title: Role of FMRP in neurogenesis

status: Public on Jul 04 2016

city: Valbonne - Sophia-Antipolis

first: Kevin

last: Lebrigand

address: 660 route des lucioles

country: France

institute: IPMC/CNRS

summary: Fragile X syndrome (FXS) is a rare disease but is the most common form of inherited intellectual disability and a leading cause of autism. FXS is due to the absence of the Fragile X Mental Retardation Protein (FMRP), an RNA-binding protein mainly involved in translational control. Even if this molecular defect is known, no specific therapy is available for FXS. The first alteration observed in the brain of FXS patients and of Fmr1 KO mice, model for FXS, is represented by an abnormal dendritic morphology that is associated with an altered synaptic plasticity. These findings led to numerous studies focused on mature neurons. However, recently, an increasing body of evidence is pointing out the importance of FMRP in the early steps of brain development. Thus, with the purpose to decipher the earliest molecular events leading to FXS we developed a stem-cell-based disease model by knocking-down the expression of Fmr1 in mouse embryonic stem (ES) cells. To gain insights in the pathways that are affected when FMRP is repressed, we performed a gene expression profile analysis comparing total RNA from shFmr1 and shControl ES cells using whole genome mouse microarrays. Transcripts were clustered according to their Gene Ontology classification using the DAVID software. Surprisingly, the most altered functional category was Nervous system development and function, highlighting the role of FMRP also during the earliest steps of neural development.

overall_design: To study the precise role of FMRP in Embryonic stem (ES) cells, we used an RNAi-based loss-of-function strategy by transducing mouse ES cells with a lentivirus expressing GFP and a shRNA targeting the constitutive exon 1 of Fmr1 (shFmr1). A random shRNA (shCT) was used as a control sequence. Transduced cells were sorted by flow cytometry and established as non-clonal cell populations. RNA samples were harvested and profiling experiments were performed in “dye-balance” as indicated for each replicate.

first: B

last: Bardoni

last: Mari

first: K

first: P

last: Barbry

first: N

last: Nottet


title: Titered FOXO overexpression maintains cardiac proteostasis and ameliorates age-associated functional decline

status: Public on Jul 01 2016

city: Claremont

first: Alexander

middle: C

last: Zambon

state: CA

address: 517 Watson Drive

department: Biopharmaceutical Sciences

country: USA

institute: Keck Graduate Institute

summary:
Heart performance declines with age. Reduced protein quality control (PQC) due to decreased function of the ubiquitin/proteasome system (UPS), autophagy, and/or chaperone-mediated protein refolding is a likely contributor to age-associated cardiac performance decline. The transcription factor FOXO participates in the regulation of genes involved PQC and a host of other processes. Here, the effect of cardiac-restricted dFOXO overexpression was investigated in Drosophila, a genetically pliable and rapidly aging model. Modest dFOXO overexpression in the heart was protective, ameliorating functional decline with age. Increased expression of genes associated predominantly with UPS relative to other PQC components accompanied dFOXO-mediated cardioprotection, which was corroborated by a significant decrease in ubiquitinated myocardial proteins.
In agreement, knockdown of upregulated UPS components seemingly induced premature aging. Despite these findings, excessive dFOXO overexpression or knockdown proved detrimental to heart function and overall organismal development. This study highlights Drosophila as a model of cardiac aging and FOXO as a tightly-regulated mediator of proteostasis and heart performance over time.

overall_design: Two replicates of 4 different samples were analyzed. Two of these samples were controls (GMH5 x yw 1 week and GMH5 x yw 5 week).

first: Anna

last: Blice-Baum

first: Gaurav

last: Kaushik

first: Meera

last: Viswanathan

first: Adam

middle: J

last: Engler

first: Rolf

last: Bodmer

first: Anthony

last: Cammarato


title: Food protein-induced activation and death of CD4+ Helios+ Foxp3- T cells is required for IL-10 production and intestinal homeostasis

city: Berlin

first: Hans-Joachim

last: Mollenkopf

address: Charitéplatz 1

country: Germany

institute: Max-Planck-Institute for Infection Biology

summary: The impact of dietary proteins on homeostasis and immune function of the intestine is poorly understood. We here show that physiological uptake of dietary proteins induced an activated, CD4+CD44+Helios+ T cell population, predominantly in Peyer's patches (PP). These cells are distinct from Foxp3+regulatory T cells and microbiota-independent. Dietary protein-reactive T lymphocytes remained innocuous due to an equilibrium between activation and apoptosis. Macrophage mediated uptake of apoptotic T cells from the PP but not from other tissues resulted in strong IL-10 expression. In contrast, replacement of dietary proteins by amino acids resulted in low numbers of activated and apoptotic CD4+CD44+Helios+ T cells together with reduced amounts of IL-10 and downregulation of genes involved in intestinal integrity such as trefoil factors and gastrokines. The impaired intestinal barrier function of these animals was restored after switching to conventional diet, demonstrating the essential role of food proteins for induction of epithelial repair mechanisms and immunological homeostasis.

overall_design: Microarray experiments were performed as dual-color hybridizations on Agilent-014868 Whole Mouse Genome 4x44K catalog arrays. To compensate for dye-specific effects, a dye-reversal color-swap was applied.

last: Visekruna

first: Sabrina

last: Hartmann

first: Hans

first: Ulrich

last: Steinhoff


title: Glis3 plays a crucial role in spermatogenesis [923]

city: RTP

first: NIEHS

last: Microarray Core

state: NC

address: 111 T.W. Alexander Drive

department: DIR

institute: NIEHS

summary: We show that Glis3 is expressed in gonocytes, SSCs and SPCs, but not in differentiated spermatogonia or subsequent stages of spermatogenesis nor in Sertoli or Leydig cells. We further demonstrate that Glis3-deficiency causes a severe impairment in spermatogenesis in mice. Although the number of gonocytes was slightly diminished in Glis3KO testis, the number undifferentiated, PLZF+ spermatogonia was dramatically reduced leading to a virtual block in the progression of spermatogenesis. Gene expression profiling showed that the expression of a number of genes associated with self-renewal and differentiation of spermatogonial cells was significantly decreased in 1-week-old Glis3KO2 testis. These included a set of GDNF-dependent genes, such as Etv5, Bcl6b, Lhx1, Brachyury, Id4, and Pou3f1, and GDNF-independent genes, such as FoxO1, Oct4, and Zbtb16. Impairment of the nuclear localization of FoxO1 may be in part responsible for the reduced expression of Ret, Lhx1, and Sall4 in Glis3KO2 testis. Our study identifies Glis3 as a novel and critical regulator of early stages of spermatogenesis.

overall_design: Thy1+ cells were isolated from 3 WT and 3 Glis3KO2 testis at postnatal day 4, and total RNAs were purified from them. Then the samples were applied to Agilent mouse genome chip.

first: Hong

last: Kang

first: Anton

middle: M

last: Jetten


title: Glucocorticoids in maintaining cardiac homeostasis in C57bl/6 (wild-type) mice

status: Public on Jun 09 2016

summary:
To further understand the genomic effects of glucocorticoids in the heart we performed microarray studies on hearts collected from long-term ADX-mice.
Our objective is to find cardiac specific genes regulated by glucocorticoids.

overall_design: C57bl/6 (wild-type) mice were adrenalectomized. Hearts were collected from sham-adrenalectomized and adrenalectomized mice 6 months following the surgery. Three biological replicates were used for this study.

first: John

middle: A

last: Cidlowski

first: Diana

last: Cruz-Topete


title: Transcriptome analysis of  satellite cells isolated from an animal model of skeletal muscle hypertrophy

status: Public on Jun 28 2016

city: Geneva

first: Flavio

middle: Lorenzo

last: Ronzoni

address: rue Michel Servet 1

department: Pathology and Immunology

country: Switzerland

institute: University of Geneva

summary: Skeletal muscle is a post-mitotic tissue with unique plasticity. It has an extraordinary ability to adjust to changes in its physiological environment by altering its metabolic phenotype and its mass. Satellite cells are the most important myogenic progenitor cells involved in muscle regeneration and remodeling. The activation of these cells is governed by genetic programs involving complex transcriptional responses and can be involved in muscle hypertrophy adaptations. We described here gene expression variations evaluated by microarray analysis in satellite cells isolated from wild type and Magic-F1 transgenic mice, a model of skeletal muscle hypertrophy. The transcriptome analysis shows  an altered gene signature in proliferating Magic-F1  satellite cells compared to controls, involving genes associated to muscle growth and vasculogenesis.

overall_design: Biological triplicates of Magic-F1+/+ and control satellite cells were used for microarray analysis.

first: Gabriele

last: Ceccarelli

first: Ilaria

last: Perini

first: Laura

last: Benedetti

first: Daniela

last: Galli

first: Francesca

last: Mulas

first: Martina

last: Balli

first: Giovanni

last: Magenes

first: Riccardo

last: Bellazzi

first: Gabriella

last: De Angelis

first: Maurilio

last: Sampaolesi


title: Glis3 regulates pancreatic beta cells development and maturation

summary: Glis3 is expressed in pancreatic beta and PP cells. To identify down stream target genes of Glis3, we performed microarray analysis using pancreas total RNAs from 1 week-old WT and Glis3KO2 mice.  insulin and pancreatic polypeptide (Ppy) was significantly decreased together with several other β cell markers, Glut2 and MafA by microarray analysis. Immunohistochemistry, QRT-PCR, and transmission electron microscopy indicated that postnatal Glis3KO2 pancreas still contains a large population of β cells that express Pdx-1, Nkx6.1, and Isl-1; however, insulin production and secretory granules were greatly reduced in these cells. In addition, chromogranin A (ChgA) and Urocortin 3, which are associated with mature β cells, was dramatically decreased in Glis3KO2 pancreas. These observations suggest that Glis3 plays a critical role in the maturation of pancreatic β cell phenotype.

overall_design: Pancreatic total RNAs were purified from 4 WT and 4 Glis3KO2 at 1 week old age. Then the samples were applied to Agilent mouse genome chip.

middle: S


title: Glis3 plays a crucial role in spermatogenesis [848_827]

overall_design: Testis total RNAs were purified from 4 WT and 4 Glis3KO2 at 1 week old age, and 3WT and 3 Glis3KO2 at 3 week-old age. Then the samples were applied to Agilent mouse genome chip.


title: Glis3 plays a crucial role in spermatogenesis

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

overall_design: Refer to individual Series


title: Bone marrow-derived macrophage responses to classical activation: wild-type vs. MLL1-deficient (Lys2Cre MLL1 fx/fx)

status: Public on Jun 02 2016

city: Ann Arbor

first: William

middle: Franklin

last: Carson

state: MI

address: 109 Zina Pitcher Place

department: Pathology

institute: University of Michigan Medical School

summary: mRNA from wild-type (Cre-) and MLL1-deficient (Cre+) BMDMs were analyzed via gene chip (Mouse Gene ST 2.1, Affymetrix) for relative expression changes. Isolated mRNA from Cre- and Cre+ BMDMs stimulated with classical activation signals (IFNg, LPS or IFNg+LPS) was analyzed using a gene chip panel of >40,000 RefSeq transcripts, and resulting fold expression was determined by analyzing quality-controlled expression values for validated probesets.

overall_design: Bone marrow derived macrophages from wild-type (Cre-) or MLL1-deficient (Cre+) mice were stimulated in vitro with IFNgamma (10 ng/ml), LPS (100 ng/ml) or the combination of IFNgamma+LPS for six hours. Cells were then processed in Trizol reagent for RNA extraction.

