene Array ST version 1.0 was performed in a total of 221 bronchial biopsies that were available from 90 COPD patients at baseline and after 6 and 30 months of therapy. Linear mixed effects modeling was used to analyze treatment-specific changes in gene expression. A validation set was included and pathway analysis was performed with Gene Set Enrichment Analysis (GSEA). Results: The expression of 138 genes significantly decreased after both 6 and 30 months of treatment with fluticasone ± salmeterol versus placebo, whereas the expression of 140 genes increased. A more pronounced treatment-induced change in expression of 51 of these 278 genes was associated with a slower rate of decline in FEV1. Genes that decreased with treatment were involved in pathways related to cell cycle, oxidative phosphorylation, epithelial cell signaling, p53 signaling and T cell signaling. Genes that increased with treatment were involved in pathways related to focal adhesion, gap junction and extracellular matrix deposition. Conclusion: The present study suggests that gene expression in biological pathways of COPD is dynamic with treatment and reflects disease activity. This study opens the gate to targeted and phenotype-driven therapy of COPD.

overall_design: First, a total of 162 samples were analysed  (RNA derived from bronchial biopsies from COPD patients before and after treatment with fluticasone +/- salmeterol or placebo [GLUCOLD study]), 107 samples before and after 6 and 30 months of treatment with fluticasone +/- salmeterol and 55 samples before and after treatment with placebo. A total of 278 genes were found that changed in expression after both 6 and 30 months of treatment with fluticasone +/- salmeterol versus placebo. Next, an additional number of 59 samples from the fouth GLUCOLD treatment were put on array. In this study arm, COPD patients were treated for 6 months with fluticasone and then fluticasone was discontinued and patients switched to placebo for the remaining 24 months of the study.


title: Effect of Valproic Acid on Endothelial Cells

status: Public on Mar 14 2012

city: Gothenburg

first: Per-Arne

last: Svensson

department: Department of molecular and clinical medicine

country: Sweden

institute: institute of medicine

summary: Valproic acid (VPA) is a short-chain fatty acid used in the treatment of epilepsy and also considered to be an epigenetic modifier by functioning as a histone deacetylase (HDAC)-inhibitor. The aim of this study was to search for gene altered by VPA in human endothelial cells.

overall_design: Human umbilical vein endothelial cells (HUVEC) from five individuals were cultured in the absence or presence of 4mM VPA for 24h. Cells were cultured in EGM-2 medium and all experiments were performed in passages 1 or 2.

first: Mia

last: Magnusson

first: Pia

last: Larsson

first: Erik

last: Ulfhammer

first: Lena

last: Karlsson

first: Sverker

last: Jern


title: Fibroblasts under adipogenic, chondrogenic or osteogenic differentiation medium and controls

status: Public on Mar 01 2012

city: Brisbane

first: Stefan

last: Thor

state: QLD

address: Skerman Bldg (65) room 506  Faculty of Medicine

department: School of Biomedical Sciences

country: Australia

institute: The University of Queensland

summary:
Global gene expression analysis was performed to investigate the changes of the fibroblast phenotype after four-week inductions toward adipocytic, osteoblastic and chondrocytic lineages. Human cells.
Differential gene regulation, interpreted through Gene Set Enrichment Analysis, highlight important similarities and differences of induced fibroblasts compared to control cultures of human fibroblasts, adipocytes, osteoblasts and articular chondrocytes.

overall_design: Fibroblast controls were compared to Adipogenic induced fibroblasts and adipocytes. Gene sets were analysed with GSEA (webgestalt). Repeated for each lineage.

first: Jonathan

last: Rakar


title: Identification of molecular pathways involved in oxaliplatin-associated sinusoidal dilatation

first: Florent

last: Dumont

summary: Oxaliplatin-based chemotherapy for colorectal liver metastases (CRLM) can result in vascular liver lesions such as sinusoidal dilatations. Physiopathology remains unclear and variability between patients suggests that there is individual susceptibility. A better understanding of the molecular mechanisms of oxaliplatin liver toxicity may allow to identification of biomarkers and adaptation of chemotherapy delivery.

overall_design: non-tumor frozen liver samples were obtained from patients operated on for CRLM after an exclusive oxaliplatin-based chemotherapy. Gene-expression profiles were first analyzed by microarray on a selected population of 20 patients; 9 patients with severe sinusoidal dilatation (SD) after a short period of chemotherapy and 10 patients without any sinusoidal dilatation after a long period of chemotherapy. These were compared with a control group of 5 patients without any chemotherapy and lesions

first: Marie

last: Seman


title: phosphatidic acid in gene expression-Phosphatidic acid in gene expression

city: evry

first: Soubigou-Taconnat

last: Ludivine

address: 2 rue gaston crémieux

department: URGV

institute: INRA

summary: au10-12_pa - phosphatidic acid in gene expression - Role of DGK in gene expression - Compounds were added 4h before cell harvesting.

overall_design: 6 dye-swap - treated vs untreated comparison

first: Sandrine

last: Balzergue

first: Ludivine

last: Taconnat

first: Eric

last: Ruelland

first: Marie-Laure

last: Martin-Magniette


title: Interconversion between active and inactive TATA-binding protein transcription complexes in the mouse genome.

city: Illkirch

first: Celine

last: Keime

address: 1 rue Laurent Fries

institute: IGBMC (CNRS/INSERM/UDS)

type: Genome binding/occupancy profiling by high throughput sequencing

summary: The conserved core domain of the TATA binding protein (TBP) interacts with multiple partners forming the complexes required for transcription by RNA Polymerases I, II and III. We use genetically modified mouse embryonic fibroblasts to show that many TBP core domain mutants complement loss of endogenous TBP, but this often results in a slow growth phenotype. Two TBP mutations, R188E and K243E, disrupt the TBP-BTAF1 interaction and B-TFIID complex formation. Transcriptome and ChIP-seq analyses show that loss of B-TFIID does not affect global genomic distribution of TBP, but positively or negatively affects TBP and/or RNA Polymerase II (Pol II) recruitment to a selected set of promoters. We identify a set of promoters where wild-type TBP assembles a partial inactive preinitiation complex lacking Pol II and TAF1. Our results suggest that an exchange of the B-TFIID complex in wild-type cells for TFIID in R188E and K243E mutant cells at these primed promoters recruits Pol II to activate their expression. We also observe that both Wt and mutant TBP can occupy promoters without concurrent Pol II recruitment and active transcription. Our data reveal a novel regulatory mechanism involving the formation of a partial preinitiation complex that primes the promoter for productive preinitiation complex formation in mammalian cells.

