title: Analysis of the role of Micu1 in maintaining functional homeostasis in mouse liver

status: Public on Jan 10 2016

city: Philadelphia

first: Egle

last: Juskeviciute

state: PA

address: 1020 Locust st. JAH 527

department: Pathology

institute: Thomas Jefferson University

summary: In this study, we analyzed global liver gene expression in MICU1 knock-down (KD) mice. To generate liver-specific MICU1 KD mice, MICU1loxp/loxp male mice were treated with an AAV8-Cre under the control of a hepatocyte specific promoter (TBG). AAV8-TBG-Null treated littermates were used as controls. Liver samples were collected 3-5 weeks after injection. Knockdown was verified by protein and mRNA (94%, 98%, respectively). Mouse Gene 2.0 ST (Affymetrix, Santa Clara, CA) arrays were used to obtain global gene expression data.

overall_design: Gene expression was profiled in control and in liver-specific Micu1 knockdown mice liver samples; 4 biological replicates per condition.

first: György

last: Hajnóczky

first: Jan

middle: B

last: Hoek

first: Erin

last: Seifert

first: Cynthia

last: Moffat

first: Melanie

last: Paillard

first: Anil

last: Antony


title: Emodin inhibits macrophage classical activation [Control-LPS-IFNg-Emodin]

status: Public on Jan 02 2016

city: Columbia

first: Diego

last: Altomare

state: SC

address: 715 Sumter Street, Room 617

department: Department of Drug Discovery and Biomedical Sciences

country: USA

institute: University of South Carolina

summary: In order to fully characterize emodin's effects on macrophage activation, peritoneal macrophages were stimulated with LPS+IFNg with or without emodin and gene expression was analyzed using a whole genome microarray. Emodin significantly attenuated the IFNg/LPS induced changes in a large percentage of responsive genes (31%) through inhibiting multiple signaling pathways. RT-qPCR was used to confirm the results in several genes associated with M1 macrophage activation including: TNF, IL6, IL1b, iNOS, MMP2, and MMP9.

overall_design: Three-condition, one-color experiment: Vehicle control, LPS-IFNg or LPS-IFNg-Emodin treated periferal WBC PMN samples: 4 biological replicates each.

first: Stephen

last: Iwanowycz

first: Dapin

last: Fan


title: Expression data from mouse amygdala

status: Public on Jan 21 2016

city: Seoul

first: Sooyoung

last: Chung

address: Ewhayeodae-gil

department: Department of Brain and Cognitive Sciences

country: South Korea

institute: Ewha Womans University

summary:
Inositol 1,4,5-trisphosphate 3-kinase A (IP3K-A) is a molecule enriched in the brain and neurons that regulates intracellular calcium levels via signaling through the inositol trisphosphate receptor. In the present study, we found that IP3K-A expression is highly enriched in the central nucleus of the amygdala (CeA), which plays a pivotal role in the processing and expression of emotional phenotypes in mammals.
We used microarray to identify differentially expressed genes in the amydala of wild type (WT) and IP3K-A KO mice.

overall_design: Male IP3K-A KO mice and their wild-type (WT) littermate controls from a C57BL/6N background were used at 10 to 15 weeks old. Mice were housed in temperature (22°C-23°C)- and humidity (50%)-controlled quarters under a 12-hr light/dark photoperiod (lights on at 08:00a.m.) with free access to food and water. Mice were sacrificed by cervical dislocation between 02:00p.m. and 04:00p.m. Amygdala tissue was rapidly dissected from 1-mm thick slices and frozen in liquid nitrogen.

first: Hyun

last: Kim


title: Transcriptional reprogramming and resistance to colonic mucosal injury in PARP1-deficient mice

status: Public on Jan 08 2016

city: Tucson

first: Pawel

middle: R.

last: Kiela

state: AZ

address: 1501 N. Campbell Ave.

department: Pediatrics

institute: University of Arizona

summary: Poly(ADP-ribose)     polymerases (PARPs)  synthesize  and  bind  branched  polymers of  ADP-ribose  to acceptor  proteins using NAD  as a  substrate,  and  participate  to  the  control  of  gene transcription  and  DNA  repair.  PARP1,  the  most abundant   isoform,   regulates   the   expression   of proinflammatory        mediator        -        cytokines, chemokines     and     adhesion     molecules,     and inhibition of PARP1 enzymatic activity reduced or ameliorated    autoimmune    diseases    in    several experimental  models,  including  colitis.  However, the mechanism(s) underlying the protective effects of PARP1 inhibition in colitis and the cell types in which Parp1  deletion  has  the  most  significant impact are unknown.  The objective of the current study   was   to   determine   the   impact   of Parp1 deletion   on   the   innate   immune   response   to mucosal   injury. Genome-wide  analysis  of  the  colonic  transcriptome  was   performed.  Compared  to  WT,  we  demonstrated  that Parp1-/-were  protected  from  DSS-induced  colitis  and  that this  protection  was  associated  with  a  dramatic transcriptional    reprogramming in    the    colon.

overall_design: WT or Parp1-/- mice were treated with drinking water administered ad libitum without ot with 4% dextran sulfate (DSS) for seven days. Whole colon was collected for RNA extraction and hybridization on Affymetrix microarrays. Thee mice from each genotype/treatment groups were used in the analysis.

first: Claire

last: Larmonie

middle: R


title: Expression data from Glioma-Initiating Cells (GICs) cultured under hypoxia and normoxia

status: Public on Jan 01 2016

city: Durham

first: Xiao-Fan

last: Wang

address: Duke University

institute: Duke University

summary:
Glioblastoma (GBM) is the most common and aggressive primary brain tumor in adults, with glioma initiating cells (GICs) implicated to be critical for tumor progression and resistance to therapy. The hypoxic tumor microenvironment has been shown to play an important role to maintain the GICs; however, the mechanisms regulating responses of GICs to hypoxia remain poorly understood.
We used microarray to  to detail the global change of gene expression in GICs cultured under hypoxia compared to normoxia and identified de-regulated genes during hypoxia.

overall_design: CD133+ D456MG GICs were cultured under 1% O2 or 20% O2 for 12 hours. Then RNA was extracted and gene expression was profiled by microarray.

first: Jing

last: Hu


title: Increased DNA Methylation of Dnmt3b-Targets Impairs Leukemogenesis (expression)

status: Public on Jan 11 2016

city: Heidelberg

first: Christian

last: Rohde

address: Im Neuenheimer Feld 410

country: Germany

institute: Heidelberg University

summary: Here, we analyzed global gene expression changes that were associated with over expression of Dnmt3b in MLL-AF9 induced leukemias using the Affymetrix microarray platform.

overall_design: Changes in global gene expression were determined with Affymetrix microarrays in MLL-AF9 induced leukemias over expressing Dnmt3b.

first: Isabell

last: Schulze

first: Carsten

last: Müller-Tidow


title: Primary lung fibroblasts treated with hedgehog agonist, purmorphamine

first: Michael

middle: Patrick

last: Morley

address: 3400 Civic Center Blvd, Bldg 421

department: Penn Cardiovascular Institute

institute: Perelman School of Medicine at the University of Pennsylvania

summary: Postnatal tissue quiescence is generally thought to be a default state in the absence of a proliferative stimulus such as injury. We now demonstrate that in the lung, quiescence in the adult is an actively maintained state and is regulated by paracrine hedgehog signaling. Epithelial-specific deletion of Sonic Hedgehog during normal homeostasis results in a proliferative expansion of the adjacent lung mesenchyme. Injury to the lung epithelium results in decreased hedgehog activation, accompanied by proliferative expansion of the adjacent mesenchyme. Moreover, reconstitution of Hedgehog signaling during epithelial injury attenuated the proliferative expansion of the adjacent mesenchyme. Hedgehog signaling maintains lung quiescence by attenuating PDGF signaling through blocking post-translational processing of PDGF receptor α/β into the mature isoforms. These results indicate that in postnatal tissues, epithelial cells can actively maintain mesenchymal quiescence via paracrine hedgehog activation, and that imbalances in this pathway could lead to aberrant mesenchymal expansion and postnatal disease.

overall_design: Fibroblasts were isolated from mouse lungs and grown in culture in triplicate wells. Samples were treated with vehicle or purmorphamine 5um for 24 hours and RNA was isolated for microarray.

first: Tien

last: Peng

first: Rachel

middle: S

last: Kadzik

middle: P

first: Komal

last: Rathi

first: Lan

last: Cheng

first: Edward

middle: E

last: Morrisey


title: Emodin inhibits macrophage alernative activation

first: Diego

last: Altomare

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

overall_design: Refer to individual Series


title: Development of gene sets after deleting Rb or Rb and Pten in p53 null background primary prostate cells

status: Public on Dec 31 2015

city: Kanazawa

first: Takumi

last: Nishiuchi

address: 13-1 Takaramachi

country: Japan

institute: Kanazawa University


title: Emodin inhibits macrophage alernative activation [Control-IL4-Emodin]

summary: In order to fully characterize emodin's effects on macrophage alternative activation, peritoneal macrophages were stimulated with IL4 with or without emodin and gene expression was analyzed using a whole genome microarray. Emodin significantly attenuated the IL4 induced changes in a large percentage of genes (60%) through inhibiting multiple signaling pathways. RT-qPCR was used to confirm the results in several genes associated with M2 macrophage activation including: Arg1, Chi3l3, and CD206.

overall_design: Three-condition, one-color experiment: Vehicle control, IL4 or IL4-Emodin treated periferal WBC PMN samples: 4 biological replicates each.

first: Stephen

last: Iwanowycz

first: Dapin

last: Fan


title: Development of gene sets after deleting Rb and Pten in p53 null background primary prostate cells [Rb and Pten]

summary: Our findings suggested that cytokines were upregulated in p53 null primary prostate cells after deleting Rb and/or Pten. Rb and Pten deletion are important for prostate cancer progression.

overall_design: p53-/- Rbf/f vs p53-/- Rb∆f/∆f primary prostate cells. Three independent experiments were performed.  p53-/- Rbf/f vs p53-/- Rb∆f/∆f Pten∆f/∆f primary prostate cells. Four independent experiments were performed.

first: Mohammed

last: Salah

first: Chiaki

last: Takahashi


title: Gene expression profiling of pancreatic stem cell derived islet like clusters vs native islets

status: Public on Dec 30 2015

city: Bangalore

first: Renjitha

last: Gopurappilly

state: Karnataka

address: GKVK PO, Bellary Rd, Allalasandra, Yelahanka

department: Regenerative Medicine

country: India

institute: SORM, Manipal University

summary: We have earlier reported the presence of mesenchymal stromal cell (MSC) - like cells in adult mouse pancreas and their ability to differentiate into islet-like clusters (ILCs). To determine the global relationship of these cells to native islets  Agilent 8X60K microarray profiling was done.More than 9000 probes were differentially regulated (≥ 1.5-fold, P ≤ 0.05) in the ILCs when compared to primary mouse islets. The mature pancreatic markers were significantly downregulated whereas markers associated with replication and cell cycle entry, inflammation, fatty acid metabolism and so on were predicted to be increased. . As a whole the ILCs though immature offer certain compensations including the infinite number of initiator MSCs which can be expanded and cryopreserved and also the amenity to genetic modifications to create robust mature cells resistant to immune attack in a transplantation perspective

overall_design: Agilent one-color experiment,Organism: Mouse ,Agilent Whole Genome Mouse 8x60k  (AMADID: 28005)  , Labeling kit: Agilent Quick-Amp labeling Kit (p/n5190-0442)

first: Ramesh

last: Bhonde


title: ISR target genes in muscle of hSA::Fv2E-PERK

status: Public on Dec 26 2015

city: Tokushima

first: Seiichi

last: Oyadomari

state: Tokushima

address: 3-18-15 Kuramoto

department: Division of Molecular Biology

institute: Institute for Genome Research

summary: To identify the target genes of integrated stress reponse (ISR) in skeletal muscle, we have employed whole genome microarray expression in muscle specific Fv2E-PERK transgenic mice and C2C12 myotubes expressed in Fv2E-PERK. As a result, we identified that Fgf21 mRNA expression was commonly induced in skeletal muscle and C2C12.

