title: Granulomatous response to Coxiella burnetii, the agent of Q fever: Activation of type I interferon-related genes

city: Lyon

first: Julien

last: Textoris

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

department: Medical Diagnostic Discovery Department (MD3)

institute: bioMérieux

summary: The formation of granulomas is associated with the resolution of Q fever, a zoonosis due to Coxiella burnetii; however the molecular mechanisms of granuloma formation remain poorly understood. We generated human granulomas with peripheral blood mononuclear cells and beads coated with C. burnetii, using BCG extracts as controls. A microarray analysis showed dramatic changes in gene expression in granuloma cells compared with peripheral blood mononuclear cells. About 60% of modulated genes were common to C. burnetii and BCG granulomas including M1-related genes. C. burnetii granulomas also expressed a specific transcriptional profile that was essentially enriched in genes associated with type I interferon response (IFI44, IFI44L, IFI6, OAS1, OAS2, OAS3, ISG15, IFIT1, IFITM2, IFITM3, MX1 and MX2). Real-time RT-PCR confirmed that C. burnetii especially increased the expression of interferon-stimulated genes in granulomas generated from controls or Q fever patients. Our results showed that granuloma formation is associated with a core of transcriptional response, but that the granulomatous response to C. burnetii is characterized by the activation of type I interferon-related genes, conferring a new role for type I interferon response in the control of C. burnetii infection.

overall_design: Human Peripheral Blood Mononuclear Cells (PBMC) were co-cultured with beads coated with  Mycobacterium bovis strain Bacille Calmette Guerin (BCG) extracts or Coxiella burnetii (C.burnetii) extracts  for 8 days and PBMC at day 0 were used as controls. For each condition ( unstimulated, BCG and C.burnetii), each microarray is a replicate of the same biological sample.

first: Delphine

last: Faugaret

first: Amira

last: Ben Amara

first: Amélie

last: Delaby

first: Catherine

last: Lépolard

first: Eric

last: Ghigo

first: Christian

last: Capo

first: Didier

last: Raoult

first: Jean-Louis

last: Mège


title: microRNA-27a contributes to rhabdomyosarcoma cell proliferation through suppression of RARA and RXRA

status: Public on May 04 2015

city: Padova

first: Gerolamo

last: Lanfranchi

address: Via U. Bassi, 58/B

department: CRIBI - Biotechnology Center and Biology Department

country: Italy

institute: University of Padova

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

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

Background: Rhabdomyosarcomas (RMS) are rare but very aggressive tumors of childhood that arise as a consequence of regulatory distruption of the growth and differentiation pathways of myogenic precursor cells. Based on morphology, two major RMS subtypes can be identified: embryonal RMS (ERMS) and alveolar (ARMS). So, it is essential to unravel the molecular mechanisms involved in cancer pathogenesis and in disease progression. MicroRNAs are endogenous small non-coding RNAs with a key role in tumorigenesis.
Methodology/Principal Findings: To better understand the involvement of miRNAs in RMS, we analyzed the expression profile of 8 different RMS cell lines (4 ARMS and 4 ERMS). The miRNA population from each cell line was compared to a reference sample consisting of a pool of each total RNA sample mixed in equal amount. We identified a 16 miRNAs signature that discriminates translocation positive (ARMS) and negative RMS (ERMS). We focused our attention on the role of miR-27a that is up-regulated in the more aggressive RMS cell lines (ARMS translocation positive) where probably it acts as an oncogene. miR-27a-overexpressing cells showed a significant enhance of the proliferation rate, paralleled by a decrease of cells in G1 phase. We demonstrated that miR-27a is implicated in cell cycle control by targeting the retinoic acid alpha receptor (RARA) and retinoic X receptor alpha (RXRA).
Conclusions: Our results demonstrated the potential of miRNA expression signature to better classify different RMS subtypes and settled the basis for a potential therapeutic role of miR-27a in RMS through modulation of retinoic acid receptors expression.

platform_organism:
Homo sapiens
Mus musculus

overall_design: Refer to individual Series


title: Gene Expression Profiles in erythroblasts and progenitor cells of mDia2 conditional KO mice

status: Public on Apr 30 2015

city: Chicago

first: Peng

last: Ji

state: IL

address: 303 E. Chicago Ave

department: Pathology

country: USA

institute: Northwestern University

summary: The goal of this study is to investigate the transcriptional network regulated by DIAPH3 gene (mDia2) using the conditional hematopoietic specific knockout mouse model, especially in the cell proliferation, cell survive (including oxidative stress), cell adhesion & migration, cell cycle and hematopoiesis pathway-related genes.

overall_design: Two groups of mice (WT vs KO) were sacrificed to purify erythroblast (Ter119+) cells from total bone marrow for RNA preparation. Each group contains three mice, the WT group includes 917,1125,1136 and 907,914,1122 belong to the conditional KO group. There is biological triplication in each group.

first: Yang

last: Mei


title: TK6 toxicogenomics reference database

status: Public on May 01 2015

city: Logan

first: Daniel

middle: R

last: Hyduke

state: UT

address: 4105 Old Main Hill ENGR 402S

department: Biological Engineering

institute: Utah State University

summary: TK6 cells were exposed to various perturbations and then the transcriptome profiles were collected at 4 hours to assemble a reference database to generate a Genotoxic / Nongenotoxic classifier using the nearest shrunken centroids method.

first: Henghong

last: Li

first: Renxiang

last: Chen

first: Jiri

last: Aubrecht

first: Albert

middle: J

last: Fornace Jr


title: Genome wide expression analysis of bone marrow derived macrophage cells (BMDMs) stimulated with IFNg and effect of Batf2 knockdown in BMDMs stimulated with IFNg

city: Yokohama

first: Harukazu

last: Suzuki

address: 1-7-22 Suehiro-Cho, Tsurumi-Ku,

department: Division of genomic technology

country: Japan

institute: Riken yokohama, Riken center for life science technology

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


title: Chondrosarcoma cells: sphere vs adherent

city: Naples

first: Angela

last: Nebbioso

state: Italy

address: Vico Luigi De Crecchio 7

department: Biophysics, Biochemestry and General Patology

institute: Seconda Università degli Studi di Napoli

summary: Transcriptional profiling of human chondrosarcoma sphere vs adherent cells

overall_design: Two different growth conditions, sphere vs adherent

first: Virginia

last: Tirino


title: Genome wide expession analysis of mouse bone marrow derive macrophage (Bmdm) cell stimulated with IFNg

summary:
Bmdm cells were differentiated for 10 days and harvested and culture in six well plate followed by cytokine stimulation
total RNA was harvested at 2, 4, 6, 24 hrs

overall_design: Total RNA was collected from bmdm cells stimulated with IFNg at different time point

first: Sugata

last: Roy


title: Modulation of murine bone marrow derived dendritic cells by IL-4

status: Public on Apr 28 2015

city: Edinburgh

first: Alasdair

last: Ivens

address: Kings Buildings

country: United Kingdom

institute: Centre for Immunity, Infection and Evolution

summary: The archetypal Th2 cytokine interleukin 4 (IL-4) has previously been shown to alternatively activate dendritic cells (DCs) both in vitro and in vivo.To more fully understand the impact of IL-4 dependent alternative activation of DCs, we used mRNA microarrays to define their transcriptional profile.

overall_design: RNAs were extracted from bone marrow-derived dendritic cells (BMDCs).  Two groups of samples were taken, with three biological replicates in each: control untreated, and treated with recombinant-IL4 (at 20 ng/ml).

first: Lucy

middle: H

last: Jones

first: Peter

middle: C

last: Cook

first: Graham

middle: D

last: Thomas

first: Alexander

middle: T

last: Phythian-Adams

first: Judith

middle: E

last: Allen

first: Andrew

middle: S

last: MacDonald


title: Deregulation of focal adhesion pathway mediated by miR-659-3p is implicated in bone marrow infiltration of stage M neuroblastoma patients

status: Public on Apr 20 2015

city: Genova

first: Sara

last: Stigliani

address: largo R Benzi 10

institute: IRCCS AOU San Martino-IST

summary: Presence of BM-infiltrating neuroblastoma (NB) cells occurs in about 50% of patients affected by this peculiar pediatric cancer. Children aged more than 18 months at diagnosis with metastatic NB are high-risk patients with 25-30% overall survival at 5 years, despite multimodal aggressive therapy. Little is known about the metastatic process in NB patients.   Hereby, we focused on miRNA expression profiles of BM-infiltrating as compared to those of primary NB tumors. For this purpose, we analyzed 22 BM-infiltrating NB cells, 22 primary NB tumors, and 4 paired BM-infiltrating and primary tumor specimens, all from patients with metastatic disease and aged > 18 months at diagnosis. Statistical analysis indicated that in human BM-infiltrating cells miR-659-3p was down-modulated as compared to primary tumors, in all sets of samples. Functional studies in HTLA and SH-SY5Y NB cell lines by miR-659-3p mimic and inhibitors demonstrated that miR-659-3p regulates the expression of the transcription factor CNOT1, that in turn regulates the expression of AU-rich element (ARE)-containing target genes AKT3, BCL2, THSB2 and CYR61, all belonging to the focal adhesion pathway. Indeed, CNOT1 expression was found significantly higher, whereas that of the ARE-containing target genes was significantly lower in BM-infiltrating cells than in primary tumors.   Our findings about a role of the focal adhesion pathway, regulated by miR-659-3p through CNOT1, in NB metastatic process are intriguing for the development of new therapeutic strategies aimed to interrupt the metastatic process.

overall_design: To evaluate the effect of miR-659-3p up- and down-regulation on gene expression,  HTLA-230 and SH-SY5Y cells were transfected with specific miR-659-3p mirVana™ mimic and inhibitor, respectively (Ambion, Life Technologies, Carlsbad, CA, USA, catalog# MC and MH 11582). Samples transfected with mirVana™ miRNA Mimic Negative Control #1 and mirVana™ miRNA Inhibitor Negative Control #1 were used as reference conditions. Transfection was performed at 20 nM miRNA concentration in OptiMEM© medium (Sigma-Aldrich), using Lipofectamin RNAiMAX© (Life Technologies), according to manufacturer’s protocol. Cells were then cultured for 48 hours, checked for viability and processed for total mRNA and miRNA extraction, as described below. Transfection experiments were performed twice with similar results.  HTLA-230 (kindly donated by Dr E. Bogenman, Los Angeles, USA) and SH-SY5Y (purchased from Banca Biologica and Cell Factory, Genoa, Italy) NB cell lines were cultured in RPMI 1640 medium supplemented with 10% heat inactivated FCS, 50 mg/ml streptomycin, 50 mg/ml penicillin and 2 mM glutamine (Sigma-Aldrich, Milan, Italy). The HTLA-230 cells present MYCN amplification and SH-SY5Y cells have normal MYCN status. Both cell lines were checked for MYCN amplification, morphology, proliferation rate and mycoplasma contamination, after thawing and within four passages in culture.  To evaluate the effect of miR-659-3p up- and down-regulation on gene expression, 1x106 HTLA-230 and SH-SY5Y cells were transfected with specific miR-659-3p mirVana™ mimic and inhibitor, respectively (Ambion, Life Technologies, Carlsbad, CA, USA, catalog# MC and MH 11582). Samples transfected with mirVana™ miRNA Mimic Negative Control #1 and mirVana™ miRNA Inhibitor Negative Control #1 were used as reference conditions. Transfection was performed at 20 nM miRNA concentration in OptiMEM© medium (Sigma-Aldrich), using Lipofectamin RNAiMAX© (Life Technologies), according to manufacturer’s protocol. Cells were then cultured for 48 hours, checked for viability and processed for total mRNA and miRNA extraction, as described below. Transfection experiments were performed twice with similar results.

