title: Microarray analysis of IL-10 stimulated adherent peripheral blood mononuclear cells

city: Sacramento

first: Dennis

middle: Jay

last: Montoya

address: 2700 Stockton Blvd #2354

department: Biochemistry and Molecular Medicine

institute: UC Davis School of Medicine

summary: The immune mechanisms that control resistance vs. susceptibility to mycobacterial infection in humans were investigated by studying leprosy skin lesions, the site where the battle between the host and the pathogen is joined.  Using an integrative genomics approach, we found an inverse correlation between of IFN-beta and IFN-gamma gene expression programs at the site of disease.  The Type II IFN, IFN-gamma and its downstream vitamin D-dependent antimicrobial genes were preferentially expressed in the lesions from patients with the self-healing tuberculoid form of the disease and mediated antimicrobial activity against the pathogen, Mycobacterium leprae in vitro.  In contrast, the Type I IFN, IFN-beta and its downstream genes, including IL-27 and IL-10, were induced in monocytes by M. leprae in vitro, and were preferentially expressed in the lesions of disseminated and progressive lepromatous form.  The IFN-gamma induced macrophage antimicrobial response was inhibited by IFN-beta/IL-10, by a mechanism involving blocking the generation of bioactive 1,25-dihyroxy vitamin D as well as inhibiting induction of antimicrobial peptides cathelicidin and DEFB4.  The ability of IFN-B to inhibit the IFN-gamma induced vitamin D pathway including antimicrobial activity was reversed by neutralization of IL-10, suggesting a possible target for therapeutic intervention.  Finally, a common IFN-beta and IL-10 gene signature was identified in both the skin lesions of leprosy patients and in the peripheral blood of active tuberculosis patients.  Together these data suggest that the ability of IFN-beta to downregulate protective IFN-gamma responses provides one general mechanism by which some bacterial pathogens of humans evade protective host responses and contribute to pathogenesis.

overall_design: Peripheral blood monuclear cells derived through Ficoll-Hypaque from the blood of healthy human donors (n=4).  Cells adhered to tissue culture treated 6-well plates for 2 hours in 1% Fetal Bovine Serum (FBS) RPMI and then stimulated by IL-10 (R&D Systems) 10ng/ml or media alone in 10% FBS RPMI for 24 hours at 37°C, 5% CO2.   After stimulation, cells harvested and monocytes isolated through CD14 positive selection (Miltenyi Biotec).  RNA from purified monocytes extracted by Trizol and purified by Qiagen RNeasy Kit.  RNA probe and microarray performed by UCLA Clinical Microarray Core using Ambion labeling kit and Affymetrix Human U133 Plus 2.0 array.

first: Rosane

last: Teles


title: Microarray analysis of differentiation of human glioblastoma neurospheres

status: Public on Mar 05 2013

city: Pamplona

first: Raquel

last: Malumbres

state: Navarra

address: Avenida Pio XII 55

department: Hemato-Oncology

country: Spain

institute: University of Navarra/ Clínica Universidad de Navarra

summary: Brain tumor neurospheres (BTCSs) are cancer cells with neural stem cell-like properties found in the fatal brain tumor glioblastoma multiforme (GBM). These cells account for less than 1% of total tumor cells, are poorly differentiated and are believed to be involved in tumor induction, progression, treatment resistance and relapse. Specific miRNAs play important roles in modulating the proliferation and differentiation of neural stem cells, therefore, we aimed to identify miRNAs controlling differentiation in GBM-BTSCs through high throughput screening miRNA array profiling. We compared the miRNA expression profiles at the neurosphere state and upon 4 and 14days of differentiation by using LIMMA, finding 21 differentially expressed miRNAs : hsa-miR-103, hsa-miR-106a, hsa-miR-106b, hsa-miR-15b, hsa-miR-17, hsa-miR-19a, hsa-miR-20a, hsa-miR-25, hsa-miR-301a and hsa-miR-93 were found up-regulated upon differentiation, while hsa-miR-100, hsa-miR-1259, hsa-miR-21, hsa-miR-22, hsa-miR-221, hsa-miR-222, hsa-miR-23b, hsa-miR-27a, hsa-miR-27b, hsa-miR-29a and hsa-miR-29b were down-regulated. Expression of 11 of the 21 miRNAs was examined by qPCR and 7 of them were validated: hsa-miR-21, hsa-miR-29a, hsa-miR-29b, hsa-miR-221 and hsa-miR-222 increased their expression upon differentiation, while hsa-miR-93 and hsa-miR-106a were inhibited. Functional studies demonstrated that miR-21 over-expression induced the expression of glial and/or neuronal cell markers in the neurospheres, possibly due to SPRY1 targeting by miR-21 in these cells, while miR-221 and miR-222 inhibition at the differentiated state reduced the expression of those differentiation markers. On the other hand, miR-29a and miR-29b targeted MCL1 in the GBM neurospheres and increased apoptotic cell death.

overall_design: Gene expression in differentiated cells relative to neurospheres in four different glioblastoma cultures

first: Beatriz

last: Aldaz

first: Jose

middle: L

last: Luna

middle: A

last: Martinez-Climent

first: Elizabeth

last: Guruceaga

first: Victor

last: Segura


title: Dysregulated expression of genes in regulatory T cells from metastatic castration-resistant prostate cancer patients

city: Bethesda

first: Alan Lap-Yin

last: Pang

state: MD

address: 49 Convent Drive, Room 2C08, MSC 4429

department: NICHD/LCG/SDG

country: USA

institute: National Institutes of Health

summary: We analyzed the global gene expression pattern of Tregs between healthy donors and prostate cancer patients.  We found that genes related to cell cycle, cellular proliferation, immune responses, hematological system development and function were differentially expressed in Tregs from prostate cancer patients.

overall_design: Total RNA samples of Tregs, isolated from peripheral blood, were obtained from three separate healthy donors and three metastatic castration-resistant prostate cancer patients.  Global gene expression pattern was examined by performing GeneChip microarray hybridization.  Genes differentially expressed between the two groups of donors were sorted and categorized based on their biological functions.

first: Ngar-Yee

last: Huen

first: Alan

first: Tin-lap

last: Lee

first: Matteo

last: Vergati

first: Caroline

last: Jochems

first: Jo

last: Tucker

first: Chiara

last: Intrivici

first: Vittore

last: Cereda

first: Wai-Yee

last: Chan

first: Owen

middle: M

last: Rennert

first: Ravi

last: Madan

first: James

last: Gulley

first: Jeffrey

last: Schlom

first: Kwong

middle: Y

last: Tsang


title: Transcriptional responses to GSK3 inhibitor and MEK inhibitor on 2i-adapted mouse embryonic stem cells

status: Public on Mar 01 2013

city: Cambridge

first: Xiaoxiao

last: Zhang

state: MA

address: 7 Divinity Ave.

department: Molecular and Cellular Biology

institute: Harvard University

summary: The objective of this study was to investigate the roles of GSK3 inhibitor CHIR99021 and MEK inhibitor PD0325901 on 2i-adapted mouse embryonic stem cells (ESCs) in serum-free conditions.Canonical Wnt signaling supports the pluripotency of mouse ESCs but also promotes differentiation of early mammalian cell lineages. To explain these paradoxical observations, we explored the gene regulatory networks at play. Canonical Wnt signaling is intertwined with the pluripotency network comprising Nanog, Oct4, and Sox2 in mouse ESCs. In defined media supporting the derivation and propagation of mouse ESCs, Tcf3 and β-catenin interact with Oct4; Tcf3 binds to Sox motif within Oct-Sox composite motifs that are also bound by Oct4-Sox2 complexes. Further, canonical Wnt signaling up-regulates the activity of the Pou5f1 distal enhancer via the Sox motif in mouse ESCs. When viewed in the context of published studies on Tcf3 and β-catenin mutants, our findings suggest that Tcf3 counters pluripotency by competition with Sox2 at these sites, and Tcf3 inhibition is blocked by β-catenin entry into this complex. Wnt pathway stimulation also triggers β-catenin association at regulatory elements with classic Lef/Tcf motifs associated with differentiation programs. The failure to activate these targets in the presence of a MEK/ERK inhibitor essential for mouse ESC culture suggests that MEK/ERK signaling and canonical Wnt signaling combine to mouse promote ESC differentiation.

overall_design: Triplicates of mouse embryonic stem cells cultured under the following conditions: 1) CHIR99021+PD0325901+LIF; 2) CHIR99021+PD0325901; 3) CHIR99021; 4) PD0325901; 5) DMSO

first: Andrew

middle: P

last: McMahon


title: Transcriptional responses to Wnt pathway stimulation in mouse embryonic stem cells cultured in serum+LIF condition

summary: The objective of this study was to identify genes regulated by canonical Wnt signaling in  mouse embryonic stem cells (ESCs).Canonical Wnt signaling supports the pluripotency of mouse ESCs but also promotes differentiation of early mammalian cell lineages. To explain these paradoxical observations, we explored the gene regulatory networks at play. Canonical Wnt signaling is intertwined with the pluripotency network comprising Nanog, Oct4, and Sox2 in mouse ESCs. In defined media supporting the derivation and propagation of mouse ESCs, Tcf3 and β-catenin interact with Oct4; Tcf3 binds to Sox motif within Oct-Sox composite motifs that are also bound by Oct4-Sox2 complexes. Further, canonical Wnt signaling up-regulates the activity of the Pou5f1 distal enhancer via the Sox motif in mouse ESCs. When viewed in the context of published studies on Tcf3 and β-catenin mutants, our findings suggest that Tcf3 counters pluripotency by competition with Sox2 at these sites, and Tcf3 inhibition is blocked by β-catenin entry into this complex. Wnt pathway stimulation also triggers β-catenin association at regulatory elements with classic Lef/Tcf motifs associated with differentiation programs. The failure to activate these targets in the presence of a MEK/ERK inhibitor essential for mouse ESC culture suggests that MEK/ERK signaling and canonical Wnt signaling combine to promote mouse ESC differentiation.

overall_design: Triplicates of mouse embryonic stem cells cultured with GSK3 inhibitor CHIR99021 or with Wnt pathway inhibitor XAV939.

first: Shinsuke

last: Ohba


title: Involvement of miRNAs in the Differentiation of Human Glioblastoma Multiforme Brain Tumor Stem-Like Cells

first: Raquel

last: Malumbres

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

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

platform_organism:
Homo sapiens
Mus musculus
Rattus norvegicus
Human alphaherpesvirus 1
Human alphaherpesvirus 2
Human betaherpesvirus 5
human gammaherpesvirus 4
JC polyomavirus
Human immunodeficiency virus 1
Murid gammaherpesvirus 4
Human gammaherpesvirus 8
Merkel cell polyomavirus
Mus musculus cytomegalovirus 2
Betapolyomavirus hominis
Betapolyomavirus macacae

overall_design: Refer to individual Series


title: Macrophage Microvesicles Induce Macrophage Differentiation and miR-223 Transfer

status: Public on Mar 08 2013

city: Indianapolis

first: Leni

last: Moldovan

state: IN

address: 980 W Walnut St., Rm. C422

department: Ophthalmology

institute: Indiana University

summary:
Microvesicles (MV) are small membrane-bound particles comprised of exosomes and various sized extracellular vesicles. These are released by a number of cell types. Microvesicles have a variety of cellular functions from communication to mediating growth and differentiation. Microvesicles contain proteins and nucleic acids. Previously, we showed that plasma microvesicles contain microRNAs (miRNAs). Based on our previous report, the majority of peripheral blood microvesicles are derived from platelets while mononuclear phagocytes, including macrophages, are the second most abundant population. Here, we characterized macrophage-derived microvesicles and whether they influenced the differentiation of naïve monocytes. We also identified the miRNA content of the macrophage-derived microvesicles. We found that RNA molecules contained in the macrophage-derived microvesicles were transported to target cells, including monocytes, endothelial cells, epithelial cells and fibroblasts. Furthermore, we found that miR-223 was transported to target cells and was functionally active. Based on our observations, we hypothesize that microvesicles bind to and activate target cells. Furthermore, we find that microvesicles induce the differentiation of macrophages. Thus, defining key components of this response may identify novel targets to regulate host defense and inflammation.
We used GeneChip microarrays to examine changes in gene expression induced by MV in primary monocyte-derived macrophages (MDM) and in THP1 cells, and compare this to cells treated with GM-CSF and PMA, respectively.

