title: Function of LIM-only protein FHL2 in vascular smooth muscle cells

status: Public on Oct 07 2014

city: Amsterdam

first: Perry

middle: D

last: Moerland

address: Meibergdreef 9

department: Epidemiology and Data Science

institute: Amsterdam UMC

summary: The LIM-only protein FHL2 is expressed in SMCs and inhibits SMC-rich lesion formation. However, the underlying mechanism behind FHL2's action in SMCs has been only partially resolved. To further elucidate the role of FHL2 in SMCs we compared the transcriptome of cultured SMCs derived from wild-type (WT) and FHL2-knockout (KO) mice.

overall_design: Comparison of gene expression in aortic smooth muscle cells (SMCs) isolated from WT and FHL2-knockout (FHL2-KO) mice. SMCs isolated from three mouse aortas were pooled (Kurakula et al, PLOS One, 2014). Both for WT and FHL-KO mice three batches of SMCs (derived from 9 mice) were cultured. The SMCs were grown to confluency and maintained in serum-free medium for 48 hrs before harvest. Subsequently, RNA was isolated for gene expression profiling.

first: Kondababu

last: Kurakula

first: Claudia

last: van Tiel

first: Carlie

last: de Vries


title: The basic leucine zipper transcription factor NFIL3 directs the development of   a common innate lymphoid cell precursor

status: Public on Oct 16 2014

city: Dallas

first: Lora

middle: V

last: Hooper

state: TX

address: 5323 Harry Hines Blvd.

department: Immunology

country: USA

institute: The University of Texas Southwestern Medical Center at Dallas

summary: Innate lymphoid cells (ILCs) are recently identified lymphocytes that limit infection and promote tissue repair at mucosal surfaces. However, the pathways underlying ILC development remain unclear. Here we show that the transcription factor NFIL3 directs the development of a committed bone marrow precursor that differentiates into all known ILC lineages. NFIL3 was required in the common lymphoid progenitor (CLP), and was essential for the differentiation of CLP, a bone marrow cell population that gives rise to all known ILC lineages. Clonal differentiation studies revealed that CXCR6+ cells within the CLP population differentiate into all ILC lineages but not T- and B-cells. We further show that NFIL3 governs ILC development by directly regulating expression of the transcription factor TOX. These findings establish that NFIL3 directs the differentiation of a committed ILC precursor that gives rise to all ILC lineages and provide insight into the defining role of NFIL3 in ILC development.  This experiment is to compare gene expression profiles between wild-type and Nfil3-/- common lymphoid progenitor (CLP) cells to identify genes regulated by NFIL3.

overall_design: There are 6 samples in this experiment, including 3 biological replicates for wild-type CLPs and 3 biological replicates for Nfil3-/- CLPs. All mice used are on the C57BL/6 background.

first: X

last: Yu

first: Y

last: Wang

first: M

last: Deng

last: Li

first: K

middle: A

last: Ruhn

first: C

middle: C

last: Zhang

first: L


title: Gene expression changes initiated by miR-34c in Dicer/Pten double knockout mouse serous epithelial cancer

status: Public on Oct 03 2014

city: Houston

first: Chad

last: Creighton

address: One Baylor Plaza, Mail Stop: BCM305

department: Biostatistics, Ducan Cancer Center

institute: Baylor College of Medicine

summary: miR-34c inhibits Dicer/Pten double knockout mouse serous epithelial cancer cell proliferation by inducing cell cycle arrest and apoptosis. We found that miR-34c had a more dramatic effect on inhibiting tumor cell viability than let-7b. The action of miR-34c induced tumor cell cycle arrest in G1 phase and apoptosis and was accompanied with the regulation of key genes involved in cell proliferation and cell cycle G1/S transition. miR-34c suppressed the expression of EZH2 and MYBL2, which may transcriptionally and functionally activate CDKN1C.

overall_design: Total RNA was extracted from DKO tumor cell lines transfected with miR-34c (n=3) and control miRNA (n=3).

first: Zhifeng

first: Jaeyeon

last: Kim

first: Marty

last: Matzuk


title: Effects of differences in donors and passage numbers of endothelial progenitor cell (EPC)-derived vascular endothelial cells (VECs) on the phenotype determination of VECs (type-I versus type-II).

status: Public on Sep 30 2014

city: Shinjuku-ku

first: Kumiko

last: Saeki

state: Tokyo

address: 1-21-1 Toyama

department: Department of disease control

country: Japan

institute: National Center for Global Health and Medicine

summary: EPC-derived VECs (EPCdECs) are categorized into two group according to their effects on the proliferation of vascular smooth muscle cells: type-I pro-proliferative VECs and type-II anti-proliferative VECs. Type-II EPCdECs were converted to type-I VECs by repetitive subcultures. Not only subculture-dependent cellular stresses but also donor differences greatly affect the phenotype determination of VECs. By comparing the gene expression profiles of type-II EPCdEC of the first donor (EPC1dEC) at early passage and those of type-II EPC1dEC at late passage and EPCdEC of the second donor at early passage, characteristic gene expression patterns that discriminate Type-I and type-II EPCdECs will be comprehended.

overall_design: Totally three samples of type-I EPC-derived VECs (EPC1dEC[P12], EPC2dEC[P7]) and type-II EPC-derived VEC (EPC1dEC[P7]) were subjected to the analyses.

first: Miwako

last: Nishio

first: Chikako

last: Sato

first: Akira

last: You


title: Genome-wide expression analysis of submandibular salivary gland tumours of Smgb-Tag mice

city: Turku

first: Johannes

last: Routila

address: Tykistökatu …

department: Centre for Biotechnology

country: Finland

institute: University of Turku

summary:
To reveal novel molecular factors behind the development of salivary gland cancer, we performed gene expression analyses from Smgb-Tag mouse salivary gland samples. The overall purpose was to apply these results for clinical use to find new approaches for both possible therapeutic targets and more accurate diagnostic tools in identification of salivary gland cancers.
Smgb-Tag mouse strain, in which salivary neoplasms arise through a dysplastic phase in submandibular glands, was investigated using genome-wide microarray expression analysis, Ingenuity pathway analysis, RT-PCR, and immunohistochemistry.

overall_design: 3 normal, 3 dysplastic, and 3 adenocarcinomatous submandibular gland tumours of Smgb-Tag mice.

first: Juho-Antti

last: Mäkelä

first: Heikki

last: Luukkaa

first: Ilmo

last: Leivo

last: Irjala

first: Jukka

last: Westermarck

first: Antti

last: Mäkitie

first: Sami

last: Ventelä


title: Human Whole Blood: Psoriatic Arthritis [PsA] vs. Cutaneous Psoriasis Without Arthritis [PsC] vs. Controls

status: Public on Sep 24 2014

city: Toronto

first: Dafna

last: Gladman

state: Ontario

address: 60 Leonard Ave

department: Rheumatology Research

country: Canada

institute: Toronto Western Research Institute

summary: Transcriptional profiling of human whole blood comparing PsA, PsC, and unaffected controls

overall_design: Three condition experiment: PsA, PsC, unaffected controls. Biological replicates: 20 PsA, 20 PsC, 12 controls

first: Remy

last: Pollock


title: Gene induction in mouse C57BL6 kidney cortex by angiotensin converting enzyme inhibition (captopril)

status: Public on Oct 02 2014

city: Montreal

first: Timothy

middle: L

last: Reudelhuber

state: Quebec

address: 110 Avenue des Pins Ouest

institute: IRCM

summary: Attempt to identify genes whose expression changed in the kidney cortex with angiotensin converting enzyme inhibition.

overall_design: Eleven week-old male C57BL6 mice were treated with captopril at 10mg/kg/day in drinking water for 7 days. The kidney cortex was surgically excised and total RNA was isolated using Trizol (Invitrogen) from three treated and three control mice and was further purified using RNeasy MinElute Cleanup spin columns (Qiagen) according to manufacturer’s instructions. Probes generated from the resulting RNA were hybridized to Illumina Expression BeadChips (mouseWG-6_V2).

first: Chantal

last: Mercure


title: NORMALvs late stage OSCC

city: Waurnponds

first: sivapriya

last: pavuluri

state: VIC

address: 75, Pigdons Road

department: School of Medicine

country: Australia

institute: Deakin University

summary:
In order to identify genes with differential gene expression or alternative splicing between the groups Normal and late stage OSCC (Stage III and IV), we study 16 hybridizations (6 normal; 10 late stage OSCC) on the HumanGene10ST array using mixed model analysis of variance.  1323 genes with significant gene expression differences between the groups and 357 genes with significant exon-group interaction (a symptom of alternative splicing) were found, including 129 genes with both gene and possible splicing differences (p<0.01).  Contingency table analysis of the set of studied genes and a dataset of known pathways and gene classifications revealed that the set of alternatively spliced and expressed genes were found to be significantly over-represented in groups of the GOMolFn, GOProcess, GOCellLoc, and Pathway classes  (p<0.01).
Algorithm ANOVA study of 16 HumanGene10ST files.

overall_design:
Factorial arrangment
NORMALvs late stage OSCC samples

first: Sivapriya

last: Pavuluri

first: Christophe

last: Lefevre

first: Julie

last: Sharp

first: Sivalinga

middle: P

last: Vasireddi

first: Kevin

middle: R

last: Nicholas


title: Loss of SOX2 expression induces cell migration via Vimentin up-regulation and serves as unfavourable risk factor for poor survival of head and neck squamous cell carcinoma patients

status: Public on Sep 23 2014

city: Heidelberg

first: Chunxuan

last: Shao

address: Im Neuenheimer Feld 280

country: Germany

institute: German Cancer Research Center

summary: Transcriptional profiling of patient derived HNSCC (head and neck squamous cell carcinoma) cell line HNO223 comparing control cells transfected with shRNA against luciferase (shLuci) with cells transfected with two different shRNAs targeting SOX2. The goal was to determine the effects of SOX2 knockdown on global gene expression.

overall_design: Total RNA was extracted from stably transfected HNSCC cells with shLuci (control) and two different SOX2 shRNAs (shSOX2#1 and shSOX2#2), comparing the control with each of the two SOX2 shRNAs (replicate1: shLuci vs. shSOX2#1 and replicate2: shLuci vs. shSOX2#2). The biological replicates were from two independent transfection experiments (transfection 1 and transfection 2). Gene expression profiling was performed using the Human GE 4x44K v2 Microarray according to manufacturer`s instructions (Agilent, Santa Clara, CA).

first: Adriana

last: Jou

first: Elena

last: Orlova

first: Pilar

last: Bayo

first: Albrecht

last: Stenzinger

first: Madeleine

last: Gross

first: Alexandra

last: Jensen

first: Niels

last: Grabe

first: Christel

middle: H

last: Mende

first: Pantelis

last: Rados

first: Juergen

last: Debus

first: Wilko

last: Weichert

first: Peter

middle: K

last: Plinkert

last: Lichter

first: Kolja

last: Freier

first: Jochen

last: Hess


title: Expression profiling of murine lung 70 days following exposure to fractionated or acute dose of 1.0 Gy 56Fe- particle irradiation

status: Public on Sep 22 2014

first: Kimberly

last: Batten

address: 5323 Harry Hines Blvd

department: Cell biology

institute: UT Southwestern Medical Center

summary: Irradiation of the K-rasLA1 mouse model with a fractionated dose of 1.0Gy 56Fe- particles increases the incidence of invasive carcinoma compared to unirradiated controls or those irradiated with an acute dose.  Microarray profiling was perfromed on whole lungs from K-rasLA1 mice in order to determine global expression changes in the lung following radiation exposure.  RNA was extracted from K-rasLA1 lungs from unirradiated control animals or those irradiated with a fractionated or acute dose of 1.0Gy 56Fe- particles 70 days post-irradiation when  lungs are still histologically indistiguishable and only contain benign lesions.

