title: Transcriptional profiling of mouse inner cell mass of the blastocyst, primordial germ cells and cultured pluripotent stem cells

status: Public on Jan 31 2012

city: San Francisco

first: Miguel

last: Ramalho-Santos

address: 35 Medical Center Way

department: Eli and Edythe Broad Center of Regeneration Medicine

institute: UCSF

summary: Pluripotent stem cells are derived from culture of early embryos or the germline, and can be induced by reprogramming of somatic cells. Barriers to reprogramming are expected to exist that stabilize the differentiated state and have tumor suppression functions. However, we have a limited understanding of what such barriers might be. To find novel barriers to reprogramming to pluripotency, we compared the transcriptional profiles of the mouse germline to pluripotent and somatic cells, in vivo and in vitro. There is a remarkable global expression of the transcriptional program for pluripotency in Primordial Germ Cells (PGCs). We identify parallels between PGCs reprogramming to pluripotency and human germ cell tumorigenesis, including the loss of LATS2, a tumor suppressor kinase of the Hippo pathway. We show that knockdown of LATS2 increases the efficiency of induction of pluripotency in human cells. LATS2 RNAi, unlike p53 RNAi, specifically enhances the generation of fully reprogrammed iPS cells without accelerating cell proliferation. We further show that LATS2 represses reprogramming in human cells by post-transcriptionally antagonizing TAZ but not YAP, two downstream effectors of the Hippo pathway. These results reveal transcriptional parallels between germ cell transformation and the generation of iPS cells, and indicate that the Hippo pathway constitutes a barrier to cellular reprogramming.

overall_design: Mouse pluripotent cells isolated directly from embryos or cultured in vitro as stem cells were analyzed using Affymetrix expression microarrays, together with several non-pluripotent cell controls, in 2-6 replicates per sample.

first: Han

last: Qin


title: Gene expression profile of classical Hodgkin lymphoma according to Epstein-Barr infection status

status: Public on Dec 31 2011

city: São Paulo

first: Renato

middle: David

last: Puga

state: São Paulo

address: Dr Ovidio Pires de Campos,785

department: Instituto de Psiquiatria

country: Brazil

institute: Universidade de São Paulo

summary: Transcriptional profiling of Human Hodkin Lymphoma lineages infected or not by Epstein Baar Virus (EBV).  We compared EBV infected lineage L591 and not EBV infected lineages L428, L1236 and KMH2.  Goal was to determine presence versus absence of EBV infection on global gene expression of Hodkin Lymphoma cell lines.

overall_design: EBV infected Hodkin Lymphoma lineage L591 vs 3 Hodkin Lymphoma lineages not EBV infected L428, L1236 and KMH2. Dye Swap and direct comparisom between L591 (EBV infected) and the three others not infected cell lines.

first: Antonio

middle: M

last: Campos

first: Alex

middle: F

last: de Carvalho

first: Cesar

middle: H

last: Torres

first: Louise

middle: D

last: de Carvalho Mota

first: Helena

last: Brentani

first: Jose

last: Vassallo

first: Fernando

middle: A

last: Soares


title: CRTC2 couples genotoxic stress and plasma cell differentiation in the germinal center

status: Public on Jan 01 2012

city: Newbury Park

first: Chetan

last: Deshpande

state: CA

address: One Amgen Center Dr

department: Molecular Sciences

country: USA

institute: Amgen Inc

type: Genome binding/occupancy profiling by genome tiling array

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

overall_design: Refer to individual Series


title: Expression Profiling of Pancreatic Xenografts and Cell Lines

status: Public on Dec 15 2011

first: Alan

middle: Hunter

last: Shain

address: 555 MISSION BAY SOUTH BLVD RM 282 # 3118

department: Pathology and Dermatology

institute: University of California San Francisco

summary: Expression profiling of 70 Pancreatic Ductal Adenocarcinoma (PDAC) samples was performed on Agilent 44K expression arrays for cancer gene discovery. Additionally, matched aCGH on Agilent 244K arrays was performed. These two datasets were integrated in order to identify driver mutations leading to pancreatic cancer. Promising candidates were interrogated further using functional studies.

overall_design: 68 tumor samples (48 xenografts, 20 cell lines). 2 color arrays hybridized against a common reference pool of RNA from 11 cancer cell lines


title: Interlaboratory study to determine the reproducibility of toxicogenomics datasets

city: Sharnbrook

first: Yeyejide

last: Adeleye

state: Bedfordshire

address: Colworth Science Park

country: United Kingdom

institute: Unilever

summary: The application of toxicogenomics as a predictive tool for chemical risk assessment has been under evaluation by the toxicology community for more than a decade. However, toxicogenomics predominately remains a tool for investigative research rather than for regulatory risk assessment. In this study, we aimed to determine whether the current generation of microarray technology in combination with an in vitro experimental design was capable of generating robust, reproducible data of sufficient quality to show promise as a tool for regulatory risk assessment. To this end, we designed a prospective collaborative study to determine the level of inter- and intra-laboratory reproducibility between three independent laboratories.  All test sites adopted the same protocols for all aspects of the toxicogenomic experiment including cell culture, chemical exposure, RNA extraction, microarray data generation and analysis. As a case study, the genotoxic carcinogen B[a]P and the human hepatocyte cell line HepG2 were used to generate three comparable toxicogenomic data sets.    High levels of technical reproducibility were demonstrated using a widely employed gene expression microarray platform.  While differences at the global transcriptome level were still observed between the test sites, a common subset of  B[a]P responsive genes was identified across all test sites which included both genes previously reported in the literature as B[a]P responsive in addition to the same most highly up and down regulated genes. Pending further analysis, these preliminary data show promise that the current generation of microarray technology in combination with a standard in vitro experimental design can produce robust data that can be reproducibly generated in independent laboratories. Future work will need to determine whether in vitro model(s) can be not only reproducible but also predictive for a range of toxic chemicals with different mechanisms of action. Such an approach may potentially be part of future in vitro testing regimes for regulatory risk assessment.

overall_design: The aim of this study was to evaluate the inter- and intra-laboratory reproducibility of toxicogenomics data for toxicity testing in a regulatory setting. 3 Test Centres performed the same experimental protocol treating HepG2 cells with 3 mM Benzo[a]pyrene (B[a]P) (in 0.5% DMSO) for 24 hours prior to RNA extraction and microarray analysis. Three biological replicates of B[a]P and DMSO treatments were analysed by microarray analysis in each Test Centre. Two Test Centres analysed one sample in triplicate to determine technical reproducibility of the chosen array platform. One Centre analysed two samples in duplicate. 24 samples in total were used in this study

first: Daniel

middle: J

last: Scott

first: Alison

last: Devonshire

first: Andrew

last: Bennett

first: Laura

last: Gribaldo

first: Robim

last: Rodrigues

first: Maria

middle: G

last: Sacco

first: Marco

last: Fabbri

first: Timothy

last: Wilkes

first: Maaike

last: Schutte

first: Carole

last: Foy

first: Andy

last: White


title: Global transcriptomic profiling of lactacystin-mediated neuronal death

status: Public on Jan 03 2012

city: Hobart

first: Minghui Jessica

last: Chen

state: Tasmania

address: Menzies Research Institute, University of Tasmania, Private Bag 24

department: Neuroscience group

country: Australia

institute: Menzies Research Institute

summary:
Inhibition of proteasome degradation pathway has been implicated in neuronal cell death leading to neurodegenerative diseases such as Parkinson’s disease and Alzheimer’s disease.  Pharmacological proteasomal inhibitors such as lactacystin can induce apoptosis in cultured mouse cortical neurons through the activation of caspase-3.  Furthermore, proteasomal inhibitors are also reported to mediate deleterious alterations in cell cycle regulation, inflammatory processes and protein aggregation and trigger the cell death pathway.
We discovered by microarray analysis that lactacystin treatment modulates the expression of both potentially neuroprotective as well as pro-apoptotic genes in neurons.  However, the genes, upon transcriptional modulation, contribute to proteasomal inhibition-induced apoptosis, remains unidentified.  By employing microarray analysis to decipher the time-dependent changes in transcription of these genes in cultured cortical neurons, we discovered different groups of genes were transcriptionally regulated at different phases of lactacystin-induced cell death.

overall_design: Microarray analysis was carried out using 10 murine genome U74A and U74Av2 Genechips array (Affymetrix, Santa Clara, CA). The assignment of the arrays (GeneChip) was as follows: Control at 24 h (n=2), 48 h (n=2); exposure to 1 μM lactacystin for 24 h (n=3) and 48 h (n=3).

first: Nam

middle: S

last: Cheung

first: Minghui

first: Zhao

last: Peng

first: Jayapal

last: Manikandan


title: A Universal RNA Polymerase II CTD Cycle Is Orchestrated by Complex Interplays Between Kinase, Phosphatase and Isomerase Enzymes Along Genes

status: Public on Feb 01 2012

city: Montreal

first: Francois

last: Robert

state: QC

address: 110 av des Pins Ouest

country: Canada

institute: IRCM

type: Genome binding/occupancy profiling by array

summary: Transcription by RNA polymerase II (RNAPII) is coupled to mRNA processing and chromatin modifications via the C-terminal domain (CTD) of its largest subunit, consisting of multiple repeats of the heptapeptide YSPTSPS. Pioneering studies showed that CTD serines are differentially phosphorylated along genes in a prescribed pattern during the transcription cycle. Genome-wide analyses challenged this idea, suggesting that this cycle is non-uniform among different genes. Moreover, the respective role of enzymes responsible for CTD modifications remains controversial. Here, we systematically profiled the location of the RNAPII phospho-isoforms in wild type cells and mutants for most CTD modifying enzymes. Together with results of in vitro assays, these data reveal a complex interplay between the modifying enzymes, and provide evidence that the CTD cycle is uniform across genes. We also identify Ssu72 as the Ser7 phosphatase and show that proline isomerization is a key regulator of CTD dephosphorylation at the end of genes.

overall_design: We took a systematic approach to examine the genome-wide distribution of the various CTD modifications using a panel of RNAPII CTD phospho-specific antibodies; both in wild type cells and in mutants for most of the CTD kinases, phosphatases and the isomerase. Immunoprecipitation of CTD phospho-isoforms were done using the following antibodies: H14 and 3E8 for Ser5, H5 and 3E10 for Ser2, 4E12 for Ser7, 8WG16 (anti-Rpb1-CTD) and W0012 (anti-Rpb3) for RNAPII (global localization). A list of the mutant strains and their genotypes can be found  in the supplemental files of the related publication. Most ChIPs (in Cy5) were hybridyzed against a non-immunoprecipitated (whole cell extract, WCE) in Cy3. Ssu72, Pti1 and Rpb1 were immunoprecipitated using tagged proteins (3myc-Ssu72, Pti1-3myc, Rpb1-9myc) and the ChIP DNA hybridized in competition with a control ChIP DNA prepared from an isogenic untagged strain (NoTag). ChIP from wild type strains yFR116 (W303) and yFR117 (S288C) were used to obtains wild type profiles that can be compared to mutants strains of the same background. All ChIP-chip experiments were done at least in duplicates. Each microarray was normalized using the Lima Loess and replicates were combined using a weighted average method as previously described  (Pokholok et al., 2005).

