title: Fibrotic and Immune Pathway Signatures in Systemic Sclerosis Suggest a Progressive, Multi-step Model of Disease Pathogenesis

status: Public on Apr 01 2015

city: Lebanon

first: Tammara

last: Wood

state: NH

address: WTRB 674

department: Biomedical Data Science

institute: Dartmouth Medical School

summary:
Pathway expression analysis in systemic sclerosis revealed key mediators driving pathology within each of the intrinsic gene expression subsets.

Genome-wide expression profiling in systemic sclerosis (SSc) has identified four 'intrinsic' subsets of disease (fibroproliferative, inflammatory, limited, and normal-like), each of which appear to be driven by distinct signaling pathways. Here we examine experimentally derived gene expression signatures for thirteen agonists to better understand the molecular mechanisms underlying each intrinsic subsets. Pathway-specific gene signatures were compared against skin biopsy microarray data consisting of 329 microarray hybridizations from 287 unique biopsies representing 111 patients. Hierarchical clustering recapitulated the four SSc 'intrinsic' gene expression subsets, along with an intermediate subset exhibiting both inflammatory and fibroproliferative gene expression signatures. The fibroproliferative subset is most strongly associated with the PDGF gene signature, while the inflammatory subset demonstrated strong activation of NF-kappaB, characterized by early induction of TH2 signals, which transitions to a more TH17-like immune response over time. The limited subset was associated with IFNalpha signaling, combined with strong downregulation of PDGF signaling. The inflammatory-proliferative subset shows downregulation of NF-kappaB-associated pathways in conjunction with increased PDGF signaling, suggestive of a transitional state linking the inflammatory and fibroproliferative subsets. IL-13 signaling was strongly associated with early disease, while TGFbeta signaling was associated with more severe disease. Together these data suggest a multi-step, progressive model of disease pathogenesis driven by distinct pathways. Targeting these pathways based upon a patient's underlying disease subset should improve therapeutic outcomes.

overall_design:
In vitro treatment of human dermal fibroblasts was performed to identify pathway-specific gene signatures. These gene signatures were then compared against systemic sclerosis skin biopsy microarrays to determine the overall contribution of each pathway to disease.

This study includes re-analysis of 247 skin biopsy samples from GSE9285, GSE32413, and GSE45485. Links to these Samples are provided below. The re-processed normalized data for these Samples are included in the supplementary file 'GSE56308_247_Skin_Biopsy_Reanalysis_Samples.txt'.

first: Michael

last: Johnson

first: J

middle: M

last: Mahoney

first: Jaclyn

last: Taroni

first: Jennifer

last: Sargent

first: Eleni

last: Marmarelis

first: Ming

last: Wu

first: John

last: Varga

first: Monique

last: Hinchcliff

last: Whitfield


title: Gene expression profile of human endothelial cells with or without nanoparticles

status: Public on Jun 01 2014

city: Philadelphia

first: Sezin

last: Aday

state: Pennsylvania

address: 210 South 33rd Street, Skirkanich Hall

country: USA

institute: University of Pennsylvania

summary: To understand the the effect of poly(lactic-co-glycolic acid) nanoparticles (NPs) encapsulating a fluorine contrast agent on human umbilical vein endothelial cells (HUVECs), we have employed whole genome microarray expression profiling. The NPs used in this study were prepared in our lab. HUVECs were ordered from Lonza (Cat# C2517A). HUVECs were incubated with NPs for 4 hours. After 4 h, the cells were washed couple of times to remove the NPs and gene expression profiles were detected after 20 h (total time: 24 h) and 7 d in the absence of NPs.  HUVECs  after 24 h without nanoparticles were used as controls.

overall_design: The gene expression in HUVECs was measured at 24 h and 7 d after incubation with nanoparticles. Three independent experiments were performed at each time.


title: Inflammation-Driven Carcinogenesis is Mediated through STING

status: Public on May 31 2014

city: Silver Spring

first: BIJU

last: ISSAC

state: MD

address: 503 Robert Grant Ave, Rm 2W123

department: Military HIV Research Program

institute: Walter Reed Army Institute of Research

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

overall_design: Refer to individual Series


title: Lung adenocarcinoma subtypes definable by lung development-related miRNA expression profiles in association with clinicopathologic features

status: Public on Jun 19 2014

city: Nagoya

first: Takashi

last: Takahashi

state: Aichi

address: 1-1 Kanokoden, Chikusa-ku

country: Japan

institute: Aichi Cancer Center

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


title: Mutations in the microtubule-associated protein Eml1 lead to ectopic progenitors and heterotopia formation during cortical development in mouse and human

status: Public on May 25 2014

city: Evry Cedex

first: Robert

last: Olaso

address: 2 rue Gaston Cremieux

department: CNRGH

country: France

institute: CEA-DRF

summary: Neuronal migration disorders such as lissencephaly and subcortical band heterotopia (SBH) are associated with epilepsy and intellectual disability. Doublecortin (DCX), LIS1 and alpha1-tubulin (TUBA1A), are mutated in these disorders, however corresponding mouse mutants do not show heterotopic neurons in the neocortex. On the other hand, the spontaneously arisen HeCo mouse mutant displays this phenotype. The study of this model reveals novel mechanisms of heterotopia formation. While, HeCo neurons migrate at the same speed as WT,  abnormally distributed dividing progenitors were found throughout the cortical wall from E13. Through genetic studies we identified Eml1 as the mutant gene in HeCo mice. No full length transcripts of Eml1 were identified due to a retrotransposon insertion in an intron. Re-expression of Eml1, coding for a microtubule-associated protein, rescues the HeCo progenitor phenotype. We further show that EML1 is mutated in giant ribbon-like heterotopia in human. Our data link abnormal spindle orientations, ectopic progenitors and severe heterotopia in mouse and human.

overall_design: 16 samples analyzed corresponding to 8 wild type brain and 8 HeCo mutant brain

first: Jean-Francois

last: Deleuze

first: Francoise

middle: P

last: Tuy

first: Fiona

last: Francis


title: Inflammation-Driven Carcinogenesis is Mediated through STING [skin]

summary: Chronic stimulation of innate immune pathways by microbial agents or damaged tissue is known to promote inflammation-driven tumorigenesis by unclarified mechanisms1-3. Here we demonstrate that mutagenic 7,12-dimethylbenz(a)anthracene (DMBA), etoposide or cisplatin induces nuclear DNA leakage into the cytosol to intrinsically activate STING (Stimulator of Interferon Genes) dependent cytokine production. Inflammatory cytokine levels were subsequently augmented in a STING-dependent extrinsic manner by infiltrating phagocytes purging dying cells. Consequently, STING-/- mice, or wild type mice adoptively transferred with STING-/- bone marrow, were almost completely resistant to DMBA-induced skin carcinogenesis compared to their wild type counterparts. Our data emphasizes, for the first time, a role for STING in the induction of cancer, sheds significant insight into the causes of inflammation-driven carcinogenesis, and may provide therapeutic strategies to help prevent malignant disease

overall_design: Total RNA obtained from DMBA or acetone treated wild type (WT) or STING deficient (SKO) mouse skin or skin tumor was examined for gene expression.

first: Jeonghyun

last: Ahn

first: Tianli

last: Xia

first: Hiroyasu

last: Konno

first: Keiko

first: Phillip

last: Ruiz

first: Glen

middle: N

last: Barber


title: SCL008: icSARS CoV, icSARS-deltaNSP16 or icSARS ExoNI infections of the 2B4 clonal derivative of Calu-3 cells - Time course

status: Public on May 23 2014

city: Seattle

first: Michael

last: Katze

state: WA

address: Rosen Building 960 Republican St.

department: Microbiology

institute: University of Washington

summary: Purpose of experiment was to compare transcriptomics of 2B4 cells (clonal derivative of Calu-3 cells) infected with either icSARS CoV, icSARS-deltaNSP16 or icSARS ExoNI mutants.

overall_design: 2B-4 cells (clonal derivatives of Calu-3 cells) were infected with either icSARS CoV, icSARS deltaNSP16 or icSARS ExoNI.  Wild type and deltaNSP16 mutant infections were at an MOI of 5 while the ExoNI infections were at an MOI of 1.  Cells samples were collected at 0, 7, 12, 24, 36, 36, 48, 60 or 72h post infection. Each infected sample was done in triplicate. (Triplicates are defined as 3 different wells, plated at the same time using the same cell stock for all replicates.)  There are triplicate time-matched Mock for each time point from the same cell stock as rest of samples.  Culture medium (the same as what the virus stock is in) was used for the Mock infections.

first: Amy

last: Sims

first: Ralph

last: Baric

first: G

middle: L

last: Law

first: Jean

last: Chang


title: The role of microRNA miR-17-92 in MYC oncogene addiction

status: Public on May 29 2014

city: stanford

first: Dean

last: Felsher

address: 269 Campus Drive

department: Medicine

institute: Stanford University

summary: miR-17-92 mediates the MYC oncogene addiction in a conditional mouse lymphoma model. To identify targets of miR-17-92 in this model, miR-17-92 was expressed in the conditional lymphoma cell lines using MSCV-puro.

overall_design: Both control and  miR-17-92-expressing conditional lymphoma cell lines were treated with doxycycline (DOX) (20ng/ml) for 48 hours to shut off MYC expression.

first: Yulin

last: Li

first: Peter

middle: S

last: Choi

first: Stephanie

middle: C

last: Casey

first: David

last: Dill

middle: W


title: Effects of dexamethasone on cultured lung explant

status: Public on May 22 2014

city: Houston

first: Jichao

last: Chen

state: TX

address: 2121 W. Holcombe Blvd, RM716

department: Pulmonary Medicine

institute: MD Anderson Cancer Center

summary: The lung is a branched tubular network with two distinct compartments — the proximal conducting airways and the peripheral gas exchange region — separated by a discrete boundary termed the bronchoalveolar duct junction (BADJ).   Here we image the developing mouse lung in three-dimensions and show that two nested developmental waves demarcate the BADJ under the control of a global hormonal signal.  A first wave of branching morphogenesis progresses throughout embryonic development, generating branches for both compartments.  A second wave of conducting airway differentiation follows the first wave but terminates earlier, specifying the proximal compartment and setting the BADJ.  The second wave is terminated by a glucocorticoid signaling: premature activation or loss of glucocorticoid signaling causes a proximal or distal shift, respectively, in BADJ location.  The results demonstrate a novel mechanism of boundary formation in complex, three-dimensional organs and provide new insights into glucocorticoid therapies for lung defects in premature birth.

overall_design: RNAs were extracted from E14 lungs cultured in control and dexamethasone media for 24 hours using Trizol reagents and Qiagen RNeasy Micro kit.  Two control and two treated samples were analyzed.


