title: Gene expression in mouse leukocytes after CAWS administration

status: Public on Sep 30 2013

city: Suita

first: Daisuke

last: Okuzaki

state: Osaka

address: Yamadaoka 3-1

department: Immunology Frontier Research Center

institute: Osaka univ.

summary: We performed DNA microarray analyses and compared the difference in the transcriptome between B6 and DBA/2 mice with modest or dramatic sensitivity to CAWS-vasculitis, respectively. Candida albicans water-soluble fraction (CAWS), a mannoprotein-β-glucan complex obtained from the culture supernatant of C. albicans NBRC1385, causes CAWS mediated vasculitis (CAWS-vasculitis) with distinct sensitivity among mouse strains.

overall_design: The mouse leukocyte derived from B6 and DBA/2 mice after 2-, 4-, 8-, 9- weeks administration were examined. Each mice was run in singlete or duplicate. Microarray analyses were performed as single-color hybridizations.

first: Hiroshi

last: Nojima


title: Gene expression profiling to identify genes that are differentially expressed between murine MHCIIlo and MHCIIhi dendritic cell subpopulations [MHCIIhi vs. MHCIIlo]

status: Public on Dec 22 2013

city: South San Francisco

first: Jason

middle: A

last: Hackney

state: CA

address: 1 DNA Way

department: Department of Bioinformatics and Computational Biology

country: USA

institute: Genentech, Inc.

summary: Hematopoietic progenitors from mouse bone marrow were differentiated into dendritic cells for 5 days with GM-CSF and IL-4. On day 6, MHCIIhi and MHCIIlo BMDC subpopulations were sorted to purify by flow cytometry. RNA was extracted and processed for microarray analysis.

sample_organism:
Homo sapiens
Mus musculus

overall_design: Two condition experiment; Biological replicates: 4 replicates per condition.

first: Zora

last: Modrusan

first: Bryan

last: Vander Lugt

first: Aly

last: Khan

first: Smita

last: Agrawal

first: Justin

last: Lesch

first: Meijuan

last: Zhou

first: Wyne

middle: P

last: Lee

first: Summer

last: Park

first: Min

last: Xu

last: DeVoss

first: Chauncey

middle: J

last: Spooner

first: Cecile

last: Chalouni

first: Lelia

last: Delamarre

first: Ira

last: Mellman

first: Harinder

last: Singh


title: Gene Regulation in Bob1-/- and miR-146a-/- Murine Pre-B Cells

status: Public on Sep 07 2013

city: Freiburg

first: John

last: Lindner

address: Stübeweg 51

department: Reth

country: Germany

institute: MPI-IE Freiburg

summary:
5d IL-7-supported bone marrow cultures from C57BL/6 mice deficient for either the transcription factor Bob1 or microRNA-146a
Micro-RNAs (miRNAs) are required for many processes during hematopoietic development and activation, including B-cell differentiation. The lymphocyte-specific transcription factor Bob1 is critical for the proper development and function of B cells. Bob1-/- mice are immunodeficient and lack germinal centers. Microarray expression analysis of Bob1-deficient B cells shows numerous up-regulated genes, suggesting that Bob1 may affect targets indirectly via the control of miRNAs. Using a gain-of-function/loss-of-function approach in WEHI-231 and primary pro-B and pre-B cells, we  identified miR-146a as a direct target of Bob1. Ttranscriptome-wide analysis of miR-146a-/- B cells shows a number of misregulated genes involved in immune regulation, while analysis of Bob1-/- cells shows increased expression of cell cycle-related genes. These results support previous evidence that Bob1 suppresses proliferation, a previously underappreciated role for Bob1 that is in line with the cancer-prone phenotype of mir-146a-/- mice.

overall_design: 8 samples in total; 2 biological duplicates each of Bob1wt, Bob1KO, wild-type C57BL/6Ncrl, and mir-146aKO

middle: M


title: MicroRNA expression profile of breast cancer patients with adjacent normal control group.

status: Public on Nov 12 2013

city: Taipei

first: Chia-Hsien

address: No. 1, Sec. 4, Roosevelt Road, Taipei, 10617 Taiwan(R.O.C)

country: Taiwan

institute: National Taiwan University

summary: To discriminate miRNA expression differences between adjacent normal and tumor tissues of breast cancer.

overall_design: 101 breast tumor + 15 adjacent breast normal tissue samples.

first: Wen-Hong

last: Kuo

first: Yen-Jen

last: Oyang

first: Hsuan-Cheng

last: Huang

first: Hsueh-Fen

last: Juan


title: Dual Roles of the Transcription Factor Grainyhead-like 2 (GRHL2) in Breast Cancer

status: Public on Sep 05 2013

city: Hamburg

first: Christian

last: Schulze

address: Falkenried 94

institute: ZMNH

summary: Using a retrovirus-mediated cDNA expression cloning approach we identified the grainyhead-like 2 (GRHL2) transcription factor as novel protooncogene. Overexpression of GRHL2 in NIH3T3 cells induced striking morphological changes, an increase in cell proliferation, anchorage-independent growth, and tumor growth in vivo. By combining a microarray analysis and a phylogenetic footprinting analysis with various biochemical assays we identified the epidermal growth factor receptor family member Erbb3 as a novel GRHL2 target gene. In breast cancer cell lines, shRNA-mediated knockdown of GRHL2 expression or functional inactivation of GRHL2 using dominant-negative GRHL2 proteins induce downregulation of ERBB3 gene expression, a striking reduction in cell proliferation and morphological and phenotypical alterations characteristic of an epithelial-to-mesenchymal transition (EMT), thus implying dual roles of GRHL2 in breast carcinogenesis. Interestingly, we could further demonstrate that expression of GRHL2 is directly suppressed by the transcription factor zinc-finger-enhancer binding protein 1 (ZEB1) which in turn is a direct target for repression by GRHL2, suggesting that the EMT transcription factors GRHL2 and ZEB1 form a double negative regulatory feedback loop in breast cancer cells. Finally, a comprehensive immunohistochemical analysis of GRHL2 expression in primary breast cancers showed loss of GRHL2 expression at the invasive front of primary tumors. A pathophysiological relevance of GRHL2 in breast cancer metastasis is further demonstrated by our finding of a statistically significant association between loss of GRHL2 expression in primary breast cancers and lymph-node metastasis. We thus demonstrate a crucial role of GRHL2 in breast carcinogenesis.

overall_design: To evaluate the role of the GRHL2 transcription factor in carcinogenessis we overexpressed the human GRHL2 protein in NIH3T3 cells. Parental NIH3T3 cells do not express the orthologic protein. Alterations in genome-wide transcriptional profiles were determined by microarray analysis.

first: Stefan

last: Werner

first: Sabrina

last: Frey

first: Sabine

last: Riethdorf

first: Malik

last: Alawi

first: Lea

last: Kling

first: Vida

last: Vafaizadeh

first: Guido

last: Sauter

first: Luigi

last: Terracciano

first: Udo

last: Schumacher

first: Klaus

last: Pantel

first: Volker

last: Assmann


title: Potential Roles of miR-29a in the Molecular Pathophysiology of T-Cell Acute Lymphoblastic Leukemia

status: Public on Sep 01 2013

city: Ribeirao Preto

first: Rodrigo

middle: Alexandre

last: Panepucci

state: São Paulo

address: R. Tenente Catao Roxo, 2501

country: Brazil

institute: Regional Blood Center of Ribeirâo Preto (FUNDHERP, HC-FMRP-USP)

summary: The miR-29 family is an important player in the molecular pathophysiology of distinct types of cancer, with roles that seems to depend on cellular context. Reduced miR-29 levels are associated with more aggressive disease and its overexpression in cancer and leukemic cell lines inhibits proliferation. In contrast, its overexpression in hematopoietic progenitors, promotes leukemogenesis. We explored the potential roles of miR-29a in the molecular pathophysiology of T-cell acute lymphoblastic leukemia (T-ALL). As compared to normal T-cells, miR-29a levels are extremely reduced in T-ALL and in the Jurkat cell line. Microarrays analysis in Jurkat cells, following the introduction of synthetic miR-29a mimics, revealed the down-regulation of several predicted targets, including previously described targets (DNMT3a/b, CDK6, PXDN, MCL1, PIK3R1 and CXXC6), and novel targets with roles in active DNA demethylation, such as members of the ten-eleven-translocation (TET) family and TDG. Reduced miR-29a levels contribute to altered epigenetics, as its introduction in Jurkat cells, promotes the demethylation of the AHR gene (commonly methylated in T-ALL). In T-ALL patients, miR-29a levels are significantly associated with blast counts and disease free survival. Our results highlight the relevance of miR-29 in T-ALL physiopathology, and may help to clarify some contrasting findings reported in the literature.

overall_design: In order to identify potential miR-29a targets in T-cell lymphoblastic leukemia, Jurkat cells were electroporated with synthetic RNA molecules corresponding to miR-29a mimics (pre-miR) or inhibitors (anti-miR); and microarray profiles were compared to the profiles of Jurkat cells eletroporated with the corresponding negative controls. Transcripts with levels reduced following the introduction of the pre-miR-29a (as compared to pre-miR-Control), or transcripts acumulated folowing introduction of the anti-miR-29a inhibitor (as compared to anti-miR-Control), were considered potential targets; and were further compared to microRNA target prediction databases. Two paired samples were used for this analysis.

first: Lucila

middle: H

last: Oliveira

first: Josiane

middle: L

last: Schiavinato

first: Antônio

middle: R

last: Lucena-Araújo

last: Haddad

first: Mariane

middle: S

last: Fráguas

first: Amélia

middle: G

last: Araujo

first: Eduardo

last: Rego

first: Dimas

middle: T

last: Covas

first: Marco

last: Zago


title: Chronic alcohol consumption from adolescence-to-adulthood in mice — Effect on gene expression in the hypothalamus

status: Public on Jun 30 2013

city: Shanghai

first: ke

last: wang

address: 151 Libing Road

country: China

institute: Shanghai Biochip Co., Ltd.

summary: We employed a paradigm of chronic moderate alcohol intake from adolescence-to-adulthood in mice, and analyzed the alcohol effect on both behavioral and hypothalamic gene expression changes.

overall_design: We employed a paradigm of chronic moderate alcohol intake from adolescence-to-adulthood in mice. Before chronic alcohol drinking began, mice (3 weeks old) were allowed to adapt to drinking tubes with both tubes containing water from experimental day 1-5. After adaptation period, mice were randomly aside to 5% alcohol group, 10% alcohol group or water-only control group (n=16-18). Chronic alcohol drinking lasted to day 57 of the experiment without any change and interruption. Then each mouse is sacrificed by decapitation, and the hypothalamus was dissected for rapid freeze and storage at -80 ºC. Hypothalamus tissue samples were used for total RNA extraction. RNA samples were pooled for microarray. For water-only group, nine mice were used to make three pools, with three equal amounts of RNA samples per pool. For alcohol group, nineteen mice were used to make nine pools, with one to three equal RNA samples per pool.

first: Hong

last: Zou

first: Lei

last: Yu

first: Ke

last: Wang


title: Gene expression analysis of iTregs and nTregs

status: Public on Jul 03 2013

city: London

first: MARC

last: MARTINEZ-LLORDELLA

address: 3rd Floor Cheyne Wing, Denmark Hill

department: Liver Science Department

country: United Kingdom

institute: King's College London

summary: MBP TCR Tg mouse (1B3) generates only iTregs when crossed onto RAGKO background. Tregs from 1B3.RAG mouse were used for gene expression analsysis to determine genes selectively expressed in peripherally generated iTregs

overall_design: iTregs from 1B3.RAG mice (>90% Foxp3+) were run against total Tregs from 1B3 and WT NOD mice. Foxp3- CD4+T cells were used as control from all strains as Tconv. (1B3 denotes MBP-TCR Tg mouse).


title: Gene expression of mouse embryonic gonad [wild type male]

status: Public on Aug 01 2013

city: Mishima

first: Rie

last: Saba

state: Shizuoka

address: Yata 1111

department: Genetic Strain Research Center

country: Japan

institute: National Institute of Genetics

summary: To analyze the gene expression profiles of the developing embryonic male gonad, we performed expression microarray analysis of the wild type male gonads from E12.5 to E15.5.