overall_design: 129S2 K-rasLA1 mice were either irradiated with an acute (1.0Gy x1; n = 15) or fractionated (0.2Gy x5; n=13) dose of 1.0Gy 56Fe- particles or left unirradiated (n=13).  Animals were euthanized 70 days post-irradiation and RNA was extracted from the whole left lung of each animal.

first: Oliver

last: Delgado

middle: G

first: Jerry

middle: W

last: Shay


title: Adjuvant induced attenuation of excessive inflammation in mice infected with pandemic H1N1 (H1N1pdm) virus

status: Public on Sep 10 2014

first: Longsi

last: Ran

state: ON

address: 101 College Street

department: Division of Experimental Therapeutics

institute: Toronto General Research Institute

summary: The reassorted human 2009 pandemic H1N1 (H1N1pdm) virus infected millions of people and caused thousands of deaths with associated immunopathology.  Traditional immunosuppressants have limited capabilities in controlling inflammatory responses associated with severe influenza infections.  A new therapeutic strategy, therefore, must be developed.  We evaluated several adjuvants including toll-like receptor (TLR) agonists, TLR independent adjuvants and Complete Freund’s adjuvant (CFA) for limiting severe H1N1pdm infection outcomes in a mouse model.  In contrast to the TLR agonists and TLR independent adjuvants, CFA which contains multiple pattern recognition receptor (PRR) agonists significantly restrained pro-inflammatory responses and promoted survival in mice from lethal H1N1pdm infection.  CFA reduced expression of the plamacytoid dendritic cell (pDC) markers and interferon alpha (IFN-α) after infection, whereas it elevated the T regulatory (Treg) cell suppressive molecules galectin-1 and CTLA-4 expression. Consequently, Th1 cell differentiation and CD8+ effector T cell responses were diminished via downregulated myeloid DC (mDC) costimulation.  Furthermore, CTLA-4 expressing Treg cells were dramatically increased when the CFA primed splenocytes were restimulated with its stimuli-killed mycobacterium tuberculosis (M. TB).  The elevated CTLA-4 on Treg cells led to reduced CD86 expressing pDCs/mDCs and less CD4+ effector T cells. Overall, our study highlights that the stimuli of innate immunity potentially controls overactive host immune responses in certain situations, and the uncovered mechanism(s) sheds light on the development of anti-influenza therapies.

overall_design: C57B6/J Mice were treated with CFA at day -2 and day 2 post H1N1pdm infection. Weight loss and lethality were monitored post infection. At day 3 and day 5 lung tissues were collected for RNA extraction and expression array analysis.

first: David

middle: J

last: Kelvin


title: Effect of FDC-SP on Gene Expression of Human Periodontal Ligament Cells

status: Public on Sep 13 2014

city: chengdu

first: Lin

last: Xiang

address: No. 14, Third Section Renmin Nan Road.

country: China

institute: SCU

summary:
Previous research has reported that FDC-SP had similar molecular properties to statherin, a protein exists in saliva which plays important roles in preventing Ca precipitation. Further biomolecular study has suggested that the expression of FDC-SP may be associated with periodontal ligament (PDL) phenotype expression. Therefore, we hypothesized that FDC-SP may play specific roles in the inhibition of calcium precipitation during periodontal regeneration, as well as affect phenotype expression of periodontal ligament cells (PDLCs) during the differentiation process.
To investigate this, we applied microarray technology to identify gene expression changes in hPDLCs transfected with FDC-SP and then clustered them according to their biological functions.

overall_design: We firstly established a recombinant lentiviral vector containing FDC-SP and obtained safe and efficient FDC-SP overexpression in human periodontal ligament cells (hPDLCs). After that, we applied Agilent Whole Human Genome Oligo Microarray (4×44K) to identify differentially expressed genes between empty vector-transfected hPDLCs and FDC-SP -transfected ones and then clustered them according to their biological functions. 3 independent experiments were performed and the empty vector-transfected hPDLCs were used as control.

last: Wei

first: Ping

last: Gong


title: Development of gene expression signatures for knock down expression of semaphorin 3F

status: Public on Sep 16 2014

city: Chongqing

first: Jun

last: Rao

address: No 183, Xinqiao street, Shapingba

department: Medical center of hematology

institute: Xinqiao hospital

summary: To further development of our gene expression approach to biodosimetry, we have employed whole genome microarray expression profiling as a discovery platform to identify genes with the potential to distinguish expression of semaphorin3F. Human colorectal cancer cell HCT116 was infected with empty control or eGFP-Sh-SEMA3F lentivirus,1468 genes was found altered significantly,709 genes was upregulated and 759 genes was downregulated significantly

overall_design: knock down expression of semaphorin3F induced gene expression in human colorectal cancer cell was measured.  Three independent experiments were performed for each experiment

first: Jing

last: Yang

first: Feng

last: Wu

first: Zhi

middle: h

last: Zhou


title: Silica nanoparticles effects on gene expression of A549 cells

status: Public on Sep 08 2014

city: Padova

first: Gerolamo

last: Lanfranchi

address: Via U. Bassi, 58/B

department: CRIBI - Biotechnology Center and Biology Department

country: Italy

institute: University of Padova

summary: Expansion of nanotechnology will bring many potential benefits as adversely effects on human health. Protection of the human respiratory system from exposure of volatile nanoparticles has become an emerging health concern. The understanding of the biological processes involved in the development and maintenance of a variety of pathologies is improved by genome-wide approaches. Technical feasibility of this type of experiment has perfected in recent years, but data analysis remains challenging. In this context, gene set analysis has emerged as a fundamental tool for the interpretation of the results. We demonstrate how the use of a combination of gene-by-gene and gene set analyses can enhance the interpretation of results. Gene set analyses are able to distinguish responses due to nanoparticle size also discriminating between long and short time recovery after exposure. Transcription regulation and cell proliferation modulation appear to be an early response while oxidative stress and mitochondrial perturbation are late response. Moreover, smaller the particle higher the effect on inflammatory response and DNA damage activation. By integrating the two approaches, we evidenced the importance of MMP1, MMP9, MMP7 and MMP14 genes in response to Ludox® silica nanoparticles and the involvement apoptosis process in cell viability.

overall_design: This study is based on the treatment of A549 cells with two different silica nanoparticles (SM30, 9 nm of diameter, and AS30, 18 nm of diameter). Treatment with nanoparticles were performed independently. We performed three biological replicates for each condition.

first: Caterina

last: Fede

last: Millino

first: Beniamina

last: Pacchioni

first: Barbara

last: Celegato

first: Paolo

last: Martini

first: Francesco

last: Selvestrel

first: Fabrizio

last: Mancin

first: Lucia

last: Celotti

first: Maddalena

last: Mognato

first: Stefano

last: Cagnin


title: Knock out of NOTCH1-bound MYC enhancer (N-Me)

status: Public on Sep 07 2014

city: New York

first: Alberto

last: Ambesi-Impiombato

state: NY

address: 1130 St. Nicholas Avenue

department: ICG

institute: Columbia University

summary: Analysis of Gene Expression in KO mice lacking the NOTCH1-bound MYC putative enhancer located at +1.43K downstream of the MYC gene. Enrichment of MYC signature genes were analyzed by GSEA. Results show that MYC expression signature is indeed significantly enriched.

overall_design: Conditional Knockout or WT mice were treated with Tamoxifen or Veicle

first: Daniel

last: Herranz

first: Teresa

last: Palomero

first: Stephanie

last: Schnell

first: Agnieszka

last: Wendorff

first: Laura

last: Belver

first: Luyao

last: Xu

first: Mireia

last: Castillo-Martin

first: David

last: Llobet-Navás

first: Carlos

last: Cardo

first: Emmanuelle

last: Clappier

first: Jean

last: Soulier

first: Adolfo

last: Ferrando


title: Identification of Tra2β-associated mRNAs in HCT116 cells

status: Public on Sep 03 2014

city: Toskushima

first: Yuki

last: Kuwano

address: Kuramoto-cho

department: Pathophysiology

institute: The University of Tokushima Graduate School

summary: Human transformer 2β (Tra2β) is a serine/arginine-rich (SR)-like protein splicing factor and is now implicated to play wide-ranging roles in gene expression as an RNA-binding protein. In this study, we identified a subset of Tra2β-associated mRNAs in HCT116 human colon cancer cells using RNA immunoprecipitation with an anti-Tra2β antibody and microarray analysis.

overall_design: Whole-cell extracts from HCT116 cells were incubated with protein-A Sepharose beads precoated with 3 μg anti-Tra2β antibody or control rabbit IgG for 2 h at 4°C. RNA in the immunoprecipitation (IP) materials was measured by human whole-genome microarray (Agilent Technology).

first: Kazuhito

last: Rokutan


title: Comparison of the transcription profile of B. subtilis clpX strain with B. subtilis clpX spx strain, reporting on Spx activity

status: Public on Sep 01 2014

city: Hannover

first: Kürsad

last: Turgay

address: Schneiderberg 50

department: Institut für Mikrobiologie

institute: Leibniz Universität Hannover

summary:
In B. subtilis the unusual transcription factor Spx controls the thiol stress response regulon (Nakano et al 2003 PNAS 100:13603; Rochat et a. 2012 NAR 40:9751). Under normal growth conditions Spx is constantly degraded by the AAA+ protease complex ClpXP (Nakano et al 2001 MolMi 42:383). Comparing a B. subtilis clpX strain, where Spx levels are high, with a B. subtilis clpX spx double mutant strain which lacks Spx, will report on Spx dependent transcriptional control.
We prepared total RNA of exponentially grown B. subtilis clpX  and of B. subtilis clpX spx cells.

overall_design: Using a merged dye swap experiments of red or green labelled cDNA of the above described RNA preparations-


title: KSHV microRNA transfection and human mRNA expression changes

city: Bethesda

first: Joseph

middle: M

last: Ziegelbauer

state: MD

address: 10 Center Dr. 6N110

institute: NIH / National Cancer Institute

summary:
Transcriptional profiling of HUVECs transfected with KSHV miRNA mimics (vMix) or a negative control mimic (neg).
To identify host RNA targets of KSHV miRNAs, we took advantage of the observation that RNAs targeted by miRNAs can display small reductions in their steady-state levels.

overall_design:
Cells transfected with negative control miRNA compared to cells transfected with KSHV miRNAs.
Experimental treatment versus control treatment

first: Amelia

last: Gallaher


title: Genome-wide analysis of gene expression in the paraventricular nucleus of Sim1-Cre specific DNMT3a deletion mice.

city: Maebashi

first: Daisuke

last: Kohno

state: Gunma

institute: Gunma University

summary: Analysis of gene expression in the paraventricular nucleus in the hypothalamus (PVH) of WT and Sim1-Cre specific DNMT3a deletion mice. Results provide important information about genes regulated by DNMT3a.