first: Alain

middle: R

last: Bataille

first: Célia

last: Jeronimo

first: Pierre-Étienne

last: Jacques

first: Louise

last: Laramée

first: Marie-Ève

last: Fortin

first: Audrey

last: Forest

first: Maxime

last: Bergeron

first: Steven

last: Hanes

first: François


title: Long-term in vitro expansion of epithelial organoids from human colon, adenoma, adenocarcinoma and Barrett's Esophagus

status: Public on Dec 07 2011

city: Dresden

first: Daniel

middle: E.

last: Stange

address: Fetscherstr. 74

country: Germany

institute: University Clinic Dresden

summary: Background & Aims: We have recently established long-term culture conditions under which single crypts or stem cells derived from murine small intestine expand over long periods of time. Growing crypts undergo multiple crypt fission events, whilst simultaneously generating villus-like epithelial domains in which all differentiated cell types are present. We have now adapted the culture conditions to grow similar epithelial organoids from mouse colon and human small intestine and colon. Methods: Based on the murine small intestinal culture system, we optimized the murine and human colon culture system. Results: Addition of Wnt3A to the growth factor cocktail allowed mouse colon crypts to expand indefinitely. Further addition of nicotinamide, a small molecule Alk inhibitor and a p38 inhibitor was essential for long-term human small intestine and colon culture. The  culture system also allowed growth of murine Apcmin adenomas, human colorectal cancer and human esophageal metaplastic Barrett’s epithelium. Conclusion: The culture technology should be widely applicable as a research tool for infectious, inflammatory and neoplastic pathologies of the human gastrointestinal tract. Moreover, regenerative applications may become feasible with ex vivo expanded intestinal epithelia.

overall_design: Human organoids were grown embedded in Matrigel in HISC (Human intestinal stem cell culture) medium. Additionally, human small intestinal crypts and villi were isolated independently from a freshly operated sample. RNA was isolated using the RNeasy Micro kit (Qiagen). Samples were labled according to Agilent guidelines with Cy3, whereas human reference RNA (Stratagene) was labeled in Cy5. Feature Extraction Software was used to extract and normalize data.

middle: E

first: Sato

last: Toshiro

first: Hans

last: Clevers


title: Expression Profiling and Array Comparative Genomic Hybridization of Pancreatic Xenografts and Cell Lines

first: Alan

last: Shain

type: Genome variation profiling by genome tiling array


title: Host response transcriptional profiling of typhoid fever infected Nigerian children

status: Public on Nov 29 2011

city: Grand Rapids

first: Mrutyunjaya

last: Parida

state: MI

address: 333 Bostwick Ave N.E.

department: Research

institute: Van Andel Institute

summary: We were able to obtain distinct gene expression profile between children with typhoid fever and other bacteremic infections.

overall_design: Peripheral blood of Nigerian children with typhoid fever and other bacteremic infection were obtained in Paxgene tubes.  Total RNa were extracted using Paxgene blood RNA kit and 4x44K (G4112F) human GE array were processed according to standard Agilent procedures

first: M

first: S

middle: K

last: Khoo

last: Obaro

first: J

last: Resau

first: A

middle: C

last: Tan

first: D

last: Petillo


title: Peripheral blood lymphocytes: ALS patients vs. healthy controls

status: Public on Dec 11 2011

city: Charlotte

first: Jean-Luc

last: Mougeot

state: NC

address: 1542 Garden Terrace

department: Internal Medicine

institute: Carolinas Medical Center

summary:
Transcripional profiling of lymphocytes from patients with amyotrophic lateral sclerosis (ALS) (n=11) and healthy control subjects (n=11).
The goal was to determine disease response expression signatures relevant of ALS pathogenesis that affect brain and spinal cord.
The reference design was used: each Cy5-labeled cRNA sample from ALS patient or healthy control subject was cohybridized on Agilent-014850 Whole Human Genome Microarray 4x44K G4112F with the reference pool formed with equal amounts of Cy3-labeled cRNAs from each sample from the healthy control group.

overall_design: Eleven lymphocyte samples from definite sporadic ALS patients and eleven samples from healthy control subjects were used.


title: Proinflammatory role of histamine-releasing factor in asthma and allergy

status: Public on Dec 04 2011

city: Tokyo

first: Kenji

last: Matsumoto

address: 2-10-1 Okura, Setagaya-ku

department: Allergy and Immunology

country: Japan

institute: National Research Institute for Child Health and Development

summary: Immunoglobulin (Ig) E-mediated activation of mast cells and basophils underlies allergic diseases such as asthma. Histamine-releasing factor (HRF), also known as translationally controlled tumor protein (TCTP) and fortilin, is a highly conserved protein with both intracellular and extracellular functions. Secreted HRF can stimulate histamine release and IL-4 and IL-13 production from IgE-sensitized basophils and mast cells. HRF is found in nasal, skin blister and bronchoalveolar lavage (BAL) fluids during late-phase allergic reactions (LPRs), which implicates HRF in the LPR and chronic allergic inflammation. Here we identify a subset of IgE and IgG antibodies as HRF-interacting molecules. HRF can exist as a dimer and bind to immunoglobulins (Igs) via interactions of its N-terminal and internal regions with the Fab region of Igs. Therefore, HRF together with HRF-reactive IgE can activate mast cells in vitro. The Ig-interacting HRF peptides that block HRF-Ig interactions can inhibit IgE+HRF-induced mast cell activation and in vivo cutaneous anaphylaxis and airway inflammation. Intranasally administered HRF can recruit inflammatory immune cells to the lung in naïve mice in a mast cell- and Fc receptor-dependent manner. These results strongly suggest the proinflammatory role of HRF in asthma and skin immediate hypersensitivity.

overall_design: A total of 6 samples were analyzed; wild type C57BL/6, FcRg KO and FceRIa KO mice were challenged with PBS (control) or mouse histamien-releasing factor

first: Jun-ichi

last: Kashiwakura

first: Tomoaki

last: Ando

first: Miho

last: Kimura

first: Jiro

last: Kitaura

first: Michael

last: Matho

first: Dirk

last: Zajonc

first: Tomomitsu

last: Ozeki

first: Chisei

last: Ra

first: Susan

last: MacDonald

first: Reuben

middle: P

last: Siraganian

first: David

last: Broide

first: Yuko

last: Kawakami

first: Toshiaki


title: Expression of Epithelial-to-Mesenchymal Transition (EMT)-associated genes in extratumoral microenvironment predicts poor clinical outcome in breast cancer patients

city: Chapel Hill

first: Melissa

last: Troester

address: 135 Dauer Drive, CB 7435

department: Epidemiology

institute: University of North Carolina at Chapel Hill

summary:
Introduction: A gene expression signature indicative of active wound responses is common to more than 90% of non-neoplastic tissues adjacent to breast cancer, but these tissues also show substantial heterogeneity, suggesting different microenvironmental subtypes. Genomic variation in the extratumoral microenvironment has received limited study.

Methods: Gene expression analysis from 72 patient-derived samples adjacent to invasive breast cancer or ductal carcinoma in situ was evaluated. Unsupervised clustering identified two distinct gene expression subgroups that differed substantially in expression of genes associated with epithelial-to-mesenchymal transition (EMT). We evaluated the prognostic and biological relevance of this extratumoral EMT-like signature using clinical and experimental approaches.

Results: We found that the extratumoral EMT-like signature was not significantly associated with overall survival among all patients [Hazard Ratio (HR) = 1.4, 95% CI 0.6 - 2.8, p=0.337], but there was a strong association with overall survival among estrogen receptor (ER)-positive patients [HR = 2.5, 95% CI 0.9 – 6.7, p=0.062] or hormone-treated patients [HR=2.6, 95% CI 1.0 – 7.0, p=0.045]. In addition, co-culturing of ER-positive MCF-7 cells with cells undergoing EMT increased migration of MCF7 cells in a TGF-β1 dependent manner.

Conclusion: Together, these results suggest that the presence of an EMT-like signature in the cancer-adjacent extratumoral microenvironment may influence the aggressiveness of the ER-positive tumors and that ER-positive patients with these extratumoral signatures may require additional treatments or more aggressive surgeries.

overall_design: Reference vs. test sample. 74 test samples (12 breast tumors, 62 normal tissue adjacent to breast tumor) from 72 patients.

first: Erick

last: Román-Pérez


title: Castration-Resistant Prostate Cancer (CRPC)

city: Arlington

first: Heng

last: Huang

state: TX

address: 500 UTA Blvd.

department: Computer Science and Engineering

institute: University of Texas at Arlington

summary: Gene expression data from Agilent-014850 4x44K human expression array for CRPC Prostate Cancer study with Xenograph data.

overall_design:
RNA was isolated using the mirVana total RNA protocol (part #AM1560, Ambion, Austin, TX). RNA integrity was verified using a 2100 Bioanalyzer (part #G2938A) with nano chips (parts #5067-15101 and #G4411B; Agilent Technologies, Alto, CA). RNA concentrations were determined using a Nanodrop spectrophotometer (Thermo Scientific, Wilmington, DE). Tumor messenger RNA expression was assessed using a human whole-genome oligo TMA kit from Agilent (prod #G4112F) according to the manufacturer’s protocol and as described previously.

In the Characteristics field, we have the notation like "Pt Dxed in 2001; hormone Tx; chemo Tx 2002; HRPC by 2002". That means the patient was admitted in 2001, did hormone and chemo treatment in 2002, and HRPC 2002. They are standard prostate cancer treatments.

first: Kanishka

last: Sircar


first: Chetan

last: Deshpande

summary: Transcriptional profiling of Ramos germinal center B cells, comparing untreated cells to cells treated with etoposide, and untreated cells to cells treated with anti-IgM.  Both treatments, engagement of the B-cell receptor with anti-IgM and induction of DNA double-strand breaks with etoposide, result in phosphorylation and cytoplasmic sequestration of CRTC2, and cause downregulation of known CRTC2 target gene TCL1.  The goal of these experiments was to determine what other genes are downregulated by both of these CRTC2-inactivating treatments, and to compare this list to the list of genes whose promoters were occupied by CRTC2 in our ChIP-on-chip assay.

overall_design: Untreated samples vs. etoposide-treated samples, untreated samples vs. anti-IgM-treated samples.  Each comparison was done in biological triplicate plus dye swap.

first: Mara

last: Sherman


title: Gene expression signature in platelets from healty vs. glioma patients

status: Public on Dec 01 2011

city: Umeå

first: Jonas

last: Nilsson

address: NUS

country: Sweden

institute: Radiation Sciences, Oncology

summary: Identify upregulated genes in platelets from patients with brain tumors.

overall_design: Platelets from 12 healty controls vs. 8 glioma patients where isolated from whole blood collected in purple-cap BD vacutainers containing EDTA as anti-cogulant.

