title: Expression changes in cultured endothelial cells upon infection with HHV-8

city: Seattle

first: Lynn

last: Amon

state: WA

address: 1100 Fairview, M1-C108

department: Division of Public Health Sciences

institute: Fred Hutchinson Cancer Research Center

summary: Tert-immortalized microvascular endothelial (TIME) cells are infected with human herpesvirus (HHV-8) or mocked infected to determine expression changes upon infection.

overall_design: Three samples to TIME cells are infected with HHV-8 and three samples are mock-infected.

first: Michael

last: Lagunoff


title: Donor-specific NK cells exert potent cytolytic effector functions against patient-specific leukemic blasts in an IL-7 and IL-15 supplemented humanized NOD/SCID/IL2Rγnull mouse model

status: Public on Aug 01 2011

city: Tuebingen

last: Bonin

state: BW

address: CAlwerstr. 7

department: Medical Genetics

country: Germany

institute: University Tuebingen

summary: Surrogate models have so far been missing that might allow the evaluation of graft-versus-leukemia effects in an individualized donor-patient-specific context. We here describe the generation of a NOD/SCID/IL2Rγnull (NSG) leukemia mouse model that ideally resembles the biology of miscellaneous patient-specific leukemias. Following transfer of patient-derived blasts into NSG mice, various forms of pediatric haematological malignancies readily engrafted NSG recipients and NSG-derived leukemic cells indeed resembled the individual leukemia with respect to phenotype, chromosomal aberrations, transcriptome and MRD marker expression.

overall_design: Comparison of bone marrow-derived human- and mouse-derived leukemia samples.

first: Maya

last: C. André

first: Udo

middle: F

last: Hartwig

first: Kai

middle: E

last: Witte

first: Barbara

last: Goecke

first: Vanessa

last: Heininger

first: Martin

last: Philippek

first: Matthias

middle: M

last: Pfeiffer

first: Andre

last: Schrauder

first: Silja

last: Röttgers

first: Wolfgang

last: Herr

first: Peter

last: Lang

first: Rupert

last: Handgretinger

last: Ebinger


title: Endothelial differentiation potential of human amnion-derived mesenchymal stromal cells (hAMSC)

status: Public on Jul 29 2011

city: Graz

first: Julia

last: König

address: Harrachgasse 21/7

department: Institute of Cell Biology, Histology and Embryology

country: Austria

institute: Medical University of Graz

summary:
Mesenchymal stromal cells (MSC) are multipotent cells that potentially promote angiogenesis. Especially MSC derived from the amnionic membrane of human term placentas (hAMSC) are promising candidates for a therapeutic use in vascular diseases, as cells can be isolated using non-invasive methods and are immunologically tolerated in vivo. In this study, we wanted to evaluate the endothelial differentiation potential of hAMSC.
We used microarrays to investigate the effect of endothelial culture conditions on gene expression of hAMSC.

overall_design: Mesenchymal stromal cells were isolated from from the amnionic membrane of three different human term placentas (hAMSC 1, 2, 3). To investigate the endothelial differentiation potential, aliquots of passage 1 cells were cultured in endothelial cell medium EGM-2 (induced hAMSC 1, 2, 3) or in control medium DMEM (non-induced hAMSC 1, 2, 3) for 14 days before RNA isolation.

first: Karin

last: Wagner


title: Effect of EGF and/or HER2 on the growth of MCF10A cells on extracellular matrix: time course

status: Public on Jul 30 2011

city: Rehovot

first: Amit

last: Zeisel

address: Weizmann Institute

department: Physics of complex systems

country: Israel

institute: Weizmann Institute of Science

summary: Mammary epithelial cells MCF10A  and HER2 overexpressing MCF10A  cells were grown on matrigel in the absence or presence of epidermal growth factor. Cells were lysed and RNA was collected  at 1.5,3,5,7,9 days.

overall_design: Total 20 arrays from four time course experiments. MCF10A and MCF10A-HER2 (overexpressed HER2) were plated on  Matrigel in the absence or presence of 20 ng/ml of EGF. This design creates four panels of experiments of 5 time points each.

first: Pradeep

last: Chaluvally-Raghavan

first: Eytan

last: Domany

first: Yosef

last: Yarden


title: Resveratrol induces downregulation of DNA repair genes in MCF7 human breast cancer cells.

city: Mexico City

first: Laura

middle: I

last: Uribe

state: DF

address: Periferico Sur 4124 Col. Ex rancho de Anzaldo

department: Research

country: Mexico

institute: INMEGEN

summary:
Breast cancer is a worlwide health problem. One of the factors involved in carcinogenesis is diet. Several studies indicate that resveratrol, a polyphenol present in diet, has several antitumor
properties. The purpose of the study is gain an insight of resveratrol effect in cancer by determining the gene expression profile of breast cancer cell lines treated with the compound.

overall_design: MCF7 cell lines were treated for a 48 hour period with two concentrations (150 and 250 uM) of resveratrol. 9 plates were used for each condition. The RNA obtained from 3 plates of the same condition was pooled, processed and hybridized to the Affymetrix Human Gene 1.0 ST array. The arrays were analyzed using Partek Genomics suite software-.

first: I

last: León-Galicia

first: J

last: Diaz-Chavez

first: E

last: Garcia-Villa

first: L

last: Uribe-Figueroa

first: A

last: Hidalgo-Miranda

last: Alvarez-Rios

last: García-Mena

first: P

last: Gariglio


title: Gene expression in hypoxic non-small cell lung cancer

status: Public on Jul 28 2011

first: Katharina

last: Leithner

address: Auenbruggerplatz 20

department: Department of Internal Medicine, Division of Pulmonology

summary: Hypoxia triggers aggressive cancer growth and contributes to chemotherapy resistance. Novel therapeutic strategies aim at targeting hypoxia activated signaling pathways. Tumor hypoxia not only affects neoplastic tumor cells but also the surrounding stroma cells. Therefore, a novel ex vivo model was established, which allows the study of hypoxia effects in fragments of non-small cell lung cancer (NSCLC) with preserved tumor microenvironment and 3D-structure. Microarray analysis identified 107 significantly regulated genes with at least two-fold expression change in hypoxic compared to normoxic fragments. However, only four genes were significantly regulated in both subtypes, adenocarcinoma and squamous cell carcinoma. The hypoxic regulation of these four genes was verified in an independent set using quantitative PCR.

overall_design: Non-small cell lung cancer (NSCLC) fragments were cultured ex vivo under hypoxia or normoxia for three days. cDNA microarray analysis was performed in hypoxic and normoxic lung cancer fragments from ten patients.

first: Birgit

last: Ebner

first: Christian

last: Guelly


title: Microarray Analysis of West Nile Virus infected Human Retinal Pigment Epithelium

city: Sydney

first: Luis

last: Munoz-Erazo

state: NSW

address: Room 260, Blackburn building D06

department: Department of Pathology

country: Australia

institute: University of Sydney

summary:
Low-level infection is believed to play a role in the degradation of the outer blood retinal barrier, which is composed of retinal pigment epithelial (RPE) cells.
By investigating immunopathogenic West nile virus (WNV) infected RPE via microarray, we sought to find key genes involved in a low-level viral infection, which are vital for normal immune responses.

overall_design: We infected primary human RPE cells and an human RPE cell line with WNV and extracted RNA to hybridize onto Affymetrix arrays. We were interested in the global expression of differentially regulated genes in WNV infected RPE cells, at 24h post infection. We were also interested in seeing the differences in response between infected primaries and the infected ARPE19 cell line.

first: Riccardo

last: Natoli

first: Jan

last: Provis

first: Michele

middle: C

last: Madiagn

first: Nicholas

middle: J

last: King


title: High apoptotic threshold mediates p53 dependent decision between arrest and apoptosis

status: Public on Jul 20 2011

city: New York

first: Ajish

middle: D

last: George

state: NY

address: 1425 Madison Ave

department: Dept of Genetics & Genomics

country: USA

institute: Mt Sinai School of Medicine

summary:
In response to stress, the p53 tumor suppressor induces arrest or apoptosis by transcriptionally regulating genes that mediate these processes. It has been proposed that the levels of p53 can influence the choice between these different outcomes, but the mechanisms involved are not clear. To gain mechanistic understanding of this p53-dependent cell fate decision, we generated a p53 inducible system that allowed tight regulation of p53 expression in human mammary epithelial cells.
We used microarrays to detail the global programme of gene expression underlying cellularisation and identified distinct classes of up-regulated genes during this process.

overall_design: Using microarray and chromatin immunoprecipitation analysis, we showed that low and high levels of p53 bind to and activate the same set of pro arrest and pro apoptotic target genes, induced to lower and higher levels, respectively. We propose that the cell fate decision between arrest and apoptosis in these cells is determined by a higher threshold required for p53 dependent apoptosis. We suggest that high level p53 activation is crucial in order to achieve maximum efficacy of p53 targeted cancer therapies.

first: Martina

last: Kracikova

first: Gal

last: Akiri

first: Ravi

last: Sachidanandam

first: Stuart

middle: A

last: Lee

last: Aaronson


title: DMSO control and DZNep treated MOLM-14 cells

status: Public on Jul 01 2011

city: Singapore

first: Jianbiao

last: Zhou

address: 28 Medical Drive

country: Singapore

institute: Cancer Science Institute Singapore

summary:
We demonstrated that 3-Deazaneplanocin A (DZNep), a histone methyltransferase inhibitor, induce robust apoptosis in AML cells through increased ROS production and ER stress.
We identified a core gene signature including TXNIP, a major redox control molecule which is crucial in DZNep-induced apoptosis.

overall_design: MOLM-14 cells were treated with DMSO and DZNep 2 µM for 24 hours


title: Insulin-producing cells generated from dedifferentiated human pancreatic beta cells expanded in vitro

status: Public on Jul 19 2011

city: Tel Aviv

first: Metsada

last: Pasmanik-Chor

address: Ramat Aviv

department: Biology

institute: Tel Aviv University

summary: Expansion of beta cells from the limited number of adult human islet donors is an attractive prospect for increasing cell availability for cell therapy of diabetes. However, while evidence supports the replicative capacity of adult beta cells in vivo, attempts at expanding human islet cells in tissue culture resulted in loss of beta-cell phenotype. Using a genetic lineage-tracing approach we have provided evidence for massive proliferation of beta-cell-derived (BCD) cells within these cultures. Expansion involves dedifferentiation resembling epithelial-mesenchymal transition (EMT). Epigenetic analyses indicate that key beta-cell genes maintain a partially open chromatin structure in expanded BCD cells, although they are not transcribed. Here we report that BCD cells can be induced to redifferentiate by a combination of soluble factors. The redifferentiated cells express beta-cell genes, store insulin in typical secretory vesicles, and release it in response to glucose. The redifferentiation process involves mesenchymal-epithelial transition, as judged from changes in gene expression. Moreover, inhibition of the EMT effector SLUG using shRNA results in stimulation of redifferentiation. BCD cells also give rise at a low rate to cells expressing other islet hormones, suggesting  transition through an islet progenitor-like stage during redifferentiation. These findings suggest that ex-vivo expansion of adult human islet cells is a promising approach for generation of insulin-producing cells for transplantation, as well as basic research, toxicology studies, and drug screening.

overall_design: Gene expression was studied in unexpanded islets (4 donors), expanded and dedifferentiated islet cells (4 donors), and re-differentiated islet cells (3 donors). The experiment was performed in 3 batches (see Date in the description table below).