overall_design: For the gene expression profiling, total RNA was extracted from PVH of WT and Sim1-Cre specific DNMT3a deletion mice (C57BL6 background) at 6 weeks old using Qiagen RNeasy Lipid Tissue Mini Kit (Qiagen) and Phase Lock Gel (5 Prime Inc., Gaitherburg, MD). To make sure reproducibility and biological significance, triple hybridizations were performed for each genotype with the RNA from 3 indipendent PVH samples, each sample contains RNA from 5 animals. Genomics and Microarray Core Facility at UTSW (http://microarray.swmed.edu/) checked RNA quality with Bioanalyzer Chip and processed the samples for hybridization with Illumina Mouse-6 V2 BeadChip (Illumina Inc., San Diego, CA). We used GeneSpring GX (Agilent Technologies, Santa Clara, CA) for data analysis.

first: Joel

last: Elmquist


title: Luteolin attenuates lipid dysregulation and insulin resistance thorough interplay of liver and adipose tissue in diet-induced obese mice

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: Analysis of effect of luteolin on lipid metabolism at gene expression level. The hypothesis tested in the present study was that luteolin treatment with obesogenic diet suppressed the hepatic lipogenesis pathways. Conversely, in adipose tissue, luteolin stimulated the lipogenesis pathway and it also simultaneously increased the expression of genes controlling lipolysis and TCA cycle. Results provide important information about the effect on diet-induced obesity and its metabolic complications.

overall_design: Total RNA of liver and adipose tissues was obtained from normal diet, high-fat diet and luteolin added high-fat diet-fed mice and mRNA expression-associated with lipid metabolism was measured.

first: Eun-Young

last: Kwon


title: CCR5 controls neuronal damage in an in vivo model of HIV glycoprotein 120-induced brain injury

status: Public on Sep 09 2014

city: La Jolla

first: Roy

last: Williams

state: CA

address: 3030 Science Park Road

department: Regenerative Medicine

institute: The Scripps Research Institute

summary: The chemokine receptor CCR5 is a major co-receptor for human immunodeficiency virus 1 (HIV-1) mediating infection of target cells1,2. Beyond its function as co-receptor, CCR5 also influences the course of HIV disease and progression to AIDS3. However, it is unclear how CCR5 affects HIV-associated damage to the central nervous system (CNS) and development of HIV-associated neurocognitive disorders (HAND) independently of its co-receptor function. Here we show in a transgenic model of brain damage induced by HIV envelope protein gp1204 that genetic ablation of CCR5 prevents neuronal injury and loss and limits microglial activation, but fails to abrogate astrocytosis. CCR5 deficiency also protected gp120-transgenic mice against impairment of spatial learning and memory. Thus, CCR5-deficiency revealed that astrocytosis, a prominent pathological feature of AIDS brains5, can occur independently from neuronal demise and behavioral impairment. Since the viral envelope protein expressed in the transgenic mouse model originated from HIV-1 LAV4, a CXCR4-preferring virus that can infect macrophages6, CCR5 appeared to exert its control of neuronal injury predominantly in an indirect fashion and independently from its function as a co-receptor. Using analysis of genome-wide CNS gene expression we identified a subset of 734 genes that were differentially regulated in association with neuronal injury in the presence of CCR5. This subset of genes indicated that neuronal injury was associated with activation of macrophages and microglia. A set of 1305 genes was only differentially regulated in association with gp120 in the absence of CCR5 and indicated changes to leukocyte function and the anti-viral immune response besides a down-regulation of components in the GABAergic neurotransmission system.  Interestingly, the most significantly differentially expressed genes were observed in a separate subset of 461 genes that was regulated in association with gp120 but independently of the CCR5 genotype. The finding that differential regulation of the 461 and 1305 gene sets was not necessarily linked to neuronal damage and loss suggested that altered expression of at least some of these factors may represent a protective adaptive response of the brain to the presence of viral gp120. Additional experiments using quantitative RT-PCR, protein assays and flow cytometry further supported the notion that CCR5 deficiency blunted microglial activation, a hallmark of HIV-associated brain injury7-9 without significantly affecting the expression of viral gp120. These results provide in vivo evidence for a significant role of CCR5 in HIV-associated CNS injury and behavioral impairment that is independent of the molecules’ function as HIV co-receptor.

overall_design: To characterize the neuroprotective effect of CCR5 ablation in the presence of HIV gp120, we next performed a genome-wide gene expression analysis using whole brain RNA preparations of mice from lines 1 and 2. We decided to collect samples from two time points before and after the ages of when we analyzed histopathology (6 months) and behavior (8 to 9 months) in order to identify genes for which differential regulation may be affected by an interaction of HIVgp120 expression and age. Accordingly, we collected brain tissue of gp120tg, CCR5KO x gp120tg, WT and CCR5KO mice at five different ages: 1.5, 3, 6, 12, and 20 (line 1) or 16 (line 2) months.

first: Ricky

last: Maung

first: Marcus

last: Kaul


title: Transcriptional analysis of Calu-3 2B-4 cells stimulated with Interleukin-1a and TNFa.

status: Public on Aug 31 2014

city: Seattle

first: Michael

last: Katze

state: WA

address: Rosen Building 960 Republican St.

department: Microbiology

institute: University of Washington

summary: Calu-3 2B-4 cells were stimulated with interleukin-1a or TNFa.  Transcriptional analysis of the extracted RNA was done by microarray.

overall_design: Calu-3 2B-4 cells were washed with phosphate-buffered saline (PBS) and treated with either IL-1a (0.001ng/ml) or TNFa (0.05ng/ml) or mock diluted in PBS for 40 min at 37°C.  Following treatment, cells were washed 3 times, and fresh medium was added.  Triplicate Calu-3 2B4 cultures and triplicate time-matched mock-infected controls were harvested at 3, 6 and 24h for IL-1a and 6 and 24h for TNF post-exposure for transcriptional analysis.

first: Jenny

last: Tisoncik-Go

first: Christian

last: Selinger

first: Sara

last: Kelly


title: Myeloid cells stimulate liver metastasis through downregulation of ANGPTL7 in cancer cells

city: Oxford

first: Su Yin

last: Lim

address: Old Road Campus Research Building

department: Oncology

country: United Kingdom

institute: University of Oxford

summary: Investigation of the molecular effects of myeloid cells on cancer cells. Myeloid cells were shown to promote metastatic liver progression but the mechanisms involved is unknown. Here we examined gene expression changes in cancer cells upon myeloid cell depletion.

overall_design: Total RNA was isolated from FACS sorted MC38 colon cancer cells in tumor bearing livers of CD11bDTR transgenic mice after PBS (control) or DT (depletion) treatments.

first: Su

middle: Y


title: Vagotomy-dependent stomach gene expression

status: Public on Sep 02 2014

city: Trondheim

first: Duan

last: Chen

address: Erling Skjalgssons Gate 1

department: Department of Cancer Research and Molecular Medicine

country: Norway

institute: Norwegian University of Science and Technology

summary: A vagotomy of the anterior region of the stomach of INS-GAS mice was performed at 6 month of age. The mice were sacrificed at 8, 10 and 12 months of age, The gene expression of the anterior and posterior regions of the stomach was compared at each time point.

overall_design: The gene expression of the posterior and anterior regions of the stomach of INS-GAS mice which were anterior vagotomized at 6 months, were compared at 8, 10, and 12 months.

first: Yosuke

last: Kodama

first: Chun-Mei

last: Zhao

last: Quante

first: Sureshkumar

last: Muthupalani

first: Arnar

last: Flatberg

first: Richard

last: Friedman

first: Arne

last: Sandvik

first: James

last: Fox

first: Timothy

last: Wang


title: The genes associated with the response to S-1,cisplatin and docetaxel combination chemotherapy (DCS therapy) for metastatic gastric cancer:

city: tokushima city

first: Shinji

last: Kitamura

address: kuramotocho 3-18-15

institute: tokushima university

summary:
Despite the effort in defining the molecular mechanisms for the drug resistance, predictors of response to chemotherapy have yet to be developed in gastric cancer.
With microarray of whole human genes, we determined 29 genes associated with the response to cisplatin and docetaxel combination chemotherapy for metastatic gastric cancer.

overall_design: We obtained Fresh-frozen samples of tumor tissue and background gastric mucosa tissue from 19 patients with gastric cancer by endoscopic biopsy before DCS therapy. Total RNA was extracted from individual microdissected populations of cancer cells and background mucosa cells using RNAeasy mini kits and amplified with a random primer, WT-Ovation FFPE RNA Amplification System V2; NuGEN, Cincinnati, Ohio) according to the manufacturer’s protocols. The amplified fragmented RNA was hybridized on a Whole Human Genome Oligo Microarray Chip (Agilent Technologies) containing 44,000 cDNA clones.


title: Human Lung Fibroblasts treated with TGFbeta, IL1, EGF and small molecule inhibitors of TGFBR1 and p38

status: Public on Aug 29 2014

city: Stevenage

first: Glyn

last: Bradley

address: Medicines Research Centre

department: Computational Biology

institute: GSK

summary:
Experiment conducted to reverse engineer the transriptional response network of cytokines, growth factors and small molecular inhibitors in HLF cells.
Global gene expression was analysed by microarrays

overall_design: HLF cells were incubated with each agent for 0.5 hours, 1 hour, 2 hours or 8 hours  in standard conditions before total RNA was prepared and hybridised to Affymetrix microarrays


title: Comparison of gene expression profiling of human lung at four developmental stages and lung adenocarcioma

status: Public on Aug 25 2014

city: Beijing

first: Lin

last: Feng

address: Panjiayuan nanli 17#

institute: Peiking union medical school

summary: It is gradually becoming a new aspect in research to search and explore embryo development for malignant information hidden in tumor cells. In this study, the gene expression profiles for human lungs at four developmental stages and lung adenocarcinoma (ADC) were depicted, respectively. The molecular dynamics was compared for development and lung ADC, and it was proposed that primary lung ADC may hijack part of the molecular mechanisms of lung development to down-regulate homeostasis-associated genes and up-regulate stemness-associated genes; and it was revealed that the genes with monotonely decreasing expression trend during lung development process are enriched with lung ADC prognostic information.

overall_design: The study material for developing lung consisted of 29 cases of therapeutic or spontaneous abortion. The samples included whole embryos aged 3 to 5 weeks post ovulation (n = 10, named WholeE), lungs at 6 to 8 postovulatory weeks (PWs) (n = 10, named EarlyL) and lungs at 16 to 24 PWs (n = 9, named MiddleL). WholeE and EarlyL samples were carefully obtained from medical waste with the guidance of a Nikon stereo microscope SMZ1500 (Japan). MiddleL were collected when autopsies were performed. Embryo/Fetuses with known or suspected genetic disorders were excluded. Uninvolved peripheral lung tissue from adults (named MatureL) was obtained from fifteen patients operated on for benign lung diseases. 69 Lung ADC samples used for expression profiling analysis were obtained from patients. All these samples were examined with Agilent Whole Human Genome 4×44k microarray.

first: Jiamei

first: Bangrong

last: Cao

first: Bo

last: Wu

first: Ning

last: An

first: Dan

last: Lu

first: Xuebing

last: Di

first: Deshan

last: Zhou

first: Xiaohong

last: Liu

first: Yunping

last: Zhang

first: Kaitai

first: Jie

last: He

first: Shujun

last: Cheng


title: Gene expression profile of mouse liver cancer (Sav1 and Mst1/2 Knockout models)

status: Public on Aug 23 2014

city: Houston

first: Sangbae

last: Kim

address: 1 Baylor plaza

department: HGSC

institute: Baylor Colleage of Medicine

summary: Hippo pathway is evolutionarily well conserved. All core components of the pathway identified to date have one or more mammalian orthologs, including MST1/2 (Hippo), SAV1 (Salvador, also known as WW45), LATS1/2 (Warts), MOB1 (Mats), YAP1 and its paralog WWTR1 (also known as TAZ) (Yorkie), and TEAD1/2/3/4 (Scalloped). Ectopic over-expression of YAP1 in mouse liver led to develop hepatocellular carcinoma (HCC). HCC is the third most common cause of cancer-related death in the world, and accounts for an estimated 600,000 deaths annually. Lack of molecular classification and clinical heterogeneity of this malignant disease hampered the development of standardized treatment. To investigate roles of Hippo pathway in liver carcinogenesis, we generated liver-specific Mst1/2 -/- and Sav1 -/- mouse models and collected gene expression data from them. Our study provided new understanding on molecular characteristics of HCC.