overall_design: All experiments were done in triplicates. Primary monocytes were collected from buffy coats (BC). The freshly isolated monocytes from three donors (Mono1-3) were either treated with GM-CSF or subjected to RNA isolation. Following treatment, MVs were isolated from the GM-CSF-treated macrophage cultures. RNA was isolated from the remaining cells for profiling (GM1-3). The isolated MVs were then used to treat new BC monocytes for 24 h (BC-GMCSF-MV24). A fraction of the new BC monocytes was subjected to RNA extraction for profiling (BC1-3). For THP1 cells, they were treated with either DMSO or PMA to produce MVs. The MVs were collected and the remaining cells lyzed for RNA extraction and profiling (DMSO1-3 and PMA1-3). The collected MVs from the DMSO or PMA-treated THP1 cells were incubated with new THP1 for 24 h and designated DMSO-MV24 or PMA-MV24. We had a total of 24 samples.

first: Noura

last: Ismail

first: Yijie

last: Wang

first: Duaa

last: Dakhlallah

first: Kara

last: Batte

first: Prexy

last: Shah

first: Jon

last: Wisler

first: Tim

middle: D

last: Eubank

first: Susheela

last: Tridandapani

first: Melissa

middle: G

last: Piper

first: Clay

middle: B

last: Marsh


title: Expression profiling of human prostate non-tumorigenic RWPE-1 cells after overexpressing ERG and ETV1, and ERG and ETV1 silencing on prostate cancer cells LNCaP and  VCaP, respectively

city: Boston

first: Esther

last: Baena

address: 300 Longwood Avenue

department: Hematology/Oncology

institute: Childrens Hospital Boston

summary: Chromosomal rearrangements involving ETS factors, ERG and ETV1, occur frequently in prostate cancer. We here examine human prostate non-tumorigenic RWPE-1 cells with ERG- or ETV1-expressing stable RWPE-1 cell.

overall_design: RWPE-1 stable cell clones overexpressing ERG and ETV1 were grown under normal conditions.  Total RNA was extracted from three biological replicates. This was used to hybridize to Affymetrix expression arrays using the HG-U133 Plus 2.0 platform.

first: Zhen

last: Shao

first: Zhe

last: Li

first: Stuart

middle: H

last: Orkin


title: Expression profiling of human prostate VCaP and LNCaP cancer cells after silencing ERG or ETV1, respectively

summary: Chromosomal rearrangements involving ETS factors, ERG and ETV1, occur frequently in prostate cancer. We here examine human prostate cancer cells control VCaP and LNCaP cells with ERG- or ETV1-silenced VCaP or LNCaP cells, respectively, in hormone deprived and stimulated conditions.

overall_design: VCAP and LNCaP cells, 24 hr after ERG or ETV1 RNA interference, respectively, were grown in hormone-depleted conditions for 2 days, and then in the presence of EtOH (vehicle) or 10nM DHT for 16hr. Total RNA was extracted from three biological replicates. This was used to hybridize to Affymetrix expression arrays using the HG-U133 Plus 2.0 platform.


title: Distinct transcriptional programs controlled by ERG and ETV1 in prostate cells

type: Genome binding/occupancy profiling by genome tiling array

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus


title: mRNA analysis of diaphragm and gastrocnimius of WT and Cox6a2 knockout mice

city: Leuven

first: Katleen

last: Lemaire

address: Herestraat 49, bus 901

country: Belgium

summary: We used microarrays to compare gene expression across different murine tissues.

overall_design: 12 samples were analysed in this comparison, 3 biological replicates were used per tissue

first: Leentje

last: Van Lommel

first: Frans

last: Schuit

first: Roel

last: Quintens


title: Valproic acid achieves its anticancer activity by re-expression of cyclin D2

city: Goettingen

first: Gabriela

last: Salinas

state: Lower-Saxony

address: Kreuzbergring 57

department: Department of Pathology

country: Germany

institute: Universitaetsmedizin Goettingen

summary: In this study we could show that the treatment of primary murine prostate cancer(PCa) cells derived from the well-established TRAMP (transgenic adenocarcinoma ofmouse prostate) model with the histone deacetylase inhibitor (HDI) valproic acid (VPA) has an anti-proliferative, anti-migrative and anti-invasive effect on the cells.To our knowledge this is the first study that identified that treatment of PCa cells with VPA leads to the re-expression of cyclin D2, which is known to be frequently inactive  in patients with PCa. Additionally, we could demonstrate that VPA specifically induces re-expression of cyclin D2 as a family member of the highly conserved Dtype cyclins in human colorectal and mammary gland adenocarcinoma cell lines, whereas VPA treatment has no effect in NIH/3T3 fibroblasts. The observed cyclin D2 re-expression in cancer cells is activated by an increase of histone acetylation in the promoter region of the cyclin D2 gene and might be the underlying molecular mechanism of the inhibition of proliferation of cancer cells after VPA treatment. Taken together, our results confirm VPA as an anticancer therapeutic option in tumors with epigenetically repressed cyclin D2 expression.

overall_design: For the comparison of vpa treatment in murine protate cancer cells we hybridized 3 replicates per condition

first: Daria

last: Witt

first: Peter

last: Burfeind

first: Sandra

last: von Hardenberg

first: Lennart

last: Opitz

last: Salinas-Riester

first: Stefan

last: Schweyer

first: Paul

last: Thelen

first: Silke

last: Kaulfuss


title: Gene expression profiling of resistant and vulnerable motor neuron subtypes in amyotrophic lateral sclerosis

city: Sheffield

middle: Roy

last: Heath

state: S. Yorks

address: SITraN, 385a Glossop Road

department: Academic Neurology Unit

country: United Kingdom

institute: University of Sheffield

summary: A consistent clinical feature of amyotrophic lateral sclerosis (ALS) is the sparing of eye movements. Pathological studies have confirmed that there is relative sparing of the cranial motor nuclei of the oculomotor, trochlear and abducens nerves, although pathological changes resembling those seen in anterior horn cells are present to a lesser degree. The aim of the present study is to combine LCM and microarray analysis to study the differences between motor neurons that are selectively resistant (oculomotor neurons) and those that are vulnerable (lumbar spinal motor neurons) to the disease process in amyotrophic lateral sclerosis.

overall_design: We used microarray analysis to determine the differences in gene expression between oculomotor and lumbar spinal motor neurons, isolated by laser capture microdissection from the midbrain and spinal cord of neurologically normal human controls.

first: Alice

last: Brockington

first: Ke

last: Ning

first: Elizabeth

last: Wood

first: Nicolo

last: Fusi

first: Neil

last: Lawrence

first: Stephen

last: Wharton

last: Ince

first: Pamela

last: Shaw


title: Expression data from Ly-6C- and Ly-6C+ Naive CD4 T cells

city: 91400 Orsay

first: Florent

last: Dumont

state: Ile de France

address: 17 avenue des sciences

country: France

institute: Université Paris-Saclay

summary: The naive CD4 T cell compartment is heterogeneous. Ly-6C- and Ly-6C+ Naive CD4 T cells were compare by microarrays.

overall_design: Ly-6C- and Ly-6C+ Naive CD4 T cells were purified for RNA extraction and hybridization on Affymetrix microarrays.

first: Bruno

last: Lucas


title: Treatment of AML patient samples with decitabine

status: Public on Mar 06 2013

city: Birmingham

first: sarah

last: leonard

address: Edgbaston

department: School of cancer sciences

institute: University of Birmingham

type: Methylation profiling by genome tiling array

summary:
Genome wide DNA methylation profiling of AML patient samples treated with PBS or DAC. The Illumina Infinium 450 Human DNA methylation was used to examine the methylation profile of 8 patient samples and 2 cell lines.

Genome wide DNA methylation profiling of AML xenografts treated with either PBS control or with decitacine (DAC) alone, cytarabine (Ara-C) alone, DAC and Ara-C together (D+A), DAC followed by Ara-C (D/A) or with Ara-C followed by DAC (A/D).

overall_design: DNA was extracted from patient bone marrow samples and xenograft bone marrow samples using Qiagen Allprep kit. Bisulphite converted DNA from all samples were hybridised to the Illumina Infinium 450 Human Methylation arrays and for each analysis the drug treated sample was compared to the corresponding PBS control sample.

first: Sarah

last: Leonard


title: Transcriptomic effects of caloric restriction reflected in primate difference

status: Public on Feb 28 2013

city: Shanghai

first: Zhao

last: Guodong

address: Yueyang Road

country: China

institute: PICB

summary:
Caloric restriction (CR) can delay morbidity and mortality in a broad range of species, including mice and macaques. Mutations and chemical agents, such as resveratrol or rapamycin that partly mimic the CR effect, can similarly increase survival or extend lifespan. In humans, however, the effects of CR or other life-extending agents have not been investigated systematically. Humans already display lower mortality and greater maximal lifespan compared to closely related species, including chimpanzees and macaques. It is thus possible that humans, during their evolution, have acquired genetic mutations mimicking the CR effect. To address this question, we compared transcriptome differences between humans and other primates, with transcriptome changes observed in mice subjected to CR [see references below]. We show that the human transcriptome state examined in multiple tissues and across different ages resembles the transcriptome state of mice fed ad libitum, relative to CR mice or mice treated with resveratrol. Furthermore, transcriptome changes induced by CR were enriched among genes showing age-related changes among primates, concentrated in specific expression patterns, and could be linked with specific functional pathways, including insulin signalling, cancer, and immune response. These findings indicate that the evolution of human longevity was likely independent of CR-induced lifespan extension mechanisms. Consequently, application of CR or CR-mimicking agents may offer a promising direction in the extension of healthy human lifespan.