first: Tom

last: Wurdinger


title: Expression profile of maliganant mesothelioma cell lines

status: Public on Dec 18 2011

city: Nagoya

first: Futoshi

last: Ishiguro

address: 1-1 Kanokoden, Chikusa-ku

department: Molecular Oncology

institute: Aichi Cancer Center Research Institute

summary: transcriptional profiling of makignant mesothelioma cell lines comparing control one immortalized mesothelial cell line, MeT-5A, and 2 primary normal mesothelial cultures collected from ascites of non-cancer patients, OV-M1 and GAS-M1

overall_design: Two-condition experiment, mesothleioma  cells vs. normal mesothelial cells

first: H

last: Murakami

first: F

last: Osada

first: Y

last: Sekido


title: Gene expression profiles of bone marrow mesenchymal stem cells in pediatric patients with severe aplastic anemia

status: Public on Nov 19 2011

city: Taichung

first: Kuan-Chih

last: Chow

address: 250 Kuo Kuang Road

department: Graduate Institute of Biomedical Sciences

country: Taiwan

institute: National Chung Hsing University

summary: Pediatric severe aplastic anemia (PSAA) is a rare and life-threatening disease, which has been suggested to result from deficiency in essential cytokines or growth factors in bone marrow mesenchymal stem cells (MSCs). In this study, we examined expression profiles of the essential cytokines and growth factors, which were involved in proliferation and differentiation of MSC, in 5 PSAA patients using oligonucleotides microarrays. Following evaluation of gene expression patterns using cluster analysis and gene ontology classifications, fifteen potential genes that were cell proliferation- and cytokine-related and significantly down-regulated in PSAA were selected. The findings of the microarray analysis were validated by quantitative reverse transcription-polymerase chain reaction (qRT-PCR). Interestingly, silencing of chemokine ligand 12 (CXCL12, also named stromal cell-derived factor 1, SDF1) or hepatocyte growth factor (HGF) gene expression reduced cell growth and response to adipogenic factor-induced differentiation, but increased osteogenesis, which possibly derived from hematopoietic stem cells (HSCs). Re-introduction of the CXCL12 gene or exogenously added HGF, on the other hand, partially recovered cell function of PSAA MSC. These results suggest that gene expression in PSAA MSC is globally down-regulated by a yet-to-be-determined mechanism. Among these down-regulated genes, CXCL12 and HGF played vital roles in regulating cell growth and differentiation.

overall_design: Mesenchymal stem cells from five pediatric SAA patients vs. MSC from five healthy donors, which were pooled together.


title: ISR target genes in the liver of mock-injected and AP20187-treated mice of wildtype and Atf4-/- genotype

status: Public on Dec 23 2011

city: Tokushima

first: Seiichi

last: Oyadomari

state: Tokushima

address: 3-18-15 Kuramoto

department: Institute for Genome Research

institute: The University of Tokushima

summary:
The molecular mechanisms linking the stress of unfolded proteins in the endoplasmic reticulum (ER stress) to glucose intolerance in obese animals are poorly understood. In this study enforced expression of a translation initiation 2α (eIF2α)-specific phosphatase, GADD34, was used to selectively compromise signaling in the eIF2(αP)-dependent arm of the ER unfolded protein response in liver of transgenic mice. The transgene resulted in lower liver glycogen levels and susceptibility to fasting hypoglycemia in lean mice and glucose tolerance and diminished hepato-steatosis in animals fed a high fat diet. Attenuated eIF2(αP) correlated with lower expression of the adipogenic nuclear receptor PPARγ and its upstream regulators, the transcription factors C/EBPα and C/EBPβ, in transgenic mouse liver, whereas eIF2α phosphorylation promoted C/EBP translation in cultured cells and primary hepatocytes. These observations suggest that eIF2(αP)-mediated translation of key hepatic transcriptional regulators of intermediary metabolism contributes to the detrimental consequences of nutrient excess.
Keywords: genotype comparison

overall_design: The low expressing Ttr::Fv2E-Perk transgene (#58) was bred into the Atf4 knockout strain and the derivative compound heterozygous mice (in the mixed FvB/n; Swiss Webster background) were backcrossed to the Atf4+/- parental stock and Ttr::Fv2E-PERK positive siblings with Atf4+/+ and  Atf4-/- genetypes were analyzed.

first: Heather

last: Harding

first: Yuhong

last: Zhang

first: Miho

last: Ron


title: Effects of dexamethasone on human skeletal muscle and adipose tissue

status: Public on Nov 28 2011

city: Toulouse

first: Nathalie

last: Viguerie

address: Avenue Poulhes

country: France

institute: INSERM

summary:
Context:  Glucocorticoids are frequently prescribed drugs with important side-effects such as glucose intolerance and tissue remodelling.
Objective: The goal was to explore the molecular basis of the crosstalk between adipose tissue and skeletal muscle during short term glucocorticoid treatment.
Design and Intervention: Healthy male subjects were assigned to a 4-d treatment with dexamethasone at 4mg/d.
Main Outcome Measures: Primary outcome measures were gene expression profiling of adipose tissue and skeletal muscle. Urinary cortisol and metabolic biochemistry were also assessed.

overall_design: Dexamethasone was provided in 0.5 mg tablets as 4mg per day during 4 days to male healthy volunteers. Skeletal muscle and adipose tissue biopsies were obtained at the beginning and at the end of the protocol. The transcriptome analysis compared before vs. after the 4 days dexamethasone treatment using a dye swap design and whole genome 4x44k oligonucleotide arrays (Agilent Technologies).

first: Flora

last: Picard

first: Gabby

last: Hul

first: Balbine

last: Roussel

first: Pierre

last: Barbe

first: Jason

last: Iacovoni

first: Carine

last: Valle

first: Dominique

last: Langin

first: Wim

last: Saris


title: The tumor suppressor gene rap1GAP is silenced by mir-101-mediated EZH2 overexpression in invasive squamous cell carcinoma

status: Public on Nov 02 2011

city: ANN ARBOR

first: NISHA

last: D'SILVA

state: MICHIGAN

address: 1011 N. UNIVERSITY AVE, ROOM 5217

department: PERIODONTICS AND ORAL MEDICINE/ SCHOOL OF DENTISTRY

institute: UNIVERSITY OF MICHIGAN SCHOOL OF DENTISTRY

summary: Rap1GAP is a critical tumor suppressor gene that is down-regulated in multiple aggressive cancers such as head and neck squamous cell carcinoma, melanoma and pancreatic cancer. However, the mechanistic basis of rap1GAP down-regulation in cancers is poorly understood. By employing an integrative approach, we demonstrate polycomb-mediated repression of rap1GAP that involves EZH2, a histone methyltransferase in head and neck cancers. We further concomitant down-regulation of rap1GAP in head and neck cancers. EZH2 represses rap1GAP by facilitating the trimethylation of H3K27, a mark of gene repression, and also hypermethylation of rap1GAP promoter. These results provide a conceptual framework involving a microRNA-oncogene-tumor suppressor axis to understand head and neck cancer progression.

overall_design: OSCC3-siRNA Non-Targeting Vs. siRNA EZH2 with dye-swap, HOK-Adeno CMV Vs. Adeno EZH2.

first: Rajat

last: Banerjee

first: Ram-Shankar

last: Mani

first: Nickole

last: Russo

first: Christina

last: Scanlon

first: Alexander

last: Tsodikov

first: Xiaojun

last: Jing

first: Qi

last: Cao

first: Nallasivam

last: Palanisamy

first: Tarek

last: Metwally

first: Ronald

last: Inglehart

first: Scott

last: Tomlins

first: Carol

last: Bradford

first: Thomas

last: Carey

first: Gregory

last: Wolf

first: Shanker

last: Kalyana-Sundaram

first: Arul

last: Chinnaiyan

first: Sooryanarayana

last: Varambally

first: Nisha


title: TCL001: Calu-3 cells treated with either IFN alpha or gamma

status: Public on Nov 01 2011

city: Seattle

first: Michael

last: Katze

state: WA

address: Rosen Building 960 Republican St.

department: Microbiology

institute: University of Washington

summary: Purpose of experiment was to compare transcriptomics of Calu-3 cells treated with either INF alpha or gamma.

overall_design:
Calu-3 cells were treated with 1000 Units/ml of INFa (Sigma I4276) or 500 Units/ml of IFN γ (Sigma I3265). Cells were collected for RNA isolation at 0, 3, 6, and 18 or 22 h post treatment.  Each treated sample was done in triplicate. (Triplicates are defined as 3 different wells, plated at the same time using the same cell stock for all replicates.)There are triplicate time-matched mock for each time point from the same cell stock as rest of samples.
The NIAID Systems Virology Center

first: Armand

last: Bankhead

first: Jean

last: Chang

first: Shannon

last: McWeeney


title: ICL002: Time course of Calu-3 cells infected with Influenza A/VN/1203/04

summary: Purpose of experiment was to perform transcriptomics on Calu- 3 cells infected with Influenza A/VN/1203/04.

overall_design:
Calu-3 cells were infected with Influenza A/VN/1203/04, at MOI of 1.0.  Cells samples were collected at 0, 3, 7, 12, 18, and 24 h post infection. Each infected sample was done in duplicate. (Duplicates are defined as 2 different wells, plated at the same time using the same cell stock for all replicates.)There is one time-matched mock for each time point from the same cell stock as rest of samples. Culture medium (the same as what the virus stock is in) was used for the mock infections.
The NIAID Systems Virology Center

first: Amie

last: Eisfeld

first: Yoshihiro

last: Kawaoka


title: Transcriptome of SATB1 transduced Hut78 cells

city: Vancouver

first: Youwen

last: Zhou

address: 835 W 10th Ave

institute: University of British Columbia

summary: Hut78 cell line was used as Sezary syndrome cell model. Comparative transcriptome profiles of SATB1 transduced Hut78 cells (Hut78-SATB1) relative to empty MIG vector transduced control Hut78 cells (Hut78-MIG) were analyzed. The primary goal is to establish a list of genes with differential expression between SATB1 transduced Hut78 cells and control Hut78 cells to identify the gene expression regulation effect of SATB1 expression in Sezary cells.

overall_design: Two color experiment, 3 biological replicates (3 unique cell clones) with Hut78 cells, each compared with a distinct individual clone from cells transduced with empty MIG vector.

first: Mingwan

last: Su

first: Yang

last: Wang


title: Gene expression signatures in gastrointestinal stromal tumors (GISTs)

city: Sapporo

first: Hiromu

last: Suzuki

state: Hokkaido

address: S1, W17, Chuo-ku

department: Department of Molecular Biology

institute: Sapporo Medical University

summary: To analyze the gene expression signatures in gastrointestinal stromal tumors (GISTs), a series of 14 GIST specimens were analyzed using Agilent Whole Human Genome Microarray (4x44K, G4112F).

overall_design: Total RNA was extracted from 32 fresh frozen GIST specimens obtained from surgical resections. Gene expression was analyzed using Agilent Whole Human Genome Microarray (4x44K, G4112F, Agilent technologies, Santa Clara, CA, USA). Risk grade was assessed according to the risk definition system proposed by Fletcher et al. (Hum Pathol. 2002;33:459-65.)

first: Minoru

last: Toyota


title: Gene expression profiling of human vascular cells following gene transfer

city: Nesher

first: Diana

last: Gershtein

address: Bar Yehuda Rd

country: Israel

institute: MGVS

summary: For further understanding of the gene expression profile of human vascular cells following gene transfer in vitro, we have employed whole genome microarray expression profiling as a discovery platform to identify gene families or single genes with the potential to distinguish between responders and non-responders to a particular gene therapy. Human vascular cells from deseased donors were derived and transduced in vitro. Total RNA was isolated from the cells and subjected to microarray analysis using the Agilent technology.