middle: F

last: Carson IV


title: Global gene expression comparation among testes, ovaries, Smad4flox/floxMerCreMer Stra8+/− ovaries and Smad4flox/floxMerCreMer Stra8−/− ovaries

status: Public on May 11 2016

city: Mishima

first: Quan

last: Wu

state: Shizuoka

address: 1111 Yata

country: Japan

institute: National Institute of Genetics

summary: To confirm that female-to-male sexual fate reversal in Smad4flox/floxMerCreMer Stra8−/− ovaries occurs independently of somatic environment. We analyzed transcriptome of samples using RNA from control testes, ovaries, Smad4flox/floxMerCreMer Stra8+/− and Smad4flox/floxMerCreMer Stra8−/− ovaries.

overall_design: Biological triplicates were examined at each situation. For each situation, RNA was extracted from one pair of gonads.


title: Effect of Tff2 on mouse Gr1+Cd11b+

status: Public on May 30 2016

city: New York

first: Timothy

middle: Cragin

last: Wang

state: NY

address: 1130 St. Nicholas Av

department: Medicine

institute: Columbia University

summary:
The gene expression of murine splenic myeloid derived suppressor cells treated with Tff2 is characterized. The motivation of the study originates in the fact that Gr1+Cd11b+ myeloid-derived suppressor cells (MDSCs), which resemble immature myeloid cells (IMCs), expand during cancer in response to inflammatory cytokines and accumulate in the spleen. MDSCs promote neoplastic progression through their suppression of anti-tumourigenic cytotoxic T-cells. MDSCs are also rapidly expanded following acute insults, but in cancer as opposed to acute inflammation, MDSCs persist. It is now recognized that a vagally-mediated, anti-inflammatory reflex arc promoting acetylcholine secretion by Cd4+ (Cd44hiSelllo) T cells, is necessary for a return to homeostasis after an acute insult. Failure of this restorative neural circuit might contribute to unabated procarcinogenic inflammation, with the chronic expansion of MDSCs driving carcinogenesis. Trefoil factor 2 (Tff2) is a secreted anti-inflammatory peptide produced by both epithelial cells and a small subset of splenic T cell.

In this study, we show that splenic Tff2 is induced in vagally-modulated memory T cells to suppress the expansion of MDSCs in response to chemical and carcinogenic injury. Deletion of Tff2 interrupts this anti-inflammatory neural arc and leads to expanded MDSCs and a dramatically increased incidence of colorectal cancer. Tff2 directly suppresses proliferation of myeloid progenitors, in a large part through upregulation of cell-bound Apolipoprotein E (ApoE), which has previously been shown to suppress proliferation of haematopoietic stem and progenitor cells. The predisposition to inflammation-associated cancer can be rescued through transgenic overexpression of splenic Tff2, adenoviral transfer of Tff2 expression or transplantation of Tff2-expressing haematopoietic cells. Thus, Tff2 production in memory T cells, is regulated by the vagus nerve, plays a central role in arresting procarcinogenic MDSC proliferation, and offers a novel approach to the prevention and treatment.

overall_design:
A. Gr1+Cd11b+ splenic cells from Tff2-/- mice treated with Csf2 (n=4).
B. Gr1+Cd11b+ splenic cells from Tff2-/- mice treated with Tff2 and Csf2 (n=4).

first: Zinaida

last: Dubeykovskaya

first: Yiling

last: Si

first: Xiaowei

last: Chen

first: Daniel

middle: L

last: Worthley

first: Bernhard

last: Renz

first: Alexander

last: Dubeykovskiy

first: Duan

first: Richard

last: Friedman

first: Samuel

last: Asfaha

first: Karan

last: Najar

first: Yagnesh

last: Tailor

first: Suresh

last: Muthupalani

first: James

last: Fox

first: Jan

last: Kitajewski


title: Gene dosage imbalance contributes to chromosomal instability-induced tumorigenesis

status: Public on May 23 2016

city: Barcelona

first: Camille

last: Stephan Otto Attolini

state: Select a State or Province

address: Baldiri Reixac 10

department: Biostatistics and bioinformatics Unit

country: Spain

institute: IRB Barcelona

summary: Chromosomal instability (CIN) is thought to be a source of mutability in human cancer. However, CIN is highly deleterious for the cell, and the resulting aneuploidy induces metabolic stress and compromises cell fitness. Here we utilized the X-chromosome dosage compensation mechanism and changes in X-chromosome number to demonstrate in Drosophila epithelial cells the causal relationship between CIN, aneuploidy, gene dosage imbalance and tumorigenesis. Whereas the harmful effects of CIN can be buffered by resetting the X-chromosome dosage compensation to compensate for changes in X-chromosome number, interfering with the mechanisms of dosage compensation suffices to induce tumorigenesis. In addition, multiple mechanisms buffer the deleterious effects of CIN including DNA-damage repair, activation of the p38 signalling pathway, and induction of cytokine expression to promote compensatory cell proliferation. These data reveal a key role of gene dosage imbalances to CIN-induced programmed cell death and tumorigenesis and the existence of robust compensatory mechanisms.

overall_design: Wing imaginal discs expressing p35, a dsRNA form of asp (ID 110177, VDRC) and UAS-RFP (ID 31417, Bloomington Stock Center) under the control of the en-gal4 driver and carrying an MMP1-GFP reporter construct (Wang et al., 2010) were dissected from ~8-day-old larvae. Cells from the anterior compartment (RFP-negative, MMP1-GFP-negative), posterior compartment (RFP-positive, MMP1-GFP-negative) and delaminating cell population (RFP-positive, MMP1-GFP-positive) were sorted by FACS. Differential expression was performed between the cell populations. 3 biological replicates per cell population.

last: Stephan-Otto Attolini

first: Annie

last: Rodolosse

first: Marta

last: Clemente-Ruiz

first: Marco

last: Milan


title: Myelin-allied gene expression profile of adult neural progenitors shortly after onset of differentiation

status: Public on Jun 01 2016

city: Ramat-Gan

first: Michael

last: Gurevich

address: Tel-Hashomer

department: Multiple Sclerosis Center

country: Israel

institute: Sheba Medical Center

summary:
Spontaneous neural repair from endogenous neural stem cells (NSCs) occurs in response to central nervous system (CNS) injuries or diseases to only a limited extent from endogenous NSCs niches. Uncovering the mechanisms that control neural repair and can be further manipulated to promote towards oligodendrocyte progenitors cells (OPCs) and myelinating oligodendrocytes is a major objective.
Our aim was to identify myelin specific transcriptional regulators amongst large transcriptional changes shortly after differentiation of neural stem cells from the subventricular zone (SVZ) of adult mice

overall_design: SVZ-NSCs from adult mice were differentiated for 12 and 24 h in absence of growth factor (bFGF, EGF) and subjected for gene array as compared with undifferentiated NSCs cultured in presence of growth factors (n=5 samples per condition).

first: Rina

last: Zilkha-Falb

first: Erez

last: Hanael

first: Anat

last: Achiron


title: Expression data from whole Drosophila pupa of 16-17 hr APF stage

status: Public on Apr 28 2016

city: Varanasi

first: Subhash

last: Lakhotia

state: UP

address: Cytogenetics Lab

department: Zoology

country: India

institute: Banaras Hindu UNiversity

summary:
Expression of activated Ras along with alteration in levels of non-coding RNA hsromega in the eye disc results in lowered ecdysone levels in post pupation stages, resulting in early pupal death.
This microarray analysis of total pupal RNAs was undertaken to know how could expression of activated Ras with altered levels of hsromega RNA in eye discs could reduce ecdysone levels

overall_design: 16-17 hr old pupae expressing activated Ras under sevGAL4 either alone or in background of altered  levels of hsromega non coding RNA were selected for RNA extraction  and hybridization on Affymetrix microarrays. Pupae of same stage of individuals expressing only UAS-GFP under the same driver were used as control

first: Mukulika

last: Ray


title: Increased antigenicity of NURF-depleted tumors enhances CD8 T cell-mediated antitumor immunity

status: Public on Apr 29 2016

city: Jacksonville

first: Catherine

last: Dumur

state: FL

address: 5008 Mustang Rd

department: Anatomic Pathology

institute: Sonic Healthcare USA

summary:
Depleting the NURF chromatin remodeling complex results in enhanced antitumor immunity using mouse tumor models syngenic to two strain backgrounds.
Selective depletion of immune cells from tumor-bearing mice discovers that both CD8+ and CD4+ cells are necessary for enhanced antitumor immunity to NURF-depleted cells. Our results suggest that NURF-depleted cells have significant differences in antigenicity compared to control cells.

overall_design: Cloning, functional and molecular assays of CD8 T cells were performed to identify clones with enhanced activity to NURF-depleted tumor cells in NSG mice compared to control tumors.

first: Joseph

last: Landry

middle: I

first: Kimberly

last: Mayes


title: Gene expression profiling of Six2-positive nephron progenitors from mouse embryo

status: Public on Apr 14 2016

city: Kuamomoto

first: Shunsuke

last: Tanigawa

state: Kumamoto

address: 2-2-1 Chuou-ku honjyo

department: Institute of Molecular Embryology and Genetics

institute: Kumamoto University

summary: Nephron progenitors in the embryonic kidney propagate while generating differentiated nephrons. However, the progenitors in mice terminally differentiate shortly after birth. We defined culture conditions to selectively propagated nephron progenitors in vitro in an undifferentiated state. To understand how expression profiles of Six2+ cells changed during culture in vitro compared with in vivo, we performed microarray analysis of Six2+ cells at E11.5 (starting material) and P0 (experiencing 8 days in vivo), and cultured Six2+ cells at E11.5 for 8 days or 19 days.

overall_design: Microarray analysis were performed with isolated Six2-positive nephron progenitors from transgenic mice embryo at E11.5 or P0, and cultured E11.5 Six2+ cells for 8 or 19 days in conditioned media. P0 non-progenitors represent Six2-GFP-negative cells at P0.

first: Ryuichi

last: Nishinakamura


title: Effect of squalene on liver transcriptome of mice lacking apolipoprotein E

status: Public on Mar 30 2016

city: Zaragoza

first: Jesus

last: Osada

address: Miguel Servet, 177

institute: Universidad de Zaragoza

summary:
The hypothesis that the squalene of olive oil might influence hepatic gene expression in an apoE and sex-dependent ways was tested in mice.
Gene expression was analyzed using DNA microarrays in male apoE-deficient mice that received 1 g/kg/day of squalene for 10 weeks.

overall_design: As initial screening of potential candidate genes involved in a differential response, only genes with remarkably modified expression (signal log2 ratio > 1.5 or < -1.5) were further considered

first: Adela

last: Ramírez-Torres

first: Roberto

last: Martínez-Beamonte

first: María

last: Navarro

first: Carmen

last: Arnal

first: Natalia

last: Guillén

first: Sergio

last: Acín

first: Valentina

last: Ruiz-Gutierrez

first: Jesús


title: Gene expression profiling of selenophosphate synthetase 2 knockdown in Drosophila melanogaster

status: Public on Apr 06 2016

city: Shanghai

first: Yan

last: Zhang

address: 294 Tai Yuan Road Shanghai, 200031 P.R.China

country: China

institute: Institute for Nutritional Sciences, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences

summary:
Selenium (Se) is an important trace element for many organisms and is incorporated into selenoproteins as selenocysteine (Sec). In eukaryotes, selenophosphate synthetase SPS2 is essential for Sec biosynthesis. In recent years, genetic disruptions of both Sec biosynthesis genes and selenoprotein genes have been investigated in different animal models, which provide important clues for understanding the Se metabolism and function in these organisms. However, a systematic study on the knockdown of SPS2 has not been performed in vivo.
Herein, we conducted microarray experiments to study the transcriptome of fruit flies with knockdown of SPS2 in larval and adult stages. Several hundred differentially expressed genes were identified in each stage.

overall_design: Genes expression profiles of 12 fruit fly samples corresponding to larval and adult stages of SPS2 knockdown and control groups (3 replicates for each group) were analyzed using an Affymetrix Drosophila genome microarray.