References for the transcriptome changes observed in mice subjected to CR:
1)  Barger JL, Kayo T, Vann JM, Arias EB, Wang J, Hacker TA, Wang Y, Raederstorff D, Morrow JD, Leeuwenburgh C, et al: A low dose of dietary resveratrol partially mimics caloric restriction and retards aging parameters in mice. PLoS One 2008, 3:e2264.
2)  Tsuchiya T, Dhahbi JM, Cui X, Mote PL, Bartke A, Spindler SR: Additive regulation of hepatic gene expression by dwarfism and caloric restriction. Physiol Genomics 2004, 17:307-315.
3)  Baur JA, Pearson KJ, Price NL, Jamieson HA, Lerin C, Kalra A, Prabhu VV, Allard JS, Lopez-Lluch G, Lewis K, et al: Resveratrol improves health and survival of mice on a high-calorie diet. Nature 2006, 444:337-342.

sample_organism:
Macaca mulatta
Pan troglodytes
Homo sapiens
Mus musculus

overall_design:
We collected post-mortem brain, heart, and liver samples from 16 human, 16 chimpanzee and 4 rhesus macaque seperately. All these individuals are adults. RNA extracted from the dissected tissue was hybridized to Affymetrix® Human Gene 1.0 ST arrays to quantify gene expression level.
We collected prefrontal cortex tissues of mice with age ranging from postnatal 2 days to 2.5 years. The strain of the mice is C57BL/6. RNA extracted from the dissected tissue was hybridized to Affymetrix® Mouse Gene 1.0 ST Arrays to quantify gene expression level.

first: Guodong

last: Zhao


title: Microarray analysis of cultured gastric myofibroblasts

city: Liverpool

first: Bahram

last: Ebrahimi

address: Crown Street

institute: Liverpool University

summary: Neuronal, endocrine and exocrine cells exhibit regulated exocytosis but there is also a body of evidence for regulated exocytosis from other cell types. Myofibroblasts are a stromal cell type that secretes extracellular matrix proteins, growth factors and cytokines; they are important in wound healing and increasingly are recognised to play a role in modifying the cellular microenvironment in cancer. We have established calcium dependent regulated secretion in a subset of myofibroblasts from gastric cancers, adjacent tissue and from normal tissue. We have used microarrays to look for the expression of genes associated with the regulated secretory phenotype.

overall_design: A panel of different myofibroblast lines generated from gastric cancers, adjacent tissue, and normal tissue, were assayed for the ability to exhibit regulated exocytosis in response to acute stimulation with IGF. From this database lines were designated as either “responders” or “non-responders” ie exhibited a regulated exocytosis phenotype, or not. The transcript profiles of the two classes of cell were examined using Affimetrix microarrays.

first: Andrea

last: Varro


title: Expression data from hiPSCs-NSCs towards 4T1

city: Singapore

first: Can

last: Chen

address: Science Drive 4

department: Department of Biological Sciences

country: Singapore

institute: National University of Singapore

summary:
Neural stem cells can migrate towards tumors of both neural and non-neural origins, which is crucial for the success in treating disseminated tumors. Although the understanding of the molecular mechanisms underlying NSC tumor tropism is limited, it has been noted that several cytokines, growth factors and receptors direct the migration in vitro. A proper understanding of the basic molecular mechanisms of NSC migration towards tumors, especially identification of key cellular regulators of the migration, will have important implications in improving the effectiveness of engineering and employing NSCs as tumor therapy agents.
We compared gene expression profiles between migratory and non-migratory hiPSC-NSCs towards cancer cells using cDNA microarray profiling.

overall_design: We collected human iPSCs derived NSCs migrating and not migrating towards mouse 4T1 breast cancer cells in an in vitro migration system for total RNA extraction and hybridization to Affymetrix microarrays


title: Expression data from hiPSCs-NSCs towards U87

overall_design: We collected human iPSCs derived NSCs migrating and not migrating towards human U87 glioma cells in an in vitro migration system for total RNA extraction and hybridization to Affymetrix microarrays


title: Inhibition of neuronal nitric oxide synthase activity promotes migration of human induced pluripotent stem cell-derived neural stem cells towards cancer cells


title: Expression data from G1E erythroid cells expressing GATA1 mutants

status: Public on Mar 04 2013

city: Aurora

first: Amy

middle: E.

last: Campbell

state: CO

institute: University of Colorado Anschutz Medical Campus

summary:
Missense mutations in transcription factor GATA1 underlie several distinct forms of anemia and thrombocytopenia. Clinical severity depends on the site and type of substitution, and distinct substiutions of the same residue produce disparate phenotypes. To investigate the effect of GATA1 missense mutations on erythroid differentiation we expressed conditionally activated wild type or mutant versions of GATA1 in GATA1-null G1E cells.
We used gene expression microarrays to explore how GATA1 missense mutations affect erythroid transcription programs.

overall_design: GATA1-null G1E cells ectopically expressing conditionally activated versions of GATA1 (GATA1-ER, GATA1(R216Q)-ER, GATA1(R216W)-ER, GATA1(D218G)-ER, or GATA1(D218Y)-ER) were treated with estradiol for 24 hours to initiate erythroid differentiation. Total RNA from treated cells was extracted for Affymetrix microarray. All data were generated from three biological replicates. Transcript levels were compared in wild type vs. mutant lines.

middle: E

first: Gerd

last: Blobel


title: Sex and aging effect on skeletal muscle transcriptome in humans

city: Ann Arbor

first: GORDON

last: PAUL

state: MI

address: 325 E Eisenhower

institute: University of Michigan

summary: The aim of this investigation was to develop a global view of muscle transcriptional differences between older men and women and with aging for each sex.

overall_design: Muscle biopsies were obtained from the biceps brachii of young (age 19~28yrs) and older (age 65~76 yrs) men (7 young, 4 older) and women (7 young, 4 older). Total RNA was extracted and gene expression profiling was performed using the Affymetrix Human Genome U133 Plus 2 chip.

first: Dongmei

last: Liu

first: Maureen

last: Sartor

first: Gustavo

last: Nader

first: Emidio

last: Pistilli

first: Leah

last: Tanton

first: Charles

last: Lilly

first: Laurie

last: Gutmann

first: Heidi

last: IglayReger

first: Paul

last: Visich

first: Eric

last: Hoffman

last: Gordon


title: Wound response in fs-THz-irradiated mouse skin

status: Public on Feb 26 2013

city: Seoul

first: Kyu-Tae

last: Kim

address: Irwon-Ro 81

department: Samsung Genome Institute

country: South Korea

institute: Samsung Medical Center

summary: Terahertz (THz) technology has emerged for biomedical applications such as scanning, molecular spectroscopy, and medical imaging. However, the biological effect of THz radiation is not fully understood. Non-thermal effects of THz radiation were investigated by applying a femtosecond-terahertz (fs-THz) pulse to mouse skin. Analysis of the genome-wide expression profile in fs-THz-irradiated skin indicated that wound responses were predominantly through NFκB1- and Smad3/4-mediated transcriptional activation. Repeated fs-THz radiation delayed the closure of mouse skin punch wounds due to up-regulation of transforming growth factor-beta (TGF-β). These findings suggest that fs-THz radiation provokes a wound-like signal in skin with increased expression of TGF-β and activation of its downstream target genes, which perturbs the wound healing process in vivo.

overall_design: To identify non-thermally induced in vivo mode action of THz radiation, gene expression profile of fs-THz-irradiated skin (at post 24-hours after 1 hour exposure) was explored. Purified total RNAs from independent 3 mice of each sham and THz group were labeled and hybridized on the Mouse Gene 1.0 ST Array (Affymetrix, Santa Clara, CA), according to manufacturer's standard protocol. Statistically filtered THz-responsive genes were examined for possible interactions with other molecules, canonical signaling pathways, and bio-functions.

first: Woong-Yang

last: Park


title: Expression data from injured murine kidney

city: Nashville

first: James

last: West

state: TN

address: 4200 E 9TH Ave, Box B133

department: Medicine

institute: Vanderbilt University

summary:
Renal recovery following injury relies on cellular regeneration. In the mouse kidney following injury, injured epithelial cells undergoes de-differentiate, proliferate and re-differentiate into functional cells, following a a tightly controlled genetic programme where specific sets of genes are up-regulated.
We used microarrays to detail the global programme of gene expression underlying cellular regeneration following injury with or without a HDAC inhibitor, m4PTB, treatment and identified distinct classes of up-regulated genes during this process.

overall_design: Male BALB/c mice underwent 26 minute unilateral ischemia-reperfusion (IR) with contralateral nephrectomy treated with vehicle or 100 mg/kg m4PTB 24 h after inducing renal injury, and kidneys harvested for RNA extraction 12 h later. We sought to obtain kidneys within a similar degree of injury in order to carefully evaluate the effect of m4PTB on expression profiles. To that end, we selected kidneys according to three different criteria of injury: (1) level of serum creatinine at Day1, (2) the level of blood urea nitrogen (BUN) (3) Kim1 expression by qPCR at Day1.5 using haevested kidneys

first: Takuto

last: Chiba

first: Nataliya

last: Skrypnik

first: Mark

last: de Caestecker


title: Expression data from wild-type and microRNA-155 (miR-155) deficient CD8 T cells

city: Philadelphia

first: E

middle: John

last: Wherry

address: 421 Curie Blvd.

institute: University of Pennsylvania

summary: MicroRNA-155 (miR-155) is upregulated in primary effector CD8 T cells but is expressed at low amounts in naïve cells.  Anti-viral CD8 T cell responses and viral clearance were impaired in miR-155 deficient (bic-/-) mice, and this defect was intrinsic to CD8 T cells, as adoptively transferred bic-/- CD8 T cells generated greatly reduced primary and memory responses during infection. To understand the mechanism by which miR-155 regulates CD8 T cell activation, we analyzed the gene expression profiles of naive and in vitro activated wild-type and bic-/- CD8 T cells.

overall_design: CD8 T cells were purified from uninfected C57BL/6 mice and stimulated in vitro with plate-bound anti-CD3 and anti-CD28 antibodies for 48 h or left unstimulated. RNA from these CD8 T cells was processed, amplified, labeled, and hybridized to Affymetrix GeneChip MoGene 1.0 st microarrays.

middle: J

first: Erietta

last: Stelekati

first: Donald

middle: T

last: Gracias

first: Travis

last: Doering

first: Peter

last: Katsikis


title: WNT pathway activation promotes phenotypic reprogramming of glioblastoma derived cells in zebrafish nervous system microenvironment

city: padova

first: silvia

last: bresolin

state: padova

address: via giustiniani 3

department: department of women's and children's health

country: Italy

institute: università di padova

summary: phenotypic reprogramming ability of teh zebtafish brain microenviroment on GBM derived cells controlled by the activation of endogenous Wnt pathway

overall_design: Class comparison between different time point of human GBM cells trasplanted into zebrafish

first: Silvia

last: Bresolin

first: Elena

last: Rampazzo


title: Gene expression profile in patients inoculated with E. coli 83972

status: Public on Feb 23 2013

city: Lund

last: Lutay

address: Sölvegatan 23

country: Sweden

institute: Lund University

summary:
Urinary tract infections (UTIs) constitute a highly relevant model of microbial adaptation, in which the contrasting effects of pathogens and commensals on host tissues are clearly displayed. While virulent Escherichia coli cause severe, potentially life-threatening disease by breaking the inertia of the mucosal barrier and infecting the kidneys, the most common outcome of bacteriuria is an asymptomatic carrier state resembling commensalism at other mucosal sites. It remains unclear if the lack of destructive inflammation merely reflects low virulence or if carrier strains actively inhibit disease associated responses in the host. To address this question, we examined the effects of asymptomatic bacterial carriage on host gene expression.
Therapeutic urinary tract inoculation with the prototype ABU strain E. coli 83972 is a safe alternative approach in patients with therapy-resistant recurrent UTI. The strain establishes persistent bacteriuria, protecting patients against super-infection with more virulent strains. Using this protocol, we examined if the establishment of asymptomatic bacterial carriage alters host gene expression.

overall_design: After antibiotic treatment to remove prior infection, patients were inoculated with E. coli 83972 through a catheter. Blood samples were obtained before and 24 h after inoculation.