title: Chronic hypoxia in patients with colon carcinoma

city: Leuven

first: Rekin's

last: Janky

address: Herestraat 49 Box 816

department: Nucleomics Core

country: Belgium

institute: VIB

summary: In Western countries, colorectal cancer (CRC) is the third most common cancer in both men and women and the second leading cause of cancer-related deaths (approximately 500,000 deaths annually). For CRC, the tumor stage is the main prognostic factor for survival or relapse after surgery. Current staging is based on the AJCC classification which takes into account tumor size/depth, lymph node involvement and distant metastases. Surgical intervention can cure a significant portion of the patients, especially those that are presented in stages I, II or III (around 75% of patients). Patients in stage II undergo surgery only, whereas stage III patients receive adjuvant chemotherapy. However, a major fraction of these patients either have no need for adjuvant treatment (40% stage III) or would benefit when they were given adjuvant therapy in stage II. Therefore, in the current practice, the majority of patients receive not the optimal treatment. An accurate and reliable method that identifies patients with low and high risk for recurrence could improve the selection for adjuvant therapies in these groups, reducing over- or under-treatment. Molecular profiling of mRNA expression by microarray is an approach to identify relevant genes and gene signatures and has been used already for different types of cancer, like breast and HCC. Most studies, however, resulted in their own classification with a specific separation into groups. Most of these microarray studies show remarkably little overlap and it is difficult to find a clear correlation between the molecular classes and prognosis. The results of the studies seem to be center-dependent because of the different microarray techniques used, the small heterogeneous cohorts that are studied and the different clinical parameters used for the evaluation. Recently, we used a mechanism-driven approach to find a correlation between gene expression in HCC and prognosis in which we tried to overcome most shortcomings (van Malenstein et al. CCR 2010). In this study, we want to apply the approach which we used for HCC now in CRC with the aim to improve the prognosis prediction for patients in AJCC stage II and III. We determined the gene expression by microarray in the colon cancer cell line Caco2 and identified the genes that are differentially expressed under hypoxia (72 hours, 2% O2). Using a bioinformatic approach, we used 5 sets of expression data with corresponding clinical information (training: 3 sets, 234 patients and validation: 2 sets, 322 patients). This resulted in a unique 21 gene set with good performance in retrospective analysis. A second improvement we wanted to achieve is the development of a method that can be applied on FFPE material, which would expand the use of the technique to samples outside the university or research setting. We used the nCounter technique that uses hybridization of labeled probes and quantification without an amplification step. We tested our 21 genes on a cohort of 384 well-characterized patients that were collected between 2004 and 2006 at the University Hospitals of Leuven.

overall_design: We compared cells under hypoxia 2% O2 versus 20% O2 conditions. This was done for two cell lines (Caco2 human colorectal adenocarcinoma cell line and HPAC pancreas adenocarcinoma cell line). Each sample has a biological replicate. Samples are hybridized in dye-swap, resulting in 4 hybridizations per cell line.

first: J

last: van Pelt

first: D

last: Hompes

first: H

last: van Malenstein

last: Popovic

first: X

last: Sagaert

first: L

last: Libbrecht

first: A

last: Daemen

first: B

last: De Moor

first: E

last: Van Cutsem

last: D'Hoore

first: C

last: Verslype


title: Inhibition of p38 MAPK in DC progenitor cells endows DCs with superior immunogenicity

city: cleveland

first: Yong

last: Lu

address: 9500 euclid avenue, NB40

institute: Cleveland Clinic

summary: Analysis of the p38 MAPK pathway in regulation of dendritic cells (DCs) differentiation at the gene expression level. Bone marrow cells were cultured with mGM-CSF (20 ng/ml) in the presence of 1.5 mM of SB202190 or 0.1% DMSO. At day 7, semi-adherent cells were collected as immature DCs (iDCs). iDCs were matured by TNF-a (10 ng/ml) and IL-1b (10 ng/ml) for 48 hours. Results showed that p38 MAPK activity in DC progenitor cells acts as an antigen presentation attenuator, and disabling this critical brake during DC differentiation endows DCs with enhanced immunogenicity, which may be useful for the induction of antitumor immune responses.

overall_design: Total RNA was obtained from 2-day-cultured bone marrow cells, iDCs and mature DCs.

first: Qing

last: Yi


title: The 5p12 breast cancer susceptibility locus affects MRPS30 expression in estrogen-receptor positive tumors

city: San Francisco

last: Quigley

state: CA

address: 1450 Third St. Room 207

department: Helen Diller Comprehensive Cancer Center

institute: UCSF

summary: Uninvolved tissue taken at the time of primary surgical resection of an adenocarcinoma. Uninvolved status determined by surgical margin and gross appearance, not pathology

overall_design: 35 biologically distinct samples, no replicates, no controls

middle: A

first: Vessela

last: Kristensen

first: Ida

middle: R

last: Bukholm


title: Inhibition of Met results in concomitant inhibition of Akt and STAT3 signaling pathways, while abrogation of negative feedback permits Erk reactivation

status: Public on May 19 2014

city: Montreal

first: Sean

last: Cory

state: QC

address: 3649 Promenade Sir William Osler

department: Bioinformatics

country: Canada

institute: McGill University

summary: Amplification and activation of the Met receptor tyrosine kinase occurs up to 23% of gastric cancers, suggesting that Met is a therapeutic target in these cancers.  However, the steady-state signaling events that occur during chronic Met activation, and mechanisms for resistance to Met small-molecule inhibitors, are poorly understood.  Here we show that multiple gastric cancer cell lines harboring MET amplifications are dependent on Met signaling for proliferation and anchorage-independent growth.  In these cells, short-term inhibition of Met leads to coordinated changes in gene expression; these include a rapid loss in expression of immediate-early genes, followed by decreased expression of genes involved in cell cycle and proliferation.   Activation of Ras-Erk, PI3K-Akt and STAT3 pathways is attenuated by acute Met inhibition.  STAT3 inhibition alone, but not individual inhibition of Mek or Akt, is sufficient to abrogate Met-dependent growth of these cells.  However, following chronic Met inhibition, reactivation of Mek-dependent Erk phosphorylation occurs even in the presence of Met inhibitor corresponding with a downregulation of Erk negative regulators DUSP4/6.  This provides a mechanism for the emergence of drug resistance.  Our findings provide insights into innate resistance to a small-molecule Met inhibitor and highlight rational combination therapies that could be evaluated in clinical trials.

overall_design: Time series experiment, four cell lines, 2 treatments

first: Andrea

last: Lai

first: Morag

last: Park


title: Histone Demethylase JARID1B Controls Mammary Gland Development by Regulating Key Developmental Genes

city: New Haven

first: Qin

last: Yan

state: CT

address: 310 Cedar St

department: Pathology

institute: Yale University

summary: The jmjC-domain containing H3K4 histone demethylase JARID1B/KDM5B/PLU1 is over-expressed in human breast cancer and is a potential target for breast cancer treatment. To investigate the in vivo function of JARID1B, we developed a new strain of Jarid1b knockout mice and characterized the phenotypes in detail. Unlike previously reported knockout strains, the majority of our Jarid1b knockout mice are viable beyond embryonic and neonatal stages. Nonetheless, these mice exhibit decreased body weight, higher incidence of adult mortality and decreased female fertility.  Furthermore, Jarid1b knockout mice show delayed mammary gland development. Mechanistically, loss of JARID1B leads to decreased serum estrogen levels and reduced proliferation of mammary epithelial cells in early puberty.  In addition, in mammary epithelial cells, loss of JARID1B diminishes the expression of key regulators of mammary morphogenesis, including FOXA1, estrogen receptor α (ERα), and GATA3. Taken together, these results indicate that JARID1B positively regulates mammary ductal development through both extrinsic and cell-autonomous mechanisms.

overall_design: Compare gene expression of Jarid1B Knock Out and Wild type Mammary Epithelial Cells (MECs).

first: Mike

last: Zou

first: Jian

last: Cao

first: Zongzhi

last: Liu

first: David

middle: F

last: Stern

first: William

middle: G

last: Kaelin


title: The highly specific role of the insulin receptor in breast cancer progression

city: Haifa

first: Ran

last: Rostoker

state: Israel

address: Efron st

department: faculty of medicne

country: Israel

institute: Technion

summary: In order to investigate insulin effect on cancer cells transcripts we stimulated the mouse mammary cancer cell line, Mvt-1 with insulin.

overall_design: RNA samples were extracted from Mvt-1 cells following 10nM insulin treatment for 90min and from control cells (vehicle)

first: Sagi

last: Abelson

first: Keren

last: Bitton-Worms

first: Inna

last: Genkin

first: Sarit

last: Ben-Shmuel

first: Zila

last: Orr

first: Avishay

last: Caspi

first: Maty

last: Tzukerman

first: Derek

last: LeRoith


title: Analysis of miR-143/145 wild-type and null mouse intestinal myofibroblasts before and after LPS stimulation

city: Dallas

first: Joshua

last: Mendell

state: Texas

address: 6000 Harry Hines Blvd NA 6.200

department: Molecular Biology

institute: UT Southwestern Medical Center

summary:
In a series of mouse genetic studies, we concluded that miR-143/145 expression in intestinal subepithelial myofibroblasts (ISEMFs) promotes epithelial regeneration after DSS-mediated injury in the colon. This experiment aims to identify miR-143/145 target genes that are involved in this function.
We generated primary ISEMFs from wildtype and miR-143/145 null mouse colons and analyzed their gene expression profile. We further subjected ISEMFs to LPS treatment, in order to measure gene expression changes that are only revealed after inflammatory stress.

overall_design: Three wild-type and three miR-143/145 null ISEMF cell lines were isolated from mouse colons. Cells were treated with or without 1 ug/mL LPS for 24 hours and total RNA was isolated.  Gene expression was profiled using Illumina microarrays.

first: Raghu

last: Chivukula

first: Guanglu

last: Shi

middle: T


title: Illumina array to compare whole-genome expression change in miR-127 KO mice at E18.5 in 3 tissues: brain, skin and muscle

status: Public on May 20 2014

city: Cambridge

first: Sarah

middle: E

last: Allen

address: Downing Street

department: PDN

country: United Kingdom

institute: University of Cambridge

summary: miR-127 is an imprinted microRNA on mouse chromosome 12, strongly expressed during late embryogenesis and known regulator of placental gene Rtl1. miR-127-knockout (KO) mice appear phenotypically normal. An Illumina beadchip whole genome microarray experiment was carried out on embryonic stage 18.5 (E18.5) mice with a deletion in the miR-127 gene, and compared with wild type (WT) mice. Three tissues with varying expression of miR-127 were analysed: brain, skin and muscle.

overall_design: For each tissue (brain, skin, muscle) and genotype (WT or miR-127 KO), total RNA from 15 different embryos was extracted. These RNA samples were divided into three pools of five, to make three biological replicates. Each biological replicate was applied to two separate Illumina Mouse WG-6 v2.0 beadchips, to make two technical replicates.


title: Foxp1 is a rate-limiting and essential negative regulator of Tfh cell differentiation

status: Public on May 18 2014

first: Priyankara

middle: J

last: Wickramasinghe

state: PA

address: 3601 Spruce Street

institute: The Wistar Institute

summary: CD4+ T follicular helper (Tfh) cells are essential for germinal center (GC) and high-affinity antibody responses. Yet the regulation that determines the initial development of Tfh cells is still largely unknown. Here we find that transcription factor Foxp1, previously shown to be essential in maintaining T cell quiescence, is a rate-limiting and essential negative regulator of Tfh cell differentiation. Naïve CD4+ T cells constitutively express Foxp1A, and stimulation through the T cell receptor (TCR) transiently induces the expression of a shorter Foxp1D isoform. In T cell-dependent (TD) humoral responses, CD4+ T cells deficient in all Foxp1 isoforms preferentially differentiate into Tfh cells, resulting in substantially increased GC and antibody responses. This negative regulation of Foxp1 on Tfh cell differentiation shows profound dominance: even in the absence of B cells, Foxp1-deficient CD4+ T cells differentiate into Tfh cells with high frequencies and sustained Bcl6 expression. Further, in the absence of Foxp1, Tfh cells are generated in higher frequencies than seen with Bcl6 overexpression and Tfh cell differentiation becomes significantly resistant to Blimp1-mediated repression. Finally, our experiments reveal specific roles of Foxp1A and Foxp1D in inhibiting Tfh cell differentiation: TCR-induced Foxp1D functions as a ‘gatekeeper’ to block the initial Tfh cell development, and together Foxp1A and Foxp1D proteins inversely determine Tfh cell generation in a dosage-dependent manner. Our study suggests that two Foxp1 isoforms provide a “double check” mechanism as fundamental regulators in Tfh cell differentiation and humoral responses.