first: Gaopeng

last: Li


title: Gene expression profiles of mouse liver tissues in response to choline deficient diet

status: Public on Feb 25 2016

city: Higashi-Hiroshima

first: Yanaka

last: Noriyuki

address: Kagamiyama 1-4-4

department: Graduate School of Biosphere Science

institute: Hiroshima University

summary: The objective of this study is to explore gene expression profiles of liver tissues in response to choline defficient diet by DNA microarray data analysis.

overall_design: Male CD-1mice (5 weeks) were fed either a choline-deficient diet (F2CDD, Oriental Yeast) or F2CDD plus 0.2% choline bitartrate for 3 weeks. Liver tissue from control versus choline-deficient samples were analyzed for gene expression on an Agilent Whole Mouse Genome Microarray.

first: Noriyuki

last: Yanaka

first: Koji

last: Mitsumoto


title: RAS signalling through PI3-Kinase controls cell migration via modulation of Reelin expression

status: Public on Feb 12 2016

city: London

first: Esther

last: Castellano

state: London

address: 44 Lincoln's Inn Fields

country: United Kingdom

institute: The Crick Institute

summary: RAS signalling through Phosphoinositide 3-kinase (PI3-Kinase) has been shown to have an essential role in tumour initiation and maintenance. RAS also regulates cell motility and tumor invasiveness, but the role of direct RAS binding to PI3-Kinase in this remains uncertain. Here, we provide evidence that disruption of RAS interaction with PI3-Kinase p110adecreases cell motility and prevents activation of Rac GTPase. Analysis of gene expression in cells lacking RAS interaction with p110areveals increased levels of the extracellular matrix glycoprotein Reelin and activation of its downstream pathway resulting in upregulation of E-Cadherin expression. Induction of the Reelin / E-Cadherin axis is also observed in Kras mutant lung tumours that are regressing due to blockade of RAS interaction with PI3-Kinase. Furthermore, loss of Reelin correlates with decreased survival of lung and breast cancer patients. Reelin thus plays a role in restraining RAS and PI3-kinase promotion of cell motility and potentially tumour metastasis.

overall_design: MEFs with or without RAS binding to p110a were seeded in a 10cm dish and left to attach during 24 hours. Full serum media was then removed and media with no FBS was added to the plates. Starvation was carried out during a period of 16 hours (over night starvation). Assay was performed in triplicates: for each genotype two diferent fibroblasts clones (and a mix of both of the clones) were used on the analysis. After starvation RNA was extracted using RNAsy kit (Quiagen). RNA was quantified and sent to Oxford Gene Technology microarray facility.

first: Miriam

last: Molina-Arcas

first: Agata

last: Krygowska

first: Philip

last: East

first: Patricia

last: Warne

first: Alastair

last: Nicol

first: Julian

last: Downward


title: Cyp1b1-mediated suppression of lymphoid progenitors in bone marrow coordinately impacts spleen and thymus

status: Public on Jun 06 2016

city: Madison

first: Colin

last: Jefcoate

state: WI

address: 1111 Highland Ave

department: Cell and Regenerative Biology

institute: UW-Madison

summary:
C57BL/6j mice were treated with polycyclic aromatic hydrocarbons (benzo(a)pyrene, 7,12-dimethylbenz(a)anthracene, and 2,3,7,8 tetrachlorodibenzo-p-dioxin)
Cyp1a1 and Cyp1b1 deletion separately and in combination were evaluated relative to the intact WT mice

overall_design: Nine comparison experiment. Comparison of C57BL/6J WT oil-treated control with BP (6h post-treatment), DMBA (12h post-treatment) and  TCDD (12h post-treatment). Comparison of Cyp1b1-null (1b1-ko) oil-treated control with WT oil-treated control and DMBA (12h post-treatment). Comparison of Cyp1a1-null (1a1-ko) oil-treated control with WT oil-treated control and BP (12h post-treatment). Comparison of Cyp1b1/1a1-null (DKO) oil-treated control with WT oil-treated control and BP (12h post-treatment).

middle: R


title: Searching genes responsible for developmental origins of health and disease (DOHaD) by comparing adult and fetal mouse undernutrition models

status: Public on Mar 03 2016

city: Tsukuba

first: RANDEEP

last: RAKWAL

state: Ibaraki

address: 1-1-1 Tennodai

department: Institute of Health and Sport Sciences

institute: University of Tsukuba

summary: A large number of rodent studies have supported the developmental origins of health and disease (DOHaD) hypothesis that interauterine undernutrition (IU) is a risk factor for non-communicable diseases. The effect of IU is considered to be induced thorough epigenetic programming in the fetal tissues. We have recently carried out global transcriptome expression and promoter DNA methylation analyses on the fetal mouse liver following maternal 50% food restriction (FR) during late gestation, and reported a list of fetal liver genes that were transcriptionally or epigenetically regulated by IU (Ogawa et al., 2014, Congenital Anomalies). We have already reported the genes that were regulated oppositely between maternal and fetal livers (Ogawa et al., 2014, Congenital Anomalies). Here, we considered that the fetal liver is a hematopoietic organ, and exposed nine-week-old male mice (C57BL/6J from Japan SLC, Hamamatsu, Japan; n=8 / group) to 50% FR (chow; CE-2, CLEA, Tokyo Japan) for two weeks and carried out global gene expression analysis on the whole blood by a method reported previously (Ogawa et al., 2014, Congenital Anomalies).

overall_design: Male C57BL/6J mice at 9 weeks (Japan SLC, Hamamatsu, Japan ; n=8 / group) were exposed to 50% FR (chow; CE-2, CLEA, Tokyo Japan) for 2 weeks. After 2 weeks, the mice were anesthetized with somunopentyl®(Kyoritsu eiyaku, Tokyo) at a dose of 0.5 mL/kg, and blood was taken from the right ventricle of the heart. Blood samples were immediately immersed in liquid nitrogen and stored at -80°C. All animal care and experimental procedures were approved by the Institutional Animal Care and Use Committee of Showa University, and caried out at animal facilities in Showa University. DNA Microarray analysis was carried out on 3 pools, respectively. Pool 1 included samples from animal No. 1-8 in each group (control and 50% FR). Pool 2 included samples from animal No. 1-4 in each group. Pool 3 included samples from animal No. 5-8 in each group.

first: Tetsuo

last: Ogawa

first: Junko

last: Shibato

first: Randeep

last: Rakwal

first: Seiji

last: Shioda


title: Expression data from Drosophila mutants´ (misexpression and overexpression) of cabut/dTIEG gene

status: Public on Mar 29 2016

city: BURJASSOT

first: YAIZA

last: BELACORTU

state: VALENCIA

address: DR. MOLINER

department: GENETICS

institute: UNIVERSITY OF VALENCIA

summary:
cabut (cbt), is the Drosophila ortholog of the human TGF-β Inducible Early Gene 1 (dTIEG). It  encodes a transcription factor involved in Drosophila dorsal closure (DC), and it is expressed in embryonic epithelial sheets and yolk cell during this process upon activation of the Jun N-terminal kinase (JNK) signaling pathway. Additional studies suggest that cbt may have a role in multiple developmental processes.
We used microarrays to detail the target genes of Cbt during dorsal closure process

overall_design: cbtEP(2)2237E1 homozigote Drosophila mutant embryos were selected  at 10-13 stage (during dorsal closure process)  from non-GFP embryos from the line cbtEP(2)2237E1/Cy0, twi-eGFP line  by embryo sorter assays. In parallel, samples of white embryos at same stages (as control) were sorting also by embryo sorter. Also using UAS-GAL4 system, Cbt was overexpressed  in the embrionic epidermis during 10-13 stage by epidermal driver (69B-Gal4) and UAS-Cbt line.

first: Yaiza

last: Belacortu

first: Nuria

last: Paricio


title: Effect of mannose-binding lectin (MBL) on pulmonary gene expression in response to ozone

status: Public on Apr 25 2016

city: RTP

first: NIEHS

last: Microarray Core

address: 111 T.W. Alexander Drive

institute: NIEHS

summary: Ozone is a common pollutant and a potent oxidant in industrialized nations. The mechanisms of ozone-induced lung injury and differential susceptibility are not fully understood.  Ozone-induced lung inflammation is mediated, in part, by the innate immune system.  We hypothesized that mannose binding lectin (MBL), which has a central role in the activation of the complement pathway of innate immunity, is a necessary component of the pro-inflammatory events caused by ozone-mediated activation of the innate immune system.  Wild-type (Mbl+/+) and MBL deficient (Mbl-/-) mice were exposed to ozone (0.3 ppm) for 24, 48, and 72 hours, and bronchoalveolar lavage fluid (BALF) was examined for inflammatory markers.  Compared to Mbl+/+ mice, significantly greater mean BALF eosinophils, neutrophils and neutrophil attractants CXCL2 (MIP-2) and CXCL5 (LIX) were found in Mbl-/- mice exposed to ozone.  Using genome-wide mRNA microarray analyses, we identified significant differences in expression response profiles and networks at baseline (e.g. NRF2 mediated oxidative stress response) and after exposure (e.g. humoral immune response) between Mbl+/+ and Mbl-/- mice.  The microarray data were further analyzed using a pattern recognition analysis for Extracting Patterns and Identifying co-expressed Genes (EPIG), and discovered several informative differential response patterns and subsequent gene sets, including antimicrobial response and inflammatory response.  These novel findings demonstrate that targeted deletion of Mbl caused differential expression of inflammation-related gene sets basally and after exposure to ozone, and significantly reduced pulmonary inflammation thus indicating an important innate immunomodulatory role of the gene in this model.

overall_design: Gene expression was measured in lungs of wild type or MBL knockout mice exposed to filtered air or ozone (0.3ppm) for 24, 48, or 72 hours.

first: Steven

last: Kleeberger

first: Jonathan

last: Ciencewicki

first: Kirsten

last: Verhein


title: Whale (Koiwashi kujira, Minke whale) Meat Extract Supplementation in Diet of Senescence-Accelerated Prone Mouse (SAMP8) Positively Affects Learning Memory Formation and Genome-Wide Changes in the Brain

status: Public on Jan 01 2016

summary: The present study examines the effects of whale meat extract (WME) supplementation on the senescence-accelerated mouse prone 8 (SAMP8) model at the level of learning memory formation and gene expression profiles genome-wide. Our present study builds up on these previous studies by focusing on two sets of experiments examining WME-supplemented diet, on SAMP8 and SAMR1 (senescence-accelerated mouse resistant 1) learning and memory deficits (experiment 1) and whole-genome DNA microarray-based transcriptomics profiling in conjunction with Ingenuity Pathway Analysis (IPA) (experiment 2). We also examined the SAMP8 and SAMR1 mice fed with the regular (control; low-safflower oil, LSO) diets specifically to know the gene profiles in the brain of the SAMP8 mouse. Results revealed that WME supplementation on SAMP8 mouse resulted in an increase in the level of learning memory formation and positive changes in the transcriptome of the brain, suggested through the observation of recovery of gene expressions in the SAMP8 model over the not-supplemented mouse.