first: Jenny

last: Grönberg Hernandez

first: Björn

last: Wullt

first: Bryndís

last: Ragnarsdóttir

first: Petter

last: Storm

first: Catharina

last: Svanborg


title: Expression data profile of A498 cells treated with DRB or E. coli 83972

summary:
Urinary tract infections (UTIs) constitute a highly relevant model of microbial adaptation, in which the contrasting effects of pathogens and commensals on host tissues are clearly displayed. While virulent Escherichia coli cause severe, potentially life-threatening disease by breaking the inertia of the mucosal barrier and infecting the kidneys, the most common outcome of bacteriuria is an asymptomatic carrier state resembling commensalism at other mucosal sites. It remains unclear if the lack of destructive inflammation merely reflects low virulence or if carrier strains actively inhibit disease associated responses in the host. To address this question, we examined the effects of asymptomatic bacterial carriage on host gene expression.
The asymptomatic strain E. coli 83972  caused reduction in  Pol II phosphorylation in the nuclei of human kidney epithelial A498 cells. To specifically address if Pol II inhibition alters the response to infection, A498 cells were pretreated with 5,6-dichloro-1-b-D-ribofuranosylbenzimidazole (DRB). This adenosine analogue has been proposed to specifically and reversibly inhibit Pol II transcription without directly affecting other cellular functions.  A498 cultered cells were infected with E. coli 83972 or DRB for 4 hours. The culture medium with DMSO was used as a background control.

overall_design: A498 cells were infected with E. coli 83972 or DRB for 4 h. Isolated RNA was subjected to whole genome transcriptome analysis.

first: Ines

last: Ambite


title: Gene expression profiling in periimplantation mouse uterine luminal epithelium

status: Public on Feb 25 2013

city: ATHENS

first: Shuo

last: Xiao

state: GA

address: 501 DW BROOKS DR

department: Physiology and Pharmacology

institute: University of Georgia

summary: We used the microarray analysis to determine the differential gene expression profiles in mouse uterine luminal epithelium between preimplantation gestation day 3.5 and postimplantation gestation day 4.5, and investigeate the molecular mechanism of the establishment of uterine receptivity and embryo implantation. Uterine luminal epithelium (LE) is critical for the establishment of uterine receptivity during embryo implantation. Many genes are known to have differential expression in the periimplantation LE  but the global profiling of the altered genes in the periimplantation LE is unknown. To fill in this knowledge gap, microarray analysis was performed in gestation day 3.5 (D3.5, preimplantation) and D4.5 (postimplantation) mouse LE from natural pregnancy. There were 382 significantly upregulated and 245 significantly downregulated genes (>2 fold, P<0.05) in the D4.5 LE.

overall_design: There are 6 samples. 3 for gestation day 3.5 uterine luminal epithelium, the other 3 for gestation day 4.5 uterine luminal epithelium

first: Xiaoqin

last: Ye

first: Honlu

last: Diao

first: Fei

last: Zhao

first: Rong

last: Li


title: Expression data of host gene response to Escherichia coli 83972

first: Nataliya

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

overall_design: Refer to individual Series


title: A Cell Epigenotype Specific Model for the Correction of Cellular Heterogeneity in the Brain

status: Public on Feb 22 2013

city: Baltimore

first: Jerry

last: Guintivano

address: 720 Rutland Avenue, Ross 1068

institute: Johns Hopkins University

summary: Cellular heterogeneity may bias cell type specific epigenetic patterns leading to a dramatic increase in false positive or negative findings in psychiatric epigenetic studies. To address this issue, we performed fluorescence activated cell sorting (FACS) of neuronal nuclei in post mortem frontal cortex 58 samples followed by Illumina HM450 microarray based DNA methylation profiling. We characterized the extent of neuron and glia specific DNA methylation variation independent of disease status and identified significant cell type specific epigenetic variation at 51% of loci.

overall_design: DNA methylation was profiled for sorted neuronal nuclei from post mortem frontal cortex of 29 major depression and 29 matched control samples using Illumina HM450 microarrays

first: J

first: M

last: Aryee

first: Z

last: Kaminsky


title: Kdm2b maintains murine embryonic stem cell status by recruiting PRC1 complex to CpG islands of lineage genes [Expression profiling]

status: Public on Feb 20 2013

city: Boston

first: Li

last: Shen

address: 200 Longwood Ave

institute: HHMI/Boston Children's Hospital/Harvard Medical School

summary:
Polycomb group (PcG) proteins play important roles in repressing lineage-specific genes and maintaining the undifferentiated state of mouse embryonic stem cells (mESCs). However, the mechanisms by which PcG proteins are recruited to their targets are largely unknown. Here, we show that the histone demethylase Kdm2b is highly expressed in mESCs and regulated by the pluripotent factors Oct4/Sox2 directly. Depletion of Kdm2b in mESCs causes de-repression of lineage-specific genes and induces early differentiation. The function of Kdm2b depends on its CXXC-ZF domain, which mediates Kdm2b’s genome-wide binding to CpG islands (CGIs). Kdm2b interacts with the core components of the Polycomb repressive complex 1 (PRC1) and recruits the complex to the CGIs of early lineage-specific genes. Thus, our study not only reveals a novel Oct4/Sox2-Kdm2b-PRC1-CGI regulatory axis and its function in maintaining undifferentiated state of mESCs, but also demonstrates a critical function of Kdm2b in recruiting PRC1 to the CGIs of lineage-specific genes to repress their expression.
In this dataset, we include the expression data for control and Kdm2b knockdown mouse embryonic stem cells.

overall_design: We analyzed the gene expression in control and Kdm2b knockdown mouse embryonic stem cells using the Affymetrix MoGene-1_0-st-v1 platform.

first: Jin

last: He

first: Ma

last: Wan

first: Olena

last: Taranova

first: Hao

last: Wu

first: Yi

last: Zhang


title: Expression data from chronic lymphocytic leukemia (CLL) tumors in two time points

status: Public on Feb 21 2013

first: Dan

last: Landau

address: 77 Avenue Louis Pasteur

department: Medical Oncology

institute: DFCI

summary:
As part of a large genetic evolution study we also acquired 3'UTR expression arrays at two time points for the same 18 patients with CLL.
We have analysed the data to evaluate whether genetic evolution (somatic mutations and Somatic copy number alterations) also manifested at the transcriptome level, either globally, or at the level of pre-defined curated geneset that correspond to specfic evolving genetic lesions.

overall_design: Samples were collected at two time points along the patients clinical course, with 13 patients having samples before treatment and at relapse, and 5 patients that were long term non progressors had sampling at two time points without intevening therapy.

first: D

last: Brown

first: C


title: Identification of mRNAs bound and regulated by human LIN28 proteins and molecular requirements for RNA recognition [Affymetrix]

city: New York

first: Miguel

state: New York

address: 1230 York Ave Box 186

institute: The Rockefeller University

summary:
Human LIN28A and B are RNA-binding proteins (RBPs) conserved in animals with important roles during development and stem cell reprogramming. We used Photoactivatable-Ribonucleoside-Enhanced Crosslinking and Immunoprecipitation (PAR-CLIP) in HEK293 cells and identified a largely overlapping set of ~3,000 mRNAs at ~9,500 sites located in the 3’UTR and CDS. In vitro and in vivo, LIN28 preferentially bound single-stranded RNA containing a uridine-rich element and one or more flanking guanosines, and appeared to be able to disrupt base-pairing to access these elements when embedded in predicted secondary structure. In HEK293 cells, LIN28 protein binding mildly stabilized target mRNAs and increased protein abundance. The top targets were its own mRNAs and those of other RBPs and cell-cycle regulators. Alteration of LIN28 protein levels also negatively regulated the abundance of some, but not all let-7 miRNA family members, indicating sequence-specific binding of let-7 precursors to LIN28 proteins and competition with cytoplasmic miRNA biogenesis factors.
To assess whether the transcripts identified by PAR-CLIP are regulated by LIN28B we analyzed the mRNA levels of LIN28B overexpressing and LIN28B-depleted cells using microarrays. Transcripts crosslinked to LIN28B were slightly downregulated upon LIN28B knockdown compared to LIN28B overexpression indicating that LIN28B stabilizes transcripts. The RBP LIN28B was depleted by siRNAs and the expression levels was compared to mock-transfected HEK293 cells

first: Markus

last: Hafner

first: Thomas

last: Tuschl


title: Genome-wide polysome analysis in poly(I:C)-treated WT and Oasl1-/- BMDM.

status: Public on Feb 17 2013

first: Byungil

last: Kim

address: 134 Shin-chon-dong, Seodaemun-gu

department: Biochemistry

institute: Yonsei University

summary:
OASL1 is a novel translation inhibitor for the type I IFN master transcription factor IRF7. To examine whether OASL1 specifically inhibit IRF7 translation, we used a genome-wide gene expression microarray to screen for the polysome-associated mRNAs more enriched in the OASL1 KO BMDMs.
The microarray analysis on the polysomal fractions identified 145 candidate transcripts, including IRF7, that showed a signal greater than two-fold higher in poly(I:C)-treated Oasl1-/- BMDM.

overall_design: We analyzed polysomal fractions from poly(I:C)-treated WT and Oasl1-/- BMDM using the Affymetrix Mouse Gene 1.0 ST array. Array data were processed by Affymetrix GCOS software. We compared these using Affymetrix Expression console1.1, R affy-package(2.9.2), DAVID.

first: Myeong

middle: S

last: Lee

first: Goo

last: Oh

first: Young-Joon


title: Molecular pathways of early CD105-positive erythroid cells as compared to CD34-positive common precursor cells by high-sensitive flow cytometric cell sorting and gene expression profiling

status: Public on Feb 16 2013

city: Linz

first: Johannes

last: Pröll

address: Krankenhausstrasse 7

country: Austria

institute: Red Cross Transfusion Service for Upper Austria

summary:
Gene network of erythropoietic cells
Special attention has recently been drawn to the molecular network of different genes that are responsible for the development of erythroid cells. The aim of our study was to establish in detail the phenotype of early erythroid cells and to compare the gene expression profile of separated early erythroid precursors with the CD34-positive compartment. Multicolor flow cytometric analyses of human bone marrow mononuclear cell fractions (n=20) defined three distinct early erythroid stages. Sorted populations were analyzed for their gene expression profile using Affymetrix array technology. In 4,524 genes, a differential regulation was found in CD105-positive erythroid cells as compared to the CD34 common progenitor compartment (2,362 upregulated genes). A highly significant difference was observed in the expression level of genes with known functions, e.g. transcription factors, heme synthesis, iron and mitochondrial metabolism and transforming growth factor-ß signaling. A comparison with recently published data showed over 800* genes which as yet have not been reported to be upregulated in the early erythroid lineage as compared to the CD34 compartment . The gene expression level within distinct pathways can be illustrated directly by applying the Ingenuity software program. The results of the gene expression analyses can be seen at http://www.ncbi.nlm.nih.gov/geo/info/submission.

overall_design: We analyzed bone marrow CD14 positive, CD105-positive erythroid cells and CD34-positive common precursor cells from  healthy subjects using the Affymetrix HG-U133_Plus_2 platform. Array data was processed by Affymetrix Array Computational Tool. No techinical replicates were performed.

first: Sigrid

last: Machherndl-Spandl

first: Susanne

last: Suessner

first: Martin

last: Danzer

first: Christian

last: Gabriel

first: Jeroen

last: Lauf

first: Rene

last: Sylie

first: Hans-Ullrich

last: Klein

first: Ansgar

last: Weltermann

first: Peter

last: Bettelheim


title: Naïve pluripotency is associated with global DNA hypomethylation

city: London

first: Kirsten

middle: R

last: McEwen

address: Du Cane Road

department: MRC Clinical Sciences Centre

institute: Imperial College London

summary: Naive pluripotent embryonic stem cells (ESCs) and embryonic germ cells (EGCs) are derived from the preimplantation epiblast and primordial germ cells (PGCs), respectively. We investigated whether differences exist between ESCs and EGCs, in view of their distinct developmental origins. PGCs are programmed to undergo global DNA demethylation; however, we find that EGCs and ESCs exhibit equivalent global DNA methylation levels. Importantly, inhibition of Erk and Gsk3b by 2i conditions leads to pronounced reduction in DNA methylation in both cell types. This is driven by Prdm14 and is associated with downregulation of Dnmt3a and Dnmt3b. However, genomic imprints are maintained in 2i, and we report derivation of EGCs with intact genomic imprints. Collectively, our findings establish that culture in 2i instills a naive pluripotent state with a distinctive epigenetic configuration that parallels molecular features observed in both the preimplantation epiblast and nascent PGCs.