first: Holger

last: Russ

first: Elad

last: Sintov

first: Leeat

last: Anker-Kitai

first: Orr

last: Friedman

first: Ayelet

last: Lenz

first: Ginat

last: Toren

first: Chen

last: Farhi

first: Varda

last: Oron-Karni

first: Philippe

last: Ravassard

first: Shimon

last: Efrat


title: Gene expression of induced neural stem cells

city: Seoul

first: Soon-Tae

address: 28, Yeongon-dong, Jongno-gu

country: South Korea

institute: Seoul National University Hospital

summary: Neural stem cell (NSC) transplantation replaces damaged brain cells and provides disease-modifying effects in many neurological disorders. However, there has been no efficient way to obtain autologous NSCs in patients. Given that ectopic factors can reprogram somatic cells to be pluripotent, we attempted to generate human NSC-like cells by reprograming human fibroblasts. Fibroblasts were transfected with NSC line-derived cellular extracts and grown in neurosphere culture conditions. The cells were then analyzed for NSC characteristics, including neurosphere formation, gene expression patterns, and ability to differentiate. The obtained induced neurosphere-like cells (iNS), which formed daughter neurospheres after serial passaging, expressed neural stem cell markers, and had demethylated SOX2 regulatory regions, all characteristics of human NSCs. The iNS had gene expression patterns that were a combination of the patterns of NSCs and fibroblasts, but they could be differentiated to express neuroglial markers and neuronal sodium channels. These results show for the first time that iNS can be directly generated from human fibroblasts. Further studies on their application in neurological diseases are warranted.

overall_design:
We generated induced neural stem cells (iNS) and compared the gene expressions with control cells, which included primary human dermal fibroblast cultured in DMEM media (FB), primary human dermal fibroblast cultured in neurosphere-forming condition (FB_con), and neural stem cell line (F3). The four cell lines (iNS, FB, FB_con, and F3) showed different gene expression patterns.
  In detail, RNA was isolated using Trizol (Invitrogen) according to the manufacturer's instructions, and was labeled and hybridized to an Affimetrix GeneChip human gene 1.0 ST array (Affimetrix, Santa Clara, CA, USA) as described according to the manufacturer’s instructions. Data were analyzed using Expression Console software version 1.1 (Affimetrix), in which gene expression ratios were normalized by Robust Multichip Analysis according to the manufacturer’s protocol.

first: Kon

last: Chu

first: Keun-Hwa

last: Jung

first: Manho

last: Kim

first: Jae-Kyu

last: Roh


title: Waves of early transcriptional activation and pluripotency program initiation along human preimplantation development.

city: Barcelona

first: Stephanie

last: Boue

address: Dr Aiguader 88

country: Spain

institute: CMRB

summary: The events regulating human preimplantation development are still largely unknown, due to scarcity of material, ethical and legal limitations, and lack of reliable techniques to faithfully amplify the transcriptome of a single cell. Nonetheless, knowledge in human embryology is gathering renewed interest due to its close relationship with both stem cell biology and epigenetic reprogramming to pluripotency, and their centrality to regenerative medicine. Using carefully timed genome-wide transcript analyses on single oocytes and embryos, the analysis of the data allowed us to uncover a series of successive waves of embryonic transcriptional initiation which start as early as the 2 cell stage. In addition, we identified hierarchical activation of genes involved in the regulation of pluripotency. Finally, we developed HumER, a free database of human preimplantation human development gene expression to serve the scientific community. Importantly, our work links early transcription in the human embryo with the correct execution of the pluripotency program later in development, and paves the way for the identification of factors to improve epigenetic reprogramming.

overall_design: Gene expression profiling of human pre-implantation was followed with biological triplicates of oocyte to blastocyst stages, and compared with ESCs.

first: Rita

last: Vassena

first: Stéphanie

last: Boué

first: Eva

middle: G

last: Roca

first: Begoña

last: Aran

first: Herbert

last: Auer

first: Anna

last: Veiga

first: Juan

last: Belmonte


title: The effects of the 5' pocket motif of Dicer on miRNA biogenesis

status: Public on Jul 13 2011

first: Hyeshik

last: Chang

state: South Korea

address: Building 203 Room 525, School of Biological Sciences, Seoul National University, 1 Gwanak-ro, Gwanak-gu

department: School of Biological Sciences

institute: Seoul National University

type: Non-coding RNA profiling by high throughput sequencing

summary: A hallmark of RNA silencing is a class of ~22 nt RNAs which are processed from dsRNA precursor by Dicer. Accurate processing by Dicer is critical for the functionality of microRNAs (miRNAs). According to the current model, Dicer measures the length by anchoring the 3' overhang of the dsRNA terminus. Here we find that human Dicer binds to the 5' end of RNA and utilizes the 5' end as an additional reference point for cleavage site selection (5' counting rule). We further identify a novel motif (5'-pocket) in Dicer, which recognizes the 5' end of RNA. By analyzing miRNA population from 5'-pocket mutant Dicer expressing Dicer-null mES, we provide that the 5' pocket is significant for Dicer processing in vivo.

overall_design: Examination of small RNA profiles from Dicer-null mouse embryonic stem cells transfected with either wild-type or 5' pocket mutant Dice expression plasmids.

first: Jong-Eun

last: Park

first: Inha

last: Heo

first: V

middle: N


title: Gene expression after treatment with anti-miR-191 or control

first: Einat

last: Sitbon

address: 10 Plaut St

institute: Rosetta Genomics

summary:
The goal of this experiment was to identify possible genes affected directly or indirectly by anti-miR-191.
Hepatocellular carcinoma (HCC) is a fatal disease with currently very limited beneficial therapies. MicroRNAs (miRs), which are considered to be master regulators of gene expression, have significant influence on cellular pathways and phenotype, and are de-regulated in HCC, and hence are thought to be of great therapeutic potential as novel targets. We identified hsa-miR-191 as a potential target for HCC therapy. Inhibition of this miR causes decreased cell proliferation and induction of apoptosis in vitro as well as a significant reduction of tumor mass in vivo in an orthotopic liver xenograft model. This miR was also found to be up-regulated by a dioxin, a known liver carcinogen, and was found to be a key regulator of cancer related pathways.

overall_design: HCC cell line treated with anti-miR-191, and treated with negative control anti-miR. Treatment was done twice (duplicates) but in independent studies.

first: Noga

last: Yerushalmi

first: Eran

last: Elyakim


title: hsa-miR-191, a potential target for  Hepatocellular carcinoma therapy

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

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

overall_design: Refer to individual Series


title: Pneumococcal conjugate vaccination at birth induces robust recall responses at 9 months of age.

status: Public on Jun 27 2011

city: Subiaco

first: Anthony

last: Bosco

address: 100 Roberts Road

institute: Telethon Kids Institute

summary: The objective of this study was to compare recall responses to vaccine antigens at 3 months and 9 months of age in infants who were vaccinated at birth or at 1 month.

overall_design: PBMC were obtained at 9 months of age from infants who were vaccinated at birth (n=25) or 1 month (n=25). The PBMC were cultured in the presence or absence of CRM197 antigen for 72 hours. At the termination of the cultures, total RNA was extracted from the PBMC. The RNA was pooled into groups of n=5 subjects per group, following by labeling and hybridization to Affymetrix microarrays.

first: Anita

middle: H

last: van den Biggelaar

first: William

last: Pomat

first: Suparat

last: Phuanukoonnon

first: Catherine

last: Devitt

first: Marie

last: Nadal-Sims

first: Peter

last: Siba

last: Richmond

first: Deborah

last: Lehmann

first: Patrick

last: Holt


title: MiRNA expression profiles from adult mouse frontal cortex and hippocampus

status: Public on Jun 22 2011

city: Helsinki

first: Iiris

last: Hovatta

address: Haartmaninkatu 8

country: Finland

institute: University of Helsinki

summary: MicroRNAs (miRNAs) are small regulatory molecules that cause post-transcriptional gene silencing. Although some miRNAs are known to have region-specific expression patterns in the adult brain, the functional consequences of the region-specificity to the gene regulatory networks of the brain nuclei are not clear. Therefore, we studied miRNA expression patterns by miRNA-seq in two brain regions, frontal cortex (FCx) and hippocampus (HP), which have separate biological functions. We identified 354 miRNA from FCx and 408 from HP. Several miRNA families and clusters were differentially expressed between FCx and HP, including the miR-8 family, miR-182|miR-96|miR-183 cluster, and miR-212|miR-312 cluster overexpressed in FCx and miR-34 family overexpressed in HP. To visualize the clusters, we developed support for viewing genomic alignments of miRNA-seq reads in the Chipster genome browser. We carried out pathway analysis of the predicted target genes of differentially expressed miRNA families and clusters to assess their putative biological functions. Interestingly, specific pathways were identified that are predicted to be regulated by several miRNAs from the same family/cluster. We have developed a miRNA-seq approach with a bioinformatic analysis workflow that is suitable for studying miRNA expression patterns from specific brain nuclei. FCx and HP were shown to have distinct miRNA expression patterns which were reflected in the predicted gene regulatory pathways. This methodology can be applied for the identification of brain region-specific and phenotype-specific miRNA-mRNA-regulatory networks from the adult and developing rodent brain.

overall_design: miRNA-seq of 3 replicates from frontal cortex, 3 replicates from hippocampus, and pooled sequence runs from both

first: Katherine

last: Icay

first: Juuso

last: Juhila


title: Impact of miR-132 and miR-381 on endogenous forskolin responsive CREB targets in HEK293T cells

city: Philadelphia

middle: O

last: Olarerin-George

state: PA

address: 835 BRB II/III, 421 Curie Blvd

department: Pharmacology

institute: University of Pennsylvania

summary: Expression profiling of HEK293T cells transfected with miR-neg (negative control), miR-132 or miR-381 mimics and treated with forskolin for 0, 1 or 4hrs.

overall_design: HEK293T cells were reverse transfected with the respective miRNA mimics.  72hrs post-transfection, cells were treated with forskolin for 0, 1 or 4hrs.  Total RNA was then extracted.  Expression profiling was carried out with Affymetrix arrays.  Experiment was performed in duplicate.  Total of 18 samples.

first: Antonio

middle: L

last: Amelio

first: Michael

last: Conkright

first: John

middle: B

last: Hogenesch


title: Transcriptomic impact of microRNAs-449 or microRNAs-34 overexpression in proliferating human airway epithelial cells

status: Public on Jun 07 2011

city: Valbonne - Sophia-Antipolis

first: Kevin

last: Lebrigand

address: 660 route des lucioles

country: France

institute: IPMC/CNRS

summary: We used microarrays to detail the global programme of gene expression that occurs in response to miR-449 or miR-34 overexpression in proliferating HAECs.

overall_design: Each donors were transfected with pre-miR-Negative control, pre-miR-449a and pre-miR-449b. The donors 3 and 4 were morever transfected with pre-miRs-34 (34a, 34b-5p, 34c-5p).

first: B

last: Marcet

first: P

last: Barbry

first: K


title: Effect of TGF-B treatment on human vascular smooth muscle cells

status: Public on Jun 16 2011

city: New Haven

first: Amir

middle: Hossein

last: Lebastchi

state: CT

address: 10 Amistad

department: Surgery

institute: Yale University

summary: The authors did a microarray analysis to investigate the effect of TGF-B treatment on cultured smooth muscle cells from the human aorta. In particular, the authors were interested to see which cell types were upregulated or downregulated after treatment with TGF-B.