overall_design: Biological duplicates were examined at each stage for each experiment.

first: Saba

last: Rie

first: Sato

last: Aya

first: Saga

last: Yumiko


title: Transcriptomic response to long time ethanol production in the cyanobacterium Synechocystis sp. PCC6803

status: Public on Aug 06 2013

first: Jens

last: Georg

address: Schänzlestr. 1

institute: University of Freiburg

summary: The production of biofuels in photosynthetic microalgae and cyanobacteria is considered a promising alternative to the generation of fuels from fossil resources.   However, to be economically competitive, producer strains need to be established that synthesize the targeted product at high yield and over a long time.   Engineering cyanobacteria to forced fuel producers should considerably interfere with overall cell homeostasis, which in turn might counteract productivity and sustainability of the process. Therefore, in-depth characterization of the cellular response upon long-term production is of high interest for the targeted improvement of a desired strain. Here we report the results of a monitoring experiment, in which the transcriptome-wide response to continuous ethanol production in the unicellular model cyanobacterium Synechocystis sp. PCC6803 was examined using high resolution microarrays. In two independent experiments, ethanol production rates of 0.0338% (v/v) EtOH d-1 ± 0.002 and 0.0303% (v/v) d-1 ± 0.002 were obtained over 18 consecutive days, measuring biological triplicates in fully automated photobioreactors. Ethanol production caused a significant (~40%) delay in biomass accumulation in the producer strains and the development of a bleaching phenotype. Absorption spectroscopy indicated in particular a down-regulation of light harvesting capacity. Microarray analyses performed at day 4, 7, 11 and 18 of the experiment revealed only three mRNAs with a strongly modified accumulation level throughout the course of the experiment. In addition to the overexpressed adhA (slr1192) gene, this was an about 4 fold reduction in cpcB (sll1577) and an about 3 to 6 fold increase in rps8 (sll1809) mRNA levels. Much weaker modifications of expression level or modifications restricted to day 18 of the experiment were observed for genes involved in carbon assimilation (Ribulose bisphosphate carboxylase and Glutamate decarboxylase). Molecular analysis of the reduced cpcB levels revealed a post-transcriptional operon discoordination in the cpcBA operon leaving a truncated mRNA cpcA* likely not competent for translation. Moreover, Western blots and zinc-enhanced bilin fluorescence blots confirmed a severe reduction in the amounts of both phycocyanin subunits, explaining the cause of the bleaching phenotype. We conclude that the changes in gene expression upon induction of long term ethanol production in Synechocystis sp. PCC6803 are highly specific. in particular we did not observe a comprehensive stress response contributing to a complex phenotype as might have been expected.

overall_design: Gene expression of Synechocystis sp. PCC 6803 WT (#621) and the isogenic ethanol producing  strain #309 was monitored at 4, 7, 11 and 18 days after induction of ethanol production by copper depletion. Each condition was sampled in biological duplicates

first: Dennis

last: Dienst

first: Thomas

last: Abts

first: Lew

last: Jakorew

first: Ekaterina

last: Kuchmina

first: Annegret

last: Wilde

first: Ulf

last: Dühring

first: Heike

last: Enke

first: Wolfgang

last: Hess


title: Role of Per2 in the control of liver glycogen metabolism

status: Public on Sep 02 2013

city: Trento

first: Alessandro

last: Provenzani

address: via delle regole 101

department: CIBIO

country: Italy

institute: University of Trento

summary: To investigate the role of Per2 in glucose metabolism in-vivo we used mice bearing a targeted gene mutation in the Per2 gene (Per2brdm) and thus unable to express a functional Per2 protein. Mice were hosted in our standard mouse facility in a 12-hour light and 12-hour dark cycle. Wt and Per2brdm mice were fed with either standard chow diet or high-fat diet for 24 weeks and analyzed for glucose homeostasis. Glucose tolerance test (GTT) and insulin tolerance test (ITT) were performed on mice food deprived for 7 hours. For pyruvate tolerance test (PTT) mice were fasted for 14 hours. Glucose levels were measured over 12 hours starvation time-courses during the light and the dark phase. Fed and fasting blood glucose and hepatic glycogen content were measured over different circadian time-points. To investigate the role of Per2 in the control of liver gene expression we performed DNA-microarray analysis of RNA preparations from liver of Per2brdm and WT mice.

overall_design: We extracted total RNA from liver of four different Per2brdm and WT mice. Mice from the same cohort were sacrificed after 8 hours of starvation. After normalization we performed a fold change comparison selecting probes with a p value < 0.05.

first: Fabio

last: Zani

first: Barbara

last: Becattini

first: Anja

last: Stauffer

first: Jean-Pierre

last: Montani

first: Urs

last: Albrecht

first: Giovanni

last: Solinas


title: Misregulation of the broad-range phospholipase C activity increases the susceptibility of Listeria monocytogenes to intracellular killing by neutrophils

status: Public on Aug 14 2013

city: Ithaca

first: Helene

last: Marquis

state: NY

address: Vet Medical Center, Room C5-169

department: Microbiology & Immunology

institute: Cornell University

summary: Listeria monocytogenes is a facultative intracellular bacterial pathogen that tightly regulates the activities of various virulence factors during infection. A mutant strain (the plcBΔpro mutant) that has lost the ability to control the activity of a phospholipase C (PC-PLC) is attenuated a hundred fold in mice. This attenuation is not due to a lack of bacterial fitness, but appears to result from a modified host response to infection. The transcriptomic pattern of immunerelated genes in infected macrophages indicated no differential response to wild-type L. monocytogenes vs the plcBΔpro mutant.

overall_design: Cultures of bone marrow derived macrophages from BALB/c were infected with either wild type or mutant L. monocytogens for 3, 6, or 9 hrs.  The macrophages were then collected and RNA isolated for microarray analysis of gene expression.

first: Bryant

last: Blank

first: Delbert

last: AbiAbdallah

first: Justin

last: Park

first: Evgeniya

middle: V

last: Nazarova

first: Alan

last: PavinskiBitar

first: Kirk

last: Maurer


title: Expression profiling of lung adenocarcinoma TPC tumor cells in Kras-driven NSCLC mouse model

status: Public on Jul 08 2013

city: Stanford

first: Yanyan

last: Zheng

address: 265 Campus Drive

institute: Stanford University

summary: Sustained tumor progression has been attributed to a distinct population of tumor-propagating cells (TPCs). To identify TPCs relevant to lung cancer pathogenesis, we investigated functional heterogeneity in tumor cells isolated from Kras-driven mouse models of non-small cell lung cancer (NSCLC).  CD24+ITGB4+Notchhi cells are capable of propagating tumor growth in both a clonogenic and an orthotopic serial transplantation assay.  While all four Notch receptors mark TPCs, Notch3 plays a non-redundant role in tumor cell propagation in two mouse model and in human NSCLC.  The TPC population is enriched after chemotherapy and the gene signature of mouse TPCs correlates with poor prognosis in human NSCLC. The unique role of Notch3 in tumor propagation may provide a therapeutic target for NSCLC

overall_design: Primary lung adenocarcinoma tumor cells were FACS sorted based on expression of CD24, ITGB4 and Notch. TPC cells are defined by Cd24+ITGB4+ Notch(high), and the remainder tumor cells are non-TPC cells.  Samples were derived from six mice.

first: E

last: Sweet-Cordero


title: Focal Adhesion Kinase Dependent Expression

status: Public on Sep 17 2013

city: Zurich

first: Berend

last: Snijder

address: Winterthurerstrasse 190

department: IMLS

country: Switzerland

institute: University of Zurich

summary: The goal of this study was to identify transcripts, which are differentially regulatulated in the presence and absence of Focal Adhesion Kinase. As Focal Adhesion Kinase activity can depend upon cell density (Snijder et al. Nature 2009), biological replicates where cells, were seeded very sparsely or confluently, were used.

overall_design: Focal Adhesion Kinase Knockout (ATCC CRL-2644) and Rescue Cells (Sieg et al. 1998, clone DA2) were seeded at two different concentrations. Replicas refer to biological replicates, performed on different days. Only one single technical replicate has been done per biological replicate.

first: Thomas

last: Stoeger

first: Andrea

last: Patrignani


title: Expression profiling of CD24+ and CD24-  tumor cells in Kras-driven NSCLC mouse model

overall_design: Highly purified primary tumor cells were FACS  sorted based on expression of CD24.  Samples were derived from six mice.


title: Reprogramming fibroblasts into bi-potential hepatic stem cells by defined factors

status: Public on Jul 19 2013

first: Pu

last: You

address: 800 Xiangyin Road

institute: Second Military Medical University

summary: Recent studies have demonstrated direct reprogramming of fibroblasts into a range of somatic cell types, but to date stem/progenitor cells have only been reprogrammed for the blood and neuronal lineages. We previously reported generation of induced hepatocyte-like (iHep) cells by transduction of Gata4, Hnf1α, and Foxa3 in p19 Arf null mouse embryonic fibroblasts (MEFs). Here, we show that Hnf1β and Foxa3, liver organogenesis transcription factors, are sufficient to reprogram MEFs into induced hepatic stem cells (iHepSCs). iHepSCs can be stably expanded in vitro and possess the potential of bi-directional differentiation into both hepatocytic and cholangiocytic lineages. In the injured liver of fumarylacetoacetate hydrolase (Fah)-deficient mice, repopulating iHepSCs become hepatocyte-like cells. They also engraft as cholangiocytes into bile ducts of mice with DDC-induced bile ductular injury. Lineage-conversion into bi-potential expandable iHepSCs provides a strategy to enable efficient derivation of both hepatocytes and cholangiocytes for use in disease modeling and tissue engineering.

overall_design: iHepSCs were converted form fibroblasts by transduction of Hnf1β and Foxa3. iHepSCs were induced to differentiate into hepatocyte-like cells and cholangiocytes in vitro. Totally, 9 samples including four clones of iHepSCS, one clone of LEPCs, two samples of MEFs and two samples of iHepSCs-derived cholangocytes were analyzed.

first: Bing

last: Yu

first: Zhi-Ying

last: He

first: Qing-Wang

last: Han

first: Dao

last: Xiang

first: Fei

last: Chen

first: Min-Jun

last: Wang

first: Chang-Cheng

last: Liu

first: Xi-Wen

last: Lin

first: Uyunbilig

last: Borjigin

first: Xiao-Yuan

last: Zi

first: Jian-Xiu

last: Li

first: Hai-Ying

last: Zhu

first: Wen-Lin

first: Chun-Sheng

last: Wangensteen

first: Yufang

last: Shi

first: Li-Jian

last: Hui

first: Xin

first: Yi-Ping

last: Hu


title: Oncogenic alterations in multiple core signaling pathways are required for glioblastoma pathogenesis in vitro and in vivo

city: Chapel HIll

first: Ryan

last: Miller

state: North Carolina

department: Pathology

institute: University of North Carolina

summary: Here, we use a series of genetically-defined murine cortical astrocytes with conditional inactivation of Rb/Pten and activated Kras to systematically investigate the individual and combinatorial roles of these pathways during gliomagenesis.  We show that genetic disruption of all three pathways, which frequently occurs in human GBM, leads to maximal in vitro growth, migration, and invasion and produces stem-like transcriptomal profiles similar to the proneural subtype of human GBM.  Genetic alterations in all three pathways are also required for efficient tumorigenesis in an orthotopic syngeneic allograft model system in vivo.  These findings show that cortical astrocytes can form GBM and identify a potential model for proneural GBM that can be used to test subtype-specific therapies. Transcriptional profiling of transformed murine cortical astrocytes shows correlation between mutated genes, invasive capability, neural lineage, and human astrocytoma/GBM signatures.  10 samples

overall_design: Cortical astrocytes were isolated from neonatal mice (C57BL/6 background strain) and cultured.  Cells were infected with adeneoviral-Cre for 6 hours to induce  recombination.  This resulted in expression of an N-terminal 121 amino acid truncation mutant of SV40 large T antigen (T121, hereafter called T) from the human glial fibrillary acidic protein (GFAP) promoter, which inactivates all three members of the Rb family (Rb, p107, p130) and results in proliferation and defective G1/S ratios. Additionally, cells contained KrasG12D mutant (R) and/or contained either heterozygous or homozygous deletion of Pten (P+/- or P-/-) .   Here are 23 cell lines comprising 6 different genotypes.  10 Samples (Sample Title: TR_2, T_1, TRP_null_3, TR_1, TRP_null_4, TRP_het_1, T_2, TRP_null_2, T_3, TRP_null_5) from one batch were combined with the remaining 13 samples to remove batch related effects (see data processing for method).