overall_design: Gene expression analysis of ex vivo OT-II Foxp1-WT Tfh cells and OT-II Foxp-conditional knockout (CKO) Tfh cells 5 days after immunization.

first: Haikun

last: Wang

first: Xiaomin

last: Wen

first: Enguang

last: Bi

first: Andrew

last: Kossenkov

first: Hui

last: Hu


title: Inflammation-Driven Carcinogenesis is Mediated through STING [MEFs]

first: BIJU

last: ISSAC

overall_design: Total RNA obtained from wild type murine embryonic fibroblasts (WT MEFs), STING deficient MEFs (SKO), Trex1 deficient MEFs (TKO), and both STING and Trex1 deficient MEFs (STKO) treated with DMBA and examined cytokine production by these cells.

first: Jeonghyun

last: Ahn

first: Tianli

last: Xia

first: Hiroyasu

last: Konno

first: Keiko

first: Phillip

last: Ruiz

first: Glen

last: Barber


title: Severe preeclampsia: new blood circulating biomarkers

status: Public on May 14 2014

city: Lyon

first: Julien

last: Textoris

address: Hôpital Edouard herriot - Pavillon P; 5 place d'Arsonval

department: Medical Diagnostic Discovery Department (MD3)

institute: bioMérieux

summary:
Background: Preeclampsia (PE) is a placental disease characterized by hypertension and proteinuria in pregnant women, which is associated with a high maternal and infantile morbidity. However, circulating biomarkers able to predict the prognosis of PE are lacking.
Methods: Thirty-eight women were included in the study. They consisted of 19 patients with PE (13 with severe PE and 6 women with non-severe PE) and 19 gestational age-matched normal pregnancy controls. We measured coagulation pathway, endothelial responses and microparticle release and circulating gene expression in PE patient groups and normotensive controls.
Results: The measurement of markers associated with coagulation pathway, endothelial activation and circulating microparticles enabled to discriminate PE from normal pregnancy but were not sufficient to distinguish severe from non-severe PE. PE patients also exhibited a specific transcriptional program distinct from that of control women and subtle differences were observed between severe and non-severe PE. Functional annotation of the up-modulated signature in PE highlighted two main functions related to ribosome and complement. Importantly, we found that 8 genes were specifically up-modulated in severe preeclampsia. Among these genes, the expression of VSIG4 was significantly increased in patients with severe preeclampsia in comparison with controls and patients with non-severe preeclampsia.
Conclusion: Using transcriptional signatures of blood samples, we identified the gene encoding the estrogen receptor as a potential diagnostic marker of severe preeclampsia. In addition, the determination of this gene may improve the prognostic assessment of severe preeclampsia.

overall_design:
Thirty-eight women were included in the study: 19 patients with PE, including 6 women with non-severe PE and 13 with severe PE, and 19 women with normal pregnancy (NP) selected according to age, weight, smoking status, race, gestational age at the inclusion, and blood pH (Table 1 of manuscript). Women with NP had no history of medical illness or medication, and received routing prenatal care. The diagnostic of PE was based on a blood pressure of ≥ 140/90 mmHg taken twice, uricemia above normal laboratory range (120-420 µmol/L), and proteinuria higher than 300 mg in a 24 hour-collection, occurring after 20 gestational weeks in previously normotensive women (Table 2). The criteria used to define severe PE included one of the following conditions: a blood pressure higher than 160/110 mmHg, a proteinuria higher than 1500 mg/24h), a multisystem disorder, maternal cerebral symptoms (seizures, stroke) or intrauterine growth restriction below the 3° percentile. Women with multiple gestations, fetal congenital malformations/chromosomal abnormalities, recent infection, antiphospholipid antibodies, trauma, drug or alcohol abuse during pregnancy, preexisting hypertension, thrombophilia with PE history, or women receiving anticoagulant or antiaggregation therapy were excluded from the study.
Two microarrays (one non-severe PE and one normal) were discarded from the analysis for technical reasons. Thus, only 36 microarrays are included here.

first: Delphine

last: Ivorra

first: Amira

middle: B

last: Amara

first: Jean

last: Ménard

first: Hélène

last: Heckenroth

first: Florence

last: Bretelle

last: Mège


title: Gene expression in murine pancreatic tumor tissues in response to the blockade of macrophage colony-stimulating factor receptor (CSF1R) signal

status: Public on May 15 2014

city: St. Louis

first: David

last: DeNardo

state: MO

address: 425 S. Euclid Ave.

department: Internal Medicine

institute: Washington University in St. Louis

summary: Analysis of responses induced upon the blockade of CSF1R signaling at the gene expression level. Hypothesis of this study was that CSF1R signal blockade alters the local immune responses in a murine pancreatic tumor model. Results provide important information on changes in the immune responses in the tumor microenvironment.

overall_design: Total RNA obtained from whole mouse pancreatic tumor tissues after vehicle or CSF1Ri treatment for 8 days

first: Yu

last: Zhu

first: Brett

last: Knolhoff

first: Melissa

last: Meyer

first: Timothy

last: Nywening

first: Brian

last: West

first: Jingqin

last: Luo

first: Andrea

last: Wang-Gillam

first: S

last: Goedegebuure

last: Linehan

first: D


title: Human gingival fibroblasts: control vs. lysophosphatidic acid (LPA 18:1)-treated

status: Public on May 12 2014

city: Omaha

first: D.

middle: Roselyn

last: Cerutis

state: NE

address: 2500 California Plaza

department: Oral Biology

institute: Creighton University

summary: Transcriptional profiling of pass 2 primary human gingival fibroblasts (GF) comparing control untreated GF with GF treated with LPA 18:1 for 2h or 8h. The goal of this study was to determine the effects of LPA 18:1 on global GF gene expression.

overall_design: Three-condition experiment, GF vs. LPA-treated (2h, 8h) GF cells. Biological replicates: 3 control replicates, 3 LPA-treated replicates.

first: Michael

middle: D

last: Weston

first: Afolabi

middle: O

last: Ogunleye

first: Martha

last: Nunn

last: McVaney

first: Takanari

last: Miyamoto


title: Molecular effects of capsaicin on human gingival epithelial cells

status: Public on May 17 2014

city: Niigata

first: Naoki

last: Takahashi

address: 2-5274 Gakko-cho, Chuo-ku

department: Oral Biological Science

institute: Niigata University Faculty of Dentistry

summary: In order to explain the molecular mechanisms of capsaicin-induced proliferation of gingival epithelial cells (GECs), a microarray analysis was performed. Several cell proliferation related genes were significantly up-regulated. These data suggest that TRPV1 signaling in GEC may induce transcriptional upregulation of growth factors, which results in an increased proliferation rate.

overall_design: Simian virus 40 (SV40) T-antigen-immortalized human gingival epithelial cell line, epi4, were stimulated with 1 μM capsaicin for 4 hours. Total RNA was isolated and subjected to gene expression analysis using Agilent whole human genome oligo microarray.


title: Loss of Fas (CD95) expression by dendritic cells protects from a chronic viral infection

status: Public on May 09 2014

city: Chicago

first: Aly

middle: Azeem

last: Khan

state: IL

address: 6045 S. Kenwood Ave.

institute: University of Chicago

summary: Chronic viral infections incapacitate adaptive immune responses by 'exhausting' virus-specific T cells, inducing their deletion and reducing productive T cell memory. Viral infection rapidly induces death receptor Fas (CD95) expression by dendritic cells (DCs) making them susceptible to elimination by the immune response. Lymphocytic Choriomeningitis Virus (LCMV) Clone 13, which normally establishes a chronic infection, is rapidly cleared in C57Black/J mice with conditional deletion of Fas in DCs. The immune response to LCMV is characterized by an extended survival of virus-specific effector T cells. Moreover, transfer of Fas-negative DCs from non-infected mice to already-infected animals results in either complete clearance of the virus or a significant reduction of viral titers. Thus, DC-specific Fas expression plays a role in regulation of anti-viral responses and suggests a strategy for stimulation of T cells in chronically infected animals and humans in order to achieve the clearance of persistent viruses.

overall_design: We compared gene expression between splenic DCs from B6.FasKI and B6.CD11c-Cre.FasKI mice. DCs were isolated on day 5 after LCMV infection with 3 mice in each group, for a total of 6 samples.  Spleens were collagenase-DNAse digested and sorted by flow to isolate DCs.

first: Vineeth

last: Varanasi

first: Alexander

middle: V

last: Chervonsky


title: GATA6 dependent gene regulation in peritoneal macrophages

status: Public on May 02 2014

first: Yasutaka

last: Okabe

address: 300 Cedar Street

department: Immunobiology

institute: Yale University School of Medicine

summary: Peritoneal macrophages from control and Mac-Gata6 KO (LysM-cre;Gata6-floxed) mice were determined for genome wide gene expression.

overall_design: Sorted peritoneal macrophages from control and Mac-Gata6 KO mice were performed for whole genome expression analysis by Illumina microarray

first: Ruslan

last: Medzhitov


title: Distinct functional programming of human fetal and adult monocytes [set 1]

first: Joseph

middle: M

last: McCune

state: California

address: 1001 Potrero Ave

summary: Microarray profiling of unstimulated human fetal and adult bone marrow classical monocytes

overall_design: Classical monocytes were sort purified, RNA isolated, and amplified. 4 of each sample was collected and used

first: Elisabeth

last: Krow-Lucal

first: Charles

last: Kim

first: Trevor

last: Burt


title: Distinct functional programming of human fetal and adult monocytes

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

overall_design: Refer to individual Series


title: Basal progenitors during cortical neurogenesis

status: Public on May 01 2014

city: Paris

first: Matthias

last: Groszer

address: 17, rue du Fer à Moulin

department: Developmental Neuroscience

institute: INSERM U839

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


title: Gene expression profile for NGAL overexpression in esophageal squamous carcinoma cell

city: shantou

first: Enmin

last: Li

state: guangdong

address: 22 Xinling Road

country: China

institute: Shantou university, medical college

summary: Neutrophil gelatinase associated lipocalin (NGAL), also known as oncogene 24p3, uterocalin, siderocalin or lipocalin 2 (Lcn2), is a member of the lipocalin family. Elevated NGAL involves various functions in malignant cells, even sometimes the conclusions were controversial. NGAL inhibits apoptosis in thyroid cancer and decrease invasion and angiogenesis in pancreatic cancer, but it increase proliferation and metastasis in breast and colon cancer. Nonetheless, the molecular functions and mechanisms of NGAL in ESCC are unknown.  To address these issues and to identify genes and biological pathways associated with NGAL functions and mechanism, NGAL was overexpressed by pcDNA3.0 plasmid in ESCC cell line EC109 with an empty plasmid as a control, these two cells were applied for mRNA expression profile analyses to find the differentially expressed genes.

overall_design: Plasmids of pcDNA3.0-NGAL and pcDNA3.0 were transfected into ESCC cell line EC109, respectively. Stable transfected cell clones were selected by G418. The overexpression of NGAL protein was confirmed by western blot. Total RNAs from NGAL overexpressed cells and control cells were extracted for Agilent whole genome oligo microarray. A dye flip was performed for duplicate.

first: Fei

last: Zhou

first: Zepeng

last: Du

first: Liyan

last: Xu

first: Bingli

last: Wu


title: Transcrioptome analysis of human primary macrophages stimulated by bacterial endotoxin lipopolysaccharide (LPS), and (1,3)-b-glucans, curdlan and glucan from baker´s yeast (GBY)

city: Helsinki

first: Tiina

last: Öhman

address: P.O.Box 65

country: Finland

institute: Institute of Biotechnology

summary: We performed gene expression microarray experiments to compare the global transcriptional response induced by b-glucans and LPS with their secretomes. We identified 1683, 767 and 1447 genes with over two-fold increase or decrease in LPS-, curdlan- or GBY-stimulated macrophages, respectively. We show that both LPS and b-glucan induces significant gene expression changes in macrophages, but only b-glucans activate a robust protein secretion.