overall_design: Sav1 and Mst1/2 Knockout models

first: Ju-Seog

last: Lee

first: Soo-Mi

first: Yun-Yong

last: Park


title: Short-term rapamycin treatment in mice have few effects on the transcriptome of white adipose tissue compared to dietary restriction

status: Public on Aug 18 2014

city: Saint Louis

first: Wilson

middle: Chun Yim

last: Fok

state: MO

address: 660 S Euclid Ave

department: Hematology

institute: Washington University in St. Louis

summary: Analysis of the transcriptome in the epididymal fat of young mice (8 months of age) from treatment of dietary restriction, or rapamycin

overall_design:
Total RNA extracted from epididymal fat of 8 month old C57BL6/J mice started on ad libitum (AL) , 40% dietary restriction (DR), or 14 ppm rapamycin (Rapa) from 2 months of age on 6 months of treatment.
Number of samples total: 24, with 8 samples in AL, 8 samples in DR, and 8 samples in Rapa

first: Carolina

last: Livi

first: Alex

last: Bokov

first: Yidong

last: Chen

first: Arlan

last: Richardson

first: Viviana

last: Pérez


title: Gene expression changes in  Apc-mutant mouse intestinal organoids with and without deleting the Prox1 transcription factor

status: Public on Aug 15 2014

city: Helsinki

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 villin-CreER; Apcflox/flox and villin-CreER; Apcflox/flox; Prox1flox/flox mice and added tamoxifen to induce the deletion of the Apc and Prox1 genes in the intestinal epitheliul ex vivo.  Microarray experiments were carried out 7 days after the addition of tamoxifen.

overall_design: Total RNA obtained from  villin-CreER; Apcflox/flox and villin-CreER; Apcflox/flox; Prox1flox/flox organoids were compared 7 days after the addition of tamoxifen and 5 days after the selection for Apc-mutant organoids in the absence of the Wnt-agonist R-Spondin1.

first: Jenny

last: Hogstrom

first: Ville

last: Hyvonen

first: Kari

last: Alitalo


title: Genome-wide analysis of Schwann cell gene expression in LKB1-SCKO mutant mice prior to occurrence of axon degeneration

status: Public on Aug 12 2014

city: St. Louis

first: Jinsheng

last: Yu

address: 660 S. Euclid Ave.

department: Genetics

institute: Washington University School of Medicine

summary: Analysis of gene expression in LKB1(Stk11)-depleted sciatic nerves (LKB1-SCKO) vs control nerves from age-matched mice. Gene expression profiles are predominantly derived from Schwann cell glia and provide important information about the response of peripheral nerve Schwann cells to inactivation of the metabolic regulator protein LKB1(aka Stk11).

overall_design: Total RNA obtained from  sciatic nerve segments from 6 LKB1-SCKO mutant mice compared to RNA from nerve segments from 6 control mice (floxed LKB1 mutant mice that do not express Cre recombinase).

first: Bogdan

last: Beirowski

first: Jeffrey

last: Milbrandt


title: Expression data from Synovial Sarcomas

status: Public on Aug 09 2014

city: Bordeaux

first: céline

last: brulard

address: 229 cours de l'argonne

country: France

institute: Institut Bergonié

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

overall_design: Refer to individual Series


title: Human cathelicidin antimicrobial peptide LL37 effect on human neonatal epidermal keratinocytes (NHEKs).

status: Public on Aug 01 2014

city: Sendai

first: Kenshi

last: Yamasaki

address: Seiryo-machi 1-1, Aoba-ku

department: Deparment of Dermatology

institute: Tohoku University Graduate School of Medicine

summary: Analysis of undifferentiated keratinocytes or differentiated keratinocytes stimulated with or without human cathelicidin antimicrobial peptide (CAMP) LL37. Results provide insight into the biological effects of CAMP on human keratinocytes.

overall_design: NHEKs were divided into two groups; low calcium (0.05 mM) and high calcium condition (1.6 mM). Then keratinocytes were stimulated with human cathelicidin antimicrobial peptide LL37 at 0, 2.56, and 7.68 μM for 12 h to 24 h.

last: Li

last: Yamsaki

first: Sawako

last: Fukushi-Takahashi

first: Ryoko

last: Shimada-Omori

first: Masayuki

last: Asano

first: Rumiko

last: Saito

first: Setsuya

last: Aiba


title: Molecular Analysis and Characteristics of Ethnic Skin

status: Public on Jul 31 2014

first: Vincent

middle: J.

last: Hearing

address: 37 Convent drive

department: Lab of cell biology

institute: National Cancer Institute

summary: In this study, we used microarray analysis to investigate molecular differences underlying the determination of pigmentation in various skin types, and we used immunohistochemistry to validate the expression patterns of several interesting targets that were identified.

overall_design: Whole skin gene expression profile were investigated in three ethnic groups:1) Caucasian 2)Asian 3)African. In each group, 4 mm whole skin punch biopsies were taken from forearm of 10 subjects, and gene expression level were tested by agilent whole human genome microarray. Samples with mRNA degraded: African_skin_03, Asian_skin_02, Asian_skin_06, and Caucasian_skin_7.

first: Lanlan

last: Yin

first: Sergio

last: Coelho

first: Dominik

last: Ebsen

first: Christoph

last: Smuda

first: Andre

last: Mahns

first: Sharon

last: Miller

first: Janusz

middle: Z

last: Beer

first: Ludger

last: Kolbe


title: Gene expression profile of human epidermoid carcinoma KB cells that overexpress thymidine phosphorylase

status: Public on Aug 03 2014

city: Suita

first: Sho

last: Tabata

state: Osaka

address: 3-2 Yamadaoka

department: Institute for Protein Research,ces

institute: Osaka University

summary: Thymidine phosphorylase (TP) catalyzes the reversible phosphorolysis of thymidine, deoxyuridine, and their analogs to the respective bases and 2-deoxy-D-ribose-1-phosphate. TP is identical to platelet-derived endothelial cell growth factor (PD-ECGF). TP was reported to induce many angiogenic factors. However, the molecular mechanism of the TP function is still obscure. To elucidate the molecular basis for the TP function in human epidermoid carcinoma KB cells, we performed a whole genome-wide microarray analysis. Genes upregulated in KB cells overexpressing TP are supposed to represent potential molecular targets of TP in KB cells.

overall_design: KB cells (4 × 10^5) in 5 ml of culture media were cultured for 24 hours, then the growth medium was replaced with serum-free medium.  These cells were maintained at 37 ˚C in a humidified atmosphere of 5% CO2 for 12 hours, then these cells were collected for RNA extraction and quantification of the transcripts by microarray analysis.

first: Ryuji

last: Ikeda

first: Shin-ichi

last: Akiyama


title: Total Gene expression analysis of H3f3b constitutive knockout testis RNA

city: Sacramento

first: Paul

last: Knoepfler

address: 2425 Stockton Blvd

department: Cell Biology and Human Anatomy

institute: UC Davis

summary: Total gene expression analysis was performed on RNA from testes extracted from two litters of constitutive homozygous and heterozygous H3f3b knockout mice compared to WT littermates.

overall_design: Constitutive knockout mice were obtained by mating H3f3b Fl/Fl mice to Zp3Cre mice. Heterozygous knockout mice were crossed until homozygous knockout mice were obtained. Testes were surgically removed from 8 week old homozygous knockouts, heterozygous knockouts and WT, and RNA was extracted from one testis from each mouse for total gene expression.

first: Kelly

last: Bush


title: Expression data from 58 Synovial Sarcomas

first: céline

last: brulard

summary:
Background: Synovial sarcoma (SS) occur in children as well as in adults, although metastatic events are much more common in the latter. Whereas the importance of the t(X;18) translocation in SS oncogenesis is well established, the genetic basis of SS metastasis is still poorly understood. We recently reported expression (CINSARC) and genomic (GI) prognostic signatures related to chromosome integrity in sarcomas and gastrointestinal stromal tumors (GISTs). Here we investigate whether these signatures can also predict outcomes in SS.
Methods: One hundred primary untreated SS were selected for expression and genomic profiling in a training/validation approach.
Results: CINSARC and GI have strong, independent and validated prognostic values (p<0.0001). Comparing expression profiles of tumors with or without metastasis, 14 genes common with the CINSARC signature were identified and the two top-ranked genes, KIF14 and CDCA2, were validated as prognostic markers in an independent cohort. Comparing genomic profiles of adult vs. pediatric SS, we show that metastasis is associated with genome complexity in both situations and that the adult genome is more frequently rearranged. Accordingly, pediatric patients with an even genomic profile do not develop metastasis.
Conclusions: Metastasis development in SS is strongly associated with chromosome complexity, and CINSARC and GI are validated independent prognostic factors. The differences in metastasis frequency between adults and children are associated with genome instability, which is much more frequent in adults. GI is potentially the best overall biomarker, and clearly the most clinically relevant, considering that genome profiling from formalin fixed samples is already used in pathology.

overall_design: 58 Synovial Sarcomas hybridized to Agilent-014850 Whole Human Genome Microarray 4x44K G4112F

first: Frederic

last: Chibon

first: Maria

last: Debiec-Rychter


title: Matrix Elasticity Does Not Affect Replicative Senescence or DNA Methylation Patterns of Mesenchymal Stem Cells [gene expression profiling]

status: Public on Jul 29 2014

city: Aachen

first: Wolfgang

last: Wagner

address: Pauwelsstrasse 20

department: Helmholtz Institute for Biomedical Engineering

institute: RWTH Aachen University

summary: Matrix elasticity influences differentiation of mesenchymal stem cells (MSCs) but it is unclear if these effects are only transient - while the cells reside on the substrate - or if they reflect persistent lineage commitment. In this study, MSCs were continuously culture-expanded in parallel either on polydimethylsiloxane (PDMS) gels of different elasticity or on tissue culture plastic (TCP) to compare impact on replicative senescence, in vitro differentiation, gene expression, and DNA methylation (DNAm) profiles. The maximal number of cumulative population doublings was not affected by matrix elasticity. Differentiation towards adipogenic and osteogenic lineage was increased on soft and rigid biomaterials, respectively - but this propensity was no more evident if cells were transferred to TCP. Global gene expression profiles and DNAm profiles revealed relatively few differences in MSCs cultured on soft or rigid matrices. Furthermore, only moderate DNAm changes were observed upon culture on very soft hydrogels of human platelet lysate. Our results support the notion that matrix elasticity influences cellular differentiation while the cells are organized on the substrate, but it does not have major impact on cell-intrinsic lineage determination, replicative senescence or DNAm patterns.

overall_design: MSCs cultivated either on polydimethylsiloxane (PDMS) gels of different elasticity or on tissue culture plastic (TCP) to compare impact on gene expression profiles.