overall_design: 6-week-old mice (SAMP8 and SAMR1; CLEA, Tokyo, Japan) were housed at the Animal Institution Facility in Showa University, and maintained in individual cages in a ventilated animal room with controlled temperature and relative humidity under a 12-h light: 12-h dark regime (8:00 AM, lights turned on). Mice were fed chow (CE-2, CLEA Japan) and tap water ad libitum until 24-weeks-old. Then, 24-week-old SAMs mice were given experimental diet, LSO diet as a control diet and WME-supplemented diet, both in a powder form. The WME was made from red meat of Antarctic minke whale (Balaenoptera bonaerensis), taken from the Japanese Whale Research Program under Special Permit in the Antarctic-Phase II in 2009/2010 by heat, enzyme and drying treatments. The quality standard of WE were measured by Marugei Co. Ltd. (Hyogo, Japan). SAMP8 mice were randomly given LSO or WME diet, respectively. SAMR1 mice were given LSO diet only until 50-weeks-old. The behavioral tests were performed at the timing of 49-weeks-old for 8 days. At the end of the experiment (50 weeks of age) following the behavioral analysis (open field test, Y-maze test, new object recognition test (NOR), and water-filled multiple T-maze) and the last day of the feeding, the mice were removed from their cages, decapitated and their brains carefully removed on ice. The whole brains were quickly frozen in liquid nitrogen in a sterile freeze tube and stored at -80ºC till extraction of total RNA followed by DNA microarray analysis using a whole-genome mouse chip (Agilent-014868, 4 x 44K (G4122F)) with two-color dye-swap approach in conjunction with IPA bioinformatic analysis. All animal studies were conducted in accordance with the Standards Relating to the Care Management of Experimental Animals” (Notice No. 6 of the Office of Prime Minister dated March 27, 1980) and with approval from the Animal Use Committee of Showa University (Approval Number: #04093).

first: Nobuhiro

last: Wada

first: Satoru

last: Yamanaka

first: Satoshi

last: Hirako

first: Yuzuru

last: Iizuka

first: Honju

middle: Y

last: Kim

first: Akiyo

last: Matsumoto

first: Kazue

last: Satoh

first: Michiru

last: Ootsuka

first: Ai

last: Kimura

first: Fumiko

last: Takenoya

first: Genta

last: Yasunaga


title: Expression data of Normal versus Mutant MPS VII Bl6 mouse

status: Public on Dec 23 2015

city: Philadelphia

first: Michael

middle: K.

last: Parente

state: PA

address: 3615 Civic Center Blvd.

department: Neurology

institute: Children's Hospital of Philadelphia

summary:
We used microarray to detect pathway differences in the hippocampus in mucopolysaccharidosis type VII ( MPS VII ), a mouse model of a lysosomal storage disease
Pathway changes were similar to those found in different strain where MPS VII mutation was backcrossed on a C3h-heouj background and implicated immune, vesicle and other pathways

overall_design: 8 samples, no replicates, made up of half normals and half MPS mutant mice

middle: K

first: Ramona

last: Rozen

first: John

middle: H

last: Wolfe


title: The Six1 oncoprotein represses translation of p53 via concomitant regulation of RPL26 and microRNA-27a

status: Public on Mar 21 2016

city: Chapel Hill

first: Charles

middle: M.

last: Perou

address: 12-044 Lineberger Comprehensive Cancer Center CB# 7295

department: Professor of Genetics, and Pathology & Laboratory Medicine; Lineberger Comprehensive Cancer Center

institute: University of North Carolina at Chapel Hill

summary: TP53 is mutated in 50% of all cancers, and is often functionally compromised in cancers where it is not mutated.  We demonstrate that the pro-tumorigenic/metastatic Six1 homeoprotein decreases p53 levels through a mechanism that does not involve the negative regulator of p53, MDM2. Instead, Six1 regulates p53 via a dual mechanism involving upregulation of microRNA-27a and downregulation of the ribosomal protein L26 (RPL26), a positive regulator of p53 translation. Mutation analysis confirms that RPL26, whose expression inversely correlates with Six1 expression in numerous tumor types, inhibits miR-27a binding to the p53 3’UTR and prevents microRNA-mediated translational inhibition of p53. Thus, through simultaneous downregulation of RPL26 and upregulation of miR-27a, Six1 efficiently lowers p53 levels despite regulation of p53 at the level of the proteasome.  Consequently, Six1 overexpression, which is observed in numerous tumor types, leads to dramatic resistance to nutlins, as well as other therapies targeting the p53-MDM2 interaction.

overall_design: reference x sample

first: C

middle: G

last: TOWERS

first: Chuck

last: Harrell

first: H

last: FORD


title: Mouse-specific skin and blood transcriptional responses after intradermal administration of flagellin

city: Berlin

first: Hans-Joachim

last: Mollenkopf

address: Charitéplatz 1

institute: Max-Planck-Institute for Infection Biology

summary: The study aimed at defining the local and systemic innate responses after intradermal injection of flagellin. For this purpose, mice were immunized by intradermal route with flagellin. Skin and blood were then sampled at selected times for microarray analyses.

overall_design: Mice were then immunized with the TLR5 agonist flagellin by intradermal route. Blood samples and punch biopsies of skin were sampled post-immunization and on mock animals. Total RNA was extracted and microarray experiments were performed as single-color hybridizations on Agilent 4x44K mouse whole genome catalog arrays (Agilent-014868) according supplier's recommendations.

first: Jean-Claude

last: Sirard


title: Characterization of Glucocorticoid Receptor (GR) in Mouse Liver

status: Public on Dec 11 2015

first: NIEHS

last: Microarray Core

summary: We proposed an experiment that determines liver gene regulation profiles in GRLKO. By comparison to the wide type C57BL/6 mouse, we determined the contribution of GR on liver gene expression either at basal level or after  Dexamethasone (DEX) injection.

overall_design: WT and GR knockout mice were divided into two groups, one with dexamethasone treatment and one with out.  Each group has four replicates.

first: Bo

last: He

last: Cidlowski


title: p53 Contributes to Differentiating Gene Expression Following Exposure to Acetaminophen and Its Less Hepatotoxic Regioisomer Both In Vitro and In Vivo

city: Seattle

first: James

middle: William

last: MacDonald

state: WA

address: 4225 Roosevelt Way NE

department: Environmental and Occupational Health Sciences

institute: University of Washington

summary: The goal of the present study was to compare hepatic toxicogenomic signatures across in vitro and in vivo mouse models following exposure to acetaminophen (APAP) or its relatively nontoxic regioisomer 3'-hydroxyacetanilide (AMAP). Two different Affymetrix microarray platforms and one Agilent Oligonucleotide microarray were utilized. APAP and AMAP treatments resulted in significant and large changes in gene expression that were quite disparate, and likely related to their different toxicologic profiles. Ten transcripts, all of which have been implicated in p53 signaling, were identified as differentially regulated at all time-points following APAP and AMAP treatments across multiple microarray platforms. Protein-level quantification of p53 activity aligned with results from the transcriptomic analysis, thus supporting the implicated mechanism of APAP-induced toxicity. Therefore, the results of this study provide good evidence that APAP-induced p53 phosphorylation and an altered p53-driven transcriptional response are fundamental steps in APAP-induced toxicity.

overall_design: Preliminary study utilizing 9 arrays, 9 experimental groups, 2 h AMAP, 2 h APAP, 2 h control, 6 h AMAP, 6 h APAP, 6 h control, 24 h AMAP, 24 h APAP, 24 h control.

first: Theodor

last: Bammler

first: Richard

middle: P

last: Beyer

first: Brendan

middle: D

last: Stamper


title: Tip60 HAT action mediates environmental enrichment induced cognitive restoration

status: Public on Jan 07 2016

first: Songjun

last: Xu

address: 3245 Chestnut street

department: Biology

institute: Drexel University

summary:
Environmental enrichment (EE) conditions have profound beneficial effects for reinstating cognitive ability in neuropathological disorders like Alzheimer’s disease (AD).   While EE benefits involve epigenetic gene control mechanisms that comprise histone acetylation, the histone acetyltransferases (HATs) involved remain largely unknown.  Here, we examine a role for Tip60 HAT action in mediating activity- dependent beneficial neuroadaptations to EE using the Drosophila CNS mushroom body (MB) as a well-characterized cognition model.   We show that flies raised under EE conditions display enhanced MB axonal outgrowth, synapse protein production, histone acetylation induction and transcriptional activation of cognition linked genes when compared to their genotypically identical siblings raised under isolated conditions.  Further, these beneficial changes are impaired in both Tip60 HAT mutant flies and APP neurodegenerative flies.   While EE conditions provide only slight beneficial neuroadaptive changes in the APP neurodegenerative fly MB, such positive changes are significantly enhanced by increasing MB Tip60 HAT levels.  Our results implicate Tip60 as a critical mediator of EE-induced benefits, and provide insight into synergistic behavioral and epigenetic based approaches for treatment of cognitive disorders.
EE has been shown to positively impact gene expression profiles in the mouse brain that are enriched in functions such as neuronal structure, synaptic plasticity and neurotransmission.  Thus, we asked whether the EE induced beneficial MB structural and synaptic changes we observe are accompanied by neuroadaptive transcriptional benefits in the Drosophila MB, and if so, is Tip60 HAT action required for this process. To address this question, we accessed EE induced beneficial transcriptional changes using microarray.

overall_design: We crossed our UAS-mCD8-GFP;Tip60E431Q flies or control UAS-mCD8-GFP flies to MB GAL4 OK-107 to simultaneously induce Tip60 HAT loss in the MB while tagging MB cells with GFP. Adult progeny were exposed to EE or ISO conditions.  After conditioning, the GFP tagged MB Kenyon neurons were FACs purified from conditioned fly brains from each genotype to enrich for detection of an EE induced MB transcriptional response.   RNA was isolated from the purified Kenyon MB neurons and transcriptional changes for each genotype were assessed using microarray analysis

first: Felice

last: Elefant


title: Transcriptional profiling of HBV-naïve subjects before vaccination against Hepatitis A/B viruses, Diphtheria/Tetanus toxoids and Cholera.

status: Public on Jan 09 2016

city: Chicago

first: Slim

last: Fourati

state: Illinois

address: 300 E Superior St

institute: Northwestern University

summary: Mechanisms of poor responses to vaccines remain unknown. Hepatitis B virus-naïve elderly subjects received three vaccines, including a vaccine against hepatitis B virus (HBV). Pre-vaccination high dimensional analyses of blood using transcriptional profiling and flow cytometry revealed that subjects having increased memory B cell frequencies and higher expression of genes downstream of B cell receptor signaling responded more strongly to the HBV vaccine whereas subjects having higher expression of inflammatory related genes and greater numbers of activated innate immune cells showed a weaker response to this vaccine. The heme-induced response was associated with the poor response to the hepatitis B vaccine. Transcriptional profiling and flow cytometry results were validated in a distinct set of elderly subjects with accuracy greater than 60%. Our study is the first that identifies baseline predictors of responses to vaccines in a population of subjects known to be highly susceptible to infections.

overall_design: One hundred and seventy four (174) generally healthy, Hepatitis B virus (HBV) naïve, adult residents of Québec were vaccinated with two doses of Twinrix® (HBsAg and Hepatitis A virus - Glaxo Smith-Kline), generic Tetanus-diphtheria booster (tetanus and diphtheria - Sanofi-Pasteur), and Dukoral (recombinant cholera toxin B subunit and whole killed Vibrios - Sanofi Pasteur) according to the respective product labels. Blood samples were taken immediately prior to vaccination. Blood samples were conserved in PAXgene tubes. RNA was extracted and hybridized to Affymetrix arrays. 5 technical replicates were included in the study.

first: Razvan

last: Cristescu

first: Andrey

last: Loboda

first: Aarthi

last: Talla

first: Ali

last: Filali

first: Radha

last: Railkar

first: I-Ming

last: Wang

first: Leonidas

middle: N

last: Carayannopoulos

first: Rafick-Pierre

last: Sékaly


title: Gene expression data of RNA from liver sample of DUhTP and DUC

status: Public on Sep 29 2015

city: Dummerstorf

first: Andreas

last: Hoeflich

address: Wilhelm-Stahl Allee 2

department: Genome Biology

institute: Leibniz Institute for Farm Animal Biology

summary:
Liver gene expression following longterm selection for high treadmill performance in mice
Liver probe-sets were screened, analysed for differential expression between high treadmill performance selected mouse line (DUhTP) and control line (DUC)

overall_design: RNAs of liver from mouse line were hybridized to Affymetrix GeneChip Murine Genome Array.