overall_design: The gene expression of human primary macrophage cells was measured at 6 hours after exposure the cells to 1 µg LPS or 10 µg Curdlan or 100 µg GBY (glucan from baker´s yeast), also 0-group was included. Three independent experiments were performed using three different donors for each experiment.

first: Laura

last: Teirilä

first: Anna

last: Lahesmaa-Korpinen

first: Wojciech

last: Cypryk

first: Henrik

last: Wolff

first: Sampsa

last: Hautaniemi

first: Tuula

last: Nyman

last: Matikainen

first: Ville

last: Veckman


title: Wip1 regulates adult neurogenesis and Wnt signaling during aging

status: Public on Apr 26 2014

city: Singapore

first: Dmitry

last: Bulavin

address: 61Biopolis Drive

country: Singapore

institute: Institute of Molecular and Cell Biology

summary:
The number of newly-formed neurons declines rapidly during aging. Here we describe an important mechanism that contributes to this decline via Wip1-dependent regulation of neuronal differentiation. We found that Wip1 is expressed in neural stem/progenitor cells (NPCs) of the mouse subventricular zone and its upregulation at physiological levels maintained higher NPC numbers and neuronal differentiation in old mice. This resulted in markedly improved neuron formation and rescued a functional defect in fine odor discrimination in old mice. We identified Dkk3 as a key downstream target of Wip1 and found that its expression in SVZ is restricted to NPCs. Functionally, Dkk3 inhibited neuroblast formation by suppressing Wnt signaling, while deletion of Dkk3 or pharmacological reactivation of the Wnt pathway improved neuron formation and olfactory function in aged mice. We propose that Wip1 controls a Dkk3-dependent inhibition of neuronal differentiation during aging and thus regulating Wip1 levels could prevent certain aspects of functional decline of the aging brain.
We found if neurospheres were derived from 18 months old mice, Wip1 transgenic neurospheres were more neurogenic than wt ones. This microarray was a pilot experiment to search the mechanism how Wip1 Transgene promoted neurogenesis, and found Dkk3 as a potential mediator.

overall_design: WT vs Wip1Tg neurospheres were cultured from mouse brain, and gene expression was compared using Illumina mouseWG-6 array

first: Yunhua

last: Zhu


title: Genome-scale analysis in blood progenitor and mast cells reveals how lineage-affiliated transcription factors control distinct regulatory programs [Beadchip Experiments]

status: Public on Apr 24 2014

first: Felicia

last: Ng

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

institute: Cambridge Institute for Medical Research

summary: Despite major advances in the generation of genome-wide binding maps, the mechanisms by which transcription factors (TFs) regulate cell type identity have remained largely obscure. Through comparative analysis of 10 key haematopoietic TFs in both mast cells and blood progenitors, we demonstrate that the largely cell-type specific binding profiles are not opportunistic, but instead contribute to cell-type specific transcriptional control, because (1) mathematical modelling of differential binding of shared TFs can explain differential gene expression, (2) cell-type specific binding is largely mediated through consensus binding sites, and (3) knock-down of blood stem cell regulators Gata2 and Erg in mast cells reveals mast cell specific genes as direct targets. Finally we show that the known mast cell regulators Mitf and c-Fos likely contribute to the global reorganisation of TF binding profiles. Taken together therefore, our study elucidates how key regulatory TFs contribute to transcriptional programmes in several distinct mammalian cell types.

overall_design: Total RNA from primary mast cells transfected with retroviral shRNA vectors were compared to negative controls (shRNA against luciferase).

first: Fernando

last: Calero-Nieto

middle: S

first: Nicola

middle: K

last: Wilson

first: Rebecca

last: Hannah

first: Evangelia

last: Diamanti

first: Victoria

last: Moignard

first: Ana

middle: I

last: Leal-Cervantes

first: Isabel

last: Jimenez-Madrid

first: Lorenz

last: Wernisch

first: Berthold

last: Gottgens


title: Memory B cell subset defined by CD80 and PD-L2 surface expression

status: Public on May 06 2014

first: Hailong

last: Meng

address: 300 George Str

summary: NP-reactive murine splenic memory B cells were sorted based on the expression of the surface markers CD80 and PD-L2

overall_design: AM14 tg+ X Vk8R+/- recipients of B1-8+ B cells were immunized with NP-CGG and 8 weeks later splenic EMA-, CD19+ and NP+ memory B cells were sorted based on their surface expression of CD80 and PD-L2 (DN=CD80- PDL2-, SP=CD80- PDL2+, DP=CD80+ PDL2+). 1x10E5 up to 3x10E5 cells per sample were sorted and total RNA was isolated using the RNeasy plus micro kit and cRNA was prepared using the Illumina TotalPrep RNA Amplification Kit.

first: Florian

last: Weisel

first: Mark

last: Shlomchik

first: Steven

last: Kleinstein


title: Regulation of p21 by TWIST2 contributes to its tumor suppressor function in human acute myeloid leukemia

status: Public on May 07 2014

city: Jiangsu

first: Yun

last: Zhao

address: No. 1, Shizi Street

institute: Cyrus Tang Hematology Center, Soochow University

summary: TWIST2 is deregulated in about 1/3 human acute myeloid leukemia (AML) patients partially due to hypermethylation. Overexpression of TWIST2 in various AML cell lines and primary AML cells leads to growth arrest, reduced colony forming cell (CFC) capacity, inhibited cell migration and tumorigenic ability in nude mice, suggesting its tumor suppressor role in AML. To explore the molecular insight of how TWIST2 acts as a tumor suppressor in AML cells, control and TWIST2 expressed THP-1 cells have been analyzed with microarray.

overall_design: 4 independent biological replicates of control and TWIST2 expressed THP-1 cells have been used for RNA extraction and microarray analysis with Agilent platform.

first: Zhao

last: Yun


title: Gene induction by all trans retinoic acid (ATRA) and/or omentum culture supernatant in bone marrow derived macrophages (BMDMs)

first: Yasutaka

last: Okabe

summary: BMDMs were stimulated with ATRA and/or omentum culture supernatant and gene expression was determined by Illumina microarray

overall_design: 8 BMDM Samples

first: Ruslan

last: Medzhitov


title: Investigation of temporal changes in cellular gene expression upon infection with HIV-1.

city: Seattle

first: Michael

last: Katze

address: Rosen Building 960 Republican St.

institute: University of Washington

summary: The purpose was to study temporal changes in cellular gene expression upon infection with HIV-1.  The T lymphoblastic leukemia cell line SUP-T1 was infected with HIV-1

overall_design: The purpose was to study temporal changes in cellular gene expression upon infection with HIV-1.  1x10^6 homo sapien were infected with LAI/lab strain at MOI giving infection of almost 100% of cells; this was visible in a QC step in which cells 24 hours after infection were stained for p24 antigen.  MOI was set so that this infection rate was achieved after 1 hour incubation of cells with virus.  Mock, UV-inactivated virus, and live virus infections were carried out in three (each) separate tubes and infected cells were maintained in separate suspensions (9 samples each).  Time point aliquots were then collected in 4-hr intervals from each suspension, cells were pelleted, and lysed in 1 ml Trizol.  Lysed samples were immediately frozen on dry ice and moved to -80°C until RNA extraction, probe labeling and microarray analysis.

first: Stewart

last: Chang

first: Pavel

last: Sova

first: Lauri

last: Aicher


title: A role for Tac2, NkB and Nk3 receptor in normal and dysregulated fear memory consolidation

city: Atlanta

first: Raul

last: Andero Gali

state: GA

address: 954 Gatewood Rd

department: Department of Psychiatry and Behavioral Sciences

institute: Emory University

summary: Analysis of amygdala RNA expression after auditory fear conditioning in mice.

overall_design: Total RNA from three groups was obtained: 1) Home Cage (HC) 2) 30 minutes after Fear Conditioning (FC) 3) 2 hours after FC.

first: Raül

last: Andero

first: Brian

last: Dias

first: Kerry

last: Ressler


title: Gene expression analysis of epidermis of skin equivalent model by treatment of BIPBIPU and CGS27023A

status: Public on Apr 16 2014

city: Yokohama

first: shunsuke

last: iriyama

address: 2-2-1, Hayabuchi, Tsuzuki-ku,

institute: Shiseido Research Center

summary:
Increase of differentiation markers and barrier function in response to BIPBIPU and CGS27023A
Gene expression in epidermis of skin equivalent model was measured by treatment of BIPBIPU, CGS27023A, BIPBIPU and CGS27023A and control. Four independent experiments were performed at Day 4.

overall_design: Total 16 samples are analyzed. (control sample;4 samples, treatment of BIPBIPU;4 samples, treatment of CGS27023A; 4 samples, treatment of BIPBIPU and CGS27023A; 4 samples)

first: Shunsuke

last: Iriyama


title: Gene expression changes in oncogenic Kras-containing, Apc-mutated mouse intestinal organoids in the presence or absence of TGF-beta

status: Public on Apr 18 2014

first: Zoltan

last: Wiener

address: Haartmaninkatu 8

department: Molecular Cancer Biology Programme

institute: University of Helsinki

summary: We isolated and selected intestinal adenoma organoids from Apc1638N/+ and Apc1638N/+; Kras mice. After the selection procedure, we maintained the cultures with or without TGF-beta for 18h. RNA was isolated to determine the effect of oncogenic Kras on the gene expression changes.

overall_design: Total RNA obtained from  Apc1638N/+; Kras  organoids were compared to Apc1638N/+ samples in the absence or presence of 3 ng/ml TGF-beta (18h).

first: Z

first: V

last: Hyvonen

first: Kari

last: Alitalo


title: Mechanism of tissue-specific functional polarization of peritoneal macrophages

city: New Haven


title: Microarray expression data from HDAC1 and HDAC2 conditional knock-out mouse embryonic stem cells

city: LEICESTER

first: RICHARD

middle: DAVID WILLIAM

last: KELLY

address: LANCASTER ROAD

department: BIOCHEMISTRY

institute: UNIVERSITY OF LEICESTER

summary:
Histone deacetylase 1 and 2 (HDAC1/2) are the core catalytic components of co-repressor complexes which modulate gene expression.  In most cell types, deletion of both Hdac1 and Hdac2 is required to generate a discernible phenotype, suggesting their activity is largely redundant.  We have therefore generated an embryonic stem cell (ES) line in which Hdac1 and Hdac2 can be inactivated simultaneously using a Tamoxifen inducible CreER fusion.  Loss of HDAC1/2 results in a 60% reduction in total HDAC activity and a loss of cell viability.  Cell death is cell cycle dependent, since differentiated, non-proliferating cells, retain their viability. Furthermore, we observe increased mitotic defects, lagging chromosomes and micronuclei, suggesting HDAC1/2 maintain chromosomal stability.  Consistent with a critical role in the regulation of gene expression, microarray analysis of Hdac1/2 deleted cells reveals 1,708 differentially expressed genes.  Significantly for the maintenance of stem cell self-renewal, we detected a reduction in the expression of the pluripotent transcription factors, Oct4, Nanog and Rex1.  HDAC1/2 activity is regulated through binding of inositol tetraphosphate molecule [Ins(1,4,5,6)P4] (IP4) sandwiched between the HDAC and its cognate co-repressor.  This raises the important question of whether the IP4 actually regulates the activity of the complex in cells.  By rescuing the viability of DKO cells, we demonstrate for the first time that mutations which abolish IP4 binding reduce the activity of HDAC1/2 in vivo.  Our data indicate that HDAC1/2 have a generic, but essential role in cellular proliferation and regulate stem cell self-renewal by maintaining expression of key pluripotent transcription factors.
Comparative gene expression profiles of wild type (Day 0) were compared to Hdac1lox/lox, Hdac2lox/lox; CreER ES cells on days 1, 2 and 3 following for OHT treatment using the Illumina mouseWG-6 v2 expression BeadChip platform.