overall_design: Using homologous recombination, we generated ES cells and mice harbouring a null allele in the Tbp gene by insertion of a hygromycin resistance cassette in exon III and a floxed allele, in which exon III is surrounded by LoxP sites. From these mice, we generated an embryonic fibroblast Tbplox/- cell line in which TBP expression can be inactivated by expression of the Cre recombinase leading to cell death. We adopted a two-step strategy to generate Tbp-/- cell lines expressing human (h)TBP. Cells were first infected with pBABE retrovirus vectors expressing Wt hTBP or a series of mutants in the TBP core region, all of which carry a Flag-HA tag on their N-terminus. Cells expressing endogenous mTBP and exogenous hTBP were then infected with a second retrovirus expressing the 4 hydroxy-tamoxifen (OHT) inducible Cre-ERT2.  Subsequently, multiple clonal populations from the OHT treated cells were isolated and genotyped by PCR to identify the Tbp-/-clones. At least two independent clones where expression of the endogenous mTBP was lost and replaced by the exogenous hTBP were isolated.

first: Mohamed-Amin

last: Choukrallah

first: Dominique

last: Kobi

first: Igor

last: Martianov

first: W

last: Pijnappel

first: Nikolai

last: Mischerikow

first: Tao

last: Ye

first: Albert

last: Heck

first: H

last: Timmers

first: Irwin

last: Davidson


title: CD20 positive cells are undetectable in the majority of multiple myeloma cell lines and are not associated with a cancer stem cell phenotype

status: Public on Feb 27 2012

city: Salamanca

first: Teresa

last: Paíno

address: Campus Miguel de Unamuno

institute: Centro de investigación del cáncer

summary: Although new therapies have doubled the survival of multiple myeloma (MM) patients, this remains an incurable disease. It has been postulated that the so-called MM Cancer Stem Cells (MM-CSC) would be responsible for tumor initiation and relapse but their unequivocal identification remains unclear. Here, we investigated in a panel of MM cell lines the presence of CD20+ cells harboring a MM-CSC phenotype. Among the multiple cell lines investigated, only a small population of CD20dim+ cells (0.3%) in the RPMI-8226 cell line was found. CD20dim+ RPMI-8226 cells expressed the plasma cell markers CD38 and CD138 and were CD19-CD27-. Additionally, CD20dim+ RPMI-8226 cells did not exhibit stem-cell markers as shown by gene expression profiling and the aldehyde dehydrogenase (ALDH) assay. Moreover, we demonstrated that CD20dim+ RPMI-8226 cells are not essential for CB17-SCID mice engraftment and show lower self-renewal potential than the CD20- RPMI-8226 cells. These results do not support CD20+ expression for the identification of MM-CSC.

overall_design:
For detailed description of Material and Methods, see supplementary Methods.
The human MM cell lines RPMI-8226, U266, MM1S, MM1R, NCI-H929, RPMI-LR5, U266-LR7 and U266-Dox4 were studied. Cells were cultured as previously described [Ocio, 2009, 3781].
MM cell lines were immunophenotyped using a 7-color immunofluorescence technique [Paiva, 2011, 697], with the following combination of monoclonal antibodies (Pacific Blue (PB)/ anemonia majano cyan (AmCyan)/ fluorescein isothiocyanate (FITC)/ peridinin chlorophyll protein-cyanin 5.5 (PerCP-Cy5.5)/ PE-cyanin 7 (PE-Cy7)/ allophycocyanin (APC)/ alexafluor 700 (AF700)): CD19/CD45/CD20/CD138/CD27/CD56/CD38. Data were stored for a minimum of 3x105 events. CD20dim+ and CD20- RPMI-8226 cells were sorted after incubation with CD20-APC/7AAD and acquisition on a FACSAria cytometer (Becton Dickison Biosciences). Sorting was performed only for viable cells (7AAD-) and debris were excluded by scatter properties. The CD20- and CD20dim+ RPMI-8266 sorted cells had a final purity of 98% and 88%, respectively.
CD20dim+ and CD20- RPMI-8226 cells were extensively characterized. Morphological characterization was done with May-Grünwald-Giemsa staining. Characterization of VDJH and IGKappa rearrangements was performed as described elsewhere [BIOMED-2, BMH4-CT98-3936]. The expression of aldehyde dehydrogenase (ALDH) was assessed using the Aldefluor Kit (StemCell Technologies) following manufacturer’s instructions with further staining with a CD20-APC antibody. For gene expression profile studies, RNA was isolated, labeled and hybridized to Human Gene 1.0 ST array (Affymetrix) according to Affymetrix protocols [Gutiérrez, 2005, 402]. The arrays were analyzed using the DNA-Chip Analyzer software (DChip). Fold change ≥2 was considered significant.

first: Enrique

middle: M

last: Ocio

first: Bruno

last: Paiva

first: Laura

last: San-Segundo

first: Mercedes

last: Garayoa

first: Norma

last: Gutiérrez

first: María

last: Sarasquete

first: Atanasio

last: Pandiella

first: Alberto

last: Orfao

first: Jesús

last: San Miguel


title: Gene expression data from  human metastatic melanoma tumors that may predict response to RAF265

status: Public on May 02 2012

city: Nashville

first: Pengcheng

last: Lu

address: 2200 Pierce Avenue

institute: Vanderbilt University

summary: To determine how mutation of BRAF affected the response to RAF265, we utilized a tumor orthotopic implant model of early passage melanoma tumors in nude mice from a series of 17 patients with advanced metastatic Tumor growth was compared between RAF265 treatment (40 mg/kg, QD) and diluent control groups. The melanoma associated gene mutation profile and global gene expression profile were determined on these human melanoma samples by SNaPshot and Affymetrix Human Gene ST 1.0 Array, respectively. Tumors were evaluated for growth response to RAF265 in an orthotopic implant model using nude mice. Comparisons were made between gene expression profiles of responders and non-responders, BRAF mutant and BRAF wild type tumors. Analysis of the microarray data revealed responders exhibited enriched expression of genes involved in cell cycle, apoptosis, cell-cell adhesion and initiation of epithelial/mesenchymal transition. It is concluded that RAF265 significantly inhibits the growth of a sub-population of V600E mutant and wild type BRAF human melanoma tumors in vivo and the gene expression profile of this subset of tumors that may predict response to RAF265.

overall_design: RNA from 17 human metastatic melanoma tumors was extracted and hybridized on Affymetrix microarrays.