first: Christina

last: Walz

last: Höflich


title: GRα-independent transcriptional activity of hGRβ in GR Liver Knockout Mouse

first: NIEHS

last: Microarray Core

department: DIR

summary: We used AAV as a vector to deliver hGRβ to the liver of GR Liver Knockout mice. We collected liver samples for microarray analysis to investigate any phenotype as well as the underlying specific signaling pathway. In particular, we would like to determine if and how hGRβ overexpression in liver affects mGRα’s gene transcription profile in GR Liver Knockout  mice.

overall_design: GR Liver Knockout mice were treated with PBS,  AAV-GFP and AAV-hGRB, respectively.  Each treatment group has four replicates.

first: Bo

last: He

first: John

middle: A

last: Cidlowski


title: Functional characterization of hGRβ Isoform in mouse liver

summary: We used AAV as a vector to deliver hGRβ to C57BL/6 mouse liver. We collected liver samples for microarray analysis to investigate any phenotype as well as the underlying specific signaling pathway. In particular, we would like to determine if and how hGRβ overexpression in liver affects mGRα’s gene transcription profile in C57BL/6 mice.

overall_design: Three replicates for each group: untreated WT liver, AAV-GFP treated liver, and AAV-hGRB treated liver.


title: Gene expression data from wild-type (WT) and ribbon (rib) mutant Drosophila mid through late stage embryos

status: Public on Dec 21 2015

city: Baltimore

first: Deborah

middle: J

last: Andrew

state: MD

address: 725 N. Wolfe St., Hunterian G-1

department: Cell Biology

institute: Johns Hopkins University School of Medicine

summary: Transcription factors, which regulate the spatiotemporal patterns of gene expression during organogenesis, often regulate multiple aspects of tissue morphogenesis, including cell-type specification, cell proliferation, cell death, cell polarity, cell shape, cell arrangement and cell migration. In this work, we describe a distinct role for Ribbon (Rib) in controlling cell shape changes during elongation of the Drosophila salivary gland (SG). Notably, the morphogenetic changes in rib mutants occurred without effects on general SG cell attributes such as specification, proliferation and apoptosis. Moreover, the abnormal cell/organ shape in rib mutants occurred without compromising epithelial-specific morphological attributes such as apicobasal polarity and junctional integrity. To identify the genes regulated by Rib that control cell and organ shape, we performed ChIP-seq analysis in embryos driving rib expression specifically in the SGs. To learn if the Rib binding sites identified in the ChIP-seq analysis were linked to changes in gene expression through transcriptional activation, repression, or both, we performed microarray analysis comparing RNA samples from age-matched wild-type and rib null embryos. From the superposed ChIP-seq and microarray gene expression data, we identified 60 genomic sites of bound Rib most likely to regulate SG-specific gene expression. We confirmed several of the identified Rib targets by qRT-pCR and/or in situ hybridization. Our results indicate that Rib regulates cell shape change in the Drosophila salivary gland via a diverse array of targets through both transcriptional activation and repression. Furthermore, our results suggest that a critical component of the SG morphogenetic gene network involving Rib is its autoregulation.

overall_design: Three independent collections of stage 11 – 16 rib1/ribP7 embryos and three of wild-type embryos were used for hybridization to Drosophila Genome 2.0 Chips. Scanned intensity values were normalized using RMA (Partek software) and statistical analysis analyses were performed using the Spotfire software package (TIBCO). Target genes were identified as those that were upregulated/downregulated (1.5-fold change cutoff, P < 0.05) in rib1/ribP7 embryos when compared with Oregon R controls.

first: Rajprasad

last: Loganathan


title: Modulation of T cell responses by type I interferons

status: Public on Dec 31 2015

city: Braunschweig

first: Andrea

last: Kröger

address: Inhoffenstrasse 7

department: Regulation and Differentiation

institute: Helmholtz Centre for Infection Research

summary: Type I interferons (IFNs) play a key role in linking the innate and adaptive immune responses. IFNs can have both positive and negative effects on the development of memory CD8+ T cells, but their contribution to the priming of naïve T cells is unclear. Using OT-I TCR transgenic T cells, we show strong effects on TCR-induced functional response when sensitized by IFN-β prior to their stimulation with cognate antigen. These effects are only seen in the absence of co-stimulation and at suboptimal TCR stimulation conditions. Pre-stimulation of naïve T cells inhibits certain TCR-mediated functions like cell proliferation and the induction of genes such as IFN-γ and IL-2. However, type I IFN does not influence the induction of other TCR-induced functions like the expression of the T cell activation marker CD25 and a number of other genes. IFN-mediated impairment of proliferation is due to the lack of IL-2 induction since it can be compensated by exogenous IL-2. Further analysis reveals an IFN-mediated inhibition of Ca2+ flux and ERK phosphorylation. In vivo studies confirm that pre-stimulation with IFNs inhibits early T cell responses, whereas long-term responses are positively affected. Our results reveal that IFN exerts negative effects on naïve T cells in a timely defined range under sub-optimal TCR stimulation conditions. These results highlight the importance of timing of immune-regulatory events and reveal a novel role for type I IFNs by shaping the immune response, such that T cells are not able to react until optimal stimulation is provided.

overall_design: 8 Arrays, untreated cells as references, IFNb treatment and/or TCR stimulation at various lengths of time

first: Berit

last: Neumann

first: Hansjörg

last: Hauser

first: Oliver

last: Dietrich-Breitholtz


title: The Mechanisms Underlying α-Amanitin Resistance in Drosophila melanogaster: A Microarray Analysis

status: Public on Dec 01 2015

city: Bar Harbor

first: Michael

middle: C.

last: Saul

state: ME

address: 600 Main St

institute: The Jackson Laboratory

summary: The rapid evolution of toxin resistance in animals has important consequences for the ecology of species and our economy. Pesticide resistance in insects has been a subject of intensive study, however, very little is known about how Drosophila species became resistant to natural toxins with ecological relevance, such as α-amanitin that is produced in deadly poisonous mushrooms. Here we performed a microarray study to elucidate the genes, chromosomal loci, molecular functions, biological processes, and cellular components that contribute to the α-amanitin resistance phenotype in Drosophila melanogaster. We suggest that toxin entry blockage through the cuticle, phase I and II detoxification, sequestration in lipid particles, and proteolytic cleavage of α-amanitin contribute in concert to this quantitative trait. We speculate that the resistance to mushroom toxins in Drosophila melanogaster and perhaps in mycophagous Drosophila species has evolved as a cross-resistance to pesticides or other xenobiotic substances.

overall_design: In the study presented here, we had a total of 3 experimental conditions using 2 stocks of Drosophila melanogaster: 5 biological replicates of the Canton-S stock raised on non-toxic food (CS), 5 biological replicates of the α-amanitin resistant Ama-KTT/M/2 stock raised on non-toxic food (KTT), and 6 biological replicates of the the α-amanitin resistant Ama-KTT/M/2 stock raised on food containing the LC-50 concentration of α-amanitin for this stock (KTT-LC50).  For each of biological replicate, we extracted total RNA from a pooled 10 larvae in the late third instar.

first: Chelsea

last: Mitchell

middle: C

first: Liang

last: Lei

first: Hairong

last: Wei

first: Thomas

last: Werner


title: Hyperosmotic-induced changes in lymphoid cell gene expression

state: NC

summary: We have taken S49 Neo cells (an immature murine T-cell line) through repeated exposures of 500 mOsm Mannitol for 4 hours, killing over 90% of the cells, and then allowed them to recover.  After 25 rounds of Mannitol exposure, we observed that these cells now have the ability to volume regulate upon an acute exposure to an osmotic stress, an ability not observed in the parental cell line.  Interestingly, we found that these repeated Mannitol treated cells to be resistant to glucocorticoid-induced apoptosis, whereas the parental cell line is highly sensitive to glucocorticoid-induced cell death.

overall_design: The RNA was prepared from cultured cells (~1x106 cells/ml) of the parental cell line S49 Neo and the Mannitol Recovered cell line MR 4-25 using the Qiagen RNeasy mini-kit and including DNase treatment.  Three replicates were used for each cell line.

first: Carl

last: Bortner


title: Mammary Gland from hNAG-1 overexpressing mice

status: Public on Nov 10 2015

summary: Non-steroidal anti-inflammatory drug activated gene 1 (NAG-1) plays some role in reducing obesity in mice overexpressing human NAG-1, even on a high fat diet. Male and female hNAG-1 expressing mice have reduced body weight, increased longevity and metabolic activity. This study investigates the role of hNAG-1 in female reproduction and finds that the female mice have reduced fertility and pup survival after birth. Examination of the mammary glands in these mice suggests that hNAG-1 overexpressing mice have altered mammary epithelial development during pregnancy, including reduced occupancy of the fat pad and increased apoptosis via TUNEL positive cells at lactation day 2. Pups nursing from hNAG-1 overexpressing dams have reduced milk spots compared to pups nursing from WT dams. When CD-1 pups were cross-fostered with hNAG-1 or WT dams; reduced milk volume was observed in pups nursing from hNAG-1 dams compared to pups nursing from WT dams in a lactation challenge study. Milk was isolated from WT and hNAG-1 dams, and the milk was found to have secreted NAG-1 protein (approximately 25ng/mL) from hNAG-1 dams compared to WT dams, which had no detectable NAG-1 in the milk. A decrease in non-esterified free fatty acids in the milk of hNAG-1 dams was observed. Altered milk composition suggests that the pups were receiving inadequate nutrients during perinatal development; to examine this hypothesis serum was isolated from pups and clinical chemistry points were measured. Male and female pups nursing from hNAG-1 dams had reduced serum triglyceride concentrations. Cidea/CIDEA expression was reduced in hNAG-1 mammary glands, and microarray analysis suggests that genes involved in lipid metabolism are differentially expressed in hNAG-1 mammary glands. This study suggests that overexpression of hNAG-1 impairs lactational differentiation and pup survival due to altered milk quality and quantity

overall_design: 4 WT mammary glands on lactation day 2 and 5 hNAG-1 transgenic mice mammary glands on lactation day 2 were used.

first: April

last: Binder

first: Justin

last: Kosak

last: Eling

first: Kenneth

last: Korach


title: Gene expression of fly testes with Med22 knock down

status: Public on Nov 07 2015

city: Stanford

first: Chenggang

last: Lu

state: CA

address: 279 Campus Drive

institute: Stanford University

summary:
The effect of Med22, spermatocyte arrest (sa) and always early (aly) loss of function on the gene expression in spermatocytes was assessed by microarray.
Title: Recruitment of Mediator complex by cell type and stage-specific factors required for tissue-specific TAF dependent gene activation in an adult stem cell lineage

overall_design: RNA was obtained from whole testes of flies with following mutations: 1)bam-gal4: UAS-Med22RNAi (VDRC#104581). Three biological replicates were included. Experiments were performed at 25C.

first: Margaret

middle: T

last: Fuller


title: Transcriptional effects of CTGF inhibition in a transgenic mouse model of dilated cardiomyopathy

status: Public on Nov 20 2015

city: San Francisco

first: Mark

middle: D.

last: Sternlicht

address: 409 Illinois Street

department: Molecular Biology

institute: FibroGen, Inc.