overall_design: wild type (Day 0) were compared to Hdac1lox/lox, Hdac2lox/lox; CreER ES cells on days 1, 2 and 3 following for OHT treatment. Four time points were analyzed in triplicate.

first: Richard

last: Kelly

first: Shaun

last: Cowley


title: Cross-species analysis of genome-wide regulatory networks identifies a synergistic dependency between FOXM1 and CENPF that drives prostate cancer malignancy

city: Newark

first: Antonina

last: Mitrofanova

state: NJ

address: 65 Bergen Street, Rm 923B

institute: Rutgers University

summary:
Analysis of the transcriptome of mouse models of prostate cancer to assemble a mouse prostate cancer interactome.
To assemble the mouse prostate cancer interactome, we collected 13 distinct mice or genetically-engineered mouse models (GEMMs), which together represent the full spectrum of prostate cancer phenotypes including: normal epithelium (i.e., wild-type), low-grade PIN (i.e., Nkx3.1 and APT), high-grade PIN and adenocarcinoma (i.e., APT-P; APC; Myc; NP; Erg-P; and NP53), castration-resistant prostate cancer (i.e., NP-AI), and metastatic prostate cancer (i.e., NPB; NPK; and TRAMP). To further enhance the heterogeneity afforded by this diversity of mouse models, we pharmacologically perturbed each GEMM using 13 different drugs (or appropriate vehicle). The resulting mouse prostate tissue/tumor dataset encompassed 384 expression profiles

overall_design: Total RNA obtained from prostate tumors/tissues of 13 mouse models of prostate cancer treated with 13 different drugs for 5 consecutive days. Prostate tumors/tissues were harvested and processed for RNA isolation and transcriptome analysis.

first: Alvaro

last: Aytes

first: Celine

last: Lefebvre

first: Andrea

last: Califano

first: Cory

last: Abate-Shen


title: Genome-wide comparative analysis of gene expression in  wild type (WT3) and TRPM7-/- (K09) mouse embryonic stem cells

status: Public on Apr 15 2014

city: Boston

first: David

middle: E.

last: Clapham

state: MA

address: Enders 1309

department: Cardiology

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

summary: TRPM7 is a ubiquitous ion channel and kinase, a unique ‘chanzyme’, required for proper early embryonic development. In order to assess the effects of TRPM7 activity on cellular gene expression, mouse embryonic stem cells with TRPM7 gene deletion (TRPM7-/- mESC) were established. By using microarray analysis, we identified genes with transcription significantly different in TRPM7-deficient mESC.

overall_design: Total RNA was extracted from cells using Qiagen RNAeasy Plus mini Kit. Triplicate samples were made for each wild type  clone 3 (WT3) and and TRPM7-/- clone 9 (KO9) mESC

first: Grigory

last: Krapivinsky


title: Modulation of gene expression induced by supercritical fluid rosemary extract in colon cancer cells

status: Public on Apr 04 2014

city: MADRID

first: ROBERTO

last: MARTIN-HERNANDEZ

address: CANTOBLANCO

department: BIOSTATISTICS AND BIOINFORMATICS UNIT

country: Spain

institute: IMDEA ALIMENTACION

summary: Supercritical rosemary extract (containing 16.90% carnosic acid, 1.90% carnosol and 13.59% volatile compounds) showed antitumor activity on colon cancer cells in vitro. We treated colon cancer cells with the extract and we employed whole genome microarray expression profiling to identify genes potentially involved in its antitumor mechanism of action.

overall_design: We analyzed gene expression of colon cancer SW620 cells after treating during 48h with supercritical rosemary extract at concentrations that cause 50% inhibition of cell viability (30 μg/mL), citostatic effect (60 μg/mL) and 50% cell death (100 μg/mL), in comparison to control cells (0 μg/mL). Two independent experiments were performed in triplicate. Each sample is the pool of the triplicates of one of the experiments (a or b) at the indicated concentration.

first: Ana

last: Ramírez de Molina

first: Margarita

last: González-Vallinas

first: Roberto

last: Martín-Hernández

first: Susana

last: Molina


title: The effect of TGF-beta in Apc-mutated mouse intestinal organoids

first: Zoltan

last: Wiener

summary: Intestinal crypts isolated from Apcflox/flox; villin-CreERT mice were treated with Tamoxifen to induce the deletion of Apc. Tamoxifen-treated organoids were selected in the absence of Wnt agonists and then treated with TGF-beta.

overall_design: Total RNA obtained from Tamoxifen-treated, Apc-deleted intestinal organoids in the absence or presence of 3 ng/ml TGF-beta (18h).

first: Z

first: V

last: Hyvonen


title: Transcriptional response in influenza-infected lungs from C57BL/6 wt, 129S7 wt and IFNAR-/- (129) mice

status: Public on Apr 30 2014

city: London

first: Stefania

last: Crotta

address: The Ridgeway

department: IR

institute: The Crick- Mill Hill Laboratories

summary: We used microarrays to analyse the global program of gene expression in response to Influenza A (X31) infection in lungs from C57BL/6 wt, 129S7 wt and IFNAR-/- (129) mice.

overall_design: Mock- or 5 day influenza A (X31)-infected total lungs from mice with the indicated genotypes were collected and processed for expression profiling.

first: S

last: Davidson

first: A

last: Wack


title: Comparison of genes regulated in P0 Klhl40 WT and KO skeletal muscle

status: Public on Apr 08 2014

city: Dallas

first: Ankit

last: Garg

address: 6000 Harry Hines Blvd, NA 8.500

institute: UT Southwestern Medical Center

summary: Nemaline myopathy (NM) is a congenital myopathy that can result in lethal muscle dysfunction and is thought to be a disease of the sarcomere thin filament. Recently, several proteins of unknown function have been implicated in NM, and their role in the disease remains unresolved. Here, we demonstrate that loss of a muscle-specific protein, Klhl40, results in a nemaline-like myopathy in mice that closely phenocopies the muscle abnormalities observed KLHL40 deficient patients. We show that Klhl40 dynamically localizes to the sarcomere I-band and A-band and binds to Nebulin (Neb), a protein frequently implicated in NM, as well as a putative thin filament protein, Lmod3. Klhl40 belongs to the BTB-BACK-Kelch (BBK) family of proteins, some of which have been previously shown to promote degradation of their substrates.  In contrast, we find that Klhl40 promotes stability of Neb and Lmod3 and blocks Lmod3 ubiquitination.  Accordingly, loss of Klhl40 reduces Neb and Lmod3 protein in skeletal muscle of mice and KLHL40 deficient patients. Because loss of sarcomere thin filament proteins is a frequent cause of NM, our data establishes a possible molecular basis for NM in KLHL40 deficient patients by establishing a novel pro-stability function of Klhl40 for Neb and Lmod3.

overall_design: Total RNA was harvested from quadriceps muscle of three Klhl40 WT (control) and three Klhl40 KO mice. Each KO mouse was sacrificed with a corresponding WT littermate. Tissues were also taken at 0 days of age to minimize confounding gene changes occurring due to malnourishment as the phenotype worsens.

first: Garg

last: Ankit


title: The effects of M3 muscarinic receptor gene ablation on murine colon neoplasia and gene expression

status: Public on Apr 07 2014

city: Baltimore

first: Kunrong

last: Cheng

state: MD

address: 22 S. Greene St., N3W62

institute: University of Maryland Baltimore

summary: In mice treated with azoxymethane (AOM), an intestine-selective carcinogen, both colon tumor number and size were robustly reduced in Chrm3-/- compared to WT mice.   In the present study, a microarray approach was used to identify genes that might have mechanistic relevance regarding the effects of M3R expression and activation on colon neoplasia, and also to identify potential biomarkers and therapeutic targets for colon cancer

overall_design: Total RNA obtained from isolated colon tumor in WT mice compared to M3KO mice.

first: Jean-Pierre

last: Raufman


title: Development of gene expression signatures for ANP in HUVEC

status: Public on Apr 23 2014

city: Suita

first: Takashi

last: Nojiri

state: Osaka

address: 5-7-1, Fujishirodai

department: Biochemistry

institute: National Cerebral and Cardiovascular Center Research Institute

summary: Analysis of HUVEC treated with ANP. ANP is a cardiac hormone, binding to the guanylate cyclase-A (GC-A) receptor with a major role in cardiovascular homeostatic mechanisms. Results provide insight into the molecular mechanisms of ANP in vascular endothelial cell.

overall_design: ANP induced gene expression in HUVEC was measured at 0, 1 and 6 hours.  Four independent experiments were performed at each time (0, 1 or 6 hours) for each experiment.

first: Takeshi

last: Hasegawa


title: Study of gene networks in basal progenitors during cortical neurogenesis

city: Paris

first: Matthias

last: Groszer

address: 17, rue du Fer à Moulin

institute: INSERM U839

summary: During cortical development neurons are generated sequentially from basal progenitors (BPs) which specifically express the transcription factor Tbr2. We used fluorescent-activaed cell sorting (FACS) to isolate BPs from Tbr2GFP knockin reporter mice (Arnold SJ et al. Genesis, 2009) at early (embryonic day, E13) and late (embryonic day, E16) stages of cortical neurogenesis and determined mRNA expression profiles using mouse mRNA microarray  (Illumina MouseWG-6 v2). Comparison of E13 and E16 mRNA expression profiles allowed us to identify regulatory gene networks for maintaining stage specific homeostasis of BPs throughout neurogenesis.

overall_design: FACS isolated BPs at E13 and E16 mouse brain cortex were used for microarray analyses.  Six biological replicates (embryonic cortex from three different litters) for E13 and five biological replicates (embryonic cortex from three different litters) for E16 were analysed.

first: Tanay

last: Ghosh


title: The effect of deficiency of BLT2 receptor on the gene expression in mouse skin during wound healing process

status: Public on Apr 21 2014

city: Tokyo

first: Takehiko

last: Yokomizo

address: Hongo 2-1-1, Bunkyo-ku

institute: Juntendo University School of Medicine

summary: Examination of gene expression in the skin of C57Black6 mice deficient in BLT2 receptor and control WT before and after skin punching.

overall_design: Total RNA was prepared from punch biopsies (5 mm in diameter) by using the Qiagen RNeasy Fibrous Tissue Kit (Qiagen, Valencia, CA, USA). In case of punched skin, the samples were taken after 2 days of skin punching. RNA from three mice per group was mixed and used for labeling. Probe cDNA was amplified and labeled with an Illumina total prep RNA amplification kit (Illumina, San Diego, CA, USA) according to the manufacturer’s protocol and then used for hybridization with Illumina MouseWG-6 Expression BeadChip arrays. The signals were quantified by using the Illumina BeadStation with BeadArray technology, and the raw data were obtained by using Illumina BeadStudio software.

first: Min

last: Liu

first: Kazuko

last: Saeki


title: Thermotolerance in B. subtilis

city: Hannover

first: Kürsad

last: Turgay

address: Schneiderberg 50

department: Institut für Mikrobiologie

country: Germany

institute: Leibniz Universität Hannover

summary:
During thermotolerance development, B. subtilis cells can be primed by a short mild heat shock to survive a subsequent severe, otherwise lethal, heat stress. We wanted to assess the influence of transcriptional regulation during thermotolerance development in B. subtilis.
We prepared total RNA of four differently treated samples of B. subtilis cells. For this purpose, exponential B. subtilis cells grown at 37 °C were divided and exposed for additional 15 min to temperatures of 37 °C, 48 °C, 53 °C or 15 min 48 °C followed by 15 min at 53 °C.