overall_design: Human Smooth muscle cells from 4 different donors in triplicates were analyzed. The cells were either untreated (n=12) or were treated with TGF-B (1 ng/ml)

first: Lingfeng

last: Qin

first: Salman

last: Khan

first: Jing

last: Zhou

first: Arnar

last: Geirsson

first: Richard

middle: W

last: Kim

first: Wie

last: Li

first: George

last: Tellides


title: Human iPSCs derived under feeder free conditions displays an unqiue cell cycle and DNA replication genotype

status: Public on Jun 03 2011

first: Henry

last: Chung

address: High St

department: Clinical Sciences Bld

institute: Prince of Wales Hospital

summary:
Induced pluripotent stem cells (iPSCs) have been generated from various somatic cells under feeder-layer conditions. These feeder-derived iPSCs generated in different labs exhibit greater variability than between different traditional embryo derived hESC lines. For that reason, it is important to develop a standard and defined system for deriving autologous patient stem cells. We have generated iPSCs under feeder-free conditions using Matrigel coated vessels in chemically defined medium, mTeSR1. These feeder-free derived iPSCs are in many ways similar to feeder-derived iPSCs and also to hESCs, with respect to their pluripotent gene expression (OCT4, NANOG, SOX2), protein expression (OCT4, NANOG, SSEA4, TRA160) and differentiation capabilities.
We conducted a whole genomic transcript analysis using Affymetrix Human Gene 1.0 ST arrays to elucidate the important differences between traditional feeder-derived iPSCs and feeder-free derived iPSCs. We reveal that feeder-free iPSCs have over-represented terms belonging to DNA replication and cell cycle genes which are lacking in feeder-derived iPSCs. Feeder-free iPSCs are in many aspects more similar to hESCs including; apoptosis, chromatin modification enzymes and mitochondrial energy metabolism. We have also identified potential biomarkers for fully reprogrammed iPSCs (FRZB) and partially reprogrammed iPSCs (POTEG, MX2) based on their expression trends across all cell types. In conclusion, feeder-free derived iPSCs is transcriptomically more similar to hESCs than feeder derived iPSCs, in many biological functions.

overall_design: For each cell sample, 2 to 3 biological replicates were obtained.

first: Ruby

last: Lin

first: Kuldip

middle: S

last: Sidhu


title: Transcriptome analysis during the time course of regeneration of the human airway mucociliary epithelium

summary:
The regeneration of the airway mucociliary epithelium involves several sequential events including migration, proliferation, polarization and final differentiation (i.e ciliogenesis).
We used microarrays to detail the global programme of gene expression that occurs during regeneration and ciliogenesis of the human airway mucociliary epithelium.

overall_design: The four time points of regeneration of the airway epithelium (ALI-D0 which corresponds to the end of proliferation step; ALI-D7 which corresponds to the polarization step; ALI-D14 which corresponds to the onset of ciliogenesis and ALI-D21 corresponding to the terminal differentiation step) for RNA extraction and hybridization on Affymetrix microarrays.

first: Brice

first: Pascal

last: LeBrigand

first: Chimène

last: Moreilhon


title: An early inflammatory gene profile in visceral adipose tissue in children

status: Public on Jun 04 2011

city: Darlinghurst

first: Mark

last: Cowley

address: 384 Victoria St.

department: Genome Informatics & Clinical Genomics

institute: Garvan Institute of Medical Research

summary: The aim of this study was to characterize expression profiles of visceral and subcutaneous adipose tissue in children. Adipose tissue samples were collected from children having elective surgery (n=71, [54 boys], 6.0 +- 4.3 years). Affymetrix microarrays (n=20) were performed to characterize the functional profile and identify genes of interest in adipose tissue. Visceral adipose tissue had an overrepresentation of Gene Ontology themes related to immune and inflammatory responses and subcutaneous adipose tissue had an overrepresentation of themes related to adipocyte growth and development. Likewise, qPCR performed in the whole cohort showed a 30-fold increase in haptoglobin (P < 0.005), 7-fold increase in IL-10 (P < 0.001), 8-fold decrease in VEGF (P < 0.01) and a 28-fold decrease in TBOX15 (P < 0.001) in visceral compared to subcutaneous adipose tissue.The inflammatory pattern in visceral adipose tissue may represent an early stage of the adverse effects of this depot, and combined with chronic obesity, may contribute to increased metabolic and cardiovascular risk.

overall_design: 20 human samples from pre-pubertal boys and girls were assessed for differences in expression between subcutaneous (n=15) and visceral fat (n=5), with 1 microarray per subject

first: Charmaine

last: Tam

first: Leonie

middle: K

last: Heilbronn

first: Corneliu

last: Henegar

first: Melanie

last: Wong

first: Christopher

middle: T

last: Cowell

first: Warren

last: Kaplan

first: Karine

last: Clément

first: Louise

last: Baur


title: mRNA Content of Human Sperm

status: Public on Jun 02 2011

city: Providence

first: Sara

last: Pacheco

state: RI

address: 70 Ship Street, Room 510

department: Pathology and Lab Medicine

institute: Brown University

summary: BACKGROUND: In previous studies using candidate gene approaches, low sperm count (oligospermia) has been associated with altered sperm mRNA content and DNA methylation in both imprinted and non-imprinted genes. We performed a genome-wide analysis of sperm DNA methylation and mRNA content to test for associations with sperm function. METHODS AND RESULTS: Sperm DNA and mRNA were isolated from 21 men with a range of semen parameters presenting to a tertiary male reproductive health clinic.  DNA methylation was measured with the Illumina Infinium array at 27,000 CpG loci.  Unsupervised clustering of methylation data differentiated the 21 sperm samples by their motility values. Recursively partitioned mixture modeling (RPMM) of methylation data resulted in four distinct methylation profiles that were significantly associated with sperm motility (P=0.01).  Linear models of microarray analysis (LIMMA) was performed based on motility and identified 9,189 CpG loci with significantly altered methylation (Q<0.05) in the low motility samples, with many loci located in genes associated with subfertility and epigenetic regulation. In the low motility samples, the majority of disrupted CpG loci (80%) were hypomethylated.  Of the aberrantly methylated CpGs, 194 were associated with imprinted genes almost equally distributed into hypermethylated (predominantly paternally expressed) and hypomethylated (predominantly maternally expressed) groups. Sperm mRNA was measured with the Human Gene 1.0 ST Affymetrix GeneChip Array. LIMMA analysis based on motility identified 20 candidate transcripts as differentially expressed in low motility sperm, including HDAC1 (NCBI 3065), SIRT3 (NCBI 23410), and DNMT3A (NCBI 1788).  Altered expression of these epigenetic regulatory genes was associated with RPMM DNA methylation class. CONCLUSIONS:  Using integrative genome-wide approaches to study epigenetic and gene expression patterns in human sperm we identified CpG methylation profiles and mRNA alterations associated with low sperm motility, and that low motility sperm may have aberrant genome-wide hypomethylation due to excess HDAC1 activity.

overall_design: See "summary" above

middle: E

first: Kim

last: Boekelheide


title: Integrative DNA methylation and gene expression analyses identify DNA packaging and epigenetic regulatory genes associated with low motility sperm

status: Public on Jun 01 2011

type:
Expression profiling by array
Methylation profiling by array

first: E

last: Houseman

first: Brock

last: Christensen

first: Carmen

last: Marsit

first: Karl

last: Kelsey

last: Sigman

last: Boekleheide


title: Expression profiling of host genes modulated by Epstein-Barr virus Rta in nasopharyngeal carcinoma cells

status: Public on May 22 2011

city: Miaoli Conunty

first: Su-Fang

last: Lin

address: No 35, Keyan Road, Zhunan Town

department: NICR

country: Taiwan

institute: National Health Research Institutes, Taiwan

summary: EBV Rta is a transcriptional activator that functions to disrupt EBV latency in cells of epithelial origin. This series of experiment is to identify host genes that are moduated by the expression of doxycycline-inducible EBV Rta in nasopharyngeal carcinoma cells. Designations for the two EBV Rta inducible cell lines are TW01TetER_cl7 (lower expression level) and TW01TetER_cl19 (higher expression level); for the control line is TW01Tet.

overall_design: All the three inducible cell lines were grown to log-phase before doxycycline induction. Same number of cells from the three cell lines were treated with doxycycline for 24 h. Total RNAs from the three samples were extracted and subjected to microarray analysis (Affymetrix Human Gene 1.0 ST Array , n=33,297). We sought to identify genes up- or down-regulated in the two doxycycline-treated EBV Rta cells, but not in the treated control cells.

first: Yen-Ju

last: Chen

first: Wan-Hua

last: Tsai

first: Yu-Lian

first: Ying-Chieh

last: Ko


title: FZD7 Plays a Critical Role in Triple Negative Breast Cancer Proliferation

city: Duarte

first: Xiwei

last: Wu

state: CA

address: 1500 E. Duarte Rd.

department: Computational and Quantitative Medicine

institute: City of Hope National Medical Center

summary: Breast cancer is genetically and clinically heterogeneous. Triple negative cancer (TNBC) is a subtype of breast cancer usually associated with poor outcome and lack of benefit from target therapy. A pathway analysis in a microarray study was performed using TNBC compared with non-triple negative breast cancer (non-TNBC). Overexpression of several Wnt pathway genes, such as frizzled homolog 7 (FZD7), Low density lipoprotein receptor-related protein 6 (LRP6) and transcription factor 7 (TCF7) has been observed in TNBC. Focus was given to the Wnt pathway receptor, FZD7. To validate its function, inhibition of FZD7 using FZD7shRNA was carried out. Notably decreased cell proliferation, suppressed invasiveness and colony formation in triple negative MDA-MB-231 and BT-20 cells were observed. Mechanism study indicated that these effects occurred through silencing the canonical Wnt signaling pathway, as evidenced by loss of nuclear accumulation of beta-catenin and decreased transcriptional activity of TCF7. In vivo study revealed that FZD7shRNA significantly suppressed the tumor formation in xenotransplation mice due to decrease cell proliferation. Our finding suggests that FZD7 involved canonical Wnt signaling pathway is essential for tumorigenesis of TNBC. Thus, FZD7 may be a biomarker and a potential therapeutic target for triple negative breast cancer.

overall_design: 14 pretreatment non-triple negative breast tumors compare with 5 triple negative breast tumor.

first: Lixin

last: Yang

first: Yun

last: Yen


title: Expression profiling of host genes modulated by Epstein-Barr virus (EBV) Rta in HEK293 cells

summary: EBV Rta is a transcriptional activator that functions to disrupt EBV latency in cells of epithelial origin. This series of experiment is to identify host genes that are moduated by the expression of doxycycline-inducible EBV Rta in HEK293 cells. Designations for the pooled EBV Rta inducible cell lines is 293TetER; pooled luciferase inducible lines is 293TetLuc (control).

overall_design: Both 293TetER and 293TetLuc cells were grown to log-phase before doxycycline induction. Same number of cells from the two cell lines were treated with doxycycline for 48 h. Experiments were performed in duplicates. Total RNAs from the four samples were extracted and subjected to microarray analysis (Affymetrix Human Gene 1.0 ST Array , n=33,297). Compared to doxycycline treated 293TetLuc, we sought to identify genes up- or down-regulated in by EBV Rta in doxycycline treated 293TetER cells..


