title: Genome-wide analysis of different response of hepatocytes and oval cells to hepatitis B virus expression during HBV-related hepatocarcinogenesis

status: Public on Jul 12 2012

city: Wuhan

first: Lei

last: Zhang

state: Hubei

address: 1095# Jiefang Avenue

institute: Hepatic Surgery Center, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology

summary: Analysis of genetic changes of hepatocytes and oval cells induced by HBV. The hypothesis tested in the present study was that hepatic progenitor cells (oval cells) are the founder cells of hepatocellular carcinoma (HCC). Results provide important information of the different responses of hepatocytes and oval cells to HBV expression during HBV-related hepatocarcinogenesis, such as up- or down-regulated oncogenes,tumor suppressor genes and signaling pathways.Results also provide new insights into the biology of human HCC.

overall_design: Total RNA obtained from primary cultured hepatocytes and oval cells isolated from the healthy and HBV transgenic mice.

first: Yan

last: Chen


title: Gene expression comparison in between mitoNEET transgenic vs wild type subcutaneous adipose tissue

city: Dallas

first: Thomas

middle: Nathan

last: Person

state: Texas

address: 5323 Harry Hines Blvd

department: Clinical Sciences

country: USA

institute: UT Southwestern

overall_design: RNA was isolated from subcutaneous adipose tissue from male FVB mice in the light phase. mRNA expression was compared in between wild type and mitoNEET transgenic subcutaneous adipose tissue.

first: Christine

middle: M

last: Kusminski

first: Philipp

middle: E

last: Scherer


title: Subgroup specific somatic copy number aberrations in the medulloblastoma genome

status: Public on Jul 27 2012

city: HEIDELBERG

first: Paul

middle: A.

last: Northcott

address: Im Neuenheimer Feld 280

country: Germany

institute: German Cancer Research Center (DKFZ)

type:
Expression profiling by array
Genome variation profiling by SNP array
SNP genotyping by SNP array

summary:
Medulloblastoma, the most common malignant pediatric brain tumour is currently treated with non-specific cytotoxic therapies including surgery, whole brain radiation, and aggressive chemotherapy. As medulloblastoma exhibits marked intertumoural heterogeneity, with at least four distinct molecular variants, prior attempts to identify targets for therapy have been underpowered due to small samples sizes.  Here we report somatic copy number aberrations (SCNAs) in 1087 unique medulloblastomas.  SCNAs are more common than SNVs in medulloblastoma, and are predominantly subgroup enriched.  The most common region of focal copy number gain is a tandem duplication of the Parkinson's disease gene SNCAIP, which is exquisitely restricted to Subgroup 4alpha. Recurrent translocations of PVT1, including PVT1-MYC and PVT1-NDRG1 that arise through localized chromosomal shattering (topochromothripsis) are restricted to Group 3 tumours. Numerous actionable SCNAs, including recurrent events targeting TGFbeta signaling in Group 3, and NF-kappaB signaling in Group 4 suggest future avenues for rational, targeted therapy

This SuperSeries is composed of the SubSeries listed below.

overall_design: Refer to individual Series


title: Transcriptome profiles of mouse and human monocyte and dendritic cell subsets

city: Singapore

first: Pavandip Singh

last: Wasan

address: 8A Biomedical Grove, #03-06, Immunos

department: Bioinformatics

country: Singapore

institute: Singapore Immunology Network

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

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus


title: Transcriptome profiles of mouse and human monocyte and dendritic cell subsets (mouse data)

summary: Dendritic cells (DCs) are critical in mediating immunity to pathogens, vaccines, tumors and tolerance to self. Significant progress has been made in the study of DC subsets in murine models but the translation of these findings to human DC immunobiology has not been fully realized.  Murine splenic CD8+ DC and CD103+ DC possess potent antigen cross-presenting capacity.  Although recent evidence points to human blood CD141+ DCs as the functional equivalent of CD8+ DC, the precise identity of the human migratory cross-presenting DC has remained elusive.  We performed phenotypic and functional analyses to interrogate the DC compartment of human non-lymphoid tissues and identified three distinct subsets: i) CD141high DCs, ii) CD1c DCs and iii) CD14+ DCs.  Only CD141high DCs were capable of cross-presenting soluble antigen. Comparative transcriptome analysis of steady state monocyte and DC subsets between mouse and human confirmed conservation between species, aligning the following subsets together: i) human CD141high DCs with mouse CD8+ and CD103+ DCs, ii) human CD1c+ DCs with mouse CD4+ DCs and iii) human CD14+ DC with mouse monocyte subsets.  The lack of positive association between human CD1c+ DCs and mouse non-lymphoid tissue CD11b+ DCs highlights heterogeneity and predicts the existence of a monocyte-like cell within the CD11b+ DCs.

overall_design: Gene expression analysis using total RNA from specific human and mouse monocyte and dendritic cell subsets purified by FACS.

first: Florent

last: Ginhoux

first: Michael

last: Poidinger

first: Pavandip

first: Muzlifah

last: Haniffa

first: Matthew

last: Collin


title: Whole genome transcription profile showing early changes in gene expression in antigen receptor activated B cells

status: Public on Jul 11 2012

city: Umeå

last: Grundström

address: Analysvägen 1

department: Department of Molecular Biology

country: Sweden

institute: Umeå University

summary: To search for rapid changes in gene expression following BCR activation, we performed DNA microarray analysis of activated splenic B cells with and without anti-IgM treatment for 1 and 2 hour.

overall_design: Primary B-lymphocytes were purified from mouse spleens and stimulated with IL-4 (Pepro-Tech) and CD40L (R&D Systems) as indicated at 5 ng/ml and 200 ng/ml, respectively. The BCR of stimulated cells  was  activated by incubation with goat F(ab’)2 anti-mouse IgM (Southern Biotechnologies) at 2.5 μg/ml for 3 hour.

first: Jiyoti

last: Verma-Gaur


title: Whole genome transcription profile of antigen receptor activated B cells expressing wildtype or Calmodulin (CaM) - resistant E12

summary: To elucidate the genome-wide role of Ca2+/ calmodulin inhibition of E2A in regulation of BCR activation, we performed DNA microarray analysis of activated splenic B cells expressing wildtype or CaM-resistant E12 mutant m8N47 with and without anti-IgM treatment for 3 hour.The expression of a remarkably large set of genes differed significantly.

overall_design: Primary splenic B-lymphocytes were purified from mice heterozygous for the deletion of E2A gene and infected with retroviruses expressing either wildtype or mutant E12 after activation with CD40L plus IL-4 for 14 h. After 12 h incubation, the infection was repeated for 12 h, followed by incubation for a further 22 h post-infection in fresh complete medium with the stimulants to allow expression of GFP and E12. In addition to CD40L plus IL-4, the medium was supplemented with LPS (200 ng/ml) during retroviral infection incubations to improve infection efficiency. To study gene expression following  B-cell receptor activation, anti-mouse IgM (2.5 μg/ml) was added for 3 hour. For DNA microarray analysis of infected B-lymphocytes, the infected cells were purified with a FACSAria cell sorter instrument (BD Biosciences) using their green fluorescence from expression of the GFP.


title: MiR-374a Promotes Epithelial-Mesenchymal Transition (EMT) and Metastasis of Breast Cancer

status: Public on Jul 14 2012

city: Guangzhou

first: Mengfeng

last: Li

state: Guangdong

address: 74# zhongshan 2 Rd.

department: Zhongshan school of medicine

country: China

institute: Sun Yat-sen University

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


title: Glioblastoma Orthotopic Xenograft Transcriptome

city: Phoenix

first: Brock

last: Armstrong

state: AZ

address: 445 N. 5th Street

department: Cancer and Cell Biology

institute: TGen

summary: Transcriptional profiling of glioblastoma orthotopic xenografts

overall_design: Descriptive experiment, comparison of 39 glioblastoma tumors as orthotopic xenografts

first: Mike

last: Berens


title: Glioblastoma Orthotopic Xenograft Transcriptome and Glioblastoma Xenograft Comparative Genomic Hybridization Arrays

type: Genome variation profiling by genome tiling array


title: A genetic basis for a postmeiotic X vs. Y chromosome intragenomic conflict in the mouse

status: Public on Jul 06 2012

city: Canterbury

first: Peter

middle: James

last: Ellis

state: Kent

address: Stacey Building

department: School of Biosciences

country: United Kingdom

institute: University of Kent

summary: The Y-encoded multicopy gene Sly has been shown to repress X and Y genes in spermatids, among which are its X-linked homologs Slx and Slxl1, via modulation of post-meiotic sex chromain (PMSC). In this experiment, we compared expression in spermatids from mice that are deficient for Sly (shSLY), for Slx/Slxl1 (shSLX1) or both (shSLX1shSLY).  We observed that Slx/Slxl1 has an opposite role to that of Sly, and stimulates expression of X and Y genes in spermatids when Sly is absent. Slx/Slxl1 deficiency rescues the sperm differentiation defects and near sterility caused by Sly deficiency and vice versa. Slx/Slxl1 deficiency also causes a sex ratio distortion towards the production of male offspring that is corrected by Sly deficiency.

overall_design: Wild type strain-matched spermatids are used as a control (4 biological replicates), and 3 biological replicate samples are analysed for each genotype of interest (shSLY, shSLX1 and shSLX1shSLY)

first: Julie

last: Cocquet

middle: J

first: Shantha

middle: K

last: Mahadevaiah

first: Nabeel

middle: A

last: Affara

first: Daniel

last: Vaiman

middle: S

last: Burgoyne


title: Gene expression profile of purified tumor cells from primary breast cancer tumor tissues and metastatic lymph nodes

status: Public on Jul 07 2012

city: Stanford

middle: P.

last: Lee

state: CA

address: CCSR room 1155, 269 Campus Drive

department: Department of Medicine

institute: Stanford University

summary:
Gene expression profiling of whole tumor tissues consists of a heterogeneous population of tumor and stromal cells. We performed gene expression profiling of flow cytometry purified tumor cells from primary breast tumor tissues and metastatic lymph nodes in order to segregate tumor signatures from stromal signatures. The goal of this set of expression profiles was to understand the underlying mechanism of lymph node metastatic processes by comparing primary breast tumor cell gene expression profiles with that of lymph node metastatic tumor cells.
Keywords: breast cancer, lymph node metastasis

overall_design: Gene expression was performed on 14 primary breast tumors and 6 metastatic lymph node samples, of which there were 3 paired tissues. Common universal human reference design. 20 samples replicated twice as dye swaps generating 40 arrays.