first: Paola

last: Scaruffi

first: Maria

middle: V

last: Corrias

first: Corrado

last: Lagazio

first: Luca

last: Persico


title: A dominant role for the methyl-CpG-binding protein Mbd2 in controlling Th2 induction by dendritic cells [gene expression]

summary: Dendritic cells (DCs) direct CD4+ T cell differentiation into distinct T helper (Th) subsets that are vital for protection against diverse types of infection.  However, the mechanisms employed by DCs to initiate Th2 responses, which are important for immunity to helminth infection as well as being a major contributor to allergic disease, remain poorly understood.  We demonstrate a crucial role for methyl-CpG-binding domain-2 (Mbd2), a protein that links DNA methylation to repressive chromatin structure, in regulating DC gene expression and ability to promote Th2 immunity against either helminths or allergens.

overall_design: RNAs were extracted from murine (C57BL/6) Bone marrow-derived dendritic cells (BMDC) samples.  Two groups of samples (three replicates each) were processed: (1) wild type, and (2) a homozygous knock-out of the Mbd2 locus.

first: Heather

last: Owen

first: Aimée

middle: M

last: Deaton

first: Jessica

middle: G

last: Borger

first: Sheila

middle: L

last: Brown

first: Thomas

last: Clouaire

first: Gareth-Rhys

first: Rachel

last: Lundie

middle: K

last: Marley

first: Vicky

last: Morrison

first: Elisabeth

last: Wachter

first: Lauren

last: Webb

first: Tara

last: Sutherland

first: John

last: Grainger

first: Jim

last: Selfridge

middle: N

last: McKenzie

first: Susanna

last: Fagerholm

first: Rick

last: Maizels

first: Adrian

last: Bird


title: C-Myb+ erythro-myeloid progenitor-derived fetal monocytes give rise to adult tissue-resident macrophages

status: Public on Apr 23 2015

city: Singapore

first: jinmiao

last: chen

address: 8A Biomedical Grove, #04-06 Immunos

country: Singapore

institute: Singapore Immunology Network

summary: Although classified as hematopoietic cells, tissue-resident macrophages are selfrenewing and maintained independently of adult hematopoiesis. While most macrophages originate from embryonic precursors that seed tissues prior to birth, their exact origin is unknown. Using an in utero macrophage depletion strategy and fatemapping of yolk sac (YS) and fetal liver (FL) hematopoiesis, we found that YS macrophages are the main precursors of microglia, while most other macrophages derive from fetal monocytes. Both YS macrophages and fetal monocytes arise from erythro-myeloid progenitors (EMP) generated in the YS. In the YS, EMP gave rise to macrophages without monocytic intermediates, while EMP seeding the FL upon the establishment of blood circulation acquired c-Myb expression and gave rise to fetal monocytes that then seed embryonic tissues to differentiate into macrophages. Thus, adult tissue-resident macrophages established from HSC-independent embryonic precursors arise from two different developmental programs.

overall_design: 12 samples of progenitors, monocytes or macrophages are analyzed from 2 to 4 replicate. Each replicate derived from at least 5 embryos or adult mice

first: Guillaume

last: Hoeffel

first: Jinmiao

last: Chen

first: Yonit

last: Lavin

first: Donovan

last: Low

first: Francisca

middle: F

last: Almeida

first: Peter

last: See

first: Anna

last: Beaudin

first: Josephine

last: Lum

first: Ivy

first: Camilla

last: Forsberg

first: Michael

last: Poidinger

first: Francesca

last: Zolezzi

first: Anis

last: Larbi

first: Lai

last: Ng

first: Melanie

last: Greter

first: Burkhard

last: Becher

first: Igor

last: Samokhvalov

first: Miriam

last: Merad

first: Florent

last: Ginhoux


title: Genome wide expession analysis of effect of Batf2 knock down in bone marrow derived macrophage cells stimulated with IFNg

first: Harukazu

last: Suzuki

summary:
Bmdm cells were differentiated for 10 days and harvested and culture in six well plate followed by transfection with Batf2 ShRNA.
Media was replanished in every two days and on 10th day cells were stimulated with IFNg for 4 hrs. Total RNA was obtain after 4 hrs of stimulation.

overall_design: Total RNA was colloected from control ShRNA transfected Bmdm cells and Batf2 shRNA transfected Bmdm cells stimulated with/with out IFNg

first: Sugata

last: Roy


title: The neuronal transcription factor NeuroD and its impact on the regulation of dendricity and pigmentation of melanocytes in postinflammatory hyperpigmentation of human skin

status: Public on Apr 11 2015

city: BETHESDA

first: Vincent

middle: J.

last: Hearing

state: MD

address: BG 37 RM 2132B 37 CONVENT DR

institute: National Cancer Institute

summary: In order to test the gene expression profile in postinflammatory hyperpigmentation, micoarray studies were performed.

overall_design: Totally 14 subjects ( 7 at each phase) were treated by suction blister, and samples from treated area and corresponding control area ( from the same subjects) were taken at 1 week(t1), 2 weeks(t2), 4 weeks(t3), 6 weeks(t4), and 16 weeks(t5) after treatment. Paired samples from subject 6382 at  6th week were missing for microarray hybridization. Therefore, there are 138 array chips available for statistical analysis.

first: Dominik

last: Ebsen

first: Lanlan

last: Yin

first: Christoph

last: Smuda

first: André

last: Mahns

first: Ludger

last: Kolbe


title: Molecular and Histological Characterization of Age Spots

status: Public on Apr 15 2015

summary: In this study, we used immunohistochemical analysis and microarray analysis to investigate the mechanism underlying the development of age spots, focusing on the expression of specific markers associated with the functions and proliferation of melanocytes and keratinocytes

overall_design: 10 subjects of phototypes I or II (all female, age = 53-70) with various sizes and colors of age spots on their forearms were recruited for the study. Four mm whole skin punch biopsies were taken from age spots on the forearm of each subject and from a perilesional control area in the vicinity of each age spot.

first: Wonseon

last: Choi

first: Andre


title: Translatome and transcriptome profiling of SH-SY5Y cells treated with staphylococcal alpha-hemolysin oligomers

status: Public on Apr 01 2015

city: Povo

first: Toma

last: Tebaldi

state: Trento

address: via Sommarive n. 9

department: Centre for Integrative Biology

institute: University of Trento

summary:
Genome-wide analysis of translation has the potential to provide major contributions in understanding the pathophysiology of infection processes, given the complex interplay between pathogens and host cells. This study uncovers the reshaping undergoing in the translational control system of the host in response to staphylococcal α-hemolysin oligomers (rAHL).
Keywords: translatome profiling, polysomal profiling, polysomal RNA, translational control, translational profiling, polysome profiling, post-transcriptional regulation, staphylococcal α-hemolysin, pore forming toxins, PTF.

overall_design: The comparison between translatome and transcriptome profiling was used to discover mRNA-specific changes of the SH-SY5Y cells transcriptome and translatome in response to staphylococcal α-hemolysin oligomers (rAHL). To identify translationally regulated mRNAs, gene expression signals derived from the polysomal mRNA populations were compared by microarrays analysis to those obtained from total RNAs. Polysomal mRNA and total mRNA were isolated from SH-SY5Y cells treated with 3nM of extracted oligomers (rAHL) for 2 hours. Cells lysates were collected from untreated cells (control) and from treated cells. All experiments were run in biological triplicates.

first: Massimiliano

last: Clamer

first: Marta

last: Marchioretto

first: Paola

last: Bernabò

first: Valentina

last: Adami

first: Pamela

last: Gatto

first: Michael

last: Pancher

first: Alessandro

last: Quattrone

first: Gabriella

last: Viero


title: Protein phosphatase PP1-NIPP1 activates mesenchymal genes in HeLa cells

status: Public on Apr 04 2015

city: Leuven

first: Rekin's

last: Janky

address: Herestraat 49 Box 816

department: Nucleomics Core

country: Belgium

institute: VIB

summary: The deletion of the protein phosphatase-1 (PP1) regulator     NIPP1 is embryonic lethal during gastrulation, hinting at a key role of     PP1-NIPP1 in lineage specification. Consistent with this notion we show     here that a mild, stable overexpression of NIPP1 in HeLa cells caused a     massive induction of genes of the mesenchymal lineage, in particular     smooth/cardiac-muscle and matrix markers. This reprogramming was     associated with the formation of actin-based stress fibers and     retracting filopodia, and a reduced proliferation potential. The     NIPP1-induced mesenchymal transition required functional substrate and     PP1-binding domains, suggesting that it involves the selective     dephosphorylation of substrates of PP1-NIPP1.

overall_design: In total 16 samples were processed. Four different cell lines were analysed: HTO_parental, HTO_NIPP1wt, HTO_NIPP1m (= alias NIPP1-Pm) and HTO_NIPP1-Pa. For each cell line 4 replicates were obtained. The HTO_parental cell line is the control cell line. For the HTO_NIPP1wt and the HTO_NIPP1-Pa the 4 replicates were obtained from two replicates of two different transgenic cell lines expressing FlagNIPP1wt (cell line wt n°1 and 2) and FlagNIPP1-Pa (cell line n°1 and 2), respectively. Each cell line was derived from the same parental control cell line.

first: Nele

last: Van Dessel

first: Shannah

last: Boens

first: Aleyde

last: Van Eynde

first: Mathieu

last: Bollen


title: Gene expression comparison between WT, U17 snoRNA knockdown and U17 overexpression NIH-3T3 cells to identify target mRNAs regulated by U17 snoRNA

city: St Louis

first: Daniel

last: Ory

state: MO

address: Box 8086 660 S Euclid Ave

institute: Washington University

summary: Comparison of mRNA transcriptome after differential expression of U17 snoRNA. We hypothesiaed  that if U17 snoRNA regulates cholesterol homeostasis by modulating the expression of target mRNAs, genes that are differentially expressed by the loss-of-function or gain-of-function of U17 snoRNA would be candidate U17 targets. Results revealed negative regulation of target genes by U17 snoRNA, in which increasing dosage of U17 snoRNA from U17 knockdown to WT to U17 overexpression lead to decreases in target levels.

overall_design: Total RNA were isolated by TRIzol reagent (Invitrogen) from WT, U17 snoRNA KD (ShSnhg3 stable clone), and U17 snoRNA OE (pMDβglobinU17b stable clone) cells grown in LPDS media for 24 hours.

first: Sarah

last: Jinn


title: The kinase DYRK1A reciprocally regulates the differentiation of Th17 and regulatory T cells [array]

status: Public on Apr 29 2015

city: Boston

first: Bernard

last: Khor

state: MA

address: 185 Cambridge St MCPZN 7106

institute: Massachusetts General Hospital

summary: Using an unbiased chemical biology approach, we discover harmine as a novel regulator of Treg/Th17 differentiation. Harmine enhances Treg differentiation (working in conjunction with low levels of exogenous TGFb) and inhibits Th17 differentiation. Analysis of global gene expression of Tregs generated using low TGFb + harmine reveals significant similarity to Tregs generated using high TGFb only and suggests relevance of harmine-engaged mechanisms to IBD.

overall_design: Naïve CD4+CD62L+ T cells were purified from Foxp3GFP mice either by MACS or FACS, then cultured in either low TGFb + harmine or high TGFb conditions. GFP+ Tregs were sorted by FACS at day 4.