first: Anne

last: Schellenberg

first: Sylvia

last: Joussen

first: Kristin

last: Moser

first: Nico

last: Hampe

first: Niels

last: Hersch

first: Hatim

last: Hemeda

first: Bernd

last: Denecke

first: Qiong

last: Lin

first: Norbert

last: Pallua

first: Martin

last: Zenke

first: Rudolf

last: Merkel

last: Hoffmann


title: Effect of HIC1 and miR-212/132 expression on MCF7 cells

city: Freiburg

first: Yoko

middle: Fukuda

last: Yuzawa

address: Stübeweg 51

institute: Max-Planck Institute of Immunobiology

summary: To identify the target of miR-212, miR-132 and HIC1, we have employed whole genome microarray expression profiling on the human breast cancer MCF7 cells.

overall_design: To generate miR-212/132 or HIC1 inducible MCF7 cells, doxycycline-dependent miR-212/132 or HIC1 gene expression system was used. Either Tet-ON miR-212/132 MCF7 or Tet-ON HIC1 MCF7 were treated with 1μg/ml of Doxycycline for 36 hours with EMEM containing 0.01 mg/ml bovine insulin and 10% FCS. Two independent experiments were performed.

first: Kotaro

last: Kiga

last: Fukuda-Yuzawa

first: Taro

last: Fukao


title: Gene expression profiling of human peripheral blood lymphocytes cultured in modeled microgravity

status: Public on Jul 17 2014

city: Padova

first: Gerolamo

last: Lanfranchi

address: Via U. Bassi, 58/B

department: CRIBI - Biotechnology Center and Biology Department

institute: University of Padova

summary: In the present study we analyzed miRNA and mRNA expression profiles in human peripheral blood lymphocytes (PBLs) incubated in microgravity condition, simulated by a ground-based Rotating Wall Vessel (RWV) bioreactor. Our results show that 42 miRNAs were differentially expressed in MMG-incubated PBLs compared with 1g-incubated ones. Among these, miR-9-5p, miR-9-3p, miR-155-5p, miR-150-3p, and miR-378-3p were the most dysregulated. To improve the detection of functional miRNA-mRNA pairs we performed gene expression profiles on the same samples assayed for miRNA profiling and we integrated miRNA and mRNA expression data. The functional classification of miRNA-correlated genes evidenced significant enrichments in the biological processes of immune/inflammatory response, signal transduction, regulation of response to stress, regulation of programmed cell death and regulation of cell proliferation. We identified the correlation between miR-9-3p, miR-155-5p, miR-150-3p and miR-378-3p expression with that of genes involved in immune/inflammatory response (eg. IFNG and IL17F), apoptosis (eg. PDCD4 and PTEN) and cell proliferation (eg. NKX3-1 and GADD45A). Experimental assays of cell viability and apoptosis induction validated the results obtained by bioinformatics analyses demonstrating that in human PBLs the exposure to reduced gravitational force increases the frequency of apoptosis and decreases cell proliferation.

overall_design: Gene expression profiling was carried out in MMG-incubated PBLs vs. 1g-incubated PBLs on total RNA extracted from the same PBL samples assayed for miRNA profiling. We used the ‘‘Whole Human Genome Oligo Microarray’’ (Agilent), consisting of ~41.000 (60-mer) oligonucleotide probes, which span conserved exons across the transcripts of the targeted full-length genes.

first: Cristina

last: Girardi

first: Cristiano

last: De Pittà

first: Silvia

last: Casara

first: Enrica

last: Calura

first: Chiara

last: Romualdi

first: Lucia

last: Celotti

first: Maddalena

last: Mognato


title: Analysis of Molecular Alterations in Oral Cell Lines

status: Public on Jul 15 2014

city: Vancouver

first: Christopher

middle: Trevor Daniel

last: Dickman

state: BC

address: 675 West 10th Ave

institute: BC Cancer Research Center

type:
Expression profiling by array
Genome variation profiling by array

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

BACKGROUND: Cell lines have been developed for modeling cancer and cancer progression. The molecular background of these cell lines is often unknown to those using them to model disease behaviors. As molecular alterations are the ultimate drivers of cell phenotypes, having an understanding of the molecular make-up of these systems is critical for understanding the disease biology modeled. METHODS: Six immortalized normal, one immortalized dysplasia, one self-immortalized dysplasia, and two primary normal cell lines derived from oral tissues were analyzed for DNA copy number changes and changes in both mRNA and miRNA expression using SMRT-v.2 genome-wide tiling comparative genomic hybridization arrays, Agilent Whole Genome 4x44k expression arrays, and Exiqon V2.M-RT-PCR microRNA Human panels. RESULTS: DNA copy number alterations were detected in both normal and dysplastic immortalized cell lines?as well as in the single non-immortalized dysplastic cell line. These lines were found to have changes in expression of genes related to cell cycle control as well as alterations in miRNAs that are deregulated in clinical oral squamous cell carcinoma tissues. Immortal lines?whether normal or dysplastic?had increased disruption in expression relative to primary lines. All data are available as a public resource. CONCLUSIONS: Molecular profiling experiments have identified DNA,mRNA,andmiRNAalterations for a panel of normal and dysplastic oral tissue cell lines. These data are a valuable resource to those modeling diseases of the oral mucosa, and give insight into the selection of model cell lines and the interpretation of data from those lines.


title: Gene expression profiles at the day 5 blastocyst implantation and interimplantation sites of the hamster [mouse array]

city: Nashville

first: Bibhash

middle: C

last: Paria

state: TN

address: 2215 B. Garland Avenue

institute: Vanderbilt

summary:
Current knowledge of the molecular regulation of the blastocyst implantation event has been largely derived from studies in the mouse that requires ovarian estrogen for initiation of the implantation event. However, there are species such as the hamster, guinea pig, pig, horse, rhesus monkey and perhaps the human where the blastocyst implantation event initiates only in the progesterone-primed uterus. Despite this fundamental difference in the requirement of ovarian hormones in initiating blastocyst implantation among species, efforts to identify gene networks relevant for the blastocyst implantation event in progesterone–dependent species are limited. In this study, cDNA prepared from RNAs of day 5 blastocyst implantation and interimplantation sites were hybridized with mouse and human oligonucleotide microarray platforms to discern the transcriptional networks underlying the regulation of blastocyst implantation in hamsters. Compared with the inter-implantation site, blastocyst implantation sites showed upregulation and downregulation of a sizable number of genes by both cross-species arrays.The merit of the cross-species hybridization and reliability of the identified up- and down-regulated genes at the implantation sites were validated by detecting differential expression of a few randomly selected genes from both arrays by real-time PCR. Function gene ontology and pathway analysis revealed that differentially expressed genes are associated with several biological events and molecular pathways that are likely to be taking place at the blastocyst implantation site. This is the first study that identified the differential gene expression profile at the blastocyst implantation site of the hamsters, and revealed molecular pathways that are possibly associated with the progesterone-dependent blastocyst implantation process.
We used microarrays to detail the expression differences in hamster implantation and interimplantation sites.

overall_design: Total RNAs were prepared from the hamster day 5 blastocyst implantation and interimplantation sites. Three sets of RNAs were isolated from three different animals and were subjected to microarray analysis using Affymetrix mouse and human array platforms.


title: Analysis of Molecular Alterations in Oral Cell Lines [mRNA]

status: Public on Jul 10 2014

summary: BACKGROUND: Cell lines have been developed for  modeling cancer and cancer progression. The molecular  background of these cell lines is often unknown to those  using them to model disease behaviors. As molecular  alterations are the ultimate drivers of cell phenotypes,  having an understanding of the molecular make-up of  these systems is critical for understanding the disease  biology modeled.  METHODS: Six immortalized normal, one immortalized  dysplasia, one self-immortalized dysplasia, and two  primary normal cell lines derived from oral tissues were  analyzed for DNA copy number changes and changes in  both mRNA and miRNA expression using SMRT-v.2  genome-wide tiling comparative genomic hybridization  arrays, Agilent Whole Genome 4x44k expression arrays,  and Exiqon V2.M-RT-PCR microRNA Human panels.  RESULTS: DNA copy number alterations were detected  in both normal and dysplastic immortalized cell lines—as  well as in the single non-immortalized dysplastic cell line.  These lines were found to have changes in expression of  genes related to cell cycle control as well as alterations in  miRNAs that are deregulated in clinical oral squamous  cell carcinoma tissues. Immortal lines—whether normal  or dysplastic—had increased disruption in expression  relative to primary lines. All data are available as a public  resource.  CONCLUSIONS: Molecular profiling experiments have  identified DNA,mRNA,andmiRNAalterations for a panel  of normal and dysplastic oral tissue cell lines. These data  are a valuable resource to those modeling diseases of the  oral mucosa, and give insight into the selection of model  cell lines and the interpretation of data from those lines.

overall_design: Total RNA from oral cancer cell lines were hybridized to Agilent 4x44k gene expression microarray

first: C

first: R

last: Towle

last: Saini

last: Garnis


title: Intrinsic self-DNA triggers inflammatory disease dependent on STING

status: Public on Jul 09 2014

city: Silver Spring

first: BIJU

last: ISSAC

address: 503 Robert Grant Ave, Rm 2W123

department: Military HIV Research Program

institute: Walter Reed Army Institute of Research


title: Gene expression profiles at the day 5 blastocyst implantation and interimplantation sites of the hamster

platform_organism:
Homo sapiens
Mus musculus


title: Expression data from miR-132 overexpressing immortalized human mammary fibroblasts and from mammary epithelial columnar cell hyperplasia cells co-cultured with miR-132 overexpressing fibroblasts

city: Malmö

first: Sofie

last: Björner

address: Jan Waldenströms gata 59

country: Sweden

institute: Lund University

summary:
Columnar cell hyperplasia (CCH) is the first histologically identifiable lesion in the breast with premalignant potential. Altered miRNA expression in the stroma surrounding CCH compared to normal tissue was discovered. The effect of upregulation of one specific miRNA was investigated  by gene expression array in human mammary fibroblasts as well as in epithelial CCH cells coculterd with miR-132 oversexpressing human mammary fibroblasts.
We used microarrays to detail the effects of miR-132 in human mammary fibroblasts and identified multiple altered genes and gene pathways both in the fibroblasts and in cocultured human mammary epithelial CCH cells.

overall_design: Immortalized human mammary fibroblasts were transfected in duplicates with miRNA mimics for miR-132 or negative control and RNA was extracted 24 h after transfection. Human mammary epithelial columnar cell hyperplasia cells were cocultured with immortalized human mammary fibroblasts transfected with either miR-132 mimic or negative control 24 hours prior to RNA extraction. The RNA from all six samples was hybridized on Affymetrix microarrays.

first: Göran

last: Landberg

last: Nilsson


title: Integration analysis of microRNA and mRNA expression profiles in human peripheral blood lymphocytes cultured in modeled microgravity

last: Lanfranchi

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

overall_design:
This SuperSeries is composed of the SubSeries listed below.
Refer to individual Series


title: Intrinsic self-DNA triggers inflammatory disease dependent on STING (II)

summary: Inflammatory diseases such as Aicardi-Goutieres Syndrome (AGS) and severe systemic lupus erythematosus (SLE) are generally lethal disorders that have been traced to defects in the exonuclease Trex1 (DNAseIII). Mice lacking Trex1 similarly die at an early age through comparable symptoms, including inflammatory myocarditis, through chronic activation of the STING (stimulator of interferon genes) pathway. Here we demonstrate that phagocytes rather than myocytes are predominantly responsible for causing inflammation, an outcome that could be alleviated following adoptive transfer of normal bone marrow into Trex1-/- mice. Trex1-/- macrophages did not exhibit significant augmented ability to produce pro-inflammatory cytokines compared to normal macrophages following exposure to STING-dependent activators, but rather appeared chronically stimulated by genomic DNA. These results shed molecular insight into inflammation and provide concepts for the design of new therapies.