title: Two phases of mitogenic signaling unveil roles for p53 and EGR1 in elimination of inconsistent growth signals

city: Jerusalem

first: Yotam

last: Drier

state: Israel

address: Faculty of Medicine, The Hebrew University, Ein Kerem

department: Immunology and Cancer Research

institute: The Hebrew University of Jerusalem

summary: Normal cells require continuous exposure to growth factors, in order to cross a restriction point and commit to cell cycle progression. This can be replaced by two short, appropriately spaced pulses of growth factors, where the first pulse primes a process, which is completed by the second pulse, and enables restriction point crossing. Through integration of comprehensive proteomic and transcriptomic analyses of each pulse, we identified three processes that regulate restriction point crossing: (i) The first pulse induces essential metabolic enzymes and activates p53-dependent restraining processes. (ii) The second pulse eliminates, via the PI3K/AKT pathway, the suppressive action of p53, as well as (iii) sets an ERK-EGR1 threshold mechanism, which digitizes graded external signals into an all-or-none decision obligatory for S-phase entry. Together, our findings uncover novel gating mechanisms, which ensure that cells ignore fortuitous growth factors, and undergo proliferation only in response to consistent mitogenic signals.

overall_design: 17 samples; one control sample, time zero.

first: Yaara

last: Zwang


title: Mutant thyroid hormone receptors (TRs) isolated from distinct cancer types display distinct target gene specificities: a unique regulatory repertoire associated with renal clear cell  carcinomas.

status: Public on May 10 2011

city: Houston

first: Scott

middle: Andrew

last: Ochsner

state: TX

address: One Baylor Plaza

department: Molecular and Cellular Biology

institute: Baylor College of Medicine

summary: Thyroid hormone receptors (TRs) are hormone-regulated transcription factors that regulate a diverse array of biological activities, including metabolism, homeostasis, and development.  TRs also serve as tumor suppressors, and aberrant TR function (via mutation, deletion, or altered expression) is associated with a spectrum of both neoplastic and endocrine diseases.  A particularly high frequency of TR mutations has been reported in renal clear cell carcinoma (RCCC) and in hepatocellular carcinoma (HCC). We have shown that HCC-TR mutants regulate only a fraction of the genes targeted by wild-type TRs, but have gained the ability to regulate other, unique, targets.  We have suggested that this altered gene recognition may contribute to the neoplastic phenotype.  Here, to determine the generality of this phenomenon, we examined a distinct set of TR mutants associated with RCCCs. We report that two different TR mutants, isolated from independent RCCC tumors, possess greatly expanded target gene specificities that extensively overlap one another, but only minimally overlap that of the WT-TRs, or those of two HCC-TR mutants.  Many of the genes targeted by either or both RCCC-TR mutants have been previously implicated in RCCC, and include a series of metallothioneins, solute carriers, and genes involved in glycolysis and energy metabolism.  We propose that TR mutations from RCCC and HCC are likely to play tissue-specific roles in carcinogenesis, and that the divergent target gene recognition patterns of TR mutants isolated from the two different types of tumors arises from different selective pressures during development of RCCC versus HCC.

overall_design: Gene expression was analyzed in HepG2 transformants expressing ectopic wildtype THRA, wildtype THRB, HCC-TR mutants αΙ and βN, and RCCC-TR mutants 6α and 15β using Affymetrix Human Gene 1.0 ST arrays in the presence or absence of T3.  Each HepG2 transformant was assayed in triplicate.

first: Meghan

last: Rosen

first: Ivan

last: Chan

first: Martin

last: Privalsky


title: Gene expression profiles based on Pulmonary Artery Pressures in Pulmonary Fibrosis

city: Toronto

first: Marco

last: Mura

state: Ontario

address: 585 University Avenue

department: Medicine/Surgery

country: Canada

institute: Toronto Lung Transplant Program

summary:
Pulmonary Hypertension (PH) is a frequent complication of Pulmonary Fibrosis (PF). PH can be seen in PF in the abscence of hypoxemia, irrespective of the degree of fibrosis. At the same time, a consistent number of patients with advanced PF never develop PH. The pathogenesis of PH secondary to PF remains unclear. PF patients are often referred to lung transplantation, but they present a higher incidence of pimary graft dysfunction than other diseases. The cause of this is unknown, and the relationship with PH remains unclear.
We used microarray to identifiy the gene expression profiles in PF patients with and without PH

overall_design: Fresh frozen lung samples were obtained from the recipients organs of 116  PF patients undergoing lung transplantation. RNA was extracted and hybridized on Affymetrix microarrays. Pulmonary artery pressures were recorded intraoperatively with right heart catheters before starting lung transplantation. Patients were divided in different groups based on the mean pulmonary artery pressure. We compared the gene expression profiles in the group with severe PH (mPAP>40 mmHg, n=17) and in that without PH (mPAP<20 mmHg, n=22)) and obtained a gene signature, which was used for clusterying analysis. The clustering analysis based on the gene signature was then validated in an Intermediate PH group (mPAP 21-39 mmHg, n=45) and in a Validation Set (n=32).

first: Marc

last: De Perrot


title: Gene expression profiles after knockdown of Nardilysin in TMK-1 gastric cancer cells

status: Public on May 16 2011

city: Kyoto

first: Hideyuki

last: Komekado

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

department: Gastroenterology and Hepatology

country: Japan

institute: Graduate School of Medicine, Kyoto University

summary:
Nardilysin (NRDc), a metalloendopeptidase of the M16 family, has been reported to promote the ectodomain shedding and resulting activation of various growth factors and cytokines, but its role in cancer biology have not been elucidated.
Microarray experiments were performed to analyze the chnages of gene expression profiles after knockdown of NRDc by microRNA (miR)-based RNA interference (RNAi).

overall_design: RNAi experiments were perfomed using BLOCK-iT Pol II miR RNAi Expression Vector Kit with EmGFP (Invitrogen).  TMK-1 cells stably expressing conrol or NRDc-targeting miR vector were established.

first: Keitaro

last: Kanda

first: Hiroshi

last: Seno

first: Eiichiro

last: Nishi


title: Controlled ErbB receptor dimerization

status: Public on May 13 2011

city: Nashville

first: Ritwik

last: Ghosh

state: TN

address: 2220 Pierce Avenue, 777 PRB

institute: Vanderbilt University

summary:
In order to better understand signaling events following receptor dimerization involving HER2, we have generated an experimental system in which ErbB dimerization can be controlled.
We used gene expression microarrays to identify genes and pathways that are differentially activated by HER2 homodimers and HER2 containing heterodimers.

overall_design: MCF10A-HER2-FKBP-HA cells were treated with AP1510, TGFalpha or heregulin for 48 hrs prior to RNA harvest for array analysis.

first: Carlos

last: Arteaga

first: Justin

middle: M

last: Balko


title: Comparing Control and Schizophrenic hiPSC-derived Neurons

status: Public on May 01 2011

city: New York

first: Kristen

last: Brennand

address: 1425 Madison Ave, 9-20B

department: Psychiatry

institute: Icahn School of Medicine at Mount Sinai

summary: Schizophrenia is a debilitating neurological disorder for which no cure exists. Few defining characteristics of schizophrenic neurons have been identified and the molecular mechanisms responsible for schizophrenia are not well understood, in part due to the lack of patient material for study. Human induced pluripotent stem cells (hiPSCs) offer a new strategy for studying schizophrenia. We have created the first cell-based human model of a complex genetic psychiatric disease by generating hiPSCs from schizophrenic patients and subsequently differentiating these cells to hiPSC-derived neurons in vitro. Schizophrenic hiPSC-derived neurons showed diminished neuronal connectivity in conjunction with decreased neurite number, PSD95-protein levels and glutamate receptor expression. Gene expression profiles of schizophrenic hiPSC-derived neurons identified altered expression of many components of the cAMP and WNT signaling pathways. Key cellular and molecular elements of the schizophrenic phenotype were ameliorated following treatment of schizophrenic hiPSC-derived neurons with the antipsychotic loxapine.

overall_design: 3 independent differentiations (biological replicates) for each of four control and four schizophrenic patients were analyzed.

first: Fred

last: Gage

middle: J


title: Gene expression profiling of low-grade fibromyxoid sarcoma (LGFMS)

status: Public on May 02 2011

city: Lund

first: Emely

last: Möller

address: Lund University Hospital

department: Clinical Genetics

country: Sweden

institute: Lund University

summary:
Analysis of gene expression in 17 low-grade fibromyxoid sarcoma (LGFMS) samples compared to that of histologically similar tumors. LGFMS is characterized by the specific translocations t(7;16)(q33;p11) or t(11;16)(p11;p11) and corresponding fusion genes FUS-CREB3L2 or FUS-CREB3L1.
The results identifies a LGFMS-specific gene expression profile and provide insight into FUS-CREB3L2 regulated gene expression.

overall_design: RNA was extracted from 17 LGFMS tumor biopsies and hybridized to Affymetrix arrays. RNA from 6 myxofibrosarcoma (MFS), 6 desmoid fibromatosis (DFM), 5 solitary fibrous tumor (SFT) and 6 extraskeletal myxoid chondrosarcoma (EMCS) tumor biopsies was used as comparison. Two pools of skeletal muscle RNA was also included in the comparison.

first: Jason

last: Hornick

first: Linda

last: Magnusson

first: Srinivas

last: Veerla

first: Henryk

last: Domanski

first: Fredrik

last: Mertens


title: Gene expression pattern of skin biopsies of epidermolysis bullosa simplex patients in comparison with control subjects

status: Public on Apr 02 2011

city: Chicoutimi

first: Catherine

last: Laprise

state: Qc

address: 555 Boul. Université

institute: Université du Québec à Chicoutimi

summary: Tha altered biological pathways in Epidermolysis bulloda simplex, a rare monogenetic skin disease, have not been well characterized. Thus, the goal of this study is to characterize the expression profile of EBS patients compared with normal subjects using genomic expression analyses. Microarray analyses were performed with RNA isolated from skin biopsies. Robust multiarray analysis (RMA) normalization and Smyth’s moderated t test were used to select differentially expressed genes. Expression profiling comparisons show that 28 genes are differentially expressed in EBS patients compared to control subjects and 41 genes in EBS-DM compared to their matched controls. Nine genes involved in fatty acid metabolism and 2 genes in epidermal keratinisation are common altered expressed genes between the two subgroups. These two biological pathways contribute both to the formation of the cell envelope barrier and seem to be defective in the severe EBS phenotype. This study demonstrates, for the first time, the relevance of metabolic cluster, specifically fatty acid metabolism in EBS biology. Difference of expression for three (AWAT2, ELOVL , and SPRR4 ) of the five selected genes were validated using real-time reverse transcription–polymerase chain reaction. To our knowledge, the distinctive pattern of gene expression that characterizes EBS versus healthy skin tissue has never been reported.

overall_design: RNA used for the microarrays analysis was isolated from superficial 2mm punch biopsies composed of mainly epidermis with minimal dermis amounts of normal-appearing skin of six EBS patients ( two females and four males) and six healthy volunteers.