first: Gautam

last: Goel

first: Ramnik

last: Xavier


title: Molecular Signature of Erythroblast Enucleation in Human Embryonic Stem Cells

status: Public on Apr 14 2015

city: Paris

first: Hélène

last: LAPILLONNE

address: 27 Rue de Chaligny

department: UMR_S938 CDR Saint-Antoine

country: France

institute: UPMC Univ Paris 06

summary:
While enucleation is a critical step in the terminal differentiation of human red blood cells, the molecular mechanisms underlying this unique process remain unclear. To investigate erythroblast enucleation, we studied the erythroid differentiation of human embryonic stem cells (hESCs), which provide a unique model for deeper understanding of the development and differentiation of multiple cell types. First, using a two-step protocol, we demonstrated that terminal erythroid differentiation from hESCs is directly dependent on the age of the embryoid bodies. Second, by choosing hESCs in two extreme conditions of erythroid culture, we obtained
an original differentiation model which allows one to study the mechanisms underlying the enucleation of erythroid cells by analyzing the gene and miRNA (miR) expression profiles of cells from these two culture conditions. Third, using an integrated analysis of mRNA and miR expression profiles, we identified five miRs potentially involved in erythroblast enucleation.
Finally, by selective knockdown of these five miRs we found miR-30a to be a regulator of erythroblast enucleation in hESCs.

overall_design: We compared the gene expression profles of sample groupe A (EB9) to sample goupe B (EB20). Microarray analysis was performed in triplicate for both sample groups at each time point: Day0, cells at the level of embryoid body (A-D0, B-D0) and Day18 of erythroid culture(A-D18, B-D18) , Twelve RNA samples were hybridized to 12 Agilent 4X44K Whole Human Genome Oligo microarrays one color.

first: Shaghayegh

last: ROUZBEH

first: Ladan

last: KOBARI

first: Marie

last: CAMBOT

first: Christelle

last: MAZURIER

first: Nicolas

last: HEBERT

first: Anne-Marie

last: FAUSSAT

first: Charles

last: DURAND

first: Luc

last: DOUAY

first: Helene


title: Gene expression signatures of MEF2D-silencing hepatocellular carcinoma cells

status: Public on Apr 07 2015

city: ChongQing

first: leina

last: ma

address: Gaotanyan Main Street, No. 35

department: Southwest Hospital

country: China

institute: Third Military Medical University

summary: Global expression profiles in Huh7 after infection with Lv-shMEF2D and Lv-scrambled, as well as transfection with siRNA-MEF2D and siRNA-control, were compared to investigate the molecular mechanisms involved in MEF2D-mediated regulation of cell cycle.

overall_design: In order to investigate the molecular mechanisms involved in MEF2D-mediated regulation of cell cycle, we assessed gene expression profiles in Huh7 cells after infection with Lv-shMEF2D and Lv-scrambled, as well as transfection with siRNA-MEF2D and siRNA-control, by cDNA microarray. Analysis of global mRNA expression profile indicated a shift toward G2/M arrest in the cells after downregulating MEF2D expression. The genes that inhibit G2/M transition were found to be expressed in high level in MEF2D-downregulated group, as compared with control group. Meanwhile, mRNA abundance of G2/M transition-promoting genes, except CDC2 and CDC25C, was reduced when MEF2D expression was depressed in Huh7 cells

first: Leina

last: Ma

first: Jia

last: Liu

first: Limei

first: Guangjie

last: Duan

first: Qingliang

last: Wang

first: Yanmin

last: Xu

first: Feng

last: Xia

first: Juanjuan

last: Shan

first: Junjie

last: Shen

first: Zhi

last: Yang

first: Xiaochu

last: Yan

first: Ping

last: Bie

first: Youhong

last: Cui

first: Xiu-wu

last: Bian

first: Cheng

last: Qian


title: Gene expression profiling of Human 293 embryonic kidney (HEK293) cells transfected with 2 different siRNAs against WRN mRNA compared to cells transfected with scrambled siRNA.

status: Public on Mar 23 2015

city: Quebec

first: Michel

last: Lebel

state: Qc

address: 2705 Laurier Blvd, Local T-2-04

department: Centre Hospitalier de l’Université Laval (CHUL)

country: Canada

institute: Centre de Recherche du CHU de Québec

summary: Werner syndrome (WS) is a rare disorder characterized by the premature onset of a number of age-related diseases. The gene responsible for WS when mutated is believed to be involved in different aspects of transcription, replication, and/or DNA repair. We depleted the human WRN protein in HEK293 cells by transfecting them with small interference RNAs (siRNAs) against the WRN mRNA. The transcription profile of these transfected cells was compared to the transcription profile of HEK293 cells transfected with a scrambled siRNA that does not deplete the WRN protein.

overall_design: Microarray analyses were performed on HEK293 cells transfected with the siRNA against WRN mRNA (siWRN385 molecule 5'-UUAACCAGACUGUUAAGGCUCCAGG-3 (HSS111385, Invitrogen, Burlington, ON, Canada) or with a second siRNA against WRN mRNA ( siWRN387 molecule 5'-AUUAUAACAAUGCUCUUUGGUGCCC-3' (HSS111387, Invitrogen, Burlington, ON, Canada). HEK293 cells transfected with a scrambled siRNA that does not recognize the WRN mRNA was used as reference. Dye swap was also performed.

first: Eric

last: Paquet


first: Hélène

last: LAPILLONNE

sample_organism:
Homo sapiens
synthetic construct

platform_organism:
Homo sapiens
Mus musculus
Rattus norvegicus

overall_design: Refer to individual Series


title: Gene expression profile associated with loss of IFNAR signaling or loss of LTβR singlaing in spleen marginal zone macrophages (MZM) in autoimmune BXD2 mice

city: Birmingham

first: Hui-Chen

last: Hsu

state: AL

address: SHEL 311, 1825 University Blvd

department: Medicine

institute: University of Alabama at Birmingham

summary: Loss of the interactions between lymphotoxin and its receptor was associated with MZM apoptotic cell clearance defects in BXD2 mice whereas loss of IFNAR in BXD2 mice normalized the function of MZMs. The analysis also intended to use MZMs isolated from BXD2-Ifnar-/- mice and BXD2 mice treated with sLTbR-Fc to identify the common pathways regulating the MZM function in these mice.

overall_design: Samples were derived from MZMs of the spleen of BXD2 mice which exhibit spontaneous defects in MZMs, BXD2-Ifnar-/- mice which exhibit normalized MZMs, and BXD2 mice administered sLTβR-Fc which exhibit further defects in MZMs

first: Hao

last: Li

first: David

last: Crossman

first: John

last: Mountz


title: Effect of Clock deletion in parvalbumin-positive interneurons (PV-cells)

status: Public on Mar 19 2015

city: Cambridge

first: Yohei

last: Kobayashi

address: 52 Oxford Street

institute: Harvard University

summary: Identification of CLOCK-regulated genes expressed in PV-cells in mouse cerebral cortex.

overall_design: Total RNA obtained from sorted PV-cells at Zeitgeber time (ZT) 16.

first: Takao

last: Hensch


title: Expression profile of human breast cancer cells with CEBPB overexpression

status: Public on Mar 31 2015

city: Shanghai

first: Pei Yi

last: Xia

address: 320 Yue Yang Road

institute: Shanghai Institute of biochemistry and cell biology, Chinese Academy of Sciences

summary: CEBPB contributes to the migration of breast cancer cells. We used microarrays to detail the mechanism of CEBPB with downstream targets that drive breast cancer cell migration.

overall_design: CEBPB were overexpressed in MDA-MB231 cell for RNA extraction and hybridization on Agilent microarrays. We sought to obtain the mechanisms of CEBPB with downstream proteins that drive breast cancer cell migration.

first: Peiyi

first: Gaoxiang

last: Ge


title: Gene Expression profiles of Bapx1 sorted cells from hindlimbs (HL) of wildtype (WT) and Bapx1 null (HOMO) E12.5 mouse embryos

city: Potsdam

first: Thomas

last: Lufkin

state: NY

address: 8 Clarkson Avenue

department: Biology

institute: Clarkson University

summary: This study aims to look at gene expresion profiles between wildtype and Bapx1 knockout cells of the hindlimbs in a E12.5 mouse embryo. Instead of looking at the whole hindlimbs,only cells expressing Bapx1 were sorted by Fluroscent Activated Cell Sorting (FACS) and subjected to expression profiling by microarray.

overall_design: EGFP was knocked into the Bapx1 locus by homologous recombination in mESC followed by generation of stable mice line. Wildtype and homozygous embryos expressing EGFP was was used to dissected out the hindlimbs and Fluroscent activated cell sorting was used to sort out cell expressing Bapx1 as marked by EGFP. Total RNA was extracted and hybidized to an Illumina WG6 v2 mouse array.

first: Sumantra

last: Chatterjee


title: Gene Expression profiles of Bapx1 sorted cells from spleen of wildtype (WT) and BApx1 null (HOMO) E12.5 mouse embryos

summary: This study aims to look at gene expresion profiles between wildtype and Bapx1 knockout cells of the spleen in a E12.5 mouse embryo. Instead of looking at the whole spleen,only cells expressing Bapx1 were sorted by Fluroscent Activated Cell Sorting (FACS) and subjected to expression profiling by microarray.

overall_design: EGFP was knocked into the Bapx1 locus by homologous recombination in mESC followed by generation of stable mice line. Wildtype and homozygous embryos expressing EGFP was was used to dissected out the spleen and Fluroscent activated cell sorting was used to sort out cell expressing Bapx1 as marked by EGFP. Total RNA was extracted and hybidized to an Illumina WG6 v2 mouse array.


title: Gene Expression profiles of Bapx1 sorted cells from vertebral column of wildtype (WT) and Bapx1 null (HOMO) E12.5 mouse embryos

summary: This study aims to look at gene expresion profiles between wildtype and Bapx1 knockout cells of the vertebral column in a E12.5 mouse embryo. Instead of looking at the whole vertebral column ,only cells expressing Bapx1 were sorted by Fluroscent Activated Cell Sorting (FACS) and subjected to expression profiling by microarray.

overall_design: EGFP was knocked into the Bapx1 locus by homologous recombination in mESC followed by generation of stable mice line. Wildtype and homozygous embryos expressing EGFP was was used to dissected out the vertebral column and Fluroscent activated cell sorting was used to sort out cell expressing Bapx1 as marked by EGFP. Total RNA was extracted and hybidized to an Illumina WG6 v2 mouse array.


title: Translatome and transcriptome profiling of SH-SY5Y cells treated with sublytic doses of staphylococcal alpha-hemolysin

first: Toma

last: Tebaldi

summary:
Genome-wide analysis of translation has the potential to provide major contributions in understanding the pathophysiology of infection processes, given the complex interplay between pathogens and host cells. Informations about the translational state of mRNAs or the activity of RNA binding proteins and ncRNAs after treatment with sublytic doses of pore forming toxins are completely missing. This study uncovers the reshaping undergoing in the translational control system of the host in response to sublytic doses of staphylococcal α-hemolysin (AHL).
Keywords: translatome profiling, polysomal profiling, polysomal RNA, translational control, translational profiling, polysome profiling, post-transcriptional regulation, staphylococcal α-hemolysin, pore forming toxins, PTF.

overall_design: The comparison between translatome and transcriptome profiling was used to discover mRNA-specific changes of the SH-SY5Y cells transcriptome and translatome in response to sublytic doses of staphylococcal α-hemolysin (AHL). To identify translationally regulated mRNAs, gene expression signals derived from the polysomal mRNA populations were compared by microarrays analysis to those obtained from total RNAs. Polysomal mRNA and total mRNA were isolated from SH-SY5Y cells treated with sublytic doses (3nM) of AHL for 2 hours. Cells lysates were collected from untreated cells (control) and from treated cells. All experiments were run in biological triplicates.

first: Massimiliano

last: Clamer

first: Valentina

last: Adami

first: Alessandro

last: Quattrone

first: Gabriella

last: Viero


title: Gene Expression profiles of Bapx1 sorted cells from forelimbs (FL) of wildtype (WT) and Bapx1 null (HOMO) E12.5 mouse embryos

summary: This study aims to look at gene expresion profiles between wildtype and Bapx1 knockout cells of the forelimbs in a E12.5 mouse embryo. Instead of looking at the whole forelimbs, only cells expressing Bapx1 were sorted by Fluroscent Activated Cell Sorting (FACS) and subjected to expression profiling by microarray.