first: Mark

last: Vitucci


title: Epigenetic regulation of sex determination by the histone demethylase Jmjd1a

status: Public on Aug 03 2013

city: Tsukuba

first: Shogo

last: Matoba

state: Ibaraki

address: 3-1-1, Koyadai

institute: RIKEN BioResource Research Center

summary: Developmental gene expression is defined through cross-talk between the function of  transcription factors and epigenetic status including histone modification. Although  several known transcription factors play crucial roles in mammalian sex determination,  how chromatin regulation contributes to this process is unknown. We observed  male-to-female sex reversal in mice lacking the H3K9 demethylase Jmjd1a, and found  that Jmjd1a directly regulates expression of the mammalian Y chromosome  sex-determining gene Sry, by regulating H3K9me2 marks. These studies reveal a pivotal  role for epigenetic regulation in mammalian sex determination, and provide new  impetus for identifying additional causes of disorders of sex determination by  environmental factors.

overall_design: Gene expression patterns were measured in gonadal somatic cells of Jmjd1a mutant and control embryos at E11.5.  Three biological replicates were performed in each group.

first: Shunsuke

last: Kuroki

first: Mika

last: Akiyoshi

first: Yasuko

last: Matsumura

first: Hitoshi

last: Miyachi

first: Nathan

last: Mise

first: Kuniya

last: Abe

first: Atsuo

last: Ogura

first: Dagmar

last: Wilhelm

first: Peter

last: Koopman

first: Masami

last: Nozaki

first: Yoshiakira

last: Kanai

first: Yoichi

last: Shinkai

first: Makoto

last: Tachibana


title: The gene sml0013 of Synechocystis sp. strain PCC 6803 encodes for a novel subunit of the NDH1 complex that is ubiquitous distributed among cyanobacteria.

status: Public on Jun 29 2013

first: Jens

last: Georg

summary: The NDH1 complex fulfils numerous tasks in the cyanobacterial cell such as respiration, cyclic electron flow, and inorganic carbon concentration. Despite the immense progress in our understanding of structure/function relation of the cyanobacterial NDH1 complex, the subunits catalysing the NAD(P)H docking and oxidation are still missing. The gene sml0013 of Synechocystis 6803 encodes for a small protein of unknown function for that homologs exist in all completely known cyanobacterial genomes. The protein exhibits weak similarities to the NDF6 protein, which was reported from Arabidopsis chloroplasts as a NDH subunit (Ishikawa et al. 2008). A sml0013 inactivation mutant of Synechocystis 6803 was generated and characterized. It showed only weak differences regarding growth and pigmentation at various culture conditions; most remarkably it exhibited a glucose-sensitive phenotype in the light. The genome-wide expression pattern of the Δsml0013::Km mutant was almost identical to wild type when grown under high CO2 conditions as well as after shifts to low CO2 conditions. However, measurements of the photosystem I redox kinetic in cells of the Δsml0013::Km mutant revealed differences to wild type such as a decreased capability of cyclic electron flow as well as of utilization of electrons from catabolic processes. These results suggest that the Sml0013 protein (named NdhP) represent a novel subunit of the cyanobacterial NDH1 complex mediating its coupling to the respiratory or photosynthetic electron flow.

overall_design: Gene expression of Synechocystis sp. PCC 6803 WT and a Δsml0013::Km mutant was monitored at HC conditions (5% CO2) and at 24h after a shift to LC conditions (ambient air containing 0.035% CO2). Each condition was sampled in biological duplicates.

first: Doreen

last: Schwarz

first: Hendrik

last: Schubert

first: Wolfgang

last: Hess

first: Martin

last: Hagemann


title: The hierarchy of transition metal homeostasis: Iron controls manganese accumulation in a unicellular cyanobacterium.

summary: Iron and manganese are part of a small group of transition metals required for photosynthetic electron transport. Here, we present evidence for a functional link between iron and manganese homeostasis. In the unicellular cyanobacterium, Synechocystis sp. PCC 6803 Fe and Mn deprivation resulted in distinct modifications of the function of the photosynthetic apparatus. For example, iron limitation modifies the rate of QA re-oxidation in photosystem II, a complex that contains more Mn than Fe. The intracellular elemental quotas of Fe and Mn are also linked. Fe limitation reduces the intracellular Mn quota. Mn limitation did not exert a reciprocal effect on Fe quotas. Microarray analysis comparing Mn and Fe limitation revealed a stark difference in the extent of the transcriptional response to the two limiting conditions, reflective of the physiological data. The effects of Fe limitation on the transcriptional network are widespread while the effects on Mn limitation are highly specific. Our analysis also revealed an overlap in the transcriptional response of specific Fe and Mn transporters. This overlap provides a framework for explaining Fe limitation induced changes in Mn quotas. Fe transporters can serve as a low affinity Mn transport system. Under iron limitation the specificity of the Fe transport system changes, making it a less efficient Mn transport system.

overall_design: We monitored the gene expression of Synechocystis PCC6083 at standard conditions and after 2 days of iron limitation (0Fe), manganese limitation (0Mn) and combined iron and manganese limitation (0Fe0Mn). Each timepoint and condition was sampled in triplicates. Due to strong deviations in one of the three repeats for the 0Mn and 0Fe0Mn conditions, the corresponding replicates were excluded from further analysis.

first: Shir

last: Sharon

first: Eitan

last: Salomon

first: Robert

last: Lehmann

first: Nir

last: Keren


title: subventricular zone progenitors healthy vs. Experimental Autoimmune Encephalomyelitis mice

status: Public on Sep 09 2013

city: Marseille

first: Myriam

last: CAYRE

address: Parc Scientifique de Luminy

country: France

summary: Transcriptional profiling of subventricular zone (SVZ) progenitors comparing control healthy mice to mice induced to develop an autoimmune demyelination (EAE model). Goal was to unveil genes involved in demyelination-induced reactivity of SVZ progenitors.

overall_design: Two-condition experiment, healthy vs. EAE derived SVZ progenitors. Biological replicates: 2 control replicates, 2 EAE replicates. SVZ progenitors were sorted in two cell populations: neuronal progenitors (PSA-NCAM magnetic sorting) and glial progenitors (NG2 magnetic sorting). Progenitors from healthy mice are reference samples.

first: Pascale

last: Durbec

last: Cayre

first: Cristina

last: Cantarella


first: Kimiko

last: Inoue

address: 3-1-1 Koyadai

department: Bioresource Engineering Division

institute: BRC, RIKEN

summary: The great majority of embryos generated by somatic cell nuclear transfer (SCNT) display defined abnormal phenotypes after implantation, such as an increased likelihood of death and abnormal placentation. To gain better insight into the underlying mechanisms, we analyzed genome-wide gene expression profiles of day 6.5 postimplantation mouse embryos cloned from three different cell types (cumulus cells, neonatal Sertoli cells and fibroblasts). The embryos retrieved from the uteri were separated into embryonic (epiblast) and extraembryonic (extraembryonic ectoderm and ectoplacental cone) tissues and were subjected to gene microarray analysis. Genotype- and sex-matched embryos produced by in vitro fertilization (IVF) were used as controls. Principal component analysis revealed that whereas the gene expression patterns in the embryonic tissues varied according to the donor cell type, those in extraembryonic tissues were relatively consistent across all groups. Within each group, the embryonic tissues had more differentially expressed genes (DEGs) (> 2-fold vs. controls) than did the extraembryonic tissues (P < 1.0 × 10–26). In the embryonic tissues, one of the common abnormalities was upregulation of Dlk1, a paternally imprinted gene. This might be a potential cause of the occasional placenta-only conceptuses seen in SCNT-generated mouse embryos (1–5% per embryo transferred in our laboratory), because dysregulation of the same gene is known to cause developmental failure of embryos derived from induced pluripotent stem cells. There were also some DEGs in the extraembryonic tissues, which might explain the poor development of SCNT-derived placentas at early stages, although these alterations were not always statistically significant for all three SCNT groups because of variability. These findings suggest that SCNT affects the embryonic and extraembryonic development differentially and might cause further deterioration in the embryonic lineage in a donor cell-specific manner. This could explain donor cell-dependent variations in cloning efficiency using SCNT.

overall_design: Comparative gene expression analyses using E4.0 cloned blastocysts were performed by microarray. Cloned embryos were produced with cumulus cells by two different methods (cell fusion and nuclear injection). As controls, sex- and genotype-matched embryos produced by in vitro fertilization were used.

first: Ryutaro

last: Hirawasa

first: Shogo

last: Matoba

first: Atsuo

last: Ogura


title: The microRNA cluster miR-17~92 promotes TFH cell differentiation and represses subset-inappropriate gene expression

city: Bonn

first: Dirk

last: Baumjohann

state: NRW

address: Venusberg-Campus 1

department: Medical Clinic III

institute: University Hospital Bonn

summary: Follicular helper T cells (TFH cells) are the prototypic helper T cell subset specialized to enable B cells to form germinal centers (GCs) and produce high-affinity antibodies. We found that expression of microRNAs (miRNAs) by T cells was essential for TFH cell differentiation. More specifically, we show that after immunization of mice with protein, the miRNA cluster miR-17~92 was critical for robust differentiation and function of TFH cells in a cell-intrinsic manner that occurred regardless of changes in proliferation. In a viral infection model, miR-17~92 restrained the expression of genes ‘inappropriate’ to the TFH cell subset, including the direct miR-17~92 target Rora. Removal of one Rora allele partially ‘rescued’ the inappropriate gene signature in miR-17~92-deficient TFH cells. Our results identify the miR-17~92 cluster as a critical regulator of T cell–dependent antibody responses, TFH cell differentiation and the fidelity of the TFH cell gene-expression program.

overall_design: Gene expression analysis of control versus miR-17~92 knockout (KO) LCMV-specific SMARTA TFH cells 5.5 days after viral infection.

first: Robin

last: Kageyama

first: Lukas

last: Jeker

first: K

last: Ansel


title: Gain and loss of H4K16 acetylation during ES cell differentiation [Agilent arrays]

status: Public on Aug 23 2013

city: Edinburgh

first: Gillian

last: Taylor

address: MRC HGU Crewe Road South

institute: IGMM

summary: Genome wide gain and loss of H4K16ac upon differentiation correlated with changes in expression.

overall_design: Gene expression in undifferentiated ES cells, and cells after 3 days of differentiation in retinoic acid.  3 biological replicates with two technical replicates were performed for each sample.

first: Ragnhild

last: Eskeland

first: Madapura

last: Pradeepa

first: Wendy

last: Bickmore


title: Interleukin-17 mediated paracrine network promote tumor resistance to anti-angiogenic therapy

status: Public on Jun 27 2013

city: South San Francisco

first: Zhaoshi

last: Jiang

address: 1 DNA Way

department: Bioinformatics

institute: Genentech, Inc

summary: While angiogenesis inhibitors have provided significant clinical benefit as cancer therapeutics, the mechanisms of anti-VEGF resistance remain incompletely understood. We uncovered an interleukin-17 mediated paracrine network of signaling between the adaptive and innate immune system associated with resistance to anti-VEGF treatment in multiple tumor models.

overall_design: The expression of tumor-associated fibroblasts and tumor-associated granulocytes (defined as CD11b+Gr1+) and tumor-associated monocytic cells (defined as CD11b+Gr1-) were compared between wildtype and IL-17RC knockout tumor bearing mice.