first: Hongxiang

last: Yu

first: Diana

middle: L

last: Simons

first: Erich

last: Schwartz

first: Ning

last: Yan

first: Frederick

last: Dirbas

first: Denise

last: Johnson

first: Susan

middle: P

last: Holmes


title: miRNA and mRNA expression profiling of hepatocellular carcinoma induced by AAV in vivo gene targeting at the Rian locus

status: Public on Jul 03 2012

city: Seattle

first: Mei

last: Xu

address: 1959 NE Pacific ave N

institute: University of Washington

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

first: Pei-Rong

last: Wang

first: Sara

last: Toffanin

first: Yi

last: Li

first: Josep

last: Llovet

first: David

middle: W

last: Russell


title: mRNA expression profiling of hepatocellular carcinoma induced by AAV in vivo gene targeting at the Rian locus

summary: The distinct phenotypic and prognostic subclasses of human hepatocellular carcinoma (HCC) are difficult to reproduce in animal experiments.  Here we have used in vivo gene targeting to insert an enhancer-promoter element at an imprinted chromosome 12 locus in mice, thereby converting ~1 in 20,000 normal hepatocytes into a focus of HCC with a single genetic modification.   A 300 kb chromosomal domain containing multiple mRNAs, snoRNAs and microRNAs was activated surrounding the integration site.   An identical domain was activated at the syntenic locus in a specific molecular subclass of spontaneous human HCCs with a similar histological phenotype, which was associated with partial loss of DNA methylation.   These findings demonstrate the accuracy of in vivo gene targeting in modeling human cancer, and suggest future applications in studying various tumors in diverse animal species.  In addition, similar insertion events produced by randomly integrating vectors could be a concern for liver-directed human gene therapy.

overall_design: Three individual liver tumor tissue and their adjacent normal liver tissue were used for mRNA array analysis


title: Expression data from GNMT knockout mice in Hepatocytes and OKER cell lines

status: Public on Jul 01 2012

city: Barcelona

first: Juanjo

last: Lozano

address: C/ Rosselló 153

department: Plataforma de Bioinformatica

country: Spain

institute: CIBEREHD

summary: Hepatocellular carcinoma (HCC) is the first cause of death in cirrhotic patients. Liver cirrhosis at a high risk of HCC has abnormal S-Adenosylmethionine (SAMe) levels. Catabolism of SAMe is mainly mediated by Glycine N-methyltransferase (GNMT), Lack in GNMT expression leads to epigenetic regulation of critical carcinogenesis pathways and mounting evidence assigns an essential role of GNMT in HCC. Methods: Here we have studied the role of LKB1-AMPK and RAS in the proliferation and transformation of GNMT-deficient HCC. Results. GNMT-deficient HCC was characterized by LKB1-AMPK misconnection, leading to resistance of apoptosis response mediated by a positive regulation of cAMP-PKA-CaMKKβ cascade. Additionally, Ras-mediated hyperactivation of LKB1 contributes to the proliferation of GNMT-deficient HCC in an ERK/p90RSK-dependent manner. The observed LKB1-induced Ras activation, was due to the regulation of RASGRP3 expression. Notably, the human HCC tumors with poorer prognosis showed the lowest levels of GNMT, p-AMPKα(Thr172) and the highest activation of Ras/LKB1/RASGRP3 axis. The present data suggest a correlation between LKB1 and RAS activity in a context of HCC with low GNMT expression, indicating that activation of the RAS/LKB1/RASGRP3 cascade might possess an important prognostic role in human liver cancer. Furthermore, these findings open the possibility to design new therapeutic strategies for the treatment of liver cancer.

overall_design: HCC induced wild-type or Gnmt knockout mice at 3 weeks old were used for RNA extraction and hybridization on Illumina microarrays. The study comprises three groups of samples: OKER cell line(n=3), GNMT-KO mouse hepatocytes (n=3) ,GNMT-WT mouse hepatocytes(n=3)

first: J

first: M

last: Martínez-Chantar


title: Dual targeting of the Akt/mTOR signaling pathway inhibits castration-resistant prostate cancer in a genetically engineered mouse model

status: Public on Jul 04 2012

city: Newark

first: Antonina

last: Mitrofanova

state: NJ

address: 65 Bergen Street, Rm 923B

institute: Rutgers University

summary: Analyses of differential gene expression analyses from intact versus castrated Nkx3.1CE2/+ or Nkx3.1CE2/+; Ptenf/f mice

overall_design:
Total RNA isolated form phenotypically wild-type (intact) Nkx3.1CE2/+ (n = 3), intact Nkx3.1CE2/+; Ptenf/f (n = 6), and castrated Nkx3.1CE2/+; Ptenf/f (n = 6) prostate.

Please contact Cory Abate-Shen (cabateshen@columbia.edu) for questions about the submission.

first: Nicolas

last: Floc’h

first: Carolyn

last: Kinkade

first: Takashi

last: Kobayashi

first: Alvaro

last: Aytes

first: Celine

last: Lefebvre

first: Robert

middle: D

last: Cardiff

first: Andrea

last: Califano

first: Michael

last: Shen

first: Cory

last: Abate-Shen


title: Gene expression analysis of the antiviral effect of chloroquine and derivatives on in vitro HCV infected cells.

city: Marseille

first: Claire

last: Camus

address: 163, avenue de Luminy - Case 928

department: GENOMIC

country: France

institute: TAGC UMRs928

summary:
The main goal of this study is to characterize the transcriptional modulations induced by antiviral compounds derived from chloroquine on Huh7 cells infected with HCV. And thus to identify among the genes modulated by infection, those who are regulated by chloroquine and potentially involved in the antiviral activity of the compound.Two HCV cell models were used: a non-infectious HCV replicon and the infectious HCV cell culture (HCVcc). In addition, this study aimed to highlight the characteristics of derivatives of antiviral chloroquine, compared with chloroquine itself.
Abstract from the associated publication: Autophagy is a process of self-degradation of cellular components in which double-membrane autophagosomes sequester organelles or portion of cytosol and fuse with lysosomes or vacuoles for breakdown by resident hydrolases. Autophagy is upregulated in response to extra- or intracellular stress and signals such as starvation, growth factor deprivation, ER stress, and pathogen infection. Indeed, infection with hepatitis C virus (HCV) was shown to induce autophagy through ER stress signaling and subsequent Unfolded Protein Response (UPR) activation. Moreover, a role of autophagy in promoting HCV infection has been suggested and chloroquine (CQ), a lysosomal protease inhibitor, has been seen blocking autophagy as well as inhibiting HCV replication. In the present report, mechanisms accounting for these inhibitory effects were investigated. Gene expression profiling was performed on CQ treated JFH-1-infected Huh7 cells to identify the host cellular genes that are transcriptionally regulated by infection, and silenced by CQ-based treatment. Herein, we demonstrate that CQ reduces the expression of genes induced by the viral infection such as those encoding autophagic key factors triggering the turn-off of mTOR activity as well as factors involved in p53 and NF-KappaB activities. However, we present several lines of evidence demonstrating that the CQ repressive effect observed on the HCV-induced pathways results from a decrease of ER stress due to the upstream pH-dependent inhibitory effect of CQ on viral replication.

overall_design: Gene expression modulations were measured in Huh7 harboring replicon cells stimulated with a 10µM of a Chloroquine derivative compound called CQd, during 6h, 12h and 24h. Two  independent experiments were performed at each time. An untreated control condition was performed in each experiment, expression was measured at the 24h time point.   For the HCVcc model, gene expression analysis was analyzed in two conditions: infection and treatment of infected cells. To characterize modulations in time course of infection, Huh7 naïve cells were infected with JFH1/CS-N6-A4 viral stock and gene expression was measured at 6h, 24h and 48h  postinfection. For each kinetic time point, an uninfected condition was performed and gene expression was measured. An additional control testing the interferon (IFN) induced modulations on infected cells was included and gene expression was measured after a 48h stimulation with 100 IU of IFN (alpha 2 b).  To characterize the antiviral modulations resulting from treatment with Chloroquine (CQ) or a derivative compound (CQd), gene expression was measured in JFH1/CS-N6-A4 infected Huh7 cells treated with 40µM of CQ or CQd during 12h or 48h post-treatment and infection. For each kinetic time point 12h and 48h, an untreated infected control was also performed and gene expression measured.

first: Angela

last: Patatian

first: Florence

last: Joly

first: Catherine

last: Nguyen

first: Philippe

last: Benech

last: Halfon


title: Global gene expression analysis in cord blood reveals gender-specific differences in response to carcinogenic exposure in utero

status: Public on Jun 27 2012

city: Maastricht

first: Kevin

last: Hochstenbach

address: Universiteitssingel 50

department: Health Risk Analysis and Toxicology

country: Netherlands

institute: Maastricht University

summary: Gender effects in the incidence of childhood cancers have been described but the aetiology still needs to be fully examined. Given the latent period of e.g. leukemia, its very early onset in childhood might indicate the foetal period as a critical period. We consequently hypothesize that gender-specific differences in childhood cancer incidence (males have a much higher incidence of leukaemia and lymphomas) may be due to gender-specific responses to exposure to environmental carcinogens in utero. We considered that whole genome transcriptomics analysis in cord blood may provide mechanistic insight into possible gender-specific effects of carcinogen exposure in utero. Thus, the objective of the current study was to investigate whether transcriptomic responses to dietary genotoxic and non-genotoxic carcinogens (i.e. acrylamide and endocrine disruptors) as analyzed in umbilical cord blood samples, demonstrate gender-specific mechanisms-of-action relevant for chemical carcinogenesis. For internal exposure assessment, the CALUX® assay was applied for measuring dioxin(-like), androgen(-like) and estrogen(-like) exposure, and acrylamide-hemoglobin adduct levels were determined by mass spectrometry. To link gene expression to an established phenotypic biomarker of cancer risk, micronuclei frequencies were investigated in T-lymphocytes. While exposure levels did not differ significantly between sexes at birth, important gender-specific differences were observed in gene expressions associated with these exposures. These genes appeared linked with cell cycle-related processes and general cellular processes such as (post) translation, as well as with immune-related pathways. Moreover, oppositely correlating leukemia and lymphoma genes between male and female newborns were identified in relation to the different biomarkers of exposure which might be relevant to male-specific predisposition to develop these cancers in childhood. This study reveals different transcriptomic responses to environmental carcinogens between the sexes In particular, male-specific TNF-alpha-NF-kB signaling upon dioxin exposure and activation of the Wnt pathway in boys upon acrylamide exposure might represent possible mechanistic explanations for the male predominance in the incidence of childhood leukemia.

overall_design: Umbilical cord blood samples were collected immediately after birth from the cord vein of 45 male and 66 female babies whose mothers participated in the Norwegian BraMat cohort. For analyses, each individual cord blood sample was labelled by means of Cyanine-5 and competitively hybridized against a common reference sample (pooled RNA cord blood samples, labelled with Cyanine-3) onto Agilent 4x44k human oligonucleotide microarrays (Agilent Technologies, Palo Alto, CA, USA) according to the manufacturer’s instructions.