first: Ann

last: Richmond

first: Yingjun

last: Su

first: Shawn

last: Levy

first: Aixiang

last: Jiang

first: Yu

last: Shyr

first: Jeffrey

last: Sosman

first: Mark

last: Kelley

first: Kimberly

last: Dahlman

first: Darrin

last: Stuart

first: Ryan

last: Splittgerber

first: Sara

last: Kantrow

first: Sarah

last: Short

first: Tammy

last: Sobolik-Delmaire

first: Snjezana

last: Zaja-Milatovic


title: Genome-wide changes in subcutaneous adipose tissue expression in HIV negative adults after 2 weeks of zidovudine or stavudine with lamivudine.

city: Dublin

first: Claudette

last: Satchell

address: Belfield

country: Ireland

institute: University College Dublin

summary: As controversy remains as to the exact mechanisms by which the thymidine-analogue nucleoside reverse transcriptase inhibitors, zidovudine (AZT) and stavudine (d4T) induce subcutaneous adipose tissue toxicity, we used microarrays to dentify patterns of gene expression in human subcutaneous adipose tissue that change as a result of exposure to these drugs for 2 weeks.

overall_design: Paired RNA samples (baseline and week 2), isolated from the adipose tissue of HIV-uninfected healthy adults randomized to 6 weeks of either AZT/ lamivudine (3TC) or d4T/ 3TC were analysed by microarray.

first: Padraig

last: Doolan

first: Eoin

last: Feeney

first: Jai

last: Mehta

first: Martin

last: Clyne

first: David

last: Cooper

first: Andrew

last: Carr

first: Paddy

last: Mallon


title: Common PIK3CA mutants and a novel 3’UTR mutation are associated with increased sensitivity to saracatinib

status: Public on Feb 24 2012

city: Salt Lake City

first: Aik Choon

last: Tan

state: UT

address: 2000 Circle of Hope

department: Oncological Sciences

institute: Huntsman Cancer Institute

summary: Sensitive versus Resistant patient-derived colorectal cancer tumor xenografts with PIK3CA mutant against saracatinib (AZD0530)

first: Aik-Choon

first: John

last: Arcaroli

first: Wells

last: Messersmith


title: A novel role of stem cell factor SALL4 as an oncofetal protein in hepatocellular carcinoma

status: Public on Feb 22 2012

city: Singapore

first: Henry

last: Yang

address: 28 Medical Drive

country: Singapore

institute: Cancer Science Institute of Singapore

summary:
Hepatocellular carcinoma (HCC) is the third leading cause of cancer-related deaths worldwide. Treatment of HCC remains abysmal; discovery of novel pathways implicated in hepatocarcinogenesis is needed for more effective therapeutics. SALL4 is a stem cell factor essential for the maintenance of embryonic stem cell self-renewal properties and expressed in fetal liver, but silenced in normal adult liver. We observed that expression of SALL4 in murine liver in a transgenic model led to development of HCC. In humans, SALL4 is re-expressed as an oncofetal protein in a subgroup of HCC patients with unfavorable prognoses. Loss-of-function studies demonstrated that SALL4 is essential for human HCC cell survival and tumorigenicity.
We demonstrated that a peptide can block the oncogenic function of SALL4 in HCC by modulating the PTEN/AKT pathway. Our findings reveal a novel role of SALL4 in HCC with important implications for understanding disease mechanisms and development of innovative therapeutics.

overall_design: Cultured cells from HCC cell line SNU-398 with scrambled or SALL4 shRNA knockdown were used for RNA extraction and hybridization on Affymetrix microarrays.

first: Kol

last: Yong

first: Chong

last: Gao

first: Benedict

last: Yan

first: Joline

last: Lim

first: Todor

last: Dimitrov

first: Akira

last: Kawasaki

first: Chee

last: Ong

first: Sanghoon

last: Lee

first: Sharada

last: Ravikumar

first: Supriya

last: Srivastava

first: Xi

last: Tian

last: Luk

first: Yock

middle: Y

last: Dan

first: Manuel

last: Salto-Tellez

first: Li

last: Chai

first: Daniel

middle: G

last: Tenen


title: Sorafenib treatment of FLT3-ITD+ acute myeloid leukemia: favorable initial outcome and mechanisms of subsequent non-responsiveness associated with a D835 mutation

status: Public on Feb 18 2012

city: Hong Kong

first: Cheuk Him

last: Man

address: L816, LAB BLK, FMB, HKU

country: Hong Kong

institute: HKU

summary: Internal tandem duplication (ITD) of the fms-related tyrosine kinase-3 (FLT3) gene occurs in 30% acute myeloid leukemias (AML) and confers a poor prognosis.  Thirteen relapsed or chemo-refractory FLT3-ITD+ AML patients were treated with sorafenib (200-400 mg twice daily). Twelve patients showed clearance or near clearance of bone marrow (BM) myeloblasts after 27 (range 21–84) days with evidence of differentiation of leukemia cells.  The sorafenib response was lost in most patients after 72 (range 54–287) days but the FLT3 and downstream effectors remained suppressed. Four pairs patients (before sorafenib treatment and after sorafenib relapse), total eight samples from four patients at the two time-points were subjected to microarray analysis. Gene expression profiling showed that leukemia cells which have become sorafenib resistant expressed a number of genes including ALDH1A1, JAK3 and MMP15, whose functions were unknown in AML. NOD/SCID mice transplanted with leukemia cells from patients before and during sorafenib resistance recapitulated the clinical results. Both ITD and tyrosine kinase domain (TKD) mutations at D835 were identified in leukemia initiating cells (LIC) from samples before sorafenib treatment.  LIC bearing the D835 mutant have expanded during sorafenib treatment and dominated during the subsequent clinical resistance. These results suggested that sorafenib have selected more aggressive sorafenib-resistant subclones carrying both FLT3-ITD and D835 mutations and might provide important leads to further improvement of treatment outcome with FLT3 inhibitors.

overall_design: RNA from CD33+CD34+ myeloblasts at pre-sorafenib-treatment and post-sorafenib-relapse were collected and subjected to microarray analysis

first: Cheuk-Him

first: Tsz-Kan

last: Fung

first: Leung

last: Anskar


title: Expression data from cytoplasmic hybrid (cybrid) and rho0 cells

status: Public on Apr 01 2012

city: Daejeon

first: Seungwoo

last: Hwang

address: 52 Eoeun-dong Yuseong-gu

department: Korean Bioinformation Center

country: South Korea

institute: Korea Research Institute of Bioscience and Biotechnology

summary:
Mitochondria have been implicated in insulin resistance and beta cell dysfunction, both of which comprise the core pathophysiology of type 2 diabetes mellitus (T2DM). It has also recently been found that mtDNA haplogroups are distinctively associated with susceptibility to T2DM at least in Koreans and Japanese.
To investigate the functional consequences of different mtDNA, we compared gene expression profiles between cybrid clones harboring three different mtDNA haplogroups (D5, F, and N9a). To produce hybrid clones, we fused mtDNA-depleted osteosarcoma cell line (143B TK- rho0) with nucleus-lacking platelets from twelve donors harboring the three haplogroups.