first: Alicia

last: Chung

first: Napoleone

last: Ferrara

first: Zora

last: Modrusan


title: Analysis of miRNA profile in Ago2-IP fraction after miR-195 or miR-497 overexpression

status: Public on May 31 2013

city: Tokyo

first: Johji

last: Inazawa

address: 1-5-45 Yushima, Bunkyo-ku

institute: Tokyo Medical & Dental University

summary:
To explore functionally crucial tumor-suppressive (TS)-miRNAs in hepatocellular carcinoma (HCC), we performed integrative function- and expression-based screenings of TS-miRNAs in six HCC cell lines.  The screenings identified seven miRNAs, which showed growth-suppressive activities through the overexpression of each miRNA and were endogenously downregulated in HCC cell lines.  Further expression analyses using a large panel of HCC cell lines and primary tumors demonstrated four miRNAs, miR-101, -195, -378 and -497, as candidate TS-miRNAs frequently silenced in HCCs.  Among them, two clustered miRNAs miR-195 and miR-497 showed significant growth-suppressive activity with induction of G1 arrest.  Comprehensive exploration of their targets using Argonute2-immunoprecipitation-deep-sequencing (Ago2-IP-seq) and genome-wide expression profiling after their overexpression, successfully identified a set of cell-cycle regulators, including CCNE1, CDC25A, CCND3, CDK4, and BTRC.  Our results suggest the molecular pathway regulating cell cycle progression to be integrally altered by downregulation of miR-195 and miR-497 expression, leading to aberrant cell proliferation in hepatocarcinogenesis.
Analysis of miRNA profile change in the Ago2-IP fraction after overexpression with miR-195 or miR-497

overall_design: miRNA expression analysis using Immunopreticipated RNA fractions with anti-human-Argonute 2 antibody for non-treated, miR-195 or miR-497 overexpressed Hep G2 cell.

first: Mayuko

last: Furuta


title: ATF3 links host adaptive-response to breast cancer metastasis

status: Public on Jul 10 2013

city: Columbus

first: Tsonwin

last: Hai

state: OH

address: 1060 Carmack Road #148

department: Molecular and Cellular Biochemistry

institute: Ohio State University

summary: Cancer-host interactions play an important role in cancer development.  We identified ATF3, an adaptive-response gene, in the host to facilitate metastasis.  We also demonstrated that the macrophage is one of the key cell types for host-ATF3 to function.  Furthermore, matrix metalloproteases 9 is a functionally important target gene of ATF3 in co-culture assays.  Gene profiling with bioinformatics analyses indicated that ATF3 downstream gene-signatures derived from tumor-associated macrophages in a mouse model can distinguish human tumor stroma from “distant” stroma in and can stratify the patients into high- versus low-risk groups.  Importantly, multivariate analyses indicated that high expression of ATF3 itself in mononuclear cells within breast tumors is an independent predictor for breast cancer-specific death in a cohort of patients.

overall_design: Approximately 21 days after orthotopic injection of PyMT breast cancer cells into syngeneic C57BL/6 mice (WT or ATF3 KO hosts) tumors were removed (tumors were ~1 cm cubic in volume), enzymatically digested to generate single cell suspensions, stained, and sorted for F4/80 and CD45 double positive cells by FACS.  Isolated cells were lysed in TRIzol, processed to generate total RNA, and gene expression analyzed by microarray.  Four replicate WT TAM samples and four replicate ATF3 KO TAM samples were analyzed.

first: Christopher

middle: C

last: Wolford


title: Genes affected by PAD4 deficiency in LSK cells obtained from mouse bone marrow.

status: Public on Jun 01 2013

city: Bunkyo-ku

first: Katsuhiko

last: Nakashima

state: Tokyo

address: 7-3-1 Hongo

department: Faculty of Medicine

institute: The University of Tokyo

summary: We found PAD4, which is one of the transcriptional co-regulator by histone modification, was highly expressed in lineage-, Sca-1+, c-kit+ (termed as LSK) cells of mouse bone marrow. To find the target genes which are regulated by PAD4 in LSK cells, we analyzed gene expression in PAD4-deficient mouse as compared with wild-type mouse.

overall_design: Gene expression in wild-type and PAD4-deficient LSK cells

first: Kazuhiro

last: Sato

first: Toru

last: Miyazaki

first: Osamu

last: Ohara


status: Public on Sep 01 2013

first: Kimiko

last: Inoue

overall_design: Comparative gene expression analyses using post-implanted E6.5 cloned embryos were performed by microarray. Cloned embryos were produced with three different types of donor cells (cumulus cells, neonatal Sertoli cells and fibroblasts). As controls, sex- and genotype-matched embryos produced by in vitro fertilization were used. Each embryos were mechanically dissected into the embryonic and extraembryonic parts at E6.5 and were subjected to gene expression microarray.

first: Ryutaro

last: Hirawasa

first: Shogo

last: Matoba

first: Atsuo

last: Ogura


title: Gene regulation during colitis-associated colon cancer in Muc1 hematopoietic KO chimeric mice

status: Public on May 30 2013

city: Scottsdale

first: Tze Wei

last: Poh

state: AZ

address: 13400 E Shea Boulevard

institute: Mayo Clinic

summary: MUC1 is a tumor-associated antigen that is aberrantly expressed in cancer and inflammatory bowel disease (IBD). Even though immune cells express low MUC1 levels, their modulations of MUC1 are important in tumor progression. Consistent with previous clinical data that show increased myeloid-derived suppressor cells (MDSCs) in IBD, we now show that down-regulation of MUC1 on hematopoietic cells increases MDSCs in IBD, similar to our data in tumor-bearing mice. We hypothesize that MDSC expansion in IBD is critical for tumor progression. In order to mechanistically confirm the linkage between Muc1 down-regulation and MDSC expansion, we generated chimeric mice that did not express Muc1 in the hematopoietic compartment (KO→WT). These mice were used in 2 models of colitis and colitis-associated cancer (CAC) and their responses were compared to wildtype chimeras (WT→WT). KO→WT mice show increased levels of MDSCs during colitis that was responsible for the larger colon tumors that eventually developed in these mice. Using microarray and qRT-PCR analysis, we observed increased pro-tumorigenic signaling in the colons of KO→WT mice during colitis as compared to WT→WT mice. Our RNA (microarray and qRT-PCR analysis) and protein analysis demonstrate increased up-regulation of metalloproteinases, collagenases, defensins, complements, growth factors, cytokines and chemokines in KO→WT mice as compared to WT→WT mice. Antibody-mediated depletion of MDSCs in mice during colitis reduced colon tumor formation during CAC. Development of CAC is a serious complication of colitis and our data highlight MDSCs as a targetable link between inflammation and cancer.

overall_design: A total of 12 samples were analysed. RNA was made from the mucosa of the colon of WT→WT and KO→WT mice that were either untreated or treated with azoxymethane (AOM) and dextran sodium sulfate (DSS). There are 4 groups, n=3 for each group: untreated WT→WT mice, untreated KO→WT mice, AOM+DSS treated WT→WT mice, AOM+DSS treated KO→WT mice = 12 samples in total.

first: Tze

middle: W

first: Sandra

last: Gendler


title: Temporal examination of Clofibrate and WY-14,643 elicited gene expression in C57BL/6 mice

status: Public on Jun 12 2013

city: East Lansing

first: Rance

last: Nault

state: United States

address: 1355 Bogue St. B403

department: Department of Pharmacology and Toxicology

institute: Michigan State University

summary: Temporal hepatic gene expression elicited by PPARα agonists Clofibrate and WY-14,643 was examined. These data were used to select PPARα regulated genes that may demonstrate species-specific regulation for assessment by QRT-PCR in a novel human adult stem cell model.

overall_design: Three biological replicates for each treatment were compared to time-matched vehicle control

first: Suntae

last: Kim

first: Naoki

last: Kiyosawa

first: Lyle

middle: D

last: Burgoon

first: Chia-Cheng

last: Chang

first: Timothy

last: Zacharewski


title: Whole genome expression analysis of tumor regulatory T cells expressing interleukin-10

status: Public on Aug 31 2013

city: Frederick

first: Charles

middle: Andrew

last: Stewart

state: MD

address: 1050 Boyles Street

department: Center For Cancer Research

institute: National Cancer Institute

summary: The tumor microenvironment contains high frequencies of inflammatory regulatory T (Treg) cells. These Treg exhibit superior regulatory function compared with those from other environments such as the spleen, partially due to expression of anti-inflammatory interleukin-10. In order to gain insight into the origins and functional roles of different Treg subsets, we used whole genome microarray analysis to characterize tumor IL-10+ and tumor IL-10- Treg subsets obtained from VERT-X reporter mice bearing transplantable tumors, along with total tumor Treg and spleen Treg from FoxP3-EGFP reporter mice. Few genes were found to differ between IL-10+ and IL-10- tumor Treg subsets (29 upregulated, 88 downregulated), suggesting a common origin of each Treg subset. The specific gene expression profile of IL-10+ tumor Treg was associated with the tumor microenvironment and absent from spleen Treg, suggesting it to be driven by components of the inflammatory tumor microenvironment. The IL-10+ tumor Treg gene expression profile displayed upregulation of genes associated with a higher activation state and greater effector function.

overall_design: Pooled MC38 tumor tissue from VERT-X or FoxP3-EGFP reporter mice were used to obtain IL10+ tumor Treg (VERT-X), IL10- tumor Treg (VERT-X) and total tumor Treg (FoxP3-EGFP). Spleens from tumor-free FoxP3-EGFP mice were used for spleen Treg. Three experiments for each population gave a total 12 RNA samples.

first: C

first: Giorgio

last: Trinchieri


title: Donor cell type-specific gene expression in embryonic but not extraembryonic tissues of postimplantation embryos cloned from somatic cells

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

overall_design: Refer to individual Series


title: A daily temporal program for rhythmic expression of protein-coding and non-coding genes in response to light and dark in Synechocystis sp. PCC 6803

city: Berlin

first: Christian

middle: Johannes

last: Beck

state: Berlin

address: Invalidenstrasse 43

department: Institute for Theoretical Biology

institute: Humboldt-University Berlin

summary: We investigated Synechocystis high-density microarray data of three high-resolution time-series experiments with alternating light/dark rhythm, transition to continuous light, and transition to continuous darkness. Using ‘least oscillating set’ normalization and a clustering approach we found a daily temporal program for rhythmic expression of protein-coding and non-coding genes under light/dark conditions. All rhythms, however, damped out rapidly under continuous conditions.

overall_design: We quantified gene expression of wild type Synechocystis PCC 6083 over 48 hours under three different light regimes; 12:12-h light/dark cycle (LDLDL), transfer to continuous light (LDLLL), and transfer to continuous dark (LDDDD). Samples were taken every two hours starting at CT 5.5 with an extra sample 30 minutes after dawn. Before the transfer to continuous light/dark in the LDLLL and LDDDD experiment, samples were taken every 6 with an extra sample 30 minutes after dawn.

first: Anne

last: Rediger

first: Robert

last: Lehmann

first: Anika

last: Wiegard

first: Adrian

last: Kölsch

first: Beate

last: Heilmann

first: Jens

last: Georg

first: Wolfgang

last: Hess

first: Stefanie

last: Hertel

first: Ilka

last: Axmann


title: Mutant TDP-43 in Astrocytes Kills Motor Neurons in Rats through Neurotoxic Gain and Neuroprotective Loss in Astrocytes

status: Public on May 20 2013

city: philadelphia

first: jianbin

last: tong

address: locust street

department: anatomy

institute: thomas jefferson university

summary: Mutation in TDP-43 is causative to amyotrophic lateral sclerosis (ALS). TDP-43 is a multifunctional ribonucleoprotein and is reproted to regulate thousands of genes in neurons, but how astrocytes contribute to TDP-43 pathogenesis is not known. This study examined how mutant TDP-43 in astrocytes kills motor neurons and causes ALS phenotypes. Primary astrocytes were isolated from transgenic rats expressing mutant TDP-43 or from control rats without mutant TDP-43 expression. Cultured astrocytes were induced to express mutant human TDP-43 and their gene expression profiles were determined by microarray assays. Microarray analysis revealed that hundreds of genes were altered in astrocytes in response to mutant TDP-43 expression.