overall_design: The hSA::Fv2E-PERK transgenic mice were injected by AP20187 or mock. C2C12-Fv2E-PERK was also stimulated with AP20187.

first: Masato

last: Miyake

first: Akitoshi

last: Nomura

first: Atsushi

last: Ogura

first: Takahara

last: Kazuna

first: Kiyoe

last: Kurahashi

first: Ryousuke

last: Sato

first: Hiroshi

last: Inoue


title: Muscle expression of SOD1G93A modulates microRNA and mRNA expression pattern associated with the myelination process in the spinal cord of transgenic mice.

city: Roma

first: Camilla

last: Bernardini

address: L.go F.Vito 1

country: Italy

institute: Università Cattolica del Sacro Cuore

type:
Expression profiling by array
Other


title: Identification of drugs that enhance skin repair using dermal stem cell-based screens [Mouse]

status: Public on Dec 24 2015

city: Toronto

first: Freda

last: Miller

state: ON

address: 686 Bay St

country: Canada

institute: Hospital for Sick Children

summary: Here, we asked whether we could identify pharmacological agents that enhance endogenous stem cell function to promote skin repair, focusing on SKPs (skin-derived precursors) a dermal precursor cell population. Libraries of compounds already used in humans were screened for their ability to enhance the self-renewal of human and rodent SKPs. We identified and validated 5 such compounds, and showed that two of them, alprostadil and trimebutine maleate, enhanced the repair of full thickness skin wounds in middle-aged mice. Moreover, SKPs isolated from drug-treated skin displayed long-term increases in self-renewal when cultured in basal growth medium without drugs. Both alprostadil and trimebutine maleate likely mediated increases in SKPs self-renewal by moderate hyperactivation of the MEK-ERK pathway. These findings identify candidates for potential clinical use in human skin repair, and provide support for the idea that pharmacological activation of endogenous tissue precursors represents a viable therapeutic strategy.

overall_design: We obtained three independent isolates of SKPs from 9 month old CD57/Bl6 mice which were either uninjured and treated with vehicle, injured and treated with vehicle, trimebutine maleate, or alprostadil. RNA samples deriving from these cells were analyzed on the Affymetrix GeneChip Mouse Gene 2.0 ST Array.

first: Sibel

last: Naska

first: Scott

middle: A

last: Yuzwa

first: Adam

last: Johnston

first: Smitha

last: Paul

first: Kristen

last: Smith

first: Maryline

last: Paris

first: Michael

middle: V

last: Sefton

first: Alessandro

last: Datti

middle: D

first: David

last: Kaplan


title: Haploinsufficiency of interstitial genes between TMPRSS2 and ERG contributes to prostate tumorigenesis

city: Boston

first: Zhe

last: Li

state: MA

address: 77 Avenue Louis Pasteur, Room 466

department: Medicine, Genetics Division

institute: Brigham and Women's Hospital

summary: TMPRSS2-ERG gene fusions that are frequently identified in prostate cancer can be generated either through chromosomal translocation or via interstitial deletion. The latter mechanism deletes an interstitial region of ~3Mb and it remains largely unanswered whether genes deleted within this region contribute to prostate cancer. By characterizing two knockin mouse models recapitulating TMPRSS2-ERG fusions with or without the interstitial deletion, we found that only those with deletion developed poorly differentiated adenocarcinomas with epithelial-to-mesenchymal transition, when under a Pten-null background. We identified several interstitial genes, including ETS2 and BACE2, whose reduced expression correlates with worse disease-free survival and lethal disease. By using an Ets2 conditional knockout allele, we demonstrated that loss of one copy of Ets2 was sufficient for prostate cancer progression when under a Pten-null background. Collectively, our data suggest that ETS2 is a prostate tumor suppressor and haploinsufficiency of one or more interstitial genes contributes to prostate cancer progression.

overall_design: Genotyped male mice were euthanized at 12 months of age and prostates isolated. Prostates were fixed overnight in 10% formalin and stored in 70% ethanol until tissue processing and paraffin embedding. Serial sections were cut from paraffin blocks which were stained for H&E and analyzed by a trained rodent histopathologist. Using these sections as a visual guide for specific types of lesions, the sequential sections were stained with hematoxylin and used for laser capture microdissection on ArcturusXT system. Epithelial cells within notable high grade prostate intraepithelial neoplasia (HG-PIN) lesions were microdissected from 3 mice from each corresponding genotype. In addition, poorly differentiated adenocarcinomas from PbCre;T-3Mb-Erg/+;PtenL/L mice were also dissected. RNA was isolated from the microdissected tissue using the Qiagen RNeasy FFPE kit and subjected to Nugen Amplification before microarray analysis on an Affymetrix Mouse Gene 2.0 ST chip.

first: Douglas

last: Linn


title: Muscle expression of SOD1G93A modulates microRNA and mRNA expression pattern associated with the myelination process in the spinal cord of transgenic mice [microarray]

summary: Expression profiling of lumbar spinal cord from MLC/SOD1G93A mice and age matched controls at 120 days of age. We used Affymetrix GeneChip Mouse Gene expression 2.0 st Array to determine differential gene expression.

overall_design: Samples were collected from mice MLC/SOD1G93A and controls FVB age matched at 4 month-old. Samples were collected representing each genotype and age group for RNA extraction and hybridization on Affymetrix Microarrays.

first: Gabriella

last: Dobrowolny

first: Martina

last: Martini

first: Mirko

last: Baranzini

first: Marta

last: Barba

first: Antonio

last: Musarò


title: QS wild type and Aldh1a1-/- preadipocytes 2015

city: Columbus

first: Lianbo

last: Yu

state: OH

address: 1800 Cannon Drive

department: Center for Biostatistics

institute: The Ohio State University

summary: The goal of this study was to identify preadipocyte signature genes that are dependent in aldehyde dehydrogenase 1a1 (Aldh1a1) by comparison genomes of the immortalized wild type and Aldh1a1-/- preadipocytes. Gene expression was measured using theAffymetrix GeneChip Mouse Gene ST 2.0 arrays.

overall_design: Murine wild type (n=3, control) and Aldh1a1-/- preadipocytes (n=3) were cultured in standard DMEM medium containing 10% of calf serum. mRNA was isolated by RNeasy (Qiagen, Valencia, CA). RNA integrity was interrogated using the Agilent 2100 Bioanalyzer (Agilent Technologies). A 100ng aliquot of total RNA was linearly amplified.  Then, 5.5ug of cDNA was labeled and fragmented using the GeneChip WT PLUS reagent kit (Affymetrix, Santa Clara, CA) following the manufacturer's instructions. Labeled cDNA targets were hybridized to Affymetrix GeneChip Mouse Gene ST 2.0 arrays for 16 h at 45 °C rotating at 60rpm.  The arrays were washed and stained using the Fluidics Station 450 and scanned using the GeneChip Scanner 3000. Signal intensities were quantified by Affymetrix Expression Console version 1.3.1. Background correction and quantile normalization was performed to adjust technical bias, and probe-set expression levels were calculated by RMA method. After filtering above noise cutoff, there are 9,528 probe-sets that were tested by linear model. A variance smoothing method with fully moderated t-statistic was employed for this study and was adjusted by controlling the mean number of false positives. With a combined cutoff of 2-fold change and p-value of 0.0001 (controlling 1 false positive over all probe-sets), we declared 500 probe-sets as differential gene expression between Aldh1a1-/- and WT preadipocytes.

first: Ouliana

last: Ziouzenkova

first: Qiwen

last: Shen

first: Paolo

last: Fadda

first: Sarah

last: Warner


title: mESCs cultured in microfluidic chambers take control of their fate by producing endogenous signals including LIF

status: Public on Dec 18 2015

city: Davis

first: Joshua

middle: Daniel

last: Guild

state: CA

address: 451 East Health Sciences St. #2619

department: Biomedical Engineering

institute: University of California Davis

summary: mESCs cultured in microfluidic chambers secrete endogneous signals which accumulate to facilitate expression of pluripotency associated genes

overall_design: ES-D3 [D3] ATCC® CRL-1934™ mouse embryonic stem cells (strain: 129S2/SvPas) were culture in standard tissue culture wells or microfluidic chambers prior to RNA extraction and hybridization on Affymetrix microarrays. We sought to assess gene expression of mESCs cultured in microfluidic chambers under conditions of minimal perfusion. Microarray probe intensity values (CEL files) were background-corrected, summarized, log2-transformed, and normalized using the Robust Multi-array Average (RMA16) algorithm and filtered for raw signal intensity values in the range of the 20th-100th percentile (lower/upper cut-off).


title: Inducible Gata1 Suppression Expands Erythro-Megakaryocytic Progenitors from Embryonic Stem Cells

status: Public on Dec 09 2015

city: Memphis

last: Finkelstein

state: TN

address: 332 N. Lauderdale St.

department: Computational Biology

institute: St Jude Children's Research Hospital

summary: Embryonic stem (ES) and induced pluripotent stem (iPS) cells represent a potential source of megakaryocytes and platelets for transfusion therapies. However, most current ES/iPS cell differentiation protocols are limited by low yields of hematopoietic progeny. Mutations in the mouse and human genes encoding transcription factor GATA1 cause accumulation of proliferating, developmentally arrested megakaryocytes. To exploit this clinical observation, we engineered wildtype (WT) murine ES cells to express doxycycline (dox)-regulated Gata1 short hairpin (sh) RNAs. In vitro differentiation with dox and thrombopoietin (Tpo) resulted in approximately 1013-fold expansion of immature hematopoietic progenitors. Upon dox withdrawal with multilineage cytokines, GATA1 expression was restored and the cells differentiated into erythroblasts and megakaryocytes. With Tpo alone, dox-deprived progenitors formed mainly mature megakaryocytes that generated functional platelets in vivo. Our findings provide a novel, readily reproducible strategy to expand ES-cell derived megakaryocyte-erythroid progenitors and direct their differentiation into megakaryocytes producing functional platelets in clinically relevant numbers.