overall_design: A total of twelve cybrid clones from the three mtDNA haplogroups were obtained: D5 (n=3), F (n=5), and N9a (n=4). For each clone, four technical replicates were obtained and hybridized to the array. For rho0 cell, six technical replicates were obtained and hybridized to the array.

first: Young

last: Cho


title: Whole genome expression data from human urinary bladder cancer

city: Lucknow

first: Pankaj

middle: Kumar

last: Singh

state: Uttar Pradesh

address: Chowk

department: Radiotherapy

country: India

summary: At diagnosis approximately 75% of bladder urothelial carcinomas are non muscle invasive bladder cancers (Ta, T1 and Tis), 20% are muscle invasive bladder cancer (T2-T4) and 5% are already metastatic. Non muscle invasive bladder cancers are characterized by tumor recurrence in 60% to 85% of cases and, therefore, long-term followup is needed.  The current standard methods to detect and monitor bladder cancer are cystoscopy and cytology. Cystoscopy is an invasive method and cytology is hampered by low sensitivity, especially for low grade tumors. So there is need to develop reliable and noninvasive methods to detect and predict bladder cancer biological behavior. So we have performed high density oligonucleotide microarray for discovery of new molecular markers to diagnose and predict the outcome of bladder cancer.

overall_design: Under an ethical guideline of Chhatrapati Shahuji Maharaj Medical University, India histologically confirmed seven bladder cancer patients were recruited from Department of Urology, Chhatrapati Shahuji Maharaj Medical University, Lucknow, India. Total RNA was extracted from tumor biopsies and hybridized on affymetrix Human Gene ST 1.1 array to determine differentially expressed genes in urinary bladder cancer with muscle invasion in comparison of normal human urinary bladder.

middle: K

first: Srikanta

last: Rath

first: Madan-Lal

middle: B

last: Bhatt


title: FOSL1 as a candidate target gene for 11q12 rearrangements in desmoplastic fibroblastoma

status: Public on May 09 2012

city: Lund

first: Karolin

middle: H

last: Nord

address: BMC C13

department: Dept of Clinical Genetics

institute: Lund University

type:
Expression profiling by array
Third-party reanalysis

summary: Global gene expression analysis of desmoplastic fibroblastoma (DF) and histologically similar tumors. FOSL1 is identified as a candidate target gene for the 11q12 rearrangments in DF.

overall_design:
RNA was extracted from 3 frozen desmoplastic fibroblastoma (DF) biopsies and hybridized onto Affymetrix Human Gene 1.0 ST arrays. RNA from 6 myxofibrosarcoma (MFS), 6 desmoid fibromatosis (DFM), 5 solitary fibrous tumor (SFT) and 17 low-grade fibromyxoid sarcomas (LGFMS) were used as controls.

The control dataset has been previously published and is available in the GEO database under Series accession GSE24369.

The complete dataset representing: (1) the 3 desmoplastic fibroblastoma Samples and (2) the 34 control Samples from Series GSE24369 (re-processed using RMA), is linked below as a supplementary file.

first: Gemma

last: Macchia

first: Domenico

last: Trombetta

first: Emely

last: Möller

first: Fredrik

last: Mertens

first: Clelia

middle: T

last: Storlazzi

first: Maria

last: Debiec-Rychter

first: Raf

last: Sciot


title: Epigenetic silencing of PKD1 in autosomal dominant polycystic kidney disease

status: Public on Feb 16 2012

city: Seoul

first: Yu Mi

last: Woo

address: Cheongpa-ro 47-gil 100 (Cheongpa-dong 2(i)-ga), Yongsan-gu

institute: Sookmyung Women's University

summary:
ADPKD (Autosomal dominant polycystic kidney disease) is the most common inherited disorders and is characterized by growth of numerous cysts filled with fluid in the kidneys. Ultimately, it leads to kidney failure. The mutations of PKD1 and PKD2 account for approximately 85 and 15 percent of ADPKD, respectively. However, the mechanisms related to genetic mutation of PKD1 and PKD2 are still unclear.
To investigate altered gene expression levels, Affymetrix microarray was performed using the kidney tissue from normal and ADPKD patients.

overall_design: Total RNAs were isolated from kidney of human normal (49 years old/ male) and ADPKD patients (62 years old/ male, 67 years old/ male) using NucleoSpin® RNA Kit (MACHEREY-NAGEL) according to the manufacturer’s instructions. We used tha Affymetrix GeneChip Human Gene 1.0 ST Array. Per RNA sample, 300 ng was used as the input into the Affymetrix procedure as recommended by the manufacturer's protocol.

first: Yu

first: Jong

last: Park


title: Polyunsaturated fatty acids acutely affect triacylglycerol-derived skeletal muscle fatty acid uptake and increases postprandial insulin sensitivity

status: Public on Feb 21 2012

city: Wageningen

first: Guido

last: Hooiveld

address: HELIX, Stippeneng 4

department: Div. Human Nutrition & Health

institute: Wageningen University

summary:
Dietary fat quality may influence skeletal muscle lipid handling and fat accumulation, thereby modulating insulin sensitivity. Objective: To examine acute effects of meals with various fatty acid (FA) compositions on skeletal muscle FA handling and postprandial insulin sensitivity in obese insulin resistant men. Design: In a single-blinded randomized crossover study, 10 insulin resistant men consumed three high-fat mixed-meals (2.6MJ). Meals were high in saturated FA (SFA), in monounsaturated FA (MUFA) or in polyunsaturated FA (PUFA). Fasting and postprandial skeletal muscle FA handling were examined by measuring arterio-venous concentration differences across forearm muscle. [2H2]-palmitate was infused intravenously to label endogenous triacylglycerol (TAG) and FFA in the circulation and [U-13C]-palmitate was added to the meal to label chylomicron-TAG. Skeletal muscle biopsies were taken to assess intramuscular lipid metabolism and gene expression. Results: Insulin and glucose responses (AUC) after SFA meal were significantly higher compared with PUFA meal (p=0.003 and 0.028, respectively). Uptake of TAG-derived FA was significantly lower in the early postprandial phase after PUFA meal as compared with other meals (AUC60-120, p<0.001). The PUFA meal induced less transcriptional downregulation of oxidative pathways compared with other meals. The fractional synthetic rate was higher in DAG and PL fraction after MUFA and PUFA meal. Conclusion: Intake of a PUFA meal reduced TAG-derived skeletal muscle FA uptake, which was accompanied by higher postprandial insulin sensitivity and a tendency towards a higher muscle lipid turnover. These data suggest that the effects of replacement of SFA by PUFA may contribute to less muscle lipid uptake and may be therefore protective against the development of insulin resistance.