overall_design: EGFP was knocked into the Bapx1 locus by homologous recombination in mESC followed by generation of stable mice line. Wildtype and homozygous embryos expressing EGFP was was used to dissected out the forelimbs and Fluroscent activated cell sorting was used to sort out cell expressing Bapx1 as marked by EGFP. Total RNA was extracted and hybidized to an Illumina WG6 v2 mouse array.


title: Fate specification of neural plate border by canonical Wnt signaling and Grhl3 is crucial for neural tube closure.

status: Public on Apr 17 2015

city: Isumi

first: Chiharu

last: Kimura-Yoshida

state: Osaka

address: 840 Murodo-cho

department: Department of Molecular Embryology

institute: Osaka Medical Center and Research Institute for Maternal and Child Health

summary: During primary neurulation, the separation of a single-layered ectodermal sheet into the surface ectoderm (SE) and neural tube specifies SE and neural ectoderm (NE) cell fates. The mechanisms underlying fate specification in conjunction with neural tube closure are poorly understood. Here, by comparing expression profiles between SE and NE lineages, we observed that uncommitted progenitor cells, expressing stem cell markers, are present in the neural plate border/neural fold prior to neural tube closure.

overall_design: To identify what type of signaling pathways and transcriptional factors are involved in the fate specification between SE and NE cells during neurulation.

first: Kyoko

last: Mochida

first: Kristina

last: Ellwanger

first: Christof

last: Niehrs

first: Isao

last: Matsuo


title: Microarray analysis of gene expression in aging in mouse sabmandibular gland.

status: Public on Mar 17 2015

city: Shinagawa

first: Atsushi

last: Yamada

state: Tokyo

address: 1-5-8 Hatanodai

department: School of Dentistry

institute: Showa University

summary: Expression pattern of young (8 weeks old) and old (50 weeks old) mice sabmandibular gland was analyzed for aging dependent gene expression in sabmandibular gland.

overall_design: Total RNA  obtained from isolated mouse sabmandibular gland subjected to 50 weeks old mice compared to  8 weeks old mice.

first: Yoshiro

last: Saito

first: Tatsuo

last: Shirota

first: Ryutaro

last: Kamijo


title: Gene Expression profiles of Bapx1 sorted cells from gut of wildtype (WT) and Bapx1 null (HOMO) E12.5 mouse embryos

summary: This study aims to look at gene expresion profiles between wildtype and Bapx1 knockout cells of the gut in a E12.5 mouse embryo. Instead of looking at the whole gut, only cells expressing Bapx1 were sorted by Fluroscent Activated Cell Sorting (FACS) and subjected to expression profiling by microarray.

overall_design: EGFP was knocked into the Bapx1 locus by homologous recombination in mESC followed by generation of stable mice line. Wildtype and homozygous embryos expressing EGFP was was used to dissected out the gut and Fluroscent activated cell sorting was used to sort out cell expressing Bapx1 as marked by EGFP. Total RNA was extracted and hybidized to an Illumina WG6 v2 mouse array.


title: Identification of signatures specific to the epithelial or mesenchymal phenotypes from the heterogeneous mammary epithelial HMLER cells

city: Seattle

first: Anne

last: Grosse-Wilde

state: WA

address: 401 Terry Ave N

institute: Institute for Systems Biology

summary:
To understand the role of the epithelial-to-mesenchymal transition (EMT) and its reverse MET dynamics between health and disease, the identification of epithelial (E)- and mesenchymal (M)-specific genes is essential. The aim of the study was to derive genes that are characteristic E and M phenotypes in breast-derived cells. Their identification can help to understand the functional meaning of their expression and dynamic changes of individual cells, whole cell populations, and tumors, and even patients.

Breast cancer stem cells (CSCs) are thought to drive recurrence and metastasis. Their identity has been linked to the epithelial-to-mesenchymal transition (EMT) but remains highly controversial since -- depending on the cell line studied -- either epithelial (E) or mesenchymal (M) markers, alone or together, have been associated with stemness. Using distinct transcript expression signatures characterizing the three different E, M and hybrid E/M cell types, our data support a novel model that links a mixed E/M signature with stemness in 1) individual cells, 2) luminal and basal cell lines, 3) in vivo xenograft mouse models, and 4) in all breast cancer subtypes. In particular, we found that co-expression of E and M signatures was associated with poorest outcome in luminal and basal breast cancer patients, as well as with enrichment for stem-like cells in both E and M breast cell lines. This link between a mixed E/M expression signature and stemness was explained by two findings: first, mixed cultures of E and M cells showed increased cooperation in mammosphere formation (indicative of stemness). Second, single-cell qPCR analysis revealed that E and M genes could be co-expressed in the same cell. These hybrid E/M cells were generated by both E or M cells and had stem-like character since they displayed increased plasticity, produced ALDH1+ progenies self-renewal and mammosphere formation compared to the more differentiated E and M cell types. Thus, the hybrid E/M state reflecting stemness and its promotion by E-M cooperation offers a dual biological rationale for the robust association of the mixed E/M signature with poor prognosis, independent of cellular origin. Together, our model explains previous paradoxical findings that breast CSCs appear to be M in luminal cell lines but E in basal breast cancer cell lines. Our results suggest that targeting E/M heterogeneity by eliminating hybrid E/M cells and cooperation between E and M cell types could improve breast cancer patient survival independent of breast cancer-subtype.

overall_design:
We chose to identify genes characteristic of the E and M phenotypes isolated from the same individual, which are therefore independent of genetic differences that are the usual problem when comparing cancer cell lines derived from different individuals. HMLER cells are derived from normal mammary epithelial cells from a healthy individual (HMEC) and immortalized and transformed by transduction with hTERT, SV40LT and RAS oncogenes (Elenbaas et al., 2001). The parental HMLER cell line (HP) is heterogeneous as it usually contains both epithelial and mesenchymal subpopulations that can be identified and discriminated by inverse expression of CD24 and CD44 cell surface markers.
Single HMLER cells were sorted using flow cytometry and expanded in adhesion cultures. Morphology with respect to cobble stone-like epithelial phenotype or fibroblast-like solitary growing mesenchymal phenotypes was assessed. Epithelial clones were designated as E clones and mesenchymal clones were designated as M clones. Expression of the cell surface markers CD24 and CD44 strongly correlated with the E (CD24+/CD44-) and M (CD24-/CD44+) phenotypes, and only clones with 95% homogeneity for CD24+/CD44- or CD24-/CD44+ were used for determination of E versus M genes.
In order to determine genes specific for the respective epithelial or mesenchymal phenotypes, we generated gene expression arrays (Agilent) by comparing stable (with respect to morphology and cell surface CD24/CD44 profile) E clones (E1 to E6) with M clones (M2-M5), which were collected as biological replicates by at least two passages and usually a freezing cycle to test biological reproducibility of the gene expression profiles. Clones E1 to E3 and M2 and M3 were generated in a first batch of single cell-cloning, and after another freezing cycle of the parental HMLER cell line, clones E4 to E6 and M1, M4 and M5 were generated. Data normalization was performed in Genedata Analyst using central tendency followed by relative normalization. Transcripts showing differential expression (p value < 0.01) between two different morphological phenotypes (E clones E1, E2, E3, E4, E5, E6 and M clones M2, M3, M4, M5) were identified by Limma and ranked according to their effect size.
As control for genes that are not specific for homogeneous single cell-derived E clones or M clones, we generated gene expression arrays from the adherent heterogeneous parental HMLER cells (=HP) that has also an epithelial phenotype and about 10-30% CD24+/CD44- cells. M1 was a CD44+ clone that also contained a stable subpopulation of CD24+/CD44+ cells, could change phenotype and had either E or M morphology, which was thus excluded from the E versus M comparison. As a control for genes that are not specific for adhesion cultures (supposedly differentiated cultures, _adh) but rather for stem cell-enriched populations, we analyzed gene expression profiles from mammospheres (_sus) from the epithelial HP cell line and the mesenchymal clone M4.

Biological replicate adherent E cell lines - E1 cell line: E1_adh_0629, E1_adh_0826; E2 cell line: E2_adh_0616, E2_adh_0629, E2_adh_0826; E3 cell line: E3_adh, E3_adh_0629, E3_adh_0826; E4 cell line: E4_adh_0210, E4_adh_0607; E5 cell line: E5_adh_0210, E5_adh_0607; HP cell line: HP_adh_2210, HP_adh_0607c, HP_adh_0607sc, HP_adh_0629.

Biological replicates adherent M cell lines - M1: M1_adh_0210, M1_adh_0607; M2 cell line: M2_adh, M2_adh_0629, M2_adh_2210; M3 cell line: M3_adh, M3_adh_2210, M3_adh_2810; M4 cell line: M4_adh_0607, M4_adh_0210.

Biological replicates mammospheres - HP cells: HP_sus_0603_1, HP_sus_0603_2; M4 cells: M4_sus_0603_1, M4_sus_0603_2.

first: Adrian

last: Ozinsky

first: Rolf

last: Kuestner


title: In vivo-selected ID8 ovarian cancer cells display accelerated peritoneal metastasis accompanied with increased macrophage recruitment and M2 polarization

status: Public on Mar 16 2015

city: Dallas

first: yun

last: lian

state: TX

address: 5323 Harry Hines Blvd.

institute: UT Southwestern Medical Center

summary: Ovarian cancer is the leading cause of gynecological cancer related death. The overall 5 year survival rate is only 29%. Over 85% of ovarian cancer patients present with advanced stage III or IV disease characterized by intraperitoneal metastasis when diagnosed. However, the process and mechanism of ovarian tumor metastasis remain poorly understood partially because of the lack of a mouse model which could recapitulate the development of metastatic lesion in an appropriate timeframe. In order to generate a convenient ovarian cancer model with accelerated peritoneal metastasis, we performed an in vivo selection study using ID8 ovarian cancer cells to establish a rapid metastasizing mouse ovarian cancer cell line, designated ID8-M. Syngeneic mice with intraperitoneal inoculation of ID8-M cells showed measurable ascites average 35 days after the inoculation and survived only an average of 52 days, while those inoculated with parental ID8 cells showed measurable ascites after 67 days and survived over 81 days. Further analysis showed that, compared with ID8 tumors, ID8-M tumors resulted in more macrophages in the ascites; and compared to ID8 cells, ID8-M cells were more potent to promote macrophages to acquire a M2 phenotype. A microarray analysis provided information to explain the accelerated metastatic phenotype of ID8-M cells.

overall_design: Parental ID8 cells were intraperitoneally injected into 8-week-old, female C57BL/6 mice. Twelve weeks after the inoculation, mice were sacrificed while the mice displayed abundant ascites. Hemorrhagic fluid was collected from the peritoneal cavity, then centrifuged and lysed with red blood cell lysis buffer to remove erythrocytes and supernatant. After filtered with 70-μm strainer, cells were re-suspended with complete medium and seeded in 35 mm plates at 37 °C in a humidified 5% CO2 atmosphere. Four days later, cell clones were picked and after several times of trypsinization and passage, we obtained a new cell line designated ID8-M. For microarray analysis, 3 samples of ID8-M cells and 3 samples of parental ID8 cells were used.

first: Xuemei

last: Jia

first: Junfeng

last: Wang

first: Fatma

last: Saaoud

first: Stephen

last: Iwanowycz

first: Yuzhen

first: Fang

last: Yu

first: Quanzhen

last: Li

first: Daping

last: Fan


title: Transcriptomic analysis of human polarized macrophages: more than one role of alternative activation?

status: Public on Mar 12 2015

city: Parma

first: Eleonora

last: Derlindati

address: via gramsci, 14

institute: University of Parma

summary:
Background:  Macrophages are a heterogeneous cell population which in response to the cytokine milieu polarize in either classically activated macrophages (M1) or alternatively activated macrophages (M2). This plasticity makes macrophages essential in regulating inflammation, immune response and tissue remodeling and a novel therapeutic target in inflammatory diseases such as atherosclerosis. The aim of the study was to describe the transcriptomic profiles of differently polarized human macrophages to generate new hypotheses on the biological function of the different macrophage subtypes.