overall_design: Two human donors, with two cell types per donor, were tested, including transduced cells and two different control samples. Technical triplicates were tested for each sample type. Thus, a total of 36 whole genome arrays were processed and analyzed. Expression of candidate genes from this signature will be quantified in the same RNA samples by real-time PCR, allowing further simplified analysis of a large pool of human donors.


title: Chlamydia trachomatis serogroup D disturbs epithelial tissue homeostasis in Fallopian tubes via paracrine Wnt signalling

status: Public on Nov 21 2011

city: Berlin

first: Hans-Joachim

last: Mollenkopf

address: Charitéplatz 1

institute: Max-Planck-Institute for Infection Biology

summary: Chlamydia trachomatis is the causative agent of sexually transmitted disease with the highest prevalence in the world today. Although, sensitive to antibiotic treatment, Ctr is also a major cause of infertility due to significant cell damage caused to the genital tract of affected women. Occlusion of Fallopian tubes is a frequent consequence of advanced ascending Ctr infection. So far the mechanisms of Ctr caused pathogensis are widely unclear. Here we show, by using an ex vivo infection model of human Fallopian tubes that Ctr causes changes in epithelial homeostasis within 2 days of inoculation, by disrupting cell adhesion and increasing cell proliferation. We demonstrate by imaging and expression analysis that tissue response to invading pathogen has also a paracrine component. We identify Wnt signalling activation as one of the hallmarks of Ctr infection which transmits effects of the infection beyond inclusion containing cells. Mechanisms of phenotypic changes involve up regulation of Epcam and Olfactomedin 4, biomarkers and regulators of cell adhesion and cell differentiation. Our findings bring focus to the pleiotropic effects of Ctr infection within epithelium and could be provide the basis for better understanding the pathological sequels in vivo.

overall_design: Microarray experiments were performed as dual-color hybridizations. To compensate for dye-specific effects, an independent dye-reversal color-swap was applied. Quality control and quantification of total RNA amount was assessed using an Agilent 2100 bioanalyzer (Agilent Technologies) and a NanoDrop 1000 spectrophotometer (Kisker).

first: Mirjana

last: Kessler

first: Thomas

last: Meyer

first: Christina

last: Fotopoulou


title: Transcriptional responses to nanoparticulate matter in human skin-derived cancer cells

city: Salt Lake City

first: Philip

last: Moos

state: UT

department: Pharmacology & Toxicology

institute: University of Utah

summary:
This study evaluated transcriptional effects of particles smaller than 100 nm of TiO2 and ZnO.  Based on previous data in colon cancer cells (GSE14910), we evaluated HaCaT and Sk Mel-28 cells for transcriptional responses to 1 and 5 ug/cm2 ZnO, or 5 and 10 ug/cm2 TiO2.  No particle controls were also included.
Again, the most pronounced transcriptional response resulted from ZnO treatement with little responses to TiO2. We identified increased protein stress responses, decreased regulation of transcription, and responses to Zn ions.  We did not observe the protein stress response and regulation of transcription with soluble Zn.
Keywords: skin-derived cancer cells - response to ZnO nanoparticulate

overall_design: Two skin-derived cancer cell types (HaCaT and SK Mel-28) were treated with media containing the nanoparticulate,  ZnCl2, or ZnO separated from the HaCaTs by a Transwell insert, and RNA was collected after 4 hrs.  Generally, the RNA from 4 independent samples were combined for one microarray.

first: Sancy

last: Leachman


title: Normal breast tissue of obese women is enriched for macrophage markers and macrophage-associated gene expression

status: Public on Nov 08 2011

first: Melissa

last: Troester

summary: Activation of inflammatory pathways is one plausible mechanism underlying the association between obesity and increased breast cancer risk. However, macrophage infiltration and local biomarkers of inflammation in breast adipose tissue have seldom been studied in association with obesity. Gene expression profiles of normal breast tissue from reduction mammoplasty patients were evaluated by whole genome microarrays to identify patterns associated with obesity status (normal-weight, body mass index (BMI) <25; overweight, BMI 25-29.9; obese, BMI > or equal to 30). The presence of macrophage-enriched inflammatory loci with immunopositivity for CD68 protein was evaluated by immunohistochemistry (IHC). After adjusting for confounding by age, 760 genes were differentially expressed (203 up and 557 down; FDR = 0.026) between normal-weight and obese women. Gene ontology analysis suggested significant enrichment for pathways involving IL-6, IL-8, CCR5 signaling in macrophages and RXRalpha and PPARalpha activation, consistent with a pro-inflammatory state and suggestive of macrophage infiltration. Gene set enrichment analysis also demonstrated that the genomic signatures of monocytes and macrophages were over-represented in the obese group with FDR of 0.08 and 0.13, respectively. Increased macrophage infiltration was confirmed by IHC, which showed that the breast adipose tissue of obese women had higher average macrophage counts (mean = 8.96 vs. 3.56 in normal-weight women) and inflammatory foci counts (mean = 4.91 vs. 2.67 in normal-weight women). Obesity is associated with local inflammation and macrophage infiltration in normal human breast adipose tissues. Given the role of macrophages in carcinogenesis, these findings have important implications for breast cancer etiology and progression.

overall_design: 72 normal breast tissue samples from patients undergoing reduction mammoplasty. Reference design.

first: Xuezheng

last: Sun

first: Patricia

last: Casbas-Hernandez

first: Carol

last: Bigelow

first: Liza

last: Makowski

first: D

last: Jerry

first: Sallie

last: Schneider


title: 17beta-estradiol (E2)-regulated gene expression across time in estrogen-dependent and estrogen deprivation-resistant MCF-7-derived breast cancer cell lines.

city: Philadelphia

first: Michael

last: Slifker

state: PA

address: 333 Cottman Ave.

institute: Fox Chase Cancer Center

summary:
A series of MCF-7 variants were previously developed that are either estrogen-dependent for growth (MCF-7:WS8 cells), or resistant to estrogen deprivation and refractory (MCF-7:2A) or sensitive (MCF-7:5C) to E2-induced apoptosis.
To identify genes associated with E2-induced apoptosis, estrogen deprivation-resistant/apoptotic-sensitive 5C cells were compared to both estrogen-dependent MCF-7:WS8 and estrogen deprivation/apoptotic-refractory MCF-7:2A cells

overall_design: Each cell line was treated with 10-9 M E2 or vehicle control over a 96 h time course consisting of 7 time points (2, 6, 12, 24, 48, 72 and 96 h) using 6 biological replicates per condition. cRNA probes from individual E2-treated samples were competitively hybridized against time-matched pooled control probes using 2-color Agilent 4x44k human oligonucleotide microarrays.

first: Eric

last: Ariazi

first: Heather

last: Cunliffe

first: Pilar

last: Ramos

first: Amanda

middle: L

last: Willis

first: V

last: Jordan


title: HO-1 modulates the expression of genes involved in inflammation, angiogenesis, proliferation, apoptosis and cell adhesion in human lung cancer cells.

status: Public on Oct 19 2011

city: Krakow

first: Slawomir

last: Golda

address: Gronostajowa 7

department: Faculty of Biochemistry, Biophysics adn Biotechnology

country: Poland

institute: Jagiellonian University

summary: The enzymatic activity of HO-1 results in decreased oxidative stress, attenuated inflammatory response, and very often in a lower rate of apoptosis. This is due to removal of heme, a potent prooxidant and proinflammatory agent, but mainly because of generation of biologically active products such as CO and bilirubin. In order to find the correlation between the HO-1 level and the expression of different genes of interest we have utilized human lung cancer cell line NCI-H292 stably overexpressing HO-1. Additionally we have checked if HO-1 can modulate genes expression in NCI-H292 cells treated with TNF. The effect of HO-1 overexpression on transcriptome was assessed by microarray analysis. We have observed that the increase in HO-1 level may affect the expression of different genes involved in cytokine synthesis, angiogenesis, apoptosis, proliferation and cell adhesion. Additionally, HO-1 may interact with the TNF treatment and influence the expression of some genes like IL-1, IL-6, IL-8, FAS and NF-kB.

overall_design: NCI-H292 cells, control (pcDNA) and stably overexpressig HO-1 (pcHO1) were treated for 24 h with TNF (30 ng/ul), then the cells were lysed and RNA was collected. The whole human gene expression profile was assessed with Agilent microarray analysis. Three independent experiments were performed at each time using different batch of cells.

first: Jerzy

last: Kotlinowski

first: Jozef

last: Dulak


title: Transcriptional analysis of normal and pathological synovial fibroblasts

status: Public on Oct 25 2011

city: Madrid

first: Manuel

last: Del Rey

address: Avda Córdoba s/n

department: Grupo de Enfermedades Inflamatorias y Autoinmunes

country: Spain

institute: Instituto de Investigación Hospital 12 de Octubre

summary: The aim of this study was  to compare gene expression between two pathological groups of human synovial fibroblasts (SF) from rheumatoid arthritis (RA) and osteoarthritis (OA) synovial tissues with normal SF from healthy individuals (HSF). We used microarray expression profiling in SF cultured from OA, RA and normal synovial tissues.   We found larger numbers of transcripts with differential expression in OASF compared to the other groups than in RASF compared to HSF. This data demonstrate that cultured OASF display a more robust transcriptomic profile than RASF when compared to HSF.

overall_design: Synovial fibroblasts were obtained from 9 patients with rheumatoid arthritis (RASF), 11 sex and age matched adult healthy donors (HSF) and 11 sex and age matched patients with OA (OASF). SF were collected under similar subconfluent conditions 24h after serum addition. 31 microarray data were used for determine the statistical significance (p value) of the differences in gene expression.

first: Alicia

last: Usategui

first: Elena

last: Izquierdo

first: Juan

last: Cañete

first: Francisco

last: Blanco

first: Gabriel

last: Criado

first: José

last: Pablos


title: Expression profiling of LSK cells from Bmi1 cKO mice in hematopoiesis versus LSK control cells from WT mice

status: Public on Oct 30 2011

city: MADRID

first: Lorena

last: Arranz

address: MELCHOR FERNANDEZ ALMAGRO

department: CARDIOVASCULAR DEVELOPMENT AND REPAIR

institute: CNIC

summary:
Bmi1 is a protein member of PRC1 and plays a major role in the maintenance of gene repression. We are studying the role of Bmi1 in the context of hematopoietic stem cell aging.
We used microarray to study the gene expression profile of LSK cells in relation to the knocking-out of Bmi1 in vivo

overall_design: LSK cells were labeled using antibodies against specific surface markers and isolated by fluorescence-activated cell sorting in trizol.

first: Susana

last: González


title: Coordinated regulation of polycomb group complexes through microRNAs in cancer

status: Public on Oct 21 2011

city: Ann Arbor

first: Christopher

last: Maher

address: 1500 E. Medical Center Drive

institute: Michigan Center for Translational Pathology

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

summary: To determine the altered mRNA expression signatures upon overexpressing EZH2 regulated microRNAs in cancer. To identify EZH2 regulated microRNAs in cancer.