Keywords: expression profiling by array

overall_design: randomized crossover dietary intervention study

first: Anneke

last: Jans

first: Ellen

last: Konings

first: Gijs

last: Goossens

first: Freek

last: Bouwman

first: Chantalle

last: Moors

first: Mark

middle: V

last: Boekschoten

first: Lydia

middle: A

last: Afman

first: Michael

last: Müller

first: Edwin

last: Mariman

last: Blaak


title: Mutant p53 Disrupts Mammary Acinar Morphogenesis via the Mevalonate Pathway

status: Public on Feb 13 2012

city: New York

first: William

last: Freed-Pastor

department: Biological Sciences

country: USA

institute: Columbia University

summary: p53 is a frequent target for mutation in human tumors and previous studies have revealed that these missense mutant proteins can actively contribute to tumorigenesis.  To elucidate how mutant p53 might contribute to mammary carcinogenesis we employed a three-dimensional (3D) culture model. In 3D culture non-malignant breast epithelial cells form structures reminiscent of acinar structures found in vivo, whereas breast cancer cells form highly disorganized and in some cases invasive structures.  We found that mutant p53 depletion is sufficient to phenotypically revert breast cancer cells to a more acinar-like morphology. Genome-wide expression analysis identified the sterol biosynthesis, or mevalonate, pathway as significantly upregulated by a tumor-derived mutant p53.  Using statins and sterol biosynthesis intermediates, we demonstrate that this pathway is both necessary and sufficient for the phenotypic effects of mutant p53 on breast tissue architecture. Mutant p53 associates with the sterol gene promoters at least partly via the SREBP transcription factors.  Finally, p53 mutation correlates with higher levels of sterol biosynthesis genes in human breast tumors. This activity of mutant p53 not only contributes insight into breast carcinogenesis, but also implicates the mevalonate pathway as a new therapeutic target for tumors bearing such mutations in p53.

overall_design: RNA was isolated from three independent experiments of MDA-468.shp53 cells cultured under 3D conditions for 8 days in the presence or absence of DOX, reversed transcribed and hybridized to an Affymetrix GeneChip expression array.  Data was processed using the Robust Multichip Average (RMA) algorithm to give expression signals and paired t-test was applied for each probe. Probes with 1% significance were selected for Ingenuity Pathway Analysis.

first: Hideaki

last: Mizuno

first: Xi

last: Zhao

first: Anita

last: Langerød

first: Sung-Hwan

last: Moon

first: Anthony

last: Barsotti

first: Agustin

last: Chicas

first: Wencheng

last: Li

first: Alla

last: Polotskaia

first: Mina

middle: J

last: Bissell

first: Timothy

last: Osborne

first: Bin

last: Tian

first: Scott

last: Lowe

first: Anne-Lise

last: Børresen-Dale

first: Arnold

last: Levine

first: Jill

last: Bargonetti

first: Carol

last: Prives


title: Gene expression from MDA-MB-231

status: Public on Feb 09 2012

city: Barcelona

first: Sandra

last: Peiró

address: Aiguader 88

department: Programa de Recerca en Càncer

institute: IMIM-Hospital del Mar

summary: Gene expression from MDA-MB-231 cells shControl and shLOXL2.

overall_design: We analyzed 3 arrays from each condition: shControl and shLOXL2.

first: S

last: Peiro


title: Gene expression analysis of urine sediment: evaluation for potential noninvasive markers of interstitial cystitis/bladder pain syndrome

status: Public on Feb 06 2012

city: Lexington

first: Eric

last: Blalock

state: KY

address: 800 Rose St.

department: Molecular and Biomedical Pharmacology

institute: University of Kentucky

summary: Purpose: Determine if gene expression profiles in urine sediment could provide non-invasive candidate markers for painful bladder syndrome (PBS) with and/or without Hunner lesions. Materials and Methods: Fresh catheterized urine was collected and centrifuged from control (n = 5), lesion-free (n = 5), and Hunner lesion bearing (n = 3) patients. RNA was extracted from the pelleted material and quantified by gene expression microarray (Affymetrix Human Gene ST Array). Results: Three biologically likely hypotheses were tested: A) all three groups are distinct from one another; B) controls are distinct from both types of PBS patients combined, and C) Hunner lesion PBS patients are distinct from controls and non-Hunner-lesion PBS combined.  For statistical parity an unlikely fourth hypothesis was included: non-Hunner-lesion PBS patients are distinct from controls and Hunner lesion PBS combined.  Analyses supported selective upregulation of genes in the Hunner lesion PBS group (hypothesis C), and these were primarily associated with inflammatory function. This profile is similar to that reported in a prior microarray study of bladder biopsies in Hunner lesion PBS. Conclusions: Urine sediment gene expression from non-Hunner-lesion PBS patients lacked a clear difference from that of control subjects, while the array signatures from PBS patients with Hunner lesions showed a clear, primarily inflammatory, signature.  This signature was highly similar to that seen in a prior microarray study of bladder biopsies. Thus, although sample sizes were small, this work suggests that gene expression in urine sediment may provide a non-invasive biomarker for Hunner lesion, but not non-Hunner lesion, PBS.

overall_design: Urine (40-100 ml) was immediately placed on ice, transported to the laboratory and centrifuged at -4C for 5 minutes.  Pellets were washed twice with ice-cold phosphate-buffered saline, suspended in 0.8 ml TRIzol and RNA was extracted according to the manufacturer's instructions.  RNA was stored at -80oC until all samples had been collected, then analyzed at our Microarray Core Facility using the Affymetrix GeneChip Whole Transcript (WT) Sense Target Labeling Assay protocol, added to Human Gene 1.0 ST array chips, and annotated with gene symbol and functional information (Affymetrix). Probe level data were produced by Partek GS (6.10) using the gcRMA output option. Probe set signal intensities < 4.2 were considered absent, and if > 10 chips rated a probe set absent, that probe set was not considered for further analysis. Additionally, probe sets that did not have a gene symbol-level annotation (e.g., were considered 'hypothetical', or 'expressed sequence tags') were not considered for further analysis.