Methods and Results: M1 polarization was obtained by IFN-γ and LPS, M2a by IL-4, whereas IL-10 induced a “deactivated” state (M2c). Transcription profile of M1, M2a and M2c macrophages was performed at 6, 12 and 24h after polarization with Whole Human Genome Agilent Microarray technique. Gene Ontology (GO) classification revealed that M1 showed a significant up-regulation whereas M2a a down-regulation of GO terms involved in immunity and inflammation compared to resting macrophage (RM). Unexpectedly, canonical and non-canonical Wnt genes and gene groups, promoting inflammation and tissue remodeling, were up-regulated in M2a compared to RM. Key results were confirmed by real time-PCR.

Conclusion: Results from gene expression profile confirmed the specific properties of differentially polarized macrophages. However, the enhanced expression of canonical and non-canonical Wnt pathways in M2a suggests a possible dual role for alternative activation in the modulation of low-grade inflammation.

overall_design: Four-condition experiment, RM, M1, M2a, M2c. Three point of time course, three replicates for each condition. Dual color experiment, reference sample: human leucocytes


title: Histone Methyltransferase Ezh2 Controls Cell Adhesion and Migration through Direct Methylation of the Extra-Nuclear Protein-Talin

status: Public on Mar 09 2015

city: Singapore

first: Michael

last: Poidinger

address: #04-06, 8A Biomedical Grove

department: Bioinformatics

institute: Singapore Immunology Network

summary: Previously, we suggested a cytosolic role for the histone-methyltransferase Ezh2 in regulating lymphocyte activation, but molecular mechanisms underpinning this extra-nuclear function remained unclear. Here we show that Ezh2 regulates integrin-signaling and adhesion dynamics of neutrophils and dendritic cells. Ezh2 deficiency impaired integrin-dependent transendothelial migration of innate leukocytes and restricted disease progression in an animal model of multiple sclerosis. Direct methylation of talin, a key regulatory molecule in cell migration, by Ezh2 disrupted talin binding to F-actin and thereby promoted adhesion structure turnover. This regulatory effect was abolished by targeted disruption of Ezh2 interactions with Vav1. Our studies reveal a novel extra-nuclear function for Ezh2 in regulating adhesion dynamics with implications for leukocyte migration, immune responses and potentially pathogenic processes.

overall_design: Control and Ezh2-deficient bone marrow derived immature and mature dendritic cells were analyzed in triplicates

first: Merry

last: Gunawan

first: Nandini

last: Venkatesan

first: Jia

last: Loh

first: Jong

last: Wong

first: Hanna

last: Berger

first: Wen

last: Neo

first: Liang

middle: Y

first: Myint

last: Win

first: Yin

last: Yau

first: Tiannan

last: Guo

first: Peter

last: See

first: Sayuri

last: Yamazaki

first: Keh

last: Chin

first: Alexandre

last: Gingras

first: Susana

last: Shochat

first: Lai

last: Ng

first: Siu

last: Sze

first: Florent

last: Ginhoux

first: I-hsin

last: Su


title: A Grhl2-dependent gene network controls trophoblast branching morphogenesis [array]

status: Public on Mar 10 2015

city: Hannover

first: Christian

last: Hinze

address: Carl-Neuberg-Str. 1

department: Department of Nephrology and Hypertension

country: Germany

institute: Hannover Medical School

summary: Healthy placental development is essential for reproductive success; failure of the feto-maternal interface results in preeclampsia and intrauterine growth retardation. We found that grainyhead-like 2 (GRHL2), a CP2-type transcription factor, is highly expressed in chorionic trophoblast cells, including basal chorionic trophoblast (BCT) cells located at the chorioallantoic interface in murine placentas. Placentas from Grhl2-deficient mouse embryos displayed defects in BCT cell polarity and basement membrane integrity at the chorioallantoic interface, as well as a severe disruption of labyrinth branchingmorphogenesis.Selective Grhl2 inactivation only in epiblastderived cells rescued all placental defects but phenocopied intraembryonic defects observed in global Grhl2 deficiency, implying the importance of Grhl2 activity in trophectoderm-derived cells. ChIPseq identified 5282 GRHL2 binding sites in placental tissue. By integrating these data with placental gene expression profiles, we identified direct and indirect Grhl2 targets and found a marked enrichment of GRHL2 binding adjacent to genes downregulated in Grhl2−/− placentas, which encoded known regulators of placental development and epithelial morphogenesis. These genes included that encoding the serine protease inhibitor Kunitz type 1 (Spint1), which regulates BCT cell integrity and labyrinth formation. In human placenta, we found that human orthologs of murine GRHL2 and its targets displayed co-regulation and were expressed in trophoblast cells in a similar domain as in mouse placenta. Our data indicate that a conserved Grhl2-coordinated gene network controls trophoblast branching morphogenesis, thereby facilitating development of the site of feto-maternal exchange. This might have implications for syndromes related to placental dysfunction.

overall_design: Differential gene expression was examined by Illumina Mouse WG6 v2.0 Expression Bead Chip microarray analysis. Expression profiling was done at embryonic day 9.5 (E9.5) and E7.5; wild-type placenta versus Grhl2-/- placenta; n=3 biological replicates, respectively.

first: Katharina

last: Walentin

first: Max

last: Werth

first: Nadine

last: Haase

first: Saaket

last: Varma

first: Robert

last: Morell

first: Annekatrin

last: Aue

first: Elisabeth

last: Pötschke

first: David

last: Warburton

first: Andong

last: Qiu

first: Jonathan

last: Barasch

first: Bettina

last: Purfürst

first: Christoph

last: Dieterich

first: Elena

last: Popova

first: Michael

last: Bader

first: Ralf

last: Dechend

first: Anne

last: Staff

first: Zeliha

last: Yurtdas

first: Ergin

last: Kilic

first: Kai

last: Schmidt-Ott


title: Gene expression analysis in mesenteric arteries and veins in Crohn's disease compared to controls from nonIBD samples

status: Public on Mar 05 2015

city: Saint Louis

first: Gwendalyn

last: Randolph

address: 425 S Euclid Ave

department: Pathology and Immunology

institute: Washington University School of Medicine

summary: Histology in the mesentery pointed to altered blood vessels. This experiment was designed to define the differences in gene expression in vessels from Crohn's disease versus controls. Crohn's disease was separately evaluated in inflamed (central disease) areas and in adjacent noninflamed areas.

overall_design: Laser capture microdissection was carried out on Carnoy's fixed mesenteric samples, comparing normal arteries or veins with Crohn's inflamed or nonifnlamed arteries or veins.


title: A New Type of Human iPS Cells: Human Induced Hepatic Lineage-Oriented Stem Cells

status: Public on Mar 13 2015

city: Chuo-ku

first: Tetsuya

last: Ishikawa

address: 1-1, Tsukiji 5-chome

department: Research Institute

institute: National Cancer Center

type:
Expression profiling by array
Third-party reanalysis

summary: Human induced hepatic lineage-oriented stem cells (hiHSCs) can be established as a new type of human induced pluripotent stem cells (hiPSCs) with only some modifications of their culture conditions in both generation and self-renewal. hiHSCs were generated and expanded at a very high density under non-typical coculture with feeder cells in a chemically defined hiPSC medium . In detail, hiHSCs were generated from human non-hepatic cells by gene transfer with pantropic retrovirus vectors carrying the three transcription factor genes OCT3/4, SOX2, and KLF4. They were expanded at a very high density under non-typical coculture with mouse embryonic fibroblasts (MEF) in a chemically defined mTeSR1 medium on gelatin-coated dishes. Self-renewing hiHSCs expressed markers of both human embryonic stem cells (hESCs) and hepatocytes. The potential hepatic specification of hiHSCs was defined by their expression profiles of hepatic markers under a self-renewal culture.

overall_design: Using the AllPrep DNA/RNA Mini kit (Qiagen), total RNA was prepared from a hepatocellular carcinoma cell line (HuH-7) and human primary adult hepatocytes (obtained from the Health Science Research Resources Bank) as well as clones AFB1-1, NGC1-1, and NGC1-2 that were cultured on the MEFs (5 X 10^4 cells/cm^2) with mTeSR1 (StemCell Technologies) medium in gelatin-coated 100-mm dishes before long-term serial passage. The microarray study was carried out using a Whole Human Genome Oligo microarray 4X44K (Agilent). The analysis was performed by Bio Matrix Research according to Agilent technical protocols. Data from these experiments and the GEO database for hESCs (hES_ES01, GSM194392; hES_BG03, GSM194391; hES_H9, GSM194390) and hiPSCs (201B7, GSM241846) established from human adult fibroblasts (fibroblast, GSM242095) were analyzed with GeneSpring GX 11.5 software (Agilent). The 50th percentile of fluorescent intensity distribution was normalized across arrays.


title: Host Age is a Systemic Regulator of Gene Expression Impacting Cancer Progression

status: Public on Mar 03 2015

city: Mountain View

first: Afshin

last: Beheshti

state: CA

address: Moffett Blvd

institute: NASA Ames Research Center

summary: Given that aging is the major determinant of cancer incidence, and that cancer incidence is dictated in large part by processes modulating progression of existing subclinical cancers, we demonstrate that aging may be an organizing axis for identifying cancer progression-modulating processes. This would permit the broad understanding of the aging process to directly inform the question of what changes in aggregate host signaling favor cancer progression. Exploring this idea, a syngeneic murine Lewis lung cancer model in adolescent (68 days), young adult (143 days), middle-aged (551 days), and old (736 days) C57BL/6 mice was used to identify the signaling and functional processes varying significantly with host age. As anticipated, many of these specific endpoints proved to be major determinants of cancer progression. Older hosts demonstrated decreased angiogenesis, decreased metabolism and dysregulated apoptosis, all identified as hallmarks of cancer progression. Transforming growth factor 1, downregulated in older hosts, was also identified as a central player in these systemic processes. It is concluded that the strong host-age dependence here observed for tumor advancement facilitates the identification of an overarching tumor control dynamic exerted by the host. Revealed is insight into a mechanistic basis for the role of aging on modulation of tumor progression that may be therapeutically exploitable.

overall_design: For genome-wide expression profiling of tumor tissue, Mouse WG-6 BeadArray chips (Illumina, San Diego, CA) were used. Total RNA was amplified with the Ambion Illumina TotalPrep Amplification Kit (Ambion, Austin, TX) and labeled from all replicate biological samples for each condition. For tumor replicates, 20 tumor samples from adolescent, 10 from young adult, 10 from middle-aged, and 20 from old mice, were used. All replicate samples were run individually. Total RNA was isolated and purified using TRIzol (Invitrogen) and quantified using an Agilent Bioanalyzer. Samples were deemed suitable for amplification and hybridization if they had 28s/18s = 2:1, RIN >7. Total RNA of 500ng per sample was amplified using AmbionTotalPrep, and 1.5ug of the product was loaded onto the chips. Following hybridization at 55C, the chips were washed and then scanned using the Illumina iScan System. The data was checked with GenomeStudio (Illumina) for quality control. Data were corrected through normalization of the housekeeping genes, quantile normalized, then imported into MultiExperiment Viewer, MeV for analysis. Statistically significant genes were determined by applying a one-way ANOVA with an adjusted Bonferroni correction and false discovery rate (FDR) < 0.05 that resulted in a list of significant genes.