first: Danitsja

last: van Leeuwen

first: Hans

last: Gmuender

first: Ralph

middle: R

last: Gottschalk

first: Martinus

last: LÃ vik

first: Berit

last: Granum

first: Unni

middle: C

last: Nygaard

first: Ellen

last: Namork

first: Micheline

last: Kirsch-Volders

first: Ilse

last: Decordier

first: Kim

last: Vande Loock

first: Harrie

last: Besselink

first: Margerata

last: TÃ¶rnqvist

last: von Stedingk

first: Per

last: Rydberg

first: Jos

last: Kleinjans

first: Joost

middle: H

last: van Delft

first: Henk

last: van Loveren


title: MKN28 Cells: Vector vs ZIC1 Transfected

status: Public on Jun 26 2012

city: Hangzhou

first: Jing

last: Zhong

address: Second Affiliated Hospital, School of Medicine Zhejiang University

summary: MKN28 cell lines were transfected with pCDNA3.1-ZIC1 or pCDNA3.1 empty vector. Then, an Agilent oligonucleotide microarray was conducted to systematically determine downstream targets of ZIC1.

overall_design: Two samples are analyzed with one two channnel experiment.

first: Liang-Jing

last: Wang


title: Role of Interleukin-6 in Influenza Pandemic A (H1N1pdm) Infection in Mice

status: Public on Jun 25 2012

city: Toronto

first: Longsi

last: Ran

state: ON

address: 101 College Street

department: Division of Experimental Therapeutics

country: Canada

institute: Toronto General Research Institute

summary: Profile of host response in C57BL6/J mice infected with A/Mexico/4108/2009 (H1N1), spanning days 1 through 6 post-infection.  Focused analysis on the involvement of IL-6 in the host response.

overall_design: Total RNA obtained from lung tissue collected from infected C57BL6/J mice at t = 1, 2, 3, 4, 5, 6 days post-infection (n=3/time point). Uninfected control samples were also obtained (n=3).

first: David

last: Kelvin


title: Global expression profiling of globose basal cells and neurogenic progression within the olfactory epithelium

status: Public on Jul 02 2012

city: Boston

first: Richard

last: Krolewski

state: MA

address: 136 Harrison Ave

department: Anatomy and Cellular Biology

institute: Tufts University School of Medicine

summary: Ongoing, lifelong neurogenesis maintains the neuronal population of the olfactory epithelium in the face of piecemeal neuronal turnover and restores it following wholesale loss. The molecular phenotypes corresponding to different stages along the progression from multipotent globose basal cell (GBC) progenitor to differentiated olfactory sensory neuron are poorly characterized. We used the transgenic expression of GFP and cell surface markers to FACS-isolate Sox2-GFP(+) GBCs, Neurog1-GFP(+) GBCs and immature neurons, and OMP-GFP(+) mature neurons from normal adult mice. In addition, the latter two populations were also collected 3 weeks after olfactory bulb ablation, a lesion that results in persistently elevated neurogenesis. Global profiling of mRNA from the populations indicates that all stages of neurogenesis share a cohort of >2100 genes that are upregulated compared to sustentacular cells. A further cohort of >1200 genes are specifically upregulated in GBCs as compared to sustentacular cells and differentiated neurons. The increased rate of neurogenesis caused by olfactory bulbectomy had little effect on the transcriptional profile of the Neurog1-GFP(+) population. In contrast, the abbreviated lifespan of OMP-GFP(+) neurons born in the absence of the bulb correlated with substantial differences in gene expression as compared to the mature neurons of the normal epithelium. Detailed examination of the specific genes upregulated in the different progenitor populations revealed that the chromatin modifying complex proteins LSD1 and coREST were expressed sequentially in upstream Sox2-GFP(+) GBCs and Neurog1-GFP(+) GBCs/immature neurons. The expression patterns of these proteins are dynamically regulated after activation of the epithelium by methyl bromide lesion.

overall_design: Total RNA was isolated from dissected, dissociated and FACS-purified olfactory mucosal cells from normal adult mice or mice 3 weeks after unilateral bulbectomy. Cells were purified with FACS using endogenous GFP fluorescence from various transgenic lines and cell surface labeling. Two to seven adult mice were used per replicate and three replicates per condition were performed using Illumina bead arrays.  21 samples from olfactory mucosa were analyzed in this series and 3 samples were from a commercially available reference RNA sample. Universal mouse reference RNA from Stratagene was used as a general control and Normal olfactory mucosa was used as a tissue specific control.

first: Adam

last: Packard

first: James

last: Schwob


title: Gene expression profile in Lmna knockout mouse embryonic fibroblast

status: Public on Jun 19 2012

first: Xiaoyu

address: ND3 200, 6001 Forest Park Rd

department: Cancer Center

institute: Ut Southwestern Medical Center

summary: Alteration of gene expression profile due to Lmna knockout was studied in MEF.

overall_design: Total RNA obtained from Lmna +/+ MEF and Lmna -/- MEF were compared.


title: Baseline gene expression in w.t and MFG-E8 deficient mice

first: YuFeng

last: Peng

state: WA

address: 1959 Pacific  Street

department: Rheumatology

summary: To examine whether MFG-E8 deficiency affects gene expression in spleen.

overall_design: Total RNA samples were extracted whole spleen of 4 month old B6 and MFG-E8 deficient mice


title: A Gene Expression Profile in the Kidney After Cisplatin Treatment

status: Public on Jun 30 2012

city: Seoul

first: Sang Geon

last: Kim

state: Seoul

address: San56-1, Sillim-dong, Kwanak-gu

department: College of Pharmacy

country: South Korea

institute: Seoul National University

summary:
Clinical use of a major cancer chemotherapeutic agent, cisplatin, is restricted to dose-limiting renal toxicity. A transcriptomic approach enabled us to extract putative molecules including Pleckstrin homology-like domain, family A, member-3 (Phlda3) contributing to the renal injury. This study investigated the expression of Phlda3 and its regulatory role in tubular injury induced by cisplatin in vivo and in vitro. Real-time PCR and immunoblot assays confirmed that Phlda3 was highly up-regulated in the kidney of mice after a single dose of cisplatin treatment, which preceded increases in the blood urea nitrogen or serum creatinine levels. Particularly, the level of Phlda3 transcript was substantially increased at an early time than that of kidney injury molecule-1, and remained elevated. The effect of cisplatin or acetaminophen treatment on Phlda3 expression in the liver was minimal. Consistently, treatment of NRK52E, a renal tubular cell line, with cisplatin caused increases in Phlda3 mRNA and protein. Knockdown of Phlda3 reversed the decrease in cell viability by cisplatin, supporting the role of Phlda3 in cell death. Akt phosphorylation initially increased after cisplatin treatment, but decreased thereafter. Cisplatin treatment elicited p53 accumulation via mdm2 repression, inducing its target genes, p21 and cyclin G1. Phlda3 deficiency attenuated a decrease in Akt phosphorylation by cisplatin, and prevented p53 accumulation, supporting the role of Phlda3 for p53-mediated tubular cell death. Other renal toxicants, cyclosporine A and CdCl2, also enhanced Phlda3-dependent cell death. Overall, nephrotoxicants including cisplatin induce Phlda3, which leads to p53-mediated tubular cell death via mdm2 repression caused by Akt inhibition.

Since the datasets reported on the effect of cisplatin on the kidney were obtained from animals treated with multiple and relatively high doses of cisplatin, we did our cDNA array analyses day 3 after a single dose of cisplatin administration to mice (i.p., 15 mg/kg) and compared the profiles of kidney microarray data. The transcriptomic approach enabled us to find the putative genes encoding molecules contributing to renal injury. Among those genes represented on the microarray, 33 genes were found to be differentially expressed by cisplatin treatment when a 2-fold change cutoff was used. The regulation of exemplary mRNAs identified in the array analysis was confirmed by qRT-PCR.

overall_design: C57BL/6 mice (9 weeks old) were intraperitoneally injected with a single dose of cisplatin (15 mg/kg body weight) or vehicle (saline). The cDNA microarray experiments were done for the kidney of mice 3 days after treatment. Each group contained 3 males.

first: Chan

middle: G

last: Lee

first: Il

last: Cho

first: Dal

last: Choi

first: Sang


title: Confined 3D microenvironment regulates early differentiation in Human Pluripotent Stem Cells

status: Public on Jun 12 2012

city: Padova

first: Barbara

last: Di Camillo

address: via Gradenigo 6B

department: Information Engineering Department

country: Italy

institute: University of Padova

summary: We aimed to investigate how different three-dimensional microenvironments regulate the early differentiation of the three germ layers in human embryonic stem cells derived embryoid bodies. In particular, a permeable, biocompatible, hydrogel microwell array was specifically designed for recreating a confined niche in which EB secreted molecules accumulate in accordance with hydrogel diffusional cut-off. Fluorescence recovery after photobleaching technique was performed to accurately evaluate hydrogel permeability, mesh size and diffusional cutoff for soluble molecules. EBs culture in microwells promotes the expression of genes involved in pattern specification processes, brain development, ectoderm and endoderm differentiation. On the contrary, suspension EBs express instead genes involved in mesoderm specification and heart development. These results suggest that local accumulation of EBs secreted molecules drives differentiation patterns, as confirmed by immunofluorescence of germ layer markers, in hydrogel confined EB culture.

overall_design: Three different culture conditions of EB culture were analyzed: suspension (standard condition), confinement in microwells of width/depth ratio 1:1 and 1:2. EBs cultured in microwells are viable and have comparable average size after 8 days culture. Whole genome microarrays show that significative differential gene expression was observed between suspension and confined EBs culture.

first: Giovanni

last: Giobbe

first: Monica

last: Zagallo

first: Massimo

last: Riello

first: Elena

last: Serena

first: Giulia

last: Masi

first: Luisa

last: Barzon

first: Nicola

last: Elvassore


title: Gene expression profiling of novel antigen presenting cells (APC) inducing pathogenic T helper cells of lupus

status: Public on Jun 21 2012

city: Chicago

first: Syamal

middle: Kumar

last: Datta

state: IL

address: MCGAW 240 E Huron

institute: Northwestern Univ.