overall_design: 3 classes of samples were compared 1) fetal liver derived megkaryocytes 2) G1ME (Gata1– megakaryocyte-erythroid)  3) G1ME2 (engineered wildtype (WT) murine ES cells to express doxycycline (dox)-regulated Gata1 short hairpin (sh) RNAs)

first: Ji-Yoon

last: Noh

first: Shilpa

last: Gandre-Babbe

first: Yuhuan

last: Wang

first: Vincent

last: Hayes

first: Yu

last: Yao

first: Paul

last: Gadue

first: Spencer

middle: K

last: Sullivan

first: Stella

middle: T

last: Chou

first: Kellie

last: Machlus

first: Joseph

last: Italiano

last: Kyba

first: Jacob

middle: C

last: Ulirsch

first: Vijay

middle: G

last: Sankaran

first: Deborah

middle: L

last: French

first: Mortimer

last: Poncz

first: Mitchell

middle: J

last: Weiss


title: Antibody-based selective isolation of atrial and ventricular cardiomyocytes by differential expression of integrin α6 (CD49f)

status: Public on Dec 14 2015

city: Bergisch-Gladbach

first: Stefan

last: Tomiuk

address: Friedrich-Ebert-Str. 68

department: Bioinformatics

institute: Miltenyi Biotec GmbH

summary: Central questions like cardiomyocyte subtype emergence during cardiogenesis or availability of cardiomyocyte subtypes for cell replacement therapy require selective identification and purification of atrial and ventricular cardiomyocytes. However, characterization and implementation of pure cardiomyocyte subtypes is still challenging due to technical limitations. Our aim was to identify surface markers enabling the selective detection and purification of atrial and ventricular cardiomyocytes from mouse hearts. In a surface marker screen we found differential expression of CD49f in atrial and ventricular embryonic cardiomyocytes (E13.5). By flow cytometry we could correlate a high CD49f expression with MLC-2a on the single cell level; a low CD49f expression corresponded to MLC-2v. Based on the persisting differential CD49f expression we developed purification protocols for cardiomyocytes subtypes from the developing mouse heart. Flow sorting of E15.5 hearts into ErbB-2+/CD49flow and ErbB-2+/CD49fhigh cells led to a selective depletion (CD49flow) or enrichment of MLC-2a+ cells (CD49fhigh). We found a corresponding CD49f-dependent distribution of MLC-2a when pre-enriched neonatal cardiomyocytes (P2) were flow-sorted into CD49flow and CD49fhigh. Atrial and ventricular identity was confirmed by expression profiling and patch clamp analysis of sorted embryonic hearts, which unequivocally demonstrated that the sorted cells were viable and functional. For the first time, we introduce a non-genetic, antibody-based approach to specifically isolate atrial and ventricular cardiomyocytes from mouse hearts of various developmental stages. This newly gained capability of obtaining highly pure, viable cells will facilitate in-depths characterization of the individual cellular subsets and will aid translational research and therapeutic applications.

overall_design: The dataset comprises four different cardiomyocytes subtypes from the developing mouse heart. Embryonic (E15.5) hearts were dissociated and flow-sorted into ErbB-2+/CD49flow and ErbB-2+/CD49fhigh cardiomyocytes. Neonatal (P2) hearts were dissociated, contaminating non-myocytes were removed by MACS depletion, and the purified cardiomyocytes were flow-sorted into CD49flow and CD49fhigh cardiomyocytes. Four biological replicates were available for each sample groups. Microarray analysis was conducted on the Agilent Whole Mouse Genome Oligo Microarray 8x60K platform.

first: Anne

middle: M

last: Wiencierz

first: Dominik

last: Eckardt


title: Expression data from mouse neonatal hindlimb muscles

status: Public on Dec 08 2015

first: Sandya

last: Liyanarachchi

address: Rm 830, 460, W 12th Avenue

department: Human Genetics

institute: OSU

summary:
During neonatal development, skeletal muscle grows dramatically by myonuclei accretion to existing fibers and hypertophic growth of fibers with protein synthesis.
To understand molecular mechanism underlying neonatal muscle growth, we used microarray to profile the global program of gene expressions especially involved in myoblast fusion, migration, and muscle fiber growth by itself.

overall_design: Mouse hindlimb muscles at postnatal day (P) 2, 7, and 14 were isolated and used for RNA extraction and hybridyzation on microarrays. We used three biological replicates for each time point.

first: Jinmo

last: Gu

first: Denis

last: Guttridge


title: CAF-1 safeguards somatic cell identity during factor-induced reprogramming

status: Public on Dec 10 2015

first: Peter

last: Park

address: 10 Shattuck St

department: Center for Biomedical Informatics

institute: Harvard Medical School

summary: Cellular differentiation involves profound changes in the chromatic landscape, yet the mechanisms by which somatic cell identity is subsequently maintained remain incompletely understood.  To further elucidate regulatory pathways that safeguard the somatic state, we performed two comprehensive RNAi screens targeting chromatin factors during transcription factor-mediated reprogramming of mouse fibroblasts to induced pluripotent stem cells (iPSCs). Remarkably, subunits of the chromatin assembly factor-1 (CAF-1) complex emerged as the most prominent hits from both screens, followed by modulators of lysine sumoylation and heterochromatin maintenance. Suppression of CAF-1 increased reprogramming efficiency by several orders of magnitude and facilitated iPSC formation in as little as 4 days. Mechanistically, CAF-1 suppression led to a more accessible chromatin structure at enhancer elements early during reprogramming. These changes were accompanied by a decrease in somatic heterochromatin domains, increased binding of Sox2 to pluripotency-specific targets and activation of associated genes. Notably, suppression of CAF-1 also enhanced the direct conversion of B cells into macrophages and fibroblasts into neurons. Together, our findings reveal the histone chaperone CAF-1 as a novel regulator of somatic cell identity during transcription factor-induced cell fate transitions and provide a potential strategy to modulate cellular plasticity in a regenerative setting.

overall_design: Gene expression analysis in CAF-1 knockdown and Renilla control during early OKSM-induced reprogramming by microarray

first: Konrad

last: Hochedlinger

first: Sihem

last: Cheloufi


title: Aneuploidy shortens replicative lifespan in Saccharomyces cerevisiae

status: Public on Dec 04 2015

city: Seattle

first: Maitreya

middle: J.

last: Dunham

state: WA

address: Foege Building, S403B, Box 355065

department: Genome Sciences

institute: University of Washington

type: Genome variation profiling by genome tiling array

summary: Aneuploidy and aging are correlated; however, a causal link between these two phenomena has remained elusive.  Here we show that yeast disomic for a single native yeast chromosome generally have a decreased replicative lifespan.  In addition, the extent of this lifespan deficit correlates with the size of the extra chromosome.  We identified a mutation in BUL1 that rescues both the lifespan deficit and a protein trafficking defect in yeast disomic for chromosome 5.  Bul1 is an E4 ubiquitin ligase adaptor involved in a protein quality-control pathway that targets membrane proteins for endocytosis and destruction in the lysosomal vacuole thereby maintaining protein homeostasis.  Concurrent suppression of the aging and trafficking phenotypes suggests that disrupted membrane protein homeostasis in aneuploid yeast may contribute to their accelerated aging.  The data reported here demonstrate that aneuploidy can impair protein homeostasis, shorten lifespan, and may contribute to age-associated phenotypes.

overall_design: These are all CGH arrays comparing DNA content between the indicated strain of interest and a wt control.

first: Anna

last: Sunshine


title: A dynamic role of Tbx3 in the pluripotency circuitry

city: Aachen

first: Martin

last: Zenke

state: NRW

address: Universitatsklinikum Aachen, RWTH

department: Cell Biology

institute: Institute for Biomedical Engineering

summary: Pluripotency represents a cell state comprising a fine-tuned pattern of transcription factor activity required for embryonic stem cell (ESC) self-renewal. TBX3 is the earliest expressed member of the T-box transcription factor family and is involved in maintenance and induction of pluripotency. Hence, TBX3 is believed to be a key member of the pluripotency circuitry, with loss of TBX3 coinciding with loss of pluripotency. We report a dynamic expression of TBX3 in vitro and in vivo using genetic reporter tools tracking TBX3 expression in mouse ESCs (mESCs). Low TBX3 levels are associated with reduced pluripotency, resembling the more mature epiblast. Notably, TBX3-low cells maintain the intrinsic capability to switch to a TBX3-high state and vice versa. Additionally, we show TBX3 to be dispensable for induction and maintenance of naive pluripotency as well as for germ cell development. These data highlight novel facets of TBX3 action in mESCs.

overall_design: 12 samples in total

first: Ronan

last: Russell

first: Marcus

last: Ilg

first: Qiong

last: Lin

first: Guangming

last: Wu

first: André

last: Lechel

first: Wendy

last: Bergmann

first: Tim

last: Eiseler

first: Leonhard

last: Linta

first: Pavan

last: Kumar

first: Moritz

last: Klingenstein

first: Kenjiro

last: Adachi

first: Meike

last: Hohwieler

first: Olena

last: Sakk

first: Stefanie

last: Raab

last: Moon

first: Thomas

last: Seufferlein

first: Hans

last: Schöler

first: Anett

last: Illing

last: Liebau

first: Alexander

last: Kleger


title: Expression data from prostate tumors of TRAMPxPWK/PhJ F2 cross

status: Public on Dec 15 2015

city: Bethesda

first: Nigel

last: Crawford

state: MD

address: 50 South Drive, Room 5154

institute: Human Genome Research Institute

summary:
We hypothesize that germline variation influences susceptibility to aggressive prostate tumor
We examined the changes in gene expression in tumors obtained from TRAMPxPWK/PhJ F2 mice

overall_design: Transgene-positive (Tg+) F2 males were bred by crossing Tg- sires to Tg+ dames. 27 tumor samples were analyzed, which were obtained from Tg+ F2 males

first: Minnkyong

last: Lee

first: Kendra

last: Williams

first: Jonathan

last: Andreas

first: Shashank

last: Patel


title: GFRα1+, NGN3+ and KIT+ spermatogonia of adult mouse testes

status: Public on Dec 02 2015

city: Okazaki

first: Shosei

last: Yoshida

state: Aichi prefecture

address: 5-1,Higashiyama, Myodaiji-cho

department: Division of Germ Cell Biology

institute: National Institute for Basic Biology

summary: In adult mouse testis, undifferentiated spermatogonia include GFRα1+ and NGN3+ populations. The former mainly act as self-renewing stem cells that support steady-state spermatogenesis. Whilst, the latter are primed for differentiation, but retain the potential of self-renewal and contribute to regeneration and post-transplantation colony formation (Nakagawa et al. science .2010; Hara et al. cell stem cell. 2014). And, NGN3+ cells can differentiate to KIT+ cells, which are also mentioned differentiated spermatogonia, by retinoic acid signal. The gene expression profiles of GFRα1+, NGN3+ and KIT+ spermatogonia, as well as the whole testis samples, were investigated here by microarray (Ikami et al. development. 2015).

overall_design: GFRα1+ spermatogonia were isolated by FACS from cell suspensions prepared from the testes of GFRα1-EGFP knock-in (Enomoto et al. development. 2000). NGN3+ and KIT+ spermatogonia were isolated from Ngn3-EGFP transgenic (Yoshida et al. Dev Biol. 2004) mice as GFP+/KIT- and GFP+/KIT+ fractions, respectively. Each GFRα1+ or KIT+ fraction was collected from a single individual, while each NGN3+ fraction was pooled from two mice. In addition, whole testes samples were prepared from WT littermates of GFRα1-EGFP knock-in mouse. All animals were sacrificed at the age of 10-11 weeks old.


title: Over-expression of hsa-miR-221 in JSC1 cells and identification of miRNA targets expressed in a panel of B-cell lines

status: Public on Dec 05 2015

city: London

first: Dan

last: Frampton

address: Gower Street

department: Infection

country: United Kingdom

institute: UCL

summary:
1) To identify changes in gene expression upon over-expression of hsa-miR-221 in JSC1 cells. 2) To identify human miRNA targets expressed in a panel of B-cell lines.
Gammaherpesvirus and host cell microRNAs (miRNAs) together modulate gene expression in normal and malignant cells. Using microRNA microarrays, we determined the expression of mature viral and host cellular miRNAs in a series of B cell tumours that include Kaposi’s Sarcoma-associated herpesvirus (KSHV) infected Primary Effusion Lymphoma (PEL) and Epstein-Barr virus (EBV) infected Burkitt’s lymphoma (BL) cell lines. We show that 35 host miRNAs were constitutively expressed in all the B cell lymphomas and differences in viral miRNA expression were evident between herpesvirus positive tumour types. Furthermore, we show that in PEL, miR-221 and miR-222 expression is defective due to a lack of transcript expression rather than mutation in the miRNA encoding loci. Absence of miR-221 and miR-222 resulted in the enhanced expression of the known target gene p27 (CDKN1B) and reintroduction of miR221 in PEL reduces p27 protein expression.

overall_design: The dataset comes in two parts. 1) 6 JSC1 samples: 2 with miR-221 lentiviral vector, 2 without and 2 with K5 short hairpin RNA as control. 2) A panel of 14 B-cell line samples.  Each of the 20 samples was Cy5 labelled and run with Cy3-labelled Stratagene reference RNA.