overall_design: Total RNA obtained from wild type murine embryonic fibroblasts (WT MEFs), Trex1 deficient MEFs (TKO) or STING and Trex1 double deficient MEFs (STKO) transfected with or without double strand DNA 90 (ISD) and examined cytokine production by these cells.

first: Jeonghyun

last: Ahn

first: Phillip

last: Ruiz

first: Glen

middle: N

last: Barber


title: Intrinsic self-DNA triggers inflammatory disease dependent on STING (I)

overall_design: Total RNA obtained from wild type (WT), Trex1 deficient (TKO), STING deficient (SKO), or Trex1 and STING double deficient (STKO) mouse Heart


title: Gene expression for transformed YAMC clones

status: Public on Jul 03 2014

city: Nantong

first: Xingmin

last: Wang

state: Jiangsu

address: 399 Century Ave.

department: Institute of Genetics and Reproductive Medicine

institute: Nantong Maternity and Child Healthcare Hospital

summary: YAMC murine colonic epithelial cells were repeatitively treated with commensal bacteria-polarized macrophages or 4-HNE. Following 10 treatments, 25 clones were selected to engraft immunodeficient mice, and 10 out of 25 clones grew tumors in these mice. To explore gene expression associated with cellular transformation, whole-genome profiling was performed on 10 transformed clones and compared with untreated YAMC controls using Illumina Mouse WG-6 v2.0 Expression BeadChip.

overall_design: Total RNA obtained from 10 transformed clones and compared to untreated YAMC controls.

first: Wang

last: Xingmin

first: Yang

last: Yonghong

first: Huycke

last: Mark


title: Columnar cell hyperplasia

status: Public on Jul 14 2014

type:
Expression profiling by array
Other


title: PEGylation of ORMOSIL nanoparticles differently modulates the in vitro toxicity toward human lung cells

first: Gerolamo

summary:
ORganically MOdified SILica (ORMOSIL) nanoparticles (NPs) appear promising carriers for the delivery of drugs to target tissues and cells but some concerns on possible cytotoxic effects still exist. We therefore studied the in vitro responses to ORMOSIL NPs in different types of human lung cells (i.e. CCD-34Lu normal fibroblasts, carcinoma alveolar type II A549 cells, NCI-H2347 adenocarcinoma cells) to determine the effects of polyethylene glycol (PEG) coating on NP cytotoxicity.
Our results show that non-PEG NPs caused a concentration-dependent decrease of viability of all types of cells. On the contrary, PEG-coated NPs increased plasma membrane permeability and induced cell death only in carcinoma alveolar type II A549 cells, while did not produce deleterious effects on CCD-34Lu and NCI-H2347 cells. PEG-coated NPs promoted the formation of reactive oxygen species (ROS) in A549 and CCD-34Lu cells; nevertheless, the decrease of ROS levels in the presence of superoxide dismutase and catalase did not protect A549 cells from death, suggesting that the oxidative stress was not the main determinant of cytotoxicity.
Analysis of gene expression in A549 cells exposed to PEG-coated NPs showed alterations in genes involved in inflammation, signal transduction and cell death, while the transcriptional response was not significantly affected in CCD-34Lu fibroblasts.
Our transmission electron microscopy analysis evidenced a unique intracellular localization of PEG NPs in the lamellar bodies of A549 cells, which could be the most relevant factor leading to cytotoxicity by reducing the production of surfactant proteins and by interfering with the pulmonary surfactant system.

overall_design: Gene expression signature was defined in A549 and CCD-34Lu controls and treated  cells, incubated with PEGylated ORMOSIL nanoparticles. Three replicates for each single sample were performed for both untreated and NP-treated A549 and CCD-34Lu cells at the end of each incubation time (24 h; 24+24h). The level of each transcript was represented as Log2.

first: Francesca

last: Moret

first: Francesco

last: Selvestrel

first: Elisa

last: Lubian

last: Mognato

last: Celotti

first: Fabrizio

last: Mancin

first: Elena

last: Reddi


title: Unraveling the Sox4-orchestrated pro-B cell differentiation program: Intricate roles of the RAG and CK1ε genes (RNA array)

status: Public on Jul 02 2014

first: Xiaoping

last: Sun

state: Texas

address: 2130 Westholcombe Blvd, LSP12.3014

department: Laboratory Medicine

institute: The University of Texas MD Anderson Cancer Center

summary:
One of the main objective of this study is to identify Sox4 controlled gene networks and their roles in progenitor B cells.
Commitment of hematopoietic stem cells to B lineage precursors and development of B lineage precursors into mature B cells is attained through the coordinated function of multiple signaling networks, which are in turn controlled through stringent functioning of stage-specific transcription factors. Here, we describe the essential role of Sox4, an HMG (high mobility group)-box-containing transactivator, in B cell development. In the absence of Sox4, differentiation from pre-pro B to pro-B, from pro-B fraction B to pro-B fraction C and further to the immature B cell stage was severely impaired. Loss of differentiation was associated with reduced expression of Rag1 and Rag2 and markedly reduced DJ (diverse, joining) and VDJ (variable DJ) recombination at immunoglobulin heavy chain gene loci. We uncovered Sox4-regulated transcriptional circuits and a landscape of Sox4-chromatin interactions in pro-B cells. Sox4 ensured the negative regulation of Wnt signaling, which is critical for self-renewal of hematopoietic stem cells and early progenitors, by inducing one of its downstream effectors, casein kinase 1 epsilon. Our findings suggest that Sox4 orchestrates a unique transcriptional program and coordinates multilevel control in the differentiation of early-stage B cells.

overall_design: Total RNA isolated from triplicate samples were used for each cell type. Gene expression signatures were compared between Sox4fl/fl and Sox4fl/fl SE-Cre progenitor B cells (Loss-of-function array); p190 Bcr-Abl-immortalized Sox4fl/fl SE-Cre HA and Sox4fl/fl SE-Cre HA-Sox4 progenitor B cells (Gain-of-function array).

first: Saradhi

last: Mallampati


title: Aneuploid T-ALL

status: Public on Jul 01 2014

city: Groningen

first: Floris

last: Foijer

address: Antonius Deusinglaan 1

department: European Institute for the Biology of Ageing

country: Netherlands

institute: University Medical Center Groningen

type: Genome variation profiling by genome tiling array

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

overall_design: Refer to individual Series


title: Transcriptomes of aneuploid mouse T-ALL

summary: Transcriptome analysis to map transcriptomes of Mps1DK p53null-driven aneuploid T-ALL, to determine correlation between copy number changes and expression changes and to map the transcriptional response to CIN

overall_design: Transcriptomes of T-ALL samples described in the accompanying manuscript were compared to the transcriptomes of thymocytes of 6-weeks old wild type mice

first: Peter

last: Sorger


title: Gene regulation by Ffr2 in the conjunctival epithelium

first: David

middle: Cy

last: Beebe

department: Ophthalmology and Visual Science

summary: Wild type or Fgfr2 fx/fx; Le-Cre-positive (Fgfr2-/-) conjunctival epithelium of E14.5 mouse embryos was laser micodissected from three embryos of each genotype. Total RNA was purified and reverse transcribed and amplified using a NuGEN kit. cDNA was biotinylated and hybridized to Illumina MouseWG-6 v2.0 bead arrays.

overall_design: Three wild type and three Ffr2 knockout embryos were used. cDNA obtained from each was used for microarray analysis. Statistical analysis was performed using Illumina Genome Studio software.

first: Ziyan

last: Chen

first: Jie

last: Huang

first: Ying

last: Liu


title: Genome-wide analysis of brown adipose tissue gene expression of IL15-depleted mice under normal diet or diet enriched with the beta3-adrenergic agonist CL 316243

city: Montréal

first: Mathieu

last: Vernier

address: 2900 Edouard Montpetit

department: Biochemistry

institute: Université de Montréal

summary: Chronic inflammation is one of the major players in the obesity related metabolic syndrome. However the various inflammatory mediators appear to promote insulin resistance directly or indirectly through their ability to induce the inflammatory cascade. Interleukin-15 (IL-15) is a pro-inflammatory cytokine that is involved in the pathogenesis of different autoimmune diseases such as rheumatoid arthritis, inflammatory bowel disease and type 1 diabetes. We postulated that as a pro-inflammatory cytokine, IL-15 promotes obesity during fat excess by promoting insulin resistance from tissues involved in energy metabolism. We used microarrays to characterize the gene expression profile of the brown adipose tissue of IL-15 mice under normal diet or diet enriched with  the beta3-adrenergic agonist CL 316243

overall_design: Total RNA obtained from adipose tissue of wt- or IL15-KO mice under normal diet or diet enriched with the beta3-adrenergic agonist CL 316243

first: G

last: Lacraz

first: M

first: Donates

last: Cepero

first: S

last: Labbé

last: Mayhue

last: Grenier

first: J

last: Stankova

first: A

last: Giaid

last: Menendez

first: D

last: Richard

last: Ferbeyre

last: Fradette

first: M-F

last: Langlois

last: Ilangumaran

last: Rola-Pleszczynski

last: Ramanathan


title: Expression data from murine myogenic cells

city: suita

first: so-ichiro

last: fukada

address: 1-6 yamadaoka

institute: osaka University

summary:
Skeletal muscle has great regenerative capacity, which is dependent on muscle stem cells, also known as satellite cells. We established the purification system of myogenic cells.
We used microarrays to identify specific genes during the muscle regenerative process.

overall_design: Myogenic cells were purified at regenerative stages for RNA extraction and hybridization on Affymetrix microarrays. CTX-2d, 3d,  5d, or 14d are the samples derived from injured muscles 2 days, 3days, 5 days  or 14 days after cardiotoxin-injection, respectively.

first: So-ichiro

last: Fukada


title: Transcriptomic analysis of neuroblastoma SH-SY5Y cells in response to stable over-expression of histone H2A type 2-B

city: Wuhan

first: Qiangsong

last: Tong

state: Hubei

address: 1277 Jiefang Avenue

department: Department of Surgery

institute: Union Hospital of Tongji Medical College

summary: Neuroblastoma is the most common extracranial solid malignancy derived from neural crest cells. Better elucidation of the mechanisms underlying the aggressive progression of neuroblastoma is needed for improving the therapeutic efficiencies. Since previous studies indicate that histone H2A type 2-B (H2AB), a histone H2A variant locating at chromosome 1q21.2 region, is up-regulated in neural progenitor cells and early motor neurons, we hypothesized that H2AB might participate in the progression of neuroblastoma. We employed the human whole genome microarray expression profiling as a discovery platform to analyze the transcriptome profiling changes of human neuroblastoma SH-SY5Y cells in response to stable over-expression of H2AB. The results showed that stable over-expression of H2AB led to altered expression of 514 human mRNAs, including 249 up-regulated genes and 265 down-regulated genes. Then we found the possible roles of these differentially regulated mRNAs in selected pathways including cell cycle/proliferation, apoptosis, and cytokine/chemokine responses by Bioinformatic analysis. Furthermore, we validated the microarray results by real-time RT-PCR with high identity. Overall, our results provided fundamental information about the transcriptomic changes in response to H2AB over-expression in human neuroblastoma cells, and these findings will help us to understand the pathogenesis of neuroblastoma.