first: Garrett

last: Korrect

last: Stromberg

first: Deborah

middle: R

last: Erickson


title: Expression data from human bronchial airway smooth muscle (ASM) cells

city: Winnipeg

first: Abdelilah

last: Gounni

state: Manitoba

address: 750 McDermot Avenue

department: Department of Immunology

institute: University of Manitoba

summary: Interleukin (IL)-17 plays an important and protective role in host defence and has been demonstrated to orchestrate airway inflammation by cooperating with and inducing proinflammatory cytokines. Mircoarrays were used to identify immediate-early/ primary response IL-17A-dependent gene transcripts in primary human bronchial ASM cells from mild asthmatic and healthy individuals.

overall_design: To evaluate IL-17A-inducible gene transcripts, primary human bronchial ASM cells from 3 mild asthmatic and 3 healthy donors were treated for 2h with IL-17 [10ng/ml] and were probed with the Affymetrix GeneChip array. The 2h time point was carefully chosen in order to identify primary response gene targets and to avoid confounding autocrine mechanisms mediating indirect, or late-phase gene expression responses. Non-stimulated ASM cells from the same patients were used as controls.

first: Stephane

last: Dragon


title: Expression data from patient iPSC and iPSC-derived cardiomyocytes

status: Public on Feb 01 2012

city: Stanford

first: Leng

last: Han

state: CA

address: 265 Campus Dr

institute: Stanford University

summary:
Dilated cardiomyopathy (DCM) is the leading cause of heart failure and transplantation worldwide. We used iPSCs to model this disease and compared gene expression change before and after gene therapy of cardiomyocytes derived from DCM-specific iPSCs.
We used microarrays to detail the global gene expression of patient specific iPSCs, iPSC-derived cardiomyocytes and its response to gene therapy.

overall_design:
Skin fibroblasts and iPSCs derived from a family exhibiting familial dilated cardiomyopathy and H7 human ESCs were subjected to RNA extraction and hybridization on Affymetrix microarrays.Global gene expression pattern were compared and analyzed.
Cardiomyocytes derived from iPSCs generated from this DCM family were treated with or without adenoriral Serca2a and subjected to RNA extraction and hybridization on Affymetrix microarrays. Global gene expression pattern were compared and analyzed.

first: Ning

last: Sun

first: Joseph

middle: C

last: Wu


title: The mRNA expression patterns in macaque brains from prenatal to neonatal

status: Public on Feb 02 2012

city: Shanghai

first: Xiling

last: Liu

address: 320 Yue Yang Road

country: China

institute: Partner Institute for Computational Biology

summary: We search for developmental changes specific to humans by examining gene expression profiles in the human, chimpanzee and rhesus macaque prefrontal and cerebellar cortex. In both brain regions, developmental patterns were more evolved in humans than in chimpanzees. To distinguish whether the human specific developmental pattern represent novel human-specific developmental patterns or a shift in the timing of the existing patterns, we measured mRNA expression patterns in macaque brains from prenatal to neonatal. Our results show that the major human-specific developmental patterns identified in the PFC reflects an extreme shift in timing of synaptic development.

overall_design: Rhesus macaque post-mortem brain samples from the superior frontal gyrus region of the prefrontal cortex were collected. Six fetal and six newborn samples were used. RNA extracted from the dissected tissue was hybridized to Affymetrix® Human Gene 1.0 ST arrays.

first: Mehmet

last: Somel

first: Lin

last: Tang

first: Zheng

last: Yan

first: Philipp

last: Khaitovich


title: Genome-wide map of DNaseI hypersensitivity in mouse erythroid cells.

status: Public on Jan 30 2012

city: Oxford

first: Monika

middle: S

last: Kowalczyk

state: Oxfordshire

address: Headley Way

department: MRC Molecular Haematology Unit

institute: Weatherall Institute of Molecular Medicine, University of Oxford

summary: We generated genome-wide maps of DNaseI hypersensitivity in mouse erythroid cells by DNase-Seq.

overall_design: Examination of DNaseI hypersensitivity in mouse erythroid cells.

first: Marco

last: de Gobbi

first: Mona

last: Hosseini

first: Jim

last: Hughes

first: Jonathan

last: Flint

first: Douglas

last: Higgs


title: Effect of FadR overexpression in an engineered fatty acid overproducer

status: Public on Jan 28 2012

city: Emeryville

first: Mario

last: Ouellet

address: 5885 Hollis St., 4th Floor

institute: Joint BioEnergy Institute

summary:
Transcriptome analysis of strains LT-ΔfadE (control) and FRT-ΔfadE (FadR overexpressor) after 12h of fatty acid production.
The strains used are described in detail in Zhang F, M Ouellet, TS Batth, CJ Petzold, A Mukhopadhyay and JD Keasling. Enhancing fatty acid production by the expression of the regulatory transcription factor FadR. (In preparation)

overall_design: Three independent cultures of control strain LT-ΔfadE and four independent cultures of FadR overexpressor strain FRT-ΔfadE were induced. One sample derived from each culture was hybridized.

first: Fuzhong

last: Zhang

first: Aindrila

last: Mukhopadhyay

first: Jay

middle: D

last: Keasling


title: Effects of Ars2 or DGCR8 siRNA on gene expression

first: Scott

last: Olejniczak

state: NY

address: 417 E68th St

institute: Memorial Sloan Kettering Cancer Center

summary: Ars2 is a component of the nuclear cap-binding complex that is required for cellular proliferation and contributes to microRNA biogenesis. Arrays were performed to determine the repertoire of genes that change following knock-down of Ars2.  Knock-down of DGCR8 was also performed to determine which changes in Ars2 knock-down cells resulted from defects in microRNA expression.

overall_design: 9 samples were analyzed including: three biological replicates of control siRNA-transfected HeLa cells, HeLa cells transfected with three independent siRNAs targeting Ars2, or HeLa cells transfected with three independent siRNAs targeting DGCR8.

first: Josh

last: Gruber

first: Gideon

last: Dreyfuss

first: Craig

last: Thompson


title: Transcriptiome of mouse erythroid cells (part2) poly(A)-

type: Expression profiling by high throughput sequencing

summary: We report genome-wide maps of transcription in mouse erythroid cells. We used an approach to survey poly(A)+ (mRNA) (Transcriptiome of mouse erythroid cells (part1) GSE26877) and non-polyadenylated RNA separately. This provides an alternative framework for comprehensive transcriptome profiling in mammalian cells.

overall_design: Examination of non-polyadenylated RNA in mouse erythroid cells  (Ter119+).


title: Niche modulated versus niche modulating genes in multiple myeloma

status: Public on Feb 23 2012

city: Be'er Yacob

first: Yossi

last: Cohen

address: Zeriffin

department: Hematology

country: Israel

institute: Asaf Harofeh University Hospital

summary:
Background. Multiple myeloma (MM) cells depend on the bone marrow (BM) niche for growth and survival. However, the tumor genes regulated by the niche are largely unknown.