first: Mbarka

last: Bchetnia

first: Marie-Lou

last: Tremblay

first: Georgette

last: Leclerc

first: Audrey

last: Dupérée

first: Julie

last: Powell

last: McCuaig

first: Charles

last: Morin

first: Valérie

last: Legendre-Guillemin


title: Site-specific heterogeneity of melanocytes in human skin

city: Nagoya

first: Motoki

last: Nakamura

address: 1-Kawasumi, Mizuho-cho, Mizuho-ku

department: Nagoya City University

institute: Department of Geriatric and Environmental Dermatology

summary: Little is known about the mechanisms underlying the localization of human melanocytes during embryogenesis, and how the characteristics of melanocytes differ in various body sites. Immunohistochemical studies of biopsy tissue obtained from four different anatomic sites (scalp, back, abdomen, and sole) of 31 aborted fetuses following the approval of the ethics committee for the study of human gene analysis revealed that the melanocyte-associated marker gp100 was expressed earlier in embryogenesis than other melanocyte markers. Human fetal melanocytes are initially localized in the epidermis, and then migrate to the hair buds from the epidermis but not the dermis. In the sole, melanocytes localize in eccrine sweat gland ducts. Cultured fetal melanocytes did not stain positively for any melanocyte markers other than MITF and nestin. When co-cultured with normal human keratinocytes and fibroblasts, fetal melanocytes stained positively for gp100. Gene expression studies indicated that fetal melanocytes were topographically diverse, especially sole-derived melanocytes compared with other melanocytes. Expression of several genes, including CHI3L1 and FGF7, was higher in sole-derived melanocytes. These findings suggest that human fetal melanocytes derived from the sole have different profiles both in vivo and in vitro compared with melanocytes from other sites.

overall_design: In this study, microarray analyses were performed using cultured fetal melanocytes from 4 different sites (scalp, back, abdomen and sole) obtained at 19WG(case27), 13WG(case29), 17WG(case30) and newborn normal epidermal melanocyte as a control.  RNA purification was performed using an RNeasy Mini kit (Qiagen, Germany) and those 5 samples, were analyzed using GeneChip 1.0 ST Array (Affymetrix, CA, USA).

first: Mizuho

last: Fukunaga-Kalabis

first: Yuji

last: Yamaguchi

first: Takuya

last: Furuhashi

first: Emi

last: Nishida

first: Hiroshi

last: Kato

first: Toshihiko

last: Mizuno

first: Mayumi

last: Sugiura

first: Akimichi

last: Morita


title: Expression Profiling of Inflammatory Breast Cancer Cells Treated with the Novel Histone Deacetylase Inhibitor, CG-1521

status: Public on Apr 12 2011

city: Rensselaer

first: Sridar

middle: V

last: Chittur

address: One Discovery Drive, CRC 342G

department: Center for Functional Genomics

institute: SUNY-University at Albany

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

overall_design: Refer to individual Series


title: Microarray-based identification of age-dependent differences in gene expression of human dermal fibroblasts

status: Public on Apr 01 2011

first: Andrea

last: Maier

address: postbox 9600

country: Netherlands

institute: LUMC

summary: Gene expression approach to differences in stress response between human skin fibroblasts derived from chronologically young (~20 years) and old (~90 years) subjects. Expression of CDKN2A was most different between fibroblasts from young and old subjects and

overall_design: Human skin fibroblasts were isolated from skin biopsies of 6 young subjects and 6 old subjects and were treated for 3 hours and 3 days with 0.6 uM rotenone. Also there were control samples, not treated but grown for 3 days, making a total of 36 samples. No experimental replicates were included. The expression of CDKN2A  was quantified in the same RNA samples by real-time PCR.

first: Pim

last: Dekker

first: David

last: Gunn

first: Tony

last: McBryan

first: Peter

last: Adams


title: Passing the anaerobic threshold is associated with substantial changes in the gene expression profile in white blood cells

status: Public on Apr 09 2011

city: Moscow

first: Evgeniy

last: Riabenko

address: Elizavetinskiy per., 10

country: Russia

institute: VNIIFK

summary: High and moderate intensity endurance exercise alters gene expression in human white blood cells (WBCs), but the understanding of how this effect occurs is limited. To increase our knowledge of the nature of this process, we investigated the effects of passing the anaerobic threshold (AnT) on the gene expression profile in WBCs of athletes. Nineteen highly trained skiers participated in a treadmill test with an incremental step protocol until exhaustion (ramp test to exhaustion; RTE). The average total time to exhaustion was 14:40 min and time after AnT was 4:50 min. Two weeks later, seven of these skiers participated in a moderate treadmill test (MT) at 80% peak O2 uptake for 30 min, which was slightly below their AnTs. Blood samples were obtained before and immediately after both tests. RTE was associated with substantially greater leukocytosis and acidosis than MT. Gene expression in WBCs was measured using whole genome microarray expression analysis before and immediately after each test. A total of 310 upregulated genes were found after RTE, and 69 genes after MT, of which 64 were identical to RTE. Both tests influenced a variety of known gene pathways related to inflammation, stress response, signal transduction and apoptosis. A large group of differentially expressed, and previously unknown, small nucleolar RNA and small Cajal body RNA was found. In conclusion, a 15 min test to exhaustion was associated with substantially greater changes of gene expression than a 30 min test just below the AnT.

overall_design: After a general medical checkup, the subjects performed a ramp-type progressive exercise test on a treadmill. Blood samples were taken from the antecubital vein using indwelling catheter before (T0) and immediately after ramp test to exaustion (T1), and before (T2) and immediately after moderate treadmill test (T3).

first: Dmitry

middle: A

last: Sakharov

first: Diana

last: Maltseva

first: Anatoly

middle: I

last: Grigoriev

first: Alexander

last: Tonevitsky


title: Expression Profiling of Inflammatory Breast Cancer Cells Treated with the Novel Histone Deacetylase Inhibitor, CG-1521 (Affymetrix HuGene-1_0)

summary: Studies of gene expression profiles using the whole genome wide microarray analysis in SUM149PT cells (ER-, p53mut) and SUM190PT cells (ER-, p53mut) when treated with 5 or 7.5 µM CG-1521 alone and in combination with 10 nM 17β-Estradiol. Comparisons between each treatment group provides evidence for the dysregulation of genes associated with the spindle assembly checkpoint.

overall_design: Three independent experiments were carried out in SUM149PT and SUM190PT cells, which were treated with vehicle (ethanol/DMSO), 10nM 17β-Estradiol, 5 or 7.5µM CG-1521, and the combination of 17β-Estradiol and CG-1521. Total RNA was extracted from cell lysates using QIAGEN RNeasy mini kit after 48h of treatment.

first: Martin

last: Tenniswood

first: Namita

last: Chatterjee


title: Peripheral blood cells expression data form 7 patients with severe pdm(H1N1) influensa and 7 gender and age matched healthy controls

city: Lørenskog

first: Jan-Erik

last: Berdal

state: Akershus

address: Sykehusvn.

department: medical department

country: Norway

institute: AHUS

summary:
Using PAXgene tubes, peripheral blood samples were collected  from seven patients >18 years with documented pdm(H1N1) influenza, bilateral chest infiltrates, and in need of ventilation support. Significant co-morbidity was exclusion criterion. Expression profiles were compared with 7 age matched controls. Using  a false discovery rate < 5% and  an absolute fold change > 2, 370 genes  were differentially expressed in case and controls.
A second sample was collected after ca 6 days in the 7 patients and temporal changes in expression profiles investigated. Over expressed putative mediators of inflammatory lung dammage were measured on the protein level.

overall_design: 14 patient samples (7 paired samples) and 7 control samples were performed.

first: Ole

last: Olstad

first: Christine

last: Jonassen


title: Expression data from BJ-hTERT cells  expressing vector, Cyclin E, c-Myc or coexpression of both

status: Public on Mar 31 2011

first: Batsheva

last: kerem

address: Edmond Safra Campus

department: Department of Genetics

summary:
Chromosomal instability in early cancer stages is caused by stress on DNA replication. The molecular basis for replication perturbation in this context is currently unknown. We studied the replication dynamics in cells in which a regulator of S-phase entry and cell proliferation, the Rb-E2F pathway, is aberrantly activated.  Aberrant activation of this pathway by HPV-16 E6/E7 or cyclin E oncogenes, significantly decreased the cellular nucleotide levels in the newly transformed cells. Exogenously supplied nucleosides rescued the replication stress and DNA damage, and dramatically decreased oncogene-induced transformation. Increased transcription of nucleotide biosynthesis genes, mediated by expressing the transcription factor c-Myc, increased the nucleotide pool and also rescued the replication-induced DNA damage. Our results suggest a model for early oncogenesis in which uncoordinated activation of factors regulating cell proliferation leads to insufficient nucleotides that fail to support normal replication and genome stability.
In order to understand the molecular basis for the low nucleotide pool in cells enforced to proliferate by oncogene expression, we performed unbiased whole transcriptome analysis of BJ cells in comparison to BJ cells expressing cyclin E, c-Myc and cells co-expressing both oncogenes.  Our results suggest that Rb-E2F aberrant activation enforces cell proliferation but fails to activate the nucleotide biosynthesis pathway leading to insufficient pool of nucleotides required for normal replication.

overall_design: We analyzed two sets of BJ cells infected with empty pBabe, Cyclin E, c-Myc or coexpression of Cyclin E and c-Myc

last: Kerem

first: Assaf

last: Bester


title: Non-phosphorylated FTY720 induces apoptosis of human microglia by activating SREBP2

status: Public on Apr 16 2011

city: Tokyo

first: Jun-ichi

last: Satoh

address: 2-522-1 Noshio, Kiyose

department: Bioinformatics

institute: Meiji Pharmaceutical University

summary: A synthetic analog of sphingosine named FTY720 (Fingolimod), phosphorylated by sphingosine kinase-2, interacts with sphingosine-1-phosphate (S1P) receptors expressed on various cells. FTY720 suppresses the disease activity of multiple sclerosis (MS) chiefly by inhibiting S1P-dependent egress of autoreactive T lymphocytes from secondary lymphoid organs, and possibly by exerting anti-inflammmatory and neuroprotective effects directly on brain cells. However, at present, biological effects of FTY720 on human microglia are largely unknown. We studied FTY720-mediated apoptosis of a human microglia cell line HMO6. The exposure of HMO6 cells to non-phosphorylated FTY720 (FTY720-non-P) induced apoptosis in a dose-dependent manner with IC50 of 10.6±2.0 microM, accompanied by the cleavage of caspase-7 and caspase-3 but not of caspase-9. The apoptosis was inhibited by Z-DQMD-FMK, a caspase-3 inhibitor, but not by Pertussis toxin, a Gi protein inhibitor, suramin, a S1P3/S1P5 inhibitor, or W123, a S1P1 competitive antagonist, although HMO6 expressed S1P1, S1P2, and S1P3. Furthermore, both phosphorylated FTY720 (FTY720-P) and SEW2871, a S1P1 selective agonist did not induce apoptosis of HMO6. Genome-wide gene expression profiling and molecular network analysis indicated activation of transcriptional regulation by sterol regulatory element-binding protein (SREBP) in FTY720-non-P-treated HMO6 cells. Western blot verified activation of SREBP2 in these cells, and apoptosis was enhanced by pretreatment with simvastatin, an activator of SREBP2, and by overexpression of the N-terminal fragment of SREBP2. These observations suggest that FTY720-non-P-induced apoptosis of HMO6 human microglia is independent of S1P receptor binding, and positively regulated by the SREBP2-dependent proapoptotic signaling pathway.