overall_design: As mutant TDP-43 transgene is under the control of tetracycline-regulated pomoter elements (TRE), mutant TDP-43 expression is subjected to Doxycline regulation. Astrocytes isolated from GFAP-tTA/TRE-TDP43M337V rats were desiginated as M337V groups and astrocytes isolated from GFAP-tTA single transgenic rats were desiginated as tTA control groups. Total RNA was isolated from cultured astrocytes at varying times (3, 4, or 6 days after Dox withdrawal) after mutant TDP-43 was induced in astrocytes. Upon mutant TDP-43 induction in astroyctes, gene expression profiles in astroyctes were determined by Illumina Direct Hybridization Assay and compared between tTA and M337V groups at the varying time points of mutant TDP-43 induction.

first: Jianbin

last: Tong

first: Cao

last: Huang

first: Fangfang

last: Bi

first: Bo

first: Qinxue

last: Wu

first: Fang

last: Li

first: Xionghao

last: Liu

first: Hongxia

last: Zhou

first: Xu-Gang

last: Xia


title: GR and Klf15 regulate gene expression dynamics and integrate signals through feed forward circuitry

status: Public on May 13 2013

city: San Francisco

first: Andrea

last: Barczak

address: 1550 4th St Rock Hall 545

institute: UCSF Sandler Center Functional Genomics Core Facility

summary: The glucocorticoid receptor (GR) regulates adaptive transcriptional programs that alter metabolism in response to stress. Network properties that allow GR to tune gene expression to match specific physiologic demands are poorly understood. We analyzed the transcriptional consequences of GR activation in murine lungs deficient for Klf15, a transcriptional regulator of amino acid metabolism that is induced by glucocorticoids and fasting

overall_design: Wild type and Klf15 KO mice were treated with dexamethsone or saline control for 4 and 8 hours.

first: Anthony

middle: N

last: Gerber

first: Sarah

middle: K

last: Sasse

first: Christina

last: Mailloux

first: Qian

last: Wang


title: Cytosolic Phospholipase A2α and Eicosanoids Regulate Expression of Genes in Macrophages Involved in Host Defense and Inflammation

status: Public on May 02 2013

city: Denver

last: Leslie

address: 1400 Jackson street

institute: National Jewish Health

summary: The role of Group IVA cytosolic phospholipase A2 (cPLA2α)  activation in regulating macrophage transcriptional responses to Candida albicans infection was investigated. cPLA2α releases arachidonic acid for the production of eicosanoids. In mouse resident peritoneal macrophages, prostacyclin, prostaglandin E2 and leukotriene C4 were produced within minutes of C. albicans addition before cyclooxygenase 2 expression. The production of TNFa was lower in C. albicans-stimulated cPLA2a+/+ than cPLA2a-/- macrophages due to an autocrine effect of prostaglandins that increased cAMP to a greater extent in cPLA2a+/+ than cPLA2a-/- macrophages. For global insight, differential gene expression in C. albicans-stimulated cPLA2a+/+ and cPLA2a-/- macrophages (3 h) was compared by microarray. cPLA2α+/+ macrophages expressed 86 genes at lower levels and 181 genes at higher levels than cPLA2α-/- macrophages (≥2-fold, p<0.05 ). Several pro-inflammatory genes were expressed at lower levels (Tnfa, Cx3cl1, Cd40, Ifng, several IFNg-inducible GTPases, Ccl5, Csf1, Edn1, CxCr7, Irf1, Irf4, Akna). Genes that dampen inflammation (Socs3, Il10, Crem, Stat3, Thbd, Thbs1, Abca1) and genes involved in host defense (Gja1, Csf3, Trem1, Hdc) were expressed at higher levels in cPLA2a+/+ macrophages. Representative genes expressed lower in cPLA2a+/+ macrophages (Tnfa and Csf1) were increased by treatment with a prostacyclin receptor antagonist and protein kinase A inhibitor, whereas genes expressed at higher levels (Crem, Nr4a2, Il10, Csf3) were suppressed. The results suggest that C. albicans stimulates an autocrine loop in macrophages involving cPLA2a, cyclooxygenase 1-derived prostaglandins and increased cAMP that globally effects expression of genes involved in host defense and inflammation.

overall_design: Resident peritoneal macrophages from Group IVA cytosolic phospholipase A2 (cPLA2a) +/+ and -/- mice were stimulated with Candida albicans (m.o.i. 2) for 3 hours and RNA isolated to evaluate the role of cPLA2a-derived lipid mediators on gene expression. Three independent experiments were analyzed.


title: A novel small compound SH-2251 suppresses Th2 cell-dependent airway inflammation through selective modulation of chromatin status at the Il5 gene locus

status: Public on Apr 30 2013

city: Toon

first: Junpei

last: Suzuki

address: Shitukawa

department: Graduate School of Medicine

institute: Ehime University

summary: IL-5 is a key cytokine that plays an important role in the development of pathological conditions in chronic allergic inflammation.  Identification of a strategy to inhibit IL-5 production is important for establishment of new therapies for allergic inflammation.  We found that SH-2251, a novel thioamide-related compound, selectively inhibits the differentiation of IL-5-producing Th2 cells.  SH-2251 inhibited the formation of the active histone modifications (H3K4me3, H3K9ac, H3K27ac) at the Il5 gene locus during Th2 cell differentiation.  The recruitment of RNA polymerase II and the induction of Th2 cell-specific intergenic transcription between the Rad50 and Il5 gene locus was also inhibited.  Furthermore, Th2 cell-driven airway inflammation in mice was suppressed by oral administration of SH-2251.  We identified Gfi1 as a downstream target molecule of SH-2251 treatment.  The expression of Gfi1 was dramatically decreased in SH-2251-treated Th2 cells.  SH-2251-mediated inhibition of the IL-5-producing Th2 cell generation was restored by transduction of Gfi1.  Thus, our study unearths SH-2251 as a novel therapeutic candidate for allergic inflammation that selectively inhibits IL-5 production.

overall_design: Gene expression in SH-2251-treated and untreated Th2 cells

first: Makoto

last: Kuwahara

first: Soichi

last: Tofukuji

first: Masashi

last: Imamura

first: Fuminori

last: Kato

first: Toshinori

last: Nakayama

first: Osamu

last: Ohara

first: Masakatsu

last: Yamashita


title: mRNAs and miRNAs expression data from AOM/DSS, AOM, DSS and control mouse colon epithelial tissue at day100 when tumor formed in AOM/DSS bearing mice --- mRNA expression data

status: Public on May 10 2013

city: Harbin

first: yanqiao

last: zhang

state: Heilongjiang

address: Haping Road # 150, Nangang District,Harbin, Heilongjiang Province, P. R. China

institute: Harbin Medical University Cancer Hospital

summary: To find out which mRNAs are significantly differential expression and potentially  involved in the process of inflammation promoting carcinogenesis of colorectal cancer (CRC). We established a colitis-associated CRC (AOM/DSS, Azoxymethane/Dextran sulfate sodium salt) model, colitis (DSS) model and high dose carcinogen (AOM, about 5 times AOM amount given than AOM/DSS model) model. At day 100 when tumor formed in AOM/DSS bearing mice (colitis-associated CRC mice) but no tumor was found in AOM (high dose carcinogen) and DSS model, we employed whole genome microarray expression profiling as a discovery platform to identify genes with the potential to involve in the progression of CRC promoted by inflammation.

overall_design: 5-7 weeks female BALB/c mice, (1) AOM/DSS group: AOM 12.5mg/kg i.p. at day 1, DSS drinking 5d/21dx3circles from day 5; (2) AOM group: AOM 10mg/kg i.p. 1/weekx6 from day 1; (3) DSS group: DSS drinking 5d/21dx3circles from day 5. The distal colon epithelial tissues were collected at day100 when tumor formed in AOM/DSS bearing mice. The whole genome microarray expression profiling experiments were performed together.

first: Yanqiao

last: Zhang

first: Yuyan

last: Gao


title: Traumatic Brain Injury Induces Macrophage Subsets In The Brain

status: Public on May 01 2013

first: Christine

middle: L.

last: Hsieh

address: 4150 Clement St. 111R

department: Immunology

institute: UC San Francisco/ San Francisco VA Medical Center

summary:
We compared arginase-1+ macrophages (macrophages were defined by flow cytometry as CD45hi CD11b+ Ly6G-) with arginase-1- brain macrophages following traumatic brain injury (TBI) by isolating these cells from YARG transgenic mice, which express YFP under the arginase-1 promoter. Both cell populations were isolated from YARG brain tissues one day following TBI. We also examined the expression profile of peripheral blood monocytes (monocytes were defined by flow cytometry as CD11bhi F4/80+) from injured YARG mice and from normal YARG mice. Peripheral blood samples were compared to TBI brain macrophages to assess gene expression changes before and after infiltration into the brain.
TBI macrophage subsets were identified by using a reporter mouse strain (YARG) that expresses eYFP from an IRES inserted at the 3' end of the gene for arginase-1 (Arg1), a hallmark of alternatively activated (M2) macrophages. One day after TBI, 21±1.5% of ipsilateral brain macrophages expressed relatively high levels of Arg1 as detected by YFP. Gene expression analysis of Arg1+ and Arg1- brain macrophage populations revealed that these populations were distinct from either classically activated (M1) macrophages or M2 macrophages, with features of both. The Arg1+ cells differed from Arg1- cells in multiple aspects, most notably in their chemokine repertoires. Thus, the macrophage response to TBI involves recruitment of at least two major macrophage subsets. Overall, our data indicate that the macrophage response to TBI is heterogeneous and unique.

overall_design: Four groups (Arg1- brain macrophages post-TBI, Arg1+ brain macrophages post-TBI, normal blood monocytes, blood monocytes post-TBI) were analyzed. Four replicates of each group were analyzed for a total of 16 samples (only 3 replicates of the blood monocyte groups are included in this submission).

first: William

middle: E

last: Seaman

first: Mary

last: Nakamura

first: Erene

last: Niemi


title: Role of omega-3 fatty acids regulating the brain functions and associated disorders: Transcriptomic analysis of the effect of a fish oil enriched diet on murine brains

status: Public on May 15 2013

city: Fort Detrick

first: Meskerem

last: Jibitu

address: 568 Doughten Drive

department: Integrative Systems Biology

institute: US Army Center for Environmental Health Research

summary:
Based on the comprehensive inhibition of a pool of inflamamsome and apoptosome networks, FD likely reduces the amyloidal burden, attenuates oxidative stress and assist somatostatin activation.
Thus FD is a potential therapeutic agent for Alzheimer’s disease, Parkinson’s disease and affective disorder

overall_design: A total of 10 mice were  randomly chosen from a strain of  C57BL/6j.Those  mice consumed  two diets  customized n-3 PUFA enriched diet (FD)  and standard lab diet (SD )from weaning age until 5 month. Hemi brain samples were harvested from these mice and Transcriptomic Expression Analysis, Cluster and Functional analysis, Real time polymerized chain reaction and assay to validate microarray results were done to collect data. A comparative analysis of the diet compositions reveals relatively comparable amount of major nutrients and consumable calories derived from both diets .The major difference between the two diet types emerges from the percentage of n-3 PUFA and n-6 PUFA present in each type .

first: Rasha

last: Hammamieha

first: Stacy-Ann

last: Miller

first: Nabarun

last: Chakraborty

first: Aarti

last: Gautam

first: Marti

last: Jett

first: Seid

last: Muhie


title: Bmi1

status: Public on Apr 12 2013

first: Brian

last: Biehs

address: 505 Parnassus Ave

institute: UCSF


title: Francisella tularensis subsp. tularensis Induces a Unique Pulmonary Inflammatory Response: Role of Bacterial Gene Expression in Temporal Regulation of Host Defense Responses

status: Public on Apr 15 2013

city: Seattle

first: kathie

last: walters

state: WA

address: 401 Terry Ave N

institute: Institute for Systems Biology

summary: Virulent Francisella tularensis induces a unique pulmonary inflammatory response characterized by temporal regulation of innate immune pathways correlating with altered bacterial gene expression patterns.