summary:
In lupus autoimmunity, pathogenic IgG autoantibodies that fix complement and bind FcGammaR on inflammatory cells, are produced with help from T helper (Th1 and Th17) cells specific for peptides from nucleosomes of apoptotic cells; and these Th cells also infiltrate vital organs (1-9).  Macrophages (e.g. tingible body MΦ), and DCs are normally tolerant to apoptotic cell antigens (10), but they are activated to present such autoantigens after binding to IgG immune complexes (IC) containing apoptotic cell derived DNA/RNA, which then dually stimulate their TLR and FcGammaR (11-16). Hence, to generate the activating IC, IgG-switched autoantibodies have to be made first by T cell help. Moreover, B cells become efficient antigen presenting cells (APC) to Th cells pre-primed by other APC (17), or if the B cells have developed high affinity somatically mutated receptors by T cell help (18). Thus, conventional APCs participate as disease progresses, but it is unknown who initially primes autoimmune Th cells. We fractionated spleen cells of lupus prone SNF1 mice in search of such APC.
To produce lupus-prone SNF1 mice, NZB and SWR mice were purchased from The Jackson Laboratory, ME to breed the lupus-prone SNF1 hybrids (19).  Female SNF1 mice, like BWF1, have high serum levels of IgG class anti-DNA and other anti-nuclear autoantibodies by 2 mo, and spontaneously begin to develop severe lupus nephritis by 5 mo age (20).
We depleted spleen cells of lupus-prone SNF1 mice of cells with mature lineage markers, including conventional APC, and then isolated pure CD117+ (c-Kit+ or K+) cells from the lineage– (Lin– or L–) cells. These Lin–c-Kit+pure cells, which had morphology of hematopoietic progenitor cells, were the main type of APC inducing nuclear autoantigen-specific T helper cell (Th17) response upon feeding them with nucleosomes.
These Lin–c-Kit+pure cell isolate is called "LinminuscKitplus pure" in the Sample titles shown below.
CD117 (c-Kit) is also a marker for macrophage/dendritic cell precursors (MDP), which also express CX3CR1 (21-23). Therefore, from T and B-cell depleted spleen cells, we sorted out CD117+CX3CR1–, CD117+CX3CR1+, CD117–CX3CR1+, and CD117–CX3CR1– cell subsets, and then tested their abilities to induce Th responses to nucleosomes. The CD117+CX3CR1– cells were Lin– (Lin–c-Kit+CX3CR1– or L–K+Cx–;  named as "LinminuscKitplusCX3CR1minus" in the sample titles below) were very similar to L–K+pure cells (LinminuscKitplus pure), which are also CX3CR1–, although isolated in a different way. Therefore, we compared gene expression profiles of nucleosome-pulsed APC that were isolated in those two ways, namely purified Lin–c-Kit+ pure (LinminuscKitplus pure) cells or the Lin–c-Kit+CX3CR1– (LinminuscKitplusCX3CR1minus) cell subset, with other types of APCs, namely the Lin–c-Kit+CX3CR1+ subset (named as "LinminuscKitminusCX3CR1plus" in sample titles below), or CD11c+CD11blowc-Kit– cells (Dendritic cells in the sample titles below).
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21. Fogg, D. K., C. Sibon, C. Miled, S. Jung, P. Aucouturier, D. R. Littman, A. Cumano, and F. Geissmann. 2006. A clonogenic bone marrow progenitor specific for macrophages and dendritic cells. Science 311:83-87.
22. Onai, N., A. Obata-Onai, M. A. Schmid, T. Ohteki, D. Jarrossay, and M. G. Manz. 2007. Identification of clonogenic co

overall_design: Gene profiling microarray and data analysis.  Spleen cells from 3 batches of three 5 mo SNF1 female mice each time were used to obtain three independent isolations of each type of APC population.  Total RNA was purified from each APC after incubation with nucleosomes (20µg/ml) for 6h.  RNA expression analysis of each type of APC isolate in triplicate was performed at our Genomics Core Facility using Illumina Mouse WG-6 v2.0 Expression Beadchips, which provides coverage of around 45,281 genes and expressed sequence tags. Raw signal intensities of each probe were obtained using data analysis software (Beadstudio; Illumina) and imported to the Lumi package of Bioconductor for data analysis. Before transformation and normalization (24-26), A/P call detection was performed based on detection p value. 20,890 out of 45,281 probes with less than 0.01 were considered as valid signals. For each pairs of four comparisons: Lin–c-Kit+CX3CR1– versus Lin–c-Kit+ CX3CR1+; Lin–c-Kit+pure vs. Lin–c-Kit+CX3CR1+; Lin–c-Kit+CX3CR1– vs. DC; and Lin–c-Kit+pure vs. DC; differentially expressed genes were identified using an Analysis of Variance (ANOVA) model with empirical Bayesian variance estimation (27). Thus, 1,619 genes were identified as being differentially expressed (up or down) on the basis of a statistically significant (raw P-value < 0.01 and false discovery rate adjusted P-value < 0.05), and 1.5-fold change (up or down) in expression level in at least one of the comparisons, and out of these 230 genes were significantly UP-regulated by the above criteria in all 4 pair comparisons.

first: Hee-Kap

last: Kang

first: Ming-Yi

last: Chiang

first: Diane

last: Ecklund

first: Li

last: Zhang

first: Rosalind

last: Ramsey-Goldman


title: Transcriptional effects of chronic heroin and methamphetamine treatment in the mouse striatum

city: Krakow

first: Marcin

last: Piechota

address: Smetna 12

department: Molecular Neuropharmacology

country: Poland

institute: Institute of Pharmacology PAS

summary: To identify molecular effects of chronic drug treatment, heroin and methamphetamine treated animals were compared with saline treated animals at multiple time-points using microarray technology. Gene expression profile was assessed 14 h after the last dose of 1, 3, 6 or 12 days drug treatment and after 13, 15, 18 or 24 days of withdrawal.

overall_design: Animals were injected intraperitoneally with saline (SAL) (Polfa, Lublin, Poland), heroin (synthesized from morphine in Institute of Pharmacology PAS, Krakow, Poland) or D-methamphetamine (Sigma-Aldrich, Poznan, Poland) twice a day for consecutive 12 days in increasing doses. The Methamphetamine last dose (8 mg/kg) was four times greater than the first dose (2 mg/kg). It was also the case for heroin (40 and 10 mg/kg respectively). Mice were sacrificed by decapitation after 1, 3, 6 or 12 days of treatment or after 13, 15, 18 or 24 days of withdrawal.

first: Michal

last: Korostynski


title: Conversion of mES to cXEN cells

status: Public on Jun 05 2012

city: Hinxton

first: Isheng

middle: Jason

last: Tsai

address: Wellcome Trust Genome Campus

institute: Wellcome Trust Sanger Institute

summary: The inner cell mass of the mouse pre-implantation blastocyst is comprised of epiblast progenitor and primitive endoderm cells of which cognate embryonic (mESCs) or extra-embryonic (XEN) stem cell lines can be derived. Importantly, each stem cell type retains the defining properties and lineage restriction of their in vivo tissue of origin. Recently, we demonstrated that XEN-like cells arise within mESC cultures. This raises the possibility that mESCs can generate self-renewing XEN cells without the requirement for gene manipulation. We have developed a novel approach to convert mESCs to XEN cells (cXEN) using growth factors. We confirm that the down-regulation of the pluripotency transcription factor Nanog and the expression of primitive endoderm-associated genes Gata6, Gata4, Sox17 and Pdgfra are necessary for cXEN cell derivation. This approach highlights an important function for Fgf4 in cXEN cell derivation. Paracrine FGF-signalling compensates for the loss of endogenous Fgf4, which is necessary to exit mESC self-renewal, but not for XEN cell maintenance. Our cXEN protocol also reveals that distinct pluripotent stem cells respond uniquely to differentiation promoting signals. cXEN cells can be derived from mESCs cultured with Erk- and Gsk3-inhibitors (2i) and LIF, similarly to conventional mESCs. However, we find that epiblast stem cells (EpiSCs) derived from the post-implantation embryo are refractory to cXEN cell establishment, consistent with the hypothesis that EpiSCs represent a pluripotent state distinct from mESCs. In all, these findings suggest that the potential of mESCs includes the capacity to give rise to both extra-embryonic and embryonic lineages.

overall_design: A total of eight samples were analyzed. Three mouse embryonic stem cell (mESC) lines were used as a negative control, 2 embryo-derived extraembryonic endoderm (XEN) cell lines were used as a positive control, 3 converted XEN (cXEN) cells were used as the experiemental cell lines.

first: Kathy

last: Niakan

first: Lily

middle: T

last: Cho


title: Transcriptome analysis of endometriotic stromal cells treated with hydrogen peroxide

status: Public on Jun 04 2012

city: Nagoya

first: Shinya

last: Toyokuni

state: Aichi

address: 65 Tsuruma-Cho, Showa-Ku

department: Pathology

country: Japan

institute: Nagoya University

summary: In ovarian endometrioma, much iron, which is derived from blood in cyst, deposit in stroma. This iron generates oxidative stress by Fenton reaction, which is supposed to affect endometriotic stromal cells. We used gene expression microarrays to find influence of oxidative stress on endometriotic stromal cells. Gene expression microarrays revealed no statistically differences caused by oxidative stress.

overall_design: 9 samples, which were 3 immortalized eutopic endometrial cells from patients without endometriosis, 3 immoralized eutopic endometrial cells from patients with ovarian endometrioma and 3 immortalized endometriotic stromal cells from patients with ovarian endometrioma, were treated with 1uM hydrogen peroxide for 60 hours and 9 controls untreated with hydrogen peroxide were prepared.  A total of 18 microarrays were used for 9 samples treated with hydrogen peroxide and 9 controls.

first: Toyokuni

last: Shinya

first: Kobayashi

last: Hiroharu

first: Yamashita

last: Yoriko

first: Akatsuka


title: Effects of plasmids transfection on the RO82_W1 human thyroid cell line

status: Public on Jun 01 2012

city: angers

first: frederique

last: savagner

address: 4 rue larrey

institute: Inserm

summary: The goal of this study was to identifiy cellular pathways modified by RO82_W1 cell transfection with PRC, ERRalpha or PRC+ERRalpha plamids relative to transfection with PGl3 plasmid

overall_design: In duplicate, cells transfected with PRC, ERRalpha or PRC+ERRalpha plamids during 48h compared to PGl3 treated cells

first: D

last: Guillotin

last: Prunier

first: F


title: The histone demethylase Kdm3a is essential to progression through differentiation

status: Public on Jun 15 2012

city: Brussels

first: Sarah

last: Dedeurwaerder

address: Route de Lennik, 808

country: Belgium

institute: Université Libre de Bruxelles

summary: Histone demethylation has important roles in regulating gene expression and forms part of the epigenetic memory system that regulates cell fate and identity, by still poorly understood mechanisms. Here we examined the role played by the histone demethylase Kdm3a, which demethylates lysine 9 of histone H3, during cellular differentiation. Using F9 mouse embryonal carcinoma cells as a model for progression through terminal differentiation, we showed that Kdm3a is essential to differentiation into parietal endoderm-like (PE) cells. On gene expression microarrays, we found several genes whose expression is upregulated by Kdm3a during endoderm differentiation, including the three developmental master players Dab2, Pdlim4, and FoxQ1. The role of Kdm3a as a transcriptional activator of these genes was correlated with its effect by demethylating dimethyl-lysine 9 of histone H3 (H3K9me2) at their promoters. We further demonstrated that Dab2 depletion, like Kdm3a depletion, prevents F9 cells from fully differentiating into PE cells. Nevertheless, the only overexpression of Dab2 in Kdm3a-depleted cells is not sufficient to completely restore the PE differentiation in Kdm3a-knockdown cells. Overall, our findings reveal that Kdm3a is crucial for progression through terminal differentiation, likely by regulating the expression of a set of master players in endoderm differentiation. The emergence of Kdm3a as a key modulator of cell fate decision strengthens the notion that histone demethylases are at the nexus of cell differentiation and development.