overall_design: The HMO6 cell line was established by immortalizing cultured microglia isolated from human embryonic telencephalon tissues with a retroviral vector PASK1.2 encoding v-myc oncogene (Nagai et al. Neurobiol. Dis. 8: 1057-1068, 2001). HMO6 cells express the markers of the microglia/macrophage lineage cells, including CD11b, CD68, CD86, HLA-ABC, HLA-DR, and ricinus communis agglutinin lectin-1 (RCA), serving as a model of human microglia both in vitro and in vivo. The cells were exposed for 2 hours to 10 microM FTY720-non-P dissolved in dimethyl sulfoxide (DMSO) or ethanol or exposed to the vehicle.

first: Hiroko

last: Tabunoki


title: Epstein–Barr virus (EBV) Rta-mediated cell cycle arrest enables permissive replication of EBV and Kaposi’s sarcoma-associated herpesvirus in 293 cells

first: Su-Fang

last: Lin

address: No 35, Keyan Road, Zhunan Town

summary:
Epstein-Barr virus (EBV) Rta is a latent-lytic molecular switch evolutionarily conserved in all gamma-herpesviruses. In previous studies, doxycycline-inducible Rta was shown to potently produce an irreversible G1 arrest followed by cellular senescence in 293 cells. Here, we demonstrate that in this system the inducible Rta not only reactivates resident genome of EBV but also that of Kaposi’s sarcoma-associated herpesvirus (KSHV), to similar efficiency. However, Rta-induced senescence program was terminated by the robust viral lytic cycle replication that eventually caused cell death. Furthermore, prior to the abrupt expression of immediate-early protein (EBV BZLF1 or KSHV RTA), Rta simultaneously down-regulates cell cycle activators (c-Myc, CDK6, CCND2) and up-regulates senescence-related genes (p21, 14-3-3s). Since Rta is a viral immediate-early transcriptional activator, it is envisioned that during the initial stage of viral reactivation, Rta may engage to modulate the host transcriptome, to halt cell cycle progression, and to maintain an ideal environment for manufacturing infectious virions.

This SuperSeries is composed of the SubSeries listed below.

overall_design: Refer to individual Series.

first: Yen-Ju

last: Chen

first: Wan-Hua

last: Tsai

first: Yu-Lian

first: Ying-Chieh

last: Ko


title: Gene expression profiling of human DLBCL tumor samples (FF and FFPE pairs)

status: Public on Mar 16 2011

city: South San Francisco

first: Peng

last: Yue

address: 1 DNA Way

institute: Genentech Inc

summary:
We profiled human DLBCL tumor samples (FF and FFPE matched pairs) to identify the transcripts which are less prone to degradation in FFPE
Keywords: DLBCL FF FFPE

overall_design: RNA profiles of human FF and FFPE samples (DLBCL)

first: David

last: Dornan


title: Gene expression profiling of human DLBCL tumor samples (SGN-40 trial)

summary:
We profiled human DLBCL patient samples to discover predictive biomarkers
Keywords: DLBCL SGN-40 FFPE

overall_design: RNA profiles of human FFPE samples (DLBCL)


title: Expression data of HepG2C3A treated by acetaminophen during 72 hours

status: Public on Mar 14 2011

city: 91400 Orsay

first: Florent

last: Dumont

state: Ile de France

address: 17 avenue des sciences

institute: Université Paris-Saclay

summary:
Evaluation of acetaminophen treatment on Hepatic cell line cultivated in conventionnal method and in a new cell culture device (microfluidic biochip)
The aim of this study is to understand the transcriptomic responses of cells cultivated in a microsystem by comparison to conventionnal culture method. As a pharmacological example, we choose to used a well known hepatotoxicant : acetaminophen to illustrate the potential of our microsystem.

overall_design: 12 samples were analysed corresponding of 4 conditions : 3 replicates cell control in microsystem, 3 replicates cell treated in microsystem, 3 replicates cell control in Petri, 3 replicates cell treated in Petri cultivated during 96 hours including 72 hours of treatment

first: Jean-Mathieu

last: Prot


title: Crosstalk between gene body DNA methylation, H3K9me3 and H3K36me3 chromatin marks and transcription [HuGene-1_0-st]

first: Xiwei

last: Wu

address: 1500 E. Duarte Rd.

institute: City of Hope National Medical Center

summary: This is one of expressional parts of the study. These data were correlated to epigenetic marks and CG density of genes in analyzed cells. The whole study has a following summary: To elucidate possible roles of DNA methylation and chromatin marks in transcription, we performed epigenetic profiling of chromosome 19 in human bronchial epithelial cells (HBEC) and in the colorectal cancer cell line HCT116 as well as its counterpart with double knockout of DNMT1 and DNMT3B (HCT116-DKO). We found that H3K9me3 forms intragenic chromatin blocks along genes with low CpG density in the gene body. Analysis of H3K36me3 profiles indicated that this mark associates either with active genes with low CpG density and H3K9me3 in the gene body or with active genes with high CpG density and DNA hypermethylation in the gene body. In HCT116 cells with double knockout of DNMT1 and DNMT3B, transcription of genes with low CpG density in the gene body was highly elevated and associated with promoter DNA demethylation and rearrangement of H3K9me3 and H3K36me3 occupation. Our finding suggests that similar to DNA methylation, H3K9me3 may play a role in intragenic gene regulation. Further, we observed that a combination of low CpG density in gene bodies together with H3K9me3 and H3K36me3 marking is a specific epigenetic feature of zinc finger (ZNF) genes, which comprise 90% of all genes carrying both histone marks on chromosome 19. For high CpG density genes, transcription and H3K36me3 occupancy were not changed in condition of partial or intensive loss of DNA methylation in gene bodies in the HCT116-DKO cell line. siRNA experiments with SETD2 knockdown in both HBEC and HCT116-DKO cell lines failed to reduce DNA methylation in gene bodies under conditions of H3K36me3 depletion. Our study suggests that the H3K36me3 and DNA methylation marks in gene bodies are established independently from each other and points to similar functional roles of intragenic DNA methylation and intragenic H3K9me3 for CpG-rich and CpG-poor genes, respectively.

overall_design: Expression profile of human bronchial epithelia cells (HBEC) immortalized with hTERT and CDK4. To elucidate possible roles of DNA methylation and chromatin marks in transcription, we performed epigenetic profiling of chromosome 19 in human bronchial epithelial cells (HBEC) and analyzed gene expression by Affymetrix expression arrays in these cells. This is the expressional part of study.

first: Maria

last: Hahn

first: Arthur

middle: X

last: Li

first: Torsten

first: Gerd

middle: P

last: Pfeifer


title: Expression data from human periodontal ligament

status: Public on Mar 17 2011

city: Göttingen

first: Nicolai

last: Miosge

address: Robert-Koch-Str. 40

department: Prothetik, Oral biology and Tissue regeneration

country: Germany

institute: University Göttingen

summary: We used microarrays to detect the differences in gene-expression of the periontal ligament  between patients with healthy periodontal ligament and patients with periodontitis

overall_design: RNA was extracted directly from the middle third of the human periodontal ligament


title: Attenuation of EIF4E Translation Initiation Adversely Affects Multiple Myeloma Cells

status: Public on Mar 11 2011

city: Tel Aviv

first: Metsada

last: Pasmanik-Chor

address: Ramat Aviv

department: Biology

country: Israel

institute: Tel Aviv University

summary:
This work explores the therapeutic potential for the translation initiation factor eIF4E in multiple myeloma (MM). We show that targeting eIF4E is deleterious to MM cells and causes reduction of targets with established importance to the disease progression. We demonstrate that eIF4E inhibition may be achieved by treating the MM cells with the already clinically employed anti-viral drug Ribavirin.
Results indicate that tetraspanin overexpression in MM cell lines increased global protein synthesis; CD81N1/CD82N1 also caused a decrease in peIF4E, its regulators and targets; direct inhibition of eIF4E (siRNA, Ribavirin) deleteriously affected MM cell lines; and Ribavirin attenuated viability and induced death of primary BM MM cells.

overall_design: Multiple Myeloma cell lines RPMI 8226 and CAG were each transiently transfected with purified plasmids of tetraspanins: pEGFP-N1 (N1, control), CD81N1-eGFP (81N1) or CD82N1-eGFP (82N1) (Clontech). Transfected cells were separated by Sorter Flow Cytometer 24 hours after transfection. Total RNA was extracted from sorted transfected cells with the Qiagen kit. Three separate experiments were analyzed by Whole Genome Affymetrix microarray chips (N1, 81N1, 82N1 in each cell line).

first: Victoria

last: Zismanov

first: Liat

last: Drucker

first: Oshrat

last: Attar-Schneider

first: Rachel

last: Heffez-Aizenfeld

first: Shelly

last: Tartakover-Matalon

first: Michael

last: Lishner


title: ChIP-seq analysis reveals distinct H3K27me3 profiles associated with gene regulation [ChIP-seq]

status: Public on Mar 21 2011

city: Parkville

first: Matthew

middle: Daniel

last: Young

state: Victoria

address: 1G Royal Parade

institute: Walter & Eliza Hall Institute of Medical Research

type: Genome binding/occupancy profiling by high throughput sequencing

summary: Transcriptional control is dependent on a vast network of epigenetic modifications.  One epigenetic mark of particular interest is tri-methylation of lysine 27 on histone H3 (H3K27me3), which is catalyzed and maintained by the Polycomb Repressor Complex (PRC2).  Although this histone mark is studied widely, the precise relationship between its local pattern of enrichment and regulation of gene expression is currently unclear.  We have used ChIP-seq to generate genome wide maps of H3K27me3 enrichment, and have identified three enrichment profiles with distinct regulatory consequences. First, a broad domain of H3K27me3 enrichment across the body of genes corresponds to the canonical view of H3K27me3 as inhibitory to transcription.  Second, a peak of enrichment around the transcription start site is commonly associated with âbivalentâ genes, where H3K4me3 also marks the TSS.  Finally and most surprisingly, we identified an enrichment profile with a peak in the promoter of genes that is associated with active transcription. Genes with each of these three profiles were found in different proportions in each of the cell types studied.  The data analysis techniques developed here will be useful for the identification of common enrichment profiles for other histone modifications that have important consequences for transcriptional regulation.

overall_design: Genomic DNA was extracted from ES cells and G1ME cells in mouse.  ChIP-seq with antibodies for H3K27me3, RNApol-II were run for both cell types.  As a control, whole cell extract or Input DNA was also sequenced for both cell types without the inclusion of an antibody.

middle: D


title: Expression profiles of PBMC from multiple sclerosis patients

status: Public on Mar 01 2011

first: Fanglin

last: Zhang

address: 2201 Childrens' way

summary:
Affymetrix GeneChip Human Gene 1.0 ST Array was applied to compare the expression profiles in peripheral blood mononuclear cells(PBMC) between  healthy controls and  multiple sclerosis patients(MS pt).
It suggested that certain genes involved in apoptosis pathway have been changed regulated in PBMC from MS pt.

overall_design: Applying Affymetrix GeneChip Human Gene 1.0 ST Array and the mixed effects model for gene set analysis, we compared gene expression profiles between 8 multiple sclerosis (MS) patients and 4 healthy controls (HC).

first: Subramaniam

last: Sriram


title: Combination of peripheral blood gene expression profiles and clinical parameters predicts response for tocilizumab (anti-IL6) treatment in rheumatoid arthritis

city: Debrecen

first: Bertalan

last: Mesko

address: Egyetem tér 1.

department: Department of Biochemistry and Molecular Biology

country: Hungary

institute: University of Debrecen

summary: We used microarrays to identify markers predicting responder status in tocilizumab treatment in rheumatoid arthritis in 13 patients at week 0 and week 4 of treatment.