summary: Cardiac structural changes associated with dilated cardiomyopathy (DCM) include cardiomyocyte hypertrophy and myocardial fibrosis.  Connective Tissue Growth Factor (CTGF) has been associated with tissue remodeling and is highly expressed in failing hearts.  To test if inhibition of CTGF would alter the course of cardiac remodeling and preserve cardiac function in the protein kinase Cε (PKCε) mouse model of DCM.  Transgenic mice expressing constitutively active PKCε in cardiomyocytes develop cardiac dysfunction that was evident by 3 months of age, and that progressed to heart failure, cardiac fibrosis, and increased mortality.  Beginning at 3 months of age, mice were treated with an antibody to CTGF (FG-3149) or non-immune IgG control antibody for an additional 3 months.  CTGF inhibition significantly improved left ventricular (LV) systolic and diastolic function in PKCε mice, and slowed the progression of LV dilatation.  Using gene arrays and quantitative PCR, the expression of many genes associated with tissue remodeling were elevated in PKCε mice, but significantly decreased by CTGF inhibition, however total collagen deposition was not attenuated.  The observation of significantly improved LV function by CTGF inhibition in PKCε mice suggests that CTGF inhibition may benefit patients with DCM.

overall_design: Total RNA was isolated from the left ventricle of 6-month-old PKCε transgenic mice or nontransgenic FVB/N controls 3 months after initiation of treatment with IgG (n=10 biological replicates each) or anti-CTGF antibody FG-3149 (n=12 each) and hybridized to Affymetrix 430A 2.0 microarrays.  CEL files were processed by GCRMA and rescaled using median per-gene normalization in GeneSpring GX 7.3.1.

first: Yevgeniya

middle: E

last: Koshman

first: Allen

middle: M

last: Samarel

first: Todd

middle: W

last: Seeley


title: Brown Adipose YY1 Deficiency Activates Expression of Secreted Proteins Linked to Energy Expenditure and Prevents Diet-Induced Obesity [BAT]

city: Schlieren

first: Francisco

last: Verdeguer

address: 27a Wagistrasse

institute: InSphero

summary: Analysis of brown adipose tissue from Yin Yang 1 (YY1) brown fat specific knockout mice fed a high fat diet for 3 months. YY1 deficiency in brown adipose tissue leads to strong thermogenic deficiency. The goal was to identify the genes controlled by YY1 responsible of brown fat defective function.

overall_design: Control mice YY1flox/flox versus YY1flox/flox; Ucp1Cre were fed a high fat diet for 3 months

first: Pere

last: Puigserver


title: Brown Adipose YY1 Deficiency Activates Expression of Secreted Proteins Linked to Energy Expenditure and Prevents Diet-Induced Obesity [IWAT]

summary: Analysis of subcutaneous adipose tissue (IWAT) from Yin Yang 1 brown fat specific knockout mice fed a high fat diet for 2 weeks. The goal was to identify a gene signature of IWAT browning in YY1 mutant mice.

overall_design: Control mice YY1flox/flox versus YY1flox/flox; Ucp1Cre were fed a high fat diet for 2 weeks


title: A CDK-independent function of p27kip1 in the control of cell proliferation

status: Public on Nov 02 2015

city: Aviano

first: daniela

last: marconi

address: Via franco Gallini 2

country: Italy

institute: CRO AVIANO

summary:
The integrated regulation of different intracellular signaling pathways is fundamental to ensure appropriate timing of cell division and, more in general, proper development of any living organism. Adopted mechanisms include the instauration of feedback regulations and/or to rely on a single molecule for the control of multiple processes.
We now present evidences that in mammalian cells the CDK inhibitor p27kip1, by a CDK-independent and stathmin-dependent mechanism, is implicated in the control of the MAPK pathway, eventually influencing cell proliferation in vitro and mice growth in vivo. This p27kip1 activity regulates H-Ras driven transformation in mice and controls tumor progression in humans. Altogether, our work unveils a new mechanism that in mammalian cells contributes to proper regulation of cell proliferation and whose alteration may contribute to tumor onset and/or progression.

overall_design: Four-condition experiment, 4 biological replicates of p27 Knock-out mices, 4 biological replicates of stathmin knock-out mices, 3 biological replicates of double knock-out (p27 & stathmin) mice3, 4 biological replicates of wild type mices. Reference design;

first: Ilenia

last: Pellizari

first: Linda

last: Fabris

first: Stefania

last: Berton

first: Gustavo

last: Baldassarre

first: Daniela

last: Marconi

first: Riccardo

last: Bomben

first: Valter

last: Gattei


title: Brown Adipose YY1 Deficiency Activates Expression of Secreted Proteins Linked to Energy Expenditure and Prevents Diet-Induced Obesity

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

overall_design: Refer to individual Series


title: Seeking genes responsible for developmental origins of health and disease (DOHaD) from the fetal mouse brain following maternal food deprivation (FD) and food restriction (FR) using OMICS approach

status: Public on Sep 19 2015

first: RANDEEP

last: RAKWAL

address: 1-1-1 Tennodai

institute: University of Tsukuba

summary: A non-optimal fetal environment is known to cause low birth weight, which has been epidemiologically associated with a greater risk of adult diseases. Maternal undernutrition in animal models has also revealed the increased risks for adult diseases in the offspring. In this study, pregnant mice underwent overnight food deprivation at gestation day (GD)17 or 50% food restriction (FR) from GD10 to GD17, and the fetal brains were examined for global changes in gene expression by DNA microarray analysis utilizing the dye-swap approach. We present here a list of candidate genes from the fetal brain that might be responsible for developmental origins of health and disease.

overall_design: For food deprivation (FD), the pregnant mice were deprived of the food for overnight before lights were turned off on GD17. For food restriction (FR), pregnant mice were exposed to 50% food restriction (FR) from GD 10 to 17 and caesarean section was performed between 10:00-12:00 AM on GD18. Amount of CE-2 chow supplied to FR group was calculated as 50% of CE-2 consumed by control group each gestation day. Control group was supplied with chow ad libitum. Pregnant mice were sacrificed by cervical dislocation, and the fetuses were taken out and anesthetized on ice cold phosphate-buffered saline. The fetuses were dissected under a dissection microscope, and fetal tissues are carefully removed avoiding any other tissues contamination. The brain was collected from control (n=5) and FD (n=5) or FR (n=5) fetuses, and immediately frozen by immersion in liquid nitrogen. For DNA microarray analyses, the total RNA was extracted, quality and quantity determined, and total RNA from each sample (control and treatment) in each group was pooled, followed by established protocols for genome wide expression changes for both FD and FR samples using a 60-mer probes (4 x 44K (41,090 gene probes), mouse whole genome, Agilent) DNA chip by the dye-swap approach.

first: Randeep

last: Rakwal

first: Junko

last: Shibato

first: Tetsuo

last: Ogawa

first: Tomomi

last: Saito

first: Gaku

last: Tamura

first: Seiji

last: Shioda


title: Brown fat-specific YY1 deficiency effect on subcutaneous white adipose tissue

first: Francisco

last: Verdeguer

summary: Analysis of visceral white adipose tissue (EWAT) from Yin Yang 1 adipose-specific knockout mice exposed to cold (4ºC) for 4 days.

overall_design: Control mice YY1flox/flox versus YY1flox/flox; Adiponectin Cre were cold exposed for 4 days.


title: Identification of KAT6B signature on KAT6B deficient SCLC cell Lines

status: Public on Oct 07 2015

city: L'Hospitalet de Llobregat

first: Manel

last: Esteller

state: Barcelona

address: Hospital Duran i Reynals Av. Gran Via s/n km, 2.7

department: PEBC

institute: IDIBELL

summary: To develop our gene expression experiment, we have employed whole genome microarray expression profiling as a discovery platform to identify genes potentially regulated by the transcriptional coactivator KAT6B. Expression of KAT6B gene was downregulated in two human SCLC cell lines using two different short hairpin RNAs. RNAs from these modified cell lines were hybridized in Agilent platform.

overall_design: 2 different SCLC cell lines transfected with 2 different shRNAs and 2 different Scramble plasmids. All shRNAs and Scramble samples were hybridized in Agilent platform in order to look for differentially expressed genes.

first: Laia

middle: S

last: Riudalbas

last: Badosa


type: Genome variation profiling by genome tiling array

summary: Copy number analysis of KAT6B gene deletion in small cell lung cancer cell lines

overall_design: We perform genotyping microarray (Illumina HumanOmni5) on small cell lung cancer cell lines in order to predict copy number aberrations.

last: Simo


title: KAT6B gene deletion as a predictive biomarker to Irinotecan response in small cell lung cancer


title: Identification of a Highly Immunogenic Mouse Breast Cancer Sub Cell Line, 4T1-S

status: Public on Nov 01 2015

city: Sapporo

first: Hirotake

last: ABE

state: Japan/Hokkaido

address: Kita15-Nishi7, Kitaku

department: Institute for Genetic Medicine

institute: Hokkaido University

summary: Recently, cancer immunotherapy has been paid much attention because of its improved efficacy and low frequency of adverse effects. A mouse breast cancer cell line, 4T1, has been known as poorly immunogeneic and highly metastatic cell line. In this study, we have identified a sub cell line of 4T1, designated as 4T1-Sapporo (4T1-S), which could induce a strong immune response against the same line. When 4T1-S was subcutaneously injected, striking enlargement of draining lymph nodes and increase of activated T cells were observed. The strong immune responses could not be observed when 4T1-S was injected to nude mice, indicating that this phenomenon is mediated by T cell response. Identification of 4T1-S characteristics may help to improve immunotherapy against breast cancer.

last: Abe

first: Ken-ichiro

last: Seino


title: Uterine Transcriptional Profile Following Treatment with Estradiol or Synthetic Estrogens Diethylstilbestrol and Propyl Pyrazole Triol

status: Public on Oct 01 2015

first: NIEHS

last: Microarray Core

address: 111 T.W. Alexander Drive

institute: NIEHS

summary: Transcriptional responses in ovariectomized mouse uterine tissue to estradiol (E2) and diethylstilbestrol (DES), known long-acting estrogens, and propyl pyrazole triol (PPT), an ER-alpha selective estrogen, were profiled. Profiles were used together with those from other estrogens to derive a biomarker panel.

overall_design: 2 mice each: WT saline, WT E2 2h, WT E2 24h, WT DES 2h, WT DES 24h, WT PPT 2h, WT PPT 24h.

first: Sylvia

last: Hewitt

first: Kenneth

last: Korach

first: Geofflrey

last: Greene


title: KRAS mutation-associated gene expression, p53 and STK11 mutations, proliferation and immune surveillance in lung adenocarcinoma

status: Public on Oct 21 2015

city: Tampa

first: Steven

last: Eschrich

address: 12902 Magnolia Drive

department: Biostatistics & Bioinformatics

institute: Moffitt Cancer Center

summary: While mutations in the KRAS oncogene are amongst the most prevalent in human cancer, there are few successful treatments to target these tumors. It is also likely that heterogeneity in KRAS-mutant tumor biology significantly contributes to the response to therapy. We hypothesized that presence of commonly co-occurring mutations in STK11 and TP53 tumor suppressors may represent a significant source of heterogeneity in KRAS-mutant tumors.  To address this, we utilized a large cohort of resected tumors from 442 lung adenocarcinoma patients with data including annotation of prevalent driver mutations (KRAS, EGFR) and tumor suppressor mutations (STK11 and TP53), microarray-based gene expression and clinical covariates including overall survival (OS). Specifically, we determined impact of STK11 and TP53 mutations on a new KRAS mutation-associated gene expression signature as well as previously defined signatures of tumor cell proliferation and immune surveillance responses. Interestingly, STK11, but not TP53 mutations, were associated with highly elevated expression of KRAS mutation-associated genes. Mutations in TP53 and STK11 also impacted tumor biology regardless of KRAS status, with TP53 strongly associated with enhanced proliferation and STK11 with suppression of immune surveillance. These findings illustrate the remarkably distinct ways through which tumor suppressor mutations may contribute to heterogeneity in KRAS-mutant tumor biology. In addition, these studies point to novel associations between gene mutations and immune surveillance that could impact the response to immunotherapy.