overall_design: Total RNA obtained from control and Kdm3a-depleted F9 cells at different differentiation stages

first: Marielle

last: Herzog

first: Eleonore

last: Josseaux

first: Emilie

last: Calonne

first: Michael

last: Volkmar

first: François

last: Fuks


title: The ETS transcription factor ESE3 controls prostate epithelial cell differentiation

city: Biella

first: giovanna

last: chiorino

address: via malta 3

department: Cancer Genomics

institute: Fondo Edo Tempia

summary:
ETS transcription factors have recently emerged as important elements in the pathogenesis of prostate cancer (PCa). ETS gene rearrangements leading to over-expression of ETS factors, like ERG, ETV1 and ETV4, are found in about 50% of prostate tumors. While the oncogenic potential of translocated ETS has been demonstrated in several contexts, the impact of endogenously expressed ETS factors on prostate tumorigenesis has been largely overlooked. Here we show that the epithelial-specific ETS factor ESE3, which is normally expressed in basal prostate epithelial (PrE) cells and frequently down-regulated in prostate tumors, serves as gatekeeper to maintain cell differentiation and its down-regulation leads to the acquisition of mesenchymal, stem cell (SC) and tumorigenic properties. ESE3 exerts this function by regulating critical genes involved in the epithelial to mesenchymal transition (EMT) and cell “stemness” and maintaining the equilibrium between cell differentiation and proliferation. Loss of ESE3 may be an important step in prostate tumorigenesis.
Keywords: prostate epithelial cells, prostate cancer, gene expression profiling, ETS genes, EMT, cancer stem cells

overall_design: To identify changes in the cell transcriptional profile induce by ESE3 loss, we performed a gene profiling analysis comparing ESE3 knock-down immortalized prostate epithelial cells (LHS-ESE3KD) vs control LHS cells.

first: Giuseppina

middle: M

last: Carbone

first: Domenico

last: Albino

first: Nicole

last: Longoni

first: Paolo

last: Kunderfranco

first: Erica

last: Ortelli

first: Anastasia

last: Malek

first: Laura

last: Curti

first: Maurizia

last: Mello-Grand

first: Giovanna

last: Chiorino

first: Carlo

middle: V

last: Catapano


title: Incisional hernia recurrence through genomic profiling: a pilot study

city: North Chicago

first: J

middle: Wade

last: Davis

address: 1 N Waukegan Rd

institute: AbbVie

summary: Skin and intact fascia were collected from 15 normal control (NC) patients with no hernia history and 18 patients presenting for recurrent incisional hernia (RH) repair. Microarray analysis was performed using whole genome microarray chips on NC (n = 8) and RH (n = 9). These samples were further investigated using a pathway-specific PCR array containing fibrosis-related genes.

overall_design: Total RNA extracted from skin and fascia of patients with a history of recurrent ventral hernias and a control group. There were no replicates for the same source material for the same patient.

first: Robert

last: Calaluce

first: Sharon

last: Bachman

first: Matthew

last: Gubin

first: Julie

last: Brown

first: Joseph

last: Magee

first: Timothy

last: Loy

first: Bruce

middle: J

last: Ramshaw

first: Ulus

last: Atasoy


title: Toxin-antitoxin of Rickettsia determines fatal addiction of the host cells

status: Public on May 24 2012

first: Gilles

last: Audoly

address: 27, bd J. Moulin

institute: URMITE

summary: Rickettsia spp. can cause mild to severe human disease. These intracellular bacteria are associated with arthropods, nematodes and trematodes, and usually, are efficiently transmitted transovarially to the progeny of the invertebrate host. We recently demonstrated foreign gene acquisition by lateral gene transfer in Rickettsia genomes. The unexpected presence of laterally transferred toxin-antitoxin (TA) genetic elements (including vapBC) in several Rickettsia genomes has not been connected with the pathogenic process or the host-bacteria relationship. We suspect that vapBC are selfish genetic elements that addict eukaryotic hosts to Rickettsia. We identified a statistical link between the transovarial transmission of Rickettsia in invertebrate hosts and the presence of TA operons, specifically vapBC, in the Rickettsia genome. These TA are neighboring to type IV secretion genes. Tunel assays and whole-genome expression of infected cells showed that antibiotic eradication of TA-containing Rickettsia from the host in cell culture initiates a proapoptotic program. Rickettsia VapC toxins inhibit the growth of transformed Escherichia coli and Saccharomyces cerevisiae. Rickettsia toxin presents in vitro RNase activity. Annexin-V staining and time-lapse video showed that intracytoplasmic injections of VapC toxins in cells cause apoptosis. These data demonstrate that host cells may develop a dependence on Rickettsia spp. expressing the vapBC operon. This would constitute a new evolutionary “mafia strategy” of intracellular bacteria based on host addiction.

overall_design: Fresh cells from the human microvascular endothelial cell line (HMEC-1) [26] were infected with R. felis California-2 strain in the presence and absence of antibiotics, at a rate of 5 bacteria per eukaryotic cell. Then, we added or not antibiotics (chloramphenicol 50 µg/ml or doxycycline to 40 µg/ml) in both experimental (R.felis-infected) and control, mock-infected cells for 6 hours. The cells were harvested and RNA was extracted using the RNeasy Mini Kit (Qiagen). DNA contamination was removed using the Turbo DNA-free Kit (Ambion). RNA were labeled using the Quick Amp Labeling Kit One-color (Agilent) and hybridized onto a Whole Human Genome Microarray, 4x44K (Agilent) as recommended by the manufacturer. Arrays were scanned with DNA Microarray Scanner (Agilent), and data were extracted using Feature Extractor (Agilent).

first: Oleg

last: Mediannikov

first: Renaud

last: Vincentelli

first: Grégory

last: Gimenez

first: Cristina

last: Socolovschi

first: Sophie

last: Edouard

first: Jean-Louis

last: Mège

first: Christian

last: Cambillau

first: Didier

last: Raoult


title: Gene expression analysis of 4T1 tumors expressing mouse urokinase plasminogen activitor (uPA)

status: Public on May 31 2012

city: MIAMI

first: YUQI

last: JING

state: FL

address: 1550 NW 10TH AVE PAP105

institute: University of Miami

summary: Analysis of uPA regulation of 4T1 tumor growth at gene expression level. The hypothesis tested in the present study was that overexpression of uPA in 4T1 tumor influence the tumor growth and metastasis related cell signaling pathway.

overall_design: 4T1 cells were stably transduced by lentiviral vector expressing mouse uPA or empty vector. After day 7 of inoculation of 4T1 cells into fatpad of Balb/c mice. Total RNA was extracted from tumor samples (triplicate) using Qiagen total RNA isolation kit. The Illumina MouseWG-6 v2.0 Expression BeadChip (Illumina, Wallingford, CT) was used for gene expression. The raw data from the fluorescence intensity measurements of each array experiment was processed using GeneSpringGX v.11.0 software (Agilent, Santa Clara, CA). Statistical analysis, fold change calculations, and hierarchical clustering of the data were also performed in GeneSpring software. Genes that expressed significantly differently with more than 1.5-fold change and a p-value of <0.05 with respect to controls were taken into consideration. Gene expression data were further validated by qRT-PCR analysis.  Pathway analysis was performed by MetaCore software (GeneGo, Inc, St. Joseph, MI).

first: Yuqi

last: Jing


title: Comparison of the effects of GMCSF, IL-4 and 15kDa Granulysin on elutriated monocytes: a 48 hour time point analysis

status: Public on May 19 2012

city: Bethesda

first: Luciano

last: Castiello

state: Maryland

address: 10 Center Drive

department: DTM

institute: NIH/CC

summary:
Gene expression profiling of elutriated monocytes cultured for 48 hours in RPMI-1640, 10% AB plamsa and one of the following: GMCSF (56IU/ml), IL-4 (2000 IU/ml), 15 kDa Granulysin (10 nM)
Sources tested: monocytes form 3 donors tested at time 0, 4 hours, 12 hours, 24 hours, 48 hours

overall_design: 5 time points were compared: day 0 (cells before start the culture), 4, 12, 24, 48 hours

first: Marianna

last: Sabatino


title: Leukemic hematopoietic stem cell FLA2

city: Ottawa

first: Theodore

last: Perkins

address: 501 Smyth Rd.

department: Cellular and Molecular Medicine

institute: Ottawa Hospital Research Institute

summary:
Sca1+Lineage-cKit+ fetal liver (FL) and bone marrow (BM) cells were sorted and infected with Hoxa9+Meis retroviral particles, which provided fully leukemic complement to hematopoietic cells. These cells were injected into mice and leukemia onset was monitored in vivo. Leukemic stem cell (L-HSC) frequencies of these primary leukemias were evaluated using limiting dilution stem cell transfer in secondary recipients. The L-HSC frequency is near absolute for the FLA2 leukemia (around 1 L-HSC per 1.4 total leukemic bone marrow cells), whereas the other leukemias (FLB1, FLB2 and BM-derived leukemias) generated within the same experiment have a wide range of L-HSC frequencies.
Keywords: other

overall_design: this experiment include 6 samples and 16 replicates

first: Guy

last: Sauvageau

first: Amelie

last: Faubert


title: The Mutational Landscape of Lethal Castrate Resistant Prostate Cancer

status: Public on May 23 2012

city: Ann Arbor

first: Scott

last: Tomlins

state: MI

address: 1400 E. Medical Center Dr., 5410 CCGC

institute: University of Michigan

type: Genome binding/occupancy profiling by genome tiling array

summary: Characterization of the prostate cancer transcriptome and genome has identified chromosomal rearrangements and copy number gains/losses, including ETS gene fusions, PTEN loss and androgen receptor (AR) amplification, that drive prostate cancer development and progression to lethal, metastatic castrate resistant prostate cancer  (CRPC)1. As less is known about the role of mutations2-4, here we sequenced the exomes of 50 lethal, heavily-pretreated metastatic CRPCs obtained at rapid autopsy (including three different foci from the same patient) and 11 treatment naïve, high-grade localized prostate cancers. We identified low overall mutation rates even in heavily treated CRPC (2.00/Mb) and confirmed the monoclonal origin of lethal CRPC. Integrating exome copy number analysis identified disruptions of CHD1, which define a subtype of ETS‑ prostate cancer. Similarly, we demonstrate that ETS2, which is deleted in ~1/3 of CRPCs (commonly through TMPRSS2:ERG fusions), is a prostate cancer tumor suppressor that can also be deregulated through mutation. Further, we identified recurrent mutations in multiple chromatin/histone modifying genes, including MLL2 (mutated in 8.6% of prostate cancers), and demonstrate interaction of the MLL complex with AR, which is required for AR mediated signaling. We also identified novel recurrent mutations in the AR collaborating factor FOXA1, which is mutated in 5 of 147 (3.4%) prostate cancers (both untreated localized prostate cancer and CRPC) , and showed that mutated FOXA1 represses androgen signaling and increases tumor growth in vitro and in vivo. Proteins that physically interact with AR, such as the ERG gene fusion product, FOXA1, MLL2, UTX, and ASXL1 were found to be mutated in CRPC, suggesting novel drivers of prostate cancer progression and potential resistance mechanisms to anti-androgen therapies. In summary, we describe the mutational landscape of a heavily treated metastatic cancer, identify novel mechanisms of AR signaling deregulated in prostate cancer, and prioritize candidates for future study.