first: Sébastien

last: Benzekry

first: J

last: McDonald

first: Lili

last: Ma

last: Peluso

first: Philip

last: Hahnfeldt

first: Lynn

last: Hlatky


title: Genome-wide analysis of LPS or PBS challenged DUSP3-KO and WT female mice peritoneal macrophages gene expression

status: Public on Mar 11 2015

city: Liège

first: Souad

last: Rahmouni

state: Liège

address: 1, Avenue de l'hopital. B34

department: GIGA-Signal Transduction

institute: University of Liège

summary: Analysis of gene expression profile in peritoneal macrophage extracted from LPS or PBS challenged DUSP3-/- and WT mice.  DUSP3 deletion protects mice from sepsis and endotoxemia. We performed a microarray analysis to get insights into the differentially regulated pathways between WT and KO under inflammatory conditions.

overall_design: Total RNA obtained from isolated peritoneal macrophages isolated from DUSP3-/- and WT mice 36 hours after challenging them in vivo with PBS or with 6mg/kg of LPS.

first: Pratibha

last: Singh

first: Lien

last: Dejager

first: Mathieu

last: Amand

first: Emilie

last: Theatr

first: Maud

last: Vandereyken

first: Tinatin

last: Zurashvilli

first: Maneesh

first: Matthias

last: Mack

first: Steven

last: Timmerman

first: Lucia

last: Musumeci

first: Emmanuel

last: Dejardin

first: Tomas

last: Mustelin

first: Jo

middle: A

last: Van Ginderachter

first: Michel

last: Moutschen

first: Cécile

last: Oury

first: Claude

last: Libert


title: Targeting the MLL complex in castration-resistant prostate cancer [expression]

status: Public on Mar 02 2015

city: Ann Arbor

first: Marcin

middle: Piotr

last: Cieslik

state: Michigan

address: 500 S State St

department: Pathology

institute: University of Michigan

summary: Resistance to androgen deprivation therapies and increased androgen receptor (AR) activity are major drivers of castration-resistant prostate cancer (CRPC). Prior work has focused on targeting AR directly; however, the identification and targeting of co-activators of AR signaling remains an underexplored area. Here we demonstrate that the MLL (mixed-lineage leukemia) complex, a well-known contributor in MLL-fusion-positive leukemia, acts as a co-activator of AR signaling. AR interacts with the MLL complex via its subunit, menin. Small molecule inhibition of the menin-MLL interaction blocks AR signaling and inhibits tumor growth in vivo. Furthermore, we find that menin is up-regulated in CRPC and high expression correlates with poor overall survival. Our study identifies the MLL complex as a co-activator of AR that can be targeted in advanced prostate cancer.

overall_design: ASH2L / Menin / MLL1 were knocked down using shRNA /siRNA in two prostate cancer cell lines, VCaP and LNCaP.

first: Rohit

last: Malik

first: Yang

last: Shi

first: Xiaojun

last: Jing


title: Role of PTH on Gene Expression in Osteocytes of Cortical Long Bone from Mature Mice

city: San Antonio

first: stephen

middle: e

last: harris

address: 7703 Floyd Curl Drive

department: Periodontics

institute: U. of Texas Health Sci Center at San Antonio

summary: Femur and Tibia of Mice 3 months of age were dissected, growth plate removed, and serial digested with collagenase-trypsin to remove endosteal and periosteal cells. The cortical bone tubes, highly enriched in osteocye in their natural bone matrix environment where then cultured with and and with out PTH at 250nM for 24hr, RNA extracted and biotinylated cDNA prepared, and hybrized to Illumina MouseWG-6_V2 arrays.  Data was analyzed using Genome Studio-Gene Expression Module from Illumina.

overall_design: The design was to explore gene expression in osteocytes as they reside in their bone matrix with normal lacunar-canalicular structure, and the role of parathyroid hormone (PTH) on changes in gene expression due to hormone treatment.

first: Stephen

last: Harris


title: MiR-29a maintains mouse hematopoietic stem cell self-renewal by regulating Dnmt3a

city: NEW YORK

first: WENHUO

last: HU

email: huwenhuo@gmail.com, huw@mskcc.org

state: NEW YORK

address: 1275 YORK AVENUE

department: HOPP

institute: MEMORIAL SLOAN KETTERING CANCER CENTER

summary: Gene expression profiling from fine purified hematopoietic stem and progenitor cells of WT or miR-29a deletion. This anlaysis identified the up- and down-regulated genes from miR-29a deletion, and suggest that cell cycle regulators are significantly changed.  The results demonstrate that the HSC lacking of miR-29a appeared as committed progentiors from their gene expression patterns.

overall_design: Cells are sorted into hematopoietic stem cells (HSC, Lin-c-Kit+Sca-1+Slam1+CD34-) and committed progenitor cells (Prog, Lin-c-kit+Sca-1-) with > 90% purity using FACS AriaII machine.

first: Wenhuo

last: Hu

first: James

last: Dooley

last: Chung

first: Luisa

last: Cimmino

first: Siddhartha

last: Mukherjee

first: Bart

middle: d

last: Strooper

first: Adrion

last: Liston

first: Christopher

last: Park


title: Multifaceted maturation of monocyte-derived dendritic cells stimulated by intracellular bacteria

status: Public on Feb 27 2015

city: Lyon

first: Julien

last: Textoris

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

department: Medical Diagnostic Discovery Department (MD3)

institute: bioMérieux

summary:
Background: It has been shown that intracellular pathogens hijack DC functions to evade immune defense mechanisms. In this study, we investigated the responses of human monocyte derived DCs to four intracellular bacteria, Tropheryma whipplei, Coxiella burnetii, Brucella abortus and Orientia tsutsugamushi, responsible for human infectious diseases and known to infect myeloid cells.
Methods: Whole genome microarrays were assessed to define common and specific transcriptionnal responses to bacterial pathogen. Bacterial pathogen ability to affect DC maturation was assessed by measuring lymphoproliferation and endocytosis as well as phenotypic maturation markers (CD80, CD83, CD86 and HLA-DR) expression.
Results: We found that Coxiella burnetii, Orientia tsutsugamushi and Brucella abortus induced DC maturation assessed through decreased endocytosis ability, triggering lymphoproliferation, surface expression of HLA class II molecules and phenotypic changes, whereas Tropheryma whipplei did not induce DC maturation. As revealed by microarray analysis, the response of DCs to these bacteria consisted of a core associated with the maturation of DCs and signatures specific for each pathogen. The core response represented 10% of genes modulated in response to pathogens and consisted of general cellular processes including nucleotide binding, protein transport, cell fraction, protein kinase, cell cycle, mitochondrial membrane and cytoskeleton. The specific transcriptional signature induced by C. burnetii is associated with the communication between innate and adaptive immune cells and DC maturation. B. abortus signature specifically involved arachidonic acid and lipooxygenase pathways and O. tsutsugamushi signature involved type I and type III IFN responses.
Conclusion: This study demonstrates that intracellular bacteria use multifaceted pathways to induce DC maturation which may lead to unadapted immune response. The understanding of these pathways may be useful to improve our knowledge of bacterial recognition by the immune system but also intracellular bacterial diseases.

overall_design:
IL4/GM-CSF monocyte-derived dendritic cells were stimulated by T. whipplei, B. abortus, C. burnetii, O. tsutsugamushi and LPS during 6 hours. Common and specific signatures were determined by comparison with uninfected DCs.

moDCs (5.10^6) were plated in 6 well plates and stimulated with bacteria or LPS for 6 hours, and total RNA was extracted using the RNeasy minikit (Qiagen, adresse CA) and DNase treatment. The Agilent-014850 4X44k Human Whole Genome microarrays (Agilent Technologies, CA) representing 44,000 probes were used as recently described. Reverse transcription, sample labeling and hybridization were performed according to protocols specified by the manufacturer (One-Color Microarray-Based Gene Expression Analysis). Three samples per experimental condition were included in the analysis.

first: Laurent

last: Gorvel

first: Romain

last: Banchereau

first: Amira

last: Ben Amara

first: Jean-louis

last: Mège


title: EphA6 promotes angiogenesis and prostate cancer metastasis and is associated with human prostate cancer progression

city: shanghai

first: shibao

last: li

address: libing road

institute: chip

summary: Purpose: Metastasis remains the primary cause of prostate cancer (CaP) related death. Here, we investigate the molecular, pathologic, and clinical outcome associations of EphA6 expression and its role in CaP progression and metastasis.Experimental Design: The gene expression profiling of Eph receptors (Ephs) and their ephrin ligands was performed in CaP cell lines by real-time RT-PCR. Metastatic potential of EphA6 gene was analyzed by RNAi approaches in a spontaneous CaP mouse model. The mRNA expression of EphA6 was measured in 58 benign prostate hyperplasia (BPH) and 112 CaP samples. Results: Among the tested Ephs  and ligands, EphA6 is the only consistently overexpressed member in CaP lymph node metastatic cells. EphA6 knock-down (KD) in human PC-3M cells causes decreased invasion in vitro and reduced lung and lymph node metastasis in vivo. In addition, KD of EphA6 decreases tube formation in vitro and angiogenesis in vivo. Studies on the clinical samples demonstrate that EphA6 is overexpressed in the CaP tumor tissues compared with those from BPH patients. The correlation was identified between EphA6 expression and vascular invasion (P=0.004), neural invasion (P=0.002), PSA level (P=0.013), and TNM staging (P=0.021) in 112 CaP cases.Further, genome-wide gene expression analysis in KD of EphA6 cells identified a panel of genes, such as PIK3IPA, AKT1, and EIF5A2, which could be associated with EphA6-regulated cancer progression. Conclusions: These findings identify EphA6 as a potentially novel metastasis gene, and increased EphA6 mRNA expression positively correlates with CaP progression. The mechanisms to inhibit EphA6 expression might suppress CaP metastatic aggressiveness.

overall_design: Knock-down of EphA6 induced gene expression in human prostate cell:PC-3M/shEphA6-1, PC3M/shControl, CWR22rv1/shEphA6-1, and CWR22rv1/shControl cell line.

first: Shibao

last: Li

first: Chongwei

last: Xie

first: Bing

last: Su

first: Ming

last: Guan


title: Snai1 regulates cell lineage allocation and stem cell maintenance in the mouse intestinal epithelium

status: Public on Feb 28 2015

city: Parkville

first: Gary

last: Hime

state: Victoria

address: Grattan Street

department: Anatomy and Neuroscience

country: Australia

institute: University of Melbourne

summary:
Conditional knockout of Snai1 in the mouse intestinal epithlium results in apoptotic loss of crypt base columnar cells and bias towards differentiation of secretory lineages. In vitro organoid cultures derived from Snail conditional knockout mice also undergo apoptosis when Snai1 is deleted.
Snai1 is required for regulation of lineage choice and maintenance of CBC stem cells.

overall_design: Total RNA was extracted from organoids cultured for 24 hours after treatment with 0.5µM Tamoxifen derived from Villin-Cre and Villin-Cre, Snai1fl/fl mice.

first: Victoria

last: Perreau

first: Helen

last: Abud


title: Large scale gene expression analysis uncover new molecules related to biology and HPV mediated carcinogenesis in penile tumors

city: Sao Paulo

first: Fabio

middle: Albuquerque

last: Marchi

address: Av Dr Arnaldo

department: CTO

country: Brazil

institute: ICESP

summary: Gene expression microarray was used to evaluate altered genes related and non related to HPV infection status in order to identify potential molecular markers in penile cancer (PC).

overall_design: RNA was extracted from thirty-nine fresh frozen PC samples and submitted to gene expression microarray. The normal penile pool consisted of total RNA from five autopsy glands. Specific gene expression alterations were investigated by RT-qPCR. DNA was also extracted from penile samples and submitted to HPV genotyping.