overall_design: Peripheral blood samples were obtained at week 0 and week 4 of tocilizumab treatment and global gene expression profiling identified markers of responder status.

first: Szilard

last: Poliska

first: Szilvia

last: Szamosi

first: Zoltan

last: Szekanecz

first: Janos

last: Podani

first: Laszlo

last: Nagy


title: Evaluation of differential gene expression in patients with amyotrophic lateral sclerosis (ALS)

status: Public on Feb 26 2011

first: soon gang

last: choi

address: 1468 Madison Avenue

department: Neurology

institute: Mount Sinai School of Medicine

summary: We compared gene expression profiles of ALS patients with normal patients and with multifocal motor neuropathy (MMN) patients.

overall_design: Skeletal muscle specimens from 3 ALS patients, 3 MMN patients, and 3 control patients were used to find disease markers specifically expressed in ASL and MMN patients.

first: Alexander

last: Shtilbans

first: Soon-Gang

last: Choi

first: Mary

last: Fowkes

first: Greg

last: Khitrov

first: Mona

last: Shahbazi

first: Jess

last: Ting

first: Weijia

first: Yezhou

last: Sun

first: Stuart

last: Sealfon

first: Dale

last: Lange


title: Expression data from BIO-treated human epidermal keratinocytes

status: Public on Feb 24 2011

city: Taichung

first: Hong-Lin

last: Su

address: 250, Kuo-Kuang Rd

institute: National Chung-Hsing University

summary:
Human keratinocytes isolated from foreskin were cultured and treated with a GSK-3beta inhibitor, BIO. The effect of BIO was evaluated by the cell growth, clony formation and differentiating markers.
We used microarrays to detail the global program of gene expression underlying cellularisation and identified distinct classes of up-regulated genes during this process.

overall_design: Human primary keratinocytes were subjected for RNA extraction. The total RNAs were hybridized on Affymetrix microarrays. The cultured cells exhibit a homogous cell morphology at passage 1 to passage 5. The cells were treated with BIO at passage 3 or 4.

first: Hong

middle: L

first: Jing

last: Shen


title: Integrated Genomics of Ovarian Xenograft Tumor Progression and Chemotherapy Response

city: PROVIDENCE

last: Brodsky

address: 593 Eddy St.

department: MCB

institute: Rhode Island Hospital/Brown University

summary: Xenograft ovarian tumors are useful model to test therapeutic candidates in vivo. We used microarrays to gain insight into the expression changes during tumor growth and induced by the vitamin D analog, MT19C at multiple time points.

overall_design: SKOV-3 cells were grown in 10% FBS/DMEM before injection into mice. Total RNA was collected using standard methods.


title: Host cell transcriptome response to expression of the human cytomegalovirus (hCMV) 72-kDa immediate-early 1 (IE1) protein

status: Public on Feb 12 2011

city: Regensburg

first: Michael

last: Nevels

address: Franz-Josef-Strauss-Allee 11

department: Medical Microbiology

institute: University of Regensburg

summary: Human cytomegalovirus (hCMV) is a highly prevalent pathogen that, upon primary infection, establishes life-long persistence in all infected individuals. Acute hCMV infections cause a variety of diseases in humans with developmental or acquired immune deficits. In addition, persistent hCMV infection may contribute to various chronic disease conditions even in immunologically normal people. The pathogenesis of hCMV disease has been frequently linked to inflammatory host immune responses triggered by virus-infected cells. Moreover, hCMV infection activates numerous host genes many of which encode pro-inflammatory proteins. However, little is known about the relative contributions of individual viral gene products to these changes in cellular transcription. We systematically analyzed the effects of the hCMV 72-kDa immediate-early 1 (IE1) protein, a major transcriptional activator and antagonist of type I interferon (IFN) signaling, on the human transcriptome. Following expression under conditions closely mimicking the situation during productive infection, IE1 elicits a global type II IFN-like host cell response. This response is dominated by the selective up-regulation of immune stimulatory genes normally controlled by IFN-gamma and includes the synthesis and secretion of pro-inflammatory chemokines. IE1-mediated induction of IFN-stimulated genes strictly depends on tyrosine-phosphorylated signal transducer and activator of transcription 1 (STAT1) and correlates with the nuclear accumulation and sequence-specific binding of STAT1 to IFN-gamma-responsive promoters. However, neither synthesis nor secretion of IFN-gamma or other IFNs seems to be required for the IE1-dependent effects on cellular gene expression. Our results demonstrate that a single hCMV protein can trigger a pro-inflammatory host transcriptional response via an unexpected STAT1-dependent but IFN-independent mechanism and identify IE1 as a candidate determinant of hCMV pathogenicity.

overall_design: We used a total of 18 microarrays for analyzing triplicate samples each of IE1-negative control fibroblasts (TetR cells) without induction (3 arrays), fibroblasts containing inducible IE1 (TetR-IE1 cells) without induction (3 arrays), TetR cells induced for 24 h (3 arrays), TetR-IE1 cells induced for 24 h (3 arrays), TetR cells induced for 72 h (3 arrays), and TetR-IE1 cells induced for 72 h (3 arrays)

first: Theresa

last: Knoblach

first: Benedikt

last: Grandel

first: Jana

last: Seiler

first: Christina

last: Paulus


title: Gene expression of VPA and GEM

status: Public on Feb 09 2011

city: Tokushima

first: Shuichi

last: Iwahashi

address: Kuramoto 3-18-15

department: Department of Surgery

institute: Institute of Health Biosciences, The University of Tokushima Graduate School

summary: Background: Histone deacetylase (HDAC) is strongly associated with epigenetic regulation and carcinogenesis, and its inhibitors induce the differentiation or apoptosis of cancer cells. Valproic acid (VPA) is one of the clinically available HDAC inhibitors. We investigated the anticancer effects of VPA in combination with gemcitabine (GEM) in cholangiocarcinoma cell line, and explored the mechanisms of the anticancer effects using microarray analysis. Methods: A human cholangiocarcinoma cell line (HuCCT1) was used. The anticancer effects of VPA, or gemcitabine (GEM), and the effects of VPA combined with GEM, were studied by cell proliferation assay. The microarray analysis was performed, the genes were picked up using Gene Spring GX11.5, Ingenuity Pathways Analysis (IPA) was performed, and then the gene-expression was determined by RT-PCR. Results: GEM (5nM) and VPA (0.5mM) reduced by 23%, which significantly augmented the anticancer effect of GEM alone or VPA alone (P<0.01). Using the microarray analysis, forty-three genes were identified with the comparison between GEM group and GEM plus VPA combination group. The interactions were shown between genes of the “Cellular Development” relevant to the differentiation of cancer cell using IPA.

overall_design: Total RNA was isolated from both the stimulated and unstimulated cells (HuCCT-1) using RNeasy Mini kit (Qiagen, Valencia, CA). Relative purity was examined using an Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA, USA). RNA expression was analyzed using GeneChip○R Human Gene 1.0 ST Array (Affymetrix, Santa Clara, CA, USA), containing 28,869 oligonucleotide probes for known and unknown genes. First standard cDNA was synthesized from 300 ng of total RNA by using GeneChip○R Whole Transcript (WT) cDNA Synthesis and Amplification Kit (Affymetrix) according to the manufacturer’s instructions. 10 μg of cRNA were input into the second-cycle cDNA reaction. cDNA was fragmented and end-labeled with the GeneChip○R WT Terminal Labeling Kit (Affymetrix). Approximately 5.5μg of fragmented and labeled DNA target was hybridized to the Affymetrix GeneChip○R Human Gene 1.0 ST Array at 45°C for 17h on a GeneChip○R Hybridization Oven 640  (Affymetrix) according to the manufacturer’s recommendation. Hybridized arrays were washed and stained on a GeneChip○R Fluidics Station 450 and scanned on a GeneChip○R Scanner 3000 7G (Affymetrix), and then generated CEL files for each array. The microarray data was normalized by GeneSpring GX 11.5 software (Agilent). The cut-off value was set at 0.5 to 2.0 for the ratio (more than 2.0: up-regulation, 0.5-2.0: no change, less than 0.5: down-regulation). Gene Ontology (GO) was analyzed using GeneSpring GX 11.5 software (Agilent), and p-value < 0.05 was used for significance. Then we used Ingenuity Pathway Analysis (IPA) 8.7 (http://www.ingenuity.com) to determine the functional pathways associated with the set of differentially expressed genes between genotypes. IPA utilizes the knowledge in the literature about biological interactions among genes and proteins.

first: Mitsuo

last: Shimada

first: Tohru

last: Utsunomiya

first: Yuji

last: Morine

first: Satoru

last: Imura

first: Tetsuya

last: Ikemoto

first: Hiroki

last: Mori

first: Jun

last: Hanaoka

first: Yu

last: Saito


title: Identification of KSHV, EBV and cellular miRNA targets in human B-cells using RIP-Chip

status: Public on Feb 04 2011

city: Cambridge

first: Lars

last: Dölken

state: Cambridgeshire

address: Addenbrookes Hospital, Hills Road

department: Medicine

country: United Kingdom

institute: University of Cambridge

summary: RIP-Chip was performed on DG75-eGFP, DG75-10/12, BCBL-1, BL41, BL41 B95.8 and Jijoye using anti-human Ago2 (11A9) antibodies. Anti-BrdU antibodies were used as controls for DG75-eGFP, DG75-10/12 and BCBL-1. Total RNA was used as control for BL41, BL41 B95.8 and Jijoye. Samples were analyzed on Affymetrix Gene ST 1.0 Arrays (2 independent biological replicates / sample)

overall_design: KSHV, EBV and cellular miRNA targets were determined by RIP-Chip using monoclonal antibodies to human Ago2

first: Georg

last: Malterer

first: Friedrich

last: Grässer

first: Gunter

last: Meister

first: Reinhard

last: Hoffmann

first: Ralf

last: Zimmer

first: Ulrich

middle: H

last: Koszinowski

first: Jürgen

last: Haas


title: mRNA expression profile modified by microRNA mir-517a (MIR517A) in human hepatocellular carcinoma cell line

status: Public on Feb 17 2011

city: Dallas

first: Yujin

last: Hoshida

address: 5323 Harry Hines Blvd

country: USA

institute: University of Texas Southwestern Medical Center

summary:
mRNA expression profile modified by stable transfection of microRNA mir-517a (MIR517A) in a human hepatocellular carcinoma cell line Huh-7

Keywords: Hepatocellular carcinoma, Expression array, microRNA

overall_design: microRNA mir-517a (MIR517A) was transfected to Huh-7 cells using GFP-expressing lentiviral vector. Infected cells were selected using flow cytometry and subjected to mRNA expression microarray experiment. The profiles were compared to controls cells infected with only GFP protein.