overall_design: Gene expression profiling and array CGH (aCGH) was performed on matched benign prostate tissues (n=28), localized prostate cancer (n=59), and metastatic castrate resistant prostate cancer (CRPC, n=35). For gene expression profiling, frozen prostate tissue samples (channel 2), were hybridized against a commercial pool of benign prostate tissue (Clontech, channel 1). For aCGH, frozen prostate tissue samples (channel 2) were hybridized against a commerical sample of Human Male Genomic DNA (Promega, channel 1).

first: S

middle: A

first: A

last: Chinnaiyan


title: Effect of isoflavone agonists of IRF-3 on response to RNA viruses

status: Public on May 18 2012

city: Seattle

first: Michael

last: Katze

address: Rosen Building 960 Republican St.

department: Microbiology

institute: University of Washington

summary: There is a growing need for novel antiviral therapies that are broad-spectrum, effective, and not subject to resistance due to viral mutations. Using high-throughput screening methods, including computational docking studies and an ISG54-luciferase reporter assay, we identified a class of isoflavone compounds that act as specific agonists of innate immune signaling pathways and cause activation of the IRF-3 transcription factor.  The objective of the microarray study was to examine the biological pathways associated with global gene expression changes following agonist treatment.

overall_design: Total RNA isolation and mRNA amplification were performed on equal masses of total RNA from MRC5 cells treated with either DMSO (negative control; n=3), or 10μM of the isoflavone agonist KIN 101 (n=3) at 20 hours post treatment. As a positive control for response to an RNA virus, total RNA isolation and mRNA amplification was performed on equal masses of total RNA from MRC5 cells infected with Sendai virus (n=3) at 20 hours post infection.

first: Kristin

last: Bedard

first: Myra

last: Wang

first: Sean

last: Proll

first: Yueh-Ming

last: Loo

last: Gale Jr

first: Shawn

last: Iadonato


title: Hepatic Gene Expression Profiling of 5'AMP Induced Hypometabolism in Mice

status: Public on Jun 20 2012

city: Houston

first: David

middle: S

last: Loose

state: TX

address: 6431 Fannin St, MSB 4.130

department: Integrative Biology & Pharm

institute: University of Texas

summary:
Mice injected IP with 5'-AMP enter a hypometabolic state that is an induced hybernation (AIHM). Recovery from this AIHM is marked by reverse flip (RF) behavior
Illumina arrays were used to profile control, AIHM and RF aminals in RNA prepared from the liver.

overall_design: Animals were injected with vehicle or 0.5 mg/g body weight 5'-adenosine monophosphate. At 6 hours (AIHM) or 12 hours (RF) animals were killed and total RNA prepared from the liver.

first: Zhaoyang

last: Zhao

first: Cheng

last: Lee


title: Genome-wide analysis of E157D PPARγ transcriptional activity in NIH-3T3 fibroblasts

status: Public on May 16 2012

first: Philippe

last: Campeau

address: 1 Baylor Plaza

department: Molecular and Human Genetics

institute: Baylor College of Medicine

summary: The E157D PPARγ mutation presents as an atypical case of familial partial lipodystrophy and diabetes in a human cohort and has a novel molecular mechanism. The mutation is located in the DNA-binding domain, has no dominant negative activity but disrupts transcription activation after the protein has bound the DNA. The mutation causes a transcriptional activation defect on many PPARγ target genes, while some genes are induced normally. A small number of non-PPARγ target genes are induced by the E157D mutant, possibly leading to the atypical features in this cohort.

overall_design: mRNA was amplified from total RNA collected from NIH-3T3 cells expressing either wild-type or E157D PPARγ through lentiviral infection. Cells were treated with DMSO or 20µM rosiglitazone for 24 hours prior to RNA isolation in three independent experiments.

first: Olga

last: Astapova

first: Rebecca

last: Martins

first: Jean

last: Bergeron

first: Patrick

last: Couture

first: Robert

last: Hegele

first: Todd

last: Leff

first: Claude

last: Gagné


title: Tissue-specific differentiation of a circulating CCR9- pDC-like common dendritic cell precursor

city: Singapore

first: Pavandip Singh

last: Wasan

address: 8A Biomedical Grove, #03-06, Immunos

department: Bioinformatics

institute: Singapore Immunology Network

summary: Committed precursors of conventional dendritic cells (pre-cDCs) derived from the common DC progenitor which differentiate into cDC subpopulations in peripheral tissues have been identified, but committed precursors for plasmacytoid DCs (pDCs) have not been found. Here we show that CDP-derived ‘CCR9- MHCIIlow BST2+ Siglec-H+ pDCs from murine bone marrow which enter the circulation and peripheral tissues have a common DC precursor function in vivo in the steady state. Upon adoptive transfer the fate of CCR9- pDC-like precursors is governed by the tissues they enter. In the bone marrow and liver most transferred CCR9- pDC-like precursors differentiate into CCR9+ pDCs, whereas in peripheral lymphoid organs, lung and intestine they can give rise to CCR9+ pDCs and cDCs. Thus, CCR9- pDC-like cells are novel CDP-derived circulating DC precursors with pDC and cDC potential, whose final differentiation depends on tissue-specific factors allowing adaptation to local requirements.

overall_design: Total RNA obtained from CCR9- pDC-like common DC progenitors and CCR9+ pDCs was compared for differential gene expression. 3 independent isolations were performed for the 2 samples. 6 arrays were run in total.

first: Andreas

last: Schlitzer

first: Pavandip

first: Florent

last: Ginhoux

first: Anne

last: Krug


title: Gene expression analysis of wild type and KAP1 KO splenic B cells

status: Public on May 17 2012

city: Milan

first: Francesca

middle: R.

last: Santoni de Sio

address: via Olgettina 58

department: SR-TIGET

institute: San Raffaele Scientific Institute

summary: Chromatin remodeling is fundamental for B cell differentiation. Here, we explored the role in this process of KAP1, the cofactor of KRAB-ZFP transcriptional repressors. B lymphoid-specific Kap1 knockout mice displayed reduced numbers of mature B cells, lower steady-state levels of antibodies and accelerated rates of decay of neutralizing antibodies following viral immunization. Transcriptome analyses of Kap1-deleted B splenocytes revealed an upregulation of PTEN, the enzymatic counter-actor of PIK3 signaling, and of genes encoding DNA damage response factors, cell-cycle regulators and chemokine receptors. ChIP/seq studies established that KAP1 bound at or close to a number of these genes, and controlled chromatin status at their promoters. Genome-wide, KAP1-binding sites avoided active B cell-specific enhancers and were enriched in repressive histone marks, further supporting a role for this molecule in gene silencing in vivo. Likely responsible for tethering KAP1 to at least some of these targets, a discrete subset of KRAB-ZFPs is enriched in B lymphocytes. This work thus reveals the role of KRAB/KAP1-mediated epigenetic regulation in B cell development and homeostasis.

overall_design: Follicular (FO) and Transcriptional 2 Follicular Progenitor (T2-FP) B cells were sorted out from 3 CD19-Cre/Kap1flox (KAP1 KO in the B lineage) mice and 3 wt/Kap1flox littermate controls

first: Adamandia

last: Kapopoulou

first: Didier

last: Trono


title: Retinal gene expression of low-density lipoprotein receptor-related protein 5 (Lrp5) knockout mice

status: Public on May 22 2012

city: Boston

first: Jing

last: Chen

address: 300 Longwood Ave.

department: Ophthalmology

institute: Children's Hospital Boston/Harvard Medical School

summary: Retinal gene expression was assessed from postnatal day (P) 8 old low-density lipoprotein receptor-related protein 5 (Lrp5) knockout mice with a Illumina mouse-WG6 expression BeadChip.

overall_design: RNA was extracted from the retinas of P8 Lrp5 knockout and wild type mice (n=3 each group). Total RNA (1ug each) were reverse transcribed, followed by a single in vitro transcription amplification to incorporate biotin-labeled nucleotide, and subsequent hybridization and staining with strepatavidin-Cy3 according to the manufacturer’s instructions.

first: Lois

middle: E

last: Smith


title: Carnitine palmitoyltransferase 1A (CPT1A): a transcriptional target of PAX3-FKHR and mediates PAX3-FKHR-dependent motility in alveolar rhabdomyosarcoma cells

city: Memphis

first: Yong-Dong

last: Wang

state: TN

address: 262 Danny Thomas Pl, MS1135

institute: St. Jude Children's Research Hospital

summary:
Background: Alveolar rhabdomyosarcoma (ARMS) has a high propensity to metastasize, leading to its aggressiveness and a poor survival rate among those with the disease. More than 80% of aggressive ARMSs harbor a PAX3-FKHR fusion transcription factor, which regulates cell migration and promotes metastasis, most likely by regulating the fusion protein's transcriptional targets. Therefore, identifying druggable transcription targets of PAX3-FKHR that are also downstream effectors of PAX3-FKHR-mediated cell migration and metastasis may lead to novel therapeutic approaches for treating ARMS.
Methods: To identify genes whose expression is directly affected by the level of PAX3-FKHR in an ARMS cellular-context, we first developed an ARMS cell line in which PAX3-FKHR is stably down-regulated, and showed that stably downregulating PAX3-FKHR in ARMS cells significantly decreased the cells' motility. We used microarrays analysis to identify genes whose expression level decreased when PAX3-FKHR was downregulated. We used mutational analysis, promoter reporter assays, and electrophoretic mobility shift assays to determine whether PAX3-FKHR binds directly and specifically to the promoter region of the target gene. We used siRNA and pharmacologic inhibitor to downregulate the target gene of PAX3-FKHR and investigated the effect of such downregulation on cell motility,
Results: We found that When PAX3-FKHR was downregulated, the expression of carnitine palmitoyltransferase 1A (CPT1A) decreased. We showed that PAX3-FKHR binds directly and specifically to a paired-domain binding-site in the CPT1A promoter region, indicating that CPT1A is a novel direct transcriptional target of PAX3-FKHR. Furthermore, downregulating CPT1Adecreased cell motility in ARMS cells, indicating that CPT1A is a downstream effector of PAX3-FKHR-mediated cell migration and metastasis.
Conclusions: Taken together, we have identified CPT1A as a novel direct transcriptional target of PAX3-FKHR and revealed the novel function of CPT1A in promoting cell motility. CPT1A may represent a novel therapeutic target for the treatment of ARMS.

overall_design:
Identification of transcription targets of PAX3-FKHR in human alveolar rhabdomyosarcoma:
By stably knocking down PAX3-FKHR in human alveolar rhabdomyosarcoma cell line Rh30 and comparing the gene expression profile of the knockdown clone (KD) to the parental Rh30, transcription targets of PAX3-FKHR have been identified.
Gene expression in parental Rh30 cells was compared to that in either Rh30 cells stably expressing shRNA targeting PAX3-FKHR (KD) or control non-targeting shRNA (CON), in duplicate.