first: Ariane

last: Busso


title: Genome-wide analysis of gene expression in mouse jejunum following exposure to the GLP-1R agonist exendin-4 or Fibroblast growth factor-7.

city: Toronto

first: Daniel

middle: J

last: Drucker

state: Ont

address: 600 University Ave TCP

department: LTRI

institute: Mount Sinai Hospital

summary: To determine whether Ex-4 and Fgf7 acitvate a subset of overlapping gene expression profiles in mouse jejunum.

overall_design: Total RNA islolated from mucosal scrapings taken from the jejunum of C57BL/6 male mice treated with a single dose of Ex-4 (10 nmol/kg, ip), human recombinant KGF/Fgf7 (1 mg/kg, ip), or vehicle/control (PBS) for 1 h (n=3 for each group), 5h (n=4 for each group), or 20 h (n=3 for each group).


title: Global expression profile of spleen DNAM-1+ and DNAM-1- NK cells.

status: Public on Feb 26 2015

city: Herston

first: Jason

middle: Sewoong

last: Lee

state: QLD

address: 300 Herston Road

department: Department of Cell and Molecular Biology

institute: QIMR Berghofer Medical Research Institute

summary:
We determined the global expression profile of DNAM-1+ and DNAM-1-  NK cell  purified by flow cytometry from 6 different groups of C57BL/6 WT mice.
Natural killer (NK) cells comprise a heterogeneous population of cells important for pathogen defense and cancer surveillance. However, the functional significance of this diversity is not fully understood. Here, we demonstrate through transcriptional profiling and functional studies that the activating receptor DNAM-1 (CD226) identifies two distinct NK cell functional subsets:  DNAM-1+ and DNAM-1- NK cells. DNAM-1+ NK cells have enhanced Interleukin 15 signaling, proliferate vigorously and produce high levels of inflammatory cytokines. By contrast, DNAM-1- NK cells that differentiate from DNAM-1+ NK cells, have greater expression of NK cell receptor related genes and are higher producers of chemokines. Together our findings highlight the existence of two distinct effector programs in innate lymphocytes controlled through DNAM-1 expression.

overall_design: NK1.1+NKp46+CD3- DNAM-1+ and DNAM-1-  NK cell were purified by flow cytometry from 6 different groups of C57BL/6 WT mice and total RNA were extracted

first: Ludovic

last: Martinet

first: Lucas

last: De Andrade

first: Camille

last: Guillerey

first: Jing

last: Liu

first: Fernando

last: Souza-Fonseca-Guimaraes

first: Dana

last: Hutchinson

first: Tatiana

middle: B

last: Kolesnik

first: Sandra

middle: E

last: Nicholson

first: Nicholas

middle: D

last: Huntington

first: Mark

last: Smyth


title: Genome wide expession analysis of mouse bone marrow derive macrophage (Bmdm) cell stimulated with cytokine and infected with mycobacterium tuberculosis

city: Yokohama

first: Harukazu

last: Suzuki

address: 1-7-22 Suehiro-Cho, Tsurumi-Ku,

department: Division of genomic technology

institute: Riken yokohama, Riken center for life science technology

summary: Bmdm cells were differentiated for 10 days and harvested and culture in six well plate followed by cytokine stimulation after 24 hrs cells were infected with mycobacterium tuberculosis to identify the host factors involved in infection.

overall_design: Total RNA was colloected from bmdm cells stimulated with cytokine and /or infected with mycobacterium tuberculosis in a time course experiments from 28hrs to 72 hrs.

first: Sugata

last: Roy


title: Inhibition of the miR-155 target NIAM phenocopies the growth promoting effect of miR-155 in B-cell lymphoma [ST486]

status: Public on Feb 20 2015

city: Groningen

first: Anke

last: van den Berg

address: Hanzeplein 1

department: Department of Pathology and Medical Biology

country: Netherlands

institute: University of Groningen, University Medical Center Groningen

summary: Several studies have indicated an important role for miR-155 in the pathogenesis of B-cell lymphoma. Highly elevated levels of miR-155 were indeed observed in most B-cell lymphomas with the exception of Burkitt lymphoma (BL). However, the molecular mechanisms that underlie the oncogenic role of miR-155 in B-cell lymphoma are not well understood. To identify the miR-155 targets relevant for B-cell lymphoma, we performed RNA immunoprecipitation of Argonaute 2 in Hodgkin lymphoma (HL) cells upon miR-155 inhibition and in BL cells upon ectopic expression of miR-155. We identified 54 miR-155-specific target genes in BL cells and confirmed miR-155 targeting of DET1, NIAM, TRIM32, HOMEZ, PSIP1 and JARID2. Five of these targets are also regulated by endogenous miR-155 in HL cells. Both overexpression of miR-155 and inhibition of expression of the novel miR-155 target gene NIAM increased proliferation of BL cells. In primary B-cell lymphoma NIAM-positive cases have significant lower levels of miR-155 as compared to NIAM-negative cases, suggesting that NIAM is also regulated by miR-155 in primary B-cell lymphoma. Thus, our data indicate an oncogenic role for miR-155 in B-cell lymphoma which involves targeting the tumor suppressor NIAM.

overall_design: Gene expression profiles were performed in ST486 Burkitt lymphoma cell line in 4 samples: ST486 EV (empty MXW-PGK-IRES-GFP vector) total cell lysate, ST486 miR-155 (ST486 with ectopic miR-155) total cell lysate, ST486 EV Ago2-IP, ST486 miR-155 Ago2-IP.

first: Izabella

last: Slezak-Prochazka

first: Joost

last: Kluiver

first: Debora

last: de Jong

first: Katarzyna

last: Smigielska-Czepiel

first: Gertrud

last: Kortman

first: Melanie

last: Winkle

first: Bea

last: Rutgers

first: Jasper

last: Koerts

first: Lydia

last: Visser

first: Arjan

last: Diepstra

first: Bart-Jan

last: Kroesen


title: Gene expression profiles of hepatic stellate cells isolated from Pdgfrb-knockout mice

status: Public on Feb 19 2015

city: Dallas

first: Yujin

last: Hoshida

address: 5323 Harry Hines Blvd

institute: University of Texas Southwestern Medical Center

summary: Background & Aims: Rapid induction of beta-PDGF receptor (beta-PDGFR) is a core feature of hepatic stellate cell activation, the hallmark of liver fibrogenesis. However, biological consequences of the induction are not well characterized. We aimed to determine the involvement of beta-PDGFR-mediated molecular pathway activation on hepatic stellate cells in liver injury, fibrogenesis, and carcinogenesis in vivo.   Methods: Loss and constitutive activation of beta-PDGFR were assessed in mouse models with either a stellate cell-specific beta-PDGFR knockout or the expression of an autoactivating mutation respectively. Liver injury and fibrosis were induced in two mechanistically distinct models: carbontetrachloride (CCl4) treatment and ligation of the common bile duct. Hepatocarcinogenesis with underlying liver injury/fibrosis was assessed by a single dose of diethylnitrosamine (DEN) followed by repeated injections of CCl4. Genome-wide expression profiling was performed isolated stellate cells from these models to determine deregulated pathways.  Results: Depletion of beta-PDGFR in hepatic stellate cells led to decreased histological liver injury, serum transaminases, collagen alpha 1(I) and alpha smooth muscle actin expression, and collagen deposition. Stellate cell proliferation was significantly reduced after acute hepatic injury in vivo. In contrast, autoactivation of beta-PDGFR in stellate cells accelerated liver fibrosis, most prominently after 6 weeks of CCl4 induced injury. There was no difference in development of DEN-induced pre-neoplastic loci according to the status of beta-PDGFR.   Conclusions: Depletion of beta-PDGFR in hepatic stellate cells attenuated the development of liver injury, fibrosis, and stellate cell proliferation in multiple animal models, whereas the constitutive activation of beta-PDGFR enhanced fibrosis. However, manipulation of beta-PDGFR alone did not reduce development of dysplastic nodules. These findings indicate that titration of receptor beta-PDGFR expression on stellate cells parallels fibrosis and injury, but may not impact the development of hepatic neoplasia alone.

overall_design: Hepatic stellate cells were isolated from liver of beta-PDGFR-wild-type or knockout mice, and treated with beta-PDGF ligand or vehicle control.

first: Peri

last: Kocabayoglu

first: Scott

last: Friedman


title: Defined conditions for the isolation and expansion of basal prostate stem cells of mouse and human origin [mouse]

city: Heidelberg

first: Eisen

last: Christian

state: (Click to Select US State)

address: Im Neuenheimer Feld 280

institute: German Cancer Research Center

summary: Isolation and culture of primary prostate epithelial stem/progenitor cells (PESC) has been proven difficult and ineffective. Here we present methods to grow and expand both murine and human basal PESCs long-term in serum- and feeder-free conditions. The method enriches for adherent mouse basal PESCs with a Lin-Sca1+ CD49f+Trop2high phenotype. Progesterone and sodium selenite are additionally required for the growth of human Lin-CD49f+Trop2high PESCs.  The gene expression profiles of expanded basal PESCs show similarities to ES cells and Lamin B1 and PRDX1 were identified as novel PESC markers. If transplanted in combination with urogenital sinus mesenchyme, expanded mouse and human PESCs generate ectopic prostatic tubules demonstrating their stem cell activity in vivo. The novel methods will facilitate the cellular, molecular and genomic characterization of normal and pathologic prostate glands of mouse and human origin.

overall_design: Murine prostate cells were seperately cultured under spheroid and adherent stem cell conditions and subsequently used for RNA extraction

first: Christian

last: Eisen

first: Thomas

last: Höfner


title: Defined conditions for the isolation and expansion of basal prostate stem cells of mouse and human origin

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

sample_organism:
Homo sapiens
Mus musculus

overall_design: Refer to individual Series


title: Gene expression after deletion of Bmp4 in the mouse optic vesicle

city: Saint Louis

first: David

middle: Cy

last: Beebe

state: MO

address: 660 S. Euclid Ave.

department: Ophthalmology and Visual Science

institute: Washington University School of Medicine

summary: Bmp4 was conditionally deleted from the mouse optic vesicle with Rx-Cre. The heads of wild type and knockout E10.5 mouse embryos were laser micodissected to isolate the lens ectoderm and prospective retina from three embryos of each genotype. Total RNA was purified and reverse transcribed and amplified using a NuGEN Ovation Pico WTA system V2 kit. cDNA was biotinylated and hybridized to Illumina Mouse6 V2 bead arrays.

overall_design: Three wild type and three knockout embryos were used. RNA obtained from the lens ectoderm or prospective retina (distal optic vesicle) was pooled, amplified and used for microarray analysis. Statistical analysis was performed using the values from the 25-50 beads on each array.

middle: C

first: Jie

last: Huang

first: Ying

last: Liu


title: Skeletal muscle myoblasts: GATA4-Wt, -KO, -OE; day 0, 3

status: Public on Feb 18 2015

city: Minneapolis

first: Genomics

last: Center

state: MN

address: 312 Church Street SE

institute: University of Minnesota

summary: Gene expression in satellite cell-derived primary myoblasts islolated from Gata4-loxP mice. Myoblasts were infected with nLacZ for control (Wt), Cre recombinase to knockout GATA4 (KO), or GATA4 expression vector to overexpress GATA4 (OE). Infected myoblasts were cultured in growth medium (day 0) then differentiated into myotubes in differentiation medium for 3 days (day 3).

overall_design: Total 18 samples. Three replicates in each myoblast; GATA4-Wt, -KO, and -OE myoblasts at day 0 and day 3.