overall_design: The pulmonary transcriptional response to aerosolized virulent F. tularensis was compared to other lethal and non-lethal respiratory pathogens.

first: Kathie-Anne

last: Walters

first: Shawn

last: Skerrett

first: Adrian

last: Ozinsky


title: Gene expression of mouse embryonic gonad [Cyp26b1_Stra8]

status: Public on Apr 01 2013

city: Mishima

first: Rie

last: Saba

address: Yata 1111

department: Genetic Strain Research Center

institute: National Institute of Genetics

summary: To analyze the function of retinoic acid and Stra8 in the male germ cell differentiation, we performed expression microarray analysis of the Cyp26b1-/-/Stra8-/- male gonads at E14.5.

overall_design: Biological duplicates were examined at each genotype for each experiment.

first: Saba

last: Rie

first: Kato

last: Yuzuru

first: Saga

last: Yumiko


title: Lipoic acid prevents Cr6+ induced cell transformation and the associated genomic dysregulation.

city: Lucknow

first: Dr Sushil

last: Kumar

state: Uttar Pradesh

address: M G Marg

department: Environmental Carcinogenesis

country: India

institute: Indian Institute of Toxicology Research

summary: Investigation of the transcription profile of cells transformed by Cr6+ in vivo was undertaken. The objective was to elucidate genomic changes underlying the mechanism of action of the carcinogenic dose of Cr6+and their prevention using metabolic antioxidant Lipoic acid (LA). Cr6+ was administered intraperitoneally to LPS+TPA challenged Swiss albino mice in host mediated cell transformation assay using peritoneal macrophages in vivo. The cell transforming potential of Cr6+ test doses was validated by gain of anchorage independent growth potential in soft agar and loss of Fc receptor on target cells. LA was administered in equimolar doses. Compared to non-transformed cells, the gene expression profile of transformed cells was found to be dysregulated substantially and in dose dependent manner. Genes showing down regulation were found to be involved in tumour suppression; apoptosis, DNA repair, and cell-cycle. A similar response was noted in the genes pertaining to immune system, morphogenesis, cell-communication, energy-metabolism, and biosynthesis. The co-administration of lipoic acid prevented the transcription dysregulation and cell transformation by Cr6+ in vivo. The influenced pathways seem to be crucial for progression as well as mitigation of Cr toxicity; and their response to LA indicated their critical role in mechanism of anti-carcinogenic action of LA. Results are of importance to mitigate Cr6+ induced occupational cancer hazard.

overall_design: Agilent one-color experiment, Organism: Mus musculus, Agilent-Whole Genome Mouse 4x44k (AMADID: 14868), Labeling kit: Agilent Quick-Amp labeling Kit (p/n5190-0442)

first: Akanksha

last: Nigam

first: Sushil

last: kumar


title: Gene expression in the islets of 12 wk old Non-Obese Diabetic (NOD) mice and healthy control NOD.B10 mice

status: Public on Apr 10 2013

city: Stanford

first: Linda

last: Yip

address: 269 Campus Drive West, CCSR Building Rm. 2240

department: Medicine

institute: Stanford University

summary: Gene expression in the islets of NOD and NOD.B10 mice at 12 weeks of age, prior to the onset of destructive insulitis.

overall_design: The pancreata of NOD and NOD.B10 mice (n=6) were frozen and islets were isolated by laser capture microdissection.  Cryosections (8 μm) were cut and stained using the Arcturus HistoGene Frozen Section Staining kit (Applied Biosystems) and laser dissection was performed using the Leica AS LMD and the Leica IM 1000 Image Manager Basic software. Sections from at least 40 individual islets were collected and RNA was extracted using the RNeasy micro kit (Qiagen). RNA quality was assessed using the Agilent 2100 Bioanalyzer and the RNA 6000 Pico Reagent Kit (Agilent). Samples were preamplified using the TrueLabeling-PicoAMP kit (SA Biosciences), post-labeled with Cy5 and run against a Cy3-labeled mouse Universal RNA control (SA Biosciences). Microarrays were performed using the Whole Mouse Genome Microarray Kit, 4×44K 2-color arrays (Agilent Technologies).


title: Role of Cyp26b1 in the embryonic male gonad


title: Transcriptional analysis of genes regulating the mitochondrial dNTP pool in muscle cells.

status: Public on Mar 08 2013

city: Padova

first: Gerolamo

last: Lanfranchi

address: Via U. Bassi, 58/B

department: CRIBI - Biotechnology Center and Biology Department

institute: University of Padova

summary: Mutations in genes involved in dNTP metabolism can lead to tissue-specific mitochondrial depletion syndromes (MDS), likely because the expression of key enzymes is reduced to critical levels in post mitotic cells. Our goal was to establish an in vitro skeletal muscle cell model to study the muscle specificity of MDS associated with mitochondrial dNTP pool imbalance. We performed a comprehensive analysis at the mRNA level of enzymes and transporters responsible for dNTP pool imbalance in muscle cells in vitro and in vivo. Agilent Mouse Oligo Arrays 4x44K were utilized to examine expression levels in proliferating and differentiated C2C12 cells as well as in the mouse EDL (fast glycolytic) and soleus (slow oxidative) muscles. The comparison of mRNA expression profiles supports the reliability of our in vitro cell system.

overall_design: Proliferating mouse C2C12 myoblasts were collected at about 50 percent confluence. Myoblasts were then induced to differentiate in vitro into myotubes that were harvested after 96 hours and further purified to reduce the contribution of mononucleated cells present in the culture. Gene expression in C2C12 myoblasts and myotubes was compared with fully differentiated muscle fibers in vivo. To this aim, the extensor digitorum longus (EDL) and soleus hind limb muscles were isolated from adult CD1 mice. These muscles were selected because they have different metabolic (glycolytic vs. oxidative) and twitching (fast vs. slow) properties. Triplicate total RNA samples were submitted to gene expression profiling.

first: Francesco

last: Chemello

first: Miriam

last: Frangini

last: Martinati

first: Beniamina

last: Pacchioni

first: Camilla

last: Bean

first: Chiara

last: Rampazzo

first: Paolo

last: Laveder

first: Caterina

last: Millino

first: Barbara

last: Celegato

first: Stefano

last: Cagnin


title: Muscle Ring Finger 1 (MuRF1) and MuRF2 are Necessary but Functionally Redundant During Developmental Cardiac Growth and Regulate E2F1-Mediated Gene Expression In Vivo

city: Chapel Hill

first: Monte

middle: Shaw

last: Willis

state: NC

address: 103 Mason Farm Road, MBRB 2340B

department: Pathology & Laboratory Medicine

institute: University of North Carolina

summary:
Muscle ring finger (MuRF) proteins have been implicated in the transmission of mechanical forces to nuclear cell signaling pathways through their association with the sarcomere.  We recently reported that MuRF1, but not MuRF2, regulated pathologic cardiac hypertrophy in vivo.  This was surprising since MuRF1 and MuRF2 interact redundantly with sarcomeric proteins in yeast two hybrid studies, and form both homo- and hetero-dimers with each other.  To determine if MuRF1 and MuRF2 were functionally redundant during development, we created mice lacking either 3 or 4 of the MuRF1 and MuRF2 alleles and compared them functionally.  Surprisingly, only mice missing all four MuRF1 and MuRF2 alleles (MuRF1-/-//MuRF2-/-) developed a spontaneous hypertrophic cardiomyopathy - mice that were null for one of the genes, but heterozygous for the other (i.e. MuRF1-/-//MuRF2+/- or MuRF1+/-//MuRF2-/-) were phenotypically identical to wild type mice.  Electron microscopy of the hearts of MuRF1-/-//MuRF2-/-(MuRF1/MuRF2 DN) mice identified altered Z disc and M line architecture, and a distinct swelling of mitochondria. MuRF1-/-//MuRF2-/- mouse hearts displayed increased expression of genes associated with fetal cardiac metabolism, including smooth muscle actin and b myosin heavy chain, suggesting that the cardiac hypertrophy seen in these mice was associated with a reversion to a fetal gene program. Despite our prediction that we would also see an increase in glucose compared to fatty acid oxidation (another trait of fetal cardiac metabolism) we saw that MuRF1-/-//MuRF2-/- heart homogenates oxidized significantly less glucose compared to controls, suggesting an important role for MuRF1 and MuRF2 in the regulation of glucose metabolism in vivo. This study identifies a previously unreported redundancy in the function of MuRF proteins in normal cardiac development.

Keywords: Genetic modification.

overall_design: Four strain-matched groups of 12 week old mice were investigated: 1) MuRF1 -/- MuRF2 -/-; 2) MuRF1 +/+ MuRF2 +/+; 3) MuRF1 -/- MuRF2 +/-; 4) MuRF1 +/- MuRF2 -/-.  Biological replicates:  4 WT, 4 MuRF1 -/- // MuRF2 -/-, 4 MuRF1 +/- //MuRF2 -/-, 4 MuRF1 -/- // MuRF2 +/-.  Hearts harvested.  One replicate per array.

first: Kristine

middle: M

last: Wadosky

first: Jessica

last: Rodriguez

first: Jonathon

last: Schisler

first: Pam

last: Lockyer

first: Eleanor

last: Hilliard

first: David

middle: J

last: Glass

first: Cam

last: Patterson


title: In Vivo RNA Interference Screening Identifies a Leukemia-Specific Dependence on Integrin Beta 3 Signaling

status: Public on Apr 24 2013

city: Cambridge

first: Gabriela

last: Alexe

state: MA

address: 415 Main St.

department: Computational Biology and Bioinformatics

institute: Broad Institute

summary:
We used an in vivo short hairpin RNA (shRNA) screening approach to identify genes that are essential for MLL-AF9 acute myeloid leukemia (AML). We found that Integrin Beta 3 (Itgb3) is essential for murine leukemia cells in vivo, and for human leukemia cells in xenotransplantation studies.  In leukemia cells, Itgb3 knockdown impaired homing, downregulated LSC transcriptional programs, and induced differentiation via the intracellular kinase, Syk.  In contrast, loss of Itgb3 in normal HSPCs did not affect engraftment, reconstitution, or differentiation.  Finally, we confirmed that Itgb3 is dispensable for normal hematopoiesis and required for leukemogenesis using an Itgb3 knockout mouse model.  Our results establish the significance of the Itgb3 signaling pathway as a potential therapeutic target in AML.
R940406 (R406, the active metabolite of fostamatinib) was supplied by Rigel Pharmaceuticals, Inc., South San Francisco, CA, and AstraZeneca Pharmaceuticals, Wilmington, DE, USA. R406 was resuspended in dimethyl sulfoxide (DMSO) (Sigma-Aldrich) and stored at −80°C. .   HL-60, U937 and KG-1 cell  lines were purchased from the American Type Culture Collection. MOLM-14 cell lines were provided by Dr. Scott Amstrong (Dana-Farber Cancer Institute, Boston MA, USA.)  All cell lines were maintained in RPMI 1640 (Cellgro) supplemented with 1% penicillin-streptomycin and 10% fetal bovine serum (FBS, Sigma-Aldrich) at 37 °C with 5% CO2.

overall_design: MOLM-14, U937, HL-60  and KG-1 cells were grown in 4mM R406 for 24 hours

first: Kimberley

last: Stegmaier


title: Transcriptional profiles of kidneys that underwent reversible UUO model using model mice for erythropoietin-deficiency anemia (ISAM)

status: Public on Mar 20 2013

city: Sendai

first: Masayuki

last: Yamamoto

address: 2-1 Seiryo-machi, Aoba-ku

department: Medical Biochemistry

institute: Tohoku University Graduate School of Medicine

summary: We have established a novel mouse model for postnatal erythropoietin (Epo)-deficiency anaemia, designated ISAM (inherited super anemic mouse) using a transgenic complementation rescue technique. To identify responsible signals for myofibroblastic transformation of Renal Erythropoietin-producing cells (REPs), we examined the mRNA expression profile of whole ISAM kidneys that underwent reversible UUO model.