first: Eve

last: Coulter

first: Amy

last: Buck

first: Paul

last: Kellam


title: Transcriptome comparison between WT mESC and Tet1,2,3 TKO mESC

status: Public on Dec 01 2015

city: Kyoto

first: Peter

middle: M.

last: Carlton

state: Kyoto

address: Sakyo-ku, Yoshida Honmachi, iCeMS Complex 2

department: Institute for Integrated Cell-Material Sciences

institute: Kyoto University

summary:
5-hydroxymethylcytosine (5hmC) is a DNA base created during active DNA demethylation by the recently-discovered Tet enzymes, and plays essential roles in gene expression. Here, we demonstrate that large quantities of 5hmC are found at sites of DNA damage and repair. 5hmC accumulates at damage foci induced by aphidicolin and microirradiation, and colocalizes with major DNA damage response proteins 53BP1 and γH2AX, revealing 5hmC as an epigenetic marker of DNA damage. Deficiency for the Tet enzymes eliminates damage-induced 5hmC accumulation, alters DNA repair focus formation, and elicits chromosome segregation defects in response to replication stress. Our results indicate that the Tet enzymes and 5hmC create an epigenetic switch that plays an essential role in ensuring genome integrity via DNA damage response pathways.
The purpose of the current dataset is to characterize the transcriptomes of WT and TetTKO cells, to determine the extent to which deficiency for DNA Damage and Repair (DDR) pathway genes contributes to the observed phenotypes in the study; namely, increased chromosomal errors at mitosis in response to 0.2 micromolar aphidicolin treatment.

overall_design: Three wild-type mESC samples and three Tet1,2,3 TKO samples, all grown at the same time. All steps after RNA extraction performed by DNA Chip, Inc.(dna-chip.co.jp)

first: Georgia

middle: R

last: Kafer

first: Xuan

last: Li

first: Takuro

last: Horii

first: Isao

last: Suetake

first: Shoji

last: Tajima

first: Izuho

last: Hatada


title: Transcription repression of miR-221 leads to p27 expression in PEL

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

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

overall_design: Refer to individual Series


title: FOXP1 in ABC DLBCL

first: Louis

last: Staudt

address: 9000 Rockville Pike, Bldg 10, Rm 4N114

department: Lymphoid Malignancies Branch

institute: National Cancer Institute

summary: High expression of the FOXP1 transcription factor distinguishes the highly aggressive Activated B Cell (ABC) type of Diffuse Large B Cell Lymphoma (DLBCL) from the more indolent Germinal Center (GCB) DLBCL subtype and is correlated with poor prognosis. A genetic or functional role for FOXP1 in lymphomagenesis and/or tumor maintenance, however, remains unknown. Here, we report that sustained expression of FOXP1 is necessary for ABC DLBCL cell line survival. Genome-wide transcript profiling reveals that FOXP1 acts directly and indirectly by enforcing expression of known ABC DLBCL hallmarks, including the classical NF-kappaB survival pathway. Our data further suggest that FOXP1 maintains the ABC subtype distinction by repressing gene expression programs dominant in GCB DLBCL and supports a model in which the target of ABC DLBCL transformation is a transitory cell type en route from the germinal center B cell to the terminally differentiated plasma cell.

overall_design: HBL1 (n=12) or TMD8 (n=12) cells were infected with either a Ctrl shRNA or with shRNAs targeting FOXP1. The shRNA expression was induced for 1, 2, 3, or 4 days.


title: Hair follicle aging is driven by transepidermal stem cell elimination via COL17A1 proteolysis

city: Tokyo

first: Hiroyuki

last: Matsumura

state: Bunkyo-ku

address: Room 213, Chemistry East Building, Department of Chemistry, 7-3-1 Hongo

department: Graduate School of Science

institute: The University of Tokyo

summary: Hair loss is one of the typical aging phenotypes in mammals, yet the underlying mechanism(s) is unclear. Here we report that hair follicle stem cell (HFSC) aging causes the stepwise miniaturization of hair follicles and eventual hair loss both in wild-type mice and in humans. In vivo fate analysis of HFSCs revealed that the DNA damage response in HFSCs causes proteolysis of Type XVII Collagen (COL17A1/BP180) to trigger “HFSC aging”, characterized by their loss of stemness signature and epidermal commitment. Those aged HFSCs are cyclically eliminated from the skin through their terminal epidermal differentiation, thereby causing hair follicle miniaturization. That process can be recapitulated by Col17a1 deficiency and prevented by forced maintenance of COL17A1 in HFSCs, demonstrating that stem cell homeostasis is the keystone against ultimate execution of the tissue/organ aging program.

overall_design: Hair follicle stem cells from young, aged and Col17a1cKO mice were FACS isolated and RNA was extracted before being hybridized Agillent microarray. We obtained a gene of list by comparing Young and Agedand Col17a1 cKO cells.

first: Emi

last: Nishimura


title: Skeletal muscle gene expression after high-fat diet with or without endothelial-directed deletion of FoxO

city: Stockholm

first: Eric

last: Rullman

address: C1:82 Karolinska University Hospital, Huddinge

department: Laboratory Medicine

country: Sweden

institute: Karolinska Institutet

summary: In a murine model of high-fat diet, Mx1-Cre was used to induce knockdown of forkhead box O 1,3 and 4 (FoxO 1,3 and 4) in the endothelium of adult mice. Skeletal muscle gene-expression was assessed after 8 weeks of high-fat diet in wild type versus FoxO knockdown mice.

overall_design: Total RNA isolated from gastrocnemius muscle after 8 weeks of high-fat diet in male FVB/n mice harbouring an endothelial directed deletion of FoxO1/3/4 (Mx1-Cre+);FoxO1,3,4L/L) (n=8) and corresponding MxCre-;FoxO1,3,4L/L littermates (n=8).

first: Tara

last: Haas


title: Cancerous inhibitor of Protein Phosphatase 2A promotes B-cell activation in vitro

city: Turku

first: Jukka

last: Westermarck

state: Southwest Finland

address: Tykistökatu 6 B

country: Finland

institute: University of Turku/BTK

summary: The generation of optimal immune response requires combined activation of both T- and B-cells. Here, we demonstrate that the cancerous inhibitor of protein phosphatase 2A (CIP2A) is a novel factor that governs activation of both T- and B-cells in vivo. Upon ovalbumin challenge, CIP2A-deficient (CIP2AHOZ) mice show impaired immune response. Furthermore, CIP2AHOZ mice had impaired clearance of Listeria Monocytogenesis (L.m.) infection, combined with decreased numbers of CD8+ T-cells and IFN-γ secretion. In an ovalbumin model of allergic asthma, CIP2AHOZ B-cells were impaired in IgE and IgG secretion, despite of normal Th2 differentiation and unaffected numbers of inflammatory cells or cytokines in bronchoalveolar lavage. Importantly, the cell-autonomous effect of CIP2A deficiency for both T- and B-cell activation was confirmed by in vitro assays. During the T-cell activation CIP2A, was shown to promote expression of ETS-1, whereas in B-cells CIP2A loss resulted in inhibition of MYC-mediated gene expression. Together these results identify CIP2A as a novel cell-autonomous regulator governing both T- and B-cell activation in vivo. They also identify CIP2AHOZ as a novel murine model for investigation of impaired immune response and allergic asthma.

overall_design: This dataset consists of samples used in two separate studies.  Samples were normalized together, but only total RNA obtained from 2 mutant mice was compared to 2 wild type controls (CIP2A-LacZ; TK13) was used for determination of CIP2A role in B- & T- cell immunity.    Whilst, only total RNA obtained from 2 mutant lymphoma bearing mice was compared to 2 wild type lymphom bearing controls (CIP2A-LacZ*Emu-myc; TKEM) for determination of CIP2A role in B-cell lymphoma .

first: Christophe

last: Côme

first: Anna

middle: N

last: Cvrljevic

first: Juan

last: Aguilar-Pimentel

first: Sebastian

last: Oeder

first: Teemu

last: Laajala


title: Hepatic stem cells with self-renewal and liver repopulation potential are harbored in CDCP1-positive subpopulations of human fetal liver cells

city: Yokohama City

first: Yasuharu

last: Ueno

state: Kanagawa

address: 3-9  Fuku-ura, Kanazawa-ku

department: Graduate School of Medicine

institute: Yokohama City University

summary: Comparison of hepatocyte and stem cell-related gene expressions of human hepatic stem cells (HpSCs),  and BMI1 introduced HpSCs.

overall_design: 3 Samples were analyzed

first: Yun-Wen

last: Zheng


title: Effect of PARP inhibition on Progesterone Gene Expression Profiling

city: Barcelona

first: Roni

last: Wright

address: C/ Doctor Aiguader, 88

country: Spain

institute: CRG-Centre de Regulació Genòmica

summary: T47D cells were starved 0% FCS for 24 hours. Following starvation PARP1 was inhibited via the use of 3AB and the gene expression in response to progesterone studied. Cells were stimiulated with R5020 for 1 or 6 hours.

overall_design: T47D cells T0 (Time 0), T1 (1 hours R5020), T6 (6 hours R5020)

first: Miguel

last: Beato


title: Tailoring heated intra-peritoneal Mitomycin C for peritoneal metastases originating from colorectal carcinoma –  A translational approach to improve survival

city: Amsterdam

first: Daoud

last: Sie

address: De Boelelaan 1117

department: Pathology

country: Netherlands

institute: Vrije Universiteit Medical Center

summary: Patients with peritoneal metastases (PM) originating from colorectal carcinoma (CRC) are curatively treated by cytoreductive surgery (CRS) and hyperthermic intra-peritoneal chemotherapy (HIPEC) with Mitomycin C (MMC). We aim to improve patient selection and personalize treatment for patients treated with HIPEC by predicting MMC sensitivity. MMC sensitivity was determined for 12 CRC cell lines using two separate assays. Thirty-seven genes related to the FA-BRCA pathway, ATM-ATR pathway and enzymatic activation of MMC were correlated on expression array platform to MMC sensitivity. Low sensitivity correlated with a decrease in BLM (p=0.01) and BRCA2 (p=0.02) on mRNA expression level. Both genes are part of the Fanconi Anaemia-BRCA (FA-BRCA) pathway and therefore, functionality of the FA-BRCA pathway in cell lines was determined using chromosomal breakage assay and Western Blot for key protein FANCD2. However, FA-BRCA pathway functionality showed no correlation to MMC sensitivity. BLM was further analysed by staining for the corresponding protein with immunohistochemistry (IHC) on both CRC cell lines and patient material. In cell lines, weak intensity staining by IHC correlated to high sensitivity (p=0.04) to MMC. High BLM protein expression was significantly correlated to a decreased survival in patients after CRS and HIPEC (p=0.04). We are the first to have found a possible predictive biomarker for PM with CRC.