overall_design: Two-condition experiment: Each EZH2 microRNA was overexpressed and compared to a control RNA in BT549 breast cancer cells. In DU145 prostate cancer cell EZH2 was knocked down and comapred to EZH2 scrambled siRNA. Other cell lines were monitored for miRNA expression as they are known to have high endogenous levels of EZH2.

first: Christophe


title: FTC-238/hrTPO/RSK008 treated with thyroid peroxidase-disrupting chemicals

status: Public on Nov 09 2011

city: seoul

first: mee

last: song

address: P.O. Box 131, cheongryang

country: South Korea

institute: KIST

summary: These experiments have systematically assessed the potential utility of transcriptomic endpoints as enhancements to the guaiacol assay. Previously, we demonstrated that benzophenone-2, benzophenone, perfluorooctane sulfonate, bisphenol A bis ether, and vinclozolin decreased TPO activity, and that dibutyl phthalate, carbaryl, dibenzo(a,h)anthracene, benzo(a)pyrene, and methylmercury increased TPO activity. In this study, we used human oligonucleotide chips to examine changes in the gene expression profile of FTC-238 human follicular thyroid carcinoma cells expressing human recombinant TPO, after exposure of the cells to TPO activity-disrupting agents.

overall_design: FTC-238/hrTPO/RSK008 cells were seeded and after incubation for 24 h at 37C, the cells were treated with non-toxic dose for 48 h. And after total RNA isolation, gene expression analysis was conducted using a 8x60-k or 4x44-k whole human genome microarray. Labeling and hybridization were performed using a FairPlay microarray labeling kit, followed by the coupling of Cy3 (controls) or Cy5 (treated samples) dye. The hybridized slides were scanned using a GenePix 4000B microarray scanner, and the images were analyzed using GenePix 4.1 software to obtain gene expression ratios. The fluorescence intensity of each spot was calculated by local median background subtraction. We then used the robust scatter-plot smoother LOWESS function to perform intensity-dependent normalization of gene expression. Scatter-plot analysis was performed using Microsoft Excel 2000. A significance analysis of microarray (SAM) was performed for genes with significant changes in expression.

first: Jae-Chun

last: Ryu

first: Mee

last: Song


title: Subcutaneous adipose tissue: comparison of weight maintainence and weight regain following an 8-week low calorie diet

status: Public on Sep 30 2011

city: Guelph

first: David

last: Mutch

state: Ontario

address: 50 Stone Road East

department: Human Health & Nutritional Sciences

institute: University of Guelph

summary: The present study was designed to identify determinants that foreshadow successful weight maintenance. More specifically, we examined whether subcutaneous adipose tissue (scAT) gene expression of participants who experience successful weight maintenance following caloric restriction differed from that of participants who regain weight.

overall_design: Forty women followed a dietary protocol consisting of an 8-week low calorie diet (LCD) and a 6-month weight maintenance phase. At the end of the protocol, participants were classified as weight maintainers (WM; 0-10% weight regain) and weight regainers (WR; 50-100% weight regain). Anthropometric measurements, plasma parameters, and scAT biopsies were taken before and after the LCD. Adipose tissue gene expression profiles were studied in all individuals before and after the LCD.

first: Monica

last: Wong

first: Karine

last: Clément


title: TRAIL and taurolidine enhance the anticancer activity of doxorubicin, trabectedin and mafosfamide in human fibrosarcoma cells.

status: Public on Oct 01 2011

city: Ludwigshafen

first: Kamran

last: Harati

address: Ludwig-Guttmanstrasse 13

department: Department of Hand and Plastic Surgery, Burn Centre

institute: BG University Hospital Ludwigshafen

summary: Microarray analysis revealed differential gene expression patterns of HT1080 cells treated with various chemical compounds alone and in combination (trabectedin, doxorubicin, mafosfamide, TRAIL, taurolidine)

overall_design: Microarray analysis of HT1080 cells treated with various chemical compounds alone and in combination (trabectedin, doxorubicin, mafosfamide, TRAIL, taurolidine)

first: Stephan

last: Hahn


title: Pathway and functional association analysis of whole blood gene expression profiles reveal functional networks underlying TB pathogenesis. [Agilent-014850]

status: Public on Oct 28 2011

first: Jeroen

last: Maertzdorf

address: Chariteplatz 1

institute: MPIIB

summary: Tuberculosis (TB) is an ancient infectious disease that remains one of the major health threats in humans worldwide. Biosignatures can play a significant role in the development of novel intervention measures against TB and blood transcriptional profiling is increasingly exploited for their rational design. We have compared whole blood gene expression in TB patients, as well as in healthy infected and uninfected individuals in a cohort in The Gambia, West Africa and validated previously identified signatures showing high similarities of expression profiles among different cohorts. In this study, we applied a unique combination of classical gene expression analysis with pathway and functional association analysis integrated with intra-individual expression correlations. These gene signature analyses were employed for pathognomonic associations, identifying a network of Fc gamma receptor 1 signaling with correlating transcriptional activity as hallmark of gene expression in TB. Remarkable similarities to characteristic signatures in the autoimmune disease systemic lupus erythematosus (SLE) were observed, and functional gene clusters of immunoregulatory interactions  provide detailed insights into the dysregulation of critical immune processes in TB. Transcriptomics thus (i) provides a robust system for identification and validation of biosignatures for TB diagnosis and (ii) application of integrated analysis tools yields novel insights into functional networks underlying TB pathogenesis.

overall_design: A total of 46 sputum smear and chest x-ray positive TB patients (TB), 25 latently infected healthy donors (LTBI, TB case contacts with Mantoux test induration >= 10mm) and 37 uninfected donors (NID, Mantoux test induration = 0mm) were included from a cohort in The Gambia. All subjects were HIV– and samples from TB patients were taken prior to chemotherapy. Whole blood RNA was extracted using the PAXgene Blood RNA Kit (PreAnalytix) and labeled with Agilents Fluorescent Linear Amplification Kit. Quantity and labeling efficiency were verified before hybridization of the samples to whole-genome 4×44k human expression arrays and scanned at 5 μm using an Agilent scanner.

first: Martin

last: Ota

first: Dirk

last: Repsilber

first: January

last: Weiner

first: Hans

last: Mollenkopf

first: Philip

last: Hill

first: Stefan

last: Kaufmann


title: SCL005: icSARS CoV Urbani or icSARS deltaORF6 infections of the 2B4 clonal derivative of Calu-3 cells - Time course

first: Michael

last: Katze

summary: Purpose of experiment was to compare transcriptomics of 2B4 cells (clonal derivative of Calu-3 cells) infected with either icSARS CoV or the icSARS deltaORF6 mutant.

overall_design:
Calu-3 cells were infected with either icSARS CoV or the icSARS deltaORF6 mutant at MOI of 5.0.  Cells samples were collected at 0, 3, 7, 12, 24, 30, 36, 48, 54, 60 or 72h post infection. Each infected sample was done in triplicate. (Triplicates are defined as 3 different wells, plated at the same time using the same cell stock for all replicates.)There are triplicate time-matched mock for each time point from the same cell stock as rest of samples. Culture medium (the same as what the virus stock is in) was used for the mock infections.
The NIAID Systems Virology Center

first: Armand

last: Bankhead

first: Jean

last: Chang

first: Amy

last: Sims

first: Ralph

last: Baric

first: Shannon

last: McWeeney


title: Gene expression-based, individualized diagnostic GC/ABC prediction for relapse/refractory diffuse large B cell lymphoma (DLBCL)

status: Public on Sep 29 2011

city: Nantes

first: Edouard

last: Hirchaud

address: 8 quai Moncousu

institute: Plateforme Bioinformatique de Nantes

summary:
Individualized diagnosis prediction classifiers were successfully constructed through expression profiling of a total of 8,644 genes in 49 patients with relapse/refractory diffuse large B cell lymphoma, prospectively treated in a randomized trial.
keyword(s): Diagnosis prediction

overall_design: All lymphoma cases were predicted as belonging either to germical center B-cell like DLBCL or activated B cell like DLBCL based on the expression of a set of 54 genes (140 probes).

first: R

last: Houlgatte

first: C

last: Thieblemont

first: E


title: The bone marrow microenvironment in patients with neuroblastoma: presence of IFN signature and significant down-regulation of CXCL12 expression

city: Genova

first: PAOLA

last: SCARUFFI

state: GE

address: LARGO R. BENZI, 10

country: Italy

institute: "San Martino" Hospital

summary: Neuroblastoma (NB) is the most common extra cranial solid tumor in infants. Although several risk factors including patient age, disease stage and genetic abnormalities, such as MYCN amplification and 11q deletion, have been shown to predict outcome, the mechanisms responsible for the heterogeneous clinical behavior of this tumor, ranging from spontaneous regression to rapid progression of disease and patient’s death, remain largely unknown. Patients with disseminated disease mainly show metastasis at bone marrow (BM) and bone. The presence of metastasis is an independent unfavorable prognostic factor for NB patients over 18 months of age at diagnosis, whose event-free and overall survivals are grim despite intensive multimodal therapies. We decided to investigate the transcriptome of both NB metastatic cells and resident hematopoietic BM cells to get insight on potential targets for diagnostic, prognostic and therapeutic purposes. Hereby, we report on the results obtained by comparing BM resident hematopoietic cells in the presence and absence of infiltrating NB hematopoietic cells with BM cells from young healthy donors.

overall_design: We analyzed gene expression profiles of 40 bone marrow samples: 8 from healthy young donor; 23 from NB patients with stage 1, 2, 3; 9 from NB patients with stage 4.

first: Paola

last: Scaruffi

first: Fabio

last: Morandi

last: Gallo

first: Sara

last: Stigliani

first: Stefano

last: Parodi

last: Moretti

last: Bonassi

first: Paolo

last: Fardin

first: Alberto

last: Garaventa

first: Vito

last: Pistoia

first: GianPaolo

last: Tonini

first: MariaValeria

last: Corrias


title: Expression data from mouse B16-F10 cells exposed to hypoxic conditions in vitro.

status: Public on Nov 11 2011

city: Warsaw

first: Michal

last: Swierniak

address: Banacha 2C

department: Centre of New Technologies

institute: University of Warsaw

summary: Analysis of gene expression profile of B16-F10 murine melanoma cells exposed to hypoxic conditions (1% oxygen) or hypoxia mimicry (cobalt chloride) for 24 hours. Gene expression profiles were analyzed using MG-U74Av2 oligonucleotide microarrays.   Data analysis revealed 2541 probesets (FDR<5%) for 1% oxygen experiment and 364 probesets (FDR<5%) for cobalt chloride, that showed differences in expression levels. Analysis of hypoxia-regulated genes (1% O2) by stringent Family-Wise Error Rate estimation indicated 454 significantly changed transcripts (p<0.05). The most upregulated genes were Lgals3, Selenbp1, Nppb (more than ten-fold increase). Both hypoxia and hypoxia-mimicry induced HIF-1 regulated genes. However, unsupervised analysis (Singular Value Decomposition) revealed distinct differences between gene expression induced by these two experimental conditions.

overall_design: We investigated transcriptional activity of B16-F10 murine melanoma cells cultured for 24h under hypoxic (nominal 1% oxygen; 9 experimental samples and 6 controls) and hypoxia-mimicking conditions (cobalt chloride, 100 μM or 200 μM, 2 samples each and 2 controls).