overall_design: Unilateral ureteral obstruction (UUO)-induced gene expression changes were analyzed. Three UUO-treated samples (Clip), three reversed UUO kidneys (ClipR-14), and two sham-treated and one untreated samples were compared.

first: Tomokazu

last: Souma

first: Shun

last: Yamazaki

first: Takashi

last: Moriguchi

first: Norio

last: Suzuki


title: Role for HA and the viral RNA polymerase complex in the virulence of the 1918 influenza virus

status: Public on Feb 23 2013

first: Michael

last: Katze

address: Rosen Building 960 Republican St.

department: Microbiology

institute: University of Washington

summary: The goal of this experiment was to examine the biological properties of reassortant viruses between the 1918 virus and a contemporary human H1N1 virus to determine the role of hemagglutinin (HA) and the viral RNA polymerase complex of 1918 virus toward pathogenesis and abberant host responses in mice.

overall_design: Six- to eight-week-old female BALB/c mice were anesthetized and inoculated with 50 μl of phosphate-buffered saline (PBS; Mock) or with 10^6 pfu of virus in a 50 μl volume. There are a total of six biological conditions: wild-type 1918 virus (A/Brevig Mission/1/1918; 1918), wild-type K173 virus (A/Kawasaki/173/2001; K173), three reassortant viruses between 1918 and K173 viruses [1918HA/K173, 1918PB1/K173, and 1918(3P+NP)/K173], and mock-infected control animals. Nine animals per virus group were inoculated, and whole lungs were collected at 1, 3 and 5 days post-inoculation from three animals per virus group per time point. Two of three mice inoculated with 1918 virus and 1918HA/K173 virus died by day 5 post-inoculation. Six animals were inoculated with PBS. Whole lungs from two mock-infected animals per time point were collected and served as the uninfected reference. All samples were processed for lung gene expression analysis using oligonucleotide microarrays. Technical replicates were performed for 9 samples.

first: Tokiko

last: Watanabe

first: Jennifer

last: Go

first: Shinji

first: Kyoko

last: Shinya

first: Nicolas

last: Tchitchek

first: Arndt

last: Benecke

first: Yoshihiro

last: Kawaoka


title: Gene expression of mouse embryonic gonad [Cyp26b1]

first: Rie

last: Saba

summary: To analyze the function of retinoic acid in the male germ cell differentiation, we performed expression microarray analysis of the Cyp26b1-/- male gonads from E12.5 to E15.5.

overall_design: Biological duplicates were examined at each stage and genotype for each experiment.

first: Saba

last: Rie

first: Saga

last: Yumiko


title: IM007 - Mouse infection with A/Vietnam/1203-CIP048_RG4/2004 (H5N1)

status: Public on Feb 21 2013

summary: A/Vietnam/1203-CIP048_RG4/2004 (H5N1) is an NS1trunc124 mutation in the wild type A/Vietman/1203/2004 (H5N1). The goal of this study was to determine the host response (C57BL/6 mouse model) to the NS1 truncation at both 10^3 PFU and 10^4 PFU.

overall_design: Groups of 20-week-old C57BL/6 mice were infected with the A/Vietnam/1203-CIP048_RG4/2004 (H5N1). This is an NS1trunc124 mutation in the wild type A/Vietnam/1203/2004 (H5N1) virus. Infections were done at 10^3 PFU or 10^4 PFU or time-matched mock infected. Time points were 1, 2, 4 and 7 d.p.i. There were 3-5 animals/dose/time point. Lung samples were collected for virus load, transcriptional and proteomics analysis. Weight loss and animal survival were also monitored.

first: Yoshi

last: Kawoaka

first: Amie

last: Eisfeld

first: Jean

last: Chang

first: Lynn

last: Law

first: Chengjun

last: Li


title: Gene expression of mouse embryonic gonad [Nanos2_Stra8]

status: Public on Feb 06 2013

summary: To examine whether the meiosis was solo factor responsible for the disruption of the male gonocyte differenitiation in the Nanos2-/- male germ cells, we deleted Stra8 function from Nanos2-null background and performed expression microarray analysis of the Nanos2+/-/Stra8+/- , Nanos2-/-/Stra8+/-, and Nanos2-/-/Stra8-/- male emnbryonic gonads at E14.5.

overall_design: Biological duplicates were examined at each stage, genotype, and sex for each experiment.

first: Yuzuru

last: Kato


title: Gene expression of adipocyte and stromal-vascular fractions

status: Public on Apr 27 2013

city: Schwerzenbach

first: Christian

last: Wolfrum

address: Schorenstrasse 16

institute: ETH Zürich

summary: In order to select mRNA transcripts strongly enriched in murine white adipocytes versus brown adipocytes or stromal-vascular fraction, gene expression data of the adipocyte and stromal-vascular fractions of the interscapular brown, inguinal subcutaneous as well as visceral epididymal adipose tissue depots of young adult male C57BL/6 mice housed at constant 23°C ambient temperature were obtained.

overall_design: 18 samples: 3 different adipose tissues separated into stromal-vascular fraction and adipocytes, analyzed in biological triplicates.

first: Matthias

last: Rosenwald


title: Transcriptional profiling of 2D colonies derived from WT, Bmi1-/-, and Bmi1-/-;Ink4a/Arf Labial cervical loops

first: Brian

last: Biehs

state: CA

summary: This experiment is aimed at determining the genetic signature of dental stem cell colonies grown in vitro and how that signature changes when Bmi1 activity is removed. Another question to be answered by the experiment is whether Bmi1 has alternate targets besides Ink4a/Arf.

overall_design: There are 12 total samples: 4 biological replicates for each genotype that consist of single colonies grown in vitro.


title: Gene expression of mouse embryonic gonad

state: Shizuoka

summary: To elucidate the function of NANOS2 to regulate the transcriptome in embryonic male germ cells, we performed expression microarray analysis of the embyornic gonads of the Nanos2+/-, Nanos2-/- male and wild type female from E12.5 to E15.5.  The Nanos2+/- and Nanos2-/-  female gonads at E15.5 were analyzed as a negative control.

first: Aya

last: Sato

first: Yumiko

last: Saga


title: Nanos2-associated mRNAs in the embryonic male gonad

summary: To identify Nanos2-associated mRNAs, we performed microarray analysis of mRNAs coprecipitated with FLAG-tagged NANOS2 with male gonad from Tg-Nanos2 enhancer-3xFLAG-Nanos2-3'UTR at E14.5.

overall_design: Biological duplicates were examined at each sample.


title: Mouse gene expression profile after transfected with miR-27a mimics and mimic NC in Raw

status: Public on Jan 31 2013

city: shanghai

first: ql

last: zheng

address: xiangyin

institute: immunity

summary:
Microarry analysis of mouse gene expression profile after transfected with miR-27a mimics (27a-7) and mimic NC (NC-9)
Goal was to determine the effects of miR-27a transfection on global gene expression.

overall_design: Two-condition experiment, 27a-7 vs.NC-9.

first: Qing

middle: L

last: Zheng

first: J

last: Hou


title: miRNA expression profiles in endometriotic cyst stromal cells (ECSCs).

city: Yufu-shi

first: Kaei

last: Nasu

state: Oita

address: Idaigaoka 1-1, Hasama-machi

department: Obstetrics and Gynecology

institute: Oita University, Faculty of Medicine

summary: To identify the miRNAs which play a role in the development of endometriosis, we explored differentially expressed miRNAs between ECSCs (N=8) and normal endometrial stromal cells (NESCs, n=8) using miRNA microarray. The expression profiles in ECSCs and NESCs were obtained, then the miRNAs were filtered by signal intensity (20.0<, at least one out of 16 samples have values within range) and flags (at least 70% of cases have good flags).  The differentially expressed miRNAs in ECSCs compared with NESCs were identified using volcano plot (Fold change >= 2.0, Mann-Whiteny U test p<0.05).

overall_design: The primary culture of ECSCs and NESCs (controls) were utilized. Total RNA was extracted from them, and miRNA microarray analysis was performed. The miRNAs differentially expressed between ECSCs and NESCs were identified, and aberrantly expressed miRNAs in ECSCs were defined as the endometriosis related miRNAs.

first: Wakana

last: Abe


title: Gene expression of mouse embryonic gonad [Nanos3]

first: Rie

last: Saba

summary: To identify germ cell- and somatic cell-specific gene expression profiles, we performed expression microarray analysis of the mouse gonads of the Nanos3+/-, Nanos3-/- female and male embryos from E12.5 to E15.5.

first: Saba

last: Rie

first: Sato

last: Aya

first: Saga

last: Yumiko


title: Gene expression profile in livers from control or Wy-14643 treated  MycF/F or MycF/F,ERT2-Cre mice

status: Public on Jan 30 2013

city: Bethesda

first: Aijuan

last: Qu

state: Maryland

address: 9000 Rockville Pike

institute: NIH

summary: Genes responsible for the effects of PPARalpha agonist Wy-14643 on liver

overall_design: 4 groups were included, MycF/F+ con, MycF/F+ Wy, MycF/F, ERT2-Cre+ Con, MycF/F,ERT2-Cre+Wy

first: Yan

last: Cai


title: Expression profiles of bone marrow cells from model mice for erythropoietin-deficiency anemia (ISAM)

status: Public on Jan 18 2013

first: Masayuki

last: Yamamoto

summary: We established a novel mouse model for postnatal erythropoietin (Epo)-deficiency anaemia, designated ISAM (inherited super anemic mouse), using a transgenic complementation rescue technique. To identify Epo-regulated genes in vivo, we examined the mRNA expression profile in the bone marrow of ISAM 6 hours after recombinant human EPO (rHuEPO) administration.

overall_design: Erythropoietin-induced gene expression in mouse bone marrow was measured at 6 hours after rHuEPO administration (3,000 U/kg). Three Epo-treated samples were analyzed, and two PBS-treated and one untreated samples were used as a control group.

first: Shun

last: Yamazaki

first: Tomokazu

last: Souma

first: Norio

last: Suzuki


title: IM006B - Mouse infection with A/Vietnam/1203-CIP048_RG3/2004 (H5N1)

first: Michael

last: Katze

summary: A/Vietnam/1203-CIP048_RG3/2004 (H5N1) is a PB1-F2 deletion in wild type A/Vietnam/1203/2004 (H5N1). The goal of this study was to determine the host response (C57BL/6 mouse model) to the PB1-F2 mutation at a 10^4 PFU dose.

overall_design: Groups of 20-week-old female C57BL/6 mice were infected with A/Vietnam/1203-CIP048_RG3/2004 (H5N1). This is a PB1-F2 deletion in wild type A/Vietnam/1203/2004 (H5N1). Infections were with 10^4 PFU or time-matched mock infections. Time points were 1, 2, 4 and 7 d.p.i. There were 1-5 animals/dose/time point. Lung samples were collected for virus load, transcriptional analysis and proteomic analysis. Weight loss and animal survival were also monitored.

first: Yoshi

last: Kawoaka

first: Amie

last: Eisfeld

first: Jean

last: Chang

first: Lynn

last: Law

first: Chengjun

last: Li


title: Role of Nanos2 in the embryonic male gonad

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

overall_design: Refer to individual Series


title: Mice with targeted deletion of Nxf7, the murine ortholog of the clinically implicated NXF5, display impaired hippocampal learning and neuroplasticity

status: Public on Jan 28 2013

city: Leuven

first: Rekin's

last: Janky

address: Herestraat 49 Box 816

department: Nucleomics Core

country: Belgium

institute: VIB

summary: Members of the Nuclear mRNA Export Factor (NXF) family are implicated in nuclear export and/or cytoplasmic transport of mRNAs in eukaryotic cells. We previously proposed NXF5 to be involved in cognitive development and aimed to study its functional role further using a mouse model. The syntenic region of the human Xcen-GLA-NXF5-NXF2-NXF3-BEX4-Xqter in the mouse is Xcen-Gla-Nxf2-Nxf7-Nxf3-Bex4-Xqter strongly indicating that mouse Nxf2 is the homolog of human NXF5. However, our functional analyses demonstrated that mouse Nxf7 is actually the functional homolog  of NXF5. Both orthologs are expressed in brain, although at low levels, show predominant cytoplasmic localization, and present a granular staining in neuronal dendrites, all indicative for a role in cytoplasmic mRNA transport or metabolism. The mouse and human Nxf2/NXF2 proteins on the other hand, show highest expression in testis, and mostly nuclear staining with incorporation in the nuclear membrane, suggesting a predominant role in nuclear mRNA export. Based on these findings we generated an Nxf7 knockout mouse, which was viable and fertile and no gross anatomical changes or morphological brain abnormalities were detected. Detailed behavioral analysis demonstrated that Nxf7 KO mice displayed a deficit in hippocampus-dependent spatial learning and memory. At the cellular level, this was accompanied by impaired hippocampal long-term potentiation, but normal long-term depression, suggesting a severe functional imbalance in NMDA-dependent synaptic plasticity. In conclusion, the present findings indicate that NXF5, and its murine ortholog Nxf7, play a crucial role in neurocognitive (memory) functions, and explain why its deletion leads to intellectual disability.