overall_design: Using four different merged dye swap experiments of red or green labelled cDNA of the above described RNA preparations, we compared and analyzed the transcriptional change of the conditions 48 °C vs. 53/48 °C (array 1), 37 °C vs. 53 °C (array 2), 37 °C vs. 48 °C (array 3) and especially 37/53°C vs. 53/48 °C (array 4)

first: Anja

last: Heinz


title: CD133+ and CD133- expression from pancreatic cancer cell line KPC001 using mouse WGA

city: Minneapolis

first: Sulagna

last: Banerjee

state: MN

address: 515 Delaware Street SE

department: Surgery

institute: University of Minnesota

summary: CD133+ and CD133 negative cells from pancreatic cancer cell line KPC001 were sorted using MACS technique. RNA was isolated using trizol (Invitrogen) and cleaned up using Qiagen RNAeasy columns. The RNA passed QC by the Biomedical Genomic Center (BMGC) of University of Minnesota. cDNA was prepared and hybridized by BMGC according to standard protocol.

overall_design: The goal of the experiment was to see changes in the expression of genes in the CD133+ vs CD133- population in the pancreatic cancer cell line derived from KPC mouse model.

first: Ashok

last: Saluja


title: Apc, Kras, and TGFbeta in intestinal organoids

city: Helsinki

first: Zoltan

last: Wiener

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

overall_design: Refer to individual Series


title: Impact of Elevated Plasma 5-HT on Global Gene Expression of Murine Megakaryocytes

city: Little rock

first: fusun

last: kilic

state: AR

address: 4301 West Markham Street, Mail Slot 516,

institute: UAMS

summary: The goal of this project was to understand the functional consequences of plasma biogenic amine serotonin (5-HT) elevation in megakaryocytes by measuring gene expression

overall_design: Total RNA was extracted from the megakaryocytes of mice treated with either 5-HT or saline and global gene expression was measured.

first: Charles

middle: P

last: Mercado

first: Fusun

last: Kilic

first: Marjorie

middle: L

last: Beggs

first: Vinay

last: Raj


title: Cyclin D:Cdk4/6 Activates Rb in Early G1 Phase by Mono-Phosphorylation

status: Public on Apr 03 2014

city: La Jolla

first: Steven

last: Dowdy

state: CA

address: 9500 Gilman Drive #0686

department: CMM

institute: UCSD

summary: The retinoblastoma tumor suppressor protein (Rb) regulates early G1 phase checkpoints, including the DNA damage response, as well as cell cycle exit and differentiation.  The widely accepted model of G1 cell cycle progression proposes that cyclin D:Cdk4/6 partially inactivates the Rb tumor suppressor during early G1 phase by progressive multi-phosphorylation, termed hypo-phosphorylation, resulting in release of E2F transcription factors.  However, this model remains largely unproven biochemically and the biologically active form(s) of Rb remains unknown.  Here we find that Rb is un-phosphorylated in G0 cells and becomes exclusively mono-phosphorylated throughout all of early G1 phase by cyclin D:Cdk4/6.  Early G1 phase mono-phosphorylated Rb is composed of 14 independent isoforms that are all targeted by the E1a oncoprotein, but each shows a preferential binding pattern to specific E2F1-4 transcription factors.  At the late G1 Restriction Point, cyclin E:Cdk2 inactivates Rb by a quantum hyper-phosphorylation (>12 phosphates/Rb).  Cells undergoing a DNA damage response activate cyclin D:Cdk4/6 to generate mono-phosphorylated Rb that regulates global transcription.  In contrast, a non-phosphorylatable ?Cdk-Rb allele was non-functional for regulating a DNA damage response, but functional for driving cell cycle exit and differentiation during myogenesis.  These observations fundamentally change our understanding of G1 cell cycle progression and show that there is no progressive multi-phosphorylation or hypo-phosphorylation inactivation of Rb during early G1 phase by cyclin D:Cdk4/6.  Instead, cyclin D:Cdk4/6 generates functionally active, mono-phosphorylated Rb that is the only Rb isoform present in cells during early G1 phase.

overall_design: Global transcriptional analysis of murine embryonic fibroblasts (MEFs) with conditional deletion of the endogenous RB gene by treatment with cell permeable TAT-Cre. Comparison to unaltered MEFs and MEFs with physiological level of exogenous wildtype or phospho-mutant RB expressed at time of RB gene deletion.

first: Anil

last: Narasimha

first: Manuel

last: Kaulich

first: Gary

last: Shapiro

first: Yoon

last: Choi

first: Piotr

last: Sicinski

middle: F


title: Whole-transcriptome microarray to identify sexually dimorphic RNA transcripts that are differentially expressed in disease-susceptible versus nonsusceptible CNS regions of male and female SJL mice

city: St. Louis

first: Seth

middle: Daniel

last: Crosby

address: 660 S. Euclid

department: Genetics

institute: Washington Univeristy School of Medicine

summary:
We hypothesized that sexual dimorphism in experimental autoimmune enecphalomyelitis arises from sexually dimorphic and CNS-region specific expression of genes that regulate BBB permeability and leukocyte entry.
To test this hypothesis, we profiled total RNA from the cerebella and frontal cortices of naïve female versus male SJL mice

overall_design: 100 ng of total RNA was extracted from cerebella and frontal cortices of naïve SJL female and male littermates to identify differential expression of gene transcripts unique to female cerebellum.

first: Sara

middle: A

last: Basak

first: Lillian

last: Cruz-Orengo

first: Robyn

last: Klein


title: Genome-scale analysis in blood progenitor and mast cells reveals how lineage-affiliated transcription factors control distinct regulatory programs [Beadchip Experiments #2]

city: Cambridge

first: Felicia

last: Ng

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

institute: Cambridge Institute for Medical Research

summary: Despite major advances in the generation of genome-wide binding maps, the mechanisms by which transcription factors (TFs) regulate cell type identity have remained largely obscure. Through comparative analysis of 10 key haematopoietic TFs in both mast cells and blood progenitors, we demonstrate that the largely cell-type specific binding profiles are not opportunistic, but instead contribute to cell-type specific transcriptional control, because (1) mathematical modelling of differential binding of shared TFs can explain differential gene expression, (2) cell-type specific binding is largely mediated through consensus binding sites, and (3) knock-down of blood stem cell regulators Gata2 and Erg in mast cells reveals mast cell specific genes as direct targets. Finally we show that the known mast cell regulators Mitf and c-Fos likely contribute to the global reorganisation of TF binding profiles. Taken together therefore, our study elucidates how key regulatory TFs contribute to transcriptional programmes in several distinct mammalian cell types.

overall_design: Total RNA from primary mast cells transfected with retroviral shRNA vectors were compared to negative controls (shRNA against luciferase).

first: Fernando

middle: J

last: Calero-Nieto

first: Nicola

last: Wilson

first: Rebecca

last: Hannah

first: Evangelia

last: Diamanti

first: Victoria

last: Moignard

first: Ana

last: Leal-Cervantes

first: Isabel

last: Jimenez-Madrid

first: Lorenz

last: Wernisch

first: Berthold

last: Gottgens


title: miR-99a/100~125b tricistrons regulate hematopoietic stem and progenitor cell homeostasis by shifting the balance between TGFβ and Wnt signaling

status: Public on Mar 28 2014

city: Frankfurt

first: Jan-Henning

last: Klusmann

address: Theodor-Stern-Kai 7

department: Pediatric Hematology and Oncology

institute: Goehte University Frankfurt

summary:
Although regulation of stem cell homeostasis by miRNAs is well studied, it is unclear how individual miRNAs, genomically encoded within an organized polycistron, can interact to induce an integrated phenotype. miR-99a/100, let-7 and miR-125b paralogues are encoded in two tricistrons on human chromosome 11 and 21. They are highly expressed in hematopoietic stem cells (HSCs) and acute megakaryoblastic leukemia (AMKL), an aggressive form of leukemia with poor prognosis.
Integrative analysis of global gene expression profiling, miRNA target prediction and pathway architecture revealed that miR-99a/100, let-7 and miR-125b functionally converge at the combinatorial block of the TGFβ pathway by targeting four receptor subunits and two SMAD signaling transducers. In addition, downregulation of tumor suppressor genes APC/APC2 stabilizes active β-Catenin and enhances Wnt signaling. By switching the balance between Wnt and TGFβ signaling the concerted action of these tricistronic miRNAs promoted sustained expansion of murine and human HSCs in vitro or in vivo, while favoring megakaryocytic differentiation.

overall_design: We lentivirally transduced cord blood CD34+-hematopoietic stem and progenitor cells (CB-HSPCs) to ectopically express miR-125b-2, miR-99a, let-7c or miR-99a~125b-2 and cultured them in megakaryocytic differentiation medium for 7 days.

first: Stephan

last: Emmrich


title: Hippocampal CA3 Transcriptome Signature and Dentate Gyrus MRI Features Correlate with Initial Precipitating Injury in Refractory Temporal Lobe Epilepsy

status: Public on Mar 31 2014

city: Sao Paulo

first: Carlos

middle: Alberto

last: Moreira-Filho

state: SP

address: Av. Dr. Eneas Carvalho de Aguiar 647

department: Departments of Pediatrics

country: Brazil

institute: Faculdade de Medicina da Universidade de Sao Paulo

summary: We analyzed the transcriptomic profile of CA3 explants surgically obtained from patients with refractory MTLE (mesial temporal lobe epilepsy) and HS (hippocampal sclerosis) in order to investigate if the initial precipitating injury (IPI) influences the molecular mechanisms underlying this condition. CA3 transcriptomic profile was found to be significantly different in cases with prolonged febrile seizures as the IPI (identified here as FS) when compared to correspondent data from cases without febrile seizure history (NFS).

overall_design: CA3 transcriptomic profiles of FS and NFS were compared in order to identify differentially expressed transcripts

first: Silvia

middle: Y

last: Bando

first: Maryana

middle: C

last: Alegro

first: Edson

last: Amaro Jr

first: Alexandre

last: Silva

first: Luiz

middle: H

last: Castro

first: Hung-Tzue

middle: T

last: Wen

first: Leandro

last: Lima

first: Helena

last: Brentani


title: GATA1s induces hyperproliferation of eosinophil precursors in Down syndrome transient leukemia

summary:
Transient leukemia (TL) is evident in 5-10% of all neonates with Down syndrome (DS) and associated with N-terminal truncating GATA1-mutations (GATA1s). Here we analyzed the effect of on gene expression upon ectopic expression of Gata1s or  Gata1, while simultaneously  knocking down endogenous GATA1, in wild-type CD34+-hematopoietic stem and progenitor cells during myeloid differentiation.
Ectopic expression of Gata1s, but not Gata1, in wild-type CD34+-hematopoietic stem and progenitor cells induced hyperproliferation of eosinophil promyelocytes in vitro. While GATA1s retained the function of GATA1 to induce eosinophil genes by occupying their promoter regions, GATA1s was impaired in its ability to repress oncogenic MYC and the pro-proliferative E2F transcription network.

overall_design: We lentivirally transduced wild-type CD34+-hematopoietic stem and progenitor cells to ectopically express Gata1s or  Gata1, while simultaneously  knocking down endogenous GATA1, and cultured them in myeloid differentiation for 0, 4 and 14 days.

first: Aliaksandra

last: Maroz


title: Human non-GCIMP gioblastoma subtypes evolve from a common proneural-like precursor glioma

city: Boston

first: Markus

last: Riester

address: 3 Blackfan Circle

department: Biostatistics & Computational Biology

institute: Dana-Farber Cancer Institute

summary: In order to understand the relationships between the human non-GCIMP glioblastoma subgroups, we performed computational analysis of human genomic data to predict the temporal sequence in which the driver events arise during tumorigenesis. The order of evolutionary events for non-GCIMP GBM is 1) chr 7 gain and loss of chr 10, followed by 2) CDKN2A loss and/or TP53 mutation, and 3) alterations canonical for specific subtypes such as NF1 loss or focal amplification of PDGFRα or EGFR. We then developed a computational methodology to identify the drivers of broad copy number changes, identifying PDGF-A (chr 7) and PTEN (chr 10) as driving the initial non-disjunction events. These predictions were validated using mouse modeling, showing PDGF-A is sufficient to induce PN-like gliomas that are enhanced by loss of Ink4a-Arf, Tp53 or Pten. Additional Nf1 loss converts PN to the MES subtype. Our findings suggest non-GCIMP GBMs arise as, and evolve from, a common proneural-like precursor.