first: Magdalena

last: Olbryt

first: Michał

last: Jarząb

first: Joanna

last: Jazowiecka-Rakus

first: Aleksander

last: Sochanik


title: The unique molecular signature of cortical tissue injury in Multiple Sclerosis

status: Public on Oct 06 2011

city: Vienna

first: Isabella

last: Wimmer

address: Spitalgasse 4

department: Center for Brain Research

country: Austria

institute: Medical University of Vienna

summary: In the present study we addressed several questions related to the mechanisms of cortical injury. We analyzed genome wide gene expression by microarrays, comparing active multiple sclerosis lesions with highly inflammatory lesions of chronic tuberculous meningitis, with neurodegenerative lesions of Alzheimer’s disease and with normal cortex of age matched controls.

overall_design: To clarify which inflammatory mediators drive demyelination in the human cortex, we characterized and compared the gene expression profile of cortices derived from patients with progressive Multiple Sclerosis (MS), Meningitis tuberculosis (TB), Alzheimer's disease (AD) as well as of normal cortex from age matched controls (CO). 3 cases of each disease were included into the study. Preceding the gene expression profiling, all cases were characterized histologically and areas of interest were identified. RNA was isolated from those areas, amplified and hybridized to Agilent G4112A whole genome microarrays.

first: Marie

middle: T

last: Fischer

first: Isabell


title: Role of Serine 134 phosphorylation of the glucocorticoid receptor (GR) in glucocorticoid signaling

status: Public on Oct 05 2011

city: RTP

first: NIEHS

last: Microarray Core

address: 111 T.W. Alexander Drive

department: DIR

institute: NIEHS

summary: In response to environmental stressors and a variety of inflammatory cytokines, p38 MAPKs become directly activated. Here we report the human glucocorticoid receptor (GR) Serine 134 as a novel target for p38 MAPK. Unlike most other phosphorylation events that occur on the GR, phosphorylation of Ser134 was found to be hormone-independent in several human and rat cell types. Instead we found phosphorylation of Ser134 was induced by a variety of stress-activating stimuli, including: glucose starvation, ultraviolet irradiation, osmotic shock, and oxidative stress. Pharmacological inhibitors and shRNA-mediated knockdown experiments correlate this phosphorylation with the activation of p38 MAPK. Compared to wild-type GR, cells expressing a mutant receptor incapable of phosphorylation at Ser134 (S134A GR) had a significantly altered hormone-dependent genome-wide transcriptional response to glucocorticoids. Moreover, we show that although WT GR regulated roughly half as many genes as S134A GR, WT receptor selectively activated significantly more genes associated with endocrine and inflammatory disease than the mutant receptor, suggesting that the phosphorylation status of Ser134 is critical for modulating GR function. Phosphorylation of Ser134 did not alter either nuclear translocation or the stability of the GR protein in the absence or presence of ligand. However, phosphorylation of Ser134 significantly increased the association of the GR with the zeta isoform the 14-3-3 class of signaling proteins, resulting in a blunted hormone-dependent transcriptional response of LAD1 and IGFBP1 but not GILZ. Together these data suggest that the phosphorylation of Ser134 acts as a molecular sensor on the GR, monitoring the level of cellular stress to allow for altered 14-3-3zeta cofactor association, ultimately modifying glucocorticoid signaling in a gene-dependent manner. Our results reveal one mechanism that may allow cellular stress to dictate the transcriptional response of cells to hormone.

overall_design: U2OS cells, a human osteosarcoma cell line, were transfected with either WT GR or S134A GR and put under antibiotic selection to produce a stable mixed population of cells expressing comparable levels of GR. 10^6 cells were treated with 100nM Dexamethasone (DEX) or vehicle control for 6 hours. Three biological and one hybridization replicate are included for each sample.

first: Amy

last: Galliher-Beckley

first: Jason

last: Williams

first: John

last: Cidlowski


title: Isolation and characterization of cancer-associated fibroblast-like cells in the glioblastoma microenvironment

status: Public on Oct 31 2011

city: Rennes

first: Amandine

last: Etcheverry

address: 2 rue Henri Le Guilloux

institute: CNRS UMR 6290 - IGDR

summary: Glioblastoma (GB) is a highly infiltrative tumor recurring in 90% of cases within a few centimeters of the resection cavity, even in cases of complete tumor resection and adjuvant chemo/radiotherapy. This observation highlights the importance of understanding this special zone of brain tissue surrounding the tumor. It is becoming clear that the non neoplastic stromal compartment of most solid cancers plays an active role in tumor proliferation, invasion and metastasis. Very little information, other than that concerning angiogenesis and immune cells, has been collected for stromal cells from GB. As part of a translational research program, we have isolated a new stromal cell population surrounding GB by computer-guided stereotaxic biopsies and primary culture. We named these cells GB-associated stromal cells (GASCs). GASCs are diploid, do not display the genomic alterations typical of GB cells and have phenotypic and functional properties in common with the cancer-associated fibroblasts (CAFs) in the stroma of carcinomas. In particular, GASCs express markers associated with CAFs such as alpha-smooth muscle actin (α-SMA) and platelet derived growth factor receptor-beta (PDGFRβ). Furthermore, as described for CAFs, GASCs have a molecular expression profile different from that of control stromal cells derived from non-GB peripheral brain tissues. GASCs were also found to have tumor-promoting effects on glioma cells in vitro and in vivo. The isolation of GASCs in a tumor of neuroepithelial origin was unexpected and further studies are required to determine their potential as a target for anti-glioma treatment.

overall_design: 3 control stromal cells and 4 GB-associated stromal cells were analysed.

first: Anne

last: Clavreul

first: Philippe

last: Menei


title: B-cell chronic lymphocytic leukemia side population cells

status: Public on Sep 27 2011

city: Houston

first: Aaron

last: Foster

address: 2130 W Holcombe Blvd

department: Product Discovery

institute: Bellicum Pharmaceuticals

summary: Analysis of Hoechst dye 33342-effluxing side population (SP) cells from B-CLL peripheral blood mononuclear cells.

overall_design: 9 biological replicates from B-CLL patients sorted into CD5+CD19+ SP and non-SP subsets. Two color comparative gene expression using Agilent microarrays.


title: Transcriptomics of the traditional Japanese medicine juzentaihoto (JTX) on large intestines on germfree mice

status: Public on Sep 14 2011

city: Shinjuku

first: Masahiro

last: Yamamoto

state: Tokyo

address: 35 Shinano-machi

department: Department of Kampo Medicine

institute: Keio University School of Medicine

summary:
Juzehtaihoto, a Japanese traditional medicine has been used for the treatment of various kinds of diseases or disorders in an enteric-flora dependent manner.
Here, we performed transcriptome analysis using Affymetrix GeneChip on large intestine (LI) of germ-free (GF)  and specific pathogen free (SPF) mice of IQI, an inbred strain established from ICR, and BALB/c SPF mice.

overall_design:
Male germ-free (GF) and specific pathogen-free (SPF) mice of IQI and BALB/c strains were bred and maintained in the laboratory of Central Institute for Experimental Animals (CIEA, Kawasaki, Kanagwa, Japan). GF mice were housed in a Trexler-type flexible film isolator in a standard germ free state and screened on a weekly basis for germ-free status by sampling feces sterilely and culturing on MRS-agar plates under aerobic and anaerobic conditions. All the GF, SPF, ex-GF mice were kept in a 12: 12-h light/dark cycle and at a temperature of 22±2°C. Nine week old mice (n=3) were sacrificed by cervical dislocation and the intestines were dissected.
comparison of the mice with or without enteric flora; comparison of the mice of different strains

first: Kaori

last: Munakata

first: Kenji

last: Watanabe


title: Transcriptomics of the traditional Japanese medicine juzentaihoto (JTX) on germfree mice

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

overall_design: Refer to individual Series


title: Transcriptomics of the traditional Japanese medicine juzentaihoto (JTX) on small intestines on germfree mice

summary:
Juzehtaihoto, a Japanese traditional medicine has been used for the treatment of various kinds of disease or disorders in an enteric-flora dependent manner.
Here, we performed transcriptome analysis using Affymetrix GeneChip on small intestine (SI) of germ-free (GF)  and specific pathogen free (SPF) mice of IQI, an inbred strain established from ICR.

overall_design:
Male germ-free (GF) and specific pathogen-free (SPF) IQI mice were bred and maintained in the laboratory of Central Institute for Experimental Animals (CIEA, Kawasaki, Kanagwa, Japan). GF mice were housed in a Trexler-type flexible film isolator in a standard germ free state and screened on a weekly basis for germ-free status by sampling feces sterilely and culturing on MRS-agar plates under aerobic and anaerobic conditions. All the GF, SPF, ex-GF mice were kept in a 12: 12-h light/dark cycle and at a temperature of 22±2°C. Nine week old mice (n=3) were sacrificed by cervical dislocation and the intestines were dissected.
comparison of the mice with or without enteric flora


title: Human Papillomavirus 16 E5 modulates the expression of host microRNAs

status: Public on Sep 01 2011

city: Tampere

first: Dario

last: Greco

address: Arvo ylpön Katu 34

department: Faculty of Medicine and Health Technology

country: Finland

institute: Tampere University

summary: The effect of human papillomavirus 16 E5 oncogene on cellular gene expression in human epithelial cells was studied.

overall_design: Alterations in cellular gene expression due to human papillomavirus type 16 E5 oncogene were studied in triplicate microarray screens. Epithelial cells where E5 expression was induced for 0, 2, 4, 24, 48, 72 and 96h were compared to control cells.

first: Niina

last: Kivi

first: Kui

last: Qian

first: Petri

last: Auvinen

first: Eeva


title: Pax6 mutant neocortex vs. wild type

city: Braunschweig

first: Robert

last: Geffers

address: Inhoffenstr. 7

department: Dep. Molecular Bacteriology

institute: HCI - Helmholtz Centre for Infection Research

summary: Pax6 is a transcription factor with key functional roles in embryonic development. In order to identify downstream effectors of Pax6 in the developing cerebral cortex we performed microarray analysis. We compared gene expression profiles of cortical tissues isolated from wild type and Pax6-/- mouse embryos.

overall_design: In order to identify Pax6 downstream targets we carried out microarray analysis of Pax6-/-  mutant mice. Pax6 is highly expressed in the mouse cerebral cortex at embryonic day E14.5, therefore we selected this tissue in order to compare gene expression profiles between wild type and Pax6-/- homozygous cortici. RNA samples were isolated from three mutant and three wild type embryos.