overall_design: Two male wild type (WT1 and WT2) and two Nxf7 knockout (KO1 and KO2) mice were used in each hybridization experiment (hippocampus or cortex). A loop-design hybridization scheme (WT1/KO1, KO1/WT2, WT2/KO2 and KO2/WT1) was performed for each experiment so as to have each sample labeled once with Cy5 and once with Cy3, and hybridised to both samples of the other genotype (WT or KO). Hybridization was done on Agilent Mouse Whole Genome arrays according to the manufacturer’s procedures.

first: Zsuzsanna

last: Callaerts-Vegh

first: Tariq

last: Ahmed

first: Joke

last: Nevelsteen

first: Anton

last: Roebroek

first: Jelle

last: Verbeeck

first: Stefanie

last: Belet

first: Tom

last: Van de Putte

first: Peter

last: Marynen

first: Detlef

last: Balschun

first: Rudi

last: D' Hooge

first: Guy

last: Froyen


title: The differentiation stage of p53- and Rb-deficient bone marrow mesenchymal stem cells imposes the phenotype of in vivo sarcoma development (part I)

status: Public on Jan 27 2013

city: Armilla

first: Alberto

last: Labarga

state: Granada

address: Av. Innovacion 1

country: Spain

institute: Experimental Serendipity S.L.

summary: We have previously reported that the deficiency of p53 alone or in combination with Rb (Rb-/- p53-/-) in adipose-derived MSCs (ASCs) promotes leiomyosarcoma-like tumors in vivo. Here, we hypothesized that the source of MSCs and/or the cell differentiation stage could determine the phenotype of sarcoma development. To investigate whether there is a link between the source of MSCs and sarcoma phenotype, we generated p53-/- and Rb-/-p53-/- MSCs from bone marrow (BM-MSCs). Both genotypes of BM-MSCs initiated leiomyosarcoma formation similar to p53-/- and Rb-/-p53-/- ASCs. In addition, gene expression profiling revealed a link between p53- or Rb-p53-deficient BM-MSCs and ASCs and muscle-associated sarcomagenesis. These data suggest that the tissue source of MSC does not seem a crucial factor in the development of a particular sarcoma phenotype. To analyze whether the differentiation stage defines the sarcoma phenotype, BM-MSCs and ASCs were induced to differentiate towards the osteogenic lineage, and both p53 and Rb were excised using Cre-expressing adenovectors at different stages along osteogenic differentiation. Regardless of the level of osteogenic commitment, the inactivation of Rb and p53 in BM-MSC-derived, but not in ASC-derived, osteogenic progenitors gave rise to osteosarcoma-like tumors which could be serially transplanted. This indicates that the osteogenic differentiation stage of BM-MSCs imposes the phenotype of in vivo sarcoma development, and that BM-MSC-derived osteogenic progenitors rather than undifferentiated BM-MSCs, undifferentiated ASCs or ASC-derived osteogenic progenitors, represent the cell of origin for osteosarcoma development.

overall_design: BM-MSC and ASC cultures were established from 3 mouse strains: (a) WT, (b) p53loxP/loxP and (c) p53loxP/loxP RbloxP/loxP. The corresponding mutant cells were generated by excision of the LoxP-flanked sequences by infection of all MSC cultures with adenoviral vectors expressing the Cre-recombinase gene (Ad-CMV-Cre). NSG mice were inoculated subcutaneously with 5×10^6 mutant cells. Animals were killed when tumors reached 1 cm3 or 150 days after infusion. Some of the obtained tumors were mechanically disaggregated to establish ex vivo MSC-transformed cell lines. Gene expression analysis was performed using BM-MSCs and ASCs from all genotypes, as well as tumor cell lines derived from p53-/- and p53-/-Rb-/- BM-MSC and ASC cultures.

first: Ruth

last: Rubio

first: Pablo

last: Menendez

first: Rene

last: Rodriguez


title: IM006A - Mouse infection with PB1-F2del: A/Vietnam/1203-CIP048_RG3/2004 (H5N1) at 10^3 PFU

status: Public on Jan 19 2013

first: Michael

last: Katze

summary: To determine the host response (C57BL/6 mouse model) to the PB1-F2del: A/Vietnam/1203-CIP048_RG3/2004 (H5N1) virus at 10^3 PFU.

overall_design: Groups of 20-week-old C57BL/6 mice were infected with the PB1-F2del: A/Vietnam/1203-CIP048_RG3/2004 (H5N1) virus at 10^3 PFU or time-matched mock infected. Time points were 1, 2, 4 and 7 d.p.i. There were 5 mice/time point for infections and 3 mice/time point for time-matched mocks. Lung samples were collected for virus load, transcriptional analysis and proteomics analysis. Weight loss and animal survival were also monitored.

first: Yoshi

last: Kawoaka

first: Amie

last: Eisfeld

first: Jean

last: Chang

first: Lynn

last: Law

first: Chengjun

last: Li


title: Genomic Reprogramming Errors Do Not Accumulate with Serial Recloning in the Mouse

status: Public on Jan 15 2013

city: Tokyo

first: Takashi

last: Kohda

address: 1-5-45 Yushima, Bunko-ku

department: Medical Research Institute

institute: Tokyo Medical and Dental University

summary: To date, the success rate of serial animal cloning has decreased with increasing iterations and recloning has failed in all species after a few generations. This has suggested that recloning might be impossible because of the accumulation of lethal genetic or epigenetic abnormalities. Here, we carried out repeated recloning in the mouse using our somatic cell nuclear transfer method combined with a histone deacetylase inhibitor. The success rate of recloning did not decrease even after 25 iterations and more than 500 viable offspring have been obtained from a single original donor. Although the genomic reprogrammability of somatic cell nuclei did not improve, reprogramming errors or clone-specific abnormalities did not accumulate with recloning. Our results provide the first evidence that iterative recloning is possible, suggesting that animals might be able to be recloned indefinitely.

overall_design: Brain and liver samples from 4 somatic cell clone (CC), 4 somatic cell clones of 20 generations (G20) and 4 normal controls (ICSI) neonate.

first: Sayaka

last: Wakayama

first: Haruko

last: Obokata

first: Mikiko

last: Tokoro

first: Chong

first: Yukari

last: Terashita

first: Eiji

last: Mizutani

first: Van

last: Nguyen

first: Satoshi

last: Kishigami

first: Fumitoshi

last: Ishino

first: Teruhiko


title: IM005 - Mouse infection with PB2-627E: A/Vietnam/1203-CIP048_RG2/2004 (H5N1)

status: Public on Jan 05 2013

first: Michael

summary: To determine the host response (C57BL/6 mouse model) to the PB2-627E: A/Vietnam/1203-CIP048_RG2/2004 (H5N1) virus at 10^4 PFU.

overall_design: Groups of 20-week-old female C57BL/6 mice were infected with the PB2-627E: A/Vietnam/1203-CIP048_RG2/2004 (H5N1) virus at 10^4 PFU or time-matched mock infected. Time points were 1, 2, 4 and 7 d.p.i. There were 5 mice/time point for infections and 3 mice/time point for time-matched mocks. Lung samples were collected for virus load, transcriptional analysis and proteomics analysis. Weight loss and animal survival were also monitored.


title: Gene expression data from AKT induced salivary gland tumors

status: Public on Jan 14 2013

city: Grand Rapids

first: Karl

last: Dykema

state: MI

address: 333 Bostwick Ave. NE

institute: Van Andel Institute

summary: Rapamycin treatment of AKT induced salivary gland tumors

overall_design: Normal tissue (parotid and submandibular), untreated tumor tissue, and tumor tissue treated for 3/14 days


title: Esophageal epithelium of 12 weeks old mice (WT, Nrf2-/-) on C57BL background with or without gastroesophageal reflux for 4 weeks.

status: Public on Jan 01 2013

city: Camden

first: Xiaoxin

middle: Luke

last: Chen

state: NJ

address: 403 Haddon Avenue

institute: Coriell Institute for Medical Research

summary: Transcriptional profiling of adult esophageal epithelium comparing wild-type mice with Nrf2-/- mice with or without gastroesophageal reflux for 4 weeks. Goal was to determine the role of Nrf2 on the barrier function of mouse esophageal epithelium.

overall_design: Two-class comparisons. Wild-type/without reflux vs. Nrf2-/-/without reflux; Wild-type/gastric reflux vs. Nrf2-/-/gastric reflux; Wild-type/duodenal reflux vs. Nrf2-/-/duodenal reflux; Wild-type/mixed reflux vs. Nrf2-/-/mixed reflux. Biological replicates: 3 replicates for each group.

first: Hao


title: Differential gene expression in the airway epithelium of beta6 ko mice chronically challenged with OVA

status: Public on Dec 31 2012

city: San Francisco

first: Xiaozhu

last: Huang

address: 1550 4th St. Rock Hall, 5th FL. Rm 545

department: medicine

institute: UCSF

summary: Expression microarrays identified 119 genes that were significantly differentially expressed in the epithelium of WT and β6 KO mice after saline or chronic allergen challenge. PAM clustering revealed two interesting clusters (6 and 8) that we had not identified in previous comparisons by whole lung microarrays. Cluster 6 genes were low at baseline in both WT and β6 KO mice and were increased in WT but not in β6 KO mice after chronic allergen challenge such as Mcpt1. Cluster 8 genes were increased at baseline in β6 KO mice, and included 6 mast cell related genes (cma1, mcpt4, cpa3, mcpt6, tpsab1, il1rl1). The most informative differentially expressed genes identified in microarrays of the epithelial microenvironment were not epithelial genes, but mast cell genes.

overall_design: Control and beta6 ko mice (wt-S (4), wt-OVA (4), ko-S (4), ko-OVA (4)) were sensitized and challenged with OVA or saline, airway epithelium were brush-harvested.

first: Dean

last: Sheppard


title: HF liver: Control vs. Plin2-ASO treated

status: Public on Dec 05 2012

city: Norfolk

first: yumi

last: imai

state: VA

address: 799W Olney Road, LH 2156

institute: Eastern Virginia Medical School

summary: Transcriptional profiling of mouse liver comparing control, scrambled-oligonucleotides (Cont)-treated mice with Perilipin 2-antisense oligonucleotides (Plin2-ASO)-treated mice. C57BL/6 mice on a high-fat diet were treated with oligonucleotides in vivo. The goal was to determine the effects of Plin2 down-regulation in the liver on global gene expression.

overall_design: Two-condition experiment, control oligonucleotides vs. Plin2-antisense oligonucleotides. Biological replicates: 4 control replicates, 4 Plin2-ASO replicates.

first: Rexford

middle: S

last: Ahima

first: Yumi

last: Imai


title: gene expression signatures of Akt1 +/- mice at 8weeks and 35weeks

city: Chiba

first: Aika

last: Nojima

institute: Chiba univeersity

summary: To know the difference of transcriptome between Wild type and Akt1+/- mice, 8weeks and 35weeks female mice were subjected to microarray analysis.

overall_design: Wild type and Akt1+/- mice in age 8weeks and 35weeks were subjected to microarray analysis. Liver, muscle and visceral fat were used. Only female mice were used.

first: Kazuhiro

last: Sato

first: Takahiro

last: Nakayama