overall_design: EGC lines were derived from E8.5 mouse embryos using three different protocols: FCS+LIF on MEFs (FCS, n = 4)), FCS+LIF on MEFs for 48 hours followed by 2i+LIF (2is, n = 4), and direct derivation into 2i+LIF (2i, n = 4). ESC lines were derived in either FCS+LIF on MEFs or in 2i+LIF conditions and once established the cell lines were also switched between the two culture environments (n = 5 for each culture condition). All cell lines were derived from genetically identical embryos.

first: Harry

last: Leitch

first: Aleksandra

last: Turp

first: Vesela

last: Encheva

first: Tom

last: Carroll

first: Nils

last: Grabole

first: William

last: Mansfield

first: Buhe

last: Nashun

first: Jaysen

last: Knezovich

first: Austin

last: Smith

first: M

last: Surani

first: Petra

last: Hajkova


title: Effects of (E)-4-bromo-5-(bromomethylene)-3-methylfuran-2(5H)-one (BF8) on E. coli RP437 persister cells (two biological replicates)

status: Public on Feb 13 2013

city: Syracuse

first: Jiachuan

last: Pan

state: NY

address: 121 Link Hall

institute: Syracuse Unievrsity

summary: Eighteen genes in RP437 persister cells were consistently induced/decreased by treatment with 5 µg/mL BF8 for 1 h.

overall_design: Persister cells were isolated from RP437 overnight cultures and treated with and without BF8 for microarray analysis.

first: Pan

last: Jiachuan

first: Ren

last: Dacheng


title: GENE-EXPRESSION ANALYSIS RELATED TO OLIVE POLLEN ALLERGY

city: Madrid

first: Miriam

last: Aguerri

address: avd/Reyes Católicos, 2

department: Immunology

institute: IIS-Fundación Jiménez Díaz

summary: Analysis of gene-expression profiles by microarrays can be very useful to characterize new potential candidate genes, key regulatory networks, and to define phenotypes or molecular signatures to improve the diagnosis or classification of the disease. We have used this approach in the study of one of the major causes of allergic diseases in Mediterranean countries, the olive pollen response, in order to find differential molecular markers among five clinical groups, Non-allergic, Asymptomatic, Allergic but not to olive pollen, Non-treated, olive pollen allergic patients and Olive pollen allergic patients (under specific-immunotherapy). The results of gene-expression by principal components analysis (PCA) clearly showed five clusters of samples that correlated with the five clinical groups. Analysis of differential gene-expression by multiple testing, and functional analysis by KEGG and Gene-Ontology revealed differential genes and pathways among the 5 clinical groups.

overall_design: The study population comprised 28 subjects, selected from a previous immunological study (Aguerri et al. Eur. J. Inflammation 2012, in press), from Andalusia, who were recruited in 2 olive pollen exposure situations: during (April-June) and outside the pollen season (October-December). We established 5 groups, and 6 subjects from each group were selected for gene-expression analysis: Group 1, non-allergic subjects; Group 2, asymptomatic subjects (diagnosed with olive pollen allergy by skin testing, with no seasonal respiratory symptoms [rhinitis and/or asthma], and who consulted for adverse reaction to drugs); Group 3, patients who were allergic, but not to olive pollen; Group 4, non-treated olive pollen–allergic; and Group 5, olive pollen–allergic patients (receiving olive pollen–specific immunotherapy).The subjects were unrelated and recruited at the Allergy Service of 4 hospitals in Andalusia (Granada, Jaén, Sevilla, and Málaga). Olive pollen–allergic patients fulfilled the following criteria: seasonal rhinitis and/or asthma from April to June, a positive skin prick test result for O. europaea pollen extract (ALK Abelló, Madrid, Spain), and no previous immunotherapy. Informed consent was obtained from each subject. Ethical approval for the study was obtained from the Ethical and Research Committee of the participating hospitals. PBMCs were isolated from heparin-containing peripheral blood samples taken during and outside pollen season, by gradient centrifugation on Lymphoprep (Comercial Rafer, Zaragoza, Spain) following the manufacturer’s instructions.

first: Blanca

last: Cárdaba

first: David

last: Calzada

first: Carlos

last: Lahoz


title: Gene expression profile analysis of mouse whole spleen following infection by lymphocytic choriomeningitis virus (LCMV), comparing LCMV-Armstrong and LCMV-Clone 13 expression patterns at 0, 5, 9, and 30 days

status: Public on Feb 15 2013

city: Cincinnati

first: Rebekah

last: Karns

state: OH

address: 3333 Burnet Ave

department: Gastroenterology, Hepatology, & Nutrition

institute: Cincinnati Children's Hospital Medical Center

summary:
To identify mechanisms behind immunosuppression during virus infections, we infected mice with LCMV-Armstrong and LCMV-Clone 13 expression patterns.  LCMV-Armstrong induces a T-cell reaction that resolves infection within 8-10 days, while LCMV-Clone13 generates a persisten infection through immunosuppression.
We used microarray to uncover splenic gene expression patterns specific to each LCMV infection at 5, 9, and 30 days

overall_design: C57BL6 mice, 6-10 weeks old, were infected with LCMV-Armstrong and LCMV-Clone 13 or left uninfected (naïve).  At days 5, 9, and 30 whole spleens were harvested for RNA extraction and hybridization on Affymetric microarray.

first: Bruce

last: Aronow

last: Brooks


title: Expression data from iMyc mouse B lymphoma and human DLBCL

city: Iowa City

first: Siegfried

last: Janz

state: Iowa

address: 500 Newton Road

department: Pathology

institute: University of Iowa

summary: Cross-species comparative gene expression profiling was performed to identify differentially expressed genes conserved in aggressive B lymphomas.

overall_design: Whole genome expression arrays from mouse B220+ splenic B cells (wild-type C57BL/6, B6) were compared to whole tumors (approximately >75% neoplastic cells) from B6.iMyc mice.  Correspondingly, isolated human peripheral blood B cells were compared to human diffuse large B cell (DLBCL) whole tumors (approximately >75% neoplastic cells) DLBCL.


title: Expression data from the comparison between poly(I:C)-treated WT and Oasl1-/- BMDMs

first: Byungil

last: Kim

summary:
Oasl1-/- BMDMs express more type I IFN upon poly(I:C) treatment. Because OASL1 seems to rather specifically suppress the type I IFN expression, we tried to address the specificity by determining the defects associated with the Oasl1 mutation using genome-wide gene expression microarray analysis under moderate poly(I:C) stimulation (5 µg/ml for 9 h); this condition was used to identify the primary targets of OASL1 while minimizing the secondary targets induced by the earlier, higher production of type I IFNs in Oasl1-/- cells.
Only 23 genes out of approximately 35,000 probed transcripts showed a signal difference greater than two-fold between the WT and KO cells; 15 showed higher signals in KO cells while 8 showed lower signals in KO cells

overall_design: We analyzed total RNA from poly(I:C)-treated WT and Oasl1-/- BMDM using the Affymetrix Mouse Gene 1.0 ST array. Array data were processed by Affymetrix GCOS software. We compared these using Affymetrix Expression console1.1, TMEV4.4, DAVID.

first: Myeong

last: Lee

first: Goo

last: Oh

first: Young-Joon


title: Dysregulated gene expression in Mef2a knockout mice subjected to cardiotoxin-induced muscle injury

status: Public on Feb 12 2013

first: Frank

last: Naya

address: 24 Cummington Mall

institute: Boston University

summary: We identified genes expressed in mouse skeletal muscle, during the process of muscle regeneration after injury, which are dysregulated in the absence of Mef2a expression. MEF2A is a member of the evolutionarily conserved MEF2 transcription factor family which has known roles in cardiac muscle development and function, but is not well studied in skeletal muscle. We performed a comparison of gene expression profiles in wild type and MEF2A knockout tibialis anterior muscle, seven days post-injury with cardiotoxin. The results indicated that a variety of genes expressed during muscle regeneration, predominantly microRNAs in the Gtl2-Dio3 locus, are dysregulated by the loss of MEF2A expression.

overall_design: Skeletal muscle RNA used in the present study included the following two sample groups: (WT) pooled total RNA from tibialis anterior muscle taken from 5 wild type mice at seven days post-injury with 10uM cardiotoxin; (KO) pooled total RNA from tibialis anterior muscle taken from 5 Mef2a knockout mice at seven days post-injury with 10uM cardiotoxin. All mice were between 2-4 months of age. Both male and female mice were used.

first: Christine

last: Snyder

first: Francisco


title: Comparing molecular assessment of implantation biopsies with histologic and demographic risk assessment.

city: Edmonton

first: Jessica

last: Chang

address: 250 Heritage Medical Research Centre

country: Canada

institute: University of Alberta

summary: In deceased donor kidney transplantation, acute kidney injury (AKI) prioir to surgery is a major determinant of delayed graft function (DGF), but AKI is histologically silent and difficult to assess. We hypothesized that a molecular measurement of AKI would add power to conventional risk assessments to predict the early poor allograft function at first week post transplantation.

overall_design: We performed microarrays on implantation biopsies taken during reperfusion in 70 deceased donor kidneys from 53 donors.  Early poor function was classified by two definitions on day 7 post-transplantation: serum creatinine greater than 265 umol/L (3 mg/dL) or the requirement for dialysis.  Donor age and related risk scores (Irish, Schold, KDRI) associated with worse early function, as expected, but histologic features (glomerulosclerosis; pathology risk scores (Remuzzi, MAPI)) correlated with donor age but not with poor function.  However, molecular AKI signal,  previously defined in kidneys with early injury, was the best single predictor of poor allograft function. The combination of donor age and the AKI signal improved the prediction of poor function.  In addition, asssessments of tissue quality particularly donor age, Banff ct, Irish and KDRI scores, showed negative correlative trend with late graft function, whereas the AKI signal did not. Thus donor age and the molecular AKI signal are the main predictors of early impaired function, but have little impact on survival.

first: Chatchai

last: Kreepala

first: Konrad

last: Famulski

first: Philip

middle: F

last: Halloran


title: Transcriptome analysis of OECM1 after expression of let-7i

status: Public on Feb 11 2013

city: Taipei

first: Muh-Hwa

last: Yang

address: No.155, Sec.2, Li-Nong Street

department: Institute of Clinical Medicine

country: Taiwan

institute: National Yang-Ming University

summary: Expression of let-7i results in transcriptome alteractions in head and neck cancer cell line, OECM1.

overall_design: Stable transfection of pmCherry-let7i in OECM1 cell and analyzed the transcriptome by cDNA microarray. OECM1 transfected with pmCherry empty vector was used as a control of experiment.