first: R

first: V

last: Tarabykin

first: S

last: Boppana


title: Bystander response to low dose (0.5 Gy) of alpha-particles in a human 3-dimensional skin model at 4h post-irradiation

status: Public on Aug 31 2011

city: New York

first: Alexandre

last: Mezentsev

state: NY

address: 630 west 168th Street, VC 15-204

department: Dermatology

institute: Columbia University

summary: Ionizing radiation (IR) not only affects cells that are directly irradiated but also their non-irradiated neighbors, which show responses known as bystander effects. While bystander and direct responses have several common end points including apoptosis and micronucleation, chromatin remodeling and altered levels or activities of regulatory proteins, they can be quantitatively and qualitatively different. The majority of studies of radiation bystander effects have utilized 2-dimensional in vitro systems, but we have recently demonstrated such effects in EPI-200 (Mat-Tek, Ashland, MA), a 3-dimensional tissue model that precisely imitates the structure and function of human epidermis.  Global gene expression is a powerful tool for uncovering both fundamental signaling processes and the mechanistic basis of cellular or physiological effects. By exposing only a thin strip across the center of the EPI-200 tissue, we have been able to measure global gene expression responses in directly irradiated and bystander cells located at 0, 0.25, 0.5, 0.75 and 1mm from the irradiation line. The data were analyzed using BRB-Array Tools (NIH), and further network analysis was performed with IPA (Ingenuity). Significantly responding genes were identified at all distances and included sets common to both direct and bystander responses. For instance, all sets demonstrated upregulation of a major component of the drug metabolism pathway, CYP1B1, and downregulation of MMP1, an enzyme involved in degradation of extracellular matrix. In contrast, PTGS2, a gene strongly implicated in the bystander response was upregulated in directly irradiated tissues, but actually downregulated in bystander cells. This effect may be time dependent, but may also suggest activation of bystander signaling mechanisms different from those observed in 2-dimensional cell cultures. According to network analysis of our results, the genes responding in bystander tissue fell into 5 major categories: cell death, cell communication, cell differentiation, stress response, and response to wounding, suggesting active intracellular communication in bystander tissue.

overall_design: Radiation induced gene expression in 3-dimensional tissue model, Epi-200, was measured at 4 hours after exposure to  0.5 Gy of alpha-particles. Three independent experiments were performed for the samples collected at different distances from the irradiation line (250-500, 500-750 and 750-1000 micrometers) using three tissue fragments per a data point.

first: Sally

last: Amundson

middle: V


title: COMPARISON OF DORSOCERVICAL TO ABDOMINAL SUBCUTANEOUS ADIPOSE TISSUE IN PATIENTS WITH AND WITHOUT ANTIRETROVIRAL THERAPY-ASSOCIATED LIPODYSTROPHY

status: Public on Sep 15 2011

summary:
Background and objective: Combination antiretroviral therapy (cART) is associated with lipodystrophy i.e. loss of subcutaneous adipose tissue in abdomen, limbs and face and its accumulation intra-abdominally. No fat is lost dorsocervically and it can even accumulates in this region (“buffalo  hump”). It is unknown how preserved dorsocervical fat differs from abdominal subcutaneous fat in HIV-1-infected cART-treated patients with (cART+LD+) and without (cART+LD-) lipodystrophy.
Results: Albeit dorsocervical adipose tissue in cART+LD+ seems spared from lipoatrophy, its mitochondrial DNA (mtDNA, copies/cell) content was significantly lower (by 62%) than that of the corresponding tissue in cART+LD-. Expression of CD68 mRNA, a marker of macrophages, and numerous inflammatory genes in microarray were significantly lower in dorsocervical vs. abdominal subcutaneous adipose tissue. Genes with the greatest difference in expression between the two depots were those involved in regulation of transcription and regionalization (homeobox genes), irrespective of lipodystrophy status. There was negligible mRNA expression of uncoupling protein 1, a gene characteristic of brown adipose tissue, in either depot.
Conclusions: As mtDNA is depleted even in the non-atrophic dorsocervical adipose tissue, it is unlikely that the cause of lipoatrophy is loss of mtDNA. Dorsocervical adipose tissue is less inflamed than lipoatrophic adipose tissue. It does not resemble brown adipose tissue. The greatest difference in gene expression between dorsocervical and abdominal s.c. adipose tissue is in expression of homeobox genes.

overall_design:
We used histology, microarray, polymerase chain reaction and magnetic resonance imaging to compare dorsocervical and abdominal subcutaneous adipose tissue in cART+LD+ (n=21) and cART+LD- (n=11).
The study consists of 17 patients on antiretroviral treatment who have developed lipodystrophy and 11 patients that are on similar treatment but have not developped lipodystrophy. All patients are HIV+ and have 2 adipose tissue samples taken from them (dorsocervical+abdominal).

first: Ksenia

last: Sevastianova

first: Jussi

last: Sutinen

first: Meline

last: Sievers

first: Kaisa

last: Salmenkivi

first: Julia

last: Perttilä

first: Vesa

middle: M

last: Olkkonen

first: Dick

last: Wågsäter

first: Martin

last: Lidell

first: Sven

last: Enerbäck

first: Per

last: Eriksson

first: Ulrich

last: Walker

first: Matti

last: Ristola

first: Hannele

last: Yki-Järvinen


title: Effetcs of several families of persistent organic pollutants on the undifferentiated and adipocyte differentiated human Multipotent Adipose-Derived Stem (hMADS) cells

status: Public on Sep 10 2011

city: paris

first: minji

last: kim

address: 45 rue des saints-pères

institute: INSERM

summary: Transcriptional profiling of hMADS cells treated or not by TCDD, PCB126 and PCB153.

overall_design: Four-condition experiment: 4 control replicates, 4 TCDD-treated, 4 PCB126-treated, 4 PCB153-treated either undiffrentitaed or differentiated cells.

first: Minjie

last: Kim

first: Véronique

last: Pelloux


title: Oxidative damage and respiratory burst in Multiple Sclerosis

status: Public on Oct 13 2011

first: Isabella

last: Wimmer

summary: In this project we focused on white matter injury in relapsing remitting MS. We concentrated on material obtained from patients who suffered from fulminant active MS to identify possible sources for ROS production in relation to demyelination and neurodegeneration.

overall_design:
We performed genome-wide microarray analyses of gene expression in carefully dissected lesions of patients with fulminant acute MS. Preceding the gene expression profiling all cases were characterized histologically and areas of interest were identified. We included 4 control cases, 2 active MS cases from which we separated 3 distinct lesions areas per case (NAWM, initial lesion and early demyelinated lesion) and 1 active MS case from which we separated 2 distinct lesion areas (NAWM and early demyelinated lesion). The RNA was isolated from those areas, amplified and hybridized to Agilent G4112A whole genome microarrays.

UPDATE in 2013! We additionally included a fourth acute MS case, from which we microdissected 2 different initial lesions and 2 different early demyelinated lesions. Data was re-normalized and re-analyzed.

first: Marie-Therese

last: Fischer

first: Rakhi

last: Sharma


status: Public on Sep 26 2011

first: Robert

last: Waterland

address: 1100 Bates St.,

institute: Baylor College of Medicine

type: Methylation profiling by genome tiling array

summary: Investigate the genome-wide DNA methylation and gene expression changes during human embryonic stem cell differentiation.

overall_design: hESCs (H1 and H13) DNA samples for 3 different differentian stage (D0, undifferentiated;D21, 21 days after undirected differentiation; D90, 90 days after undirected differentiation); two-color experiment, paired comparison (differentiated vs undifferentiated; A & B: two biological replicates). Differentian-stage variation in methylation profiling of human DNA samples were detected by MSAM. 2µg of DNA was serially digested with SmaI and XmaI followed by an adaptor ligation and adaptor mediated PCR amplification. Analysis of differentian-stage variation in gene expression of human mRNA samples were implementd following standard Agilent protocol.

first: Lanlan

last: Shen

first: Wenjuan

last: Zhang


title: Biological response to low dose of alpha-particles in a human 3-dimensional skin model, in 1 and 16h after exposure to ionizing radiation.

first: Alexandre

last: Mezentsev

summary: Direct irradiation of 3-dimensional skin model, Epi-200, with alpha-particles led to differential regulation of 166 genes: 16 and 150 genes were differentially expressed at 1 and 16 h postirradiation. Unlike the traditional 2-dimensional in vitro systems, Epi-200 made of the primary cells, epidermal human keratinocytes. It mimics the structure of the human epidermis Global gene expression is a powerful tool for uncovering both fundamental signaling processes and the mechanistic basis of cellular or physiological effects. By comparing irradiated tissues with non-irradiated control, we have been able to measure global gene expression responses and reveal the affected biological pathways and molecular functions. The data were analyzed using BRB-Array Tools (NIH), and further gene ontology analysis was performed with Panther database (Applied Biosystems). Gene ontology analysis of the samples harvested in 16h after exposure showed that irradiation presumably affected the genes involved in cell-cell signaling (15 genes, , p=9.0 x E-04) ion transport (10 genes, p=0.00189) and amino acid metabolism (5 genes, p=0.0258). Among 16 genes differentially expressed in 1h after exposure we found NOTCH2 (ENST00000401649) and methyltransferase AOF1 (KDM1B). In the mammalian cells, NOTCH signaling pathway has a role in differentiation and intracellular communication. Moreover the intercellular domain of NOTCH regulates gene expression acting as a transcription factor. In turn, AOF1 affects the transcription via histone demethylation. Thus, irradiation with alpha-particles caused predominant downregulation of multiple genes in 1 and 16h after exposure. It also suggested that changes in cell metabolism initially affected transcriptional regulation and finally led to the rearrangement in expression of genes playing a role in biosynthesis and ion trafficking.

overall_design: Radiation induced gene expression in 3-dimensional tissue model, Epi-200, was measured in 1 and 16 h hours after exposure to  0.5 Gy of alpha-particles. Three independent experiments were performed using one tissue sample per a data point.

first: Sally

last: Amundson


title: Folic acid supplementation dysregulates gene expression in lymphoblastoid cells

status: Public on Aug 24 2011

city: Staten Island

first: Mohammed

middle: A.

last: Junaid

address: 1050 Forest Hill Road

department: Developmental Biochemistry

institute: New York State Institute for Basic Research in Developmental Disabilities

summary: To prove our hypothesis that excess folic acid supplementation is responsible for widespread gene expression changes during gestational development that may be responsible for abnormal behaviors later on in the life, we have used whole genome microarray expression profiling in lymphoblstoid cells as a proof of concept. Human lymphoblastoid cells in culture were supplemented with folic acid, and four days later gene expression changes were measured. Expression of three genes (FMR1, GPR37L1 and TSSK3) from this data was confirmed by Western blot analyses. Dysregulation of other genes (ARHGAP6, EF1A1, MEST, SMAD3) was confirmed by qRT-PCR.

overall_design: Lymphoid cells at confluence were grown with or without folic acid for four days. Total mRNA was prepared and labeled with cyanine-3 (Cy3), followed by hybridization. RNA samples from three independent experiments were pooled.

first: Salomon

last: Kuizon

first: Raju

last: Pullarkat

first: W

last: Brown


title: mRNA expression profiling in nine human tissues

status: Public on Sep 20 2011

city: Santa Clara

last: Ach

state: CA

address: 5301 Stevens Creek Boulevard

department: Agilent Laboratories

institute: Agilent Technologies

summary: Profiled mRNA gene expression in nine different commercially purchased total RNA samples which were also profiled for miRNAs.

overall_design: 500ng toal RNA from each tissue was labeled and hybridized in at least duplicate, using Agilent Low Input Linear Amplification Kit.