first: Lingling

last: Liu

first: Taosheng


title: TNF-α treated HUVECs: microRNA negative control VS. miR-181b

first: Mark

middle: W.

last: Feinberg

address: 77 Avenue Louis Pasteur

department: Medicine

institute: Brigham and women's hospital

summary: Transcriptional profiling of TNF-α treated HUVECs comparing cells transfected microRNA negative control with cells transfected with miR-181b.

overall_design: Two-condition experiment, miR negative control  VS. miR-181b transfected HUVECs. Biological replicates: 4 replicates of comparison of miR negative control VS. miR-181b

first: Xinghui

last: Sun

middle: W


title: Transcriptome profiles comparison between the B220+, CD27- and CD27+ NK cell subset

status: Public on May 15 2012

city: Montréal

first: Sylvie

last: Lesage

address: 5415, boul. de l'Assomption

institute: Hopital Maisonneuve-Rosemont

summary: The cell lineage origin of interferon-producing killer dendritic cells (IKDC), which exhibit prominent anti-tumoral activity, has been subject to debate. Although IKDC were first described as a cell type exhibiting both pDC and NK cell properties, the current view reflects that IKDC merely represent activated NK cells expressing B220, which were thus renamed B220+ NK cells. Herein, we further investigate the lineage relationship of B220+ NK cells with regards to other NK cell subsets. We surprisingly find that, upon adoptive transfer, B220- NK cells did not acquire B220 expression, even in the presence of potent activating stimuli. These findings strongly argue against the concept that B220+ NK cells are activated NK cells in vivo. Moreover, we unequivocally demonstrate that B220+ NK cells are highly proliferative and differentiate into mature NK cells upon in vivo adoptive transfer. Additional phenotypic, functional and transcriptional characterizations further define B220+ NK cells as immediate precursors to mature NK cells. By analogy to pre-B cells and pre-DC, we propose that B220+ NK cells should be renamed pre-NK cells. The characterization of these novel attributes to pre-NK cells will guide the identification of their ortholog in humans, contributing to the design of potent cancer immunotherapies.

overall_design: Total RNA from B220+ NK cells compared to total RNA from CD27- and CD27+ NK cell subsets all isolated ex vivo from the spleen of B6.Rag-/-. Triplicatas were analysed.

first: Fanny

last: Guimont-Desrochers

first: Geneviève

last: Boucher


title: Acute host transcriptonal response to A/Texas/36/91 influenza and A/Texas/36/91 influenza containing the NS1 gene from r1918 in A549 cells

status: Public on May 14 2012

first: Michael

last: Katze

summary: The “Spanish influenza” of 1918 claimed an unprecedented number of lives, yet the determinants of virulence for this virus are still not fully understood. Here, we used functional genomics and an in vitro human lung epithelial cell infection model to define the global host transcriptional response to the eight-gene 1918 virus. To better understand the role of the 1918 virus NS1 gene, we evaluated the host response to A/Texas/36/91 (a seasonal isolate of human influenza virus) and a reassortant of A/Texas/36/91 containing the 1918 NS1 gene.

overall_design: A549 cells were infected at a MOI=2 with either A/Texas/36/91 (Tx/91) or A/Texas/36/91 (Tx/91) containing the NS1 gene from r1918 influenza. Virus was allowed to bind to cells for 1 h at 4°C in serum-free infection medium supplemented with trypsin (1  g/ml). Mock-infected cells were treated with allantoic fluid instead of virus.  Three replicate wells were used for each infection condition at each time point. Cells were harvested for array analysis at 2, 6, and 24hr post-infection. Cells from three individual cultures were pooled for each condition for microarray.

first: Rosalind

last: Billharz

first: Hui

last: Zeng

first: Sean

last: Proll

first: Marcus

last: Korth

first: Sharon

last: Lederer

first: Randy

last: Albrecht

first: Alan

last: Goodman

first: Elizabeth

last: Rosenzweig

first: Terrence

last: Tumpey

first: Adolfo

last: Garcia-Sastre


title: Gene expression changes in cervical motor neurons of Hoxa5fl/fl::olig2CREHoxc5-/- mice

status: Public on Oct 27 2012

city: New York

first: Polyxeni

last: Philippidou

address: 550 1st ave

institute: NYU Medical Center

summary: To compare gene expression between cervical MNs of wt and Hox5 mutant embryos

overall_design: 6 samples 3 wt vs 3 mutant e12.5 embryos

first: Jeremy

last: Dasen


title: SCL006,icSARS CoV Urbani or icSARS Bat SRBD (spike receptor binding domain from the wild type strain Urbani to allow for infection of human and non-human primate cells) infections of the 2B4 clonal derivative of Calu-3 cells - Time course

status: Public on May 07 2012

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

overall_design:
Calu-3 cells were infected with either icSARS CoV or the cSARS Bat SRBD strain at MOI of 1.0.  Cells samples were collected at 0, 7, 12, 24, 30, 36, 48, 54, 60 or 72h post infection. Each infected sample was done in triplicate. (Triplicates are defined as 3 different wells, plated at the same time using the same cell stock for all replicates.)There are triplicate time-matched mock for each time point from the same cell stock as rest of samples. Culture medium (the same as what the virus stock is in) was used for the mock infections.
Contributor: The NIAID Systems Virology Center

first: Armand

last: Bankhead III

first: Jean

last: Chang

first: Amy

last: Sims

first: Ralph

last: Baric

first: Shannon

last: McWeeney


title: Host Regulatory Network Response in Calu-3 cell Infection with A/CA/04/2009 Influenza virus

status: Public on May 05 2012

first: Michael

last: Katze

summary: Differential Expression was determined in Calu-3 cells between mock infected and infection with A/CA/04/2009 Influenza virus at nime time points post infection.

overall_design: Calu-3 cells were infected with A/CA/04/2009 Influenza virus at MOI of 3, samples were collected 0,3,7,12,18, 24, 30, 36 and 48 hpi. Expression profiles and DE genes were determined for all time points.  There are 3 mock and infected replicates for each time point.

first: Chengjun

last: Li

first: Yoshi

last: Kawaoka

first: Amie

last: Eisfeld

first: G

middle: L

last: Law


title: Acute host transcriptonal response to r1918 influenza and r1918 influenza containing the NS1 gene from A/Texas/36/91 in A549 cells

summary: The “Spanish influenza” of 1918 claimed an unprecedented number of lives, yet the determinants of virulence for this virus are still not fully understood. Here, we used functional genomics and an in vitro human lung epithelial cell infection model to define the global host transcriptional response to the eight-gene 1918 virus. To better understand the role of the 1918 virus NS1 gene, we also evaluated the host response to fully reconstructed 1918 and reassortant 1918 virus containing the NS1 gene from A/Texas/36/91 (a seasonal isolate of human influenza virus).

overall_design: A549 cells were infected with either recombinant 1918 influenza, a chimeric virus that contained seven genes from recombinant 1918 and the NS1 from A/Texas/36/91 (Tx/91), or mock. Cells were harvested for microarray analysis at 2, 6, and 24hr following infection.

first: Rosalind

last: Billharz

first: Hui

last: Zeng

first: Sean

middle: C

last: Proll

first: Marcus

last: Korth

first: Sharon

last: Lederer

first: Randy

last: Albrecht


title: Differentiation of Human Embryonic Stem Cells under Hypoxia Conditions

city: Valencia

first: David

last: Montaner

address: C/ Eduardo Primo Yufera, 3

institute: CIPF

summary: Early development of mammalian embryos occurs in an environment of relative hypoxia. Nevertheless, human embryonic stem cells (hESC), which are derived from the inner cell mass of blastocyst, are routinely cultured under the same atmospheric conditions (21% O2) as somatic cells. We hypothesized that O2 levels modulate gene expression and differentiation potential of hESC, and thus, we performed gene profiling of hESC maintained under normoxic or hypoxic (1% or 5% O2) conditions. Our analysis revealed that hypoxia downregulates expression of pluripotency markers in hESC but increases significantly the expression of genes associated with angio- and vasculogenesis including vascular endothelial growth factor and angiopoitein-like proteins. Consequently, we were able to efficiently differentiate hESC to functional endothelial cells (EC) by varying O2 levels; after 24 hours at 5% O2, more than 50% of cells were CD34+. Transplantation of resulting endothelial-like cells improved both systolic function and fractional shortening in a rodent model of myocardial infarction. Moreover, analysis of the infarcted zone revealed that transplanted EC reduced the area of fibrous scar tissue by 50%. Thus, use of hypoxic conditions to specify the endothelial lineage suggests a novel strategy for cellular therapies aimed at repair of damaged vasculature in pathologies such as cerebral ischemia and myocardial infarction.

overall_design: 26 samples in a time course experiment. Gene expression is measured at 5 different time points and under 3 different oxygen levels. Two control samples are provided.

first: Joaquin

last: Dopazo

first: Miodrag

last: Stojkovic

first: Sonia

last: Prado-Lopez


title: The global gene expression profile of gain of function miR34c in osteoblast

status: Public on May 03 2012

first: Yangjin

last: Bae

address: One Baylor Plaza

department: Molecular Human Genetics

summary: To examine the unbiased global gene expression of gain of miR34c in committed osteoblast in mouse we have performed expression microarray. This approach will allow us to define the novel targets that are negatively regulated by over-expression of miR34c in osteoblast.

overall_design: Total RNA was isolated from primary calvaria from WT and GOF miR34c mouse (n=3) at the age of P3. WT primary calvarial samples were served as control.

first: Brian

last: Dawson


title: Amorfrutins are selective PPARγ agonists with potent antidiabetic properties

status: Public on May 02 2012

city: Berlin

first: Christopher

last: Weidner

address: Ihnestraße 63

department: Otto Warburg Laboratory

institute: Max Planck-Institute for Molecular Genetics

summary: Faced by an alarming incidence of metabolic diseases including obesity and type 2 diabetes worldwide, there is an urgent need for effective strategies for preventing and treating these common diseases. The nuclear receptor PPARγ (peroxisome proliferator-activated receptor gamma) plays a crucial role in metabolism. We isolated the amorfrutins from edible parts of the plants Glychyrrhiza foetida and Amorpha fruticosa, and identified these natural products as a new chemical class to treat insulin resistance and diabetes by selectively activating PPARγ. In contrast to existing synthetic PPARγ drugs, the amorfrutins display unique properties by separating insulin sensitization from unwanted side effects. In obese mouse models, amorfrutin treatment significantly improved important metabolic and inflammatory parameters. In summary, PPARγ activation by selective amorfrutins derived from edible biomaterial is a promising approach to combat metabolic diseases and other diseases in which PPARγ is involved in.

overall_design:
GSM701612-GSM701623: Male DIO C57BL/6 mice (age 18 wks), 3 groups (n=4 each after pooling of 8 samples per group). Mice were fed over 3 wks with high fat diet (HFD) without compound (vehicle), HFD with 4 mg/kg/d rosiglitazone or with 100 mg/kg/d amorfrutin 1. Liver RNA extracted. --> 4 biological replicates, vehicle vs. rosiglitazone or amorfrutin 1