overall_design: Total RNA of cells stably transfected with empty vector or H2AB was extracted using the TRIZOL Reagent according to the manufacturer's instructions. Gene expression profiling was performed for each RNA sample separately on the Agilent Whole Human Genome Oligo Microarray 4×44K at Shanghai Technology Corporation (Shanghai, China), in which GeneChip microarray service was certificated by Agilent.

first: Tong

last: Qiangsong

first: Zheng

last: Liduan


title: Transcriptome analysis of Yap mutant kidneys

city: Toronto

first: carl

last: virtanen

address: 101 College St

department: Princess Margaret Genomics Centre

institute: University Health Network

summary: Microarrays were used to examine gene expression changes between control and mutant (YapCM-/-) kidneys to investigate molecular changes responsible for abnormal nephrogenesis seen in Yap mutants. This work identifies a list of potential genes regulated by Yap during nephron development.

overall_design: Total RNA obtained from three mutants and three controls kidneys at embryonic day E13.5 were used for the expression profiling analysis.

first: Antoine

last: Reginensi

first: Helen

last: McNeil

first: Carl

last: Virtanen


title: A high proportion of myoepithelial cells have mammary stem cell potential

status: Public on Jun 30 2014

city: Cambridge

first: Suraj

last: Menon

address: Li Ka Shing Center, Robinson Way

institute: Cambridge Research Institute, Cancer Research UK

summary:
The basal cell lineage in the mouse mammary gland is perceived to be composed mostly of differentiated myoepithelial cells intermixed with a rare subpopulation of mammary stem cells. Here, we show that a high proportion (~30%) of basal cells have colony forming capacity when actin-myosin contraction is prevented. A basal cell subpopulation enriched for mammary repopulating units (MRUs) is shown to be enriched for dividing cells. Inducing basal cells to proliferate in vitro increases MRU frequency 10-fold and permits a ~750-fold expansion of MRUs. Transplantation of single-cell-derived basal colonies into cleared fat pads demonstrates that the majority (~80%) of these colonies can repopulate a mammary gland. This suggests that a high proportion of basal cells, most of which were previously perceived to be terminally differentiated myoepithelial cells, have latent mammary stem cell potential.
Mammary glands from 10-14 week old, female, virgin C57BL/6J mice were dissociated into single cells and basal cells were sorted by flow cytometry at a purity of ~95%. Inducing basal cell proliferation in vitro causes mammary stem cell expansion over 7 days in culture. Basal cells were cultured on Matrigel-coated cell culture plastic in a keratinocyte stem cell media supplemented with the Rho kinase inhibitor Y-27632 and were co-seeded with irradiated NIH 3T3 fibroblast feeder cells. In order to determine the molecular changes that occur during culture that may contribute to mammary stem cell expansion, gene expression profiling was conducted on basal cells pre-culture and after 1- or 7-day-culture.

overall_design: Mammary glands from 6 C57BL/6J mice were pooled for each experiment. Purified basal cells sorted from the same pooled sample were split into 3 groups: pre-culture for immediate RNA extraction, 1-day-culture and 7-day-culture. Cultured basal cells were sorted to exclude fibroblast feeder cells. Total RNA was extracted for each group in 4 independent experiments

first: Michael

middle: D

last: Prater

first: John

last: Stingl


title: Loss of histone demethylase KDM6B enhances aggressiveness of pancreatic cancer through downregulation of C/EBPα

city: New York

first: Keisuke

last: Yamamoto

address: 550 First Avenue

department: Radiation Oncology

institute: NYU School of Medicine

summary: Genetic mutations in pancreatic ductal adenocarcinoma (PDAC) with critical roles have been well examined. The recent discovery of alterations in genes encoding histone modifiers suggests their possible roles in the complexity of cancer development. We previously reported loss of heterozygosity of the KDM6B gene, which encodes a histone demethylase for trimethylated histone H3 lysine 27 (H3K27me3), a repressive chromatin mark, in PDAC cells. In this study, we demonstrated that loss of KDM6B enhanced aggressiveness of PDAC cells. KDM6B has been regarded as a tumor suppressor that mediates oncogenic KRAS-induced senescence. Consistently, KDM6B was highly expressed in pancreatic precancerous lesions (pancreatic intraepithelial neoplasms); then, the expression decreased as the malignant grade progressed. We found that knockdown of KDM6B in PDAC cells promoted tumor sphere formation and increased peritoneal dissemination and liver metastasis in vivo. Microarray and chromatin immunoprecipitation analysis implicated CEBPA for aggressiveness induced by KDM6B knockdown. CEBPA knockdown recapitulated the phenotypic change of PDAC cells after KDM6B knockdown, which was reversed by forced expression of C/EBPα. Moreover, similar protein expression patterns of KDM6B and C/EBPα in human PDAC emphasized their functional correlation. Notably, pharmacological inhibition of the H3K27 methylase EZH2 in PDAC cells inhibited tumor sphere formation along with the upregulation of CEBPA expression, and this effect was impaired in KDM6B knockdown cells, highlighting the role for KDM6B in the activation of CEBPA. Together, our results propose a significant role for the KDM6B-C/EBPα axis in the PDAC phenotype.

overall_design: To identify genes regulated by JMJD3/KDM6B in pancreatic cancer, transcriptional profiling of BxPC3 cells transfected with either control vector or shKDM6B-expressing vector was performed using whole human genome microarrays. Total RNA was extracted from biologically triplicated samples.

last: Tateishi


title: Vpx of SIV modulates expression of innate immune target genes by inhibition of NF-κB activation

status: Public on Jun 28 2014

city: Langen

first: Sunitha

last: Joseph Myladoor

state: Hessen

department: Divison of Medical Biotechnology

institute: Paul-Ehrlich-Institut

summary:
Background: In contrast to HIV-1, lentiviruses of the HIV-2/SIVmac/SIVsmm lineage are capable of efficient replication in myeloid cells due to the presence of their accessory protein Vpx. Vpx has been shown to induce degradation of the dNTP triphosphohydrolase SAMHD1, which is a cellular restriction factor of lentiviral replication. Furthermore, Vpx is important for nuclear import of the viral pre-integration complex. To identify further functions of Vpx, we have analyzed the effect of Vpx on cellular gene expression in monocytes. Therefore, we performed whole genome microarray analysis of unstimulated primary human monocytes treated with SIV–based virus-like particles containing Vpx (VLP+Vpx) or lacking Vpx (VLP).
Results: Comparison of the gene expression profiles of human monocytes treated with VLP+Vpx and VLP revealed that Vpx down-regulates various genes involved in innate immunity, in particular genes that are known to be regulated by the transcription factor NF-κB. Subsequent analysis of p65 nuclear translocation revealed that Vpx inhibits the VLP-induced activation of NF-κB. Counteraction of NF-κB was also obtained using Vpx mutants lacking the capacity to induce SAMHD1 degradation.
Conclusions: Independent of its capacity to induce degradation of SAMHD1, Vpx is involved in regulation of cellular gene expression. In particular, Vpx is able to modulate innate immune responses through down-regulation of TLR-induced NF-κB activation. This points to a significant role of Vpx in the pathogenicity of SIV, as the lower pathogenicity of SIV compared to HIV-1 has been associated to lower innate immunity responses.

overall_design: Primary human monocytes were treated with virus-like particles containing Vpx (VLP+Vpx) or lacking Vpx (VLP) of SIVsmmPBJ for 6 hours, and the expression profiles were compared by whole genome microarray analysis.

last: Myladoor

first: Meike

middle: S

last: Gratz

first: Brigitte

last: Anliker

first: Matthias

last: Renner

first: Sylvia

last: Panitz

first: Tanja

last: Kearns

first: Renate

last: König

first: Klaus

last: Cichutek

last: Schweizer


title: Dexamethasone regulation of mRNAs in astrocytes in vitro

status: Public on Jun 25 2014

city: Ann Arbor

first: Bradley

last: Carter

state: MI

address: 109 Zina PItcher Place

department: Molecular and Behavioral Neuroscience Institute

institute: University of Michigan

summary: Analysis of mRNA gene expression changes mediated by synthetic GR-agonist dexamethasone in mouse cortical primary astrocyte cultures

overall_design: Total RNA obtained from astrocyte cultures subjected to 0.25, 1, 2, 4, 6, 12, 18, or 24 hours of ~100nM dexamethasone exposure compared to vehicle control astrocyte cultures

first: Robert

last: Thompson


title: Ablation of Cdh1 and Trp53 in the uterus reveals novel mechanisms controlling tumor microenvironment in endometrial cancer.

status: Public on Jun 23 2014

city: Pullman

first: Kanako

last: Hayashi

address: BLS345, 1770 NE Stadium Way

department: School of Molecular Biosciences

institute: Washington State University

summary: Because TP53 mutation and CDH1 inactivation are the most common abnormalities found in human type II endometrial carcinomas, the contribution of dysfunctional TRP53 and CDH1 in the tumor microenvironment to induce type II endometrial cancer was characterized using mouse as a model. The results of our analysis revealed that conditional deletion of Cdh1 and Trp53 in the uterus regulated most of the genes categorized by their involvement in inflammatory responses, immune cell trafficking, cellular movement, cell-to-cell signaling and interaction and cellular growth and proliferation.

overall_design: A direct comparison of mouse uteri (n=3) from control, single ablation of Cdh1 or Trp53, and ablation of both Cdh1 and Trp53 at 2 months of age.

first: Genna

middle: R

last: Stodden

first: Mallory

middle: E

last: Lindberg

first: Mandy

middle: L

last: King

first: James

middle: A

last: MacLean II


title: FGF-regulated Sox9 and Sox10 are required for the formation and branching morphogenesis of mouse ocular glands

city: Saint Louis

first: David

last: Beebe

address: 660 S. Euclid Ave.

institute: Washington University School of Medicine


title: Lung adenocarcinoma subtypes definable by lung development-related miRNA expression profiles in association with clinicopathologic features [pre-miRNA analysis - Whole Human Genome 4 x 44K Microarray]

status: Public on Jun 19 2014

city: Nagoya

first: Takashi

last: Takahashi

state: Aichi

address: 1-1 Kanokoden, Chikusa-ku

institute: Aichi Cancer Center

summary: Accumulation of genetic and epigenetic changes alters regulation of a web of interconnected genes including miRNAs, which confer hallmark capabilities and characteristic cancer features. In this study, the miRNA and mRNA expression profiles of 126 non-small cell lung cancer specimens were analyzed, with special attention given to the diversity of lung adenocarcinomas. Of those, 76 adenocarcinomas were classified into two major subtypes, developing lung-like and adult lung-like, based on their distinctive miRNA expression profiles resembling those of either developing or adult lungs, respectively. A systems biology-based approach using a Bayesian network and nonparametric regression was employed to estimate the gene regulatory circuitry functioning in patient tumors in order to identify subnetworks enriched for genes with differential expression between the two major subtypes. miR-30d and miR-195, identified as hub genes in such subnetworks, had lower levels of expression in the developing lung-like subtype, while introduction of miR-30d or miR-195 into the lung cancer cell lines evoked shifts of mRNA expression profiles towards the adult lung-like subtype. Conversely, the influence of miR-30d and miR-195 was significantly different between the developing lung- and adult lung-like subtypes in our analysis of the patient dataset. In addition, RRM2, a child gene of the miR-30d-centered subnetwork, was found to be a direct target of miR-30d. Together, our findings reveal the existence of two miRNA expression profile-defined lung adenocarcinoma subtypes with distinctive clinicopathologic features and also suggest the usefulness of a systems biology-based approach to gain insight into the altered regulatory circuitry involved in cancer development.