title: Bystander response to 2.5 Gy of protons in a human 3-dimensional skin model in 16 h after exposure

summary: Bystander mechanisms that originate in the areas surrounding a tissue damage presumably play an important role participating in wound healing and tissue remodeling. Thus, identification and characterization of bystander mechanisms will help to development of new treatments of patients with a radiation exposure. In the present study, we irradiated 3-dimensional tissue model of human epidermis, Epi-200 (Mat-Tek, Ashland, MA), with 2.5 Gy protons. By exposing only a thin strip across the center of the EPI-200 tissue, we have been able to measure global gene expression responses in directly irradiated and bystander cells located at 0.125-0.375, 0.375-0.625, 0.625-875 mm from the irradiation line. The data were analyzed using BRB-Array Tools (NIH), and further gene ontology analysis and network analysis was performed with Panther (Applied Biosystems) and IPA (Ingenuity), accordingly. Significantly responding genes were identified at all distances and included sets common to both direct and bystander responses. False discovery rate in bystander samples did not exceed 20% (p=0.001) and was sufficiently low in the samples obtained after the whole tissue exposure (0.06-1.16%). Analysis of the fragments cut at the same distance revealed 52, 54 and 88 differentially expressed genes. These gene lists overlapped each other had from 3 to 12 genes in common including CLED2, S100A7A. Samples obtained after the whole tissue exposure discovered 949 differentially expressed genes. Moreover, the performed gene ontology analysis showed there overrepresentation of TP53 pathway (pathways, p=2.04E-02), a common marker of direct irradiation response, and also overrepresentation of the following groups of genes: signal transduction (p=4.52E-04), cell communication (p=1.24E-04) and cell cycle in the category of biological processes; DNA helicase activity (p=2.54E-07), receptor binding (p=6.19E-04), calcium ion binding proteins (p=2.57E-03) as the molecular functions. Differentially expresses genes of bystander samples had few categories in common such as cell communication (p=2.36E-03) and signal transduction (p=2.42E-03) among the biological processes and receptor activity (p=4.54E-03) among the molecular functions. Categories specific for the bystander samples included G-protein coupled receptors (p=7.24E-03) and ligand-gated ion channels (p=4.16E-03) suggesting a role of external stimulation and ion trafficking in bystander mechanisms.

overall_design: Radiation induced gene expression in 3-dimensional tissue model, Epi-200, was measured in 16 hours after exposure to  2.5 Gy of protons. Four independent experiments were performed for the samples collected at different distances from the irradiation line (125-375, 375-625 and 625-875 micrometers) using three tissue fragments per a data point. Moreover, three sets of whole tissue irradited samples were also generated for 0 and 2.5 Gy  (6 samples total) and used for comparison of bystander and direct responses.


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

city: Bozeman

first: Kate

last: McInnerney

state: MT

address: 109 Lewis Hall

department: Microbiology

institute: Montana State University

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

overall_design: Human keratinocytes were grown in co-culture with mature S. aureus biofilms for 24 hours.  Keratinocytes exposed to S. aureus biofilm were analyzed in quadruplicate. Control cells were also analyzed in quadruplicate. Dye-swaps were performed.

first: Patrick

last: Secor

first: Garth

last: James

first: Philip

last: Fleckman

first: John

last: Olerud

first: Scot

last: Dowd

last: Stewart


title: Transcriptome profiling of degU expression reveals unexpected regulatory patterns in Bacillus megaterium and discloses new targets for optimizing expression

status: Public on Aug 15 2011

first: Rebekka

last: Biedendieck

address: Rebenring 56

department: Institute of Microbiology

institute: Technische Universtität Braunschweig

summary:
First whole transcriptome assessment of a Bacillus megaterium strain.
The B. megaterium DegU regulon was assessed for LB batch cultures with artificially induced degU expression. DegU is a pleiotropic regulator in B. subtilis governing adaptive responses such as secretory enzyme production.

overall_design:
8 x 15 K customer made microarrays for gene expression analysis of B. megaterium were obtained from Agilent (Agilent Technologies, USA) with up to three probes per open reading frame of the B. megaterium DSM319 genome. Finally, the hybridization and final washing steps of the microarrays  occurred as described in the Agilent manual for two color microarrays. The microarrays were scanned with the help of the Agilent C Scanner (Agilent Technologies, USA). For scanning and feature extraction the software Agilent Scan Control 8.4.1 and Feature Extraction 10.7.3.1 (Agilent Technologies, USA), respectively, was used according to the instruction. The analysis of the raw data occurred with the programming language R and Bioconductor as described in Yang and Paquet (2005). Finally, in consequence of the microarray design  three different probes belonging to one gene were matched performing mean and median summarization of the logarithmic fold changes (logFC). Nevertheless, the p-values and also the logFC values were given for each probe separately, to account for different hybridization behavior of the different probes (Bunk, 2010). Only genes with a p-value < 0.01 in all replicates and an absolute  |logFC| > 1 were considered as to be differentially expressed.
Samples from degU expressing cells (xylose induction) of a degSU deletion mutant were compared to samples obtained from the likewise induced empty vector control strain, two time points, biological replicates: 3-5

first: Claudia

last: Borgmeier

first: Kristina

last: Hoffmann

first: Dieter

last: Jahn

first: Friedhelm

last: Meinhardt


title: Knockdown and Overexpression of Cbx4 wild type and of a Cbx4 chromodomain mutant in human epidermal stem cells

status: Public on Aug 02 2011

city: Barcelona

first: Salvador

middle: Aznar

last: Benitah

address: Baldiri Reixac 10

department: Oncology

institute: Institute for Research in Biomedicine (IRB, Barcelona)

summary: Human epidermal stem cells transit from a slow cycling to an actively proliferating state to contribute to homeostasis. Both stem cell states differ in their cell cycle profiles but must remain guarded from differentiation and senescence. Here we show that Cbx4, a Polycomb Repressive Complex-1 (PRC1)-associated protein, maintains human epidermal stem cells slow-cycling and undifferentiated, while protecting them from senescence. Interestingly, abrogating the polycomb activity of Cbx4 impairs its anti-senescent function without affecting stem cell differentiation, indicating that differentiation and senescence are independent processes in human epidermis. Conversely, Cbx4 inhibits stem cell activation and differentiation through its SUMO ligase activity. Global transcriptome and chromatin occupancy analyses indicate that Cbx4 regulates modulators of epidermal homeostasis and represses factors, such as Ezh2, Dnmt1, and Bmi1, to prevent the activate stem cell state. Our results suggest that distinct Polycomb complexes balance epidermal stem cell dormancy and activation, while continually preventing senescence and differentiation.

overall_design: Primary human keratinocytes were infected with control vector pBABE, Cbx4 wildtype and a chromodomain mutant version of Cbx4 (F11A and W35L), both fused to a Estrogen Receptor to render their activaty inducible by addition of 4OHT to the media. Cells were cultured for 5 days (after infection and selection) under 4OHT treatment, after which total RNA was collected. For the knockdown, the pRetroSuperPuro was used as a control vector, in which a shRNA sequence for Cbx4 was introduced to interfere with Cbx4 expression. Cell were cultured in the same way as for the overexpression experiments.

first: Nuno

last: Luis


title: CPG stimulation for Gene Expression of mutated B-CLL

status: Public on Aug 18 2011

city: Aviano

first: daniela

last: marconi

address: Via franco Gallini 2

institute: CRO AVIANO

summary: The aim is to identify the differential gene expression profile of mutated B-CLL stimulated with CPG

overall_design: Two-condition experiment, CPG-stimulated B-CLL mutated vs. Unstimulated B-CLL mutated . Biological replicates: 8 unstimulated replicates, 8 CPG-stimulated replicates. Reference design;

first: Riccardo

last: Bomben

first: Daniela

last: Marconi

first: Michele

last: Dal Bo

first: Dania

last: Benedetti

first: Antonella

last: Zucchetto

first: Stefano

last: Volinia

first: Valter

last: Gattei


title: Knockdown and Overexpression of Cbx4 wild type, Cbx4 chromodomain mutant, and Cbx4 sumoylation mutant in human epidermal stem cells

status: Public on Aug 03 2011

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

overall_design: Refer to individual Series


title: Biological response to 2.5 Gy of X-rays  in 3-dimensional skin model, Epi-200.

first: Alexandre

last: Mezentsev

summary: Biological response X-rays traditionally serves as a standard in comparative analysis of different qualities of ionizing radiation. Most such studies have utilized 2-dimensional culture systems, which may not fully represent responses in 3-dimensional tissues. To gain insight into biological responses to X-rays in tissue, we have profiled global gene expression in EPI-200, a 3-dimensional tissue model that imitates the structure and function of human epidermis, at 4, 16 and 24 hours after exposure to 2.5 Gy of X-rays. The most significant gene ontology groups were associated with cell cycle, cytokinesis, establishment and maintenance of chromatin architecture. Remarkably, genes with a role in cell cycle were predominantly downregulated at all time points while genes involved in the cell defense response - upregulated. Methyltransferases were predominantly upregulated at 4 and 16h while transcription factors - at 16h and 24h suggesting remodeling of the chromatin. Among the genes with a role in signal transduction, irradiation affected kinase modulators and microtubule binding motor proteins at all time points. Kinases, especially non-receptor serine/threonine protein kinases were predominantly upregulated at 16 and 24h suggesting a rearrangement in the signaling pathways. The results also confirm involvement in the biological response of the genes participating in p53 pathway that were overrepresented at 4 and 16h in the set of upregulated genes and ubiquitin proteasome pathway that were predominantly downregulated at 16h and 24h In the same time, growing numbers of altered in expression genes: 449 at 4h; 720 and 3986 genes - at 16 and 24h postirradiation, accordingly suggested that ionizing radiation caused long term changes in the gene expression the exceeded the time frame proposed for this study.

overall_design: Radiation induced gene expression in 3-dimensional tissue model, Epi-200, was measured at 4, 16 and 24 hours after exposure to the dose of 2.5 Gy of X-rays. Three independent experiments were performed in the each time point using one tissue sample per a data point.

first: Sally

middle: A

last: Amundson


title: RIP-Chip analysis of Musashi (Msi1) in the Daoy human medulloblastoma cell line.

status: Public on Jul 26 2011

city: san antonio

first: raquel

last: abreu

address: 8403 Floyd Curl Drive

institute: CCRI

summary: RIP-chip analysis to identify mRNA preferentially associated with Msi1 protein.

overall_design: RIP-Chip experiments were performed on two biologically replicated samples transfected with the BAP-Msi1 construct and a control sample from cells transfected with the BAP-Control construct. A total of 8 microarrays were carried on using technical replicates of BAP-Msi1 vs. BAP-Control for each dye orientation.

first: Dat

last: Vo

first: Tarea

last: Burton

first: Dharmalingam

last: Subramaniam

first: Marc

last: Remke

first: Christine

last: Vogel

first: Raquel

last: Abreu

first: Suzanne

last: Burns

first: Mei

last: Qiao

first: Uthra

last: Suresh

first: Susan

last: Weintraub

first: Andrey

last: Korshunov

first: Adrian

last: Dubuc

first: Paul

last: Northcott

first: Stefan

last: Pfister

first: Michael

middle: D

last: Taylor

first: Shrikant

last: Anant

first: Luiz

middle: F

last: Penalva