first: Tomohide

last: Takaya

first: Atsushi

last: Asakura


title: Transcriptome and translatome profiling of CPX 90m effects in neuroblastoma cells CHP134

status: Public on Feb 04 2015

city: Povo

first: Toma

last: Tebaldi

state: Trento

address: via Sommarive n. 9

department: Centre for Integrative Biology

institute: University of Trento

summary:
Neuroblastoma (NB) is the most frequent extracranial solid tumour of childhood. Clinical courses are highly variable, ranging from spontaneous regression/maturation to rapid progression despite intensive multimodal therapy. The estimation of 5-year event free survival in high-risk patients of only about 40 % stresses an importance of novel therapeutic strategies. A number of iron chelators have demonstrated marked in vitro and in vivo anti-tumor activity and are currently being developed as novel anti-cancer agents. Therefore, the potential antitumor effect of iron chelators in NB cancer was investigated. Among the compounds tested, ciclopirox olamine (CPX) was shown to be one of the most effective intracellular iron chelators in NB cells. To unveil the molecular mechanisms underlying the effects of CPX on viability of NB cells, microarray analysis was performed in CHP134 control cells and cells treated with 5 µM CPX for 90 minutes. Inclusion of both total RNA (reflecting transcriptional status of the cells) and polysomal RNA (approximating the proteomic representation of the cells) provided us with a deeper understanding of changes in the cells upon CPX treatment.  Keywords: ciclopirox olamine, iron chelator, neuroblastoma, translatome profiling, transcriptome profiling.
Keywords: ciclopirox olamine, iron chelator, neuroblastoma, translatome profiling, transcriptome profiling, polysomal profiling, polysomal RNA, translational control, translational profiling, polysome profiling

overall_design: Microarray analysis was performed to enable a comprehensive view of the changes in the transcriptional and translational status of the cells in response to the treatment with an iron chelator CPX. Polysomal RNA and total RNA were isolated from vehicle-treated CHP134 cells and CHP134 cells treated with 5 µM CPX for 90 minutes. Each condition is represented by three biological replicates, i.e. the experiment was repeated starting each time from cells seeding yielding an independent RNA sample. In total, 12 samples corresponding to 4 conditions were subjected to microarray analysis.

first: Viktoryia

last: Sidarovich

first: Valentina

last: Adami

last: Greco

first: Alessandro

last: Quattrone


title: Nur77 overexpression in mouse skeletal muscle

city: Los Angeles

first: Lily

last: Chao

address: 4650 Sunset Blvd

institute: CHLA

summary: We isolated total RNA from gastrocnemius muscle of wildtype and muscle-specific Nur77 overexpressing transgenic mice to identify Nur77-mediated changes in gene expression. Findings confirmed changes in genes involved in carbohydrate metabolism and muscle development.

overall_design: 2 replicate Illumina Single Color Mouse WG-6_V2_0 chips were used. 6 wildtype and 6 transgenic mice overexpressing Nur77 in skeletal muscle were used.  RNA was isolated by Trizol and further purified through RNEasy column. RNA from 2 mice were pooled, for a total of 6 samples -- 3 wildtype and 3 transgenic.  The same samples were split into two technical replicate chips.  Each chip contains 3 wildtype and 3 transgenic samples.

first: Peter

last: Tontonoz

first: Omar

last: Cortez-Toledo

first: Kevin

last: Wroblewski

first: Cindy

last: Hong

first: Laura

last: Lim

first: Rogelio

last: Carranza

first: Orla

last: Conneely

first: Daniel

last: Metzger


title: Inactivation of Unr results in induction of differentiation of murine ES cells into the primitive endoderm lineage

status: Public on Feb 10 2015

city: Illkirch

first: Doulaye

last: Dembele

address: 1 rue Laurent Fries

department: Biopuces

institute: IGBMC

summary:
Unr (upstream of N-ras) is a cytoplasmic RNA-binding protein with cold shock domains, involved in regulation of messenger RNA stability and translation. To address the biological role of Unr, we inactivated the unr gene by homologous recombination in mice and embryonic stem (ES) cells. Embryos deficient for Unr die at mid-gestation, and the main phenotypic defects observed, growth deficiency and absence of neural tube closure, suggest a role of Unr in the balance proliferation/differentiation during early development. Here, we report that in Unr-null ES cell cultures, we observed a greater proportion of partially differentiated colonies, together with  dispersed, refractile cells with stellate morphology, reminiscent of primitive endoderm (PrE) cells. DNA microarray, immunostaining, and RNA analyses revealed that Unr-null ES cells express a set of PrE markers, including the GATA6 transcription factor, a key inducer of PrE. Although Unr-deficient cells did not downregulate the pluripotency regulators Oct4, Nanog and Sox2, they grew more slowly than the wild-type lines, and their clonogenicity was lower. Silencing of Unr by RNA interference in ES E14 (129 genetic background) resulted in similar phenotypic and molecular changes as those observed in unr-/- ES cells (C57Bl/6 background). Finally, we show that ectopic expression of Unr in unr-/- ES cells partially reverses the endoderm-specific gene expression and the differentiation phenotype.
We propose that Unr prevents the differentiation of ES cells into PrE, by controlling the stability of GATA6 mRNAs, since the decay of GATA6 mRNAs is increased in the absence of Unr. In summary, these results indicate that an essential function of Unr is to stabilize ES cells in a pluripotent state by repressing PrE gene expression.

Keywords: Transcriptome analysis of wild-type and unr K.O. ES cells.

overall_design: We have  compared the transcriptome of wild-type and unr-/- ES cells. Heterozygous unr+/- mice were intercrossed, and unr+/+ and unr-/- ES cell lines were established from individual blastocysts.  Total RNA were prepared from unr+/+ and unr-/- cells, either under growing conditions, or two or 24 hours after gamma-irradiation. Two or three replicates per condition.

first: Habiba

last: Elatmani

first: Virginie

last: Dormoy-Raclet

first: François

last: Dautry

first: Hélène

last: Jacquemin-Sablon


title: Genome-wide analysis of gene expression in mLTC-1 cells following siRNA-mediated Gata4 inhibition

status: Public on Feb 23 2015

city: Helsinki

first: Markku

last: Heikinheimo

address: Tukholmankatu 8

department: Children's Hospital

country: Finland

institute: University of Helsinki

summary:
The effects of Gata4 inhibition on global gene expression in mLTC-1 cells was analysed. Using microarray analysis we identified a set of genes that are downregulated or upregulated following siRNA-mediated silencing of Gata4 in the murine Leydig tumor cell line mLTC-1.  Among the downregulated genes were enzymes of the androgen biosynthetic pathway.
mLTC-1 cells were transfected with non-targeting (NT) siRNA and Gata4 siRNA respectively. 72h post transfection cells were lysed and RNA was extracted.

overall_design: n=3 of each sample group; control samples are samples 3-6 (mLTC-1 cells treated with non-targeting siRNA)

first: Anja

last: Schrade

first: Oyediran

last: Akinrinade


title: Friends not foes: CTLA-4 blockade and mTOR inhibition cooperate during CD8+ T cell priming

status: Public on Jan 31 2015

city: Cambridge

first: Martin

middle: L

last: Miller

address: Robinson Way

department: Cancer research UK, Cambridge Institute

institute: University of Cambridge

summary:
T cells receive numerous positive and negative signals during primary antigen encounter that control their proliferation and function, but how these signals are integrated to modulate T cell memory has not been fully characterized.  In these studies, we demonstrate that combining seemingly opposite signals, CTLA-4 blockade and rapamycin-mediated mTOR inhibition, during in vivo T cell priming leads to both an increase in the frequency of memory CD8+ T cells and improved memory responses to tumors and bacterial challenges.
This enhanced efficacy corresponds to increased early expansion and memory precursor differentiation of CD8+ T cells and increased mitochondrial biogenesis and spare respiratory capacity in memory CD8+ T cells in mice treated with anti-CTLA-4 and rapamycin during immunization.  Collectively, these results reveal that mTOR inhibition cooperates with rather than antagonizes blockade of CTLA-4, promoting unrestrained effector function and proliferation and an optimal metabolic program for CD8+ T cell memory.

overall_design: Total RNA was isolated from FACS-sorted, antigen-specific CD8+T cells from different treatment conditions at 5 or 35 days after primary T cell activation

first: Virginia

last: Pedicord

first: Justin

middle: R

last: Cross

first: Welby

last: Montalvo-Ortiz

first: James

middle: P

last: Allison


title: U937 scramble vs shHDAC2 upon SAHA (Vorinostat; suberoylanilide hydroxamic acid) treatment

city: Napoli

first: Mariarosaria

last: Conte

address: via De Crecchio

department: Patologia Generale

institute: Second University of Naples

summary: Transcriptional profiling of U937 scramble vs shHDAC2 before and after SAHA treatment at 5µM concentration for 6 and 24 hours.

overall_design: Different Experimental Conditions: U937 scramble (U937 trasfected with empty vector) vs shHDAC2 (U937 trasfected with shHDAC2 vector), untreated and treated with SAHA at 5 µM concentration for 6h and 24h. Biological replicates: 2 for each sample, independently grown and harvested at 6 and 24 hours. One replicate per array.

first: Carmela

last: Dell'Aversana


title: Differential gene regulation by the disease-associated short isoform of GATA1 (microarray)

city: Cincinnati

first: Timothy

middle: Michael

last: Chlon

state: OH

address: 3333 Burnet Ave

department: Oncology

institute: Cincinnati Children's

summary: The transcriptional activiy of GATA1s was compared to GATA1 through gene expression analysis in a cell line model with both erythroid and megakaryocyte differentiation.

overall_design: G1ME cells were derived from Gata1- mouse ES cells and have both megakaryocyte and erythrocyte differentiation potential upon reconstitution of GATA-1 expression (Stachura 2006).  HA-tagged full length or short GATA-1 were expressed in G1ME cells grown in TPO via retroviral transductions.  The cells were sorted for GFP positivity 68 hours post-transduction and then were allowed to recover in normal growth medium for 4h.  Total RNA was then isolated using RNeasy kit from Qiagen 72 hours post-transduction.

first: John

last: Crispino


title: Gene Expression Analysis of PDAC tumors

status: Public on Jan 20 2015

city: Houston

first: Valerie

last: LeBleu

address: 1881 East Road

institute: MDACC

summary: Analysis of myofibroblast ablation at the gene expression level of PDAC tumors.

overall_design:
Total RNA optained from pancreas of PDAC mice with and without aSMA myofibroblast ablated
In addition, late stage aSMA ablated mice were treated with anti-CTLA4 treatment

first: Raghu

last: Kalluri


title: Transcriptional interaction network analyses in dorsal nucleus of vagus nerve, locus coeruleus and substantia nigra in Parkinson's disease

status: Public on Jan 11 2015

city: Sao Paulo

first: Carlos

middle: Alberto

last: Moreira-Filho

state: SP

address: Av. Dr. Eneas Carvalho de Aguiar 647

department: Departments of Pediatrics

institute: Faculdade de Medicina da Universidade de Sao Paulo

summary: We analyzed the transcriptomic profile of post-mortem explants from dorsal nucleus of vagus nerve, locus coeruleus and substantia nigra obtained from controls and Braak 4 (BK4) and 5 (BK5) stages of Parkinson’s disease (PD) patients in order to investigate how gene-gene interaction patterns vary along different anatomical regions in patients and controls. The comparative transcriptional networks analyses indicate that the main hubs in PD networks are related to ubquitin/proteasome, oxidative stress, neuroprotection, neurogenesis and PD associated proteins.

overall_design: Transcriptomic profiles of controls and Parkinson’s disease patients were compared using SAM test for LC or Wilcoxon Mann-Whitney test for SN and VA (p<0.005 and p<0.01, respectively) in order to identify differentially expressed transcripts.

first: Beatriz

last: Corradini

first: Priscila

last: Iamashita

first: Edilaine

last: Tampellini

first: Jose

middle: M

last: Farfel

first: Lea

middle: T

last: Grinberg