Design and Methods. BM aspiration samples were obtained from MM-patients with a high tumor load. Gene expression profile (GEP) was recorded immediately following aspiration and at subsequent time points. Identification of niche-regulated genes relied on spontaneous gene modulation following loss of niche regulation.

Results. Compared to the reference samples fixed immediately following aspiration, the BM samples fixed after longer delay acquired numerous changes in GEP. The top modulated genes included a common subset of ~ 60 genes displaying prompt and sustained “switch” in expression consistently, among which were oncogenes (FOS, JUN) and genes regulating homing (CD69, RGS1), expansion and angiogenesis (AREG, PTGS2, RGS2, NR4A2). Interestingly, the “switch” in GEP was reversible and turned “off” and “on” in culture conditions resuming cell-cell-matrix contact versus re-spread into suspension, respectively. Moreover, the resuming of contact prolonged the survival of the tumor cells out-of-niche and the regression of the “contactless switch” was followed by induction of a new set of genes this time mostly encoding extracellular proteins, including angiogenic factors (IL8, CXCL5), extracellular-matrix proteins (SPP1, FN1), chemokines (CXCL5, CCL2, CCL20) and growth factors (CCL2, IL6).

Conclusions. Our dataset, being unique in authentic expression design, uncovered contact-regulated genes capable of controlling homing, expansion and tumorigenesis. The adaptive response of the tumor cells to culture conditions deficient of integral niche components (e.g., vascular vessels) uncovered inducible niche-regulating tumor genes.

overall_design: Comparative gene expression profiling of whole bone marrow samples from myeloma patients fixed either immediately following aspiration or after delayed RNA fixation (for 17, 120, 300, 420, 540, 660 minutes). Comparison was also made between cultured bone marrow cells fixed immediately following spread from the bottom well or after maintenance in suspension (for 60, 120 minutes) as well as between malignant pleural fluid sediment fixed before or after cell spread from the bottom tube and maintenance in suspension (for 270 minute).

first: Osnat

last: Garach-Jehoshua

first: Adina

last: Bar-Chaim

first: Abraham

last: Kornberg


title: Expression data from HEK293 cells with or without MIBP1 overexpression

status: Public on Jan 31 2012

city: Fukuoka

first: Yuji

last: Iwashita

state: Fukuoka

address: 3-1-1 Maidashi, Higashi-ku

department: Reseach Center for Genetic Information

country: Japan

institute: Kyushu University, Medical Institute of Bioregulation

summary: The transcription factor c-MYC intron binding protein 1 (MIBP1) binds to various genomic regulatory regions, including intron 1 of c-MYC. This factor is highly expressed in post-mitotic neurons in the fetal brain and may be involved in various biological steps, such as neurological and immunological processes. In this study, we globally characterized the transcriptional targets of MIBP1 and proteins that interact with MIBP1. Microarray hybridization followed by Gene Set Enrichment Analysis revealed that genes involved in the pathways downstream of MYC, NF-κB, and TGF-β were downregulated when HEK293 cells stably overexpressed MIBP1. In silico transcription factor binding site analysis of the promoter regions of these downregulated genes showed that the NF-κB binding site was the most overrepresented. The upregulation of genes known to be in the NF-κB pathway after the knockdown of endogenous MIBP1 in HT1080 cells supports the view that MIBP1 is a downregulator of the NF-κB pathway. We also confirmed the binding of the MIBP1 to the NF-κB site. By immunoprecipitation and mass spectrometry, we detected O-linked β-N-acetylglucosamine (O-GlcNAc) transferase (OGT) as a prominent binding partner of MIBP1. Analyses using deletion mutants revealed that a 154-amino acid region of MIBP1 was necessary for its OGT binding and O-GlcNAcylation. A luciferase reporter assay showed that NF-κB-responsive expression was repressed by MIBP1, and stronger repression by MIBP1 lacking the 154-amino acid region was observed. Our results indicate that the primary effect of MIBP1 expression is the downregulation of the NF-κB pathway, and that this effect is attenuated by O-GlcNAc signaling.

overall_design: Six total samples were analyzed. Three of empty vector transfectant and three of MIBP1 expressing HEK293 cell clones

first: Tomoko

last: Tahira

first: Kenshi

last: Hayashi


title: Expression data from peripheral blood  - blood draws at Pre and Post time points of Allergen inhalation challenge (PAX.NGR and EDTA)

status: Public on Jan 26 2012

city: Vancouver

last: Tebbutt

state: BC

address: Room 166, 1081 Burrard Street

department: Medicine

institute: University of British Columbia

summary: To determine differential gene expression in peripheral blood of asthmatic individuals undergoing allergen inhalation challenge, post-challenge compared to pre-challenge

overall_design:
Blood was collected immediately prior to, and two hours after challenge
The 8 PAXgene non-globin reduced (PAX.NGR) samples were combined with 10 EDTA samples (n=9) for one analysis (PAX.NGR+EDTA) comparing gene expression in whole blood between pre and post challenge using the following covariates: tube type, sex, age, PC20 at pre-challenge, and FEV1 after onset and 2h post challenge and the RNA integrity number.
Preprocessing and filtering were applied to the PAX.NGR+EDTA dataset using the Factor Analysis for Robust MicroArray Summarization (farms) package in R
The Linear Models for MicroArrays (limma) package was used to determine differential gene expression using a Benjamini Hochberg FDR of 5%.

first: Sarah

last: Kam

first: Amrit

last: Singh

first: Jian-Qing

last: He

first: Jian

last: Ruan

first: Gail

last: Gauvreau

first: Paul

last: O'Byrne

first: J

last: FitzGerald


title: Expression data from peripheral blood  - blood draws at Pre and Post time points of Allergen inhalation challenge (PAX.NGR)

first: Scott

summary:
Detecting differential changes in the peripheral whole-blood transcriptome, post-challenge compared to pre-challenge; using non-globin reduced PAXgene (PAX.NGR) tubes
Blood was collected immediately prior to, and two hours after challenge

overall_design:
Preprocessing and filtering were applied to the PAX.NGR dataset using the Factor Analysis for Robust MicroArray Summarization (farms) package in R
The Linear Models for MicroArrays (limma) package in R was used to determine differential gene expression using a Benjamini Hochberg FDR of 5%.