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus

overall_design:
hGBM_sphere:
Three different human GBM sphere lines expressing two different NF1-shRNAs or empty shRNA-control were generated by a lentiviral infection with the relevant pLKO.1 vectors. The total RNAs were obtained from the GBM sphere lines and the gene expression profile of the NF1-shRNA cells was then compared to the control cells.
hGBM_rapamycin:
Two human GBM sphere lines (TS543 and TS667) expressing the NF1-shRNAs were generated by a lentiviral infection with two different pLKO.1-NF1-shRNA vectors (two different target sequence; #2 and #5). The total RNAs were obtained from the NF1-shRNA lines treated with a 1nM rapamycin or 0.1% DMSO control for 5 hours and the gene expression profile was then compared between the both groups.
Murine_gliomas:
Murine brain tumors were generated by an injection of DF1 cells producing the relevant RCAS virus into newborn pups or adult mice brain. When mice presented any symptoms of disease, the mice were sacrificed and the brain tumor tissues were macroscopically dissected. Then total RNAs were extracted from the murine brain tumors or normal brain tissues and the gene expression profile was compared between various tumor types and/or normal brain tissues. In this study, two different RCAS-shNf1 (GR249 and GF249) and shp53 (R696 and mR696) was used for the generation of the murine brain tumors. Each RCAS vector has different structure but the target sequence against the Nf1 and p53 is same and similar knockdown effect was observed. Tumor grade were determined with the residual sections after a piece of tumor tissue were excised for the RNA extraction. The detail information of the experiment was described in the associated-publication.
Murine_shere:
Murine neurosphere lines were generated by a retroviral infection with the relevant RCAS viruses. The total RNAs were obtained from the murine neurosphere lines expressing the RCAS-shGL2, shNf1, shp53 or shNf1+shp53 and the gene expression profiles of the shNf1, shp53 or shNf1/p53 cells were then compared to the control shGL2 cells.


title: Gene expression in Kras-driven lung tumors in mice fed with standard or high calorie diet

status: Public on Mar 27 2014

city: Geneva

first: Giorgio

last: Ramadori

address: Michel Servet 1

country: Switzerland

institute: University of Geneva

summary:
The results provide information on the gene expression in dissected  KrasG12D-driven lung tumor in mice. Mice were fed on high-calorie diet starting 3 months before tumor induction.
Dissected tumors were obtained 11 weeks after tumor induction.

overall_design: Total RNA extracted from Kras-driven lung tumors of mice fed with standard diet or high calorie diet

first: Georgia

last: Konstantinidou


title: Genome-wide analysis of liver gene expression in male and female mice.

status: Public on Apr 01 2014

city: Houston

first: deqiang

last: sun

state: TX

address: 2121 W Holcombe Blvd

institute: Texas A&M University

summary: Analysis of gender differential gene expression levels in mouse liver.

overall_design: Total RNA was obtained from mouse liver isolated from male and female mice.

first: Sun

last: Deqiang

first: Astrid

last: Kosters


title: PHF19 isoforms induced gene expression alteration in colon cancer cells

status: Public on Mar 22 2014

city: Guangzhou

first: Mengfeng

last: Li

state: Guangdong

address: 74# zhongshan 2 Rd.

department: Zhongshan school of medicine

institute: Sun Yat-sen University

summary: This experiment is designed to evaluate gene expression alteration following silencing PHF19 isoforms in colon cancer cells.

overall_design: Total RNA were extraced from indicated stable cell lines, two biological replications for each treatment.

first: Zhe

last: Ying


title: Gene expression profiling upon PI3K inhibition using different inhibitors

city: Madrid

first: Sergio

last: Callejas

address: Melchor Fernández Almagro, 3

department: Genomics Unit

institute: Centro Nacional de Investigaciones Cardiovasculares (CNIC)

summary: Activation of the phosphoinositide 3-kinase (PI3K)/Akt signaling pathway is one the most frequent genetic events in human cancer. Therefore, the development of PI3K inhibitors has attracted much attention. We previously described the pyrazolopyrimidine derivative ETP-45658 as a potent inhibitor of PI3K p110α in vitro and in vivo. Here we report the gene expression signatures of MCF7 cells treated with ETP-45658 or the reference PI3K inhibitor PI-103. Both compounds potently inhibited proliferation of a wide range of human cancer cells. ETP-45658 most potently suppressed the growth of PIK3CA (E545K)-mutated MCF7 breast cancer cells. Treatment with ETP-45658 or PI-103 resulted in a time and concentration-dependent decrease in phosphorylation of AKT Ser473 in MCF7 cells. We conducted microarray analysis examining the gene expression profile in MCF7 cells at six hours post ETP-45658 or PI-103 incubation. Both compounds induced the expression of negative cell cycle regulators including Cyclin G2, p27kip1 and ING4 and decreased positive regulators such as Cyclin D1 without significantly affecting the expression of pro-apoptotic genes. We found FOXO transcription factor binding sites over-represented in both up- and down-regulated genes but not in those without significant changes. The expression of the breast cancer tumor suppressor Nischarin was found to be induced by ETP-45658 but not after PI-103 treatment while several genes differentially expressed specifically after ETP-45658 treatment are functionally associated with the focal adhesion pathway.

overall_design: Twelve samples have been analyzed in six different conditions. Two replicates have been included for each condition.

first: Richard

last: Hill

first: Ravi

last: Kalathur

first: Beena

last: Jeevan-Raj

first: Beatriz

last: Garcia Serelde

first: Antonio

last: Cebriá

first: Carmen

last: Blanco-Aparicio

first: Joaquín

last: Pastor

first: Matthias

last: Futschik

first: Ana

last: Dopazo

first: Wolfgang

last: Link


title: Hedgehog pathway inhibition in chondrosarcoma using the Smoothened inhibitor IPI-926 directly inhibits sarcoma cell growth

status: Public on Mar 18 2014

first: John

last: Keilty

state: Massachusetts

address: 780 Memorial Drive

department: Informatics

institute: Infinity Pharmaceuticals

summary:
Mice bearing primary human chondrosarcoma xenografts were treated with IPI 926, and mRNA levels of known Hh pathway genes and endpoint tumor volumes were measured.
Gene expression profiling of IPI-926 treated tumors was conducted to identify potential novel Hh target genes.

overall_design: 4 Control treated and 4 IPI-926 treated NSG Mice.  Primary tumor was obtained from a single chondrosarcoma patient.

first: Campbell

last: Veronica

first: Wunder

last: Jay


title: Genome-wide analysis of the gene expression profile of  in vivo induced pluripotent stem cells

status: Public on Mar 19 2014

city: Manchester

first: Kostas

last: Kostarelos

address: AV Hill Building, Upper Brook St

department: Faculty of Medical and Human Sciences

institute: University of Manchester

summary:
Analysis of the gene expression profile of a novel type of pluripotent stem cells (in vivo induced pluripotent stem cells, named i2PS cells) obtained by reprogramming BALB/c mice hepatocytes in vivo. The hypothesis tested in the present study is that in vivo induced pluripotent stem cells will have a similar gene expression profile to that of other pluripotent stem cells. Hence the embryonic stem cell line E14TG2A is used as a reference in this study.
Results provide valuable information for the overall molecular characterisation of cells that have been reprogrammed to pluripotency in vivo, together with the confirmation of their pluripotent character at the gene expression level.

overall_design: Total RNA was obtained from i2PS and E14TG2A cells cultured under standard embryonic stem cells conditions (i.e. DMEM supplemented with LIF). Three biological replicates were included for each cell type. Data were analysed using the gene expression levels of E14TG2A cells as a reference.

first: Irene

last: de Lazaro

first: Charles

last: Mein

first: Mimoza

last: Hoti


title: Gene expression in pancreatic ductal adenocarcinoma

status: Public on Mar 14 2014

city: Glasgow

first: Nigel

middle: Balfour

last: Jamieson

address: Alexandra Parade

department: Academic Department of Surgery

institute: University of Glasgow

summary: To further develop our understanding of the gene expression signature of pancreatic ductal adenocarcinoma

overall_design: Gene expression signatures in macrodissected resected pancreatic ductal adenocarcinoma specimens

first: Nige

middle: B

first: Karin

last: Oien

first: Ross

last: Carter

first: Colin

last: McKay


title: Siah2-dependent gene expression profile

city: Durham

first: Jian-Liang

last: Li

state: NC

address: 111 TW Alexander Dr

institute: NIEHS

summary: Gene expression profiling was performed to identify Siah2-dependent changes in cells subjected to ER stress, hypoxia, and combined glucose/oxygen deprivation.  To establish the magnitude of the Siah2 effect on the ER stress response, we have compared gene expression profiles of WT and Siah1a-/-::Siah2-/-  mouse embryo fibroblasts (MEFs) that were subjected to glycosylation inhibitor tunicamycin (TM), thapsigargin (TG), glucose deprivation, or glucose/oxygen deprivation.  Overall, this analysis confirmed changes associated with ER stress that had not previously been associated with Siah2 signaling, substantiating Siah2 as a key coordinator of ER stress through the ATF4 and sXbp1 pathways.

overall_design: WT and Siah1a/Siah2 KO MEF cells were treated with TM or TG for 6 h, or subjected for 12 h to oxygen deprivation, glucose deprivation or a combination of oxygen and glucose deprivation, in duplicate.

first: Marzia

last: Scortegagna

first: Jian

first: Ze’ev

last: Ronai


title: Genetic factors regulating lung vasculature and immune cells functioning associate with resistance to pneumococcal infection

status: Public on Mar 05 2014

city: Leicester

first: Peter

middle: W

last: Andrew

address: University Rd

department: Infection, Immunity and Inflammation

institute: University of Leicester

summary: Analysis of pulmonary gene expression in two mouse strains, resistant (BALB/c) and susceptible (CBA/Ca) to Streptococcus pneumoniae infection. Data collected at 6h post-infection and for control animals (PBS-treated). The list of differentially expressed genes was created by comparisons of infected versus PBS-treated animals and PBS-treated BALB/c versus CBA/Ca. The hypothesis tested in the present study was that pulmonary transcriptomes of both mouse strains differ during pneumococcal infection and in non-disease conditions. Results provided important information on differences in immune responses between both mouse strains. The results identified genes and pathways uniquely regulated by only one of the tested mouse strains helping to understand molecular mechanism behind resistance or susceptibility to pneumococcal infections.