first: R

last: Kwakman

first: E

last: de Cuba

first: J

middle: P

last: de Winter

first: I

middle: H

last: de Hingh

first: P

last: Delis-van Diemen

first: M

last: Tijssen

last: Rooimans

first: O

last: Krijgsman

first: B

last: Carvalho

first: G

last: Peters

first: H

last: Bonjer

last: Meijer

last: te Velde


title: Expression data transgenic mouse mammary tumors

status: Public on Nov 25 2015

city: Montreal

first: William

middle: Joseph

last: Muller

state: Quebec

address: 1160 Pine ave Ouest

department: Biochemistry

institute: McGill University

summary:
Immunosurveillance constitutes the first step of cancer immunoediting in which developing malignant lesions are eliminated by anti-tumorigenic immune cells. However, the mechanisms by which neoplastic cells induce an immunosuppressive state to evade the immune response are still unclear. The transcription factor Stat3 has been implicated in breast carcinogenesis and tumor immunosuppression in advanced disease, but its involvement in early disease development has not been established. Here, we genetically ablated Stat3 in the tumor epithelia of the inducible PyVmT mammary tumor model and found that Stat3-deficient mice recapitulated the three phases of immunoediting: elimination, equilibrium, and escape. Pathological analyses revealed that Stat3-deficient mice initially formed hyperplastic and early adenoma-like lesions that later completely regressed, thereby preventing the emergence of mammary tumors in the majority of animals. Furthermore, tumor regression was correlated with massive immune infiltration into the Stat3-deficient lesions, leading to their elimination. In a minority of animals, focal, non-metastatic Stat3-deficient mammary tumors escaped immunosurveillance after a long latency or equilibrium period. Taken together, our findings suggest that tumor epithelial expression of Stat3 plays a critical role in promoting an immunosuppressive tumor microenvironment during breast tumor initiation and progression, and prompt further investigation of Stat3 inhibitory strategies that may reactivate the immunosurveillance program.
We used microarrays to detail determine the transcriptional difference between PyVmT-driven mouse mammary tumors that progressed in the presence or absense of epithelial Stat3.

overall_design: Mammary tumors from transgenic mice were excise and flash frozen. Tumors were analyzed from 8 Stat3-proficient tumors and 6 Stat3-deficient tumors. RNA was extracted and hybridization on Affymetrix microarrays.

first: Laura

last: Jones

first: John

last: Ozcelik

first: Michael

last: Hallett


title: In vivo pulmonary genotoxicity of multiwalled-carbon nanotubes

status: Public on Nov 27 2015

city: Ottawa

first: Sabina

last: Halappanavar

state: Ontario

address: 251 Sir Frederick Banting Driveway, Building 22

institute: Health Canada

summary: Carbon nanotubes (CNTs) are newly developed nanomaterials with unique chemical and physical properties. Exposure to airborne CNTs in occupational settings or via consumer products is expected to increase significantly within the next decade due to the vigorous synthesis and applications of these materials in numerous consumer and industrial activities. Previous studies have shown that multiwalled CNT (MWCNT) induce pulmonary inflammation and pulmonary fibrosis. In the present study, we investigated genotoxic potential of MWCNTs.  Female MutaMouse were exposed to 42.7 ug/mouse or 128 ug/mouse doses of MWCNTs Mitsui XNRi-7 or NM 401 once a week for four consecutive weeks. Doses were administered via intratracheal instillation. Lung tissues were collected 56 days post-exposure. Bronchoalveolar lavage(BAL) fluid cellularity, BAL and lung tissue DNA damage (COMET assay), lacz mutation frequency and global gene expression  changes in lung tissue were determined.

overall_design: This experiment examined the pulmonary response of male mice exposed to Mitsui XNRi-7 and NM 401  once a week for 4 consecutive weeks via intratracheal instillation at two doses, including 42.7µg/mouse and 128µg/mouse and vehicle control.  Each dose group was examined 56 days following the final exposure.  Each dose group had 4-5 biological replicates. There were a total 26 samples (arrays) from the lung included in the final analysis using a two-colour reference design.

first: Luna

last: Rahman

first: Jake

last: Nikota

first: Dongmei

last: Wu

first: Charles

last: Guo

first: Andrew

last: Williams


title: Osteoclasts Control Re-activation of Dormant Myeloma Cells by Remodeling the Endosteal Niche

status: Public on Nov 30 2015

city: Darlinghurst

first: Peter

last: Croucher

state: New South Wales

address: 384 Victoria St

department: Bone

country: Australia

institute: Garvan Insititute of Medical Research

summary: Multiple myeloma is largely incurable, despite development of therapies that target myeloma cell-intrinsic pathways. Disease relapse is thought to originate from dormant myeloma cells, localized in specialized niches, which resist therapy and re-populate the tumor. However, little is known about the niche, and how it exerts cell-extrinsic control over myeloma cell dormancy and re-activation. In this study we track individual myeloma cells by intravital imaging as they colonize the endosteal niche, enter a dormant state and subsequently become activated to form colonies. We demonstrate that dormancy is a reversible state which is switched ‘on’ by engagement with bone lining cells or osteoblasts, and switched ‘off’ by osteoclasts remodeling the endosteal niche. Dormant myeloma cells are resistant to chemotherapy targeting dividing cells. The demonstration that the endosteal niche is pivotal in controlling myeloma cell dormancy highlights the potential for targeting cell-extrinsic mechanisms to overcome cell-intrinsic drug resistance and prevent disease relapse.

overall_design: Affymetrix microarray was performed on dormant, proliferating and transitioning multiple myeloma cells extracted ex vivo. GFP expressing 5TGM1 multiple myeloma cells were labelled with a DiD membrane label and its retention of DiD (DiDHigh) discriminates dormant from proliferating cells (DiDNeg). At 28 days post intravenous injection, cells were extracted from the bone marrow of C57BLkALwRij mice using FACS and RNA was extracted.

first: Michelle

middle: A

last: Lawson

last: McDonald

first: Natasa

last: Kovacic

first: Weng-Hua

last: Khoo

first: Rachael

last: Terry

first: Jenny

last: Down

first: Warren

last: Kaplan

first: Julia

last: Paton-Hough

first: Clair

last: Fellows

first: Jessica

last: Pettitt

first: Terence

last: Dear

first: Els

last: Van Valckenborgh

first: Paul

last: Baldock

last: Rogers

first: Colby

last: Eaton

first: Karin

last: Vanderkerken

first: Allison

last: Pettit

first: Julian

last: Quinn

last: Zannettino

first: Tri

last: Phan

middle: I


title: Deletion of hyaluronan synthase 3 inhibits neointimal hyperplasia

status: Public on Nov 24 2015

city: Duesseldorf

first: Karl

last: Koehrer

address: Universitaetsstr. 1

department: BMFZ

institute: University of Duesseldorf

summary: Affymetrix Mouse Gene 2.0 ST Gene Expression Microarrays were used to analyze differentially expressed genes after carotid artery ligation. The aim of this experiment was to detect genes regulated in Has3 deficient as compared to wildtype controls that might be involved in neointimal hyperplasia.

overall_design: Neointimal hyperplasia was induced in female Has3 deficient mice and wildtype controls by ligation of the left common carotid artery. Carotid transcriptome was analyzed 5 days after surgery in ligated and non-ligated carotid arteries.

first: Lena

middle: S

last: Kiene

first: Maria

last: Grandoch

first: Berit

last: Rabausch

first: Susanne

last: Homann

last: Müller

first: Tatsiana

last: Suvorava

first: Georg

last: Kojda

first: Inga

last: Kretschmer

first: Sören

last: Twarock

first: Guang

last: Dai

first: René

last: Deenen

last: Köhrer

first: Rashmin

last: Savani

first: Jens

middle: W

last: Fischer


title: Enhanced Phospholipase A2 group 3 expression by oxidative stress decreases the insulin-degrading enzyme

status: Public on Nov 20 2015

city: Bunkyo-ku

first: Kaoru

last: Mogushi

state: Tokyo

address: 2-1-1 Hongo

department: Intractable Disease Research Center

institute: Juntendo University

summary: Oxidative stress has a ubiquitous role in neurodegenerative diseases and oxidative damage in  specific regions of the brain is associated with selective neurodegeneration. We previously reported that Alzheimer disease (AD) model mice showed decreased insulin-degrading enzyme (IDE) levels in the cerebrum and accelerated phenotypic features of AD when crossbred with alpha-tocopherol transfer protein knockout (Ttpa-/-) mice. To further investigate the role of chronic oxidative stress in AD pathophysiology, we performed DNA microarray analysis using young and aged wild-type mice and aged Ttpa-/- mice. Among the genes whose expression changed dramatically was Phospholipase A2 group 3 (Pla2g3); Pla2g3 was identified because of its expression profile of cerebral specific up-regulation by chronic oxidative stress in silico and in aged Ttpa-/- mice. Immunohistochemical studies also demonstrated that human astrocytic Pla2g3 expression was significantly increased in human AD brains compared with control brains. Moreover, transfection of HEK293 cells with human Pla2g3 decreased endogenous IDE expression in a dose-dependent manner. Our findings show a key role of Pla2g3 on the reduction of IDE, and suggest that cerebrum specific increase of Pla2g3 is involved in the initiation and/or progression of AD.

overall_design: Gene expression in cerebral cortex and cerebellum of mice were determined using Agilent chips. To ensure higher quality results in gene expression data, we conducted microarrays on 4 mice per group. Young mice were 2 months old and the other aged mice were 29 months old at the time of use. Data were standardized using global normalization and pro-cessed by R-program. An absolute fold change threshold of greater than 1.5 was required to be considered for further analyses. Expression values were in log2 scale.

first: Daishi

last: Yui

first: Yoichiro

last: Nishida

first: Tomoko

last: Nishina

first: Mio

last: Tajiri

first: Satoru

last: Ishibashi

first: Itsuki

last: Ajioka

first: Kinya

last: Ishikawa

first: Hidehiro

last: Mizusawa

first: Shigeo

last: Murayama

first: Takanori

last: Yokota


title: Screening of genes activated by phsiological E2F induced by gorwth stimulation

city: Sanda

first: Kiyoshi

last: Ohtani

state: Hyogo

address: 2-1 Gakuen

department: Department of Bioscience

institute: Kwansei Gakuin University

summary: To identify genes activated by physiological E2F, we examined gene expression profiles using human normal fibroblasts (HFFs), which were starved of serum and re-stimulated with serum.

overall_design: To identify genes activated by growth stimulation, human normal fibroblasts (HFFs) were starved of serum for 48 hr, re-stimulated with serum or left serum-starved for 18 hr, and harvested. Gene expression profiles of each sample were examined by DNA microarray.

first: Hodaka

last: Kitamura

first: Eiko

last: Ozono

first: Ritsuko

last: Iwanaga

first: Andrew

last: Bradford

first: Junko

last: Okuno

first: Emi

last: Shimizu

first: Kenta

last: Kurayoshi

first: Kazuyuki

last: Kugawa

first: Hiroyuki

last: Toh


title: Screening of new target genes specifically activated by deregulated E2F

summary: To identify genes specifically activated by deregulated E2F, we examined gene expression profiles using human normal fibroblasts (HFFs), which were starved of serum and re-stimulated with serum, over-expressed with E2F1 or expressed with adenovirus E1a to forcedly inactivate RB.

overall_design: To identify genes activated by growth stimulation, human normal fibroblasts (HFFs) were starved of serum for 48 hr, infected with control virus, restimulated with serum or left serum-starved for 18 hr and harvested. To identify genes actived by deregulated E2F, HFFs were  starved of serum for 48 hr, infected with control virus, adenovirus expressing E2F1 or adenovirus E1a, further cultured in the absence of serum for 18 hr and harvested. Gene expression profiles of ecach sample were examined by DNA microarray.