first: Wen-Hao


title: Cardiomyocyte specific plin5 over expression

status: Public on Feb 09 2013

first: carole

last: sztalryd

state: Maryland

address: 650 West Redwwod Street

institute: University of Maryland

summary: Presence of ectopic lipid droplets (LDs) in cardiac muscle is associated to lipotoxicity and tissue dysfunction.  However, presence of LDs in heart is also observed in physiological conditions, such as at times when cellular energy needs and energy production from mitochondria fatty acid (FA) β-oxidation are high (fasting).  This suggests that development of tissue lipotoxicity and dysfunction is not simply due to the presence of LDs in cardiac muscle but due at least in part to alterations in LD function.  To examine the function of cardiac LDs, we obtained transgenic mice with heart-specific plin5 over-expression (MHC-plin5), a member of the perilipin protein family. Hearts from MHC-plin5 mice expressed at least 4-fold higher levels of plin5 and exhibit a 3.5- fold increase in triglyceride content versus non-transgenic littermate.  Chronic cardiac excess of LDs was found to result in mild heart dysfunction with decreased expression of PPARα target genes, decreased mitochondria function and left ventricular concentric hypertrophia.  Lack of more severe heart function complications may have been prevented by a strong increased expression of oxidative induced genes via NF-E2-related factor 2 anti-oxidative pathway. Perilipin 5 regulates the formation and stabilization of cardiac LDs, and promotes cardiac steatosis without major heart function impairment.

overall_design: Hearts from Four MCH-Plin5 mice and four control mice at the age of 12 weeks were harvested

first: Carole

last: Sztalryd

first: Hong

last: Wang

first: Urmila

last: Sreenivasan

first: Anup

last: mahurkar

first: Yezhou

last: Sun


title: Exome and whole genome sequencing of esophageal adenocarcinoma identifies recurrent driver events and mutational complexity

first: Shouyong

last: Peng

address: 450 Brookline Avenue

institute: Dana-Farber Cancer Institute

summary: The incidence of esophageal adenocarcinoma (EAC) has risen 600% over the last 30 years.  With an extremely poor five-year survival rate of only 15%, identification of new therapeutic targets for EAC is of great importance. Here, we analyze the mutation spectra from the whole exome sequencing of 149 EAC tumors/normal pairs, 15 of which have also been subjected to whole genome sequencing. We identify a novel mutational signature in EACs defined by a high prevalence of A to C transversions at Ap*A dinucleotides. Statistical analysis of the exome data identified 26 genes that are mutated at a significant frequency. Of these 26 genes, only four (TP53, CDKN2A, SMAD4, and PIK3CA) have been previously implicated in EAC. The novel significantly mutated genes include several chromatin modifying factors and candidate contributors to EAC: SPG20, TLR4, ELMO1, and DOCK2.   Notably, functional analyses of EAC-derived mutations in ELMO1 increase cellular invasion. Therefore, we suggest a new hypothesis about the potential activation of the RAC1 pathway to be a contributor to EAC tumorigenesis.

overall_design: The study aimed to analyze 150 primary, human esophageal adenocarcinoma samples by whole genome and whole exome sequencing (which will be deposited to dbGAP following the TCGA practice).  RNA expression data was used to determine gene expression in 14 of the samples analyzed by whole genome sequencing. No normals were analyzed.

first: Austin

last: Dulak

first: Petar

last: Stojanov

first: Tony

last: Godfrey

first: Gad

last: Getz

first: Adam

last: Bass


title: lung carcinoid

status: Public on Feb 08 2013

city: Milan

first: Gabriele

last: Bucci

address: Via Olgettina 60

department: Center of Translational Genomics and Bioinformatics

institute: Università vita e Salute Ospedale San Raffaele

summary:
Global gene expression of  13 frozen samples, 6 from typical and 7 from atypical surgically resected primary lung carcinoids
All the patients not chemo-radio naïve and with a second tumor were excluded from the study. A written informed consent for research use of biological samples was obtained from all the patients.

overall_design: tissue biopsies

first: Francesca

last: Toffalorio

first: Elena

last: Belloni

first: Massimo

last: Barberis

first: Gabrile

first: Laura

last: Tizzoni

first: Giancarlo

last: Pruneri

first: Caterina

last: Fumagalli

first: Gianluca

last: Spitaleri

first: Chiara

last: Catania

first: Flavia

last: Melotti

first: Pier

last: Pelicci

first: Lorenzo

last: Spaggiari

first: Tommaso

last: De Pas


title: Expression data from antimycin A-treated BE(2)-C cells

city: Ann Arbor

first: David

last: Miller

address: 3560B MSRB II, 1150 W. Medical Center Dr.

department: Internal Medicine

institute: University of Michigan

summary: Analysis of transcription response of undifferentiated human BE(2)-C neuronal cells to stimulation with purified antimycin A1a or unfractionated commercially available antimycin A (Sigma A8674).

overall_design: Three independent sets of BE(2)-C cells were treated DMSO control or 200 nM of either purified antimycin A1a or unfractionated antimycin A.  Total RNA was harvested at 24 h after stimulation and analyzed with Affymetrix U133 Plus 2.0 chips.


title: Expression data from wild type and globally hypomethylated mouse embryonic stem cells (ESCs) during their differentiation as embyroid bodies

status: Public on Feb 05 2013

city: Planegg-Martinsried

first: Fabio

last: Spada

state: Bavaria

address: Grosshaderner Str. 2

department: Biology

institute: Ludwig Maximilian University Munich

summary: To analyze the role of DNA methylation during differentiation, we performed genome-wide expression analysis of undifferentiated wild type, dnmt1-/- and triple knock out (TKO; dnmt1-/-, dnmt3a-/-, dnmt3b-/-) ESCs as well as respective embryoid bodies (EBs) at two stages of differentiation

overall_design: We generated EBs from wild type, dnmt1-/- and TKO ESCs using the hanging drop method and performed affymetrix microarray expression analysis at three time points; i) in the undifferentiated ESC state (d0), ii) early EB differentiation (d4) and iii) later EB differentiation stage (d16).

first: Christine

last: Schmidt


title: Expression data from mobilized human CD34+ cells

first: Maureen

last: Lane

address: 1300 York Avenue

institute: Weill Cornell Medical College

summary: Bortezomib-based secondary induction therapy and mobilization could represent alternative strategies to reduce tumor burden. We used microarrays to investigate genome-wide expression changes between bortezomib and non-bortzomib mobilizaton strategies and identified distinct genes and pathways that were significantly differentially regulated.

overall_design: CD34+ stem cells were enriched from leukapheresis products from multiple myeloma patients treated with a bortezomib- or non-bortezomib-based mobilization. RNA extraction, amplification and hybridization on Affymetrix microarrays was performed. Post-induction stem cell collection was initiated when patients' ANC reached >1.0×10^9/L.

first: Ruben

last: Niesvizky


title: Comparative gene expression analysis of mesenchymal stem cells (MSC) derived  from non-small cell lung cancer (NSCLC) and corresponding normal lung tissue (NLT)

status: Public on Feb 07 2013

city: Heidelberg

first: Ruprecht

last: Kuner

address: Im Neuenheimer Feld 460

department: Molecular Genetics

institute: German Cancer Research Center and National Center of Tumor Diseases

summary: The stromal microenvironment plays a vital role in cancer initiation and progression. We performed a comparative expression profiling of pulmonary MSC derived from NSCLC and corresponding normal lung tissue of 5 newly diagnosed patients. The analysis indicated variable expression of genes involved in DNA repair, apoptosis, proliferation or angiogenesis between NSCLC-MSC and NLT-MSC.

overall_design: MSC were derived from NSCLC and corresponding normal lung tissue of 5 patients. Paired SAM test was performed to screen for differentially expressed genes between NSCLC-MSC and NLT-MSC.

first: Holger

last: Sueltmann

first: Christian

last: Bender

first: Michael

last: Meister

first: Sandra

last: Gottschling


title: Characterization of gene expression of tumor infiltrating T cells (TILs) in previously untreated patients with follicular lymphoma (FL) compared with those of tonsils

first: Shahryar

last: Kiaii

address: Charterhouse Square

department: Centre of Haemato-Oncology

institute: Barts Cancer Institute, Queen Mary University, School of Medicine and Dentistry

summary: It has been shown that tumor infiltrating immune cells have a profound impact on the outcome of FL. To find mechanisms whereby TILs are altered gene expession analysis of highly pure TILs were performed.

overall_design: The study is composed of 4 groups, FL CD4 (n=12), FL CD8 (n=9), Tonsil CD4 (n=7) and Tonsil CD8 (n=7). All FL patients were treatment naive. Cells were flowsorted from cryopreserved single cell suspensions and purity of cells were at least 95%.

first: Ajanthah

last: Sangaralingam

first: John

last: Gribben


title: DNA methylation profiling of normal prostates and prostate cancer metastases [Illumina]

status: Public on Feb 04 2013

city: Charlestown

first: Martin

last: Aryee

address: 149 13th Street

institute: Massachusetts General Hospital

summary: DNA methylation profiling of normal prostates from organ donors and prostate cancer metastases from a rapid autopsy cohort of lethal metastatic prostate cancer

overall_design: Metastases from prostate cancer patients. Normal prostate samples from organ donors

first: Srinivasan

last: Yegnasubramanian


title: Expression data of differentiated human erythroid cells with or without Tranylcypromine (TC) treatment

first: Lihong

last: Shi

address: 3608 BSRB, 109 Zina Pitcher Place

summary:
We found that LSD1 inhibition by a monoamine oxidase inhibitor, tranylcypromine (TC), could enhance fetal gamma globin expression.
Global effects of TC on erythroid expession were conducted by HG-U219 array strips.

overall_design: Primary human erythroid cells, which differentiated from CD34+ cells for 8 days,  were harvested before or and after TC treatment (0.5 µM, 1.5 µM or 5 µM)  for the gene expression analysis.

first: Shuaiying

last: Cui

first: James

last: Engel

first: Osamu

last: Tanabe


title: Intrinsic glioma subtypes in EORTC 26951 (part 5)

status: Public on Feb 01 2013

city: Rotterdam

first: Pim

last: French

address: Dr Molewaterplein 50

department: Neurology

country: Netherlands

institute: Erasmus MC

summary: Background: Intrinsic glioma subtypes (IGS) are molecularly similar tumors that can be identified based on unsupervised gene-expression analysis. Here, we have evaluated the clinical relevance of these subtypes within EORTC26951, a randomized phase III clinical trial investigating adjuvant procarbazine, CCNU (lomustine) and vincristine (PCV) chemotherapy in anaplastic oligodendroglial tumors. Our study is the first to include gene-expression profiles of formalin-fixed and paraffin-embedded (FFPE) clinical trial samples. Methods: Gene-expression profiling was performed in 140 samples: 47 fresh frozen and 93 FFPE, on HU133_Plus_2.0 and HuEx_1.0_st arrays (Affymetrix), respectively.  Results: All previously identified six intrinsic glioma subtypes are present in EORTC26951. This confirms that different molecular subtypes are present within a well-defined histological subtype. Intrinsic subtypes are highly prognostic for overall- (OS) and progression-free survival (PFS). They are prognostic for PFS independent of clinical (age, performance, tumor location), molecular (1p19qLOH, IDH1 mutation, MGMT methylation) and histological parameters. Combining known molecular (1p19LOH, IDH1) prognostic parameters with intrinsic subtypes improves outcome prediction (Proportion of Explained Variation 30% v 23%). Specific genetic changes (IDH1, 1p19qLOH and EGFR amplification) segregate into different subtypes. We identified one subtype, IGS-9 (characterized by a high percentage of 1p19qLOH and IDH1 mutations), that especially benefits from PCV chemotherapy. Median OS in this subtype was 5.5 years after radiotherapy (RT) alone v 12.8 years after RT/PCV; P=0.0349; HR 2.18, 95% CI [1.06, 4.50]. Conclusion: Intrinsic subtypes are highly prognostic in EORTC26951 and improve outcome prediction when combined with other prognostic factors. Tumors assigned to IGS-9 benefit from adjuvant PCV

overall_design: A total of 140 samples were included in this study, profiles of 95 were FFPE derived samples run on exon arrays. 12 samples (part 2) can also be found in GSE16011 (PMID 19920198 and 16357140), and 6 from Oncomine (part 3).