overall_design: Total RNA obtained from lung tissue from BALB/cOlaHsd and CBA/CaOlaHsd mouse strains (Harlan) 6 hours post intranasal infection with Streptococcus pneumoniae serotype 2 strain D39 dose 5.0E06 or PBS-treated animals

first: Magda

middle: S

last: Jonczyk

first: Nicolas

last: Sylvius

first: Vitor

middle: E

last: Fernandes

first: Michelle

last: Simon

first: Saumya

last: Kumar

first: Paul

last: Denny

first: Ann-Marie

last: Mallon


title: Wnt5A Enhances Resistance of Melanoma Cells to Targeted BRAF Inhibitors

status: Public on Mar 06 2014

city: Boston, MA

first: Jamie

last: Anastas

state: United States of America

address: 300 Longwood Ave

department: Newborn Medicine

institute: Boston Children's Hospital

summary: About half of all melanomas harbor a constitutively active mutant BRAFV600E/K kinase that can be selectively inhibited by targeted BRAF inhibitors (BRAFi). While patients treated with BRAFi initially exhibit measurable clinical improvement, the majority of patients eventually develop drug resistance and relapse. We observe significant elevation of WNT5A in a subset of tumors from patients exhibiting disease progression on BRAFi therapy. WNT5A transcript and protein are also elevated in BRAFi-resistant melanoma cell lines generated by long-term in vitro treatment with BRAFi. RNAi-mediated reduction in levels of endogenous WNT5A in melanoma decreases cell growth, increases apoptosis in response to BRAFi challenge, and decreases the activity of pro-survival AKT signaling. Overexpression of WNT5A conversely promotes melanoma growth and tumorigenesis and activates AKT signaling. Similar to WNT5A knockdown, knockdown of the WNT receptors FZD7 and RYK inhibits growth, sensitizes melanoma cells to BRAFi, and reduces AKT activation. Together, these findings suggest that chronic BRAF inhibition elevates WNT5A expression, which then acts through FZD7 and RYK to promote AKT signaling, leading to increased growth and therapeutic resistance. Increased WNT5A expression in BRAFi-resistant melanomas also correlates with an associated transcriptional signature, which identifies potential therapeutic targets to reduce clinical resistance to BRAFi.

overall_design:
Expression of WNT5A-correlated genes was compared in melanoma cell lines generated to be resistant to PLX4032 and the their associated naïve parental line
Basal expression of the WNT5A-correlated genes was also measured in experiments comparing each naïve line to a mixed reference pool containing equal amounts of 47 melanoma cell lines.

first: Erika

middle: M

last: von Euw

first: Dennis

last: Slamon

first: Judy

last: Dering

first: Hsiao-Wang

last: Chen


title: Genome-wide analysis of transcription factor PPARγ-responsive gene expression in the nodose ganglion (NG)

status: Public on Apr 02 2014

city: Dallas

first: Chen

last: Liu

address: 5223 Harry Hines Blvd

institute: UT Southwestern Medical Center

summary:
Analysis of gene expression regulated by PPARγ in the nodose ganglion of Phox2b::Cre; PPARγ fl/+ and Phox2b::Cre; PPARγ fl/fl mice.
Resutls demonstrate potential PPARγ transcriptional targets in neurons

overall_design: RNA was purified from laser-captured nodose neurons.  Three independent biological replicates were prepared by pooling RNA of nodose neurons from multiple animals of the same genotypes.  Genomics and Microarray Core Facility at UT Southwestern ( http://microarray.swmed.edu/) checked RNA quality and performed the hybridization with a Mouse-6 V2 BeadChip (Illumina Inc.).  We used Partek Genomics Suite 6.5 (Partek Inc.) and Ingenuity Pathway Analysis (Ingenuity Systems Inc.) for data and pathway analysis respectively.

first: Joel

middle: K

last: Elmquist


title: Wnt signalling sustains an EpiSCs subpopulation similar to primitive streak with increased mesendodermal potency

status: Public on Mar 04 2014

city: Edinburgh

first: Anestis

last: Tsakiridis

address: 5 Little France Drive

institute: MRC Centre for Regenerative Medicine

summary: During gastrulation, epiblast cells are pluripotent and their fate is thought to be constrained principally by their position.  Cell fate is progressively restricted by localised signalling cues from areas including the primitive streak (PS). However, it is unknown whether this restriction accompanies, at the single cell level, a reduction in potency.  Investigation of these early transition events in vitro is possible via the use of Epiblast Stem Cells (EpiSCs), self-renewing pluripotent cell lines equivalent to the postimplantation epiblast. Strikingly, EpiSCs express various early lineage-specific markers in self-renewing conditions. However, it is unknown whether cells that express these markers are pluripotent, spontaneously differentiated, or biased towards specific lineages. Here we show that EpiSC are inherently heterogeneous and contain two major and mutually exclusive subpopulations with PS and neural characteristics respectively. Using differentiation assays and embryo grafting we demonstrate that PS-like EpiSCs are biased towards mesoderm and endoderm differentiation but they still retain their pluripotent character. The acquisition of a PS character by undifferentiated EpiSC is mediated by paracrine Wnt signalling. Elevation of Wnt activity promotes further restriction into PS-associated cell fates which occurs via the generation of distinct clonal mesendodermal and neuromesodermal precursors. Collectively, our data suggest that primed pluripotency encompasses a range of reversible lineage-biased states reflecting the birth of pioneer lineage precursors from a pool of uncommitted EpiSCs similar to the earliest cell fate restriction events taking place in the gastrula-stage epiblast.

overall_design: Total RNA obtained (3 biological replicates) from flow sorted dsRed2+, dsRed2-, and +CHIRON treated for 48h cells was isolated and labelled/amplified using the Illumina® TotalPrep™ RNA Amplification Kit (Life Technologies)

first: Yali

last: Huang

first: Guillaume

last: Blin

first: Stavroula

last: Skylaki

first: Filip

last: Wymeersch

first: Rodrigo

last: Osorno

first: Costas

last: Economou

first: Eleni

last: Karagianni

first: Sally

last: Lowell

first: Valerie

last: Wilson


title: Time-dependent network analysis reveals molecular targets underying the development of diet-induced obesity and non-alcoholic steatohepatitis.

status: Public on Mar 01 2014

city: Daegu

first: Myung-Sook

last: Choi

address: 1370, Sankyuk-Dong, Buk-gu

department: Food and Nutrition

country: South Korea

institute: Kyungpook National University

summary: Core diet-induced obesity networks were constructed using Ingenuity pathway analysis (IPA) based on 332 high-fat diet responsive genes identified in liver by time-course microarray analysis (8 time-points over 24 weeks) of high-fat diet fed mice compared to normal diet fed mice. IPA identified five core diet-induced obesity networks with time-dependent gene expression changes in liver. When we merged core diet-induced obesity networks, Tlr2, Cd14 and Ccnd1 emerged as hub genes associated with both liver steatosis and inflammation and were altered in a time-dependent manner. Further protein-protein interaction network analysis revealed Tlr2, Cd14 and Ccnd1 were inter-related through the ErbB/insulin signaling pathway.  Dynamic changes occur in molecular networks underlying diet-induced obesity. Tlr2, Cd14 and Ccnd1 appear to be hub genes integrating molecular interactions associated with the development of NASH. Therapeutics targeting hub genes and core diet-induced obesity networks may help ameliorate diet-induced obesity and NASH.

overall_design: Total RNA obtained from isolated liver of C57BL/6J mice fed normal diet or high fat diet for 0, 2, 4, 6, 8, 12, 16, 20 and 24 weeks.

first: Su-kyung

last: Shin


title: Expression data from JQ1 (0.2 uM) treated tamoxifen-resistant MCF7 cells

first: Qin

last: Feng

address: 3517 Cullen Blvd

department: Biology and Biochemistry

institute: University of Houston

summary:
Estrogen signaling pathway is critical for breast cancer development and has remained the major adjuvant therapeutic target for this disease. Tamoxifen has been used in clinic for many years to treat ER-positive breast cancer. However a great many (30%) suffer relapse due to drug resistance. In this study, the bromodomain inhibitor JQ1 was found to down-regulate ERalpha gene expression and have anti-tumor effect in cultured tamoxifen-resisant breast cancer cells.
We used microarrays to detail the global programme of gene expression in tamoxifen-resistant MCF7 cells treated with the bromodomain inhibitor JQ1.

overall_design: Tamoxifen-resistant breast cancer MCF7 cells were treated with DMSO (vehicle) or JQ1 (0.2 uM) for 24 hours before total RNA was purified for microarray. Each sample was triplicated.


title: Time-course microarrays reveal early activation of the immune transcriptome and adipokine dysregulation leads to fibrosis in visceral adipose depots during diet-induced obesity

summary: Time-course analysis of adipocyte gene expression profiles response to high fat diet. The hypothesis tested in the present study was that in diet-induced obesity, early activation of TLR-mediated inflammatory signaling cascades by CD antigen genes, leads to increased expression of pro-inflammatory cytokines and chemokines, resulting in chronic low-grade inflammation. Early changes in collagen genes may trigger the accumulation of ECM components, promoting fibrosis in the later stages of diet-induced obesity. New therapeutic approaches targeting visceral adipose tissue genes altered early by HFD feeding may help ameliorate the deleterious effects of a diet-induced obesity.

overall_design: Total RNA obtained from isolated epididymal and mesenteric adipose tissue of C57BL/6J mice fed normal diet or high fat diet for 2, 4, 8, 20 and 24weeks

first: Eun-Young

last: Kwon


title: Foxf1+/- mouse lung gene expression analysis

first: Pawel

last: Stankiewicz

state: Texas

address: One Baylor Plaza

department: Molecular and Human Genetics

institute: Baylor College of Medicine

summary: Analysis of genes dysregulated due to haploinsufficiency of Foxf1 in postnatal day 0.5 mouse lungs

overall_design: Total RNA obtained from six Foxf1+/- mouse lungs compared to six wildtype littermate mouse lungs

first: Avinash

last: Dharmadhikari

first: Tadeusz

last: Majewski


title: mRNA profiles of activated and resting T cells and their exosomes

status: Public on Feb 27 2014

first: Fatima

last: Sanchez-Cabo

address: Melchor Fernandez Almagro

institute: CNIC

summary: Microarray analysis of exosomal and cellular mRNAs in activated and resting primary human T lymphoblasts

overall_design: Primary human T lymphoblasts were obtained from eight donors and total RNA was isolated from cells and derived exosomes before and after activation with PMA plus ionomycin.

first: Carolina

last: Villarroya-Beltri

first: María

last: Mittelbrunn

first: Fátima

last: Sánchez-Cabo

first: Francisco

last: Sánchez-Madrid


title: Separated Pancreatic stellate cells (PSCs) by functional separation using modified Matrigel invasion assay

status: Public on Feb 25 2014

city: BALTIMORE

first: Kenji

last: Fujiwara

address: 1650 Orleans Street

department: Oncology

institute: Johns Hopkins University SOM

summary: We separated PSCs by functional separation using moidfied Matrigel invasion assay our previously reported (Fujiwara, PLoS One, 2012). In this culture system, we evaluated two primary cultures of human PSCs. PSCs in the upper chambers were incubated for 72 hours in culture with SUIT-2 pancreatic cancer cells in the lower chambers, or as controls without pancreatic cancer cells in the lower chambers, and were collected from the top and bottom sides of the upper chambers separately. The top side-derived PSCs were cells that did not migrate toward the cancer cells, and the bottom side-derived PSCs were cells that migrated toward the pancreatic cancer cells. We then performed a DNA microarray analysis using these cells.

overall_design: The quality of the RNA samples was evaluated using Experion™ Automated Electrophoresis Station (Bio-Rad Laboratories, Hercules, CA). We used a HumanHT-12v4 Expression BeadChip (Illumina, San Diego, CA) for these analyses. The data were analyzed using Bead Studio software version 3.2.3 (Illumina).

first: Kenoki

last: Ohuchida

first: Shin

last: Akagawa

first: Takao

last: Ohtsuka

first: Kazuhiro

last: Mizumoto

first: Masao

last: Tanaka


title: mRNA and miRNA profiles of activated and resting T cells and their exosomes

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

overall_design: Refer to individual Series