first: Sara

last: Toffanin

first: Anja

last: Lachenmayer

first: Augusto

last: Villanueva

first: Laia

last: Cabellos

first: Beatriz

last: Minguez

first: Stephen

last: Ward

first: Swan

last: Thung

first: Radoslav

last: Savic

first: Derek

middle: Y

last: Chiang

first: Clara

last: Armengol

first: Victoria

last: Tovar

first: Sasan

last: Roayaie

first: Craig

last: April

first: Jian-Bing

last: Fan

first: Myron

last: Schwartz

first: Jordi

last: Bruix

first: Scott

last: Friedman

first: Todd

middle: R

last: Golub

first: Vincenzo

last: Mazzaferro

first: Josep

last: Llovet


title: Gene Expression Profiling Predicts the Development of Oral Cancer

status: Public on Feb 01 2011

city: Houston

first: Pierre

last: Saintigny

address: 1515 Holcombe

department: Thoracic / Head and Neck Medical Oncology

institute: The University of Texas M.D. Anderson Cancer Center

summary:
Patients with oral preneoplastic lesion (OPL) have high risk of developing oral cancer. Although certain risk factors such as smoking status and histology are known, our ability to predict oral cancer risk remains poor.  The study objective was to determine the value of gene expression profiling in predicting oral cancer development. Gene expression profile was measured in 86 of 162 OPL patients who were enrolled in a clinical chemoprevention trial that used the incidence of oral cancer development as a prespecified endpoint. The median follow-up time was 6.08 years and 35 of the 86 patients developed oral cancer over the course. Gene  expression profiles were associated with oral cancer-free survival and used to develope multivariate predictive models for oral cancer prediction.
We developed a 29-transcript predictive model which showed marked improvement in terms of prediction accuracy (with 8% predicting error rate) over the models using previously known clinico-pathological risk factors. Based on the gene expression profile data, we also identified 2182 transcripts significantly associated with oral cancer risk associated genes (P-value<0.01, single variate Cox proportional hazards model). Functional pathway analysis revealed proteasome machinery, MYC, and ribosomes components as the top gene sets associated with oral cancer risk. In multiple independent datasets, the expression profiles of the genes can differentiate head and neck cancer from normal mucosa.  Our results show that gene expression profiles may improve the prediction of oral cancer risk in OPL patients and the significant genes identified may serve as potential targets for oral cancer chemoprevention.

first: Li

last: Zhang

last: Mao


title: A Bacterial Protein Targets the BAHD1 Chromatin Complex to Stimulate Type III Interferon Response

status: Public on Feb 03 2011

city: Jouy-en-Josas

first: Helene

last: Bierne

address: Domaine de Vilvert, bat 442, INRA Micalis

department: Micalis Institute

institute: INRAE - University PARIS SACLAY

summary:
Intracellular pathogens such as Listeria monocytogenes subvert cellular functions through the interaction of bacterial effectors with host components. Here we found that a secreted listerial virulence factor, LntA, could target the chromatin repressor BAHD1 in the host cell nucleus to activate IFN-stimulated genes (ISGs). IFN-λ expression was induced in response to infection of epithelial cells with bacteria lacking LntA; however, the BAHD1-chromatin associated complex repressed downstream ISGs. In contrast, in cells infected with lntA-expressing bacteria, LntA prevented BAHD1 recruitment to ISGs and stimulated their expression. Murine listeriosis decreased in BAHD1+/- mice or when lntA was constitutively expressed. Thus the LntA-BAHD1 interplay may modulate IFN-λ−mediated immune response to control bacterial colonization of the host.
In this dataset, we include the expression data obtained following infection of human Lovo cells infected with Listeria bacteria expressing (LntA-V5+) or not (DlntA) the virulence facteur LntA

overall_design: RNA from LoVo cells grown in 6-well plates and infected with either lntAV5+ or lntA– strains was extracted. Three biological replicates were analyzed for each experimental condition.

first: Béatrice

last: Régnault

first: Hélène


title: Expression data from iPS and human ES cells

status: Public on Jan 29 2011

city: BRONX

first: Chan-Jung

last: Chang

address: 1300 MORRIS PARK AVE

department: Hematology/Cell biology

institute: Albert Einstein College of medicine

summary: Assays to assess the quality of the reprogramming of human Induced pluripotent stem cells are needed. We have previously shown that hESC can be differentiated into embryonic and fetal type of red blood cells that sequentially express three types of  hemoglobins recapitulating early human erythropoiesis. We report here that we have produced iPS from three somatic cell types: adult skin fibroblasts as well as embryonic and fetal mesenchymal stem cells. We show that some of these iPS are fully reprogrammed into a pluripotent state that is undistinguishable from that of hESCs based and low and high-throughput expression analysis and detailed expression of globin expression patterns suggesting that reprogramming with the four original Yamanaka pluripotency factors leads to complete erasure of all functionally important epigenetic marks associated with hematopoietic differentiation regardless of the age or the tissue type of the donor cells. We also report that reprogramming can also lead to abnormal iPS that are undistinguishable from hES cells by morphology, and by the expression of their endogenous genes but that are grossly abnormal in their differentiation potential. The most likely cause of abnormal reprogramming is failure to silence the virally transduced reprogramming factors. The ability to produce large number of erythroid cells with embryonic and fetal-like characteristics is likely to have many translational applications

overall_design: the gene expression in different source of iPS and standard ES cells H1

first: Koyel

last: Mitra

first: Mariko

last: Koya

first: Michelle

last: Velho

first: Romain

last: Desprat

first: Jack

last: Lenz

first: Eric

last: Bouhassira


title: Ku70 Is a Novel Cytosolic DNA Sensor that Induces Type-III Rather than Type-I IFN

city: Frederick

first: Richard

last: Lempicki

state: MD

address: PO Box B

department: Clinical Services Program

institute: Leidos Biomedical Research, Inc.

summary: Cytosolic foreign DNA is detected by pattern recognition receptors and mainly induces Type-I IFN production. We found that transfection of different types of DNA into various untreated cells induces Type-III IFN (IFN-lambda1) rather than Type-I IFN, indicating the presence of uncharacterized DNA sensor(s). A pull-down assay using cytosolic proteins identified that Ku70 and Ku80 are the DNA binding proteins. The knockdown studies and the reporter assay revealed that Ku70 is a novel DNA sensor inducing the IFN-lambda1 activation. The functional analysis of IFNL1 promoter revealed that PRDI and ISRE sites are predominantly involved in the DNA-mediated IFNL1 activation. A pull-down assay using nuclear proteins demonstrated that the IFN-lambda1 induction is associated with the activation of IRF-1 and IRF-7. This is the first report of a specific induction of Type-III rather than Type-I IFN and of Ku70 that plays a key role in the activation of innate immune responses.

overall_design: To identify the nature of the anti-HIV mediators associated with the empty vector transfection, we compared patterns of gene expression between untreated and pCMV9-transfected HEK293 cells, using DNA microarray analysis.

first: Xing

first: Terrence

middle: W

last: Brann

first: Ming

last: Zhou

first: Jun

last: Yang

first: Raphael

last: Oguariri

first: Kristy

middle: B

last: Lidie

first: Hiromi

last: Imamichi

first: Da-Wei

last: Huang

first: Michael

last: Baseler

first: Timothy

last: Veenstra

first: Howard

last: Young

first: H

middle: C

last: Lane

first: Tomozumi


title: mRNA expression data from A549 exposed to fresh or aged urban air mixtures

city: Chapel Hill

first: Rebecca

middle: Catherine

last: Fry

address: 1213 MHRC

department: Environmental Sciences and Engineering

institute: UNC-Chapel Hill

summary:
We are investigating the mRNA expression profiles of human lung cells to gaseous urban mixtures
We used microarrays to compare the global mRNA expression profiles upon response to fresh against aged urban mix

Keywords: dose

overall_design: A549 cells were grown to confluency and exposed to fresh urban mix, aged urban mix, or mock-treated. RNA was collected 9 hrs after exposure.

first: Julia

middle: E

last: Rager

first: Lisa

last: Smeester

first: Ilona

last: Jaspers

first: Kenneth

middle: G

last: Sexton


title: Expression data from TGFbeta-treated control or aPKC silenced A549 cells

city: London

first: John

middle: M

last: Di Guglielmo

state: ON

address: 1151 Richmond

department: Phys/Pharm

institute: University of Western Ontario

summary:
Aberrant TGFbeta signalling is a hallmark of epithelial derived tumours. Signalling patterns can depend on the membrane trafficking and internalization of the TGFbeta receptors. Protein kinase C (PKC), particularly the atypical PKC isoforms, alter the trafficking of TGFbeta receptors and can alter TGFbeta induced gene expression.
We used microarrays to detail the programme of gene expression underlying TGFbeta induction between control or aPKC silenced A549 cells.

overall_design: Control or aPKC silenced A549 cells were serum starved and treated with TGFbeta for 1 hour. Total RNA was extracted from untreated or TGFbeta treated cells after 8 and 24 hours and analyzed using Affymetrix microarrays.  We sought to assess TGFbeta gene expression in aPKC silenced lung cancer cells, as we found that knockdown of aPKC extends TGFbeta signalling as assessed by phospho Smad2 levels. Furthermore, increased expression and oncogenic activity of aPKC (PKCiota) has been reported in lung cancer cells.

first: Adrian

last: Gunaratne

first: Hassina

last: Benchabane

first: David

last: Carter


title: Development of patient-specific neurons in schizophrenia using induced pluripotent stem cells: proof of principle and preliminary findings

status: Public on Jan 14 2011

city: Bronx

first: Herb

last: Lachman

state: NY

address: 1300 Morris Park Ave., F103

department: Psychiatry

institute: Albert Einstein College of Medicine

summary:
Induced pluripotent stem cell (iPSC) technology has the potential to address the inaccessibility of the human brain by providing investigators with patient-specific neurons that can potentially be used to carry out molecular, electrophysiological and pharmacological studies {{855 Takahashi,K. 2006}}. Although iPSC technology was primarily conceived and developed as a means to bypass the use of human embryonic stem cells (hESCs) for regenerative medicine, its potential for disease modeling may prove to be equally valuable, especially for neuropsychiatric disorders.
A total of 1207 genes were found to be differentially expressed using LIMMA (>2-fold, p-value <0.05), and these genes were hierarchically clustered to form 5 groups based on their expression in day 0, 10 and 32. These were subjected to bioinformatics analysis by Gene Ontogoly (GO) and Ingenuity Pathway Analysis (IPA) to determine enrichment profiles and associated disease processes. The largest cluster (cluster III), which showed increasing expression in both day 10 and day 32 neurons, was found to be enriched with genes involved in a number of neuronal pathways including neurogenesis, neuronal differentiation, axon guidance and adhesion, among others.

overall_design: At a p-value of 0.05, we detected 645 and 383 genes up- and down-regulated between day 0 and day 10, respectively, and 146 and 280 genes up- and down-regulated between day 10 and day 32. In total, 1207 genes were found to be differentially expressed using LIMMA, and these genes were hierarchically clustered to form 5 groups.

first: Erika

last: Pedrosa

first: Vladislav

last: Sandler

first: Abhishek

last: Shah

first: Reed

last: Carroll

first: Chanjung

last: Chang

first: Shira

last: Rockowitz

first: Xingyi

last: Guo

first: Deyou

last: Zheng

first: Herbert


title: Expression analysis of human melanoma short-term culture WM451-Lu harvested after lentiviral infection with a GFP (control) or SETDB1 (experimental) viral vector

status: Public on Jan 07 2011

city: Karp 7

first: Yariv

last: Houvras

state: MA

address: 1 Blackfan Circle

institute: Childrens Hospital Boston

summary: Investigation of expression differences induced by expression of the histone methyltransferase SETDB1 in human melanoma short-term culture WM451-Lu.

overall_design: A six-chip study using total RNA prepared from WM451-Lu melanoma short-term cultures infected with either a lentivirus encoding GFP (control) or SETDB1. Cells were allowed to grow for 2 days post-infection.

first: Craig

middle: J

last: Ceol