first: Lale

last: Erdem

first: Lonneke

middle: A

last: Gravendeel

first: Johan

last: de Rooi

first: Paul

last: Eilers

first: Ahmed

last: Idbaih

first: Wim

last: Spliet

first: Wilfred

last: den Dunnen

first: Johannes

middle: L

last: Teepen

first: Pieter

last: Wesseling

first: Peter

last: Sillevis Smitt

last: Kros

first: Thierry

last: Gorlia

last: van den Bent


title: Expression data from  SW480 cells with Gankyrin knockdown

city: Beijing

first: Bai

middle: Zhao

last: Fang

state: Beijing

address: 27 Tai-Ping Road

institute: National Center of Biomedical Analysis

summary: we performed genome-wide screening  using SW480 cells with Gankyrin knockdown on  an Affymetrix gene expression array to identify the transcriptional targets of Gankyrin

overall_design: Transcriptional profiling with samples from SW480 cells that were infected with control or gankyrin shRNA. Two condition experiment: control shRNA (three replicates) and NFIL3 shRNA (three replicates)

first: Cheng

last: Zhen

first: Zhaofang

last: Bai

first: Tao

last: Zhou


title: Intrinsic glioma subtypes in EORTC 26951 (part 4)

last: French

last: Erdem

middle: M

first: Martin


title: BL2 cells stimulated with B cell specific paracrine stimuli

city: Regensburg

first: Katharina

last: Meyer

address: Josef Engert Street 9

department: Statistical Bioinformatics

institute: Institute for Functional Genomics

summary: Expression data of BL2 Burkitt Lymphoma cell line (controls and samples treated with different B cell specific stimuli)

overall_design: BL2 cells were cultured in RPMI and stimulated with the respective agents (rhCD40L, rhIL21, rhBAFF, LPS and antiIgM F(ab) fragments) for indicated timepoints. Cells were harvested and total RNA was isolated for gene expression profiling. The experiments were conducted in 2-3 biological replicates.

first: Alexandra

last: Schrader

first: Frederike

last: von Bonin

first: Martina

last: Vockerodt

first: Neele

last: Walther

first: Elisabeth

last: Hand

first: Antje

last: Ulrich

first: Kamila

last: Matulewicz

first: Dido

last: Lenze

first: Michael

last: Hummel

first: Arnd

last: Kieser

last: Engelke

first: Lorenz

last: Trümper

first: Dieter

last: Kube


title: Gene response to major burn injuries

city: Boston

first: Wenzhong Xiao

state: MA

address: 55 Fruit Street, GRV 1302

department: Department of Surgery

summary:
Blood was sampled from severe burns patients over time as well as healthy subjects. Genome-wide expression analyses were conducted using the Affymetrix U133 plus 2.0 GeneChip™.
The Inflammation and the Host Response to Injury Large-Scale Collaborative Research Program

overall_design: Blood was sampled from 244 severe burns patients over time as well as 35 healthy subjects who consented to blood sampling. Study subjects were treated under standard operating procedures to minimize treatment variations. Patients had burns covering >20% of the total body surface area and were admitted within 96 hours of injury.  Genome-wide expression analyses were conducted using the Affymetrix U133 plus 2.0 GeneChip™.

first: David

middle: N

last: Herndon

first: Henry

middle: V

last: Baker

first: Celeste

middle: C

last: Finnerty

first: Hong

last: Gao

first: Wenzhong

last: Xiao

first: Marc

last: Jeschke

first: M

last: Lopez

first: Brian

last: Lobo

first: LaToya

last: Patterson

first: Johnathan

last: Rice

first: Matthew

last: Klein

first: Richard

last: Gamelli

first: Nicole

last: Gibran

first: Lyle

last: Moldawer

last: Mindrinos

first: Brett

last: Arnoldo

first: Ronald

last: Tompkins


title: Intrinsic glioma subtypes in EORTC 26951 (part 3)

first: Pim

last: French

first: Lale

last: Erdem

first: Lonneke

last: Gravendeel

first: Johan

last: de Rooi

first: Paul

middle: H

last: Eilers

first: Ahmed

last: Idbaih

first: Wim

middle: G

last: Spliet

first: Wilfred

last: den Dunnen

first: Johannes

last: Teepen

first: Pieter

last: Wesseling

first: Peter

last: Sillevis Smitt

last: Kros

first: Thierry

last: Gorlia

first: Martin

last: van den Bent


title: The transient chondrocyte phenotype in osteophytic cartilage - a role of PEDF?

status: Public on Jan 31 2013

city: Erlangen

first: Arif

middle: B

last: Ekici

address: Schwabachanlage 10

institute: Institute of Human Genetics

summary: Pigment Epithelium-Derived Factor (PEDF) has recently been identified as a factor that is significantly upregulated in late-stage osteoarthritic cartilage in which chondrocytes are confronted with terminal differentiation and cell death. Since PEDF is known to induce cell death of endothelial cells, it may also be responsible for terminal differentiation and cell death in cartilage.

overall_design: Using cDNA microarray analysis, we found PEDF among the factors with the strongest differential expression and significant higher levels (118.5-fold) in osteophytic cartilage compared with articular cartilage. This study explored if PEDF interferes with the stable chondrocyte phenotype by promoting terminal differentiation or cell death.

first: Patricia

last: Klinger

first: Kolja

last: Gelse


title: Gene expression profiling in bone-marrow-derived neutrophils of lcn2 deficient mouse

city: Cleveland

first: Zhuoming

last: Liu

address: 2103 Cornell Road

institute: Case Western Reserve University

summary:
Lipocalin 24p3 (24p3) is a neutrophil secondary granule protein. 24p3 is also a siderocalin, which binds several bacterial siderophores. It was therefore proposed that synthesis and secretion of 24p3 by stimulated macrophages or release of 24p3 upon neutrophil degranulation sequesters iron-laden siderophores to attenuate bacterial growth. Accordingly, 24p3-deficient mice are susceptible to bacterial pathogens whose siderophores would normally be chelated by 24p3. Specific granule deficiency (SGD) is a rare congenital disorder characterized by complete absence of proteins in secondary granules. Neutrophils from SGD patients, who are prone to bacterial infections, lack normal functions but the potential role of 24p3 in neutrophil dysfunction in SGD is not known. Here we show that neutrophils from 24p3-deficient mice are defective in many neutrophil functions. Specifically, neutrophils in 24p3-deficient mice do not extravasate to sites of infection and are defective for chemotaxis. A transcriptome analysis revealed that genes that control cytoskeletal reorganization are selectively suppressed in 24p3-deficient neutrophils. Additionally, small regulatory RNAs (miRNAs) that control upstream regulators of cytoskeletal proteins are also increased in 24p3-deficient neutrophils. Further, 24p3-deficient neutrophils failed to phagocytose bacteria, which may account for the enhanced sensitivity of 24p3-deficient mice to both intracellular (Listeria monocytogenes) and extracellular (Candida albicans, Staphylococcus aureus) pathogens. Interestingly, Listeria does not secrete siderophores and additionally, the siderophore secreted by Candida is not sequestered by 24p3. Therefore, the heightened sensitivity of 24p3-deficient mice to these pathogens is not due to sequestration of siderophores limiting iron availability, but is a consequence of impaired neutrophil function.
Key words: Lipocalin, 24p3, neutrophils, cell motility, chemotaxis, MIRNA-362-3p

overall_design: To address the role of lipocalin 2 in unstimulated and fMLP-stimulated neutrophils derived from mouse bone marrow, we performed micorarray analysis of gene expression in unstimulated wild type (N=3), unstimulated lcn2 knockout (N=3), fMLP-stimulated wild type (N=2) and fMLP-stimulated lcn2 knockout (N=2) neutrophils. Upon stimulation, neutrophils were treated by fMLP at 10 micromolar for 20 minutes at 37 centigrade.

first: L

last: Devireddy

first: Z


title: Expression profiles in response to HMGA overexpression in late-stage neural precursor cells

city: Tokyo

first: Yukiko

last: Gotoh

address: Bunkyo-ku, Yayoi, 1-1-1

department: IMCB

country: Japan

institute: the Univ. of Tokyo

summary: Neural precursor cells (NPCs) in the mammalian neocortex generate various neuronal and glial cell types in a developmental stage-dependent manner. Most neocortical NPCs lose their neurogenic potential after birth. We have previously shown that high mobility group A (HMGA) proteins confer the neurogenic potential on early-stage NPCs during the midgestation period, although the underlying mechanisms are not fully understood. Here we performed microarray analysis and compared expression profiles between control and HMGA2-overexpressed NPCs.

overall_design: Mouse neocortical neuroepithelial cells were isolated at embryonic day 11.5 and cultured as neurospheres for 9 days in vitro in the presence of fibroblast growth factor (FGF) 2 and epidermal growth factor (EGF). These cells were infected with control or HMGA2-expressing retrovirus, cultured in the presence of FGF and EGF for 3 days. Half of them were collected immediately for microarray analysis, and the other half were cultured in the absence of FGF for 12 h and then collected for microarray analysis.

first: Yuki

last: Fujii

first: Yusuke

last: Kishi


title: Expression profiling in bone-marrow-derived neutrophils of lcn2 deficient mouse

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

platform_organism:
Mus musculus
synthetic construct

overall_design: Refer to individual Series


title: DNA methylation alterations exhibit striking intra-individual stability and inter-individual heterogeneity across metastatic dissemination

last: Aryee

first: Srinivasan

last: Yegnasubramanian


title: Characterization of A Novel CRAC Inhibitor that Potently Blocks Human T cell Activation and Effector Functions

city: Nutley

first: Kai

last: Lau

address: 340 Kingsland St

institute: Hoffmann-La Roche

summary: Store operated calcium entry (SOCE) downstream of T cell receptor (TCR) activation in T lymphocytes has been shown to be mediated mainly through the Calcium Release Activated Calcium (CRAC) channel. Here, we compared the effects of a novel, potent and selective CRAC inhibitor, 2,6-Difluoro-N-{5-[4-methyl-1-(5-methyl-thiazol-2-yl)-1,2,5,6-tetrahydro-pyridin-3-yl]-pyrazin-2-yl}-benzamide (RO2959), on T cell effector functions with that of a previously reported CRAC channel inhibitor, YM-58483, and a calcineurin inhibitor Cyclosporin A (CsA). Using both electrophysiological and calcium-based fluorescence measurements, we showed that RO2959 is a potent SOCE inhibitor that blocked an IP3-dependent current in CRAC-expressing RBL-2H3 cells and CHO cells stably expressing human Orai1 and Stim1, as well as SOCE in human primary CD4+ T cells triggered by either TCR stimulation or thapsigargin treatment. Furthermore, we demonstrated that RO2959 completely inhibited cytokine production as well as T cell proliferation mediated by TCR stimulation or MLR (Mixed Lymphocyte Reaction). Lastly, we showed by gene expression array analysis that RO2959 potently blocked TCR triggered gene expression and T cell functional pathways similar to CsA and FK506. Thus, both from a functional and transcriptional level, our data provide evidence that RO2959 is a novel and selective CRAC inhibitor that potently inhibits human T cell functions.