overall_design: Resected tumors from 442 lung adenocarcinoma patients were profiled on gene expression arrays, prevalent driver mutations (KRAS, EGFR) and tumor suppressor mutations (STK11 and TP53) were assessed.

first: Matthew

last: Schabath

first: Amer

last: Beg


title: Microarry from Treg with conditional knockout of Usp7

status: Public on Sep 15 2015

first: Wayne

last: Hancock

address: 916B ARC, 3615 Civic Ctr Blvd

institute: CHOP/UPenn

overall_design: RNA from three independent samples from FACS sorted CD4+YFP+ Treg of fl-Usp7/Foxp3cre mice, compared to Foxp3cre control (C57BL/6 background).

first: Liqing

last: Wang

first: Suresh

last: Kumar

first: Satinder

last: Dahiya

first: Jack

first: Kheng

last: Newick

first: Rongxiang

last: Han

first: Arabinda

last: Samanta

first: Ulf

middle: H

last: Beier

first: Tatiana

last: Akimova

first: Tricia

middle: R

last: Bhatti

first: Benjaming

last: Nicholson

first: Wei

last: Gu

first: Joseph

last: Weinstock

first: Tauseef

last: Butt

last: Albelda


title: Microarray analysis of skeletal muscle in PGC1α transgenic mice

status: Public on Sep 18 2015

city: Kyoto

first: Yukino

last: Hatazawa

address: 1-5 Hangi-cho, Shimogamo, Sakyo-ku

institute: Kyoto Prefectural University

summary: Peroxisome proliferator-activated receptor (PPAR) γ coactivator 1α (PGC1α) is a coactivator of various nuclear receptors and other transcription factors that shows increased expression in skeletal muscle during exercise. In skeletal muscle, PGC1α is considered to be involved in contractile protein function, mitochondrial function, metabolic regulation, intracellular signaling, and transcriptional responses. Several isoforms of PGC1α mRNA have recently been identified. PGC1α-a is a full-length isoform of PGC1α that was the first to be isolated. PGC1α-b is another isoform of PGC1α, which is considered to be similar in function to PGC1α-a, differing by only 16 amino acids at the amino terminus.   We have previously generated independent lines of transgenic mice that overexpress PGC1α-a or PGC1α-b in skeletal muscle. The microarray data shows that energy metabolism-related pathways such as the TCA cycle, branched-chain amino acid metabolism, purine nucleotide pathway, and malate–aspartate shuttle are activated in PGC1α transgenic mice compared with wild-type mice.

overall_design: For microarray analysis, RNA was isolated from the gastrocnemius skeletal muscle of wild-type control mice (12 weeks of age) as well as transgenic mice [PGC1α-a (E) (Miura et al., J. Biol. Chem. 278:31385-90, 2003), 12 weeks of age; PGC1α-b (02-1) (Miura et al., Endocrinology 149:4527-33, 2008), 14 weeks of age; and PGC1α-b (03-2) (Miura et al., Endocrinology 2008), 14 weeks of age]. Samples from wild-type and transgenic mice (N = 5 for each group) were pooled before use.

first: Yasutomi

last: Kamei

first: Shinji

last: Miura


title: TG-interacting factor1 (Tgif1) maintains the identity of mouse ES cells by counterbalancing the expression of core pluripotency factors.

status: Public on Sep 26 2015

city: Austin

first: Bum-Kyu

last: Lee

state: TX

address: 2506 Speedway Stop A5000

institute: University of Texas at Austin

summary: TG-interacting factor1 (Tgif1) is well-known as a transcriptional repressor in transforming growth factor beta (TGFβ) signaling pathway. Target mapping of ES core factors in mouse embryonic stem (ES) cells revealed that Tgif1 is occupied by Oct4 and Nanog. Moreover, recent interactome study of mouse gene regulatory regions showed a preferential regulation of Tgif1 by mouse ES cell specific enhancers. However, the detailed role and mode of actions of Tgif1 in stem cell maintenance and development remains elusive. We show that Tgif1 is indispensable for self-renewal and pluripotency of mouse embryonic stem (ES) cells. Aberrant expression of Tgif1 promotes differentiation of ES cells even in the presence of LIF in part by deregulation of pluripotency factors. Intriguingly, we find that Tgif1 level is a critical factor to determine specific lineage commitment in a dosage-dependent manner. We further show that Tgif1 interacts with ES cell core factors and co-localizes at their binding sites, which eventually restricts expression of ES cell core factors including Oct4, Sox2, and Nanog. Taken together, we provide new insights into the roles of Tgif1 in maintenance as well as differentiation of ES cells.

overall_design: We investigated the roles of  Tgif1 in mouse embryonic stem (ES) cells by knocking down or overexpressing Tgif1 or Tgif2. Total RNAs were extracted from the ES cells upon KD and OE of Tgif1 or Tgif2, and then hybridized on Affymetrix Mouse GeneChip 430A 2.0. We monitored global gene expression changes upon perturbation of Tgif1 or Tgif2.

first: Jonghwan

last: Kim


title: Discovery of progenitor signatures by time series synexpression analysis during Drosophila cell immortalization [Microarray Expression]

status: Public on Sep 23 2015

city: Boston

first: Mary-Lee

last: Dequeant

email: mdequeant@genetics.med.harvard.edu, fagegalt@cshl.edu, Greg.Hannon@cruk.cam.ac.uk, perrimon@receptor.med.harvard.edu

state: MA

address: 77 Avenue Louis Pasteur

department: Genetics

institute: Harvard Medical School

summary: To characterize the sequence of events associated with RasV12 immortalization of Drosophila embryonic cells, we generated transcriptional time series during cell line establishment, from primary cultures until passage (P) 19.

overall_design: We generated two transcriptional time series from two cell lines (R3 and R7) by sampling the cultures at successive stages, early (P2-4), intermediate (P4-11), and late (P16-19), characterized by different passage times. Time points for the R3 time-series were: P2, P2 (replicate), P5, P6, P7, P8, P16, P17 and P19; for the R7 time-series: P2, P2 (replicate), P3, P4, P7, P8, P16, P17 and P19.

last: Dequéant

first: Delphine

last: Fagegaltier

first: Yanhui

last: Hu

first: Kerstin

last: Spirohn

first: Amanda

last: Simcox

first: Gregory

last: Hannon

first: Norbert

last: Perrimon


title: Expression data in dSTING knockdown and control sibling flies after mock or pathogenic infection

status: Public on Sep 22 2015

city: Miami

first: Glen

middle: N.

last: Barber

state: FL

address: 1550 NW 10th Ave

institute: University of Miami

summary:
Parental flies (y1v1;P{TRiP.JF01138}attP2 and y1w*;P{Act5C-GAL4}25FO1/CyO,y+) were mated and 4-7 day old flies were used for all subsequent experiments. dSTING RNAi flies expressed the dsRNA hairpin targeting dSTING and had straight wings, while sibling flies not expressing dSTING dsRNA had curly wings.
Pathogens used for inoculation were Listeria monocytogenes, Drosophila C Virus (DCV), and Insect Iridescent virus 6 (IIV6), at the following concentrations: 1e7 CFU/ml, 5e7 TCID50/ml, 5e6 TCID50/ml. Mock inoculation was performed with PBS. Whole flies were homogenized 24 or 72 h post-infection.

overall_design: Determining the effect of genotype on gene expression profiles following pathogenic infection was the overall goal of this project.

first: Alan

middle: G

last: Goodman


title: Expression data in S2 cells with or without dSTING knockdown followed by dsDNA treatment

summary:
S2 cells were treated with dsRNA targeting dSTING (dSTING RNAi) or non-specifically (control). 90-mer dsDNA (dsDNA90) was then transfected, which activates dSTING. Mock transfection was performed in the absence of dsDNA90 using lipofectamine alone.
Affymetrix arrays were used to profile gene expression.

overall_design: Determining the effect of dSTING knockdown in dsDNA-transfected S2 cells on gene expression profiles was the overall goal of this project.


title: The difference of gene expression for live or dead BbrY associated mice.

status: Public on Aug 30 2015

city: kunitachi-si

first: tatsuichiro

last: shima

state: Tokyo

department: basic research

institute: Yakult central institute for microbiological research

summary: To confirm epithelial gene expression of the large intestine after inoculation of dead (heat-treatment) or live Bifidobacterium probiotic strain (BbrY) we have employed whole genome microarray expression profiling. The epithelial cells were released from dead or live BbrY associated mice 3 or 28 days after association and GF mice with HANKS including EDTA and Hepes and treated by TRI-zol reagent. It was confirmed that the live BbrY associated mice were affected epithelial gene expression much more than dead cell feeding by K-means clustering and the functional categories.

overall_design: BbrY-association induced gene expression in cecal epithelial cells was measured at 3 or 28 days after BbrY-association. Four mice was used for each experiment and GF mice were used as reference.

first: Tatsuichiro

last: Shima

first: Yoshinori

last: Umesaki


title: Gene expression in third instar larval eye discs

status: Public on Aug 26 2015

city: Chicago

first: Mary

last: Truscott

state: IL

address: 900 S Ashland Ave, room 2356

department: Biochemistry and Molecular Genetics

institute: University of Illinois at Chicago

summary: We used microarrays to identify genes that are differentially expressed in the absence of miR-998 expression.

overall_design: Drosophila third instar larvae were selected for RNA extraction and hybridization on Affymetrix microarrays. Three biological replicates for each genotype were prepared. The data was normalized using the RMA algorithm.

first: Maxim

last: Frolov


title: Expression data in dSTING knockdown S2 cells and whole flies after mock or pathogenic infection


title: Development of a prognostic gene signature in pancreatic cancer

status: Public on Aug 28 2015

first: Dung-Tsa

last: Chen

department: Biostatistics and Bioinformatics

summary: Microarray analysis of 63 patients with pancreatic cancer tissues resulted in the identification of a 15-gene signature to predict overall survival

overall_design: RNA was extracted from microdissected frozen pancreatic tissues for gene array analysis

first: Mokenge

middle: P

last: Malafa


title: Gene expression regulated by transcription factor MiT in Drosophila

status: Public on Aug 01 2015

city: Syracuse

first: Francesca

last: Pignoni

state: NY

address: 766 Irving Ave, 5322 Weiskotten Hall

department: Department of Ophthalmology

institute: SUNY Upstate Medical University

summary: To understand the role of MiT in Drosophila, we set out to identify critical gene targets by looking at changes in the WT transcriptome induced by either gain or loss of MiT function. Mutant hindgut and malpighian tubules provided loss-of function tissue and nub-Gal4-driven expression of MiT in the wing epithelium was used for gain-of-function. In the wing disc experiment, 543 genes were upregulated by exogenous MiT, and 359 genes were downregulated (>1.4 fold; P value < 0.01). In the larval HG+MT, 897 genes were downregulated and 898 were upregulated (>1.4 fold; P value < 0.01) after MiT. Among these genes, 85 were both upregulated in wing discs and downregulated in mutant HG+MT, and are the common genes that regulated by MiT in both tissues.

overall_design: We set out to identify potential targets of MiT by comparing the transcriptional profiles of wing discs with and without MiT overexpression (nub-Gal4 UAS-MiT versus nub-Gal4), and separately the profiles of HG+MT tissue from WT and MiT mutant (MiTTZ2/Df(4)TZ). Then, we focused on genetic loci that were upregulated by gain of MiT in the wing and downregulated by loss of MiT in the HG+MT.

first: Tianyi

last: Zhang

first: Michael

last: Hsing

first: Sek

last: Kong


title: Differential gene expression between female hNAG-1 transgenic and Wt mice in abdominal white adipose tissue (WAT)

status: Public on Aug 10 2015

city: RTP

first: NIEHS

last: Microarray Core

summary:
To understand the mechanism of extended lifespan in hNAG-1 mice, we used whole genome microarray analysis to examine differential gene expression in abdominal WAT in hNAG-1 mice. Differential category expression analysis may show significant differences between hNAG-1 mice and WT mice in key pathways in the regulation of metabolism and mammalian lifespan.
In addition, To explore the reason why hNAG-1 mice are leaner than Wt littermates.