title: Expression data from peripheral blood  - blood draws at Pre and Post time points of Allergen inhalation challenge

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

overall_design: Refer to individual Series


title: Expression data from peripheral blood  - blood draws at Pre and Post time points of Allergen inhalation challenge (PAX.GR)

summary: Detecting differential changes in the peripheral whole-blood transcriptome, post-challenge compared to pre-challenge; using globin reduced PAXgene (PAX.GR) tubes

overall_design:
Blood was collected immediately prior to, and two hours after challenge
Blood samples from 4 subjects were used to study the effects of globin reduction on differential gene expression
Preprocessing and filtering were applied to the PAX.GR dataset using the Factor Analysis for Robust MicroArray Summarization (farms) package in R
The Linear Models for MicroArrays (limma) package in R was used to determine differential gene expression using a Benjamini Hochberg FDR of 5%.


title: Unique Transcriptome, Pathways, and Networks in the Human Endometrial Fibroblast Response to Progesterone in Endometriosis

status: Public on Jan 24 2012

city: San Francisco

first: Linda

last: Giudice

address: 513 Parnassus Ave. HSE 1619

department: OBGYN and RS

institute: University of California, San Francisco

summary: Eutopic endometrium in endometriosis has molecular evidence of resistance to progesterone (P4) and activation of the PKA pathway in the stromal compartment. To investigate global and temporal responses of eutopic endometrium to P4, we compared early (6-h), intermediate (48-h), and late (14-day) transcriptomes, signaling pathways, and networks of human endometrial stromal fibroblasts (hESFs) from women with endometriosis (hESFendo) to hESFs from women without endometriosis (hESFnonendo). Endometrial biopsy samples were obtained from subjects with and without mild peritoneal endometriosis (n = 4 per group), and hESFs were isolated and treated with P4 (1 μM) plus estradiol (E2) (10 nM), E2 alone (10 nM), or vehicle for up to 14 days. Total RNA was subjected to microarray analysis using a Gene 1.0 ST (Affymetrix) platform and analyzed by using bioinformatic algorithms, and data were validated by quantitative real-time PCR and ELISA. Results revealed unique kinetic expression of specific genes and unique pathways, distinct biological and molecular processes, and signaling pathways and networks during the early, intermediate, and late responses to P4 in both hESFnonendo and hESFendo, although a blunted response to P4 was observed in the latter. The normal response of hESF to P4 involves a tightly regulated kinetic cascade involving key components in the P4 receptor and MAPK signaling pathways that results in inhibition of E2-mediated proliferation and eventual differentiation to the decidual phenotype, but this was not established in the hESFendo early response to P4. The abnormal response of this cell type to P4 may contribute to compromised embryonic implantation and infertility in women with endometriosis.

overall_design: We compared early (6-h), intermediate (48-h), and late (14-day) in vitro whole-genome responses of hESF from women with endometriosis (hESFendo) to hESF from women without endometriosis (hESFnonendo) treated with P4 plus E2 (E2P4), E2 alone, or vehicle alone. Using this experimental paradigm, the data demonstrate unique phenotypes, gene expression processes, biochemical and signaling pathways, and networks suggestive of early, intermediate, and late responses of hESFnonendo and hESFendo to P4, giving insights into the complexity of events occurring normally in response to P4 and in the setting of endometriosis.

first: L

last: Aghajanova

first: K

last: Tatsumi

last: Horcajadas

first: A

last: Zamah

first: F

last: Esteban

first: C

middle: N

last: Herndon

first: M

last: Conti


title: An extreme human-specific delay in cortical synaptic development

first: Xiling

last: Liu

sample_organism:
Macaca mulatta
Mus musculus

platform_organism:
Homo sapiens
Mus musculus


title: Effects of Evi1 knockdown and overexpression in SKOV-3 ovarian carcinoma cells

status: Public on Jan 15 2012

city: Singapore

first: Justin

middle: Jeyakani

last: Joseph Gnanakkan

state: Singapore

address: 60, Biopolis street

department: Computational and Systems Biology

institute: Genome Institute of Singapore

summary:
We studied the variations of mRNA amounts after Evi1 knockdown or Flag-Evi1 overexpression in SKOV-3 cells.
Despites Evi1 discovery in 1988, its recognized role as a dominant oncogene in myeloid leukemia and more recently in epithelial cancers, only a few target genes were known and it was not clear why Evi1 was involved in cancer progression. Here we obtained the genomic binding occupancy and expression data for Evi1 in human ovarian carcinoma cells. We identified numerous Evi1 target cancer genes and genes controlling cell migration and adhesion. Moreover, we characterized a transcriptional cooperation between AP1 and Evi1 that regulated proliferation and adhesion through a feed-forward loop. Furthermore, this study provides human genome-wide mapping and downstream analyses for Evi1 that will be useful for the research community.

overall_design: 16 samples were collected. Each condition was done in 4 replicates, collected 65 hours after transfection. Transfections with control siRNA or Flag-expressing vector were used as controls.

first: Emilie

last: Bard-Chapeau

last: Jeyakani

first: Neal

last: Copeland

first: Guillaume

last: Bourque


title: Expression data of the splenocytes from mice at 6th of Plasmodium chabaudi infection.

status: Public on Jan 13 2012

city: Worcester

first: Ricardo

middle: Tostes

last: Gazzinelli

state: Massachusetts

address: 364 Plantation Street

institute: University of Massachusetts Medical School

summary: During malaria infection is observed a robust immune response culminating on release of inflammatory mediators. This exacerbated immune response is involved in malaria symptoms and mortality. There are evidences that this response is mediated by innate immunity where pattern recognition receptors have a key role. We used microarrays to elucidate some pro-inflammatory genes that are differential expressed during P. chabaudi infection, a malarial murine model

overall_design: Spleen from C57BL/6, MyD88, or IFN-gamma knockout mice non-infected or after 6 days post infection with 105 P. chabaudi infected red blood cells were harvested for RNA extraction and hybridization on Affymetrix microarrays. This time point was chose to coincides with rupture of red blood cells \since this event of the parasite life cycle is related with malaria outcomes.