title: Murine bone marrow c-kit+, Sca-1+ lineage neative cells (KSL) from p21CDKN1a-/- vs  p21+/+ mice,  Flt3/ITD transfected KSL cells and nontransfected KSL cells

city: Izumo

first: Seiji

last: Fukuda

state: Shimane

address: 89-1 Enya

department: Pediatrics

institute: Shimane University

summary:
Transcriptional profiling of murine bone marrow c-kit+, Sca-1+ lineage neative (KSL) cells from p21CDKN1a-/- and  p21+/+ overexpressing Flt3/ITD. The goal was to determine the effect on global gene expression by loss of p21 in Flt3/ITD transformed KSL cells
Internal tandem duplication (ITD) mutations in the Flt3 gene (Flt3-ITD) are associated with poor prognosis in patients with acute myeloid leukemia (AML). Few inhibitors of Flt3-ITD are effective against Flt3-ITD+ AML due to the development of drug-resistance. In this study, we demonstrate that Flt3-ITD activates a novel pathway involving p21Cdkn1a (p21) and pre-B cell leukemia transcription factor 1 (Pbx1) that attenuates Flt3-ITD cell proliferation and is involved in the development drug resistance. Flt3-ITD up-regulated p21 expression in mouse bone marrow c-kit+-Sca-1+-Lin- (KSL) cells and in Ba/F3 cells. Loss of p21 expression enhanced growth factor-independent proliferation and sensitivity to cytarabine as a consequence of enriching the S+G2/M phase population concomitant with a significant increase in the expression of Pbx1, but not Evi-1, in Flt3-ITD+ cells. This enhancement of cell proliferation by loss of p21 was partially abrogated when Pbx1 expression was silenced in Flt3-ITD+ primary bone marrow colony-forming cells (CFCs) and Ba/F3 cells. Antagonizing Flt3-ITD using AC220, a selective inhibitor of Flt3-ITD, decreased the expression of p21, coincident with the up-regulation of Pbx1 mRNA and a rapid decline in the number of viable Flt3-ITD+ Ba/F3 cells, however the cells eventually became refractory to AC220. Overexpressing p21 in Flt3-ITD+ Ba/F3 cells delayed the emergence of cells refractory to AC220, whereas silencing p21 accelerated their development. These data demonstrate that Flt3-ITD is capable of inhibiting the proliferation of Flt3-ITD+ cells through the p21/Pbx1 axis and that antagonizing Flt3-ITD contributes to the subsequent development of cells refractory to Flt3-ITD inhibitor by disrupting p21 expression.

overall_design: biological replicates: 3 KSL cell replicates overexpressing ITD-Flt3 from p21+/+ and p21-/- cells, 1 KSL cell replicate from  p21+/+ and p21-/- cells

first: Mariko

last: Abe


title: Transcriptional profiles of intestinal CD4 T-cells from control, HFD-induced prediabetic and diabetic mice

status: Public on Nov 18 2015

city: Toulouse

first: Lucile

last: Garidou

address: 1 Avenue J. Poulhes

country: France

institute: INSERM

summary: To determine whether diet-induced changes in gut microbiota modified intestinal immune cell gene expression, we analyzed the transcriptome of CD4 T lymphocytes isolated from the lamina propria of the small intestine from mice fed with different diets.

overall_design: Mice were fed a high fat diet to change microbiota. 10 and 30 days after the diet started, microarray were performed on lamina propria CD4 T lymphocytes.

first: Céline

last: Pomié

first: Rémy

last: Burcelin


title: IRAK1 drives intestinal inflammation by promoting the generation of effector Th cells with optimal gut homing capacity

status: Public on Nov 13 2015

city: Martinsried

first: Tobias

last: Straub

address: Großhadener Str. 9

department: Biomedical Center, Bioinformatics

institute: LMU Munich

summary: Interleukin-1 receptor associated kinase 1 (IRAK1) is an important component of the IL-1R and TLR signaling pathways, which influence Th cell differentiation. Here, we show that IRAK1 promotes Th17 development by mediating IL-1β induced upregulation of IL-23R and subsequent STAT3 phosphorylation, thus enabling sustained IL-17 production. Moreover, we show that IRAK1 signaling fosters Th1 differentiation by mediating T-bet induction and counteracts Treg generation. Cotransfer experiments revealed that Irak1-deficient CD4+ T cells have a cell-intrinsic defect in generating Th1 and Th17 cells under inflammatory conditions in spleen, mesenteric lymph nodes and colon tissue. Furthermore, IRAK1 expression in T cells was shown to be essential for T cell accumulation in the inflamed intestine and mLNs. Transcriptome analysis ex vivo revealed that IRAK1 promotes T cell activation and induction of gut-homing molecules in a cell-intrinsic manner. Accordingly, Irak1-deficient T cells failed to upregulate surface expression of α4β7 integrin after transfer into Rag1-/- mice and their ability to induce colitis was greatly impaired. Lack of IRAK1 in recipient mice provided additional protection from colitis. Therefore, IRAK1 plays an important role in intestinal inflammation by mediating T cell activation, differentiation and their accumulation in the gut. Thus, IRAK1 is a promising novel target for therapy of inflammatory bowel diseases.

overall_design: RNA isolated from CD45.1+ CD45.2- and CD45.1- CD45.2+ CD3+ CD4+ T cells 14 days after cotransfer into Rag1-/- mice. 4 replicate experiments with cells from 2 mice pooled.

first: Alexander

middle: F

last: Heiseke

first: Benjamin

last: Jeuk

first: Anamarija

last: Markota

first: Hans-Anton

last: Lehr

first: Wolfgang

last: Reindl

first: Anne

middle: B

last: Krug


title: Transcriptional profiles of intestinal APS & CD4-T cells from control, HFD-induced prediabetic and diabetic mice

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

overall_design: Refer to individual Series


title: Transcriptional profiles of intestinal antigen presenting cells from control, HFD-induced prediabetic and diabetic mice

summary: To determine whether diet-induced changes in gut microbiota modified intestinal immune cell gene expression, we analyzed the transcriptome of antigen presenting cells isolated from the lamina propria of the small intestine of mice fed with different diet.

overall_design: Mice were fed a high-fat diet to change microbiota. At 10 and 30 days after the diet start, microarrays were performed on lamina propria antigen presenting cells.


title: Characterization of molecular signature in mice that experienced an hostile social environment during cocaine abstinence

status: Public on Nov 15 2015

city: Rome

first: Luciano

last: Castiello

address: Viale Regina Elena 291

institute: Istituto Pasteur Italia - Fondazione Cenci Bolognetti

summary:
Childhood maltreatment is associated with increased severity of substance use disorder and frequency of relapse to drug use following abstinence. However, the molecular and neurobiological substrates engaged during early traumatic events and mediating the relapse risk are poorly understood. Here, we show that the exposure to an adverse/hostile social experience in juvenile mice (social stressed mice, SS) influences the propensity to reinstate cocaine seeking after withdrawal periods. This effect is associated with an increased blood coagulation  and a pauperization of brain vasculature. Moreover, a treatment with an anticoagulant agent during withdrawal abolishes the susceptibility to reinstate cocaine seeking in SS mice. These findings for the first time propose a molecular mechanism contributing to the increased susceptibility to relapse into cocaine abuse observed in individuals who had experienced childhood maltreatment.
To analyze global gene expression differences between mice experiencing an hostile/adverse social environment during the third postnatal week and juvenile social isolated (SI) mice during cocaine abstinence. Peripheral Blood Mononuclear Cells were measured with Agilent mouse gene expression microarray during cocaine abstince after undergoing cocaine-seeking behavior studies by conditioned place preference test, extinction and withdrawal.
Blood was collected 24 hours after the extinction test and genome-wide

overall_design: PBMC of mice that experienced hostile/adverse social environment during the third postnatal week (SS) (n = 8) and mice that were juvenile social isolated (SI)  (n = 6) were compared during cocaine abstinence. In particular mice were first  conditioned with under-threshold cocaine dosage (5 mg/kg), then underwent extinction and withdrawal. 24 hours after withdrawal blood samples were taken and RNA from PBMC was analyzed on Agilent One-color experiments

first: Eleonora

last: Aricò

first: Valeria

last: Carola

first: Luisa

last: Lo Iacono

first: Alessandro

last: Valzania

first: Federica

middle: V

last: Comandini

first: Maria

middle: T

last: Viscomi

first: Diego

last: Oddi

first: Francesca

last: D'Amato

first: Olga

last: Ermakova

first: Stefano

last: Puglisi-Allegra


title: Microarray analysis of gene expression profile of the spinal cord in the mice L5 spinal nerve ligation model of neuropathic pain

status: Public on Nov 17 2015

city: nantong city

first: Bao-chun

last: Jiang

address: seyuan road

country: China

institute: nantong university

summary: To search for novel chemokines that are involved in the maintenance of neuropathic pain, we harvested the ipsilateral spinal cords at 10 days after SNL and performed gene expression profiling using mouse gene expression microarrays.

overall_design: The gene expression profiles in L5 spinal cords from the lumbar 5 spinal nerve ligation group mice and sham group mice were measured at 10 days after operation, each group have two replicates.

first: Yong-jing

last: Gao


title: Dexamethasone treatment alters levels of insulin, leptin, and adiponectin but does not have metabolic effects across generations

city: Neuherberg

first: Johannes

last: Beckers

address: Ingolstaedter Landstr. 1

department: Institute of Experimental Genetics

institute: Helmholtz Zentrum Muenchen

summary: Genome-wide expression analysis of sperms did not identify significant transcriptome changes upon dexamethasone treatment in mice. These results are consistent with the observation that dexamethasone treatment of parental male mice did not induce metabolic changes in the F1 generation.

overall_design: We performed gene expression microarray analysis of sperms derived from dexamethasone-treated (n=8) or control mice (n=7).

first: Clemens

last: Bönisch

first: Peter

last: Huypens

first: Martin

last: Irmler

first: Laura

last: Brachthäuser

first: Frauke

last: Neff

first: Susan

last: Marschall

last: HrabédeAngelis


title: Bortezomib resistance in CCRF-CEM cell line [GEP]

status: Public on Nov 04 2015

first: Daoud

last: Sie

summary: Bortezomib is a proteasome inhibitor used in severel different hematological malignancies. Resistance to this drug is still poorly understood. In order get more insight in the resistance mechanism, we developed several bortezomib resistant subclones of the CCRF-CEM T-ALL cell line. On these subclones comparative Genome hybridization (arrayCGH) for DNA copy number analysis gene expression and micro-RNA expression arrays were performed.

overall_design: We performed gene expression microarray analysis on four different bortezomib resistant subclones of the CCRF-CEM cell line. The resistant subclones were compaired to treated and untreated the parental CCRF-CEM wildtype cell line.

first: Niels

middle: E

last: Franke

first: Gertjan

middle: L

last: Kaspers

first: Yehuda

middle: G

last: Assaraf

first: Johan

last: van Meerloo

first: Denise

last: Niewerth

first: Floortje

last: Kessler

first: Pino

middle: J

last: Poddighe

first: Serge

last: Smeets

first: Bauke

last: Ylstra

first: Chonglei

last: Bi

first: Wee

last: Chng

first: Terzah

last: Horton

first: Rene

middle: X

last: Menezes

first: Renée

last: Musters

first: Sonja

last: Zweegman

first: Gerrit

last: Jansen

first: Jacqueline

last: Cloos


title: The Immunobiology of Aging [II]

status: Public on Nov 07 2015

city: palo alto

first: weiqi

last: wang

state: ca

address: 1291 welch road

institute: stanford

summary: The overriding objective of this application is to seek funding for the development of a crossectional profile of immune phenotype of over 600 normal subjects between the ages of 50 and 90. As a consequence, we will infer changes in immune phenotype of normal subjects as they age. These immune phenotypic data, as well as standard laboratory tests and evaluations of questionnaires, will be used to generate a large and comprehensive database of demographic and biological information. The proposal utilizes the strengths of the Stanford Human Immune Monitoring Core (HIMC) and the unique expertise in basic immunology, immune monitoring, the development of patient registries, biostatistics and bioinformatics at Stanford.