overall_design: PBMC from healthy donors (n=4) were stimulated with anti-CD3/CD28 in the presence or absence of CRAC inhibitor, CsA or FK506 for 24 hrs

first: Gang

last: Chen

first: Sandip

last: Panicker

first: Kai-Yeung

first: Subramaniam

last: Apparsundaram

first: Vaishali

last: Patel

first: Shiow-Ling

first: Rothschild

last: Soto

first: Jimmy

middle: K

last: Jung

first: Palanikumar

last: Ravindran

first: Dayne

last: Okuhara

first: Gary

last: Bohnert

first: Qinglin

last: Che

middle: E

last: Rao

first: John

middle: D

last: Allard

first: Laura

last: Badi

first: Hans-Marcus

last: Bitter

first: Philip

last: Nunn

first: Satwant

last: Narula

first: Julie

last: DeMartino


title: Expression data from NIH-3T3 cells infected with MCMV for 2, 4 or 6h

city: Cambridge

first: Lars

last: Dölken

state: Cambridgeshire

address: Addenbrookes Hospital, Hills Road

department: Medicine

institute: University of Cambridge

summary:
Expression data from NIH-3T3 cells left uninfected or infected with MCMV for 2, 4 or 6h on total RNA as well as newly transcribed RNA labeled for 1-2, 3-4, and 5-6hpi. For newly transcribed RNA, the isolated RNA was labeled for 1h and separated from total cellular RNA following Trizol RNA preparation and thiol-specific biotinylation. We used microarrays to analyze the effects of MCMV infection in total and newly transcribed RNA.
During viral infections cellular gene expression is subject to rapid alterations induced by both viral and antiviral mechanisms. In this study, we applied metabolic labeling of newly transcribed RNA with 4-thiouridine (4sU-tagging) to dissect the real-time kinetics of cellular and viral transcriptional activity during lytic murine cytomegalovirus (MCMV) infection. Microarray profiling on newly transcribed RNA obtained from different times during the first six hours of MCMV infection revealed discrete functional networks of cellular genes regulated with distinct kinetics at surprising temporal resolution. Most of these were undetectable in total RNA, either due to low temporal sensitivity of standard gene expression profiling using total RNA, or due to rapid (viral) counter-regulation. Furthermore, metabolic labeling and purification of newly transcribed RNA detailed the real-time kinetics and regulation of viral gene expression in absence of any interfering virion-associated RNA. Both qRT-PCR and next-generation sequencing of newly transcribed RNA demonstrated an unexpected peak of viral gene expression during the first two hours of infection including transcription of immediate early, early and even well characterized late genes. Interestingly, this peak was subject to rapid gene silencing (independent of the multiplicity of infection) with similar transcriptional activity only reached late in infection. For some genes, e.g. m152, this resulted in massive down-regulation of transcriptional activity by 6 hours post infection, which was not even reversed late in infection. Our findings thus highlight the importance of transcriptional activity during the first few hours of CMV infection and hint at novel mechanisms governing the kinetics of viral gene expression. In conclusion, studying real-time transcriptional activity during lytic CMV infection provides intriguing new insights into the regulation of cellular and viral gene expression.

overall_design: NIH-3T3 cells (5th to 15th passage after thawing) were split from confluent plates 24h before start of the experiment. At the beginning of the experiment about 80% confluency was reached. The experiment was started by applying fresh, prewarmed, CO2-equilibrated medium containing either mock or MCMV particles (MOI 1). The MOI was increased by ~10-fold through centrifugal enhancement (2000g, 30min). Labeling was started 1, 3, or 5hpi after the end of centrifugal enhancement.

last: Doelken


title: HIPK2 and MED19 are new regulators of androgen receptor in prostate cancer cells

status: Public on Jan 30 2013

city: New York

first: Michael

last: Garabedian

address: 550 First Avenue

department: Microbiology

institute: NYU School of Medicine

summary:
The androgen receptor (AR) is a mediator of both androgen-dependent and castration- resistant prostate cancers.  Identification of cellular factors affecting AR transcriptional activity could in principle yield new targets that reduce AR activity and combat prostate cancer, yet a comprehensive analysis of the genes required for AR-dependent transcriptional activity has not been determined.  Using an unbiased genetic approach that takes advantage of the evolutionary conservation of AR signaling, we have conducted a genome-wide RNAi screen in Drosophila cells for genes required for AR transcriptional activity and applied the results to human prostate cancer cells.  We identified 45 AR-regulators, which include known pathway components and genes with functions not previously linked to AR regulation, such as HIPK2 (a protein kinase) and MED19 (a subunit of the Mediator complex).  Depletion of HIPK2 and MED19 in human prostate cancer cells decreased AR target gene expression and, importantly, reduced the proliferation of androgen-dependent and castration-resistant prostate cancer cells.  We also systematically analyzed additional Mediator subunits and uncovered a small subset of Mediator subunits that interpret AR signaling and affect AR-dependent transcription and prostate cancer cell proliferation.  Importantly, targeting of HIPK2 by an FDA approved kinase inhibitor phenocopied the effect of depletion by RNAi and reduced the growth of AR-positive, but not AR negative, treatment-resistant prostate cancer cells.  Thus, our screen has yielded new AR regulators including drugable targets that reduce the proliferation of castration-resistant prostate cancer cells.
HIPK2 and MED19 were identified via a genome-wide RNAi screen as new androgen receptor (AR) reulators.  Our goal in performing this microarray was to identify the gene regulated by HIPK2 and MED19 in a late stage prostate cancer cell line (LNCaP-abl), and to see what genes are in common with known genes to be regulated by AR, and what genes are unique to HIPK2 or MED19.

overall_design: Knockdown of HIPK2 and MED19 was tested in LNCaP-abl cells against control. Each was performed in duplicates. Six samples were analyzed

first: Keren

last: Imberg

first: Alex

last: Greenfield


title: Genes regulated by UCHL1 in ovarian cancer cells

city: Hangzhou

first: Chengmeng

last: Jin

state: zhejiang

address: 268 kaixuan road

department: SBP

institute: ZCNI

summary: UCHL1 is related to apoptosis and proliferation in cancers and we sought to identify genes regulated by UCHL1

overall_design: UCHL1 was knocked down in A2780 (A2780-shUCHL1). A2780-shUCHL1 and A2780-control were cultured in RPMI and total RNA was extracted and hybridizated on Affymetrix.GeneChip.HG-U133_Plus_2

first: Biaoyang

last: Lin


title: Identification of genes responsive to mild hyperthermia in human oral squamous cell carcinoma HSC-3 cells

city: Toyama

first: Yoshiaki

last: Tabuchi

state: Toyama

address: 2630 Sugitani

department: Life Science Research Center

institute: University of Toyama

summary:
Hyperthermia (HT) is widely used to treat patients with various cancers. In general, HT elicits a wide spectrum of stress responses, such as induction of heat shock proteins, protein aggregation and cell death in mammalian cells. Although many biological processes are affected by HT, the overall responses to HT in mammalian cells remain unknown.
The effects of heat stress at 41°C for 30 min (mild hyperthermia) on the gene expression in human oral squamous cell carcinoma HSC-3 cells were investigated using an Affymetrix GeneChip system.

overall_design: Human oral squamous cell carcinoma HSC-3 cells were treated with heat stress (41°C for 30 min), followed by incubation for 0, 1, or 3 h at 37°C. Non-treated cells served as control. Total RNA samples were prepared from the cells, and quality of the RNA was analyzed using a Bioanalyzer 2100. Gene expression was monitored by an Affymetrix GeneChip® system with a Human Genome U133-Plus 2.0 array. Sample preparation for array hybridization was carried out as described in the manufacturer's instructions.

first: Ayako

last: Kariya

first: Tatsuya

last: Yunoki


title: Gene expression following epigenetic drug treatment

city: Barcelona

first: Pedro

last: Jares

state: Barcelona

address: c/ Villarroel 170

department: Genomics Unit

institute: IDIBAPS

overall_design: MCL cell lines were treated with aza and aza in combination with TSA. Gene expression following drug treatment was compared with untreated cells.

first: Verónica

last: Fermández

first: Anna

last: Enjuanes


title: Gene expression of cultured human fetal liver hematopoietic stem and progenitor cells (HSPC) and their supportive ex vivo OP9 stromal niche cells

city: Los Angeles

first: Mattias

last: Magnusson

state: CA

address: 621 Charles E Young Drive South, 2204

department: MCDB

institute: UCLA


title: Gene expression analysis of human fetal liver hematopoietic stem and progenitor cells (HSPC) in culture

summary: One of the long-standing goals in the field has been to establish a culture system that would allow maintenance of HSC properties ex vivo. In the absence of such system, the ability to model human hematopoiesis in vitro has been limited, and there has been little progress in the expansion of human HSCs for clinical application. To that end, we defined a mesenchyml stem cell co-culture system for expansion of clonally multipotent human HSPCs that are protected from apoptosis and immediate differentiation, and retain the HSPC phenotype. By performing a genome-wide gene expression analysis of purified HSPCs isolated at different stages of co-culture, we asked at the molecular level, to what degree hematopetic stem cell properties can be preserved during culture. This temporal gene expression data from in vivo derived- and ex vivo expanded human HSPCs will serve as a resource to identify novel regulatory pathways that control HSC properties, and to develop clinically applicable protocols for HSC expansion.

overall_design: Human CD34+ fetal liver cells were co-cultured on a subclone of OP9 stomal cells (OP9M2 sublemented with supportive cytokines (see below)). To distinguish between molecular changes acquired over prolonged culture versus immediately after exposure to culture, gene expression in isolated CD45+CD34+CD38-CD90+ HSPCs was assessed after 12 hours, 2 weeks and 5 weeks in culture. Cultured CD45+CD34+CD38-CD90+HSPCs were compared to freshly isolated CD45+CD34+CD38-CD90+HSPCs and their more differentiated CD45+CD34+CD38+CD90- downstream progenitor cells.

first: Maria

middle: I

last: Sierra

first: Rajkumar

last: Sasidharan

first: Sacha

last: Prashad

first: Pamela

last: Saarikoski

first: Melissa

last: Romero

first: Ben

last: Van Handel

first: Andy

last: Huang

first: Xinmin

last: Li

first: Hanna

last: Mikkola


title: Analysis of embryonic day E14.5 and E16.5 mouse ureters from Tshz3LacZ/LacZ mutants and wild types

city: Marseille

first: Laurent

last: Fasano

address: Parc Scientifique de Luminy

institute: CNRS-AMU

summary:
In the urinary tract, smooth muscle (SM) is present in the renal pelvis, the ureter, the bladder and the urethra and plays a crucial role in the functional and structural integrity of these organs. In Tshz3 mutant ureters the myogenic program is not activated in the proximal region due to the absence of expression of myocardin (Myocd), a key regulator of SM differentiation. We set out to characterize TSHZ3-dependent mechanisms that participate to the process of ureteric smooth muscle cells (SMC) differentiation.
To this aim, we used microarrays to identify distinct classes of up- and down-regulated genes in Tshz3LAcZ/LacZ mutant ureters at two different time points; at E14.5, which corresponds to the onset of the myogenic program and at E16.5, when SMC express the full repertoire of differentiation marker genes.

overall_design: Mouse embryonic (E14.5 and E16.5) wild type and Tshz3LacZ/LacZ mutant ureters were dissected for RNA extraction and hybridization on Affymetrix microarrays.

first: Xavier

last: Caubit

first: Christine

last: Vola

first: Elise

last: Martin

first: Teddy

last: Fauquier

first: Herbert

last: Schulz

first: Kathrin

last: Saar

first: Sabine

last: Schmidt