overall_design: Microarray analysis using a Whole Human Genome 4 x 44K Microarray G4112F (Agilent) was conducted to examine changes in expression of 400 genes in SiGN network by transfection of Pre-miR-30d, Pre-miR-195 or Pre-miR-NC#2 (Ambion) in SK-LC-7 cells, which were then harvested at 72 hours after transfection.

first: Chinatsu

last: Arima

first: Taisuke

last: Kajino

first: Yoshinori

last: Tamada

first: Seiya

last: Imoto

first: Yukako

last: Shimada

first: Masahiro

last: Nakatochi

first: Motoshi

last: Suzuki

first: Hisanori

last: Isomura

first: Yasushi

last: Yatabe

first: Tomoya

last: Yamaguchi

first: Kiyoshi

last: Yanagisawa

first: Satoru

last: Miyano


title: Gene expression profile in PGC1b overexpressing skeletal muscle

status: Public on Jun 21 2014

city: hounston

first: vihang

last: narkar

state: texas

address: 1825 pressler street

department: IMM

institute: universuty of texas

summary: PGC1b transgenic mice were generated to selectively over-express PGC1b in skeletal muscles using human skeletal alpha-actin gene promoter. The gene expression profiles were collected from Tibialis anterior (TA) muscles of wild type (WT) and PGC1b transgenic (TG)  mice.

overall_design: Tibialis anterior muscles from three month old WT and PGC1b transgenic male mice.

first: Yadav

last: Vikas

first: Matsakas

last: Antonios

first: Lorca

last: Sabina

first: Narkar

last: Vihang


title: TLR4 ligands LPS and MPLA differentially regualte effector and memory CD8 T cell differentiation

status: Public on Jun 03 2014

city: New Haven

first: Hailong

last: Meng

state: CT

address: 300 George Str

institute: Yale University

summary: Here we implemented a simple dendritic cell (DC)-mediated immunization approach to study the effects of commonly used adjuvants, Toll like receptor (TLR) ligands, on effector CD8 T cell differentiation and memory T cell development. To our surprise, we found that the TLR4 ligand LPS was far more superior to other TLR ligands in generating memory CD8 T cells upon immunization. LPS boosted clonal expansion similar to the other adjuvants, but fewer of the activated CD8 T cells died during contraction, generating a larger pool of memory cells. Intriguingly, monophosphoryl lipid A (MPLA), another TLR4 ligand, enhanced clonal expansion of effector CD8 T cells, but also promoted their terminal differentiation and contraction; thus, fewer memory CD8 T cells formed and MPLA-primed animals were less protected against secondary infection compared to those primed with LPS. Furthermore, gene expression profiling revealed that LPS-primed effector cells displayed a stronger pro-memory gene expression signature, whereas the gene expression profile of MPLA-primed effector cells had aligned closer with terminal effector CD8 T cells.

overall_design: Mice that contain small number of P14 CD8 T cells were immunized with DC-33 either alone or in combination with LPS or MPLA. KLRG1loIL-7Rhi MPECs were purified by FACS sort, and mRNA isolated from MPECs was subjected to whole-genome expression profiling using Illumina MouseWG-6 v2.0 Expression BeadChip.

first: Weiguo

last: Cui

first: Susan

last: Kaech

first: Steven

last: Kleinstein


title: Gene Expression Analysis of Cancer-Associated Fibroblast (CAF) compared to Normal Fibroblast (NF) [microarray]

status: Public on Jun 18 2014

city: Houston

first: Valerie

last: LeBleu

state: TX

address: 1881 East Road

institute: MDACC

summary: Analysis of differentially expressed genes in CAF associated with PDAC vs NF

overall_design: Total RNA obtained from PDAC CAF and NF samples

first: Raghu

last: Kalluri


title: Transcriptional profile of Foxp3+ regulatory T cells from colon lamina propria and mesenteric lymph node in steady state mice

city: Oxford

first: Chris

last: Schiering

address: John Radcliffe Hospital

department: Nuffield Department of Clinical Medicine

institute: University of Oxford

summary: The IL-33 receptor ST2 is differentially expressed by colonic lamina propria Treg cells

overall_design: Microarray of sort-purified Foxp3+ Treg cells from colonic lamina propria over mesenteric lymph node

first: Thomas

last: Krausgruber

first: Thibault

last: Griseri

first: Julia

last: Bollrath

first: Fiona

last: Powrie


title: Gene regulation by Sox9 in the conjunctival epithelium

first: David

last: Beebe

summary: Wild type or Sox9 fx/fx; Le-Cre-positive (Sox9-/-) conjunctival epithelium from the temporal, nasal and dorsal region of E14.5 mouse embryos was laser micodissected from three embryos of each genotype. Total RNA was purified and reverse transcribed and amplified using a NuGEN kit. cDNA was biotinylated and hybridized to Illumina MouseWG-6 v2.0 bead arrays.

overall_design: Three wild type and three Sox9 knockout embryos were used. cDNA obtained from each region of the conjunctival epithelium was pooled and used for microarray analysis. Statistical analysis was performed using the values from the 25-50 beads on each array.

first: Ziyan

last: Chen

first: Jie

last: Huang

first: Ying

last: Liu


title: The Alarmin IL-33 Promotes Regulatory T Cell Function in the Intestine

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

overall_design: Refer to individual Series


title: Histone H3 Acetylation and microRNA(s) Regulate Inflammatory response in Mastitis Mice, induced by Staphylococcus aureus Infection [Microarray]

status: Public on Jun 01 2014

city: Bangalore

first: Tapas

middle: Kumar

last: Kundu

state: Karnataka

address: Jakkur P.O.

department: Molecular Biology & Genetics Unit

country: India

institute: Jawaharlal Nehru Centre for Advanced Scientific Research

summary: Bacterial infection in the mammary gland parenchyma induces local inflammation that can lead to a multietiological complex disease called mastitis. Globally Staphylococcus aureus is the single largest mastitis pathogen and the infection can ultimately result in either subclinical or chronic and sometimes lifelong infection. In the present report we have addressed the differential inflammatory response in the mice mammary tissue during intramammary infection  and the altered epigenetic context induced by two closely related strains of S. aureus. Immunohistochemical and immunoblot analysis showed strain specific hyperacetylation at histone H3K9 and H3K14 residues. Real-time PCR and genome-wide gene expression studied showed expression of a set of proinflammatory genes and cytokines in a temporal manner. Remarkably, over expression of the genes significantly correlated with the promoter specific acetylation in these residues. Furthermore, we have identified several differentially expressed known miRNAs and 4 novel miRNAs in the S. aureus infected mice mammary tissue by small RNA sequencing. By employing these gene expression data, an attempt has been made to delineate the gene regulatory networks in the strain specific inflammatory response. Apparently, one of the isolates of S. aureus activated the NFkB signaling leading to drastic inflammatory response and induction of immune surveillance, which could lead to rapid clearance of the pathogen. The other strain repressed most of the inflammatory response, which might help in its sustenance in the host tissue. Taken together, our studies shed substantial lights to understand the mechanisms of strain specific differential inflammatory response to S. aureus infection during mastitis.

overall_design: 3 samples in two biological replicates. One control and two samples infected with two different strains of S. aureus

first: Rahul

last: Modak

first: Susweta

last: Das Mitra

first: Bibek

last: Shome

middle: K


title: Lung adenocarcinoma subtypes definable by lung development-related miRNA expression profiles in association with clinicopathologic features [mRNA analysis - Whole Human Genome 4 x 44K Microarray]

first: Takashi

last: Takahashi

overall_design: Microarray analysis using a Whole Human Genome 4 x 44K Microarray G4112F (Agilent) was conducted.

first: Chinatsu

last: Arima

first: Taisuke

last: Kajino

first: Yoshinori

last: Tamada

first: Seiya

last: Imoto

first: Yukako

last: Shimada

first: Masahiro

last: Nakatochi

first: Motoshi

last: Suzuki

first: Hisanori

last: Isomura

first: Yasushi

last: Yatabe

first: Tomoya

last: Yamaguchi

first: Kiyoshi

last: Yanagisawa

first: Satoru

last: Miyano


title: Expression data from feline liver tissue

status: Public on Jun 11 2014

city: Riyadh

first: Marya

middle: Zia

last: Zaidi

state: Riyadh

address: 1 Takhassussi Road

department: Biological & Medical Research

country: Saudi Arabia

institute: KFSH&RC

summary: This study looks at the effect of dietary manipulation on the development of hepatic steatosis and changes in hepatic gene expression in a feline model. We used microarray analysis to examine changes in hepatic gene transcription in response to Trans fat, High Fructose Corn Syrup  (HFCS) and/or Monosodium Glutamate (MSG) in the domestic cat. The use of human Affymetrix arrays for the study of feline gene expression has previously been validated by Dowling and Bienzle, 2005, Journal of  General  Virology. 86(Pt 8), 2239-48 (PMID 16033971).

overall_design: Our study animals were bred from female Felis catus previously placed on one of 4 different dietary regimens for a period of 3 weeks prior to mating. The four dietary regimens used in this study were: [1] Standard Chow Control feline diet (Test Diet Purina catalog #5003); [2] MSG diet consisting of Control diet with 1.125% added Monosodium Glutamate (Diet A: Test Diet Purina catalog #5C1J); [3] Trans-fat/HFCS diet, containing  8.6% Trans fat and 24% HFCS (Diet B: Test Diet Purina catalog #5B4K); and [4] Trans-fat/HFCS and MSG diet, containing 8.6% Trans fat, 24% HFCS and 1.125% MSG (Diet C: Test Diet Purina catalog #5C1H). Following mating, the 4 groups of dams were maintained on their respective diets throughout the gestation and nursing period. Male offspring used in the following experiments were  weaned onto the same diets and maintained on their respective dietary regimens until they reached 9 months of age. Hepatic  tissues (4-5 per diet group) were used for RNA extraction and hybridization on Affymetrix microarrays.

first: Kate

last: Collison

first: Nadine

last: Makhoul


title: Identification of IL-23 target genes in intestinal CD4+ T cells

first: Chris

last: Schiering

summary: IL-23 negatively regulates St2 and Gata3 expression in intestinal CD4+ T cells

overall_design: Colitis was induced by co-transfer of WT and Il23r-/- naïve CD4 T cells into Rag1-/- recipients. Upon development of clinical signs of inflammation WT and Il23r-/- CD4+ T cells were sort-purified from the colon lamina propria on the basis of congenic markers. Total RNA was extracted immediately after the sort without further manipulation.

first: Fiona

last: Powrie


title: Gene expression profile of hematopoietic stem cells (CD34+ cells) with or without nanoparticles

city: Philadelphia

first: Sezin

last: Aday

state: Pennsylvania

address: 210 South 33rd Street, Skirkanich Hall

institute: University of Pennsylvania

summary: To understand the the effect of poly(lactic-co-glycolic acid) nanoparticles (NPs) encapsulating a fluorine contrast agent on hematopoietic stem cells (CD34+ fraction of umbilical cord blood mononuclear cells), we have employed whole genome microarray expr

overall_design: The gene expression in human CD34+ cells was measured at 24 h and 7 d after incubation with nanoparticles. Three independent experiments were performed at each time.