overall_design: A total of 6 animals from each genotype were used and WAT was extacted from each mouse, we then pooled two sample as one sample for each genotype to be used in microarray experiment.

first: Thomas

last: Eling

first: Xingya

last: Wang


title: Expression data from Brakeless mutant Drosophila embryos

status: Public on Aug 24 2015

city: Stockholm

first: Mattias

last: Mannervik

address: Arrheniuslaboratories E3

department: Molecular Biosciences, the Wenner-Gren Institute

country: Sweden

institute: Stockholm University

summary:
The Brakeless protein performs many important functions during Drosophila development, but how it controls gene expression is not understood. We previously showed that Brakeless can function as a transcriptional co-repressor. Here, we report transcriptional profiling of brakeless mutant embryos to identify additional target genes.
We used microarrays to identify gene expression changes in brakeless mutant early Drosophila embryos.

overall_design: Drosophila germline clones of the strong brakeless 278 allele (lab stock B97) were generated and compared to control germline clones generated with the original unmutagenized chromosome (FRT G13). Two-four hour old embryos from these females were used for RNA extraction and hybridization on Affymetrix microarrays.

first: Filip

last: Crona

first: Bhumica

last: Singla


title: RAS/MAPK activation drives resistance to Smo inhibition, metastasis and tumor evolution in Shh pathway-dependent tumors

status: Public on Jul 22 2015

first: Xuesong

last: Zhao

state: Massachusetts

address: 450 Brookline Ave

department: Cancer Biology

institute: Dana-Farber Cancer Institute

summary:
Aberrant Shh signaling promotes tumor growth in diverse human cancers. The importance of Shh signaling is particularly evident in medulloblastoma and basal cell carcinoma (BCC), where inhibitors targeting the Shh pathway component Smoothened (Smo) show great therapeutic promise. However, the emergence of drug resistance limits long-term efficacy and the mechanisms of resistance remain poorly understood. Using new culturing techniques, we established a cohort of Shh pathway-driven medulloblastoma cell lines derived from Ptch+/- mice. Using this new model, we identify activation of the RAS/MAPK pathway circumvents Shh pathway-dependency, drives tumor growth and enhances metastatic behavior.Together these findings reveal a critical role of RAS/MAPK pathway in drug resistance and tumor evolution of Shh pathway-dependent tumors.
We performed gene expression profile analysis of SMB cells, in vivo primary MB, as well as cerebellum of normal P6 and adult mice. We also compared gene expression profiles of SMB cells to those of growth factor treated and RAS transformed cells.

overall_design: 24 mouse samples were collected for RNA extraction and hybridization on Affymetrix microarrays, including 3 normal cerebellar as control, 3 primary tumor samples and 18 cell samples with different treatment conditions. We first compared gene expression profiles of SMB cells to those of in vivo primary MB and normal cerebellum. We then compared gene expression profiles of SMB cells to those of growth factor treated and RAS transformed cells.

first: Tatyana

last: Ponomaryov

first: Rosalind

last: Segal


title: Dazl is required for TET-mediated reprogramming to a naïve pluripotent state (II)

status: Public on Jul 01 2015

city: Utrecht

first: Niels

last: Geijsen

address: Uppsalalaan 8

country: Netherlands

institute: Hubrecht Institute

summary: Embryonic stem cell (ESC) cultures display a heterogeneous gene expression profile, ranging from a pristine naïve pluripotent state to a primed epiblast state. While it is known that the addition of inhibitors of GSK3β and MEK (so-called 2i conditions) push ESC cultures towards a more homogeneous naïve pluripotent state, the molecular underpinnings of this naïve transition are not completely understood. Here we demonstrate that Dazl, a RNA-binding protein previously thought to be expressed specifically in developing primordial germ cells (PGCs), marks a subpopulation of ESCs in vitro that is actively transitioning toward naïve pluripotency. In the absence of Dazl expression, ESCs fail to induce proper expression of Tet enzymes required for 5-hydroxymethylation in 2i-culture conditions. As a result, 5-hydroxymethylation of methylated cystosine residues is impaired. Indeed, we demonstrate that Tet1 and Tet2 are mRNA targets of Dazl, indicating that Dazl might play a role in protection or stabilizing these mRNA molecules. Our results provide insight in the regulation of the acquisition of naïve pluripotency and demonstrate that Dazl is required for TET-mediated cytosine hydroxymethylation in cells that are actively reprogramming to a pluripotent ground state.

overall_design: RNA-IP experiments were used to identify the RNA species bound to DAZL.

first: Maaike

last: Welling

first: Hsu-Hsin

first: Javier

last: Munoz

first: Lennart

last: Kester

first: Jan

last: Junker

first: Nikolai

last: Mischerikov

first: Ewart

last: Kuijk

first: Lev

last: Silberstein

first: Peter

middle: V

last: Kharchenko

first: Mike

last: Geens

first: Hilde

last: van de Velde

first: Alexander

last: van Oudenaarden

first: Albert

last: Heck


title: Polycomb PRC2 antagonizes de novo DNA methylation at the maternal Gtl2-Rian-Mirg locus [Affymetrix Expression]

status: Public on Jul 15 2015

city: Corvallis

first: David

middle: Anthony

last: Hendrix

state: OR

address: 2011 Ag & Life Sciences Bldg

department: Biochemistry and Biophysics/EECS

institute: Oregon State University

summary: Wild-type mouse embryonic stem cells are compared with mutants for components of PRC2 including  Ezh2-/-, Eed-/-, and Jarid2-/- cells. Gene expression microarrays were used to compare the expression for these.

overall_design: This experiment compares wild-type gene expression with mutants for different PRC2 components, including Ezh2-/-, Eee-/- and Jarid2-/- with two replicates for each using Affymetrix Gene Expression Arrays.

first: Partha

last: Das


title: Time course of gene expression signatures in mPTECs during ex vivo culture

city: Tainan

first: Ming-Jer

last: Tang

address: 82-0735, 7F, Department of Physiology, No.1 University Road, National Cheng-Kung University Medical College, Tainan, Taiwan

department: Department of Physiology

country: Taiwan

institute: National Cheng Kung University

summary:
To further examine the gene expression of isolated primary mouse proximal tubular epithelial cells (mPTECs) during ex vivo culture, we have employed whole genome microarray expression profiling as a discovery platform to identify genes with the potential to distinguish the key regulatory transcription factor which was significantly altered.  Primary culuture of mPTECs were cultured on culture dishes for 1 and 3 days. As compared to freshly isolated mPTECs, a 1801-gene consensus signature was identified that distinguished between day 1 and and day 3 samples.  Within these genes, 78 transcriptal factors were dramatically altered. Expression of three genes (KLF5, KLF4, and CCND1) from this signature was quantified in the same RNA samples by RT-PCR.
The proliferation of mouse proximal tubular epithelial cells in ex vivo culture depends on matrix stiffness. Combined analysis of the microarray and experimental data revealed that Krüppel-like factor 5 (Klf5) was the most upregulated transcription factor accompanied by Krüppel-like factor 4 (Klf4) downregulation when cells on stiff matrix. These changes were reversed by soft matrix via ERK inactivation. Knockdown of Klf5 or forced-expression of Klf4 inhibited stiff matrix-induced cell spreading and proliferation, suggesting that Klf5/Klf4 act as positive/negative regulators, respectively. Moreover, stiff matrix-activated ERK increased the protein level and nuclear translocation of mechanosensitive Yes-associated protein 1 (YAP1), which is reported to prevent Klf5 degradation. Finally, in vivo model of unilateral ureteral obstruction (UUO) revealed that matrix stiffness-regulated Klf5/Klf4 is related to the pathogenesis of renal fibrosis. In the dilated tubules of obstructed kidney, ERK/YAP1/Klf5/Cyclin D1 axis were upregulated and Klf4 was downregulated. Inhibition of collagen crosslinking by lysyl oxidase inhibitor alleviated UUO-induced tubular dilatation and proliferation with preserving Klf4 and suppressing the ERK/YAP1/Klf5/Cyclin D1 axis. This study unravels a novel mechanism how matrix stiffness regulates cellular proliferation and highlights the importance of matrix stiffness-modulated Klf5/Klf4 in the regulation of renal physiological functions and fibrosis progression.

overall_design: Gene expression in cultured mPTECs was measured at 0, 1 and 3 days after culturing on culture dishes.

first: Wan

last: Chen

first: Ming

first: Hsi

last: Lin


title: Dazl is required for TET-mediated reprogramming to a naïve pluripotent state (I)

first: Niels

last: Geijsen

summary: Embryonic stem cell (ESC) cultures display a heterogeneous gene expression profile, ranging from a pristine naïve pluripotent state to a primed epiblast state. While it is known that the addition of inhibitors of GSK3β and MEK (so-called 2i conditions) push ESC cultures towards a more homogeneous naïve pluripotent state, the molecular underpinnings of this naïve transition are not completely understood.  Here we demonstrate that Dazl, a RNA-binding protein previously thought to be expressed specifically in developing primordial germ cells (PGCs), marks a subpopulation of ESCs in vitro that is actively transitioning toward naïve pluripotency. In the absence of Dazl expression, ESCs fail to induce proper expression of Tet enzymes required for 5-hydroxymethylation in 2i-culture conditions. As a result, 5-hydroxymethylation of methylated cystosine residues is impaired.  Indeed, we demonstrate that Tet1 and Tet2 are mRNA targets of Dazl, indicating that Dazl might play a role in protection or stabilizing these mRNA molecules. Our results provide insight in the regulation of the acquisition of naïve pluripotency and demonstrate that Dazl is required for TET-mediated cytosine hydroxymethylation in cells that are actively reprogramming to a pluripotent ground state.

overall_design: Two independent mouse ES cell lines, Dazl-GFP and Stella-GFP, were cultured on γ-irradiated feeder MEFs in DMEM containing 15% FBS or serum-free B27N2 medium both supplemented with leukemia inhibitory factor (LIF) (Ying 2008). For the 2i experiments, 1µM MEK inhibitor PD0325901 (Axon Medchem), and 5 µM GSK3β inhibitor Kenpaullone (Tocris), were used. Cells were harvest at 0, 3 and 10 days in each condition for expression microarray analysis.

first: Maaike

last: Welling

first: Hsu-Hsin

first: Javier


title: Comparision of expression profile between CD4+ helper T cells and CD8+ cytotoxic T cells

status: Public on Jun 30 2015

city: Obu

first: Yoshinori

last: Naoe

state: Aichi

address: 35 Gengo Morioka

department: Department of mechanism of aging

institute: National Institute for Longevity and Gerontology

summary: We compared gene expression profiling between CD4+ helper T cells and CD8+ cytotoxic T cells

overall_design: CD4+ helper T cells vs CD8+ cytotoxic T cells

first: Ichiro

last: Taniuchi


title: Expression data from C3H10T1/2 cells treated with 3.3 nM BMP7 vs vehicle

status: Public on Jul 21 2015

first: Yu-Hua

last: Tseng

address: 1 Joslin Place

institute: Joslin Diabetes Center Harvard Medical School

summary:
Multipotent C3H10T1/2 cells can be induced to differentiate into mature brown adipocytes by 3-days BMP7 pretreatment followed by standard adipogenic induction.
We used microarrays to detail the global programme of gene expression in C3H10T1/2 cells after 3-day BMP7 (3.3 nM) treatment.

overall_design: C3H10T1/2 cells were treated with 3.3 nM BMP7 for 3 days, and then total RNAs were extracted for microarray using Affymetrix GeneChip mouse 430A.

first: Hongbin

last: Zhang