GSM702299-GSM702344: Biological replicates (n = 3-4 each) of human primary adipocytes were treated with the following compounds for 24 hours. 10µM rosiglitazone, 10µM pioglitazone, 30µM telmisartan, 10µM nTZDpa, 30µM amorfrutin 1, 30µM amorfrutin 2, 30µM amorfrutin 3 or 30µM amorfrutin 4 vs. 0.1% DMSO (vehicle)


title: GY118F downstream effect in EpiSCs

status: Public on May 01 2012

city: Cambridge

first: Jose

last: Silva

address: Tennis Court Road

institute: University of Cambridge, centre for stem cell research

summary: This microarray was performed to gain insight in the effect of GY118F stimulation in EpiSCs. This array is part of the following paper to be published in Nature Communications: “JAK/STAT3 signalling is sufficient and dominant over antagonistic cues for the establishment of naïve pluripotency” by Anouk L. van Oosten, Yael Costa, Austin Smith & José C.R. Silva

overall_design: Gy0 a, gy0 b, gy0 c (triplicate samples for GY118F EpiSCs in N2B27+Activin+Fgf)   c0 a, c0 b, c0 c (triplicate samples for Control EpiSCs in N2B27+Activin+Fgf)   gy3 b, gy3 c (duplicate samples for GY118F EpiSCs in N2B27+Activin+Fgf stimulated with GCSF for 3 hours)   c3 a, c3 b, c3 c (triplicate samples for Control EpiSCs in N2B27+Activin+Fgf stimulated with GCSF for 3 hours)     Within the manucript genes of interest were defined as those that were significantly upregulated (P<0.01) above a 1.4 fold change  threshold in GCSF stimulated GY118F EpiSCs as compared to those not stimulated, but for which the expression did not significantly change upon GCSF stimulation in the control.   The fold change in expression was calculated by 2^absolute value of subtracted normalised data.


title: GY118F downstream targets in iPSCs and EpiSCs

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

overall_design: Refer to individual Series


title: Complement protein C1q modulates macrophage activation and inflammasome activity during the uptake of apoptotic cells

city: Irvine

first: Marie

middle: Emeline

last: Benoit

address: 2419 McGaugh Hall

department: Molecular Biology and Biochemistry

institute: UC Irvine

summary: In this study, we developed a unique system using primary human autologous lymphocytes and HMDMs to characterize the effect of C1q on macrophage gene expression profiles during the uptake of apoptotic cells. Our results showed that C1q bound to autologous apoptotic lymphocytes (AL) significantly modulated the response of HMDMs to LPS by increasing expression of cytokines, chemokines and effector molecules associated with immunoregulation and by directly suppressing caspase-1 dependent cleavage of IL-1beta.

overall_design: Human monocyte-derived macrophages (HMDMs) were incubated with early apoptotic lymphocytes (EAL), late apoptotic lymphocytes (LAL), C1q-EAL and C1q-LAL for 1h and then and stimulated with 10 ng/ml ultra-pure LPS. After 3 h of LPS stimulation, total RNA was extracted using the Illustra RNAspin Mini Isolation Kit. Gene expression profiles were studied using the Human Gene 1.0 ST array (Affymetrix). Slides were scanned using the Affymetrix GCOS software (performed by the microarray core facility at University of California, Irvine). Data processing and analysis were performed using JMP Genomics 5.0 software (SAS Institue Inc.). Significant differences in gene expression compared to unstimulated HMDMs were identified by ANOVA test using Holm multiple testing method and a false positive rate (alpha error) of 0.05

first: Elizabeth

last: Clarke

first: Pedro

last: Morgado

first: Deborah

last: Fraser

first: Andrea

last: Tenner


title: Differences in gene expression between murine Fnip1-null pre-B cells and wild type pre-B cells.

last: Iritani

address: 1959 NE Pacific Street

department: Comparative Medicine

summary: Analysis of gene expression in FACs-sorted pre-B cells derived from Fnip1-null and normal wildtype littermate mice.  3 arrays from 3 different mice per genotype were utilized to generate the expression data (mouse WG-6 v.2.0 beadchip (Illumina Inc, San Diego CA)) and statistics.  P-values are shown.

overall_design: Total RNAs were isolated from sorted B220+CD43+ cell from Fnip1-/- and WT mice (n=3)

first: Heon

last: Park


title: Analysis of hippocampal gene expression in adult and aged male BABL/c mice with or without running wheel access

city: Urbana

first: Rachel

middle: Ann

last: Kohman

address: 405 N Mathew

department: Psychology

institute: University of Illinois

summary: Currently, the mechanisms behind the anti-aging effects of exercise are not understood. The presented study conducted a microarray on hippocampal samples from adult (3.5 month-old) and aged (18 month-old) male BALB/c mice that were individually housed with or without running wheels for 8 weeks. Results showed that aging altered genes related to chromatin remodeling, cell growth, immune activity, and synapse organization compared to adult mice. Exercise was found to modulate many of the genes altered by aging, but in the opposite direction. For example, wheel running increased expression of genes related to cell growth and attenuated expression of genes involved in immune function and chromatin remodeling. Collectively, findings show that even late-onset exercise may attenuate age-related changes in gene expression and identifies possible pathways through which exercise may exert its beneficial effects.

overall_design: In total 20 samples (4 aged exercise, 4 aged sedentary, 6 adult exercise, and 6 adult sedentary) plus 4 technical replicates (24 total) were analyzed.

first: Sandra

last: Rodriguez-Zas

first: Keith

last: Kelley

first: Robert

last: Dantzer

first: Justin

last: Rhodes


title: miR-206 modulates the pathogenesis of muscular dystrophy of mdx mice

city: Dallas

first: Ning

last: Liu

address: 6000 Harry Hines Blvd.

department: Molecular Biology

institute: UT Southwestern Medical Center

summary: In response to skeletal muscle injury, adult myogenic stem cells, known as satellite cells, are activated and undergo proliferation and differentiation to regenerate new muscle fibers.  The skeletal muscle-specific microRNA, miR-206, is up-regulated in satellite cells following muscle injury, but its role in muscle regeneration has not been defined.  Here we show that skeletal muscle regeneration in response to cardiotoxin injury is impaired in mice lacking miR-206.  Loss of miR-206 also accelerates and exacerbates the dystrophic phenotype of mdx mice, a model for Duchenne muscular dystrophy.  MiR-206 promotes satellite cell differentiation and fusion to form multinucleated myofibers by suppressing a collection of negative regulators of myogenesis.  Our findings reveal an essential role for miR-206 in satellite cell differentiation during skeletal muscle regeneration and as a modulator of Duchenne muscular dystrophy.

overall_design: total RNA obtained from TA muscle of  mdx and 3 miR-206 KO; mdx mice at 3 months of age.

first: Eric

middle: N

last: Olson


title: Gene expression in 16 dpp Tex19.1-/- mouse testes

status: Public on Apr 27 2012

city: Edinburgh

first: Ian

last: Adams

address: Crewe Road

department: Genome Regulation

institute: MRC Human Genetics Unit

summary: Microarray experiment to identify changes in gene expression in 16 day post partum prepubertal Tex19.1-/- mouse testes. Tex19.1 is expressed in germ cells in testes. Tex19.1-/- mice have spermatogenic defects and errors in progression through meiosis. Data provides insight into the changes in gene expression in developing testes at the time when meiotic defects first start to become apparent.

overall_design: Testes from four Tex19.1-/- animals (ko) and four Tex19.1+/- littermate controls (het) are included in the analysis.

middle: R

first: Judith

last: Reichmann


title: GY118F downstream targets in iPS cells

last: Silva

summary: This microarray was performed to gain insight in the downstream targets of GY118F in iPS cells. This array is part of the following paper to be published in Nature Communications: “JAK/STAT3 signalling is sufficient and dominant over antagonistic cues for the establishment of naïve pluripotency” by Anouk L. van Oosten, Yael Costa, Austin Smith & José C.R. Silva

overall_design: The samples analysed were:  - GY118F iPS cells derived and maintained in N2B27 plus GCSF (t0, indicated in data as nlng t0 a),   -same cells but from which GCSF was withdrawn for 12 or 24 hours (t-12, t-24, indicated in data as nlng t-12 a and nlng t-24 a)   -and cells to which after withdrawal for 12 or 24 hours, subsequently GCSF was added back for 2 hours and 40 minutes (t-12+2h40m, t-24+2h40m, indicated in data as nlng t-12+2.4 a and nlng t-24+2.4 a).     To obtain the data as presented in the manuscript the following was done:The values obtained for t0 were subtracted from t-12 and t-24. The values for t-12 and t-24 were subtracted from t-12+2h40m and t-24+th40m respectively.   Subsequently the data was devided into genes that appeared to go down upon withdrawal of GCSF and up upon readdition and those with the converse gene expression pattern. Then a threshold of ≥1.4 fold change was applied. If a certain gene obeyed these criteria for all described comparisons, the gene was considered a potential downstream target.   The fold change in expression was calculated by 2^absolute value of subtracted normalised data.


title: Hedgehog pathway inhibitor saridegib (IPI-926) increases lifespan in a mouse medulloblastoma model

status: Public on Apr 20 2012

first: Michelle

last: Lee

address: 1100 Fairview Avenue, D4-100

department: Clinical Research Division

institute: Fred Hutchinson Cancer Research Center

summary: The Sonic Hedgehog (Shh) pathway drives a subset of medulloblastomas, a malignant neuroectodermal brain cancer, and other cancers. Small-molecule Shh pathway inhibitors have induced tumor regression in mice and patients with medulloblastoma; however, drug resistance rapidly emerges, in some cases via de novo mutation of the drug target. Here we assess the response and resistance mechanisms to the natural product derivative saridegib in an aggressive Shh-driven mouse medulloblastoma model. In this model, saridegib treatment induced tumor reduction and significantly prolonged survival. Furthermore, the effect of saridegib on tumor-initiating capacity was demonstrated by reduced tumor incidence, slower growth, and spontaneous tumor regression that occurred in allografts generated from previously treated autochthonous medulloblastomas compared with those from untreated donors. Saridegib, a known P-glycoprotein (Pgp) substrate, induced Pgp activity in treated tumors, which likely contributed to emergence of drug resistance. Unlike other Smoothened (Smo) inhibitors, the drug resistance was neither mutation-dependent nor Gli2 amplification-dependent, and saridegib was found to be active in cells with the D473H point mutation that rendered them resistant to another Smo inhibitor, GDC-0449. The fivefold increase in lifespan in mice treated with saridegib as a single agent compares favorably with both targeted and cytotoxic therapies. The absence of genetic mutations that confer resistance distinguishes saridegib from other Smo inhibitors.

overall_design: P21 to P36 PtcC/C mice were randomized to receive either saridegib (20 mg/kg per dose) for 6 weeks or vehicle control [5% (2-hydroxylpropyl)-β-cyclodextrin (HPBCD)] for 3 weeks administered via daily i.p. injection. Triplicate total RNA samples were collected for each of the two conditions.

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