overall_design: The dataset will comprise a crossectional analysis of the local San Francisco Peninsula general population between the ages of 50 and 90 (representing equal gender and representative ethnic population, and equal distribution by decade of life). The registry will contain demographic data, race/ethnicity, prescribed medications, over the counter medications, vitamins, alternative therapies, physical function questionnaire, alternative contact person, and HIPPA release. Fasting blood will be obtained for immune phenotyping. The immune profile will contain the results of both conventional and novel immune profiling assays to develop the normative immune profile of aging (using PBMC subset analysis, cytokines, and activation induced signaling of PBMCs for phosphoepitope and gene expression analyses). Data from these analyses will be useful in identifying biomarkers of the normal immune profile associated with aging as well as correlation with phenotypic aspects of aging such as sarcopenia and disability The immune profile (as well as normal blood chemistries and demographic data) of these subjects will be made available to serve as the basis for future longitudinal study of change in the immune profile over time in association with the development of co-morbidities associated with aging. in the PBMC gene expression, 120 samples were analyzed (no replicates), containing patients and controls.

first: Garry

last: Fathman


title: Transcriptional Response of Male MutaTMMouse Spleen to Dibenzo[def,p]chrysene Exposure

first: Nikolai

last: Chepelev

address: 50 Colombine Driveway

department: Environmental Health Science and Research Bureau

summary:
Dibenzo[def,p]chrysene (DBC) is the most carcinogenic polycyclic aromatic hydrocarbon (PAH) examined to date. We investigated the immunotoxicity of DBC, manifested as spleen atrophy following acute exposure of adult Muta™Mouse males by oral gavage. Mice were exposed to 0, 2.0, 6.2, or 20.0 mg DBC /kg-bw per day, for three days.
Genotoxic endpoints (DBC-DNA adducts and lacZ mutant frequency in spleen and bone marrow, and red blood cell micronucleus frequency) and global gene expression changes were measured. All of the genotoxicity measures increased in a dose-dependent manner in both tissues.
Gene expression analysis showed that DBC activates p53 signalling pathways related to cellular growth and proliferation, which was evident even at the low dose. Strikingly, the expression profiles of DBC exposed mouse spleens were highly inversely correlated with the expression profiles of the only published toxicogenomics dataset of enlarged mouse spleen.
This analysis suggested a central role for Bnip3l, a pro-apoptotic protein involved in negative regulation of erythroid maturation. RT-PCR confirmed expression changes in several genes related to apoptosis, iron metabolism, and aryl hydrocarbon receptor signalling that are regulated in the opposite direction during spleen atrophy versus benzo[a]pyrene-mediated splenomegaly.
In addition, benchmark dose modeling of toxicogenomics data yielded toxicity estimates that are very close to traditional toxicity endpoints. This work illustrates the power of toxicogenomics to reveal rich mechanistic information of immunotoxic compounds and its ability to provide information that is quantitatively similar to that derived from standard toxicity methods in health risk assessment.

overall_design: Four to five (N=4-5) biological replicates were analyzed per sample for each of the three doses, plus a control, four or 24 h after the last treatment.

first: Alexandra

last: Long

first: Andrew

last: Williams

first: Byron

last: Kuo

first: Rémi

last: Gagné

first: Dean

last: Kennedy

first: David

last: Phillips

first: Volker

middle: M

last: Arlt

first: Paul

last: White

first: Carole

last: Yauk


title: Bortezomib resistance in CCRF-CEM cell line

first: Daoud

last: Sie

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


title: Kinetic analysis of T cell anergy induction

status: Public on Nov 01 2015

city: Seoul

first: Kyungho

last: Choi

address: 103 Daehak-ro, Jongno-gu

department: Department of Biochemistry and Molecular Biology

institute: Seoul National University College of Medicine

summary:
T cell receptor(TCR) engagement in the absence of costimulation leads to a state of T cell tolerance known as anergy. Anergy induction requires new protein synthesis since it is inhibited by cycloheximide.
In this experiment, we tried to figure out kinetic properties of the gene expression in anergy induction phase and the subsequent anergy maintenance phase.

overall_design: A.E7 cell, a murine CD4(+) T cell clone, was stimulated with anti-TCR antibody for 0, 2, 4, and 6hrs followed by RNA extraction. For the maintenance phase, A.E7 was stimulated for 16hrs and rested for 5days before RNA extraction.

first: Jun

last: Yang

first: Ronald

last: Schwartz


title: Histone chaperone CAF-1 is essential for retrotransposon silencing by mediating histone H4K20me3 deposition in mouse preimplantation embryos

city: Tsukuba

first: Kimiko

last: Inoue

state: Ibaraki

address: 3-1-1 Koyadai

department: Bioresource Engineering Division

institute: BRC, RIKEN

summary: Retrotransposons are widely spread in the mammalian genome and are usually silenced during development to avoid transposition-inducing mutations. But how they are repressed in embryos shortly before implantation remain to be identified, since the genome at this stage is globally hypomethylated. Here we show a histone chaperon, CAF-1, is responsible for retrotransposon silencing at the morula-blastocyst stages by depositing histone H4 lysine 20 trimethylation (H4K20me3). Knockdown of CAF-1 with a specific siRNA resulted in derepression of LINE-1, SINE-B2 and IAP associated with the decreased H4K20me3 level, and arrested embryonic development at the morula stage. The identical results were obtained with siRNAs against Suv420h1/2, H4K20 methyltransferases. Treatment with reverse transcriptase inhibitors rescued at least a part of these embryos. Thus, CAF-1 ensures the genomic integrity of preimplantation embryos by establishing repressive histone marks in the multiple retrotransposon classes.

overall_design: Comparative gene expression analyses using P150 knockdown (P150KD) embryos at morula stage were performed by microarray. P150KD embryos were produced with the injection of P150 siRNA into 1-cell embryos. As controls, siControl embryos were produced by the injection of control siRNA. These embryos were subjected to gene expression microarray.

first: Yuki

last: Hatanaka

first: Atsuo

last: Ogura


title: Origin-Dependent Inverted-Repeat Amplification: Tests of a Model for Inverted DNA Amplification

status: Public on Oct 30 2015

city: Seattle

first: Maitreya

middle: J.

last: Dunham

address: Foege Building, S403B, Box 355065

department: Genome Sciences

institute: University of Washington

summary: DNA replication errors are a major driver of evolution—from single nucleotide polymorphisms to large-scale copy number variations (CNVs). Here we test a specific replication-based model to explain the generation of interstitial, inverted triplications. While no genetic information is lost, the novel inversion junctions and increased copy number of the included sequences create the potential for adaptive phenotypes. The model—Origin-Dependent Inverted-Repeat Amplification (ODIRA)—proposes that a replication error at pre-existing short, interrupted, inverted repeats in genomic sequences generates an extrachromosomal, inverted dimeric, autonomously replicating intermediate; subsequent genomic integration of the dimer yields this class of CNV without loss of distal chromosomal sequences. We used a combination of in vitro and in vivo approaches to test the feasibility of the proposed replication error and its downstream consequences on chromosome structure in the yeast Saccharomyces cerevisiae. We show that the proposed replication error—the ligation of leading and lagging nascent strands to create “closed” forks—can occur in vitro at short, interrupted inverted repeats. The removal of molecules with two closed forks results in a hairpin-capped linear duplex that we show replicates in vivo to create an inverted, dimeric plasmid that subsequently integrates into the genome by homologous recombination, creating an inverted triplication. While other models have been proposed to explain inverted triplications and their derivatives, our model can also explain the generation of human, de novo, inverted amplicons that have a 2:1 mixture of sequences from both homologues of a single parent—a feature readily explained by a plasmid intermediate that arises from one homologue and integrates into the other homologue prior to meiosis. Our tests of key features of ODIRA lend support to this mechanism and suggest further avenues of enquiry to unravel the origins of interstitial, inverted CNVs pivotal in human health and evolution.

overall_design: These are all CGH arrays comparing DNA copy number between evolved yeast strains and a euploid wt strain.

first: Celia

last: Payen

first: Bonita

last: Brewer

first: Megan

last: Higgins

first: Giang

last: Ong

first: Sara

last: Di Rienzi

last: Raghuraman


title: Highly Potent and Selective Interleukin-1 Receptor-Associated Kinase 4 Inhibitors for the Treatment of Lymphoid Malignancies

city: Bethesda

first: Louis

middle: M.

last: Staudt

address: 9000 Rockville Pike, Bldg 10, Rm 4N114

department: Lymphoid Malignancies Branch

institute: National Cancer Institute

summary: Pathologic activation of the Toll-like receptor (TLR) pathway underlies various human disorders such as autoimmune diseases, chronic inflammatory diseases and lymphoid malignancies. Current therapy of these diseases relies on immunosuppressive or chemotherapeutic agents, but more effective therapeutics tailored to disease-causing mechanisms are needed. Pivotal to TLR signaling is the IL-1 receptor-associated kinase 4 (IRAK4), which is recruited to TLRs by the adaptor protein MyD88. Recruitment of IRAK kinases to MyD88, triggers the formation of a signaling competent myddosome complex, which underlies the pathogenesis of many immuno-inflammatory disorders, suggesting that IRAK4 inhibitors might be useful in the treatment of these diseases. Gain-of-function MYD88 mutations activate IRAK4 in several mature B cell malignancies, including activated B-cell-like diffuse large B cell lymphoma (ABC DLBCL). Development of selective IRAK4 inhibitors has been confounded by the challenging structure of the IRAK4 catalytic domain. Using structure-based drug design methodologies, we identified potent and selective IRAK4 inhibitors. These small molecules suppress LPS-induced TNFalpha production in vitro and in vivo, and are efficacious in mouse models of collagen-induced arthritis and MyD88-dependent inflammatory gout. Human ABC DLBCL cell lines that harbor the activating, oncogenic MyD88 L265P mutation are killed by IRAK4 inhibitors, both in vitro and in mouse xenograft models. IRAK4 inhibitors synergize with the BTK inhibitor ibrutinib, with the Syk inhibitor PRT062607, and with the Bcl-2 inhibitor ABT-199 in killing ABC DLBCL cells, suggesting new therapeutic strategies for this refractory cancer.

overall_design: Four ABC DLBCL cell lines (OCI-Ly10, TMD8, HBL1 and OCI-Ly3), were treated with either ND-2158 or the structurally related negative control compound ND-1659 for 6, 12, 24 or 36 h in culture. Gene expression profiling was performed using two-color human Agilent 4x44K gene expression arrays comparing signal from control compound-treated (ND-1659) control cells (Cy3), to cells treated with ND-2158 for the indicated times (Cy5).


title: Primary lung fibroblasts activated with constitutively active Smo

status: Public on Oct 22 2015

city: Philadelphia

first: Michael

middle: Patrick

last: Morley

state: PA

address: 3400 Civic Center Blvd, Bldg 421

department: Penn Cardiovascular Institute

institute: Perelman School of Medicine at the University of Pennsylvania

summary: Postnatal tissue quiescence is generally thought to be a default state in the absence of a proliferative stimulus such as injury. We now demonstrate that in the lung, quiescence in the adult is an actively maintained state and is regulated by paracrine hedgehog signaling. Epithelial-specific deletion of Sonic Hedgehog during normal homeostasis results in a proliferative expansion of the adjacent lung mesenchyme. Injury to the lung epithelium results in decreased hedgehog activation, accompanied by proliferative expansion of the adjacent mesenchyme. Moreover, reconstitution of Hedgehog signaling during epithelial injury attenuated the proliferative expansion of the adjacent mesenchyme. Hedgehog signaling maintains lung quiescence by attenuating PDGF induced activation. These results indicate that in postnatal tissues, epithelial cells can actively maintains mesenchymal quiescence via paracrine hedgehog activation, and that imbalances in this pathway could lead to aberrant mesenchymal expansion and postnatal disease.

overall_design: Fibroblasts were isolated from lungs of adult UBCCreERT2:R26RSmoM2 mice and incubated with or without 4-hydroxytamoxifen to activate the SmoM2 allele for 48 hours before RNA was isolated for microarray.

first: Tien

last: Peng

first: Rachel

last: Kadzik

middle: P

first: Komal

last: Rathi

first: Lan

last: Cheng

first: Edward

last: Morrisey


title: The imprinted Phlda2 gene modulates a major endocrine compartment of the placenta to regulate placental demands for maternal resources

status: Public on Oct 24 2015

city: Cardiff

first: Rosalind

last: John

address: Museum Avenue

department: Biosciences

institute: Cardiff University

summary:
Recent work suggests that imprinted genes may regulate the signalling function of the placenta by modulating the size of the endocrine compartment. Our work provides in vivo evidence that this hypothesis is well founded.
Affymetrix Mouse Microarray analysis of E16.5 placneta was used to demonstrate gene expression changes in the mutant placenta.

overall_design: E16.5 Phlda2+/+(129) (non-transgenic; 1X), Phlda2-/+(129) (maternal KO; 0X) and Phlda2+/+BACx1(129) (single copy Phlda2 transgene; 2X) placenta were used (N=3-4 of each genotype, two independent litters) were used to extract RNA and hybridize to Affymetrix microarrays.

first: S

last: Tunster

first: H

middle: D

last: Creeth

first: R


title: Gene Expression analysis of stomachs of a C/EBP beta knockout (KO) mouse model

city: Berlin

first: Susann

last: Förster

address: R. Rössle Str 10

institute: MDC

summary: In order to identify genes that are potentially regulated by the transkription factor C/EBP beta in the stomach, we have performed a microarray-based profiling of the genome-wide mRNA expression of C/EBP beta KO mouse stomach and compared it to wildtype (WT) littermates.

overall_design: newborn were killed and the stomachs were taken out. 5 KO and 4 WT stomachs were used for the profiling.

first: Goncalo

last: Regalo


title: The Immunobiology of Aging

first: weiqi

last: wang


title: Expression data from sorted monoyctes/macrophages

status: Public on Nov 06 2015

city: Kingston

first: Nader

last: Ghasemlou

address: 18 Stuart Street, room 754

institute: Queen's University

summary:
Tissue injury, such as incisional wound, results in an inflammatory response as well as acute to chronic mechanical and thermal pain. It is now understood that there is a strong contribution of these immune cells to the pain phenotype.
We used microarray analysis of sorted CD11b+Ly6G- myeloid cells extracted from the mouse hindpaw 24h after incisional wound to identify distinct classes of upregulated genes.

overall_design: CD11b+Ly6G- myeloid cells were sorted by expression of Ly6C (high, medium, and low) and used for microarray analysis. All sorted cells were collected on the same day to reduce variability.

first: Clifford

last: Woolf


title: A Comparative Analysis of Gene Expression Profiles During Skin Regeneration in Mus and Acomys

status: Public on Oct 28 2015

city: Gainesville

first: Jason

middle: Orr

last: Brant

state: FL

address: 2197 Mowry Rd

department: Biostatistics

institute: University of Florida

summary: Acomys exhibits a blunted immune response to wounding, and shares characteristics with fetal wound healing

sample_organism:
Acomys cahirinus
Mus musculus

overall_design: We used mouse microarrays to compare gene expression profiles during wound healing between the African spiny mouse (Acomys) and the house mouse (Mus)

middle: O

first: Maria-Cecilia

last: Lopez

first: Henry

last: Baker

first: W

last: Barbazuk

first: Malcolm

last: Maden


title: Global gene expression analysis of formalin-fixed paraffin-embedded (FFPE), furan-exposed mouse liver using one-colour Agilent microarrays

status: Public on Oct 14 2015

city: Ottawa

first: Anna

middle: Francina

last: Jackson

address: 50 Colombine Drive, Tunney's Pasture

department: Environmental Health Center

institute: Health Canada

summary: Furan is a mouse and rat hepatocarcinogen. We sought to determine if furan-induced gene expression changes could be detected in paired fresh-frozen and formalin-fixed paraffin embedded (FFPE) samples using one-colour microarrays.  To determine the effect of time-in-formalin on gene expression signatures we performed microarray analysis of livers that were fixed in formalin for 18 hours or 3 weeks. All samples (fresh-frozen, 18 hours in formalin, 3 weeks in formalin) were also examined using two-colour microarrays and RNA-seq (ribo-depletion and polyA-enrichment protocols) in order to determine the effect of the technology on gene expression profiles.

overall_design: In this experiment we examined the transcriptional response of liver tissue of female B6C3F1 mice exposed to furan for 3 weeks to 1, 2, 4, or 8 mg/kg bodyweight per day furan (or vehicle control) and sacrificed four hours after the final exposure.  Each dose group had 5 biological replicates. Samples were formalin-fixed (for 18 hours or 3 weeks) and paraffin embedded. We used a randomized block design and SurePrint G3 Mouse GE 8x60K microarrays (Agilent).

first: A

middle: F

last: Webster

first: Andrew

last: Williams

first: Leslie

last: Recio

first: Carole

last: Yauk


title: Expression data from the aortas of ApoE knockout and ApoE/IL-17 double knockout mice

status: Public on Oct 11 2015

first: Xiao-Feng

last: Yang

address: 3500 N. Broad St

department: Cardiovascular Research Center

institute: Temple University School of Medicine

summary: Interleukin-17 (IL-17)-secreting T helper 17 cells (Th17) are a recently identified CD4+ T helper subset that has been implicated in various inflammatory and autoimmune diseases.  The issue of whether interleukin-17A (IL-17) contributes to hyperlipidemia-induced aortic endothelial cell activation remained unknown. Here, we reported that IL-17 contributes to hyperlipidemia-induced modulation of vascular cell gene expression during early atherosclerosis in vivo. Our results has shed lights onto the role of IL-17 on EC biology and has provided important insights for future development of novel therapeutics for early intervention of cardiovascular diseases and other inflammatory diseases.

overall_design: All mice were in a C57B/L6 strain background. Male Apolipoprotein E (ApoE) gene knockout mice and ApoE/IL-17 double gene deficient mice were fed with high fat diet for 3 weeks starting from 8 weeks to induce early dyslipidemia.  At 11-week of age, aortas from these mice were used for microarray analysis. 5 biological replicates in each group.

first: Jietang

last: Mai

first: Ya-feng

last: Li

first: Xinyuan


title: Neonatal morphine exposure alters mRNA and microRNA (miR) expression in mouse hippocampus

status: Public on Oct 05 2015

first: James

middle: William

last: MacDonald

state: WA

address: 4225 Roosevelt Way NE

department: Environmental and Occupational Health Sciences

summary: Morphine is used to sedate critically ill infants to treat painful or stressful conditions associated with intensive care.  Whether neonatal morphine exposure affects microRNA (miR) expression and thereby alters mRNA regulation is unknown.  We tested the hypothesis that repeated morphine treatment in stress-exposed neonatal mice alters hippocampal mRNA and miR gene expression.  C57BL/6 male mice were treated from postnatal day (P) 5 to P9 with morphine at 2 or 5 mg/kg ip bid  (MS5) and then exposed to stress consisting of hypoxia (100% N2 1 min and 100% O2 5 min) followed by 2h maternal separation. Control mice were untreated and dam-reared. mRNA and microRNA expression profiling was performed on hippocampal tissues at P9.   Overall, MS2 and MS5 morphine treatment altered expression of a total of 150 mRNAs  (>1.5 fold change, P<0.05; 36 up, 114 down), and MS5 affected 63 mRNAs.  The most upregulated mRNAs were fidgetin, arginine vasopressin, and resistin-like alpha, and the most down-regulated were defensin beta 11, aquaporin 1, calmodulin-like 4, chloride intracellular channel 6, and claudin 2. Gene Set Enrichment Analysis revealed that morphine treatment affected pathways related to cell cycle, membrane function, signaling, metabolism, cell death, transcriptional regulation, and immune response.  MS5 decreased expression of miR-204-5p, miR-455-3p, miR-448-3p, and miR-574-3p.Nine morphine-responsive mRNAs that are involved in neurodevelopment, neurotransmission, and inflammation are predicted targets of the aforementioned differentially expressed microRNAs These data establish that morphine produces dose-dependent changes in both hippocampal mRNA and miR gene expression in stressed neonatal mice. If permanent, morphine–mediated neuroepigenetic effects may affect long-term hippocampal function, and this provides a mechanism for the neonatal morphine-related impairment of adult learning.

platform_organism:
Mus musculus
synthetic construct

overall_design: Beginning on P5, male mice were assigned to one of 3 treatment conditions: untreated control (Con), morphine 2 mg/kg + stress (MS2), and morphine 5 mg/kg + stress (MS5). Untreated control animals were housed normally and exposed to minimal handling.  Treated pups were exposed to stress, apnea, and morphine.  To produce stress, mice were separated from the dam and isolated in cups within a veterinary warmer at 32°C (08:00 h to16:00 h).  To simulate apnea, mice were exposed to 100% N2 for 1 min then 100% O2 for 5 min, twice daily (08:00 and 15:30 h). Just prior to each apnea exposure, mice received 10 µL s.c. injections of morphine.  After treatments, mice were then returned to the home cage with the untreated control littermates and could nurse overnight ad lib.

first: Theodor

middle: K

last: Bammler

first: Richard

last: Beyer

first: Ryan

last: McAdams


title: Expression profile of Ceacam1 downstream genes in NSC and NSCL61

city: Sapporo

first: Toru

last: Kondo

address: Kita-15, Nishi-7, Kita-ku,

department: Institute for Genetic Medicine

institute: Hokkaido University

summary: To identify Ceacam1 downstream factors, we compared gene expressions between NSCs and Ceacam1L-expressing NSC and between NSCL61 and Ceacam1shRNA-expressing NSCL61.

overall_design: We established Ceacam1L-expressing NSC and Ceacam1shRNA-expressing NSCL61s. We think that genes, which are differently expressed between NSC and Ceacam1L-NSC, and between NSCL61 and Ceacam1shRNA-NSCL61, are the Ceacam1 downstream factors.


title: Effect of histone deacetylase 3 (Hdac3) deficiency in second heart field on embryonic heart development.

status: Public on Oct 02 2015

city: Worcester

first: Chinmay

last: Trivedi

state: MA

address: 368 Plantation St AS7-1047

department: Cardiovascular Medicine

institute: University of Massachusetts Medical School

summary:
Analysis of whole heart samples from Hdac3-Isl1KO embryos at embryonic day E9.5. Results provide insights into the role of Hdac3 in second heart field-derived cardiac cells.
We used microarray to investigate the gene expression program affected by Hdac3 during cardiac development and identified patterns of differentially-expressed genes and pathways during this process.

overall_design: Mouse embryonic hearts were dissected from E9.5 embryos and pooled for RNA extraction and hybridization on Affymetrix microarray chips. We utilized three samples for each Hdac3-flox/flox and Hdac3-Isl1KO genotypes.

first: Sara

last: Lewandowski


title: Characterization of chemokine and chemokine receptor expression during Pneumocystis infection in healthy and immunodeficient mice (part 1)

status: Public on Oct 10 2015

city: Frederick

first: Xiaojun

last: Hu

state: MD

address: 1050 Boyles St.

department: CSP

institute: SAIC_Frederick, INc

summary: For both CD4 and micropajfe cell types, upregulated genes were primarily related to immune activation and proliferation, while down-regulated genes represented more diverse processes, including cell membranes, vasculature development, cell adhesion, and lipid-related metabolic processes.

overall_design: Gene expression microarrays were from 4 exposured samples compared with 4 unexposured samples

first: Lisa

middle: R

last: Bishop

first: Michail

middle: S

last: Lionakis

first: Monica

last: Sassi

first: Philip

last: Murphy

first: Da

middle: W

last: Huang

first: Brad

last: Sherman

first: Jun

middle: A

last: Lempicki

first: Joseph

last: Kovacs


title: Characterization of chemokine and chemokine receptor expression during Pneumocystis infection in healthy and immunodeficient mice (part 4)

last: Yang